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Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism
Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)
doubly-wound polymer, processes such as chromosome compaction and replication naturally lead to DNA overwinding, underwinding, and tangling. Topoisomerases are essential to...
Anthraquinone Photonuclease Structure Determines Its Mode of Binding to DNA and the Cleavage
E-Print Network [OSTI]
Anthraquinone Photonuclease Structure Determines Its Mode of Binding to DNA and the Cleavage recently described a set of anthraquinone derivatives that act as photonucleases.6 Three classes
Williams, Loren
Mechanistic studies of bleomycin-mediated double-stranded DNA cleavage and structural studies of DNA containing normal and 4'-oxidized abasic sites
In order to examine the role of partial intercalation in double-stranded (ds) DNA cleavage mediated by a single bleomycin (BLM), a bulky group ([-cyclodextrin) was chemically attached to the polyamine tail of BLM A5 to ...
Chen, Jingyang, Ph. D. Massachusetts Institute of Technology
4698 Biochemistry 1993, 32, 4698-4701 Sequence-Specific Cleavage of DNA via Nucleophilic Attack of Hydrogen
4698 Biochemistry 1993, 32, 4698-4701 Sequence-Specific Cleavage of DNA via Nucleophilic Attack by oxidative damage of the DNA backbone but instead is the result of nucleophilic attack by peroxide. A singleSaccharomyces cerevisae, whichactivatesthephosphodiester for attack by thediffusible smallnucleophile. While Flp
Tullius, Thomas D.
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AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr May JunDatastreamsmmcrcalgovInstrumentsrucLas ConchasPassiveSubmittedStatusButler Tina ButlerToday inm"Topo II: An Enzyme
AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr MayAtmosphericNuclear SecurityTensile Strain Switched Ferromagnetism in Layered NbS2Topo II: An Enzyme Target for Antibacterial andTopo
AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr MayAtmosphericNuclear SecurityTensile Strain Switched Ferromagnetism in Layered NbS2Topo II: An Enzyme Target for Antibacterial
AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr MayAtmosphericNuclear SecurityTensile Strain Switched Ferromagnetism in Layered NbS2Topo II: An Enzyme Target for
AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr MayAtmosphericNuclear SecurityTensile Strain Switched Ferromagnetism in Layered NbS2Topo II: An Enzyme Target forTopoisomerase II Structure
AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr MayAtmosphericNuclear SecurityTensile Strain Switched Ferromagnetism in Layered NbS2Topo II: An Enzyme Target forTopoisomerase II
Carbon Nanotube DNA Sensor and Sensing Mechanism
Carbon Nanotube DNA Sensor and Sensing Mechanism Xiaowu Tang,*,, Sarunya Bansaruntip, Nozomi; Revised Manuscript Received June 7, 2006 ABSTRACT We report the fabrication of single-walled carbon nanotube (SWNT) DNA sensors and the sensing mechanism. The simple and generic protocol for label
Le Roy, Robert J.
Three-Dimensional Structure and Reactivity of a Photochemical Cleavage Agent Bound to DNA
30332-0400 ReceiVed May 20, 1998 Abstract: Irradiation of the anthraquinone derivative N,N-Bis(3 interactions are observed in the intercalated complex, indicating that the ground-state anthraquinone and DNA (Rh),7 and a series of anthraquinone (AQ) derivatives8 provides a model for natural oxidative
Photochemistry and Photobiology, 2005, 81: 8995 Photoinduced DNA Cleavage and Cellular Damage in Human Dermal
1 Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD . Furthermore, upon irradiation with visible light, DAP is able to nick plasmid DNA in the presence of oxygen. The concentration of DAP that resulted in 50% cell death was 172 6 9 lM in the dark and 13 6 1 lM after irradiation
Turro, Claudia
Crystal structures of [lamda] exonuclease in complex with DNA suggest an electrostatic ratchet mechanism for processivity
SciTech Connect (OSTI)
The {lambda} exonuclease is an ATP-independent enzyme that binds to dsDNA ends and processively digests the 5'-ended strand to form 5' mononucleotides and a long 3' overhang. The crystal structure of {lambda} exonuclease revealed a toroidal homotrimer with a central funnel-shaped channel for tracking along the DNA, and a mechanism for processivity based on topological linkage of the trimer to the DNA was proposed. Here, we have determined the crystal structure of {lambda} exonuclease in complex with DNA at 1.88-{angstrom} resolution. The structure reveals that the enzyme unwinds the DNA prior to cleavage, such that two nucleotides of the 5'-ended strand insert into the active site of one subunit of the trimer, while the 3'-ended strand passes through the central channel to emerge out the back of the trimer. Unwinding of the DNA is facilitated by several apolar residues, including Leu78, that wedge into the base pairs at the single/double-strand junction to form favorable hydrophobic interactions. The terminal 5' phosphate of the DNA binds to a positively charged pocket buried at the end of the active site, while the scissile phosphate bridges two active site Mg{sup 2+} ions. Our data suggest a mechanism for processivity in which wedging of Leu78 and other apolar residues into the base pairs of the DNA restricts backward movement, whereas attraction of the 5' phosphate to the positively charged pocket drives forward movement of the enzyme along the DNA at each cycle of the reaction. Thus, processivity of {lambda} exonuclease operates not only at the level of the trimer, but also at the level of the monomer.
Zhang, Jinjin; McCabe, Kimberly A.; Bell, Charles E. (OSU)
Mechanisms of DNA Adsorption to Soil Particles Student: Maline Elumelu
1 Mechanisms of DNA Adsorption to Soil Particles Student: Maline Elumelu Advisor: Dr. Michael), Swiss Federal Institute of Technology (ETH), Zurich Abstract It has been found that DNA adsorbed to soil particles can be partially protected against enzymatic degradation. Soils are a very heterogeneous matrix
Fischlin, Andreas
amide bond cleavage: Topics by E-print Network
the reactions of vanadyl ion and found that incubation of DNA with vanadyl ion and hydrogen peroxide (H202) led to intense DNA cleavage. ESR spin trapping demonstrated that...
Cleavage of nucleic acids
DOE Patents [OSTI]
The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The structure-specific nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof.
Prudent, James R. (Madison, WI); Hall, Jeff G. (Waunakee, WI); Lyamichev, Victor I. (Madison, WI); Brow; Mary Ann D. (Madison, WI); Dahlberg, James E. (Madison, WI)
Prudent, James R. (Madison, WI); Hall, Jeff G. (Madison, WI); Lyamichev, Victor L. (Madison, WI); Brow, Mary Ann D. (Madison, WI); Dahlberg, James E. (Madison, WI)
Mechanical Control of Enzymes Using DNA Molecular Springs
Responses of GK to Mechanical Stresses . . . . . . .4 Mechanical Control of Renilla116 Relation of Enzymatic Activity and Mechanical Stress
Tseng, Chiao-Yu
Stochastic Ratchet Mechanisms for Replacement of Proteins Bound to DNA
Experiments indicate that unbinding rates of proteins from DNA can depend on the concentration of proteins in nearby solution. Here we present a theory of multi-step replacement of DNA-bound proteins by solution-phase proteins. For four different kinetic scenarios we calculate the depen- dence of protein unbinding and replacement rates on solution protein concentration. We find (1) strong effects of progressive 'rezipping' of the solution-phase protein onto DNA sites liberated by 'unzipping' of the originally bound protein; (2) that a model in which solution-phase proteins bind non-specifically to DNA can describe experiments on exchanges between the non specific DNA- binding proteins Fis-Fis and Fis-HU; (3) that a binding specific model describes experiments on the exchange of CueR proteins on specific binding sites.
Simona Cocco; John F. Marko; Remi Monasson
A two-step nucleotide-flipping mechanism enables kinetic discrimination of DNA lesions by AGT
A two-step nucleotide-flipping mechanism enables kinetic discrimination of DNA lesions by AGT Jie serve as a paradigm for the many nucleotide-flipping proteins that regulate genes and repair DNA in all trajectories of molecu- larly rare events now enable us to elucidate a pathway for nucleotide flipping by AGT
Dinner, Aaron
Recent developments in single-molecule DNA mechanics Zev Bryant1,2
Recent developments in single-molecule DNA mechanics Zev Bryant1,2 , Florian C Oberstrass1 University, Stanford, CA 94305, USA Corresponding author: Bryant, Zev (firstname.lastname@example.com) Current Opinion
Bryant, Zev
DNA-Binding Mechanism in Prokaryotic Partition Complex Formation
AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr May JunDatastreamsmmcrcalgovInstrumentsruc DocumentationP-Series to UserProduct: Crude OilPublicDNA Gridiron
AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr MayAtmospheric Optical Depth7-1D: Vegetation Proposed Newcatalyst phases onOrganization FY Middle SchoolARM-TR-01468This4t cDNA-Binding
E-Print Network 3.0 - apoptotic dna degradation Sample Search...
DNA cleavage on agarose gels and by classic apoptotic morphology (23... with Hoechst dye (Sigma) to differentiate between normal and apoptotic cells by DNA fragmentation....
September 15, 2014 Computational analysis key to structural understanding of molecular machine that targets viral DNA LOS ALAMOS, N.M., Sept. 15, 2014-When this week's print issue...
Brittle to ductile transition in cleavage fracture
The problem of interpretation of fracture transition from brittle to ductile or vice versa is the subject of study. An instrumented tapered double cantilever beam (TDCB) has been developed as a definitive tool in the study of the intrinsic mechanism in single crystalline samples. In this experiment, the crack velocity is directly proportional to actuator velocity. In experiments performed on TDCB shaped Si single crystals, oriented for cleavage on either [l brace]111[r brace] or [l brace]110[r brace] planes, a number of troubling features of jerky carck extension were encountered. Evidence suggests that nucleation of dislocation loops from crack tip is easier than moving these dislocations away from crack tip. 14 refs, 1 fig.
Argon, A.S.; Berg, Q.
Extracting physical chemistry from mechanics: a new approach to investigate DNA interactions with drugs and proteins in single molecule experiments
In this review we focus on the idea of establishing connections between the mechanical properties of DNAligand complexes and the physical chemistry of DNA-ligand interactions. This type of connection is interesting because it opens the possibility of performing a robust characterization of such interactions by using only one experimental technique: single molecule stretching. Furthermore, it also opens new possibilities in comparing results obtained by very different approaches, in special when comparing single molecule techniques to ensemble-averaging techniques. We start the manuscript reviewing important concepts of the DNA mechanics, from the basic mechanical properties to the Worm-Like Chain model. Next we review the basic concepts of the physical chemistry of DNA-ligand interactions, revisiting the most important models used to analyze the binding data and discussing their binding isotherms. Then, we discuss the basic features of the single molecule techniques most used to stretch the DNA-ligand complex...
Rocha, M S
Elucidation of the Mechanism of Gene Silencing using Small Interferin RNA: DNA Hybrid Molecules
The recent discovery that short hybrid RNA:DNA molecules (siHybrids) induce long-term silencing of gene expression in mammalian cells conflicts with the currently hypothesized mechanisms explaining the action of small, interfering RNA (siRNA). As a first step to elucidating the mechanism for this effect, we set out to quantify the delivery of siHybrids and determine their cellular localization in mammalian cells. We then tracked the segregation of the siHybrids into daughter cells after cell division. Markers for siHybrid delivery were shown to enter cells with and without the use of a transfection agent. Furthermore, delivery without transfection agent only occurred after a delay of 2-4 hours, suggesting a degradation process occurring in the cell culture media. Therefore, we studied the effects of nucleases and backbone modifications on the stability of siHybrids under cell culture conditions.
Dugan, L
Mechanisms of radiation interaction with DNA: Potential implications for radiation protection
The Office of Health and Environmental Research (OHER) of the US Department of Energy conducts a broad multidisciplinary research program which includes basic biophysics, biophysical chemistry, molecular and cellular biology as well as experimental animal studies and opportunistic human studies. This research is directed at understanding how low levels of radiation of various qualities produce the spectrum of biological effects that are seen for such exposures. This workshop was entitled ''Mechanisms of Radiation Interaction with DNA: Potential Implications for Radiation Protection.'' It ws jointly sponsored by the Department of Energy and the Commission of European Communities. The aim of the workshop was to review the base of knowledge in the area of mechanisms of radiation action at the DNA level, and to explore ways in which this information can be applied to the development of scientifically sound concepts and procedures for use in the field of radiation protection. The overview of research provided by this multidisciplinary group will be helpful to the Office in program planning. This report includes a summary of the presentations, extended abstracts, the meeting agenda, research recommendations, and a list of participants. Individual papers are processed separately for the data base.
Not Available
Thermal and mechanical denaturation properties of a DNA model with three sites per nucleotide
In this paper, we show that the coarse grain model for DNA, which has been proposed recently by Knotts, Rathore, Schwartz and de Pablo (J. Chem. Phys. 126, 084901 (2007)), can be adapted to describe the thermal and mechanical denaturation of long DNA sequences by adjusting slightly the base pairing contribution. The adjusted model leads to (i) critical temperatures for long homogeneous sequences that are in good agreement with both experimental ones and those obtained from statistical models, (ii) a realistic step-like denaturation behaviour for long inhomogeneous sequences, and (iii) critical forces at ambient temperature of the order of 10 pN, close to measured values. The adjusted model furthermore supports the conclusion that the thermal denaturation of long homogeneous sequences corresponds to a first-order phase transition and yields a critical exponent for the critical force equal to sigma=0.70. This model is both geometrically and energetically realistic, in the sense that the helical structure and th...
Florescu, Ana-Maria; 10.1063/1.3626870
A DNA Damage-Induced, SOS-Independent Checkpoint Regulates Cell Division in Caulobacter crescentus
Cells must coordinate DNA replication with cell division, especially during episodes of DNA damage. The paradigm for cell division control following DNA damage in bacteria involves the SOS response where cleavage of the ...
Modell, Joshua W.
Structure of DNA-Bound FEN1 Reveals Mechanism of Action
double helix. A protein called DNA polymerase does most of this work, adding nucleotides complementary to the template's nucleotides. But before polymerase builds the...
Stochastic Ratchet Mechanisms for Replacement of Proteins Bound to DNA , J.F. Marko2
- binding proteins Fis-Fis and Fis-HU; (3) that a binding specific model describes experiments processes. In [1] a single DNA was stretched out, and spontaneous dissociation of fluorescently-labeled Fis Fis or another DNA-binding protein, e.g., HU) was added, the fluorescent protein unbound rapidly
Cocco, Simona
Mechanisms that prevent DNA re-replication in the yeast Saccharomyces cerevisiae
Every time a cell divides it must faithfully duplicate its genome before the cell divides. If replication initiates a second time (re-replication) before cytokinesis, cells can accumulate extensive DNA damage, which results ...
Tanny, Robyn E
Structure and mechanism of the UvrA?UvrB DNA damage sensor
Nucleotide excision repair (NER) is used by all organisms to eliminate DNA lesions. We determined the structure of the Geobacillus stearothermophilus UvrA-UvrB complex, the damage-sensor in bacterial NER and a new structure of UvrA. We observe that the DNA binding surface of UvrA, previously found in an open shape that binds damaged DNA, also exists in a closed groove shape compatible with native DNA only. The sensor contains two UvrB molecules that flank the UvrA dimer along the predicted path for DNA, {approx}80 {angstrom} from the lesion. We show that the conserved signature domain II of UvrA mediates a nexus of contacts among UvrA, UvrB and DNA. Further, in our new structure of UvrA, this domain adopts an altered conformation while an adjacent nucleotide binding site is vacant. Our findings raise unanticipated questions about NER and also suggest a revised picture of its early stages.
Pakotiprapha, Danaya; Samuels, Martin; Shen, Koning; Hu, Johnny H.; Jeruzalmi, David (Harvard)
An unprecedented nucleic acid capture mechanism for excision of DNA damage
DNA glycosylases that remove alkylated and deaminated purine nucleobases are essential DNA repair enzymes that protect the genome, and at the same time confound cancer alkylation therapy, by excising cytotoxic N3-methyladenine bases formed by DNA-targeting anticancer compounds. The basis for glycosylase specificity towards N3- and N7-alkylpurines is believed to result from intrinsic instability of the modified bases and not from direct enzyme functional group chemistry. Here we present crystal structures of the recently discovered Bacillus cereus AlkD glycosylase in complex with DNAs containing alkylated, mismatched and abasic nucleotides. Unlike other glycosylases, AlkD captures the extrahelical lesion in a solvent-exposed orientation, providing an illustration for how hydrolysis of N3- and N7-alkylated bases may be facilitated by increased lifetime out of the DNA helix. The structures and supporting biochemical analysis of base flipping and catalysis reveal how the HEAT repeats of AlkD distort the DNA backbone to detect non-Watson-Crick base pairs without duplex intercalation.
Rubinson, Emily H.; Prakasha Gowda, A.S.; Spratt, Thomas E.; Gold, Barry; Eichmanbrand, Brandt F. (Pitt); (Vanderbilt); (Penn)
Sustained water cleavage by visible light
Sustained cleavage of water by 4 quanta of visible light is achieved in aqueous solutions by using a bifunctional redox catalyst composed of Pt and RuO/sub 2/ cosupported by colloidal TiO/sub 2/ particles. A photochemical model system containing Ru(bpy)/sub 3//sup 2 +/ as a sensitizer and methyl viologen (MV/sup 2 +/) as an electron relay is used to test the effect of catalyst composition, sensitizer concentration, pH, and temperature on the efficiency of light-induced water decomposition. Electron relay free systems also exhibit high photoactivity. Direct band gap irradiation by uv light leads to efficient water cleavage in the absence of sensitizer and relay.
Borgarello, E.; Kiwi, J.; Pelizzetti, E.; Visca, M.; Graetzel, M.
Mechanism of mismatch recognition revealed by human MutS[beta] bound to unpaired DNA loops
DNA mismatch repair corrects replication errors, thus reducing mutation rates and microsatellite instability. Genetic defects in this pathway cause Lynch syndrome and various cancers in humans. Binding of a mispaired or unpaired base by bacterial MutS and eukaryotic MutS{alpha} is well characterized. We report here crystal structures of human MutS{beta} in complex with DNA containing insertion-deletion loops (IDL) of two, three, four or six unpaired nucleotides. In contrast to eukaryotic MutS{alpha} and bacterial MutS, which bind the base of a mismatched nucleotide, MutS{beta} binds three phosphates in an IDL. DNA is severely bent at the IDL; unpaired bases are flipped out into the major groove and partially exposed to solvent. A normal downstream base pair can become unpaired; a single unpaired base can thereby be converted to an IDL of two nucleotides and recognized by MutS{beta}. The C-terminal dimerization domains form an integral part of the MutS structure and coordinate asymmetrical ATP hydrolysis by Msh2 and Msh3 with mismatch binding to signal for repair.
Gupta, Shikha; Gellert, Martin; Yang, Wei (NIH)
A New Mechanism for DNA Alterations Induced by Alpha Particles Such as Those Emitted by Radon and Radon Progeny
The mechanism(s) by which alpha (a) particles like those emitted from inhaled radon and radon progeny cause their carcinogenic effects in the lung remains unclear. Although direct nuclear traversals by a-particles may be involved in mediating these outcomes, increasing evidence indicates that a particles can cause alterations in DNA in the absence of direct hits to cell nuclei. Using the occurrence of excessive sister chromatid exchanges (SCE) as an index of DNA damage in human lung fibroblasts, we investigated the hypothesis that a-particles may induce DNA damage through the generation of extracellular factors. We have found that a relatively low dose of a-particles can result in the generation of extracellular factors, which, upon transfer to unexposed normal human cells, can cause excessive SCE to an extent equivalent to that observed when the cells are directly irradiated with the same irradiation dose. A short-lived, SCEinducing factor(s) is generated in a-irradiated culture medium containing serum in the absence of cells. A more persistent SCE-inducing factor(s), which can survive freeze-thaw and is heat labile is produced by fibroblasts after exposure to the a-particles. These results indicate that the initiating target for a-particle-induced genetic changes can be larger than a cell's nucleus or even a whole cell. How transmissible factors like those observed here in vitro may extend to the in vivo condition in the context of a-particle-induced carcinogenesis in the respiratory tract remains to be determined. Environ Health Perspect 1 05(Suppl 5):1095-1101 (1997) Key words: alpha particles, radon/radon progeny, indirect radiation effects, high LET radiation,
Bruce E. Lehnert; Edwin H. Goodwin
DUPLEX: A molecular mechanics program in torsion angle space for computing structures of DNA and RNA
DUPLEX produces energy minimized structures of DNA and RNA of any base sequence for single and double strands. The smallest subunits are deoxydinucleoside monophosphates, and up to 12 residues, single or double stranded can be treated. In addition, it can incorporate NMR derived interproton distances an constraints in the minimizations. Both upper and lower bounds for these distances can be specified. The program has been designed to run on a UNICOS Cray supercomputer, but should run, albeit slowly, on a laboratory computer such as a VAX or a workstation.
Hingerty, B.E.
AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr May JunDatastreamsmmcrcalgovInstrumentsrucLas ConchasPassiveSubmittedStatus TomAbout » Staff125,849| OSTI,Structure of DNA-Bound FEN1
AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr May JunDatastreamsmmcrcalgovInstrumentsrucLas ConchasPassiveSubmittedStatus TomAbout » Staff125,849| OSTI,Structure of DNA-Bound
Low Dose Radiation-Induced Genome and Epigenome Instability Symposium and Epigenetic Mechanisms, DNA Repair, and Chromatin Symposium at the EMS 2008 Annual Meeting - October 2008
The Low Dose Radiation Symposium thoughtfully addressed ionizing radiation non-mutational but transmissable alterations in surviving cells. Deregulation of epigenetic processes has been strongly implicated in carcinogenesis, and there is increasing realization that a significant fraction of non-targeted and adaptive mechanisms in response to ionizing radiation are likely to be epigenetic in nature. Much remains to be learned about how chromatin and epigenetic regulators affect responses to low doses of radiation, and how low dose radiation impacts other epigenetic processes. The Epigenetic Mechanisms Symposium focused on on epigenetic mechanisms and their interplay with DNA repair and chromatin changes. Addressing the fact that the most well understood mediators of epigenetic regulation are histone modifications and DNA methylation. Low levels of radiation can lead to changes in the methylation status of certain gene promoters and the expression of DNA methyltransferases, However, epigenetic regulation can also involve changes in higher order chromosome structure.
Morgan, William F.; Kovalchuk, Olga; Dolinoy, Dana C.; Dubrova, Yuri E.; Coleman, Matthew A.; Sch�r, Primo; Pogribny, Igor; Hendzel, Michael
Mechanistic Examination of C?�C? Bond Cleavages...
Mechanistic Examination of C?�C? Bond Cleavages of Tryptophan Residues during Dissociations of Molecular Mechanistic Examination of C?�C? Bond...
Mapping between the order of thermal denaturation and the shape of the critical line of mechanical unzipping in 1-dimensional DNA models
In this Letter, we investigate the link between thermal denaturation and mechanical unzipping for two models of DNA, namely the Dauxois-Peyrard-Bishop model and a variant thereof we proposed recently. We show that the critical line that separates zipped from unzipped DNA sequences in mechanical unzipping experiments is a power-law in the temperature-force plane. We also prove that for the investigated models the corresponding critical exponent is proportional to the critical exponent alpha, which characterizes the behaviour of the specific heat in the neighbourhood of the critical temperature for thermal denaturation.
Buyukdagli, Sahin; 10.1016/j.cplett.2009.11.061
Creep-induced cleavage fracture in WIPP salt under indirect tension
The phenomenon of cleavage fracture initiation in rock salt undergoing concurrent creep was studied experimentally using the Brazilian indirect tension test technique. The tensile creep and cleavage fracture behaviors were characterized for rock salt from the Waste Isolation Pilot Plant (WIPP) site. The Brazilian test consists of a compressive line load applied diametrically on a disk specimen to produce a region of tensile stress in the center of the disk. The damage processes were documented using video photography. The experimental results were analyzed in terms of a wing-crack fracture model and an independently developed, coupled time-dependent, mechanism-based constitutive model whose parameters were obtained from triaxial compression creep tests. Analytical results indicate that coupling between creep and cleavage fracture in WIPP salt results in a fracture behavior that exhibits time-dependent characteristics and obeys a failure criterion involving a combination of stress difference and tensile stress. Implications of creep-induced cleavage fracture to the integrity of WIPP structures are discussed.
Chan, K.S.; Bodner, S.R. [Southwest Research Inst., San Antonio, TX (United States); Brodsky, N.S.; Fossum, A.F.; Munson, D.E. [Sandia National Labs., Albuquerque, NM (United States)
CLEAVAGE FRACTURE MICROMECHANISMS RELATED TO WPS EFFECT IN RPV STEEL S. R. Bordet1 , B. Tanguy1 , S by warm pre-stress (WPS) on the cleavage fracture micromechanisms of a 18MND5 (A533B) reactor pressure vessel (RPV) steel. In this purpose, different WPS fracture test results obtained on compact tensile (CT
Boyer, Edmond
Exoproteolytic cleavage of N-terminal His tags QIAGEN Distributors
His tags using DAPase Enzyme 25 Buffer preparation 25 Desalting 25 Protocol 1. DAPase digestion (small-scale, and pGAPase Enzymes 30 Buffer preparation 30 Desalting 30 Protocol 4. DAPase Qcyclase digestion (small-scale with TAGZyme cleavage His tags suitable for exoproteolytic cleavage by the TAGZyme system 50 Small-scale
Lebendiker, Mario
Nucleation, propagation and cleavage of target RNAs in Ago silencing complexes
The slicer activity of the RNA-induced silencing complex resides within its Argonaute (Ago) component, in which the PIWI domain provides the catalytic residues governing guide-strand mediated site-specific cleavage of target RNA. Here we report on structures of ternary complexes of Thermus thermophilus Ago catalytic mutants with 5'-phosphorylated 21-nucleotide guide DNA and complementary target RNAs of 12, 15 and 19 nucleotides in length, which define the molecular basis for Mg{sup 2+}-facilitated site-specific cleavage of the target. We observe pivot-like domain movements within the Ago scaffold on proceeding from nucleation to propagation steps of guide-target duplex formation, with duplex zippering beyond one turn of the helix requiring the release of the 3'-end of the guide from the PAZ pocket. Cleavage assays on targets of various lengths supported this model, and sugar-phosphate-backbone-modified target strands showed the importance of structural and catalytic divalent metal ions observed in the crystal structures.
Wang, Yanli; Juranek, Stefan; Li, Haitao; Sheng, Gang; Wardle, Greg S.; Tuschl, Thomas; Patel, Dinshaw J.; (MSKCC); (HHMI)
Pre-Steady-State Analysis of ATP Hydrolysis by Saccharomyces cereVisiae DNA Topoisomerase II. 2. Kinetic Mechanism for the Sequential Hydrolysis of Two
Pre-Steady-State Analysis of ATP Hydrolysis by Saccharomyces cereVisiae DNA Topoisomerase II. 2. Kinetic Mechanism for the Sequential Hydrolysis of Two ATP Timothy T. Harkins,,| Timothy J. Lewis two ATP and rapidly hydrolyzes at least one of them before encountering a slow step in the reaction
Lewis, Timothy
Molecular Quantum Mechanics 2010: From Methylene to DNA and Beyond Conference Support
This grant was $12500 for partial support of an international conference, Molecular Quantum Mechanics 2010, which was held on the campus of the University of California, Berkeley, from 24 to 29 May 2010. The conference involved more than 250 participants. The conference schedule ran from as early as 8:00 AM to as late as 10:30 PM at night, in order to accommodate six historical lectures, 16 plenary lectures, 42 invited talks and two very strong poster sessions containing 143 contributed posters. Since 1989, the Molecular Quantum Mechanics (MQM) series of international conferences has show- cased the frontiers of research in quantum chemistry with a strong focus on basic theory and algorithms, as well as highlights of topical applications. Both were strongly in evidence at MQM 2010. At the same time as embracing the future, the MQM conferences also honour the lifetime contributions of some of the most prominent scientists in the field of theoretical and computational quantum chemistry. MQM 2010 recognised the work of Prof. Henry F. �Fritz� Schaefer of the Center for Computational Chemistry at the University of Georgia, who was previously on the faculty at Berkeley The travel of invited speakers was partially covered by sponsorships from Dell Computer, Hewlett-Packard, Journal of Chemical Theory and Computation, Virginia Tech College of Science, Molecular Physics, Q-Chem Inc and the American Institute of Physics. By contrast, the conference grant from the Department of Energy was used to provide fellowships and scholarships to enable graduate students and postdoctoral fellows to attend the meeting, and thereby broaden the participation of young scientists at a meeting where in the past most of the attendees have been more senior faculty researchers. We believe that we were very successful in this regard: 118 students and postdocs attended out of the total of 256 participants. In detail, the DOE sponsorship money was partially used for dormitory scholarships that covered the cost of shared accommodation for students and postdocs at Berkeley dormitories. This covered the $200-$305 cost of a shared room for the 5-day duration of the conference. The only condition of these scholarships was that the awardee must present a poster at the meeting. Approximately $7565 was spent for these dormitory scholarships. The remaining expenditures of $4800 was used for 12 merit scholarships which were awarded to students whose poster presentations were judged the best at the conference. This amount covered a significant part of their travel and registration fees.
alpha-dependent aggrecan cleavage: Topics by E-print Network
in both strand cleavage reactions. These structures differ Monnat, Ray 46 Refining the model for selective cleavage at acidic residues in arginine-containing protonated...
Detection of nucleic acids by multiple sequential invasive cleavages
The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The structure-specific nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof. The present invention further relates to methods and devices for the separation of nucleic acid molecules based on charge. The present invention also provides methods for the detection of non-target cleavage products via the formation of a complete and activated protein binding region. The invention further provides sensitive and specific methods for the detection of human cytomegalovirus nucleic acid in a sample.
Hall, Jeff G; Lyamichev, Victor I; Mast, Andrea L; Brow, Mary Ann D
Microbial cleavage of organic C-S bonds
A microbial process is described for selective cleavage of organic C-S bonds which may be used for reducing the sulfur content of sulfur-containing organic carbonaceous materials. Microorganisms of Rhodococcus rhodochrous and Bacillus sphaericus have been found which have the ability of selective cleavage of organic C-S bonds. Particularly preferred microorganisms are Rhodococcus rhodochrous strain ATCC 53968 and Bacillus sphaericus strain ATCC 53969 and their derivatives.
Kilbane, J.J. II.
Transferability of cleavage fracture parameters between notched and cracked geometries
and specimen geometry dependence of cleavage fracture micromechanisms of a French pressure vessel steel (A508 that only NT tests with a mean fracture strain lower than 25% have to be considered to make sure ; ¢ 50 £ C ]. Also a unique set of Weibull parameters was found to describe all the NT tests over
Application of electron backscattered diffraction to cleavage fracture in duplex stainless steel
The mechanical properties and corrosion resistance of duplex stainless steel (DSS) are generally superior to conventional austenite or ferrite grades. DSSs can have yield strengths twice the austenite grades, while retaining good ductility and toughness properties. Commercial wrought duplex stainless steels, either plates or rod, are processed by hot rolling followed by a solution annealing treatment to optimize the austenite-ferrite ratio and dissolve any pre-existing secondary phases. Processing may lead to a significant anisotropy in mechanical properties. For example, the tensile properties in cold-rolled sheet of duplex stainless steel (22Cr5Ni) reveals anisotropy of strength, i.e., the transverse direction tensile strength is 7.3% higher than tensile strength in the rolling direction (RD). It was also shown in a study of the effect of crack orientation on the impact properties of the same steel, that when the crack was oriented parallel to the direction of elongation of the austenite phase, the crack could grow along the more brittle ferrite phase for a longer distance before encountering the more ductile austenite. This decreased impact toughness. These are examples of microstructure texture. Crystallographic texture may also have an effect on properties that are related to specific crystallographic planes; such as brittle cleavage and stress corrosion cracking. This paper describes the application of electron backscattered diffraction (EBSD) to study cleavage fracture and crystal texture in age-hardened DSS.
Kim, S.; Marrow, T.J.
E-Print Network 3.0 - alkene group cleavage Sample Search Results
cleavage Page: << < 1 2 3 4 5 > >> 1 Glaser, UMC, Chem210 Notes WS97, 1997 --1 --Chemistry 210 --Winter Semester 1997Chemistry 210 --Winter Semester 1997 Summary: Cleavage of...
Nanotechnology with DNA DNA Nanodevices
Nanotechnology with DNA DNA Nanodevices Friedrich C. Simmel* and Wendy U. Dittmer A DNA actuator. Introduction.............285 2. Overview: DNA Nanotechnology.......285 3. Prototypes of Nanomechanical DNA overview of DNA nanotechnology as a whole is given. The most important properties of DNA molecules
Ludwig-Maximilians-Universität, München
Brittle to ductile transition in cleavage fracture. Final techical report, April 1, 1987--June 30, 1991
The problem of interpretation of fracture transition from brittle to ductile or vice versa is the subject of study. An instrumented tapered double cantilever beam (TDCB) has been developed as a definitive tool in the study of the intrinsic mechanism in single crystalline samples. In this experiment, the crack velocity is directly proportional to actuator velocity. In experiments performed on TDCB shaped Si single crystals, oriented for cleavage on either {l_brace}111{r_brace} or {l_brace}110{r_brace} planes, a number of troubling features of jerky carck extension were encountered. Evidence suggests that nucleation of dislocation loops from crack tip is easier than moving these dislocations away from crack tip. 14 refs, 1 fig.
Generation of DNA-Damaging Reactive Oxygen Species via the Autoxidation of Hydrogen Sulfide under Physiologically Relevant
Generation of DNA-Damaging Reactive Oxygen Species via the Autoxidation of Hydrogen Sulfide under found that micromolar concentrations of H2S generated single-strand DNA cleavage. Mechanistic studies indicate that this process involved autoxidation of H2S to generate superoxide, hydrogen peroxide, and
Gates, Kent. S.
The various processes of DNA uptake by cells can be categorized as: viral DNA entry, conjugation, or transformation. Within each category, a variety of mechanisms have been found. However, considerable similarities occur among the different mechanisms of conjugation and, especially, transformation. All of these natural mechanisms of DNA transfer are quite elaborate and involve multiple protein components, as the case may be, of the virus, the donor cell, and the recipient cell. The mechanisms of viral infection and conjugation will be discussed mainly with respect to their relevance to transformation.
Mechanistic Investigation of Acid-Catalyzed Cleavage of Aryl-Ether Linkages: Implications for Lignin Depolymerization
Carbon-oxygen bonds are the primary inter-monomer linkages lignin polymers in plant cell walls, and as such, catalyst development to cleave these linkages is of paramount importance to deconstruct biomass to its constituent monomers for the production of renewable fuels and chemicals. For many decades, acid catalysis has been used to depolymerize lignin. Lignin is a primary component of plant cell walls, which is connected primarily by aryl-ether linkages, and the mechanism of its deconstruction by acid is not well understood, likely due to its heterogeneous and complex nature compared to cellulose. For effective biomass conversion strategies, utilization of lignin is of significant relevance and as such understanding the mechanisms of catalytic lignin deconstruction to constituent monomers and oligomers is of keen interest. Here, we present a comprehensive experimental and theoretical study of the acid catalysis of a range of dimeric species exhibiting the b-O-4 linkage, the most common inter-monomer linkage in lignin. We demonstrate that the presence of a phenolic species dramatically increases the rate of cleavage in acid at 150 degrees C. Quantum mechanical calculations on dimers with the para-hydroxyl group demonstrate that this acid-catalyzed pathway differs from the nonphenolic dimmers. Importantly, this result implies that depolymerization of native lignin in the plant cell wall will proceed via an unzipping mechanism wherein b-O-4 linkages will be cleaved from the ends of the branched, polymer chains inwards toward the center of the polymer. To test this hypothesis further, we synthesized a homopolymer of b-O-4 with a phenolic hydroxyl group, and demonstrate that it is cleaved in acid from the end containing the phenolic hydroxyl group. This result suggests that genetic modifications to lignin biosynthesis pathways in plants that will enable lower severity processes to fractionate lignin for upgrading and for easier access to the carbohydrate fraction of the plant cell wall.
Sturgeon, M. R.; Kim, S.; Chmely, S. C.; Foust, T. D.; Beckham, G. T.
Cellular responses to environmental DNA damage
This volume contains the proceedings of the conference entitled Cellular Responses to Environmental DNA Damage held in Banff,Alberta December 1--6, 1991. The conference addresses various aspects of DNA repair in sessions titled DNA repair; Basic Mechanisms; Lesions; Systems; Inducible Responses; Mutagenesis; Human Population Response Heterogeneity; Intragenomic DNA Repair Heterogeneity; DNA Repair Gene Cloning; Aging; Human Genetic Disease; and Carcinogenesis. Individual papers are represented as abstracts of about one page in length.
Single-Molecule Study of DNA Polymerization Activity of HIV-1 Reverse Transcriptase on DNA Templates
Single-Molecule Study of DNA Polymerization Activity of HIV-1 Reverse Transcriptase on DNA unwinding protein, such as a helicase. In order to understand the mechanism of polymerization through secondary structures, we investigated the DNA polymerization activity of HIV-1 RT on long ssDNA templates
Xie, Xiaoliang Sunney
Useful for cleavage of organic C-S bonds Bacillus sphaericus microorganism
A mutant Bacillus sphaericus strain ATCC No. 53969 which has the property of sulfur removal and sulfur metabolism by selective cleavage of C-S bonds in organic carbonaceous materials.
DNA demethylation by DNA repair
Active DNA demethylation underlies key facets of reproduction in flowering plants and mammals and serves a general genome housekeeping function in plants. A family of 5-methylcytosine DNA glycosylases catalyzes plant ...
Gehring, Mary
Role of Magnesium Ions in DNA Recognition by the EcoRV Restriction Endonuclease
The restriction endonuclease EcoRV binds two magnesium ions. One of these ions, Mg2+A, binds to the phosphate group where the cleavage occurs and is required for catalysis, but the role of the other ion, Mg2+B is debated. Here, multiple independent molecular dynamics simulations suggest that Mg2+B is crucial for achieving a tightly bound protein DNA complex and stabilizing a conformation that allows cleavage. In the absence of Mg2+B in all simulations the protein DNA hydrogen bond network is significantly disrupted and the sharp kink at the central base pair step of the DNA, which is observed in the two-metal complex, is not present. Also, the active site residues rearrange in such a way that the formation of a nucleophile, required for DNA hydrolysis, is unlikely.
Zahran, Mai [ORNL; Berezniak, Tomasz [University of Heidelberg; Imhof, Petra [University of Heidelberg; Smith, Jeremy C [ORNL
Method for rapid base sequencing in DNA and RNA with two base labeling
Method for rapid-base sequencing in DNA and RNA with two-base labeling and employing fluorescent detection of single molecules at two wavelengths. Bases modified to accept fluorescent labels are used to replicate a single DNA or RNA strand to be sequenced. The bases are then sequentially cleaved from the replicated strand, excited with a chosen spectrum of electromagnetic radiation, and the fluorescence from individual, tagged bases detected in the order of cleavage from the strand.
Jett, James H. (Los Alamos, NM); Keller, Richard A. (Los Alamos, NM); Martin, John C. (Los Alamos, NM); Posner, Richard G. (Los Alamos, NM); Marrone, Babetta L. (Los Alamos, NM); Hammond, Mark L. (Los Alamos, NM); Simpson, Daniel J. (Los Alamos, NM)
A method is described for rapid-base sequencing in DNA and RNA with two-base labeling and employing fluorescent detection of single molecules at two wavelengths. Bases modified to accept fluorescent labels are used to replicate a single DNA or RNA strand to be sequenced. The bases are then sequentially cleaved from the replicated strand, excited with a chosen spectrum of electromagnetic radiation, and the fluorescence from individual, tagged bases detected in the order of cleavage from the strand. 4 figures.
Jett, J.H.; Keller, R.A.; Martin, J.C.; Posner, R.G.; Marrone, B.L.; Hammond, M.L.; Simpson, D.J.
The Structure of a High Fidelity DNA Polymerase Bound to a Mismatched Nucleotide Reveals an ;Ajar; Intermediate Conformation in the Nucleotide Selection Mechanism
To achieve accurate DNA synthesis, DNA polymerases must rapidly sample and discriminate against incorrect nucleotides. Here we report the crystal structure of a high fidelity DNA polymerase I bound to DNA primer-template caught in the act of binding a mismatched (dG:dTTP) nucleoside triphosphate. The polymerase adopts a conformation in between the previously established 'open' and 'closed' states. In this 'ajar' conformation, the template base has moved into the insertion site but misaligns an incorrect nucleotide relative to the primer terminus. The displacement of a conserved active site tyrosine in the insertion site by the template base is accommodated by a distinctive kink in the polymerase O helix, resulting in a partially open ternary complex. We suggest that the ajar conformation allows the template to probe incoming nucleotides for complementarity before closure of the enzyme around the substrate. Based on solution fluorescence, kinetics, and crystallographic analyses of wild-type and mutant polymerases reported here, we present a three-state reaction pathway in which nucleotides either pass through this intermediate conformation to the closed conformation and catalysis or are misaligned within the intermediate, leading to destabilization of the closed conformation.
Wu, Eugene Y.; Beese, Lorena S. (Duke)
A Mechanism of Haloalkene-Induced Renal
Several halogenated alkenes are nephrotoxic; some others induce renal tubular adenocarcinomas in rodents after lifelong administration. A bioactivation mechanism accounting for the organ-selective tumor induction has been elucidated: conjugation of the parent compounds with glutathione (GSH), catalyzed by hepatic GSH S-transferases, results in the formation of haloalkyl and halovinyl glutathione S-conjugates. Formation of S-conjugates (identified by NMR and mass spectrometry) could be demonstrated with trichloroethene, tetrachloroethene, hexachlorobutadiene, perfluoropropene, trichlorotrifluoropropene, and dichloroacetylene in incubations with rat liver microsomes and in the isolated perfused rat liver. The GSH conjugates formed are eliminated from the rat liver with the bile and may be translocated to the kidney, intact or after metabolism to the corresponding cysteine S-conjugates that are metabolized in the kidney by renal tubular cysteine conjugate 3-lyase (P-lyase) to reactive intermediates, most likely thioacylchlorides and thioketenes. Interaction of these potent electrophiles with DNA [demonstrated for intermediates formed from S-(1,2,3,4,4-pentachlorobutadienyl)-L-cysteine] causes mutagenicity in bacteria, genotoxicity in cultured renal cells, and cytotoxicity in kidney cells. As an alternative to 3-lyase-catalyzed cleavage, the cysteine S-conjugates may be acetylated to the corresponding mercapturic acids, which have been identified in urine. The ability of the kidney to concentrate GSH and cysteine S-conjugates and the intensive metabolism of GSH S-conjugates to cysteine S-conjugates in this organ are evidently responsible for the organotropic carcinogenicity.
Wolfgang Dekant; Spyridon Vamvakas; Andreas Kochling; Wolfgang Kanhai; Dirk Muller; Dietrich Henschler
Atomistic characterization of stress-driven configurational instability and its activation mechanisms
Cleavage decohesion and shear dislocation nucleation are two basic modes of localized deformation in crystal lattices, which normally result from instability of the atomic configuration driven by mechanical forces. The ...
Zhu, Ting, 1971-
A novel role for the transcriptional modulator NusA in DNA repair/damage tolerance pathways in Escherichia coli
All organisms must contend with the consequences of DNA damage, induced by a variety of both endogenous and exogenous sources. Mechanisms of DNA repair and DNA damage tolerance are crucial for cellular survival after DNA ...
Cohen, Susan E., Ph. D. Massachusetts Institute of Technology
Design of Autonomous DNA Cellular Automata , Sudheer Sahu
Design of Autonomous DNA Cellular Automata Peng Yin ¡ , Sudheer Sahu ¡ , Andrew J. Turberfield cellular computing devices, i.e. autonomous nano-mechanical DNA computing devices embedded in DNA lattices. As a prototype of such devices, we recently reported the design of an Autonomous DNA Turing Machine, which
Yin, Peng
StochasticModeling of the Independent Roles of Particle Size and Grain Size in Transgranular Cleavage Fracture
Cleavage Fracture TSANN LIN, A. G. EVANS, and R. O. RITCHIE The independent roles of grain size. INTRODUCTION CLEAVAGE fracture in most metals occurs by the nu- cleation of a microcrack, assisted by the local, concentrated, tensile stress exceeds some critical fracture stress. In mild steels, such microcracks were
Ritchie, Robert
E-Print Network 3.0 - ataxin-3 protein cleavage Sample Search...
protein, Factor Xa is removed with greater... mM Tris-HCl pH 8.0, 100 mM NaCl, 5 mM CaCl2. A Cleavage Control ... Source: Lebendiker, Mario - Wolfson Centre for Applied...
Temperature-Controlled Regioselectivity in the Reductive Cleavage of p-Methoxybenzylidene Acetals
Temperature-Controlled Regioselectivity in the Reductive Cleavage of p-Methoxybenzylidene Acetals The regioselective ring opening of pyranosidic 4,6-p-methoxybenzylidene acetals with BH3/Bu2BOTf in THF can be tuned-sensitive functional groups, including allyl and enol ethers. The presence of water does not interfere with reductive
Wei, Alexander
Metabolic Engineering to Develop a Pathway for the Selective Cleavage of Carbon-Nitrogen Bonds
The objective of the project is to develop a biochemical pathway for the selective cleavage of C-N bonds in molecules found in petroleum. Specifically a novel biochemical pathway will be developed for the selective cleavage of C-N bonds in carbazole. The cleavage of the first C-N bond in carbazole is accomplished by the enzyme carbazole dioxygenase, that catalyzes the conversion of carbazole to 2-aminobiphenyl-2,3-diol. The genes encoding carbazole dioxygenase were cloned from Sphingomonas sp. GTIN11 and from Pseudomonas resinovorans CA10. The selective cleavage of the second C-N bond has been challenging, and efforts to overcome that challenge have been the focus of recent research in this project. Enrichment culture experiments succeeded in isolating bacterial cultures that can metabolize 2-aminobiphenyl, but no enzyme capable of selectively cleaving the C-N bond in 2-aminobiphenyl has been identified. Aniline is very similar to the structure of 2-aminobiphenyl and aniline dioxygenase catalyzes the conversion of aniline to catechol and ammonia. For the remainder of the project the emphasis of research will be to simultaneously express the genes for carbazole dioxygenase and for aniline dioxygenase in the same bacterial host and then to select for derivative cultures capable of using carbazole as the sole source of nitrogen.
John J. Kilbane II
Cleavage-like fracture of austenite in duplex stainless steel
Nitrogen alloying of stainless steel has proved to be extremely successful for mechanical and corrosion properties. For duplex stainless steel, which appears to be very promising for industrial application, the beneficial influence of nitrogen has also been established for contents of about 0.2 wt-%. Duplex structures are found in many alloys and systems as, for instance, in Cu- and Ti-alloys and in stainless steel. They all are characterized by a mixture of similar amounts of two phases whose plastic behaviors are different from one another. In the case of duplex stainless steel the matrix phase is usually ferrite. However, by increasing the nitrogen content and therefore the stability of austenite, it is shown in the present work that austenite can also become the matrix. Because the partition coefficient of nitrogen between [alpha] and [gamma] is large, it is also possible to harden the [gamma] phase more than [alpha]. The question this paper attempts to answer is whether or not nitrogen alloying can exchange the roles of the [alpha] and the [gamma] phases with respect to mechanical properties.
Foct, J. (Univ. de Lille (France)); Akdut, N. (Inst. fuer Metallkunde und Metallphysik, Aachen (Germany))
The biological and metabolic fates of endogenous DNA damage products
DNA and other biomolecules are subjected to damaging chemical reactions during normal physiological processes and in states of pathophysiology caused by endogenous and exogenous mechanisms. In DNA, this damage affects ...
Chan, Wan Simon
Roles of grain boundaries in cleavage cracking and thermal crack arrest experiments in iron-silicon alloy
High-angle grain boundaries in steel offer an important resistance to the propagation of cleavage cracks that affects the fracture toughness and can modulate the ductile-to-brittle transition temperature of fracture downward. ...
Qiao, Yu, 1972-
Coordinateendonucleolytic 5' and 3' trimming of terminally blocked blunt DNA double-strand break ends by Artemis nuclease and DNA-dependent protein kinase
Previous work showed that, in the presence of DNA-PK, Artemis slowly trims 3'-phosphoglycolate-terminated blunt ends. To examine the trimming reaction in more detail, long internally labeled DNA substrates were treated with Artemis. In the absence of DNA-PK, Artemis catalyzed extensive 5' {yields} 3' exonucleolytic resection of double-stranded DNA. This resection required a 5'-phosphate but did not require ATP, and was accompanied by endonucleolytic cleavage of the resulting 3' overhang. In the presence of DNA-PK, Artemis-mediated trimming was more limited, was ATP-dependent, and did not require a 5'-phosphate. For a blunt end with either a 3'-phosphoglycolate or 3'-hydroxyl terminus, endonucleolytic trimming of 2-4 nucleotides from the 3'-terminal strand was accompanied by trimming of 6 nucleotides from the 5'-terminal strand. The results suggest that autophosphorylated DNA-PK suppresses the exonuclease activity of Artemis toward blunt-ended DNA, and promotes slow and limited endonucleolytic trimming of the 5'-terminal strand, resulting in short 3' overhangs that are trimmed endonucleolytically. Thus, Artemis and DNA-PK can convert terminally blocked DNA ends of diverse geometry and chemical structure to a form suitable for polymerase mediated patching and ligation, with minimal loss of terminal sequence. Such processing could account for the very small deletions often found at DNA double-strand break repair sites.
Povirk, Lawrence; Yannone, Steven M.; Khan, Imran S.; Zhou, Rui-Zhe; Zhou, Tong; Valerie, Kristoffer; F., Lawrence
Effect of phosphorus on cleavage fracture in -carbide N. I. Medvedeva,1,2 R. A. Howell,2 D. C. Van Aken,2 and J. E. Medvedeva2
Effect of phosphorus on cleavage fracture in -carbide N. I. Medvedeva,1,2 R. A. Howell,2 D. C. Van of the phosphorus effect on ideal cleavage energy and critical stress in -carbide, Fe3AlC, a precipitate the cleavage characteristics of -carbide. We show that strong anisotropy of the Fe-P bonds in Fe3 Al,P C under
Medvedeva, Julia E.
Asiakastyytyv�isyystutkimus - DNA Kauppa Lappeenranta.
??Opinn�ytety�n aiheena oli DNA Kauppa Lappeenrannan asiakastyytyv�isyyden tutkiminen. Tutkimuksen ensisijaisena tavoitteena oli selvitt��, kuinka tyytyv�isi� asiakkaat olivat olleet DNA Kauppa Lappeenrannan ja asiakkaan v�liseen kontaktipintaan� (more)
Pitk�nen, Jesse
Physical process Mechanical mechanisms
1 Physical process Generation · Mechanical mechanisms F = m·a · Electric/Magnetic mechanisms F Quadrupoles......shear stress fluctuations High order poles...... phys. interpretation difficult Governing
Berlin,Technische Universität
Optical probe for the cytochrome P-450 cholesterol side chain cleavage enzyme
An optical probe enables the study of enzyme activity by absorbance spectroscopy or by sensitive fluorescence methods. In particular, the probe provides the ability to monitor the activity of cytochrome P-450.sub.scc enzyme, the rate limiting enzyme for steroid biosynthesis. Located on the inner mitochondrial membrane, P-450.sub.scc catalyzes the conversion of cholesterol to pregnenolone and isocapraldehyde by sequential oxidations of the cholesterol side chain. The fluorogenic probe includes a cholesterol-like steroid linked to a chromophore through a linking group. The chromophore is selected to have little optical response when linked to the steroid substrate and an enhanced optical response when cleaved from the substrate and linking group. Thus, a fluorescent anion that can be optically detected is generated by the side-chain cleavage reaction during steroidogenesis.
Marrone, Babetta L. (Los Alamos, NM); Simpson, Daniel J. (Los Alamos, NM); Unkefer, Clifford J. (Los Alamos, NM); Whaley, Thomas W. (Santa Fe, NM)
Activation of nucleic acid-sensing Toll-like receptors requires cleavage by endolysosomal proteases: a mechanism to avoid autoimmunity
receptor DC: dendritic cell pDC: plasmacytoid dendritic celltaken up by plasmacytoid DCs (pDC) and elicit large amountsare also components of the pDC-MyD88 signaling complex (
Ewald, Sarah Elisabeth
Surface Functions during Mitosis. III. Quantitative Analysis of Ligand-receptor Movement into the Cleavage Furrow: Diffusion vs. Flow
ABSTRACT The surface distribution of concanavalin A (Con A) bound to cell membrane receptors varies dramatically as a function of mitotic phase. The lectin is distributed diffusely on cells labeled and observed between mid-prophase and early anaphase, whereas cells observed in late anaphase or telophase demonstrate a marked accumulation of Con A-receptor complexes over the developing cleavage furrow (Berlin, Oliver, and Walter. 1978. Cell. 15:327-341). In this report, we first use a system based on video intensification fluorescence microscopy to describe the simultaneous changes in cell shape and in lectin-receptor complex topography during progression of single cells through the mitotic cycle. The video analysis establishes that fluorescein succinyl Con A (F-S Con A)-receptor complex redistribution begins coincident with the first appearance of the cleavage furrow and is essentially complete within 2-3 min. This remarkable redistribution of surface fluorescence occurs during only a modest change in cell shape from a sphere to a belted cylinder. It reflects the translocation of complexes and not the accumulation of excess labeled membrane in the cleavage furrow: first, bound fluorescent cholera toxin which faithfully outlines the plasma membrane is not accumulated in the cleavage furrow, and, second, electron microscopy of peroxidase-Con A labeled cells undergoing
unknown authors
Capstan friction model for DNA ejection from bacteriophages
Bacteriophages infect cells by attaching to the outer membrane and injecting their DNA into the cell.The phage DNA is then transcribed by the cell's transcription machinery.A number of physical mechanisms by which DNA can be translocated from the phage capsid into the cell have been identified. A fast ejection driven by the elastic and electrostatic potential energy of the compacted DNA within the viral capsid appears to be used by most phages, at least to initiate infection.In recent in vitro experiments, the speed of DNA translocation from a lambda phage capsid has been measured as a function of ejected length over the entire duration of the event.Here a mechanical model is proposed that is able to explain the observed dependence of exit velocity on ejected length, and that is also consistent with the accepted picture of the geometric arrangement of DNA within the viral capsid.
Sandip Ghosal
DNA Sequencing apparatus
An automated DNA sequencing apparatus having a reactor for providing at least two series of DNA products formed from a single primer and a DNA strand, each DNA product of a series differing in molecular weight and having a chain terminating agent at one end; separating means for separating the DNA products to form a series bands, the intensity of substantially all nearby bands in a different series being different, band reading means for determining the position an This invention was made with government support including a grant from the U.S. Public Health Service, contract number AI-06045. The U.S. government has certain rights in the invention.
Tabor, Stanley (Cambridge, MA); Richardson, Charles C. (Chestnut Hill, MA)
An unusual carbon?carbon bond cleavage reaction during phosphinothricin biosynthesis
Natural products containing phosphorus-carbon bonds have found widespread use in medicine and agriculture. One such compound, phosphinothricin tripeptide, contains the unusual amino acid phosphinothricin attached to two alanine residues. Synthetic phosphinothricin (glufosinate) is a component of two top-selling herbicides (Basta and Liberty), and is widely used with resistant transgenic crops including corn, cotton and canola. Recent genetic and biochemical studies showed that during phosphinothricin tripeptide biosynthesis 2-hydroxyethylphosphonate (HEP) is converted to hydroxymethylphosphonate (HMP). Here we report the in vitro reconstitution of this unprecedented C(sp{sup 3})-C(sp{sup 3}) bond cleavage reaction and X-ray crystal structures of the enzyme. The protein is a mononuclear non-haem iron(II)-dependent dioxygenase that converts HEP to HMP and formate. In contrast to most other members of this family, the oxidative consumption of HEP does not require additional cofactors or the input of exogenous electrons. The current study expands the scope of reactions catalysed by the 2-His-1-carboxylate mononuclear non-haem iron family of enzymes.
Cicchillo, Robert M.; Zhang, Houjin; Blodgett, Joshua A.V.; Whitteck, John T.; Li, Gongyong; Nair, Satish K.; van derDonk, Wilfred A.; Metcalf, William W.; (UIUC)
Solvent dependent branching between C-I and C-Br bond cleavage following 266 nm excitation of CH{sub 2}BrI
It is well known that ultraviolet photoexcitation of halomethanes results in halogen-carbon bond cleavage. Each halogen-carbon bond has a dominant ultraviolet (UV) absorption that promotes an electron from a nonbonding halogen orbital (n{sub X}) to a carbon-halogen antibonding orbital (?*{sub C-X}). UV absorption into specific transitions in the gas phase results primarily in selective cleavage of the corresponding carbon-halogen bond. In the present work, broadband ultrafast UV-visible transient absorption studies of CH{sub 2}BrI reveal a more complex photochemistry in solution. Transient absorption spectra are reported spanning the range from 275 nm to 750 nm and 300 fs to 3 ns following excitation of CH{sub 2}BrI at 266 nm in acetonitrile, 2-butanol, and cyclohexane. Channels involving formation of CH{sub 2}Br + I radical pairs, iso-CH{sub 2}Br-I, and iso-CH{sub 2}I-Br are identified. The solvent environment has a significant influence on the branching ratios, and on the formation and stability of iso-CH{sub 2}Br-I. Both iso-CH{sub 2}Br-I and iso-CH{sub 2}I-Br are observed in cyclohexane with a ratio of ?2.8:1. In acetonitrile this ratio is 7:1 or larger. The observation of formation of iso-CH{sub 2}I-Br photoproduct as well as iso-CH{sub 2}Br-I following 266 nm excitation is a novel result that suggests complexity in the dissociation mechanism. We also report a solvent and concentration dependent lifetime of iso-CH{sub 2}Br-I. At low concentrations the lifetime is >4 ns in acetonitrile, 1.9 ns in 2-butanol and ?1.4 ns in cyclohexane. These lifetimes decrease with higher initial concentrations of CH{sub 2}BrI. The concentration dependence highlights the role that intermolecular interactions can play in the quenching of unstable isomers of dihalomethanes.
Anderson, Christopher P.; Spears, Kenneth G.; Wilson, Kaitlynn R.; Sension, Roseanne J. [Department of Chemistry and Department of Physics, University of Michigan, Ann Arbor, Michigan 48109 (United States)] [Department of Chemistry and Department of Physics, University of Michigan, Ann Arbor, Michigan 48109 (United States)
Detection and quantitation of single nucleotide polymorphisms, DNA sequence variations, DNA mutations, DNA damage and DNA mismatches
DNA mutation binding proteins alone and as chimeric proteins with nucleases are used with solid supports to detect DNA sequence variations, DNA mutations and single nucleotide polymorphisms. The solid supports may be flow cytometry beads, DNA chips, glass slides or DNA dips sticks. DNA molecules are coupled to solid supports to form DNA-support complexes. Labeled DNA is used with unlabeled DNA mutation binding proteins such at TthMutS to detect DNA sequence variations, DNA mutations and single nucleotide length polymorphisms by binding which gives an increase in signal. Unlabeled DNA is utilized with labeled chimeras to detect DNA sequence variations, DNA mutations and single nucleotide length polymorphisms by nuclease activity of the chimera which gives a decrease in signal.
McCutchen-Maloney, Sandra L. (Pleasanton, CA)
Mechanisms of chemical phototoxicity
Psoralens in combination with ultraviolet light (PUVA) are phototoxic and potent modulators of epidermal cell growth and differentiation. Using an in vitro cell culture model, the effects of psoralens and UVA light on the growth of epidermal cells were investigated. It was found that psoralen and UVA light interact synergistically to inhibit the growth of cells in culture. This synergism was also observed in the ability of PUVA to inhibit DNA synthesis, decrease cell survival, cause mutations and form psoralen-DNA adducts. Using a cell culture model for the differentiation of melanocytes, PUVA was also found to be a potent inducer of melanogenesis as evidenced by its ability to increase cellular tyrosinase, the enzyme responsible for melanin biosynthesis. Results from these studies indicate that PUVA can induce dramatic alterations in the growth rate and differentiation state of cells at dosage levels which are associated with minimal DNA damage. These findings are in conflict with the general assumption that the biological effects of psoralens and UVA light are associated with their ability to bind covalently to and cross-link DNA. Therefore, the author investigated the possibility that sites of action, other than DNA, are involved in the mechanism(s) by which photoactivated psoralens modulate epidermal cell growth and differentiation. The author's laboratory has found that mammalian epidermal cells contain specific, saturable, high-affinity binding sites for the psoralens that are distinct from DNA. This receptor for the psoralens, photolabeled with ({sup 3}H)-8-methoxysporalen, was visualized following sodium dodecyl sulfatepolyacrylamide gel electrophoresis. The psoralen receptor is shown to be a 22,000 dalton protein located in nonnuclear fractions of cell extracts.
Yurkow, E.J.
DNA nanotechnology: understanding and optimisation through simulation
DNA nanotechnology promises to provide controllable self-assembly on the nanoscale, allowing for the design of static structures, dynamic machines and computational architectures. In this article I review the state-of-the art of DNA nanotechnology, highlighting the need for a more detailed understanding of the key processes, both in terms of theoretical modelling and experimental characterisation. I then consider coarse-grained models of DNA, mesoscale descriptions that have the potential to provide great insight into the operation of DNA nanotechnology if they are well designed. In particular, I discuss a number of nanotechnological systems that have been studied with oxDNA, a recently developed coarse-grained model, highlighting the subtle interplay of kinetic, thermodynamic and mechanical factors that can determine behaviour. Finally, new results highlighting the importance of mechanical tension in the operation of a two-footed walker are presented, demonstrating that recovery from an unintended `overstepped' configuration can be accelerated by three to four orders of magnitude by application of a moderate tension to the walker's track. More generally, the walker illustrates the possibility of biasing strand-displacement processes to affect the overall rate.
Thomas E. Ouldridge
Identification of an Acyl-Enzyme Intermediate in a meta-Cleavage Product Hydrolase Reveals the Versatility of the Catalytic Triad
Meta-cleavage product (MCP) hydrolases are members of the {alpha}/{beta}-hydrolase superfamily that utilize a Ser-His-Asp triad to catalyze the hydrolysis of a C-C bond. BphD, the MCP hydrolase from the biphenyl degradation pathway, hydrolyzes 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid (HOPDA) to 2-hydroxypenta-2,4-dienoic acid (HPD) and benzoate. A 1.6 {angstrom} resolution crystal structure of BphD H265Q incubated with HOPDA revealed that the enzyme's catalytic serine was benzoylated. The acyl-enzyme is stabilized by hydrogen bonding from the amide backbone of 'oxyanion hole' residues, consistent with formation of a tetrahedral oxyanion during nucleophilic attack by Ser112. Chemical quench and mass spectrometry studies substantiated the formation and decay of a Ser112-benzoyl species in wild-type BphD on a time scale consistent with turnover and incorporation of a single equivalent of {sup 18}O into the benzoate produced during hydrolysis in H{sub 2}{sup 18}O. Rapid-scanning kinetic studies indicated that the catalytic histidine contributes to the rate of acylation by only an order of magnitude, but affects the rate of deacylation by over 5 orders of magnitude. The orange-colored catalytic intermediate, ES{sup red}, previously detected in the wild-type enzyme and proposed herein to be a carbanion, was not observed during hydrolysis by H265Q. In the newly proposed mechanism, the carbanion abstracts a proton from Ser112, thereby completing tautomerization and generating a serinate for nucleophilic attack on the C6-carbonyl. Finally, quantification of an observed pre-steady-state kinetic burst suggests that BphD is a half-site reactive enzyme. While the updated catalytic mechanism shares features with the serine proteases, MCP hydrolase-specific chemistry highlights the versatility of the Ser-His-Asp triad.
Ruzzini, Antonio C.; Ghosh, Subhangi; Horsman, Geoff P.; Foster, Leonard J.; Bolin, Jeffrey T.; Eltis, Lindsay D. (Purdue); (UBC)
Distinct kinetics of human DNA ligases I, IIIalpha, IIIbeta, and IV reveal direct DNA sensing ability and differential physiological functions in DNA repair
The three human LIG genes encode polypeptides that catalyze phosphodiester bond formation during DNA replication, recombination and repair. While numerous studies have identified protein partners of the human DNA ligases (hLigs), there has been little characterization of the catalytic properties of these enzymes. In this study, we developed and optimized a fluorescence-based DNA ligation assay to characterize the activities of purified hLigs. Although hLigI joins DNA nicks, it has no detectable activity on linear duplex DNA substrates with short, cohesive single-strand ends. By contrast, hLigIII{beta} and the hLigIII{alpha}/XRCC1 and hLigIV/XRCC4 complexes are active on both nicked and linear duplex DNA substrates. Surprisingly, hLigIV/XRCC4, which is a key component of the major non-homologous end joining (NHEJ) pathway, is significantly less active than hLigIII on a linear duplex DNA substrate. Notably, hLigIV/XRCC4 molecules only catalyze a single ligation event in the absence or presence of ATP. The failure to catalyze subsequent ligation events reflects a defect in the enzyme-adenylation step of the next ligation reaction and suggests that, unless there is an in vivo mechanism to reactivate DNA ligase IV/XRCC4 following phosphodiester bond formation, the cellular NHEJ capacity will be determined by the number of adenylated DNA ligaseIV/XRCC4 molecules.
Chen, Xi; Ballin, Jeff D.; Della-Maria, Julie; Tsai, Miaw-Sheue; White, Elizabeth J.; Tomkinson, Alan E.; Wilson, Gerald M.
Carbon-carbon bond cleavage of 1,2-hydroxy ethers b7 vanadium(V) dipicolinate complexes
The development of alternatives to current petroleum-based fuels and chemicals is becoming increasingly important due to concerns over climate change, growing world energy demand, and energy security issues. Using non-food derived biomass to produce renewable feedstocks for chemicals and fuels is a particularly attractive possibility. However, the majority of biomass is in the form of lignocellulose, which is often not fully utilized due to difficulties associated with breaking down both lignin and cellulose. Recently, a number of methods have been reported to transform cellulose directly into more valuable materials such as glucose, sorbitol, 5-(chloromethyl)furfural, and ethylene glycol. Less progress has been made with selective transformations of lignin, which is typically treated in paper and forest industries by kraft pulping (sodium hydroxide/sodium sulfide) or incineration. Our group has begun investigating aerobic oxidative C-C bond cleavage catalyzed by dipicolinate vanadium complexes, with the idea that a selective C-C cleavage reaction of this type could be used to produce valuable chemicals or intermediates from cellulose or lignin. Lignin is a randomized polymer containing methoxylated phenoxy propanol units. A number of different linkages occur naturally; one of the most prevalent is the {beta}-O-4 linkage shown in Figure 1, containing a C-C bond with 1,2-hydroxy ether substituents. While the oxidative C-C bond cleavage of 1,2-diols has been reported for a number of metals, including vanadium, iron, manganese, ruthenium, and polyoxometalate complexes, C-C bond cleavage of 1,2-hydroxy ethers is much less common. We report herein vanadium-mediated cleavage of C-C bonds between alcohol and ether functionalities in several lignin model complexes. In order to explore the scope and potential of vanadium complexes to effect oxidative C-C bond cleavage in 1,2-hydroxy ethers, we examined the reactivity of the lignin model complexes pinacol monomethyl ether (A), 2-phenoxyethanol (B), and 1,2-diphenyl-2-methoxyethanol (C) (Figure 1). Reaction of (dipic)V{sup V}(O)O{sup i}Pr (1a) or (dipic)V{sup v}(O)OEt (lb) with A, B, or C in acetonitrile yielded new vanadium(V) complexes where the alcohol-ether ligand was bound in a chelating fashion. From the reaction of 1b with pinacol monomethyl ether (A) in acetonitrile solution, (dipic)V{sup v}(O)(pinOMe) (2) (PinOMe = 2,3-dimethyl-3-methoxy-2-butanoxide) was isolated in 61 % yield. Reaction of 1b with 2-phenoxyethanol (B) in acetonitrile gave the new complex (dipic)V{sup v}(O)(OPE) (3) (OPE = 2-phenoxyethoxide), which was isolated in 76% yield. In a similar fashion, 1a reacted with 1,2-diphenyl-2-methoxyethanol (C) to give (dipic)V(O)(DPME) (4) (DPME = 1,2-diphenyl-2-methoxyethoxide), which was isolated in 39% yield. Complexes 2, 3, and 4 were characterized by {sup 1}H NMR and IR spectroscopy, elemental analysis, and X-ray crystallography. Compared to the previously reported vanadium(V) pinacolate complex (dipic)V(O)(pinOH) the X-ray structure of complex 2 reveals a slightly shorter V = O bond, 1.573(2) {angstrom} vs 1.588(2) {angstrom} for the pinOH structure. Complexes 3 and 4 display similar vanadium oxo bond distances of 1.568(2) {angstrom} and 1.576(2) {angstrom}, respectively. All three complexes show longer bonds to the ether-oxygen trans to the oxo (2.388(2) {angstrom} for 2, 2.547(2) {angstrom} for 3, and 2.438(2) {angstrom} for 4) than to the hydroxy-oxygen in the pinOH structure (2.252(2) {angstrom}).
Hanson, Susan K [Los Alamos National Laboratory; Gordon, John C [Los Alamos National Laboratory; Thorn, David L [Los Alamos National Laboratory; Scott, Brian L [Los Alamos National Laboratory; Baker, R Tom [Los Alamos National Laboratory
Damage and rupture mechanisms in an austenoferritic duplex steel
The influence of ageing on damage and rupture mechanisms in an austenoferritic duplex stainless steel is studied using conventional straining and impact toughness testing at 20 C and 320 C, and in situ SEM straining at 20 C. While the as-received alloy fails in a ductile mode, damage in the aged material starts with cleavage nucleation in ferrite. The authors show that, owing to the bipercolated topology of the alloy, these cleavage cracks can propagate while passing round austenite ligaments whose plastic stretching controls the crack extension. The variations with strain of both the crack size and the average crack separation are computed analytically and their comparison gives a good prediction of ductility.
Verhaeghe, B.; Louchet, F.; Brechet, Y. [LTPCM-CNRS, St. Martin d`Heres (France). Groupe Physique du Metal] [LTPCM-CNRS, St. Martin d`Heres (France). Groupe Physique du Metal; Massoud, J.P. [EDF, Moret sur Loing (France)] [EDF, Moret sur Loing (France)
Effect of electric field on exfoliation of nanoplates Department of Mechanical Engineering, University of Michigan, Ann Arbor, Michigan 48109
Effect of electric field on exfoliation of nanoplates Wei Lua Department of Mechanical Engineering assist or retard exfoliation depending on the angle between a collection of plates and the field. A critical electric field strength for exfoliation is predicted. Structural refinement occurs by cleavage
Lu, Wei
AMEAerospace & Mechanical
AMEAerospace & Mechanical Engineering #12;Aerospace and Mechanical Engineers design complex mechanical, thermal, fluidic, acousti- cal, optical, and electronic systems, with char- acteristic sizes space. Aerospace and Mechanical Engineering (AME) students conduct basic and applied research within
Wang, Hai
Processing of 3'-Phosphoglycolate-Terminated DNA Double-StrandBreaks by Artemis Nuclease
The Artemis nuclease is required for V(D)J recombination and for repair of an as yet undefined subset of radiation-induced DNA double-strand breaks. To assess the possibility that Artemis functions on oxidatively modified double-strand break termini, its activity toward model DNA substrates, bearing either 3{prime}-hydroxyl or 3{prime}-phosphoglycolate moieties, was examined. A 3{prime}-phosphoglycolate had little effect on Artemis-mediated trimming of long 3{prime} overhangs (>9 nucleotides), which were efficiently trimmed to 4-5 nucleotides. However, 3{prime}-phosphoglycolates on overhangs of 4-5 bases promoted selective Artemis-mediated trimming of a single 3{prime}-terminal nucleotide, while at least 2 nucleotides were trimmed from identical hydroxyl-terminated substrates. Artemis also efficiently removed a single nucleotide from a phosphoglycolate-terminated 3-base 3{prime} overhang, while leaving an analogous hydroxyl-terminated overhang largely intact. Such removal was dependent upon Ku, DNA-dependent protein kinase, and ATP. Together, these data suggest that Artemis-mediated cleavage of 3{prime} overhangs requires a minimum of 2 nucleotides, or a nucleotide plus a phosphoglycolate, 3{prime} to the cleavage site. Shorter 3{prime}-phosphoglycolate-terminated overhangs and blunt ends were also processed by Artemis, but much less efficiently. Consistent with the in vitro substrate specificity of Artemis, human cells lacking Artemis exhibited hypersensitivity to X-rays, bleomycin and neocarzinostatin, which all induce 3{prime}-phosphoglycolate-terminated double-strand breaks. Collectively, these results suggest that 3{prime}-phosphoglycolate termini and/or specific classes of DNA ends that arise from such blocked termini are relevant Artemis substrates in vivo.
Povrik, Lawrence F.; Zhou, Tong; Zhou, Ruizhe; Cowan, Morton J.; Yannone, Steven M.
Cleavage of the SARS Coronavirus Spike Glycoprotein by Airway Proteases Enhances Virus Entry into Human
have direct implications for the cell entry mechanism of SARS-CoV along the respiratory system and the susceptibility of a recombinant native full-length S-protein trimer (triSpike) of the severe acute respiratory
Supramolecular DNA nanotechnology : discrete nanoparticle organization, three-dimensional DNA construction, and molecule templated DNA assembly.
??The field of structural DNA nanotechnology utilizes DNA's powerful base-pairing molecular recognition criteria to help solve real challenges facing researchers in material science and nanotechnology,� (more)
Aldaye, Faisal A., 1979-
Patterning nanocrystals using DNA
One of the goals of nanotechnology is to enable programmed self-assembly of patterns made of various materials with nanometer-sized control. This dissertation describes the results of experiments templating arrangements of gold and semiconductor nanocrystals using 2'-deoxyribonucleic acid (DNA). Previously, simple DNA-templated linear arrangements of two and three nanocrystals structures have been made.[1] Here, we have sought to assemble larger and more complex nanostructures. Gold-DNA conjugates with 50 to 100 bases self-assembled into planned arrangements using strands of DNA containing complementary base sequences. We used two methods to increase the complexity of the arrangements: using branched synthetic doublers within the DNA covalent backbone to create discrete nanocrystal groupings, and incorporating the nanocrystals into a previously developed DNA lattice structure [2][3] that self-assembles from tiles made of DNA double-crossover molecules to create ordered nanoparticle arrays. In the first project, the introduction of a covalently-branched synthetic doubler reagent into the backbone of DNA strands created a branched DNA ''trimer.'' This DNA trimer templated various structures that contained groupings of three and four gold nanoparticles, giving promising, but inconclusive transmission electron microscopy (TEM) results. Due to the presence of a variety of possible structures in the reaction mixtures, and due to the difficulty of isolating the desired structures, the TEM and gel electrophoresis results for larger structures having four particles, and for structures containing both 5 and 10 nm gold nanoparticles were inconclusive. Better results may come from using optical detection methods, or from improved sample preparation. In the second project, we worked toward making two-dimensional ordered arrays of nanocrystals. We replicated and improved upon previous results for making DNA lattices, increasing the size of the lattices to a length greater than 20 {micro}m, and collecting atomic force microscopy (AFM) images up to 30 {micro}m. We found the lattices' requirement of divalent magnesium cations to stabilize Holliday junctions to be incompatible with the stability of charge-stabilized gold nanoparticles used for the experiments here, and gold particles added indiscriminately to the lattice surface through non-specific binding. Redesigning the lattices to avoid magnesium may improve results.
Williams, Shara Carol
DNA Cleavage by Photogenerated Rh2(O2CCH3)4(H2O)2 Patty K.-L. Fu, Patricia M. Bradley, and Claudia Turro*
,8-anthraquinone disulfonate (AQ2-) was utilized,17 whose negative charge precludes its binding to the polyanionic
Mechanistic Examination of Cβ-Cγ Bond Cleavages of Tryptophan Residues
AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr MayAtmospheric Optical Depth7-1D: VegetationEquipment Surfaces andMapping the NanoscaleMechanical Behavior ofAPS ... SearchMechanisms
Strength of semiconductors, metals, and ceramics evaluated by a microscopic cleavage model with Morse-type and Lennard-Jones-type interaction
An improved microscopic cleavage model, based on a Morse-type and Lennard-Jones-type interaction instead of the previously employed half-sine function, is used to determine the maximum cleavage strength for the brittle materials diamond, tungsten, molybdenum, silicon, GaAs, silica, and graphite. The results of both interaction potentials are in much better agreement with the theoretical strength values obtained by ab initio calculations for diamond, tungsten, molybdenum, and silicon than the previous model. Reasonable estimates of the intrinsic strength are presented for GaAs, silica, and graphite, where first principles values are not available.
Hess, Peter [Institute of Physical Chemistry, University of Heidelberg, Im Neuenheimer Feld 253, D-69120 Heidelberg (Germany)
Strandwise translocation of a DNA glycosylase on undamaged DNA
Base excision repair of genotoxic nucleobase lesions in the genome is critically dependent upon the ability of DNA glycosylases to locate rare sites of damage embedded in a vast excess of undamaged DNA, using only thermal energy to fuel the search process. Considerable interest surrounds the question of how DNA glycosylases translocate efficiently along DNA while maintaining their vigilance for target damaged sites. Here, we report the observation of strandwise translocation of 8-oxoguanine DNA glycosylase, MutM, along undamaged DNA. In these complexes, the protein is observed to translocate by one nucleotide on one strand while remaining untranslocated on the complementary strand. We further report that alterations of single base-pairs or a single amino acid substitution (R112A) can induce strandwise translocation. Molecular dynamics simulations confirm that MutM can translocate along DNA in a strandwise fashion. These observations reveal a previously unobserved mode of movement for a DNA-binding protein along the surface of DNA.
Qi, Yan; Nam, Kwangho; Spong, Marie C.; Banerjee, Anirban; Sung, Rou-Jia; Zhang, Michael; Karplus, Martin; Verdine, Gregory L. (Harvard)
Coarse-graining DNA for simulations of DNA nanotechnology
To simulate long time and length scale processes involving DNA it is necessary to use a coarse-grained description. Here we provide an overview of different approaches to such coarse graining, focussing on those at the nucleotide level that allow the self-assembly processes associated with DNA nanotechnology to be studied. OxDNA, our recently-developed coarse-grained DNA model, is particularly suited to this task, and has opened up this field to systematic study by simulations. We illustrate some of the range of DNA nanotechnology systems to which the model is being applied, as well as the insights it can provide into fundamental biophysical properties of DNA.
Doye, Jonathan P K; Louis, Ard A; Romano, Flavio; Sulc, Petr; Matek, Christian; Snodin, Benedict E K; Rovigatti, Lorenzo; Schreck, John S; Harrison, Ryan M; Smith, William P J
DNA polymerase having modified nucleotide binding site for DNA sequencing
A modified gene encoding a modified DNA polymerase is disclosed. The modified polymerase incorporates dideoxynucleotides at least 20-fold better compared to the corresponding deoxynucleotides as compared with the corresponding naturally-occurring DNA polymerase. 6 figs.
Tabor, S.; Richardson, C.
DNA Structural Nanotechnology Duke University
DNA Structural Nanotechnology John Reif Duke University Graduate Students: Harish Chandran&Caltech Tube Lattices #12;Ned Seeman New York University, USA Ned Seeman: Father of DNA Nanotechnology His Initial Ideas & Motivation for DNA Nanotechnology #12;Cube Chen & Seeman, Nature350:631 (1991) Truncated
Reif, John H.
Fleet DNA (Presentation)
The Fleet DNA project objectives include capturing and quantifying drive cycle and technology variation for the multitude of medium- and heavy-duty vocations; providing a common data storage warehouse for medium- and heavy-duty vehicle fleet data across DOE activities and laboratories; and integrating existing DOE tools, models, and analyses to provide data-driven decision making capabilities. Fleet DNA advantages include: for Government - providing in-use data for standard drive cycle development, R&D, tech targets, and rule making; for OEMs - real-world usage datasets provide concrete examples of customer use profiles; for fleets - vocational datasets help illustrate how to maximize return on technology investments; for Funding Agencies - ways are revealed to optimize the impact of financial incentive offers; and for researchers -a data source is provided for modeling and simulation.
Walkokwicz, K.; Duran, A.
Dimension Augmentation and Combinatorial Criteria for Efficient Error-resistant DNA Self-assembly
Dimension Augmentation and Combinatorial Criteria for Efficient Error-resistant DNA Self-assembly Abstract DNA self-assembly has emerged as a rich and promising primitive for nano-technology. Experimental-correction mech- anisms have been proposed for the tile model of self- assembly. These error-correction mechanisms
Goel, Ashish
RESEARCH NOTE A proposed protocol for nomenclaturally effective DNA barcoding of microalgae
RESEARCH NOTE A proposed protocol for nomenclaturally effective DNA barcoding of microalgae barcoding of microalgae. Phycologia 48: 70�74. DOI: 10.2216/08-70.1. A mechanism for giving DNA barcodes nomenclatural status in microalgae via culture-derived epitypes is demonstrated with reference to four species
Chiral Mesophases of DNA
In the hexagonal columnar phase of chiral polymers a bias towards cholesteric twist competes with braiding along an average direction. When the chirality is strong, topological defects proliferate, leading to either a tilt grain boundary phase or a new ``moire state'' with twisted bond order. This moire phase can melt leading to a new phase: the chiral hexatic. I will discuss some recent experimental results from the NIH on DNA liquid crystals in the context of these theories.
Randall D. Kamien
DNA waves and water
Some bacterial and viral DNA sequences have been found to induce low frequency electromagnetic waves in high aqueous dilutions. This phenomenon appears to be triggered by the ambient electromagnetic background of very low frequency. We discuss this phenomenon in the framework of quantum field theory. A scheme able to account for the observations is proposed. The reported phenomenon could allow to develop highly sensitive detection systems for chronic bacterial and viral infections.
L. Montagnier; J. Aissa; E. Del Giudice; C. Lavallee; A. Tedeschi; G. Vitiello
Transcription Inhibition by Platinum DNA Cross-links in Live Mammalian Cells
We have investigated the processing of site-specific Pt?DNA cross-links in live mammalian cells to enhance our understanding of the mechanism of action of platinum-based anticancer drugs. The activity of platinum drugs ...
Ang, Wee Han
Mitochondrial DNA variation in populations of Peromyscus eremicus from the Sonoran and Chihuahuan Deserts
DNA divergence suggests a lack of gene flow between the two races and supports the hypothesis that these groups represent distinct species. Pliocene or late Pleistocene pluvial-interpluvial climatic fluctuations are implicated as the primary isolating mechanism...
Walpole, Deric King
Design, fabrication, and characterization of a motion stage for scalable imprinting of DNA nanowires
This thesis work examines the scalability of an imprinting stage utilizing parallel self-aligning mechanisms in a DNA combing and imprinting (DCl) process. Scalability is vital in developing efficient, low-cost and high-yield ...
LaColla, John J. (John Joseph)
Heterolytic Cleavage of H2 by Bifunctional Manganese(I) Complexes: Impact of Ligand Dynamics, Electrophilicity, and Base Positioning
We report the synthesis, characterization, and reactivity with H2 of a series of MnI complexes of the type [(P-P)Mn(L2)CO]+ (L2 = dppm, bppm, or (CO)2; P-P = PPhNMePPh or PPh2 NBn2 ) that bear pendant amine ligands designed to function as proton relays. The pendant amine was found to function as a hemilabile ligand; its binding strength is strongly affected by the ancillary ligand environment around Mn. Tuning the electrophilicity of the Mn center leads to systems capable of reversible heterolytic cleavage of the H-H bond. The strength of pendant amine binding can be balanced to protect the Mn center while still leading to facile reactivity with H2. Neutral amine-bearing MnIH species were found to react with one-electron oxidants and, after proton and electron transfer reactions, regenerate MnI cationic species. The reactivity presented herein indicate that the Mn complexes we have developed are a promising platform for Mn-based H2 oxidation electrocatalyst development. The research was supported as part of the Center for Molecular Electrocatalysis, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences. Pacific Northwest National Laboratory is operated by Battelle for DOE.
Hulley, Elliott B.; Helm, Monte L.; Bullock, R. Morris
Photofragmentation in linked donor-acceptor molecules. Intramolecular single electron transfer induced cleavage of a 1,2-diamine
Two intramolecular donor-acceptor molecules which fragment by a single electron transfer initiated cation radical carbon-carbon bond cleavage have been synthesized and their photoreactivity studied. The intramolecular [open quotes]diads[close quotes] consist of a 1,2-diamine linked via an ester bond to either an anthraquinone or a 9,10-dicyanoanthracene electron-acceptor chromophore. As the covalent linkage between the donor and acceptor chromophores prevents solvent separation of the photogenerated radical ion pair, these systems provide a [open quotes]clock[close quotes] to examine directly competition between fragmentation and back electron transfer. The linked anthraquinone molecule fragments efficiently, with quantum yields approaching 80%, despite the inability of the photoproduced radical ions to separate. These high yields may be attributed to a slow, spin-forbidden back electron transfer and a rapid fragmentation. In contrast, the quantum yields for the dicyanoanthracene diad (reactive singlet) are markedly lower, less than 0.001 in benzene. The reactivity of comparable intermolecular donor-acceptor combinations is also reported. 54 refs., 3 figs., 2 tabs.
Leon, J.W.; Whitten, D.G. (Univ. of Rochester, NY (United States))
AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr MayAtmospheric Optical Depth7-1D: Vegetation Proposed Newcatalyst phases onOrganization FY Middle SchoolARM-TR-01468This4t c
Plectoneme tip bubbles: Coupled denaturation and writhing in supercoiled DNA
Biological information is not only stored in the digital chemical sequence of double helical DNA, but is also encoded in the mechanical properties of the DNA strands, which can influence biochemical processes involving its readout. For example, loop formation in the Lac operon can regulate the expression of key genes, and DNA supercoiling is closely correlated to rhythmic circardian gene expression in cyanobacteria. Supercoiling is also important for large scale organisation of the genome in both eukaryotic and prokaryotic cells. DNA can respond to torsional stress by writhing to form looped structures called plectonemes, thus transferring energy stored as twist into energy stored in bending. Denaturation bubbles can also relax torsional stress, with the enthalpic cost of breaking bonds being compensated by their ability to absorb undertwist. Here we predict a novel regime where bubbles form at the tips of plectonemes, and study its properties using coarse-grained simulations. These tip bubbles can occur for both positive and negative supercoiling and greatly reduce plectoneme diffusion by a pinning mechanism. They can cause plectonemes to preferentially localise to AT rich regions, because bubbles more easily form there. The tip-bubble regime occurs for supercoiling densities and forces that are typically encountered for DNA in vivo, and may be exploited for biological control of genomic processes.
Christian Matek; Thomas E. Ouldridge; Jonathan P. K. Doye; Ard A. Louis
A Model for Structure and Thermodynamics of ssDNA and dsDNA Near...
Structure and Thermodynamics of ssDNA and dsDNA Near a Surface:A Coarse Grained Approach. A Model for Structure and Thermodynamics of ssDNA and dsDNA Near a Surface:A Coarse...
Radiation can damage cellular components, including DNA. Organisms have developed a panoply of means of dealing with DNA damage. Some repair paths have rather narrow substrate specificity (e.g. photolyases), which act on specific pyrimidine photoproducts in a specific type (e.g., DNA) and conformation (double-stranded B conformation) of nucleic acid. Others, for example, nucleotide excision repair, deal with larger classes of damages, in this case bulky adducts in DNA. A detailed discussion of DNA repair mechanisms is beyond the scope of this article, but one can be found in the excellent book of Friedberg et al. [1] for further detail. However, some DNA damages and paths for repair of those damages important for photobiology will be outlined below as a basis for the specific examples of genetic and molecular analysis that will be presented below.
Mechanical memory
A first-in-first-out (FIFO) microelectromechanical memory apparatus (also termed a mechanical memory) is disclosed. The mechanical memory utilizes a plurality of memory cells, with each memory cell having a beam which can be bowed in either of two directions of curvature to indicate two different logic states for that memory cell. The memory cells can be arranged around a wheel which operates as a clocking actuator to serially shift data from one memory cell to the next. The mechanical memory can be formed using conventional surface micromachining, and can be formed as either a nonvolatile memory or as a volatile memory.
Gilkey, Jeffrey C. (Albuquerque, NM); Duesterhaus, Michelle A. (Albuquerque, NM); Peter, Frank J. (Albuquerque, NM); Renn, Rosemarie A. (Albuquerque, NM); Baker, Michael S. (Albuquerque, NM)
Gilkey, Jeffrey C. (Albuquerque, NM); Duesterhaus, Michelle A. (Albuquerque, NM); Peter, Frank J. (Albuquerque, NM); Renn, Rosemarie A. (Alburquerque, NM); Baker, Michael S. (Albuquerque, NM)
Conserved and Unconventional Responses to DNA Damage in Tetrahymena
in the transition G1/S phase to promote the loading of DNA polymerases. Additionally CDK prevent any further activation of pre-RC. CDK also induce phosphorylation of Sld2, Sld3 and Mcm5 that promotes the initiation of DNA synthesis. Diagram modified from Sclafani... and Holzen (2007). Cdc45 Sld2-3 S-CDK Initiation G1 phase G1/S transition S phase 21 21 mechanism to restrict pre-RC formation to only once per cell cycle (Lutzmann et al., 2006). Cdc6 in budding yeast stimulates the Abf1 binding activity...
Sandoval Oporto, Pamela
Structure of an aprataxin?DNA complex with insights into AOA1 neurodegenerative disease
DNA ligases finalize DNA replication and repair through DNA nick-sealing reactions that can abort to generate cytotoxic 5'-adenylation DNA damage. Aprataxin (Aptx) catalyzes direct reversal of 5'-adenylate adducts to protect genome integrity. Here the structure of a Schizosaccharomyces pombe Aptx-DNA-AMP-Zn{sup 2+} complex reveals active site and DNA interaction clefts formed by fusing a histidine triad (HIT) nucleotide hydrolase with a DNA minor groove-binding C{sub 2}HE zinc finger (Znf). An Aptx helical 'wedge' interrogates the base stack for sensing DNA ends or DNA nicks. The HIT-Znf, the wedge and an '[F/Y]PK' pivot motif cooperate to distort terminal DNA base-pairing and direct 5'-adenylate into the active site pocket. Structural and mutational data support a wedge-pivot-cut HIT-Znf catalytic mechanism for 5'-adenylate adduct recognition and removal and suggest that mutations affecting protein folding, the active site pocket and the pivot motif underlie Aptx dysfunction in the neurodegenerative disorder ataxia with oculomotor apraxia 1 (AOA1).
Tumbale, Percy; Appel, C. Denise; Kraehenbuehl, Rolf; Robertson, Patrick D.; Williams, Jessica S.; Krahn, Joe; Ahel, Ivan; Williams, R. Scott (NIEHS); (Manchester)
Integrated Microfluidic Electrochemical DNA Sensor
of small scale fluid flow Laminar flow Easy to predict the flow patterns Very little diffusion This can make mixing difficult Small volumes Don't need to waste expensive reagents Easy fluid control;DNA Purification The DNA will be extracted using Invitrogen Charge Switch beads. Cellular Lysis
Fygenson, Deborah Kuchnir
Computational mechanics
The Computational Mechanics thrust area sponsors research into the underlying solid, structural and fluid mechanics and heat transfer necessary for the development of state-of-the-art general purpose computational software. The scale of computational capability spans office workstations, departmental computer servers, and Cray-class supercomputers. The DYNA, NIKE, and TOPAZ codes have achieved world fame through our broad collaborators program, in addition to their strong support of on-going Lawrence Livermore National Laboratory (LLNL) programs. Several technology transfer initiatives have been based on these established codes, teaming LLNL analysts and researchers with counterparts in industry, extending code capability to specific industrial interests of casting, metalforming, and automobile crash dynamics. The next-generation solid/structural mechanics code, ParaDyn, is targeted toward massively parallel computers, which will extend performance from gigaflop to teraflop power. Our work for FY-92 is described in the following eight articles: (1) Solution Strategies: New Approaches for Strongly Nonlinear Quasistatic Problems Using DYNA3D; (2) Enhanced Enforcement of Mechanical Contact: The Method of Augmented Lagrangians; (3) ParaDyn: New Generation Solid/Structural Mechanics Codes for Massively Parallel Processors; (4) Composite Damage Modeling; (5) HYDRA: A Parallel/Vector Flow Solver for Three-Dimensional, Transient, Incompressible Viscous How; (6) Development and Testing of the TRIM3D Radiation Heat Transfer Code; (7) A Methodology for Calculating the Seismic Response of Critical Structures; and (8) Reinforced Concrete Damage Modeling.
Goudreau, G.L.
The TGA codons are present in the open reading frame of selenoprotein P cDNA
The TGA codon in DNA has been shown to direct incorporation of selenocysteine into protein. Several proteins from bacteria and animals contain selenocysteine in their primary structures. Each of the cDNA clones of these selenoproteins contains one TGA codon in the open reading frame which corresponds to the selenocysteine in the protein. A cDNA clone for selenoprotein P (SeP), obtained from a {gamma}ZAP rat liver library, was sequenced by the dideoxy termination method. The correct reading frame was determined by comparison of the deduced amino acid sequence with the amino acid sequence of several peptides from SeP. Using SeP labelled with {sup 75}Se in vivo, the selenocysteine content of the peptides was verified by the collection of carboxymethylated {sup 77}Se-selenocysteine as it eluted from the amino acid analyzer and determination of the radioactivity contained in the collected samples. Ten TGA codons are present in the open reading frame of the cDNA. Peptide fragmentation studies and the deduced sequence indicate that selenium-rich regions are located close to the carboxy terminus. Nine of the 10 selenocysteines are located in the terminal 26% of the sequence with four in the terminal 15 amino acids. The deduced sequence codes for a protein of 385 amino acids. Cleavage of the signal peptide gives the mature protein with 366 amino acids and a calculated mol wt of 41,052 Da. Searches of PIR and SWISSPROT protein databases revealed no similarity with glutathione peroxidase or other selenoproteins.
Hill, K.E.; Lloyd, R.S.; Read, R.; Burk, R.F. (Vanderbilt Univ., Nashville, TN (United States))
Sequence independent amplification of DNA
The present invention is a rapid sequence-independent amplification procedure (SIA). Even minute amounts of DNA from various sources can be amplified independent of any sequence requirements of the DNA or any a priori knowledge of any sequence characteristics of the DNA to be amplified. This method allows, for example, the sequence independent amplification of microdissected chromosomal material and the reliable construction of high quality fluorescent in situ hybridization (FISH) probes from YACs or from other sources. These probes can be used to localize YACs on metaphase chromosomes but also--with high efficiency--in interphase nuclei. 25 figs.
Bohlander, S.K.
The present invention is a rapid sequence-independent amplification procedure (SIA). Even minute amounts of DNA from various sources can be amplified independent of any sequence requirements of the DNA or any a priori knowledge of any sequence characteristics of the DNA to be amplified. This method allows, for example the sequence independent amplification of microdissected chromosomal material and the reliable construction of high quality fluorescent in situ hybridization (FISH) probes from YACs or from other sources. These probes can be used to localize YACs on metaphase chromosomes but also--with high efficiency--in interphase nuclei.
Bohlander, Stefan K. (Chicago, IL)
Normalized cDNA libraries
This invention provides a method to normalize a directional cDNA library constructed in a vector that allows propagation in single-stranded circle form comprising: (a) propagating the directional cDNA library in single-stranded circles; (b) generating fragments complementary to the 3' noncoding sequence of the single-stranded circles in the library to produce partial duplexes; (c) purifying the partial duplexes; (d) melting and reassociating the purified partial duplexes to moderate Cot; and (e) purifying the unassociated single-stranded circles, thereby generating a normalized cDNA library.
Soares, Marcelo B. (New York, NY); Efstratiadis, Argiris (Englewood, NJ)
This invention provides a method to normalize a directional cDNA library constructed in a vector that allows propagation in single-stranded circle form comprising: (a) propagating the directional cDNA library in single-stranded circles; (b) generating fragments complementary to the 3{prime} noncoding sequence of the single-stranded circles in the library to produce partial duplexes; (c) purifying the partial duplexes; (d) melting and reassociating the purified partial duplexes to moderate Cot; and (e) purifying the unassociated single-stranded circles, thereby generating a normalized cDNA library. 4 figs.
Soares, M.B.; Efstratiadis, A.
Local chromatin structure of heterochromatin regulates repeatedDNA stability, nucleolus structure, and genome integrity
Heterochromatin constitutes a significant portion of the genome in higher eukaryotes; approximately 30% in Drosophila and human. Heterochromatin contains a high repeat DNA content and a low density of protein-encoding genes. In contrast, euchromatin is composed mostly of unique sequences and contains the majority of single-copy genes. Genetic and cytological studies demonstrated that heterochromatin exhibits regulatory roles in chromosome organization, centromere function and telomere protection. As an epigenetically regulated structure, heterochromatin formation is not defined by any DNA sequence consensus. Heterochromatin is characterized by its association with nucleosomes containing methylated-lysine 9 of histone H3 (H3K9me), heterochromatin protein 1 (HP1) that binds H3K9me, and Su(var)3-9, which methylates H3K9 and binds HP1. Heterochromatin formation and functions are influenced by HP1, Su(var)3-9, and the RNA interference (RNAi) pathway. My thesis project investigates how heterochromatin formation and function impact nuclear architecture, repeated DNA organization, and genome stability in Drosophila melanogaster. H3K9me-based chromatin reduces extrachromosomal DNA formation; most likely by restricting the access of repair machineries to repeated DNAs. Reducing extrachromosomal ribosomal DNA stabilizes rDNA repeats and the nucleolus structure. H3K9me-based chromatin also inhibits DNA damage in heterochromatin. Cells with compromised heterochromatin structure, due to Su(var)3-9 or dcr-2 (a component of the RNAi pathway) mutations, display severe DNA damage in heterochromatin compared to wild type. In these mutant cells, accumulated DNA damage leads to chromosomal defects such as translocations, defective DNA repair response, and activation of the G2-M DNA repair and mitotic checkpoints that ensure cellular and animal viability. My thesis research suggests that DNA replication, repair, and recombination mechanisms in heterochromatin differ from those in euchromatin. Remarkably, human euchromatin and fly heterochromatin share similar features; such as repeated DNA content, intron lengths and open reading frame sizes. Human cells likely stabilize their DNA content via mechanisms and factors similar to those in Drosophila heterochromatin. Furthermore, my thesis work raises implications for H3K9me and chromatin functions in complex-DNA genome stability, repeated DNA homogenization by molecular drive, and in genome reorganization through evolution.
Peng, Jamy C.
DNA Synthesis across an Abasic Lesion by Human DNA Polymerase I
Abasic sites are among the most abundant DNA lesions formed in human cells, and they present a strong block to replication. DNA polymerase{sup I} (Pol{sup I}) is one of the few DNA Pols that does not follow the A-rule opposite an abasic site. We present here three structures of human Pol in complex with DNAs containing an abasic lesion and dGTP, dTTP, or dATP as the incoming nucleotide. The structures reveal a mechanism of translesion synthesis across an abasic lesion that differs from that in other Pols. Both the abasic lesion and the incoming dNTPs are intrahelical and are closely apposed across a constricted active site cleft. The dNTPs partake in distinct networks of hydrogen bonds in the 'void' opposite the lesion. These different patterns of hydrogen bonds, as well as stacking interactions, may underlie Pol's small preference for insertion of dGTP over other nucleotides opposite this common lesion.
Nair, Deepak T.; Johnson, Robert E.; Prakash, Louise; Prakash, Satya; Aggarwal, Aneel K.; (Sinai); (Texas-MED)
Modeling DNA Shuffling Fengzhu Sun
Modeling DNA Shuffling Fengzhu Sun 1Department of Genetics Emory University School of Medicine property are selected. Irvine et al. (1991) and Sun et al. (1996) studied in vitro evolution not involving
Sun, Fengzhu - Sun, Fengzhu
Unnatural nucleotides for DNA sequencing
Fluorescent nucleotide analogs were prepared and tested to find surrogate structures that are: (i) incorporated by DNA polymerases; (ii) spectroscopically distinct for each fluorescent tag; and (iii) easily deprotected at the 3'-position under mild...
Jacutin, Swanee E
Molecular Computing with DNA Self-Assembly
Molecular Computing with DNA Self-Assembly Urmi Majumder #12;Self-Assembly in Nature #12;Key to DNA for Molecular Computing with DNA Self-Assembly Compact: Small library of assembly primitives Complex: Capable in Tiling Assembly: vitroation tural DNA self-assembly has powerful echanisms for error correction
Agreement Mechanisms
AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr May JunDatastreamsmmcrcalgovInstrumentsruc Documentation RUCProductstwrmrAre theAdministratorCFM LEAPAgenda AgendaAgreement Mechanisms
CONSULTATION RESPONSE The Forensic Use of DNA and the National DNA Database
CONSULTATION RESPONSE The Forensic Use of DNA and the National DNA Database Wellcome Trust response on the important topic of the forensic use of DNA and the National DNA Database (NDNAD). Given the Trust Assembly; "Forensic DNA Databasing: A European perspective" - a biomedical ethics grant to Professor Robin
Rambaut, Andrew
Quantum Confinement in Hydrogen Bond of DNA and RNA
The hydrogen bond is a fundamental ingredient to stabilize the DNA and RNA macromolecules. The main contribution of this work is to describe quantitatively this interaction as a consequence of the quantum confinement of the hydrogen. The results for the free and confined system are compared with experimental data. The formalism to compute the energy gap of the vibration motion used to identify the spectrum lines is the Variational Method allied to Supersymmetric Quantum Mechanics.
da Silva dos Santos; Elso Drigo Filho; Regina Maria Ricotta
Santos, da Silva dos; Ricotta, Regina Maria
DNA polymorphism identity determination using flow cytometry
DNA polymorphism identity determination using flow cytometry. Primers designed to be immobilized on microspheres are allowed to anneal to the DNA strand under investigation, and are extended by either DNA polymerase using fluorescent dideoxynucleotides or ligated by DNA ligase to fluorescent reporter oligonucleotides. The fluorescence of either the dideoxynucleotide or the reporter oligonucleotide attached to the immobilized primer is measured by flow cytometry, thereby identifying the nucleotide polymorphism on the DNA strand.
Nolan, John P. (Santa Fe, NM); White, P. Scott (Los Alamos, NM); Cai, Hong (Los Alamos, NM)
Mechanical Engineering ME 3720 FLUID MECHANICS
Mechanical Engineering ME 3720 FLUID MECHANICS Pre-requisite: ME 2330 Co-requisite: ME 3210) to develop an understanding of the physical mechanisms and the mathematical models of fluid mechanics of fluid mechanics problems in engineering practice. The basic principles of fluid mechanics
Panchagnula, Mahesh
Regulation of DNA damage tolerance : studies of the translesion synthesis DNA ploymerase eta in Saccharomyces cerevisiae
All organisms must control the effects of DNA damage to protect the integrity of their genomes. In addition to DNA repair, this requires DNA damage tolerance pathways, which allow the continuation of essential processes ...
Woodruff, Rachel Van Etten
Accelerated search kinetics mediated by redox reactions of DNA repair enzymes
A Charge Transport (CT) mechanism has been proposed in several papers (e.g., Yavin, et al. PNAS, v102 3546 (2005)) to explain the localization of Base Excision Repair (BER) enzymes to lesions on DNA. The CT mechanism relies on redox reactions of iron-sulfur cofactors that modify the enzyme's binding affinity. These redox reactions are mediated by the DNA strand and involve the exchange of electrons between BER enzymes along DNA. We propose a mathematical model that incorporates enzyme binding/unbinding, electron transport, and enzyme diffusion along DNA. Analysis of our model within a range of parameter values suggests that the redox reactions can increase desorption of BER enzymes not already bound to their targets, allowing the enzymes to be recycled, thus accelerating the overall search process. This acceleration mechanism is most effective when enzyme copy numbers and enzyme diffusivity along the DNA are small. Under such conditions, we find that CT BER enzymes find their targets more quickly than simple "passive" enzymes that simply attach to the DNA without desorbing.
Pak-Wing Fok; Tom Chou
In vivo and in vitro effects of ethanol on the incorporation and cleavage of sialic acid moieties in the brain before, during and after withdrawal from a chronic ethanol diet
IN VIVO AND IN VITRO EFFECTS OF ETHANOL ON THE INCORPORATION AND CLEAVAGE OF SIALIC ACID MOIETIES IN THE BRAIN BEFORE' DURING AND AFTER WITHDRAWAL FROM A CHRONIC ETHANOL DIET A Thesis by NESTOR ENRIQUE ACEVEDO-PABON Submitted to the Office... of Graduate Studies of Texas A&M University in partial fulfillment of the requirement for the degree of MASTER OF SCIENCE December 1988 Major Subject: Veterinary Anatomy IN VIVO AND IN VITRO EFFECTS OF ETHANOL ON THE INCORPORATION AND CLEAVAGE OF S IALI...
Acevedo-Pabon, Nestor Enrique
Evidence for an RNA-based catalytic mechanism in eukaryotic nuclear ribonuclease P.
neighbor is itali- cized+) Inspection of Figure 4 shows that these oligo- nucleotides could result only from cleavage at the normal RNase P site, �ApUp21Afp11GpC� for pre-G1Phe and �ApUp 21Afp11ApC� for pre-A1Phe+ In contrast, RNase P treatment...Evidence for an RNA-based catalytic mechanism in eukaryotic nuclear ribonuclease P BRIAN C. THOMAS,1,2,5 JOEL CHAMBERLAIN,3,6 DAVID R. ENGELKE,3,4 and PETER GEGENHEIMER1,2 1Department of Molecular Biosciences, The University of Kansas, 2045 Haworth...
Thoms, Brian C; Chamberlain, Joel; Engelke, David R; Gegenheimer, Peter Albert
Mechanical & Aerospace Engineering
Mechanical & Aerospace Engineering An experimental methodology is presented for mechanism verification of physics-based prognosis of mechanical damage, such as fatigue. The proposed experimental methodology includes multi-resolution in-situ mechanical testing, advanced imaging analysis, and mechanism
Photodegradation of oligomeric polyesters containing anthraquinone and 1,2-diamine units. Single electron transfer induced cation radical bond cleavage in the solid state
Oligomeric polyesters containing light-absorbing anthraquinone electron acceptor chromophores and fragmentable 1,2-diamine donors have been synthesized. Irradiation with [lambda] [ge] 340 nm in solution or as solid films results in photooxidative C-C bond cleavage of the 1,2-diamine units yielding essentially the same products in either case. The solid state photodegradation reaction was monitored using size exclusion chromatography and was found to be substantially less efficient than the corresponding solution reaction. This is attributed to an inefficient forward electron transfer step and the possibility of an induced reversibility of the fragmentation. The efficiency of photodegradation is suggested to be dependent on the donor/acceptor orientations in the solid state. 49 refs., 11 figs., 1 tab.
DNA Concentration By UV Spectrophotometry Measure Absorption
DNA Concentration By UV Spectrophotometry Measure Absorption: 1. Dilute DNA to 0.5 to 50 µg 2. Measure absorption at 260 nm (A260). Start by zeroing instrument with TE buffer or dH2O alone
Aris, John P.
Micropatterned cell arrays for detecting DNA damage
Numerous agents are capable of interacting with DNA and damaging it. Permanent changes in the DNA structure can be both mutagenic and cytotoxic; therefore, methods to measure the susceptibility of cells to mutations are ...
Mittal, Sukant
Towards Privacy Preserving of Forensic DNA Databases
Protecting privacy of individuals is critical for forensic genetics. In a kinship/identity testing, related DNA profiles between user's query and the DNA database need to be extracted. However, unrelated profiles cannot be revealed to each other...
Liu, Sanmin
Chromosome specific repetitive DNA sequences
A method is provided for determining specific nucleotide sequences useful in forming a probe which can identify specific chromosomes, preferably through in situ hybridization within the cell itself. In one embodiment, chromosome preferential nucleotide sequences are first determined from a library of recombinant DNA clones having families of repetitive sequences. Library clones are identified with a low homology with a sequence of repetitive DNA families to which the first clones respectively belong and variant sequences are then identified by selecting clones having a pattern of hybridization with genomic DNA dissimilar to the hybridization pattern shown by the respective families. In another embodiment, variant sequences are selected from a sequence of a known repetitive DNA family. The selected variant sequence is classified as chromosome specific, chromosome preferential, or chromosome nonspecific. Sequences which are classified as chromosome preferential are further sequenced and regions are identified having a low homology with other regions of the chromosome preferential sequence or with known sequences of other family me This invention is the result of a contract with the Department of Energy (Contract No. W-7405-ENG-36).
Moyzis, Robert K. (Los Alamos, NM); Meyne, Julianne (Los Alamos, NM)
International Standards in Forensic DNA
International Standards in Forensic DNA John M. Butler, Ph.D. National Institute of Standards and Technology NIST Fellow & Special Assistant to the Director for Forensic Science Vice-Chair, National Commission on Forensic Science World Forensics Festival Seoul, Korea October 15, 2014 #12;Definition
Amplification of chromosomal DNA in situ
Amplification of chromosomal DNA in situ to increase the amount of DNA associated with a chromosome or chromosome region is described. The amplification of chromosomal DNA in situ provides for the synthesis of Fluorescence in situ Hybridization (FISH) painting probes from single dissected chromosome fragments, the production of cDNA libraries from low copy mRNAs and improved in Comparative Genomic Hybridization (CGH) procedures.
Christian, Allen T. (Tracy, CA); Coleman, Matthew A. (Livermore, CA); Tucker, James D. (Livermore, CA)
DNA nanotubes and helical nanotapes via self-assembly of ssDNA-amphiphiles
DNA nanotubes and helical nanotapes via self- assembly of ssDNA-amphiphiles Timothy R. Pearcea and Efrosini Kokkoli*b DNA nanotubes were created using molecular self-assembly of single-stranded DNA (ss. The nanotube structures were formed by bilayers of amphiphiles, with the hydrophobic components forming
Kokkoli, Efie
Supplementary Information for: Integrating DNA Strand Displacement Circuitry with DNA Tile Self-assembly
Supplementary Information for: Integrating DNA Strand Displacement Circuitry with DNA Tile Self-assembly of Contents: · Supplementary Figures 1. Native polyacrylamide gel electrophoresis of DNA tile self-assembly 2. UV absorbance annealing and melting curves of DNA tile self-assembly 3. Characterization
Zhang, David Yu
Probe and method for DNA detection
A hybridization probe containing two linear strands of DNA lights up upon hybridization to a target DNA using silver nanoclusters that have been templated onto one of the DNA strands. Hybridization induces proximity between the nanoclusters on one strand and an overhang on the other strand, which results in enhanced fluorescence emission from the nanoclusters.
Yeh, Hsin-Chih; Werner, James Henry; Sharma, Jaswinder Kumar; Martinez, Jennifer Suzanne
Self-assembled DNA Structures for Nanoconstruction
Self-assembled DNA Structures for Nanoconstruction Hao Yan, Peng Yin, Sung Ha Park, Hanying Li methods based on DNA self-assembly. Here we review our recent experimental progress to utilize novel DNA nanostructures for self-assembly as well as for templates in the fabrication of functional nano
HELICASE DEPENDENT AMPLICATION transfer the DNA
STEP 1 STEP 2 STEP 3 HELICASE DEPENDENT AMPLICATION HELICASE DNA POLYMERASE transfer the DNA instrumentation. MOLECULAR BIOMARKERS MADE UP DNA or RNA STRANDS ARE A POWERFUL WEAPON IN DETECTING DISEASE. USING for sample preparation at the point to care using only hand generated power.... #12;
Binary electrokinetic separation of target DNA from background DNA primers.
This report contains the summary of LDRD project 91312, titled ''Binary Electrokinetic Separation of Target DNA from Background DNA Primers''. This work is the first product of a collaboration with Columbia University and the Northeast BioDefense Center of Excellence. In conjunction with Ian Lipkin's lab, we are developing a technique to reduce false positive events, due to the detection of unhybridized reporter molecules, in a sensitive and multiplexed detection scheme for nucleic acids developed by the Lipkin lab. This is the most significant problem in the operation of their capability. As they are developing the tools for rapidly detecting the entire panel of hemorrhagic fevers this technology will immediately serve an important national need. The goal of this work was to attempt to separate nucleic acid from a preprocessed sample. We demonstrated the preconcentration of kilobase-pair length double-stranded DNA targets, and observed little preconcentration of 60 base-pair length single-stranded DNA probes. These objectives were accomplished in microdevice formats that are compatible with larger detection systems for sample pre-processing. Combined with Columbia's expertise, this technology would enable a unique, fast, and potentially compact method for detecting/identifying genetically-modified organisms and multiplexed rapid nucleic acid identification. Another competing approach is the DARPA funded IRIS Pharmaceutical TIGER platform which requires many hours for operation, and an 800k$ piece of equipment that fills a room. The Columbia/SNL system could provide a result in 30 minutes, at the cost of a few thousand dollars for the platform, and would be the size of a shoebox or smaller.
James, Conrad D.; Derzon, Mark Steven
Pliable DNA Conformation of Response Elements Bound to Transcription Factor p63
We show that changes in the nucleotide sequence alter the DNA conformation in the crystal structures of p63 DNA-binding domain (p63DBD) bound to its response element. The conformation of a 22-bp canonical response element containing an AT spacer between the two half-sites is unaltered compared with that containing a TA spacer, exhibiting superhelical trajectory. In contrast, a GC spacers abolishes the DNA superhelical trajectory and exhibits less bent DNA, suggesting that increased GC content accompanies increased double helix rigidity. A 19-bp DNA, representing an AT-rich response element with overlapping half-sites, maintains superhelical trajectory and reveals two interacting p63DBD dimers crossing one another at 120{sup o}. p63DBD binding assays to response elements of increasing length complement the structural studies. We propose that DNA deformation may affect promoter activity, that the ability of p63DBD to bind to superhelical DNA suggests that it is capable of binding to nucleosomes, and that overlapping response elements may provide a mechanism to distinguish between p63 and p53 promoters.
Chen, Chen; Gorlatova, Natalia; Herzberg, Osnat (Maryland)
Regulation of chloroplast number and DNA synthesis in higher plants. Final report
The long term objective of this research is to understand the process of chloroplast development and its coordination with leaf development in higher plants. This is important because the photosynthetic capacity of plants is directly related to leaf and chloroplast development. This research focuses on obtaining a detailed description of leaf development and the early steps in chloroplast development including activation of plastid DNA synthesis, changes in plastid DNA copy number, activation of chloroplast transcription and increases in plastid number per cell. The grant will also begin analysis of specific biochemical mechanisms by isolation of the plastid DNA polymerase, and identification of genetic mutants which are altered in their accumulation of plastid DNA and plastid number per cell.
Mullet, J.E.
The long term objective of this research is to understand the process of chloroplast development and its coordination with leaf development in higher plants. This is important because the photosynthetic capacity of plants is directly related to leaf and chloroplast development. This research focuses on obtaining a detailing description of leaf development and the early steps in chloroplast development including activation of plastid DNA synthesis, changes in plastid DNA copy number, activation of chloroplast transcription and increases in plastid number per cell. The grant will also begin analysis of specific biochemical mechanisms by isolation of the plastid DNA polymerase, and identification of genetic mutants which are altered in their accumulation of plastid DNA and plastid number per cell.
Mechanical and Aerospace Engineering
Mechanical and Aerospace Engineering seminar Three Dimensional Traction Force Microscopy with Applications in Cell Mechanics abstract The interactions between biochemical and mechanical signals during-dimensional measurement techniques are needed to investigate the effect of mechanical properties of the substrate
Mechanical Engineer Company Description
Mechanical Engineer Company Description Control Solutions Inc. is a small, dynamic, and rapidly. Position Description The Mechanical Engineer is responsible for all aspects associated with the mechanical enclosures, brackets, cabling assemblies among others. Systems include mechanisms, sensors, hydraulics, among
Kostic, Milivoje M.
MECHANICAL ENGINEERING Ross Schlueter
MECHANICAL ENGINEERING Ross Schlueter Engineering Deputy For Mechanical Engineering Russ Wells Mechanical Engineering Department Deputy ELECTRONICS, SOFTWARE & INSTRUMENTATION ENGINEERING Henrik von Der Sen Mechanical Admin. Assist. Joan Wolter Electronics Admin. Assist. Marilyn Wong Division Admin
Microfluidic DNA sample preparation method and device
Manipulation of DNA molecules in solution has become an essential aspect of genetic analyses used for biomedical assays, the identification of hazardous bacterial agents, and in decoding the human genome. Currently, most of the steps involved in preparing a DNA sample for analysis are performed manually and are time, labor, and equipment intensive. These steps include extraction of the DNA from spores or cells, separation of the DNA from other particles and molecules in the solution (e.g. dust, smoke, cell/spore debris, and proteins), and separation of the DNA itself into strands of specific lengths. Dielectrophoresis (DEP), a phenomenon whereby polarizable particles move in response to a gradient in electric field, can be used to manipulate and separate DNA in an automated fashion, considerably reducing the time and expense involved in DNA analyses, as well as allowing for the miniaturization of DNA analysis instruments. These applications include direct transport of DNA, trapping of DNA to allow for its separation from other particles or molecules in the solution, and the separation of DNA into strands of varying lengths.
Krulevitch, Peter A. (Pleasanton, CA); Miles, Robin R. (Danville, CA); Wang, Xiao-Bo (San Diego, CA); Mariella, Raymond P. (Danville, CA); Gascoyne, Peter R. C. (Bellaire, TX); Balch, Joseph W. (Livermore, CA)
Fleet DNA Project (Fact Sheet)
The Fleet DNA Project - designed by the U.S. Department of Energy's National Renewable Energy Laboratory (NREL) in partnership with Oak Ridge National Laboratory - aims to accelerate the evolution of advanced vehicle development and support the strategic deployment of market-ready technologies that reduce costs, fuel consumption, and emissions. At the heart of the Fleet DNA Project is a clearinghouse of medium- and heavy-duty commercial fleet transportation data for optimizing the design of advanced vehicle technologies or for selecting a given technology to invest in. An easy-to-access online database will help vehicle manufacturers and fleets understand the broad operational range for many of today's commercial vehicle vocations.
Electromagnetic Signals from Bacterial DNA
Chemical reactions can be induced at a distance due to the propagation of electromagnetic signals during intermediate chemical stages. Although is is well known at optical frequencies, e.g. photosynthetic reactions, electromagnetic signals hold true for muck lower frequencies. In E. coli bacteria such electromagnetic signals can be generated by electric transitions between energy levels describing electrons moving around DNA loops. The electromagnetic signals between different bacteria within a community is a "wireless" version of intercellular communication found in bacterial communities connected by "nanowires". The wireless broadcasts can in principle be of both the AM and FM variety due to the magnetic flux periodicity in electron energy spectra in bacterial DNA orbital motions.
A. Widom; J. Swain; Y. N. Srivastava; S. Sivasubramanian
Channel plate for DNA sequencing
This invention is a channel plate that facilitates data compaction in DNA sequencing. The channel plate has a length, a width and a thickness, and further has a plurality of channels that are parallel. Each channel has a depth partially through the thickness of the channel plate. Additionally an interface edge permits electrical communication across an interface through a buffer to a deposition membrane surface. 15 figs.
Douthart, R.J.; Crowell, S.L.
In Situ Live Cell Sensing of Multiple Nucleotides Exploiting DNA/RNA Aptamers and Graphene Oxide Nanosheets
Adenosine-5�-triphosphate (ATP) and guanosine-5�-triphosphate (GTP) are primary energy resources and function coordinately for numerous reactions such as microtubule assembly, insulin secretion and ion channel regulation. We have developed a novel DNA/RNA aptamer- graphene oxide nanosheet (GO-nS) sensing platform that can selectively and simultaneously detect ATP and GTP in live cells. A fluorescent tag is covalently attached to aptamers and fluorescence is quenched upon binding of aptamer to the GO-nS. Fluorescently tagged aptamers that selectively bind ATP or GTP were isolated from an aptamer library and were adsorbed onto GO-nS. Upon incubation with targets (ATP and/or GTP), the aptamers readily dissociated from GO-nS and the fluorescent signal was recovered. By covalently attaching fluorophores, both ATP and GTP sensing aptamers could be exploited to simultaneously visualize aptamer dissociation in live cells. In addition, the GO-nS appear to be biocompatible and protect the adsorbed DNA/RNA aptamers from enzymatic cleavage. Our results support the application of aptamer/GO-nS as a sensing platform for nucleotides in living cells and have implications for the development of additional sensor platforms for other bio-molecules that show selective interactions with aptamers and other biomarkers.
Wang, Ying; Li, Zhaohui; Weber, Thomas J.; Hu, Dehong; Lin, Chiann Tso; Li, Jinghong; Lin, Yuehe
Heterolytic Cleavage of Hydrogen by an Iron Hydrogenase Model: An Fe-H - - - H-N Dihydorgen Bond Characterized by Neutron Diffraction
Use of hydrogen as a fuel by [FeFe]-hydrogenase enzymes in nature requires heterolytic cleavage of the H-H bond into a proton (H+) and hydride (H-), a reaction that is also a critical step in homogeneous catalysts for hydrogenation of C=O and C=N bonds. An understanding of the catalytic oxidation of H2 by hydrogenases provides insights into the design of synthetic catalysts that are sought as cost-effective alternatives to the use of the precious metal platinum in fuel cells. Crystallographic studies on the [FeFe]-hydrogenase enzyme were critical to understanding of its reactivity, but the key H-H cleavage step is not readily observed experimentally in natural hydrogenases. Synthetic biomimics have provided evidence for H2 cleavage leading to hydride transfer to the metal and proton transfer to an amine. Limitations on the precise location of hydrogen atoms by x-ray diffraction can be overcome by use of neutron diffraction, though its use is severely limited by the difficulty of obtaining suitable crystals and by the scarcity of neutron sources. Here we show that an iron complex with a pendant amine in the diphosphine ligand cleaves hydrogen heterolytically under mild conditions, leading to [CpC5F4NFeH(PtBu2NtBu2H)]+BArF4-, [PtBu2NtBu2 = 1,5-di(tert-butyl)-3,7-di(tert-butyl)-1,5-diaza-3,7-diphosphacyclooctane; ArF = 3,5-bis(trifluoromethyl)phenyl]. The Fe-H- - - H-N moiety has a strong dihydrogen bond, with a remarkably short H � � � H distance of 1.489(10) � between the protic N-H?+ and hydridic Fe-H?-. The structural data for [CpC5F4NFeH(PtBu2NtBu2H)]+ provide a glimpse of how the H-H bond is oxidized or generated in hydrogenase enzymes, with the pendant amine playing a key role as a proton relay. The iron complex [CpC5F4NFeH(PtBu2NtBu2H)]+BArF4- is an electrocatalyst for oxidation of H2 (1 atm) at 22 �C, so the structural data are obtained on a complex that is a functional model for catalysis by [FeFe]-hydrogenase enzymes. This research was supported as part of the Center for Molecular Electrocatalysis, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences. Pacific Northwest National Laboratory is operated by Battelle for the U.S. Department of Energy.
Liu, Tianbiao L.; Wang, Xiaoping; Hoffmann, Christina; DuBois, Daniel L.; Bullock, R. Morris
) MICROFLUIDICS PLATFORMS _______________ A Thesis Presented to the Faculty of San Diego State University in Compact Disk (CD) Microfluidics Platforms by Nithesh Paramesh Master of Science in Mechanical Engineering and hybridization of DNA molecules in CD microfluidics platform where centrifugal force is used as the driving force
Kassegne, Samuel Kinde
ENGINEERING MECHANICS SEMINARSENGINEERING MECHANICS SEMINARS THINK COMPOSITE "THINK outside the box" for more competitive structural COMPOSITES Dr. Melih Papila Visiting Professor, Aero/Astro Department, Stanford University. Adv. Composites and Polymer Processing Lab., Sabanci University, Istanbul. mpapila
Ponce, V. Miguel
Heavy Mobile Equipment Mechanic (One Mechanic Shop)
Broader source: Energy.gov [DOE]
The position is a Heavy Mobile Equipment Mechanic (One Mechanic Shop) located in Kent, Washington, and will be responsible for the safe and efficient operation of a field garage performing...
The dynamic interplay between DNA damage and metabolism : the metabolic fate and transport of DNA lesions and novel DNA damage derived from intermediary metabolism
The work presented in this thesis explores two novel and complementary facets of endogenous DNA damage: the development of biomarkers of inflammation based on metabolites of DNA damage products and the formation of DNA ...
Jumpathong, Watthanachai
AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr MayAtmospheric Optical Depth7-1D: Vegetation Proposed Newcatalyst phases onOrganization FY Middle SchoolARM-TR-01468This4t c 5DMSEdrives
Enhancing the DNA Patent Database
Final Report on Award No. DE-FG0201ER63171 Principal Investigator: LeRoy B. Walters February 18, 2008 This project successfully completed its goal of surveying and reporting on the DNA patenting and licensing policies at 30 major U.S. academic institutions. The report of survey results was published in the January 2006 issue of Nature Biotechnology under the title �The Licensing of DNA Patents by US Academic Institutions: An Empirical Survey.� Lori Pressman was the lead author on this feature article. A PDF reprint of the article will be submitted to our Program Officer under separate cover. The project team has continued to update the DNA Patent Database on a weekly basis since the conclusion of the project. The database can be accessed at dnapatents.georgetown.edu. This database provides a valuable research tool for academic researchers, policymakers, and citizens. A report entitled Reaping the Benefits of Genomic and Proteomic Research: Intellectual Property Rights, Innovation, and Public Health was published in 2006 by the Committee on Intellectual Property Rights in Genomic and Protein Research and Innovation, Board on Science, Technology, and Economic Policy at the National Academies. The report was edited by Stephen A. Merrill and Anne-Marie Mazza. This report employed and then adapted the methodology developed by our research project and quoted our findings at several points. (The full report can be viewed online at the following URL: http://www.nap.edu/openbook.php?record_id=11487&page=R1). My colleagues and I are grateful for the research support of the ELSI program at the U.S. Department of Energy.
Walters, LeRoy B.
Detection and Repair of Ionizing Radiation-Induced DNA Double Strand Breaks: New Developments in Nonhomologous End Joining
DNA damage can occur as a result of endogenous metabolic reactions and replication stress or from exogenous sources such as radiation therapy and chemotherapy. DNA double strand breaks are the most cytotoxic form of DNA damage, and defects in their repair can result in genome instability, a hallmark of cancer. The major pathway for the repair of ionizing radiation-induced DSBs in human cells is nonhomologous end joining. Here we review recent advances on the mechanism of nonhomologous end joining, as well as new findings on its component proteins and regulation.
Wang, Chen [Departments of Biochemistry and Molecular Biology and Oncology, and Southern Alberta Cancer Research Institute, University of Calgary, Calgary (Canada)] [Departments of Biochemistry and Molecular Biology and Oncology, and Southern Alberta Cancer Research Institute, University of Calgary, Calgary (Canada); Lees-Miller, Susan P., E-mail: firstname.lastname@example.com [Departments of Biochemistry and Molecular Biology and Oncology, and Southern Alberta Cancer Research Institute, University of Calgary, Calgary (Canada)
DNA-guided nanoparticle assemblies
In some embodiments, DNA-capped nanoparticles are used to define a degree of crystalline order in assemblies thereof. In some embodiments, thermodynamically reversible and stable body-centered cubic (bcc) structures, with particles occupying <.about.10% of the unit cell, are formed. Designs and pathways amenable to the crystallization of particle assemblies are identified. In some embodiments, a plasmonic crystal is provided. In some aspects, a method for controlling the properties of particle assemblages is provided. In some embodiments a catalyst is formed from nanoparticles linked by nucleic acid sequences and forming an open crystal structure with catalytically active agents attached to the crystal on its surface or in interstices.
Gang, Oleg; Nykypanchuk, Dmytro; Maye, Mathew; van der Lelie, Daniel
Human Genome Research: Decoding DNA
AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr MayAtmospheric Optical Depth7-1D: Vegetation ProposedUsingFun withconfinement plasmas inPortalAllBPA addressesHowHughHumanDecoding DNA
Mechanical & Biomedical Engineering
Mechanical & Biomedical Engineering Department BACHELOR OF SCIENCE IN MECHANICAL ENGINEERING COURSE 105 Mechanical Engineering Graphics 3 CHEM 111L College Chemistry Lab (DLN) 1 ENGL 102 English PHYS 211 Mechanics, Waves & Heat (DLN) 4 UF 100 Intellectual Foundations 3 PHYS 211L Mechanics, Waves
Barrash, Warren
Assembling semiconductor nanocomposites using DNA replication technologies.
Deoxyribonucleic acid (DNA) molecules represent Nature's genetic database, encoding the information necessary for all cellular processes. From a materials engineering perspective, DNA represents a nanoscale scaffold with highly refined structure, stability across a wide range of environmental conditions, and the ability to interact with a range of biomolecules. The ability to mass-manufacture functionalized DNA strands with Angstrom-level resolution through DNA replication technology, however, has not been explored. The long-term goal of the work presented in this report is focused on exploiting DNA and in vitro DNA replication processes to mass-manufacture nanocomposite materials. The specific objectives of this project were to: (1) develop methods for replicating DNA strands that incorporate nucleotides with ''chemical handles'', and (2) demonstrate attachment of nanocrystal quantum dots (nQDs) to functionalized DNA strands. Polymerase chain reaction (PCR) and primer extension methodologies were used to successfully synthesize amine-, thiol-, and biotin-functionalized DNA molecules. Significant variability in the efficiency of modified nucleotide incorporation was observed, and attributed to the intrinsic properties of the modified nucleotides. Noncovalent attachment of streptavidin-coated nQDs to biotin-modified DNA synthesized using the primer extension method was observed by epifluorescence microscopy. Data regarding covalent attachment of nQDs to amine- and thiol-functionalized DNA was generally inconclusive; alternative characterization tools are necessary to fully evaluate these attachment methods. Full realization of this technology may facilitate new approaches to manufacturing materials at the nanoscale. In addition, composite nQD-DNA materials may serve as novel recognition elements in sensor devices, or be used as diagnostic tools for forensic analyses. This report summarizes the results obtained over the course of this 1-year project.
Heimer, Brandon W.; Crown, Kevin K.; Bachand, George David
Optical Recognition of Converted DNA Nucleotides for Single-Molecule DNA
Optical Recognition of Converted DNA Nucleotides for Single-Molecule DNA Sequencing Using Nanopore among individual nucleotides (nt). The system must be capable of differentiating among the four bases
Chemical biology of mutagenesis and DNA repair: cellular responses to DNA alkylation
The reaction of DNA-damaging agents with the genome results in a plethora of lesions, commonly referred to as adducts. Adducts may cause DNA to mutate, they may represent the chemical precursors of lethal events and they ...
Shrivastav, Nidhi
Nucleotide capacitance calculation for DNA sequencing
Using a first-principles linear response theory, the capacitance of the DNA nucleotides, adenine, cytosine, guanine and thymine, are calculated. The difference in the capacitance between the nucleotides is studied with respect to conformational distortion. The result suggests that although an alternate current capacitance measurement of a single-stranded DNA chain threaded through a nano-gap electrodes may not sufficient to be used as a stand alone method for rapid DNA sequencing, the capacitance of the nucleotides should be taken into consideration in any GHz-frequency electric measurements and may also serve as an additional criterion for identifying the DNA sequence.
Lu, Jun-Qiang [ORNL; Zhang, Xiaoguang [ORNL
Mechanical Engineering Graduate Student
......................................................................................9 Engineering Career Services ................................................................9 McMechanical Engineering Graduate Student Handbook January 2014 Department of Mechanical Engineering University of Wisconsin-Madison #12;Mechanical Engineering Web Page: http://www.engr.wisc.edu/me Graduate
Wisconsin at Madison, University of
Mechanical & Industrial Engineering
Mechanical & Industrial Engineering 1 Welcome MIE Industrial Advisory Board October 15, 2010 #12;Mechanical & Industrial Engineering 2 MIE Dorothy Adams Undergraduate/Graduate Secretary David Schmidt Associate Professor & Graduate Program Director #12;Mechanical & Industrial Engineering 3 MIE James Rinderle
Mountziaris, T. J.
Mechanical engineering Department Seminar
and the Department of Mechanical Engineering Tufts University Retooling Our Energy Ecosystem: challengesMechanical engineering Department Seminar Robert J. Hannemann The Gordon Institute and Chair of the Tufts Department of Mechanical Engineering. His technical and academic interests
HANDBOOK FOR MECHANICAL ENGINEERING UNDERGRADUATE MAJOR Old Dominion University Department of Mechanical Engineering Batten College of Engineering and Technology Norfolk, Virginia 23529-0247 #12;TABLE OF CONTENTS MECHANICAL ENGINEERING HANDBOOK
Mechanical engineering Department Seminar Katia Bertoldi Harvard University Soft materials in response to diverse stimuli. While the mechanical attributes - such as energy absorption, stiffness and switchable functionalities. Katia Bertoldi is an Assistant Professor of Applied Mechanics at Harvard
Differences in Electrostatic Potential Around DNA Fragments Containing Guanine and 8-oxo-Guanine
hanges of electrostatic potential (EP) around the DNA molecule resulting from chemical modifications of nucleotides may play a role in enzymatic recognition of damaged sites. Effects of chemical modifications of nucleotides on the structure of DNA have been characterized through large scale density functional theory computations. Quantum mechanical structural optimizations of DNA fragments with three pairs of nucleotoides and accompanying counteractions were performed with a B3LYP exchange-correlation functional and 6-31G** basis sets. The �intact� DNA fragment contained guanine in the middle layer, while the �damaged� fragment had the guanine replaced with 8-oxo-guanine. The electrostatic potential around these DNA fragments was projected on a surface around the double helix. The 2D maps of EP of intact and damaged DNA fragments were analyzed to identify these modifications of EP that result from the occurrence of 8-oxo-guanine. It was found that distortions of the phosphate groups and displacements of the accompanying countercations are clearly reflected in the EP maps.
Haranczyk, Maciej; Gutowski, Maciej S.
DNA repair efficiency in germ cells and early mouse embryos and consequences for radiation-induced transgenerational genomic damage
Exposure to ionizing radiation and other environmental agents can affect the genomic integrity of germ cells and induce adverse health effects in the progeny. Efficient DNA repair during gametogenesis and the early embryonic cycles after fertilization is critical for preventing transmission of DNA damage to the progeny and relies on maternal factors stored in the egg before fertilization. The ability of the maternal repair machinery to repair DNA damage in both parental genomes in the fertilizing egg is especially crucial for the fertilizing male genome that has not experienced a DNA repair-competent cellular environment for several weeks prior to fertilization. During the DNA repair-deficient period of spermatogenesis, DNA lesions may accumulate in sperm and be carried into the egg where, if not properly repaired, could result in the formation of heritable chromosomal aberrations or mutations and associated birth defects. Studies with female mice deficient in specific DNA repair genes have shown that: (i) cell cycle checkpoints are activated in the fertilized egg by DNA damage carried by the sperm; and (ii) the maternal genotype plays a major role in determining the efficiency of repairing genomic lesions in the fertilizing sperm and directly affect the risk for abnormal reproductive outcomes. There is also growing evidence that implicates DNA damage carried by the fertilizing gamete as a mediator of postfertilization processes that contribute to genomic instability in subsequent generations. Transgenerational genomic instability most likely involves epigenetic mechanisms or error-prone DNA repair processes in the early embryo. Maternal and embryonic DNA repair processes during the early phases of mammalian embryonic development can have far reaching consequences for the genomic integrity and health of subsequent generations.
Marchetti, Francesco; Wyrobek, Andrew J.
The 2013 Gordon Conference on Inorganic Reaction Mechanisms will present cutting-edge research on the molecular aspects of inorganic reactions involving elements from throughout the periodic table and state-of-the art techniques that are used in the elucidation of reaction mechanisms. The Conference will feature a wide range of topics, such as homogeneous and heterogeneous catalysis, metallobiochemistry, electron-transfer in energy reactions, polymerization, nitrogen fixation, green chemistry, oxidation, solar conversion, alkane functionalization, organotransition metal chemistry, and computational chemistry. The talks will cover themes of current interest including energy, materials, and bioinorganic chemistry. Sections cover: Electron-Transfer in Energy Reactions; Catalytic Polymerization and Oxidation Chemistry; Kinetics and Spectroscopy of Heterogeneous Catalysts; Metal-Organic Chemistry and its Application in Synthesis; Green Energy Conversion;Organometallic Chemistry and Activation of Small Molecules; Advances in Kinetics Modeling and Green Chemistry; Metals in Biology and Disease; Frontiers in Catalytic Bond Activation and Cleavage.
Abu-Omar, Mahdi M.
A DNA Based Implementation of an Evolutionary Search for Good Encodings for DNA Computation
lelism, capacity, and power. This potential, however, is limited by the constraints imposed by the DNA chemistry 1]. Adleman 2] introduced a way to solve combina- torial optimization problems with DNA- mental reaction in DNA based computation is hydro- gen bonding between Watson-Crick complement base pairs
Deaton, Russell J.
The androgen receptor independent mechanism of toxicity of the novel anti-tumor agent 11[beta]-dichloro
Inspired by the toxicity mechanism of cisplatin in testicular cancer, a series of bi-functional genotoxicants has been designed that supplement their DNA damaging properties with the ability to interact with tumor specific ...
Fedele?, Bogdan I
Dynamics and control of DNA sequence amplification
DNA amplification is the process of replication of a specified DNA sequence in vitro through time-dependent manipulation of its external environment. A theoretical framework for determination of the optimal dynamic operating conditions of DNA amplification reactions, for any specified amplification objective, is presented based on first-principles biophysical modeling and control theory. Amplification of DNA is formulated as a problem in control theory with optimal solutions that can differ considerably from strategies typically used in practice. Using the Polymerase Chain Reaction as an example, sequence-dependent biophysical models for DNA amplification are cast as control systems, wherein the dynamics of the reaction are controlled by a manipulated input variable. Using these control systems, we demonstrate that there exists an optimal temperature cycling strategy for geometric amplification of any DNA sequence and formulate optimal control problems that can be used to derive the optimal temperature profile. Strategies for the optimal synthesis of the DNA amplification control trajectory are proposed. Analogous methods can be used to formulate control problems for more advanced amplification objectives corresponding to the design of new types of DNA amplification reactions.
Marimuthu, Karthikeyan [Department of Chemical Engineering and Center for Advanced Process Decision-Making, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213 (United States); Chakrabarti, Raj, E-mail: email@example.com, E-mail: email@example.com [Department of Chemical Engineering and Center for Advanced Process Decision-Making, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213 (United States); Division of Fundamental Research, PMC Advanced Technology, Mount Laurel, New Jersey 08054 (United States)
DNA Motif Representation with Nucleotide Dependency
DNA Motif Representation with Nucleotide Dependency Francis Chin1 and Henry Leung1 1 Department, these representations cannot model biological binding sites well because they fail to capture nucleotide interdependence. It has been pointed out by many researchers that the nucleotides of the DNA binding site cannot
Chin, Francis Y.L.
Recombinant DNA encoding a desulfurization biocatalyst
This invention relates to a recombinant DNA molecule containing a gene or genes which encode a biocatalyst capable of desulfurizing a fossil fuel which contains organic sulfur molecules. For example, the present invention encompasses a recombinant DNA molecule containing a gene or genes of a strain of Rhodococcus rhodochrous. 13 figs.
Rambosek, J.; Piddington, C.S.; Kovacevich, B.R.; Young, K.D.; Denome, S.A.
Electric DNA chips for determination of pathogenic microorganisms
Electric DNA chips for determination of pathogenic microorganisms Yanling Liu Doctoral thesis Liu (2008): Electric DNA chips for determination of pathogenic microorganisms. School of Biotechnology, Royal Institute of Technology (KTH), Stockholm, Sweden Abstract Silicon-based electric DNA chip arrays
Enfors, Sven-Olof
Mitochondrial DNA phylogenetic analysis of Myrmecolacidae (Insecta: Strepsiptera) va
Guinea are determined. Methods were developed for extraction, amplification, and sequencing of mitochondrial DNA (mtDNA) from Strepsiptera. High-resolution mtDNA sequences obtained by these methods were used in the phylogenetic analysis of Myrmecolacidae...
Halbert, Natalie Rose
Single molecule analysis of DNA electrophoresis in microdevices
Given that current electrophoresis technology is inadequate for mapping large O[100 kilobasepair] DNA, several promising lab-on-chip designs for DNA mapping have been recently proposed that require either 1) a DNA molecule ...
Randall, Greg C
Flow cytometric detection method for DNA samples
Disclosed herein are two methods for rapid multiplex analysis to determine the presence and identity of target DNA sequences within a DNA sample. Both methods use reporting DNA sequences, e.g., modified conventional Taqman.RTM. probes, to combine multiplex PCR amplification with microsphere-based hybridization using flow cytometry means of detection. Real-time PCR detection can also be incorporated. The first method uses a cyanine dye, such as, Cy3.TM., as the reporter linked to the 5' end of a reporting DNA sequence. The second method positions a reporter dye, e.g., FAM.TM. on the 3' end of the reporting DNA sequence and a quencher dye, e.g., TAMRA.TM., on the 5' end.
Nasarabadi,Shanavaz (Livermore, CA); Langlois, Richard G. (Livermore, CA); Venkateswaran, Kodumudi S. (Round Rock, TX)
Atomic force microscopy of biochemically tagged DNA
Small fragments of DNA of known length were made with the polymerase chain reaction. These fragments had biotin molecules covalently attached at their ends. They were subsequently labeled with a chimeric protein fusion between streptavidin and two immunoglobulin G-binding domains of staphyloccocal protein A. This tetrameric species was expected to bind up to four DNA molecules via their attached biotin moieties. The DNA-protein complex was deposited on mica and imaged with an atomic force microscope. The images revealed the protein chimera at the expected location at the ends of the strands of DNA as well as the expected dimers, trimers, and tetramers of DNA bound to a single protein. 25 refs., 5 figs.
Ogletree, D.F.; Kolbe, W.; Spengler, S.; Salmeron, M. (Lawrence Berkeley Laboratory, CA (United States)); Hansma, H.G.; Bezanilla, M. (Univ. of California, Santa Barbara (United States)); Sano, T.; Smith, C.S.; Cantor, C.R. (Boston Univ., MA (United States))
Storing data encoded DNA in living organisms
Current technologies allow the generation of artificial DNA molecules and/or the ability to alter the DNA sequences of existing DNA molecules. With a careful coding scheme and arrangement, it is possible to encode important information as an artificial DNA strand and store it in a living host safely and permanently. This inventive technology can be used to identify origins and protect R&D investments. It can also be used in environmental research to track generations of organisms and observe the ecological impact of pollutants. Today, there are microorganisms that can survive under extreme conditions. As well, it is advantageous to consider multicellular organisms as hosts for stored information. These living organisms can provide as memory housing and protection for stored data or information. The present invention provides well for data storage in a living organism wherein at least one DNA sequence is encoded to represent data and incorporated into a living organism.
Wong; Pak C. (Richland, WA), Wong; Kwong K. (Sugar Land, TX), Foote; Harlan P. (Richland, WA)
Disclosed herein are two methods for rapid multiplex analysis to determine the presence and identity of target DNA sequences within a DNA sample. Both methods use reporting DNA sequences, e.g., modified conventional Taqman.RTM. probes, to combine multiplex PCR amplification with microsphere-based hybridization using flow cytometry means of detection. Real-time PCR detection can also be incorporated. The first method uses a cyanine dye, such as, Cy3.TM., as the reporter linked to the 5' end of a reporting DNA sequence. The second method positions a reporter dye, e.g., FAM, on the 3' end of the reporting DNA sequence and a quencher dye, e.g., TAMRA, on the 5' end.
Nasarabadi, Shanavaz (Livermore, CA); Langlois, Richard G. (Livermore, CA); Venkateswaran, Kodumudi S. (Livermore, CA)
Crystal Structure of the Chromodomain Helicase DNA-binding Protein 1 (Chd1) DNA-binding Domain in Complex with DNA
Chromatin remodelers are ATP-dependent machines that dynamically alter the chromatin packaging of eukaryotic genomes by assembling, sliding, and displacing nucleosomes. The Chd1 chromatin remodeler possesses a C-terminal DNA-binding domain that is required for efficient nucleosome sliding and believed to be essential for sensing the length of DNA flanking the nucleosome core. The structure of the Chd1 DNA-binding domain was recently shown to consist of a SANT and SLIDE domain, analogous to the DNA-binding domain of the ISWI family, yet the details of how Chd1 recognized DNA were not known. Here we present the crystal structure of the Saccharomyces cerevisiae Chd1 DNA-binding domain in complex with a DNA duplex. The bound DNA duplex is straight, consistent with the preference exhibited by the Chd1 DNA-binding domain for extranucleosomal DNA. Comparison of this structure with the recently solved ISW1a DNA-binding domain bound to DNA reveals that DNA lays across each protein at a distinct angle, yet contacts similar surfaces on the SANT and SLIDE domains. In contrast to the minor groove binding seen for Isw1 and predicted for Chd1, the SLIDE domain of the Chd1 DNA-binding domain contacts the DNA major groove. The majority of direct contacts with the phosphate backbone occur only on one DNA strand, suggesting that Chd1 may not strongly discriminate between major and minor grooves.
Sharma A.; Heroux A.; Jenkins K. R.; Bowman G. D.
Mechanical & Industrial Engineering 1 Welcome MIE Industrial Advisory Board May 5th, 2011 #12;Mechanical & Industrial Engineering 2 IAB 2010-2011 · David K. Anderson Alden Research Laboratory, Inc went on for three weeks Mechanical & Industrial Engineering 6 #12;Reza Shahbazian Yassar Mechanical
Mechanical engineering Department Seminar Ju Li Professor MIT Electrochemical-mechanical actions computational and experimental research on mechanical properties of materials, and energy storage and conversion Refreshments served at 10:45 AM The creation of a nanoscale electrochemical and mechanical testing platform
Lin, Xi
Mechanical Engineering Undergraduate
Mechanical Engineering Department Undergraduate Advising Manual for Bachelor of Science Degrees in Mechanical Engineering and Engineering Mechanics 2011-2012 - Updated April 15, 2012 #12;Johns Hopkins University Department of Mechanical Engineering 2011-2012 Undergraduate Student Advising Manual Page 2
Ghosh, Somnath
Mechanical engineering Department Seminar James Bird Department of Mechanical Engineering Boston are discussed. James Bird is an Assistant Professor in the Mechanical Engineering Department at Boston completed post-doctoral research at MIT. His research interests include experimental fluid mechanics
Mechanical Engineering Department Undergraduate Advising Manual for Bachelor of Science Degrees in Mechanical Engineering and Engineering Mechanics 2012-2013 - Updated July 14, 2013 #12;Johns Hopkins University Department of Mechanical Engineering 2012-2013 Undergraduate Student Advising Manual Page 2
Mechanical Engineering & Thermal Group
Mechanical Engineering & Thermal Group The Mechanical Engineering (ME) & Thermal Group at LASP has, and ground- based mechanical systems. Instrument Design Building on decades of design experience that has evolved with the complexity of instrument design demands, LASP mechanical engineers develop advanced
Mojzsis, Stephen J.
Combined Quantum Mechanical and Molecular Mechanics Studies of...
Mechanical and Molecular Mechanics Studies of the Electron-Transfer Reactions Involving Carbon Tetrachloride in Combined Quantum Mechanical and Molecular Mechanics Studies of the...
Catalytic Hydrolytic Cleavage and Oxy-Cleavage of Lignin Linkages
In this work, new strategies involving organic bases were evaluated to depolymerize lignin to reduced molecular fragments in aqueous medium. NaOH as an inorganic base was also investigated as a reference. Full nature lignin samples are used for the study. As research tools to unravel the complexity of the macro lignin structure and bulky molecular size under this study, size exclusion chromatography and high resolution mass spectrometric analysis, typically used for protein characterizations, were used to follow the progress of lignin depolymerisation by measuring the molecular weight distribution of the products and determining the key molecular fingerprints, respectively. The results show that sodium phenoxide and guanidine carbonate are effective catalysts for lignin depolymerization. It is observed that there exists a synergism between H2O2 and the organic base, which is strongest with guanidine carbonate.
Xia, Guanguang; Chen, Baowei; Zhang, Rui; Zhang, Z. Conrad
ap dna endonuclease: Topics by E-print Network
specificity Raines, Ronald T. 2 A DNA and restriction enzyme implementation of Turing Ma (Turing machines; Universal Turing machines; recombinant DNA; nonpalindromic...
adenovirus dna sequences: Topics by E-print Network
description of the given DNA string in terms of a smaller set of distinct domain labels. This yields a minimal domain description of a given DNA sequence, significantly...
Minor Groove Deformability of DNA: A Molecular Dynamics Free...
Minor Groove Deformability of DNA: A Molecular Dynamics Free EnergySimulation Study. Minor Groove Deformability of DNA: A Molecular Dynamics Free EnergySimulation Study. Abstract:...
Electrochemical Branched-DNA Assay for Polymerase Chain Reaction...
Branched-DNA Assay for Polymerase Chain Reaction-Free Detection and Quantification of Oncogenes in Messenger RNA Electrochemical Branched-DNA Assay for Polymerase Chain...
adapting dna microarray: Topics by E-print Network
Gene Expression Analysis & R Tutorial 12;DNA Microarrays An R Tutorial Functional Genomics Qiu, Weigang 3 Research tools known as DNA microarrays are Biology and Medicine...
archived dna microarrays: Topics by E-print Network
Protein Bridges DNA Base and Nucleotide Excision Repair Pathways
a nucleotide from the DNA double helix to its active site to access damaged nucleotides. But unlike AGT and most other known DNA nucleotide-flipping proteins, this...
Constraint of DNA on Functionalized Graphene Improves Its Biostability...
Constraint of DNA on Functionalized Graphene Improves Its Biostability and Specificity. Constraint of DNA on Functionalized Graphene Improves Its Biostability and Specificity....
Sandia National Laboratories: Mechanical Testing
EnergyNuclear Energy Systems Laboratory (NESL) Brayton LabMechanical Testing Mechanical Testing Mechanical Testing Overview Mechanical 1-2 (2008). Standard Test Methods for...
Method of quantitating dsDNA
A method for quantitating dsDNA in an aqueous sample solution containing an unknown amount of dsDNA. A first aqueous test solution containing a known amount of a fluorescent dye-dsDNA complex and at least one fluorescence-attenutating contaminant is prepared. The fluorescence intensity of the test solution is measured. The first test solution is diluted by a known amount to provide a second test solution having a known concentration of dsDNA. The fluorescence intensity of the second test solution is measured. Additional diluted test solutions are similarly prepared until a sufficiently dilute test solution having a known amount of dsDNA is prepared that has a fluorescence intensity that is not attenuated upon further dilution. The value of the maximum absorbance of this solution between 200-900 nanometers (nm), referred to herein as the threshold absorbance, is measured. A sample solution having an unknown amount of dsDNA and an absorbance identical to that of the sufficiently dilute test solution at the same chosen wavelength is prepared. Dye is then added to the sample solution to form the fluorescent dye-dsDNA-complex, after which the fluorescence intensity of the sample solution is measured and the quantity of dsDNA in the sample solution is determined. Once the threshold absorbance of a sample solution obtained from a particular environment has been determined, any similarly prepared sample solution taken from a similar environment and having the same value for the threshold absorbance can be quantified for dsDNA by adding a large excess of dye to the sample solution and measuring its fluorescence intensity.
Stark, Peter C. (Los Alamos, NM); Kuske, Cheryl R. (Los Alamos, NM); Mullen, Kenneth I. (Los Alamos, NM)
DNA fragment sizing and sorting by laser-induced fluorescence
A method is provided for sizing DNA fragments using high speed detection systems, such as flow cytometry to determine unique characteristics of DNA pieces from a sample. In one characterization the DNA piece is fragmented at preselected sites to produce a plurality of DNA fragments. The DNA piece or the resulting DNA fragments are treated with a dye effective to stain stoichiometrically the DNA piece or the DNA fragments. The fluorescence from the dye in the stained fragments is then examined to generate an output functionally related to the number of nucleotides in each one of the DNA fragments. In one embodiment, the intensity of the fluorescence emissions from each fragment is linearly related to the fragment length. The distribution of DNA fragment sizes forms a characterization of the DNA piece for use in forensic and research applications.
Hammond, Mark L. (Angier, NC); Jett, James H. (Los Alamos, NM); Keller, Richard A. (Los Alamos, NM); Marrone, Babetta L. (Los Alamos, NM); Martin, John C. (Los Alamos, NM)
Internal pipe attachment mechanism
An attachment mechanism for repairing or extending fluid carrying pipes, casings, conduits, etc. utilizing one-way motion of spring tempered fingers to provide a mechanical connection between the attachment mechanism and the pipe. The spring tempered fingers flex to permit insertion into a pipe to a desired insertion depth. The mechanical connection is accomplished by reversing the insertion motion and the mechanical leverage in the fingers forces them outwardly against the inner wall of the pipe. A seal is generated by crushing a sealing assembly by the action of setting the mechanical connection.
Bast, Richard M. (Livermore, CA); Chesnut, Dwayne A. (Pleasanton, CA); Henning, Carl D. (Livermore, CA); Lennon, Joseph P. (Livermore, CA); Pastrnak, John W. (Livermore, CA); Smith, Joseph A. (Livermore, CA)
An attachment mechanism is described for repairing or extending fluid carrying pipes, casings, conduits, etc. utilizing one-way motion of spring tempered fingers to provide a mechanical connection between the attachment mechanism and the pipe. The spring tempered fingers flex to permit insertion into a pipe to a desired insertion depth. The mechanical connection is accomplished by reversing the insertion motion and the mechanical leverage in the fingers forces them outwardly against the inner wall of the pipe. A seal is generated by crushing a sealing assembly by the action of setting the mechanical connection. 6 figures.
Bast, R.M.; Chesnut, D.A.; Henning, C.D.; Lennon, J.P.; Pastrnak, J.W.; Smith, J.A.
Sequential addition of short DNA oligos in DNA-polymerase-based synthesis reactions
A method of preselecting a multiplicity of DNA sequence segments that will comprise the DNA molecule of user-defined sequence, separating the DNA sequence segments temporally, and combining the multiplicity of DNA sequence segments with at least one polymerase enzyme wherein the multiplicity of DNA sequence segments join to produce the DNA molecule of user-defined sequence. Sequence segments may be of length n, where n is an odd integer. In one embodiment the length of desired hybridizing overlap is specified by the user and the sequences and the protocol for combining them are guided by computational (bioinformatics) predictions. In one embodiment sequence segments are combined from multiple reading frames to span the same region of a sequence, so that multiple desired hybridizations may occur with different overlap lengths.
Gardner, Shea N; Mariella, Jr., Raymond P; Christian, Allen T; Young, Jennifer A; Clague, David S
8-oxoguainine enhances bending of DNA that favors binding of glycosylases
Molecular dynamics (MD) simulations were carried out on the DNA oligonucleotide GGGAACAACTAG:CTAGTTGTTCCC in its native form and with guanine in the central G19:C6 base pair replaced by 8-oxoguanine (8oxoG). A box of explicit water molecules was used for solvation and Na+ counterions were added to neutralize the system. The direction and magnitude of global bending were assessed by a technique used previously to analyze simulations of DNA containing a thymine dimer. The presence of 8oxoG did not greatly affect the magnitude of DNA bending; however, bending into the major groove was significantly more probable when 8oxoG replaced G19. Crystal structures of glycosylases bound to damaged-DNA substrates consistently show a sharp bend into the major groove at the damage site. We conclude that changes in bending dynamics that assist the formation of this kink are a part of the mechanism by which glycosylases of the base excision repair pathway recognize the presence of 8oxoG in DNA.
John H. Miller
Free energy landscape and characteristic forces for the initiation of DNA unzipping
DNA unzipping, the separation of its double helix into single strands, is crucial in modulating a host of genetic processes. Although the large-scale separation of double-stranded DNA has been studied with a variety of theoretical and experimental techniques, the minute details of the very first steps of unzipping are still unclear. Here, we use atomistic molecular dynamics (MD) simulations, coarse-grained simulations and a statistical-mechanical model to study the initiation of DNA unzipping by an external force. The calculation of the potential of mean force profiles for the initial separation of the first few terminal base pairs in a DNA oligomer reveal that forces ranging between 130 and 230 pN are needed to disrupt the first base pair, values of an order of magnitude larger than those needed to disrupt base pairs in partially unzipped DNA. The force peak has an "echo," of approximately 50 pN, at the distance that unzips the second base pair. We show that the high peak needed to initiate unzipping derives...
Mentes, Ahmet; Brunk, Elizabeth; Wereszczynski, Jeff; Joyeux, Marc; Andricioaei, Ioan
Nucleotide insertion initiated by van der Waals interaction during polymerase beta DNA replication
Immortality will remain a fantasy for as long as aging is determined by the erroneous biochemical reactions during a particular DNA replication. The replication and base excision repair mechanism, associated to eukaryotic DNA polymerase-beta enzyme are central to maintaining a healthy cell. Here, we give a series of unambiguous theoretical analyses and prove that the exclusive biochemical reaction involved in a single nucleotide insertion into the DNA primer can be efficiently tracked using the renormalized van der Waals interaction of the stronger type, and the Hermansson blue-shifting hydrogen bond effect. We found that there are two biochemical steps involved to complete the insertion of a single dCTP into the 3' end of a DNA primer. First, the O3' (from a DNA primer) initiates the nucleophilic attack on P_alpha?(from an incoming dCTP), in response, O3_alpha (bonded to P_alpha) retaliates by interacting with H' (bonded to O3'). These interactions are shown to be strongly interdependent and require the form...
Arulsamy, Andrew Das
DNA unzipping, the separation of its double helix into single strands, is crucial in modulating a host of genetic processes. Although the large-scale separation of double-stranded DNA has been studied with a variety of theoretical and experimental techniques, the minute details of the very first steps of unzipping are still unclear. Here, we use atomistic molecular dynamics (MD) simulations, coarse-grained simulations and a statistical-mechanical model to study the initiation of DNA unzipping by an external force. The calculation of the potential of mean force profiles for the initial separation of the first few terminal base pairs in a DNA oligomer reveal that forces ranging between 130 and 230 pN are needed to disrupt the first base pair, values of an order of magnitude larger than those needed to disrupt base pairs in partially unzipped DNA. The force peak has an "echo," of approximately 50 pN, at the distance that unzips the second base pair. We show that the high peak needed to initiate unzipping derives from a free energy basin that is distinct from the basins of subsequent base pairs because of entropic contributions and we highlight the microscopic origin of the peak. Our results suggest a new window of exploration for single molecule experiments.
Ahmet Mentes; Ana Maria Florescu; Elizabeth Brunk; Jeff Wereszczynski; Marc Joyeux; Ioan Andricioaei
Linear Thermodynamics of Rodlike DNA Filtration
Linear thermodynamics transportation theory is employed to study filtration of rodlike DNA molecules. Using the repeated nanoarray consisting of alternate deep and shallow regions, it is demonstrated that the complex ...
Li, Zirui
Intriguing DNA Editor Has a Structural Trigger
generating a lot of excitement because, unlike earlier genome-editing tools, its basic architecture doesn't have to be rebuilt each time a new section of DNA is targeted; it...
The Initiation of Bacterial DNA Replication
that the ATP-DnaA active site is in a closed configuration, which allows it to bind nucleotides using conserved residues from neighboring AAA+ protomers. The precise geometry of...
Deoxyribose oxidation chemistry and endogenous DNA adducts
Endogenous and exogenous oxidants react with cellular macromolecules to generate a variety of electrophiles that react with DNA produce cytotoxic and mutagenic adducts. One source of such electrophiles is deoxyribose in ...
Zhou, Xinfeng
Programmable Mechanical Metamaterials
We create mechanical metamaterials whose response to uniaxial compression can be programmed by lateral confinement, allowing monotonic, non-monotonic and hysteretic behavior. These functionalities arise from a broken rotational symmetry which causes highly nonlinear coupling of deformations along the two primary axes of these metamaterials. We introduce a soft mechanism model which captures the programmable mechanics, and outline a general design strategy for confined mechanical metamaterials. Finally, we show how inhomogeneous confinement can be explored to create multi stability and giant hysteresis.
Bastiaan Florijn; Corentin Coulais; Martin van Hecke
RecA acts in trans to allow replication of damaged DNA by DNA polymerase V
, Michael M. Cox2 , Roger Woodgate3 & Myron F. Goodman1 The DNA polymerase V (pol V) and RecA proteins
Cox, Michael M.
Mechanical & Industrial Engineering Mario A. Rotea Professor and Department Head #12;2Mechanical & Industrial Engineering Outline · Undergraduate Degree Programs · Graduate Degree Programs · The Faculty · The Research · Summary #12;3Mechanical & Industrial Engineering Undergraduate Programs BSME & BSIE 0 20 40 60
efficient energy systems. Evelyn N. Wang is an Associate Professor in the Mechanical Engineering DepartmentMechanical engineering Department Seminar Evelyn Wang Depaprtment of Mechanical Engineering MIT Nanoengineered Surfaces: Transport Phenomena and Energy Applications 11:00 AM Friday, 5 April 2013 Room 245, 110
Mechanical engineering Department Seminar Domitilla Del Vecchio Department of Mechanical. A near future is envisioned in which re- engineered bacteria will turn waste into energy and kill cancer, she joined the Department of Mechanical Engineering and the Laboratory for Information and Decision
in Mechanical Engineering at the School for Engineering of Matter, Transport and Energy, working in Dr. MarcusMechanical & Aerospace Engineering The atomization of a liquid jet by a high speed cross.S.E. degree in mechanical engineering from Amirkabir University of Technology in 2006 and M.S. degree
Mechanical engineering Department Seminar Shuodao Wang Postdoctoral Fellow University of Illinois, Urbana-Champaign Mechanical Design and Fabrication Techniques for Bio-Electronic Systems 11:00 AM Friday that bridge this gap in mechanics and form will create new opportunities in bio-inspired and bio
Mechanical and Aerospace Engineering Abstract Solid materials used in energy conversion and storage that couples the mechanical and chemical (or electrochemical) fields in solids via the use of stress-chemo- mechanical theory, two examples of practical interest will be discussed, namely, solid oxide fuel cells
Mechanical engineering Department Seminar Maureen Lynch Postdoctoral Fellow Cornell University Mechanical Loading Decreases Osteolysis and Tumor Formation via Effects on Bone Remodeling 11:00 AM Friday to mechanical stimuli in the skeleton, yet the role of biomechanical loading remains poorly characterized
UNSATURATED SOIL MECHANICS IMPLEMENTATION DURING PAVEMENT CONSTRUCTION QUALITY ASSURANCE Mn !! Performance Based Construction QA !! Unsaturated Soil Mechanics !! What We've Learned !! Next Steps #12.6-6.0 5 - 7 19 0.8 5 7 - 9 24 1.1 4 9 - 11 28 1.2 4 #12;Unsaturated Soil Mechanics #12;Fundamentals
Minnesota, University of
Victor Yakhot Mechanical Engineering
to flows of strongly non-linear fluids relevant for mechanical engineering, polymers and bio-fluid dynamicsVictor Yakhot Mechanical Engineering UniversalReynoldsNumberofTransition,Renormalizationand Mechanical Engineering 11 AM Friday, October 31st Room 245, 110 Cummington Mall Refreshments served at 10
Recombinant DNA Research in Human Subjects Duke Institutional Biosafety Committee
/2010 Summary. All Duke research using recombinant DNA (rDNA) in human subjects must comply with the NIH Guidelines for Research involving Recombinant DNA Molecules (available at http://oba.od.nih.gov/rdna/nih Biosafety Committee (IBC) [NIH Guidelines Section III-C and III-C-1]. The NIH defines rDNA broadly
Mechanical seal assembly
An improved mechanical seal assembly is provided for sealing rotating shafts with respect to their shaft housings, wherein the rotating shafts are subject to substantial axial vibrations. The mechanical seal assembly generally includes a rotating sealing ring fixed to the shaft, a non-rotating sealing ring adjacent to and in close contact with the rotating sealing ring for forming an annular seal about the shaft, and a mechanical diode element that applies a biasing force to the non-rotating sealing ring by means of hemispherical joint. The alignment of the mechanical diode with respect to the sealing rings is maintained by a series of linear bearings positioned axially along a desired length of the mechanical diode. Alternative embodiments include mechanical or hydraulic amplification components for amplifying axial displacement of the non-rotating sealing ring and transfering it to the mechanical diode.
Kotlyar, Oleg M. (Salt Lake City, UT)
An improved mechanical seal assembly is provided for sealing rotating shafts with respect to their shaft housings, wherein the rotating shafts are subject to substantial axial vibrations. The mechanical seal assembly generally includes a rotating sealing ring fixed to the shaft, a non-rotating sealing ring adjacent to and in close contact with the rotating sealing ring for forming an annular seal about the shaft, and a mechanical diode element that applies a biasing force to the non-rotating sealing ring by means of hemispherical joint. The alignment of the mechanical diode with respect to the sealing rings is maintained by a series of linear bearings positioned axially along a desired length of the mechanical diode. Alternative embodiments include mechanical or hydraulic amplification components for amplifying axial displacement of the non-rotating sealing ring and transferring it to the mechanical diode.
Kinetics and mechanism of the oxidation of propylene to allyl acetate in solutions of palladium clusters
The kinetics of the oxidative acetoxylation of propylene to allyl acetate in solutions of the clusters Pd/sub 561/Phen/sub 60/(OAc)/sub 180/ and Pd/sub 561/Phen/sub 80/(PF/sub 6/) have been studied by gas-liquid chromatography over the range 40-90/degree/C. It has been established that the rate of reaction is proportional to the concentrations of propylene and the clusters in solution and its dependence on the concentrations of O/sub 2/ and acetic acid is represented by a Michaelis type of equation. For high partial O/sub 2/ pressures inhibition of the reaction by oxygen is observed. A mechanism is proposed for the reaction, according to which the cleavage of the C-H bond in the coordinated olefin molecule to form an allyl complex takes place at the limiting stage.
Stolyarov, I.P.; Vargaftik, M.N.; Moiseev, I.I.
Mass spectrometric characterization of sequence-specific complexes of DNA and transcription factor PU.1 DNA binding domain
Electrospray ionization mass spectrometry (ESI-MS) has been used to study the noncovalent interaction of the 13.5-kDa DNA binding domain of PU.1 (PU.1-DBD) with specific double-stranded DNA (dsDNA) target molecules. Mixtures of PU.1-DBD protein and wildtype target DNA sequence yielded ESI-MS spectra showing only protein-dsDNA complex ions of 1:1 stoichiometry and free dsDNA. When PU.1-DBD protein, wild type target DNA, and a mutant target DNA lacking the consensus sequence were mixed, only the 1:1 complex with the wild-type DNA was observed, consistent with gel electrophoresis mobility shift assay results, demonstrating the observation of sequence-specific protein-dsDNA complexes using ESI-MS. 22 refs., 5 figs., 1 tab.
Cheng, Xueheng; Harms, A.C.; Bruce, J.E. [Pacific Northwest National Lab., Richland, WA (United States)] [and others] [Pacific Northwest National Lab., Richland, WA (United States); and others
Transport in hybrid electronic devices based on a modified DNA nucleoside (deoxyguanosine)
We report on a new class of hybrid electronic devices based on a DNA nucleoside (deoxyguanosine lipophilic derivative) whose assembled polymeric ribbons interconnect a submicron metallic gate. The device exhibits large conductivity at room temperature, rectifying behaviour and strong current-voltage hysteresis. The transport mechanism through the molecules is investigated by comparing films with different self-assembling morphology. We found that the main transport mechanism is connected to pi-pi interactions between guanosine molecules in adjacent ribbons, consistently with the results of our first-principles calculations.
R. Rinaldi; E. Branca; R. Cingolani; R. Di Felice; E. Molinari; S. Masiero; G. P. Spada; G. Gottarelli; A. Garbesi
The mechanism for iron-catalyzed alkene isomerization in solution
Here we report nano- through microsecond time-resolved IR experiments of iron-catalyzed alkene isomerization in room-temperature solution. We have monitored the photochemistry of a model system, Fe(CO){sub 4}({eta}{sup 2}-1-hexene), in neat 1-hexene solution. UV-photolysis of the starting material leads to the dissociation of a single CO to form Fe(CO){sub 3}({eta}{sup 2}-1-hexene), in a singlet spin state. This CO loss complex shows a dramatic selectivity to form an allyl hydride, HFe(CO){sub 3}({eta}{sup 3}-C{sub 6}H{sub 11}), via an internal C-H bond-cleavage reaction in 5-25 ns. We find no evidence for the coordination of an alkene molecule from the bath to the CO loss complex, but do observe coordination to the allyl hydride, indicating that it is the key intermediate in the isomerization mechanism. Coordination of the alkene ligand to the allyl hydride leads to the formation of the bis-alkene isomers, Fe(CO){sub 3}({eta}{sup 2}-1-hexene)({eta}{sup 2}-2-hexene) and Fe(CO){sub 3}({eta}{sup 2}-1-hexene){sub 2}. Because of the thermodynamic stability of Fe(CO){sub 3}({eta}{sup 2}-1-hexene)({eta}{sup 2}-2-hexene) over Fe(CO){sub 3}({eta}{sup 2}-1-hexene){sub 2} (ca. 12 kcal/mol), nearly 100% of the alkene population will be 2-alkene. The results presented herein provide the first direct evidence for this mechanism in solution and suggest modifications to the currently accepted mechanism.
Sawyer, Karma R.; Glascoe, Elizabeth A.; Cahoon, James F.; Schlegel, Jacob P.; Harris, Charles B.
The Department of Mechanical Engineering --Engineering Mechanics
undergraduate and graduate courses in thermodynamics, fuel cell systems, sustainable energy systems, and mechanical systems design. Dr. Ellis is the director of the Sustainable Energy Research Program in Virginia. Ellis has 25 years of experience in engineering, research, and education related to the development
Endres. William J.
Optical selection and collection of DNA fragments
Optical selection and collection of DNA fragments. The present invention includes the optical selection and collection of large (>.mu.g) quantities of clonable, chromosome-specific DNA from a sample of chromosomes. Chromosome selection is based on selective, irreversible photoinactivation of unwanted chromosomal DNA. Although more general procedures may be envisioned, the invention is demonstrated by processing chromosomes in a conventional flow cytometry apparatus, but where no droplets are generated. All chromosomes in the sample are first stained with at least one fluorescent analytic dye and bonded to a photochemically active species which can render chromosomal DNA unclonable if activated. After passing through analyzing light beam(s), unwanted chromosomes are irradiated using light which is absorbed by the photochemically active species, thereby causing photoinactivation. As desired chromosomes pass this photoinactivation point, the inactivating light source is deflected by an optical modulator; hence, desired chromosomes are not photoinactivated and remain clonable. The selection and photoinactivation processes take place on a microsecond timescale. By eliminating droplet formation, chromosome selection rates 50 times greater than those possible with conventional chromosome sorters may be obtained. Thus, usable quantities of clonable DNA from any source thereof may be collected.
Roslaniec, Mary C. (Los Alamos, NM); Martin, John C. (Los Alamos, NM); Jett, James H. (Los Alamos, NM); Cram, L. Scott (Los Alamos, NM)
Does quantum entanglement in DNA synchronize the catalytic centers of type II restriction endonucleases?
Several living systems have been examined for their apparent optimization of structure and function for quantum behavior at biological length scales. Orthodox type II endonucleases, the largest class of restriction enzymes, recognize four-to-eight base pair sequences of palindromic DNA, cut both strands symmetrically, and act without an external metabolite such as ATP. While it is known that these enzymes induce strand breaks by attacking phosphodiester bonds, what remains unclear is the mechanism by which cutting occurs in concert at the catalytic centers. Previous studies indicate the primacy of intimate DNA contacts made by the specifically bound enzyme in coordinating the two synchronized cuts. We propose that collective electronic behavior in the DNA helix generates coherent oscillations, quantized through boundary conditions imposed by the endonuclease, that provide the energy required to break two phosphodiester bonds. Such quanta may be preserved in the presence of thermal noise and electromagnetic interference through decoherence shielding, the specific complex's exclusion of water and ions surrounding the helix. Clamping energy imparted by the enzyme decoherence shield is comparable with zero-point modes of the dipole-dipole oscillations in the DNA recognition sequence. The palindromic mirror symmetry of this sequence should conserve parity during the process. Experimental data corroborate that symmetric bond-breaking ceases when the symmetry of the endonuclease complex is violated, or when environmental parameters are perturbed far from biological optima. Persistent correlation between states in DNA sequence across spatial separations of any length--a characteristic signature of quantum entanglement--may be explained by such a physical mechanism.
P. Kurian; G. Dunston; J. Lindesay
Reactivity studies of a pseudo three-coordinate vanadium(II) complex: Synthesis of terminal oxo and sulfido complexes of vanadium(IV) and S?S and Se?Se reductive bond cleavage reactions
Terminal oxo and sulfido complexes in the form of (nacnac)V=E(Ntol{sub 2}) (nacnac = [ArNC(CH{sub 3})]{sub 2}CH{sup -}, Ar = 2,6-(CHMe{sub 2}){sub 2}C{sub 6}H{sub 3}, Ntol{sub 2} = {sup -}N(C{sub 6}H{sub 4}-4-Me), E = O (1), S (2)) were isolated from treatment of the masked three-coordinate vanadium(II) complex, (nacnac)V(Ntol{sub 2}), with C{sub 5}H{sub 5}NO and S{sub 8}, respectively. Both vanadium(IV) species, 1 and 2, have been characterized by room temperature X-band EPR spectroscopic studies, and in the case of complex 1, a single crystal molecular structure confirmed the presence of a terminal oxo moiety. Moreover, reaction of (nacnac)V(Ntol{sub 2}) with diphenyl-disulfide and diphenyl-diselenide results in the reductive cleavage of these compounds to produce the vanadium(III) complexes (nacnac)V(XPh)(Ntol{sub 2}) (X = S, (3), Se (4)). A molecular structure of the phenylsulfide complex, 3, confirmed formation of the d{sup 2} complex resulting from reductive cleavage of the S-S bond.
Tran, Ba L.; Chen, Chun-Hsing; Mindiola, Daniel J. (Indiana)
Mechanical Properties of Nanocrystal Supercrystals
and Its Impact on Mechanical Properties. MacromoleculesO. L. ; Minor, A. M. , Mechanical annealing and source-Mechanical Properties of Nanocrystal Supercrystals Enrico
Tam, Enrico
operating in microfluidic environment, which can dynamically diverge, collimate and focus surface plasmons in 2012, with a joint appointment in the Department of Mechanical & Industrial Engineering
Research Center. Currently he is an Assistant Prof. in the Aerospace and Ocean Engineering DepartmentMechanical engineering Department Seminar Cornel Sultan Virginia Tech Design for Control
Technology Partnering Mechanisms
expand a business with INL technologies, or require business support our Technology Transfer team is available to discuss the following contractual mechanisms: Cooperative...
Protection of cisplatin-induced spermatotoxicity, DNA damage and chromatin abnormality by selenium nano-particles
Cisplatin (CIS), an anticancer alkylating agent, induces DNA adducts and effectively cross links the DNA strands and so affects spermatozoa as a male reproductive toxicant. The present study investigated the cellular/biochemical mechanisms underlying possible protective effect of selenium nano-particles (Nano-Se) as an established strong antioxidant with more bioavailability and less toxicity, on reproductive toxicity of CIS by assessment of sperm characteristics, sperm DNA integrity, chromatin quality and spermatogenic disorders. To determine the role of oxidative stress (OS) in the pathogenesis of CIS gonadotoxicity, the level of lipid peroxidation (LPO), antioxidant enzymes including superoxide dismutase (SOD), catalase (CAT) and glutathione peroxidase (GSH-Px) and peroxynitrite (ONOO) as a marker of nitrosative stress (NS) and testosterone (T) concentration as a biomarker of testicular function were measured in the blood and testes. Thirty-two male Wistar rats were equally divided into four groups. A single IP dose of CIS (7 mg/kg) and protective dose of Nano-Se (2 mg/kg/day) were administered alone or in combination. The CIS-exposed rats showed a significant increase in testicular and serum LPO and ONOO level, along with a significant decrease in enzymatic antioxidants levels, diminished serum T concentration and abnormal histologic findings with impaired sperm quality associated with increased DNA damage and decreased chromatin quality. Coadministration of Nano-Se significantly improved the serum T, sperm quality, and spermatogenesis and reduced CIS-induced free radical toxic stress and spermatic DNA damage. In conclusion, the current study demonstrated that Nano-Se may be useful to prevent CIS-induced gonadotoxicity through its antioxidant potential. Highlights: ? Cisplatin (CIS) affects spermatozoa as a male reproductive toxicant. ? Effect of Nano-Se on CIS-induced spermatotoxicity was investigated. ? CIS-exposure induces oxidative sperm DNA damage and impairs steroidogenesis. ? Nano-Se retained sperm quality against CIS-induced free radicals toxic stress.
Rezvanfar, Mohammad Amin; Rezvanfar, Mohammad Ali [Department of Toxicology and Pharmacology, Faculty of Pharmacy, and Pharmaceutical Sciences Research Center, Tehran University of Medical Sciences (TUMS), Tehran (Iran, Islamic Republic of)] [Department of Toxicology and Pharmacology, Faculty of Pharmacy, and Pharmaceutical Sciences Research Center, Tehran University of Medical Sciences (TUMS), Tehran (Iran, Islamic Republic of); Shahverdi, Ahmad Reza [Department of Pharmaceutical Biotechnology and Biotechnology Research Centre, Faculty of Pharmacy, TUMS, Tehran (Iran, Islamic Republic of)] [Department of Pharmaceutical Biotechnology and Biotechnology Research Centre, Faculty of Pharmacy, TUMS, Tehran (Iran, Islamic Republic of); Ahmadi, Abbas [Department of Histology and Embryology, Faculty of Veterinary Medicine, Urmia University, Urmia (Iran, Islamic Republic of)] [Department of Histology and Embryology, Faculty of Veterinary Medicine, Urmia University, Urmia (Iran, Islamic Republic of); Baeeri, Maryam; Mohammadirad, Azadeh [Department of Toxicology and Pharmacology, Faculty of Pharmacy, and Pharmaceutical Sciences Research Center, Tehran University of Medical Sciences (TUMS), Tehran (Iran, Islamic Republic of)] [Department of Toxicology and Pharmacology, Faculty of Pharmacy, and Pharmaceutical Sciences Research Center, Tehran University of Medical Sciences (TUMS), Tehran (Iran, Islamic Republic of); Abdollahi, Mohammad, E-mail: firstname.lastname@example.com [Department of Toxicology and Pharmacology, Faculty of Pharmacy, and Pharmaceutical Sciences Research Center, Tehran University of Medical Sciences (TUMS), Tehran (Iran, Islamic Republic of)] [Department of Toxicology and Pharmacology, Faculty of Pharmacy, and Pharmaceutical Sciences Research Center, Tehran University of Medical Sciences (TUMS), Tehran (Iran, Islamic Republic of)
Boston University Department of Mechanical Engineering ME 303 Fluid Mechanics
Boston University Department of Mechanical Engineering ME 303 Fluid Mechanics Fall 2011 Class: EK301 Engineering Mechanics Course Textbook: Fundamentals of Fluid Mechanics, 6th ed., Munson B. Reference Texts: Fluid Mechanics, Landau and Lifshitz, Vol. 6 Fluid Mechanics, Y. Cengel and J. Cimbala
Department of Mechanical Engineering
Explore and understand applicable science Create new materials #12;Indian Railways #12;Wheel Impact Load automated system for On-Line estimation of Wheel Impact Loads and detection of Wheel Flats of running trains Detection System (WILD) #12;Derailment Mechanism Laboratory Tests Lab Brake Mechanism Placement of Sensors
Srivastava, Kumar Vaibhav
Mechanical & Aerospace Engineering In the pursuit of developing manned, reusable hypersonic & Energy Arizona State University November 9, 2012 at 1:30pm in SCOB 228 School for Engineering of Matter will experience thermal and mechanical loads. The research presented will discuss advancements in structural
Mechanical engineering Department Seminar Junjie Niu Postdoctoral Associate MIT Engineering Nano nanomaterials in applications of energy storage, biomedicine and chemo-mechanics. In 2007, Dr.Niu received young-structured Materials for Energy Storage 11:00 AM Friday, 14 February 2014 Room 245, 110 Cummington Mall Refreshments
Mechanical & Aerospace Engineering The development of high-energy storage devices has been one energy capacity over 500 cycles. Teng Ma received his BS degree in Thermal and Power Engineering from Xi and Technology of China in 2009. He is currently a Ph.D. candidate in Mechanical Engineering at School
, and nuclear energy. She is a member of the American Society of Mechanical Engineers (ASME), Fluids EngineeringMechanical & Aerospace Engineering Interfacial flows are multi-material flows comprised of two of the interface between the fluids and the interface physics (like surface tension) needs to be predicted as part
Respiratory Mechanisms of Support
Respiratory Mechanisms of Support Nasal Cannula Hi Flow Nasal Cannula CPAP Continuous positive the respiratory system is working to compensate for a metabolic issue so as to normalize the blood pH. HCO3 - 22 uses PIP Mechanical Ventilation: Volume vs. Pressure: Volume Control Pressure Control Cycle Volume Time
Kay, Mark A.
Graduate Studies Environmental Fluid Mechanics
Graduate Studies Environmental Fluid Mechanics and Water Resources Engineering ENVIRONMENTAL FLUID MECHANICS AND WATER RESOURCES ENGINEERING (EFMWR) The environmental fluid mechanics and water resources Environmental Fluid Mechanics and Hydraulic Engineering research focuses on turbulent entrainment, transport
Jacobs, Laurence J.
MECHANICAL ENGINEERING Program of Study
MECHANICAL ENGINEERING Program of Study Correspondence The Department of Mechanical Engineering offers graduate programs in the fields of thermal science and engineering mechanics. Current areas of research activity include Biomedical Engineering, Biomimetics, Composite Materials, Computational Mechanics
Thomas, Andrew
Integrated Mechanical & Electrical Engineering (IMEE)
Integrated Mechanical & Electrical Engineering (IMEE) Department of Electronic & Electrical Engineering and Department of Mechanical Engineering #12;Graduates able to work in both mechanical of Mechanical Engineers (IMechE) n Develop essential engineering skills through extensive project work n Enhance
Burton, Geoffrey R.
Mechanical code comparator
A new class of mechanical code comparators is described which have broad potential for application in safety, surety, and security applications. These devices can be implemented as micro-scale electromechanical systems that isolate a secure or otherwise controlled device until an access code is entered. This access code is converted into a series of mechanical inputs to the mechanical code comparator, which compares the access code to a pre-input combination, entered previously into the mechanical code comparator by an operator at the system security control point. These devices provide extremely high levels of robust security. Being totally mechanical in operation, an access control system properly based on such devices cannot be circumvented by software attack alone.
Peter, Frank J. (Albuquerque, NM); Dalton, Larry J. (Bernalillo, NM); Plummer, David W. (Albuquerque, NM)
The self-assembly of particles with isotropic interactions: Using DNA coated colloids to create designer nanomaterials
Self-consistent field theory equations are presented that are suitable for use as a coarse-grained model for DNA coated colloids, polymer-grafted nanoparticles and other systems with approximately isotropic interactions. The equations are generalized for arbitrary numbers of chemically distinct colloids. The advantages and limitations of such a coarse-grained approach for DNA coated colloids are discussed, as are similarities with block copolymer self-assembly. In particular, preliminary results for three species self-assembly are presented that parallel results from a two dimensional ABC triblock copolymer phase. The possibility of incorporating crystallization, dynamics, inverse statistical mechanics and multiscale modelling techniques are discussed.
Thompson, R. B.; Dion, S.; Konigslow, K. von [Department of Physics and Astronomy and Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1 (Canada)
Graduate Studies Environmental Fluid Mechanics and Water Resources Engineering GRADUATE COURSESResourcesManagement · IntermediateFluidMechanics · AdvancedFluidMechanics · EnvironmentalFluidMechanics · AdvancedEnvironmental FluidMechanics · FluidMechanicsofOrganisms · OpenChannelHydraulics · SedimentTransport · ComputationalFluidMechanics
Storici, Francesca
Localization of positive charge in DNA induced by its interaction with environment
Microscopic mechanisms of positive charge transfer in DNA remain unclear. A quantum state of electron hole in DNA is determined by the competition of the pi-stacking interaction $b$ sharing a charge between different base pairs and the interaction $\\lambda$ with the local environment which attempts to trap charge. To determine which interaction dominates we investigated charge quantum states in various $(GC)_{n}$ sequences choosing DNA parameters satisfying experimental data for the balance of charge transfer rates $G^{+} \\leftrightarrow G_{n}^{+}$, $n=2,3$ \\cite{FredMain}. We show that experimental data can be consistent with theory only assuming $b\\ll \\lambda$ meaning that charge is typically localized within the single $G$ site. Consequently any DNA sequence including the one consisting of identical base pairs behaves more like an insulating material then a molecular conductor. Our theory can be verified experimentally, for instance measuring balance of charge transfer reactions $G^{+} \\leftrightarrow G_{n}^{+}$, $n \\geq 4$ and comparing the experimental results with our predictions.
Dmitry B. Uskov; Alexander L. Burin
Role of DNA repair protein ERCC1 in skin cancer�
Nucleotide excision repair (NER) is one of the major repair systems for removal of DNA lesions. The NER pathway has evolved mainly to repair UV-induced DNA damage and is also active against a broad range of endogenously ...
Song, Liang
DNA hybridization : fundamental studies and applications in directed assembly
Programmed self-assembly using non-covalent DNA-DNA interactions is a promising technique for the creation of next-generation functional devices for electronic, optical, and magnetic applications. This thesis develops the ...
Bajaj, Manish G. (Manish Gopal)
Analysis of the structural changes caused by positive DNA supercoiling
The procession of helix-tracking enzymes along a DNA molecule results in the formation of supercoils in the DNA, with positive supercoiling (overwinding) generated ahead of the enzyme, and negative supercoiling (underwinding) ...
Barth, Marita Christine
Lectin cDNA and transgenic plants derived therefrom
Transgenic plants containing cDNA encoding Gramineae lectin are described. The plants preferably contain cDNA coding for barley lectin and store the lectin in the leaves. The transgenic plants, particularly the leaves exhibit insecticidal and fungicidal properties.
Raikhel, Natasha V. (Okemos, MI)
Mitigating security issues in the evolving DNA synthesis industry
DNA synthesis technologies are advancing at exponential rates, with production of ever longer, more complex, and less expensive sequences of double stranded DNA. This has fostered development of industrial scale design, ...
Turlington, Ralph Donald, III
Flow cytometric measurement of total DNA and incorporated halodeoxyuridine
A method for the simultaneous flow cylometric measurement of total cellular DNA content and of the uptake of DNA precursors as a measure of DNA synthesis during various phases of the cell cycle in normal and malignant cells in vitro and in vivo is described. The method comprises reacting cells with labelled halodeoxyuridine (HdU), partially denaturing cellular DNA, adding to the reaction medium monoclonal antibodies (mabs) reactive with HdU, reacting the bound mabs with a second labelled antibody, incubating the mixture with a DNA stain, and measuring simultaneously the intensity of the DNA stain as a measure of the total cellular DNA and the HdU incorporated as a measure of DNA synthesis. (ACR)
Dolbeare, F.A.; Gray, J.W.
Defining functional DNA elements in the human genome
With the completion of the human genome sequence, attention turned to identifying and annotating its functional DNA elements. As a complement to genetic and comparative genomics approaches, the Encyclopedia of DNA Elements ...
Kellis, Manolis
Single cell trapping and DNA damage analysis using microwell arrays
With a direct link to cancer, aging, and heritable diseases as well as a critical role in cancer treatment, the importance of DNA damage is well-established. The intense interest in DNA damage in applications ranging from ...
Wood, David
A model for sample stacking in microcapillary DNA electrophoresis
Sanger's method of chain termination is the method of choice in DNA sequencing, where electrophoresis is used to separate the different sized DNA. In the past decade, microfabricated capillary devices have been developed ...
Srivastava, Alok Kumar, 1967-
Photoelectrochemical array platform for genomic scale DNA synthesis
Molecular and synthetic biologists have increasing demand for large, high-fidelity constructs of synthetic DNA. Recent developments in harvesting oligonucleotides from DNA microarrays has proven that these can be assembled ...
Emig, Christopher Joseph
Bayesian models for DNA microarray data analysis
as to perform future predictions. The method is applied to cancer classi?cation via cDNA microarrays. In particular, the genes BRCA1 and BRCA2 are associated with a hereditary disposition to breast cancer, and the method is used to identify the set of signi...
Lee, Kyeong Eun
Rotary mechanical latch
A rotary mechanical latch for positive latching and unlatching of a rotary device with a latchable rotating assembly having a latching gear that can be driven to latched and unlatched states by a drive mechanism such as an electric motor. A cam arm affixed to the latching gear interfaces with leading and trailing latch cams affixed to a flange within the drive mechanism. The interaction of the cam arm with leading and trailing latch cams prevents rotation of the rotating assembly by external forces such as those due to vibration or tampering.
Spletzer, Barry L.; Martinez, Michael A.; Marron, Lisa C.
Electronic door locking mechanism
The invention is a motorized linkage for engaging a thumb piece in a door mechanism. The device has an exterior lock assembly with a small battery cell and combination lock. Proper entry by a user of a security code allows the battery to operate a small motor within the exterior lock assembly. The small motor manipulates a cam-plunger which moves an actuator pin into a thumb piece. The user applies a force on to the thumb piece. This force is transmitted by the thumb piece to a latch engagement mechanism by the actuator pin. The latch engagement mechanism operates the door latch.
Williams, Gary Lin (428 E. Third Ave., Kennewick, WA 99336); Kirby, Patrick Gerald (1010 W. Fifteenth Pl., Kennewick, WA 99337)
The invention is a motorized linkage for engaging a thumb piece in a door mechanism. The device has an exterior lock assembly with a small battery cell and combination lock. Proper entry by a user of a security code allows the battery to operate a small motor within the exterior lock assembly. The small motor manipulates a cam-plunger which moves an actuator pin into a thumb piece. The user applies a force on to the thumb piece. This force is transmitted by the thumb piece to a latch engagement mechanism by the actuator pin. The latch engagement mechanism operates the door latch. 6 figs.
Williams, G.L.; Kirby, P.G.
DNA Strands Attached Inside Single Conical Nanopores: Ionic Pore Characteristics and Insight into DNA Biophysics
Kathawalla et al. 1989; Heng et al. 2005; Keyser et al.due to the electric ?eld (Heng et al. 2005; Randall et al.DNA analysis. Nanomedicine Heng JB, Aksimentiev A, Ho C,
Nguyen, Gael; Howorka, Stefan; Siwy, Zuzanna S.
Orientational Dynamics and Dye-DNA Interactions in a Dye-Labeled DNA Aptamer
We report the picosecond and nanosecond timescale rotational dynamics of a dye-labeled DNA oligonucleotide or ��aptamer�� designed to bind specifically to immunoglobulin E. Rotational dynamics in combination with fluorescence lifetime measurements...
Wilson, George S.; Unruh, Jay R.; Gokulrangan, Giridharan; Lushington, Gerald H.; Johnson, Carey K.
DNA ruler : enhancing nanopore sizing resolution by multiple measurements on the same DNA molecule
Nanopores are versatile sensors for label-free detection of single molecules and particles that have attracted attention for applications such as DNA sequencing and nanoparticle analysis. Detection of single molecules or ...
Sen, Yi-Heng
A User's Guide to the Encyclopedia of DNA Elements (ENCODE)
The mission of the Encyclopedia of DNA Elements (ENCODE) Project is to enable the scientific and medical communities to
Bernstein, Bradley E.
Design and Characterization of Programmable DNA Nanotubes Supporting Information
. DNA sample preparation: Lyophilized HPLC- or PAGE- purified DNA oligonucleotides were purchased from Integrated DNA Technologies (Coralville, IA), resuspended in water, quanti- tated by UV absorbance at 260 nm immersion and 40X/0.75 NA air objectives. Blue light was filtered from a mer- cury arc lamp thro
Self-assembling DNA templates for programmed artificial biomineralization
Self-assembling DNA templates for programmed artificial biomineralization Enrique C. Samano created via engineered DNA self-assembly represent an important new class of soft matter. These assemblies nanostructures Our current ability to create complex DNA nanostructures via designed self- assembly owes much
Finkelstein, Gleb
Correct and incorrect nucleotide incorporation pathways in DNA polymerase b
Correct and incorrect nucleotide incorporation pathways in DNA polymerase b Ravi Radhakrishnan a nucleotide incorporations in the DNA by using a novel protocol involving energy minimizations, dynamics simu- sive transient intermediates, for nucleotide incorporation at the template/primer DNA junction. A large
Schlick, Tamar
Ultralight, ultrastiff mechanical metamaterials
The mechanical properties of ordinary materials degrade substantially with reduced density because their structural elements bend under applied load. We report a class of microarchitected materials that maintain a nearly ...
Zheng, Xiaoyu
people trained from both perspectives can result in innovative solutions. At Fraunhofer CMI coMechanical engineering Department Seminar Alexis Sauer-Budge Senior Research Scientist, Fraunhofer CMI Adjunct Research Assistant Professor, BME, Boston University Innovations at the intersection
Mechanical & Aerospace Engineering This presentation will address the development and transition of advanced structural health management (SHM) technologies from the perspective of understanding and the importance of understanding this role to increase the likelihood for transition of new technologies
Mechanical Compression Heat Pumps
MECHANICAL COMPRESSION HEAT PUMPS Thomas-L. Apaloo and K. Kawamura Mycom Corporation, Los Angeles, California J. Matsuda, Mayekawa Mfg. Co., Tokyo, Japan ABSTRACT Mechanical compression heat pumping is not new in industrial applications.... In fact, industry history suggests that the theoretical concept was developed before 1825. Heat pump manufacturers gained the support of consultants and end-users when the energy crisis hit this country in 1973. That interest, today, has been...
Apaloo, T. L.; Kawamura, K.; Matsuda, J.
Mitotic chromosomes are chromatin networks without a mechanically contiguous protein scaffold
Mitotic chromosomes are chromatin networks without a mechanically contiguous protein scaffold in the electron micro- scope by histone-depleting chromosomes; the resulting micro- graphs show 40-kb DNA loops chromosomes and was essentially a fibrous network of nonhistone proteins (3), which could be isolated
Poirier, Michael
MECH 386 INDUSTRIAL FLUID MECHANICS 1 INDUSTRIAL FLUID MECHANICS MECH 386 Contact information Dr This course is an introduction to industrial fluid mechanics. According to J. C. R. Hunt (a famous fluid mechanics specialist): "industrial fluid mechanics broadly covers those aspects of the design, manufacture
Mechanical Engineering Is Mechanical Engineering right for me?
Mechanical Engineering Is Mechanical Engineering right for me? If you are interested in the wide range of principles related to mechanical systems then Mechanical Engineering is well suited to you. A Mechanical Engineering degree programme will focus on aspects such as analysis, design, manufacture
Harman, Neal.A.
The Role of Micro-Mechanics in Soil Mechanics
The Role of Micro-Mechanics in Soil Mechanics M.D.Bolton CUED/D-Soils/TR313 September 2000;1 The Role of Micro-Mechanics in Soil Mechanics Malcolm Bolton Summary It is suggested that observations of the changing microstructure of soils will permit the selection and refinement of relevant micro-mechanisms
Bolton, Malcolm
DNA digestion protocol & hints Overview: Although it is pretty standard to digest DNA with restriction enzymes, here
Liu 4/2004 DNA digestion protocol & hints Overview: Although it is pretty standard to digest DNA in molecular biology (3.1.1-3.1.2) Materials: � DNA sample in water or TE buffer � 10x digestion buffer.1 to 4 �g 10x Digestion buffer 2 �l 5 �l Enzyme ? ? Water Rest of volume Rest of volume 2. Add the enzyme
Doering, Tamara
Preparation of DNA-containing extract for PCR amplification
Environmental samples typically include impurities that interfere with PCR amplification and DNA quantitation. Samples of soil, river water, and aerosol were taken from the environment and added to an aqueous buffer (with or without detergent). Cells from the sample are lysed, releasing their DNA into the buffer. After removing insoluble cell components, the remaining soluble DNA-containing extract is treated with N-phenacylthiazolium bromide, which causes rapid precipitation of impurities. Centrifugation provides a supernatant that can be used or diluted for PCR amplification of DNA, or further purified. The method may provide a DNA-containing extract sufficiently pure for PCR amplification within 5�10 minutes.
Dunbar, John M.; Kuske, Cheryl R.
Reactive species and DNA damage in chronic inflammation: Reconciling chemical mechanisms and biological fates
Chronic inflammation has long been recognized as a risk factor for many human cancers. One mechanistic link between inflammation and cancer involves the generation of nitric oxide, superoxide and other reactive oxygen and ...
Lonkar, Pallavi
Introduction The study of DNA repair mechanisms has been aided by the
in the fission yeast Schizosaccharomyces pombe requires microtubule-dependent oscillatory nuclear movements. These events were initially thought to result from gene conversion (GC) accompanied by crossover (Jager and Philippsen, 1989). However, other studies of direct repeat recombination have shown that deletions commonly
Orchestration of cooperative events in DNA synthesis and repair mechanism unraveled by transition path
of Chemistry and Courant Institute of Mathematical Sciences, 251 Mercer Street, New York University, New York and energetic details of the con- formational change that precedes the chemical reaction of nucle- otide
AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr MayAtmosphericNuclear Security Administrationcontroller systemsBiSiteNeutronStrategicOur MissionStructureSynthetase |Structure of
AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr MayAtmosphericNuclear Security Administrationcontroller systemsBiSiteNeutronStrategicOur MissionStructureSynthetase |Structure
AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr MayAtmosphericNuclear Security Administrationcontroller systemsBiSiteNeutronStrategicOur MissionStructureSynthetase
Cadmium sulfate and CdTe-quantum dots alter DNA repair in zebrafish (Danio rerio) liver cells
Increasing use of quantum dots (QDs) makes it necessary to evaluate their toxicological impacts on aquatic organisms, since their contamination of surface water is inevitable. This study compares the genotoxic effects of ionic Cd versus CdTe nanocrystals in zebrafish hepatocytes. After 24 h of CdSO{sub 4} or CdTe QD exposure, zebrafish liver (ZFL) cells showed a decreased number of viable cells, an accumulation of Cd, an increased formation of reactive oxygen species (ROS), and an induction of DNA strand breaks. Measured levels of stress defense and DNA repair genes were elevated in both cases. However, removal of bulky DNA adducts by nucleotide excision repair (NER) was inhibited with CdSO{sub 4} but not with CdTe QDs. The adverse effects caused by acute exposure of CdTe QDs might be mediated through differing mechanisms than those resulting from ionic cadmium toxicity, and studying the effects of metallic components may be not enough to explain QD toxicities in aquatic organisms. - Highlights: � Both CdSO{sub 4} and CdTe QDs lead to cell death and Cd accumulation. � Both CdSO{sub 4} and CdTe QDs induce cellular ROS generation and DNA strand breaks. � Both CdSO{sub 4} and CdTe QDs induce the expressions of stress defense and DNA repair genes. � NER repair capacity was inhibited with CdSO{sub 4} but not with CdTe QDs.
Tang, Song; Cai, Qingsong [The Institute of Environmental and Human Health, Texas Tech University, Lubbock, TX 79416 (United States); Chibli, Hicham [Department of Biomedical Engineering, McGill University, Montr�al, QC H3A 2B4 (Canada); Allagadda, Vinay [The Institute of Environmental and Human Health, Texas Tech University, Lubbock, TX 79416 (United States); Nadeau, Jay L. [Department of Biomedical Engineering, McGill University, Montr�al, QC H3A 2B4 (Canada); Mayer, Gregory D., E-mail: firstname.lastname@example.com [The Institute of Environmental and Human Health, Texas Tech University, Lubbock, TX 79416 (United States)
, when two bound copies are to be submitted to the Mechanical Engineering Services Office #12;PLEASE Mechanical Engineering Student Services: ¨ Application Approved ¨ Application Denied Signature of UGMECHANICAL ENGINEERING UNDERGRADUATE HONORS THESIS The Department of Mechanical Engineering
Prinz, Friedrich B.
20062007 Mechanical Engineering Student Services Building 530, Room 125 (650) 7257695 FAX (650) 7234882STANFORD UNIVERSITY MECHANICAL ENGINEERING DEPARTMENT GRADUATE STUDENT HANDBOOK Academic Year Revised 9/06 #12;MECHANICAL ENGINEERING GRADUATE STUDENT HANDBOOK 20062007 TABLE OF CONTENTS (Clickable
Determining orientation and direction of DNA sequences
Determining orientation and direction of DNA sequences. A method by which fluorescence in situ hybridization can be made strand specific is described. Cell cultures are grown in a medium containing a halogenated nucleotide. The analog is partially incorporated in one DNA strand of each chromatid. This substitution takes place in opposite strands of the two sister chromatids. After staining with the fluorescent DNA-binding dye Hoechst 33258, cells are exposed to long-wavelength ultraviolet light which results in numerous strand nicks. These nicks enable the substituted strand to be denatured and solubilized by heat, treatment with high or low pH aqueous solutions, or by immersing the strands in 2.times.SSC (0.3M NaCl+0.03M sodium citrate), to name three procedures. It is unnecessary to enzymatically digest the strands using Exo III or another exonuclease in order to excise and solubilize nucleotides starting at the sites of the nicks. The denaturing/solubilizing process removes most of the substituted strand while leaving the prereplication strand largely intact. Hybridization of a single-stranded probe of a tandem repeat arranged in a head-to-tail orientation will result in hybridization only to the chromatid with the complementary strand present.
Goodwin, Edwin H. (Los Alamos, NM); Meyne, Julianne (Los Alamos, NM)
Experimental unsaturated soil mechanics
In this general report, experimental systems and procedures of investigating the hydro-mechanical behaviour of unsaturated soils are presented. The water retention properties of unsaturated soils are commented and linked to various physical parameters and properties of the soils. Techniques of controlling suction are described together with their adaptation in various laboratory testing devices. Some typical features of the mechanical behaviour of unsaturated soils are presented within an elasto-plastic framework. An attempt to describe the numerous and significant recent advances in the investigation of the behaviour of unsaturated soils, including the contributions to this Conference, is proposed.
Delage, Pierre
Mechanical Behavior of Indium Nanostructures
Mechanical Behavior of Indium Nanostructures Mechanical Behavior of Indium Nanostructures Print Wednesday, 26 May 2010 00:00 Indium is a key material in lead-free solder...
Department of Mechanical Engineering 2014 Fast Facts Faculty Based on 2013 statistics from Master's Degrees Awarded 45 Doctorate Degrees Awarded Funding Fiscal Year 2013 $20M Total Research for Energetic Concepts Development Center for Environmental Energy Engineering Center for Risk and Reliability
Li, Teng
MECHANICAL TEST LAB CAPABILITIES · Static and cyclic testing (ASTM and non-standard) · Impact drop testing · Slow-cycle fatigue testing · High temperature testing to 2500°F · ASTM/ Boeing/ SACMA standard testing · Ability to design and fabricate non-standard test fixtures and perform non-standard tests
Mechanical engineering Department Seminar Jason Fleischer Department of Electrical Engineering Princeton University Fluid dynamics of light 11:00 AM Friday, November 4th, 2011 Room 245, 110 Cummington Street Refreshments served at 10:45 AM Fluid dynamics inspired the original wave theories of light, while
Quantum Mechanics and Gravitation
In summer 1999 an experiment at ILL, Grenoble was conducted. So-called ultra-cold neutrons (UCN) were trapped in the vertical direction between the Fermi-potential of a smooth mirror below and the gravitational potential of the earth above [Ne00, Ru00]. If quantum mechanics turns out to be a sufficiently correct description of the phenomena in the regime of classical, weak gravitation, one should observe the forming of quantized bound states in the vertical direction above a mirror. Already in a simplified view, the data of the experiment provides strong evidence for the existence of such gravitationally bound quantized states. A successful quantum-mechanical description would then provide a convincing argument, that the socalled first quantization can be used for gravitation as an interaction potential, as this is widely expected. Furthermore, looking at the characteristic length scales of about 10 mikron of such bound states formed by UCN, one sees, that a complete quantum mechanical description of this experiment additionally would enable one to check for possible modifications of Newtonian gravitation on distance scales being one order of magnitude below currently available tests [Ad00]. The work presented here deals mainly with the development of a quantum mechanical description of the experiment.
A. Westphal
, electrical, and computing sciences that allows the development of machines that are able to act to recent advances in the science of robotics, and thus the machines perform primarily as mechanical devices for manual (human) labor. However, many machines currently in use in manufacturing were developed prior
Mechanical engineering Department Seminar Wynter J. Duncanson Department of Aerospace and Ocean Engineering Virginia Tech Smart' Bubbles for Acoustic Contrast in Oil Reservoirs 11:00 AM Friday, 19 April engineering from Boston University. Her doctoral research was devoted to designing surface architectures
Mechanical engineering Department Seminar Eric Suuberg Professor Brown University Another Reason, chemicals of anthropogenic origin can migrate from soil into houses, invis- ibly, over time, impacting the soil gas migration problem, and used these to develop simple analytical approaches to estimating
Residential Mechanical Precooling
This research conducted by the Alliance for Residential Building Innovation team evaluated mechanical air conditioner pre-cooling strategies in homes throughout the United States. EnergyPlus modeling evaluated two homes with different performance characteristics in seven climates. Results are applicable to new construction homes and most existing homes built in the last 10 years, as well as fairly efficient retrofitted homes.
German, A.; Hoeschele, M.
Imaging the Antikythera Mechanism
In 1900, a party of sponge divers chanced on the wreck of a Roman merchant vessel between Crete and mainland Greece. It was found to contain numerous ancient Greek treasures, among them a mysterious lump of clay that split open to reveal 'mathematical gears' as it dried out. This object is now known as the Antikythera Mechanism, one of the most enlightening artifacts in terms of revealing the advanced nature of ancient Greek science and technology. In 2005 we travelled to the National Archeological Museum in Athens to apply our Reflectance Imaging methods to the mechanism in the hopes of revealing ancient writing on the device. We were successful, and along with the results of Microfocus CT imaging, we are able to decipher 3000 characters compared with the original 800 known. This lead to an understanding that the device was a mechanical, astronomical computer from 150 B.C.E. capable of predicting solar and lunar eclipses along with other celestial events. This talk will overview both the imaging methods as well as what they reveal about the Antikythera Mechanism.
Malzbender, Tom (Hewlett Packard Laboratories) [Hewlett Packard Laboratories
Molecular mechanisms controlling complex traits in yeast
A fundamental goal in biology is to understand how the information stored in DNA results in a cellular function. However, it is insufficient to study one variant of a particular DNA sequence because most people do not share ...
Chin, Brian L. (Brian Leland)
Department of Mechanical Engineering "From Compliant Mechanisms to
such as 3D printing with materials specialized in electro- mechanical sensing and actuation in addition
Militzer, Burkhard
MECHANICAL ENGINEERING 121 Department of Mechanical Engineering (MEE)
MECHANICAL ENGINEERING 121 Department of Mechanical Engineering (MEE) *Available for general education credit. The Department of Mechanical Engineering offers an upper- division curriculum which leads to a B.S. in mechanical engineering. The curriculum is based on a strong foundation of fundamental
Mechanical engineering Mechanical engineering is about solving problems, designing processes,
Mechanical engineering Mechanical engineering is about solving problems, designing processes, and making products to improve the quality of human life and shape the economy. Mechanical engineers apply the principles of physics, mathematics, computing and practical skills to design mechanical systems and artefacts
Waikato, University of
114 MECHANICAL ENGINEERING Department of Mechanical Engineering (MEE)
114 MECHANICAL ENGINEERING Department of Mechanical Engineering (MEE) *Available for general education credit. The Department of Mechanical Engineering offers an upper- division curriculum which leads to a B.S. in mechanical engineering. The curriculum is based on a strong foundation of fundamental
Program Transformation Mechanics A Classification of Mechanisms for Program Transformation
Program Transformation Mechanics A Classification of Mechanisms for Program Transformation with a Survey of Existing Transformation Systems Jonne van Wijngaarden Eelco Visser UU-CS-2003-048 Institute Transformation Mechanics A Classification of Mechanisms for Program Transformation with a Survey of Existing
Utrecht, Universiteit
Probing Minor Groove Hydrogen Bonding Interactions between RB69 DNA Polymerase and DNA
Minor groove hydrogen bonding (HB) interactions between DNA polymerases (pols) and N3 of purines or O2 of pyrimidines have been proposed to be essential for DNA synthesis from results obtained using various nucleoside analogues lacking the N3 or O2 contacts that interfered with primer extension. Because there has been no direct structural evidence to support this proposal, we decided to evaluate the contribution of minor groove HB interactions with family B pols. We have used RB69 DNA pol and 3-deaza-2'-deoxyadenosine (3DA), an analogue of 2-deoxyadenosine, which has the same HB pattern opposite T but with N3 replaced with a carbon atom. We then determined pre-steady-state kinetic parameters for the insertion of dAMP opposite dT using primer/templates (P/T)-containing 3DA. We also determined three structures of ternary complexes with 3DA at various positions in the duplex DNA substrate. We found that the incorporation efficiency of dAMP opposite dT decreased 10{sup 2}-10{sup 3}-fold even when only one minor groove HB interaction was missing. Our structures show that the HB pattern and base pair geometry of 3DA/dT is exactly the same as those of dA/dT, which makes 3DA an optimal analogue for probing minor groove HB interactions between a DNA polymerase and a nucleobase. In addition, our structures provide a rationale for the observed 10{sup 2}-10{sup 3}-fold decrease in the rate of nucleotide incorporation. The minor groove HB interactions between position n-2 of the primer strand and RB69pol fix the rotomer conformations of the K706 and D621 side chains, as well as the position of metal ion A and its coordinating ligands, so that they are in the optinal orientation for DNA synthesis.
Xia, Shuangluo; Christian, Thomas D.; Wang, Jimin; Konigsberg, William H. (Yale)
Fluid Mechanics and Homeland Security
Fluid Mechanics and Homeland Security Gary S. Settles Mechanical and Nuclear Engineering Department. 2006. 38:87110 The Annual Review of Fluid Mechanics is online at fluid.annualreviews.org doi: 10 security involves many applications of fluid mechanics and offers many opportunities for research
Settles, Gary S.
Mechanical Engineering Department Seminar Series
Mechanical Engineering Department Seminar Series Rational Mechanics of Viral Shells: Is Continuum Theory a Stretch? William S. Klug Associate Professor, Mechanical & Aerospace Engineering, University-assembly. The capacity of these shells to respond structurally and mechanically to physical and chemical stimuli also
Eustice, Ryan
, mechanical with nuclear engineering, and medical engineering. Engineers qualified in all these areas play MECHANICAL ENGINEERING MECHANICAL WITH NUCLEAR ENGINEERING MEDICAL ENGINEERING OTHER COURSES TO CONSIDER Entryrequirementsandhowtoapply Modules MedicalEngineering(MEng,BEng) MechanicalwithNuclearEngineering(MEng,BEng) MechanicalEngineering
Dimitrova, Vania
Osmotic pressure: resisting or promoting DNA ejection from phage
Recent in vitro experiments have shown that DNA ejection from bacteriophage can be partially stopped by surrounding osmotic pressure when ejected DNA is digested by DNase I on the course of ejection. We argue in this work by combination of experimental techniques (osmotic suppression without DNaseI monitored by UV absorbance, pulse-field electrophoresis, and cryo-EM visualization) and simple scaling modeling that intact genome (i.e. undigested) ejection in a crowded environment is, on the contrary, enhanced or eventually complete with the help of a pulling force resulting from DNA condensation induced by the osmotic stress itself. This demonstrates that in vivo, the osmotically stressed cell cytoplasm will promote phage DNA ejection rather than resisting it. The further addition of DNA-binding proteins under crowding conditions is shown to enhance the extent of ejection. We also found some optimal crowding conditions for which DNA content remaining in the capsid upon ejection is maximum, which correlates well...
Jeembaeva, Meerim; Larsson, Frida; Evilevitch, Alex
How effective is graphene nanopore geometry on DNA sequencing?
In this paper we investigate the effects of graphene nanopore geometry on homopolymer ssDNA pulling process through nanopore using steered molecular dynamic (SMD) simulations. Different graphene nanopores are examined including axially symmetric and asymmetric monolayer graphene nanopores as well as five layer graphene polyhedral crystals (GPC). The pulling force profile, moving fashion of ssDNA, work done in irreversible DNA pulling and orientations of DNA bases near the nanopore are assessed. Simulation results demonstrate the strong effect of the pore shape as well as geometrical symmetry on free energy barrier, orientations and dynamic of DNA translocation through graphene nanopore. Our study proposes that the symmetric circular geometry of monolayer graphene nanopore with high pulling velocity can be used for DNA sequencing.
Satarifard, Vahid; Ejtehadi, Mohammad Reza
Mechanics of collective unfolding
Mechanically induced unfolding of passive crosslinkers is a fundamental biological phenomenon encountered across the scales from individual macro-molecules to cytoskeletal actin networks. In this paper we study a conceptual model of athermal load-induced unfolding and use a minimalistic setting allowing one to emphasize the role of long-range interactions while maintaining full analytical transparency. Our model can be viewed as a description of a parallel bundle of N bistable units confined between two shared rigid backbones that are loaded through a series spring. We show that the ground states in this model correspond to synchronized, single phase configurations where all individual units are either folded or unfolded. We then study the fine structure of the wiggly energy landscape along the reaction coordinate linking the two coherent states and describing the optimal mechanism of cooperative unfolding. Quite remarkably, our study shows the fundamental difference in the size and structure of the folding-u...
Caruel, M; Truskinovsky, L
Design of a combinatorial dna microarray for protein-dnainteraction studies
Background: Discovery of precise specificity oftranscription factors is an important step on the way to understandingthe complex mechanisms of gene regulation in eukaryotes. Recently,doublestranded protein-binding microarrays were developed as apotentially scalable approach to tackle transcription factor binding siteidentification. Results: Here we present an algorithmic approach toexperimental design of a microarray that allows for testing fullspecificity of a transcription factor binding to all possible DNA bindingsites of a given length, with optimally efficient use of the array. Thisdesign is universal, works for any factor that binds a sequence motif andis not species-specific. Furthermore, simulation results show that dataproduced with the designed arrays is easier to analyze and would resultin more precise identification of binding sites. Conclusion: In thisstudy, we present a design of a double stranded DNA microarray forprotein-DNA interaction studies and show that our algorithm allowsoptimally efficient use of the arrays for this purpose. We believe such adesign will prove useful for transcription factor binding siteidentification and other biological problems.
Mintseris, Julian; Eisen, Michael B.
Quantitative Analysis of Clustered DNA Damages Induced by Silicon Beams of Different Kinetic Energy
Humans may b exposed to highly energetic charged particle radiation as a result of medical treatments, occupational activitie or accidental events. In recent years, our increasing presence and burgeoning interest in space exploration beyond low Earth orbit has led to a large increase in the research of the biological effects ofcharged particle radiation typical of that encountered in the space radiation environment. The study of the effects of these types of radiation qualities in terms ofDNA damage induction and repair is fundamental to understand mechanisms both underlying their greater biological effectiveness as we)) as the short and long term risks of health effects such as carcinogenesis, degen rative diseases and premature aging. Charged particle radiation induces a variety of DNA alterations, notably bistranded clustered damages, defined as two or more closely-opposed strand break , oxidized bases or abasic sites within a few helical turns. The induction of such highly complex DNA damage enhances the probability of incorrect or incomplete repair and thus constitutes greater potential for genomic instability, cell death and transformation.
Keszenman D. J.; Keszenman, D.J.; Bennett, P.V.; Sutherland, B.M.; Wilson, P.F.
Mechanically induced unfolding of passive crosslinkers is a fundamental biological phenomenon encountered across the scales from individual macro-molecules to cytoskeletal actin networks. In this paper we study a conceptual model of athermal load-induced unfolding and use a minimalistic setting allowing one to emphasize the role of long-range interactions while maintaining full analytical transparency. Our model can be viewed as a description of a parallel bundle of N bistable units confined between two shared rigid backbones that are loaded through a series spring. We show that the ground states in this model correspond to synchronized, single phase configurations where all individual units are either folded or unfolded. We then study the fine structure of the wiggly energy landscape along the reaction coordinate linking the two coherent states and describing the optimal mechanism of cooperative unfolding. Quite remarkably, our study shows the fundamental difference in the size and structure of the folding-unfolding energy barriers in the hard (fixed displacements) and soft (fixed forces) loading devices which persists in the continuum limit. We argue that both, the synchronization and the non-equivalence of the mechanical responses in hard and soft devices, have their origin in the dominance of long-range interactions. We then apply our minimal model to skeletal muscles where the power-stroke in acto-myosin crossbridges can be interpreted as passive folding. A quantitative analysis of the muscle model shows that the relative rigidity of myosin backbone provides the long-range interaction mechanism allowing the system to effectively synchronize the power-stroke in individual crossbridges even in the presence of thermal fluctuations. In view of the prototypical nature of the proposed model, our general conclusions pertain to a variety of other biological systems where elastic interactions are mediated by effective backbones.
M Caruel; J. -M Allain; L Truskinovsky
Relativistic viscoelastic fluid mechanics
A detailed study is carried out for the relativistic theory of viscoelasticity which was recently constructed on the basis of Onsager's linear nonequilibrium thermodynamics. After rederiving the theory using a local argument with the entropy current, we show that this theory universally reduces to the standard relativistic Navier-Stokes fluid mechanics in the long time limit. Since effects of elasticity are taken into account, the dynamics at short time scales is modified from that given by the Navier-Stokes equations, so that acausal problems intrinsic to relativistic Navier-Stokes fluids are significantly remedied. We in particular show that the wave equations for the propagation of disturbance around a hydrostatic equilibrium in Minkowski spacetime become symmetric hyperbolic for some range of parameters, so that the model is free of acausality problems. This observation suggests that the relativistic viscoelastic model with such parameters can be regarded as a causal completion of relativistic Navier-Stokes fluid mechanics. By adjusting parameters to various values, this theory can treat a wide variety of materials including elastic materials, Maxwell materials, Kelvin-Voigt materials, and (a nonlinearly generalized version of) simplified Israel-Stewart fluids, and thus we expect the theory to be the most universal description of single-component relativistic continuum materials. We also show that the presence of strains and the corresponding change in temperature are naturally unified through the Tolman law in a generally covariant description of continuum mechanics.
Masafumi Fukuma; Yuho Sakatani
Helical Disruptions in Small Loops of DNA
The thermodynamical stability of DNA minicircles is investigated by means of path integral techniques. Hydrogen bonds between base pairs on complementary strands can be broken by thermal fluctuations and temporary fluctuational openings along the double helix are essential to biological functions such as transcription and replication of the genetic information. Helix unwinding and bubble formation patterns are computed in circular sequences with variable radius in order to analyze the interplay between molecule size and appearance of helical disruptions. The latter are found in minicircles with $100$ base pairs and appear as a strategy to soften the stress due to the bending and torsion of the helix.
Zoli, Marco
DNA Origami: A History and Current Perspective
AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr May JunDatastreamsmmcrcalgovInstrumentsruc DocumentationP-Series to UserProduct: Crude OilPublicDNA Gridiron Nanostructures
AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr MayAtmospheric Optical Depth7-1D: Vegetation ProposedUsingFunInfrared LandResponses to EngineeredA GENERAL2RadiativeIntriguing DNA Editor
AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr MayAtmospheric Optical Depth7-1D: Vegetation ProposedUsingFunInfrared LandResponses to EngineeredA GENERAL2RadiativeIntriguing DNA
Isolation of Discrete Nanoparticle-DNA Conjugates for Plasmonic Applications
Discrete DNA-gold nanoparticle conjugates with DNA lengths as short as 15 bases for both 5 nm and 20 nm gold particles have been purified by anion-exchange HPLC. Conjugates comprising short DNA (<40 bases) and large gold particles (>_ 20 nm) are difficult to purify by other means, and are potential substrates for plasmon coupling experiments. Conjugate purity is demonstrated by hybridizing complementary conjugates to form discrete structures, which are visualized by TEM.
Alivisatos, Paul; Claridge, Shelley A.; Liang, Huiyang W.; Basu, Sourav Roger; Frechet, Jean M.J.; Alivisatos, A. Paul
Alternative Methods for Human Identification: Mitochondrial DNA Base Composition Profiling
Profiling by ESI-TOF Mass Spectrometry Kevin Kiesler Research Biologist, Applied Genetics Group Forensics · Why use Mass Spectrometry? · Abbott / Ibis Biosciences PLEX-ID Instrument · PLEX-ID mtDNA 2.0 Assay://remf.dartmouth.edu/images/mammalianLungTEM/source/8.html #12;Applied Genetics mtDNA Genotyping for Human I.D. · Mutations in mtDNA occur naturally
Perkins, Richard A.
Phase transformation and mechanical behavior in annealed 2205 duplex stainless steel welds
The phase transformations and mechanical behaviour during welding and subsequent annealing treatment of 2205 duplex stainless steel have been investigated. Detailed microstructural examination showed the presence of higher ferrite amounts in the heat affected zone (HAZ), while higher amounts of austenite were recorded in the centre region of the weld metal. Annealing treatments in the temperature range of 800-1000 deg. C resulted in a precipitation of {sigma} phase and M{sub 23}C{sub 6} chromium carbides at the {gamma}/{delta} interfaces that were found to be preferential precipitation sites. Above 1050 deg. C, the volume fraction of {delta} ferrite increases with annealing temperature. The increase of {delta} ferrite occurs at a faster rate in the HAZ than in the base metal and fusion zone. Optimal mechanical properties and an acceptable ferrite/austenite ratio throughout the weld regions corresponds to annealing at 1050 deg. C. Fractographic examinations showed that the mode of failure changed from quasi-cleavage fracture to dimple rupture with an increase in the annealing temperature from 850 to 1050 deg. C.
Badji, Riad [LPMTM-CNRS- Universite Paris 13, 99, av. J.B. Clement, 93430 Villetaneuse (France)], E-mail: email@example.com; Bouabdallah, Mabrouk [Ecole Nationale Polytechnique, 10, Avenue Hassan Badi, BP 182, El Harrach (Algeria); Bacroix, Brigitte; Kahloun, Charlie [LPMTM-CNRS- Universite Paris 13, 99, av. J.B. Clement, 93430 Villetaneuse (France); Belkessa, Brahim; Maza, Halim [Welding and NDT research Centre, B.P 64, Cheraga (Algeria)
Modeling DNA Interactions in Nucleosome Particles (A Computational Study of DNA Interactions in Nucleosome Particles)
Technology Center, University of Kansas, Lawrence, KS 66045. 2006 Annual Kansas City Area Life Sciences characterize global motions of the histone-DNA complex with respect to energy fluctuations in an assessment of energy differences resulting from the nucleotide substitutions will be presented in the context
Kansas, University of
Regulation of DNA Repair Fidelity by Molecular Checkpoints: "Gates" in DNA Polymerase 's Substrate Selection
Schlick*, Department of Chemistry and Courant Institute of Mathematical Sciences, New York UniVersity, New York, New York 10012, and Laboratory of Structural Biology, National Institute of EnVironmental Health enzymology data. Focusing on DNA polymerase (pol ), we present an emerging view of the geometric, energetic
assemble linear dna: Topics by E-print Network
compute? In his early studies of reversible computation, Bennett imagined an enzymatic Turing Machine which modified a hetero-polymer (such as DNA) to perform computation with...
assembly regulate dna: Topics by E-print Network
Fleet DNA Project - Data Dictionary for Public Download Files
Reference document for the Fleet DNA results data shared on the NREL public website. The document includes variable definitions and descriptions to assist users in understanding data.
Duran, A.; Burton, E.; Kelly, K.; Walkowicz, K.
DNA-inspired materials for 'bottom-up' nanotechnology.
??DNA is a remarkable material that is both an inspiration for polymer nanotechnology and a versatile building block for assembling well-defined nanostructures. To create polymeric� (more)
Ishihara, Yoshihiro.
ancient human dna: Topics by E-print Network
STUDY OF DNA DOUBLE-STRAND BREAKS IN BYSTANDER PRIMARY HUMAN FIBROBLASTS L. B. Smilenov-or-nothing manner(7) . Bystander cells exhibit a variety of characteristics of...
ancient dna studies: Topics by E-print Network
Ergonomics in DNA Sequencing: Standing Down to Ergonomics
Ergonomics in DNA SequencingStanding Down to Ergonomics Presented at the COEH 2009We Do: Introduction � How We Work: Ergonomics Challenges in
Naca, Christine
Nanoscale topographical replication of graphene architecture by artificial DNA nanostructures
Despite many studies on how geometry can be used to control the electronic properties of graphene, certain limitations to fabrication of designed graphene nanostructures exist. Here, we demonstrate controlled topographical replication of graphene by artificial deoxyribonucleic acid (DNA) nanostructures. Owing to the high degree of geometrical freedom of DNA nanostructures, we controlled the nanoscale topography of graphene. The topography of graphene replicated from DNA nanostructures showed enhanced thermal stability and revealed an interesting negative temperature coefficient of sheet resistivity when underlying DNA nanostructures were denatured at high temperatures.
Moon, Y.; Seo, S.; Park, J.; Park, T.; Ahn, J. R., E-mail: email@example.com [Department of Physics, Sungkyunkwan University, Suwon 440-746 (Korea, Republic of); Shin, J.; Dugasani, S. R. [Sungkyunkwan Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 440-746 (Korea, Republic of); Woo, S. H. [College of Pharmacy, Chungnam National University, Daejeon 305-764 (Korea, Republic of); Park, S. H., E-mail: firstname.lastname@example.com [Department of Physics, Sungkyunkwan University, Suwon 440-746 (Korea, Republic of); Sungkyunkwan Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 440-746 (Korea, Republic of)
Solvent resistant microfluidic DNA synthesizer{ Yanyi Huang,{a
a microfluidic DNA synthesizer out of perfluoropolyether (PFPE), an elastomer with excellent chemical characterization of the products.6 We previously reported a photocurable perfluoropolyether (PFPE) elastomer, which
Huang, Yanyi
High-Performance Integrated Genetic Analyzers for Forensic DNA Typing
Encoded evidence: DNA in forensic analysis. Nature Reviewspopulations. Journal of Forensic Sciences 48, 908-911 (identity testing. Journal of Forensic Sciences 51, 253-265 (
Liu, Peng
A Nucleotide-Analogue-Induced Gain of Function Corrects the Error-Prone Nature of Human DNA Polymerase iota
Y-family DNA polymerases participate in replication stress and DNA damage tolerance mechanisms. The properties that allow these enzymes to copy past bulky adducts or distorted template DNA can result in a greater propensity for them to make mistakes. Of the four human Y-family members, human DNA polymerase iota (hpol{iota}) is the most error-prone. In the current study, we elucidate the molecular basis for improving the fidelity of hpol{iota} through use of the fixed-conformation nucleotide North-methanocarba-2{prime}-deoxyadenosine triphosphate (N-MC-dATP). Three crystal structures were solved of hpol{iota} in complex with DNA containing a template 2{prime}-deoxythymidine (dT) paired with an incoming dNTP or modified nucleotide triphosphate. The ternary complex of hpol{iota} inserting N-MC-dATP opposite dT reveals that the adenine ring is stabilized in the anti orientation about the pseudo-glycosyl torsion angle, which mimics precisely the mutagenic arrangement of dGTP:dT normally preferred by hpol{iota}. The stabilized anti conformation occurs without notable contacts from the protein but likely results from constraints imposed by the bicyclo[3.1.0]hexane scaffold of the modified nucleotide. Unmodified dATP and South-MC-dATP each adopt syn glycosyl orientations to form Hoogsteen base pairs with dT. The Hoogsteen orientation exhibits weaker base-stacking interactions and is less catalytically favorable than anti N-MC-dATP. Thus, N-MC-dATP corrects the error-prone nature of hpol{iota} by preventing the Hoogsteen base-pairing mode normally observed for hpol{iota}-catalyzed insertion of dATP opposite dT. These results provide a previously unrecognized means of altering the efficiency and the fidelity of a human translesion DNA polymerase.
Ketkar, Amit; Zafar, Maroof K.; Banerjee, Surajit; Marquez, Victor E.; Egli, Martin; Eoff, Robert L. (Cornell); (Vanderbilt); (NCI); (Arkansas)
Physicochemical characterization of immortal strand DNA
Adult tissue differentiation involves the generation of distinct cell types from adult stem cells (ASCs). Current understanding of tissue differentiation mechanisms is based on studies of protein and RNAs that asymmetrically ...
Lansita, Janice A. (Janice Ann), 1975-
carbon composite general aviation aircraft); and Manager of Materials and Structures Research at Sikorsky temperature and bio material composite programs. In bio composite material programs Ron frequently worksENGINEERING MECHANICS SEMINARSENGINEERING MECHANICS SEMINARS BIO COMPOSITES FOR AVIATION Ron
Efficiency of stripping mechanisms
There are several physical processes to remove gas from galaxies in clusters, with subsequent starvation and star formation quenching: tidal interactions between galaxies, or tidal stripping from the cluster potential itself, interactions with the hot intra-cluster medium (ICM) through ram pressure, turbulent or viscous stripping, or also outflows from star formation of nuclear activity, We review the observational evidence for all processes, and numerical simulations of galaxies in clusters which support the respective mechanisms. This allows to compare their relative efficiencies, all along cluster formation.
F. Combes
Fields and Quantum Mechanics
The quantum field theories (QFT) constructed in [1,2] include phenomenology of interest. The constructions approximate: scattering by $1/r$ and Yukawa potentials in non-relativistic approximations; and the first contributing order of the Feynman series for Compton scattering. To have a semi-norm, photon states are constrained to transverse polarizations and for Compton scattering, the constructed cross section deviates at large momentum exchanges from the cross section prediction of the Feynman rules. Discussion includes the incompatibility of canonical quantization with the constructed interacting fields, and the role of interpretations of quantum mechanics in realizing QFT.
Glenn Eric Johnson
Metal Mechanisms | EMSL
AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr May Jun Jul(Summary)morphinanInformation Desert Southwest Regionat Cornell Batteries & Fuel Cells In ThisMetal Mechanisms Metal
Mechanical Operations and Maintenance
AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr MayAtmospheric Optical Depth7-1D: VegetationEquipment Surfaces andMapping the NanoscaleMechanical Behavior ofAPS ... Search Button
ATP AND DNA AS MICROBIAL PARAMETERS IN THE ALIMENTARY TRACT J. WOLSTRUP K. JENSEN A. JUST I. The aim of the present work was to investi- gate the use of ATP and DNA as parameters for microbial activity and biomass in the ali- mentary tract of cows and pigs. ATP was selected because of the promising
Paris-Sud XI, Université de
cDNA encoding a polypeptide including a hevein sequence
A cDNA clone (HEV1) encoding hevein was isolated via polymerase chain reaction (PCR) using mixed oligonucleotides corresponding to two regions of hevein as primers and a Hevea brasiliensis latex cDNA library as a template. HEV1 is 1,018 nucleotides long and includes an open reading frame of 204 amino acids.
Raikhel, N.V.; Broekaert, W.F.; Namhai Chua; Kush, A.
Yeast Genomic Library Genomic DNA Sau3AI partial digestion
Yeast Genomic Library Concept: Genomic DNA � Sau3AI partial digestion Vector DNA � BamHI full digestion partial Ligate and transform above products Vector Information: � use centromeric plasmid to avoid of the mcs Preparing Vector: 1) digest 3-4ug of library vector with BamHI for 2-4hrs in a total volume of 20
Odorizzi, Greg
Mechanisms of Attachment of Tobacco-Treated Streptococcus mutans to Human Endothelial Cells Alyssa R. Miller1
Mechanisms of Attachment of Tobacco-Treated Streptococcus mutans to Human Endothelial Cells Alyssa to atherosclerosis. S. mutans were treated with different concentrations of nicotine and cigarette smoke condensate reagents, enolase antibody and purified DnaK, were also used to treat the HUVEC to observe the effects
Zhou, Yaoqi
Insulation Mechanisms of in vivo Biomolecular Circuits Kayzad S. Nilgiriwala, Phillip M. Rivera and Domitilla Del Vecchio
Insulation Mechanisms of in vivo Biomolecular Circuits Kayzad S. Nilgiriwala, Phillip M. Rivera,2,3). It has been theoretically shown that a system can be insulated from retroactivity by using high gain, effectively insulating the cycle from retroactivity by downstream DNA targets. Hence, phosphorylation cycles
Del Vecchio, Domitilla
College of Engineering Mechanical Engineering
College of Engineering Mechanical Engineering Core 2.0 Completion Checklist Mechanical Engineering Science IN CHMY 141 (CHEM 131) 6 Research and Creative Experience R EMEC 489R & EMEC 499 R (ME 404R & ME
Dyer, Bill
Statistical Mechanics with focus on
Statistical Mechanics with focus on Liquids, Solutions and Colloidal Systems Course contents A. Foundations of statistical mechanics Classical dynamics Hamilton's and Liouville's equations The concept statistics. Ideal fermion or boson gases. Bose-Einstein condensation. The relationship between
Johannesson, Henrik
Probing DNA shape and methylation state on a genomic scale with DNase I
. It approximates the size and nuclear dif- fusion properties of a typical human transcription factor (TF) (1 status of genomic DNA. Analyzing millions of DNA backbone hydrolysis events on naked genomic DNA, we show
Rohs, Remo
E-Print Network 3.0 - anchored dna substrates Sample Search Results
show... that the binding of the -domain to DNA is not required for anchoring to DNA, as looping is still observed for Fts... in the new DNA tether (Supplementary ... Source:...
Extending the realm of SuNS to DNA nanoarrays and peptide features
Intense research on DNA arrays has been fostered by their applications in the field of biomedicine. DNA microarrays are composed of several different DNA sequences to be analyzed in parallel allowing high throughput ...
Akbulut Halatci, �zge
E-Print Network 3.0 - active dna replication Sample Search Results
DnaB(Ts), we examined the degradation... of the DnaB Helicase Leads to the Collapse and Degradation of the Replication Fork: a Comparison to UV... -induced DNA damage and...
Development of new tools for the production of plasmid DNA biopharmaceuticals
DNA vaccines and gene therapies that use plasmid DNA (pDNA) as a vector have gained attention in recent years for their good safety profile, ease of manufacturing, and potential to treat a host of diseases. With this ...
Bower, Diana M. (Diana Morgan)
Lecture notes Introductory fluid mechanics
Lecture notes Introductory fluid mechanics Simon J.A. Malham Simon J.A. Malham (22nd February 2013 of fluid mechanics and along the way see lots of interesting applications. 2 Fluid flow 2.1 Flow A material essential to all modern car braking mechanisms. Fluids can be further subcatergorized. There are ideal
Malham, Simon J.A.
Lecture notes Ideal fluid mechanics
Lecture notes Ideal fluid mechanics Simon J.A. Malham Simon J.A. Malham (6th Feb 2010) Maxwell and in the process learn about the subtleties of fluid mechanics and along the way see lots of interesting are generally incompressible--a feature essential to all modern car braking mechanisms. Fluids can be further
Lecture notes Introductory fluid mechanics Simon J.A. Malham Simon J.A. Malham (17th March 2014 of fluid mechanics and along the way see lots of interesting applications. 2 Fluid flow, the Continuum are generally incompressible--a feature essential to all modern car braking mechanisms. Fluids can be further
Fluid Mechanics 25 March 2009
Journal of Fluid Mechanics 25 March 2009 VOLUME 623 Journal of Fluid Mechanics 25 Mar. 2009 VOLUME 623 #12;J. Fluid Mech. (2009), vol. 623, pp. 7584. c 2009 Cambridge University Press doi:10.1017/SLCS and the capture region enable analysis of the effect of several physiological and mechanical parameters
Dabiri, John O.
Mechanical engineering COLLEGE of ENGINEERING
. Mechanical engineering is a broad, versatile and creative discipline concerned with conversion of energyMechanical engineering COLLEGE of ENGINEERING DepartmentofMechanicalEngineering CollegeofEngineering 5050AnthonyWayneDrive Detroit,MI48202 College of engineering t Educating future engineers for 80 years
Berdichevsky, Victor
Exploiting mechanical biomarkers in microfluidics
Exploiting mechanical biomarkers in microfluidics Xiaole Maoa and Tony Jun Huang*b DOI: 10.1039/c2 mechanical biomarkers in microfluidic devices. This trend makes sense because microfluidic devices often of mechanical biomarker- based microfluidic applications. We believe that these examples are just the tip
MASTER OF SCIENCE IN MECHANICAL ENGINEERING 75 DEVELOPMENT OF A MODEL TO PREDICT AND ASSESS SURFACE Master of Science in Mechanical Engineering-December 2000 Advisors: Charles N. Calvano, Department of Mechanical Engineering David W. Byers, Naval Surface Warfare Center-Carderock Division Survivability has
Information weights of nucleotides in DNA sequences
The coding sequence in DNA molecule is considered as a message to be transferred to receiver, the proteins, through a noisy information channel and each nucleotide is assigned a respective information weight. With the help of the nucleotide substitution matrix we estimated the lower bound of the amount of information carried out by nucleotides which is not subject of mutations. We used the calculated weights to reconstruct k-oligomers of genes from the Borrelia burgdorferi genome. We showed, that to this aim there is sufficient a simple rule, that the number of bits of the carried information cannot exceed some threshold value. The method introduced by us is general and applies to every genome.
M. R. Dudek; S. Cebrat; M. Kowalczuk; P. Mackiewicz; A. Nowicka; D. Mackiewicz; M. Dudkiewicz
Hybridization and Selective Release of DNA Microarrays
DNA microarrays contain sequence specific probes arrayed in distinct spots numbering from 10,000 to over 1,000,000, depending on the platform. This tremendous degree of multiplexing gives microarrays great potential for environmental background sampling, broad-spectrum clinical monitoring, and continuous biological threat detection. In practice, their use in these applications is not common due to limited information content, long processing times, and high cost. The work focused on characterizing the phenomena of microarray hybridization and selective release that will allow these limitations to be addressed. This will revolutionize the ways that microarrays can be used for LLNL's Global Security missions. The goals of this project were two-fold: automated faster hybridizations and selective release of hybridized features. The first study area involves hybridization kinetics and mass-transfer effects. the standard hybridization protocol uses an overnight incubation to achieve the best possible signal for any sample type, as well as for convenience in manual processing. There is potential to significantly shorten this time based on better understanding and control of the rate-limiting processes and knowledge of the progress of the hybridization. In the hybridization work, a custom microarray flow cell was used to manipulate the chemical and thermal environment of the array and autonomously image the changes over time during hybridization. The second study area is selective release. Microarrays easily generate hybridization patterns and signatures, but there is still an unmet need for methodologies enabling rapid and selective analysis of these patterns and signatures. Detailed analysis of individual spots by subsequent sequencing could potentially yield significant information for rapidly mutating and emerging (or deliberately engineered) pathogens. In the selective release work, optical energy deposition with coherent light quickly provides the thermal energy to single spots to release hybridized DNA. This work leverages LLNL expertise in optics, microfluids, and bioinformatics.
Beer, N R; Baker, B; Piggott, T; Maberry, S; Hara, C M; DeOtte, J; Benett, W; Mukerjee, E; Dzenitis, J; Wheeler, E K
Mechanics of Isolated Horizons
A set of boundary conditions defining an undistorted, non-rotating isolated horizon are specified in general relativity. A space-time representing a black hole which is itself in equilibrium but whose exterior contains radiation admits such a horizon. However, the definition is applicable in a more general context, such as cosmological horizons. Physically motivated, (quasi-)local definitions of the mass and surface gravity of an isolated horizon are introduced and their properties analyzed. Although their definitions do not refer to infinity, these quantities assume their standard values in the static black hole solutions. Finally, using these definitions, the zeroth and first laws of black hole mechanics are established for isolated horizons.
Abhay Ashtekar; Christopher Beetle; Stephen Fairhurst
Microfabricated therapeutic actuator mechanisms
Electromechanical microstructures (microgrippers), either integrated circuit (IC) silicon-based or precision machined, to extend and improve the application of catheter-based interventional therapies for the repair of aneurysms in the brain or other interventional clinical therapies. These micromechanisms can be specifically applied to release platinum coils or other materials into bulging portions of the blood vessels also known as aneurysms. The ``micro`` size of the release mechanism is necessary since the brain vessels are the smallest in the body. Through a catheter more than one meter long, the micromechanism located at one end of the catheter can be manipulated from the other end thereof. The microgripper (micromechanism) of the invention will also find applications in non-medical areas where a remotely actuated microgripper or similar actuator would be useful or where micro-assembling is needed. 22 figs.
Northrup, M.A.; Ciarlo, D.R.; Lee, A.P.; Krulevitch, P.A.
Electromechanical microstructures (microgrippers), either integrated circuit (IC) silicon-based or precision machined, to extend and improve the application of catheter-based interventional therapies for the repair of aneurysms in the brain or other interventional clinical therapies. These micromechanisms can be specifically applied to release platinum coils or other materials into bulging portions of the blood vessels also known as aneurysms. The "micro" size of the release mechanism is necessary since the brain vessels are the smallest in the body. Through a catheter more than one meter long, the micromechanism located at one end of the catheter can be manipulated from the other end thereof. The microgripper (micromechanism) of the invention will also find applications in non-medical areas where a remotely actuated microgripper or similar actuator would be useful or where micro-assembling is needed.
Northrup, Milton A. (Berkeley, CA); Ciarlo, Dino R. (Livermore, CA); Lee, Abraham P. (Walnut Creek, CA); Krulevitch, Peter A. (Los Altos, CA)
PEBBLES Mechanics Simulation Speedup
Pebble bed reactors contain large numbers of spherical fuel elements arranged randomly. Determining the motion and location of these fuel elements is required for calculating certain parameters of pebble bed reactor operation. These simulations involve hundreds of thousands of pebbles and involve determining the entire core motion as pebbles are recirculated. Single processor algorithms for this are insufficient since they would take decades to centuries of wall-clock time. This paper describes the process of parallelizing and speeding up the PEBBLES pebble mechanics simulation code. Both shared memory programming with the Open Multi-Processing API and distributed memory programming with the Message Passing Interface API are used in simultaneously in this process. A new shared memory lock-less linear time collision detection algorithm is described. This method allows faster detection of pebbles in contact than generic methods. These combine to make full recirculations on AVR sized reactors possible in months of wall clock time.
Joshua J. Cogliati; Abderrafi M. Ougouag
Vehicle rear suspension mechanism
A vehicle rear suspension mechanism is described which consists of: a suspension member connected with a vehicle body; wheel hub means supporting a rear wheel having a wheel center plane for rotation about a rotating axis; and connecting means for connecting the wheel hub means with the suspension member. The connecting means include ball joint means having a pivot center located forwardly of and below the rotating axis of the rear wheel and connecting the wheel hub means to the suspension member pivotably about the pivot center, first resilient means located between the wheel hub means and the suspension member rearwardly of and above the rotating axis of the rear wheel, and second resilient means located between the wheel hub means and the suspension member forwardly of and above the rotating axis of the rear wheel.
Kijima, T.; Maebayashi, J.
Mechanically expandable annular seal
A mechanically expandable annular reusable seal assembly to form an annular hermetic barrier between two stationary, parallel, and planar containment surfaces is described. A rotatable ring, attached to the first surface, has ring wedges resembling the saw-tooth array of a hole saw. Matching seal wedges are slidably attached to the ring wedges and have their motion restricted to be perpendicular to the second surface. Each seal wedge has a face parallel to the second surface. An annular elastomer seal has a central annular region attached to the seal wedges' parallel faces and has its inner and outer circumferences attached to the first surface. A rotation of the ring extends the elastomer seal's central region perpendicularly towards the second surface to create the fluid tight barrier. A counter rotation removes the barrier. 6 figs.
Gilmore, R.F.
Montana State University 1 Mechanical Engineering
mechanics, materials science, manufacturing processes, thermodynamics, heat transfer, fluid mechanicsMontana State University 1 Mechanical Engineering The specific mission of the undergraduate Mechanical Engineering (ME) program is to prepare students for successful mechanical engineering
Maxwell, Bruce D.
The Glutamate Switch of Bacteriophage T7 DNA Helicase ROLE IN COUPLING NUCLEOTIDE TRIPHOSPHATE (NTP) AND DNA BINDING TO NTP
The Glutamate Switch of Bacteriophage T7 DNA Helicase ROLE IN COUPLING NUCLEOTIDE TRIPHOSPHATE (NTP also creates nucleotide-binding sites located at the interfaces of the sub- units. DNA binding of a bound nucleoside 5 -triphosphate. However, in the absence of a nucleotide, Glu-343 changes orientation
Richardson, Charles C.
E-Print Network 3.0 - andribosomal dna sequences Sample Search...
Jiawei Hany Summary: DNA-Miner: A System Prototype for Mining DNA Sequences Jiawei Hany Hasan Jamilx Ying Luy Liangyou... biosequences is to nd sequence or repeating patterns...
E-Print Network 3.0 - alpha-1 foundation dna Sample Search Results
Medicine ; Materials Science ; Physics 76 Conductivity of a single DNA duplex bridging a carbon nanotube gap Summary: Conductivity of a single DNA duplex bridging a carbon...
Folding of a DNA Hairpin Loop Structure in Explicit SolventUsingRepli...
Folding of a DNA Hairpin Loop Structure in Explicit Solvent UsingReplica-Exchange Molecular Dynamics Simulations. Folding of a DNA Hairpin Loop Structure in Explicit Solvent...
E-Print Network 3.0 - alignment improves dna Sample Search Results
details of initiator proteins for DNA replication have provided clues... + domains in ORC contain a conserved structural element that, in DnaA, promotes formation of a right...
E-Print Network 3.0 - alkyladenine dna glycosylase Sample Search...
Thymine DNA... fusion TMZ Tmozolomide U373 Ligne cellulaire de glioblastomes humains Ugi Uracil-DNA-Glycosylase... recherche CNRS Rapporteur M. Jian-Sheng Sun Professeur MNHM,...
Sensitive method for measurement of telomeric DNA content in human tissues
A sensitive method for measurement of telomeric DNA content in human tissue, based upon the ratio of telomeric to centromeric DNA present in the tissue.
Bryant, Jennifer E. (Albuquerque, NM); Hutchings, Kent G. (Albuquerque, NM); Moyzis, Robert K. (Corona Del Mar, CA); Griffith, Jeffrey K. (Cedar Crest, NM)
E-Print Network 3.0 - amplified polymorphic dna Sample Search...
Belfast Collection: Environmental Sciences and Ecology 13 Helpful Resources on Forensic DNA Testing Butler, J.M. (2005) Forensic DNA Typing: Biology, Technology, and...
Unification of fluctuation theorems and one-shot statistical mechanics
Fluctuation-dissipation relations, such as Crooks' Theorem and Jarzynski's Equality, are powerful tools in quantum and classical nonequilibrium statistical mechanics. We link these relations to a newer approach known as "one-shot statistical mechanics." Rooted in one-shot information theory, one-shot statistical mechanics concerns statements true of every implementation of a protocol, not only of averages. We show that two general models for work extraction in the presence of heat baths obey fluctuation relations and one-shot results. We demonstrate the usefulness of this bridge between frameworks in several ways. Using Crooks' Theorem, we derive a bound on one-shot work quantities. These bounds are tighter, in certain parameter regimes, than a bound in the fluctuation literature and a bound in the one-shot literature. Our bounds withstand tests by numerical simulations of an information-theoretic Carnot engine. By analyzing data from DNA-hairpin experiments, we show that experiments used to test fluctuation theorems also test one-shot results. Additionally, we derive one-shot analogs of a known equality between a relative entropy and the average work dissipated as heat. Our unification of experimentally tested fluctuation relations with one-shot statistical mechanics is intended to bridge one-shot theory to applications.
Nicole Yunger Halpern; Andrew J. P. Garner; Oscar C. O. Dahlsten; Vlatko Vedral
Mobile linkers on DNA-coated colloids: valency without patches
Colloids coated with single-stranded DNA (ssDNA) can bind selectively to other colloids coated with complementary ssDNA. The fact that DNA-coated colloids (DNACCs) can bind to specific partners opens the prospect of making colloidal `molecules'. However, in order to design DNACC-based molecules, we must be able to control the valency of the colloids, i.e. the number of partners to which a given DNACC can bind. One obvious, but not very simple approach is to decorate the colloidal surface with patches of single-stranded DNA that selectively bind those on other colloids. Here we propose a design principle that exploits many-body effects to control the valency of otherwise isotropic colloids. Using a combination of theory and simulation, we show that we can tune the valency of colloids coated with mobile ssDNA, simply by tuning the non-specific repulsion between the particles. Our simulations show that the resulting effective interactions lead to low-valency colloids self-assembling in peculiar open structures, very different from those observed in DNACCs with immobile DNA linkers.
Stefano Angioletti-Uberti; Patrick Varilly; Bortolo M. Mognetti; Daan Frenkel
Distinct MAPK signaling pathways, p21 up-regulation and caspase-mediated p21 cleavage establishes the fate of U937 cells exposed to 3-hydrogenkwadaphnin: Differentiation versus apoptosis
Despite the depth of knowledge concerning the pathogenesis of acute myeloblastic leukemia (AML), long-term survival remains unresolved. Therefore, new agents that act more selectively and more potently are required. In that line, we have recently characterized a novel diterpene ester, called 3-hydrogenkwadaphnin (3-HK), with capability to induce both differentiation and apoptosis in various leukemia cell lines. These effects of 3-HK were mediated through inhibition of inosine 5'-monophosphate dehydrogenase, a selective up-regulated enzyme in cancerous cells, especially leukemia. However, it remains elusive to understand how cells display different fates in response to 3-HK. Here, we report the distinct molecular signaling pathways involved in forcing of 3-HK-treated U937 cells to undergo differentiation and apoptosis. After 3-HK (15 nM) treatment, a portion of U937 cells adhered to the culture plates and showed macrophage criteria while others remained in suspension and underwent apoptosis. The differentiated cells arrested in G{sub 0}/G{sub 1} phase of cell cycle and showed early activation of ERK1/2 pathway (3 h) along with ERK-dependent p21{sup Cip/WAF1} (p21) up-regulation and expression of p27{sup Kip1} and Bcl-2. In contrast, the suspension cells underwent apoptosis through Fas/FasL and mitochondrial pathways. The occurrence of apoptosis in these cells were accompanied with caspase-8-mediated p21 cleavage and delayed activation (24 h) of JNK1/2 and p38 MAPK. Taken together, these results suggest that distinct signaling pathways play a pivotal role in fates of drug-treated leukemia cells, thus this may pave some novel therapeutical utilities.
Moosavi, Mohammad Amin [Institute of Biochemistry and Biophysics, P. O. Box 13145-1384 University of Tehran, Tehran (Iran, Islamic Republic of); Yazdanparast, Razieh [Institute of Biochemistry and Biophysics, P. O. Box 13145-1384 University of Tehran, Tehran (Iran, Islamic Republic of)], E-mail: firstname.lastname@example.com
Method for construction of normalized cDNA libraries
This invention provides a method to normalize a directional cDNA library constructed in a vector that allows propagation in single-stranded circle form. The method comprises: (a) propagating the directional cDNA library in single-stranded circles; (b) generating fragments complementary to the 3` noncoding sequence of the single-stranded circles in the library to produce partial duplexes; (c) purifying the partial duplexes; (d) melting and reassociating the purified partial duplexes to moderate Cot; and (e) purifying the unassociated single-stranded circles, thereby generating a normalized cDNA library. 4 figs.
Structural aspects of catalytic mechanisms of endonucleases and their binding to nucleic acids
Endonucleases (EC 3.1) are enzymes of the hydrolase class that catalyze the hydrolytic cleavage of deoxyribonucleic and ribonucleic acids at any region of the polynucleotide chain. Endonucleases are widely used both in biotechnological processes and in veterinary medicine as antiviral agents. Medical applications of endonucleases in human cancer therapy hold promise. The results of X-ray diffraction studies of the spatial organization of endonucleases and their complexes and the mechanism of their action are analyzed and generalized. An analysis of the structural studies of this class of enzymes showed that the specific binding of enzymes to nucleic acids is characterized by interactions with nitrogen bases and the nucleotide backbone, whereas the nonspecific binding of enzymes is generally characterized by interactions only with the nucleic-acid backbone. It should be taken into account that the specificity can be modulated by metal ions and certain low-molecular-weight organic compounds. To test the hypotheses about specific and nonspecific nucleic-acid-binding proteins, it is necessary to perform additional studies of atomic-resolution three-dimensional structures of enzyme-nucleic-acid complexes by methods of structural biology.
Zhukhlistova, N. E.; Balaev, V. V.; Lyashenko, A. V.; Lashkov, A. A., E-mail: firstname.lastname@example.com [Russian Academy of Sciences, Shubnikov Institute of Crystallography (Russian Federation)
Bohmian Mechanics with Discrete Operators
A deterministic Bohmian mechanics for operators with continuous and discrete spectra is presented. Randomness enters only through initial conditions. Operators with discrete spectra are incorporated into Bohmian mechanics by associating with each operator a continuous variable in which a finite range of the continuous variable correspond to the same discrete eigenvalue. In this way Bohmian mechanics can handle the creation and annihilation of particles. Examples are given and generalizations are discussed.
R. A. Hyman; Shane A. Caldwell; Edward Dalton
Parallel GPU Algorithms for Mechanical CAD
of California, Berkeley, Mechanical Engineering Department,GPU Algorithms for Mechanical CAD by Adarsh Krishnamurthy Aof Philosophy in Engineering - Mechanical Engineering in the
Krishnamurthy, Adarsh
Mechanical and Manufacturing Engineering Mechatronics Engineering Minor
Mechanical and Manufacturing Engineering Mechatronics Engineering Minor Students pursuing a BSc in mechanical or manufacturing engineering have experience and entrepreneurship. Mechatronics is the synergistic combination of mechanical
Calgary, University of
Mechanical Behaviors of Alloys From First Principles
Some Backgrounds on The Quantum Mechanical Stresses . . .3.2.2 The Quantum Mechanical Stresses and The Generalized3.2.3 Quantum-Mechanical
Hanlumyuang, Yuranan
F. P. Knudsen, "Dependence of Mechanical Strength of BrittleMicrostruc- ture on the Mechanical Properties of Ceramics,"of Porosity on the Mechanical Properties of Lead Zirconate-
Biswas, D.R.
INL '@work' heavy equipment mechanic
ScienceCinema (OSTI)
INL's Cad Christensen is a heavy equipment mechanic. For more information about INL careers, visit http://www.facebook.com/idahonationallaboratory.
Christensen, Cad
Romanian sources on applied mechanics
This note provides a list of journals and recent books published in Romania covering topics in applied mechanics, with information on bow to obtain them.
Popescu, M.E. [Civil Engineering Inst., Bucharest (Romania)
Mechanical Behavior of Indium Nanostructures Print Indium is a key material in lead-free solder applications for microelectronics due to its excellent wetting properties, extended...
COMPLEX BIOLOGICAL MECHANISMS: CYCLIC, OSCILLATORY, AND AUTONOMOUS William Bechtel and Adele- nomological framework and its focus on laws as the primary explanatory vehicle; for them, a scientific
Bechtel, William
An exploration of sequence specific DNA-duplex/pyrene interactions for intercalated and surface-associated pyrene species. Final report, May 1, 1993--December 31, 1996
The broad objective of this DOE sponsored work on photoinduced electron transfer (ET) within covalently modified DNA was to learn about the rates of Et among various DNA bases and commonly used organic electron donor (D) and acceptor (A) molecules. This hypothesis driven, multidisciplinary project combined skills in modified nucleic acid synthesis and in continuous and time-resolved optical spectroscopies. Covalently modified DNA chemistry as investigated in this program had two specific long term goals. The first was to use experimental and theoretical insights into the mechanisms of electron transfer (ET) reactions to design supramolecular assemblies of redox-active chromophores that function as efficient vectorial ET engines. The second was to construct oligonucleotide probes for real-time monitoring of intracellular processes involving DNA and RNA such as m-RNA expression and translocation. This research project laid the groundwork for studying ET reactions within DNA duplexes by examining the photophysics of uridine nucleosides which are covalently labeled at the 5-position with 1-pyrenyl chromophores.
Netzel, T.L.
Cytogenetic status and oxidative DNA-damage induced by atorvastatin in human peripheral blood lymphocytes: Standard and Fpg-modified comet assay
To investigate the genotoxic potential of atorvastatin on human lymphocytes in vitro standard comet assay was used in the evaluation of basal DNA damage and to investigate possible oxidative DNA damage produced by reactive oxygen species (ROS) Fpg-modified version of comet assay was also conducted. In addition to these techniques the new criteria for scoring micronucleus test were applied for more complete detection of baseline damage in binuclear lymphocytes exposed to atorvastatin 80 mg/day in different time periods by virtue of measuring the frequency of micronuclei, nucleoplasmic bridges and nuclear buds. All parameters obtained with the standard comet assay and Fpg-modified comet assay were significantly higher in the treated than in control lymphocytes. The Fpg-modified comet assay showed a significantly greater tail length, tail intensity, and tail moment in all treated lymphocytes than did the standard comet assay, which suggests that oxidative stress is likely to be responsible for DNA damage. DNA damage detected by the standard comet assay indicates that some other mechanism is also involved. In addition to the comet assay, a total number of micronuclei, nucleoplasmic bridges and nuclear buds were significantly higher in the exposed than in controlled lymphocytes. Regression analyses showed a positive correlation between the results obtained by the comet (Fpg-modified and standard) and micronucleus assay. Overall, the study demonstrated that atorvastatin in its highest dose is capable of producing damage on the level of DNA molecule and cell.
Gajski, Goran [Institute for Medical Research and Occupational Health, Mutagenesis Unit, 10000 Zagreb (Croatia)], E-mail: firstname.lastname@example.com; Garaj-Vrhovac, Vera [Institute for Medical Research and Occupational Health, Mutagenesis Unit, 10000 Zagreb (Croatia); Orescanin, Visnja [Ruder Boskovic Institute, 10000 Zagreb (Croatia)
Line narrowing spectroscopic studies of DNA-carcinogen adducts and DNA-dye complexes
Laser-induced fluorescence line narrowing and non-line narrowing spectroscopic methods were applied to conformational studies of stable DNA adducts of the 7{beta}, 8{alpha}-dihydoxy-9{alpha}, l0{alpha}-epoxy-7,8,9, 10-tetrahydrobenzo[{alpha}]pyrene (anti-BPDE). Stereochemically distinct (+)-trans-, ({minus})-trans-, (+)-cis- and ({minus})-cis adducts of anti-BPDE bound to exocyclic amino group of the central guanine in an 11-mer oligonucleotide, exist in a mixture of conformations in frozen aqueous buffer matrices. The (+)-trans adduct adopts primarily an external conformation with a smaller fraction ( {approximately} 25 %) exists in a partially base-stacked conformation. Both cis adducts were found to be intercalated with significant {pi}-{pi} stacking interactions between the pyrenyl residues and the bases. Conformations of the trans-adduct of (+)-anti -BPDE in 11-mer oligonucleotides were studied as a function of flanking bases. In single stranded form the adduct at G{sub 2} or G{sub 3} (5 ft-flanking, base guanine) adopts a conformation with strong, interaction with the bases. In contrast, the adduct with a 5ft-flanking, thymine exists in a primarily helixexternal conformation. Similar differences were observed in the double stranded oligonucleotides. The nature of the 3ft-flanking base has little influence on the conformational equilibrium of the (+)-trans-anti BPDE-dG adduct. The formation and repair of BPDE-N{sup 2}-dG in DNA isolated from the skin of mice treated topically with benzo[{alpha}]pyrene (BP) was studied. Low-temperature fluorescence spectroscopy of the intact DNA identified the major adduct as (+)-trans-anti-BPDE-N-dG, and the minor adduct fraction consisted mainly of (+)-cis-anti-BPDE-N{sup 2}-dG.
Suh, Myungkoo
The equivalence principle in classical mechanics and quantum mechanics
We discuss our understanding of the equivalence principle in both classical mechanics and quantum mechanics. We show that not only does the equivalence principle hold for the trajectories of quantum particles in a background gravitational field, but also that it is only because of this that the equivalence principle is even to be expected to hold for classical particles at all.
Philip D. Mannheim
Nuclear DNA content variation in Helianthus annus and the detection of repetitive DNA sequences
. This wes shaken at 140 rpm overnight at 37 C, and the bacteria were recovered by centrifugation at 10, 000Xg for 10 min at 4 C. The bacteria were resuspended in 10 ml sterile 0. 01 N and stored at 4 C. Petri dishes were poured using 10 g agarose per... liter of NZC medium, with each dish containing 30 ml of media. Dishes were used within 24 hr. Top agarose was made using 3 g agarose per liter of media. Use of agar in plates apparently interferes with restriction endonuclease activity on DNA isolated...
Michaelson, Martin Joseph
Exploring the specificity and mechanisms of siRNA-mediated gene silencing in mammalian cells
Complementary short interfering RNAs (siRNAs) are routinely used to knockdown gene expression. siRNAs bind to their target sequence and guide transcript cleavage and subsequent degradation. This type of silencing is ...
Alem�n, Lourdes Maria
automated dna sequence: Topics by E-print Network
ethanol and Na-acetate. Place the tubes in the -20 freezer overnight. (2 tubes sit in the refrigerator overnight to allow the DNA to go into solution. (8) Measure concentration...
anonymous dna sequences: Topics by E-print Network
automated dna sequencing: Topics by E-print Network
ancient dna sequences: Topics by E-print Network
Photoelectromechanical synthesis of low-cost DNA microarrays
Recent advances in de novo gene synthesis, library construction, and genomic selection for target sequencing using DNA from custom microarrays have demonstrated that microarrays can effectively be used as the world's ...
Chow, Brian, 1978-
This invention provides a method to normalize a directional cDNA library constructed in a vector that allows propagation in single-stranded circle form comprising: (a) propagating the directional cDNA library in single-stranded circles; (b) generating fragments complementary to the 3` noncoding sequence of the single-stranded circles in the library to produce partial duplexes; (c) purifying the partial duplexes; (d) melting and reassociating the purified partial duplexes to appropriate Cot; and (e) purifying the unassociated single-stranded circles, thereby generating a normalized cDNA library. This invention also provides normalized cDNA libraries generated by the above-described method and uses of the generated libraries. 19 figs.
Optical studies of DNA-wrapped carbon nanotubes
This thesis presents a series of detailed optical studies of phonon-assisted relaxation processes in DNA-wrapped single walled carbon nanotubes. Using resonance Raman spectroscopy (RRS) and photoluminescence spectroscopy ...
Chou, Shin Grace
acetobutylicum 8-oxoguanine dna: Topics by E-print Network
Fabrice Sabathe; Lynn Doucette-stamm; Philippe Soucaille; Michael J. Daly; George N. Bennett; Eugene V. Koonin; Douglas R. Smith 2001-01-01 9 Role of a MutY DNA glycosylase in...
Spatially localized generation of nucleotide sequence-specific DNA damage
Spatially localized generation of nucleotide sequence-specific DNA damage Dennis H. Oh* , Brett A- neously manipulated at the nucleotide level and in three dimen- sions. This approach for targeting
Boxer, Steven G.
Developing a DNA vaccine to protect against brucellosis
Brucella are Gram-negative intracellular pathogenic bacteria, which represent a threat to human and animal health. Live vaccine strains are available to protect some animal species but no vaccines exist for human use. A DNA vaccine could potentially...
Owen, David Matthew
Cellular responses against DNA damaged by platinum anticancer drugs
The anticancer activity of platinum-based drugs such as cisplatin, carboplatin, and oxaliplatin is mediated by their ability to attack DNA such that generated adducts trigger numerous cellular responses. A better understanding ...
Jung, Yongwon, 1977-
Vehicle Technologies Office Merit Review 2014: Fleet DNA
Presentation given by National Renewable Energy Laboratory at 2014 DOE Hydrogen and Fuel Cells Program and Vehicle Technologies Office Annual Merit Review and Peer Evaluation Meeting about fleet DNA.
Dna electrophoresis in photopolymerized polyacrylamide gels on a microfluidic device
DNA gel electrophoresis is a critical analytical step in a wide spectrum of genomic analysis assays. Great efforts have been directed to the development of miniaturized microfluidic systems (�lab-on-a-chip� systems) to perform low-cost, high...
Lo, Chih-Cheng
Development of a microfluidic platform for integrated DNA sequencing protocols
This thesis describes the design and development of a microfluidic platform to reduce costs and improve the quality of in the DNA sequencing methodology currently implemented at the Broad Institute in Cambridge, Massachusetts. ...
Kumar, Mayank, S.M. Massachusetts Institute of Technology
An integrated encyclopedia of DNA elements in the human genome
The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of ...
Altshuler, Robert Charles
INTRODUCTION The homeodomain DNA-binding motif, initially discovered in
to the establishment and maintenance of a detailed positional reference system; homeodomain genes operating and characterization of btn cDNA and genomic clones Total RNA was prepared according to standard procedures (Sambrook
Patel, Nipam H.
Control for nematodes in cotton DNA story text
IMPACTS Control for nematodes in cotton DNA story text Studies help plants survive Battling opens in May By Donna Bowen Photo by Clemson University Site-specific controls for nematodes in cotton
Bolding, M. Chad
Method for rapid base sequencing in DNA and RNA
A method is provided for the rapid base sequencing of DNA or RNA fragments wherein a single fragment of DNA or RNA is provided with identifiable bases and suspended in a moving flow stream. An exonuclease sequentially cleaves individual bases from the end of the suspended fragment. The moving flow stream maintains the cleaved bases in an orderly train for subsequent detection and identification. In a particular embodiment, individual bases forming the DNA or RNA fragments are individually tagged with a characteristic fluorescent dye. The train of bases is then excited to fluorescence with an output spectrum characteristic of the individual bases. Accordingly, the base sequence of the original DNA or RNA fragment can be reconstructed. 2 figs.
Jett, J.H.; Keller, R.A.; Martin, J.C.; Moyzis, R.K.; Ratliff, R.L.; Shera, E.B.; Stewart, C.C.
A method is provided for the rapid base sequencing of DNA or RNA fragments wherein a single fragment of DNA or RNA is provided with identifiable bases and suspended in a moving flow stream. An exonuclease sequentially cleaves individual bases from the end of the suspended fragment. The moving flow stream maintains the cleaved bases in an orderly train for subsequent detection and identification. In a particular embodiment, individual bases forming the DNA or RNA fragments are individually tagged with a characteristic fluorescent dye. The train of bases is then excited to fluorescence with an output spectrum characteristic of the individual bases. Accordingly, the base sequence of the original DNA or RNA fragment can be reconstructed.
Jett, James H. (Los Alamos, NM); Keller, Richard A. (Los Alamos, NM); Martin, John C. (Los Alamos, NM); Moyzis, Robert K. (Los Alamos, NM); Ratliff, Robert L. (Los Alamos, NM); Shera, E. Brooks (Los Alamos, NM); Stewart, Carleton C. (Los Alamos, NM)
Linking Cell Cycle Reentry and DNA Damage in Neurodegeneration
Aberrant cell cycle activity and DNA damage have been observed in neurons in association with various neurodegenerative conditions. While there is strong evidence for a causative role for these events in neurotoxicity, it ...
Kim, Dohoon
This invention provides a method to normalize a directional cDNA library constructed in a vector that allows propagation in single-stranded circle form comprising: (a) propagating the directional cDNA library in single-stranded circles; (b) generating fragments complementary to the 3' noncoding sequence of the single-stranded circles in the library to produce partial duplexes; (c) purifying the partial duplexes; (d) melting and reassociating the purified partial duplexes to appropriate Cot; and (e) purifying the unassociated single-stranded circles, thereby generating a normalized cDNA library. This invention also provides normalized cDNA libraries generated by the above-described method and uses of the generated libraries.
People V. Castro: Challenging the Forensic Use of DNA Evidence
Lander noted that �at present, forensic science is virtuallydiagnose strep throat than forensic labs must meet to put aV. CASTRO: CHALLENGING THE FORENSIC USE OF DNA EVIDENCE �
Mnookin, Jennifer L.
Transgenic plants containing cDNA encoding Gramineae lectin are described. The plants preferably contain cDNA coding for barley lectin and store the lectin in the leaves. The transgenic plants, particularly the leaves exhibit insecticidal and fungicidal properties. GOVERNMENT RIGHTS This application was funded under Department of Energy Contract DE-AC02-76ER01338. The U.S. Government has certain rights under this application and any patent issuing thereon.
Forensic DNA data banking by state crime labortaories
This article reports the results of a survey of the responsible crime laboratories in the first 19 states with legislation establishing forensic DNA data banks. The survey inquired into the labs` policies and procedures regarding the collection, storage, and analysis of samples; the retention of samples and data; search protocols; access to samples and data by third parties; and related matters. The research suggests that (1) the number of samples collected from convicted offenders for DNA data banking has far surpassed the number that have been analyzed; (2) data banks have already been used in a small but growing number of cases, to locate suspects and to identify associations between unresolved cases; (3) crime labs currently plan to retain indefinitely the samples collected for their data banks; and (4) the nature and extent of security safeguards that crime labs have implemented for their data banks vary among states. The recently enacted DNA Identification Act (1994) will provide $40 million in federal matching grants to states for DNA analysis activities, so long as states comply with specified quality-assurance standards, submit to external proficiency testing, and limit access to DNA information. Although these additional funds should help to ease some sample backlogs, it remains unclear how labs will allocate the funds, as between analyzing samples for their data banks and testing evidence samples in cases without suspects. The DNA Identification Act provides penalties for the disclosure or obtaining of DNA data held by data banks that participate in CODIS, the FBI`s evolving national network of DNA data banks, but individual crime labs must also develop stringent internal safeguards to prevent breaches of data-bank security. 9 refs., 3 tabs.
McEwen, J.E. [Eunice Kennedy Shrive Center for Mental Retardation, Waltham, MA (United States)
Self-assembling DNA Nanostructures for Patterned Molecular Assembly Thomas H. LaBeana
1 Self-assembling DNA Nanostructures for Patterned Molecular Assembly Thomas H. LaBeana , Kurt firstname.lastname@example.com; Tel: (919)660-65685 Abstract The Chapter describes the use of DNA for molecular-scale self-assembly with a discussion of DNA-nanostructures, starting with the self-assembly of various building-blocks known as DNA
Design of an Autonomous DNA Nanomechanical Device Capable of Universal Computation and Universal Translational Motion
Design of an Autonomous DNA Nanomechanical Device Capable of Universal Computation and Universal, and in DNA computing provide a solid foundation for the next step forward: designing autonomous DNA construction of autonomous unidirectional DNA walking devices that move along linear tracks, we present
Designs for Autonomous Unidirectional Walking DNA Devices Peng Yin Andrew J. Turberfield John H. Reif
Designs for Autonomous Unidirectional Walking DNA Devices Peng Yin £ Andrew J. Turberfield Ý John H. Reif �? Abstract Imagine a host of nanoscale DNA robots move autonomously over a microscale DNA chal- lenge. The missing link is a DNA walker that can autonomously move along a route programmably em
J. Mol. Riol. (1991) 222, 1085-1108 Complementary Recognition in Condensed DNA: Accelerated
J. Mol. Riol. (1991) 222, 1085-1108 Complementary Recognition in Condensed DNA: Accelerated DNA) Condensation of denatured DNA greatly accelerates the kinetics of DNA renaturation. We propose a unifying explanation for the effects of several accelerating solvents studied here including polymers, di
Church, George M.
Creative cleavages : distributive politics and electoral alignment
Distributive politics plays an important role for political elites for their electoral goal. Since the resources that politicians can distribute are limited, they have to decide how to distribute them in order to maximize ...
Kim, Jiyoon, Ph. D. Massachusetts Institute of Technology
Atomistic Details of the Associative Phosphodiester Cleavage...
that the nature of the nucleophile is a water molecule. In the first step, the water attack on the scissile phosphorous is followed by a proton transfer from the water to the O2P...
Mechanical Engineering Professional Electives Policy
Mechanical Engineering Professional Electives Policy 3/22/11 2004-2006 & 2006-2008 Catalogs Management (d) F EMEC 403 (ME 411) CAE IV: Design Integration S ETME 430 (ME 435) Fluid Power Systems Design (d) Must successfully complete EMEC 445 before taking EELE 321 S EGEN 415 (EM 415) Advanced Mechanics
, the mechanical engineering technologist provides the professional services needed in transforming the resultsMontana State University 1 Mechanical Engineering Technology The mission of the Mechanical Engineering Technology (MET) program is to prepare students for successful Mechanical Engineering
UNDERGRADUATE STUDENT MANUAL Department of Mechanical Engineering
engineering (for example, computer-aided-design and manufacturing (CAD/CAM), energy engineering, mechanical1 UNDERGRADUATE STUDENT MANUAL Department of Mechanical Engineering and Applied Mechanics Engineering and Applied Mechanics? ........................................................................3
Plotkin, Joshua B.
Mechanical Engineering Department 06 November 2013
Mechanical Engineering Department Lecture 03 06 November 2013 WORCESTER POLYTECHNIC INSTITUTE MECHANICAL ENGINEERING DEPARTMENT Optical Metrology and NDT ME-593L, B'2013 #12;Mechanical Engineering Possible longitudinal resonant modes (cavity length = L) #12;Mechanical Engineering Department Lasers
Furlong, Cosme
Mechanical Engineering Department WORCESTER POLYTECHNIC INSTITUTE
Mechanical Engineering Department WORCESTER POLYTECHNIC INSTITUTE MECHANICAL ENGINEERING DEPARTMENT STRESS ANALYSIS ES-2502, C'2012 Lecture 15: 07 February 2012 #12;Mechanical Engineering Department Popova firstname.lastname@example.com #12;Mechanical Engineering Department Stress concentrations Ripping open candy
Mechanical Engineering Department WORCESTER POLYTECHNIC INSTITUTE MECHANICAL ENGINEERING DEPARTMENT STRESS ANALYSIS ES-2502, C'2012 Lecture 20: 20 February 2012 #12;Mechanical Engineering Department Popova firstname.lastname@example.com #12;Mechanical Engineering Department Bending Deformation of a component subjected
Mechanical Engineering Department WORCESTER POLYTECHNIC INSTITUTE MECHANICAL ENGINEERING DEPARTMENT STRESS ANALYSIS ES-2502, C'2012 Lecture 14: 06 February 2012 #12;Mechanical Engineering Department Popova email@example.com #12;Mechanical Engineering Department Stress concentrations Ripping open candy
Mechanical Engineering Department "The Lindbergh Lectures"
Mechanical Engineering Department "The Lindbergh Lectures" Thursday, November 14th, 2013 12:00 12:50 PM Room 1106 Mechanical Engineering Building MECHANICAL MICRO-MANUFACTURING RESEARCH @ CARNEGIE MELLON UNIVERSITY BURAK OZDOGANLAR, CARNEGIE MELLON UNIVERSITY Abstract: Mechanical
Mechanical and Manufacturing Engineering Petroleum Engineering Minor
of Chemical and Petroleum Engineering for their petroleum engineering minor. As well, mechanical engineeringMechanical and Manufacturing Engineering Petroleum Engineering Minor The Department of Mechanical and Manufacturing Engineering offers a minor in petroleum engineering within the mechanical engineering major
Mechanical Characterization of Fuel Injector Piezoactuators and...
Broader source: Energy.gov (indexed) [DOE]
Mechanical Characterization of Fuel Injector Piezoactuators and their Piezoceramics Mechanical Characterization of Fuel Injector Piezoactuators and their Piezoceramics 2007 Diesel...
Self-Assembly and Crystallization of Hairy (f-Star) and DNA-Grafted Nanocubes
Nanoparticle superlattices are key to realizing many of the materials that will solve current technological challenges. Particularly important for their optical, mechanical or catalytic properties are superlattices of anisotropic (nonspherical) nanoparticles. The key challenge is how to program anisotropic nanoparticles to self-assemble into the relevant structures. In this Article, using numerical simulations, we show that �hairy� (f-star) or DNA grafted on nanocubes provides a general framework to direct the self-assembly into phases with crystalline, liquid crystalline, rotator, or noncrystalline phases with both long-range positional and orientational order. We discuss the relevance of these phases for engineering nanomaterials or micromaterials displaying precise orientational order, realization of dry superlattices as well as for the field of programmed self-assembly of anisotropic nanoparticles in general.
Knorowski, Christopher [Ames Laboratory; Travesset, Alex [Ames Laboratory
A new structural framework for integrating replication protein A into DNA processing machinery
By coupling the protection and organization of single-stranded DNA (ssDNA) with recruitment and alignment of DNA processing factors, replication protein A (RPA) lies at the heart of dynamic multi-protein DNA processing machinery. Nevertheless, how RPA coordinates biochemical functions of its eight domains remains unknown. We examined the structural biochemistry of RPA's DNA-binding activity, combining small-angle X-ray and neutron scattering with all-atom molecular dynamics simulations to investigate the architecture of RPA's DNA-binding core. The scattering data reveal compaction promoted by DNA binding; DNA-free RPA exists in an ensemble of states with inter-domain mobility and becomes progressively more condensed and less dynamic on binding ssDNA. Our results contrast with previous models proposing RPA initially binds ssDNA in a condensed state and becomes more extended as it fully engages the substrate. Moreover, the consensus view that RPA engages ssDNA in initial, intermediate and final stages conflicts with our data revealing that RPA undergoes two (not three) transitions as it binds ssDNA with no evidence for a discrete intermediate state. These results form a framework for understanding how RPA integrates the ssDNA substrate into DNA processing machinery, provides substrate access to its binding partners and promotes the progression and selection of DNA processing pathways.
Brosey, Chris; Yan, Chunli; Tsutakawa, Susan; Heller, William; Rambo, Robert; Tainer, John; Ivanov, Ivaylo; Chazin, Walter
Aerospace and Mechanical Engineers design and build unique, complex mechanical, optical,
skills in the areas of mechanics, thermodynamics, fluid mechanics, heat transfer, materials and automatic including control of turbulence, emerging fuel cell technologies, computational fluid mechanics, ground20 Aerospace and Mechanical Engineers design and build unique, complex mechanical, optical
Aerospace and Mechanical Engineers design and build unique, complex mechanical, optical, and electronic
Aerospace and Mechanical Engineers design and build unique, complex mechanical-optical-
of mechanics, thermodynamics, fluid mechanics, heat transfer, materials and automatic controls. Our graduates including control of turbulence, emerging fuel cell technologies, computational fluid mechanics, ground20 Aerospace and Mechanical Engineers design and build unique, complex mechanical
20 Aerospace and Mechanical Engineers design and build unique, complex mechanical, optical, far underground, and deep inside the intricacies of our own bodies. Aerospace and Mechanical skills in the areas of mechanics, thermodynamics, fluid mechanics, heat transfer, materials and automatic
Aerospace and Mechanical Engineers design and build unique, complex mechanical, optical, and
Biology Lab 3: Small Scale Plasmid DNA Purification (Minipreps) Plasmids are small, circular pieces of DNA (about 3-5 kilobases in length on average) that
Biology Lab 3: Small Scale Plasmid DNA Purification (Minipreps) Plasmids are small, circular pieces. Plasmid purification procedures selectively enrich plasmid DNA over genomic DNA, which is present the small plasmids remain intact. Thus, when denatured, the plasmids remain linked to their complementary
Qualitative insights on fundamental mechanics
The gap between classical mechanics and quantum mechanics has an important interpretive implication: the Universe must have an irreducible fundamental level, which determines the properties of matter at higher levels of organization. We show that the main parameters of any fundamental model must be theory-independent. They cannot be predicted, because they cannot have internal causes. However, it is possible to describe them in the language of classical mechanics. We invoke philosophical reasons in favor of a specific model, which treats particles as sources of real waves. Experimental considerations for gravitational, electromagnetic, and quantum phenomena are outlined.
G. N. Mardari
Phase space quantum mechanics - Direct
Conventional approach to quantum mechanics in phase space (q,p), is to take the operator based quantum mechanics of Schroedinger, or an equivalent, and assign a c-number function in phase space to it. We propose to begin with a higher level of abstraction, in which the independence and the symmetric role of q and p is maintained throughout, and at once arrive at phase space state functions. Upon reduction to the q- or p-space the proposed formalism gives the conventional quantum mechanics, however, with a definite rule for ordering of factors of noncommuting observables. Further conceptual and practical merits of the formalism are demonstrated throughout the text.
Nasiri, S.; Sobouti, Y.; Taati, F. [Institute for Advanced Studies in Basic Sciences, Zanjan, 45195-1159 (Iran, Islamic Republic of) and Department of Physics, Zanjan University, Zanjan (Iran); Institute for Advanced Studies in Basic Sciences, Zanjan, 45195-1159 (Iran, Islamic Republic of); Institute for Advanced Studies in Basic Sciences, Zanjan, 45195-1159 (Iran, Islamic Republic of) and Department of Physics, University of Kurdistan, D-78457 Sanadaj (Iran)
A damage mechanics approach to life prediction for a salt structure
Excavated rooms in natural bedded salt formations are being considered for use as repositories for nuclear waste. It is presumed that deformation of the rooms by creep will lead to loss of structural integrity and affect room life history and seal efficiency. At projected repository temperatures, two possible fracture mechanisms in salt are creep-induced microcracking in triaxial compression and cleavage in tension. Thus, an accurate prediction of room life and seal degradation requires a reliable description of the creep and damage processes. While several constitutive models that treat either creep or fracture in salt are available in the literature, very few models have considered creep and damage in a coupled manner. Previously, Munson and Dawson formulated a set of creep equations for salt based on the consideration of dislocation mechanisms in the creep process. This set of creep equations has been generalized to include continuum, isotropic damage as a fully coupled variable in the response equation. The extended model has been referred to as the Multimechanism Deformation Coupled Fracture (MDCF) model. A set of material constants for the creep and damage terms was deduced based on test data for both clean and argillaceous salt. In this paper, the use of the MDCF model for establishing the failure criteria and for analyzing the creep response of a salt structure is demonstrated. The paper is divided into three parts. A summary of the MDCF model is presented first, which is followed by an evaluation of the MDCF model against laboratory data. Finally, finite-element calculations of the creep and damage response of a salt structure are presented and compared against in-situ field measurements.
Chan, K.S.; Bodner, S.R. [Southwest Research Inst., San Antonio, TX (United States); DeVries, K.L.; Fossum, A.F. [RE/SPEC, Inc., Rapid City, SD (United States); Munson, D.E. [Sandia National Labs., Albuquerque, NM (United States)
Free will and quantum mechanics
A simple example is provided showing that violation of free will allows to reproduce the quantum mechanical predictions, and that the Clauser-Horne parameter can take the maximum value 4 for a proper choice.
Antonio Di Lorenzo
Mechanism design with approximate types
In mechanism design, we replace the strong assumption that each player knows his own payoff type exactly with the more realistic assumption that he knows it only approximately: each player i only knows that his true type ...
Zhu, Zeyuan Allen
Renewable Auction Mechanism (RAM) (California)
The Renewable Auction Mechanism (RAM), approved by the California Public Utilities Commission (CPUC) in December 2010, is expected to result in 1,299 megawatts (MW) of new distributed generation...
The Newton Wonder in Mechanics
Application of Newton's ideas from "Principia" gives many new results in mechanics. Here we explore the question ``What form of extra force will maintain the magnitude of a vector constant of the motion while changing its direction?''
Donald Lynden-Bell
Process of labeling specific chromosomes using recombinant repetitive DNA
Chromosome preferential nucleotide sequences are first determined from a library of recombinant DNA clones having families of repetitive sequences. Library clones are identified with a low homology with a sequence of repetitive DNA families to which the first clones respectively belong and variant sequences are then identified by selecting clones having a pattern of hybridization with genomic DNA dissimilar to the hybridization pattern shown by the respective families. In another embodiment, variant sequences are selected from a sequence of a known repetitive DNA family. The selected variant sequence is classified as chromosome specific, chromosome preferential, or chromosome nonspecific. Sequences which are classified as chromosome preferential are further sequenced and regions are identified having a low homology with other regions of the chromosome preferential sequence or with known sequences of other family members and consensus sequences of the repetitive DNA families for the chromosome preferential sequences. The selected low homology regions are then hybridized with chromosomes to determine those low homology regions hybridized with a specific chromosome under normal stringency conditions.
Moyzis, R.K.; Meyne, J.
Statistical Mechanics of Amplifying Apparatus
We implement Feynman's suggestion that the only missing notion needed for the puzzle of Quantum Measurement is the statistical mechanics of amplifying apparatus. We define a thermodynamic limit of quantum amplifiers which is a classically describable system in the sense of Bohr, and define macroscopic pointer variables for the limit system. Then we derive the probabilities of Quantum Measurement from the deterministic Schroedinger equation by the usual techniques of Classical Statistical Mechanics.
Joseph Johnson
Mechanical Dissipation in Silicon Flexures
The thermo-mechanical properties of silicon make it of significant interest as a possible material for mirror substrates and suspension elements for future long-baseline gravitational wave detectors. The mechanical dissipation in 92um thick single-crystal silicon cantilevers has been observed over the temperature range 85 K to 300 K, with dissipation approaching levels down to phi = 4.4E-7.
S. Reid; G. Cagnoli; D. R. M. Crooks; J. Hough; P. Murray; S. Rowan; M. M. Fejer; R. Route; S. Zappe
Calibration of Cotton Planting Mechanisms.
per foot. To obtain a perfect stand of one plant to Foot, a minimum of 1 to a maximum of 11 plants per foot wonld have to be thinned out. The number for picker wheel- drop planting mechanisms ranged from a minimum of 2 to a maxi- mum of 27 plants... per foot, requiring the removal of from 1 to 26 nlants per foot to leave one plant per foot. CONTENTS Introduction History of cotton planter development ------------.---------------------------------- Cottonseed planting mechanisms Requirements...
Smith, H. P. (Harris Pearson); Byrom, Mills H. (Mills Herbert)
Optomechanical conversion by mechanical turbines
Liquid crystal elastomers are rubbers with liquid crystal order. They contract along their nematic director when heated or illuminated. The shape changes are large and occur in a relatively narrow temperature interval, or at low illumination, around the nematic-isotropic transition. We present a conceptual design of a mechanical, turbine-based engine using photo-active liquid crystal elastomers to extract mechanical work from light. Its efficiency is estimated to be 40%.
Milos Knezevic; Mark Warner
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