Genetic determinants of heat resistance in Escherichia coli.
Escherichia coli AW1.7 is a heat resistant food isolate and the occurrence of pathogenic strains with comparable heat resistance may pose a risk to food safety. To identify the genetic determinants of heat resistance, 29 strains of E. coli that differed in their of heat resistance were analyzed by comparative genomics. Strains were classified as highly heat resistant strains, exhibiting a D60-value of more than 6 min; moderately heat resistant strains, exhibiting a D60-value of more than 1 min; or as heat sensitive. A ~14 kb genomic island containing 16 predicted open reading frames encoding putative heat shock proteins and proteases was identified only in highly heat resistant strains. The genomic island was termed the locus of heat resistance (LHR). This putative operon is flanked by mobile elements and possesses >99% sequence identity to genomic islands contributing to heat resistance in Cronobacter sakazakii and Klebsiella pneumoniae. An additional 41 LHR sequences with >87% sequence identity were identified in 11 different species of β- and γ-proteobacteria. Cloning of the full length LHR conferred high heat resistance to the heat sensitive E. coli AW1.7ΔpHR1 and DH5α. The presence of the LHR correlates perfectly to heat resistance in several species of Enterobacteriaceae and occurs at a frequency of 2% of all E. coli genomes, including pathogenic strains. This study suggests the LHR has been laterally exchanged among the β- and γ-proteobacteria and is a reliable indicator of high heat resistance in E. coli.


Violence Against Women in Selected Areas of the United States.
We determined the prevalence of recent emotional, physical, and sexual violence against women and their associations with HIV-related risk factors in women living in the United States. We performed an assessment of women ages 18 to 44 years with a history of unprotected sex and 1 or more personal or partner HIV risk factors in the past 6 months from 2009 to 2010. We used multivariable logistic regression to examine the association of experiencing violence. Among 2099 women, the prevalence of emotional abuse, physical violence, and sexual violence in the previous 6 months was 31%, 19%, and 7%, respectively. Nonmarried status, food insecurity, childhood abuse, depression symptomology, and posttraumatic stress disorder were significantly associated with multiple types of violence. All types of violence were associated with at least 3 different partner or personal HIV risk behaviors, including unprotected anal sex, previous sexually transmitted infection diagnosis, sex work, or partner substance abuse. Our data suggested that personal and partner HIV risk behaviors, mental illness, and specific forms of violence frequently co-occurred in the lives of impoverished women. We shed light on factors purported to contribute to a syndemic in this population. HIV prevention programs in similar populations should address these co-occurring issues in a comprehensive manner.


Angiostatin-like activity of a monoclonal antibody to the catalytic subunit of F1F0 ATP synthase.
The antiangiogenic protein angiostatin inhibits ATP synthase on the endothelial cell surface, blocking cellular proliferation. To examine the specificity of this interaction, we generated monoclonal antibodies (mAb) directed against ATP synthase. mAb directed against the beta-catalytic subunit of ATP synthase (MAb3D5AB1) inhibits the activity of the F(1) domain of ATP synthase and recognizes the catalytic beta-subunit of ATP synthase. We located the antibody recognition site of MAb3D5AB1 in domains containing the active site of the beta-subunit. MAb3D5AB1 also binds to purified Escherichia coli F(1) with an affinity 25-fold higher than the affinity of angiostatin for this protein. MAb3D5AB1 inhibits the hydrolytic activity of F(1) ATP synthase at lower concentrations than angiostatin. Like angiostatin, MAb3D5AB1 inhibits ATP generation by ATP synthase on the endothelial cell surface in acidic conditions, the typical tumor microenvironment where cell surface ATP synthase exhibits greater activity. MAb3D5AB1 disrupts tube formation and decreases intracellular pH in endothelial cells exposed to low extracellular pH. Neither angiostatin nor MAb3D5AB1 showed an antiangiogenic effect in the corneal neovascularization assay; however, both were effective in the low-pH environment of the chicken chorioallantoic membrane assay. Thus, MAb3D5AB1 shows angiostatin-like properties superior to angiostatin and may be exploited in cancer chemotherapy.


Constrained customization of non-coplanar beam orientations in radiotherapy of brain tumours.
A methodology for the constrained customization of non-coplanar beam orientations in radiotherapy treatment planning has been developed and tested on a cohort of five patients with tumours of the brain. The methodology employed a combination of single and multibeam cost functions to produce customized beam orientations. The single-beam cost function was used to reduce the search space for the multibeam cost function, which was minimized using a fast simulated annealing algorithm. The scheme aims to produce well-spaced, customized beam orientations for each patient that produce low dose to organs at risk (OARs). The customized plans were compared with standard plans containing the number and orientation of beams chosen by a human planner. The beam orientation constraint-customized plans employed the same number of treatment beams as the standard plan but with beam orientations chosen by the constrained-customization scheme. Improvements from beam orientation constraint-customization were studied in isolation by customizing the beam weights of both plans using a dose-based downhill simplex algorithm. The results show that beam orientation constraint-customization reduced the maximum dose to the orbits by an average of 18.8 (+/-3.8, ISD)% and to the optic nerves by 11.4 (+/-4.8, ISD)% with no degradation of the planning target volume (PTV) dose distribution. The mean doses, averaged over the patient cohort, were reduced by 4.2 (+/-1.1, ISD)% and 12.4 (+/-3.1, ISD)% for the orbits and optic nerves respectively. In conclusion, the beam orientation constraint-customization can reduce the dose to OARs, for few-beam treatment plans, when compared with standard treatment plans developed by a human planner.


OKT3 and viral disease in pediatric liver transplant recipients.
Seventy-four consecutive pediatric liver transplant recipients were reviewed to assess the effect of the monoclonal anti-T-lymphocyte antibody OKT3 on subsequent viral infection (9 patients were excluded due to postoperative demise during the 1st week). Twenty-two patients received OKT3 in addition to standard cyclosporine-prednisone immunosuppression for either steroid-resistant acute rejection (18) or to facilitate reduction of cyclosporine due to severe renal impairment (4). Invasive infections were diagnosed by histology or culture in tissue biopsies or bronchoalveolar lavage specimens. The overall incidence of viral infection was 58%, half of which was due to cytomegalovirus (CMV). Invasive viral disease was associated with increased mortality (37% vs. 3% p = 0.001). Viral-related deaths were due to CMV (5), disseminated adenovirus (3), disseminated enterovirus (1) and respiratory syncytial viral pneumonia (1). The use of OKT3 was associated with increased viral disease (59% vs. 33% p=0.04) and invasive primary CMV disease (58% vs. 19% p=0.04). Trends were observed toward increased overall viral infection (73% vs. 51 % p=0.08), primary CMV infection (58% vs. 25% p=0.08) and overall mortality (27% vs. 9% p =0.08) following OKT3 therapy. We conclude that pediatric liver transplant recipients who require OKT3 therapy may be at increased risk for invasive viral disease and especially invasive primary CMV disease.


Hydrogen sulphide-related thiol metabolism and nutrigenetics in relation to hypertension in an elderly population.
Hydrogen sulphide (H(2)S) is a gaseous signalling molecule that regulates blood flow and pressure. It is synthesised from cysteine via cystathionine β-synthase and cystathionine γ-lyase. We examined whether thiol precursors of H(2)S, transsulphuration pathway gene variants (CBS-844ins68 and CTH-G1364T) and key B-vitamin cofactors might be critical determinants of hypertension in an elderly Australian population. An elderly Australian retirement village population (n = 228; age 65-96 years, 91 males and 137 females) was assessed for the prevalence of two transsulphuration pathway-related variant genes associated with cysteine synthesis and hence H(2)S production. Thiols were determined by HPLC, genotypes by PCR and dietary intake by food frequency questionnaire. Homocysteine levels were statistically higher in the hypertensive phenotype (p = 0.0399), but there was no difference for cysteine or glutathione. Using nominal logistic regression, cysteine, CTH-G1364T genotype, dietary synthetic folate and vitamin B(6) predicted clinical phenotype (determined as above/below 140/90 mm Hg) and then only in female subjects (p = 0.0239, 0.0178, 0.0249 and 0.0371, respectively). Least-squares regression supports cysteine being highly inversely predictive of diastolic blood pressure: p and r (2) values <0.0001 and 0.082; 0.0409 and 0.046; and <0.0001 and 0.113 for all subjects, males and females, respectively. Additionally, CTH-G1364T genotype predicts diastolic blood pressure in males (p = 0.0217; r (2) = 0.083), but contrasts with observations for females. Overall, analyses, including stepwise regression, suggest cysteine, dietary natural and synthetic folate, vitamins B(6) and B(12), and both genetic variants (CTH-C1364T and CBS-844ins68) are all aetiologically relevant in the regulation of blood pressure. Hydrogen sulphide is a vasorelaxant gasotransmitter with characteristics similar to nitric oxide. Cysteine and the G1364T and 844ins68 variants of the cystathionine γ-lyase and cystathionine β-synthase genes, respectively, are the biological determinants of H(2)S synthesis, and all three are shown here to influence the hypertensive phenotype. Additionally, B-vitamin cofactors for these three enzymes may also be important determinants of blood pressure.


Self-etching adhesives improve the shear bond strength of a resin-modified glass-ionomer cement to dentin.
Despite the improvements of resin-modified glass-ionomer cements, the dentin bond strength of these materials remains inferior to that provided by "bonding system/composite" combinations and limits the clinical use of RMGIC. The objective of this in vitro study was to investigate the effect of new self-etching bonding systems on the adhesion to dentin of Fuji II LC. Seven recent self-etching systems were studied (Clearfil SE Bond = CSE, Optibond Solo Plus Self-Etching Primer = OSP, One Up Bond F = OUP, Mac Bond II = MB2, Xeno III = XB3, ADPER Prompt-L-Pop = ADP, Unifil Bond = UB) and compared with Cavity Conditioner (C). After the bonding procedure, a resin-modified glass-ionomer cylinder (Fuji II LC) was bonded to the surface using a Teflon mold (diameter: 3 mm; height: 5 mm). The different specimens were tested in a shear bond mode (0.5 mm/min). Statistical analyses were performed with one-way ANOVA and Fischer PLSD test (p < 0.05). The one-way ANOVA revealed a significant influence of the surface treatment parameter (p < 0.0001). The lowest shear bond strength values were obtained with Cavity Conditioner. The highest values were obtained with MB2. The multiple comparisons revealed that ADP = OBP = XB3 = OUB = UB = CSE and that UB = CSE = MB2. The application of the 7 self-etching adhesives tested in this study improves the dentin shear bond strengths of Fuji II LC. This increase depended on the adhesive system and ranged from 50% for ADP up to 130% for MB2.


A colloidal quantum dot photonic crystal phosphor: nanostructural engineering of the phosphor for enhanced color conversion.
Phosphors, long-known color-converting photonic agents, are gaining increasing attention owing to the interest in white LEDs and related applications. Conventional material-based approaches to phosphors focus on obtaining the desired absorption/emission wavelengths and/or improving quantum efficiency. Here, we report a novel approach for enhancing the performance of phosphors: structural modification of phosphors. We incorporated inorganic colloidal quantum dots (CQDs) into a lateral one-dimensional (1D) photonic crystal (PhC) thin-film structure, with its photonic band-edge (PBE) modes matching the energy of 'excitation photons' (rather than 'emitted photons', as in most other PBE application devices). At resonance, we observed an approximately 4-fold enhancement of fluorescence over the reference bulk phosphor, which reflects an improved absorption of the excitation photons. This nano-structural engineering approach is a paradigm shift in the phosphor research area and may help to develop next-generation higher efficiency phosphors with novel characteristics.


Evaluation of health literacy status among patients in a tertiary care hospital in coastal karnataka, India.
People with limited health literacy are more likely to make medication errors, and they have less health knowledge, worse health status, more hospitalizations, and higher healthcare costs than people with adequate literacy. The objective of this study is to assess the health literacy status among patients who are able to read and understand English attending a tertiary care hospital by using Rapid Estimate of Adult Literacy in Medicine [REALM] technique and to compare the health literacy levels to educational status and other baseline characteristics. A widely used word recognition method [REALM] was used to assess the HL status of 200 patients attending a tertiary care hospital in Southern India. The number of correctly pronounced words was used to assign a grade-equivalent reading level. Scores 0 to 44 indicate reading skills at or below the 6th grade level, scores from 45 to 60 represent skills at the 7th or 8th grade level, and scores above 60 indicate skills at the high-school level or higher. HL status was found below adequate level in more than 50% of the patients. Younger age group showed better HL scores compared to those aged more than 25 years. General education level or the medium of education does not truly reflect HL levels as brought out in the study. Even those with postgraduate qualification had poor HL skills. The study was carried out to find out the HL levels among patients attending a tertiary care hospital. It was assumed that the general education levels may not reflect true HL status. In view of the results of this study it can be concluded that patient's HL skills should not be taken for granted and adequate attention should be paid in educating and briefing patients whenever patients are required to interpret and understand health care related documents.


A new class of antibacterials, the imidazopyrazinones, reveal structural transitions involved in DNA gyrase poisoning and mechanisms of resistance.
Imidazopyrazinones (IPYs) are a new class of compounds that target bacterial topoisomerases as a basis for their antibacterial activity. We have characterized the mechanism of these compounds through structural/mechanistic studies showing they bind and stabilize a cleavage complex between DNA gyrase and DNA ('poisoning') in an analogous fashion to fluoroquinolones, but without the requirement for the water-metal-ion bridge. Biochemical experiments and structural studies of cleavage complexes of IPYs compared with an uncleaved gyrase-DNA complex, reveal conformational transitions coupled to DNA cleavage at the DNA gate. These involve movement at the GyrA interface and tilting of the TOPRIM domains toward the scissile phosphate coupled to capture of the catalytic metal ion. Our experiments show that these structural transitions are involved generally in poisoning of gyrase by therapeutic compounds and resemble those undergone by the enzyme during its adenosine triphosphate-coupled strand-passage cycle. In addition to resistance mutations affecting residues that directly interact with the compounds, we characterized a mutant (D82N) that inhibits formation of the cleavage complex by the unpoisoned enzyme. The D82N mutant appears to act by stabilizing the binary conformation of DNA gyrase with uncleaved DNA without direct interaction with the compounds. This provides general insight into the resistance mechanisms to antibiotics targeting bacterial type II topoisomerases.


In-vivo longitudinal MRI study: an assessment of melanoma brain metastases in a clinically relevant mouse model.
Brain metastases are an important clinical problem. Few animal models exist for melanoma brain metastases; many of which are not clinically relevant. Longitudinal MRI was implemented to examine the development of tumors in a clinically relevant mouse model of melanoma brain metastases. Fifty thousand human metastatic melanoma (A2058) cells were injected intracardially into nude mice. Three Tesla MRI was performed using a custom-built gradient insert coil and a mouse solenoid head coil. Imaging was performed on consecutive days at four time points. Tumor burden and volumes of metastases were measured from balanced steady-state free precession image data. Metastases with a disrupted blood-tumor barrier were identified from T1-weighted spin echo images acquired after administration of gadopentetic acid (Gd-DTPA). Metastases permeable to Gd-DTPA showed signal enhancement. The number of enhancing metastases was determined by comparing balanced steady-state free precession images with T1-weighted spin echo images. After the final imaging session, ex-vivo permeability and histological analyses were carried out. Imaging showed that both enhancing and nonenhancing brain metastases coexist in the brain, and that most metastases switched from the nonenhancing to the enhancing phenotype. Small numbers of brain metastases were enhancing when first detected by MRI and remained enhancing, whereas other metastases remained nonenhancing to Gd-DTPA throughout the experiment. No clear relationship existed between the permeability of brain metastases and size, brain location and age. Longitudinal in-vivo MRI is key to studying the complex and dynamic processes of metastasis and changes in the blood-tumor barrier permeability, which may lead to a better understanding of the variable responses of brain metastases to treatments.


Transcription of a "silent" cyanobacterial psbA gene is induced by microaerobic conditions.
Cyanobacteria, contrary to higher plants, have a small psbA gene family encoding the reaction centre D1 protein subunit of photosystem II, the first macromolecular pigment-protein complex of the photosynthetic electron transport chain. Modulation of expression of multiple psbA genes in the family allows cyanobacteria to adapt to changing environmental conditions. To date, two different strategies for regulation of the psbA genes have emerged. One, characterized in Synechocystis PCC6803 and Gloeobacter violaceus PCC7421 involves the increased expression of one type of D1 protein to cope with the increased rate of damage. The other strategy, in Synechococcus PCC7942 and Anabaena PCC7120, is to replace the existing D1 with a new D1 form for the duration of the stress. However, most of the psbA gene families characterized to date contain also a divergent, apparently silent psbA gene of unknown function. This gene, present in Synechocystis, Anabaena and Thermosynechococcus elongatus BP-1 was not induced by any stress condition applied so far. Our data shows a reversible induction of the divergent psbA gene during the onset of argon-induced microaerobic conditions in Synechocystis, Anabaena and Thermosynechococcus elongatus. The unitary functional response of three unrelated cyanobacterial species, namely the induction of the expression of the divergent psbA gene as a reaction to the same environmental cue, indicates that these genes and the protein they encode are part of a specific cellular response to microaerobic conditions. There are no specific primary structure similarities between the different microaerobic inducible D1 forms, designated as D1'. Only three amino acid residues are consistently conserved in D1'. These modifications are: G80 to A, F158 to L and T286 to L. In silico mutation of the published D1 structure from Thermosynechococcus did not reveal major modifications. The point by point effects of the mutations on the local environment of the PSII structure are also discussed.


Novelty detection in the human auditory brainstem.
Auditory deviance detection has been associated with a human auditory-evoked potential (AEP), the mismatch negativity, generated in the auditory cortex 100-200 ms from sound change onset. Yet, single-unit recordings in animals suggest much earlier (∼20-40 ms), and anatomically lower (i.e., thalamus and midbrain) deviance detection. In humans, recordings of the scalp middle-latency AEPs have confirmed early (∼30-40 ms) deviance detection. However, involvement of the human auditory brainstem in deviance detection has not yet been demonstrated. Here we recorded the auditory brainstem frequency-following response (FFR) to consonant-vowel stimuli (/ba/, /wa/) in young adults, with stimuli arranged in oddball and reversed oddball blocks (deviant probability, p=0.2), allowing for the comparison of FFRs to the same physical stimuli presented in different contextual roles. Whereas no effect was observed for the /wa/ syllable, we found for the /ba/ syllable a reduction in the brainstem FFR to deviant stimuli compared with standard ones and to similar stimuli arranged in a control block, with five equiprobable, rarely occurring sounds. These findings demonstrate that the human auditory brainstem is able to encode regularities in the recent auditory past to detect novel events, and confirm the multiple anatomical and temporal scales of human deviance detection.


Acute Effects of Exercise on Blood Pressure: A Meta-Analytic Investigation.
Hypertension affects 25% of the world's population and is considered a risk factor for cardiovascular disorders and other diseases. The aim of this study was to examine the evidence regarding the acute effect of exercise on blood pressure (BP) using meta-analytic measures. Sixty-five studies were compared using effect sizes (ES), and heterogeneity and Z tests to determine whether the ES were different from zero. The mean corrected global ES for exercise conditions were -0.56 (-4.80 mmHg) for systolic BP (sBP) and -0.44 (-3.19 mmHg) for diastolic BP (dBP; z ≠ 0 for all; p < 0.05). The reduction in BP was significant regardless of the participant's initial BP level, gender, physical activity level, antihypertensive drug intake, type of BP measurement, time of day in which the BP was measured, type of exercise performed, and exercise training program (p < 0.05 for all). ANOVA tests revealed that BP reductions were greater if participants were males, not receiving antihypertensive medication, physically active, and if the exercise performed was jogging. A significant inverse correlation was found between age and BP ES, body mass index (BMI) and sBP ES, duration of the exercise's session and sBP ES, and between the number of sets performed in the resistance exercise program and sBP ES (p < 0.05). Regardless of the characteristics of the participants and exercise, there was a reduction in BP in the hours following an exercise session. However, the hypotensive effect was greater when the exercise was performed as a preventive strategy in those physically active and without antihypertensive medication.


Data-Driven Collective Variables for Enhanced Sampling.
Designing an appropriate set of collective variables is crucial to the success of several enhanced sampling methods. Here we focus on how to obtain such variables from information limited to the metastable states. We characterize these states by a large set of descriptors and employ neural networks to compress this information in a lower-dimensional space, using Fisher's linear discriminant as an objective function to maximize the discriminative power of the network. We test this method on alanine dipeptide, using the nonlinearly separable data set composed by atomic distances. We then study an intermolecular aldol reaction characterized by a concerted mechanism. The resulting variables are able to promote sampling by drawing nonlinear paths in the physical space connecting the fluctuations between metastable basins. Lastly, we interpret the behavior of the neural network by studying its relation to the physical variables. Through the identification of its most relevant features, we are able to gain chemical insight into the process.


Agreement of objectively measured physical activity and sedentary time in preschool children.
To determine the intra-individual agreement for objectively measured physical activity (PA) and sedentary behavior (SED) over two subsequent weeks in preschool children. Ninety-one children aged 3 to 5 years (49% boys) from three preschools in Sogn og Fjordane, Norway, provided 14 consecutive days of accelerometer data (Actigraph GT3X +) during the autumn of 2014. Week-by-week reliability was assessed using intraclass correlation (ICC), Bland-Altman plots and 95% limits of agreement for different wear time criteria (≥ 6, 8 and 10 h/day and ≥ 3 and 5 days/week). The week-by-week ICC was ≥ 0.75 for all variables across all wear criteria applied, except for absolute sedentary time (ICC 0.61-0.81). Using a ≥ 8 h/day and ≥ 3 days/week criterion (n = 78), limits of agreement were ± 209.5 cpm for overall PA, ± 68.6 min/day for SED, ± 43.8 min/day for light PA, ± 20.2 min/day for moderate-to-vigorous PA, and ± 55.9 min/day for light-to-vigorous PA, equaling 1.0-1.6 standard deviation units. Considerable week-by-week variability was found for all variables. Researchers need to be aware of substantial intra-individual variability in accelerometer-measurements and take necessary actions according to the hypothesis under study, as noise in any measurement will preclude researchers' ability to arrive at valid conclusions in epidemiology.


Home range overlap as a driver of intelligence in primates.
Various socioecological factors have been suggested to influence cognitive capacity in primates, including challenges associated with foraging and dealing with the complexities of social life. Alexander [Alexander, 1989]. Evolution of the human psyche. In: Mellars P, Stringer C, editors. The human revolution: Behavioural and biological perspectives on the origins of modern humans. Princeton: Princeton University Press. p 455-513] proposed an integrative model for the evolution of human cognitive abilities and complex sociality that incorporates competition among coalitions of conspecifics (inter-group conflict) as a major selective pressure. However, one of the premises of this model, i.e., that when confronted with inter-group conflict selection should favor enhanced cognition, has remained empirically untested. Using a comparative approach on species data, I aimed to test the prediction that primate species (n = 104) that face greater inter-group conflict have higher cognitive abilities (indexed by endocranial volume). The degree of inter-group conflict/complexity was approximated via the variable home range overlap among groups. I found a significant relationship between home range overlap and endocranial volume, even after controlling for other predictor variables and covariates such as group size and body mass. I conclude that brain size evolution cannot be attributed exclusively to social factors such as group size, but likely reflects a variety of social and ecological determinants including inter-group conflict which poses cognitive demands on monitoring both the wider social milieu as well as spatial attributes of the habitat.


Evaluation of antiretroviral therapy (ART)-related counselling in a workplace-based ART implementation programme, South Africa.
Counselling about antiretroviral therapy (ART) is thought important to prepare patients for treatment and enhance adherence. A workplace-based HIV care programme in South Africa instituted a three-step ART counselling protocol with guidelines prompting issues to be covered at each step. We carried out an early evaluation of ART counselling to determine whether patients understood key information about ART, and the perceptions that patients and health care professionals (HCP) had of the process. Among 40 patients (median time on ART 83 days), over 90% answered 6/7 HIV/ART knowledge-related questions correctly. 95% thought counselling sessions were good. 93% thought ongoing counselling was important. Recommendations included the need for continuing education about HIV/ART, being respectful, promoting HIV testing and addressing the issues of infected partners and stigma. 24 participating HCP identified additional training needs including counselling of family and friends, family planning, sexually transmitted infections and running support groups. 90% of HCP thought that counselling guidelines were helpful. The programme appears to be preparing patients well for ART. Counselling should be offered at every clinic visit. Counselling guidelines were a valuable tool and may be useful elsewhere. The evaluation helped to assess the quality of the programme and to suggest areas for improvement.


An endonuclease switching mechanism in the virion RNA and cRNA promoters of Thogoto orthomyxovirus.
An in vitro assay was developed to investigate endonuclease activity of Thogoto virus, a tick-borne orthomyxovirus. Endonuclease activity relied on an interaction between the 3' and 5' termini of virion RNA (vRNA) and not those of cRNA. Evidence was obtained that cap structures are cleaved directly from cap donors and that cleavage does not occur after pyrimidines. A 5' hook structure, present in the vRNA promoter but not the cRNA promoter, was introduced into cRNA promoter mutants. These mutants stimulated endonuclease activity, although at levels slightly lower than that of vRNA. The ability of the cRNA promoter to stimulate endonuclease activity when mutated to contain a 5' hook structure indicates that this structure constitutes a switching mechanism for endonuclease activity between the vRNA and cRNA promoters.


Relationship quality and sense of coherence in dementia: Results of a European cohort study.
Quality of life of people with dementia and their family carers is strongly influenced by interpersonal issues and personal resources. In this context, relationship quality (RQ) and sense of coherence (SOC) potentially protect and promote health. We aimed to identify what influences RQ in dyads of people with dementia and their carers and to examine differences in their perspectives. Cross-sectional data were used from the Actifcare cohort study of 451 community-dwelling people with dementia and their primary carers in eight European countries. Comprehensive assessments included the Positive Affect Index (RQ) and the Orientation to Life Questionnaire (SOC). Regression analyses revealed that RQ as perceived by people with dementia was associated with carer education, stress, and spouse caregiving. RQ as perceived by carers was associated with carer stress, depression, being a spouse, social support, reported neuropsychiatric symptoms of dementia, and carer SOC. Neuropsychiatric symptoms and carer stress contributed to discrepancies in RQ ratings within the dyad. The only factor associated with both individual RQ ratings and discrepancies was carer stress (negative feelings subscore). No significant differences in the overall perception of RQ were evident between spouses and adult children carers, but RQ determinants differed between the two. In this European sample, carer SOC was associated with carer-reported RQ. RQ determinants differed according to the perspective considered (person with dementia or carer) and carer subgroup. A deeper understanding of RQ and its determinants will help to tailor interventions that address these distinct perspectives and potentially improve dementia outcomes.


Why are GPs treating subclinical hypothyroidism? Case note review and GP survey.
Subclinical hypothyroidism (SCHo) is a common biochemical diagnosis in older age. Evidence of impact is inconclusive and guidelines are inconsistent. With increasing numbers of thyroid function tests (TFTs) performed, GPs frequently have to make management decisions regarding this diagnosis. However, little is known about how SCHo is currently being managed in primary care. To explore management of SCHo in primary care and GP reported rationale for treatment of SCHo in older individuals. Descriptive study using retrospective case note review and GP survey. Nineteen General Practices, Central England, UK. Follow-up of a large cohort with subsequent detailed review of individuals for whom therapy had been initiated following diagnosis of SCHo. Data on practice policies, and rationale behind treatment were collected via GP questionnaire. Forty-two individuals were treated following identification of SCHo. Factors regarded as supporting instigation of therapy recorded by practitioners included symptoms, a positive antithyroid antibody test and history of radioiodine therapy. In all, 55% were registered at 3/19 practices suggesting significant between practice variation. Reasons for testing included chronic disease check-up (n = 14), presenting 'thyroid symptoms' (n = 5) and presenting other symptoms (n = 9). Reasons for therapy initiation were only recorded in 26 cases and included presence of symptoms, persistently high or increasing serum thyroid stimulating hormone concentration and patient request. Only 2/15 GPs reported having practice guidelines on management. Results suggest that GPs are uncertain how to interpret symptoms and TFT results in older individuals. There is considerable variation in management of SCHo between GPs with some GPs treating patients outside of all guideline recommendations.


Chronic pain self-management support with pain science education and exercise (COMMENCE): study protocol for a randomized controlled trial.
Previous research suggests that self-management programs for people with chronic pain improve knowledge and self-efficacy but result in negligible effects on function. This study will investigate the effectiveness self-management support with pain science education and exercise on improving function for people with chronic pain in comparison to a wait-list control. A secondary objective is to determine which variables help to predict response to the intervention. This study will be an unblinded, randomized controlled trial with 110 participants comparing a 6-week program that includes self-management support, pain science education and exercise to a wait-list control. The primary outcome will be function measured by the Short Musculoskeletal Function Assessment - Dysfunction Index. Secondary outcomes will include pain intensity measured by a numeric pain rating scale, pain interference measured by the eight-item PROMIS pain interference item-bank, how much patients are bothered by functional problems measured by the Short Musculoskeletal Function Assessment - Bother Index, catastrophic thinking measured by the Pain Catastrophizing Scale, fear of movement/re-injury measured by the 11-item Tampa Scale of Kinesiophobia, sense of perceived injustice measured by the Injustice Experience Questionnaire, self-efficacy measured by the Pain Self-Efficacy Questionnaire, pain sensitivity measured by pressure pain threshold and cold sensitivity testing, fatigue measured by a numeric fatigue rating scale, pain neurophysiology knowledge measured by the Neurophysiology of Pain Questionnaire, healthcare utilization measured by number of visits to a healthcare provider, and work status. Assessments will be completed at baseline, 7 and 18 weeks. After the 18-week assessment, the groups will crossover; however, we anticipate carry-over effects with the treatment. Therefore, data from after the crossover will be used to estimate within-group changes and to determine predictors of response that are not for direct between-group comparisons. Mixed effects modelling will be used to determine between-group differences for all primary and secondary outcomes. A series of multiple regression models will be used to determine predictors of treatment response. This study has the potential to inform future self-management programming through evaluation of a self-management program that aims to improve function as the primary outcome. ClinicalTrials.gov NCT02422459 , registered on 13 April 2015.


Kriging Models Predicting Atrazine Concentrations in Surface Water Draining Agricultural Watersheds.
The performance of kriging methods in predicting maximum m-day (m = 1, 7, 14, or 30) rolling averages of atrazine concentrations in 42 site-years of Midwest Corn Belt watersheds under two systematic sampling designs (sampling every 7 or 14 d) was examined. Daily atrazine monitoring data obtained from the Atrazine Ecological Monitoring Program in the Corn Belt region (2009-2014) were used in the evaluation. Both ordinary and universal kriging methods were considered, with the covariate for universal kriging derived from the deterministic Pesticide Root Zone Model (PRZM). For the maximum 1-d rolling averages, prediction did not differ among methods. For rolling averages of longer duration (m > 1), predictions obtained by linear interpolation on a logarithmic scale were better (up to 15% lower for 7-d sampling and 22% lower for 14-d sampling in terms of the relative root mean squared prediction error) than those obtained by linear interpolation on the original linear scale and also less variable. For kriging methods, empirical semivariograms of daily atrazine time series suggest a negligible noise process, supported by replicate analysis of selected field samples; piecewise linear semivariogram models were found to perform best for predicting sampled data. We demonstrate that kriging prediction intervals offer close to nominal coverage for unsampled values.


Metabolic control of adult neural stem cell activity by Fasn-dependent lipogenesis.
Mechanisms controlling the proliferative activity of neural stem and progenitor cells (NSPCs) have a pivotal role to ensure life-long neurogenesis in the mammalian brain. How metabolic programs are coupled with NSPC activity remains unknown. Here we show that fatty acid synthase (Fasn), the key enzyme of de novo lipogenesis, is highly active in adult NSPCs and that conditional deletion of Fasn in mouse NSPCs impairs adult neurogenesis. The rate of de novo lipid synthesis and subsequent proliferation of NSPCs is regulated by Spot14, a gene previously implicated in lipid metabolism, that we found to be selectively expressed in low proliferating adult NSPCs. Spot14 reduces the availability of malonyl-CoA, which is an essential substrate for Fasn to fuel lipogenesis. Thus, we identify here a functional coupling between the regulation of lipid metabolism and adult NSPC proliferation.


Association Between Greater Cerebellar Network Connectivity and Improved Phonemic Fluency Performance After Exercise Training in Older Adults.
Little is known about the effects of exercise training (ET) on lexical characteristics during fluency task and its association with cerebellum functional connectivity. The purposes of this study were (1) to investigate whether ET alters response patterns during phonemic and semantic fluency tasks and (2) to assess the association between ET-related changes in cerebellum functional connectivity (FC) and lexical characteristics during fluency tasks. Thirty-five older adults (78.0 ± 7.1 years; 17 mild cognitive impairment (MCI) and 18 healthy cognition (HC)) underwent a 12-week treadmill ET. Before and after ET, cardiorespiratory fitness tests, phonemic and semantic fluency tests, and resting-state fMRI scans were administered. We utilized a seed-based correlation analysis to measure cerebellum FC and linear regression to assess the association of residualized ET-induced Δcerebellum FC with Δtask performance. Improved mean switches and frequency during the phonemic fluency task were observed following ET in all participants. There were significant associations between ET-induced increases in cerebellum FC and greater phonemic fluency task log frequency, increases in mean switches, and a reduction in the number of syllables in HC. Lastly, there was a significant interaction between group and cerebellar connectivity on phonemic fluency mean log frequency and number of syllables. A 12-week walking ET is related to enhanced phonemic fluency lexical characteristics in older adults with MCI and HC. The association between ET-induced increases in cerebellum FC and enhanced response patterns after ET suggests that the cerebellum may play an important role in ET-related improvement in phonemic fluency performance in cognitively healthy older adults.


Metabolism of PLTP, CETP, and LCAT on multiple HDL sizes using the Orbitrap Fusion Lumos.
Recent in vivo tracer studies demonstrated that targeted mass spectrometry (MS) on the Q Exactive Orbitrap could determine the metabolism of HDL proteins 100s-fold less abundant than apolipoprotein A1 (APOA1). In this study, we demonstrate that the Orbitrap Lumos can measure tracer in proteins whose abundances are 1000s-fold less than APOA1, specifically the lipid transfer proteins phospholipid transfer protein (PLTP), cholesterol ester transfer protein (CETP), and lecithin-cholesterol acyl transferase (LCAT). Relative to the Q Exactive, the Lumos improved tracer detection by reducing tracer enrichment compression, thereby providing consistent enrichment data across multiple HDL sizes from 6 participants. We determined by compartmental modeling that PLTP is secreted in medium and large HDL (alpha2, alpha1, and alpha0) and is transferred from medium to larger sizes during circulation from where it is catabolized. CETP is secreted mainly in alpha1 and alpha2 and remains in these sizes during circulation. LCAT is secreted mainly in medium and small HDL (alpha2, alpha3, prebeta). Unlike PLTP and CETP, LCAT's appearance on HDL is markedly delayed, indicating that LCAT may reside for a time outside of systemic circulation before attaching to HDL in plasma. The determination of these lipid transfer proteins' unique metabolic structures was possible due to advances in MS technologies.


Unexpected mobility variation among individual secretory vesicles produces an apparent refractory neuropeptide pool.
Most stored neuropeptide cannot be released from nerve terminals suggesting the existence of a refractory pool of dense core vesicles (DCVs). Past fluorescence photobleaching recovery, single particle tracking and release experiments suggested that the refractory neuropeptide pool corresponds to a distinct immobile fraction of cytoplasmic DCVs. However, tracking of hundreds of individual green fluorescent protein-labeled neuropeptidergic vesicles by wide-field or evanescent-wave microscopy shows that a separate immobile fraction is not evident. Instead, the DCV diffusion coefficient (D) distribution is unusually broad and asymmetric. Furthermore, the distribution shifts with a release facilitator. This unexpected variation, which could reflect heterogeneity among vesicles or in their medium, is shown to generate the appearance of a regulated refractory neuropeptide pool.


Vitamin D deficiency is associated with an increased autoimmune response in healthy individuals and in patients with systemic lupus erythematosus.
Vitamin D deficiency is widespread and has been associated with many chronic diseases, including autoimmune disorders. A study was undertaken to explore the impact of low vitamin D levels on autoantibody production in healthy individuals, as well as B cell hyperactivity and interferon α (IFNα) activity in patients with systemic lupus erythematosus (SLE). Serum samples from 32 European American female patients with SLE and 32 matched controls were tested for 25-hydroxyvitamin D (25(OH)D) levels, lupus-associated autoantibodies and serum IFNα activity. Isolated peripheral blood mononuclear cells were tested for intracellular phospho-ERK 1/2 as a measure of B cell activation status. Vitamin D deficiency (25(OH)D <20 ng/ml) was significantly more frequent among patients with SLE (n=32, 69%) and antinuclear antibody (ANA)-positive controls (n=14, 71%) compared with ANA-negative controls (n=18, 22%) (OR 7.7, 95% CI 2.0 to 29.4, p=0.003 and OR 8.8, 95% CI 1.8 to 43.6, p=0.011, respectively). Patients with high B cell activation had lower mean (SD) 25(OH)D levels than patients with low B cell activation (17.2 (5.1) vs 24.2 (3.9) ng/ml; p=0.009). Patients with vitamin D deficiency also had higher mean (SD) serum IFNα activity than patients without vitamin D deficiency (3.5 (6.6) vs 0.3 (0.3); p=0.02). The observation that ANA-positive healthy controls are significantly more likely to be deficient in vitamin D than ANA-negative healthy controls, together with the finding that vitamin D deficiency is associated with certain immune abnormalities in SLE, suggests that vitamin D plays an important role in autoantibody production and SLE pathogenesis.


MY7 monoclonal antibody for diagnosis of cutaneous T-cell lymphoma.
Infiltrate in cutaneous T-cell lymphomas (CTCLs) is composed mainly of CD4 helper cells with a phenotype very similar to that of benign cutaneous lymphoid infiltrate. MY7 (CD13) is a monoclonal antibody that is normally expressed on peripheral granulocytes and monocytes but also cross-reacts with an antigen expressed on epidermal basal cells. We studied MY7 expression on basal cells of the epidermis and CD4 cell infiltrate in 34 CTCLs, 11 pseudolymphomas, and 29 other benign cutaneous lesions. An indirect immunofluorescence technique with double labeling and an immunoperoxidase technique were used. We found that in benign inflammatory infiltrate, less than 10% of CD4 cells expressed MY7 antigen associated with normal MY7 monoclonal antibody labeling of basal cells, whereas in CTCLs more than 50% of CD4 tumoral cells in dermis expressed MY7 antigens; however, basal cells were MY7 negative. Thus, it is demonstrated that MY7 monoclonal antibody with its double modulation on epidermis (basal cells) and dermis (CD4 cells) has diagnostic value for differentiating CTCLs with CD4+ MY7+ tumor cells in dermis and MY7-negative basal cells from benign inflammatory lesions with CD4+ MY7- cells in dermis and MY7-positive basal cells. This modulation of MY7 labeling could be related to the secretion of epidermal cytokines.


Ten golden rules for reforestation to optimize carbon sequestration, biodiversity recovery and livelihood benefits.
Urgent solutions to global climate change are needed. Ambitious tree-planting initiatives, many already underway, aim to sequester enormous quantities of carbon to partly compensate for anthropogenic CO2 emissions, which are a major cause of rising global temperatures. However, tree planting that is poorly planned and executed could actually increase CO2 emissions and have long-term, deleterious impacts on biodiversity, landscapes and livelihoods. Here, we highlight the main environmental risks of large-scale tree planting and propose 10 golden rules, based on some of the most recent ecological research, to implement forest ecosystem restoration that maximizes rates of both carbon sequestration and biodiversity recovery while improving livelihoods. These are as follows: (1) Protect existing forest first; (2) Work together (involving all stakeholders); (3) Aim to maximize biodiversity recovery to meet multiple goals; (4) Select appropriate areas for restoration; (5) Use natural regeneration wherever possible; (6) Select species to maximize biodiversity; (7) Use resilient plant material (with appropriate genetic variability and provenance); (8) Plan ahead for infrastructure, capacity and seed supply; (9) Learn by doing (using an adaptive management approach); and (10) Make it pay (ensuring the economic sustainability of the project). We focus on the design of long-term strategies to tackle the climate and biodiversity crises and support livelihood needs. We emphasize the role of local communities as sources of indigenous knowledge, and the benefits they could derive from successful reforestation that restores ecosystem functioning and delivers a diverse range of forest products and services. While there is no simple and universal recipe for forest restoration, it is crucial to build upon the currently growing public and private interest in this topic, to ensure interventions provide effective, long-term carbon sinks and maximize benefits for biodiversity and people.


General Practitioners' intention to prescribe and prescribing patterns in selected European settings: The OTCSOCIOMED project.
The aim of this paper is to explore general practitioners' (GPs) prescribing intentions and patterns across different European regions using the Theory of Planned Behavior (TPB). A cross-sectional study was undertaken in selected geographically defined Primary Health Care areas in Cyprus, Czech Republic (CZ), France, Greece, Malta, Sweden and Turkey. Face-to-face interviews were conducted using a TPB-based questionnaire. The number of GP participants ranged from 39 to 145 per country. Possible associations between TPB direct measures (attitudes, subjective norms (SN) and perceived behavioral control (PBC)) and intention to prescribe were assessed by country. On average, GPs thought positively of, and claimed to be in control of, prescribing. Correlations between TPB explanatory measures and prescribing intention were weak, with TPB direct measures explaining about 25% of the variance in intention to prescribe in Malta and CZ but only between 3% and 5% in Greece, Sweden and Turkey. SN appeared influential in GPs from Malta; attitude and PBC were statistically significant in GPs from CZ. GPs' prescribing intentions and patterns differed across participating countries, indicating that country-specific interventions are likely to be appropriate. Irrational prescribing behaviors were more apparent in the countries where an integrated primary care system has still not been fully developed and policies promoting the rational use of medicines are lacking. Demand-side measures aimed at modifying GPs prescribing behavior are deemed necessary.


From cyst to tubule: innovations in vertebrate spermatogenesis.
Although vertebrates share many common traits, their germline development and function exhibit significant divergence. In particular, this article focuses on their spermatogenesis. The fundamental elements that constitute vertebrate spermatogenesis and the evolutionary changes that occurred upon transition from water to land will be discussed. The life-long continuity of spermatogenesis is supported by the function of stem cells. Series of mitotic and meiotic germ cell divisions are 'incomplete' due to incomplete cytokinesis, forming syncytia interconnected via intercellular bridges (ICBs). Throughout this process, germ cells are supported by appropriate microenvironments established primarily by somatic Sertoli cells. In anamniotes (fish and amphibians) spermatogenesis progresses in cysts, in which developing germ cell syncytia are individually encapsulated by Sertoli cells. Accordingly, Sertoli cells undergo turnover with germ cells that they nourish. This mode of cystic spermatogenesis is also observed in nonvertebrates as insects. In amniotes (reptiles, birds, and mammals), however, Sertoli cells do not turn over but comprise a persistent structure of seminiferous tubules. Sertoli cells nourish different stages of germ cells simultaneously in distinct regions of their surface. This function of Sertoli cells is spatiotemporally orchestrated, and the seminiferous epithelial cycle and spermatogenic wave make the seminiferous tubules a high-throughput factory for sperm production. Furthermore, contrary to the organized differentiating cells, undifferentiated spermatogonia that comprise the stem cell compartment exhibit active motion over the basal layer of seminiferous tubules and the frequent breakdown of ICBs. Thus, amniote seminiferous tubules represent a typical facultative (or open) niche environment without a stem cell tethering anatomically defined niche. WIREs Dev Biol 2016, 5:119-131. doi: 10.1002/wdev.204 For further resources related to this article, please visit the WIREs website.


Entrainment Maps.
Circadian oscillators found across a variety of species are subject to periodic external light-dark forcing. Entrainment to light-dark cycles enables the circadian system to align biological functions with appropriate times of day or night. Phase response curves (PRCs) have been used for decades to gain valuable insights into entrainment; however, PRCs may not accurately describe entrainment to photoperiods with substantial amounts of both light and dark due to their reliance on a single limit cycle attractor. We have developed a new tool, called an entrainment map, that overcomes this limitation of PRCs and can assess whether, and at what phase, a circadian oscillator entrains to external forcing with any photoperiod. This is a 1-dimensional map that we construct for 3 different mathematical models of circadian clocks. Using the map, we are able to determine conditions for existence and stability of phase-locked solutions. In addition, we consider the dependence on various parameters such as the photoperiod and intensity of the external light as well as the mismatch in intrinsic oscillator frequency with the light-dark cycle. We show that the entrainment map yields more accurate predictions for phase locking than methods based on the PRC. The map is also ideally suited to calculate the amount of time required to achieve entrainment as a function of initial conditions and the bifurcations of stable and unstable periodic solutions that lead to loss of entrainment.


Digging the New York City Skyline: soil fungal communities in green roofs and city parks.
In urban environments, green roofs provide a number of benefits, including decreased urban heat island effects and reduced energy costs for buildings. However, little research has been done on the non-plant biota associated with green roofs, which likely affect their functionality. For the current study, we evaluated whether or not green roofs planted with two native plant communities in New York City functioned as habitats for soil fungal communities, and compared fungal communities in green roof growing media to soil microbial composition in five city parks, including Central Park and the High Line. Ten replicate roofs were sampled one year after planting; three of these roofs were more intensively sampled and compared to nearby city parks. Using Illumina sequencing of the fungal ITS region we found that green roofs supported a diverse fungal community, with numerous taxa belonging to fungal groups capable of surviving in disturbed and polluted habitats. Across roofs, there was significant biogeographical clustering of fungal communities, indicating that community assembly of roof microbes across the greater New York City area is locally variable. Green roof fungal communities were compositionally distinct from city parks and only 54% of the green roof taxa were also found in the park soils. Phospholipid fatty acid analysis revealed that park soils had greater microbial biomass and higher bacterial to fungal ratios than green roof substrates. City park soils were also more enriched with heavy metals, had lower pH, and lower quantities of total bases (Ca, K, and Mg) compared to green roof substrates. While fungal communities were compositionally distinct across green roofs, they did not differentiate by plant community. Together, these results suggest that fungi living in the growing medium of green roofs may be an underestimated component of these biotic systems functioning to support some of the valued ecological services of green roofs.


Identification and comparison of oligopeptides during withering process of White tea by ultra-high pressure liquid chromatography coupled with quadrupole-orbitrap ultra-high resolution mass spectrometry.
Peptides could have specific tastes or bioactivities depending on the length and sequence of amino acids. Till date it remains unknown what peptides are formed during the white tea manufacturing process and whether they contribute to the flavor or bio-activities of white tea. As a first step to address these questions, we applied ultra-high pressure liquid chromatography coupled with quadrupole-orbitrap ultra-high resolution mass spectrometry (UPLC-Quadrupole-Orbitrap-UHRMS) to monitor peptides dynamic changes during the withering process. A total of 196 abundant peptides were identified. Most of them were oligopeptides within a molecular weight of 1000 Da. Four of them were randomly selected, synthesized peptides were applied for further confirmation and quantification. Sequence analysis suggested that some of them were potential taste contributors. Proteinase cleave site analysis identified two separate periods of active proteins degradation at 0-12 h and 30-42 h of the withering processes. Further analysis of cleavage sites also suggested that protein degradation during withering steps were random rather than a stepwise reaction.


Attitudes toward genetic research review: results from a survey of human genetics researchers.
Researchers often relate personal experiences of difficulties and challenges with Institutional Review Board (IRB) review of their human genetic research protocols. However, there have been no studies that document the range and frequency of these concerns among researchers conducting human genetic/genomic studies. An online anonymous survey was used to collect information from human genetic researchers regarding views about IRB review of genetic protocols. Logistic regression was used to test specific hypotheses. Results from the national online survey of 351 human genomic researchers are summarized in this report. Issues involving considerable discussion with IRBs included reconsent of subjects (51%), protection of participants' personal information (39%) and return of results to participants (34%). Over half of the participants had experienced one or more negative consequences of the IRB review process and approximately 25% had experienced one or more positive consequences. Respondents who had served on an IRB were about 80% more likely to report positive consequences of IRB review than their colleagues who had never served on an IRB (p = 0.03). Survey responses were mixed on the need for reconsent before data sharing and risks related to participant reidentification from genomic data. The results from this study provide important perspectives of researchers regarding genetic research review and show lack of consensus on key research ethics issues in genomic research.


Symptoms and transmission of intestinal cryptosporidiosis.
Cryptosporidium spp are a cause of diarrhoea in toddlers. Symptoms and routes of transmission were investigated in a prospective case-control study in the city and surroundings of Basel, Switzerland. Twenty one (4.6%) out of 455 children with diarrhoea who attended paediatric and general practices from June to September 1988 were positive for cryptosporidium. The mothers of each case, of two controls with diarrhoea of another origin, and of two healthy controls were interviewed with a standardised questionnaire. In comparison with controls with diarrhoea of another origin, respiratory symptoms were significantly more frequent in children with cryptosporidiosis: eight of 19 (42%) compared with five of 38 (13%). In comparison with healthy controls, preceding contact with a person suffering from diarrhoea was associated with the greatest relative risk for cryptosporidiosis, followed by travel in a Mediterranean country. Transient cryptosporidial infection of the respiratory tract may be common in immunocompetent children. In the area investigated person to person transmission may account for most cases.


Mantle phase changes and deep-earthquake faulting in subducting lithosphere.
Inclined zones of earthquakes are the primary expression of lithosphere subduction. A distinct deep population of subduction-zone earthquakes occurs at depths of 350 to 690 kilometers. At those depths ordinary brittle fracture and frictional sliding, the faulting processes of shallow earthquakes, are not expected. A fresh understanding of these deep earthquakes comes from developments in several areas of experimental and theoretical geophysics, including the discovery and characterization of transformational faulting, a shear instability connected with localized phase transformations under nonhydrostatic stress. These developments support the hypothesis that deep earthquakes represent transformational faulting in a wedge of olivine-rich peridotite that is likely to persist metastably in coldest plate interiors to depths as great as 690 km. Predictions based on this deep structure of mantle phase changes are consistent with the global depth distribution of deep earthquakes, the maximum depths of earthquakes in individual subductions zones, and key source characteristics of deep events.


Nonlinear directional coupler with a diffusive Kerr-type nonlinearity.
We present numerical results showing the effects of a diffusive Kerr-type nonlinearity on the switching characteristics of a nonlinear directional coupler. It is found that switching can still occur even when the diffusion length is equal to the waveguide separation but that then its threshold increases and becomes less pronounced.


Formation of Unstable and very Reactive Chemical Species Catalyzed by Metalloenzymes: A Mechanistic Overview.
Nature has tailored a wide range of metalloenzymes that play a vast array of functions in all living organisms and from which their survival and evolution depends on. These enzymes catalyze some of the most important biological processes in nature, such as photosynthesis, respiration, water oxidation, molecular oxygen reduction, and nitrogen fixation. They are also among the most proficient catalysts in terms of their activity, selectivity, and ability to operate at mild conditions of temperature, pH, and pressure. In the absence of these enzymes, these reactions would proceed very slowly, if at all, suggesting that these enzymes made the way for the emergence of life as we know today. In this review, the structure and catalytic mechanism of a selection of diverse metalloenzymes that are involved in the production of highly reactive and unstable species, such as hydroxide anions, hydrides, radical species, and superoxide molecules are analyzed. The formation of such reaction intermediates is very difficult to occur under biological conditions and only a rationalized selection of a particular metal ion, coordinated to a very specific group of ligands, and immersed in specific proteins allows these reactions to proceed. Interestingly, different metal coordination spheres can be used to produce the same reactive and unstable species, although through a different chemistry. A selection of hand-picked examples of different metalloenzymes illustrating this diversity is provided and the participation of different metal ions in similar reactions (but involving different mechanism) is discussed.


Overproduction of the beta subunit of DNA polymerase III holoenzyme reduces UV mutagenesis in Escherichia coli.
Overproduction of the beta subunit of DNA polymerase III holoenzyme caused a 5- to 10-fold reduction of UV mutagenesis along with a slight increase in sensitivity to UV light in Escherichia coli. The same effects were observed in excision-deficient cells, excluding the possibility that they were mediated via changes in excision repair. In contrast, overproduction of the alpha subunit of the polymerase did not influence either UV mutagenesis or UV sensitivity. The presence of the mutagenesis proteins MucA and MucB expressed from a plasmid alleviated the effect of overproduced beta on UV mutagenesis. We have previously suggested that DNA polymerase III holoenzyme can exist in two forms: beta-rich form unable to bypass UV lesions and a beta-poor form capable of bypassing UV lesions (O. Shavitt and Z. Livneh, J. Biol. Chem. 264:11275-11281, 1989). The beta-poor form may be related to an SOS form of DNA polymerase III designed to perform translesion polymerization under SOS conditions and thereby generate mutations. On the basis of this model, we propose that the overproduced beta subunit affects the relative abundance of the regular replicative beta-rich polymerase and the SOS bypass-proficient polymerase by sequestering the polymerase molecules to the beta-rich form and blocking the SOS form.


Monetary favors and their influence on neural responses and revealed preference.
Favors from a sender to a receiver are known to bias decisions made by the recipient, especially when the decision relates to the sender, a feature of social exchange known as reciprocity. Using an art-viewing paradigm possessing no objectively correct answer for preferring one piece of art over another, we show that sponsorship of the experiment by a company endows the logo of the company with the capacity to bias revealed preference for art displayed next to the logo. Merely offering to sponsor the experiment similarly endowed the gesturing logo of the company with the capacity to bias revealed preferences. These effects do not depend upon the size of the displayed art or the proximity of the sponsoring logo to the piece of art. We used functional magnetic resonance imaging to show that such monetary favors do not modulate a special collection of brain responses but instead modulate responses in neural networks normally activated by a wide range of preference judgments. The results raise the important possibility that monetary favors bias judgments in domains seemingly unrelated to the favor but nevertheless act in an implicit way through neural networks that underlie normal, ongoing preference judgments.


Growth and Growth hormone - Insulin Like Growth Factor -I (GH-IGF-I) Axis in Chronic Anemias.
Anaemia is a global public health problem affecting both developing and developed countries with major consequences for human health as well as social and economic development. It occurs at all stages of the life cycle, but is more prevalent in pregnant women and young children. Iron deficiency anaemia (IDA) was considered to be among the most important contributing factors to the global burden of disease. Prolonged and/or chronic anemia has a negative effect on linear growth especially during the rapid phases (infancy and puberty). Additionally infants with chronic IDA have delayed cognitive, motor, and affective development that may be long-lasting. In view of the significant impact of chronic anemias on growth, pediatricians endocrinologists and hematologists should advocate primary prevention and screening for growth disturbance in these forms of anemias. The extent of the negative effect of different forms of chronic anemias on linear growth and its possible reversibilty is addressed in this review. The possible mechanisms that may impair growth in the different forms of anemias are addressed with special attention to their effect on the growth hormone (GH) - insulin like growth factor -I (IGF-I).


Non-Classical monocytes display inflammatory features: Validation in Sepsis and Systemic Lupus Erythematous.
Given the importance of monocytes in pathogenesis of infectious and other inflammatory disorders, delineating functional and phenotypic characterization of monocyte subsets has emerged as a critical requirement. Although human monocytes have been subdivided into three different populations based on surface expression of CD14 and CD16, published reports suffer from contradictions with respect to subset phenotypes and function. This has been attributed to discrepancies in reliable gating strategies for flow cytometric characterization and purification protocols contributing to significant changes in receptor expression. By using a combination of multicolour flow cytometry and a high-dimensional automated clustering algorithm to confirm robustness of gating strategy and analysis of ex-vivo activation of whole blood with LPS we demonstrate the following: a. 'Classical' monocytes are phagocytic with no inflammatory attributes, b. 'Non-classical' subtype display 'inflammatory' characteristics on activation and display properties for antigen presentation and c. 'Intermediate' subtype that constitutes a very small percentage in circulation (under physiological conditions) appear to be transitional monocytes that display both phagocytic and inflammatory function. Analysis of blood from patients with Sepsis, a pathogen driven acute inflammatory disease and Systemic Lupus Erythmatosus (SLE), a chronic inflammatory disorder validated the broad conclusions drawn in the study.


SNARE selectivity of the COPII coat.
The COPII coat buds transport vesicles from the endoplasmic reticulum that incorporate cargo and SNARE molecules. Here, we show that recognition of the ER-Golgi SNAREs Bet1, Sed5, and Sec22 occurs through three binding sites on the Sec23/24 subcomplex of yeast COPII. The A site binds to the YNNSNPF motif of Sed5. The B site binds to Lxx-L/M-E sequences present in both the Bet1 and Sed5 molecules, as well as to the DxE cargo-sorting signal. A third, spatially distinct site binds to Sec22. COPII selects the free v-SNARE form of Bet1 because the LxxLE sequence is sequestered in the four-helix bundle of the v-/t-SNARE complex. COPII favors Sed5 within the Sed5/Bos1/Sec22 t-SNARE complex because t-SNARE assembly removes autoinhibitory contacts to expose the YNNSNPF motif. The COPII coat seems to be a specific conductor of the fusogenic forms of these SNAREs, suggesting how vesicle fusion specificity may be programmed during budding.


Mice lacking Nf1 in osteochondroprogenitor cells display skeletal dysplasia similar to patients with neurofibromatosis type I.
Mutations in NF1 cause neurofibromatosis type I (NF1), a disorder characterized, among other clinical manifestations, by generalized and focal bony lesions. Dystrophic scoliosis and tibial pseudoarthrosis are the most severe skeletal manifestations for which treatment is not satisfactory, emphasizing the dearth of knowledge related to the biology of NF1 in bone cells. Using reporter mice, we report here that the mouse Col2α1-Cre promoter (collagen, type II, alpha 1) is active not only in chondrocytes but also in adult bone marrow osteoprogenitors giving rise to osteoblasts. Based on this finding, we crossed the Col2α1-Cre transgenic and Nf1(flox/flox) mice to determine whether loss of Nf1 in axial and appendicular osteochondroprogenitors recapitulates the skeletal abnormalities of NF1 patients. By microtomographic and X-rays studies, we show that Nf1(Col2)(-/-) mice display progressive scoliosis and kyphosis, tibial bowing and abnormalities in skull and anterior chest wall formation. These defects were accompanied by a low bone mass phenotype, high bone cortical porosity, osteoidosis, increased osteoclastogenesis and decreased osteoblast number, as quantified by histomorphometry and 3D-microtomography. Loss of Nf1 in osteochondroprogenitors also caused severe short stature and intervertebral disc defects. Blockade of the RAS/ERK activation characteristic of Nf1(-/-) osteoprogenitors by lovastatin during embryonic development could attenuate the increased cortical porosity observed in mutant pups. These data and the skeletal similarities between this mouse model and NF1 patients thus suggest that activation of the RAS/ERK pathway by Nf1 loss-of-function in osteochondroprogenitors is responsible for the vertebral and tibia lesions in NF1 patients, and that this molecular signature may represent a good therapeutic target.


Loss of Xist imprinting in diploid parthenogenetic preimplantation embryos.
We have analysed Xist expression patterns in parthenogenetic and control fertilised preimplantation embryos by using RNA FISH. In normal XX embryos, maternally derived Xist alleles are repressed throughout preimplantation development. Paternal alleles are expressed as early as the 2-cell stage. In parthenogenetic embryos, we observed Xist RNA expression and accumulation from the morula stage onwards, indicating loss of maternal imprinting. In the majority of cells, expression was from a single allele, indicating that X chromosome counting occurs to establish appropriate monoallelic Xist expression. We discuss these data in the context of models for regulation of imprinted and random X inactivation.


Expression, isolation, and purification of soluble and insoluble biotinylated proteins for nerve tissue regeneration.
Recombinant protein engineering has utilized Escherichia coli (E. coli) expression systems for nearly 4 decades, and today E. coli is still the most widely used host organism. The flexibility of the system allows for the addition of moieties such as a biotin tag (for streptavidin interactions) and larger functional proteins like green fluorescent protein or cherry red protein. Also, the integration of unnatural amino acids like metal ion chelators, uniquely reactive functional groups, spectroscopic probes, and molecules imparting post-translational modifications has enabled better manipulation of protein properties and functionalities. As a result this technique creates customizable fusion proteins that offer significant utility for various fields of research. More specifically, the biotinylatable protein sequence has been incorporated into many target proteins because of the high affinity interaction between biotin with avidin and streptavidin. This addition has aided in enhancing detection and purification of tagged proteins as well as opening the way for secondary applications such as cell sorting. Thus, biotin-labeled molecules show an increasing and widespread influence in bioindustrial and biomedical fields. For the purpose of our research we have engineered recombinant biotinylated fusion proteins containing nerve growth factor (NGF) and semaphorin3A (Sema3A) functional regions. We have reported previously how these biotinylated fusion proteins, along with other active protein sequences, can be tethered to biomaterials for tissue engineering and regenerative purposes. This protocol outlines the basics of engineering biotinylatable proteins at the milligram scale, utilizing a T7 lac inducible vector and E. coli expression hosts, starting from transformation to scale-up and purification.


Phosphorylation of Toxoplasma gondii Secreted Proteins during Acute and Chronic Stages of Infection.
The intracellular parasite Toxoplasma gondii resides within a membrane-bound parasitophorous vacuole (PV) and secretes an array of proteins to establish this replicative niche. It has been shown previously that Toxoplasma secretes kinases and that numerous proteins are phosphorylated after secretion. Here, we assess the role of the phosphorylation of strand-forming protein 1 (SFP1) and the related protein GRA29, two secreted proteins with unknown function. We show that both proteins form stranded structures in the PV that are independent of the previously described intravacuolar network or actin. SFP1 and GRA29 can each form these structures independently of other Toxoplasma secreted proteins, although GRA29 appears to regulate SFP1 strands. We show that an unstructured region at the C termini of SFP1 and GRA29 is required for the formation of strands and that mimicking the phosphorylation of this domain of SFP1 negatively regulates strand development. When tachyzoites convert to chronic-stage bradyzoites, both proteins show a dispersed localization throughout the cyst matrix. Many secreted proteins are reported to dynamically redistribute as the cyst forms, and secreted kinases are known to play a role in cyst formation. Using quantitative phosphoproteome and proteome analyses comparing tachyzoite and early bradyzoite stages, we reveal widespread differential phosphorylation of secreted proteins. While we found no direct evidence for phosphorylation playing a dominant role for SFP1/GRA29 redistribution in the cyst, these data support a model in which secreted kinases and phosphatases contribute to the regulation of secreted proteins during stage conversion.IMPORTANCEToxoplasma gondii is a common parasite that infects up to one-third of the human population. Initially, the parasite grows rapidly, infecting and destroying cells of the host, but subsequently switches to a slow-growing form and establishes chronic infection. In both stages, the parasite lives within a membrane-bound vacuole within the host cell, but in the chronic stage, a durable cyst wall is synthesized, which provides protection to the parasite during transmission to a new host. Toxoplasma secretes proteins into the vacuole to build its replicative niche, and previous studies identified many of these proteins as phosphorylated. We investigate two secreted proteins and show that a phosphorylated region plays an important role in their regulation in acute stages. We also observed widespread phosphorylation of secreted proteins when parasites convert from acute to chronic stages, providing new insight into how the cyst wall may be dynamically regulated.


Ultra-small dye-doped silica nanoparticles via modified sol-gel technique.
In modern biosensing and imaging, fluorescence-based methods constitute the most diffused approach to achieve optimal detection of analytes, both in solution and on the single-particle level. Despite the huge progresses made in recent decades in the development of plasmonic biosensors and label-free sensing techniques, fluorescent molecules remain the most commonly used contrast agents to date for commercial imaging and detection methods. However, they exhibit low stability, can be difficult to functionalise, and often result in a low signal-to-noise ratio. Thus, embedding fluorescent probes into robust and bio-compatible materials, such as silica nanoparticles, can substantially enhance the detection limit and dramatically increase the sensitivity. In this work, ultra-small fluorescent silica nanoparticles (NPs) for optical biosensing applications were doped with a fluorescent dye, using simple water-based sol-gel approaches based on the classical Stöber procedure. By systematically modulating reaction parameters, controllable size tuning of particle diameters as low as 10 nm was achieved. Particles morphology and optical response were evaluated showing a possible single-molecule behaviour, without employing microemulsion methods to achieve similar results. Graphical abstractWe report a simple, cheap, reliable protocol for the synthesis and systematic tuning of ultra-small (< 10 nm) dye-doped luminescent silica nanoparticles.


Diuretic induced long term hemodynamic changes in hypertension. A retrospective study in a MRFIT clinical center.
Retrospective analysis of hemodynamic factors was performed on hypertensive participants of our Multiple Risk Factor Intervention Trial (MRFIT) center to determine whether these may have a role in the higher mortality in a subgroup of special intervention (SI) participants with minor baseline electrocardiographic abnormalities. Stroke volume was estimated by a formula [SV = K(LVETxPP)x(1 + LVET/DP) where the K factor was determined using a separate group of individuals undergoing cardiac catheterization. The Pearson correlation between the two methods (dye dilution and above formula) was 0.7744 with a 95% confidence interval of 0.57-0.89 for the true correlation. In 222 SI and 186 usual care (UC) participants with no differences in stroke volume index (SVI) and cardiac output index (CI) at baseline, SVI and CI were systematically lower during the entire period of treatment in SI receiving higher average doses of thiazide diuretics. There was a moderate increase of SVI and CI in SI participants toward baseline after hydrochlorothiazide was replaced by other antihypertensive medication in the fourth year of the trial. We conclude that the lower SVI and CI could have been a contributing factor in the higher mortality in the SI group with ECG abnormalities resulting in decreased coronary flow reserve under stress conditions in these participants with probably pre-existing asymptomatic coronary artery disease.


Insights into centriole geometry revealed by cryotomography of doublet and triplet centrioles.
Centrioles are cylindrical assemblies comprised of 9 singlet, doublet, or triplet microtubules, essential for the formation of motile and sensory cilia. While the structure of the cilium is being defined at increasing resolution, centriolar structure remains poorly understood. Here, we used electron cryo-tomography to determine the structure of mammalian (triplet) and Drosophila (doublet) centrioles. Mammalian centrioles have two distinct domains: a 200 nm proximal core region connected by A-C linkers, and a distal domain where the C-tubule is incomplete and a pair of novel linkages stabilize the assembly producing a geometry more closely resembling the ciliary axoneme. Drosophila centrioles resemble the mammalian core, but with their doublet microtubules linked through the A tubules. The commonality of core-region length, and the abrupt transition in mammalian centrioles, suggests a conserved length-setting mechanism. The unexpected linker diversity suggests how unique centriolar architectures arise in different tissues and organisms.


A perspective on genomic-guided anthelmintic discovery and repurposing using Haemonchus contortus.
High-throughput molecular and computer technologies have become instrumental for systems biological explorations of parasites. Investigating the genomes and transcriptomes of different developmental stages of parasitic nematodes can provide insights into gene expression, regulation and function in the parasite, which is a significant step toward understanding their biology as well as host interactions and disease. This article covers aspects of a talk given at the MEEGID XII conference in Thailand in 2014. Here, we refer to recent studies of the genomes and transcriptomes of socioeconomically important parasitic nematodes of animals; provide an account of the barber's pole worm (Haemonchus contortus) and emerging drug resistance problems in this and related worms; we also propose a genomic-guided drug discovery and repurposing approach, involving the prediction of the druggable genome, prioritization of drug targets, screening of compound libraries against H. contortus and, briefly, a hit-to-lead optimization approach. We conclude by indicating prospects that molecular tool kits for nematodes provide to the scientific community for future comparative genomic, genetic, proteomic, metabolomic, evolutionary, biological, ecological and epidemiological investigations, and as a basis for biotechnological outcomes and translation.


Multiwave associations between depressive symptoms and endothelial function in adolescent and young adult females.
Depression has been linked to endothelial dysfunction, and some research suggests that past depressive episodes are associated with a lasting, negative impact on the endothelium. However, investigations in this area have been predominantly cross-sectional, raising questions about the direction of these associations. Using a multiwave design, we sought to extend previous research in this area by examining whether depressive symptoms have a lasting negative influence on endothelial function. A total of 135 adolescent and young adult females with no known or suspected major health problems were followed for 2½ years. Endothelial function was assessed at three time points throughout the study. The Beck Depression Inventory was administered, and information about health practices was collected every 6 months. Self-reported depressive symptoms covaried with endothelial functioning on a within-person basis (β = -0.23, p < .05). As a participant's depression symptoms rose beyond her typical level, her endothelial function declined commensurately. This association persisted after controlling for health practices and adiposity. There was no evidence that depressive symptoms predicted endothelial function at later time points or interacted with time to predict the trajectories of endothelial function over the follow-up period. Depressive symptoms were concurrently associated with endothelial function in this cohort of healthy adolescent girls and young women. On visits when participants endorsed depressive symptoms that were higher than their mean level of depression, they tended to have worse endothelial function. We did not observe a lasting negative effect of depression on endothelial function.


Biased Competition during Long-term Memory Formation.
A key task for the brain is to determine which pieces of information are worth storing in memory. To build a more complete representation of the environment, memory systems may prioritize new information that has not already been stored. Here, we propose a mechanism that supports this preferential encoding of new information, whereby prior experience attenuates neural activity for old information that is competing for processing. We evaluated this hypothesis with fMRI by presenting a series of novel stimuli concurrently with repeated stimuli at different spatial locations in Experiment 1 and from different visual categories (i.e., faces and scenes) in Experiment 2. Subsequent memory for the novel stimuli could be predicted from the reduction in activity in ventral temporal cortex for the accompanying repeated stimuli. This relationship was eliminated in control conditions where the competition during encoding came from another novel stimulus. These findings reveal how prior experience adaptively guides learning toward new aspects of the environment.


The effects of seagrass (Zostera japonica) canopy structure on associated fauna: a study using artificial seagrass units and sampling of natural beds.
The importance of seagrass canopy to associated fauna was assessed by comparing the species richness, abundance and diversity of the epi- and infaunal macroinvertebrate assemblages in a seagrass (Zostera japonica Ascherson and Graebner) bed and the adjacent unvegetated area in Hong Kong. Seagrass cover had significant effects on the composition and abundance of the associated fauna and the amount of detritus accumulated on the sediment surface. Detritus abundance was significantly higher in the seagrass bed, and was positively correlated with both the above- and belowground biomass of Z. japonica. Both the abundance and species richness of the epi- and infauna were significantly positively correlated with the belowground biomass of the seagrass and detritus standing crop. Macrofaunal species richness was higher (118) in the seagrass bed than the adjacent unvegetated areas (70), with a higher degree of similarity between the infauna than the epifauna of the two habitats. While all species recorded from the unvegetated areas were found in the seagrass bed, 48 species occurred only in the seagrass-covered areas. Species richness of epifauna was significantly higher in the seagrass bed, but there was no difference between infaunal species of the two habitats. On the contrary, faunal (epi- and infauna) abundance was significantly higher in seagrass areas. The seagrass bed also supported species of small tellinid bivalves previously not recorded from Hong Kong. Artificial seagrass units (ASUs, 0.2 m(2)) with four combinations of leaf density and leaf length and a control (bare sand) were placed at short distances from natural patches of Z. japonica. The composition, abundance and biomass of the epibenthos associated with the ASUs and the control were recorded after 3 months in the field. While species richness did not differ among the treatments, total abundance of epibenthos was significantly higher in the high density-long leaves (HL) treatment than in the control. Results of a discriminant analysis using log-transformed abundance data suggest that the gastropod Clithon oualaniensis, the mussel Musculista senhousia and the crab Thalamita sp. were important species distinguishing the assemblages in the various treatments. All the three species were significantly more abundant in the HL treatment than in the low density-short leaves (LS) treatment and the control. By contrast, there was no significant difference in the biomass of the epifauna, but discriminant analysis again separated the five treatments based on the composition of the biomass, with the same three species identified as the most important discriminating species. The species richness and abundance of the epifauna associated with the ASUs were similar to the adjacent unvegetated areas, but significantly lower than in the Zostera patches. The physical canopy structure of Z. japonica beds increased the abundance of the epibenthos, potentially through provision of canopy and indirectly through trapping of detritus.


Pyrethroid insecticide residues on vegetable crops.
Pyrethroid insecticides were applied on various vegetable crops as foliar treatments to determine dissipation rates. On Chinese broccoli (Guy Lon), Chinese mustard (Pak Choi) and Chinese cabbage (Kasumi, napa), fenvalerate was persistent with residues of 0.10, 0.14 and 0.11 mg kg-1, respectively, by day 21. Cypermethrin residues on head lettuce were below 0.1 mg kg-1 by day 10 but on the leafier romaine and endive varieties it was more persistent and required 14-19 days to dissipate below this concentration. After three applications, residues of cypermethrin in harvested carrots and of permethrin in eggplant were not detected on the day of application. On asparagus, deltamethrin and cypermethrin residues declined to less than 0.1 mg kg-1 by days 1 and 2, respectively; permethrin was more persistent, requiring more than 2 days to decline to less than 0.1 mg kg-1. Deltamethrin on dry (cooking) and Spanish onions was not detected on the day of application. On tomatoes, the concentration of permethrin was 0.093 mg kg-1 on the day of application and declined to about 0.05 mg kg-1 after 2-4 days. In general, permethrin, cypermethrin and deltamethrin residues declined to acceptable concentrations within an acceptable pre-harvest interval. Fenvalerate may be too persistent on these speciality crops unless a maximum residue limit > 0.1 mg kg-1 is permitted.


The ubiquitous nature of Listeria monocytogenes clones: a large-scale Multilocus Sequence Typing study.
Listeria monocytogenes is ubiquitously prevalent in natural environments and is transmitted via the food chain to animals and humans, in whom it can cause life-threatening diseases. We used Multilocus Sequence Typing (MLST) of ∼2000 isolates of L. monocytogenes to investigate whether specific associations existed between clonal complexes (CCs) and the environment versus diseased hosts. Most CCs (72%) were not specific for any single source, and many have been isolated from the environment, food products, animals as well as from humans. Our results confirm that the population structure of L. monocytogenes is largely clonal and consists of four lineages (I-IV), three of which contain multiple CCs. Most CCs have remained stable for decades, but one epidemic clone (CC101) was common in the mid-1950s and very rare until recently when it may have begun to re-emerge. The historical perspective used here indicates that the central sequence types of CCs were not ancestral founders but have rather simply increased in frequency over decades.


Repeated parallel evolution reveals limiting similarity in subterranean diving beetles.
The theory of limiting similarity predicts that co-occurring species must be sufficiently different to coexist. Although this idea is a staple of community ecology, convincing empirical evidence has been scarce. Here we examine 34 subterranean beetle communities in arid inland Australia that share the same habitat type but have evolved in complete isolation over the past 5 million years. Although these communities come from a range of phylogenetic origins, we find that they have almost invariably evolved to share a similar size structure. The relative positions of coexisting species on the body size axis were significantly more regular across communities than would be expected by chance, with a size ratio, on average, of 1.6 between coexisting species. By contrast, species' absolute body sizes varied substantially from one community to the next. This suggests that self-organized spacing according to limiting-similarity theory, as opposed to evolution toward preexisting fixed niches, shaped the communities. Using a model starting from random sets of founder species, we demonstrate that the patterns are indeed consistent with evolutionary self-organization. For less isolated habitats, the same model predicts the coexistence of multiple species in each regularly spaced functional group. Limiting similarity, therefore, may also be compatible with the coexistence of many redundant species.


A novel Hsp70 inhibitor prevents cell intoxication with the actin ADP-ribosylating Clostridium perfringens iota toxin.
Hsp70 family proteins are folding helper proteins involved in a wide variety of cellular pathways. Members of this family interact with key factors in signal transduction, transcription, cell-cycle control, and stress response. Here, we developed the first Hsp70 low molecular weight inhibitor specifically targeting the peptide binding site of human Hsp70. After demonstrating that the inhibitor modulates the Hsp70 function in the cell, we used the inhibitor to show for the first time that the stress-inducible chaperone Hsp70 functions as molecular component for entry of a bacterial protein toxin into mammalian cells. Pharmacological inhibition of Hsp70 protected cells from intoxication with the binary actin ADP-ribosylating iota toxin from Clostridium perfringens, the prototype of a family of enterotoxins from pathogenic Clostridia and inhibited translocation of its enzyme component across cell membranes into the cytosol. This finding offers a starting point for novel therapeutic strategies against certain bacterial toxins.


Full-screen magnification for windows using DirectX Overlays.
This paper presents the basic features of software-based magnifiers used by some visually impaired people to read information from a computer screen. The paper briefly presents two major approaches to full-screen magnification for modern multiple window systems (the paper focuses on Microsoft Windows). This paper describes in detail the architecture and operation of a full-screen magnifier that uses Microsoft DirectX Overlays. This approach leads to a robust magnifier that has a low computational overhead. The magnifier has problems with video cards that use a YUV color model but these problems may be addressed by RGB to YUV translation software--an issue that is still to be investigated. The magnifier also has problems when the generic device driver, rather than the manufacturer's device driver, is installed on the system. The paper presents two further strategies for full screen magnification, namely, using multimonitor support and true type fonts for text enlargement.


HIV-Associated Cognitive Impairment in Perinatally Infected Children: A Meta-analysis.
Research shows, conclusively, that perinatal HIV infection has negative effects on cognitive functioning of children and adolescents. However, the extent of these cognitive impairments is unknown. Current literature does not document specific cognitive domains most affected in HIV-infected children and adolescents. To systematically review and meta-analyze the degree of cognitive impairment, and the specific cognitive domains affected, in children and adolescents with perinatally acquired HIV infection. We systematically searched 5 electronic bibliographic databases, namely: PubMed, PsychINFO, Academic Search Premier, Scopus, and WorldCat, by using a search protocol specifically designed for this study. Studies were selected on the basis of set a priori eligibility criteria. Titles, abstracts, and full texts were assessed by 2 independent reviewers. Data from included studies were extracted into Microsoft Excel by 2 independent reviewers. Twenty-two studies were identified for inclusion in the systematic review and of this, 6 studies were included in the meta-analysis. Results from the meta-analysis indicated that working memory and executive function were the domains most affected by the HIV virus. Only 27% of the included studies were suitable to enter into the meta-analysis. There was significant geographic bias in published studies, with only 32% (7/22) of included studies from sub-Saharan Africa. The evidence supports an association between HIV infection in children and adolescents and cognitive impairment in the domains of working memory, executive function and processing speed, with effect size estimates also providing some support for deficits in visual memory and visual-spatial ability.


Relationships of wild and domesticated rices (Oryza AA genome species) based upon whole chloroplast genome sequences.
Rice is the most important crop in the world, acting as the staple food for over half of the world's population. The evolutionary relationships of cultivated rice and its wild relatives have remained contentious and inconclusive. Here we report on the use of whole chloroplast sequences to elucidate the evolutionary and phylogenetic relationships in the AA genome Oryza species, representing the primary gene pool of rice. This is the first study that has produced a well resolved and strongly supported phylogeny of the AA genome species. The pan tropical distribution of these rice relatives was found to be explained by long distance dispersal within the last million years. The analysis resulted in a clustering pattern that showed strong geographical differentiation. The species were defined in two primary clades with a South American/African clade with two species, O glumaepatula and O longistaminata, distinguished from all other species. The largest clade was comprised of an Australian clade including newly identified taxa and the African and Asian clades. This refined knowledge of the relationships between cultivated rice and the related wild species provides a strong foundation for more targeted use of wild genetic resources in rice improvement and efforts to ensure their conservation.