How do you express and detect GLP-1 receptors?

The question is slightly unclear since it fails to clarify whether the GPL-1 receptor is endogenous or is over-expressed. Also does the GLP-1 belong the same species that Min-6 originates from or it belongs to a different species? Those are important points since if the receptor is endogenous then the main problem is sensitivity of the detection method, which can be difficult sometimes to detect an endogenous protein relative to an over-expressed one. Also if the GPL-1 belongs to a different species, which you are trying to over express in Min-6 it might not work since the cellular machinery might not support its production (tho unlikely) or its transport to the cell surface, which I have had this problem before. It could be that for the particular expression levels you have in those cells, if the GLP-1 is over expressed or if its non-endogenous, it causes toxicity and kills the cells that are expressing it hence why you do not see any GLP-1 expression (e.g due to excessive receptor activation). Also could you clarify what you mean by "analogue for glp-1"? does this mean it is not exactly GPL-1 or its a homologue or orthologue, which you are trying to detect using a GLP-1 specific antibody? that might again be a problem if the GLP-1 Ab you are using detects a region of the receptor, which is not conserved in its homologues.

In terms of solutions as pointed in the comments, the best way to go about this is to use a polyclonal Ab, which is raised against a large section of the peptide in question, allowing you a better chance of its detection. If that did not work, you might have to resort to GLP-1 mRNA detection using RT-PCR or qPCR, which you would need to design primers for based on you GPL-1 sequence which you can get help with here.


How large is the variability in human bone thickness, and is "big boned" a real thing or not?

Since the argument with my girlfriend was finished days after this was posted(sadly we were waiting for this but it took so long, we posted this question to have an answer right away) I'll just post here what I conclude about the "big-boned theory" based on searching through internet.

Let me site this link; that says,
"However, the initial findings of this study show that having big bones does not make you fat, being fat gives you big bones". What the link says, having more fats forced our body to increase the size of our bones for it to endure the stress brought by having heavier weight. Which means big-boned really do exists. (Damn lost the argument with my girlfriend because of this link)

Another site that says, "If your scale weight indicates that you’re overweight, it’s most likely because you’re carrying too much body fat.   Not because you’ve got 'big bones'". This site says that we cannot use the "big-bone theory" to reason out being fat. In the article, The heavier weight was caused mostly by fats and not by bones. Also the article says that tall person having 6'2 height will have of course bigger bones that a person with height of 4'2. Also the article says that "Still others definitely seem to have a larger “frame” as evidenced by a larger circumference of the wrist and ankles.  [NOTE:  The wrist and ankle joints typically do not have much fat or muscle, it’s mostly skin and bone.  So a person with a larger wrist would most likely have a larger bone circumference.]" (My girlfriend's face would be so happy to read this)

The last site that I would like to post here have chart to know if you're big-boned or not. The site also agrees that there is big boned

TL;DR

I lost, "Big-boned theory" is real but having heavier weight not mean your big-boned.

P.S. : Also instead of saying "ohh, you're not fat, you're just 'BIG BONED'" to someone just to make their feelings well, you're not doing it right! Just tell them the truth and tell them to do more exercise and have healthy lifestyle. :)


Why don't birds in flocks fly into each other?

Richard Dawkins discusses this in his book The Greatest Show on Earth: The Evidence for Evolution.

The birds, in the aforementioned example Starlings, 'know' which direction to fly and where to be by obeying simple local rules concerning the distance and spacing of other members of the flock in their immediate vicinity, without any global knowledge of the size or shape of the flock in its entirety.

The key to this behavior is that there is no choreographer and no leader.  Order, organization and structure all emerge as by-products of rules obeyed locally, many times over.

Dawkins equates this to 'bottom-up' design or 'self-assembly'.  This is also how embryology works.  Beautifully 'designed' bodies emerge as a result of single cells obeying local rules.  The idea of a blueprint is a misconception.

Dawkins mentions a man in the book named Craig Reynolds who wrote a program in 1986 called 'Boids' which models the flocking behavior of thousands of birds - http://en.wikipedia.org/wiki/Boids


Does current evidence support the use of resveratrol as an anti-ageing drug?

It's worth noting that earlier this month a large body of resveratrol research was retracted:

  The University of Connecticut, in what clearly seems like an attempt to get ahead of damaging news, has announced an “extensive”
  investigation into research misconduct involving one of its
  scientists, Dipak K. Das.

  According to a press release, the university has notified 11 journals
  that published Das’ work about the alleged fraud. One area of interest
  for Das, a government-funded professor of surgery and director of the
  Cardiovascular Research Center, has been resveratrol, a substance in
  red wine that has allegedly been linked to improved cardiac health.

Retraction Watch's coverage has been pretty thorough and includes comments and citations:

UConn resveratrol researcher Dipak Das fingered in sweeping
misconduct case
So how peripheral was Dipak Das’ resveratrol
work, really?
Resveratrol fraud case update: Dipak Das loses
editor’s chair, lawyer issues statement refuting all charges


Cellular Respiration in Boiling Conditions

Extending on @ANONGOODNURSE, @SAPPHIRA and @JAMES.

Something you should know about proteins, they have primary, secondary, tertiary and quaternary structures all due to specific folding of the proteins. These foldings are mainly connected via hydrogen bonds to each other along with other bonds (Alberts et al., 2002). On the action of heat, the molecules composing the bonds are vibrated due to higher kinetic energy resulting in the breaking of the bonds which causes unfolding of proteins (Wikipedia denaturation of proteins). This phenomenon is called Denaturation of Proteins which causes the loss of protein function due to loss of shape.

Read this QandA in Reference.com for more information about denaturation of proteins.

Read this for more information about proteins: Molecular Biology of the Cell. 4th edition.

Link this idea to cellular respiration and how Electron Transport Chain and the Krebs Cycle (Citric acid cycle) involve proteins for the completion of the respective processes.


How can I estimate the CO₂ uptake of a plant?

Can I calculate the estimate through a simple measurement (e.g. of plant weight) or does it require tight lab experiments? In the former case, how is that measurement made?

In the textbook Plant Physiological Ecology*, they state that about 40% of the dry weight of plants is carbon, and I believe the vast majority of that is from CO2 from the atmosphere. You can take a fresh weight of an entire plant, and then dry it at the lowest temperature in your kitchen oven for a couple of days to get a reasonably accurate dry weight. That dry weight times 0.4 will give you an estimated total carbon, though I have seen other factors used. Plants can also be analyzed for Total Organic Carbon in some agricultural laboratories. Fast growing plants are going to absorb more carbon than slow growing ones.

* Lambers, H, Thijs L. Pons, and F S. Chapin. Plant physiological ecology. New York: Springer Verlag, 2008. Print. ISBN:978-0-387-78341-3


Majority of transcripts are from sense strand?

From my understanding sense and anti sense is contextual. If you are looking at a gene from 5'->3'(which is convention) that strand is the sense strand and the complement to the gene is the anti sense strand.

However further along the DNA there could be a gene on the 'original' anti sense strand, if you are discussing this new gene, there is a new context and it is now on the sense strand (oriented 5'->3'), and it's complement on the anti sense strand.

I hope that's clear.


What is the signal conversion from hair cells to cochlear nerve cells?

Short answer
Sound level is coded in spike rate, frequency is coded by a place-frequency map.

Background
Spiral ganglion cells (SGCs, the secondary sensory neurons making up the auditory nerve) are continuously firing cells in a healthy ear (they fall silent when the hair cells degenerate, leading to deafness). In fact, their base frequency in silence is pretty high. The only thing the hair cell input does is lowering, or elevating the threshold and hence affecting firing rate. During a sine wave stimulus (a pure tone), the stereocilia of the hair cells deflect in one phase, and inflect on the other. One phase hence depolarizes the SGC, the other hyperpolarizes it. This generates a near-perfect representation of the sine wave input at low frequencies. At high frequencies the SGCs may skip a phase or two, but because multiple SGCs are involved, the population code is still stochastically spot on.

Sound level is coded in spike rate, frequency is coded by a place-frequency map (Müller, 1996). The base of the cochlea codes high frequencies, the apex low frequencies. Hence, loudness is coded by every SGC, while frequency determines which SGC is activated. An informative overview of hair cell signalling is provided in Fig. 1.

Fig. 1. Hair cell transduction. source: Pasadena City College

References
- Kandel et al., Principles of Neural Science, 4th ed.
- Müller, Hear Res (1996), 94(1-2): 148-56


Interpretation of faint band for Linear Array HPV Genotyping Test

I received this answer privately and was given permission (in fact asked) to share it without attribution.

The package insert for the Linear Array assay defines any visible band as a positive band, so a faint band counts as a positive.
The difference in band intensity could be related to viral type abundance but really depends on which bands are being compared.  Because this is an end-point assay, it's possible that some virus types amplify with better efficiency than others when found in a mixed infection and it is also likely that overall sensitivity or detection limits may be different for each type.  Additionally the probe for HPV52 is cross-reactive with types 33, 35, 58 and in the presence of any of those additional types, it may increase its intensity.

The driver of the disease process is the virus with the most oncogenic potential (but I assume that is only when we are talking about cancer or dysplasia, perhaps not when referring to recurrent respiratory papillomatosis or genital warts), which does not change in the presence or absence of other viruses (and regardless of the band intensity).  Additionally, it's important to remember that the resulting disease is clonally derived, originating with a single-type infection (ie. each lesion will be linked to only one HPV type).  When multiple viral types are found within an exfoliated sample it signifies multiple different infection sites (and not multiple virus types within single cells).  Not all of these will progress to high-grade disease, but rather, the lesions caused by genotypes with the highest associated risk are the most likely.


Can you tell if a corpse was male or female by only examining its skull?

According to textbook of forensic medicine and toxicology by Ks Narayan reddy:

Qualitative differences are:

Male mandible has everted ramus, but female have inverted ramus.
Males have chin U shaped, but it's rounded in females

Quantitative differences:

Suparaorbital ridges are prominent in males but often absent in females.
Mastoid process is wider, longer and blunt in males but is narrow and pointed in females.

And there are many more differences, see the pics below:


Why do plants have pith and how is it useful to them?

The pith (medulla) forms part of the ground tissue system of a plant, and specifically it is the ground tissue which lies interior to a plants vascular tissues (xylem, phloem etc.)

The ground tissue system is responsible for much of a plants metabolic functioning, and contains various specialized cell types which aid in photosynthesis and storage of photosynthesis products. The pith is made from parenchyma cells.


How can promoter binding sites be determined?

I don't have a definitive answer, but I can perhaps offer some insight. Given the necessary function of rpoA, I would be willing to bet that SigA is the factor responsible for its transcription, so I will focus my discussion there.

Predicting promoters without experimentation can be very challenging given their immense variability. The idealized core promoter consists of a -10 region, a spacer and a -35 region. Recognition of the promoter by a sigma factor is done at the -10 and -35 regions: each sigma factor recognizes a different consensus sequence. Bacillus subtilis SigA recognizes the consensus sequences TTGACA (-35) and TATAAT (-10). They key word there is consensus however, as it is rare that a promoter will actually contain these exact sequences. In reality, 3/6 nucleotides matching could be considered reasonable. Between the -10 and -35 regions is a spacer with conserved length. In the absence of transcription activators, SigA requires a 17 +/- 1 nucleotide spacer. This is due to thermodynamic constraints. Very briefly, promoter melting (at -10) is dependent the angle between the -10 and -35 regions. Given the helical nature of DNA, this angle is in turn dependent on the distance between the -10 and -35 regions. If the angle is just right, the untwisting of the DNA to align the promoter elements and thus allow sigma binding provides the energy to melt the promoter. If the angle is too large, the regions can never align. If the angle is to small, alignment will not provide enough energy for melting. Complicating this are non-standard core promoters and various flanking sequences that all play a role in transcription initiation. As a direct answer to one of your question, a single sigma factor can bind to many different DNA sequences with some conserved regions.

Fortunately, the B. subtilis genome has been sequenced. Your search for the promoter might involve looking for the -10 and -35 regions 5' to the rpoA gene. This however doesn't take into account that rpoA might be part of a polycistronic operon and thus under the control of a promoter further upstream. Suh et al. (1986) did basically this and reported:

  Our DNA sequence analysis suggests further experiments to study regulation within the rpoA region. Because inhibition of polycistronic message translation by free protein S4 is one of the chief controls of alpha operon expression in E. coli (16, 23), the apparent absence of S4 from the B. subtilis alpha region suggests different regulation. Although the close coupling of the rpsM and rpsK genes in our sequence (Fig. 3) supports the notion of a translational coupling similar to E. coli, the putative rpoA promoters in the relatively large intercistronic distance following rpsK are also different (28, 29). However, the apparent absence of a rho-independent terminator in this region could indicate that significant transcription occurs from additional upstream promoters in B. subtilis as well as in E. coli (28).

Albeit this is an old paper, but I was unable to find more recent studies in my quick research. Basically they compared the B. subtilis rpoA gene to that of Escherichia coli, where it is located in an operon with ribosomal proteins rpsM, rpsK, rpsD and rplQ (under the control of a single promoter). They found both similarities and differences. They were able to find two possible SigA core promoters in the region between rpoA and rpsK (the next gene 5' to rpoA in B subtilis). There was also a relatively large distance between the two genes, suggesting that they are not part of the same operon. Furthermore, they were able to find a ribosome binding site (Shine-Dalgarno sequence) between the hypothetical promoters and the translation start site. On the other hand there is no transcription terminator between rpsK and rpoA which suggested that a promoter further upstream regulated rpoA expression. After their sequence analysis, they suggested that further experimentation was required.

In conclusion, it's hard to find promoters just by looking at the sequence. Even if you do find a possible promoter, it's impossible to say whether or not it is utilized without experimentation. That said, given that the alpha subunit is necessary for cell function, that the rpoA gene appears to be transcriptionally tied to ribosomal proteins (which are also necessary for cell function) and that SigA is the predominant factor in log phase B. subtilis, I feel that it is very likely that SigA is ultimately the factor responsible for rpoA expression

I also thought I'd mention that there are various online bioinformatics tools that attempt to predict promoters, but I will not comment more on them because I have not used them.


How much does sprayed water remove bacteria?

Though conditions are not exactly the same (the water is not sprayed, the duration of water exposition is different, and samples are not Petri dishes ; I am not competent enough in biology to compare methodologies), I found two relevant papers.

Listeria innocua/monocytogenes, pure rinsing

The first paper used Listeria innocua "as a surrogate for L. monocytogenes", while the EMSL report linked in the question tested the latter.

They found the following bacterial log-reduction after rinsing for 15 s under running cold tap water at room temperature and without prior soaking :

on brocoli and lettuce : 1.41 (96.11 %) ;
on apples : 2.01 (99.02 %) ;
on tomatoes : 2.10 (99.21 %).

To be compared to the report from the EMSL which found, after spraying modified water for 10 s on an inoculated Petri dish (which surface is obviously smoother than that of a tomato) :

at 20 °C : 4.24 (99.994 %) ;
at 25 °C : 3.01 (99.903 %) ;
at 30 °C : 3.37 (99.957 %).

Note that although not mentioned, uncertainties on the EMSL numbers must be fairly large since the quantitative counts are below the detection level of the apparatus (but would actually make the numbers conservative…).

Link to the paper : Efficacy of Home Washing Methods in Controlling Surface
Microbial Contamination on Fresh Produce (open access PDF), Agnes Kilonzo-Nthenge, Fur-Chi Chen, Sandria Godwin, Journal of Food Protection, 69, 2, 2006.

(NB : it contains further testing which are out of scope for this question but may be of interest, e.g. soaking, rubbing or wiping with paper towel.)

Escherichia coli O157:H7, rinsing while thoroughly rubbing

The second paper tested Escherichia coli 0157:H7, which has also been tested by the EMSL.

The paper reports the following log-reduction after thoroughly rubbing during 15 s under running tap water (no indication of temperature, but flow of 2.0 L/min ; the values in the abstract seem wrong for tomatoes, here are the in-paper values) :

lettuce leaves (not rubbed ?) : 1.16 (93.08 %) ;
cabbage leaves (not rubbed ?) : 2.02 (99.05 %) ;
lemons : 4.10 (99.99 %) ;
tomatoes : 5.78 (99.9998 %).

Note that the same reduction is reached for tomatoes after only 8 s of washing.

To be compared to the EMSL results (sprayed "modified" water, 10 s rinsing, no rubbing, Petri dish) :

at 20 °C : 5.67 (99.9998 %) ;
at 25 °C : 5.14 (99.9993 %) ;
at 30 °C : 4.88 (99.998 %).

(Same comment about uncertainties applies.)

Interestingly, in this study they also tested the effects of alkaline electrolyzed water, which may not be too far from "ionized water" (I have yet to dig into details), which itself may not be too far from what is supposed to exit the device tested by the EMSL.  And… they found no significant difference with regard to plain tap water.  (Though they did find significant effects with acidic electrolyzed water and by applying both successively — but that's out of the scope of this question.)

Link to the paper : Reduction of Escherichia coli O157:H7 on Produce by Use of Electrolyzed Water under Simulated Food Service Operation Conditions (open access PDF), Pangloli et al, Journal of Food Protection, 72, 9, 2009.


In what ways have plants and animals evolved to support each other throughout history?

There are probably a few cases of this and exactly how animals and plants co-evolve probably differs between different scenarios. One 'famous' example I like is between ants and acacia plants. The acacia plant has evolved to produce food for a particular species of ant and in return the ants protect it from the grazing of herbivores.

Explained better here: http://bioblog.biotunes.org/bioblog/2007/10/02/cool-bug-9-acacia-ants/


Is it possible to purify antigens from a vaccine and to separate them from the adjuvant?

The major component of a vaccine is the adjuvant, and according to Wikipedia the most commonly used adjuvants in human vaccines are aluminium salts.

Here for example is the composition of Recombivax HB, a hepatitis B vaccine produced by Merck Frosst and used in Canada (source of information is a Canadian website)

  RECOMBIVAX HB ® [hepatitis B vaccine (recombinant)] is a non-infectious subunit viral vaccine consisting of surface antigen (HBsAg or Australia antigen) of hepatitis B virus produced in yeast cells. A portion of the hepatitis B virus gene, coding for HBsAg, is cloned into yeast and the vaccine for hepatitis B is produced from cultures of this recombinant yeast strain according to methods developed in the Merck Research Laboratories.
  Two formulations are available:
   •  10 µg/1.0 mL formulation: each 1.0 mL dose contains 10 µg of hepatitis B surface antigen adsorbed onto approximately 0.5 mg of amorphous aluminum hydroxyphosphate;
   •  40 µg/1.0 mL formulation: each 1.0 mL dose contains 40 µg of hepatitis B surface antigen adsorbed onto approximately 0.5 mg of amorphous aluminum hydroxyphosphate;
  Thimerosal (mercury derivative) 1:20,000 (50 µg/mL) has been added only to the preservative-containing formulations. All preparations have been treated with formaldehyde prior to adsorption onto amorphous aluminum hydroxyphosphate. The vaccine is of the adw subtype.

As explained in   Exley, C. et al. (2010) The immunobiology of aluminium adjuvants: how do they really work? Trends in Immunology, 31:103-109:

  The vaccine preparation is primarily micrometer-sized clusters of nano-sized primary particles of the aluminium salt with which the antigen is associated by adsorption and entrapment. The avidity with which the adjuvant associates with the antigen will depend upon multiple factors, including the form of aluminium salt (usually oxyhydroxide or hydroxyphosphate), the physico-chemical properties of the antigen (including its overall charge and molecular weight), the mode of preparation of the antigen-adjuvant complex (for example, ratio of adjuvant to antigen), and the final solution pH. The latter will usually be around neutral (pH 7.0 +/-0.5), and, along with the highly super-saturated state of the aluminium salt, this will ensure that the concentration of soluble aluminium in the vaccine preparation remains below ca 2 mM. Similarly, there will be a variable proportion of antigen, often <1% of the total antigen load, that is not associated directly with the adjuvant, and some of this ‘free’ antigen may also be in a complex with aluminium., what this means is that the protein antigen is not soluble in the vaccine, but rather is adsorbed and/or entrapped in the inorganic particulate material.

What this means is that the protein antigen is not soluble in the vaccine, but rather is adsorbed and/or entrapped in the inorganic particulate material. The antigen itself has of course already been extensively purified before being incorporated into the vaccine, so the task of purifying the antigen from the Recombivax vaccine is one of releasing it from the inorganic adjuvant. The obvious thing to try first would be to isolate the particulate material by centrifugation, and then attempt to release the antigen from this in a soluble form: things to try would be extremes of pH, high salt concentrations, and detergents. SDS-PAGE would be used to monitor how much was released by these treatments.

Now the example that I gave above (Recombivax HB) is fairly straightforward because it contains a single protein antigen. Compare this to Pentacel, given as first vaccination to babies in Canada (same source as before).

  Act-HIB ® Reconstituted with QUADRACEL ®Haemophilus b Conjugate Vaccine (Tetanus Protein – Conjugate) Reconstituted with Component Pertussis Vaccine and Diphtheria and Tetanus Toxoids Adsorbed Combined with Inactivated Poliomyelitis Vaccine.
  Each single dose (approximately 0.5 mL) after reconstitution contains:
   •  purified polyribose ribitol phosphate capsular polysaccharide (PRP) of Haemophilus influenzae type b covalently bound to 20 µg of tetanus protein 10 µg
   •  pertussis toxoid (PT) 20 µg
   •  filamentous haemaglutinin (FHA) 20 µg
   •  fimbrial agglutinogens 2 + 3 (FIM) 5 µg
   •  pertactin (PRN) 3 µg
   •  diphtheria toxoid 15 Lf
   •  tetanus toxoid 5 Lf
   •  poliovirus type 1 (Mahoney) 40 D-antigen units
   •  poliovirus type 2 (MEF1) 8 D-antigen units
   •  poliovirus type 3 (Saukett) 32 D-antigen units
   •  aluminum phosphate 1.5 mg
   •  2-phenoxyethanol (not as a preservative) 0.6% v/v
   •  polysorbate 80 10 ppm (by calculation)
   •  bovine serum ≤50 ng
   •  trace amounts of formaldehyde
   •  trace amounts of polymyxin B and neomycin may be present from the cell growth medium

This vaccine is clearly much more complex, so in this case, once the desired antigen(s) were freed from the adjuvant there would be a need to use standard protein purification techniques to separate the various contaminants.

Finally it's worth pointing out that unless you have access to large amounts of vaccine, you are going to be starting with quite small amounts of antigen (see above) so it will probably be quite a challenging purification.


Why do animals only eat some parts of their food?

It all depends on hunger. As in comment (@Remi.b), it has been mentioned, an animal won't throw if they are starving.

  For example monkeys/apes only eat part of a fruit and then throw the rest.

Monkeys and apes can differentiate between good and bad part of the fruits. So, they eat what they can and if the color looks different (or however they differentiate them) they will throw the rest of them.

  Cats (big and small species) only eat some parts of their prey and then they abandon it.

Cats in general are very picky eaters. They actually have a very short digestive tract, so, they need something easy to breakdown into energy rather than complex processes of digestion. Their main food consist of meat, they leave the inner organs as such.

Source:

http://en.wikibooks.org/wiki/Wikijunior:Big_Cats/Complete_Edition
http://bigcatrescue.org/feed-cats/

Image Source:

http://wordpress.as.edu.au/rspiers/2013/05/22/comparing-animals-digestive-systems/
http://cats56971.wordpress.com/2012/10/30/eating-habits-of-a-african-lion/


How many species can have the same scientific name?

The scientific name (better known as latin name or binomial name) of a species is unique to this species. No two species can have the same latin name. Also, a single species cannot have two different latin names. But of course, mistakes happen and we don't seem to bother too much about them (esp. when the two species are very unrelated; see What instances are there in which two species share the same binomial name? (thanks @fileunderwater and @HRA).

Of course, the above is true as long as there is agreement in the limits of the definition of a species. In absence of such general agreement, there can be some issues. Consider for example, Homo neanderthalis who is often called Homo sapiens neanderthalis. See the post How could humans have interbred with Neanderthals if we're a different species? for more information about the definition and delimitations of species.

Have a look at wikipedia > Binomial nomenclature for more information.


Book request: biology of sensation and perception

This is a very broad range of topics. I doubt you'll be able to find a single reference on all of it. I'm providing below some references with a focus on more introductory approaches.

  The mechanisms underlying our “five senses,” i.e. the eye, inner ear, tongue, nose, and nervous system, and how (chemically/physically) they are triggered

Bear, Connors & Paradiso "Neuroscience: Exploring the Brain" is pretty extensive. It covers chemical senses, vision, audition, the vestibular system and touch. It is not cheap, but that's the only reference that will cover most of the topics you are interested in. However it focuses mostly on the physiology of the senses, and not really about perception

Otherwise I'm afraid you'll immediately have to read specialized books such as Palmer's "Vision Science", Moore's "introduction to the psychology of hearing", Goldberg et al. "The vestibular system". Those are fairly readable introductory books. I don't know much about chemical senses.

  How our brain makes inferences from the raw sensory data we receive, e.g. using our depth perception to infer distance from a two-dimensional projection onto each of our eyes

For the topic of inference specifically a classical reference is Richard Gregory's "Eye and Brain: The Psychology of Seeing". It is dated (60s) but still very relevant. This is somewhat contradictory with your first point because inference is a behavior while you asked for more physiological references. Stereopsis specifically is a classical field of vision science so any descent book will cover it.

  Comparison with other species of animals

I cannot recommend enough Sarah Shettleworth's "Cognition, evolution, and behavior". Though focusing only on behavior, it is a very extensive and interesting book.

  Experimental results relating to the three points above

Any good book would include data and plots from classical experiments.

  An evolutionary perspective hypothesizing about why these sense-detecting organs were important for human survival

Again, Shettelworth's book.


What is the state-of-the-art algorithm for multiple sequence alignment?

My Vote goes to Mafft(insi) as it have ~86% accuracy and results in ~1.2 hour. Though fastest will be kalign takes only ~3 minutes to finish with an accuracy of 74.3%.

For testing:

  For each of the 218 reference alignments in the benchmark, we applied
  eight alignment programs, resulting in a total of 1744 automatically
  constructed MSAs. The overall quality of these automatic alignments
  was measured using the Column Score (CS) described in Methods.

FIGURE 1: Overall alignment performance for each of the MSA programs tested.

(A) Overall Accuracy

(B) Total run time for constructing all alignments (a log10 scale is used for display purposes).

doi:10.1371/journal.pone.0018093.g003

Compared Tools

http://www.plosone.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pone.0018093.t001&representation=PNG_L

Source and Photo Credits:

A Comprehensive Benchmark Study of Multiple Sequence Alignment Methods: Current Challenges and Future Perspectives

PS: This is from an old paper of 2011. If you want the new statistics you can always test on your own, by the process described in the source paper.


Can a portion of human skin cells be modified in some way to generate light?

Genetic modification of any cell to overexpress a fluorescent protein will not 'generate' light, per-say: fluorophores absorb particular wavelengths and re-emit in less energetic wavelengths, dispersing some energy as heat. (Perhaps there is some semantic choice here, but there is no transduction to light from another form of energy.)

Bio-luminescence, on the other hand, can be considered generation of light. There are proteins commonly found in marine animals (which skin cells could be engineered to express) which convert chemical energy to emit light.

With regards to generation of electricity, I think this gets a bit interesting...

The electron transport chain (ETC) in the inner membranes of our mitochondria carry out a series of redox reactions which serve to oxidise food metabolites (thus freeing electrons). In order to maintain the free energy gradient that favours this directional cascade of reactions, electrons and protons are finally accepted by a continual supply of oxygen atoms, producing water. (You may be aware that aerobic respiration consumes oxygen and produces water.) In nature (in aerobes), oxygen acts as the final electron acceptor, or an electron sink.

Bacteria also have electron transport chains for their respiration (mitochondria were once bacteria, after all), and people have wondered whether these redox reactions could be used to produce a current instead of reducing oxygen to water as the final step. We normally use current in the form of electrons moving along a metal wire.

This is the idea of a "microbial fuel cell". Just like a battery produces a current from a chemical redox reaction, the ETC might be recruited in to producing a current from its chemical redox reactions.

I think this is a very difficult piece of bioengineering, since the ETC is integrated in to respiration and needs to be de- & re-coupled to some kind of inorganic mediator and ultimately a circuit; and also because the ETC produces very low voltages, I think.

There is a nice wikipedia page on microbial fuel cells that you might find interesting, if you think this is relevant to your question.


Gene located on Which strand? Want reference.

Assume that you are given the gene in the "forward direction"; the one where the starting ATG is on the left, that the sequence you are looking at is what the single stranded RNA will be.


How and where do nerves share pathways to the brain?

The first layer of sensory integration from neural interconnection lies in the spinal dorsal horns (for somatosensory stimuli), and the spinal anterolateral system (for painful stimuli). It resembles option #2 much more than option #1.

Addenda: Since you are asking a lot about neuroanatomy and neurophysiology, I suggest those 2 beginner books:

Neuroanatomy Text and Atlas, John Martin
Neuroscience, Dale Purves


Possibility of orthogonal view for a creature?

Many creatures have eyes on the sides of their head where they cannot have both eyes simultaneously look at the same target. For example whales. Chameleons are well known for having independently moving eyes (though they can align them for binocular vision)

Since all the significant processing of vision occurs in the brain's occipital lobes there is no problem with optics.


Short answer
The total number of photoreceptors ('pixels') in the human retina is 63 million. Approximately 3 million of them transmit focused, color-coded information.

Background
In essence, each photoreceptor on the retina acts as a photosensitive sensor. We have rods and cones in our retinae. Rods confer gray scale vision, while cones are responsible for color vision.

The raw average tally of rods in the human retina is 60 million, and cones count a little over 3 million (Jonas et al, 1992). Hence, we could conclude we have 63 megapixels per eye available.

However, this does not mean that 63 million pixels are sent off to the brain. Instead, just as with a JPG image, it's instantly reduced in size even before the information leaves the retina.

Most importantly, rods are specialized for scotopic (night) vision and 10 to 30 rods connect to a single bipolar cell (Kolb, 2011). Hence, this feat only reduces the number of 'rod pixels' to about 3 million. Cones generally synapse onto a single bipolar. Hence, 6 megapixels leave the retina approximately.

The retinal image is generally focused onto the fovea, which is the central 18o of the total ~160o that is covered by a retina (Fig. 1). The remainder of the retina may receive a blurred image projection.

Fig. 1. Image focussing through accommodation on the retina. Source: Health Problem and Solutions

The fovea is densely packed with cones and contains nearly all of them (fig. 2).

Fig. 2. Distribution of rods and cones in human. Source: (Kolb, 2011)

Hence, the focused part of the image may be encoded by as little as 3 million cones. Since rods don't provide color information, it can be concluded that focused, color-coded information is conveyed by 3 million photoreceptors per retina.

Ultimately, however, it is important to note that the brain fills in missing gaps. For example, the optic disc, i.e. the point where the optic nerve leaves the eye, measures about 1.5 mm in diameter (Kolb, 2011). Given that the total diameter of the retina is about 30-40 mm this is quite a big blind spot. The brain simply fills in that gap by estimating what supposed to be there. In fact, many people with degenerative diseases of the retina don't even notice their deficits until they start bumping into objects that they did not notice. However, they do not see black holes, but instead their brain has been filling in the gaps with the information available in the remaining image, just like it does with the optic disc in normally-seeing people.

References
- Jonas et al, Graefes Arch Clin Exp Ophthalmol (1992); 230(6):505-10
- Kolb, Webvision, The Organization of the Retina and Visual System, Simple Anatomy of the Retina (2011)
- Kolb, Webvision, The Organization of the Retina and Visual System,
Circuitry for Rod Signals Through The Retina (2011)


What is the difference between "hamstring tendon" and "common hamstring tendon"?

In the paper you cite, they are talking about the tendon on the other side from the ones you've listed, at the "origin from the ischial tuberosity" (quoted from the abstract).

In this case, the word "common" is used in the dictionary sense of "same" rather than "ordinary": it's "common" because it's the same origin for the different muscles that make up the hamstrings. This terminology is used elsewhere in anatomy, too, for example the common carotid artery splits into the internal carotid and external carotid; the "common" portion is the larger proximal vessel.


How does Sodium Valproate cause neural plasticity

As far as I can see this paper is being a little misleading, by saying "VPA mimics Nogo-66 receptor deletion".

The action of VPA doesn't seem to be related to this receptor.

It seems that blocking this receptor and applying VPA both increase plasticity, but it is like taking a car or taking a train -- entirely different modes of transport that achieve the same effect.

VPA seems to facilitate LTP through increased availability of relevant proteins.

That is unconnected with growing new neural structure.

The principal problem with growing new structure is, as hinted at the end of the question, that the adolescent/adult brain secretes a chemical that gets picked up by Nogo 66 receptor, which signals to collapse the axon growth cone.

It's why adult humans can't recover from spinal injuries. The axons won't reconnect.

It so happens that a small molecule Nogo Antagonist has recently been developed by Professor Strittmatter.  He was kind to reply to my query, and I learned that this molecule is currently in the early stages of FDA approval. It's a very exciting discovery!

I would caution anyone against taking VPA -- I have been encountering chest pains since experimenting with it (even though I dropped the experiment after a week due to pain). It looks as though this pain is inflammation of the stomach lining and a common reaction to VPA (VPA is an acid!).

If someone is determined to take VPA, they should at least investigate taking it together with Omeprazole, which discourages the stomach from producing excess acid.

I am disappointed that I now need to take omeprazole quazi-regularly, it appears that my brief VPA experiment has caused some long-term upset in my chemical balance.

Also of note is that (again discovered by Strittmatter) Ibuprofen has been found to also interrupt the signalling pathway that leads to axon growth collapse. But it requires a high dosage, and ibuprofen also causes a similar imbalance.


The process is self-reinforcing but the argument is not circular (no tautology implied).

As soon as some male traits are considered more sexy than others, then there is selection for females to like those traits even more, which causes those traits to raise in frequency, which increases the selection for liking these traits. In other words, in this model, the state where there are no sexy traits in males is an unstable equilibrium.


How do roots absorb water instead of presence of waxy - material suberin in the form of casparian strips on the wall of endodermis?

The plants do  have waxy walls and stuff, the plants use "Suction Method" to suck the water from the ground. Due to transpiration plants loose water from the top or aerial region of the plant and since water is absent in that region there is vacuum present so it sucks water from the ground. This is how plants absorb water.

[Reference--- https://en.wikipedia.org/wiki/Xylem ]

[Ref. Wiki Images and text part and cross check for better understanding]


How can P450 distinguish between foreign and native compounds?

False Premise

The false premise in this question lies in the end of the last sentence:

  …the ability to distinguish the foreign compounds that are substrates
  from the normal metabolic intermediates that are not substrates,
  if they are structurally similar

The assumption here would seem to be that the similarity between normal metabolic intermediates and foreign compounds is too great for discrimination to occur. There is no reason to assume this.

Explanation

  The substrate specificity of those P450 enzymes that metabolise
  xenobiotics is such that they will not metabolize normal cellular
  constituents.

There is a wealth of evidence that enzymes can have substrate specificity that is either extremely narrow or relatively wide. This obviously depends on the structure of the substrate binding site — its shape and size and the chemical nature of the amino acid residues there. Thinking in these terms one can envisage an enzyme that will discriminate against substrates with a single substituent at a particular position, but metabolize a variety of similar compounds that lack this. The evolution of P450 enzymes can be imagined as a process whereby mutations that allowed metabolism of toxic environmental compounds would convey an advantage and be selected for, but mutations that disrupted normal metabolism would be lethal (or disadvantageous) and be selected against.

The Broader context of P450 Enzymes

The question is posed in terms that might suggest that the only function of P450 enzymes is in removal of xenobiotics, and perhaps that they are only a feature higher organisms. In fact neither of these are true. Details of their occurrence in bacteria can be found in the Wikipedia article. However, a paper which I, as a non-expert, found interesting in this respect was published by Kawashima and Satta in PLOS ONE in 2014. This makes the point that there are two classes of P450 genes — those involved in normal cellular biosynthesis (e.g. steroids, cholesterols, vitamin D3 and bile acids), and those active against xenobiotics (e.g. plant alkaloids, aromatic compounds and fatty acids). Comparison of the genes for these in a variety of (mainly) vertebrates implies those involved in the metabolism of xenobiotics evolved from those involved in normal cellular metabolism, and such detoxification genes have arisen not just once, but on several occasions.


What is the relationship between the e value reported by HMMER and BLAST? (Are they equivalent?)

They use very different algorithms so they should not have the same E-value. BLAST uses a position-independent substitution matrix (e.g. BLOSUM) while HMMER uses a position-dependent substitution matrix that is different for every profile. Check out the "Background and Brief History" section in the HMMER's user guide. It explains the conceptual differences at a very broad level.

Therefore, I don't think there's any way to make them equivalent.


It looks like southern platyfish (Xiphophorus maculatus) to me.

Courtesy: http://aquaticszone.blogspot.in/2011_04_01_archive.html


My dog and I are wondering: is this a biting midge, or another bug?

It seems to be a Yellow-banded polybia wasp (Polybia occidentalis), a species of Potter wasp.

my doubts with this conclusion is that the abdomen of the insect in your photo is quite large compared to other observations of the species. Also, Polybia occidentalis is a species that exists in South and Central America, not up north in New York, Perhaps it is able to exist there due to the warm summer weather though I am not entirely sure.
It might be another species of potter wasp. Potter wasps are able to sting but rarely do so to large organisms and their stings don't hurt much. They usually prey on caterpillars and beetle larvae and use those to feed their own. They create these nests that look like a ceramic pot. each of these "pots" contains one larva of the wasp (along with all the food the wasp has collected for their larva when it hatches).
here's a photo of the pots (wasps seem to be willing to create these pots on pretty much any solid surface including under leaves):

Wasps are not parasites, they are hunters of other insects, if my identification of this species is correct, then you and your dog are likely not going to suffer any direct harm from this species let alone parasitic behaviour.


Transport mechanism in absorption of monosaccharides in small intestine

From my initial reading on this, the SGLT1 does not itself directly use energy in the form of ATP. https://en.wikipedia.org/wiki/Sodium-glucose_transport_proteins It appears the uptake of the sugars by this protein are achieved by cotransport. In this case, they "hitch a ride" into intestinal epithelium by following the flow of sodium ions back into the epithelial cells. The reason the Na+ ions flow into the epithelial cells is because of their higher concentration outside the cells. This concentration gradient is created and maintained by the Na-K Pump. So, ATP is used to create a chemical gradient, higher [Na+] outside compared to inside. Then the natural flow of Na+ down its gradient "drags in" the sugars.


Summary
The poster’s answer to his own question focuses on the end results of the anti-viral action of poly- and mono- ADP-ribosyl transferases — PARPs. The references he provided stimulated me to read about the molecular aspects of this topic, which is where my own interests lie. The ‘answer’ emerging from this reading is somewhat extensive, but can be summarized as:

  The molecular details of the way in which PARPs act as anti-virals against
  coronaviruses, and in particular whether and how they antagonize viral
  protein NSP3, are still unknown. There is indirect evidence to
  implicate PARP9, PARP14 and PARP15, which — like NSP3 — share a
  structural feature known as a macrodomain, although their mode of
  action is complicated by the fact that PARP9 does not catalyse
  ADP-ribosylation. The viral NSP3 protein has the ability to remove
  ADP-ribose from proteins in vitro, but whether this is its mode of
  action in the cell is yet to be established.

The role of PARPs in the cell (1)
The name PARP is an acronym for poly-ADP-ribosyl transferase, although the 17 human PARPs are defined, not by this catalytic activity, but by the possession of a domain homologous the catalytic domain of the founder member, PARP1 (2). On the basis of assaying the cloned, expressed proteins for self-ribosylation activity most of these (eleven) have only mono-ADP-ribosyl transferase activity, and two (PARP1 and PARP13) are inactive — a conclusion consistent with the substitution of a key catalytic residue at the active site (3).
   One can consider three stages in the involvement of catalytically active PARPs in cellular metabolism: activation, catalytic action and effect.

A common feature of activation seems to be the response to some stress signal, which may result in increased transcription of PARP genes or activation of an inactive form, for example by combination with an accessory protein (4).
   Catalytically active PARPs covalently attach one or more ADP-ribose groups most commonly to specific glutamate residues (less frequently to asp, arg, or ser residues) of target proteins (or in some cases themselves) using NAD+ as a donor:

For those PARPs that catalyse poly-ADP ribosylation (PARP1, -2, -5a and -5b)) linear or branched chains are formed by glycosidic bonds between the 2′ and 1″ positions of ribose rings.
   Although all PARPs — by definition — contain the PARP domain, they vary considerably in the other domains they possess, and this would be expected to be the basis for different substrate specificities. However for many PARPs these substrates have not been identified — only the processes they affect, the main processes (other than anti-viral action) appearing to be DNA integrity, telomere homeostasis, RNA transcription, regulation of mRNA translation by cytoplasmic stress granules and degradation of proteins through the ubiquitin pathway. Most effort has been directed at the substrates of PARP1, which include histones H1 and H2B and  the chromatin insulator binding protein, CTCF (in response to DNA strand breakage) and the transcription factors NELF and C/EBPβ.
   The effect of modification of the substrate protein may be a change in its activity (as exemplified by the inhibition of translation EF-2 by diphtheria toxin) or more generally interaction with some other protein that recognizes the ADP-ribose moiety. One feature of this recognition — particularly significant in the context of virus–host interaction — is that it often involves a specific domain called the macrodomain (5), named after the C-terminal domain of the histone H2A variant, MacroH2A.

Macrodomain from Archaeoglobus fulgidus protein AF1521 showing binding of ADP-ribose (red)

The macrodomain is found in certain classes of enzyme responsible for the turnover of the reversible modification of proteins by ADP-ribose. These include the polyADP-ribose glycohydrolases — which cleave ribose–ribose glycosidic bonds — and MacroD1 and MacroD2 — which hydrolyse the ester bond between the amino acid and the terminal ribose.
   Also of interest is the fact that, several macrodomains are found in three PARPs: PARP9, PARP14 and PARP15.

PARPs in cellular anti-viral responses and viral anti-PARP proteins (6)
   In different classes of viruses PARPs can act in a pro-viral or anti-viral manner. In coronaviruses (human SARS-CoV has been the subject of most study) they exert an anti-viral effect, as indicated by the effect of inhibitors of PARPs. Furthermore certain PARPs (-9, -12, -13 and -14) are induced in response to interferon, itself a consequence of viral infection. As mentioned by the poster, PARP13 binds directly to viral RNA resulting in its eventual destruction. However in most cases it is unclear which PARPs are involved, what their targets are, and whether their anti-viral action is a result of their catalytic activity — clearly not in the cases of PARP9 and PARP13. This is an important proviso to what follows.
   A study of the evolutionary conservation of the all 17 PARPs in different primate species showed that five of these underwent rapid evolution, typical of proteins involved in host–viral conflict (7).
   One of these was the catalytically inactive PARP13, which before its assignment to the PARP family had been shown to have anti-retroviral properties and was termed ‘ZAP’ (Zinc-finger Antiviral Protein).  The zinc-finger domain binds directly to a long stretch of viral RNA (8), but the details of the recognition and how binding leads to the destruction of the viral RNA (is the PARP domain involved?) remain to be elucidated.
   More relevant to coronaviruses, perhaps, is the positive selection of PARP9, PARP14 and PARP15, which all contain the ADP-ribose binding macrodomain. In contrast to PARP13, the mutations in these PARPs are found throughout the proteins, including the macrodomain, where they are found distributed in surface patches, rather than in the ADP-ribose pocket. The relevance of this to anti-viral action is that there is a virulence protein, NSP3, in SARS-CoV which posses three macrodomains, one of which (MAC1) is structurally homologous to the macrodomain of the PARPs. (This macrodomain is also found in the virulence protein of hepeviruses and togaviruses.)

Structure of SARS-CoV genome and domains in gene nsp3 (from (6))

This macrodomain has been shown to bind ADP-ribose, and mutations in the macrodomain of nsp3 have been generated at key residues at the binding site. Using these mutants it has been established first, that such mutants have reduced virulence compared with the wild-type virus, but that this difference is abolished when infection was in cells with knockdowns in the gene for macrodomain-containing PARP14  (although also in PARP12 knockdowns) (9).
   It has been demonstrated that NSP3 can remove ADP-ribose from proteins in vitro, suggesting that this catalytic activity may be the basis of its virulence (6). However evidence for such action during infection is lacking.
   If indeed the continual mutation of the macrodomain of PARP9, -14 and -15 is part of an “evolutionary arms race” with NSP3, the nature of the postulated interaction or antagonism between these proteins remains to be determined.

References
   1. Gupte et al. (2020) Genes & Development 31, 101–126.
   2. Schreiber et al. (2006) Nature Reviews: Molecular Cell Biology 7, 517-528.
   3. Vyas et al. (2014) Nature Communications 5, 1–13
   4. Suskiewicz et al. (2020) Nature 579, 598–605
   5. Leung et al. (2018) PLOS Pathogens 14(3): e1006864
   6. Fehr et al. (2018) Trends in Microbiology 26 598–610
   7. Daugherty et al. (2014) PLoS Genetics 10(5): e1004403
   8. Guo et al. (2004) Journal of Virology 78, 12781-12787
   9. Grunewald et al. (2019) PLoS Pathogens 15 (5): e1007756.


Since the sequence starts with an initiation codon and ends with a stop codon I think it's safe to conclude that this is the coding strand.  The coding strand has the same sequence as the transcribed RNA (except T>U). This is because it is the other strand of the DNA that is the template for the synthesis of an RNA. The RNA is indeed made 5'>3', but the template it uses has to run in the opposite direction.

5’-ATGTACTTCCATCTGGAATAG-3’
3'-TACATGAAGGTAGACCTTATC-5' template strand

5'-AUGUACUUCCAUCUGGAAUAG-3’ mRNA transcript
3'-TACATGAAGGTAGACCTTATC-5' template strand (read from left to right by the polymerase)

and the sequence of the protein is MetTyr...etc


Are there any bacterial lineages which are particularly well adapted to becoming endosymbionts?

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0027909

  Members of the genus Xenorhabdus are entomopathogenic bacteria that associate with nematodes. The nematode-bacteria pair infects and kills insects, with both partners contributing to insect pathogenesis and the bacteria providing nutrition to the nematode from available insect-derived nutrients. The nematode provides the bacteria with protection from predators, access to nutrients, and a mechanism of dispersal. Members of the bacterial genus Photorhabdus also associate with nematodes to kill insects, and both genera of bacteria provide similar services to their different nematode hosts through unique physiological and metabolic mechanisms.


What is the mechanism of monofunctional glycosylases?

The article referred to in the question is Fromme et al. (2004). I was able to find several proposed mechanisms for the monofunctional uracil-DNA glycosylase but I'll discuss two that seem most relevant in the context of your question.

The first I'll mention was outline by Parikh et al. (2000) who studied recombinant human mitochondrial uracil-DNA glycosylase. They report a mechanism where the glycosidic bond cleavage is not induced by a nucleophilic attack by water but rather by valence electron rearrangement, induced by conformational changes of the substrate by the enzyme, leading to a resonance stabilized oxocarbenium intermediate. This figure shows an electron pushing representation as well as the various stabilizing effects produced by orbital overlaps which favours cleavage of the C-N bond:

  Original caption: Structure-based reaction mechanism that resolves the apparent orthogonal paradox for electron transpositions by altering the substrate stereochemistry. (A) A simplified valence-bond representation of the glycosylic bond dissociation hides the paradox that the three electron pairs to be transposed are involved in orthogonal orbitals. (B) In the normal anti-conformation of deoxyuridine, the σ*-orbital involved in the anomeric effect and the π-orbital of the C2⩵O bond are orthogonal to one another, thus preventing orbital overlap. (C) Severe distortions of the deoxyribose and the glycosylic bond in the strained conformation of deoxyuridine enforced by the UDG active center align the pairs of atomic orbitals participating in each electron transposition, thereby electronically coupling the anomeric and σ-πArom effects to promote bond cleavage.

They also go on to say (emphasis added):

  A water is tightly positioned 3.54 Å below the deoxyribose C1′ by four hydrogen bonds (Fig. 3B) but is likely a poor nucleophile. Instead, the UDG–DNA substrate structure suggests this water is well positioned to become the 1′-α-OH after dissociation of the incipient deoxyribose oxocarbenium ion from the uracil ring.

Here is Fig. 3B from the article, where the water molecule is the red sphere at the bottom of the image coordinated by four hydrogen bonds:

The next mechanism involves a nucleophilic attach by an activated water molecule and was outlined by Drohat et al. (1999) studying Escherichia coli uracil-DNA glycosylase. Here is the first step of the mechanism:

  From the Wikipedia article on uracil-DNA glycosylase (accessed 15 Jul 2014)

Drohat et al. (1999) describe this:

  UDG apparently follows a [...] mechanism by deprotonating the incoming water nucleophile using the completely conserved residue Asp64 as the general base. Site-directed mutagenesis studies of the human enzyme support the structural evidence that His187 and Asp64 act as a general acid and base, respectively, because conversion of these groups to leucine and asparagine resulted in 300- and 2500-fold losses in activity (11). However, structural and mutagenesis data alone cannot establish the catalytic roles and ionization states of active site groups; thus other complementary approaches must be utilized to establish a chemical mechanism.

To answer your question, the water molecule is considered activated because it is a better nucleophile due to proton abstraction by the aspartate residue side chain. Thus the electrons used in in the original O-H bond in water (which are polarized towards the electronegative oxygen) are free to attack the partial positive 1' carbon of the deoxyribose. Although it is a concerted mechanism, you could perhaps think of the nucleophile being the hydroxide anion, which is much stronger than water.

So which mechanism is correct you might ask. Well, I don't know, but I refer you to a paragraph from Parikh et al. (2000):

  Despite the importance of UDG and the many proposed mechanisms for its catalysis of glycosylic bond cleavage, the structural chemistry underlying efficient catalysis by UDG has remained elusive. Two groups, including our own, have proposed a traditional acid-base catalysis carried out by a cationic His-268 and an absolutely conserved Asp-145 (13, 26). Two proposals (27, 28) invoke only general base catalysis via the same catalytic aspartate and a neutral histidine. Another proposal (29), based on a computationally simulated uncleaved-substrate complex, predicts that Asp-145 is fully solvated in the substrate complex so that it cannot act as a general-base catalyst. These proposed mechanisms are inconsistent with each other and with the uncleaved-substrate crystal structure presented here. Moreover, they are problematic in that they rely entirely on functional group chemistry and thus do not adequately explain UDG's efficiency or the activity of mutants that alter evidently key functional groups (13, 27). UDG mutations that remove apparently key active site functional groups are actually faster enzymes than several wild-type DNA glycosylases (30). Thus, without knowledge of a substrate complex structure, the characterization of UDG mechanism is severely hindered. Here, we present the structures of UDG bound to both uncleaved-substrate analog at 1.8-Å resolution and cleaved-product DNA oligonucleotides at 2.0-Å resolution. These high-resolution cocrystal structures suggest how UDG applies part of the DNA-binding energy to glycosylic bond cleavage by conformationally altering its deoxyuridine substrate to take advantage of stereoelectronic and strain effects in what is then an apparently dissociative process.

References:

Drohat AC, Jagadeesh J, Ferguson E, Stivers JT. 1999. Role of electrophilic and general base catalysis in the mechanism of Escherichia coli uracil DNA glycosylase. Biochemistry-US. 38(37):11866-11875.

Fromme JC, Banerjee A, Verdine GL. 2004. DNA glycosylase recognition and catalysis. Curr Opin Struct Biol. 14(1):43-49.

Parikh SS, Walcher G, Jones GD, Slupphaug G, Krokan HE, Blackburn GM, Tainer JA. 2000. Uracil-DNA glycosylase–DNA substrate and product structures: Conformational strain promotes catalytic efficiency by coupled stereoelectronic effects. P Natl Acad Sci USA. 97(10):5083-5088.


This is a Sawfly larvae, and is most likely of the species Perga dorsalis or Perga affinis. The larvae you depict appears to be quite young, but as it matures it'll gain a much darker color, and, depending on whether it's P. affinis vs. P. dorsalis, the abdomen will grow fairly long.

I imagine the developmental progress of your larvae is somewhere between the two following larvae.

A few more images:


Help identifying spider found in central Indiana US

This looks like a black lace-weaver, or Amaurobius ferox. Based on the size you described it seems as though this one is an adult female. These spiders avoid bright spaces and if they feel cornered they might bite you.

For pictures of it you can look here https://www.arkive.org/black-lace-weaver/amaurobius-ferox/ and for more information you can look here https://en.wikipedia.org/wiki/Amaurobius_ferox


Fibrinoid swelling involves necrosis and swelling so no.
Organisation of thrombus refers to some very large space of organising thrombus in different ways - so no, since there is an exact mechanism under.
Based on my interpretation of Robbins -book.

The correct answer is 3. thromboembolism.
Thromboembolism is a combination of thrombosis and its main complication, embolism.


How does the specificity to bind to antibody differs between 'hot' and 'cold' antigen in radioimmunoassay?

The specificity is the same, but protein-ligand binding is an equilibrium process. In other words, the antigen is constantly associating with and dissociating from the antibody. As a hot antigen dissociates, it is possible that a cold antigen can take its place, and vice-versa. As the ratio of cold to hot antigen increases, there is a greater probability that cold antigens will take the place of hot antigens.

You can read more on Wikipedia.


Could a trans-female person ever become pregnant?

Medical science has reached the point where it is able to consider performing uterine transplants in genetically female (cis-female) patients born without a uterus.
In the MedlinePlus report, First Uterus Transplant Planned in U.S. doctors at The Cleveland Clinic have plans to perform the first uterus transplant in the US sometime in 2016.
The article does however go on to state that the women will need to have been born with ovaries. The same matching process of blood and tissue typing that goes along with any organ transplant would still be in effect for this surgery.
It is also unlikely that the procedure would be open to women that lost their uterus due to cancer, as the recipients would be required to be on immunosuppression medication, and the risk of cancer recurrence would be too great.
As for your question about transplantation into Male-to-Female transgender patients, it is unlikely, at least with present technology that the person would be able to receive the transplant. There is a complex cascade of hormone signaling required for implantation of the embryo.
There could also be implications as to the formation of the placenta and how the person's body react to that. We have many examples of surrogacy, so we know that a woman can carry the embryo formed from the egg of another woman, but how the transgender person's somatic cells would react, given that they all have y-chromosomes is unknown.
According to a Yahoo! news article that interviewed Dr. Karine Chung, director of the fertility preservation program at the University of Southern California’s Keck School of Medicine and Dr. Christine McGinn, a New Hope, Pa., plastic surgeon who performs transgender surgeries on men and women, they foresee possibilities that this could happen in the future, however they do not cite any research that has been performed to date.
One of the issues would be the differing pelvic vasculature that a cis-male has to a cis-female, and what would need to be done to provide an adequate blood supply to sustain not only the uterus but the growing fetus as well.

...biological women have a leg up on biological males when it comes to accepting and nurturing a transplanted uterus. Women already have: vasculature needed to feed the uterus with blood, pelvic ligaments designed to support a uterus, a vagina and cervix, and natural hormones that prepare the uterus for implantation and support the pregnancy.
Men have none of those support systems — naturally — but none are impossible to create. “Male and female anatomy is not that different,” says Chung. “Probably at some point, somebody will figure out how to make that work.” (2)

The article does go on to point out that

Hormone therapy can shut off testosterone and introduce progesterone and estrogen needed to prepare the uterus for pregnancy.

Even though males do not have uterine veins and arteries needed to nurture the womb, it’s possible to attach a branch of a large vessel, like the internal iliac, to the uterus. “It’s doable, it just hasn’t been done,” Chung says.

Although it’s preferable for a vagina to support the uterus, it’s possible to attach a transplanted uterus to other ligaments in the pelvis.


How much solar energy required to produce enough food for a herbivore?

BMR is the amount of energy an animal uses just by being alive. BMR is proportional to the mammal's mass. More precisely, BMR is proportional to the mammal's mass to the power of 3/4. A 0.1 kg mammal has a BRM of 10 kcal/day. Using the aforementioned proportionality, a 600 kg mammal (average mass of a cow) will have a BMR of 6800 kcal/day.

This means that a cow would need about 6800 kcal of energy per 24 hours (1440 minutes) to survive.

The amount of solar energy reaching the earth’s atmosphere is 0.00194 kcal per square centimeter per minute. Since, according to you, there is 10 times the amount of sun in Mercury, there should be 0.0194 kcal per square centimeter per minute hitting Mercury.

0.0194 kcal per minute for 720 minutes (counting only day - since there is no sun during the night) equals 13.968 kcal per square centimeter per day. At this rate, the sun has to hit an area of 486 cm squared to harness enough energy for the cow.

In summary:

The average cow needs about 6800 kcal per day to survive (BMR)
On Mercury, the sun generates 13.968 kcal per square cm
Which means, the sun has to hit an area of 486 square cm

In one sentence:

In order to power a cow on Mercury, the sun has to hit an area of 486 cm for 720 minutes.

To learn more:

https://en.wikipedia.org/wiki/Kleiber%27s_law
http://www.ase.org/resources/measuring-number-calories-sunlight


Deletion errors with Phusion Polymerase?

In my own personal lab experience, I got some unexpected results using Phusion polymerase. However, I have not seen deletions, only insertions (ranging from single bases to 3 tandem copies of a primer sequence). This is not an answer to your deletion question, but it does suggest unusual things might happen.

I have seen deletions with T4 DNA polymerase during "blunting" reactions. According to the NEB website:

Q10: Is T4 DNA Polymerase active at room temperature?

A10: We suggest 12°C. The DNA ends "breathe" at higher temperatures allowing the exonuclease to remove nucleotides past blunt.


Energy released during the production of ATP?

This is difficult to answer exactly since the thermodynamics of cellular metabolism are not well understood.
These are spontaneous reactions, so there is certainly a loss of Gibbs' energy $\Delta G < 0$; this energy corresponds to your "energy" term on the product side of the reactions. For the anaerobic case (glycolysis) a balanced reaction formula is

Glucose + 2 ADP + 2 Pi $\rightarrow$ 2 Lactate + 2 ATP + 2 H2O

Details like phosphate (Pi) and water is important here. Now, if we know the free energies $G$ of each substrate and product, we can calculate the $\Delta G$ as the sum of the products' energies minus the sum of the reactants. Unfortunately, this energy $G$ is hard to get at. It depends on a number of things, like the molecule structure, concentration, temperature and the pH and ion strength of the solution. These things are not exactly known, so the answer will be uncertain. This is actually an active area of research, and sophisticated methods have been developed for calculating $G$. One of the best are from a groyp at the Weizmann institute in Israel, and is available at http://equilibrator.weizmann.ac.il

If we assume all concentrations to be 1mM, this method gives $\Delta G = -118.7$ for the glycolytic reaction above. This is the energy lost (mainly as heat) in the reaction. For comparison with energy captures by ATP, we can break up the reaction into two parts and calculate

Glucose $\rightarrow$ 2 Lactate $\quad\quad\quad\quad\quad \Delta G = -206.7$

2 ADP + 2 Pi $\rightarrow$ 2 ATP + 2 H2O $\quad\quad\Delta G = 87.0$

which sums to -118.7, as expected. This tells us the fraction of the Gibb's energy captured as ATP is 87/206.7 = 42%, while 58% is lost as "heat". So glycolysis has an efficiency of 42%. (For comparison, a combustion engine is somewhere at 15--20%.)

The aerobic case is more difficult, because the stoichiometry is not even fixed: the number of ATP molecules actually obtained from 1 molecule of glucose depends on the efficiency of the respiratory chain, on cytosolic NADH oxidation, and otherthings. But let's say we get 30 ATP. Then

Glucose + 30 ADP + 30 Pi + 6 O2 $\rightarrow$ 6 CO2 + 30 ATP + 36 H2O

has $\Delta G = -1608$, which can be broken up into

Glucose + 6 O2 $\rightarrow$ 6 CO2 + 6 H2O $\quad\quad\Delta G = -2913$

30 ADP + 30 Pi$\rightarrow$  30 ATP + 30 H2O $\quad\quad\Delta G = 1305$

So here 1305/2913 = 45% of the energy is captured. So in this sense, glycolysis and respiration are similar in efficiency. Varying the number of ATP changes this value; try it! Of course, glycolysis can only partially oxidize glucose (into lactate), while respiration achieves complete oxidation to CO2, extracting much more energy.

Again, these values depends heavily on concentrations of metabolites inside cells, which are not well known. Try changing them at the equilibrator web site and note the effects! Unfortunately, many biochemistry textbooks present values of $\Delta G$ assuming reactants at 1M (!) which is completely irrelevant to actual conditions in living cells.


There are. But they are not that universal. See kappa-particle in Paramecium and Wolbachia in insects. Also, there are different origins of plastids (compare red algae and green algae). Some organisms like Rhopallodia gibba even have plastids of multiple origin.

  So do most organelles just lose all their DNA? Or is it something that
  occurs fairly rarely?

The organelles of endosymbiotic origin lose their genes gradually. The extent and rate of loss is correlated with the number of organelle the cell harbours. The limited transfer window hypothesis speculates a probable mechanism.


How does temperature influence the rate of protein degradation?

This is a general answer for all three of your related questions:

This one
How does Temperature influences the rate of protein turnover?
How is the rate of transcription influenced by temperature?

Since you said:

  I want to simulate the evolution of genetic architecture when after a
  sudden change in temperature or in an environment that is temporally
  heterogeneous in terms of the temperature

You should see this paper. They have studied the dependence of growth rate on temperature. This was measured for different organisms (all poikilotherms).

See this figure:

Figure S1 from Dell et. al 2011. PNAS

  The unimodal thermal response of radial growth rate of sac fungi (m/(colony*s)). Green and brown curves are OLS regressions to the Boltzmann-Arrhenius model (Eq. 1) for the subset of data that are the rise and fall components, respectively. These components were extracted by the algorithm described in the Materials and Methods. For
  this particular response, the rise was obtained by the algorithm
  through removal of the measurements at the 4 highest temperatures and
  the fall through removal of measurements at the 5 lowest temperatures.
  The blue curve is the best fit to the Johnson & Lewin model (SI
  Methods) (1). Values shown are estimated activation energies with 95%
  confidence intervals for the respective response components. Dotted
  vertical arrows are estimated temperatures for Topt –the temperature
  at which the trait value is optimal–calculated from the direct method
  (red) and Johnson & Lewin model (blue). See SI for more details. Data
  are from Fargues et al. (9)

As you can see, the curve is skewed. The left side of the curve from Topt follows the activation energy model (Arrhenius/Boltzmann). The right side, though they say in the figure legend also fits the model, it seems to me that the phenomenon is somewhat different. The steepness of the curve is perhaps because of denaturation of enzyme active site and therefore a loss of activity. For different enzymes the denaturation kinetics would vary.

I happened to stumble into the author of this paper and that is how I got to know of this work. He seemed to agree that the right half steepness might be because of enzyme denaturation.

Also have a look at this article which is about the temperature dependence of the activity of the proteasome of a thermophile (same principles apply for mesophiles).

Figure 2 of the article:

  Normalized Cbz-Ala-Ala-Leu-pNA hydrolysis activity of (filled squares)
  purified native and (filled circles) 70°C heat-purified recombinant (α
  + β) Mj proteasome. To normalize recombinant activity to native activity a multiplier of 1.92 was used. Error bars for the native
  sample represent one standard deviation for triplicate assays.
  Measured temperature errors were ±2°C.

Bottomline (From my comments)

You can assume that the enzymes are at their optimum. You can model the loss of activity due to increased temperature (protein denaturation) as gamma/chi square or exponential function (or the fitted function on the denaturation kinetics) and the effect of low temperature using the chemical thermodynamic equations. But the point is that we don't know if they are at their optimum or not or how each of they may perform at different temperatures.


Is chromosomal DNA more likely to interfere with restriction mapping or PCR analysis in E. coli?

Welcome to Biology.SE!

I think you've come to a reasonable conclusion, but not for exactly the right reasons.

The genomes of several strains of Escherichia coli have been sequenced (e.g. https://www.ncbi.nlm.nih.gov/nuccore/U00096) so you could predict the sizes of the fragments you would expect from your digest.

The genome size of E. coli is about 4.6 million base pairs and six-cutters like EcoRI and BamHI cut on average about once every 4096 bp (you should be able to figure out how to come up with that number). From that what would you expect to see if you did a restriction digest on this bacteria's genomic DNA?

Does that help you improve your answer?

(If you have access to the appropriate software, I encourage you to download that sequence and check your conclusions.)

((Also note that the specificity of PCR is dependent on primer selection, so your answer is assuming that the primers were well designed!))


Is there any complex organism that is both autotroph and heterotroph?

For example sundews are plants (so autotrophic), but they "hunt" for insects to get additional nutrients, e.g. nitrogen. As far as I remember the nitrogen is the main reason for eating other organisms but they also use other substances, including carbohydrates, from their prey.


Is the Michael Jackson skin pigmentation disease realistic?

1) Is this plausible?

It is absolutely plausible. His particular condition was called Vitiligo
 (as stated in your quote) and isn't that uncommon, albeit not usually as severe.

Skin pigmentation expression changes over time, sometimes dramatically.

  2) Is it likely to be an actual disease, or would there be so many mitigating factors that it is unlikely a person would suffer to the extent he did?

Vitiligo is a very well-documented disease, and like every disease, there's a broad range of affectation. Treatments options are very limited, and so makeup or other methods are often used to disguise the affected skin.

Here's some more pictures of people with Vitiligo at varying stages:


Is death by cyanide the same as suffocation?

In suffocation or asphyxiation you are actually deprived of breathing oxygen. The arterial blood oxygen concentration decreases (hypoxemia) which is detected by the chemoreceptors of the carotid body and aortic arch. This induces a neuronal response in the medulla that increases respiratory rate, force of contraction and relaxation of respiratory muscles and heartbeat rate. Simply put, you get panicked. Prolonged suffocation may lead to seizures, cardiac and respiratory arrest and death.

Cyanide poisoning is an example of histotoxic hypoxia resulting from tissue poisoning by $\rm CN^-$. Unlike other forms of hypoxia, where the concentration of oxygen is less in tissues, in cyanide poisoning, the concentration of oxygen is actually perfectly normal in ECF and ICF. It is the cell which is unable to utilize the oxygen present in it. As a result the arterial blood doesn't lose much oxygen to the tissue as they themselves have adequate oxygen, resulting in an increase in $\rm HbO_2$ concentration in blood.
Thus your skin gets cherry red, not blue like when you get deprived of breathing oxygen which happens due to an increase in concentration of deoxygenated hemoglobin in blood.

Here is what happens at the molecular level.

The $\rm CN^-$ ions diffuse into the mitochondria. They have high affinity to the ferrous ion of the mitochondrial enzyme cytochrome c oxidase involved in the Electron Transport Chain, one of the phases of cellular respiration where $\rm ATP$ is generated from $\rm NADH$ and $\rm FADH_2$. And it is this process which actually requires oxygen. The inhibited cytochrome c oxidase is no good, thus no $\rm ATP$ molecules are generated from ETS. And, the oxygen molecules waiting for those electrons remain empty handed explaining the increase in molecular oxygen concentration. Remember, ETS occurs in almost all living cells except few like RBC which get their major share of ATP from the highly inefficient anaerobic glycolysis. Note, $\rm ATP$ is the energy currency of our body and is required in a wide variety of bodily processes like osmotic balance, nerve impulse transmission, muscle contraction etc. With no $\rm ATP$ your heart muscles and respiratory muscles can't contract, your medulla can't regulate breathing. You will go into cardiac and respiratory arrest. It may result into seizures and coma. Death is iminent if a high concentration of cyanide gets into your blood.
The symptoms of panic are not usually seen unless the victim himself knows he is poisoned . Well, that is due to your fight/flight response. The effects like cardiac and respiratory arrest, seizures and coma are similar to those of suffocation because it is due to low $\rm ATP$ production in both cases.

Reference:

https://www.ncbi.nlm.nih.gov/books/NBK54113/


Does a plant have to have leaves to produce fruit?

In short: yes, a plant have to have leaves to produce a fruit. Both from the evolutionary viewpoint as from the anatomical viewpoint.

All the fruit producing plants belong to a group we call Anthophyta (or Magnoliophyta), meaning in greek "plants with flowers". These fruit producing plants are all descendant from ancestors that have leaves, specifically what we call megaphyll ("big leaves").

Even Anthophyta that apparently stopped producing leaves, as cactuses, still have them. According to Mauseth (Botany: An Introduction to Plant Biology):

  Although all flowering plants possess leaves, stems and roots, these parts have been modified so extensively in some species that they may not be recognizable without careful study. For example, cacti are often described as leafless, but they actually have small green leaves between 100 and 1000 micrometers long.

More important, spines are highly modified leaves (and that's the difference between spines and thorns). In a cactus, these highly modified leaves come from a structure called areole, that also produces another highly modified leaf: the flower.

Now to the anatomical part: flowers are specialised leaves:

http://www.ncbi.nlm.nih.gov/pubmed/11440721
http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1677-04202005000400001
http://dx.doi.org/10.1016/S0960-9822(01)00024-0
http://www.ijdb.ehu.es/web/paper/052020pr

...and the list continues. According to Lodish, "Molecular Cell Biology" (http://www.ncbi.nlm.nih.gov/books/NBK21561/):

  Genetic studies have shown that normal flower development requires three classes of floral organ – identity genes. In plants with mutations in all three classes, concentric whorls of leaf-like structures replace the floral organs, indicating that these structures are modified leaves. (emphasis mine)

And according to Durner, "Principles of Horticultural Physiology":

  Flowers are modified leaves. Upon exposure to specific environmental signals such as daylength or temperature or at a specific point of plant development, shoot meristems start to form flowers rather than leaves. (emphasis mine)

And from a paper published in Nature, 2001 (http://www.nature.com/nature/journal/v409/n6819/full/409469a0.html):

  Goethe was right when he proposed that flowers are modified leaves. It seems
  that four genes involved in plant development must be expressed together to
  turn leaves into floral organs. (emphasis mine)

Flowers have several parts, and one of them is the ovary, which will turn into the fruit after (but not necessarily) the fecundation. Thus, in conclusion, fruits are a modified part of a flower, and flowers are specialised leaves.

It's worth mentioning that all fruit plants have leaves, but of course not all plants with leaves have fruits.


Why has the human eye evolved to become sensitive only to the visible light?

Actually, it's got nothing to do with evolution or even human biology.

Why?

  What’s in a name? That which we call a rose,
  By any other name would still smell as sweet. William Shakespeare.

First, try to define visible yourself. Next look at the definition of it in various respected dictionaries; in our context it means

  that can be seen

Consider the case of Goffin's cuckatoo, they can see as far up to as ultra-violet spectrum. They don't speak English (or Portuguese for that matter) but for them visible would mean "what they can see".

So, coming back to your question, even if we had capability to see, say, infrared spectrum, visible would have meant: VIBGYOR + infra. And then we'd have complained about not being able to see bacteria with naked eye :P


How do carrier RNAs increase yield in sequencing experiments?

If you are adding phenol-chloroform extracted tRNA then that is a carrier for the precipitation steps. Some people use linear acrylamide for the same purpose.


Why are some viruses not communicable person-to-person?

Viruses can have many different conditions necessary for transmission.  Viruses which have membrane surface coats (like HIV ) need to be in water all the time to survive.  Cold and flu viruses are more resilient and can survive on a surface such as a doorknob with a halflife of 18 hours(!).  Fortunately we are also have a reasonable intrinsic resistance to cold and flu and I think most infections do not result in symptoms.

Viruses often only infect some parts of the body.  Venerial diseases are a classic example of this where only contact of genitalia might cause transmission. Its probable that Hantavirus is not excreted through the sweat glands or in saliva.  If it did it would certainly be a more devastating disease.   It may also only be serious when the virus is introduced into the lungs, which may make transmission difficult.

For Hantavirus human to human transmission looks possible as observed by these folks. Even so, transmission is still so rare that there is no accounting for it in public health policy.  (they might also have been mistaken!).   Its possible that the virus requires transmission from a mouse to be virulent in humans. Its possible that the human transmission mechanism is so improbable (ingestion of faeces of infected human for instance) that you just dont' see it happening with the few cases of Hantavirus infection we have on the books.


What is a detailed chemical explanation for describing how an enzyme may lower the activation energy of a reaction?

BACKGROUND

We should first understand what activation energy really is and what does Arrhenius equation mean. For any chemical reaction to happen you need to break some existing bonds in order to form new bonds. Breaking existing bonds consumes some energy; in other words you have to convert the reactant to an active form which undergoes a reaction readily. The energy that is required to do so is called activation energy.

It is essential to note that activation energy is an empirical term because it does not actually consider the reaction mechanism. The above example of bond-breaking and re-formation can happen in many ways. Some mechanisms may require less activation energy than the others.

The Arrhenius equation denotes the relationship between reaction rate and activation energy:

$$k=Ae^{-\frac{E_a}{RT}}$$

where $k$ is the reaction rate constant, $A$ is the Arrhenius constant (an arbitrary proportionality constant), $E_a$ is the activation energy, $R$ is the universal gas constant and $T$ is the absolute temperature.

This equation tells you that the rate of reaction decreases with increase in activation energy and increases with increase in temperature.

The temperature indicates the internal energy of the system i.e. the movement of molecules. Collision between molecules is essential for chemical reaction to happen and increased temperature increases the chance of collisions (due to higher molecular movement).

How do enzymes lower activation energy of a reaction?

They either do that by increasing the chance of interaction between the reactants or diverting the reaction to follow a different mechanism that has a lower activation energy.

As you know, the enzyme binds to the reactants and forms a complex. This effectively brings the reactants closer thereby increasing the probability of their "collision" which in turn increases the reaction rate. This can be further extended to the level of molecular orientation. The analogy presented by AMR in their comment is great. It is one of the mechanisms by which the free energy of the system would increase — by reduction of entropy. Clamping the substrate in place can expose its reactive groups to the co-reactants, thereby allowing the reaction to proceed faster.

In most other mechanisms of enzyme catalysis, the functional groups in the enzyme active site react with the substrate to form intermediates and these intermediates which have lower activation energy give rise to product faster than the substrate in absence of the enzyme.

It is to be noted that this entire process of catalysis adds a few extra steps to the actual reaction (binding,  formation of intermediates etc). The catalyst would be effective only if these combined rates are still faster than that of the uncatalyzed reaction.


Does someone know of a website that keeps track of a species population?

How about human?

You will find the data of human population growth on the webpage "Our World in Data". Scroll to the second graph, click on the tab "data" and download the .csv file.

Just google for any specific species of interest

Otherwise you can just google things of interest. Look for large emblematic mammals or commercially important species.

If you google "bald eagle population growth", you will easily find these data.
If you google "moose growth population breeding pairs", you will find these data.
If you google "killer whale population growth", you will find these data.
If you google "tuna population growth", you will find these data.

COMADRE

COMADRE is a database of animal matrix population models. It can be of interest to you.


Hearing and neurons- do ears have a sampling period?

Inner hair cells (IHC) do not fire action potentials themselves. It's the auditory-nerve that synapses with IHC that generates action potentials. The firing rate of the auditory nerve can be as high as few hundred Hz with a refractory period as short as 1 ms or so (depends on the animal).

However, it is important to note that the signal is not sampled at this rate. As you may know, the auditory signal is first transformed to the "frequency" domain through the physical structure of cochlea. Each inner hair cell therefore is roughly only encoding the relative strength of a frequency band. There are presumably inner hair cells in the human cochlea that correspond to a range centered around 18 kHz for example, but neither the neurotransmitters of the corresponding IHC nor the auditory nerve can fire at 18 kHz. Nevertheless, the amplitude modulation at this high frequency is what is transmitted.

Also, thinking of neural firing as a "sampling period" is not always a good analogy. There are debates about this, but it could be that precise timing of action potential carries large amount of information about the stimulus (perhaps not so much so in early auditory system.)

If you want to see some computational modeling work for inner ear, IHC, and auditory nerve, I recommend the Meddis IHC model:

C. J. Sumner, E. A. Lopez-Poveda, L. P. O'Mard, R. Meddis. A revised model of the inner-hair cell and auditory-nerve complex, J. Acoust. Soc. Am. 111 (5) 2002


It's its ovipositor & it's trying to dig a hole to lay its eggs.

  "How Do Grasshoppers Dig Holes to Lay Their Eggs? After breeding, female grasshoppers dig a hole in the ground in which to lay their eggs by using a special tube in their abdomen known as an ovipositor. The ovipositor is first used to dig the hole, and then to deposit the eggs one by one into the hole"

Probably not having much success on tarmac, did it eventually move onto soil?


Terminology for inefficacy of selection on recessive alleles

I think recessive refuge is the term you are looking for (this is the best link I could find, sorry: https://quizlet.com/4176029/bio-experiment-1-and-2-flash-cards/)


Unless someone has already done the work to determine genetic distance between the two species you're interested in, unfortunately the answer is "no, there is no such database".  If representative members of the two species have had their DNA fully sequenced, any of the relevant metrics (e.g., those described in Wikipedia https://en.wikipedia.org/wiki/Genetic_distance) can be used to calculate a value for the genetic distance.  But it's important to keep in mind that "genetic distance" is a pretty vague notion when talking about different species.  There are all sorts of epigenetic factors and gene rearrangements that can play important roles in determining the developmental and phenotypic differences between species; and those factors won't show up in most methods for calculating genetic distance.


Is the 6th rib attached to 7th rib, and 7th rib to 8th?

Those are just a part of the costal cartilage, which is only found at the anterior ends of the ribs, providing medial extension. This connects the ribs to the sternum and is made of hyaline cartilage. Here is a clearer diagram of the cartilage part:

Ribs 8–12 are called false ribs (vertebrochondral ribs- attached to vertebra and cartilage). The costal cartilages from these ribs do not attach directly to the sternum, but are all attached to the cartilage of the 7th rib. For ribs 8–10, the costal cartilages are attached to the cartilage of the next higher rib. So, in a way, you are right in saying that the 8th and 7th ribs are attached.
The 6th and 7th ribs, though, are not attached. There are just cartelagenous bridges present in between them. The first seven are called vertebrosternal ribs. (attached to vertebra and sternum)

Sources:

https://opentextbc.ca/anatomyandphysiology/chapter/7-4-the-thoracic-cage/

https://en.wikipedia.org/wiki/Rib

https://www.pulsus.com/scholarly-articles/cartilaginous-bridges-between-the-adjacent-costal-cartilages--a-case-report.html


Appears to be a larviform female firefly (order Coleoptera; family Lampiridae).

I cannot find a good source for listing/IDing Palestinian fireflies, so I unfortunately cannot give you a definitive answer. I do want to provide some of an answer and an example specimen to get you going on the path of accurately IDing your specimen.

To get you started, your specimen appears similar to Photinus bromleyi (seen here) and below:

Photinus are a group of North American fireflies, so not likely your species.
According to firefly.org, the subfamily Luciolinae is found throughout Eurasia, while the genus Lampyris is a "wastebin taxon" used as a "catch all" for misfit fireflies that is found throughout the world. So I'd start looking in those groups.

I'll dig around for a more Palestinian-oriented bug guide. Again, this is not meant to be an exact answer but just a starting point for you or another user who might have access to Palestinian resources. I'll update if I find something definitive.


J. Von Rustizky, a Russian pathologist working in the laboratory of Friedrich von Recklinghausen (1833–1910) in Strassburg in 1873, introduced the term “multiple myeloma.” At autopsy, a 47-year-old patient examined had eight separate tumors of bone marrow, which Von Rustizky called “multiple myelomas,” and he noted that the nucleus of the tumor cells was located in the periphery of the cell membrane — a morphology highly suggestive of plasma cells.

source: Kyle, RA, Steensma, DP (2011) History of multiple myeloma. Recent Results Cancer Res., 183: 3-23

From the same item:

  The most commonly recognized [first documented] case is that of Thomas Alexander McBean, a highly respectable tradesman from London in 1850. Mr. McBean excreted a large amount of protein that was described by Henry Bence Jones in the middle of the 19th century. Jones was a well-known physician and made many contributions to medicine.

The Bence Jones protein is in fact an immunoglobulin light chain. Purified Bence Jones protein were sequenced by FW Putnam, and
variations between patients were some of the first clues to the existence of the variable regions of immunoglobulin molecules.


Basic Local Alignment Search Tool (BLAST)

Because it has a poor statistical model. It's basically a local alignment tool aided by a fixed-length k-mer index. It estimates homology in terms of sequence identity and while this is often enough to find homology in relatively conservative sequences, the heuristic scoring model doesn't really allow to search motifs. A motif in terms of bioinformatics can be seen as a series of state-switch events, hence you need a model that estimates similarity in terms of likelihood of observing such a sequence of state switches under  your prior state-switch matrix (inferred from a training sample). These models are known as Markov models and people usually utilize Hidden Markov Models to find motifs. There are good popular tools, such as HMMER

EDIT as per OP's comment

  As motifs are locally conserved regions & BLAST also performs local
  alignment then why it should not be able to search for motifs?

A motif is not just a "locally conserved region", it's a specific sequence profile. BLAST doesn't extract any sequence profiles, it wasn't created for that. Given a pair of sequences it simply shows you similar patches. Hence BLAST is simply not the right tool for the task. They made PSI-BLAST for that very sake.
Moreover, many motifs comprise amino acids or nucleotides that can be quite separated in a primary sequence and only get close in a folded (secondary or tertiary) structure. Here your definition of "locally conserved region" fails as does BLAST.
As I've already mentioned, BLAST performs a heuristic local alignment, that is it assumes that two related sequences must contain at least one common k-mer (word) of specific length. This, given a precomputed word index, significantly increases performance in terms of speed and RAM consumption. But similar motifs can be present in non-homologous sequences or in highly divergent sequences that hardly evince any homology, and BLAST won't find anything at all.


When harvesting agave nectar, generally the whole plant is harvested at once to get to the core, where most of the sap is. There isn't exactly an easy way to continually get nectar from the agave plant since it is herbaceous, whereas something like maple trees can be tapped because the wood can support the spigot.


Species identification please - Bug is a plague for Italian Stone Pines (Pinus Pinea)

That's and aphid (Hemiptera:Sternorrycha). Most likely, it belongs to the genus Cinara, which is common on trees. https://en.wikipedia.org/wiki/Cinara