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Is uncoating required for completion of reverse transcription of HIV?
The p24 capsid plays an important role in the replication of HIV, particularly in the reverse transcription and nuclear entry processes. The capsid protects the viral reverse transcription complex (RTC) from antiviral sensors of the host cells, and breaks apart to release the pre-integration complex (PIC) for integration. However, the precise timing of the uncoating is unclear. It’s generally accepted that HIV can initiate reverse transcription in intact viral capsids because the p24 hexamers can alternate between closed and open conformation, which opens up a tiny pore that allows nucleotides to get in and out. So the uncoating is likely to occur during or after reverse transcription. Some researchers speculate that the capsid is uncoated before the reverse transcription is finished. The reason is that the capsid is too small to accommodate the DNA product (however, the RNA template is hydrolyzed at the same time of reverse transcription, which means the volume of nucleic acids should remain the same), and double stranded DNA is more rigid than single stranded RNA. As the reverse transcription proceeds, the pressure builds up inside, which eventually ruptures the capsid. The rupture of the capsid also makes room for the reverse transcription to finish.
So I come up with an interesting idea. If the uncoating of the capsid is mandatory for the  completion of the reverse transcription, can we test it by using mutations or small molecules like lenacapavir to stabilize the capsid and prevent its rupture? If the reverse transcription is unable to finish inside intact capsids, the uncoating must occur before its completion.

Reference:
Jacques, D., McEwan, W., Hilditch, L. et al. HIV-1 uses dynamic capsid pores to import nucleotides and fuel encapsidated DNA synthesis. Nature 536, 349–353 (2016). doi.org/10.1038/nature19098
Zila, V., Müller, T. G., Müller, B., and Kräusslich, H.-G. (2021b). HIV-1 capsid is the key orchestrator of early viral replication. PLoS Pathog. 17:e1010109. doi: 10.1371/journal.ppat.1010109

Note - you should provide attribution for your images - it is good practice for writing, and also because links are susceptible to rot, so ideally your article links should also be listed as references.

Could you provide an example about how references are added?

It seems the image is adapted from the first linked publication. Here is a link to a blog that contains the composite image.

That’s why I didn’t include the link to the blog. The rearrangement is too trivial to be included.

@哲煜黄 it's still good practice to link all sources of images that are not your own.

@哲煜黄 simply by quoting the reference details, your first one is: Jacques, D., McEwan, W., Hilditch, L. et al. HIV-1 uses dynamic capsid pores to import nucleotides and fuel encapsidated DNA synthesis. Nature 536, 349–353 (2016). https://doi.org/10.1038/nature19098. Most articles have a "cite this article" link or simply a cite button that will produce a pop-up with 1 or more citation styles.

Thanks for giving insight about the interesting characteristics of HIV Capsids and Reverse transcription! In order to fully judge the viability of your proposed experiment, we need more information about your model. How does culturing HIV work? Does it work like any other viral culture using a host cell culture? Or are there simpler/safer in vitro models? I suspect that one needs the full length HIV-genome? If so, you could run a PCR of the medium using primers that span the complete/incomplete genome to test for complete reverse transcription?

At the time I couldn't find any info on this, but I recently came across a review covering the recent literature investigating this subject. To summarize, evidence currently supports entry of the intact capsid into the nucleus through the nuclear pore complex (NPC), (this is a surprising result!) reverse transcription occurring mostly in 'nuclear speckles', and capsid uncoating most likely occurs near the end of or shortly after cDNA transcript is complete.
The authors suggest the conical shape of the HIV capsid facilitates NPC entry, but there's no direct evidence for that yet.
Electron tomography and AFM studies directly observed partially broken capsids with nucleic acid exiting, both in cell nucleus and isolated capsids. This means there's likely no signal-mediated disassembly of the capsid and makes it more likely rupture is caused by internal stress.

Two observations that undercut the "cDNA > internal pressure > ruptured capsid" hypothesis are as follows:

However, the in silico model (130) also predicts that compaction of HIV-1 nucleic acids by the viral nucleocapsid (NC) protein, present within the core at high concentration, strongly alleviates outward forces acting on the capsid shell, and NC-mediated condensation of DNA into a tightly packed globule has been demonstrated in vitro (135). The limit of dsDNA length that can be accommodated within the HIV-1 capsid under authentic conditions is currently not known.

lentiviral vectors packaging RNA much smaller than 10,000 nucleotides have been shown to efficiently transduce cells and are thus capable of genome uncoating and integration.

OP seems to be familiar with the details of the subject, so I recommend reading the review in full if you have access.


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How does the recently discovered nitroplast fix nitrogen?
Nitroplast is a newly discovered eukaryotic organelle that can perform nitrogen fixation. Like chloroplast, nitroplast was derived from a cyanobacteria species (UCYN-A). Cyanobacteria are the only photosynthetic organisms capable of nitrogen fixation. Because oxygen is very toxic to nitrogenase, cyanobacteria evolved a special photosynthetic pathway which uses the light energy to make ATP without electrolyzing water molecules (cyclic photophosphorylation). Does that mean nitroplast also use this mechanism to fix nitrogen?
I found this question interesting because there is a lot of interest to incorporate nitrogen fixation into plants. However, nitrogen fixation is extremely costly. It’s calculated that it takes two glucose molecules to fix one nitrogen molecule. Even though legumes can fix nitrogen with the help of bacteria, they only do so when nitrogen is scarce. Because the amount of sunlight typically exceeds the requirement of carbon fixation, if nitroplast can use photon energy directly, it can fix nitrogen without consuming organic materials. In another word, the crops can get extra nitrogen without compromising their yields.

Please provide a link to information about the "nitroplast". If you know about it and I have never heard of it because of its recent discovery, the chances are that you are as well placed to find out about its biochemistry than anyone on this list. What research have you done?

I added the link. I can’t provide more details because those papers are paywalled.

The Wikipedia page Nitroplast has references worth following. New Nitrogen-Fixing Microorganisms Detected in Oligotrophic Oceans by Amplification of Nitrogenase (nifH) Genes is salient. There doesn't seem to be much to indicate that it's an energy-free process though.

Ok. I’ll download it and have a glance when I’ve a moment.

source: Stack Exchange

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Can you measure plasma glucose with a regular glucose meter?
I'm wondering if plasma glucose can be measured with a regular glucose meter and strips like this. I know these meters are normally used to measure whole blood glucose, but can they measure plasma glucose levels as well?
Thanks.

What is blood: Mostly red blood cells, white blood cells and serum. So if you want to divide cells and serum, you should be able to measure the serum glucose levels with equipment like this as well.

ABSOLUTELY NOT - using those meters for measuring glucose in fluids besides blood is inaccurate and dangerous - you should never do that clinically or experimentally

Excellent question... "Can you measure plasma glucose with a blood glucose meter?"
Absolutely Not! In my experience, if you try to measure plasma glucose with a whole blood glucose meter the results are highly variable for a number of reasons (mentioned below). Using blood glucose meters to measure plasma glucose is dangerous. The meters are calibrated for whole blood and not plasma, which is chemically different and will yield different results. Depending on the clinical situation (or experimental situation), the results can be significantly different and non-linear across a huge spectrum of concentrations.
Here is a nice link from the University of Virginia demonstrating the basics of how one type of these meters works.
There are a number of types of glucose meters commercially available to the public as well as healthcare facilities. Most of these meters use varying solid-state chemistry techniques to drive the production of an electrical current that can be measured by the glucose meter. In other words, when the blood is taken up by the strip in the meter the glucose takes part in a redox chemical reaction that creates a small "electrical current" that is detected by the meter. The amount of glucose in the sample is proportional to the electrical current produced. However, there are a number of assumptions that the meters make (which can differ between meters). One of the most clinically significant assumptions is that the meter assumes that the hematocrit (i.e. the percentage of blood volume that is erythrocytes) is normal or approximately 45%. If you use these types of meters on plasma (which has no erythrocytes in it), the chemistry is inaccurate because the meter "thinks" all the glucose that it is detecting is actually dispersed within a pool of erythrocytes in a hematocrit of 45%. There are a number of other issues and important points discussed in this review.
When the clinical trials (e.g. NICE-SUGAR) began showing that intensive glucose control was associated with improved mortality, clinical practices changed from keeping blood glucose concentrations in critically ill patients between 150 and 250 mg/dl to a much lower concentrations (i.e. 80-120 mg/dl). As these new guidelines began rolling out, there were a number of subsequent studies that showed that intensive glucose control was actually associated with more frequent hypoglycemia episodes. There were likely a number of issues to explain this, but one of those was that if your meters were not correcting for differences in hematocrit the blood glucose meters would read spuriously higher than what the true measurement was (thus, you could be treating someone with insulin to lower their glucose that was 160 mg/dl - when in true the value was much, much lower).

I assume you mean that using the measurements is dangerous. There is nothing dangerous about doing the measurement, right?

Dangerous, if the patient is monitoring their blood glucose concentrations in order to maintain a safe bodily state. I.e. if the pateint has Type 2 diabetes. The incorrect reading could lead to incorrect administration.

@daniel yes - using the measurement is potentially very dangerous – that's what happened in some of the early intensive glucose control studies. Glucose was being monitored with glucose meters at the bedside and those meters were giving inaccurate results because the meters assume certain physiological parameters like hematocrit that were not normal. The patients were then getting treated with insulin who had normal blood glucose but high "measurements" – and then those patients were becoming hypoglycemic and having adverse events because of insulin they didn't actually need.

While I agree with the basic conclusion - that glucometers do not reflect plasma glucose, I think you're assertations can be misleading. Glucometers can be invaluable in predicting plasma glucose.  Also, this is a funny phrase "associated with improved mortality". Better death? Should that be "improved mortality rate" or something similar? This language is a bit loose.

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Is there a metabolic pathway that generates methanol?
I've been looking for help topics about methanol in metabolism. Specifically, I wish to know what is a common dietary component that generates methanol following metabolism and comment on its toxicity?  I cannot seem to find any relevant data and i'm seeking to know if anyone here has any experience and knowledge of this.

This source may be a good place to start.

This is an old question by now, but I found it interesting, so here's my two cents :)
Methanol has long been known to normally occur in humans; one study from 1963 demonstrates its presence in breath.
One major source for methanol in humans is breakdown of pectin by bacteria in the gut. Pectin is a complex carbohydrate found in many fruits and other non-woody parts of plants. Pectin is not well metabolized by humans, and so has low nutritional value and counts as dietary fiber. Still, some species of bacteria in the gut are able to degrade pectin, and this process produces methanol.
This article reports measurements of methanol levels in the breath of subjects consuming pectin. Here, 10--15 grams of pectin (equivalent to ~1 kg of apples) was estimate to yield about 0.4--1.4 grams of methanol. The authors also state that there is a basal production of methanol in humans as well, of about 0.3 grams per day; the origin of this methanol seems unclear.
There are also pathways in human cells capable of forming methanol. This study demonstrates this fact by showing that infusion of ethanol (bypassing the gut) leads to a rise in methanol levels.
A recent review of metanol metabolism in humans can be found here.

So this is a really recent and IMO good review of methanol metabolism in humans: Metabolic Methanol: Molecular Pathways and Physiological Roles, there's a paywall though. Humans also encode their own PPME that generates methanol in regulating PP2A (same protein that generates methanol from pectin in plants I think).

@CMosychuk  Fantastic! I will add it to the answer, many thanks!

I can't comment on dietary components or toxicity, but the Kegg database has an entry for methanol with links to the pathways in which it is an intermediate. You might find it useful to check that if you haven't already done so.
http://www.genome.jp/dbget-bin/www_bget?C00132

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How are drug metabolism and detection related?
If someone is taking treatment for a psychiatric disorder (e.g. diazepine), then would traces of the metabolized drug be detectable in their sweat or saliva?
Any links to resources regarding this, or any help is greatly appreciated!

Short answer: Yes.
Diazepine is a ring-structure that forms the basis for the class of drugs called benzodiazepines. This class includes long acting and short acting agents. If you're actually talking about diazepam, it's one of the long acting agents, which means the half-life of the metabolite in your body (and it's detection) is long.
The National Highway Traffic Safety Administration has good reasons to want to collect samples of various drugs non-invasively, and, indeed, they're headed toward saliva for screening. A neat little item called a Drugwipe can pick up traces of diazepam from not only saliva and sweat, but from surfaces people have touched.*
The real kicker, though, is hair, from any part of your body. Drug use(including diazepam) can be  detected in hair for months after (even single) use, and many employers are now going for hair sample testing to screen for drug use.
*Saliva and Sweat Testing With Drugwipe®.


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Can Helicobacter pylori be eradicated naturally?
This question is not to discuss whether substances that have anti-H. pylori activity work or not, or to discuss the pros and cons of such but from a medical perspective.
Assuming that one is able to control, reduce, or eliminate H. pylori via foods containing natural anti-bacterial activity targeted at H. pylori without the consumption of antibiotics, what is the possibility of reinfection or an overgrowth with H. pylori?

In this study, the bactericidal activity of Korean and Japanese wasabi roots, stems and leaves against Helicobacter pylori were examined... All parts of wasabi showed bactericidal activities against H. pylori strain NCTC 11637, YS 27 and YS 50.

My questions are:

If this method was carried out in vivo and the results were found to be consistent with the research mentioned above, what is the chance of developing resistance to H. pylori?
Will developing resistance prevent recolonization of the stomach lining with H. pylori?

Bactericidal activity of wasabi (Wasabia japonica) against Helicobacter pylori

Your sentence is quite confusing. Could you break it up in some meaningful way?

Do you have any evidence that you can clear H. pylori with foods? Can you share that?

To clarify - By eradication, I mean symptoms disappear, but not confirmed by testing.

Then you have not eradicated the infection.

Ok I tried, but here's what I've come up with http://www.ncbi.nlm.nih.gov/pubmed/15246236

So my questions is, if this method is carried out in-vivo, what is the chance of developing a resistance to h.pylori? And will developing a resistance prevent the re-colonization of the stomach lining?

+1 for showing your research. This is the response that saves a question from closure. I've edited your question to add the research and revised questions.

There is a flaw in your logic. You are saying that the foods have antibacterial properties and then say can the infection be eradicated without consuming an antibiotic. If you eating something that actually has antibacterial properties, then whether you like it or not, you are consuming an antibiotic. Just because it didn't come in a pill made by GlaxoWellcome, Pfizer, Merck, etc, doesn't mean it isn't an antibiotic, just that it hasn't been standardized, had safety and efficacy tests done, and been proven in clinical trials to be scientifically effective.

If I understand you correctly you would want to eat lots of wasabi and the likes to decrease/eliminate the bacterial load of H. pylori in your body.
Concerning your questions -

to be perfectly blunt here - The chance to develop resistance to a bacterium by temporarily eating something is close to 0. This can be explained by two factors:

1 - resistance could develop spontaneously due to mutations and the likes, however the chance is incredibly low if not 0 (nothing in biology is ever impossible ;) ).
2 - if you only temporarily consume an antibiotic substance you will only be protected as long as the substance is active in your system. Surely you could eat wasabi every day, but would you want to for the rest of your life? Additionally, resistance to bacterial pathogens seems to be a temporal situation since their "ability" to incorporate foreign DNA into their own arsenal as well as spontaneous mutations turns the pathogens into ever changing organisms and while you might have been resistant to the "old" bacterium, the newly mutated or modified version could still harm you - unfortunately (This is one of the reasons why it is so hard to develop anti bacterial vaccines).

If - and only if! - you would be resistant to the bacterium, than this should in theory protect you from further colonization of said bacterium. As previously mentioned this is a currently very unlikely scenario due to the limitations science is facing.

IF sources shall be needed just comment and I will search the web for something suitable ;) Hell, I might even get the chance to cite some of my own papers, finally ;)

Yes please add sources to allow users to background read on your answer

H.pylori is a bacteria that is a cause for Peptic ulcer disease of human being. It helps to create more acidic product and causes ulcer. But human body is naturally protected to H.pylore, but excess stress,irregular life style etc helps H.pylori to growth and causes ulcer. Simple measure can escape you from this infection. 1. Intake enough water 2. Maintain oral hygiene is very Imp, 3, at bed time gurgle by H2o2 ( Hydrogen per Oxyde) 3. If you are infected then triple therapy for 3 weeks is the choice of treatment

Can you please add some references for your claim?

I am a registered physician and from that respect I answered

@fazlerabbi Still best to add references.

@fazlerabbi Great to have experts here. Still references are required. If they come from your practice, there should be something available like guidelines etc.

My answer was from my own knowledge,but Here I am giving a ref. Hope it will be helpful. JOHN HOPKINS MEDICINE Health Library (p00373)

There is many possible antibacterial natural treatment using probiotics provided by natural product such kambucha,Baikkimchi,kefir (1,2,3).In the other side,plant oil extracts also studied in vivo and in vitro (4,5,6) ,but in  general, all result was relative that we can not be cured 100% with such therapy.
source:

http://nordicfoodlab.org/blog/2013/2/komboooucha
http://link.springer.com/article/10.1007%2Fs13765-014-4198-6
http://www.ijaaonline.com/article/S0924-8579(05)00054-3/abstract?cc=y=
http://cmr.asm.org/content/12/4/564.short
http://onlinelibrary.wiley.com/doi/10.1111/j.1348-0421.2004.tb03521.x/full
http://www.sciencedirect.com/science/article/pii/S0378874107004370

Which of those links are you claiming shows in vivo efficasy in humans?  Because as far as I can tell, none of them do.


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Is there nutrient absorption in the large intestine of hindgut fermenters?
In hindgut fermenters, plants are digested in the caecum by microbes. I want to know whether hindgut fermenters can absorb the nutrients obtained from the digestion in the large intestine because the absorption of digested materials is not the main function of the large intestine in other animals. I know some hindgut fermenters reingest the materials created in the caecum, but I think not all hindgut fermenters perform this behavior. I want to know the main site of absorption after the caecum.

There is quite a difference between a horse and a rabbit - for example, the colon is enormous in the horse compared to the rest of the GI tract, much less so in the rabbit. it would help if you could specify what hindgut fermenter your question pertains to.

Maybe I want to know different kinds. Is it that the ones that cannot absorb nutrients in the large intestine will reingest (e.g., coprophagy)? And others that can absorb nutrients in the large intestine will not reingest?

I have divided this answer into a section on horse and rabbit. While there are many other hindgut fermenters, these species are good illustrations of  different ways hindgut fermenters can digest and absorb nutrients from their food.
Horse
As you know, absorption of "nutrients" occurs along the intestines, but at varying degrees at different sites. Most compounds are primary absorbed in the small intestine of the horse. This includes protein, glucose (soluble carbohydrates), fats, calcium, and magnesium.
Any carbohydrates that are not absorbed in the small intestine reach the hind gut. Here they are fermented by bacteria to short-chain volatile fatty acids  (VFAs) and lactic acid. Horses can use the VFAs (propionate, butyrate, and acetate) as an energy source, but a diet too high in grain can also lead to excessive lactic acid production in the hindgut, and as a result the horse may experience colic.  As your question pertains to the hind gut, a nutrient of main concern is therefore volatile fatty acids.
The hindgut of the horse is very long and developed. To review with the anatomy of the horse hindgut, it consists of the caecum, ventral colon, dorsal colon, transverse colon, descending colon (or small colon), and rectum.

In a study in 1974, RA Argenzio et al. determined that among the parts of the horse hindgut, most VFAs were produced and absorbed in the ventral colon, 8-12 hours after feeding. This is depicted by the graph below, which shows a large negative net production of VFAs after 8-12 hours (i.e. more VFAs absorbed than produced). Note that the caecum and dorsal colon are also important sites of VFA production and absorption.

The hindgut is also an important site for phosphorus absorption in the horse, unlike many other species that primarily absorb phosphorus in the small intestine. This is thought to be because most of the dietary phosphorus in the horse in phytin phosphate, which must be exposed to the enzyme phytase produced by the microbial flora in order to be absorbed. Studies such as Schryver et al. (1972) and T. Matsui et al. (1999) have shown that most phosphorus is excreted by the small intestine and caecum, and most is absorbed in the dorsal colon and small colon. The figure below from Schryver shows the net absorption of phosphorus on the various experimental diets. Note that this is oriented opposite to the VFA figure above; absorption is positive rather than negative on this graph.

Rabbit
To begin with the rabbit anatomy, you will note that the colon of the rabbit is much less developed than that of the horse. However, both are hindgut fermenters, and what they do have in common is a very large caecum.

As in the horse, much of the digestion and absorption of nutrients occurs in the small intestine. This includes protein, fats, and simple carbohydrates (glucose), as well as some vitamins.
Also like the horse, the digestable material not absorbed by the small intestine passes to the caecum, where it undergoes fermentation by the microbial flora. The large fibrous material passes directly to the colon, where water is absorbed and forms hard faecal pellets, while the small digestible material passes through reverse peristalsis into the caecum. What is different in a rabbit to a horse, however, is that the about 8 hours after feeding, the caecal material is packaged into a small pellet called a caecotrophe. As or shortly after the caecotrophe is excreted, the rabbit re-ingests the caecotrophe. As this food has been digested once already, the small intestine is better able to absorb nutrients from it.
As an example, important nutrients that are able to be absorbed due to caecotrophy in the rabbit are the B vitamins such as niacin, riboflavin, folate, and cobalamin (vitamin B12). One of the early studies on this topic is Kulwich et al. (1953).
Summary
The reason for the difference between the horse and rabbit is fundamentally an anatomical difference. Both species have a large caecum which enables fermentation of plant matter. However, the horse has a long, voluminous colon in which it can absorb many nutrients, but they will lose protein and other nutrients in this process because the colon is less adapted to absorb them. In coprophagic (rat) or caecotrophic species (rabbit), they do not have as long a colon, but can absorb vitamins and proteins lost in the faeces during the second pass through the gastrointestinal tract.
An excellent and very detailed review of the gastrointestinal tracts and nutrient absorption in a variety of species is this freely accesible paper by Stevens and Hume, "Contributions of Microbes in Vertebrate Gastrointestinal Tract to Production and Conservation of Nutrients."
References
Argenzio, R.A., Southworth, M., and Stevens, C.E. (1974) Sites of organic acid production and absorption in the equine gastrointestinal tract. Am. J. Physiol. 226:1043-1050.
Bugaut, M. (1987) Occurence, absorption and metabolism of short chain fatty acids in the digestive tract of mammals. Comp. Biochem. Physiol. 86B(3):439-472.
Hornincke H., and Bjornhag, G. (1980) Coprophagy and related strategies for digesta utilization. In Digestive Physiology and Metabolism in Ruminants, 707-730. Avi Publishing, Westport, CT.
Kulwich, R., Struglia, L. and Pearson, P.B. (1953) The effect of coprophagy on the excretion of B vitamins by the rabbit. J. Nutr. 49:639-645.
Matsui, T., Murakami, Y., Yano, H., et al. (1999) Phytate and phosphorus movements in the digestive tract of horses. Equine Vet. J. Suppl. 30:505-7.
Schryver, H.F., Hintz, H.F., Craig, P.H., Hougue, D.E. and Lowe, J.E. (1972) Site of phosphorus absorption from the intestine of the horse. J. Nutr. 102: 143-148.
Stevens, C.E., and Hume, I.D. (1998) Contributions of Microbes in Vertebrate Gastrointestinal Tract to Production and Conservation of Nutrients. Physiological Reviews, 78(2):393-427.


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Is there a way to quantify in vivo cholesterol transport rates?
I have always had trouble grasping the physiology of lipoprotein cholesterol transport. The "standard" description found in the literature is that liver synthesizes cholesterol which is carried in "forward" transport to peripheral organs by VLDL (and LDL?), while "reverse" transport is mediated by HDL. Most tissues can synthesize their own cholesterol as well (which makes one wonder what cholesterol transport is needed for in the first place). The figure below sums it up (shamelessly taken from this review).

My question: what are the net rates of transport (fluxes) in this system?
Does the liver actually provide net cholesterol to pheripheral tissues, or is it the other way around? Or is the net close to zero? I can imagine this differs between peripheral tissues, some might be net producers and others may be net consumers, but reviews typically lump everything except the liver together as "the periphery". Perhaps some tissues become net cholesterol producers in certain situations, and consumers in others?
I can't find any data on this in the literature (reviews tend to focus on molecular details of lipoproteins, receptors etc.) but this is not my field and I'm sure the data is out there somewhere. I imagine people have done isotope tracing studies to quantify the rates of transport.

fantastic question! (I think) cholesterol flux is inherently difficulty to study... really depends on the state of the person - fasting or fed. Not sure if anyone has good tracer methods... in my dissertation we did some work with VLDL secretion from the liver (but that was just to look at triglyceride-VLDL secretion rates from the liver)... you give tyloxapol (detergent) which inhibits all peripheral lipoprotein lipase and then increase in VLDL/Triglyceride over time is estimate of liver VLDL secretion see http://www.ncbi.nlm.nih.gov/pubmed/20494946  for that technique

Wolf & Chinkes book - Isotope Tracers in Metabolic Research would probably have the techniques if they exist  https://books.google.com/books/about/Isotope_Tracers_in_Metabolic_Research.html?id=ZlA79DrpNQEC&printsec=frontcover&source=kp_read_button#v=onepage&q&f=false

@VanceLAlbaugh  Thanks, will check out the book!

If I'm not mistaken, shouldn't the CE exchange occur between HDL and VLDL? as opposed to HDL and LDL as shown here.. I mean the CETP thing.


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Can leukopenia in a person with an otherwise normal immune system lead to non-infectious diseases in the long-term?
If a person has developed leukopenia as a side-effect of long-term use of anti-convulsant medications and his/her immune system appears normal otherwise (does not get infections any more often than a healthy person, and bone marrow biopsy did not indicate anything abnormal), does the condition need to be treated? Is it even possible to treat leukopenia effectively as long as the person is on anti-convulsant medication?
Does leukopenia increase a person's chances of getting some non-infectious diseases too? I know WBC is primarily responsible for fighting infectious micro-organisms, but does it have any significant role in cleaning up body's own malfunctioning or ageing cells?

What do you mean by "non-infectious diseases"? The white blood cells are part of the adaptive immune system and play a very important role to keep us healthy.

@Chris - By non-infectious diseases, I meant chronic and potentially degenerative diseases not caused by infectious microorganisms (bacteria, viruses etc.) but due to undesirable changes happening at a sub-cellular, cellular or organ level. If WBCs have a role in eliminating malfunctioning or degenerate cells of the human body, then they may be helping prevent some diseases caused by accumulation of such cells. Hope this clarifies.

Leukopenia is just a definition. In medicine, there's a saying:

Treat the patient, not the numbers.

Numbers can mislead people, sometimes quite seriously. Definitions of leukopenia vary: some define it as less than 5,000 WBCs per µL of blood; others define it as less than 4,000.
Decreases in specific WBCs is usually described as neutropenia, lymphocytopenia, monocytopenia, etc. This, too, is important information, as each cell has a different function, and thus different results are possible.
In leukopenia, bone marrow biopsies are very informative. They reveal if the cause is a decreased production of WBCs due to destruction of precursor cells, replacement of marrow by other tissue, invasion of marrow by cancer, etc. If a bone marrow biopsy is normal, that is very comforting.

does the condition need to be treated?

Most people with anti-epileptic drug (AED) induced leukopenia are just fine. Some common-sense precautions (such as avoiding other drugs which might also cause leukopenia, and checking a white count if you fall significantly ill) should be heeded. If your doctor is a neurologist, they should be thoroughly versed in the side effects of AEDs, as this constitutes a very large patient population for them. Some of the newer AEDs have a lower incidence of leukopenia. Talk to your doctor about the potential benefits and drawbacks of switching.

Does leukopenia increase a person's chances of getting some non-infectious diseases too?

Theoretically possible, but not particularly likely.
If you are truly concerned, ask if you can get a referral to see a hematologist. They should be able to give you a real picture of the problems with long-term AED-induced leukopenia.
Remember: treat the patient, not the numbers. If you're healthy now, you're likely to continue to be so. Maybe you'll need more blood tests than others, but that doesn't mean you're not healthy. Talk to your doctors, not the internet.

Thanks for the detailed answer! Biopsy done by a hematologist some years ago didn't provide any actionable diagnosis. Since an accompanying blood test coincidentally revealed liver enzyme imbalance, was redirected to a gastroenterologist to check if liver is affected and causing low WBC as side-effect. Liver found to be normal now but WBC still low as it was years ago. Went back to hematologist who recommends repeating the biopsy to reassess bone marrow function but he was unclear as to what treatment could be given if the result is again inconclusive and only AED is the cause

Particularly appreciate you advice on taking to doctors, not the internet - hope the message reaches all internet users! Unfortunately, have to take multiple AEDs as per neurologist's advice and there doesn't seem to be a way out of these for the next few years, Even though the main AED is the latest generation one, the informational leaflet in the package mentions leukopenia as a possible side-effect.

@so2 - biopsies are necessary until there are "data points" for predictability. Also, inferno's answers is theoretical - if you had a neutrophil abnormality - that is, the ones you had didn't phagocytize appropriately - you'd know it by now. That you've not been prone to dangerous infections is evidence that you have enough neutrophils and that they're working correctly. You are likely relatively neutropenic - you have the usual complement of lymphocytes. Your WBC is low because  normally neutrophils = 75-80% of WBC count. You're probably closer to 40-50%. Again, treat the patient, not the #s.

Finally, one test you might consider is an ultrasound of the spleen, if you haven't already had one. Your hematologist will tell you why.

Thanks to you and @inf3rno! Hematologist said spleen seems normal (not through ultrasound though). Will let hematologist reassess bone marrow and advice on the next steps.

I know WBC is primarily responsible for fighting infectious
  micro-organisms, but does it have any significant role in cleaning up
  body's own malfunctioning or ageing cells?

They kill the pathogens, infected, senescent, mutated or unnecessary cells, clean up the cell fragments, clean up the oxidized LDL from the surface or arteries, etc... So I think the shortage of leukocytes can cause for example cancer, cardiovascular diseases (dependent on the nutrient composition of the food), etc... in severe cases, but it is hard to find any evidence, since these people die because of infections caused by normally harmless (or well controlled) pathogens, for example HHV8 - causes a cancer type called Kaposi's sarcoma in immunodeficient patients, saccharomycosis (S. cerevisiae, S. boulardii, etc... members of the normal flora), aspergillosis (A. niger - it is everywhere in the air), etc...
I guess there are experiments with NOD/SCID mice (which lack T-cells, B-cells, and NK cells, so a huge part of their immune system is defective), but I cannot find anything about cancer or cardiovascular diseases by them. They are usually engrafted with human cancer, etc... in the experiments, which is not the same as naturally developing cancer. Maybe if you have time to google a day or two, you can find more.
Be aware that there are many different types of leukocytes (WBCs), which have their own role in the immune system. Some of the people with leukopenia have lack only of a single type of leukocytes and not all of them. For example HIV patients have helper T-cell deficiency, people with neutropenia have neutrophil granulocyte deficiency, and so on...
I don't know anything of the treatment, I guess bone marrow transplant is involved in the severe cases. If it is caused by medication as a side effect, or you are seeking for medical advice, I think you should consult a doctor.

@inf3mo - Thanks for your response! Obviously, it is depressing to hear of these diseases, but then that seems to be nature's nature - design something very complex, make the complexity appear to be a boon, and make that very same complexity turn out to be a bane for many.
Posted the question because the previous biopsy did not lead reveal anything actionable. Was wondering if a repeat biopsy suggested by the doctor would be useful at all, especially since he could not tell if any treatment is even possible if the result is the same and AED is the only suspect. Stopping AED is not an option :(

@so2 Using another AED is your doctor's choice. There are many drugs, and I guess not all of them is immunotoxic. Your doctor should measure your WBC levels and decide what to do. I found only this article in the topic. AEDs increase the risk of relapse in patients with cancer according to this article.

Thanks for those links! Will let the hematologist do a reassessment & if he feels the condition warrants a change in prescribed AEDs then send his recommendation to the neurologist. Many specialists work in a silo-mode and don't take a holistic view of a patient's health - neurologist never ever told about the side-effects of AEDs & it was from the internet & later from medicines' informational leaflets that I came to realize they have hematologic side-effects.
Site doesn't allow me to accept 2 answers. Chose anongoodnurse's answer on 1st-come basis but your replies were equally helpful!

@so2 No problem.


text:
Why would yeast grow but not produce alcohol?
I'm studying for my intro to microbiology test and I have a question asking why a culture of yeast responsible for producing alcohol would be growing, but not producing alcohol?
The multiple choice answers are:
a) the maltose is toxic
b) O2 is in the medium
c) Not enough protein is available in the agar
d) The temperature is too low
e) The temperature is too high
EDIT: There is not much more context that what I gave here. The question simply asks me to assume the position of a scientist at a wine production company, and then asks the question I posed above - nothing too specific.
I think it is (b) because the presence of O2 would cause the yeast to respire aerobically, but I can't eliminate (d) and (e)
I figure it probably isn't (a) because a toxic chemical would inhibit the growth of the yeast. I don't believe protein is relevant so I don't think it is (c).

I think we generally ask people with homework questions to explain their work and reasoning as much as they can first. Look up some stuff about yeast fermentation and you might answer this yourself. And please clarify how the yeast is making bacteria?

Changing the temperature would tend to cause the rate of metabolism to increase/decrease, but it would not tend to cause the actual metabolic products to change significantly.

I think only b.) is true.

a. I cannot find evidence that maltose is toxic to yeasts (and I would hardly believe it, because it is a glucose dimer), however I found evidence, that yeasts might need the presence of oxygen to process maltose.

1977 - The Requirement of Oxygen for the Utilization of Maltose, Cellobiose and D-Galactose by Certain Anaerobically Fermenting Yeasts (Kluyver Effect)
1994 - Effects of oxygen limitation on sugar metabolism in yeasts: a continuous-culture study of the Kluyver effect.

b. Alcoholic fermentation is an anaerob process, so it won't work in the presence of oxygen.
c. Alcoholic fermentation is for creating energy. Proteins are normally not involved as substrate (maybe by gluconeogenesis, but that's another story). If the yeast grows, then there is enough protein available to build fermentation enzymes as well.
d. I found some articles about the temperature dependency of alcoholic fermentation:

Juices fermented at 10°C exhibited ethanol concentrations between 7.4
  and 13.4% and populations of K. apiculata, C. stellata and C. krusei
  in the range 106-108 cells/ml.

1988 - The effects of temperature and pH on the growth of yeast species during the fermentation of grape juice

At low temperatures, alcohol yield was higher. Secondary metabolites
  to alcoholic fermentation increased as the temperature increased.
  Glycerol levels were directly affected by temperature.

2003 - Effects of fermentation temperature on the strain population of Saccharomyces cerevisiae

The immobilized yeast showed an important operational stability
  without any decrease of its activity even at low temperatures (1−12
  °C). Specifically, at 6 °C the biocatalyst favored wine production
  within 8 days, which is less time than is required for the natural
  fermentation of grape must.

2001 - Wine Production Using Yeast Immobilized on Apple Pieces at Low and Room Temperatures

It seems like low temperature does not necessary have an adverse effect, but this could depend on strain.
e. Just the same as the previous answer. I think the main fermentation products will be always ethanol in the yeasts chosen for alcoholic fermentation (if the other conditions are right), so it is not temperature dependent in this case. A growing yeast will produce alcohol on both low and high temperatures. The ratio of ethanol and the byproducts can depend on the temperature, but not the presence of the ethanol itself. By too low or too high temperature the yeast will die or will stop to grow. (My experience that CO2 production is faster by high temperature, so it is because everything is faster or because the ethanol/CO2 ratio is lower.) An example of temperature dependence by wine making:

Temperature control is vital in the production of fine table wines as:

High temperatures encourage the loss of alcohol and aroma and flavour compounds due to volatilisation. If the temperature goes above
  30 -35ºC, the yeast becomes sluggish and fermentation may stop.
Low temperatures will lead to a poor extraction of colour and tannins in red wines and can also cause sluggish fermentations and the
  production of high levels of ethyl acetate.

Managing the alcoholic fermentation

I think "sluggish" means stop growing in this case, and ofc. stop fermenting due to the death of the yeast cells.

I think you put in way more effort than this question required. Not that that's a bad thing.

@canadianer Maybe. Btw. your answer is perfectly valid too, and you solved it with pure logic, +1 :-) Ohh I have not known that this is an old question.

Depends on the yeast but some (most notably S. Cerevisiae) readily ferment in the presence of oxygen. So this question is a little ambigious. Although not surprising for biology, Im surprised the microbio prof did not clarify the question.

IMO, the answer to this one is (b). The reason is the (often overlooked) Pasteur effect: oxygen inhibits fermentation.
The Pasteur effect occurs in many cell types, including skeletal muscle, brain, heart, liver, bacteria and yeast (Tejwani,1978) .
The mechanism of the Pasteur Effect has been much studied and debated and it it probably true to say that it has still not been fully explained. However, in abstract terms, it  be explained to a good approximation in terms of the allosteric regulation of the the enzyme phosphofructokinase, a key regulatory enzyme of glycolysis, where ATP, inorganic phosphate, and citrate (among other allosteric effectors) play critical roles. (Krebs, 1972, Tejwani, 1978).
Refs
Krebs, Hans (1972). The Pasteur effect and the relations between respiration and fermentation. Essays in Biochemistry 8, 1–34.
Tejwani, G. A (1978)  The role of phosphofructokinase in the Pasteur effect.  Trends in Biochemical Sciences, Volume 3, pages 30-33

You're right, the answer is b since the presence of oxygen would lead to aerobic respiration and not fermentation.
If maltose was toxic, the yeast wouldn't grow.
Proteins are required for growth, but the yeast is growing.
Any temperature that is extreme enough to prevent fermentation would also prevent other cellular processes and the yeast wouldn't grow.

all_licenses: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/


text:
Why do neurons have long axons but short dendrites?
Cian O'Donnell, a British neuroscientist, originally asked this question on Twitter: https://twitter.com/cian_neuro/status/1075432086692089857. I am not a biophysicist by training but I wonder whether there might be existing publications that have shed light on this question.
My primitive back-of-the-envelope analysis involves the following:

If we suppose that most neurons are limited to a volume V, give or take epsilon volume, and the function of axons is to carry a signal over a large distance whereas the function of dendrites is to integrate information from different sources then a semi-spherical radiation of dendrites should be the norm.
This becomes an extremal optimisation problem where there are specific constraints on the minimal axon thickness, the minimal dendrite thickness and an upper-bound on the average number of dendrites that fan out of a given axon.
This becomes an extremal optimisation problem where there are specific constraints on the minimal axon thickness, the minimal dendrite thickness and an upper-bound on the average number of dendrites that fan out of a given axon.

This is a very sloppy analysis which ignores biophysical constraints but I think that we have an extremal optimisation problem here.

Axons are used to transfer electrical signals from Point A to Point B.
Dendrites are for receiving electrical signals from different neuron cells via their respective Axons.
There are mainly two different types of Axons, insulated and non-insulated.
Insulated Axons allows extremely high velocity of electrical signals to propagate from Point A to Point B. Please note that insulated axons are not entirely insulated, the axons are only insulated at every given interval for a certain length (in measurement of distance). This forces the electrical signal to jump from one gap to another gap between insulation and result in extreme speed of electrical signal propagation down the axon.
Non-insulated axons still allow high velocity of electrical signal propagation but it is very much slower as compared to insulated axons. This is why when you have a stomach ache, its a slow and dull pain due to non-insulated axons which gives you prolonged pain signal. However, if you accidentally knock into a sharp object, you receive an instant sharp pain for a split second for you to react at that instant (Its a biological life saving function) due to insulated axons that gives you extreme speed of pain signal propagation.
On the other hand, dendrites are not built for signal transmitting but for signal receiving. Dendrites comes in different configurations, one such examples are your color sensory cells in your retina.
This is why dendrites are short while axons are long. They are configured for different purpose. Just a bit more information, electrical signal in biofluid are actually ionic current. Ionic current are different from electron current, the charge carrier are different. Lastly, electrical signal are generated due to electrochemical gradient on cellular level. When a certain membrane potential threshold is reached, action potential will be triggered and they resulted in the firing of electrical signal down the axons.
I hope you find these useful.
Best Regards
Price

To me it makes sense. Axons are optimized for speed, dendrites are optimized for networks. It explains why the size is different in the "typical" neuron.

I'm not sure that statement holds true. Pyramidal cells are one of the primary excitatory cells in the cortex and are characterized by their long apical dendrites.


text:
What happens exactly in the electron transport chain when there's no oxygen
what is the mechanism of hypoxia in the electron transport chain? It stops because there's no terminal electron acceptor so the IV complex become "stuck" with an electron? There's no other molecule that can accept electrons just like the oxygen?

This article suggests fumarate is an alternative terminal acceptor under low-oxygen conditions

@Aditya thank you.


text:
How often are diseases caused by more than a single mutation of a gene?
Many genetic diseases are caused by mutations in a gene and often, it is a single nucleotide polymorphism (SNP) that has dramatic consequences (e.g. the E6V hemoglobin mutation in sickle cell disease). Other diseases are the result of multiple mutations, that have occurred within various genes (often in cancer).
My question is, are there also many (or any?) known diseases that only manifest if two or more particular mutations arise in the same gene? My assumption is that they exist, but are rather rare; an ideal answer would point me to a publication with quantitative data: how many known diseases are caused by a single mutation, how many by double, etc.
Regarding alleles: I am not asking whether mutations have to occur homozygously to manifest; I'm talking about mutations in the same copy of the gene; for coding sequences, we would be talking about a double (triple,...) mutant of a protein.

I doubt that such data exist: it would mean a) enumerating all the possible (genetic) diseases, and b) knowing exactly what kinds of mutations are responsible for each of them. There may be also ambiguity in defining what are different diseases and what is not - liek in the case of cancers.

Would Huntingtin mutations fit?

@RogerVadim OMIM is a good database for that but one would have to look at specific diseases. However, I didn't a table of mutations and the associated diseases.

I think that this question cannot be quantitatively answered, because the baseline "non-disease" state is not well defined.
Let's take as a starting point the example that you gave, of sickle cell disease. It turns out there is not actually a single mutation that can lead to the disease, but a number of different mutations. A person with only one of the two copies of their hemoglobin genes affected will be a carried but will not have a sickle cell disease. A person who is affected in both copies will have some form of sickle cell disease, though the specifics will depend on the mixture of mutations present. Does this count as one or two mutations? Would it be counted differently if each copy has the same mutation or a different mutation? What about for the carriers, who have the same mutations, but not the disease?
For another example, consider the case of BRCA1. A person with this gene disabled is highly susceptible to cancer. Should this be counted as a mutation that causes a disease, or should only the mutations on the path to the cancer itself?
It only gets worse when we start considering more complicated questions of susceptibility and potential risk, such as associations between SNPs and heart disease, where the causal relationship becomes extremely murky indeed.
Bottom line: I think that biology has too much fuzziness for a crisp answer to this question in this form.

Updated question to clarify alleles; but question is clear: "are there diseases that only manifest if two or more mutations arise in the same gene". Yes, sickle cell can also manifest with >1 mutation, but one suffices --> not an example of a disease that only manifests if there are >1 mutations. Arguing about disease definitions is also not helpful; there are ressources online that define diseases e.g. here. Ok, there's no IUPAC defintion, but that's okay. For any given definition of a disease: how often are they caused by double mutants?

@Anonymous I still think the concept is ill-defined, because you can't distinguish between "gene with one of two mutations required for disease" and "gene requiring only one mutation for disease"


text:
How to generate PDB file for custom DNA squence(10 base pairs)
I am trying to study docking of drug-DNA interaction and for that I need PDB file.
How can I get a pdb file for my custom dsDNA sequence (10-11 base pairs long)?
I will really appreciate if you can please guide me.
Thank you all for your time.

Pymol can build nucleic acids and is free for students.

Please edit the question to limit it to a specific problem with enough detail to identify an adequate answer.

Further to @canadianer here ins a link that looks as if it might be helpful https://pymolwiki.org/index.php/Builder .


text:
Neuron Growth and Regeneration
Are nerves and/or neurons able to grow and repair after damage, but not regenerate? Is this specific to humans? I have heard of people being paralyzed, but after much therapy are able to use their legs again. Is this just through the creation of new connections from healthy nerves, or is there nerve repair to an extent?

the following is true for humans, I dunno about other animals:
schwann cells in peripheral nervous system can rebuild a severed axon if the perineurium of the nerve fibers are sutured together ... the same is not true for oligodendrocytes in the central nervous system. Thus only peripheral nerves can regenerate and not nerves located in the central nervous system (ie. spinal cord or brain).
surgical nerve regeneration after a nerve is severed is not the only possible form of nerve regeneration, another example would be when the facial nerve is damaged by bells palsy and then it regenerates itself. so a fun example of what can go wrong is when some of the nerves switch when they regenerate, so your brain thinks it's doing one thing, but since the nerves switched when they regenerated, it does the other. The example would be "crocodile tears syndrome", it has nothing to do with crocodiles (thats just the name) but rather this is where the facial nerves salivation fibers get switched with the crying fibers... so when they eat they cry...
as for neuro-rehabilitation in people suffering paralysis, this is a broad question. As I understand it, if it's the spinal cord thats cut then it will never regenerate, but if its a nerve that left the spinal cord (a peripheral nerve) than it may possibly regenerate. Here are some specific conditions:
Also it could be a temporary thing like Guillain-Barré syndrome where the immune system (hyper sensitized by a previous campylobacter bacteria or CMV virus, or for some other reason) temporarily injures the peripheral nerves and then after about 2 weeks they recover)
also there is there are drugs and toxins which are temporary, so one your body metabolizes/excretes (bile or urine) it is gone: botulinum toxin (from bacteria Clostridium botulinum), curare (south american plant poison), the many chemically modified versions of curare produced by pharmaceutical used in surgery to relax the muscles, and the list goes on for drugs/toxins. Again, drugs/toxins are temporary.
Stroke, though in the central nervous system, might be able to be rehabilitated since maybe everything wasn't destroyed (even though what was destroyed was destroyed permanently), and the patient can salvage what is left and use their neuroplasticity to try and use their brains slightly differently to be able to recover.
ALS, affects the ventral horn of the spinal cord... this one is irreversible at least today.
there are many other causes of paralysis which may nbe reversible or irreversible
glossary

schwann cell= the fatty cell that wraps around an individual nerve in order to myelin ate it... myelination being the fatty insulating of axon so they send electric signals faster...
axon= a projection off of the cell body that sends an electrical impulse to the end of the nerve that ultimately communicates with the target nerve/muscle/gland/etc
perineurium= outside protective sheath composed of connective tissue covering many nerve fibers
oligodendrocytes= the equivalent of a schwann cell, but in the central nervous system, it myelinates many nerves, unlike the schwann cell which only myelinates 1 nerve.
nerve fibers= a collection of many nerves running together
facial nerve= facial nerve innervated the muscles of the face and there are 2 facial nerves, one for each side of the face. the facial nerve doesn't only do face muscles, but also taste, salivation, and tear formation
bell's palsy= when the facial nerve stops working and half the face gets droopy... there are a lot of possible causes, like virus bacteria, and many many noninfectious causes...

That is really helpful and interesting, thank you!


text:
Is Insulin-Glucose dynamic Lotka-Volterra?
From Wikipedia:
The Lotka–Volterra equations, also known as the predator–prey equations, are a pair of first-order, non-linear, differential equations frequently used to describe the dynamics of biological systems in which two species interact, one as a predator and the other as prey. The populations change through time according to the pair of equations:
\begin{align}
\frac{dx}{dt} = \alpha x - \beta x y \\
\frac{dy}{dt} = \delta x y  - \gamma y
\end{align}

This looks very similar to how Insulin and Glucose interact with each other in the body.

Glucose uptake release insulin and glucagon offsets the effect of insulin through glycogenesis.
Can the Glucose-Insulin dynamic be described as Lotka Volterra?

Is there a model for glucose-insulin relationship. I guess there may be several. Lotka-Volterra is basically a negative feedback model and there are several examples of negative feedbacks (they are not referred to as Lotka-Volterra because it is model for a specific case and not a modelling strategy). You should clarify your question. Without looking at the model no conclusions can be made.

Is the standard Lotka-Volterra (LV) model an exact fit for insulin-glucose (IG) dynamics? No. Can a similar model built on the same principles capture most of the essential features of the IG dynamics? Absolutely.
How to capture most of the insulin-glucose dynamics using a slightly modified Lotka-Volterra model
We can figure out how to change the LV equations to fit the IG dynamics by figuring out how our assumptions have changed. Like Daan mentioned, neither insulin nor glucose undergo self-reproduction. So we'll drop those terms from the equation, and we'll represent an influx of glucose (as from, say, a meal) as a simple time-dependent linear spike. Your rate equations will now look like:
$\frac{dx}{dt} = \alpha[t_{gi} < t< t_{gf}]-\beta x y$
$\frac{dy}{dt} = \delta x-\gamma x y$
where $x$ is glucose concentration, $y$ is insulin concentration, and $[t_{gi} < t< t_{gf}]$ is equal to 1 if the current time $t$ is greater than the time when the glucose spike starts $t_{gi}$ and less than the time when the glucose spike ends $t_{gf}$, and is equal to zero if the time $t$ does not meet this condition.
Simulation of insulin-glucose dynamics using the above LV model
I ran a simulation of the above model in Matlab, and here's what it looks like:

The basic features of the insulin-glucose dynamics from the example graph the OP posted are present. Just like in the real system, first the glucose spikes, then the insulin spikes after a short lag, then they both return to baseline.
With some small improvements, the LV model can capture the dynamics of the infamous "sugar crash" phenomenon
Now for the really cool part.
As can be seen on the OP's graph, glucose levels tend to fall somewhat below their baseline following a large glucose spike. This is the physiological basis for the sugar crash that people sometimes get a little while after eating something really sugary like a candy bar. Regardless of whether the psychological symptoms actually occur, the dip in glucose levels is a real thing.
In order for a model to be considered "good", it has to be able to capture these kinds of complex but important phenomena in their underlying systems. The glucose dip did not show up in my original LV model, so the question is, can the model be modified in a simple way so that it will capture the dip? Let's take another crack at it!
Part of the problem with trying to study phenomena related to baseline levels using the previous model is that the baseline levels of both insulin and glucose are effectively fixed at 0 in that model. We can set the baseline levels by adding what's called a zeroth-order production term (essentially a fixed constant that isn't multiplied by the concentration of anything) to each of our rate equations. The rate equations now look like:
$\frac{dx}{dt} = \alpha[t_{gi} < t< t_{gf}]+\epsilon-\beta x y$
$\frac{dy}{dt} = \delta x+\eta-\gamma x y$
where $\epsilon$ is the 0th order glucose production term, $\eta$ is the 0th order insulin production term, and everything else is exactly the same.
Simulation of insulin-glucose dynamics using the "dip-enabled" LV model
Again using Matlab, I ran a simulation of the "dip-enabled" LV model:

and this time the dip shows up.
Notes:
-The term with the times in it is called an Iverson Bracket.
-You could make this model more physiologically relevant by using a more complex function for the glucose spike, but for simplicity's sake we'll stick with a linear function. A smoother function, like for example a Hill function, would probably help to reproduce your original graph of the IG dynamics.
Matlab code
function dxdt = insulin_glucose_birth_death_dxdt(t, x, kip, bip, kid, kgp, bgp, kgd)
dxdt = [kip*x(2) + bip - kid*x(1),
    kgp*(t>1 && t<2) + bgp - kgd*x(1)*x(2)];
end

function [t,x] = insulin_glucose_birth_death_odesol(tspan, x0, kip, bip, kid, kgp, bgp, kgd)
opts=odeset();
[t,x]=ode45(@(t,x)insulin_glucose_birth_death_dxdt(t, x, kip, bip, kid, kgp, bgp, kgd), tspan, x0, opts);
end

function [t,x] = insulin_glucose_birth_death_plot(tspan, x0)
%run with:
%   tspan = [-10, 5];
%   x0 = [0,0];
%   [t,x] = insulin_glucose_birth_death_plot(tspan,x0);

kip = 2;
bip = 0;  % set to .01 for the "dip" simulation
kid = 1;
kgp = .1;
bgp = 0;   % set to .1 for the "dip" simulation
kgd = 50;

[t,x] = insulin_glucose_birth_death_odesol(tspan, x0, kip, bip, kid, kgp, bgp, kgd);

figure(gcf)
hold on
plot(t, x(:,1), 'b', t, x(:,2), 'r')
legend('insulin','glucose')
xlabel('time')
ylabel('concentration')
axis([0 inf -inf inf])
hold off
end

You need not include the code. That is not really necessary. Instead you can explain the mathematical model better.

Interpreting your question as "would the Lotka-Volterra predator-prey model be a good model for the glucose-insulin system?" my answer is "no". The predator-prey equations capture assumptions about how prey and predator interact with each other, and how they would fare on their own. These assumptions are not equivalent to any reasonable assumptions about the glucose-insulin system. The fact that both prey and predator population sizes as well as glucose and insulin concentrations oscillate is not enough to say the two systems may be modelled by the same equations. In fact, the oscillations in the figures you show are very different form each other.
Let us go through some of the assumptions of the Lotka-Volterra predator-prey model to see why most of them do not resemble anything related to the glucose-insulin system.
1) In the absence of predators, the prey population grows exponentially without limits. This follows from self-reproduction. If glucose were likened to prey, glucose would increase exponentially in the absence of insulin. If prey were likened to insulin, insulin would increase exponentially in the absence of glucose. Is that reasonable?
2) The population growth rate of the prey is reduced by a quantity proportional to the population sizes of both prey and predator. The underlying assumption is that prey and predator meet a rate proportional to their population densities and that a fraction of these encounters leads to the death of the prey. The assumption about the encounter rate is called the Law of Mass-Action, and applies well to chemical compounds in a liquid, like glucose and insulin. However, glucose and insulin do not interact directly, and it is not clear to me how realistic assumptions abut their interaction would work out.
3) New predators are born at a rate proportional to the encounter rate in 2). In the glucose-insulin system this would mean that more insulin is produced if more insulin is present. Is that realistic?
The answer to these questions is, according to me, "no".
(On a side note: the Lotka-Volterra model is structurally unstable, meaning that slightest change in the assumptions would fundamentally alter the outcome of the model. One of these outcomes are neutrally stable predator-prey cycles, that is, cycles of which the amplitude and period depend on the initial population sizes. Changing the assumption that the prey population grows exponentially by including a term - $m \times x^2$ to the first equation changes the oscillations into damped oscillations so that the populations settle at a stable equilibrium.)

No, the Lotka-Volterra model is a description of predator-prey dynamics. Although in some respects over-simplifying it is well suited for educating population dynamics and basic research.
The physiology of carbohydrate homeostasis is different. Although, similar to population count in the Lotka-Volterra model, the elimination of both glucose and insulin depend on their respective concentrations (which represents a very basic form of autoregulation), their interdependence is different. Here, we have to consider distribution processes, receptor binding, enzyme kinetics etc.
Numerous mathematical and cybernetic models have attempted to describe glucose-insulin homeostasis. The following review articles provide a good overview of the topic:

Ajmera I, Swat M, Laibe C, Novère NL, Chelliah V. The impact of mathematical modeling on the understanding of diabetes and related complications. CPT Pharmacometrics Syst Pharmacol. 2013 Jul 10;2:e54. doi 10.1038/psp.2013.30. PMID 23842097; PMCID PMC3731829.
Palumbo P, Ditlevsen S, Bertuzzi A, De Gaetano A. Mathematical    modeling of the glucose-insulin system: a review. Math Biosci. 2013    Aug;244(2):69-81. doi 10.1016/j.mbs.2013.05.006. Epub 2013 Jun 1. Review. PMID 23733079.

There is an important difference in the dynamics of the 2 situations.
The Lotka-Volterra model undergoes repeated oscillations in predator and prey levels. Changes in one population affect the changes in the other population, and vice versa.
In the glucose-control model, what you have plotted are the changes in glucose and insulin levels following a meal or infusion of glucose. Note that there is no subsequent peak of glucose after the insulin levels have dropped, unlike the peaks in prey levels after predator levels have dropped in the Lotka-Volterra model.

Negative feedbacks can lose oscillations if certain parameters are  changed. This is called the Hopf bifurcation. Just because a system ceases to oscillate doesn't mean that the model structure has changed. Anyways, since the OP has not really shown the mathematical equations underlying the glucose-insulin plot, nothing can be said. I am surprised why this question is not closed yet.


text:
How does core-conductor model correspond to an actual neuron?

Hi guys, looking at your average neuron, it is very difficult for me to imagine how this could be translated into a core-conductor model

On the neuron above, where would be the intracellular space and where would be the extracellular space? Also, where is this membrane we are talking about?

What may be confusing is that the myelin is wrapped around the membrane of the axon.
The easiest way to see this is in cross-section:

From here.
The axon is indicated by #1 in the diagram and the myelin sheath is #4
The intracellular space (as represented by the horizontal resistors in the case of your model of the axon) is the fluid, replete with ions, that is contained within the membrane of the axons.
At the nodes of Ranvier, there is a break in the myelin sheath, exposing the underlying membrane of the axon.  In membrane in those gaps of the sheath, there are sodium channels (voltage gated) and potassium channels that facilitate the influx and efflux of ions that "refresh" the action potential as it travels down the axon.  The extracellular space is simply the milieu of fluid in the space between the axon and any adjoining cells.  For the purposes of analyzing the currents of the neuron, the sodium and potassium ions (and the conductances of the channels) are all that you really need to be concerned with.
What is confusing about your diagram is that it represents the conductance -- the inverse of the resistance of the channels -- of the channels (inwards and outwards) as a single vertical resistor in between the horizontal resistors of the intracellular membrane. This oversimplification is handy when doing the cable theory-type analysis, but it betrays the actual physiology of the neuron.
From a model standpoint, I'm breaking all the rules here, but you can think of things like this:

where one "rung" of your resistor ladder has $r_m$ broken out into the 2 components and drawn differently.

That's probably clear as mud, and I've glossed over a lot, so feel free to ask questions and I'll fill in the gaps.

Hi just to clarify. So the membrane is the axon membrane, the intracellular space is lies within the axon (so the cytoplasm within the axon) and the extracellular space lies outside of the axon and between the neurons (another type of fluid I guess). The breaks between the myelin sheath is used to refresh the action potential and is not modelled. could you provide a realistic example of core-conductor cable model of a neuron? You said the verticle resistors are not realistic and does not represent a part of the neuron.

@IllegalImmigrant The breaks (nodes of Ranvier) on the myelin sheath are modeled by the electrical nodes between the horizontal resistors in your model.  These are the only places between the hillock of the axon (the pointy part at the end of the cell body) and the terminal where ions are being exchanged.  At the other points along the axon, the receptors are covered over by the myelin, so no current leaks out with the movement of the ions.  The vertical resistors are realistic, they just betray the complexity of the actual voltage-gated influx through sodium channels

and the potassium efflux.  There are different subtypes of these potassium channels as well (so Rm take a lot of information about conductances/resistances and jams it down into one component).  My "grounds" in my circuit are a bit exaggerated, since the currents leaving and entering the axon can propagate through the ions in the extracellular milieu.  I just wanted to illustrate that the conductances could be split off into the different components, but it was still justifiable to combine them.

The core conductor model is very limited in scope.  It may be helpful for you to take a look at Hodgkin and Huxley's work with the compartmental models as a way of exploring the limitations of cable theory.


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What is the so called "hepatic glucose production"
I came across this term in my readings but I do not understand how this works. Can someone direct me to some reference as to what this "hepatic" glucose production is all about?

Hepatic refers to the liver, which is the predominant location of gluconeogenesis.

Silly me, I mixed hepatic with haptic (as in haptic feedback) and got totally confused

"Hepatic glucose production" is the gluconeogenesis process (the opposite of the gycolysis process), that is the formation of glucose primarily from lactate and amino acids. This process takes place in the liver's cells and it is regulated by hormones (insulin and glucagon).
Look here and here for a better explanation!


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Why should or shouldn't we allow the human body to take its natural course?
For example, when you are sick but don't feel thirsty, this could be due to baroreceptor reflex that is attempting to readjust salt and water balancing.
Why shouldn't a patient be left thirsty and let the body to adjust until he or she feels thirsty again?

Are you suggesting that we should throw away modern medicine and go back to natural selection?

I find this very unclear and broad (there are a huge number of processes and responses to consider).

imagine you have diarrhea and eventually will lose a lot of water. Would you like an IV with saline/vitamins or to be left alone?

I am assuming that your question is: "why can a human intervention improve health?". Let me know if I misunderstood your question.
Why can a human intervention improve health?
Let's first avoid going into the details of your example. It is quite obvious that human intervention can often improve health in a way that your body alone cannot. To me, an intuitive way to classify the reasons why human intervention are important to improve health into two categories.

The body does not always react in an adaptive manner.

Example: Anaphylaxis is a serious and sudden allergic reaction that may cause death. An allergic reaction is what is happening when your immune system recognize a chemical as a infectious element while it is not. The reaction of the body is not adaptive and taking medication such as an anti-histaminic can force the body to stop this "stupid" reaction.
Note: There are reasons why the body cannot be always perfect but it is a bit long to make an overview here. There is stochasticity in the developmental processes, there is genetic variation for example due to always occurring deleterious mutations, there is also an arms race between parasites and host. This arm race leads parasites to take advantage of normal host physiological pathways. There are tons of other reasons that relate to the stochasticity and to the physic and physiological constraints of evolutionary processes.

The body sometimes cannot (physical constraint) produce the action that is required to be performed to improve health.

Example:  If you have an important wound, then a human-made compression can by far improve your chance of the survival. The body is not able by itself to simulate this external compression to prevent blood to exit the body through the wound.

You might easily find semantic issues with these categories though such as the question of cancer and its removal for example and some may argue against this categorization.
Dehydration and thirst
Your example would fall into the first category. It is not so uncommon that the body needs water while not causing thirst. Because after 50 years old, the sensation of thirst start to diminished, dehydration without the sensation of thirst is common among old people. Dehydration along with hyperthermia is a relatively important cause of death during hot weather in summer. It is especially true in old people as the sensation of thirst diminishes with age. Dehydration following diarrhea is also a common and important issue in old people sometimes leading to death.

Dehydration/hyperthermia isn't just an issue for elderly people, it can affect anyone.

I meant that it is an issue of particular importance in old people as old people the sensation of thirst decreases with age. Feel free to edit my answer to clarify this point if it is a bit unclear.

I'd also add that many pathogens have evolved to abuse reflexes that would otherwise be beneficial. Coughing for transmission of airborne disease, fungi causing itch...

It is a good point. I felt it quite complicated to add this point without having to make consideration of the other evolutionary processes that may explain why an individual does not always react adaptively. I put all that in some kind of messy text as a "note" under the first category.


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What is the insight of Frank Starling law of the heart?
The Frank Starling law appears to be a trivial observation:
stroke volume is directly related to the end diastolic volume
In everyday language, as more blood fills the heart, the heart pumps more blood out.
Can someone point out whether there are some inaccuracies in the above description because I don't understand why every article on FS law requires upward 20 pages. Even youtube video on this topic is 8 minutes long.
What is the big idea here that I am missing?

This is the short answer from wikipedia :) :

As the heart fills with more blood than usual, the force of cardiac
  muscular contractions increases.[2] This is a result of an increase in
  the load experienced by each muscle fiber due to the extra blood load
  entering the heart. The stretching of the muscle fibers augments
  cardiac muscle contraction by increasing the calcium sensitivity of
  the myofibrils, [3] causing a greater number of actin-myosin
  cross-bridges to form within the muscle fibers. The force that any
  single cardiac muscle fiber generates is proportional to the initial
  sarcomere length (known as preload), and the stretch on the individual
  fibers is related to the end-diastolic volume of the left and right
  ventricles.
In the human heart, maximal force is generated with an initial
  sarcomere length of 2.2 micrometers, a length which is rarely exceeded
  in the normal heart. Initial lengths larger or smaller than this
  optimal value will decrease the force the muscle can achieve. For
  larger sarcomere lengths, this is the result of less overlap of the
  thin and thick filaments; for smaller sarcomere lengths, the cause is
  the decreased sensitivity for calcium by the myofilaments.

in one sentence, it is a response to tension.


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Tribes outside humanity
All humans are a group with common ancestry but some humans distinct themselves into sub-groups by "distinctive ancestry" and tend to ask other humans "where are you originally from" as to get a satisfying answer about the other side's "distinctive ancestry".
Asking for a precise meaning of this vague question might bring different "exact" versions such as "where were you born?" (some people were born in a ship or an airplane) or "What is your country"? (some people don't affiliate themselves with any country / "stateless") but in the end it generally boils down to "distinctive ancestry".
Is this tendency of many humans to classify other humans into these groups of two or more families with a "distinctive ancestry" (but not by the general group of humanity and not by nuclear family) exist in animals (of course, not by asking "where are you originally from" but with much more simple or "primitive" ways of communication)?
Do cows/lizards/sheep/squirrels/cats, etc. have a similar classification mechanism?

Do you mean as wolves do?

Welcome to Biology.SE. As written essentially any animal with even the most rudimentary social structure (e.g. anything that forms pair bonds for a breeding season) would fit your criteria. Questions on this site are expected to be focused, clear, and demonstrate evidence of prior research (see [tour], [ask], and other [help] for details). In addition, questions that would seem trivial to biology professionals (such as this) are considered "homework" — please read the rules for such questions and [edit] or delete your question accordingly.

Question broadly edited.

Any of the ungulates, felidae, canids, most schooling fish and social insects still fit the description as I read it.

@bob1 I know that wolves and birds pack themselves into groups / migrate but I don't know if this must be based on some "middleground ancestry".

Also, human "tribes" are often not about shared ancestry, but shared beliefs: religion, fans of sports teams, being a supporter of a certain former US President...

@jamesqf 100% but these are not "at minimum" or at least don't bring a question such as "where are you originally from".

@al-harumi-jidan - but to the best of our knowledge neither do animals, other than recognizing a "foreigner" by scent or sight, AFAIK most animals don't have the mental abilities to think more than "us" and "not us"

@al-harumi-jidan: Because "Where are you originally from?" is not usually relevant to those kinds of tribes.

It seems like your underlying question may be more psychological/social than biological. If you want to know why some people seem obsessed with labelling  people who don't look like them that really doesn't belong on this site. To make this a biological question, you probably need to find a word that doesn't carry the connotations that "tribe" has. For example, are you interested in the question if you replace tribe with something like extended family group? If you are then do some reading based on the multiple hints above and rewrite accordingly. If not please delete it.

@tyersome My question is about biology; I have described a phenomenon common between humans and want to know if there is anything near to it with animals. I think you would need to excuse me from not knowing which term to use instead tribe (which is obviously the nearest thing I could come with). Non registered users can't delete questions and I would not have deleted the question even if could !

Historically distinct human ancestry was to a large extent due to limited mobility (although also some assortative mating) - this has been changing obly in the last few decades, and mostly in developed countries.

Your problem is questions like "were were you born?" require adaptations and concepts that to do not appear outside humans in extant animals. The very idea of a question is a human thing. you may however be interested in the tribal behavior of chimpanzees. https://scholar.harvard.edu/files/glowacki/files/wrangham_glowacki_2012_warfare_hunter_gatherers.pdf


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Ants carrying metal scew
Today I saw a few ants carrying a metal screw with them.
Video
What might be the reason behind this?  (nesting material?)

Is there any reason why they shouldn't be doing that?

I think the question is reasonable - this seems like very unusual behaviour. Perhaps there was organic material (food stuff) in the threads of the screw and they assumed it was wholly made of food.

Damn. It's just fascinating watching them cooperate like that. From the way they are sometimes stumble from lack of perfect coordination, they could probably carry it with fewer ants than there are. If you see a bunch of humans moving a couch, if we stumble like that the entire couch falls so those ants are working below capacity I think.

+1 for the video. Maybe they're building something. If so, please post the video of them using the screwdriver, which ought to be even more fascinating.

ants use the materials avaliable to them it is why you can find glass plastics and other non natural building materials in many ant hills.

How can you be sure the screw was made of metal?


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What is this plant (see the photo)?
EDIT: Found in Asia, China, latitude ~25 degree. Size about several centimeters.
I wonder what this plant is? It looks quite unlike the plants we see everyday. I have tried photo search engines and apps, but cannot find anything.

Looks like a fungus. Please [edit] your post to include location info about the photo and approximate size

Possibly: Genus Cordyceps (Kingdom: Fungi).
Greater than 600 species of this fungus exist worldwide, their fruiting body's are club-shaped and range in colour from white to bright orange.
The spores being entomopathogenic, find an insect-host and proliferate within until the insect's behaviour is conditioned for the survival of the fungi. This has earned some varieties the name of the Zombie Fungus for the strange behaviour observed in inoculated individuals.
The Wikipedia article indicates that is a part of the ascomycota division which indicating it's reliance on a sack-like (or "wineskin") fruiting body to reproduce, just like common edible mushrooms.
Popular in Chinese traditional medicine and as a food supplement increasingly in other parts of the world, there is yet no conclusive benefit medicinally.
Another photograph, showing a cluster of fruiting bodies.

In https://www.reddit.com/r/whatsthisplant/comments/qj0jj6/what_is_this_plant_have_used_photo_search_engines/ , @TinySpookyGhost mentions:

I think it's a fungus. Maybe like this https://en.wikipedia.org/wiki/Xylaria_longipes ?
Here you can see similar ones https://mushroomobserver.org/196852?q=2pXG

I think it is that one.


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How to customize the output of my BLASTP output form
I'm trying to align the output of I got previously to against the swissprot database, and I need to have an output in tabular form with -qseqid -sacc -qlen -slen -length -nident -pident -evalue -stitle and I want to set the evalue less than 1e-10. Here is my code :
#!/usr/bin/env bash
blastp -query Trinity.fasta.transdecoder.pep \
    -db swissprot \
    -outfmt "6 qseqid sacc qlen slen length nident pident evalue stitle" -evalue 1e-10 1>Predict.txt \
    2>wrongPredicted.err

However this is the first several lines of output I got in the txt file :
TRINITY_DN0_c0_g1::TRINITY_DN0_c0_g1_i1::g.132::m.132   Q964E0  400     376     376     364     96.81   0.0     RecName: Full=Actin, cytoplasmic; Contains: RecName: Full=Actin, cytoplasmic, intermediate form; Flags: Precursor
TRINITY_DN0_c0_g1::TRINITY_DN0_c0_g1_i1::g.132::m.132   Q964D9  400     376     376     364     96.81   0.0     RecName: Full=Actin, cytoplasmic; Contains: RecName: Full=Actin, cytoplasmic, intermediate form; Flags: Precursor
TRINITY_DN0_c0_g1::TRINITY_DN0_c0_g1_i1::g.132::m.132   P53472  400     376     376     364     96.81   0.0     RecName: Full=Actin, cytoskeletal 1A; AltName: Full=Actin, cytoskeletal IA; Flags: Precursor
TRINITY_DN0_c0_g1::TRINITY_DN0_c0_g1_i1::g.132::m.132   P92179  400     376     376     364     96.81   0.0     RecName: Full=Actin, cytoplasmic; Contains: RecName: Full=Actin, cytoplasmic, intermediate form; Flags: Precursor
TRINITY_DN0_c0_g1::TRINITY_DN0_c0_g1_i1::g.132::m.132   Q964E1  400     376     376     363     96.54   0.0     RecName: Full=Actin, cytoplasmic; Contains: RecName: Full=Actin, cytoplasmic, intermediate form; Flags: Precursor
TRINITY_DN0_c0_g1::TRINITY_DN0_c0_g1_i1::g.132::m.132   Q964E2  400     376     376     364     96.81   0.0     RecName: Full=Actin, cytoplasmic; Contains: RecName: Full=Actin, cytoplasmic, intermediate form; Flags: Precursor
TRINITY_DN0_c0_g1::TRINITY_DN0_c0_g1_i1::g.132::m.132   P69004  400     376     376     364     96.81   0.0     RecName: Full=Actin-15B; Flags: Precursor
TRINITY_DN0_c0_g1::TRINITY_DN0_c0_g1_i1::g.132::m.132   O17320  400     376     376     361     96.01   0.0     RecName: Full=Actin

The problem is that all the evalue is 0.0 for some reasons, cuz what I want is something like this :
TRINITY_DN8_c0_g1_i1 Q5ZKK7 283 788 64 53 82.81 1e-30 RecName: Full=General transcription and DNA repair factor IIH helicase subunit XPB; Short=TFIIH subunit XPB; AltName: Full=DNA excision repair protein ERCC-3
TRINITY_DN8_c0_g1_i1 Q7ZVV1 283 782 64 53 82.81 3e-30 RecName: Full=General transcription and DNA repair factor IIH helicase subunit XPB; Short=TFIIH subunit XPB; AltName: Full=DNA excision repair protein ERCC-3
TRINITY_DN8_c0_g1_i1 Q1RMT1 283 782 64 52 81.25 6e-30 RecName: Full=General transcription and DNA repair factor IIH helicase subunit XPB; Short=TFIIH subunit XPB; AltName: Full=DNA excision repair protein ERCC-3
TRINITY_DN8_c0_g1_i1 Q5RA62 283 782 64 52 81.25 7e-30 RecName: Full=General transcription and DNA repair factor IIH helicase subunit XPB; Short=TFIIH subunit XPB; AltName: Full=DNA excision repair protein ERCC-3
TRINITY_DN8_c0_g1_i1 Q60HG1 283 782 64 52 81.25 7e-30 RecName: Full=General transcription and DNA repair factor IIH helicase subunit XPB; Short=TFIIH subunit XPB; AltName: Full=DNA excision repair protein ERCC-3

The 8th column should be valid evalue. Need some help! Thank you!

Very low e values are rounded to zero, so that’s a valid output.

Welcome to Biology.SE! Please take the [tour] and then go through the [help] pages starting with [Ask] questions effectively on this site. In particular, this question seems like it might be a better fit for [Bioinformatics.SE], but please do not crosspost, instead request migration after consulting that sites help and checking for duplicates.

0 is a valid e-value. It is the strongest e-value you can get.
the sequence identifier in a FASTA file (and thus what BLAST uses) is "everything up to the first space". If what you have behind "::" is indeed useless, you should remove it from your query before submitting it.

FWIW, my lab makes SequenceServer, a powerful graphical interface for running BLAST. It enables you to run BLAST in the cloud or on your local computer.

Good answer, but three links to your own application? Really!

Hi @David - Sorry I didn't mean to cause offence. I'm quite proud of what our app has accomplished: SequenceServer helps me and 1000s of others perform and interpret BLAST analyses every week. Anyhow, I've removed 1 of the 2 links to the app.


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Are there taxonomic keys for members of the family poeciliidae in America?
I wish to know what are the taxonomic aspects necessary for the identification of certain species of poecilids, specifically what is the role in the counting of rays and spines and also the measurements of the organism. Which documents can I guide myself from? Am looking to know the exact measurements of a specific fish, in this case Poecilia salavatoris.
The fish was found in Honduras, Central America in the state of Francisco Morazán in a fast-moving, shallow, seasonal brook.

The fish in question is 4.5 cm in total length and 3.5 cm in standard length.


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Pedigree Diagram help

I am asked to fill the genotypes in the spaces provided but looks like I am aving a little bit of trouble. can anyone help? thanks in advance!

Here are a few hints that might help:
Talking about Maria's pedigree:
Firstly, it seems as if you have mixed up with $X^a$ and $X^A$, see that the disorder is X-linked DOMINANT. Anyone with either heterozygous or homozygous dominant expression would have the disease expressed. So the first generation male should have a genotype: $X^aY$, because if it were $X^AY$ then Amelogenesis imperfecta would be expressed as his phenotype and the first generation female should have a homozygous recessive genotype. Also no child in the second generation would suffer from the same.
(NOTE: The one suffering from Amelogenesis in the second generation would have genotype $X^AY$)
As for Gunther disease, both the parent in the first generation should have a heterozygous dominant expression and the offspring suffering must have a homozygous recessive expression. And you can apply the same basics in Peter's pedigree.
I think this much should be enough to complete the task, but if you still have some doubt you can put it forward in the comments.

Thank you very much Shefali for the explanation. I truly appreciate it. Here is my second attempt: http://s837.photobucket.com/user/apothemnew/media/attempt2_zps419409e5.jpg.html?filters[user]=138960233&filters[recent]=1&filters[publicOnly]=1&sort=1&o=0 does it look ok now? Thanks in advance. Sorry for the inconvenience :)

Well, in the first place I did not understand what does H or h and - indicate?

@ApothemCyte U have written Gg for peter's father but he could also be GG !

@Shefali Hello Shefali. Would you please if at all possible be able to help with my new question: http://biology.stackexchange.com/questions/15142/genetic-linkage-mapping-question-help Thank you so much in advance!!


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Genetics independent assortment?

As indicated in this question, what do you think is is the best explanation for the observed progeny, is it because distance between genes affects recombination frequency? My main concern is question b).
Any help would be greatly appreciated thanks in advance!!

Until now, it looks good. When you are looking at basic mendelian gene linkage problems like these and you find out that the chi square analysis rejects your hypothesis, it means that there is linkage. In that case, you should have a case where your two recombinant genotypes have an approximately equal number of progeny and your two parental genotypes also have an approximately equal number of progeny. In your case, 220 is about 230, and 270 is about 280.

(source: k12.ny.us)
This image is just like your problem. I want you to imagine that b+ and b represent A and a in your problem and that vg+ and vg represent B and b in your problem, respectively. You start out with an AaBb crossed with an aabb. On the gametes line, it lists all of the possible gametes of this cross. On the line where it describes testcross offspring, we see a situation very similar to yours. In this case, AaBb = 965, aabb = 944, Aabb = 206, and aaBb = 185. We have our two pairs: AaBb/aabb and Aabb/aaBb. Sound familiar?
The recombinant offspring are defined as the offspring that do not have a genotype of either parents. The reason this is important is because you need a crossover to get a recombinant. The closer two alleles are together on the same chromosome, the harder it is to get one of the alleles to cross over without the other one crossing over with it.
Let's clarify. This means that if the alleles are closer, you get less crossovers. All recombinant exist because of a crossover. Therefore, the closer two alleles are, the less recombinants you get.
Quick note: the formula for the distance two alleles are from each other is expressed by this formula:
100(recombinant frequency) / (total offspring) = distance apart.
This is consistant with everything we have said, because as recombinant frequency decreases, distance apart decreases as well.
Another way to explain it: on the gametes, AB and ab really like to stay together, as they are LINKED. It is very difficult to separate them. That is why there are more AaBb and aabb; they only require the gametes AB and ab.
Apply the formula to find out how far they are apart. I think you can figure out the rest from here. I want you to try and answer the question.
Hope this helped! :)


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Population Genetics Question

Can someone please help with this question? Here is my working (just in case it is not clear: 1/300*1/30*1/2) but is this actually correct or do I need to multiply by 0.5 once again? I appreciate any help!

Question is: If an Ashkenazi(1/30) and(multiply) French-Canadian(1/30) ....
Where 1/300 came from ?
I duno, I may missing something - but may it be like  that
Parrent1(=1/30 * 1/2)*Parrent2(=1/30 * 1/2) = P(child with both mutations)


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Gene Complementation Question

Hi everyone! Here is a diagram of a genetics complementation problem. My main concern is regarding number 3d. I'm assuming that in this case, it would be complementary interaction and thus exhibiting a ratio of nine to seven. because if we cross F1, 3 will be mutant while one will exhibit wild-type phenotype. Is this right? Thanks in advance!

Yes 9:7 seems to be the right answer.
F1 progeny should be AaGg... and crossing it will give a ratio of 9:7 as is of any complementary genes