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Why can't this be 1st meiotic division non-disjunction as well?

The child has gotten 2 "sick" chromosomes from his dad and 1 healthy from his mom, leaving it with trisomy 13.
I can see how this can happen in the second meiotic division of the father but I can ALSO see how this can happen in the FIRST meiotic division by non-disjunction.
Let me illustrate both ways which I see it and you can tell me where I go wrong as my book only illustrates that is the second division:

The black is the healthy chromosome and the red is the "sick" one. As you can see, we should end up with a double sick chromosome in both cases??

I'm starting to believe that my professors/whoever made the material has misunderstood nondisjunction as everything I read seems to indicate that it can happen in both 1. and 2.? Example: http://genetics.thetech.org/sites/default/files/NonDisjunction12.gif
If the "small" chromosome is the blue one you can notice that it can happen in both. Anyone else agree?

A) you are combining trisomy with translocation B) your final question is a bit unclear— are you asking why non-disjunction cannot happen in first division?

How am I combining trisomy with translocation? Nobody mentioned translocation. The small allele is the product of translocation, yes but it has nothing to do with the way the question is formulated. The final question asks if you can get trisomi from a nondisjunction in 1st meiotic division.

So you can remove the reference to the "sick" chromosome. It is unnecessary and confusing.

It's there to illustrate the fact that these are 2 different variations of the same chromosomes. Else people may think it was a different chromosome adding even more confusion. I don't know why this confuses you. I answered my own question anyhow.

This was a little confusing to answer because there is no explanation of why you thought non-disjunction could not happen in meiosis I. Another difficulty highlighted by @WYSIWYG is that you tackle both a specific disease resulting from non-disjunction and general non-disjunction diseases in the same question. I've tried to lay out my answer accordingly. Personally, I always find meiosis is a tricky one to visualise so the more we talk about it the better!

Non-disjunction and trisomy 13.

Why can't this be 1st meiotic division non-disjunction as well?

It absolutely can be 1st meiotic division non-disjunction as well. Patau syndrome can occur as a result of either meiotic non-disjunction event, and furthermore a mosaic form of the disorder can occur after mitotic non-disjunction.
Non-disjunction generally.
Non-disjunction can occur in meiosis I, but it's not necessarily the same result as non-disjunction event in meiosis II. This image helps describe the formation of the gametes from non-disjunction events.

(source: bioninja.com.au)
The most obvious point is that there are more aneuploidy cells born from a meiosis I non-disjunction event than a meiosis II non-disjunction event.
Furthermore non-disjunction occurs between homologous chromosomes in meiosis I or between sister chromatids in meiosis II. Was this subtlety perhaps what your lecturers/teachers were trying to describe?
Confusion somewhere in the question perhaps.
I think the problem comes from your first diagram, which appears to be an inaccurate sketch of what trisomy 13 looks like in a karyotype. This is what trisomy 13 actually looks like:

(source: iupui.edu)
How non-disjunction leads to a disease karyotype.
Lets pretend that the 'long' chromosomes in the first diagram of this answer are chromatids of chromosome 13. Thinking about the fusion event between gametes - the aneuploidy (n+1) gamete formed from either meiotic non-disjunction event and a normal (n) gamete could fuse to make the trisomy 13 result shown in the karyotype above; there would be three 'long' chromatids rather than two.

Your illustration is wrong. During second meiosis the sister chromosomes go to each their cell, not the same cell.
This would correspond to switching the colors up in your illustration like this:

What textbook are they using for your genetics course in the First year of medical school?


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Is there evidence to suggest that sleeping requires more energy than watching TV?
I have heard the claim:

sleeping requires more energy than watching TV.

I have heard the counter-claim - watching TV requires large amounts of energy.
My question is: Is there evidence to suggest that sleeping requires more energy than watching TV?

This sounds like a better fit for skeptics.SE.

So your sources are 3 "news" websites that don't share sources and a parenting SE post?

It sounds like you have a better one. Please enlighten us.

So you have this question after reading a couple of "news" and lifestyle sites and a parenting site, which btw do not point to any external source? I think that before worrying about who would win between an elf and a troll I should check if those thing exist. I'm not sure they do, but the links you provided aren't it.

No, I'm saying this exists in the Zeitgeist. In common conversation. It is something that people talk about. These were the sites that came up when I searched for a truth that is commonly known.

I never wrote anything about calories in my answer over at Parenting SE. I simply started that the brain is active while the body may be relaxed when kids are sitting in front of a TV. I don’t think that it’s a suitable example for your question.

From Harvard Health Publishing. The weights are in pounds, and the energy is shown in calories. These values are for over a 30 minute period.

This suggests that the claim is false; watching TV uses more energy than sleeping does.

Data is in pounds? Really? Pounds of what? Pounds sterling?

Pounds are a valid measurement of mass, see https://en.wikipedia.org/wiki/Pound_(mass). If you want me too, I can use kilograms, however for simplicity the data was in pounds and the conversion to kilograms gives decimal places, the removal of which reduces accuracy.

But that, I imagine, refers to the figures in bold. One could ask "mass of what?"  But as the question is about energy, I assume the non-bold figures are energy, which does not have units of mass.

Oh, sorry. I didn't realise that. Fixing that up now, and I'll fix the table up when I get on a PC

source: Stack Exchange

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Are there any viruses or bacteria which have evolved to withstand higher temperatures due to fever
My question was raised after receiving this information:

The primary reason the body raises its temperature (via the Hypothalamus in this case) is that bacteria and viruses tend to optimally thrive at 98.6F, which is also your body's optimal operating temperature.

I am just wondering if there are any viruses or bacteria that have gained the ability to prosper under fever temperatures through evolution? If not, why not?  Is there any biological restriction stopping such viral evolution?
Update:
I will try to explain my question.  As far as I know, evolution helps species to adapt to their environment.  For example, when people started using antibiotics we got new bacteria resistant to those antibiotics.
If fever is part of the innate immune reaction to viruses and bacteria, why hasn't this resulted in selection for fever-resistant variants? Why has evolution apparently stopped in this case?

There are bacteria that live in hotsprings, for them 100c is comfortable.

Are you asking if there are pathogenic bacteria that thrive at higher body temperatures?

I have updated my question and tryied to explain it.

Does anyone else cringe whenever stumbling upon 98.6°F?

Fever is just one of the many ways of the body's defense mechanism work. Under infection, human body can raise body temperature, release cytokins and activate white blood cells etc. Sometimes the bacteria can evade immune suppression or immune complement fixation so that they can stay inside a "fever-ish" body like they just don't care. Example: Pseudomonas aeruginosa. They can grow in 42 degree Celsius which surpass the normal fever temperature.
My answer may not be the best for your question. All I'm trying to say is that fever acts as a supportive role during an infection. Human body relies on heavy artilleries such as white blood cells and cytokin to clear the infection. That's why it will be more beneficial for the bacteria to evolve abilities to evade immune suppression and immune complement fixation. And bacteria know how to do those.

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Do pale skinned people show other low light adaptations?
So, pale skin is, fundamentally, an adaptation to living in low light conditions. Pros: reduce energy spent on producing melanin, increase vitamin D production. Cons: more vulnerable to sunburns and skin cancer.
Do populations with this sort of adaptation have an increased rate of other low light adaptations? Specifically, I'm thinking of vision in low light situations. Examples of possible adaptations: increased rod count in the retina (pro: better low light vision, con: worse bright light vision), or faster production/resetting of rhodopsin (pro: better low light vision, con: greater energy expenditure).

Light intensities that are "low" for vitamin D production are still far more intense than needed for vision.  Indeed, one might reasonably regard the evolution of dark skin as an adaption to living in light that's too intense.

@jamesqf That seems to be a semantic difference, to me. Though it suggests another possible adaptation: greater light transmission through lens/fluid in eye. Pros: more sensitivity, cons: more vulnerable to retina burn/snow blindness, possibly also cataracts.

Not really semantic, just looking at the question from a different angle.  Why do dark-skinned people native to tropical countries wear sunglasses?

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Mechanics of Chromosomal Crossover
When chromosomal crossover occurs, two matched chromosomes swap matched sections of their chromosomes. My question is: how does the cell select where to to make the break on both chromosomes? Is it based on some attempt to match sequences on the two chromosomes, or purely on distance from the centromere? The mechanics of the former could be achieved by breaking the two strands of each chromosome at different places. The mechanics of the second is a simple walk from the centromere with a random(?) selection of where to cut.
The purpose of this question: if the process is based on distance from the centromere then it would provide an explanation the presence of junk DNA. Successful crossover requires that the number of functioning genes on the two chromosomes not be radically altered in quantity. A failed crossover would result in at least one of the gametes being non-viable, reducing fertility. If crossover is based on centromere distance then the location of genes becomes a factor in the success of a crossover, erecting a fitness barrier between populations with radically different gene placement, even if gene content is identical.
If this is a question without an answer, currently, one way to address it would be to try to cross breed knockout mice that don't have junk DNA with ordinary mice that do. If the fertility of the cross breeding is significantly lower than than knockout with knockout and normal with normal, or if the cross breeds are less fecund, then that would provide evidence for position based crossovers, and a function for junk DNA in the crossover process.

How does the cell select where to to make the break on both chromosomes?

There are proteins that direct the selection of a site where a double strand break will be made on one chromatid.

Crossovers are not randomly distributed: The histone methyltransferase PRDM9 recruits the recombination machinery to genetically determined hotspots in the genome and each incipient crossover somehow inhibits formation of crossovers nearby, a phenomenon called crossover interference. Each chromosome bivalent, including the X-Y body in males, has at least one crossover and this is required for meiosis to proceed correctly.
  Credit; Reactome

.

Is it based on some attempt to match sequences on the two chromosomes, or purely on distance from the centromere?

The sequences are matched but not as you have assumed. Following the introduction of a double-strand break in one chromosome the regions around the break are processed (by proteins) and these processed ends invade the opposite chromatid. The formation of a Holliday junction follows, these are the "X" structures between strands in the image below, and they requires base-pairing;

Image credit; EMW2012

Interesting. How does the protein "know" where to look on the blue DNA for the matching sequence (the strand invasion part before the process split)? Or does the protein that opens the blue pair along it until a match is found? Those genetically determined hotspots are particularly interesting. Is each crossover hot-spot's (CHS) sequence unique? In other words, can the crossover mechanism accommodate radically different chromosome lengths if the relationship among CHS's and genes is right?

Yep, it's top-shelf interesting. The chromatids are aligned with one another as a tetrad during Prophase I of meiosis. This animation shows how the steps progress by showing only the DNA but note that many proteins regulate the steps; including locating the matching sequence (see Reactome link in answer for key proteins). The linked paper above shows the differing binding sites for alleles of human PRDM9.

I guess you could put it, succinctly, this way: the search for the matching sequence in the blue DNA has to start somewhere, and it has to complete in a limited amount of time for the process to succeed. How do the relative lengths and positions of matching sequences affect the success rate of the operation of the mechanism? Does it succeed at the same rate for radically different lengths with the same relative configuration of functional regions as for more matched ones?

Just my take here. I have difficulty envisioning a mechanism that would insure the "walking" distance from the centromere was the same on both chromatids. How would that be coordinated? Since the chromatids are not in continual contact their entire length, this would entail two "walkers" that somehow coordinated their steps.
Furthermore, there is a lot of truly "junk DNA" between genes. By truly junk, I exclude the non-gene DNA portions we haven't fully documented the function of but which have uses that require their conservation. But there is a significant portion of DNA that is not conserved (which provides the basis for RFLP analysis in DNA fingerprinting). This means that, while the nucleotide lengths within genes and other important regions may be identical between homologous chromatids, the length of segments in between is not guarenteed to be so. An error of "walking" just one extra base within a gene would result in a frame-shift mutation likely rendering that allele useless.
I think there must some local exposure of the base pairs in some areas of contact between chromatids for chiasmata to form. This would also seem necessary simply for the chromatids to recognize their homologues.

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What is (probably) the closest living relative of the trilobite?
The trilobites vanished from the fossil record many millions of years ago, but they were obviously arthropods of some sort. Do we know which animals are their closest living relatives? I've heard both Armadillidiidae and horseshoe crabs. Can we tell which is right (or if there is a different answer), and how?

Without their DNA, it's difficult to know the answer to that, from physiology of >250mn year old fossils, perhaps crayfish and scorpions also come from trilobites, also arthropods, they appeared 100 million years afterwards. it's best to content ourselves with a map of genetic distance between shrimps, earwigs, horeshoe crabs, crayfish, and find a map of animals that comes from them. I can't find a genetic distance mapping tool on the web.

There were so many species of trilobites for 300 million years, so perhaps some trilobites species are closer to horseshoe crabs whilst others are closer to woodlice, some trilobites were amphibious and could walk onto the seashore.
If you check this research about horseshoe crabs, there are a dozen fossils that are hybrids between a trilobite and a horseshoe crab, i.e. bellinatus trilobitoides.

 From the family tree you can see some early horseshoe crabs:

this is a harpetida trilobite:

The morphology of the fossils is mostly saved as dorsal morphology and ventral morphology. from the top the are similar to horseshoe crabs, and the different legs are similar to woodlice and bathynomus and horseshoe crabs in different fossils:

There are other living animals that resemble them like Serolina Delaria:

Tadpole Shrimps:

That's from this cool page with images of lots of things like trilobites.
Silverfish:

Bathynomus, similar to woodlice:

The videos of bathynomus are cool: https://www.youtube.com/watch?v=jfnHQPkta-Q

The Tree of Life Web Project is a good resource for these kinds of questions. It looks like we cannot distinguish trilobites' origin from the origin of arthropoda: link. Also, some references on trilobite evolution and systematics from the same source: link.


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How complete is the information in DNA?
Everyone talks about how DNA is the "molecule of life" and "the set of instructions for building you." How complete are the instructions, really, though? To make the question concrete, say I were to remove all of the DNA from a bacterium and replace it with the nuclear DNA from a eukaryote, would the cell (and it's daughters) be able to transition into the same sort of eukaryote as the DNA source? Granted, the lack of mitochondria would be a huge hindrance, but assume we could add some when the bacteria swelled up to a large enough size to accomodate them inside of it. Are there other barriers to this process?
I know that adding any single gene for producing a protein would function as expected when added to a bacterium, but would the lack of a nucleus and organelles prove fatal, or does the nuclear DNA have the information needed to build them up using only the machinery available in a bacterium?
What about an archaea? Or going the other direction - remove the nucleus from a eukaryote, add bacterial DNA, does the cell and its daughters survive to become bacteria?

If you want an analogy, it would be like having a hard drive containing all the specifications for all of the hardware and software necessary to read the information on the drive, as well as the manufacturing instructions for all of the machinery need to manufacture the computer, to manufacture the machinery needed to manufacture the machinery to manufacture the computer, and down the line to extraction of raw resources. The information is 100% complete, and totally sufficient to build a second set of all the machinery, but can't do it if you are just holding the bare drive.

Barrier? Yes Prokaryotic and eukaryotic cells differ in DNA replication.
So a prokaryotic cell would never replicate to form a eukaryotic cell. As of Mitochondria, Mitochondria have their own DNA and would replicate normally. I am not so sure about swapping with Archae though

@Soura Not to mention, bacterial DNA is partially methylated. Replacing bacterial DNA with the DNA from some eukaryote would not even if only for the reason that bacterial replication machinery requires this methylation.

This is a good question, because the answer to the overall question (is the information in DNA complete - yes) is not the same as the one to the more specific ones (would a cell survive if the DNA was swapped with that of another life form - no). Let me elaborate:
The information in the DNA of in any given organisms (except for a virus) IS complete. This means that the DNA has 'code' for all the molecules required to build and sustain this organism.
However, the DNA of an organism alone (or placed inside an unnatural environment like a completely different cell) is not sufficient to actually make or build that organism. The reason for this is that, while the DNA has all the necessary code, without the correct machinery to actually read that code nothing can or will happen. Eukaryotes and bacteria are so vastly different (which is to be expected after millions of years of evolution for both), basically all the different machineries are not compatible anymore: transcription binding sites are different, gene structure (exons/introns vs. operons) is different, Ribosomes are different, ... [btw this also means that just putting the gene of an eukaryote into a bacterium doesn't work, researchers have to modify it accordingly to work].
Even between different eukaryotes (and probably some bacteria but I'm not sure about that) exchanging the nuclear DNA would not produce viable cells (or at least not ones that could grow into an organism), since again the transcription machinery would not match up sufficiently.

"[btw this also means that just putting the gene of an eukaryote into a bacterium doesn't work, researchers have to modify it accordingly to work]" Thanks, in particular, for clearing up that misconception of mine. Is it a difference in the codon to peptide mapping, or maybe something in how the dynamics of folding work?

@SeanLake The main problem is the difference in gene structure (bacteria don't have introns). Codon usage (the frequencies of individual codons, not their meaning) can make problems, but will not prevent expression. Folding problems can also exist, but you can still make pretty much eukaryote protein in bacteria - just not necessarily always functional/correctly folded.


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Are fish averse to extreme heat?
Terrestrial animals face two common sources of heat extreme enough to pose a danger to them: Sunlight and fire.
It therefore stands to reason that they would evolve systems for sensing heat and behavior making them averse to extreme levels of heat, and most terrestrial animals have indeed done so.
Fish, on the other hand, live in an environment where neither of the above heat sources have a profound impact, and the one source of high temperatures underwater (geothermal activity, such as underwater volcanoes) does not exist within the habitat of many species of fish.
In summary, there does not appear to be any pressure for fish to evolve or retain an aversion to heat like terrestrial animals have.
Are fish averse to extreme heat?

Welcome to BiologySE, you should add some references to the background knowledge that you nicely put in your question. That way people that are unfamiliar with heat response can get a deeper look into the topic, too. And, generally speaking, people on BiologySE will frequently ask for evidence to claims made in answers and questions.

Temperature affect pretty much all metabolic pathways. There are incentive in fishes as well to control their internal temperature.
Control of Body temperature can be categorize along two axes, one concerning the source of heat and the other the magnitude of temperature variation. Please have a look at this post to understand the terms endo-, exo-, poikilo-, homeo- terms.
Below is a figure to give a general overview of the diversity of species in terms of temperature regulation.

As you can see fishes are found in different parts of the figure.
So, yes there is incentive in fishes to control their internal temperature and to avoid extreme heat as well as extreme cold.

This is true. Some species of salmon adjust their depth in the water column to regulate their body temperature as a means to control metabolic processes including digestion to improve efficiency between twilight feeding times. While many have a wider temperature tolerance range than mammals, a preferred temperature range exists for fish.


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Why doesn't Poison Ivy cause a reaction under one's fingernails?
Okay, so I pulled up a bunch of Poison Ivy last week and I got itchy up and down my arms. I scratch and I think that causes the oil to spread causing more misery. However I notice that I don't get a reaction under my nails where I would think the oil might accumulate. Why not? The skin under the nail seems relatively delicate and yet it doesn't react. ?


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How diverse are species in remote, isolated areas on Earth?
If we consider land areas that have been largely isolated from each other from a human point of view, but with a similar climate – for example, a part of Europe and a part of Americas with a similar climate before the time of Columbus – generally how different can one expect the flora and fauna to be between the places?
I realize there can be quite different approaches to measuring the biological differences. Not being a biologist, I probably miss some quite important metrics. Some ideas that come to my mind:

How distinct are the species in each environment? For example, can we expect to see the same ant species? Same grass species? Same bacteria?
DNA difference based approaches: How much of the DNA material in each environment does not exist in the other one? How large a proportion of organisms in one environment does not have a close relative on the other, given some threshold closeness value?
Historical approach (probably overlaps the DNA approach quite a bit): How long ago (alternatively: how many generations ago) did the common ancestor of similar organisms in each environment live? Do the organisms share this number, i.e. is the common ancestor of, say, humans in Europe and America as ancient as that of ants and grasses?

You might narrow this down a bit. There are q number of questions, and to answer them all, the answer would need to be quite long.

The concept that you hint at, has been studied at the example of the island of Australia, where marsupials often look quite similar as their counterparts in the same ecological niche, which live outside Australia and have a placenta, and are less related on the DNA level (e.g.: squirrel-like animals, wolf-like, and the now everywhere extinct saber-toothed tiger-like...).
If you are interested to learn more, I would highly recommend to read Jerry Coyne's "Why evolution is True" ( http://jerrycoyne.uchicago.edu/index.html )
The specific example of Europe and Americas (which does not fully capture the complexity of your question), also is quite interesting - although it is very short on an evolutionary time-scale. E.g.: American squirrels, which lack predators in Europe, and only arrived in Europe because of human journeys following the rediscovery of Americas, are partially outcompeting the beloved red squirrels ( https://en.wikipedia.org/wiki/Eastern_grey_squirrels_in_Europe )


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Have bacteria evolved antibiotic resistance in a laboratory setting?
Is it possible to breed a strain of bacteria in a laboratory setting so that it gains resistance to an antibiotic, replicating the kinds of resistance seen in wild, and has that been done?

Yes, many times.
For just one example, see this paper; you could also see this review for numerous examples.
These are examples of spontaneous mutations that lead to antibiotic resistance, so this is sort of an extreme version of evolution of antibiotic resistance. You could also say that antibiotic resistance "evolves" in terms of selection any time an experiment is done that uses a resistance gene to mark a subset of cells, which occurs on a daily basis in labs all over; fortunately these experiments use antibiotics that aren't used to treat patients.


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How can evolution make such complicated beings?
So what I understand is, evolution is a mere mistake in the replication of DNA and this change is sometimes good and sometimes bad.
And the other day, in our biology class, we were told the functioning of the lungs and how the RBCs fetch the O2 from the alveoli and dump the CO2 out.
And I also know a little bit about some complicated processes in the body like, how the digestive system works, how the muscle cells switch to  anaerobic mode when we run out of O2 causing cramps, how the cells make ATPs in the mitochondrea.
And 1 more notable thing- the amount of complicatedness and all the neural networks in brain.
My question is- how can evolution(a mere mistake in copying a strand of DNA) make such a complicated machine, like our body. There are SO many organs, all working in collaboration to make the body work. And all of those organs are doing SO many things.
I know that this is a result of 3.8 billion years of evolution...but still... how can even a million "mistakes" make a body which is so well deisgned?
ALSO was the whitening of the polar bears a mistake too? Then what are the chances of such a mistake occuring in the replication of DNA? If it was evolution then why don't birds become the colour of the sky?

I'm afraid you need to learn a bit more about how evolution works. Evolution is not just a series of random mistakes, it also involves natural selection which is not random at all. A good starting point to learn about evolution is: http://evolution.berkeley.edu/evolibrary/home.php

@Roland I know about natural selection- its like the survival of the fittest right? Like if there are 5 species of dogs in an environment, then only the fittest species will survive.

@Roland im a 10th grade kid and all the knowledge that i have gathered about evolution is from 2 or 3 youtube videos

Yes, that's natural selection. It acts as a "force" directing evolution, which means that the way things evolve is not random at all. Many people have questioned how evolution can come up with such incredible complex structures, but it does happen over billions of years, with countless organisms alive and evolving at any moment. It's really hard to grasp the enormous scale of it all. But evolution is a large topic, and we can't provide textbook material on this site, so check out the Berkeley page I mentioned for more information!

@Roland ok, but 1 more question. Was there a species of animal with their brain not in their head? And maybe it went exist because the "brain in the heads" species was more fit? This is a silly question but it makes sense to me.

Well I'm no expert on evolution of the brain, but it doesn't sound silly to me. You might want to look at  https://en.wikipedia.org/wiki/Evolution_of_nervous_systems  If you don't find what you're looking for, you can post this as a separate question!

One example of an animal with a brain not in their head is the human species: http://www.scientificamerican.com/article/gut-second-brain/

Mistake is the wrong word. You want the word 'difference'.

@Adi, from my experience it is difficult to get an answer which is to the point in this web site. every entity will have (to a certain level) random mutation and it is very strange the barriers between species are very clear in this world.

We see many breeds of dogs, and cats but not something between. They are discrete. And the mutation that affects to evolution should occur to the germ(reproductive) cells before massive cell differentiation during embryo development(because after massive cell differentiation, mutation is minority and will be repaired, will not survive in the reproduction activity) and those period is very short term in an animal's life. So I think evolution is like a belief at the end deep inside people not thinking though it out.

Biologists talk about 64 mutations per generation in average (coincides with simple math by the way) and this should happen all in very early stage during embryo development. Do those 'believing' in evolution know about this? Is the probability a real measurement?

If this is a general question about how evolution works then Roland's comment is correct - you should start with one of the excellent resources available online, like http://evolution.berkeley.edu/evolibrary/home.php. However, this specific question sounds more like something we used to call the 'argument from personal incredulity' to me - you're willing to accept that evolution occurs, you're just not sure whether it is sufficient to create something as complex as the organisms you see around you. This is quite a common issue people have with evolution by natural selection, and it's a perfectly reasonable question to ask. Essentially, it originates in the difficulty of appreciating the sheer scale of the processes involved. To paraphrase Douglas Adams, "[life] is big. Really big. You just won't believe how vastly, hugely, mind-bogglingly big it is." But I'll do my best to try to help you understand this a bit better.
The number of single-celled organisms on the ocean floor is estimated at 2.9×10^29 - that's roughly three hundred billion billion billion. The current global human population is about seven billion - that's already effectively impossible to imagine. If every one of those people had seven billion tiny people living on them, and every one of those had seven billion people living on them, that's roughly the number of single-celled organisms on the ocean floor right now. Many of those appeared less than 24 hours ago and will be gone tomorrow. Natural selection is acting on every aspect of every one of those organisms simultaneously and has been doing for roughly 1.5 trillion generations. One-and-a-half thousand, thousand, thousand, thousand, thousand, thousand generations.
Natural selection is also a fantastic mechanism for homing in on solutions to complex problems - so good that we've started using it to solve mathematical and computational optimisation problems.
Essentially, it's one of the best approaches to solving complex problems we have been able to conceive of and it's had an insanely, mind-bogglingly long time to act on a planet-sized test tube. That's how we ended up with so much amazing stuff on our planet.

@arbrviral but still, like that complicated mechanics? Is the ability of the brain to switch itself off when we are hit on head also a mistake? Like I once saw in brain games that as light travels faster than sound, our brain perceives them both at the same time by lagging the light perception a little behind.  Now that is a really complicated process and I don't think that was caused by a mere mistake and natural selection. If it was caused by natural selection then wouldn't some organisms might have existed on the planet who lag behind the sound perception?

@Adi: It's not by mistake. It's by natural selection. And yes, there have existed many individuals that lagged behind in many aspects when you compare them to existent individuals. many of those did not contribute to future generations because of their lagging behind. And there are still individuals that lag behind and they will also more likely not contribute to future generations. You have to keep in mind that what we see on earth today is a very, very, very (...) short evolutionary time frame, say a glimpse or a snapshot, and therefore not very informative.

@Adi Some aspects of any organism's environment are highly unpredictable; one is contact with parasites and pathogens, one is social environment. In situations like this the optimal response can be to evolve a system which is itself adaptive, rather than a pre-programmed solution. The brain and the immune system are the most obvious (and most complex) examples of this. I'm not sure I follow your brain-switching-off example, but this partially explains how we learn to integrate sensory inputs. See also: https://www.theguardian.com/education/2012/nov/12/improbable-research-seeing-upside-down

Douglas Adams said "The Universe is big," not life.


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Why does cutaneous respiration need moist skin?
My teacher told me the other week, that respiration through skin (cutaneous respiration) cannot happen without moist skin. That is why frogs have moist skin.
My question- Why does cutaneous respiration needs moist skin? Can't it happen on dry skin?
ALSO - Why does cutaneous respiration happen in the first place? It uses diffusion right? And diffusion doesn't produce enough energy for an organism as big as a frog to live does it?
Please help.

Cutaneous respiration does take place through dry/keratinous skin to some extent, so I think it's an overstatement to say that it cannot happen. The answer to your first question is in your second question: diffusion. Think about the similarities of moist skin to the epithelial lining of the lungs.

They are both moist and uses diffusion right? But the lungs have millions of allveoli (700 millions if I remember correctly) which helps in more surface area. BUT why does diffusion need water? It just refers to substances going from area of high concentration to low concentration right? Why does it need moisture(water) then?

The gas has to diffuse to an aqueous medium in order to be absorbed by the body (the entire body has an aqueous medium). How can a dry skin ensure that? It would just pose as an additional barrier to diffusion.

@WYSIWYG i dont understand. It should be easier for oxygen to diffuse as a gas shouldn't it be? Gases are more "fluid" and movement is easier. How does aqueous solution facilitate diffusion more than air then?

@Adi the gas has to eventually dissolve in an aqueous medium. How else would it reach the cells and mitochondria?

@WYSIWYG but.. can't it just reach it in gaseous form?

How, in the form of bubbles??!

@WYSIWYG does diffusion only take place in water?

No. Why are you making extreme assumptions?? Diffusion happens in any medium (except in perfect solids). Your body is made up of water and the reactions happening in your body need oxygen then how can it be in a different phase?? Diffusion doesn't need water. But all your cell stuff is suspended in water. Oxygen has to dissolve in water to be available to them. Gas bubbling through a liquid is not diffusion. The bubbles do not move according to diffusion gradient, they move according to surface tension/buoyancy.

@WYSIWYG ok now i understand. Thanks for the explanation. :)


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Why are human eye colours limited?
Related to the question What causes the colors we see in eyes?, I am wondering why human eyes are restricted in colour. Most common eye colours are blue, green and brown. Why not yellow, orange, purple, red and so on?
I am guessing this is related to the function of the iris and that other colours do not have the same effect on light absorbing or something like that.

@UV-D Even though that answer sort-of answers my question, it doesn't do so directly. There are certain proeprties to the colours blue, green and brown that explain their occurence. But why not other colours then?

I was going through and cleaning up some of my old answers when I came to this one.  Was there something else you were looking for in an answer?

There is only one main "coloring" agent, or pigment, in the eyes.  That pigment is melanin.  To a much lesser extent, at least in health individuals, you can have lipofuscin produced which gives a golden-amber color to the eyes.  It should be noted that lipofuscin is most likely produced because of oxidation damage/stress in your eye, and not something to be hoping for (Beatty et al has a good review of the subject (1)).
Indeed, lipofuscin in the eyes can be seen as a symptom to physicians, so for the rest of the answer I will only consider melanin, eumelanin and pheomelanin in particular, as the normative pigment in the iris.
To make additional colors, we would need to develop an additional pigment, and or modify eumelanin so that it produces different scattering properties.  So why do we have melanocytes in the eye producing melanin in the first place?
As much as we might consider it as a factor now, sexual selection was probably not the main pressure for having pigment in the eyes.  Instead UV protection almost assuredly is (2, 3).  Thus for another pigment to be selected for, it would probably need to do a better job protecting us vs. UV (also, further selection in humans is hampered by all kinds of things like behavior, medicine, and life span).
Eumelanin does a good job protecting us from UV (2, 3) and in fact does a better job than phenomelanin (4).  It seems incredibly unlikely that we would develop the necessary evolutionary pressure to have our pigment epithelium to produce a totally foreign pigment.
And that is what prevents us from naturally having a whole rainbow of colors in our iris.  One could conceivably engineer a better pigment, and have the genetic information needed to produce it delivered in gene therapy (I hate to think of people purposefully infecting their pigment epithelia).  I, for one, wouldn’t sign up for that.
(1) Beatty S. et al. The role of oxidative stress in the pathogenesis of age-related macular degeneration. Surv Ophthalmol. 2000 Sep-Oct;45(2):115-34.
(2) Hu DN. et al. Role of ocular melanin in ophthalmic physiology and pathology. Photochem Photobiol. 2008 May-Jun;84(3):639-44. doi: 10.1111/j.1751-1097.2008.00316.x. Epub 2008 Mar 8.
(3) Simon JD, Peles DN. The red and the black.  Acc Chem Res. 2010 Nov 16;43(11):1452-60. doi: 10.1021/ar100079y. Epub 2010 Aug 24.
(4) Hu DN et al. Uveal melanocytes, ocular pigment epithelium, and Müller cells in culture: in vitro toxicology. Int J Toxicol. 2002 Nov-Dec;21(6):465-72.


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How is it possible to breathe perfluorocarbon?
I have heard of liquid breathing, where an organism, usually a person, would be breathing in perfluorocarbon. Now I looked up perfluorocarbon on Wikipedia and I noticed, no oxygen at all, but fluorine that would rather bind to the molecules inside you and kill you. I mean, fluorine is electronegative enough to oxidize oxygen. So why doesn't perfluorocarbon fluoridate every oxygen molecule in your body preventing your cells from working and form calcium fluoride in your bones?
How would a person not be killed by breathing perfluorocarbon? Is oxygen more soluble in perfluorocarbon? Does perfluorocarbon not even get into the blood and instead stay in the lungs? And even then, why wouldn't the oxygen coming in be turned into oxygen fluoride? Is it simply because oxygen fluoride has such a short half-life, especially at body temperature that it never forms in significant enough amounts? But even then you would still be breathing out fluorine gas of which some will come back in the next breath. Fluorine gas is toxic because it is such a powerful oxidizer that it will oxidize anything.

At a guess, the fluorine in such molecules is in a stable enough state that it doesn't bind to haemoglobin. Perfluorocarbons have very high gas solubility. Perfluoromethylcyclohexane is one commonly studied for its gas solubility and potential use as an oxygen delivery system. There's a paper on this, but it's paywalled unfortunately.

Fluorine (or any atom) that's bound in a molecule has very different properties from the pure element.  Consider common salt, composed of sodium, a highly-reactive metal that spontaneously bursts into flame on contact with water, and chlorine, a poisonous gas used in chemical warfare (WWI).  Yet the combination is necessary for life.  Or the fluorine atoms in such things as toothpaste & non-stick cookware, or any number of rocks: https://en.wikipedia.org/wiki/Category:Fluorine_minerals

I think that's a chemistry.stack quesiton... Toxic chemicals are absorbed differently depending on their organic chemistry compatibility with the body... you can hold 200g of pure mercury in your hand without any risk of death, all day, but the lethal dose of certain mercury compounds is 1 drop for a minute, because pure mercury is not absorbed, whereas certain organic mercury compounds are so reactive that they can't even by synthesized without killing the researchers.

In liquid breathing systems the perfluorocarbons are simply an inert carrier for dissolved oxygen. It turns out that oxygen and other atmospheric gasses readily dissolve in perfluorocarbons without chemically reacting with them. Some perfluorocarbons can carry over 300 times as much oxygen as the equivalent amount of water. Perfluorocarbons are incredibly stable under conditions compatible with life, they aren't being broken down into free fluorine in you lungs or blood, or reacting with your tissues much at all. The perfluorocarbons don't cross the lung-blood interface in significant amounts.


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Presence of reaction module in bacteria but not in Eukaryotas (human)
From the statistics page, I found that the Module-M00008 is present only in bacteria and not Eukaryotes. Why so? I noticed that all the compounds necessary or the reaction are present in human body and also all the enzymes required for the reactions are present in human body too. Then why does that reaction not happen in humans?

That module represents Entner-Duodoroff pathway, which is an alternative pathway to the Embden-Mayerhof-Parnas pathway of glycolysis.
Entner-Duordoff pathway exists only in prokaryotes.

so does this mean that the enzymes required for this particular pathway in bacteria are not present in Eukaryotas ?

@Rishika Precisely

so if these enzymes would have been present then which pathway would have had the more probability of occurring?

@Rishika That is a hypothetical question and the only answer would be that it would depend of different regulators of the glycolytic flux (in a manner how the fluxes through glycolysis and pentose phosphate pathway are regulated). Now don't ask me what those regulators could be because this question is as such hypothetical.

But according to the statistics , both the pathways of glycolysis are present in procaryotes, but the Entner-Duodoroff pathway is present only in procaryotes and not eucaryotes ... Any biological reason for this??

@Rishika, to add to this answer, there are three possibilities for discrepancy in coverage. 1) Limited information, i.e. even if the module exists in other species it has not been found (missing enzymes, proteins, etc.). 2) The information has not been added to the database (remember that this resource is manually curated). 3) It actually refers to different evolutionary paths. As WYSIWYG says, this is an alternative pathway. Either only the ancestors of prokaryotes found it or if other species found it, it did not increase fitness and was lost. You will find many more examples.

@Rishika And actually, reading the link to the Entner-Duodoroff pathway in wikipedia, it mentions that some prokaryotes use it as they lack enzymes critical for glycolysis. This suggests that even if "prokaryotes" have both glycolysis and this alternative according to the KEGG Module, maybe not the same prokaryote has both. At least it seems the case here.


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Query from a ppt slide
I came across this slide:

Now I haven't understood what the last two grey colored lines mean. Can't ORFS be of any size? What is overlapping frames here?

Can't ORFS be of any size?
I think the point being made is that in a random sequence of 64 amino acids, on average 3 out of 64 should be stop codons, because there are three possible nucleotide sequences for stop codons (UAA, UAG, UGA). ORFs could theoretically be any size but the longer the sequence the more likely you are to come across a stop codon purely due to probability.
What is overlapping frames here?
An example of overlapping frames is shown in the slide:

For instance, you can see that the first "CU" in the first frame produces an alanine (as GCU), while the "CU" in the second frame produces a leucine (as CUU).
They have the same nucleotide sequence, but are offset to produce different amino acids. Viruses have very "condensed" genomes and often can use the same nucleotide sequence for different genes, just starting at different points in that nucleotide sequence. This means they have functional overlapping frames.

"but the longer the sequence the more likely you are to come across a stop codon purely due to probability." what does this line mean

so they have considered the frame size to be 3 here

@Rishika A reading frame is always 3 nucleotides. All I am saying is that in a random sequence of nucleotides, if you select any three at random you should come across a stop codon 3 out of 64 times. Think of it like driving down a road, where there are traffic lights every few blocks. You might get lucky and have a green light for 5 lights in a row, but it is statistically unlikely that you can avoid a red light for a very long distance. Think of the stop codon like a red light.


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Availability of a database containing the proteins of Vibrio cholerae and their corresponding gene sequences
I wanted a list of all the proteins (amino acid sequences) and their corresponding gene sequences of Vibrio cholerae. I tried to search in patric, but the number of amino acid sequences and gene sequences do not match, as they have provided the whole genome. I need to know if there is a database where all the proteins of Vibrio cholerae and their corresponding gene sequences can be obtained in a single file or in a couple of files. Copy pasting 4000-5000 genome and protein sequences individually from the internet seems cumbersome to me.

You want to go to PATRIC > Data > Download Tool.
From the Taxonomy tree, find Vibrio cholerae, choose Type of annotation as either PATRIC/RefSeq or both, choose the type of file you want (gbk or faa) and download from there.

have tried that. the number of gene and protein sequences do not match

Did you get the genes from PATRIC or NCBI? If the number of genes do not match the genes would be more. Considering that you have non-coding sequences, rRNA and tRNA genes and also hypothetical and predicted sequences.

i got it from patric.


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What are the types of interactions in biological network (protein networks)?
In the KGML files, the types of relations between genes or proteins are precisely activation, inhibition, expression, repression, indirect effect, state change, binding/association, dissociation, phosphorylation, dephosphorylation, glycosylation, ubiquitination, and methylation. I want to know more about these interactions. Is there a particular source from where I would understand what these interactions mean in depth?

Most of them are pretty self-explanatory. KEGG pathways are often vague, as a lot of the specific biology for some proteins has yet to be properly investigated - sometimes you only know that two proteins associate, not what they actually do.
The relationship between the two is easier to predict when you know the function of one, e.g. a protein interacting with a kinase is likely phosphorylated by said kinase. A lot of those relationships correlate to post-translational modifications (glycosylation, phosphorylation, ubiquitination, acetylation, methylation, etc) made to one protein by another. Wikipedia actually has a decent overview of these with lots of examples.
Several of the other relationships have to do with regulating protein activity or expression. This goes somewhat hand in hand with what I stated above. Some proteins are only activated once phosphorylated or demethylated, etc. Other enzymes may remove phospho groups, leading to repression. Others still may interact directly with a protein, inhibiting it from binding its substrate or target. Maybe the binding induces a conformational change in one protein that allows it to bind its substrate when it can't normally. Some proteins function as transcription factors that activate or repress the expression of certain genes, indirectly affecting protein levels.
There are all sorts of possibilities - the KGML files try to represent them in a way that at least gives some indication of how the interactions between two proteins may affect each. I hope that provides some insight.


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Propensity Score for amino acid
What is the meaning of propensity score of amino acid? How is it calculated? (I have not studied biology since last 8 years and now I am going through it because I need it for my research. So if someone can describe it in simple language it would be very helpful)

As a simplified response:
Propensity score is used to predict protein secondary structure. It is derived from looking at the aa residue of the accessible surface of the protein and also the interface which enables interactions between other proteins.
The equation is as follows:
Propensity= [probability of the residue in the interface / probability of the residue on the surface]
where,
prob of the residue in the interface = [number of amino acids in the interface / total number of amino acids of any type of interface]
and,
prob of the residue on the surface =  [number of surface amino acids / total number of surface amino acids]
Check out this PLOS paper for an example. PLoS One. 2014; 9(5): e97158.


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Immunodominant Peptide
Can someone please explain me the concept of Immunodominant peptide in simple language?? I did read the wiki article but did not understand it clearly. Please help!
(I have not studied biology since last 8 years and now I am going through it because I need it for my research. So if someone can describe it in simple language it would be very helpful)

This article is indeed written in a complicated way.

If you have an antigen (something foreign for the immune system, for example a virus or bacteria) this consists of many different epitopes (immunogenic regions), as shown in the figure below (from the German Wikipedia, Antikörper means antibodies). The antigens are taken up by special cells of the immune system and processed to get small peptides:

To produce highly specific antibodies, the body has to undergo a specific immune reaction against these peptides. In the beginning of this reaction antibodies usually have a rather low affinity (bind only weak) against their antigen. This is changed by the so called affinity maturation in which the antibodies are mutated to make a variety of different new antibodies. These are then again "checked" against the antigen and the ones with a higher affinity are positively selected.
So antibodies with a strong binding to their antigen are favoured against such which have a less strong binding which can lead the selection of only a few antibodies, even if a complex antigen which has many immunogenic peptides is used. This is positive in the way that these antibodies are very effective in directing an immune response against the virus/bacteria but can be critical if the pathogen has a high mutation rate as this leads to a pathogen which does not have this antigen anymore.

It is about recognizing the intracellular pathogens. Every cell with nucleus splits up some of its intracellular protein to small chunks called oligopeptide (OP hereafter). So if there is an intracellular pathogen inside a cell, then its protein will be split up as well. After that the cell select the OPs it wants to show up on the surface. After an OP is selected, the cell binds it to a protein called MHC1 and sends it to the cell surface. So there is a lot of different MHC1-OP on the surface of every cell with nucleus. An immune cell group called T-cells are recognizing the MHC1 with their T-cell receptor (TCR hereafter). The TCR has a constant part and a variable part. The constant part depends on the species and person, it recognizes the MHC1. The variable part is random, it recognizes the OP. Each (not activated) T-cell has different variable part on the TCR on their surface, so each of them recognizes a different OP set. If a T-cell has strong binding to an intracellular pathogen's OP (IPOP hereafter), then it will be activated and it will destroy the cell infected with the pathogen. If a T-cell has only weak binding to an IPOP, or it recognizes an OP of a harmless own cell, then it won't be activated and it will die after a while, or in the second case it can become a regulator cell, which prevents autoimmune diseases. After the activation the T-cell start to proliferate, it divides many times and these clones try modify their receptor to bind even stronger to the selected IPOP, so they can find and destroy infected cells even more effectively. There is a mechanism in the immune system which prevents the activation of more than a few T-cells with different TCRs against the IPOPs of a single pathogen. So for example against a single pathogen there will be about a dozen different T-cell lines, which recognize a dozen IPOP. These IPOPs are the immunodominant peptides. Ofc. there can be IPOPs which are specific to the pathogen, but the T-cells which recognize them, are not or less activate. Those are the subdominant peptides.
You can find more info about immunodominance on wikipedia.


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What is the biological significance of finding palindromes in DNA sequence?
I found a function called palindromes in Matlab that finds palindromes from DNA sequence. Now what is the biological intention behind incorporating this function? What the biological significance of finding palindrome in DNA sequences?

In regards to a Matlab function, it is probably used to find Restriction Enzyme digestion sites. Many, but not all of the recognition sites of Restriction Enzymes are palindromic, and having a function that can search a sequence and find these site will give you the location where restriction enzymes will cut. Palindromes also can represent places in genomes where viral DNA has been incorporated. So the basis of Bacterial adaptive immunity are these short palindromic repeats that encode RNA template strands for an enzymes such as Cas that can identify and cleave infecting DNA.

My knowledge of biology is extremely limited, but this is what I know of palindromic sequences:
Palindromic sequences are their own reverse complements. I have seen many restriction sites be palindromic. Also, some Transcription Factor Binding sites are palindromic. The canonical E-box site, for example, can be expressed as CANNTG.
Also, these palindromes, when occurring in pairs with a sequence between the occurrences, can double back and bind to each other (when the DNA is transcribed to RNA, say), and this would result in the RNA stem and loop structure.

Are these the only biological significance? do you have the extensive list of all possible significances ?

I wish I did. In my opinion, you learn as you go. Maybe Google+dig deep would help get a longer list of potential areas of significance, but an extensive list serves no purpose as it is not constant, and because most problem solving is done with the thought process "What are the available solutions to this problem" and not "What are the problems this individual piece of a larger solution can address"

@Rishika Please take a look at my answer

@RamRS what must be the length of such palindromes??

I've encountered 6 and 8-mers, and I remember a colleague saying those are the typical length you see, but that statement may be specific to human TFBS sites.

Palindrome sequences are important in bioinformatics understanding, it helps us to extract patterns in the genomic sequences. I'll give an example in HIV (very important application).
HIV has a nasty requirement that the virus must keep the cell alive. It does that by inserting itself into the host's genome. We know from biology that cutting and pasting of DNA works best when the sequences at either end of the cut site are identical. In fact, we usually look for palindromes, sequences that read the same backward and forward. We know the virus prefer to integrate at a palindromic sequence.
Therefore we should look at those palindromic patterns for HIV. Once we find those regions, we might do an alignment with known HIV sequences.
Please Google "restriction sites" for more information.

I'd recommend you Google restriction sites, because that's exactly what you've described here. Good example though!

@StudentT what should be the size of these palindromes?

This information is mainly from my bioinfo class notes. Palindromes or inverted repeats in genome can help in

Predicting regions in RNA that are self-complementary and that, therefore, have the potential of forming secondary structure.
Identification of binding site of regulatory proteins involved in regulation of transcription. This is because sometimes the binding protein has a couple of monomers which bind to both sequences (orignal and inverted) resulting in stronger interaction than cases where only one monomer binds.
Inverted repeats of small length are also present in some transposons (though I am not really aware of their function there).

I also came across a section on function of inverted repeats (palindromes) on google books that discusses the topic in more detail.

what must be the length of such palindromes??


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How does the counter current mechanism concentrate urine?
The movement of ions like sodium into the interstitial space causes water to passively diffuse out the descending loop of Henle. How does this concentrate the urine? The solvent is removed at one place, and the solute at another. Shouldn't the concentration remain the same? Or does the removal of a little solute remove a lot of solvent? Why?

There are actually two places where water is removed (Descending limb and the Collecting tubules) and only one where solute is expelled(Ascending limb). Does this help? Ask If you want further clarifications.

Have a look at this figure (from here):

In the descending loop the NaCl concentration is lower than in the surrounding tissue which leads to a passive water transport along the gradient, which leads to a concentration effect. In the ascending loop then NaCl is actively transported out of the loop which then prevents the diffusion of water back into the loop.
In the collecting tube water is actively transported out leading to an even higher concentration effect. A nice animation of this can be found here.


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Long-Term EMG studies
I am having trouble differentiating onset/offset of muscle activation. Is there anyone in the field has a specific way to set the threshold for both time and magnitude?

Can you give more information about the system you are working in? What species? Indwelling or surface electrodes? etc.

I am using OpenBCI with surface electrodes  link I am testing on average human adults.


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Definition for different arrhythmia
I am wondering if there is an organization, a document or a research that standardize all the rhythms? Such as describing how long should the ECG be flatline to be considered as asystole? The rhythm I am focusing on is:

Asystole
Missed beat
Tachycardia
Bradycardia
PAC
PVC
Bigeminy
Trigeminy
Atrial Fibrillation

Basic Cardiac Rhythms – Identification and Response (The University of Toledo, Medical Center)
This quite thorough one-page source describes:

Basic heart anatomy and physiology
The meaning of the waves in ECG
Examples of ECGs for most arrhythmias with timing, causes, symptoms and treatment

Here's Pocket Guide to Neonatal ECG Interpretation (NICU INK Book Publishers) - an one-page source about arrhythmias in infants.


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Does neural network in brain form cycles?
In other words is it possible for dendrite of neuron A to be connected with axon of neuron B and at the same time dendrite of neuron B to be connections with axon of neuron A (or similarly for any larger number of neurons)?
If so, are there any statistical data on number of such cycles in average human brain?

I don't think such direct loops exist. I haven't even heard much about small indirect feedback loops in neurons though feedforward are well known.

I wouldn't call them "cycles". "Both inhibitory and excitatory coupling were observed between pairs of mitral cells." from Reciprocal intraglomerular excitation and intra- and interglomerular lateral inhibition between mouse olfactory bulb mitral cells. It's dense reading but I think it's giving an example of your A and B.

In general neural networks are a lot less simple and directed than ANNs or artificial circuitry - connections can be inhibitory or excitatory, vary widely in strength etc etc. So unsurprisingly yes, recurrence is observed in actual neural networks. I don't know of any statistics on the frequency of such network structures, or even if such exists. Our knowledge of the brain at this fine level is still limited I think, the more global attempt to map 'the connectome' generally consider things at a higher resolution.

"...inhibitory or activating." I believe the official term is excitatory, not activating.

@CDB - true, fixed


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Is it possible for virus infected cells to continue to present a self-antigen on the MHC1?
Forgive my ignorance, as I'm new to immunology, however it seems like there would be some amount of positive selective pressure for viruses to develop the ability to continue to present the host's self-antigen on the MHC1 of a newly infected cell, thereby disguising the infection from the body's immune system (or at least from the cytotoxic T cells).
Is this in theory possible? Or is there a reason it cannot occur.

Self antigen is presented throughout viral infections.  You seem to think that cytotoxic T lymphocytes respond to absence of self. That’s backward. CTL respond to their specific peptide target no matter how much self antigen there is. In a typical response, there may be 100,000 self peptide/MHC complexes and 100 viral peptide/MHC complexes, and that’s enough for a CTL response.
One trigger for NK cells is absence of self, so perhaps that’s the source of your confusion.

So viruses cannot avoid displaying at least some viral peptides on the MHC complex?

Many viruses, especially members of the herpesvirus family, try, in that they express inhibitors of MHC Class I antigen processing. Even those viruses don't seem to completely succeed. So no, viruses can't avoid it completely

From what I know, the cell does not actively choose to display viral antigens on its MHC 1 receptors. As proteins within the cell are inevitably degraded as a part of garbage disposal, these peptides are transported to the ER, where they bind to MHC 1 and display on the cell surface. When a virus infects a cell, some of its proteins are similarly degraded, either by the cell's own defenses or as a part of their normal life cycle.
So, there will inevitably come a time when a viral antigen will make its way to a cell's surface. The only way to stop it would be to stop protein degradation in the cell entirely, which is not a good idea. What viruses do try is downregulating MHC 1 molecules themselves, so there are less receptors to display antigens, but a reduced MCH 1 expression attracts the attention of NK cells.


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What is a gene transcript, how is it different from an allele?
Within human genetics,
My current understanding of a transcript for a particular gene is that it's the exact nucleotide sequence and position of a particular instance of said gene in some individual.
My current understanding of an allele is that it's a less granular breakdown of the instances of a gene in a population.  That is to say, one allele for a particular gene likely covers many (millions of?) unique transcripts for that particular gene, and groups them together due to their tendency to all have a similar phenotypic expression.
Is this correct?

Related http://biology.stackexchange.com/q/42521/3340

No.
A gene is a unit of the genome stored in the form of DNA. It can be transcribed into mRNA  (the transcript) to be used as a template in protein synthesis.
A gene can come in many different versions unique to an individual. That is, individuals can have different alleles, or versions of the same gene.
For example, in mice you can have many different fur colors. The color of their hair is determined by a series of biochemical reactions that are catalyzed by proteins. If each protein is functional, the mice will have a certain color of hair. If any of these proteins are not functional (because they are carrying a certain allele), then the mouse will end up being a different color than it would be if each protein functioned.
You can also have genes that produce somewhat faulty protein-products. As is the case with insulin-resistant diabetes.

But how come particular genes have so few recognized alleles then?  Isn't there way more variation in a particular gene across the population than the 2-3 alleles commonly associated to it?

Not really. Think of it this way. You are trying to assemble a car; you have ten sets of intructions, only one of the instructions will build you a functional car. How many types of cars can you build from these ten sets?

Two. It will either function, or it won't.

So you're saying that in a gene of say a million bp, that everyone will have one of ten possible million bp nucleotide sequences, without even a single SNP somewhere in there which deviates from one of these ten exact sequences?

Not necessarily. Not all mutations have an affect on the protein-product. Because of things like wobble-base pairing, and the overlap in amino acids to trinucleotide sequences. And some mutations might not have that much of an affect on the product. Usually, for a phenotypic change to occur, a protein needs to stop functioning, or have its function drastically reduced.

But wouldn't these SNPs then technically give rise to separate alleles?  Or must they result in some change in the protein product?

They could give rise to a separate allele if the protein is changed in such a way to produce a new phenotype.

So alleles are at a higher level of granularity with respect to the actual variation in the DNA nucleotide sequence.  What is a particular instance of a gene referred to then at the most granular level (SNPs included and all), just an instance?

I can't recall if there's a word for it. But, say an SNP occurred in a 800bp gene. You would jist refer to it at its particular point, eg. "the SNP at the 25th base"

Ah I see, since if it doesn't have a significant affect on the protein coded for then there's no point in referring to it beyond that, ok thanks!

I thought a transcript was the RNA sequence produced from transcription. The RNA copy of an allele that gets spliced and translocated to the cytoplasm for translation. Not sure if Wikipedia references are allowed here, but they seem to agree with my understanding.
An allele is a specific copy of a gene, i.e. you have two copies (alleles) of gene X; allele X1 comes from your mum, allele X2 from your dad.
I haven't heard of the less granular breakdown description of genes, so that might just be a different way of looking at it.

Yes I've seen the word 'transcript' used in that context as well, but I've also seen it used in the context of a particular 'gene transcript'.  As for alleles, just reading from here: https://en.wikipedia.org/wiki/Allele#Multiple_alleles, it says "For example, at the gene locus for the ABO blood type carbohydrate antigens in humans,[6] classical genetics recognizes three alleles, IA, IB, and i, that determine compatibility of blood transfusions"  But that can't be all, since basically every time you sequence another person's genome you should get a new allele.

Not quite, an allele can be the same between different people and a person can carry two of the same allele as two copies of the same gene.

Alleles in the traditional sense represent genetic variation in a population at a given locus. Usually this is related to a given phenotype or observable trait. They can refer to areas of the genome that may or may NOT be transcribed into RNA, whether or NOT that RNA gets translated into protein.
Alleles can refer to a single nucleotide difference (SNP), or an insertion/deletion of one more more bases (indels). Thus for a given SNP associated with heart disease, if 97% of the population has a T and the other 3 percent have an A at that locus, then the alleles are the A and T alleles for that SNP.
Note: the variation could be in a regulatory region of DNA and never get transcribed. But the phenotype associated would be varied expression of a transcribed region it regulates.
A transcript is merely an antisense strand of a region of DNA with U replacing T. Note there are many kinds of RNA transcripts, not all of which get translated to protein. The transcript always mirrors the DNA below. If the DNA has genetic variation, the transcript will reflect it.
In the last 10 years, with the discovery of epigenetics, we also have started thinking about a genetic locus where the variation is a modification of base or histone that the base binds to as DNA is compacted. So some now also include methylation of a CpG as an allele, where one person might have 40% of CpG at that location methylated, and another have 67%.  This difference can explain a trait difference and thus also be referred to as an allele (high methylation vs. lower).
Last but not least, much genetic variation results in no discernible phenotypes. Sometimes both Alleles still result in the same base being encoded during translation for example.


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What is the concentration/molecules per cell of iodothyronine deiodinase in a cell?
I'm trying to parameterize an in silico model and need the approximate concentration (M), or molecules per cell, of iodothyronine deiodinase type II (D2) enzyme in a human cell, ideally a glial cell.  I can only find specific activity values in the literature. Could anyone point me in the right direction, please?


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Do humans squint more readily at green light?
I know that humans won't squint their eyes even if exposed to dangerous levels of ultraviolet or infrared light because our eyes simply don't have the capability to detect it. Neither do the irises constrict.
Since the human eye is most sensitive to green light, does this mean that we will squint and/or constrict our irises more readily for green light? Perhaps even when the intensity is safe for our eyes? (Albeit close to dangerous levels)

If it is below danger level, there is no reason for eye to squint even for green light.

As the intensity increases, energy transferred increases, which would cause sensation of heat causing closing of eyes.

Yes.  According to Action spectrum for photophobia Journal of the Optical Society of America A, Vol. 20, pp. 1852-1858 (2003), the most squinting-sensitive wavelength is ~510 nm, which is green.  Squinting sensitivity progressively falls above 510nm, and below 510nm squinting falls to a local minimum at 460 nm, and then rises again below 460nm, but did not reach a higher maximum in the range studied, which ended at 420 nm.

Since this article is behind a paywall, all I have to go off of is the abstract which says "...a trend of increasing sensitivity with decreasing wavelength."

@Myridium if there is something specific you want me to tell you from the full text, let me know, but I can't copy the whole article.

Is there a visual which exhibits the main results? What you tell me in your answer contradicts what I read in the abstract.

@Myridium Yes, there are graphs of sensitivity verse wavelength.  I am telling the actual squinting sensitivity vs. wavelength, whereas the abstract is telling you "After correction for absorption by macular pigment and the ocular media".


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Can anybody recognize this cardiac waveform?
Is this an artifact or an arrhythmia?

What animal is this recording from? What is the nature of the recording? Where was the electrode placed? Did the animal move during the recording? Etc. I think we need more information.

There is also a Medical Science Stack Exchange site, I think that after you collect more information to address the questions in the comment above, you might consider asking there. But be sure to supply a lot more information than this.

To be conclusive, another couple of leads recorded at the same time as this event would be helpful though the fact that you do have a recognisable QRS complex and a T wave and that the QRS happens before you would expect it to based on the prior rhythm and the P wave, if that is one, prior to it is to close to the QRS complex to have caused it would suggest a premature supraventricular arrhythmia.  There are many technical texts to consult to refine this further, if this is a small animal ECG, I recommend Larry Tilley's textbook entitled ECG for the small animal practitioner.


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How can axons shrink?
I' ve read that some diseases result in the shrinking of neurons in the brain.
Does the axon shrink or the cell body? And what' s the underlying mechanism that shortens the axons, if that' s the case?
And is it possible that axons shrink even without any diseases?

It might be helpful to know which diseases you have in mind, and where you've read about this; personally, I'm curious whether you are referring broadly to degradation of "white matter" or of something more specific and it would help to know what motivated your question.

I've read this about alzheimer's disease, but don't know where I read about this. My actual interest is to find out whether axons can shrink and if there is any biological necessity for axons to shrink.

Demyelinating disorders like multiple sclerosis cause the insulating myelin around axons to shrink, but that isn't the same as the axon itself shrinking. Alzheimers isn't my area of research but I am aware that damage to the "white matter" is part of the disease - white matter consists of axons and their myelin, but my understanding is that white matter degradation in Alzheimers is due to loss of fibers, not shrinking of the individual axons. It's possible this is what you read but without a citation I don't know for sure.


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Can this system of mutual promoting and repressing proteins be simulated using Gillespie algorithm?
Consider an axon of length $L$ with the soma located at $x=0$ and the tip located at $x=L$.
We assume that there is a constant input of Kinesin motors to location $x=0$ coming in from $x \le 0$.
Assuming that all Kinesin motors travel at the same speed $v$, the proteins reach the location $x=L$ after a time $\tau = \frac{L}{v}$.
At $x=L$, incoming Kinesin motors induce Dynein motors to travel from $x=L$ to $x=0$.
Assuming that all Dynein motors travel also at the same speed $v$, they reach the Location $x=0$ after a time $\tau = \frac{L}{v}$.
At $x=0$, incoming Dynein motors inhibit Kinesin motors from travelling to $x=L$.
Thus, we get a negative feedback.
My question:
Can this system of mutual promoting and repressing preoteins be simulated using Gillespie algorithm?
I already simulated it with a mathematical model of delay-differential equations, but as this model doesn' t show all effects, I would like to try using Gillespie algorithm.

Why don't you just try it and find out?

Yes Gillespie's algorithm has been used to study such feedbacks. Are you also modelling diffusion? In that case you should also incorporate Brownian motion.

Yes, I' m also modelling diffusion. Thank you for your help!


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Protein degeneration/excretion in cell
If I inject a dose of GFP or some other types of protein into a long-living human cell like brain neuron cell. Will these proteins being degenerated or excreted over time?

This paper gives a half-life of 26 hours for wild-type GFP expressed in mouse cells.


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Why HIV need integrase enzyme to integrate their DNA into host cell?
In gene transfer by microinjection, the gene of interest is injected into the nucleus of host cell without using integrase enzyme. So why does HIV need that enzyme? Why they not just place their DNA into the nucleus and let it stay there?

During gene transfer by microinjection the DNA has at least some fragments of identical DNA sequence to the host genome. Usually DNA that is used for microinjection will have flanks on either side identical in sequence to two nearly situated, sometimes adjacent blocks of DNA sequence. This allows homologous recombination to occur which engages proteins already present in the host cell: https://en.wikipedia.org/wiki/Homologous_recombination
In case of HIV, there are no fragments of identical sequence flanking the genome of the virus, so no homologous recombination can occur, therefore integrase is necessary. Furthermore, integrase inserts viral genome into random parts of the host genome unlike homologous recombination, which would always localize that viral genome into the same spot each time.
Now, this is my wild guess, as I couldn't really find any evidence in the literature but I'd say it gives the virus certain advantage. Site-specific insertion could be easily inhibited in the course of evolution by mutations within the host genome and eventually the virus would be eliminated. This is not the case with random allocation, as no mutations in the host genome will ever substantially change the probability of integration.
Here is a good review on the process of DNA integration regarding HIV: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3385939/
Let me know if this helps, confront your opinions with what I think.
Cheers,
Krzysztof


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What happens when the bacteria in the petri dish lack nutrients for long time?
If I put some E.coli in a petri dish filled with limited nutrition in room temperature and forget them for months or years. What will happen in the final after they overgrowth and used all nutrition left? Will they die or just stop dividing?

They will die, eventually.
The requirement for energy is a thermodynamic constraint; maintaining cellular structures, repairing molecules that spontaneously damage etc takes some energy, and E. coli is not able to reach a level of quiescence sufficient to survive for years. However some cells might survive longer than expected if they enter low-metabolic activity states; that would not be enough to survive years in a petri dish, though.
Note that other species may be able to survive, through special stress-induced processes such as sporulation or cryptobiosis.


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Predict if a given protein is recognized by antibodies
Assume that i have a 3d-protein structure in a PDB file on a computer. Is there any bioinformatic method to predict if that protein is recognized by all known antibodies of human and cause an immune response or not?
If the answer is yes, how accurate of these method?

First of all: It is important to appreciate tha antibodies do not recognize antigens, they recognize epitopes borne on antigens.
There are several software (online) that allow to predict these epitopes with high accuracy. I´m going to describe some of them next:
Prediction of B-cell epitopes:
You have to be in mind that B-cell epitopes can be continuous and conformationals.
Continuous epitopes can be predicted using Bcepred. This prediction methods is based on physico-chemical properties on a non-redundant dataset. The dataset consists of 1029 B-cell epitopes obtained from Bcipep database and equally number of non-epitopes obtained randomly from Swiss-Prot database. The prediction accuracy for models based of various properties varies from 52.92% and 57.53%. Also It achived highest accuracy of 58.70% at threshold 2.38, when  combined four amino acid properties( hydrophilicity, flexibility, polarity and exposed surface).
Conformational epitopes can be predicted using DiscoTope 2.0. This method predicts discontinuous B cell epitopes from protein three dimensional structures. The method utilizes calculation of surface accessibility (estimated in terms of contact numbers) and a novel epitope propensity amino acid score. The final scores are calculated by combining the propensity scores of residues in spatial proximity and the contact numbers. Besides, Using the benchmark data set from the original DiscoTope paper, has been demonstrated that the updated method has a significantly increased predictive performance.
Important: Discotope allows to get a 3D structure of this epitopes.
I propose to use DiscoTope for prediction of discontinuous epitope residues for several reasons. First, I have shown on a data set of discontinuous epitopes that the average predictive performance of the DiscoTope is significantly higher than the Parker propensity scale and marginally higher than the surface localization score defined by the NACCESS RSA score. Second, several authors have shown that DiscoTope correctly predicts residues in epitopes that have been identified using different techniques such as phage-display, point mutation, and sequence analysis. Third, the DiscoTope prediction method is publicly available on www.cbs.dtu.dk/services/DiscoTope, and the output of the method is easily interpreted.
I would recommend you to check if this epitopes borne on the protein have possible allergenic sites that can contain experimentally proven IgE
epitope. For this you can use Algpred

Very interesting answer, but please make it clear when you are directly quoting a source.

Also note that, while you are (excellently) covering the 'how' of epitope prediction, this will not allow the OP to predict if the immune system can make antibodies against a certain protein or not (see my answer)

The answer of polonio210 is an excellent summary of bioinformatic tools, that allow comparisons with databases of known antibodies - which is helpful to find a specific antibody that could bind your protein.
It's important to note, that this approach will not allow you, to discern whether or not the human immune system will be able to make an antibody against this protein. Based on the answers & comments to this question the number of possible antibodies a single human can make ranges from $10^{12}$ to $10^{16}$. These numbers are so high, that it's likely that not database will ever be able to cover all possible antibodies and allow you to predict if the immune system could make an antibody against a specific protein.


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Predict if a given protein can pass through the intestine
Assume that i have a 3d-protein structure in a PDB file on a computer.
Is there any bioinformatic method to predict if that protein can pass through the intestine or not?

No, you can only make such prediction with experimental data, such as pH stability and vulnerability studies with the relevant proteases.

You could start with a structural BLAST search, so a BLAST search against the Protein databank and look through the significant matches and search whether these can pass through the intestine (based on literate e.g.) and then align the PDB file of this BLAST match with yours. This will at least give you some information and as suggested by Jeppe further information could probably only be found using experiments.

@RickBeeloo that's a very smart idea.Thank you very much!


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Was the frequency of mutations more during primitive earth due to radioactivity?
Primitive earth was more radioactive (or was it really?) according to radiometric analysis of C14 which suddenly appeared at 4250 million years in the Hadeon eon. Is it possible that ancient high levels of radioactivity could affect the mutation rate of early organisms? Does mutation frequency accelerate evolutionary process and/or speciation?

Can you give a reference to the "higher $^{14}{C}$ radioactivity" assertion? It sounds a priori unlikely, given that the cosmic ray processes making carbon-14 from nitrogen would surely have operated equally at that time. Moreover, since the half-life of carbon-14 is about 5700 years, I can't see how any of it can have survived from a time almost a million half-lives ago. A reference could make everything clear.


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How to explain the colour of these scots pines?
I would like to know why the trunks of scots pines have a particular colour, at least in Estonia, as shown here.

The bottom part of the trunks is darker than the upper part. What could explain this?
Thank you for your help!

Let me know if I can improve my question, add relevant tags, and so on. I'm new on this SE site, so I may not ask suitable questions…

Looks like they've lost a good deal of their bark on the upper trunks. Could be a result of a severe weather event, but more likely it's some sort of disease or insect infestation.

Or maybe that's just the way it looks in the wild. I'm from the northeastern US, and we generally only see Scotch pine on Christmas tree farms, where they are tended to grow well, but don't grow that high, for obvious reasons. If you do see them in the wild, they're often stunted and twisted, as they're not adapted to our soil that well. I've also heard from tree farmers that they're susceptible to some fungal or insect infestation (I don't remember which) that can kill them pretty quickly, so you have to keep a close eye on them and treat them with various chemicals to keep them healthy.

Could be squirrels...

I'm fairly sure it's intrinsic, not extrinsic causes (i.e. not squirrels etc. just something that the tree does) because the pattern is observed so ubiquitously across the species and its range.

The bark of some pinus species, like pinus sylvestris and pinus pinaster naturally turns orange when they are a bit older. Other species stay grayisch black, like pinus nigra (hence the name).
By the way: I have never seen pinus sylvestris grow so straight. Is it possible this is another species, for example P. pinaster?
Sources: Den nya nordiska floran (Mossberg&Stenberg 2003) and Heukels' flora van Nederland (van der Meijden 2005).

I'm not sure this answers the question - the question asks why the pattern is present, you've simply stated that some species do this. I also think the original species ID is correct, they often grow straight, especially in managed forests.

@rg255 It depends if you think the question aks for a fysiological explanation or that the question (and some responses) seem to assume the colour is caused by some external factor. I think it asks for the latter, in which case my answer is valid. And from your comment i see we agree on the intrinsic nature of the colour.


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Indian tropical fruit trees and fruit bearing

Most Indian tropical fruit trees produce fruits in April-May. The best possible explanation for this is

optimum water availability for fruit production.
the heat allows quicker ripening of fruit.
animals have no other source of food in summer.
the impending monsoon provides optimum conditions for propagation

This was asked in a competitive examination, and being a mathematician with interest in plants, this caught my attention. Please note that this was asked in aptitude section, and I feel it more aptly belongs this SE, correct me if I am wrong.
My thoughts:

April-May is summer in (tropical) India (where I live, Kerala) hence optimum water availability looks out of option.
Considering fruit production being a part of process of propagation, though this is a favourable factor, I doubt if it is a determining factor
Animals help disperse the fruits, and less availability of food may be a favouring factor attracting animals to fruits, it is not a determining factor.
which for me looks like the factor influencing increased fruit production more than the other two.

Sorry for the layman language, I would be grateful if someone can correct me if my reasoning is wrong and explain it more precisely (preferably in layman language, though I can understand some botanical terms)

Trees fruit before the monsoon season to maximize seed germination and seedling recruitment. previous studies have shown that in many species, fruiting occurs just before the wet season such that seeds germinate and establish during the wet season when conditions are most favourable.
Smythe N. 1970 Relationships between fruiting seasons and seed dispersal methods in a Neotropical forest. Am. Nat. 104, 25–35. (doi:10.1086/282638)
So the answer is 4.

So you say faster ripening influences the tree to produce more trees in summer?

Adding: Something to be noted here is that question is about "increased fruit production" and not (just) "ripening"!

Evolutionarily, these tropical fruit trees would want to maximize the amount of offspring that are produced and that survive to reproduce. This would increase their fitness and ensure that their genes are passed on to the next generation.

Tropical fruit trees would "want" (they're not actively strategizing) to produce their fruit at a time when other sources of food for animals are limited as this would increase the likelihood of most of their fruit being eaten and these seeds being dispersed (through the feces of animals) to many different areas to grow and reproduce themselves. This ensures the continuation of these species of trees.

So you say (3) is the best possible reason for increased production of fruits in April-May? I doubt!


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Why there is no typical cells
My physiology book says that cell specialization is so great that no cell in the body could be called a typical cell.
I don't understand the above sentence, why couldn't there be typical cells? After mitosis don't we get two typical cells? Or what is meant by the sentence??
Thanks in advance!

Its because there are different kinds of cells in our body for example a neuron can't represent different types of cells found in our body like goblet cells etc., just like F1 car can't be representative of all cars. I presume that the word typical is in the context of human body.

I'm voting to close this question as off-topic because it is about language, not Biology.

It is about biological terminology which is relevant. Asmaa in this case a "typical cell" would be a cell that represents all cells in the body equally well, like an average of all cells in the body..

Typical here means representative of the whole.
from the google dictionary

typ·i·cal ˈtipik(ə)l/Submit adjective having the distinctive qualities
  of a particular type of person or thing. "a typical day"
  synonyms: representative, classic, quintessential, archetypal, model,
  prototypical, stereotypical, paradigmatic;

There is such a variety of cells in the body no one is really typical.  Like a typical human.  Who would that be?  Me?  Chinese lady?  Indian kid?  There are many of us and a lot of variety.  Maybe you could say "typical older Scotsman" or "typical arrogant Stack Question answerer".  You could definitely say "typical liver cell"; narrowing down the zone limits the variety possible and lets you more accurately characterize a call as prototypical or representative.


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The difference between the beta-sheets and the quaternary structure of proteins
My biochemistry book says that beta-pleated sheets is a form of secondary structure of proteins, and it is formed between two or more polypeptide chains.
I wonder why the sentence in bold doesn't belong to the quaternary structure instead?!

Beta strands can form both intra- and interchain sheets. I wouldn't get too caught up in the latter case when deciding what level of protein structure beta sheets fit into.

Quarternary structure is between separate protein chains or proteins themselves. Beta sheets are a form of secondary structure which is within a single polypeptide.
Sure, some of the structures in quarternary complexes will be between “two or more peptide chains”, but the stipulation that these not be part of the same polypeptide chain would be necessary.

You say that beta sheet is a structure within a "single polypeptide", but my text book says that it is between "two or more extended polypeptide chains". Is the book wrong?!!

No its just a symantic issue. A beta sheet requires 2 stretches of peptide to run parallel to one another. Those 2 stretches of peptide are part of one continuous chain at the secondary structure level. Whether it counts as Beta sheet when 2 stretches polypeptides from totally separate proteins are in close proximity enough to hydrogen bond, I'm not 100% sure. But generally it refers to secondary structure which must be within a single continuous peptide.


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Nerve excitability and K+ concentration
My book says that the excitability of the nerve is increased when increasing the the potassium ion (K+) concentration in the extracellular fluid and vice versa.
I don't understand this mechanism could someone explain it for me!
Thanks in advance!

Just for reference, what book are you speaking of?

my physiology book which my college provide.


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Has there been a measurement of a stalling force for myosin molecular motors?
For processive molecular motors like kinesin, in vitro assays have allowed to measure directly a stalling force beyond which they do not progress anymore or detach.
As far as I know, the literature has only very indirect ways of evaluating what a stall force may be for myosin molecular motors, is this true? If so, is it because of the nonprocessivity of most myosin motors, or are there other experimental obstacles to this measurement?


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Question regarding an Escherichia coli reaction
With respect to this link
http://www.biocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=RXN-14479
Here the enzyme is mentioned and the two reacting compounds. Now , my question is
1. When these two compounds react, do they initially get attached to the enzyme before reaction?
2.If they Do both these compounds get attached to the enzyme, what is such an interaction called? Protein compound interaction??

As far as I can tell, enterochelin esterase (Fes) utilizes an Alpha/Beta hydrolase fold to catalyze it's reactions, which means there's a triad of catalytic amino acid side chains. Where Fes differs from other proteins in the pathway is an amino terminal lid domain which confers specificity to the substrates of Fes ((1) dictates this forms a deep pocket in the protein). I'm having trouble finding the exact catalytic amino acids, but homology modeling between IroE and Fes from the same source shows this may be a triad of Glu, His and Ser. If we kind of visualize what a catalytic triad's mechanism looks like, and the following image is a generic lipase/esterase catalytic site,

A sort of transition state is formed between the target molecule and the serine, where the water reacts with help from the asp/glu and histidine to catalyze the hydrolysis. You'd just call it protein-ligand interactions.

Okay now I found this article in wikipaedia : http://en.wikipedia.org/wiki/Ligand , this has got a list of ligands... but the reaction I provided, doesnt contain the list of ligands as mentioned in wikipaedia, then how is it called a protein ligand interaction? Is it because the compound may contain a ligand group which binds to the protein which is why you called it protein ligand binding?

In biochemistry, we'd refer to the ligand as anything that forms a complex with the protein. That includes inhibitors, substrates, etc. The ligand that binds to the active site of the protein is it's substrate, and the following wikipedia page explicates ligands from a biochemical perspective.