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Can enzymes catalyze thermodynamically unfavorable reactions?
Can biological enzymes catalyze thermodynamically unfavorable reactions? I read that an enzyme lowers the activation energy of a reaction by offering an alternative reaction pathway with a lower activation energy, however the ΔG of the reaction is unchanged. If enzymes can do this, then how exactly does this work?

I've deleted the comments as the question has an accepted answer and flags started to pour in. Please go to chat to resolve outstanding matters, if any. They served their purpose as a few good quality answers are in place now. Q and A's also seem to be on the same page now in terms of the can and how issue.

"I read that [...]" - for completeness, could you add where you read this?

I read this in my school homework question, hence the tag. But there's a link here that mentions something to that effect: http://www.rsc.org/Education/Teachers/Resources/cfb/enzymes.htm

Enzymes can catalyze a thermodynamically unfavorable reaction by coupling it with a thermodynamically favorable reaction. Most often, enzymes use ATP hydrolysis reaction (energetically favorable) as a source of energy (in simple terms) to drive the unfavorable reaction forward. One important point to keep in mind here is that enzymes don't drive a reaction equilibrium forward or backward; they just help in achieving the reaction equilibrium faster. Also pay attention that enzyme itself does not change the thermodynamics of a reaction (as you say, ∆G of the concerned reaction remains the same, except at equilibrium), coupling of a favorable reaction with an unfavorable one only helps in making the overall reaction favorable. This phenomenon, of one reaction changing the rate of another reaction, is called induced catalysis and has nothing to do with the enzyme itself.
I will talk about how enzymes do this using examples, while the other answer talks about the semantics. An example which will help you understand this concept is ATP synthase. It is an enzyme found in the inner mitochondrial membrane which allows the movement of H+ from the inter-membrane space towards the mitochondrial matrix, using the energy of movement (since this is favorable and exergonic) to generate ATP. The reaction would look like this:
$$\ce{ADP + P_i + 3 H^+_{IMS} \rightarrow ATP + 3 H^+_{matrix}}$$ (remember that exactly 3 H+ are not required, this is a simplified version)
But, ATP synthase does not drive the reaction forward; it just helps in reaching the following equilibrium faster:
$$\ce{H^+_{IMS} \leftrightharpoons H^+_{matrix}}$$ i.e. keeping the amount of H+ in inter-membrane space and matrix the same. This is why a constant gradient is required to keep them in working condition. For this, the electron transport chain continuously throws H+ into the inter-membrane space to maintain an electrochemical gradient. Along with this, enzymes ATP-ADP translocase and phosphate carrier continuously take out ATP from the matrix and throw in ADP and Pi. However, this lowers the electrochemical gradient (exchanging ADP3- for ATP4- in inter-membrane space, while phosphate carrier catalyzes electroneutral reaction), making the final reaction: $$\ce{ADP + P_i + 4 H^+_{IMS} \leftrightharpoons ATP + 4 H^+_{matrix}}$$
However, since the enzyme just helps in maintaining equilibrium, it can also work backwards i.e. it can also transport H+ against electrochemical gradient (unfavorable), coupling it with ATP hydrolysis (favorable) to reach equilibrium. The enzyme is now called ATPase and the reaction becomes: $$\ce{ATP + 4 H^+_{matrix} \rightarrow ADP + P_i + 4 H^+_{IMS}}$$
There are many more such enzymes which couple ATP hydrolysis (or other favorable reactions) to catalyze reactions which are either unfavorable or very slow (i.e. require a source of activation energy) under normal cellular conditions. Another factor, as the other answer explains, which helps in this is changing the concentration of products. As seen above, ATP-ADP translocase and phosphate carrier continuously decrease the concentration of products (ATP) and increase concentration of reactants (ADP and Pi) so that the overall equilibrium shifts forward and the enzyme keeps on driving the reaction forward (this, again, has nothing to do with with the enzyme itself, it is called Le Chatelier's Principle). Again, the other answer focuses on this issue.
References:

Enzyme - Wikipedia
Cellular Respiration

This is at the best a misreading of the question and at the worst casuistry. If an energetically unfavourable reaction is coupled to a more energetically favourable reaction you have an overall reaction that is energetically favourable. The enzyme has nothing to do with the thermodynamics. The fact that the poster has accepted the answer implies that this answer has mislead him or, more likely, bamboozled him by giving such an unnecessarily esoteric and long example of the concept of coupled reactions which could be written as three simple A+B=C type equations.

@david Well, I reread my answer and don't find any line which says that enzyme has something to do with thermodynamics. In fact, it is this point itself, to disregard which I say again and again that enzymes only help in attaining equilibrium faster. I don't know how you concluded that point from my answer, but I don't think anybody with even basic knowledge of enzymes would get misled by my answer. Also, I don't like giving one-line answers & try to add as many details as possible. Yet, you can post an answer if mine 'bamboozles' you.

Excellent, clear answer. I don't know what David is on about, I can't see any way this answer would be misleading to the OP.

What does "Yes they can" mean in relation to an question that asks "how"? It would be good if people were encouraged to pose clearly researched and defined questions so they could be answered (or not) properly at the appropriate level.

Ah, I wrote that before editing the question, thanks for pointing out :) as for the lack of research effort, I too have voted to close this question. I just answered this because I find the question itself rather interesting and worthy to be answered. And I don't think I can do much after voting to close, downvoting, and warning about lack of research (as a matter of fact, I'll retract all these once proper research effort is shown by OP).

@David Is that really the basis of your complaint about this answer? The original question was "can" - the rest of this answer addresses "how".

Perhaps coupled reactions is what the OP was looking for, but it so that's not clear from the question. Coupling two reactions is an entirely different concept than catalysis, which simply means lowering the activation energy, so I think the wording of this answer is confusing. The correct answer is that catalysis has nothing to do with whether the reaction is favorable or not, as @David points out. (Also, ATP synthase is a rather poor example of a coupled reaction I think, as it is not fully stoichiometric; something like hexokinase would be better.)

@BryanKrause — I made clear the basis of my objection in my original comment. Roland, at least, seems able to understand it.

@Roland I don't think OP was looking for anything in particular in a correct answer. I suspect, though I don't know for sure, that the OP is trying to come to terms with two obvious facts: 1) Not all reactions in biology are, by themselves, energetically favorable, and 2) Enzymes can't change ΔG, effectively they only alter reaction rates. So how does this work? This answer clearly answers that question.

@BryanKrause  Yes, I think you're right.  I don't mean it's a bad answer.  It's just that this is a difficult topic where there is a lot of confusion in the biological sciences, and therefore I think it's particularly important to be crystal clear about the definitions.  It's not just arguing about terminology.  If one believes that catalysis and coupling are the same thing, then one might conclude that, for example, coupling ATP hydrolysis to a reaction makes it go faster ...

@tomd (and others too) why can't we...say, assume, that when OP talks about ∆G, they know the difference between ∆G and ∆G°? Also, I still don't find any line in my answer which says that enzymes do change either the equilibrium constant or ∆G°. I still don't find the answer misleading buddy, these are just the points which I did not mention.

@tomd better now? I don't get "A coupled reaction is a biochemical abstraction, without any thermodynamic 'slight of hand'"

Can enzymes catalyze thermodynamically unfavourable reactions?
Enzymes don't change the equilibrium of a reaction, but the fact that an equilibrium exists means that the reaction proceeds in both the forward and reverse directions. Before equilibrium is attained, ΔG for the reaction is not 0. Thus, by definition, one direction is thermodynamically favourable (ΔG<0) while the other is thermodynamically unfavourable (ΔG>0). Since an enzyme lowers the activation energy of a reaction, it is catalysing both the forward and reverse reactions. This is a semantic argument since the reaction will still proceed in the direction which is thermodynamically favourable.

How can enzymes catalyze thermodynamically unfavourable reactions?
Other than in the sense I described above, enzymes do not catalyze thermodynamically unfavourable reactions. However, biological systems can make unfavourable reactions favourable. In addition to the reaction coupling discussed in the other answer (sometimes referred to as pushing) thermodynamically unfavourable reactions can be made favourable by pulling. In this case, for reactions where ΔG°>0 (ie the reaction under standard conditions is unfavourable), the reaction can be made favourable by decreasing the concentration of products relative to reactants, such as by immediately using them in a subsequent, thermodynamically favourable reaction. Mathematically, the relationship between the free energy change of the reaction under standard conditions and the actual reaction is given by:
$$\Delta G=\Delta G^{\circ} +R T\ln\left(\frac{[P]}{[R]}\right)$$
As the ratio of product to reactant concentrations decreases, the actual free energy change of the reaction decreases and can be made thermodynamically favourable.
To be clear, it is not the enzyme that makes an unfavourable reaction favourable (again, it only lowers activation energy). Rather, the enzyme is catalyzing a reaction that is now thermodynamically favourable.

Sorry for cluttering your answer again, but I just love the dualistic approach. +1 it also points out a fundamental problem on the why versus how questions though. Often they seem to go hand in hand and obscuring the question core. Your approach solves matters nicely :)

Nice answer, +1! At least now I understand what I was missing in my answer ;) I've edited my answer to make clear the difference between what mine and your answers discuss :)

Annoying pedantic guy here :)  Two points: (1) I think it's a bit dangerous to argue using equilibrium, as this often leads people to think that enzymes are at equilibrium in living organisms. A lot of biochemistry textbooks do this, and it causes no end of confusion. The key point is not that enzymes "don't change the equilibrium";  it's that enzymes don't change the Delta G.  (2) Strictly speaking, the second part is not an answer to the new question, because it's not about the enzyme at all. It says "maybe other enzymes can help drive the reaction", which just shifts the problem.

@Roland (1) I'm not sure I appreciate this point, yet. (2) The answer is that enzymes don't make unfavourable reactions favourable. Then I go on to explain what can make unfavourable reactions favourable.

@Roland (this applies to your comment here and on the other answer as well) - I think the discrepancy here is between biochemistry of enzymes as functionally interesting in and of themselves, and the OP and the answers are in a different mode of thinking, where enzymes are a means to an end, part of the rest of biology. Neither approach is wrong, but for the second approach, it is still within the scope of the problem to include other helper mechanisms, because the goal is to understand the whole process, not the action of one enzyme or one specific reaction.

If we were talking about cars, in answering "how does pressing the accelerator make a car go faster?" someone could answer that "well it lets fuel and air enter the engine faster which increases RPMs and translates to torque that makes the car go fast." Then someone else says no no the accelerator pedal doesn't do any of that, that's the job of the butterfly valve and the transmission and the wheels. The pedal just signals the car, mechanically or electrically, to open the butterfly valve. Both answers are right, but at OP's level of understanding the first answer makes more sense.

@tomd,  I disagree. Reactions in living cells are not at equilibrium, because at equilibrium there can be no net flux.  The precise magnitude of Delta-G is less important, but I would say that modern studies disagree with Newsholme's 1973 textbook; see for example  http://www.nature.com/nchembio/journal/v12/n7/abs/nchembio.2077.html
Delta-G-0 is just one particular choice of units, it's not very important here. The key is that, whatever the Delta-G is for a reaction system (at steady state), adding an enzyme does not change it.

@tomd,  I did not quote you at all ...  I'm saying the conceptually important point is that enzymes are not at equilibrium in living cells, and therefore it is usually not helpful to to explain enzyme thermodynamics using equilibrium arguments. Precisely how far (or close) to equilibrium various enzymes are in cells is less important, and experimental data like Rabinowitz' paper often disagree with textbooks on Delta-Gs anyway.
But I think this discussion should be moved to chat.  When I have time I will write up an answer of my own to highlighting these issues.


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How do plants maintain air spaces in leaves?
As we know, there are air spaces in the mesophyll layer which allows carbon dioxide to diffuse in and oxygen to diffuse out, but cell membranes are partially permeable and allow water to diffuse to regions with lower concentration. Yet these air spaces still manage to not get flooded by liquid water.
How does this happen?

Welcome to Biology.SE! This question is off-topic since you don't show any research effort. Also, it might be a better fit for Physics.SE

I in-fact did some research but i came up empty handed as all the resources i have got my hand on to don't address this problem directly and the only helpful resource was this research https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1066361/pdf/plntphys00565-0087.pdf

That is wrong, yes it will displace it eventually making it move out the stomata unless ur saying that air is compressed (which is not and can't be as its content actually diffuse to and from cells) that it won't let water molecules through the pores that it fits through which again can't be the case, it is water and it can go out of the cell but why doesn't it?

in the end all sciences interlock, diffusion and osmosis for example are from physics, so if a question is asked about it relating living things u can't just claim it is off-topic

There has not been not much research on this topic, which has caused lack of definite answer. Sibbernsen et al, 2017 performed a study on response of stomatal opening on filling these air spaces with water. They suggest the existence of a vapor-phase signal (from water) that originates in the mesophyll and causes stomata to open in the light. In another research, Wiebe et al, 1976 were able to remove the air spaces with the use of paraffin oil which infiltrated the spaces. They show that leaf air spaces contain invaginations which are extensions of air space system and increase conductivity of CO2 to the chloroplasts which line these invaginations.
Stomatal transpiration gives a clue to this. When the stomata open, they expose the internal environment to the atmosphere. Due to this, the air spaces get filled with water vapors which, due to concentration gradient, flow outwards from the leaf. To maintain the inner water vapors, more water is evaporated from the nearby cells, which leads to more transpiration. This hints that some water is present all the time in these air spaces in the form of water vapors. However, when the concentration of vapors becomes high, the nearby cells might take in some water or the stomata might open to maintain the concentration. See this article for some details on this.

At last, there is Woolley et al, 1983 which concludes that the mechanism behind the maintenance of these air spaces is still largely unknown.

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T7 Tagging in Synthetic Biology
What is a T7 tag and can if be used to purify synthesized proteins? Is it charge based like a His tag?

The T7 tag is the first 11 amino acids of the T7 gene 10 protein. Basically, if you engineer a protein with the T7 tag, you've engineered a small, known epitope to the protein of interest which may be detected immunologically. The small size of the epitope reduces the chance it will disrupt the protein's normal function (to which it's tagged). If we look at the affinity purification kit on the following product page we can see that specific vectors can be used to express T7-tagged proteins, and an immunoaffinity column can be used to purify the protein of interest. The T7 tag chemical structure is denoted here.

It also allows the discrimination of engineered protein from in vivo expressed proteins and you don't have to make specific antibodies for each protein but use antibodies against the t7 tag instead.

What makes it different from the FLAG-Tag? (Besides sequence of course)

I don't have any data on how each epitope may affect stability or what have you, but it generally follows that whether it be T7, FLAG, HA or Myc etc. they're just method of recognition through the use of an anti-tag antibody (anti-HA, anti-FLAG, etc.) in immunoassay.

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T7 Tagging Next to Met
Will a T7 tag still work if it is placed next to a start codon? Meaning, will it still work with a Met attached to it in the amino acid sequence?
Thank you!

Homework questions are off-topic unless you show some effort solving them yourself. Not doing any research yourself is the same.

This isn't a homework question. We are an undergraduate research team (iGEM) asking a question as we need to know this to design our research project. I just worded my thoughts very clearly, no teacher nor professor wrote this.

Then you should probably explain this better in your question. Otherwise it might be closed.

@Kathryn if your team cannot find any local resources to answer your questions about designing your research project you may find the New England Biolabs Catalog a valuable resource with lots of plasmid maps and bacterial strain genotypes. If you have access to a research lab they very likely have some molecular cloning manuals and and lab recipe books that could also be valuable. Based on my brief experience here It seems like actual homework questions risk portraying the questioner as "too lazy to do it themselves". If you have a larger goal then disclosing that at the outset may help

By "still work" I assume you are asking if it will still be recognized by an antibody? It might. Internal T7 tag fusions are done, though they may require different antibodies than terminally tagged fusions.
That said, do you have a reason for inserting the the tag after methionine? The T7 tag already starts with methionine and naturally functions to initiate translation of T7 gene10. pET based vectors also contain it for this purpose.

[source]
In this vector, your gene of interest is typically inserted after the tag to create a fusion protein (using BamHI) or immediately after the start codon (using NheI). In either case, the T7 tag start codon is used.

Thank you very much. We didn't know that the T7 tag contained a methionine, and we were placing this tag after a stop codon, so we assumed we needed to place it after a start codon (Met).

You need a ribosomal binding site before the initial codon.

Or I am mistaken about what is asked...

This is more of a comment and you have enough rep to do so


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Proline Iminopeptidase v Proline Aminopeptidase
We're an undergraduate independent research team and we are having trouble purchasing commercial proline iminopeptidase as it is unavailable on Sigma Aldrich and very expensive on other websites. We need to test that this peptidase will cut a series of tripeptides we are synthesizing in e coli.
Could we purchase proline aminopeptidase instead of proline iminopeptidase; will the peptidase function the same way?
This paper says that they are the same, but this paper says that they are different. Does anyone have any experience with this commercial peptidase?

Chemically, proline does not contain an imino group. http://goldbook.iupac.org/I02959.html More on topic, you can send an email to the manufacturer of the aminopeptidase and ask if it cuts the tripeptides.

The peptidase cuts the tripeptides after the proline in that sequence. The purpose of purchasing this peptidase is to compare our experimental results (the results of the cleavage) to the results of the commercial peptidase cleavage. We work in synthetic biology so both the tripeptides and the peptidase will be in a single plasmid.

There are two related enzymes that cleave an N-terminal residue. Enzyme 3.4.11.9 cleaves any residue from a peptide when the next residue is proline. Enzyme 3.4.11.5 cleaves an N-terminal proline from a peptide. Unfortunately, it appears that both are sometimes referred to as proline aminopeptidase. However, only 3.4.11.5 is referred to as proline iminopeptidase.
The vendor should certainly specify which enzyme they are offering.


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Vegetable Cellulose
I'm a pharmacy student working on my thesis. I just want to ask the probable sources of vegetable cellulose found in vegetable capsule? Note: I'm referring to the capsule itself not for its possible content. Thanks.

There are "vegetarian" capsules?? I didn't know about this..

Vegetarian capsules are made of hydroxypropylmethylcellulose (also called hypromellose). The cellulose from which this material is prepared is usually from tree fiber, commonly from pine or poplar species (as noted here).


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Are there examples of now-living species where one is descended from the other?
I'm not a biology person so please forgive me if this question is formulated badly :)
I'm curious. Are there any species that has an ancestor species that is still alive today?

http://www.quora.com/Is-there-any-species-living-today-that-is-the-ancestor-of-any-other-living-species

Wolves and dogs.. They are still considered the same species though

First, you probably want to have a look at this answer who offers an introduction to phylogeny.
There are few subjects that yield to as many semantic issues than the definition of species and the definition of life. Your question is at the border of the species definition. Therefore the question is not so much about Biology than about Philosophy, so let me advertise: The following answer is nothing else than a semantic discussion (philosophy) and has no relevance of our understanding of evolutionary processes. Note however that semantic discussions might be very helpful to evolutionary biologists as well.
Sexual organisms
Dogs and wolves
Commonly, in sexual organisms, species are defined by the concept of reproductive isolation. To address @WYSIWYG's comment, wolves can breed with dog. The offspring is called a wolfdog and it suffers from little inbreeding depression.
Is the MRCA contained in the species of one descendent
But I'll use the wolf example anyway and make some fake assumptions. There are probably better examples I could pick though. Let's assume that wolves and dogs can't interbreed, that they are therefore separate species. Let's assume as well that somehow we manage to recreate the Most Recent Common Ancestor (MRCA) of wolves and dogs (which has some issue due to parental effect incl. culture and epigenetic) and this MRCA can breed with wolves and but not with dogs, then we could eventually say that the MRCA and the current wolf (there are actually 3 species of wolves that are probably not real species) are the same species. One could then say that dogs descend from the wolf.
Feeling that we talk about improvement over another species
I think that much of the issue in saying that the dog descend from the wolf is that some people would understand things like "dog is more evolved than the wolf", which makes no sense. Both the current wolf and the current dog has evolved for exactly the same amount of time. Any living species on earth has evolved for exactly the same amount of time (almost 4 billion years).
Temporal constraint in the definition of species
Therefore, it is eventually possible to say that one node on a phylogenetic tree is of the same species that the previous and the next node. I think that in reaction to the misleading feeling that early evolutionary biologists and current non-biologists people have in hearing that one species descent from another one, we tend to make a temporal constraint to the species. A species is what it is only at the exact moment we talk about it. This prevents us to consider a MRCA as being of the same species of any descendent.
Note that the definition of species yield to various issues such as the case of ring species.
Asexual organisms
Same issue as above
Now, if we talk about asexual species. There is no clear definition of what is a species there. Of course if we were to use the definition based on reproductive isolation, then any asexual individual would be a new species. We therefore define a species when we see a group of phylogenetically related individuals that all share some feature that we find "interesting enough" (very arbitrary) to describe this group as a different species from the some other group of individuals. In asexuals, you may see one lineage that accumulate 10 mutations, while the other lineage accumulates 1000 mutations (this other lineage may eventually live in a different environment than the MRCA of the two lineages). Therefore, you get to the same issue when thinking about asexuals than about sexual organisms. If one lineage ressemble more their MRCA than the other lineage, then is their MRCA part of the species of one lineage?
Is a species a thing?
Well... the concept of species is useful in the sense that it is often not ambiguous to classify one individual into one species or into another. The concept of species allows us to better communicate.. so yes I guess it is useful.
The concept of species existed way before we had any understanding of natural selection, mutations, genetic drift and other basic concepts in evolutionary biology. Aristotle used the concept of species (he also thought without having any good evidence that life evolves). This concept of species has been very well conserved because of the static view we had on what a species is before Darwin. Now that we have a better understanding of evolutionary biology, ecology and reproductive biology we discover that the concept of species is not a natural category but is a man-made unclear category.
Other discussion on the subject
In this post I made an overview of the issue related to the concept of species. I did not go into the details but tried to list important concepts.
You will find many websites that address the concept of species in philosophy. I particularly like discussion in the concern of how current bad semantic may yield to bias in the way we think nature and may yield to bad decision in applied science. Here is a podcast (in french) on the origin and consequences of the concept of species.

Very interesting, thank you. The thought that species is a man-made categorization had never occurred to me before. Non parlez francaise I'm afraid though :(

Very nice breakdown, +1. One nitpick, however: the unit of "evolvedness", if such a thing could be said to exist, would not be years but generations. A bacterial species is way more "evolved" than a mammal since they've had several orders of magnitude more generations in which to evolve. While I agree that saying "X is more evolved than Y" is nonsensical, if you do choose to make such a statement, you need to think in terms of generations and not time. Time is irrelevant, it is only the number of generations that counts.

There's a TetZoo podcast where one of the two pod-casters, I think it was Darren Naish, observed that species as a taxonomic grouping are inherently paraphyletic.


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Plasmid gene knockout
How do delete a single gene encoded in an operon on a plasmid using E. coli? Could you use the same principle as when knocking out a gene from the bacterial chromosome which is e.g. suicide vector-derived allelic replacement through homologous recombination?
Thanks for your response.

So you have a plasmid and you want to delete a section? Why not do the deletion outside the cell with PCR or something and then transform into new cells?

Well the simplest way is to cut the gene at the both ends from operon by means of proper restriction enzymes but in case that you get more than one recognition site then you can use microRNA or proper oligo to make a hairpin loop and break that part
If you only want to silence the operon then you just need to cut it nearly at middle of the gene and ligate it with a nonsense sequence, then it will loose it's functionality.


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What is the meaning of conservation site in miRNA-mRNA pairing context?
I am not biologist and just work in Bioinformatics field.
Does anyone know what is the meaning of conservation in the context of miRNAs and their pairings to mRNAs?
Example:
Each of these duplexes has a region called the “seed”, a site located at 5’ part of miRNA (positions 2-7) which is characterized by a strict or almost strict Watson-Crick pairing between miRNA and its target site and shows the best conservation among the miRNA sequence.
(from http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3182075/)

As far as I know this is unknown. Binding sequences for miRNA where empirically found to be more conserved overall (this is actually used by and very important for algorithms to predict miRNA binding sites) than the rest of the transcriptome but the actual reasons behind it are still unclear. For the meaning, well the seed in particular is very conserved which means that this information can be used to better predict where miRNA will bind and therefore which genes they will silence, i.e. mismatches in the seed regions are more heavily penalized than mismatches in non-seed regions.

What the conservation scores denote is how well is the miRNA binding site conserved between different organisms (orthologs). PicTar uses an HMM based methodology to do that. TargetScan and miRanda also provide conservation scores. I shall give you a detailed answer in a while.

So, generally miRNA binds several different target RNA? If yes is it relevant? Thanks.

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Accuracy of best plant growth models?
Given a plant $P$, predict its height $H$ at time $t$ since planting given some environmental variables $E_1, \dots, E_n$. How accurate are the state-of-the-art models for such thing? What data is used to make the prediction?

You should add some more details. What do you mean by state-of-art models. Note that the utility of models depends on the question that is asked.

I've worked on a couple of these for biofuel production. The answer varies widely according to plant P and how well studied plant P is. In terms of what data is used, it includes but is not limited to: temperature, insolation, length of the day, cloud cover, rain, soil composition, soil type, soil density, other local effects like wind or pests, altitude, humidity, and pH. For corn(food) and miscanthus(experimental biofuel crop) the models are quite good if the year is pretty normal and you're in a well-studied parameter space, mostly because corn and grass grows straight up. For trees, non-crops, non-corn crops, etc the models are almost completely useless. It's a question of testing nearly every possible combination of parameters for each plant P, and how much people care about how tall it gets.
Given how much data goes in, it surprises me that even under ideal conditions(well-studied) some of the parameters the model spits out are impossible/wrong. There's a measure of leaf overlap(just as an example) that's especially poorly defined but a rough proxy might be "number of leaves that shade a specific point, on average" and it's regularly measured at <10 and regularly predicted at well north of 50.


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BLAST, using Smith-Waterman in the last step and S-score
In my bioinformatics course we studied the BLAST agorithm. After finding the HSP's and joining the HSPs together that are close enough and in a correct diagonal trend, we perform a next step: namely a Smith-Waterman alignment. Why do we do this? Didn't BLAST already find the alignment by joinging the HSPs?
I also have a second question about BLAST. When calculating the E-value with the formula:
$E=K \times m \times n \times e ^{\lambda S}$
Which score is this S exactly? Is it the score found for the HSP with the used substitution matrix? What is the score if we have multiple HSPs in one database entry? Is the E-value, and thus the S-score, calculated seperatly for every HSP or is it a value for the entry in total?

You may be interested in bioinformatics.stackexchange.com

Please post your two questions separately.

The BLAST algorithm is a heuristic to find which the path through the matrices formed between a query sequence and a target sequences from the database is ‘best’. Such paths represent an alignment which is has a completely different basis to that of the Smith-Waterman dynamic programming algorithm. Not only is it ungapped, but it based on comparison of tuples with matches scored according to frequency, and then proceeds by trying to join those with certain relative scores.
The speed of the program is partly the result of rapidly discarding unpromising paths, storing and continually refining only the current best candidates. The alignments will not be Smith-Waterman alignments, but there is no point in performing a Smith-Waterman alignment on each high-scoring sequence pair as this is not the basis of inclusion in the pool of best candidates. Performing such an alignment would be a waste of time for those candidates that will ultimately be discarded.
Only when the run is complete is it appropriate to perform the Smith–Waterman alignment on the final top candidates to produce a gapped alignment from which statistics such as the E-value are calculated (using S, the raw score from such Smith–Waterman alignments).

I have revised my answer to include both points as the second is now readable thanks to @anotherHomoSapien, and happens to be related.

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What is C-terminal tryptic peptide?
A biologist wrote to me:
... C- or N-terminus,... For example, a C-terminal tryptic peptide like AGWRGSDSHSR, would be...
I don't have any idea what that is. When I google the term ("C-terminal tryptic peptide"), nothing obvious came up. What's that? Why AGWEGSDSHSR is a "C-terminal tryptic peptide"?

Did a biologist really write this to you? Seems strange as it's clearly not your field. But really how do you expect a decent answer unless you give us the full text and context of what appears to me as a quite bizarre communication.

Its quite simple if you look at the basics! Lets have a look at the sequence you give:

AGWRGSDSHSR

Write that in 3-letter terms1:

Ala-Gly-Trp-Arg-Gly-Ser-Asp-Ser-His-Ser-Arg

Pay attention to the C-terminus. The last amino acid residue in the sequence is Arginine. Now, its well established that Trypsin cleaves a polypeptide after (i.e. towards the C-terminal side of) Lysine and Arginine2.
Thus, C-terminal tryptic peptide is the peptide that remains after a polypeptide has been treated with Trypsin.

Its just about getting the clues @smallchess

Ah, so it refers to where the peptide was cleaved, not where the peptide was located on the original protein. Unintuitive for me :)

@armatus haha I've been working on peptide sequencing for a while now, so I got the point there ;)

Why the downvote? I get that the question is pretty naive, but is there something wrong in the answer?

Trypsin does not cleave at the "carboxy-terminus" of any amino acid, as that term is used to designate one end of a protein (that with a free alpha-COOH). I also do not believe "C-terminal lysis by trypsin" means anything, or if it did it would mean the removal of the C-terminal amino acid, which is here not the case. Your answer does not represent usage and is clearly wrong.

@david I agree with you in that I should have framed my sentences more carefully since there are terms which represent something but are used to mean something else. I've edited my answer. Does it make sense to you now?

@xusr yup I get what you mean, so I edited the answer a bit to make it clearer :)

Downvotes are free that is why instead of giving input to improve the answer people go around anon downvoting.

@ronisaiba TBH I quite agree with you. Most of the time David has something to say about my answer, I see him talking like "here's a -1 and a comment for you". AFAIK what SE encourages is "all right you touch the correct point, lemme just edit these finer details to make it more presentable". Downvotes on answers do give -1 to downvoter though :/

Unless your corespondent is off their rocker (or I am), this is rather unambiguously referring to the peptide released from the C-terminal end of a polypeptide by tryptic digestion.
This means that the final arginine in your sequence would have been the C-terminus of the original polypeptide, not the trypsin cleavage site. It also means that your sequence was preceded by R or K.

Quite, which is why it looks like some sort of homework question, with the R in the sequence as red herring.


text:
Why are bruises not lethal?
Given the following:

bruises are caused by minor trauma which breaks blood vessels beneath the skin, causing bleeding
the mechanism by which bleeding stops is clotting
blood clots inside the body have an unfortunate tendency to get into the bloodstream and cause blockages, leading to severe problems such as strokes or heart attacks

why is it that people don't die from bruises?  What mechanism does the human body have to keep this from happening?

In addition to the serious answers which are given below, I'd like to point out the real reason bruises are not lethal is because our clotting system is beautiful and borderline miraculous in every way.

I would note that clotting around a bruise or similar injury is a reaction that was "learned" in the process of evolution, and it exists precisely to protect the body from further damage.  No doubt, during the evolutionary process, there were times when a mutation made things a bit worse, but over a few hundred million years it got sorted out.

Your question can be answered without any factual knowledge: Because of evolutionary pressure. To some individuals minor trauma is life threatening. Until recently they did not tend to survive long, let alone procreate.

blood clots inside the body have an unfortunate tendency to get into the bloodstream and cause blockages, leading to severe problems such as strokes or heart attacks

This statement is primarily true only for blood clots within blood vessels, especially in the veins. When you are talking about bruising, you are talking about clots outside of the vasculature.
When a blood clot occurs in an artery, it can block that artery or break off, flow downstream, and block some smaller distal vessel. These events are most severe when they affect crucial organs like the brain and heart ("stroke" or "heart attack"), though of course any organ can be damaged in this way. However, blood clots in arteries can't ever directly affect a tissue that is not distal from where the clot starts, because they can never pass through capillaries or travel backward.
When a blood clot occurs in a vein and is dislodged, it can follow the increasingly larger venous system back to the heart, where it can cause a pulmonary embolism (blockage in the lungs) or, via a patent foramen ovale, travel to the left-side circulation and end up anywhere, including the coronary arteries or blood vessels of the brain. Similarly, clots that form in the venous return from the lungs to the heart or in the left side of the heart itself can travel anywhere (except the lungs) and create a blockage.
For a clot outside the vasculature, for it to have an effect somewhere else systemically it must re-enter the vasculature. This is simply not possible in most situations, because the vessels involved are very small, and during bleeding the blood is flowing out of vessels: there is no pressure gradient to push the clot back into the vessels.
In more severe cases of injury where major vessels are involved, clotting in those major vessels can indeed be a problem, but not for common occurrences of bruising.
(see also @anongoodnurse's answer that contains a good clarification of what exactly a bruise is, as well as how there are risks from very serious bruises but not the same way the original question implied)

"...travel to the left-side circulation and end up anywhere, including the coronary arteries or brain" How would a blood clot get past the blood-brain barrier?

I don't mean that it could actually enter the brain, or any other organ or tissue for that matter, but rather that it could close off circulation to the brain; that's what an embolism does.

I also want to point out that the blood-brain barrier really just refers to the special regulatory interface between capillaries and actual nervous tissue in the CNS that prevents a lot of molecules from entering the brain that can more freely do so in other tissues. There are lots of blood vessels all in and through the brain (as a whole organ) that are exposed to the same circulation as the rest of the body.

"bleeding the blood is flowing out of vessels: there is no pressure gradient to push the clot back into the vessels" Doesn't the heart both push blood away and pull blood in, so wouldn't there also be a negative pressure trying to draw clots back in?

@IshouldchangemyUsername There isn't any negative pressure anywhere in the vasculature relative to the outside.

@IshouldchangemyUsername: To elaborate: during diastole -- when the heart refills, which is not the same as "pulling blood in" -- there is still pressure. When your doc tells you you have a 130 / 80 blood pressure, the lower number is the pressure during diastole -- pressure above ambient. So, as, Bryan said, the vasculature is always under pressure.

@DevSolar That is true about the heart refilling, but the 130/80 number is arterial pressure, the 80mmHg is for arterial diastole. On the venous side, there is very little oscillation (right by the heart there are some effects on pressure from atrial systole and the mechanical motion of the heart) and much lower pressure (~10-20mmHg). Instead, the veins on constantly "full" and a bit distended. The connective tissue and the muscles in the veins hold a constant pressure on the blood, a lot like a stretched balloon would, and this is the pressure that refills the heart.

@Bryan Krause's answer is quite correct. I just want to clarify what a bruise is, because I think you have a misconception of what happens.
There are bruises (blood leakage into tissue because of damage to capillaries) and there are hematomas (a collection of blood in a tissue caused by breakage of either many capillaries or normally a larger blood vessel.)
A capillary is small. As an analogy, imagine someone injects a small amount of blood, say, .5cc, under your skin with a very fine needle, but leaves the needle there. The blood will spread out as much as it can over time. The blood does not need to clot; only at the level of the injured capillary does the blood need to clot. So if the fine needle represents the capillary, the .5cc of blood won't clot then go back up into the needle; it can't happen. It's stuck in the tissue (the extracellular fluid of the skin.) A tiny clot near the tip of the needle will stop more blood from pouring out. No problem. No bleeding to death.
Since the blood has nowhere to go once it spreads out, the blood cells die in the tissue, and heme degradation begins. Initially the blood is reddish, then reddish blue, then dark purple, followed by purplish-brown, to brown-greenish, to yellow, to normal.
A hematoma is a collection of blood that can't spread out because it is unable to penetrate the tissue very well (maybe there's a fibrous capsule in the way.) The blood will stay there and will eventually clot, but it can't get into the end of the fine needles (capillaries) or the bigger needle (arteriole). The body doesn't work that way. Hematomas are eventually broken down by the body as well, but it takes more time, and often there is a residual "scar" in the tissue where it was. That's why sometimes you feel a little bump forever afterwards where you had a really bad bruise.
Bruises - really bad bruises - can cause major damage if there is insufficient or no clotting factor, but not because clots form and kill us, but because the bleeding doesn't stop and if it's bad enough, one can bleed so much into a tissue that the swelling can cut off the blood flow into the tissue (e.g. see compartment syndrome).

I would like to add a point which I feel others have missed: our body already has a safety system to prevent such a thing from happening, called fibrinolysis.
Obviously, this system is not solely for degrading clots that might have come into the bloodstream, but this is an important part of all of its functions. The main character here is plasmin: a serine protease (just like trypsin) whose function is to degrade blood proteins, including fibrin clots. It is synthesized by the liver and secreted into the bloodstream in an inactive form, namely plasminogen. It comes with two levels of safety systems. In the zymogen form, it is in the closed form i.e. the active site is hidden and inactive. When it encounters a blood clot, it gets a conformational change and exposes its activation site. Now, enzymes like tissue plasminogen activator (tPA), urokinase plasminogen activator (uPA), kallikrein and even factor XII convert it into its active form (by breaking a peptide bond between Arg561 and Val562). This two level safety system helps in preventing unnecessary activation of plasminogen (since both the zymogen and its activators are flowing in the bloodstream).

So what prevents it from chewing off all the blood proteins? The secret: its inhibitors are also flowing with it in the bloodstream. Plasmin is inactivated by proteins like $\alpha_2$-macroglobulin and $\alpha_2$-antiplasmin. Plasmin cleaves $\alpha_2$-macroglobulin at the bait region, causing a conformational change. In the resulting $\alpha_2$-macroglobulin-plasmin complex, the active site of plasmin is hidden so that its efficiency is greatly reduced. This conformational change also allows the clearance proteins to bind this complex and let it get out of circulation. You can see the Wikipedia article to know more.

This is all factual, but bears no relation whatsoever to the OP's question. The point of our answers was that it is impossible for a clot to enter the bloodstream the way the OP proposed. This is an answer that might support the OP's faulty supposition.

@anongoodnurse I have supposed that the OP did not take blood vessel size into consideration while asking the question. I don't think just telling why it would be impossible for clots to reach capillaries is enough, if there is something to add, it must be added, and that is what I did; just in case the OP would become curious about how any clot is removed eventually. Anyways, the OP has already selected an answer, so my answer can be taken as a bonus point too.

This answer is IMHO the best... it explains the exact mechanism needed to prevent all of the blood from clotting up. Without this mechanism any minor wound would be lethal.

I think fibrinolysis should be included in a complete answer. Not all injuries producing bruises behave so that the clotting would be fully outside the capillaries. Hemostasis includes fibrinolysis.

Bruises usually damage capillaries (think of them as being side roads well away from the expressway and major routes). Just as closing down a few side roads in a lightly populated suburban or rural area a mile away from a major interstate is unlikely to cause a backup/traffic jam, blood clotting in capillaries at a bruise shouldn't generate dangerous blockages.

I don't think this analogy works at all. Blood clots aren't like closing a road in the abstract; rather, they're a blockage on the road that can break loose and move around. But there isn't any sort of blockage like that on the road network.


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What happens to our body when we undergo a sudden temperature change from 40℃ to 20℃?
We know that a glass gets cracked when it undergoes sudden change in temperature. But what will happen in the case of a human body if it changes from the maximum(>35℃) to the minimum temperature(<35℃) suddenly?

That depends entirely on the range of temperatures you're talking about. Please [edit] your question and add some additional details, because as it stands now your question is unclear.

The edit is not an improvement of the question. (>35 C) and (<35 C) is not a range.

Others have given the scientific literature, I'll just add an experience. I am 32, male, 5'7" tall. Went for a hike in the Himalayas. Was cold enough to wear a sweatshirt and half sleeved sweater even after few kilometers of quick hike. Encountered a waterfall, decided to take a dip. And boy was it cold. The dip under the fall perhaps I could have easily tolerated, but then I went to do some floating in the shallow pool underneath it. When I tried to get out, I just wasn't strong enough to stand. My feet weren't steady, I instantly knew something was wrong, and I just felt very low...continued

...continued...It wasn't like sick low, it was just like the entire system wasn't doing what I expected it to do, and I felt I might fall. It alarmed and scared me. I knew I needed to heat up my very cold body and started doing some jumps and shakes and stuff. Only after I was confident that Humpty-Dumpty had been put together again (metaphorical, I am not fat but reasonably fit) did I put every piece of cloth I had on and moved on the trail. That day I decided never to enter such freezing glacial water again....continued...

...continued...So, whether at that moment the best thing to do is to just dry yourself, put clothes on and sit tight, or to do what I did - exercise, I'll let any doctors here be the guide. Just in case someone finds themselves taking a stupid dip in glacial waters again.

Disclaimer: the answer is very broad and covers both the situations I am confident about, as well as those I understand only superficially.
The outcome depends on particular temperatures.
Example - cold shock response: "Cold shock response is the physiological response of organisms to sudden cold, especially cold water. In humans, cold shock response is perhaps the most common cause of death from immersion in very cold water, such as by falling through thin ice. The cold water can cause heart attack due to vasoconstriction, the heart has to work harder to pump the same volume of blood throughout the body. For people with heart disease, this additional workload can cause the heart to go into arrest. Inhalation of water (and thus drowning) may result from hyperventilation. Some people, due to body type or mental conditioning, are much better able to survive swimming in very cold water." But: " A person who survives the initial minute of trauma (after falling into icy water), can survive for at least thirty minutes provided they don't drown."
Sudden heat at entering sauna - I am not sure, but probably it also may cause heart attacks. Recent heart attack is a contraindication for sauna visits. Healthy individuals do O.K. due to thermoregulation mechanisms in the body.
As we move to more extreme temperatures, where the thermoregulation of human body simply has no chance at all to keep up, you can percieve the human body as a chunk of meat. The proteins denature, the water in the body gets boiled. The meat gets cooked, turns coal like, burns to ashes... Or by freezing, the water forms crystals, damages and breaks the cells. Eventually the meat freezes to be stone hard and does not change for a long time if kept at such temperature.

Blood vessels  tighten as the diferencial between the body temperature and the external temperature start to even out and the excess heat/energy disperses from the body to the environment. There should be a slowdown of heartbeat rate as less effort is applied to regain homeostasis.On the negative side, the sudden tightening of the blood vessels will add strain on the blood pressure until the heart starts pumping blood at a regular rate again, causing pains like muscle spasms and headaches. This can be minimizes if u got to a temperature of 25ºC instead of 20ºC and do a gradual decrease in temperature.
Reference
Alexiou. The effect of water temperature on the human body
and the swimming effort. JBE – VOL. 10.2, 2014


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Why do the humans become sleepy after meals?
I don't know about all the mankind, but I know enough people, who becomes sleepy after their meals. Also, I'm not sure, what kind of food do they consume, but I personally get sleepy almost from any food: sweet, fat, spicy, salty, liquid, tasty, not tasty, etc.
Is this phenomenon well known? And, if yes, how does it occur?

The functions of Parasympathetic nervous system - Rest and digest !

The name used frequently for this phenomenon is "Post-lunch dip".
"The post-lunch dip is a real phenomenon that can occur even when the individual has had no lunch and is unaware of the time of day. This dip has its roots in human biology, and may be linked to the size of the 12-hour harmonic in the circadian system. It is certainly exacerbated by a high-carbohydrate lunch, and may be more likely to occur in extreme morning-type individuals."
PubMed Source
Another PubMed source
"The 'post-lunch' dip is a bi-circadian phenomenon, largely unrelated to lunch, and worsened by a disturbed prior night's sleep. Despite anecdotal claims of adverse effects of larger lunches on afternoon driving ability, there is little actual driving data to support this belief."
For other reading and research...

What can be done to avoid Post-lunch dip? @Ilan

Coffee drink would improve the feeling I thing. In addition, meal with low glycemic index will lessen the phenomenon as well.

A relatively simple answer to explain your observation (yes, its not just you, it is something that actually occurs):
Orexin (or hypocretin) is a neuropeptide that controls arousal, wakefulness and appetite (Davis et al, 2011). As you might have understood, it acts as a critical link between what you eat and how much you sleep.
Generally, all kinds of foods contain glucose (ignoring some very rare examples, none of which I know honestly). When this glucose enters your bloodstream, it acts on not only insulin levels, but also orexin levels. Glucose has an inhibitory effect on orexin production, similar to leptin and opposite to ghrelin (Inutsuka et al, 2013).
Now, since increased orexin levels promote wakefulness, inhibition of orexin production causes sleepiness (Mochizuki et al, 2003). This helps explain how almost all kinds of meals cause a person to become sleepy.
References:

Davis JF, Choi DL, Benoit SC (2011). "24. Orexigenic Hypothalamic Peptides Behavior and Feeding - 24.5 Orexin". In Preedy VR, Watson RR, Martin CR. Handbook of Behavior, Food and Nutrition. Springer. pp. 361–2. ISBN 9780387922713.
Inutsuka A, Yamanaka A. The physiological role of orexin/hypocretin neurons in the regulation of sleep/wakefulness and neuroendocrine functions. Frontiers in Endocrinology. 2013;4:18. doi:10.3389/fendo.2013.00018.
Takatoshi Mochizuki, Thomas E. Scammell, Orexin/Hypocretin: Wired for Wakefulness, In Current Biology, Volume 13, Issue 14, 2003, Pages R563-R564, ISSN 0960-9822

What should we do to avoid it? @another 'Homo sapien'

@Pie not consuming heavy diets or meals rich in carbs might prove effective (I'm no expert in foods), or maybe a bit of caffeine (I wouldn't recommend it though, due to its addictive effects)

As far as I know it happens due the histamine release after meals. It leads to vasorelaxation and blood flow to the gastrointestinal tract. So, brain does not receive enough blood and you feel sleepy.

Please add some references for your answer.

Source : Here
Sugary foods lead to the production of insulin. Insulin stimulates cells to take up glucose from blood. It also mobilizes tryptophan to brain. Once in brain, tryptophan triggers formation of serotonin, a hormone involved in controlling mood and slumber.

the best sources are PubMed publications. Any other source are unreliable, especially site not related to any scientistic research and activity.

@llan Ohk..Will search and add some reliable references.

Digestion burns a lot of energy as many muscles enter the mechanism as well as many chemical reactions.
Therefore, you feel tired as your body has less energy for other functions than it usually do.
I remember a lecture at the university about sciences' history in which they explained an experiment, a long time ago, led on death sentenced men. After a very good meal, one guy was going out for a ride while the other was going to sleep. After 6 hours, they killed both of them : the one who slept had fully digested the meal whereas, for the other, digestion was not complete. They guessed it did not go as well as part of the energy needed for digestion was used for skeletal muscles and that sleeping afer eating helped for a better digestion.

That is a very biased experiment, to say the least. Why, for example, do people then go for a "digestion walk" and actually feel it helps them to digest?

@skymninge: pure speculation, they mistake the effects on their metabolism of exercise, for the effects on their metabolism of having completed digestion. Or repeated contraction of the abdominal muscles while walking helps shift wind that they associate with poor digestion. Doesn't really matter why, the conclusions of a study of two people can be explained or waved away with any old crazy theory ;-)


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Do the bacterial species X, Y, Z code for proteins A, B, C?
My PI has assigned me a task to gather evidence to determine whether or not a list of particular species of
Campylobacter and Helicobacter code for a list of several proteins.  To put it simply I’ve been asked, “Do species X, Y, Z code for proteins A, B, C?”  The genomes of these bacterial species have been fully sequenced and I am able to retrieve the FASTA files for each of them.  I am having trouble deciding on the proper method to screen these genomes for the genes.  I have been given the names of the proteins, i.e. VgrG and HCP, but the amino acids sequences listed on databases are annotated to different species of the bacteria.  I seem to be stuck in a grey area and am having trouble connecting the overwhelming amount of resources available on the NCBI website.  I have not found a specific guide to perform this task - Could you please provide me with a solution to my problems?

First of all, don't reinvent the wheel, search for annotated homologs first. Assuming you don't find them, the next step is:

Collect the sequences of your query proteins (not genes) from one species in a multifasta file.
Run a tBLASTn with those sequences against the genomes of all the other species of interest.
Analyze. Look for HSPs with a certain level of sequence identity. The details of what threshold you choose will depend on your data, I can't help you  there.

While the tBLASTn approach is going to be more sensitive, an easier method that can find gene structures and not just HSPs is to use exonerate:
exonerate -m p2g proteins.fa genome.fa

Finally, for a more sensitive search than either of the above, useful for finding more distant homologs, run a Psi-tBLASTn of your proteins against the genomes of interest.
In all of these approaches, the tricky bit is to choose the right threshold. Unfortunately, there is no golden rule here. It all depends on how closely related your species are and how similar the homologs. You will have to try a few different ones before you can choose the right one.

I am unclear as to how I could go about obtaining these query proteins.  They are not listed in any databases yet. I think my PI wants me to predict whether or not a protein exists in these organisms.

@codax that's a completely different question! What are you trying to do? WHat do you have and what are you looking for? Don't you have a list of proteins in species X and want to find them in species Y?

I'm really sorry if I was unclear, but your advice is invaluable to me and I'm learning so much. I have a list of species and I need to find if they contain genes that code for specific proteins.  Ex. Campylobacter Jejuni and VgrG.

@codax OK, if you have a list of proteins you want, get their sequences from a related species of bacterium, the closer the better, and use those sequences to query your target genomes. The methods I describe are sensitive enough to deal with small differences in sequence.

I've tried your approach to this problem.  The HSP's indicate an overall similarity to all of the sequences entered into the query.  From what I understand, there is a near 100% identity ranging from 97-100%. Now I know that there is a high similarity between the list of proteins entered and the species I've entered. Would I have to put one query at a time and blast it against one species to confirm if the sequences code for the individual proteins?

@codax no, each query protein should have its own set of HSPs. You are looking for HSPs that have i) high sequence identity and ii) cover the entire length of the query sequence (or nearly). Now that you know they are there and have high similarity, you  can also use exonerate to match the genes more precisely.

Do multiple sequence alignment of your protein sequences. This will give you evolutionary relationship between your sequences.

I think the OP needs to identify genes in the genomic sequence and only has proteins from one species. Multiple alignment won't help.

I have to identify if these genes exist in a list of species.  I have the names of a few proteins.  MSA would not apply in this situation.  I can retrieve the FASTA containing the entire genomes of these species.  Is there a way that I could retrieve the protein sequences and compare them with the nucleotide sequence somehow?


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What is the name of cellular respiration that Prokayotic cells use?
Eukaryotic cells use mitochondria using anaerobic or aerobic respiration. Prokayotic cells lack mitochondria but are bacteria. Mitochondria originated from bacteria and can be used in the same way. Bacteria produce ATP the same way that Mitochondria do.
So, what is that kind of cellular respiration called?

"Prokayotic cells lack mitochondria but use bacteria instead" ??

@Dexter Yes. Here's some extra info.  http://biology.stackexchange.com/questions/5430/how-do-prokaryotes-perform-cellular-respiration-without-membrane-bound-organelle

Prokaryotic cells don't 'use' bacteria. Bacteria are prokaryotic cells. Is it some wrong formation of sentence ?

@Dexter I fixed it.

Check this.

I think I figured it out from someone else

Prokayotic cells use anaerobic respiration.
Glycolysis is the only stage of cellular respiration that does not occur in mitochondria.
The glycolysis process does not need oxygen and uses anaerobic respiration. The other stages require oxygen and use aerobic respiration.


text:
Is global life expectancy normally distributed?
I am trying to find out what the world distribution of life expectancy looks like.

Statistician here. The answer would depend on what, exactly, you're asking about. The answer you have now wasn't explicit about what precise question it was answering but seems to be answering "if I randomly chose a country, each with equal probability, and looked up its life expectancy, what would the distribution of that life expectancy look like?". I expect you want something different to that (e.g. perhaps something closer to "if I randomly chose a person from the world, what would their life expectancy at birth have been?"). The most interesting/useful questions may be harder to answer.

Let's see!
I took the most recent WHO data from here and did a quick an dirty analysis in R. Here is the histogram as well as a normal distribution with the same mean and standard deviation as the actual data:

Does not look very normally distributed. In fact, the shapiro test confirms this impression:
Shapiro-Wilk normality test

data:  df$life_expectancy
W = 0.94141, p-value = 4.338e-07

Edit
Commenters requested to weigh the life expectancy by population size.Well...the result is pretty ugly:

Apparently, the large populations of China and India produce disproportionally high bars. However, keep in mind that we are using averaged values which means that all the variation within countries is not represented by the histogram. We would actually have to have data on individual ages of death for a random sample of the world population to finally settle the question. :/

Have you tried weighing by the number of inhabitants? It's true that there's no reason to expect a gaussian. But the distribution you show also seems rather weird :)

Who kills all those people just before they turn 80?

It would definitely be interesting to see how the distribution looks when weighted for population.

I'll see what I can do

Both graphs can't answer the question, since they're done by the mean in each country. So, all people from India and China fall in a single column each, when with real data they would be more spread, and, who knows, make something closer to normal distribution. Though it's probably hard to get the real data.

That's what I said in the last paragraph.

A few people thought it would be interesting to see what the distribution looked like if we plotted the number of people dying at each age, so I took data from the SSA (which admittedly isn't global data, but it's probably fairly reflective of the world overall) and plotted the number of deaths per 100,000 at each age.

This looks like it makes sense - the high death rate at birth, the plateau during the 20-40 range, then the rapid escalation past middle age, and eventual decline shortly after reaching the average life expectancy range.
However, while it looks a lot smoother than plotting the averages of individual countries, it's definitely not normally distributed.
EDIT:
If you extrapolate the above death rates using the global life expectancy of 71.0 instead of US life expectancy, the chart looks roughly the same, but is adjusted to reflect what the death rates of the planet most likely look like.


text:
How do I read a species description that uses both ≡ (triple bar) and "incl." to denote synonymy?
I'm trying to understand the relationship of plants formerly classified as Dorstenia crispa with distinct individuals continuously classified as Dorstenia foetida. I would assume that the distinctive phenotype would warrant a var. or forma, if not a subspecies, but I haven't seen it written as such anywhere.
I turned to monographs, which in one case stated:

incl. Dorstenia crispa Engler (1898); ... incl. Dorstenia crispa var. lancifolia Rendle (1915) ≡ Dorstenia foetida ssp. lancifolia (Rendle) Friis (1983);

Would this indicate that a specimen identified as D. crispa is properly identified no more specifically than as D. foetida?
Does this indicate that a specimen of D. crispa v. lancifolia is properly D. foetida ssp. lancifolia; or simply recognising that D. crispa v. lancifolia and D. foetida ssp. lancifolia would refer to the same individuals, which are properly still called nothing more than D. foetida?
Since these formerly-recognised infraspecific taxa do exist as separately-kept lines in cultivation, would they be properly recognised as cultivars?

My answer may simply be the closing remark in the above-quoted description, "Since the various forms are connected by intermediates, it is impossible to recognize infraspecific taxa." However, that's deeply-unsatisfying if cataloguing a collection that contains several now-synonymous specimens.

Welcome to Biology Stack Exchange! I think this is a fine question, and I look forward to hearing (or rather seeing) the answers!

Thank you! I appreciate the welcome, and hope this gets some answers myself. :-D

This seems like the type of thing that might vary from publication to publication. If you have access to the full book, maybe there's a key/glossary where you can find what the authors mean by these symbols

According to the Taxon guidelines for authors (pdf, pg 205), a triple-bar (≡) indicates a homotypic synonym:

Homotypic names are cited in chronological order in a single paragraph with
  the identity sign (≡), followed by the type.

So, in your example, Dorstenia foetida was described on the basis of the same type specimen used by Forsskål in 1775 to describe Kosaria foetida -- or possibly a neotype was designated linking these two names, possibly by Schweinfurth in Bull. Herb. Boissier 4(App. 2): 120 in 1896. More information about the relevant type specimens would help sort this out.

That makes sense. How does it play with "incl.", then? I see, then, that D. crispa var. lancifolia shares a type with the superceding name D. foetida ssp. lancifolia. What relationship does that type have to D. foetida, indicated by the incl.? Is it simply that the taxonomist preparing this monograph is indicating his belief that they all should share a type, even though currently they don't?

I'm afraid I have  no idea! If I had to guess, I'd guess that "A: incl. B" means that all individuals associated with the name B are considered by the taxonomist to belong to their circumscription of name A, without the requirement that they share a homonym. In some cases, it looks like B is a subspecies or variety, suggesting that these should be subsumed into A and not considered a separate entity. I'd hoped someone more knowledgeable would chime in but since that hasn't happened yet, here's my somewhat-informed guess!


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Clarification on RefSeq Genes track on IGV
The following picture is a snapshot of the RefSeq Genes track (collapsed) on IGV. I know that the bold blue line indicates exons and the thin one indicates introns.
However, I cannot find what the medium line stands for. Is it part of the exon? Why is it different?
I have checked into the manual but I couldn't find any relevant info.

When you expand the track (bottom picture) even more diverse lines appear.

medium blue line without arrows
medium line with arrows
bold line with arrows

Can anyone explain to me what is the difference between all of them?

The thinnest blue line is intron, so not in your transcript.  The medium thickness segment is untranslated exon, the thickest blue segment is translated.

Thanks for the answer. It makes sense. Do you have any insight on the meaning of the arrows? Why some medium blue lines have it and some not?


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How to grow fibroblast colonies from single cells?
I need to establish a cell line starting from single cells seeded on a 96 wells plate by a FACS sorter. The cells I am using are human fibroblasts RPE-1 cultured in F12 medium supplemented with 10% FBS and antibiotics. After having seeded 5x96 cells (one cell per well in 5 plates) I have obtained only 4 colonies. Does anyone know any good (preferably personally tested) protocol to efficiently grow fibroblast colonies from single cells?

Why do you sort the cells when you use a cell line? Additionally: What kind of colonies do you want? 2D, 3D?

I have engineered the cells using the CRISPR/Cas system and I sort the transfected one (GFP expressing vector). However, since only 1% of the transfected will have the right modification and since my final goal is to obtain a new cell line, I need to grow colonies out of single cells (2D, 3D doesn't matter), and then screen them to find the one carrying the correct modification.

This should be relatively straight forward. Sort the cells into single wells so all descendants are clones of the sorted cell and let them grow until they are dense enough to be transferred into a bigger plate (probably 48 or 24 well). Continue this process until you can go into big cell culture flasks or plates and make sure that you freeze away a number of aliquots as a backup if something goes wrong. Expand the cells further until you have enough cells to do an analysis.
Keratinocytes need some time to get highly proliferative (around a week or so) and if you don't grow them on a layer of feeder cells, usually also need a special conditioned medium. See the references below (if you have trouble accessing the papers, let me know).
What often also helps is the use of conditioned media. I know this from other cells in the skin which often don't like to grow (at least not as primary cells) unless you use conditioned media. For this, take of the media from the same sort of cells (here it would be keratinocytes) before it is completely used (typically yellow if the media contains pH indicators), centrifuge it to remove any cell debris and then mix it with fresh media to let your cells grow. You might need to experiment a bit with the mixing ratio between the "used" and the fresh media, but 50%:50% is usually a good starting point.
References:

Isolation and cultivation of human keratinocytes  from skin or
plucked hair for the generation of  induced pluripotent stem cells
Culture techniques for human keratinocytes
Improvement of human keratinocyte isolation and culture using
thermolysin

I did that but I got only 4 cells (out of almost 500) to grow into colonies and it took 3 weeks! Fibroblasts don't like to grow alone (at least this is what I am experiencing) so I was looking for suggestions about the protocol to use to make them grow well even if isolated.. I tried to seed different amount of cells but less than 1000 cells per well nothing grows. I will look to the links you posted.

What media and what kind of plates do you use?

F12 medium supplemented with 10% FBS and antibiotics. Very standard 96 wells plates for cell cultures. The cells grow perfectly if I seed them in large number but a single cell will not grow. I think I need to tweak the medium, maybe use 50% conditioned medium... But before rushing in tens of tests I wanted to ask if someone have a nice running protocol to accomplish the task.

That's what I would suggest as well, the use of conditioned medium. We rarely do keratinocytes, more melanocytes and melanoma and they often don't like to grow if there are not enough cells.

This is just to let all of you know that I am trying your suggestions. As soon I will have the results I will sign the correct answer.

Conditioned medium worked very well! in few days I can see colonies growing from single cells!

Although I have not yet done, in general, cells are happier in a conditioning medium. Grow the original cells in 10cm dishes and save the medium and use it to grow single colonies. You might want to mix used and fresh medium (1:1 ratio).
Growth factors are another option. Insulin is sometimes used, but it also depends on cells.
Coating the surface of well with extracellular matrix such as collagen could be effective.
If your cells are normal human fibroblast, cells get senescent, stopping growing. You might want to use immortalized cells like hTERT RPE-1, although you should be careful because immortalization could cause characteristic changes.

Thank you for the suggestion, I am indeed using hTERT RPE-1, I will try growing them in 1:1 conditioned medium and see..


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What animal produces male gametes by mitosis?
The following question came up in my biology examination but I could not answer it:

"What animal produces male gametes by mitosis?"

I know that some plants produce their gametes by mitosis in the gametophytes, but found no references to any animals doing so.

I don't think gametes are ever produced by mitosis. There can be modified meiosis in which there is no halving of the number of chromosomes. This can be seen in haploid organisms such as male honeybees.

@WYSIWYG correct, but it is so because male honey bees are produced by parthenogenesis. So all cells in them are haploid and can act as gametes.

@another'Homosapien' No the cells do not automatically act as gametes. Sperm is a very specialized cell. Spermatogenesis does happen (see my answer).

I think the answer of honeybees is much correct,as their cells are haploid they have to produce their gametes by mitosis, because the worker bees are diploid and they are produced after fertilization so the queen and the male gametes have to be haploid.

@WYSIWYG It actually does happen: they can automatically act as gametes. I don't know any reference, but I was taught earlier that meiosis cannot occur in such cases. Also, as you say in your answer, only meiosis-II occurs which is also very similar to mitosis.

@Asmaa did you ask your teacher about the correct answer? (because only your teacher can solve this dilemma now ;)

@another'Homosapien' yes that does not mean that cells do not differentiate. Gametogenesis is also differentiation (along with haploidization). Since the germ cells are already haploid, meiosis-I is abortive. When you say they automatically act as gametes, you are just ignoring all these processes which are quite critical for the formation of the sperm.

@WYSIWYG okay I apologize for saying that they can automatically act as gametes. But you can't deny that they produce gametes by mitosis, not meiosis.

@another'Homosapien' yes and as I mentioned in my answer, it still behaves like a meiosis but is finally just like mitosis.

In organisms which have haploid males (such as honeybees), there is a variation of meiosis during spermatogenesis. The meiosis-I is abortive i.e. the chromosomal events such as crossover and separation of homologous chromosomes, do not happen. However, some cytological changes do happen which is described by Sharma et al (1961) as "simulation of the normal meiosis I". This is followed by meiosis II (which is mechanistically same as mitosis). So, basically there is no halving of the number of chromosomes and the gametes are also haploid.
So, as far as I can guess, the question in your exam sheet probably refers to spermatogenesis in Hymenopteran haploid males.

Reference:
Sharma, G. P., Brij L. Gupta, and C. G. Kumbkarni. "CYTOLOGY OF SPERMATOGENESIS IN THE HONEY‐BEE, APIS INDICA (F.)." Journal of the Royal Microscopical Society 79.4 (1961): 337-351.


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Why doesn't the rest of the body have something like the "blood-brain" barrier to protect itself from pathogens?
According to Wikipedia:

"The blood–brain barrier acts very effectively to protect the brain from most pathogens".

This is because the pathogens cannot pass through the tight junctions of the endothelial cells lining the inside of the blood vessels delivering blood to the brain through BBB.
But if so, why don't tissues/organs in the rest of the body employ the same barrier, and thus avoid pathogens from ever entering those tissues/organs through the bloodstream?

There are many physical barriers actually (not like BBB, though). Skin, for example ,is a very strong barrier.

That's true, but if there is a very strong barrier, such as the BBB, which is stronger than others, why isn't it used universally throughout the body? That is, what advantages are there to use a weaker barrier when there is a stronger one available?

There can be many reasons to why BBB-like barrier is not present in all the capillaries of the body. Let's talk about them one at a time.

Source
Blood-brain barrier has its own side effects. Some major side effects are cerebral edema (accumulation of excess water in the extracellular space of the brain, which can result when hypoxia causes the blood–brain barrier to open) and (possibly) Epilepsy. See this wikipedia article:

Several clinical and experimental data have implicated the failure of blood–brain barrier function in triggering chronic or acute seizures. Some studies implicate the interactions between a common blood protein (albumin) and astrocytes. These findings suggest that acute seizures are a predictable consequence of disruption of the BBB by either artificial or inflammatory mechanisms.

Another problem is that BBB doesn't allow passage of drugs, diagnostic and therapeutic agents through it. Again, see this article:

Overcoming the difficulty of delivering therapeutic agents to specific regions of the brain presents a major challenge to treatment of most brain disorders. In its neuroprotective role, the blood–brain barrier functions to hinder the delivery of many potentially important diagnostic and therapeutic agents to the brain. Therapeutic molecules and antibodies that might otherwise be effective in diagnosis and therapy do not cross the BBB in adequate amounts.

Now, if you want to know why the body doesn't have BBB-like barrier (not exactly BBB), then there are three parts of the answer.

These kinds of barriers are highly specialized for a particular organ or organ system, which may not be useful for another organ/organ system. Also, creating specialized barriers for all the parts of the body will take a lot of energy, cells and even more time to develop completely. Possibly, in the evolutionary course, body preferred to have phagocytic cells circulating in the body instead of having specialized barriers throughout the body.
These barriers might not be a total solution for immunity or restriction of pathogens. See this part:

It is believed that latent HIV can cross the blood–brain barrier inside circulating monocytes in the bloodstream ("Trojan horse theory") within the first 14 days of infection. Once inside, these monocytes become activated and are transformed into macrophages. Activated macrophages release virions into the brain tissue proximate to brain microvessels. These viral particles likely attract the attention of sentinel brain microglia and perivascular macrophages initiating an inflammatory cascade that may cause a series of intracellular signaling in brain microvascular endothelial cells and damage the functional and structural integrity of the BBB. This inflammation is HIV encephalitis (HIVE).

Also, it is not necessary that those pathogens would infect only those tissues to which they reach via bloodstream. Pathogens like HIV cause infection in the blood cells. See this image from here:

Once a person is infected with HIV, the virus begins to attack and destroy the CD4 cells of the immune system. CD4 cells are a type of white blood cell that play a major role in protecting the body from infection. HIV uses the machinery of the CD4 cells to multiply (make copies of itself) and spread throughout the body. This process, which includes seven steps or stages, is called the HIV life cycle.

Similar barriers are already present in many parts of the body. For example- Blood-Ocular Barrier, Blood-Testis Barrier, Blood-Thymus Barrier, etc. They may also have some loopholes. For example, see this article-

Possible consequences of blood-thymus barrier failure are trophoblast-specific or tumor-specific antigens penetrate into the thymus, deletion or anergy of antigen-specific clones and acquired thymic tolerance induction.


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Why does too much candy cause nausea?
As I sit here after eating too much chocolate, I wonder:
What are the biological mechanisms behind eating too much candy candy causing nausea in a healthy individual?  Is it a spike in blood sugar, or does the stomach run out of a particular chemical, or is it a pH shift?
Is it the same reason that greasy meals can cause nausea?
From an evolutionary perspective, candy causing nausea seems counter-intuitive since candy is easy calories.  Then again, candy and concentrated carbs are modern inventions...

There can be many reasons about why too much candy (chocolate) can cause nausea. Lets talk about them one by one.

Hyperglycemia - chocolate contains sugar, and too much sugar consumption can cause high blood sugar levels i.e. hyperglycemia. When blood sugar levels remain high for some time, it can cause nausea and vomiting, among many other symptoms including dizziness, itchy skin, dry mouth, thirst, etc. If left untreated, it can lead to diabetic ketoacidosis or diabetic coma. See this article for more information.
Artificial Sweeteners - often chocolates contain artificial sweeteners instead of table sugar or glucose to prevent risk of hyperglycemia without compromising with taste. But many times, these artificial sweeteners can cause side-effects too. For example, there have been reports that sucralose causes nausea and vomiting in some people. Other alernatives, like mannitol, sorbitol, xylitol, maltitol, isomalt, etc. can also cause nausea and similar symptoms.
Dumping Syndrome - sweet foods, like chocolate, are hyperosmolar i.e. have high osmolarity. When these are ingested in large amounts, they cause the small intestine to expand quickly, due to which the ingested food passes too quickly through the stomach, largely in undigested form. This condition is called Rapid Gastric Emptying (RGE) or Dumping Syndrome. The initial symptoms of dumping syndrome include nausea, dizziness, diarrhea, fatigue, etc. See the Wikipedia page for more information.
Fats - chocolate contains cocoa butter, and cocoa butter is a source of saturated fats. Ingestion of large amounts of fats can lead to indigestion, and indigestion can become a cause of nausea and vomiting. This also explains why greasy foods can cause nausea; because they have high fat content.

Some other factors could include candy allergy, pregnancy, etc. or something I failed to mention. But I hope this much would help too.


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Has the human body the greatest total length of nerves of all animals?
I've read that a human body contains about 150,000-180,000 km (Pakkenberg et al., 1997; 2003) of nerve wiring in the whole body. But does this length increase with the size of the animal? For example, an elephant is much bigger than a human and perhaps even his brain is bigger but is an elephant also the animal with the longest nerve cells in total?

Of course this length increases. Elephants are bigger than humans, so they need longer nerves to reach distant parts of body (say, tail) which obviously increases total nerve length. But I doubt whether anyone would have calculated total nerve length of elephant/any other big animal.

There is no reason to believe that total nerve "wiring" (or combined length) does not increase with the size of the animal, although the number of neurons in the brain (and the number of connections they make via dendrites) matters as well.
Animals with long necks, legs and tails have long nerves. Ancient sauropods may have had the longest nerves (referring not only to nerve bundles but single neurons) in history. Their brains were not as large compared to their body size, however, as humans.
But whales - the largest animals on earth - do have larger brains. Modern cetacean brains are among the largest in both absolute size and in relation to body size of all mammals. The brain of an average adult sperm whale weighs 8 Kg; by comparison, the average adult human brain weighs about 1.3 Kg.
Blue whales are the largest animals in existence today. With a large brain (3.6 Kg) and a long body, I can't see a particular reason to believe that the total amount of "wiring" in a blue whale doesn't exceed that present in a human.
[Normal weight of the brain in adults in relation to age, sex, body height and weight]
Normal organ weights in men: part II-the brain, lungs, liver, spleen, and kidneys.
Cortical complexity in cetacean brains


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When you take a very cold or hot bath how is that influencing your breath?
It looks like when you take a cold shower or bath your veins get smaller and when you take hot shower your veins get wider. But is that right and do you need to breath more in both cases because you got less oxygen? If so how does it work in both cases?

There is an adaptation to being submerged in cold water in mammals called the Mammalian diving reflex.  Have you ever noticed when you jump into cold water, or enter a really cold shower you take a big breath?  While not exactly correlated with the dive reflex, it shows that there is a neurological reflex of entering cold water.  Here is a brief overview of what can happen when you submerge yourself in cold water:

Lower heart rate - aka Bradycardia, slowing down the rate of blood pumped will decrease the oxygen requirement of red blood cells, which in turn allow organs like the brain to use oxygen.
Smaller veins - aka Vasoconstriction, the blood flow in your fingers and toes is reduced, allowing more blood to be used in the more important organs.  Eventually the vasoconstriction will apply to hands and feet.
Blood shift - this adaptation allows the submerged animal to dive without having their thorax to collapse due to increased pressure.  Not necessarily attributing to breathing patterns though, so I left the boring stuff out and paraphrased.

In hot water, the opposite happens with respect to #'s 1 and 2.  Increased heart rate, like when you go running, tends to increase breathing frequency.  Vasodilation allows blood to flow more easily and is primarily for heat exchange.  Have the warmer blood in your fingers exchange heat to the environment will cool it for the return to systemic circulation.  Surface area is a large factor with heat exchange.  Hope this provided some insight.

Do you perhaps know what chemical proces causes the drop of heart rate in cold water. And is it true that when you take of hot shower you veins are getting bigger and because of that the bloodpressure drops so you get less oxygen and need to breath more?

The chemical process is just nerve signals that lower the heart rate.  I'm fairly certain it is parasympathetic regulation including the vagus nerve.  When your "veins" get bigger, and blood pressure drops, the heart compensates by increasing the pumping.  So technically you may need to breath more due to the increased heart rate.  You do not get less oxygen though.


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How do chameleons signal cells to change color?
I have read about how they can change color, but is there literature about the chemical signaling process they use to do so?  I read that it could be some combination of hormones and neurotransmitters, but I couldn't find specific information on the receptors or chemical mechanisms.

As said by @dblyons, there has not been a lot of research (biochemical) on chameleons. So, the exact part of mechanism that you're looking for is still not understood. However, we have recently caught the broad end of the stick. Chameleons don't have special cells for color, their complete skin has a layer of pigments (dermal iridophores) which helps them in changing color. See this (or this) article:

Chameleon skin has a superficial layer which contains pigments, and under the layer are cells with guanine crystals. Chameleons change color by changing the space between the guanine crystals, which changes the wavelength of light reflected off the crystals which changes the color of the skin.

These guanine crystals are actually like colorless mirrors, but by changing the distance between these crystals, wavelength of light absorbed (and reflected) can be changed. It is quite similar to how the color of ozone changes from pale blue in gas to violet-black in solid form. However, how chameleons trigger this change in distance of crystals, is not yet known.
This is how these crystal lattice works:
sourcesource
This is what a guanine crystal looks like ((a) is guanine):

You can also see a nice real-time video of guanine crystals changing color of chameleon here.
The color changing portion of skin has 3 main layers:

superficial s-iridophores which help in changing color in visible region rapdily.
deep d-iridophores which reflect light in infrared refion and are thought to provide thermal protection to chameleon.
layer of melanin which is actually yellow in color, making chameleons naturally yellow(!) in color. When the guanine crystals come closer, they reflect the blue portion of visible spectrum. This blue light, along with the natural yellow color of melanin, becomes green which gives green color to chameleon. So, the actual color visible to us is a combination of color reflected by guanine crystal and yellow color of melanin.

As I said already, the exact biochemical signalling process behind this process is not known yet. It could be complex hormonal or neurotransmitter signals. However, hormones are considered as the main triggers because chameleons have been shown to change color due to changes in mood instead of environmental protection.

Cephalopods such as the octopus have complex chromatophore organs controlled by muscles to achieve this, whereas vertebrates such as chameleons generate a similar effect by cell signalling. Such signals can be hormones or neurotransmitters and may be initiated by changes in mood, temperature, stress or visible changes in the local environment.

the thing i didn't like about the chameleon wiki was that they cited a national geographic article... no primary source

@dblyons I have added another citation in the first paragraph which has (quite) plenty of references. Please let me know if it helps.

it doesn't.  the original citation is this paper: http://www.nature.com/articles/ncomms7368

@dblyons This nature article has also been cited in the reference I added. Along with it are many other citations including some books too.

This is a good question and... kind of remarkable because I don't think there is a specific body of literature regarding chameleons.
Generally though, vertebrate skin cells responsible for color (these cells are called chromatophores and arise from the neural crest during development) are responsive to the hormones melatonin, MSH, and others.  These hormones, which are released from the pineal (melatonin) or pituitary (MSH), bind GPCRs on the surface of the chromatophores which elicit intracellular activation of PKA, for instance.  This activity can cause mobilization of pigment within the cells.  This article about fish coloration may help guide you somewhat in your studies, but chameleons in particular seem like an understudied clade of color-changing animals!