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How does one experimentally obtain a hemoglobin-oxygen dissociation curve?
I've always wanted to do comparative eco-physiology studies looking at Hemoglobin-Oxygen affinity of populations in different environments, but I can't find a protocol to experimentally measure the relationship. Does anyone know where I can find a protocol, or know a protocol themselves?
I'm assuming an answer would include what the necessary instrumentation would be, what condition the blood needs to be in (fresh?), if the heme is isolated (and if so, how), and what an appropriate sampling scheme would look like.

There are existing instruments commercially available to measure hemoglobin-oxygen saturation curves. Whole blood or lysed blood can be used; I would expect the instrumentation to come with specific directions for sample preparation because it may depend on the exact equipment.
These devices use a spectrophotometer to measure saturation, taking advantage of the same color difference between arterial and venous blood that is visible to the human eye.
To collect a curve, you start with the sample saturated in room air or oxygen, and the instrument gradually introduces nitrogen to replace the oxygen, while also monitoring oxygen concentrations using a Clarke electrode.
Here is an example paper that uses one of these devices. Their precise methods may or may not be appropriate to your research approach.
References

Head, C. A., Brugnara, C., Martinez-Ruiz, R., Kacmarek, R. M., Bridges, K. R., Kuter, D., ... & Zapol, W. M. (1997). Low concentrations of nitric oxide increase oxygen affinity of sickle erythrocytes in vitro and in vivo. Journal of Clinical Investigation, 100(5), 1193.

Thanks! This sounds not terribly difficult, given the right equipment. Something for me to think about if I ever have my own lab/startup funds.


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Does all the citrus fruit contain Citric acid and Ascorbic acid?
While reading a sixth class book about acid bases and salts. I figured that that citrus fruits like lemon, orange etc.. contains citric acid. But in the same book they also given that amla contains Ascorbic acid. Amla being a citrus fruit should contain Citric acid. I am just confused with this.

Just tell me whether all the citrus fruits contains both citric acid as well as ascorbic acid.

I checked in wikipedia & also in oxford dictionary.

Welcome to Biology.SE! What research have you done before asking it here?

You might be interested in the meaning of citrus.

It seems most of the fruits has citric acid! @another'Homosapien'

Whatever the colloquial/vernacular/etymological meaning of "citrus"; when it comes about scientific names; Citrus is a particular genus. It do have many species.

"Amla being a citrus fruit"

No. Amla (Phyllanthus emblica) is not a member of genus Citrus; not even allied.
Ascorbic acid is just another name for Vitamin C. It is also present in common edible citrus fruits.

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How do I compare bacteria growth curves?
I have bacteria growth curves for 5 different temperature conditions and these were created using %red-light transmittance. How do I compare these growth curves? Should I calculate the growth rate and if so how do I do that?

Please do not create different accounts and ask the same question

If you are interested in learning about the site. You could visit the tour-page for basic informations, the help-page for more detailed informations about what could be asked or could not be.

The other question: https://biology.stackexchange.com/questions/58350/how-to-calculate-growth-rate-analyse-growth-curve-of-bacteria

1) A Bacterial growth curve:
When we provide a favorable medium for bacteria to divide regulary and increase in number, we get what's called a "growth curve", measuring the concentration of cells against time as time passes.
2) Phases:
A) The first phase is called the "lag phase", in this phase bacteria are adapting to the new medium, preparing enzymes etc, to start dividing. Therefore little to no growth is observed.
B) The second phase is the "Exponential growth phase", bacterial cells are well adjusted to their medium and ready to reach full potential, "maximum division and growth" happens here.
C) The third phase is the "stationary phase", bacteria are no longer able to grow or feed, they run out of nutrients, and growth is stationary/zero again. It can persist for a long period of time. (Cell growth=cell death, no actual increase in cell number=stationary)
D) The final growth phase is the "death phase", no nourishment is available and toxic metabolites have been accumulating during the stationary phase, death occurs (death here means that an increasing number of bacterial cells are dying, unlike the stationary phase where the number of cells dead equals the number of cells viable), following cell death (which now happens at a faster rate than cell growth), the cell concentration starts to decline. However, it doesn't really reach zero and bacteria might be able to regenerate again when the conditions are healthy again.
3) Recording bacterial growth using transmittance or spectrophotometer:
As bacterial cells increase in number, the turbidity of their medium increases (depends on the concentration of cells), and the incident light (if you shoot a beam of light across the medium) is more deflected away from the receiving detector (to detect the intensity of light), which makes spectrophotometer a reliable and accurate method to measure cell growth (proportional to the intensity of light detected).
4) How to compare growth curves?
Looking at the growth curve will give some idea of the rate of growth in relation to a standard growth curve or some other available growth curves (compare phases and their durations, the exponential phase, etc). However there is a way to calculate growth curve and generation time (doubling time) from a growth curve.
The difference in cell concentration/difference in time = growth rate constant. Or dN/dt = kN or you may use this advanced equation: log10N2 – log10N1 = k(t2 – t1)/2.303
Simply plot any two random points of time on your curve: the first point is t1, the second point is t2, N1 is the number of cells (cell concentration) at t1, N2 is cell concentration at t2.
Or you can simply use dN/dt = (N1 – N2)/(t1 – t2) and compare the resulting k between curves.
I hope this answers your question, please know that I am by no means an expert on the subject and you may search further or get expert advice if you need to.
References:
Textbookofbacteriology.net
Miller-lab.net/MillerLab
biotek.com/
Academic.pgcc.edu
Web.mst.edu

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Calculating maximal growth rates
Maximal growth rates are indeed important to compare, when evaluating the differences between different growth curves. The higher the value is, the fastest is the exponential phase. In order to calculate the growth rate of each curve, you have at least to possibilities:
The quickest and easiest way is to select two points from the exponential phase and use the following formula:
$\mu_{max} = \frac{ln(X_2) - ln(X_1)}{t_2 - t_1}$
where $X_i$ is your measure of cell density (e.g. dry weight, optical density, etc.) at time $t_i$, and $\mu_{max}$ is the maximal growth rate.
Another way to estimate $\mu_{max}$ is to use modeling techniques. A classical model for bacterial growth is the Gompertz model:
$y(t) = A \cdot exp \left[ - exp \left(1 + \frac{\mu \cdot e}{A} (\lambda - t) \right) \right]$
Where $y$ is the measure of cell density, $A$ the asymptotic value of cell density and $\lambda$ is the duration of the lag phase. Tools exist that can help you fit your curves with this kind of model, like the grofit package for R (it's free!). This package can provide you with estimations of $A$, $\lambda$ and $\mu_{max}$, along with the corresponding intervals of confidence (see figure below).

Comparing growth curves
When comparing growth curves, key values to compare are: $\mu_{max}$ the maximal growth rate, $A$ the asymptotic value and $\lambda$ the lag phase duration. One should not neglect one of them over the others. Low $\mu_{max}$, low $A$ or high $\lambda$ are each a sign of possible bacterial stress.

Source of the figure: Kahm, M., Hasenbrink, G., Lichtenberg-Fraté, H., Ludwig, J., Kschischo, M. (2010) grofit: Fitting Biological Growth Curves with R, Journal of Statistical Software (33)7

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Why are monocotyledonous plants considered more evolved than dicotyledonous?
Why are the following characteristics advantageous for a plant?

to have atactostele instead of eustele
to have less stamens
to lose secondary growth
to switch to anemophily pollination (also if it's not always the case)
to use the cotyledon as storage media instead of endosperm

Why are there so much similarities between liliopsida and gymnospermae?

This wasn't an homework question, but a genuine curiosity that arose studying such organisms. I'll be glad to modify it to fit the rules of the community if possible.


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Do telomeres appear at just one end of the chromosome?
I have just studied DNA Replication for my Biology Class and I have this question that leaves me stuck, though I have tried to figure it out myself.
During telomere replication, I am aware Telomerase elongates the 3' end of the template strand on both molecules and then DNA repair Polymerase comes in to fill in the gap that could not be previously synthesised after the last primer.
After this is complete, we would have the T-loop formation and Shelterin complex arrangement to protect these ends and form what we know as telomeres. However, if we take both DNA molecules, this only happens at one end of each of them, right? As the other end would correspond to the leading strand.
So I am confused: do telomeres just appear at one end of the chromosome?

The term "leading strand" only makes sense in the context of a gene. Both strands can contain genes, it only depends on where is the promoter. I think this is where your confusion comes from. So, correcting your question you were probably looking for to the 5'->3' strand and the 3'->5' one. As both ends have both strands (one's 5'->3' is the other's 3'->5'), yes, telomeres appear at both ends.

Ah, okay, I see. In my class, we did not see any specificity as to replication being made about a gene but rather as a whole strand, so I just figured that for a 5'->3' strand, every left replication fork would give rise to a continuously synthesised strand and the right one to a lagging one.

This answer might help you (if you’re still interested in getting help 2 years later). You’re right that this has nothing to do with genes.

This is a great question!  The issue- the "paradox" of replication of linear chromosomes- of trying to filling in the unreplicated region (an overhanging 3' end) should technically be an issue only for one 3' end of each chromosome on any round of replication, as one new 3' end is produced by leading stand synthesis, and the other- the one with the issue- by lagging strand synthesis. However, both ends will have telomeres, they simply trade off being the end with the issue, in each round of replication.  Or you could say, in a single round of replication, one sister will have an issue at the right end end, and the other sister will have the issue at the left hand end.

Welcome. Can you add sources?

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What are "primary amino acids and secondary amino acids"? Context: analysis of amino acid content using reversed-phase HPLC
In a Russian document I'm translating, an HPLC system is used to analyse the amino acid content of a substance.

The detector wavelength is set at 262 nm for "secondary amino acids" and 338 nm for "primary amino acids". But what are those?
I googled and found a lot of mentions with exactly these wavelengths being used, but I haven't been able to quickly understand how a "primary" amino acid differs from a "secondary" one. Is it that the secondary amino acids are the products of the destruction of the primary amino acids (those that initially existed in the substance)?
What is the difference between a "primary amino acid" and a "secondary amino acid"?

You might be interested in this.

@another'Homosapien' - thank you, I'll read it.

@tomd - in my paper, they do 'hydrolyse' the substance, but they don't use OPA. But the term 'secondary' must apply whatever chemical you use to break the bonds. I'll abstain from disclosing too much from my paper.

@tomd - I should have looked further in the document. They do use OPA and FMOC. So the 'secondary amino acids' must be amino acids affected by derivatization.

Could someone — tomd or the poster — make this into an answer when they are satisfied it is correct. Then the question can be marked as answered.

I would guess that 'secondary' refers to amino acids that have been derivatized in some way, possibly by reacting with o-phthalaldehyde. (To measure the fluorescence of an OPA-derivatized amino acid, you excite at 340 nm, so I presume the derivative will absorb at this wavelength?).

Based on the reference I read for my biochem exam, secondary amino acids are those which are made of primary amino acids by adding some materials to them for ex :

hydroxylysine is made by hydroxilation of lysine
cystine is made by integrating two cysteins so cysteine is primary but cystine is secondary
etc but in other references the explanation maybe different :)


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How is the concept of species defined in asexual organisms?
In asexual organisms such as bacteria, archea and some fungi, as well as in some plants where asexual reproduction is the only reproductive strategy, how can we be unambiguous in defining if an organism belong to a different species from another or not?

I have edited your question — there is no English word ‘specie’ (except an archaic word meaning coined money). Both singlular and plural have an ‘s’ (as an observant biologist might have noticed). This is because the word is derived from the Latin singular, species.

Related: How could humans have interbred with Neanderthals if we're a different species?.

The term species is poorly defined anyway- no reason to change the concept based on sexual reproduction. Dozens of definitions.

There is no taxonomic category called "asexual organism". It is rather a phenotypic trait of scattered occurrence.
However the absence of sexual-reproduction in a group of organisms sometimes causes problems in scientific classification. This caused development of the artificial-group fungi-imperfecti (or deuteromycota) at one time, for fungal strains which lack sexual reproduction.
Bacteria and archaea (prokaryotes) are not known to show sexual reproduction. However  they  show  some gene transfer processes like conjugation and transformation; but this is not the same as sexual reproduction because cell fusion does not take place.

Yes, sorry for my English. For asexual organisms I meant the organisms that aren't characterized  by sexual reproduction. I was thinking most of all about prokariotes, and because as you said there is HGT, but they lack real sexuality, is there a criteria used for classification or there isn't universal agreement on the topic?

Classification depend on many evidences. Not only macroscopic and microscopic structures but also biochemical composition and DNA and RNA sequence data also used.

Defining a species or describing how one species differs from another goes beyond an animal's ability to mate with another. I get the idea that's where you were heading with this train of thought and you're not entirely wrong. An early technique of classification, developed by Carl Linnaeus, relied on the number of stamens a plant had to define a species. Differences in reproductive organs, mating behaviours and gametes are certainly characteristics that can and do help taxonomists to categorize organisms.
Modern taxonomy takes a number of characteristics into account and there a number of different branches of taxonomy that focus on a certain set of characteristics.
Many forms of taxonomy rely on shared descent to classify organisms based on  shared common ancestors. This is called phylogenetics. Taxonomy also uses shared characteristics, rank-based classification and genetics to define species.
Asexual species can also be classified with these techniques but there some challenges associated. Sometimes asexual species have rapid life cycles (eg. bacteria) and therefore evolutionary change can occur rapidly. Horizontal gene transfer can occur transmitting DNA from one species to another and makes the process of classification tricky.
That being said, evolution is a constant process and genomes are constanly changing. Classifying any species that are continually changing is challenging.


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Why do (almost) all energy carriers contain adenine?
Unlike this question which is specific to just ATP, this one includes all energy carriers.

When thinking of common energy carrying molecules, I can think of Adenosine triphosphate (ATP), Nicotinamide Adenine Dinucleotide (Phosphate) (NADH/NADPH), Flavin Adenine Dinucleotide (FADH2), S-adenosylmethionine, coenzyme-A (derived from cysteine, pantothenic acid and ATP), etc. Recalling exceptions, I can only think of biotin (carboxylated) and uridine diphosphate glucose. Just talking about ATP, we could have called its preference over others just a matter of chance. But when so many carriers contain adenine, there has to be some selection against other energy carriers (or adenine was so lucky?). Note that when saying 'common energy carriers', I exclude GTP, CTP, TTP and UTP since they are not very commonly used (or at least their use is confined to only some metabolic reactions, unlike ATP which finds its use in almost all metabolic reactions requiring energy).
Why do the majority of energy carrier molecules contain adenine (or its derivative) instead of any other nucleobase?

This question is open for discussion i.e. everybody is welcome to post their (scientifically backed-up) opinion as an answer while none of those answers will be selected because of lack of conclusive proofs, which are very likely to remain elusive forever.

I know questions like this are likely to get primarily opinion-based answers, but I still wish to keep it on this site since some opinions might be scientifically more sound and may get back-up references either now or later on.

What is even commonly used if  GTP is produced during the citrate cycle and is needed to synthesize every single protein that's existing in a cell?

@adjan in that sense, even CTP, UTP and TTP find uses somewhere. But I was talking about the diversity of functions, in which ATP is by far at the top. But I'll edit that point to make it clearer

@adjan — Just for the record, the GTP produced in the TCA cycle isn't used for cytoplasmic proteins synthesis as it is made in the mitochondrion. However, I do agree on its importance in protein synthesis, although, paradoxically it is not used for peptide bond formation, but is thought to be a timing device as in other G-protein systems.

@David well i did not mean to imply that it was the same GTP that was used for both, i just found these are two very essential processes in the cell.

As @canadianer comments, this question is unanswerable, and it verges on being classified as ‘opinion-based’. However, because I do not find the answer from the OP appealing, I’ve set out a few points of my own. Hardly an answer — more a list of alternatives as food for thought.
I can imagine adenine being chosen for one of the following reasons (others are welcome to suggest additions):

Functionally best suited
Was there first
Easiest or cheapest to synthesize originally (which would explain why
it was there first, if this were the case)
Random choice

Let’s look at them in turn.
Adenine functionally best suited
There seems nothing in the function of NAD that suggests the adenine ring could not have been replaced by another of the bases, and we know that the free energy of hydrolysis of the beta–gamma phosphodiester bonds of GTP, CTP and UTP can be utilized in an analogous way to that of ATP, so this doesn’t seem very likely.
However one does wonder if a purine (rather than a pyrimidine) ring conveys some sort of advantage in that the other purine-based triphosphate, GTP, is used so widely in the (ancient and essential) process of protein biosynthesis. Perhaps the greater area of contact of the purine ring favoured interaction with proteins (if you don’t argue that these came later).
Adenine was there first
One might consider that early in the evolution of life the bases (or nucleosides and nucleotides) emerged one at a time, in which case the first might have been used for NAD etc. and stuck. One might also consider whether a two-base world preceded a four-base world. If A and U (but not G and C) were in the first RNA (which may have been single-stranded, so I don’t see that the GC content of contemporary thermophiles is relevant) then it may have been a choice between A and U, which A might have won because U is subject to spontaneous deamination (or for the protein-interaction argument mentioned above).
Adenine as easiest or energetically cheapest to synthesize originally
Clearly, the first base might have been the one favoured by chemistry in relation to its synthesis. Contemporary biosynthesis is unlikely to reflect primeval biosynthesis, but it is amusing to observe that adenosine biosynthesis is the only one that doesn’t involve NAD-dependent oxidation. Of course all the contemporary biosyntheses utilize ribosyl pyrophosphate, which requires ATP in its synthesis from ribose phosphate. (Talk about chicken and egg!)
Random choice that stuck
In the absence of any more sophisticated explanation, then it could just be this. Once a choice was made and enzymes evolved to use NAD etc. the choice of adenine couldn’t be changed (or there was no strong enough functional advantage to doing so).
Postscript: When and how did NAD appear on the scene?
One of the reasons I don’t favour the OP’s answer is because it envisages NAD arising after DNA genomes and as a separate entity. I would suggest that it is likely that RNA preceded DNA and that catalytic RNA was responsible for some of the early oxido-reductions. (The first ones were probably catalysed by iron–sulphur centres, either inorganic or associated with simple proteins.) It seem feasible that the nicotinamide ring was an elaboration of a ribozyme which was ultimately almost completely replaced by protein. The adenosine was retained with the functional nicotinamide because it could interact better with the protein. Gross speculation, and it doesn’t explain why adenine was the chosen base, but an antidote to thinking NAD evolved in the fully grown form we see it today.

@tomd — Thanks. I'm pretty ignorant about that sort of thing, which is rather embarrassing seeing I proffered an answer of sorts. But it does suggest a different approach to that of the poster.

+1 although you would need to get some back up papers, like the one @tomd has suggested. I did not wish to get completely speculative answers (at least some of the claims must be backed-up in some way or the other) in which sense "contemporary thermophiles" seems more relevant than "maybe adenine came first" (although I wasn't talking about 'contemporary' thermophiles in my answer).

I think a lot of David's answer was just common sense, though. The arguments of "adenine came first" and "it was random" seem perfectly rational to me and it would be nigh on impossible to justify them with evidence.

@jam if I say "adenine is preferred because I say it is" that seems perfectly rational to me, but there is no way I can prove it either. Just giving common sense points as arguments is not sufficient, lest everything in biology can be justified by common sense. I have no problem with david's answer, I just mean I don't understand your perspective.

I’ve added a postscript which is even more speculative than the main part of my answer. @another'Homosapien' asks for “claims to be backed up in some way” — this isn‘t a claim, it is a set of ideas explored in the context of what fossils we have of the chemistry of early life. It‘s not for the poster to accept or reject either — that‘s not what questions here are for — it‘s for interested parties to read (and vote for or against if they wish). In fact the development of oxio-reduction in general is probably a more fruitful area, although my own chemistry is not really up to it.

@david I meant just backing-up any of your claims if the speculations in your answer can be related to it (knid of "I know we ppssibly had A [see this], so I speculate A -> B -> C and C is the present scenario"). I appreciate that you brought up another possibility in your answer, and I know you can't back it up.

One of the reasons why adenine is by far the most common component in energy carriers might be its less utility in DNA. Naitoh (2008) also describes this opinion. Keeping in mind the conditions on earth when first life would have evolved, this becomes easy to conceptualize. Naitoh (2008) compared RNAs of many different species of hyper-thermophiles and found that it contained a larger percentage of guanine and cytosine instead of adenine and uracil. They suggested that this could be because guanine and cytosine form stronger base pairs than adenine and uracil. Thus, while guanine and cytosine were being preferred as the constituents of DNA and/or RNA, adenine and uracil found place in other processes. While uracil would have become usable in polysaccharide generation reactions, adenine would have been a preferred choice for energy carrier molecules. PS: we could also apply the same hypothesis with a dsRNA virus which might have evolved GC rich RNA and left more AU content in its host. In this manner, this process seems more likely to cause AU buildup in the host.
To give a better idea of what might be happening, suppose there is a unicellular organism with the following DNA sequence:
5'-GCATGCATGCATGCAT-3'
3'-CGTACGTACGTACGTA-5'
and some free nucleotides, suppose 5 GTP + 5 CTP + 5 ATP + 5 TTP. Now, since G and C are being favored because of the greater stability they provide to the DNA, they would eventually replace some of the A and T in DNA, which would later become:
5'-GCGCGCATGCGCGCAT-3'
3'-CGCGCGTACGCGCGTA-5'
giving some free nucleotides as 1 GTP + 1 CTP + 9 ATP + 9 TTP. These extra ATP and TTP could be preferred in other reactions over GTP and CTP because of higher availability. Now, it could be mere chance or better functionality of adenine (as another answer says) due to which it was chosen over thymine (or uracil).
For why many other energy carriers contain adenine, the following is just speculation. Beginning with the assumption that nucleotide triphosphates were the first energy carrier molecules (since they are the precursors of genetic materials), they would have been derived for many other processes. And in some such processes, they would have got incorporated in another molecule in such a way that the formed new molecule would have acted as an energy carrier molecule too. For example, NAD+ (Nicotinamide Adenine Dinucleotide, although it is technically a hydride ion i.e. H- carrier) biosynthesis requires ADP ribose as a precursor (Wikipedia). See the diagram below for the biosynthesis pathway (from PNAS):

Flavin adenine dinucleotide (FAD) is also synthesized in a similar manner. See this diagram (from Wikipedia):

From this, we can suggest that ATP once acted as a substrate in a reaction whose product (or intermediate) was NAD+/FAD. This molecule turned out to be a useful energy carrying molecule. We could also explain the occurence of adenine in other energy carriers through this hypothesis.

So why not NUDH? In my opinion, this doesn't really answer the question (which is actually unanswerable).

@canadianer because UTP is preferred in polysaccharide synthesis reaction and ATP would be the only carrier left to react with NaMN (as I say, this is purely speculation). And who says this question can be answered? If it could be, then there would be no need for a discussion post. And obviously, your own opinion is most welcome as another answer, which I have already made clear in the question ;-)

Also NUDH does exist, at least in vitro :P

because UTP is preferred in polysaccharide synthesis Okay, but the question is why? Truthfully, the only reason why I didn't vote to close this question is because you are an experienced user, which is perhaps an unfortunate double standard which I think others are following as well. Certainly the answers will be opinion based, which is explicitly off-topic on this site. I'm also not sure that this question is sufficiently different from the one you linked to to justify it.

@canadianer I know the question is primarily opinion-based. All I wanted to have was a discussion post just to know the different theories and opinions present out there regarding this. This is what I have tried to make  clear in the question itself: none of the answers posted will be selected since none of them can be proved true. Its much similar to "why some bad traits evolve" question: simply because they do, there's nothing stopping it, same thing here. And yes, why 'adenine' is a component of many energy carriers is certainly different from why 'ATP' is preferred energy carrier ;)

Are you arguing that if early genomes were high GC, there would be a surplus of adenine? If so I don't follow this argument.

@david honestly (no hard feelings, if it seems so) I hope you know the difference between argument and speculation. Nobody can prove it, all we can do is criticism. BTW if you and @ canadianer have another theory in mind, why not post it as answer? I am waiting for more responses :)

I have just posted my own answer, but wanted to be clear about your answer. I'm not criticizing it as speculation, but I want to be clear I understand it before criticizing it on (speculative) scientific grounds. For example, if there was little need for adenine, I don't see why it would be made in excess, as I understand (or misunderstand) you are speculating.

@david suppose you have an RNA as 5'-GCAUGCAUGCAUGCAU-3' You replace some As and Us with Gs and Cs (what evolution might have done) and you have 5'-GCGCGCAUGCGCGCAU-3' + 2 A + 2 U which can be used elsewhere. This is my speculation. I'll comment on your answer...

OK. Now you have clarified, let me put forward my criticism of your hypothesis. My main reason  is that I do not see why the synthesis of adenine would not be regulated by demand, i.e. by some sort of feedback inhibition. It would seem that you would have to postulate that regulation hadn't developed then, but as you reproduce detailed contemporary pathways, this seems special pleading. In any case I think that if an RNA world preceeded a DNA world,  I would expect NAD to have arisen in the RNA world  — for which the adenine of NAD seems to me the smoking gun. The DNA world seems too late.

Another reason which might have played a crucial role in preference of adenine could be its greater stability over other nucleobases.
Dividing nucleobases into purines (A, G) and pyrimidines (C, T, U), lets first look at the pyrimidines. It is a well established fact that pyrimidines are more prone to damage, especially damage caused by UV radiation. It is known that due to UV radiation, pyrimidines form dimers, such as cytosine dimer, thymine dimer and uracil dimer (see Wikipedia). Also, researches have concluded that once the aromaticity of a pyrimidine is lost, its C4 position becomes a hotspot for a tetrahedral intermediate, whose degradation can cause major problems including DNA strand breaks (Lin et al, 2014).
Coming to purines, it has been shown that guanine is more prone to covalent attack than adenine. It could be due to the differing electronic charge distributions in the two bases. The sites O6, N7 (in major groove), N1, N2 and N3 (in minor groove) are the preferred sites for covalent attacks (Neidle, 2002). This point also gets support by the fact that the most common modified purines, xanthine and 7-methylguanine, are actually the modified forms of guanine (see Wikipedia), again meaning greater stability of adenine over guanine (although hypoxanthine is made from adenine, but the reaction is multi-step and requires many enzymes).
Why talk about stability?
The most obvious question which arises now is why are we talking about stability? If a nucleobase is more stable, it should be a preferred component of nucleic acid (which contradicts my own claim in another answer). To answer this part, we are talking about stability in different contexts in different answers. In this answer, we talk of the stability of the nucleobase itself, while in the other answer, we talk of the overall stability that the nucleobase provides to the nucleic acid. If a nucleobase is modified in a nucleic acid, it can be repaired easily through different repair mechanisms (think about repair mechanisms of strand break and dimers). On the other hand, if a free nucleobase (in the form of NTP or dNTP) is modified, it can cause serious damage to other components of the cell. Another point is that when a nucleobase is modified, its structure changes. This modified structure can prevent other proteins from recognizing this molecule. For example, if guanine would have been a component of NADH (which we would call NGDH), it might get modified to xanthine (forming NXDH...?). Now the NGDH binding sites of different proteins would not be able to recognize this molecule, and since this molecule is not a part of DNA, repair mechanisms would not help here much either. Hence, the most stable nucleobase (adenine) gets preference as the component of different energy carriers because of its stability too.
P.S.: the point of stability can also explain why GTP is also used in some crucial metabolic reactions, like protein synthesis and TCA cycle, since guanine is the most stable nucleobase after adenine.

Do free pyrimidines form dimers in solution at an appreciable rate?

@canadianer thats a nice point, although I could not find any papers regarding this (maybe nobody else has thought about this). I suppose the rate would not be appreciable (but would surely be detectable). But, the point here is that dimerization is not the only way 'active' pyrimidines could cause damage.


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Functions of tracrRNA and crRNA in the CRISPR/Cas9 system
I need some help about Crispr / Cas9.
The CRISPR/Cas9 technic consists (for bacterias) in "cut" bacteriophage's DNA, in order to make it unfunctional.
When the RNA is transcribed (RNA which is complementary to the bacteriophage's DNA), it will be associated with crRNA and tracrRNA to form the sgRNA (single guide RNA).
But I would like to know where crRNA and tracrRNA are from? and what are their function(s)/ goal(s).
Sorry If I made mistakes I'm French.

Note that the sgRNA is not present in the natural CIRSPR system and is only used in engineering as a replacement for both the crRNA and the tracrRNA.

I have also been wondering the same thing for a while now and I think that the best answer that I could find after reading several review papers on CRISPR/Cas9 and online information, points to tracrRNA as serving the role of multiplexing with pre-crRNA which helps pre-crRNA mature to crRNA. This process activates the crRNA. I'm not exactly sure how this multiplexing action "matures" the pre-crRNA or what exactly that even means, but that is as much insight as the literature provides (see e.g. this abstract to a conference talk).
There most likely are some more important functions that have not yet been discovered for tracrRNA yet.

Welcome to Biology.SE and thank you for your answer. Could you please also add the references to the review papers and online information you are mentioning? Thanks!


text:
Is the worm brain understood?
Is the relationship between worm (C. elegans nematode or any worm) behavior and the worm brain understood? Is the learning technology within the worm brain understood? If so, what's a summary of the mathematical processes and biological implementations used? If not, what is the impediment to understanding?

Hi! This is an interesting question but you might have more success if you narrow it down to a specific question about worm or C. elegans brain function. It's also helpful to show you've done some research by summarizing what you already know so that answerers know where to begin with an explanation.

"Understood" is also incredibly broad and nearly impossible to actually obtain: you can read about the Dunning-Kruger effect. Or this image, which I happened to find just now unsourced on a LinkedIn blog but it is definitely not the original, there are dozens and dozens of variants on the same idea.


text:
Cell dye in red fluorescence spectrum
There are some cell dyes available for stianing cells intracellularly / membrane. I am aware of other channels (CFSE \ PKH26). But I want to stain cells for flow cytometry with a 'red' dye.
I have looked at a few options from Thermo but did not find sufficient data on either.
Specifically I am planning to stain a single cell population with two different dyes, treat each stained population somewhat different in between, and then culture them together and distinguish read-outs later. Antibody-staining for a surface marker would be possible with Fab fragments (the antibodies itself may interfere with cell activation during culturing). Therefore I would rather use a red-spectrum dye like CFSE or PKH26 as this may be cheaper and possible for secondary use with other cell lines.
I have multiple cytometers available and the specific emittance doesn't matter as we can pick what is generally possible (LSR/Fortessa).
Thus, I am looking for a dye with emittance in the red fluorescence spectrum which has staining protocols available that can be adapted for my purposes.
Is anybody willing to share their experiences?
Edit

Clarified that I needed a 'no-antibody-staining'
Clarified question with regard to biological question and FACS

What is your question? Are you looking for a product recommendation?

So you're doing a dye dilution proliferation experiment? Please explain what you're doing! Especially what cytometer you plan to use in case the stock filter set up is ill-suited to certain spectra.

I've used the ThermoFisher brand of CellTrace dyes. Specifically, I co-cultured two populations of cells, one with CellTrace Far Red in the APC channel and another with CellTrace Yellow in the PE channel. My choice was in part guided by a product review by another lab touting the relatively low cytotoxicity of these products.
The protocol is quite straight forward. It's also available in CFSE and Violet, though I haven't tested those. These dyes are also optimized for lymphocytes, and so I'd recommend titrating if you're staining anything else.
The dyes are quite bright, and so there were issues with costaining APC-Cy7, for example. I ended up leaving my CellTrace dyes as the only markers on their respective lasers and stacking my phenotyping on the 355nm and 405nm lasers.
For compensation, you might just stick with cells, but in the product manual for CellTrace, however, it says:
"The CellTrace™ reagents readily diffuse into cells and bind covalently
to intracellular amines, resulting in stable, well-retained fluorescent staining that can
be fixed with aldehyde fixatives."
So if you use the ArC amine-reactive comp beads for LIVE/DEAD kits, you might be able to just make comp beads with those. I'll verify this when I'm back at work if need be, as I haven't done it myself, but it's a nice thought!

There is a number of different dyes possible, as you can see in this figure (from here):

A good overview can be found in the "Selecting Reagents for
Multicolor Flow Cytometry" application note publication from BD (in reference 1) and also the Fluorochrome Specifications from BD (reference 2).
References:

Selecting Reagents for  Multicolor Flow Cytometry
BD Life Sciences Fluorochrome Specifications

Thanks for your answer, Chris. I realize that I was a bit vague about my question, and have edited it above.


text:
How do we feel temperature?
Recently I watched a Youtube Video by
Veritasium
He said we are actually feeling the rate of heat transfer, not the temperature.
But how do we feel temperature?
How is feeling temperature different from feeling heat and heat transfer?

Welcome to the Biology Stack Exchange. Please take the [tour] and carefully read through the [help] to learn more about the site, including what is on-topic and what is not, and how to ask a good question.

@Mesentery - although your links are highly useful, new users are likely overwhelmed and do not know what you are after. If you have certain critiques, please make them explicit, especially to new users. Posting a standard welcome message with all sort of links within the site may have its merits, but is arguably not the best thing to do. Other users have started doing that and have eventually been discouraged. Specific pointers are, imho, better.

@AliceD I have seen that this user has not got the informed badge. I just want him to guide him about how this site works. So, if he/she asks further any questions, they are also on-topic on the site.

@Mesentery - that is awesome. Mentioning this explicitly will help this new user even more I think. Thanks for all your good work here and for your efforts. I'm not aiming to criticize, just trying to be constructive. Cheers.

After all that being said, a summary would be - did you try finding an answer? 'Provide details. Share your research', else it is likely to be closed as a low effort question. I'm voting as one.

use google.  "nerve temperature response" = https://en.wikipedia.org/wiki/Thermoreceptor afaik they have different ranges for different precision/speed of response. the topic takes 30 40 minutes of going on good pages to be knowledgeable on for the rest of your life, and one day you can use all your knowledges as a combined power of generalist science knowledge. research is good.


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What happens to the nitrogen when an oxygen machine delivers only oxygen?
My father recently began using an oxygen machine. He would like to know where the nitrogen goes when the machine takes in air and puts out only oxygen.

I'm voting to close this question as off-topic because are OP doesn't show attempt at an answer.

Did you try finding an answer? ' Provide details. Share your research. '

The nitrogen is returned to the air around the machine.  See Wikipedia's article on the oxygen concentrator for details about how the machine separates the nitrogen and oxygen.


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How do the flowers of Diphylleia grayi become transparent after rain?
Known as the skeleton flower, its flowers turn transparent in rain. How does it do so? How can it gain transparency in rain when water is already present in flower? Or is it because other components present in the rain? Also is there any  advantage of this for the plant? I research using Google, but I couldn't find an answer.

YouTube

I have to hypthesise here:
the white colour you perceive is most likely near-to-full diffusion (or possibly better phrased: reflection with effectively undirected refraction due to multiple reflections) of light by structures on the surface of the petals and/or air space encapsulated in the petals. (This is true for most white flowers, by the way.)
Water fills the structures and/or the air space, which changes the refractive index of the petal surface.
In other words: the flower becomes like water, because the air is driven out.
Edit: seems I was right. SE asked me to add links to my answer, so I asked GoogleScholar about D. grayi and found this: "The inner part of the petal comprises numerous lacunae and intercellular spaces that are filled with air."
(source: Yong et al. (2015). Bioinspired transparent underwater superoleophobic and anti-oil surfaces. Journal of Materials Chemistry A, 3(18), 9379-9384.)

Could you find whether it is an adaptation or not?

I don't think there's data to support that hypthesis, but then, there's also no data to reject it. (Seriously, though: I can't see why this would be an adaption. Maybe it has an obscure evolutionary advantage, but IDK which that would be. Maybe it just isn't an evolutionary disadvantage. Ecologists, to the research!)

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


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Why do membrane proteins at lower temperatures contain more alpha helices than beta sheets?
Why do organisms found at low temperatures have membrane proteins with a higher percentage of alpha helices compare to beta sheets?

This is an interesting question that I've not really come across before. Is there a citation for this claim? I'd be interested to read more.

@James Porins are beta barrel but yeah many membrane proteins are alpha-helical, though I don't have an exact number.

@WYSIWYG I once looked at the difference between the two and TMHs are far more common (~13k proteins 90% redundant with a TMH in humans, and only around ~1k TM beta sheet containing proteins in Swissprot without selecting a specific taxonomy or redundancy ). What I have not come across is something saying that the ratio shifts in organisms that are at lower temperatures.The annotation of beta sheet TMDs is nowhere near as high quality as TMHs, so I assumed that nobody had looked into this.

The reason could be the greater motility of the alpha helix, compared with the more rigid beta sheet.
This allows the enzyme to remain functional at low temperature.
The proteins of such organisms tend also to have less hydrophobic regions and covalent bonds.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1692995/pdf/12171655.pdf
Molecular basis of cold adaptation
Salvino D’Amico, Paule Claverie, Tony Collins, Daphne´ Georlette,
Emmanuelle Gratia, Anne Hoyoux, Marie-Alice Meuwis, Georges Feller
and Charles Gerday*
This doesn't refer to alpha helix explicitly, however alpha helix are known to allow more flexibility than beta sheets, so it's reasonable to argue that the increase in alpha helix could be one of several strategies used to obtain more flexible enzymes, as well as other means cited in the paper.
This point is also made by Brock-Biology of microorganisms(2015) pag.161

Several cold-active enzymes whose structure is known show a
  greater content of α-helix and lesser content of β-sheet secondary
  structure ( Section 4.14) than do enzymes that show little
  or no activity in the cold. Because β-sheet secondary structures
  tend to be more rigid than α-helices, the greater α-helix content of cold-active enzymes allows these proteins greater flexibility
  for catalyzing their reactions at cold temperatures.

However unfortunately no reference is provided about this claim.

This is a great idea for a comment, but it's not an answer. It would be if it had sources, or calculations etc.


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What is this insect in this picture?
I recently found this insect  near our veranda wall. What insect is this ?
Is it poisonous?

As you can see, it has multiple legs fine as hair, but it is not like a common millipede or centipede.
I searched for this insect by reverse Google image search without result.
Location: Kolkata, India
Nature: fast-moving, aggressive.
Unlike earthworms, this insect loves basking in sunlight.

It looks like Scutigera coleoptrata. From Wikipedia: Bites are uncommon, and the forcipules of house centipedes are not strong enough to easily penetrate human skin. Bites are similar to a bee's sting, with its venom causing redness and mild to severe swelling.

I think it's Scutigera coleoptrata.

Source of the image.

About copy righted image. Also if an image is not your own work it's source needs to be mentioned.

While using copyrighted image on SE it is advisable (as in the link)  that the copy right allows sharing image as being done, if not it is right to replace it with one that allows.

@SanjuktaGhosh, I edited the post.

It looks like a house centipede, which are harmless to people.  The ones I encounter love cool, dark, damp places like the basement, and move lightning fast.  They are also prone to dropping off legs when you try to catch them.

Welcome to Bio.SE. Please add a picture and provide references. You can visit the help center for more details about how this site works.


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Which are the best programs to analyze circular RNA?
Hello I'm just started with bioinformatics and I would like to know which programs are best for the task of finding circRNA (circular RNA) in sequences of tissues and different cellular types. I have heard about circRNA finder, find circ, CIRCexplorer, CIRI, and MapSplice which all are different programs to find circRNA, but I really don't know which one is the most used and easy to use, and which one is most accurate for finding circRNA.

Welcome to SE Biology. Just to let you know why I changed "algorithm" to "program". An algorithm is the strategy by which a problem can be solved computationally, a program is its implementation in code. You would ask about the best algorithm if you wanted to write your own implementation or you knew which algorithms the different programs you mention used and wished to choose from those using the best algorithm. I assume that in fact you just want recommendations from the programs named.

According to the most recent paper (https://doi.org/10.1093/bib/bbx014), CIRI2 shows a balanced performance on sensitivity and FDR.
"Computational detection methods have been widely used in studies on the biogenesis and the function of circular RNAs (circRNAs). However, all of the existing tools showed disadvantages on certain aspects of circRNA detection. Here, we propose an improved multithreading detection tool, CIRI2, which used an adapted maximum likelihood estimation based on multiple seed matching to identify back-spliced junction reads and to filter false positives derived from repetitive sequences and mapping errors. We established objective assessment criteria based on real data from RNase R-treated samples and systematically compared 10 circular detection tools, which demonstrated that CIRI2 outperformed its previous version CIRI and all other widely used tools, featured with remarkably balanced sensitivity, reliability, duration and RAM usage."


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Why is secretin sensitive to acid?
My textbook says, secretin secretion is triggered by the presence of acidic chyme in intestine.
But why is secretin sensitive to acidic environment? I checked the wikipedia page of secretin and found no related information.
Is there some mechanism for secretin to secrete in presence of acidic chyme?

The exact mechanism by which secretin is released is still not known.

The mechanism by which acid brings about secretin release is not fully understood but probably involves acid sensing ion channels of the Trp family present in the brush border of S-cells.

Physiological reason for susceptibility to acid: It is because this hormone acts on pancreas and increases the secretion of bicarbonates to increase the pH. It also reduces gastric motility thereby allowing longer digestion within the stomach. So, it effectively prevents deterioration of duodenal mucosa and helps in efficient absorption of lipids by increasing ph in duodenum which is required for better action of lipases. So, its secretion is induced by increased acidity from chyme (so that it can increase pH).
Thus, we can conclude that secretin is acid sensitive.

Source: https://www.pancreapedia.org/molecules/secretin

You forgot to connect your last paragraph to "thus it is acid-sensitive" (its not easy to draw this conclusion from your paragraph). Anyways, +1! ;)


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Did migratory birds' ancestors live in the places of migration?
I was studying birds' migration as a type of instinctive behaviour. But my textbook points out that other than for warm climate and easy food, migratory bird migrate to places where their ancestors lived.
Is it a real point? Or the writers just made it up.

An anecdotal comment, as it doesn't address your question about birds: This is the case in eels. European (Anguilla anguilla ) + American  (A. rostrata ) eels are sister taxa; both go to the Sargasso Sea to spawn. The working hypothesis is that the original N. Atlantic eel pop migrated through the Tethys Sea to the spreading Atlantic, and spawned in what would become the modern Sargasso. As the Atlantic Basin spread through continental drift, the 2 spp differentiated--but both still return to the Sargasso to spawn. ref: Aoyama, J. 2009. Aqua-BioSci. Monogr. (ABSM), Vol. 2, No. 1, pp. 1–42

do migratory birds have same kind of analogous history?

ancestors can refer to 2 generations ago and to 1000ds of years ago. that's why my interpretation of it was vague.

haven't the foggiest. @comprehensible -- I actually really liked your answer.

Edited for a different consideration: Do birds migrate to and from zones defined only by ecological and climate choice, or do they evolve to migrate away to and from an ancestral home?
Later studies of migration searched for evolutionary definitions of bird migration as opposed to ecology/geography definitions which were the initial focus. Various theories of evolution and migration have been developed, although ice ages and climate change make the definition of a bird ancestral land vague.
If you search google for "sister taxa, migration, evolution" you will find a lot
A study for American Thrush species starts with previous research:

range expansion and speciation for the
evolution of long-distance migration. In brief,
resident, tropical species expand their ranges
into the seasonal subtropics. Further range
expansion into temperate areas due to competition
and other selective pressures creates a partially
migratory species. The partially migratory
birds continue to expand into higher latitudes,
where they breed successfully; migratory behavior
becomes fi xed (Stiles 1980).

It's results for the thrush are very complex, and you can see the map and the conclusions at the end, which state that:

The migratory species tree does not have a clear single ancestor.
The ancestor's range was probably very widespread, over 1000ds of
kilometers.
They migrated by stepping stone, rather than by diet
constraints of being frugivorous versus insectivorous.

http://www.sonoma.edu/users/g/girman/outlawetal2003.pdf
also
http://www.bioone.org/doi/abs/10.1642/0004-8038%282007%29124%5B410%3AASROMM%5D2.0.CO%3B2?journalCode=tauk
The data is erased in history, the migration routes and maps are very complex, the ancestral homeland shifts as forests and boreal ranges change latitude, so it's a balance in between the ability for birds to have fixed ancestral lands, given their great mobility, and the speed of their evolution. For the moment there are some theories on mechanisms and causes for selection by migratory advantage which are not general enough to apply to many clades of bird.
for precise and recent return to homeland:
Yes it's absolutely true, that many birds return to the exact same nest in Europe for example after wintering in Africa, and they also return to the same cliff/forest as where their parents were born, and some species vaguely follow the flocks very broad zones:
One study showed that most swallows returned to the same colony, with 44 per cent of pairs reoccupying the same nest. “This is remarkable given the length of a swallow’s return migration from its wintering grounds in South Africa,” says Rob Robinson, associate director of research at the BTO. Robinson has studied this iconic species’ unusually strong nest-faithfulness, a phenomenon called natal philopatry.
https://en.wikipedia.org/wiki/Philopatry

I don't think your answer really answer s my question. have u read Kara's comment? My question is do migratory birds have same kind of analogous history?

some birds have specialized into migrators millions of years ago, like Geese, and some of them are more generalized species, like thrush, with recent ancestry that can be studied. There are geese in hawaii and S africa. The hawaiian goose may have evolved from an off-course flock that arrived there 500,000 years ago. euro and ozzy swan also demonstrates geography vagueness of bird origins, and euro small bird species ranges are normally pan european for 1000ds of km so it makes the geography of ancestry complex, same as eels except radiative/ ranges that change easily.

Now it's a very nice answer.

Thanks, someone knowledgeable about evolution of bird ecology would give a summary of different types of migrating species, coastal, forest, boreal, tropical, thrush, goose, range geography and climate change, which selective pressures are prevalent for temps and predators in different ranges and seasonal foods, and combine that knowledge with current research of migration genetics and evolution to give a very good text about it, it would be interesting to read an actual textbook chapter on evolution of migration with examples and theory. At my town have 1000ds HiRondElles which are martins.


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Do bacteria with flagella self-rotate?
The bacterial flagellum uses rotation for generating forward motion, just like a helicopter main rotor does. Helicopters must utilize a secondary rotor to avoid self-rotation due to preservation of angular momentum. Alternatively they can have multiple rotors rotating at opposite directions. But all flagella rotate in the same direction.  Does this mean that the bacterial cell rotates in the opposite direction?
If so, what is the typical frequency of such rotation? Shouldn't the rotation disturb sensing and nevigation in the environment by the cell?

Welcome to Biology.SE! What research have you done before asking it here?

Google, and a bit of common sense. But no definitive conclusion...

My opinion as a physicist would be that yes, they do.
Assuming a sperm-like structure with a single flagellum at the centre of a long, thin cell of uniform density. They would rotate around the axis of travel.
However, for other cells, this could be mitigated in several ways:

If the cell was submersed in or floating on a liquid, it is likely that the effects of Archimede's Principal would be sufficient to keep it in a fixed orientation (this is how ships and submarines stay upright despite rotors that all go in the same direction - the least dense parts of a body always attempt to restore themselves to the highest position).
Fluid in the cytoplasm could act as ballast, providing a counterrotation force thanks to the gravitational effect on it.
If the cell happened to be particularily masseous in relation to the force the flaggela were providing, this would make any rotational force negligible.
If the flagella were located away from the axis of travel (through the centre of gravity - ie to the sides) the torque would have less of an effect.

As for the navigational aspect of your question, if these cells do auto-rotate, they will have done so throughout their evoloutionary histories and therefore in all likelihood will have evolved navigation methods capable of dealing with this.
I will however put a disclaimer on this, I am not a biologist and am weighing in from the point of view of a physicist.

1+2 are indeed nice ways to stabilize the cell. Has any such mechanism  been found?

3 sounds wrong. if the cell is too massive in relation to the force, then the flagella will not be useful for motility. I would say that if the flagella applies a forward force F on the cell, it must generate torque of approximately F*r, where r is the radius of the flagellum helix, probably ~1 micron. Thus, with similar approximations I would say that using flagellum to move in velocity of 100 body lengths per second must compel auto-rotation with frequency of about 100 Hz. This is reasonable as it is a typical rotation frequency of flagella.

@UriM, I agree, the flagella wouldn't be much use in that situation, but the cell would still be fairly stable

As for whether or not any such mechanism has been found, 1 + 2 must be true for any cell of non-uniform density with a non-rigidly located cytoplasm

point 4 applies to E. coli which has peritrichous flagella i.e. they arise at points over the entire cell surface and coalesce to form a flagellar bundle. There is a flexible component, the hook,  between the motor and the filament which enables this.

Yes, the bacterial cell body rotates, but more slowly than you might think.
Bacteria are examples of 'life at low Reynold's number'. Here are some extracts from  Howard C. Berg Random Walks in Biology (1993) Princeton University Press pp 75-80.

The Reynolds number is a dimensionless parameter in the equations of motion of a fluid that indicates the relative size of terms that describe intertial forces (forces required to accelerate masses) and viscous forces (forces due to viscous shear).

For a fish R is approximately 105; for a bacterium it is approximately 10-5. This difference has a profound effect on the physics of swimming.

The fish propels itself by accelerating water, the bacterium by using viscous shear.

To illustrate the lack of inertial effects at low Reynolds number, Berg estimates that if a bacterium stops swimming it comes to rest within about 1 µs and coasts for approximately 0.4 nm.

Flagellated bacteria swim by rotating one or more thin helical filaments... Torque generated by rotation of the filaments is balanced by viscous drag due to the counter-rotation of the cell and thrust generated by rotation of the filaments is balanced by viscous drag due to translation of the body of the cell.

In a recent paper from Berg's group direct measurements of the rotation of the flagellar filament and the cell body (for E. coli) are presented: the filament rotates at approximately 100 Hz; the cell body at 20 Hz.
The supplementary question is: Shouldn't the rotation disturb sensing and nevigation in the environment by the cell? Bacterial chemotaxis, at least in E. coli, relies upon time-averaged sensing of the concentrations of attractants in the surroundings via ligand-receptor interactions. Rotation of the cell body will not have any effect on these interactions.


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How to combine gene set enrichment analysis with hierarchical clustering?
I would like to find out how to combine gene set enrichment analysis with hierarchical clustering. The motivation for this combination is that potentially
too many gene-set symbols for leukemia may pass the p-value significance threshold. We are using an R-package for fast preranked gene set enrichment analysis (GSEA) with the URL, https://github.com/ctlab/fgsea.
Subsequent to the fast gene set enrichment analysis on a ranked list of gene symbols with different expression t-statistics, we specifically need to identify gene-set symbols belonging to a common functional group using the R language hclust function intended for supervised hierarchical clustering with a Euclidean distance between features in a timely manner, for example 15 or fewer minutes.
Quoting from Alan Moses 2017 book, "Statistical Modeling and Machine Learning for Molecular Biology" , "Clustering is meant for exploratory data analysis and therefore doesn't really have a strong framework for hypothesis testing".A new R package ClusterProfiler provides enrichment analysis of gene clusters as reported in this URL,  http://guangchuangyu.github.io/2015/05/use-clusterprofiler-as-an-universal-enrichment-analysis-tool/
The fact that most quality measures found in the literature have been conceived to evaluate non-overlapping clusterings, even when most real-life problems are better modeled using overlapping clustering algorithms is analyzed
in detail in the following paper and University of Texas Ph.D thesis
Academic paper: CICE-BCubed: A New Evaluation Measure for Overlapping Clustering Algorithms. Available from: https://www.researchgate.net/publication/260421976_CICE-BCubed_A_New_Evaluation_Measure_for_Overlapping_Clustering_Algorithms [accessed Apr 16, 2017].
and
https://repositories.lib.utexas.edu/bitstream/handle/2152/ETD-UT-2010-08-2022/KRUMPELMAN-DISSERTATION.pdf?sequence=1&isAllowed=y
As I am a novice to this type of bioinformatics research, please correct any inaccuracies in my problem statement.

The article, What to Do When K-Means Clustering Fails: A Simple yet Principled Alternative Algorithm with the URL, http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0162259 discusses MAP-DP which is a more flexible clustering technique using a probabilistic model.

You can try Enrichr for enrichment analysis. On 'Results' page you can use Clustergram view.
Or you can upload your results to Clustergrammer itself.

Thank you for your nice answer. Is it possible to measure and refine the quality of hierarchical clustering results generated by the R language function hclust() using Euclidean distance by automatically computing p-values for all clusters contained in the clustering of original data. Could we use the paper "Multiscale mutation clustering algorithm identifies pan-cancer mutational clusters associated with pathway-level changes in gene expression", http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005347 to refine clustering analysis? Thank you.

Is it mathematically correct to use the R function for combining gene set enrichment analysis p-values from  https://github.com/ctlab/fgsea. in this URL, https://www.biostars.org/p/211307, to calculate the quality of a hclust() clustering result tree? Thank you. I am awarding reputation points to your nice answer.

How does your answer address overlapping clustering? Thank you.

A rising young M.I.T professor told me just now that the volcano plot with 1og(p value) vertical axis can in many cases differentially visualize overlapping clusters where p values come from gene set enrichment analysis,


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Are RNA transcripts always synthesised from the same DNA strand?
The DNA is read 3'->5' (and RNA synthesized 5'->3'). But due to the DNA strands having to be complementary, it seems to me that the origin can only appear on the correct side of the ORF on one of the strands. And even if it were possible to synthesise RNA from the other strand, due to the directionailty of the strands/RNA the RNA transcript would then code for the protein in reverse. Surely the reverse synthesis of a protein, even if containing all of the same amino acids, would lead to dfferent folding and thus only on eof the proteins is correct?
Now that I am considering the origin, it seems likely to me that the strand on which the origin is dictates which strand acts as the RNA template (perhaps both starnds can, however for a given GENE the RNA is always synthesised from the same strand.
Is this the case? I have read this post: Majority of transcripts are from sense strand? however I found it slightly confusing. I think what the answerer said is similar to what I have suggested here, however I am not quite sure. Would greatly appreciate some input.

By "origin" do you mean "promotor"? You might wish to consult https://en.wikipedia.org/wiki/Promoter_(genetics) and then edit your question if appropriate and you feel it not answered in  https://biology.stackexchange.com/questions/39046/how-does-rna-transcription-determine-which-half-of-the-dna-to-use.

@David Thanks I did mean promoter! I realised when I re-read my question now- it is easy to get mixed up with the terms when learning about DNA replication and transcription simultaneously! As it transpires my question was answered in the post suggested by another 'Homo Sapien'. Thank you for your input.


text:
Can dopamine antagonists be used as dopamine upregulation?
Can dopamine antagonists such as Thorazine that are used to treat schizophrenia and bipolar be used to upregulate dopamine in the long term in healthy (non schizophrenic or bipolar) users to get a similar effect as a stimulant high without inducing neurotoxicity? Due to tolerance buildup of the dopamine blocker, my assumption is that it should result in dopamine upregulation when dopamine antagonist use is stopped.
As an example, in extremely high doses of methamphetamine, meth induces temporary schizophrenia (skin picking, crank bugs, paranoia, hallucinations, etc), and extremely similar, if not exact, effects to bipolar, which are the only two neurological diseases resulted from dopamine over-production and release. Over time, tolerance to meth builds up and it stops being effective, unless it is stopped for a period of time resulting in reverse-tolerance. Can this same dopamine downregulation effect be used in dopamine antagonists as dopamine upregulation, creating the same euphoric feeling resulted from meth use or bipolar hypomania if the dopamine antagonist is taken for a period of time then stopped?

Neurologically and physiologically in general the body is programmed to find it's state of homeostasis. Dopamine as a molecule within neurology can not in fact pass the Blood Brain Barrier in which is why the precursor L-Dopa is administered for deficiency. Regard to homeostasis in a non naturally deficient person, both down and or up regulation to find this balance over time can occur in which cessation is not a good idea without medical assistance as natural production may well have changed gene expression.

@kirill2485 - please be nice to people spending their time on your questions. The answer from Max was reverted to a comment by the mod team, explaining the reason it pops up again.

@kirill2485 - it's already clear that it's not an answer, because the post was converted to a comment. You wrote 'I already told you, this is NOT an answer...' - The capitals imply screaming, like 'oh my, not you again, dude, can't you read my question?'. You could say something along the lines of 'Thanks for the comment, but....'


text:
Are acid-fast bacteria Gram-positive or Gram-negative?
Both procedures involve using a stain, decolorising agent, and then a second stain. I am tempted to conclude that acid-fast bacteria, which resist decolorisation (eg. by strong carbol fuchsin), also resist decolorisation in the Gram staining test (eg. by gentian violet) and are thus Gram-positive.
After all, there are much fewer acid-fast bacteria than Gram-positive bacteria.
Is this line of thinking incorrect?

Image URL: http://www.scienceprofonline.com/images/science-image-library/microbiology/staining/differential-bacterial-stain-controls-diagram.JPG

Taxonomic Classification:
The most salient acid-fast bacteria are Mycobacterium spp., which are part of a phylum of gram-positive bacteria called Actinobacteria. This classification is based on 16S rRNA sequencing. However, based on genetic conservation, this paper makes the claim that they are more closely related to gram negative bacteria.
Gram Reaction:
Acid-fast bacteria are characterized by cell walls rich in mycolic acids. This characteristic causes both poor stain penetration and high stain retention which forms the basis of acid-fast stains. However, it also means that crystal violet will not penetrate the cell wall efficiently. Thus their gram reaction is variable and they generally stain light purple. The result is dependent on technique as well as mycolic acid content variation between genera (Nocardia spp, for example, are less acid-fast and stain gram positive). Needless to say, their cell walls don't fit well with the classic dichotomy of thin versus thick peptidoglycan which the gram stain differentiates between.
Example Gram Stains:

For comparison, the left image is of Bacillus subtilis, a gram positive, non-acid-fast bacilli. In the middle is M. phlei and on the right is M. smegmatis, both of which are acid-fast but show a weakly positive gram reaction. Images from Napa Valley College.

B. subtilis is again on the left for comparison. In the middle is M. fortuitum staining positive but more weakly than B. subtilis. On the right is N. astroides which is partially acid-fast but stains strongly gram positive. Images from Microbe Canvas.


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Chromosome related problems.
1.) How many versions (alleles) of a gene can we carry if every chromosome is in pair?
2) What happens during the gamete formation (meiosis) ? Do the gene pairs stay together?
3) What happens then to the paternal and maternal sets of genes that we inherited ?
My attempts
1) I think that it could be any number, but confused with 2 as an answer.
2) Gene pairs must refer to homologous chromosome pairs which remain together in meiosis-I and get separated in meiosis-II. So in net process, it get separated.
3) It is used for producing proteins essential for body functioning by the process of transcription and translation. These genes with some changes (due to crossover) will also be transferred to second generation.

How many versions (alleles) of a gene can we carry if every chromosome is in pair?

The phrasing "if every chromosome is in pair" sounds a little bit funny. But it probably mean "or a diploid individual".
If an individual is diploid, then it has two copies of any given locus. If the term is new to you, a locus is a position in the genome (it may correspond to a gene or not). With two copies an individual can carry maximum two different copies, that is two alleles. The answer is two.

What happens during the gamete formation (meiosis) ? Do the gene pairs stay together?

You nailed it!

What happens then to the paternal and maternal sets of genes that we inherited ?

This is a slightly vague question IMO but I would suppose the main point that is being expected is a description of segregation and recombination (cross-over). You answer was good but I would suggest.
"The maternally and paternally inherited haplotype will recombine (cross-over) during meiosis so that a gamete resulting from meiosis will contain a single haplotype which is a 'mixture' of the maternally inherited and paternally inherited haplotypes."


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Interpretation of picture of human chromosomes

Does this picture show sister chromatids or homologous chromosomes? If they are homologous then what is YY? If they are sister chromatids then do homologous chromosomes ever appear like this (with the centromere)? Do sister chromatids exist only in prophase-I to anaphase-I of meiosis?

Since I have used more than 1 image in my answer; with numbers starting from 1; I'll call your provided figure as figure-0

What is shown in following picture?

Though the image showing many things; in overall it is an image of a set of chromosomes; seemingly almost certainly from human. The chromosomes has been stained with a banding method (though I'm not sure about which banding method used).

Are they sister chromatids?

Could not be answered in few words. The image contains sister chromatids. But the entire image in OP (fig-0) could not be described as "image of sister chromatids".
All the chromosomes in this image are in metaphase. so each chromosome is made up of 1-pair of chromatids which are sister-chromatids to each-other.
Fig 1.   This total image showing 1 chromosome (on or before metaphase) showing 2 chromatids (written as A and B). A and B are sister chromatids because their DNA-content resulted from same mother-DNA molecule when replication happened at S-phase of cell-cycle; so their DNA content is basically same.

or homologous chromosome?

No. They are Not homologous. However Chromosome X and Y do have some homologous portion (Pseudo-autosomal regions). Question-figure (Fig-0) neither shows a complete set (46 chromosomes) from 1 diploid cell; nor shows its half (the haploid set) (that is causing your confusion about X and Y; let me proceed...) . Fig-0 shows each-type of human chromosome in 1 piece.

If they are homologous then what is YY?

YY karyotype does not normally exist in human.

Karyotype of human male:
2 x (22 autosome) + 1 X-chromosome + 1 Y-chromosome.

Karyotype of human female
2 x (22 autosome) + 2 x X-chromosome.

Then how are homologous chromosomes?

Fig-2 (photo Taken from iGenetics; by peter J russell; Ed-3 ebook). Slightly modified.

it shows a complete set of chromosome from a human male cell. Note that it doesn't contain YY but only a single X plus Single Y.

And from same photo; what are sister and nonsister chromatids, and homologous and heterologous (non-homologous) chromosomes.
Fig-3 .

Reference:  iGENETICS by Peter J. Russell, Ed-3.

@ruakh Yes you pointed it correctly. I'm correcting it immediately.

While typing in a flow I put the wrong term. Thanks for correction.

The picture can be a bit misleading because it represents 22 autosomes (autosome = non-sexual chromosome) while there are 22 pairs of autosomes (so the homologous chromosome is not represented). And it represents the whole pair of sexual chromosomes (the individual is a male).
homologous chromosome
For each autosome represented, there is another one which would be its homologous chromosome.
Sister chromatids
As you can see, each chromosome looks like an X. The right and left side of this X there are chromatids (two chromatids per chromosome here). The chromatids are attachedf by the centromere.
Note
Please note that 1) chromosomes looks like they are represented here only during the metaphase (when they are condensed). 2) A chromosome is not always made of two chromatids. Sometimes it is made of single chromatid only. It depends on the moment in the cell life cycle.


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Are differing shapes of the acromion congenital or acquired?
In the human body, the acromion is located here:

There exist different shapes of acromion, at least 3:

The frequency varies according to the acromion type:

Some clinicians consider that there exist more than 3 types of acromion:

Are differing shapes of the acromion are congenital or acquired?
{1} says:

Debate continues as to whether the differing shapes of the acromion are congenital or acquired. […] We conclude that the different shapes of acromion are, therefore, acquired as a response to traction forces applied via the coracoacromial ligament and are not congenital in origin.

However, this study was published 16 years ago. What is the current scientific consensus, if any, regarding whether differing shapes of the acromion are congenital or acquired?

References:

{1} Shah, Nirav N., N. C. Bayliss, and Archie Malcolm. "Shape of the acromion: congenital or acquired—a macroscopic, radiographic, and microscopic study of acromion." Journal of Shoulder and Elbow Surgery 10, no. 4 (2001): 309-316. https://scholar.google.com/scholar?cluster=2046701264133216154&hl=en&as_sdt=0,22 ; http://doi.org/10.1067/mse.2001.114681; http://sci-hub.cc/10.1067/mse.2001.114681


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Trying to understand a scientific text about neurons and dopamine
I'm in the process of reading https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1564381/ and I'm trying to understand how the predicting is done in the neuron.
What I distilled so far: A cell gets an input, it calculates a probability of reward(bliss potential i like to call it), if it could cause a reward it releases dopamine in a quantity of expected reward.
So right now I'm wondering,  what is the process that goes on to make that calculation. Which input variables does the neuron use to calculate the probability of a reward and how much dopamined to release?
Does it take account which synapses provided the input signals? Or is it the type of input signals? Or a combination of both? Is it the frequency inputs occur?
II need an explaination how the neuron calculates its "bliss potential" as i like to call it, in normal peoples english instead of academia english.
P.s. I don't have an academic background.  I'm just interested in science related things without having a formal education.


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Is there any math formula that can be used to describe shape of leaves?
There can be great variation in shape of leaves. Neverthless they are fairly simple shapes. How far are we in describing the shape of leaves in a mathematically rigorous way? Do we have a general formula that can be used to describe all shapes of leaves (or, at least, a reasonably large subset)?

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3419012/

L-systems.  Search on-line for examples, or read "The Algorithmic Beauty of Plants".  There's a freely downloadable PDF version online somewhere.

I don't think there is one equation that describes all leaf patterns. As the article linked by @CountIblis says, the mathematical description of the final forms using fractals or "golden ratio" can be biologically misleading. More accurate mathematical models would consider the developmental dynamics. L Mahadevan from Harvard works on pattern development in different biological tissues (not just leaves). Have a look at his site.

Related: This post

There are algorithms which can be used to describe leaves, if that is what you mean.
The following description takes into account that leaf shape is not solely a function of genetics, but is also effected by environment. It also models how different growth rates within the cells have consequences. Mutant, cloning cells are also factored into the description.
The mathematical model has interesting allometric implications.
Here is a very readable paper (PDF),which endeavours to describe differences using mathematics and for which for which we can thank Cornell University Library for hosting the paper and Lawrence Livermore National Laboratory.


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Can any organisms see non-electromagnetic radiation?
Some examples would be cosmic rays, neutron radiation, alpha radiation, beta radiation, muon radiation, and antimatter radiation.
Some related questions: How is non-electromagnetic radiation detected, and would it ever be evolutionarily beneficial?

Welcome to Biology.SE! Is any of these radiations naturally found in a habitable space? If no, then evolving ability to detect it would be senseless. And how would an organism know that it can see something that is not found nearby anywhere?

@another 'Homo sapien', thanks. Off the top of my head, I can think of high-altitude birds & bacteria, organisms living near nuclear reactors & radioactive waste deposits, and organisms living in uranium mines.

When people are exposed to radiation they can see flashes of light. An astronaut on board the MIR space station has told about this when he had to take shelter during a solar storm in a room with thick shielding. The light flashes are caused by protons moving through the brain, causing spurious electric signals in the visual part of the brain. So, you could say that you can become a walking Geiger counter when exposed to radiation.

Increase in the mutation rate (single and double strand breaks) caused by those radiations is harmful for most life forms on earth.

What exactly is antimatter radiation? Things like positrons are not gonna make it very far through our matter atmosphere. As for the rest, about the most any creature can detect is the noxious effects. I am not aware of any species which can directly "see" such radiation. It wouldn't be particularly advantageous anyway, since there are very few places on Earth where the radiation levels are not (relatively) constant. Perhaps in time, organisms like radiotrophic fungi may evolve to have more sophisticated detection mechanisms (though they use electromagnetic radiation, specifically gamma rays).

What do you mean by see. Just detection will be enough?

Some fungi have radiotropism; they grow toward radiation sources. Melanin-expressing (melanotic) fungi migrate toward radioactive sources, which  enhance their growth. According to this paper.

These Melanotic fungi inhabit some of the most extreme habitats on earth such as the damaged nuclear reactor at Chernobyl and the highlands of Antarctica, both of which are high-radiation environments.
Radiotropism was triggered primarily by gamma radiation, but it is possible that both alpha and beta radiation could be  “ sensed ” by the fungi as well.

It seems like these melanotic fungi can detect gamma and beta or alpha that they can use as energy source.


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Example of species that went extinct because of excessive hunting by non-humanoid predators?
I was wondering if there were any species that went extinct for being excessively hunted/eaten by predators? I don't mean human hunting. For example, I wish to know if there's a species of frog that are now extinct, because they were driven to extinction by predation by snakes. In fact I'm also OK with examples where a species/class of plant or grass went extinct due to overgrazing? I want to know because I've always heard people say "Nature corrects itself" or "hunting is under control in the natural environment" etc. Is this argument valid?

I've always heard people say "Nature corrects itself" or "hunting is under control in the natural environment"

I wouldn't say that extinction of a species necessarily goes against that. You could call it a 'natural event', and not a problem.

nearly all pre human extinct prey animals must have perished also due to excessive predation. most striking is cats and rats and rabbits through human introduction, for example preying on flightless birds of NZ or natural bridge crossing, which is too long ago to map precisely. like mammals arrived in america, nearly all the marsupials of old america vanished, preyed and outcompeted.

The Brown Tree snake (Boiga irregularis) is responsible for five extinctions on the island of Guam. Some of these species existed only on Guam, while others exist elsewhere and so it is the Guam subspecies that has been lost.
Guam flycatcher (Myiagra freycineti). Last sighted in 1983.
Guam rail (Gallirallus owstoni) is extinct in the wild, but is now bred in captivity and has been introduced to the island of Rota.
Guam kingfisher (Todiramphus cinnamominus) is also extinct in the wild and exists only in a captive breeding program.
Guam flying fox (Pteropus tokudae). Went extinct in the late 1960's possibly as a result of the Brown Tree snake.
I had a suprisingly difficult time obtaining accurate lists of the Guam extinctions.
For an example of overgrazing leading to a local extinction, see St. Matthew island in the Bering Sea. The US Coast Guard introduced reindeer in 1944. By 1963 there were ~6,000. Without any natural predation to control the population, they are considered to have overgrazed, causing a population collapse to 42 by 1965 and no reindeer population by the 1980's.

Could you add your sources to your answer?

WHen new connections form between formerly isolated land masses there is usually a drastic shift in the ecosystem as new hunters and herbivores enter that the native animals have no defense for. Snakes, and rats are not native to many islands, when introduced they often decimate local animals. The same thing happens when humans introduce species. See the brown tree snake in Guam or rabbits in Australia or nile perch in lake Victoria.


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Enhanced Spectrum Chloroplasts
As far as I'm aware, chloroplasts produce energy through the use of photosynthesis which essentiall converts CO2 and Water into Glucose (I'm an engineer by trade so really wracking my brains to the last time I studied biology formally).
The pigment in chloroplasts, chlorophyll, makes the plant appear green due to the fact that it absorbs red and blue light, reflecting the green.
My question is this, would it be possible to extend the light spectrum absorbed by the chloroplasts, perhaps through the use of very careful genetic engineering and manipulation of the pigments contained within, in order to increase their energy absorbtion rate.
In essence, could you could make them absorb a wider range of frequencies for use with photosynthesis and thus enable much faster glucose/ATP synthesis?
If this were possible, how much of an evolutionary advantage would it provide?


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Impact of latitude on agriculture?
I live in southern California, where the difference between seasons is mild, and the dominant limitation on agriculture is the lack of water. (Spring is whenever it rains, not a place on the calendar.)
In my early education, as is usual, I learned the growing season is shorter in more northern latitudes. The natural deduction is to expect less effective agriculture, further north.
Recently, I spent a week in early April in Vancouver (Canada). The weather was very (very!) nice, much warmer than I expected, and the hours of daylight longer. On reflection, all this was obvious ... but I was surprised at the time.
Northern latitudes may have shorter growing seasons, but the hours of daylight during that season are much(!) longer. What is the potential agricultural productivity of more northern latitudes?
Much of the past century of agricultural research was centered on the American mid-west. How much is possible if we further optimize agriculture for more northern latitudes, and higher levels of technology?
As the Earth warms, large expenses of Russia and Canada will thaw. Seedlings started early in artificially warmed and lit greenhouses could jump-start crops. (Or transported from more southern latitudes.) If we took full advantage of the longer hours of daylight in northern growing seasons ... what is the limit to agriculture?
With global warming, could Canada and Russia become the bread-basket of the world? Can agriculture as a technology be adapted to more northern latitudes, and take best advantage of a shorter season with longer daylight?
(In imagination, I see seedlings started in greenhouses, and robot-planters placing seedlings in just-warm fields, to capture every hour and day of longer sunlight.)
Do we know how to best take advantage of long northern days for agriculture?

The days may be longer but the light is much less intense, hence why it is colder.

Is it really much less intense? What does the longer hours of daylight do to plant growth? Are plants only responsive to total cumulative energy from the sun? Vancouver in early April was not colder than southern California ... so, what is the sum?

I know this response is coming a bit late but in case you're still curious I have a response!
I'm a M.Sc. student working in Agricultural entomology in Northern Canada (between 55 and 59 degrees North). You are correct, up at more Northern latitudes our short growing season mainly limits what crops we can grow, but less so our yield. We are also restricted in where we can farm by soil conditions as the further north you go the more you are on the Canadian Shield - so less fertile. If you look at growing regions in Northern Alberta, North West territories, etc. you'll see that they tend to stick fairly close to rivers. Further south in Canada, moisture conditions play a much bigger role in determining yield. Mainly we stick to crop species and cultivars that can produce a good yield in a short time - canola, wheat, barley, peas (although corn and soybeans have some large acreages in the Eastern prairies and Ontario).
Climate wise, the comment about light intensity is not really accurate in the summer. The longer daylength definitely compensates for any differences in light intensity. Even at 59 degrees latitude it can get well into the 30's (Celcius) in the summer.
Canada already produces a large amount of wheat and canola, we are the 6th largest exporter of wheat according to a quick google search. So I would argue that while Canada may not be the bread basket of the world it is pretty close already.
It's tough to say how climate change will affect agriculture, because it's really tough to determine how climate change will affect local climate. The changes to weather patterns (changes in amount and timing of rain and moisture, changes in spring or fall frost timing) will have a large impact on agricultural outputs.

Ag Canada actually has a nice little description of ways that climate change is predicted to affect Canadian agriculture! http://www.agr.gc.ca/eng/science-and-innovation/agricultural-practices/agriculture-and-climate/future-outlook/impact-of-climate-change-on-canadian-agriculture/?id=1329321987305

Understand you are more focused on insects, but still curious about specialization of plants (crops) to the shorter growing season. The varieties developed for more southern (central US) latitudes are probably not optimal.
Also, increasing automation (smarter/cheaper machines) means crops could be jump-started in greenhouses (or warmer latitudes) and placed in northern fields when temperatures permit.
Curious about the state of research for the above. :)


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Anabolic reactions and reaction energy
My textbook says,

In general, the formation of a [chemical] bond releases energy

and continues to state,

Anabolic reactions (collectively called anabolism) link simple molecules to form more complex molecules. Anabolic reactions require an input of energy because strong bonds within the smaller molecules must be broken to form the more complex molecules.

Do these two statements contradict each other? The first statement says that when two chemicals combine to form a bond, energy is released; the second statement says that when simple molecules are linked, presumably through a bond, an input of energy is required.
Any help is appreciated.

Both statements are correct, but an understanding of why they are not contradictory requires a bit of explanation.
For "spontaneous" reactions, those which occur naturally, entropy must always increase.  As a general rule, one of the easiest ways to increase entropy is to release energy, so we generally find that spontaneous reactions release energy.*  It's a pretty decent rule of thumb to use.
In the case of an anabolic reaction, we're putting together complex molecules from simple ones, and for these particular reactions we see they don't release energy.  They in fact "consume" energy in their formation.  This is reasonable, so what we find is that such reactions are not "spontaneous."  We don't see them just occurring on their own.
To make an anabolic reaction occur, we need to change the environment such that the reaction becomes spontaneous. We need to change the environment such that the reaction releases energy.  To do that, we start off with inputs which have even more energy than the final product should (such as extra kinetic energy from heat, or a strong oxidizer to reduce one of the reagents, or any one of a number of chemical and mechanical approaches).  Now the formation of the complex molecule can release energy, so it can occur spontaneously.  When we do this, we release some energy, but not all of it.  The rest of the energy is consumed in building the bonds of this molecule that would not otherwise have spontaneously come into being.  The released energy is typically seen as waste, and the energy pent up in the molecule is your desired product.
So in the end, the reason why there's no conflict is the "In general..." bit in the first quote.  You can cause a reaction to occur that consumes energy, but you typically have to do some clever things to put the energy into it.  Reactions which release energy occur spontaneously.  In general, we find "spontaneous" reactions occur far more often, hence the rule of thumb.
* I'm pretty loose with energy and entropy here to try to paint a simple picture without all of the confusion that entropy always brings to a discussion.  As you learn more, do expect to need to be more precise than I am here.

Thanks for your answer, but I'm still a little confused on the concept. Take, for example, the following reaction: $\ce{2H_{2}+O_{2} \rightarrow 2H_{2}O+heat}$. Is this an example of an anabolic reaction that is exergonic? Or are anabolic reactions a special type of endergonic reaction, to which the above reaction is not classified as?

Ahh, I see the confusion.  Anabolic and catabolic are terms typically used when talking about complex molecules like protiens and other polymers, where the term "complex" is more easily meaningful.  Adding amino acids to a protein, for example, is anabolic.  When you get to the small reactions, like your redox of hydrogen example, our intuitive concept of "complex" gives way to basic chemistry rules.  I could argue that maintaining a mixture of hydrogen and oxygen is actually more complex than maintaining a body of water, and thus it was not anabolic, but really, I'd be better to say...

... it' just a "simple" reaction which doesn't easily fit the mold used for more complicated reactions.

Although the answer from @CortAmmon is generally admirable, I think there needs to be a distinction between the type of veracity of the two statements. I would say that:

Statement 1 (bond formation releases energy) is a fundamental truth which emerges from the definition of bond energy.
Statement 2 (anabolic reactions require energy) is a generalization
  that is true in most circumstances but is not a fundamental truth, as
  illustrated by exceptions.

The first problem is the definition of anabolism. Let us take an uncontraversial one from an internet site:
“Anabolism is… the generation of complex molecule from simple molecules”
or, as in Berg et al. Biochemistry, “Biosynthetic processes”.
It is immediately obvious that this is a much less precise concept than bond energy, and and the distinction arises between anabolism as a whole (e.g. the overall synthesis of glucose from pyruvate in gluconeogenesis) and individual anabolic reactions (e.g. the aldolase reaction in gluconeogenesis).
Now in anabolism in biology we are generally concerned with the the creation of complex molecules containing new carbon–carbon bonds, peptide bonds, glycosidic bonds, phospho-diester bonds and the like. As @CortAmmon makes clear, the second statement is valid because (I would say “if”) the bonds in the molecules that have to be broken for the likage to occur have a greater total bond energy than that of the new bond in the product. This depends on the particular chemistries involved, and may turn out to be true for the whole process, but there seems to be no fundamental reason why it should be so.
Certainly, it need not be true for individual anabolic reactions, as illustrated by the aldolase reaction, mentioned above:

This is a reversible reaction, which in the anabolic direction forms a C–C bond between two trioses. The standard free energy change in this reaction is near zero.
If the poster’s textbook had made this distinction, the poster’s confusion on the matter need not have arisen.

This is old news, and so will likely never be seen by the original poster. However, it came up recently because of a new answer, and I found the question intriguing and felt there was unfinished business here that was worth addressing.

I think both statements are correct.When they consider the entlapy change they consider the overall change. Energy is needed for the reaction to start for breaking old bonds allowing new bonds to form hence on the other hand when bond forms energy is released. The energy released is more as compared to energy absorbed hence bond formation releases energy.

It would be helpful if you could perhaps add some sources that can back up your answer. That way the person who asked the question is able to go and look at those sources as well.