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Why don't bacteria eat food leftovers?
I have thrown a dirty spoon after eating some pasta into one of my desk drawers (doesn't do me much honor). It stayed there for around a year. My house is warm and I think there is enough humidity for bacteria to multiply, however I have found it today with seemly same amount of food on it when I left it.
I assume given enough time all food should get converted into bacteria (bacteria would eat and multiply until food is there and stop when it is all consumed). Is this assumption incorrect?
Why didn't bacteria decomposed the food on my spoon?
EDIT: This question has nothing to do with fried McDonald foods and is referring to bacteria consuming 'ordinary' food, plus I am asking if food should disappear completely while the other question is about it being decomposed,  answers are completely different.

why would you assume that a bacterial colony looks "clean"?

@rumtscho I assumed given enough time all food should get converted into bacteria (bacteria would eat and multiply until food is there and stop when it is all consumed). Is this assumption incorrect?

The crucial point is water availability. The Antarctic is a big mass of water. Yet it is frozen and your spoonful would survive there too. The air may be humid in your place, but that doesn't mean organisms can deploy that moist and thrive.

The assumption is indeed wrong. But even if it were right, the spoon would be covered in gunk consisting of dead bacteria bodies + their waste product.

@AliceD So had I placed spoon in conditions perfect for bacteria I would have found it 'eaten off' clean?

@rumtscho Could you post it as answer please. Thanks.

@MatasVaitkevicius - I would suspect fungi to decompose it, yes. However, as posed above, the 'clean' I am unsure of, as certain components of organic material may, or may not be digested fully.

Possible duplicate of Why don't McDonald's fries decompose?

First, your assumption is wrong. Bacteria multiplication is not limited by food availability only, it is one of many constraints.
Oxygen availability, water availability and the absence of toxins also play a role. You can easily start a thriving bacterial colony somewhere, but once one of these conditions changes sufficiently, the colony can die off. And it can be the growth itself which changes the conditions. A classic example is found in wine fermenting. The yeast there multiplies freely until it has produced so much alcohol as a waste product that it dies off. This is why wine is always in the 12 to 18% ABV range, anything above is "fortified wine" where the concentration was increased after the yeast's death. Yeast are not bacteria, but bacterial colonies' growth is limited in similar ways.
Second, even if the assumption were true, the spoon wouldn't be clean. Bacteria converting food in waste doesn't result in nothing, nor does it result in something gaseous which would literally disappear into thin air. OK, part of their byproducts are likely to be some gas. But you certainly get lots of bacterial bodies (alive, later dead) and also lots of waste product. Together, it forms some kind of sticky organic goo (frequently a biofilm).
So, about your spoon

it is entirely possible that it never got a thriving bacterial colony, because the conditions weren't right despite food availability
it is also possible that it got some kind of colony (pathogenic or not), and it died off before the food was consumed
in the case of a colony, it doesn't matter how much it got to consume before dying off. The spoon wouldn't have ended up clean under any circumstances, including the very unlikely "death by food going out" scenario
depending on the conditions in which the spoon is held, the colony which dominates the spoon can be bacterial, or fungal (mold, yeast), or you can end up with different species building their colonies in parallel. Still, the previous points hold under the "mold colony" or "multiple colonies" scenarios just as under the "single bacterial colony" scenario.

Thanks, I appreciate your patience with someone as ignorant as myself.  I am working on a different angle - that they simply didn't like the pasta :)

Wouldn't you think fungi would be better candidates than bacteria?

Heh, no problem - if I didn't have the patience, I wouldn't have written an answer. Also, you're raising an interesting philosophical question - can bacteria "like" something?

@AliceD both are possible, I suspect it's the circumstances which determine which ones will get the upper hand - I think it's mostly up to temperature, with bacteria being more likely at room temperature and fungi preferring it below 20 C. I can say from "standard food safety knowledge" (sorry that I can't point to a specific reference right now) that B. cereus is very fond of cooked starches, and can confirm from personal slob experience that you certainly can incubate a nice bacterial colony on pasta or rice - I didn't do anything to confirm that it's B. cereus, though.


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What differences in effect does fast repetitive exercise have compared to slower muscle-building exercise?
As a drummer who likes to play high-energy music (fast, aggressive metal) it's safe to say I burn a fair amount of calories when doing so. But I've been drumming for over a decade and despite the amount of it that I've done, it hasn't really had any (visible) effect on muscle growth. Every time I drum I try and push the limit of how fast I can go until I start to ache, so I'm definitely doing something to the muscles in my arms and legs, but it definitely isn't building mass.
I remember reading somewhere that speed based exercise can actually reduce muscle mass as the body tries to make itself more efficient, but heard no evidence to support this or an explanation of how.
Can someone please explain to me how exercise such as fast drumming affects muscle growth and development in relation to traditional muscle building exercise like lifting weights?
I am looking for a explanation of the biology behind this by the way, not fitness advice.
Clarification - for non-drummers, the "speed exercise" I'm referring to is what are called blast beats, where the aim is to keep an often inhumanely fast repetitive beat going. It's common in more "extreme" music such as death metal. While trying to maximise efficiency by minimising the amount of effort required is the goal, the muscles required are undergoing a rapid contraction-release cycle, often sustained for minutes at a time, and sometimes for an entire song.

That's an interesting question +1. Just as a comment, body building is typically done by using weights/force and to increase the weights/force over time. Those drumsticks are too light. Although it consumes energy, it doesn't need muscle mass to do it. It needs endurance to complete an hour or two of intense practice, but no muscle mass per se. Further, I worked for a long time unloading trucks. Day in day out lifting ~15 kg boxes for months on end didn't do anything either.

With that in mind, what factors determine a muscle's endurance?

I think that's an entirely different question altogether. Muscle building is akin to body building. Endurance quite another. Do you want muscles or endurance? Perhaps a clarification in your question proper is appropriate.

what do you mean by "speed based exercise?"

In this case I mean what drummers would call blast beats, where the aim is to keep a continuous but very fast beat going (some would refer to it as a wall of noise). Usually the aim is to minimize the amount of movement required because of the extreme speeds, so it's really about efficiency. But even though the movement is as minimal as it can be, the fast "back and forth" can still tire you out.

Your body creates muscle after an exercise through a process where it fuses muscle fibers together to form new muscle protein strands called myofibrils. these myofibrils increase in size as workout intensity increases, leading to muscle growth. Muscle growth occurs when muscle protein synthesis happens faster than muscle tissue breakdown 1.
Since you are never really increasing the amount of strain on your muscles(i.e. by adding more weight to a workout) there is no incentive for your body to create more myofibrils, rather it will just replace the ones that were torn during your drumming.

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What is the change in ratio of histone to protamine in men with infertility called?
I am neither a biology researcher nor a student. In a paper (written by a biology researcher) I am translating into English, there is the following statement which, according to the text, must have a name and I fail to find the English name:

It is showed that in men with infertility histone to protamine ratio changes and the change is called ...

What is the change called? I guess it's something unnatural/abnormal.

It is termed "abnormal packing".
Source: "Sperm Chromatin: Biological and Clinical Applications in Male Infertility and Assisted Reproduction" by Armand Zini & Ashok Agarwal (2011), p 172.

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Nerve fiber responses to intense stimuli
Can one instantaneous, high-intensity stimulus performed on a nerve fiber generate a series of action potentials? Or are nerve fibers limited to one response action potential, no matter how intense the stimulus?

Short answer
It depends on your definition of 'instantaneous' and on your definition of 'stimulus'. I can safely say that secondary neurons can fire multiple action potentials to a single, short physical stimulus delivered to the associated sensory neuron.
Background
Physiologically, external stimuli are processed by sensory neurons. Sensory neurons generally work with graded potentials, not action potentials. Sensory neurons typically convey their graded response onto a secondary neuron that translates it into a frequency-modulated pulse train.
Hence, I interpret your question as "can a single, short stimulus delivered to a receptor generate multiple action potentials in the associated secondary neuron".
If sensory neurons were restricted to one action potential per stimulus, then a stimulus could only be detected in terms of its onset or offset. We can, however, sense prolonged stimuli. For example, we can perceive a continuous auditory tone and we can look at an image for extended periods without it fading away.
However, it all depends on the sensory system. A great example is the tactile system, where some receptors mediate prolonged sensations, whereas others only mediate onset or offset responses. Their associated secondary neurons are therefore classified as rapidly adapting and slowly adapting fibers.
Figure 1 shows the response profiles of various secondary neurons connected to different mechanoreceptors in the skin.

Fig. 1. Responses of various secondary neurons to tactile stimulation. Source: Mann (1997)
For example, the Pacinian corpuscle is a rapidly adapting mechanoreceptor. If it receives a static pressure difference, its associated neuron fires only a single action potential (or very few action potentials) at the start and end of the stimulus. Slowly adapting receptors causes their associated neurons to continue firing even after prolonged stimulation. Slowly adapting mechanoreceptors are Merkel's disks and Ruffini endings (fig. 2)

Fig. 2. Skin receptors. Source: Purves et al. (2001).
If you, however, mean with an 'instantaneous' stimulus a nearly infinitesimal short stimulus, then this question becomes a search for the shortest possible stimulus still capable of evoking a response in the secondary nerve fiber. In the auditory field, the shortest acoustic stimulus possible is probably the click stimulus, which is akin to a pulse stimulus. An acoustic click is hence about the shortest possible stimulus known to activate a sensory neuron. An acoustic click can be as short as 30 microseconds. A short stimulus like that, however, still evokes multiple action potentials in auditory nerve fibers (Parham et al., 1996). Admittedly, due to the mechanics of the inner ear, most notably the basilar membrane and the travelling wave the click evokes, the factual physiological stimulus may be longer, but in the auditory field at least, tens of microseconds is about as short as it gets.
Hence, I would answer "yes, instantaneous stimuli can evoke multiple action potentials in a given nerve fiber'.
References
- Mann. The nervous sytem in action (1997)
- Parham et al., J Neurophysiol; 76(1): 17-29
- Purves et al., Neuroscience. 2nd ed. Sunderland (MA): Sinauer Associates (2001)

If by 'nerve fiber' you mean a single neuron, the answer is definitely not.
Once a nerve 'fires', it fires completely. It depolarizes 100%, and further stimulus can't make it depolarize further. Once the stimulus is off and the nerve is finished repolarizing, further stimulus is needed to fire another action potential.
The nerve can't 'remember' that the previous stimulus was particularly intense and fire again.
If by 'nerve fiber' you mean a bundle of neurons, the answer is almost certainly not. Maybe you could get some cross-talk where some neurons didn't fire and then further down the fiber the action potential 'jumped rails' and propagated back to the site of stimulus, maybe you could count that. I wouldn't rule it out but the layout of neurons would need to be really strange.


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What are 'acid stable' amino acids?
I tend to see terms amino acid, acid stable amino acid, and free amino acids used often in the field of nutrition, but they are sometimes used interchangeably which confuses me.
I know that:

amino acid is a general term to describe organic compounds that encompass both essential and non-essential amino acids.
free amino acids is a general term for amino acids that are not broken down from a protein source; instead it exists in its original form 'freely'.
acid stable amino acid ... no idea

Is that right (correct me if I'm wrong)? What is the larger relationship amongst all three terms? Would consuming a free amino acid be better than one from a protein, or from an acid stable amino acid? Why would one choose to consume a particular class of amino acids over another?

a reference to the source of acid stable amino acid may help place it into context. If its is 'acid-stable amino acid' it may refer to its stability in acidic environments like the stomach?

The amino acids asparagine and glutamine have hydrolysable amide groups on their R groups, as shown here:

Note the leftmost amide group on both amino acids. When exposed to acid, these groups would hydrolyse, releasing ammonia.
This was of interest when people used to determine amino acid compositions by acid hydrolysing purified proteins (example paper which does this) and then running them through HPLC or mass spectroscopes. This method, however, fails to distinguish asparagine/aspartate and glutamine/glutamate due to their acid-unstable nature.
So to answer your question, an acid-stable amino acid is any amino acid that does not degrade under acid treatment.
Additional amino acids that degrade under such treatment can be found here, and includes serine, threonine, tyrosine, tryptophan and cysteine in addition to the two above amino acids. These amino acids degrade by alternative pathways distinct from the one by which the above amino acids degrade.
Finally, assuming you are talking about amino acids in dietary supplements, the reason acid-stable amino acids are reported is because acid hydrolysis is usually the method used to hydrolyse the proteins into amino acids, and therefore the manufacturer would not be able to produce acid-unstable amino acids by this method, leading to that label on your supplements.


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What if there are no bacteria such as Streptococcus mutans
If someone removed all bacteria such Streptococcus mutans in her mouth by starving long time, or by some chemical method, would she never have such bacteria?
In my thought, because S.mutans only spread out through human teeth, and if there are some in the air, white blood cell might kill all from the air completely because they are very little.
Is this foolish hypothesis of mine possible?
Thanks for your answer in advance.

no kissing.  no licking.  no eating food touched by other people's mouths. (sharing an apple for instance.) seems unlikely...  also total removal is hard but that's another matter.

As shigeta touched on, there's no practical way to avoid cross-contamination from other humans. Assuming by magic you delete all your mouth bacteria, there are so many paths to re-inoculation you couldn't avoid it without living in extreme isolation.
A non-exhaustive list of all the ways you could get re-inoculated:

kissing
licking
aerosolized saliva from coughing/sneezing
eating food exposed to same
Touching something contaminated then brushing your teeth
Essentially putting anything another human has touched in your mouth

Other humans get saliva on things they touch and things they breathe on. You can't breathe or eat those things without cooking them. No fresh vegetables.
Your white blood cells or your immune system in general won't help, because S. mutans is already adapted to live in your saliva and there's not (to my knowledge) any adaptive immune system components active in your saliva.


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Why my base-quality in alignment is not perfect?
I have a fasta file with some DNA sequences. I would like to simulate next-generation sequencing reads from it. I'm doing it without any base error and mutation error.
wgsim -e 0 -r 0 sequence.fa seq_0_1.fq seq_0_2.fq

To my knowledge, this is a perfect simulation. Next, I give the paired alignments to bwa for alignment.
bwa mem -M sequence.fa seq_0_1.fq seq_0_2.fq > P0.sam

Now, I check the ASCII of base quality (column 11 in the SAM format, the specification is here).
head -n 3 P0.sam | cut -f11

IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII

According to this page, the ASCII (in order of quality) is:
!"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~

Question: My experiment is supposed to be perfect, so my base-quality metrics are expected to appear near the right-end of the list (like x,y,z). However, my metric I is no-where near the top of the list. In particular, I'm unable to achieve anything from J to ~. Why?

When fasta reads are aligned they are by default assigned the phred score of 40, which in phred+33 encoding is represented by I. Phred+33 uses ASCII characters from ! to I:
!"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHI

Phred+33 was originally used by sanger machines but it is now used by all popular platforms such as Illumina, Ion-torrent (also Ion-proton) and Roche 454. Since most platforms now use phred+33, most aligners also assume it by default. You can specify other quality encoding formats if you want (such as phred+64 or Solexa).
Have a look at wikipedia page on FASTQ format for the different quality encoding formats.


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What is the role of the tissue surrounding neurons in decision making and taking control of impulses?
How does the fatty tissue surrounding neurons supports and enhances the speed of electrical impulses? How does it stabilize connections that take control of impulses and decision-making? The cells surrounding the neurons in this case being either glial cells (neuroglia) which provide support and protection for neurons in the central nervous system and peripheral nervous system, or myelin an insulating sheath around many of the nerve fibers consisting of proteins and phospholipids.

This is a broad question. There are different types of cells that surround the neurons and they have critical roles in ensuring proper function of the nervous system. Each of these cell types have a unique function. Please edit your question to add some details or else this question would be closed.

I hope you aren't confusing "impulse" with action potential (sometimes called nerve impulse).

@Memming Apologies if was not specific/clear enough, I mean impulse as in the relaying of a coded signal that travels along a nerve membrane to an effector, such as muscle or other nerve cells

Possible duplicate of http://biology.stackexchange.com/q/14249/3340

Short answer
This question is pretty broad as it basically translates to "what purpose serves neuroglia in neuronal communication"? In short: next to everything.
Background
In the adult brain there are three types of glia: oligodendrocytes, astrocytes, and microglial cells (Purves, 2001). A few notable examples of their functions:

Oligodendrocytes (peripherally called Schwann cells) generate myelin sheaths around neurons, which increases conduction speeds (saltatory nerve conduction) and increases the metabolic efficiency of neural communication.
Astrocytes are a highly heterogeneic group of supportive cells. To put the impact of glia in perspective: this class of cells is considered to contain as many cell types as there are types of neurons in the brain. They are thought to mediate transfer of nutrients from blood capillaries to neurons, and they also assist in removal of neurotransmitters from the synaptic cleft and thereby speed up the recovery from synaptic activity and hence they increase the speed of information transfer (Tsacopoulos & Magistretti, 1996).
Microglia are the brain's immune cells, and are similar to peripheral macrophages. They act as the major inflammatory cell type in the brain, and respond to pathogens and injury.

References
- Purves  et al (eds). Neuroscience, 2nd edition. Sunderland (MA): Sinauer Associates (2001)
- Tsacopoulos & Magistretti, J Neurosci (1996); 76(3): 877-85

Microglia are also involved in synaptic pruning thereby regulating the development of the neural network and reducing noisy impulses (http://www.ncbi.nlm.nih.gov/pubmed/21778362).

@WYSIWYG - there are really a myriad of functions. I mentioned a few notable examples above, as explicitly mentioned in my answer.


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Is there a blood panel lab test that measures all the hormone-producing glands?
I understand that there are gland-specific hormone tests, such as:

Secretin: for the pancreas; and
Prolactin/ACTH: for the pituitary; and
PTH: for the payathyroid, etc.

However, are there any "composite" blood panels that test the "entire gamut/spectrum" of organs/glands, similar to what composite metabolic panels do for your cell counts?

There are no composite tests that measure all the clinically important hormone producing glands. There are too many hormones produced by too many hormone producing cells/tissues in the body to test for all of them all at once (i.e. in a panel).
For illustrative purposes only... if you go to wikipedia they have a list of all hormones in the human body which is definitely far from complete! But it gives you an indication of just "how many" hormones there are and why testing for all of them is impossible in a panel.
Even with regard only to pancreatic hormones, there are several hormones produced (e.g. insulin, glucagon, somatostatin) that aren't necessarily a marker of the glands overall function (because they are not necessarily involved in the same function). Each of these hormones has different functions even though they are produced by the same gland.
Regardless, from a medical perspective you would never have a reason to test for all of them anyway. If you tested enough of them you'd find at least one of them that would - by chance - be abnormal.
Additionally, if you asked a handful of scientists to name fifty hormones there would be a lot of different hormones on each of their lists. The definition of hormone is vague, and we are learning more about new hormones every day. In the last decade we have learned that bile acids - chemicals predominately produced by the liver that are involved in dietary fat absorption - also act as hormones. There aren't clinical reasons to study all of these molecules just yet, but this demonstrates that it would be impossible to measure all of them all at the same time in one particular "panel".

Good answer.  Lipase and amylase are enzymes to my knowledge. Also many hormones are difficult to measure at all due to instability or low concentration.

+1 - Not to mention new hormones are being discovered constantly, it seems. They are actually pretty hard to keep up with.


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Where would the majority of the Indoleacetic acid (IAA) be in the shoot and what would the effect be?
If I propose that a plant is 2D and then a light source was shone on both horizontal side of the shoot, in which direction would positive phototropism occur (or would positive phototropism occur at all?).
I am presuming that light intensity is the same and there has been no modification of the tip.


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How is achieved the loss of heat through vasodilation?
I know it is the widening of blood vessels, loosing heat in this way. But is it achieved through: sweat evaporation, the increase of cardiac rhythm, the increase of respiratory/ breathing rhythm or frequent urination?

It's unclear, are you asking what is/causes vasodilation or how it contributes to heat loss in the body?

@Nathan the loss of heat through vasodilation is achieved through____???

See help pages regarding homework questions.

Sweat evaporation is the most correct answer you have mentioned.  Vasodilation increases blood flow, allowing for more blood to be cooled be vessels closer to the surface of the skin.  It's increasing the surface area the blood interacts with, which always allows for faster heat transfer.


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Trees ability to transport water
How can trees be able to transport hundreds of liters of water all the way up to the crown and out in the leaves?

This question places much emphasis on quantity, I vote to leave open.

The most popular theory is the ‘hydraulic limitation hypothesis’ (Ryan & Yoder, 1997), which suggests that as trees grow taller, it becomes more difficult to supply water to their leaves. This hydraulic limitation results in reduced transpiration and less photo-synthesis, causing reduced growth.
It is known that in larger/taller trees water supply is limited by two factors — distance and gravity. Larger trees have a longer pathway of transporting tissue, this tissue is known as xylem. This is known as hydraulic resistance and makes it more strenuous for the water to move around in the tree. So now not only is the pathway long, but the water also has to beat gravity. Increased force is necessary to pull the water up to the highest leaves. Additional difficulty comes from the trees growing upright. Fast - growing/short trees frequently have shorter life-spans. They achieve their expeditious growth by having broader, wider xylem vessels, this increasing their hydraulic efficiency. At the same time this provides space for embolisms. An embolism makes it unable for a xylem vessel to transport water. Taller, slow-growing trees are longer-lived, this is caused by them having multiple xylem vessels, rather than having only a few wider ones like the fast-growing trees. Short-growing trees also have a more secured hydraulic system, preventing the forming of air-locks.


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How is the Concept of Simple Diffusion Possible
How can a substance pass through a lipid membrane in a cell through simple diffusion? In order for something to be able to go through the membrane, in simple diffusion, it must be hydrophobic, or non polar. The reason for this is that in order for it to easily interact and pass the fatty acid part of the lipid membrane, which is hydrophobic or non polar, it must also be hydrophobic and non polar. But in order for this substance to pass the phosphate part of the membrane, which is hydrophilic, or polar, doesn't it also need to be polar and hydrophilic?

Simple diffusion is the movement of solutes from an area of high solute concentation to an area of low solute concentration.
Here are a few ways molecules will make it through membrane into cell:
(A) Fuse with the membrane and enter due to like polarities i.e non-polar subtance fuses with non-polar membrane and passes through membrane
(B) Small polar molecules CAN move into cell but at a much slower rate
(C) Through transmembrane integral protein channels such as aquaporins, K+ leak channels, and other channels that DO NOT require energy, and are ALWAYS open
If you want to understand how it was determined which molecules were able to pass through the membrane look for some resources about Overton's Plasmolytic Method.
Alongside that the definition of the partition coefficient will give you some insight on how fast molecules will pass through membrane, if at all.
Good luck on the searching!
@ Ro Siv - Simple diffusion is not facilitated diffusion


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What contributes to the variation of protein sequence across different species?
What contribute to the variation of protein sequence across different species (e.g. phenotype, environment, evolutionary pressure) and how do those factors contribute to the variation?
I have tried to search using google + google scholar but they generally show papers discussing why and how the protein conserved across species rather than why/how the protein diverged across species. Please help me on this and references/sources are very important and highly appreciated. Thank you!
An example to clarify my question. The gene CD81 is not identical among human, chimp, rat, chicken based on this identity matrix from ClustalW2. Why is CD81 not identical in all species? What factors cause the different in CD81s? How do those factors cause that (e.g. evolutionary pressure)?
#
#
Percent Identity  Matrix - created by Clustal2.1
#
#
 1: sp|P60033|CD81_HUMAN    100.00  100.00   93.22   82.55
 2: sp|P60034|CD81_PANTR    100.00  100.00   93.22   82.55
 3: sp|Q62745|CD81_RAT       93.22   93.22  100.00   82.55
 4: tr|F1NW06|F1NW06_CHICK   82.55   82.55   82.55  100.00

Welcome to Biology.SE. What contribute to the variation [..]. The maintenance of genetic (and therefore protein and phenotypic) variation is one of the main question of evolutionary biology. It is extremely studied and there are a lot of processes that either retain or remove genetic variation. The question is too broad. [..] and how do they influence? How do they influence what? (I am not sure what they stands for either) It is unclear.

Thanks Remi.b for your feedback! I have clarified my word and add an example.

I didn't like my answer so I deleted it. It is hard to answer such a broad question. However, there is one result you probably want to remember. If you can assume that both species and all of their ancestral lineages up to their Most Recent Common Ancestor, had the same mutation rate $\mu$, then, the substitution rate is $\mu$ as well.

It is indeed general so that's why I have such a hard time answering as well as finding literature. Anyway, I have found my answer related to the keyword "Neutral evolution" or "Molecular evolution".

I've edited the English in your title. Hope you don't mind.

I have found an acceptable answer for my question. Just post here if any interest in it. Pardon my English.
Source:
Nei et. al. 2010. The Neutral Theory of Molecular Evolution in the Genomic Era. Annu. Rev. Genom. Human Genet.
Evolution and point mutation cause the sequence difference of the same functional protein across species. Neutral theory of molecular evolution shows that speciation level of evolution is an accumulation of molecular level of neutral evolution. In neutral evolution, the mutation only occur at a scope of point mutation in sequence in the manner that the function of the protein is retained. Overtime, speciation occurs yet the function carried out by that specific protein is still necessary and is conserved across species. Difference in protein sequence of the same functional protein is the residuals of random point mutation.

I would dispute your conclusion that it is simply neutral evolution. Neutral change absolutely does occur but it is not a complete answer to your question. Similar proteins in different organisms are not in the same environment and rarely do exactly the same thing.
For example, your three mammals will have similar but not identical body temperatures while the chicken's body temperature will be slightly higher at 42 degrees. Enzyme efficiency is highly temperature dependent so it is likely that some of the difference is attributable to optimal function at different temperatures. I don't know anything about CD81 specifically but it is often the case that gene regulation pathways are similar, but not identical, between organisms so that you may find that it needs to interact with slightly different proteins in a slightly different way.


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Is there a better lysis buffer than this for fungal DNA extraction?
I've being using this lysis buffer for fungal DNA extraction,lysis buffer - 400mM TRis-HCl(pH8.0), 60mM EDTA(pH8.0), 150mM NaCl, 1% SDS and containing 40microgram/ml RnaseA.
It is keep giving very light bands on 1% agarose gel and shear appearence. After extraction I have to follow PCR and sequencing. If there are inhibitors, how can I get rid of those ?

Do you Fungi contain pigment, especially melanin? This is a potent inhibitor for PCR. If not, you could start by trying a phenol/chloroform extraction.

yeah they have pigments,one sample was a penicillium,  i did PCR for these DNA extractions (didn't make any changes to the lysis buffer) but I got good bands after PCR,my primers were ITS1 and ITS4. But I didn't get PCR results for extractions I did more than 4 days ago. thank you for the answer.


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Where should one start if they want to go about identifying phytoplankton and dinoflagellates?
I'm a first year university student and I really need help on how to identify and recognize the different organisms observed in my water samples. Are there any good references/tips on how to?


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Why are there splice variants within the same organism? What might contribute to the need for the feature?
I only know splice variants are produced by different combinations of introns and exons. I wish to know why there is a need of such function. Perhaps using the same amount of DNA sequence to produce multiple proteins saves genetic material. Also, I want to know what contribute to the need for splice variants feature (e.g. evolutionary pressure, the need to increase the complexity)
I find that in human, protein CD81 is predicted by Ensembl to have a lot of splice variants (http://grch37.ensembl.org/Homo_sapiens/Gene/Splice?db=core;g=ENSG00000110651;r=11:2398547-2418649;t=ENST00000475945). However, only 1 of them is characterized. Thus, splice variants seem redundant. Any examples of splice variants actually carry different function?

The reason is very simply to provide enough variation in a limited sized genome to produce the repertoire of proteins produced by the cells of multicellular organisms. It is also a matter of efficiency and reduced energy consumption.
Consider that on average there are about 100,000 unique protein types being produced in a human cell [1], but the human genome is estimated to contain only 19,042 protein coding genes [2], then the cell needs some way to vary that limited instruction set.
Also remember that differentiated cell types express certain genes but not others, and produce different proteins that other cells do. So that implies that there are more than 100,000 different types of human proteins, and far fewer than 19,042 genes being expressed in any one cell at the same time.
So without splice variants, our genomes would either need to be far larger than the approximately 3 billion base pairs it is already or our repertoire of proteins would be significantly less. We would also have a lot of redundancy, as many common exons would have to be repeated over an over again. That would require a lot more energy for DNA synthesis, and nucleic acid synthesis, etc. The process would become inefficient rather quickly and would likely make complex multicellular animal life untenable.
There is a bit of an error in your question. Splice variants are identified by the mRNAs that are produced, and exons are defined by the sequence that is in the mature mRNA. Introns are, by definition spliced out of the pre-mRNA, meaning that splice variants are not "produced by different combinations of introns and exons." Splice variants will only consist of different combinations of exons. The only time an intron would be found in a mature mRNA is if a splice site is mutated and it is no longer recognized by the spliceosome, so it leaves the intron in incorrectly. This will generally result in a non functional protein.
EDIT

The collection of components required to carry out the intricate processes involved in generating and maintaining a living, breathing and, sometimes, thinking organism is staggeringly complex. Where do all of the parts come from? Early estimates stated that about 100,000 genes would be required to make up a mammal; however, the actual number is less than one-quarter of that, barely four times the number of genes in budding yeast. It is now clear that the 'missing' information is in large part provided by alternative splicing, the process by which multiple different functional messenger RNAs, and therefore proteins, can be synthesized from a single gene.

-Expansion of the eukaryotic proteome by alternative splicing: Nilsen and Graveley

Alternative splicing of pre‐messenger ribonucleic acid (pre‐mRNA) allows the generation of different mRNAs from the same gene. Evolution of alternative splicing affecting translated regions of mRNAs permits the synthesis of different proteins from a single gene, significantly increasing the diversity of the protein repertoire.

-Patthy, László(Apr 2008) Alternative Splicing: Evolution. In: eLS. John Wiley & Sons Ltd, Chichester.
Also while I am not one to accept a Nobel Prize at face value, they are usually awarded when the field accepts the explanation of the hypothesis. The 1993 Nobel Prize in Physiology and Medicine was awarded to Richard J. Roberts and Phillip A. Sharp "for their discovery of 'split genes'."

Thanks AMR! Do you know any sources to back the argument? I feel like the answer is rather a deduction from the two cited numbers. Or the deduction you gave is widely accepted?

You cannot escape the deduction, but it is pretty much universally accepted.

An interesting application of splicing is in CD45 on T cells. Essentially, effector and memory T cells express a splice variant that is shorter than the CD45 expressed by naive T cells, and it facilitates faster TCR signalling. The splice mechanisms that catalyze this variant are activated during the effector/memory state. In this case we're not trying to fit more genes into less DNA, we're actually increasing efficiency of a system! Some light reading on CD45.

@Kendall, I am not sure I see your point? The entire pre-mRNA of the gene encoding CD45 will be transcribed. The regulation of splicing determines the isoform that the cell expresses and significantly increases the probability of that isoform, but does not change the fact that there are several possible isoforms present on the on the pre-mRNA to chose from. That the isoform expressed is more efficient is a function of the conformation of the molecule that alternate splicing choses. No? Somatic recombination of BCRs and TCRs are more in line with what I think you are trying to point out.

There was no point other than an example of utility, but if that was a poor example I apologize!

@Kendall Not a poor example, just an example of regulated alternative splicing, which is something I did not address in my answer. That is probably worthy of an answer of its own if you are up for it.

Insofar organismal complexity is defined as the number of known cell types, there is a strong relationship between splicing, the repertoire of isoforms and organismal complexity.
See paper here

I personally think that you embark up a slippery slope when you try to qualify or quantify organismal complexity. It is only a veiled attempt at trying to justify ones place in an arbitrary hierarchy of living things. More important than complexity is the study of homology, as it gives us insight into processes and allows us to test hypotheses without having to rely on empiricism. If we can amass evidence by studying flies or worms or yeast that can be translated to humans, then all the better, as the costs are far lower and the time to obtain results is far less.

Also, I want to know what contribute to the need for splice variants feature.

One common function of splice variants no one mentioned is to function as a dominant negative of a longer functional full length transcript. dominant negative splice variants So it allows for additional regulation of post-transcriptional processing.
This is actually quite a common function of splice variants.
In addition, as others have mentioned, it adds complexity at a reduced cost.  Many transcription factor proteins have both transactivation domains (ability to interact with and regulate DNA transcription) and protein-protein interacting domains. With splicing variants, the organism can make different parts of that protein that are functional for only one subset of activity.


text:
Producing a genetically modified animal with cell walls
I'm curious if there has been any genetic experiments transferring cell wall producing genes into the genome of a animal model organism such as the fruit fly (Drosophila melanogaster) or a larger animal such as a mouse (Mus musculus).
If there hasn't what do you think would happen, if anything at all?
Thanks!

They already have cells with walls.

I don't know of any animals with cell walls unlise your considering something like chitin as a cell wall, which it isn't. Please provide examples if you have any. Thanks!

The short answer is it's very complicated. Plants devote a significant portion of their genomes to cell wall construction and integrating that into an animal, I imagine, would be like integrating a helicopter into a battle tank.

Unless some experiments have been made testing this (which I doubt) this question can only generate speculation.  Voting to close as primarily opinion-based.

Mammalian cells have a semi permeable membrane not a true cell wall like a plant cell. I could imagine that if the semi permeable membrane were replaced with a plant like cell wall then osmosis and other biochemical processes necessary to the organisms growth and survival could not occur correctly.


text:
Which Darwin book (and today edition) is illustrated by his own drawings?
I am interested in buying Charles Darwin books and mostly drawings (nowadays editions, I am not a collector). Please, can you advise in which book and which edition I can find the most of his drawings? I found some books as On the Origin of Species ad the Geology of The Voyage of The Beagle but I am not sure if there are his drawings too. I am a student so I couldn't spend too much money on it, but I was interested in his texts and drawings, supporting each other in one book/journal/publication. Thank you !

I believe that there is only one drawing in the first edition of On the Origin of Species, and it is Darwin's.  Any good edition such as the fascimile edition with an introduction by Ernst Mayr, will include this drawing.  I'm not sure about other editions of the Origin or other books of Darwin's.  However, maybe you don't need to buy anything.  Darwin Online is a wonderful collection that includes many (all?) of Darwin's writings over the years, including images of many of them; the drawings are no doubt included.
It's possible that the History of Science and Mathematics StackExchange site would be a better place for this question.

Very good answer +1. I did not know about History_of_Science_and_Math.SE. Darwin Online is a nice resource as well.

Thank you @Mars, I neither didn't know about History of Science... thanks for the book link and  Darwin online, I also found this resource later. Thank you again ! :)


text:
Is there a lower temperature limit, below which we cannot sense a difference in temperature?
At work I have to handle samples stored at -20 and -70 degrees Celsius, and they don't feel that different to me.

So you're handling things nearly as cold as dry ice without protection? Sounds like a bad idea.

I touched -70 accidentally, it didn't felt as cold as I had expected.

Are you referring to the difference limens in the -20oC range at normal hand temperature, or when the hand is cooled to such temperatures? One way or another, scientific studies addressing either question have probably not been carried out due to ethical considerations. Very brief touching of cold objects may be ethically OK since the skin is not under-cooled, but such experiments are for the same reason futile because they don't tell you anything.

@AliceD Normal hand temperature.

This article goes into detail about what affects thermal thresholds in human skin.  http://www.scholarpedia.org/article/Thermal_touch

I always hated opening the -80 freezer, because it felt... just incredibly cold! (With protection, but obviously not to my face over the freezer.) You just touched something shortly, probably with a short area of skin contact. With larger area of contact and longer exposure you will feel the difference. Like it is the case for hot things. But as far as reflexes go, you're supposedly already letting go/getting away before you really feel the full cold/heat.


text:
Please identify organ

This is the gut area of an Eastern Grey Kangaroo taken of a property in the Southern Highlands of NSW, Australia. The top red organ appears to be the spleen but what is the elongated tubular organ extending from the spleen? Is it a deformation or the result of disease?

You are aware that all species of kangaroo are protected?

You mean the long red "tube"? At a guess I'd say it just looks like a lobe of the spleen.

Thank you vervet for your response and thank you for clarifying the issue with AliceD. This kangaroo was taken on a cattle farm under the following provision: http://www.environment.nsw.gov.au/wildlifelicences/OccupierLicences.htm

An evidence? http://www.appendicitis.pro/the-sir-frederick-treves/sir-frederick-treves/the-dissection-drawings-of/brush-tailed-kangaroo-gi.html

As far as it can be deducted from the picture you ask about Appendix or just Coecum. This is a normal finding and not abnormal one. (You can see a terminal Ileum as well).
If other pictures were provided it could be possible to give more exact answer.

I don't know if the question is asking about this organ or the extention of the spleen. But in any case here is some information on the kangaroo "appendix": http://onlinelibrary.wiley.com/doi/10.1111/j.1420-9101.2009.01809.x/full It's perhaps more blown up than it would be in a living animal, but that's probably a post mortem change as there's still living bacteria in the GI tract producing gas.

I was under the impression that macropods did not have an appendix


text:
Why does NAD+ become reduced if it gains a hydrogen proton?
I've heard that $\ce{NAD^+}$ gains a Hydrogen proton during glycolysis and the Krebs cycle and becomes reduced to $\ce{NADH}$. However, isn't reduction when a molecule receives an electron?
Maybe I've been misinformed? Does $\ce{NADH}$ gain a Hydrogen electron, not a proton?

You are correct that reduction is simply a gain of electrons. This results in a decrease in oxidation number.
You know that NAD+ is reduced by this process because it starts off with a positive charge (+1) and ends up with a neutral charge (0).
The reducing agent that is donating the electrons is the hydrogen. More correctly, the electrons come from the hydride (H-).
The hydride is represented by 2 electrons on this redox diagram:

As you can see, the reduction reaction transfers a proton (H+) and hydride electrons (H- or 2e-) to NAD+. One electron goes to the nitrogen, and the other to the carbon where the proton binds. More details on the redox reaction of NAD can be found here.

Hydride anions do not exist in biochemical reactions.

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


text:
How do molecular recognition features work?
The occurrence of relatively short (10–70 residues), loosely structured protein regions bind within longer, largely disordered sequences that were characterized as bound to larger proteins. These regions are MoRFs. But how do these high specificity regions combined with low affinity proteins?


text:
Understanding Illumina Adapters
I am currently working on a project where I need to trim the adapters off of some single end read RNA-Seq data, and I want to know which sequences to cleave.  Illumina TruSeq adapters were used.  I have tried following Tuft's explanation and make sense of Illumina's video, but I am left with several unresolved questions.
The TruSeq Universal adapter, seems to be what binds to the flow cell and is
AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT

The TruSeq Adapter Index N is
 GATCGGAAGAGCACACGTCTGAACTCCAGTCAC-NNNNNN-ATCTCGTATGCCGTCTTCTGCTTG

My impression of how the cDNA fragment attached to the adapters is :
(flow cell)
||
||
||                                             (Index Adapter)                                               (Universal Adapter)
||    3'                                                                5'                          3'                                                        5'
||    GTTCGTCTTCTGCCGTATGCTCTA-NNNNNN-CACTGACCTCAAGTCTGCACACGAGAAGGCTAGA                           TCTAGCCTTCTCGCAGCACATCCCTTTCTCACATCTAGAGCCACCAGCGGCATAGTAA
||                                                         ||||||||||||||                           ||||||||||||||                                                              <----- Must get denatured!
||        5'   AATGATCGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT--(5' MY DNA FRAGMENT 3')--AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC‐NNNNNN‐ATCTCGTATGCCGTCTTCTGCTTG
||-------------TTACTAGCCGCTGGTGGCT                                     3'                           5'                                                                3'
||
||             ^(Flow cell oligo)              ^(Universal Adapter)                                            ^(Index Adapter)
||
||                                     TGTGAGAAAGGGATGTGCTGCGAGAAGGCTAGA                           TCTAGCCTTCTCGTGTGCAGACTTGAGGTCAGTGTG
||
||                                             ^(Read 1 Primer)                                                ^(Read 2 Primer)
||
||
||                                                                                TAGAGCATACGGCAGAAGACGAAC----------||
||
||                                                                                ^(Flow cell oligo)
||

Here are my questions :

Is this image correct in the single stranded case?
Do I have the correct primer binding site (used for the actual sequencing)?
Do I have the correct oligo for paired end reads, i.e. TAGAGCATACGGCAGAAGACGAAC---------?
Do I have the correct primer (and it's site) for the index read?

 Per Illumina, I guess I need to include this :
"Oligonucleotide sequences © 2007-2013 Illumina, Inc. All rights reserved. Derivative
works created by Illumina customers are authorized for use with Illumina instruments
and products only. All other uses are strictly prohibited."


text:
how does one apply for masters in genetics abroad?
Please can some one give me step wise instructions for applying for a masters degree in genetics or biological sciences?

This may be more on-topic in Academia SE!

I am voting to close as off-topic. The question would be on-topic in Acedemia.SE.

A bit more than a year ago I applied for a PhD position abroad in population genetics. Here are my steps: 1) Find a supervisor that a) does the kind of things I like, b) is good, c) is friendly, d) has trained people who got job in the academia. 2) Read some of his/her recent and most cited papers, 3) Evaluate the place 4) get a rough idea of what you would like to work on, 5) Contact him/her 6) If (s)he showed interest in your application, go through the formal application.

Note that it will take some time reading on the website to understand a new system. I have studied in 4 (or 5) different universities in 3 (or 4) different countries. It always take some time to get used to a new system. Your supervisor (and/or future lab mates) will be happy to help you.

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text:
How the brain is affected by Alzheimer's disease

What exactly happens to the neurones in the brain?
why can't they be repaired/restored?
Why is it that there are so called 'good days'? What happens to the brain on such days?

Essentially, there's a net dysregulation of a number of genes where the additive effect of each dysregulation causes neurotoxic amyloid plaque formations, and neurofibrillary tangles of hyperphosphorylated tau protein. Not only so, these mutations induce calcium and cytokine dysregulation, and increase oxidative stress.
Specific to molecular mechanisms of amyloid beta (abeta) oligomer toxicity, a good article here makes some good descriptions. For example, abeta can reduce copper and iron ions. Oxygen reacting with these reduced metals become reactive oxygen species. They also noted that abeta reacts with many receptors, like TLR's which ended up promoting JNK-mediated apoptosis. I'd give that article a read, and I'll try to get some molecular pathology mechanisms for other facets of AD on board here.
They can't generally be repaired because the issue is with genetic mutations, and some of the mutations engage in positive feedback loops with existing conditions that make a more pronounced effect. For example, tau protein is regulated in part by O-GlcNAcylation. This is like phosphorylation, but with sugar moieties, but it becomes downregulated when glucose is low, thus increasing phosphorylation on tau (Liu et al., 2004) . Mutations that affect GSK-3, insulin resistance and/or diabetes thus can play a role in AD pathogenesis.
Some data exists to show restoration of potentially AD-causing abnormalities involving HDACs. For example, abnormal HDAC2 in AD brains hypoacetylated promoter regions for some housekeeping and plasticity genes, and they rescued the AD phenotype by knocking down HDAC2 (Gräff et al., 2012) . These are of course mouse models typically.
As for question three, I really can't say except for stochasticity. I did a review for an undergraduate course that goes over some of the recent literature involving AD genetics/pathogenesis. It might not be professional quality but it gets the message across, linked https://drive.google.com/open?id=0BwKiapIJL9T2ajc4ajhTVVRvRWc


text:
What product of cellular respiration creates an acid when in solution with water?
What product of cellular respiration creates an acid when in solution with water?
Topic question really, haven't been able to find a direct answer.

A lot of them do, like malate, and citrate

So does carbon dioxide :)

@TanMath, the presence of organic acids like malate and citrate in central metabolism is not in itself acidifying. These species typically a produced in deprotonated forms and do not release protons. Acidification only occurs if there is a net release of protons during metabolism.

They are the cation of the acid. An acid is not just protons...

Well, they are anions, but they are conjugate bases to the acid, yes.  The point is that there is no acidification unless protons are released, and the existence of intermediates like malate and citrate does not imply proton release. Acidification is by definition release of protons.

Of course they are anions . I just gave an example there are many products from cellular respiration that can form acids in many ways and the ATP hydrolysis is not the only way a proton can be sourced. I don't know where you got that last bit from

It's not classed as an acid until the proton and the anion have interacted then it is a molecule that can be deprotonated ( an acid)

The question asks for a product of cellular respiration that creates an acid when in solution with water. Since H+ can form hydronium with water an example could be a proton or one of many anions.

@Roland sure, but it can be found as malic or citric acid, and then it would be and acid.

@TanMath There is some confusion here, maybe this deserves a question of its own ... Acidification is the lowering of pH, meaning increase of H+ concentration. That's the definition. An acid is so called because it is a compound capable of releasing H+. The conjugate base (anion) is not relevant here, besides determining pKa. Biochemical processes are only acidifying if they produce protons, or compounds that can release protons (which is really the same thing). TCA cycle produces a net of 1 H+ I think. Citrate and malate are weak bases; they do not release protons.

Cellular respiration itself, defined as the activity of the respiratory chain complexes I -- V (including ATP synthase), is not acidifying. On the contrary, free protons are captured during ATP synthesis, so cellular respiration acts to raise pH. But then ATP synthesis is always matched with ATP breakdown in reactions that utilize energy (muscle contraction, for example), and ATP breakdown liberates the captured protons again. So the complete cycle of ATP turnover is pH neutral. (For more information, see for examplle http://www.ncbi.nlm.nih.gov/pubmed/6298937)
The activity of the TCA cycle, on the other hand, produces CO$_2$ when oxidizing carbohydrates, and CO$_2$ dissolved in water is slightly acidic (pK$_a$ = 6.3) and so tends to lower pH. This is the main acidifying effect of oxidative metabolism. In animals, the CO$_2$ generated is of course released via the lungs, so the amount of CO$_2$ dissolved in body water is (more or less) constant, and therefore pH is stable.

Nice answer! :-)

CO2 is likely the answer you're looking for. This is especially true if this is in response to a 100 or 200 level biology course question. Based on the framing of the question, I would assume this is the case.
Though, as others have pointed out, there are other products that would qualify.

In tissue and cell culture I recall that after the vascular smooth muscle cell line i was working with had used up the compounds in the buffer the supernatant started to turn acidic due to presence of lactic acic.
The cells aerobicaly produce lactate which most likely converts to lactic acid with the H2O and other byproducts ( such as a H+ )present in the supernatant.
CO2 respiration can also form carbonic acid (H2CO3) with water. These are just a couple of examples.
A proton (which forms H3O+ with water) or one of many anions that could be produced by a cell or present in an aqueous  buffer, could create an acid when in solution with water.
Take into account there are many different cellular types and types of respiration.

Glycolytic metabolism is indeed overall acidifying, but the question was regarding oxidative metabolism. Also, the source of protons during glycolytic metabolism is not lactate production, but ATP hydrolysis.

Lactate is produced and the proton source is ATP hydrolysis. Two different things but the by products resulting from the processes form an  acidic solution . The H+ does come from the ATP hydrolysis but the cation of the acid does not.

I also mentioned the CO2 + H2O → H2CO3 in my answer.


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NCBI E-utility to Find Shortest Citation Path Between Two Publications
I'm trying to perform a thorough review of Hi-C and RNAi developments and have found myself looking at publication A (2011) and publication B (2015). B doesn't cite A explicitly but I'm sure there are papers linking the two and I'd like to find them. Are there existing utilities to help with this? I've used NCBI E-utilities in the past but would prefer not to rewrite an application that already exists.

I'm going to pursue Neo4j. Example usage, similar to what I'm looking for, is given here. (per a tip from the blog's author in response to my cross-posting on biostars)

AFAIK the full citation graph is locked away in proprietary databases like Google Scholar and Web of Science, writing a program would be hard. However, in Web of Science you can save the list of papers citing A, and the list of papers cited by B. Then I'm sure you can find a way to get their intersection.


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Argentine Ant Trails
What is the maximum distance for an argentine ant (Linepithema humile) trail?  I imagine that there is some point where the ants are unable to make the return trip either through exhaustion or from the chemicals of the trail failing somehow.

I don't think that the chemicals evaporating would be the limiting factor, because a trail isn't created by a single ant, it's created by many ants following the same track. Meaning as long as the trail is active the chemicals can be replenished. Offhand I would say a good indicator of the maximum length a trail gets is the amount of territory a single colony controls - but Argentine ants form supercolonies, so not only might this be hard to measure, but maybe they could share trails in which case ant exhaustion won't be a factor either. I will see if "Adventures among Ants" says something.

I was reading "Adventures among Ants", by Mark Moffett, to see if he said something about the length of the trails of Argentine ants and I was about to give up and give a general answer based on the other information about Argentine ants in the book, when I hit upon this quote by "Physicist turned biologist Jean-louis Deneubourg":

The Argentine ants' exploratory behavior is exceptional in that they mark continually and explore collectively. Whereas other recruitment trails are constructed between two points (e.g., nest and food), their exploratory trails have no known destination, progressively advancing into the unknown. They rapidly lead new explorers to the frontier between the just explored and the about to be explored zones, avoiding situations where ants will end up exploring the same zone twice, and help returning explorers reach the next directly. A wide corridor of the chemically unmarked area is thus systematically "swept' and marked in a minimum time with maximum economy.

The things to know about Argentine ants are, they form supercolonies in which all ants from the same supercolony can mingle indifferently, regardless of the nest they are from. There is no theoretical limit on the size of such a supercolony; if there is one, it is over thousands of kilometers:

The largest [Argentine ant supercolony] extends from Italy to Spain's Atlantic coast, a distance approaching 2,000 kilometers

This means that the length of an Argentine ant trail is definitely not limited by ant exhaustion or chemical evaporation, depending on what we mean by "trail". If interconnected trails can be counted as a single one you could theoretically have a 2000-km Argentine ant trail that is maintained by ants all along its length. In practice the trail lengths are probably still limited, but by their purpose instead of hard physical limitations. The Deneubourg quote says recruitment trails are built between two specific points, such as a nest and food: this example clearly implies a distance limited by nest density (the trail between a nest and food will be from the nest closest to the food, so if nests are all 10m apart the length of the trail will be 5m at most). This would be true of any trail that has a nest as an endpoint, and what other kind are there?
He also says exploratory trails have no fixed destination, but that doesn't mean they cover unlimited distance either: the exploratory front as described clearly moves forward gradually and deliberately, and as Argentine ants are constantly building nests within the territory of the colony, the exploration front will always be a certain limited distance from the nearest nest.
Then again we could also argue that nest density is itself determined by a physical limit on maximum trail length, which could indeed be ant exhaustion (or ant loss of efficiency at least), risk of the trail being perturbed, chemical evaporation (as in, a longer trail would need more ants to maintain it), etc. I can't speak to that.
Trying to find numbers on Argentine ant nest density I fell upon this paper, which gives more information about ant colony structure and gives the closest thing I think you will find to a definite answer to your question:
Nest connectivity and colony structure in unicolonial Argentine ants

In experiments using labeled food, and in a 3-year census of nests and trails, we found that food was shared and nests were linked by trails at distances up to 50 meters.

Note that this is "path distance", i.e. the length of interconnected sets of trails. I couldn't find statements on a single trail, but they show a figure and the longest trail on it is between nests that are about 12m apart.
As an aside, this very interesting paper breaks up the "supercolony" concept a bit; while supercolonies are defined by seeing which ants will attack one another, meaning you can legitimately drop an ant from one end of the colony into the other end and it will go to work unmolested as if it were home, the authors of this paper looked at actual worker movement and food sharing, and found that

Argentine ant populations do not function ecologically as single, large supercolonies, but instead as mosaics of smaller, distinct colonies consisting of groups of interacting nests.

It also says the distribution pattern of nests is seasonal (Argentine ants have very ephemeral nests to begin with); this could give some clue as to what determines nest density and whether physical limits on trail length play a role.


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Transmission of HIV from Mother-to-Child Through Breastfeeding
If a mother is HIV+ and was on medications which would help her deliver a HIV negative baby, can the baby contract the HIV through her breast milk?

Hi there and welcome to biology.S.E. Currently the question is a bit unclear. To try to move this away from being to hypothetical, what medication is the mother taking? Also note that this site shouldn't be used to seek personal medical advice.

I am not seeking personal medical advice ,i was just curious to know.Thanks for the answer

In short, yes. Breast milk can contain virions which can be transferred from Mother-to-Child.
These are the guidelines from the National Institute of Health in the United States regarding the Prevention for Mother-to-Child Transmission of HIV and how the prevent Mother-to-Child Transmission of HIV After Birth
While the guidelines in the US are geared towards the fact that we have alternatives to breast milk, the World Health Organization has compiled evidence that suggests that Antiretroviral therapies along with exclusive breastfeeding may provide the most benefit for the health of the infant. This likely has to do with the access to suitable nutritional alternatives, clean water, and vaccines in developing countries, and in fact, it appears that mothers in wealthy countries that have HIV are advised not to breastfeed at all. This site outlines the different guidelines in place. The choice between breastfeeding and not in lesser developed countries has to do with the fact that the risk from waterborne illnesses and their impact on infant mortality rates is likely far greater than the risk of HIV transmission from mother to child through breastfeeding while both are on Antiretroviral therapy. The reason that exclusive breastfeeding is recommended is that it keeps the viral concentration in breast milk lower than if the baby was suckling only part of the time.
Italics in previous paragraph indicate an edit to the answer in order to clarify the reason why breastfeeding is recommended in lesser developed countries, even though it poses a risk for HIV transmission
Please note that these guidelines are in flux and as more evidence is obtained and as the virus mutates, things may change. It is always best to consult with a physician on the most current recommendations in the care of your infant if you are HIV+.

Wow, I would never have expected a 'yes (maybe)' on this question... +1

@AliceD I think that we in the developed world forget that what works for us may be untenable for the rest of the world. The WHO guidelines are likely a lesser of two evils approach....

@AliceD Breastmilk is a really easy way to spread the virus, but part of the problem is that in many sub-Sarahan communities access to clean water is not reliable.  Thus, the option frequently becomes a choice between breastfeeding and giving your child HIV, or mixing formula with water and giving your child life-threatening illnesses.  Not good.

@Amory, my goodness, that is terrible. I never realized HIV to be transmitted orally via breastmilk.

@AliceD It's fairly efficacious too; transmission rate is somewhere around 20%, if not higher.  Only birth (25%?) and blood transfusions (90%) are higher.


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Infection of urinary tract if the pH of urine is made alkaline
It is very well known that drugs like phenobarbiton,morphine are unionized, lipid soluble.So,in case if there is toxicity due to these drugs,the only way to save the patient is make the pH of urine alkaline and thus facilitating its excretion.But,the normal pH of the urine is acidic which protects the person from various urinary tract infections,if the pH is made alkaline is there a increased for the patient to have urinary tract infections?

There is a huge misconception here.  Morphine overdose is treated with Narcan (naloxone).  Phenobarbiton overdose is treated with artificial respiration (in extreme cases), blood pressure medication, and management of low heart rate.  The concept of lowering the pH of the urine to increase a drug excretion is (to my knowledge) never used in emergency settings.  Dialysis, which filters the blood, would be used to 'clean' the blood of toxins.  Think about it.  Time is life, and changing the composition of your fluids would take a lifetime compared to the implemented measures in emergency rooms.  You body has an extremely sensitive acid-base balance.  You do not want to try to increase or decrease the pH of your bodily fluids.


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How can the number of chromosome change during evolution
I found an explanation here, which is basically saying that sometimes the centromeres are duplicated, breaking a chromosome into two halves. But how could this propagate?  I don't think inbreeding is efficient enough for this mutation to become dominant, and it should take a lot of pregnancies for the mutants and the regular ones to produce an healthy offspring. Is the explanation in the link backed by any evidence?
Thank you!
By the way, do we know how many chromosomes did the latest common ancestor of human and chimpanzee have, and when did chimpanzee gain the extra pair of chromosomes (or when did we lose it)?

We cannot have direct evidence as the DNA of common ancestors have either not been found or are degraded to a point where it cannot be analyzed. However when looking at modern genomes we can do syntenic analysis and look at the synteny between chromosomes. Whether you believe it or not, the evidence is within our genome and many other genomes. All you need for it to take hold is an isolated population that is put under selective pressure.

@arax There are two different questions in your post. A post should always be limited to one question. I suggest that you get rid of the second one. You may ask it later.

@arax Speciation due to change in chromosomal number by hybridization between two species, yielding to a third species has typically be quite nicely studied. Would such an example answer your question?

Note btw that a change in chromosomal number is often (not always) associated with a shift in the ecological niche toward more extreme environments. Why is it so? Last time I heard of it, I have been told that nobody really knows why.

Someone asked and then deleted their comment, but to clarify, "direct evidence" in my comment would be intact, sequenceable genomic DNA from a Common Ancestor. Syntenic analysis provides inferential evidence of the events of translocation that have survived in evolution, but without the ability to compare to the actual data of the common ancestor, we can only infer the events.

This article may be useful.  The author goes into several ways that chromosomal rearrangements can go wrong resulting in a change in chromosome number. http://scienceblogs.com/pharyngula/2008/04/21/basics-how-can-chromosome-numb/


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What is the effect of reduced gravity on human height?
There has been talk recently of building a base on either the Moon or Mars. What I'm wondering is, if you are born and grow to adulthood on the Moon, where the gravity is a tenth of the Earth's, would you be taller than if you had been born and grown up on Earth?

This sounds like a question about biology rather than physics.

apologies - by all means if this needs to be moved go ahead

I doubt there will be significant conceptual differences, just severe disorders, low bone density, etc. The more physical question is, how would life evolve if earth's gravity was larger/smaller... I read somewhere, that the linear dimensions would scale inversely proportional to gravity, as the bone would be able to support more or less mass. Nice question anyhow.

the height of astronauts is affected by gravity http://www.space.com/19116-astronauts-taller-space-spines.html .

As far as I am aware, no one has ever been born in space, so your answer cannot be answered directly. However, it is known that the absence of gravity results in an increase in body height by a few centimeters. This is due to stretching of the vertebral column, which is no longer being pressed together by the downward pull of gravity1. For example, the astronaut Richard Hieb, who spent 2 weeks in space, found that his height had increased by 1 inch (~2.5 centimeters)2. Loss of gravity also causes the blood and other fluids to migrate from the legs to the upper part of the body, resulting in swelling of the face and protrusion of the veins of the neck1. I assume that these effects reported at zero gravity at least partially apply to 10% gravity.
Sources
- Airbus Defence & Space
- NASA


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How do I generate a phylometric tree given species names?
I have a list of species. I want to put those names into a tool and get back a visualized tree that includes names of shared order, suborder, family and genus.
Is there an existing tool that does this job for me or do I need to program my own solution?
(The solutuion in the other thread only shows the name of the species but not order/suborder/family/genus)

Possible duplicate of Visualising a subset of the tree of life

Biopython may have a module for this. I know it can parses phyloxml files and render a tree. You can query the ncbi database for the xml files. Here is some sample code that will render an ascii tree given a phyloxml file...
from Bio import Phylo
tree = Phylo.read("examplephylo.xml", "phyloxml")
Phylo.drawascii(tree)

There is also support for drawing more graphically rich trees using matplotlib. There is a .pdf book for Biopython that you can download from this url http://biopython.org/DIST/docs/tutorial/Tutorial.pdf
Hope that helps

There is support for other file types besides phyloxml, but I can only speak for the phyloxml files, because I have used them personally.

As far as I am aware, there isn't an easy one-stop-shop solution for what you'd like to do.
My own solution for doing something similar (with the caveat that the NCBI taxonomies are not always up-to-date with the latest data) is to a) use NCBI's Common Tree page to build out the lineages you'd like to include and download it as a text tree (e.g. in Phylip format, which includes internal nodes), b) visualize the tree on a local computer using something like TreeView X or FigTree
It's a bit of a pain, but if you'd like to add additional metadata to the tree before visualizing it, you can edit the Phylip-formatted text file directly before opening it in one of the viewers.

This is easily doable in the R package 'rotl' with only three simple commands.
E.g.
library(rotl)
taxa<-tnrs_match_names(names= c("Danaus plexippus",
                       "Sylvia atricapilla",
                       "Acrocephalus arundinaceus",
                       "Anas platyrhynchos",
                       "Oncorhynchus nerka",
                       "Hirundo pyrrhonota",
                       "Progne subis"))

tree <- tol_induced_subtree(ott_ids = ott_id(taxa))

plot(tree, cex = .8, label.offset = .1, no.margin = TRUE)

Full details outlined here: http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12593/full


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QTL mapping in Drosophila
I have already googled it before but yet unsuccessful in finding the whole topic with intuition. Please help.
A guide to an associated book would be greatly valued.

First you need two, hopefully homozygous, strains that differ in some measurable quantitative trait. In worms it has been done with lifespan; in mice injected with ethanol it has been done with long-sleep and short-sleep periods. The two strains need to differ in their RFLPs. For flies there are probably lots of behavioural traits one could use.
You set up a cross, and then mate individual brothers to sisters, and keep repeating this breeding pattern for multiple generations to establish recombinant inbred lines. After 10 generations they are basically homozygous, and you take the individual lines and assay them first for the trait you are scoring, and second for the molecular markers. The results of the molecular mapping let your draw the haplotype along each chromosome, so you know which parental strain contributed which portion or each chromosome.
The results of each quantitative trait scoring let you classify each recombinant inbred line into one of the two parental phenotype classes (or if it is a multi-locus trait then you may get some intermediate lines).
With those two results you will be able to correlate the absence, or presence, of molecular markers along the chromosomes, with the quantitative trait you are studying.
If it works you will be able to narrow in on a genomic region that co-segregates with the trait. If there are multiple genes involved you may be able to assign a probability or LOD score to different regions.


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Calculating the frequency of a recessive allele in case of three segregating alleles
Is it correct to say:
A. f(A) = p; f(a) = q
B. p = f(AA) + ½ f(Aa)=$\sqrt{f(AA)}$?
Also,

For a gene locus segregating more than two alleles, the frequency of
  each allele is the frequency of its homozygote plus 1/2 the sum of the
  frequencies of all heterozygotes in which it can occur.

For example, I have this data on blood-types from a population: 42,4% type A, 8.3% type B, 1.4% type AB, 47.9% type O. Plus we know that p(A)=0.250, p(B)=0,050, p(O)=0,692.
When I try to calculate p(O) in different ways, I get p(O)= $\sqrt{0.479}$=0,692
If I calculate p(O) as:p(O)= 0.479+½*0.424+½*0,083=0,7325
 As the result, I am getting two different frequencies for p(O). What am I getting wrong here?

Welcome to Biology.SE
A few issues about your post
You should always limit your post to a single question.
Make sure to define what the function f() and p() mean.
Use points (.) instead of comas (,) for the numbers.
You should show how you made your calculations otherwise we can't tell what is right and wrong.
Your question

is $p = f(AA) + \frac1{1}{2} f(Aa)=\sqrt{f(AA)}$ correct?

$$f(AA) = p^2$$
$$f(Aa) = 2pq = 2p(1-p)$$
$$f(Aa)/2 = pq = p(1-p) = p - p^2$$
, therefore
$$f(AA) + f(Aa)/2 = p^2 + (p - p^2) = p = \sqrt{p^2} = \sqrt{f(AA)}$$
So, yes you are correct