text:
Why don't we feel hungry after waking up?
Yesterday, I was fasting (drinking only water until I had dinner at 9 pm). After dinner, I went back to my lab (I am a Master's student) and worked till 1:30 AM. By 1 o' clock, I was feeling quite hungry, probably because I hadn't eaten anything all day and only had a light meal for dinner. However, I didn't eat anything then and just slept. Today morning I wake up (around 9 AM) and I don't feel hungry! I could surely eat something if I wanted, but I am not feeling the acute hunger that I was feeling last night!
More generally, what could be the reason for the behavior that a human experiences acute hunger, but after sleeping for an extended period of time, he/she may no longer have the hunger. Since a passage of time has passed, one would expect the hunger to increase, which would have certainly happened if the person had not slept. Is it the case that sleeping somehow affects the overall hunger/glucose demands of the body?
I suspect that it is possible that the body's food needs could be majorly affected by the circadian clock, but I wanted an explanation to contrast the situation when one is not hungry and when one is very hungry before sleep. How can the difference between both the situations be easily trumped by the circadian rhythm's effect? (if it is the explanation!)

Do u think its normal to feel hungry when we wake up?

@JM97, no its not. but the interesting question then is, that it means that the hunger situation of the body before sleeping seems to have no bearing on the hunger situation post sleeping. This I feel would warrant an explanation

@another'Homosapien', I have edited the question to make it more specific and non-personal (and interesting, i think!). Could you have a look?

@JM97, I have tried to do now. Feel free to edit to improve it

Yeah, rewording seems to have made it better. I have voted to reopen this (in fact, I voted to close as I thought I would have chance to retract my vote by the time you edit it, but this was too fast :P). And, I can answer this as soon as the question opens again :)

My suggestion is to perform this ritual repeatedly and record your hunger levels several times. This might give you a better picture, and might help us make a clearer analysis

I will try to keep the answer as simple as possible, but feel free to point out if I make this too simple.
Well, you are not alone with this observation. This is quite a common, but rather complex, phenomenon which controls our apetite and causes us to not feel hungry after waking up.
The feeling of being hungry is under constant regulation by two antagonistic (having opposite effects) hormones:

leptin, released from adipose tissue, decreases our apetite and suppresses our hunger
ghrelin, released from stomach, does just the opoosite i.e. increases our hunger.

And guess what, these hormones are controlled through the circadian cycle. When you sleep, your body produces more leptin and stops the production of ghrelin. Why? The answer is quite obvious: because you're sleeping. While sleeping, your metabolism is lowered because your body needs to repair the damaged cells and tissues. To control metabolism, we need to control our apetite, and to control our apetite, we need to suppress our hunger. So...? When you wake up, you still have a hangover of this effect. In other words, it takes some time to change the secretion rates of leptin and ghrelin and the resulting effects.
Lets get into some analytical details now. According to Sharma et al, 2010, metabolic rate and brain temperature are lowered during non-REM sleep to deal with the damages that may have occured during time of wakefulness. In their study, the subjects were deprived of sleep for 2 nights (4 hours per night) and then allowed to sleep for next 2 nights (10 hours per night). The result? Leptin levels decreased by 18% and ghrelin levels increased by 28%. The subjects also craved for more carbs. Also, craving for salty foods increased by 45%. Overall hunger increased by 23% due to reduction in leptin levels. They also showed that people who sleep less than 5 hours have increased Body Mass Index (BMI). All this points to the fact that sleep does cause reduction in apetite and hunger. In short, don't think of missing your breakfast.
References:

Sharma, Sunil; Kavuru, Mani (2 August 2010). "Sleep and Metabolism: Overview". International Journal of Endocrinology. 2010: 1–12. doi:10.1155/2010/270832.
Wikipedia contributors. "Sleep and metabolism." Wikipedia, The Free Encyclopedia. Wikipedia, The Free Encyclopedia, 8 Feb. 2017. Web. 26 May. 2017.

so if you're hungry and you can't eat, just sleep! BTW, you can't suppress hunger by sleep for long, right?

Yeah, when the body really needs energy, it will cause you to wake up. Also, IMO normal sleep duration is not enough to deplete body's food reserves. "If you're hungry and you can't eat..." I must say I didn't get that :/

i meant that if you are hungry and have nothing to eat, you can just sleep as it would reduce the hunger. is this right?

Seems you used (kinda) improper words here. I'd say if you are hungry and have nothing to eat, you can just sleep as it would 'delay' your hunger for some time. ;)

yes, fair enough

of course! just want to give it a couple days before accepting, for obvious reasons


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Why do Kupffer cells not attack malarial sporozoites?
During malaria, why don't Kupffer cells (hepatic macrophages) attack  the Plasmodium sporozoites and stop schizogony, thus saving us from the disease?

I assume the parasite has developed some coating to prevent Kupffer cell uptake, but I don't know what. Of course, once it enters a blood cell, Kupffer cells uptake won't be an issue anymore. This might be interesting to look at in more detail, people doing nanoparticle research are also interested in making particles avoid Kupffer cell uptake while getting hepatocyte uptake.

I know only tardigrade is only being capable of creating bio-glass coating to prevent itself being dessicated.I didn't know sporozoite having same capability.

Indeed the process is even more interesting than thought: sporozoites actively attack Kupffer cells and let themselves get eaten! In a 2001 research, Pradel et al found that sporozoites pass through a layer of Kupffer cells in order to enter hepatocytes for the next stage of their life cycle. They observed that in rat liver cells, Plasmodium berghei and Plasmodium yoelii sporozoites attach to and enter the Kupffer cells, but not the sinusoidal endothelia. During experiment, the number of intracellular sporozoites kept increasing for upto 12 hours, unlike hepatocytes and other non-phagocytic cells which were invaded in vitro for only the first hour of parasite exposure. The sporozoites entered the Kupffer cells via endocytosis in specialized vesicles which did not interact with lysosomal markers. From Kupffer cells, sporozoites traversed to hepatocytes where they developed into exoerythrocytic schizonts. In another 2015 research, Cha et al concluded that the sporozoites interact with CD68 receptor on the surface of Kupffer cells for endocytosis. In short, sporozoites literally pass through Kupffer cells without letting Kupffer cells doing any harm to them. See this diagram for illustration:

EDIT: What happens in Kupffer cells during traversal of sporozoites remains unkown to some extent. However, Frevert et al, 2008 has shown that sporozoites render Kupffer cells insensitive to pro-inflammatory stimuli and force them towards apoptosis (aka programmed cell death or "cell suicide"). This happens as sporozoite-exposed Kupffer cells are stimulated by lipopolysaccharide or IFN-$\gamma$, causing down-modulation of TNF-$\alpha$, IL-6 and MCP-1 and upregulation of IL-10. Nuclear factor NF-$\kappa$B is also activated, which causes apoptosis in Kupffer cells (Punsawad et al, 2014). However, if Kupffer cells are activated, in particular by immunization caused due to high antivody levels, they may phagocytoze the sporozoites and thus prevent their traversal (Krzych et al, 2015).
References:

Pradel, G. and Frevert, U. (2001), Malaria sporozoites actively enter and pass through rat Kupffer cells prior to hepatocyte invasion. Hepatology, 33: 1154–1165. doi:10.1053/jhep.2001.24237
Cha, S.-J., et al. CD68 acts as a major gateway for malaria sporozoite liver infection. J. Exp. Med., July 2015 DOI: 10.1084/jem.20110575
Klotz C, Frevert U. Plasmodium yoelii sporozoites modulate cytokine profile and induce apoptosis in murine Kupffer cells. International journal for parasitology. 2008;38(14):1639-1650. doi:10.1016/j.ijpara.2008.05.018
Viriyavejakul P, Khachonsaksumet V, Punsawad C. Liver changes in severe Plasmodium falciparum malaria: histopathology, apoptosis and nuclear factor kappa B expression. Malaria Journal. 2014;13:106. doi:10.1186/1475-2875-13-106.
Frevert U, Krzych U. Plasmodium cellular effector mechanisms and the hepatic microenvironment. Frontiers in Microbiology. 2015;6:482. doi:10.3389/fmicb.2015.00482.

Does the Kuppfer Cells get affected while letting sporozoites pass through them?  @another 'Homo Sapien'

Does the Kupffer cells get affected while letting the sporozoites pass through them?

@swastik I've that part in the answer. If you have any further queries, please ask them here or add them in your question with an "EDIT" :)

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Do acetic acid bacteria use the electron transport chain when converting ethanol to acetic acid?
Do acetic bacteria use the electron transport chain when converting ethanol to acetic acid?
And is wikipedia inconsistent here in its definition of fermentation. It says fermentation

Fermentation takes place when the electron transport chain is unusable

(and this is consistent with (academic) microbiology books searchable on google books).
Wikipedia defines acetic acid bacteria as

produce acetic acid during fermentation.

also

Some genera, such as Acetobacter, can oxidize ethanol to carbon dioxide and water using Krebs cycle enzymes. Other genera, such as Gluconobacter, do not oxidize ethanol, as they do not have a full set of Krebs cycle enzymes.

I read in microbiology books on google books, that acetic acid bacteria use oxygen as the terminal electron acceptor, and have a respiratory mechanism.
Brewing Microbiology edited by Fergus Priest p165

Acetobactor spp. possess a respiratory mechanism...Acetobactor spp. are obligately aerobic with a respiratory metabolism (O2 as the terminal electron acceptor)

So is wikipedia wrong to describe acetic acid bacteria as using fermentation?
I see mention of krebs cycle though, which I understand to be associated with respiration rather than fermentation. Also in this reaction/process :
$C_2H_6O\hspace{1mm}(ethanol) + O_2 \rightarrow C_2H_4O_2\hspace{1mm}(acetic\hspace{1mm}acid) + H_2O$
I see water mentioned but not carbon dioxide(if it had both I'd say that really looks like respiration, though it's being called oxidative fermentation).  So I still can't really see whether it's respiration or fermentation, though it's being called fermentation (oxidative fermentation), yet there is the mention of krebs cycle enzymes (krebs cycle being associated with respiration), so it makes me unsure whether the electron transport chain is used or not.

also aside from ethanol->acetic acid,  apparently they might also do glucose straight to acetic acid, skipping ethanol.. not sure whether that uses the ETC or not.  the additional part to this question is related http://web.archive.org/web/20170312205200/http://chemistry.stackexchange.com/questions/69388/in-the-production-of-vinegar-where-does-water-come-from/

Yes
I find it somewhat ironic that in a response a recent post from the poster concerning itself with the precise definition of ‘fermentation’ I argued that this was a semantic question because of the use of the term in the English language before any biochemistry was known. I now discover that the term is used in an even looser sense than I was aware of — in an aerobic context. The conversion of ethanol to acetic acid by acetic acid bacteria is apparently referred to as oxidative fermentation as explained in this extract from a paper in The Journal of Bacteriology:

Acetic acid bacteria are obligate aerobes that belong to the α-Proteobacteria and have a strong ability to oxidize ethanol, sugar alcohols, and sugars into their corresponding organic acids. Such oxidation reactions are traditionally called oxidative fermentation, since they involve incomplete oxidation of these compounds. These bacteria accumulate the corresponding incomplete oxidation products in large quantities in their surrounding environment.

The biochemistry is summarized by Gómez-Manzo et al.:

Ethanol fermentation by acetic acid bacteria is carried out by two sequential reactions catalyzed by pyrroloquinolinequinone (PQQ)-dependent alcohol dehydrogenase enzymes (ADH) and aldehyde dehydrogenase (ALDH), which are located in the cytoplasmic membrane [6] and transfer electrons to ubiquinone Q10 [7]. PQQ-ADH is a periplasmic quinohemoprotein-cytochrome c complex and catalyzes the first step of ethanol oxidation by transferring electrons to Q10 and producing acetaldehyde which usually is the substrate for another enzyme (ALDH), and converted to acetic acid during the second step of ethanol fermentation.

The fact that the reduced pyrroloquinolinequinone is re-oxidised by ubiquinone, indicates that the conversion of ethanol to acetic acid requires the electron transport chain in the bacterial membrane to continue, and that the ultimate electron acceptor is oxygen.

I do not know about the prokaryotic mechanism for ethanol metabolism. However, in eukaryotes, the metabolism of ethanol does indeed eventually show an effect in the ETC.
When ethanol is metabolised in eukaryotes, alcohol dehydrogenase will remove a proton with the help of NAD+ to create acetate and NADH. Of course, NADH is used within the ETC. So basically, the metabolism of ethanol serves as one of many ways a cell can balance its redox potential.
Some organisms fermentative pathways are inhibited by the presence of oxygen, and some are not. I can not tell you with certainty whether or not this is the case for you in particular. But, I would define a fermentative process as, a process which does not result in the complete oxidation of a carbon-substrate.

Apparently bacteria are related to mitochondria. And some bacteria have an ETC in their cell membrane, rather like all mitochondria have an ETC in their membrane.

This is true! But, my point still stands. The ETC would work to provide a means to convert the NADH produced from ethanol oxidation, back to NAD+, provided that there is an electron acceptor present.

Ah thank you for clarifying my answer @tomd. The acetaldehyde step slipped my mind. But also, in regards to yeast, they are capable of both ethanol production, and ethanol metabolism - so ADH will work in both directions.

It appears that the 'main' acetic acid bacteria — Acetobactor sp — do not use NAD to oxidize the ethanol to acetic acid, but pyrroloquinolinequinone. The situation is not the same is in mammalian liver. (See my answer.)

@xusr Yes this had already been noted, nearly 7 months ago.. thanks

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What flower is this blue flower?
What flower is this?  All help would be appreciated

Could you add further information as to e.g. where you found it?

Was it spray-painted blue? Do you have a picture of the whole plant? Thanks!

Do you have an image which shows the whole flower (ideally with some leafs)?

Species identification questions are on topic as long as sufficient details are provided. This question does not have enough details.

Without more detail about the whole plant (including leaves), where it came from, and about whether or not it was spray-painted, watered with dyed water, etc. it would be difficult to ID.
It seems to be in the Asteraceae family, and in the pompon class, as seen in these vender's pictures. (Disclosure: I have no affiliation with the company.)
http://www.fiftyflowers.com/product/Blue-Cushion-Bulk-Flower_10.htm
http://www.fiftyflowers.com/product/Blue-Cremon-Bulk-Flowers_24307.htm
http://www.fiftyflowers.com/product/Electric-Blue-Flowers_10.htm
It is most similar to a blue chrysanthemum.

http://john-hallett.co.uk/2013/04/04/blue-crysanthemum/

Sources:

as listed above for images
http://en.wikipedia.org/wiki/Chrysanthemum (pink image)
http://www.mums.org/chrysanthemum-classes/


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Evolutionary selection pressure for human hair patterns?
Are there hypotheses or conjectures that postulate any selection pressures or benefits that account for the patterns of non-pubic human hair?  Particularly:

Humans do not grow notable (i.e., non-vellus) body hair until puberty.
Terminal body hair growth in adults is not only sexually dimorphic but also peculiar in its patterning:

Source
As with any trait: it is quite possible that the evolution of human hair patterns had no selective significance.  It could also have been the result of a sexually-selective feedback loop, and therefore are an arbitrary sex trait.
I am looking for hypotheses or conjectures that suggest some objective benefit to terminal body hair.  I struggle to imagine one particularly because of the sexual dimorphism in adult hair patterns:  E.g., if facial hair provides some benefit to men, why would it not provide the same one to women?
If we stipulate that the pattern is only fully expressed in males then it is still peculiar: For example, I can't see any functional characteristic that would make hair on the front torso beneficial while not conferring a benefit if present on the shoulders or top of the torso.

At least some of it is a side effect of the way human skin develops. Humans actually have the same number and density of hair follicles as great apes, it is merely that our hair develops as short vellum hair rather than the thicker, longer hair of great apes. This is a side effect of the same genes that control eccrine sweat gland development, turning on the genes causes the skin to develop more sweat glands at the cost of reducing hair thickness across the body. For humans, a primarily tropical species, having sweat glands was evolutionarily more useful than being hairy, so we largely traded hair for sweat glands. As a result, the distribution of hair across our bodied may be at least in part a side effect of where it would be most useful to have sweat glands. Hair is typically retained in the armpits and groin because it helps trap odors that may elicit sexual signalling.
Hormones may also play a role. Testosterone has been linked to changes in hair development, and may actually be related to male-pattern baldness.

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Location of t tubule in muscle
Why do mammalian skeletal muscles have t-tubules at the junction of the anisotropic and isotropic band, whereas non-mammalian muscles and cardiac muscles have it at Z-line? What could have been the functional significance?
If skeletal muscle would have it at the Z-line then I think it would have been more effective in contraction of muscle fibre. So which arrangement is more efficient?
Also, why is a common arrangement (the more efficient one) not seen in all those muscle types?

Interesting question. Indeed it is related to the working of cardiac muscles. First of all, lets have a look at the structure of a sarcomere of a cardiac muscle from here:

Here, what we can see is that the t-tubule is a depression formed in myocyte. It is important to know this fact here. Why? See this:

In contrast to skeletal muscle, cardiac muscle requires extracellular calcium ions for contraction to occur. Like skeletal muscle, the initiation and upshoot of the action potential in ventricular cardiomyocytes is derived from the entry of sodium ions across the sarcolemma in a regenerative process. However, an inward flux of extracellular calcium ions through L-type calcium channels sustains the depolarization of cardiac muscle cells for a longer duration. The reason for the calcium dependence is due to the mechanism of calcium-induced calcium release (CICR) from the sarcoplasmic reticulum that must occur during normal excitation-contraction (EC) coupling to cause contraction.

First, cardiac muscles don't work by external action potentials, they work on a cycle governed by themselves, known as the cardiac cell cycle.

Second, as is clear from above paragraph, these cells depend on extracellular Ca2+ ions for initiating contraction, a clear difference from skeletal muscles which need Ca2+ stored in SR. Hence, they require t-tubule at a place where a sarcomere ends. Obviously, having a depression in the middle of a sarcomere (i.e. between I- and A-band) would not work here.
Also, the structure of t-tubules is also different between the two. Compare my first image with the image below from here:

In the second one (from skeletal muscle), t-tubule seems like a mere little pit covering the muscle cell in 360° like a duct tape. In the first image, the t-tubule is more like a double wall dividing 2 sarcomeres. It is so because in skeletal muscles, t-tubules have to just transfer the action potential to SR while in cardiac muscle, they have to transfer calcium ions into the cell. So, at the end, the difference is not in efficiency, but in function.
If we look at non-mammalian muscles, then the cause of presence of t-tubules at z-lines couls be associated with presence of large amount of sarcoplasmic reticulum at z-lines. See this article:

Electron microscopic examination of developing myofibrils in regenerating skeletal muscle of Rana pipiens tadpole tails reveals that SR is in regular and close association with Z-lines of young sarcomeres before t-tubules have formed alongside the myofibrils. SR is also associated with M-lines of young sarcomeres but on a less regular basis than with Z-lines...This suggests the formation of a specific bond between SR and Z- and M-lines...These observations support the conclusion that SR does not initiate formation of Z-line precursor elements, but rather associates with Z-lines as they condense from more diffuse Z-bodies.

Since SR is thought to be bonded with z-lines during their formation from z-bodies, hence large amount of SR should be present at the site of association. Hence, it might be beneficial for t-tubules to be present at z-lines to efficiently transfer action potential to SR. However, such association might be absent in mammalian muscles, which can partly answer your next question.
EDIT 1: As you asked in comments
what it would have been if duct like to tubules of skeletal muscle would were present at z line instead of a-i junction?
Now we head towards evolution aspect. Yes, it might have been more effective for skeletal muscles to have t-tubules at z-line instead of A-I junction, but it would not be effective enough to create an evolutionary pressure. Both of these could have same effectiveness too, but during the course of evolution, only those traits which have much greater and direct benefit to an organism's survival and fitness are selected. There is no specific answer for 'why we have 5 fingers instead of 6 or 4', the answer is just that there is no such benefit in having 6 or 4 fingers which would cause it to be selected against 5 fingers.
EDIT 2: Obviously, its exact cause can never be known, but following might also be partly helpful. In mammalian muscles, close communication between SR and mitochondria has been observed. Such so- called "through-space" communication is an important feedback system for effiecient muscle functioning. See this article:

the SR and mitochondrial function in muscle are not independent as calcium uptake into the mitochondria increases ATP production by stimulating oxidative phosphorylation and mitochondrial ATP production and production/detoxification of ROS/RNS, in turn modulates SR calcium release and reuptake...The resultant anchoring of mitochondria to the Calcium Release Units provides a structural basis for maintaining bi-directional SR-mitochondrial “through-space” communication during vigorous contraction.

Now, for such critical communication, SR, t-tubule and mitochondrion need to be as close as possible for fastest & direct communication. Hence, SR & t-tubules need to be as near mitochondrion as possible.

Ogata and Yamasaki used electron microscopy to provide the first detailed description of mitochondrial localization in adult mammalian skeletal muscle (Ogata and Yamasaki, 1985). These studies revealed that mitochondria are located within the I-band, adjacent to the CRU on either side of the Z-line. Precise localization of mitochondria adjacent to the CRU at the A-I band junction was subsequently confirmed in non-fixed rat skeletal and cardiac muscle (Vendelin et al., 2005). Juxtapositioning of mitochondria adjacent to sites of Ca2+ release that occur during EC coupling provides a structural basis for potential local or privileged communication between these two organelles (Rossi et al., 2009).

Thus, presence of mitochondrion at A-I junction and of a "through-space" communication also tend to answer this question.

Yes, I do understand that tubules are different, but what it would have been if duct like to tubules of skeletal muscle would were present at z line instead of a-i junction? Wouldn't that be more effective in contracting two adjacent sarcomeres simultaneously? So why not that configuration?

Why only a-i junction? What's the speciality in that?


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Which frequency of UV light damages DNA?
I have read that UV light can damage pure DNA (DNA that has been extracted and purified). Is there a particular frequency threshold where this damage occurs or is it more of a gradient where the high frequency, the more damage. I want to understand how much damage light can do at what frequencies.

Not only pure DNA, UV radiations are one of the main causes of skin cancer because they damage cellular DNA in skin cells. Talking about frequency range, two different types of UV radiations damage DNA in two different ways:

UV-A radiation damages DNA in indirect ways. UV-A radiation easily generates free radicals, such as hydroxyl and oxygen radicals, which in trun cause the main damage1. The damage caused by such radicals is mostly single-stranded breaks in DNA. In fact, it has only recently been established that UV-A radiations do damage DNA, while these were originally considered as not (or less) harmful2. UV-A also has immunosuppressize effects on the entire body and is also mutagenic for keratinocytes in skin.
Wavelength range: 315 - 400 nm
Effect: source
UV-B radiation is in fact what causes most damages and deadliest damages to DNA. UV-B radiation directly attacks DNA, it excites atoms of adjacent thymine molecules, which in turn form covalent bonds with each other and lead to formation of thymine dimers. These dimers, because of being bonded side-by-side instead of being bonded to opposite strand base, form a bulge which interrupts structure and function of DNA. Such dimers are removed by a process known as nucleotide excision repair, which involved about 30 diffeeent proteins3, meaning UV-B is more harmful for the body than UV-A. UV-B also causes double-stranded breaks in DNA, which are a major problem for DNA replication and a threat for cell's survival.
Wavelength range: 280 - 315 nm
Effect: source
Other effects of UV radiation on the body include damage to collagen fibers and vitamin-A in the body and accelerated ageing effects 4. Apart from this, UV radiations, because of harmful effects on DNA, are used for sterilization as they destroy microbes' DNA and thus prevent them from replication.
Wavelength range: 10 - 400 nm (complete UV spectrum)

References:

Svobodová AR, Galandáková A, Sianská J, et al. (January 2012). "DNA damage after acute exposure of mice skin to physiological doses of UVB and UVA light"
Halliday GM, Byrne SN, Damian DL (December 2011). "Ultraviolet A radiation: its role in immunosuppression and carcinogenesis"
Bernstein C, Bernstein H, Payne CM, Garewal H (June 2002). "DNA repair/pro-apoptotic dual-role proteins in five major DNA repair pathways: fail-safe protection against carcinogenesis"
Torma, H; Berne, B; Vahlquist, A (1988). "UV irradiation and topical vitamin A modulate retinol esterification in hairless mouse epidermis"


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How do bile salts affect lipase activity?
BACKGROUND: It is well known that bile salts are needed for emulsification of fats. It is then said that this increases the surface area for activity of pancreatic lipase, implying that bile salts make pancreatic lipase more effective. But it is also said that pancreatic lipase do need a colipase to overcome the inhibitory effect from bile salts.

QUESTION: So what does bile salts actually do? Do they increase or decrease lipase activity? How does colipase overcome it?

MY ATTEMPT: After some research , I found that bile salts above critical micelle concentration have inhibitory effect, but could not still comprehend how does the colipase makes lipase more efficient. Also if greater concentration is inhibitory then why does our body just secrete it in sufficient amounts? Isn't it be more efficient than to make a whole protein(colipase)?

Let us first clear out some basic concepts regarding lipase, colipase and bile salts. The pancreatic lipase has an optimum pH range of about pH 8.0 (Worthington). This can be understood easily by Le Chatelier's principle: as the reaction moves forward, there is reduction of pH (due to formation of fatty acids). So, a basic pH would help the reaction in moving forward. See this diagram (Worthington):

It can also be understood on the basis of lipase's optimum pH, which lies between pH 8-9. See the graph (orange line) (Chegg):

This optimum pH is brought about by bile salts. Bile salts are slightly alkaline, with pH range of about 7-8 (Britannica). This helps lipase in catalysing its reaction. Bile salts also help lipase by increasing the surface area of fat droplets. Bile molecules have a hydrophobic and hydrophilic part. The hydrophobic part is attracted towards fat while the hydrophilic part is attracted towards water. This helps stabilize fat droplets by emulsification i.e. breaking the fat droplet(s) into smaller parts. This also increases the surface area of fat droplets.
Now, the matter gets complicated when we talk about concentration. Since bile molecules contain hydrophilic and hydrophobic ends, they tend to form micelles with increasing concentration (just like soap). As long as its concentration is below critical micelle concentration, it will carry on emulsification and increase lipase activity. But when its concentration becomes more than the critical micelle concentration, it will form micelles and not carry on emulsion. This significantly reduces lipase activity by not only decreasing surface area, but also reducing pH to slightly acidic (Erlanson et al, 1973). This is where colipase helps. Colipase binds to the C-terminal, non-catalytic domain of lipase and stabilizes its active conformation and increases the hydrophobicity binding site (Verger et al, 1999). Colipase strongly binds to the ester bond of the triglyceride molecule, by which its hydrolysis by lipase becomes easy (Mansbach, 2011). Thus, colipase helps in overcoming the inhibitory effect or bile salts on lipase.

Thanks. Why don't our body secrete bile salts in less than CMC. Won't that be more energy efficient than making a protein( in this case colipase)?

It might be due to lack of regulation. All mechanisms I know about (CCK, secretin, enterohepatic circulation) only act as positive feedback loops. Also, gallbladder performs the job of concentrating bile, which doesn't seem to have any strong regulative mechanism either.

The optimal pH of lipase probably has more to do with general acid/base catalysis than Le Chatelier.

@canadianer I just used Le Chatelier to give an idea of effect of pH on lipase. I'll check that point out too. Thanks for suggesting :)

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text:
Do all organs of our body secrete hormones?
My teacher says that all organs of our body secrete some kind of hormone so they are all glands.
Is the statement entirely correct without any exceptions?
Till date I am unable to find any exception for that statement.
Could anybody provide an exception if any present?

Oesophagus is one such e.g that comes to mind

Oesophagus contain adipose tissue which secretes hormones like leptin, adiponectin and resisting.

How do you define an organ? Paracrine signalling factors are not considered hormones. If you consider interferons and chemokines as hormones, then cells that secrete these are found almost everywhere.

Good question! The major and most common endocrine glands in the human body include pituitary, thyroid, parathyroid, thymus, adrenal, pancreas, gonads and pineal gland, along with neuroendocrinol glands like hypothalamus. Some other, not-so-common, examples include heart (Anti-Natriuretic Factor), GI tract organs (gastrin, secretin, etc.), placenta (estrogen, progesterone, etc.), kidneys (erythropoietin, renin), skin (cholecalciferol) and adipose tissue (leptin)1. Even the lungs are known to secrete calcitonin2.
In spite of this, I can think of quite a few examples of organs which do not act as endocrine glands. That is because there is a difference between the organs secreting hormones and endocrine glands. The definition of endocrine glands is as follows1, 5, 6, 7, 8:

Endocrine glands are glands of the endocrine system that secrete their products, hormones, directly into the blood rather than through a duct.

So, if these organs don't directly secrete the hormones into the bloodstream, then they are not endocrine glands. Leading this way, emotional tears are known to consist of hormones such as prolactin, ACTH and leucine-enkephalin3, 4. Thus, though eyes do secrete hormones, they are not endocrine glands. Also, not sure about this, but lungs still do not seem to fit in the category of endocrine glands.
In short, all the organs of the body might secreted hormones, but they all cannot be considered as endocrine glands.
References:

Endocrine gland - Wikipedia
[Hormone expression and opioid receptors in fetal and adult lung]
Gómez-Román JJ, Cifrián Martínez JM, Fernández Rozas S, Fernando Val-Bernal J.
Frey W. H., DeSota-Johnson D., Hoffman C., McCall J. T. (1981). Effect of stimulus on the chemical composition of human tears. Am. J. Ophthalmol. 92 559–567. 10.1016/0002-9394(81)90651-6
What biological functions does crying serve? - Biology Stack Exchange

Mesentery too contains adipocytes implying that these adipocytes too secrete leptin and other hormones, thanks for efforts.

It would be much better to add definition from a authority holding site, Wikipedia page there does not cite any source either.


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experimental procedure regarding AceCS1 overexpression
I'm new to biology and was just as to curious on how one can experimentally prove/disprove that AceCS1 overexpression in mammalian cells would yield enhanced rates of fatty acid synthesis through acetate.
Thanks.


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What puts a lower bound on the size of warm-blooded animals?
The smallest known vertebrates are frogs that range down to 0.01 grams.  I would take that as evidence that at smaller sizes an endoskeleton is more of a liability than an asset.
1-2 grams is a lower limit of what has evolved across all phyla of warm-blooded animals.  Are there physical reasons that this would be the case?
One I can imagine is that any smaller and the surface-area/volume ratio makes it too expensive to regulate body temperature, but that's just a broad guess.

This is a guess, not a proper, sourced answer, but my bet is that below ~2 grams is where a warm-blooded organism has so much body surface area relative to internal volume that it can't eat quickly enough to make up for body heat loss. It's why shrews eat several times their body mass daily.

@KEY_ABRADE so that would be a sort of surface/volume constraint, but on digestive-system processing capacity rather than heat regulation.  Sounds plausible, given that (AFAIK) hummingbirds consume almost pure sugar, which I assume is the most efficient/concentrated means of getting bio-available energy.

Is there any reason to believe that the current smallest known vertebrates actually represent the lower bounds? We know that the current upper bounds are not the largest ever (for terrestrial mammals at keast).


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Can (or have) antiviral drugs created drug-resistant viruses?
Evolution/emergence of antibiotic-resistance in bacteria is a known effect of extensive use of pharmaceutical antibiotics.
Pharmaceutical antivirals have come into extensive use in recent decades – e.g., Tamiflu for influenza; Harvoni for hepatitis C; Valtrex for herpes.  Some are even prescribed as ongoing "suppressants."
Has anything analogous to antibiotic resistance (i.e., antiviral resistance) been observed in viruses treated with pharmaceutical antivirals?  If not, are there theoretical reasons this would be unlikely (or impossible) to occur?

Resistance to antiviral therapy is a problem in the treatment of many viral illnesses.
Influenza is particularly significant given the epidemiological characteristics of the disease. This Nature Medicine article gives a good overview of oseltamivir resistant pandemic H1N1, which is a useful example, since our assumption that resistant virus would not spread very effectively was (probably predictably) not valid.
HIV is an excellent case study as well, since antiretroviral resistance is such an important issue in the treatment of that particular infection, and demonstrates the challenges of outwitting a pathogen with such a high error rate. This became apparent quite soon after introduction of (initially successful) monotherapy with AZT. In fact, preventing the emergence of resistant virus within the population of virus in a given patient is typically the primary consideration in choosing a drug regimen.
With regard to the other examples of antiviral treatment you mentioned, HCV resistance is well reviewed here. HSV resistance is reviewed here. Resistance has been observed in both examples, though it is more often considered in the normal course of treatment for HCV than HSV. I'd note that Harvoni, which you mentioned, is a combination therapy (ledipasvir-sofosbuvir). Combination therapy is one common strategy for preventing the emergence of resistance


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Which side of the DNA helix is used for describing SNPs?
In genetic research I often come across references to single-nucleotide polymorphisms (SNPs).  An example is rs3184504(C;T).  As far as I understand it: In this case rs3184504 refers to a specific point in the DNA genome, and (because this one occurs in a non-sex human chromosome) it indicates the nucleotides at that point in each copy of that chromosome.
But how does one determine which strand of the DNA helix it references?  Is there a convention?  Or is the strand indicated in the SNP reference (in this case rs3184504)?
If one strand is C;T then the opposing strand will be G;A ... but in the context of the gene in question I assume it matters which strand is referenced in the SNP.  E.g., if the code following this SNP on the chromosome in which rs3184504 has C is:
CTCGA...
GAGCT...

this is a different genotype from the SNP indicating a C on the other strand:
GTCGA...
CAGCT...

So the SNP description is only meaningful if it also indicates the strand, right?  If so, how does the SNP descriptor do that?

@WYSIWYG is correct, but in view of the brevity of his answer (and a second answer contradicting him) I provide chapter and verse.
The definition of RefSNP reference number is given by NCBI as:

“A reference SNP ID number, or “rs” ID, is an identification tag
  assigned by NCBI to a group (or cluster) of SNPs that map to an
  identical location.”

It is important to realize that this number bears no relationship to the numbering of the DNA sequence:

“The rs ID number, or rs tag, is assigned after submission.”

To find information about the position of an SNP from its rs number one can search the NCBI dbSNP. In the case of rs1384504 the first few lines of the first entry in the search results is:
Variant type:   SNV
Alleles:        T>A,C,G
Chromosome:     12:111446804 (GRCh38)

This indicates that the SNP is at position 111446804 on Chromosome 12, which has a T in the reference genome, and this lies in a gene designated SH2B3. (You can find this from the links on this page.)
It can be seen on this page that the orientation of this gene happens to coincide with that of the reference chromosome. However a nearby gene, PPP1CC, is in the opposite orientation and contains a SNP rs367543175 C/T. The start of the entry for this is
Variant type:   SNV
Alleles:        C>T
Chromosome:     12:110720185 (GRCh38)

…indicating that the SNP is at position 110720185 on Chromosome 12, which has a C in the reference genome, i.e. on the anti-sense strand of this gene.

And, of course, most human SNPs lie outside genes, so the concept of sense and anti-sense strand does not apply.
Conclusion
To find out whether the reference base in a designation for a SNP lying in the coding region of gene corresponds to the sense or anti-sense strand of that gene, one has to access the documentation for that SNP. This information is not embodied in the allele data appended to the reference SNP ID number.

It is described with respect to the reference sequence. See the VCF format description.

DNA has a "sense" strand and an antisense strand. The sense strand for that gene is the one you care about when discussing SNPs in that gene, because its the one being transcribed (and, as a result, the one affecting the organism). For more information about sense and antisense strands, there are some pretty good explanatory youtube videos and Wikipedia entries.

Whether or not you are interested in the sense strand of a gene (and most SNPs fall outside genes) the allele variation in an RefSNP reference number, about which the poster asks, does not necessarily relate to that strand. @WYSIWYG was correct, as I document in my own answer.


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Do all proteins start with methionine?
Start codon AUG also codes for methionine and without start codon translation does not happen. And even the ambiguous codon GUG codes for methionine when it is first. So does this mean that all proteins start with methionine as the first amino acid.

You are correct in thinking that since the translation of mRNA begins with AUG, which codes for methionine, then all proteins should contain a methionine at their N-terminus (aka start site). But, it is indeed not so. First of all, I want to mention about variations in start codon. As you say, AUG is not the only, but actually the most common, start codon, and it codes for methionine in eukaryotes, or formylmethionine in prokaryotes but only at the start site. But, this start codon can also vary and become GUG or even UUG, coding for valine and leucine respectively. And the twist is, it still codes for methionine or formylmethionine1. In rare cases, such as heat shock, other codons like CUG, ACG, AUA and AUU, are also used for initiation 2. It is so because start codon itself is not sufficient to begin translation, other nearby factors, like the Shine-Dalgarno sequence, or initiation factors, also play a role. One such factor is the initiation tRNA. At the beginning of translation, tRNAMet or tRNAfMet binds to the small subunit of ribosome. So, whatever be the start codon, the first amino acid will be methionine3.
Now, coming back to the main question, N-terminal methionine, although being the first amino acid, is not present at N-terminus of all proteins. This is because of a process that is known as post-translational modification. After a polypeptide is completely translated from mRNA, it is modified at different places by different enzymes, which are regulated by different (internal or external) factors. There are more than a hundred post-translational modifications known4, one of which is the removal of methionine from the N-terminus of a polypeptide. N-terminal methionine is removed from a polypeptide by the enzyme methionine aminopeptidase5.
The question which immediately comes to mind is Why are proteins modified after translation? Well, there can be various different causes of it. First of all, post-translational modifications are regulated by many factors, and this process is called post-translational regulation6. Another point is cell targeting. Attaching different groups to polypeptides makes them more stable at their target location. For example, by attaching lipid molecules to polypeptides (in a process called lipidation) makes the polypeptide more stable and suitable for cell membranes4. A yet another factor is increasing stability. Yes, you read it right, in some cases, N-terminal methionine can destabilize a protein! For example, an extra N-terminal methionine not only destabilizes but also disrupts the native folding configuration of $\alpha$-lactalbumin7. There can be numerous other factors too, which promote removal of N-terminal methionine from polypeptides.
Thus, in short, No, not all proteins contain a methionine at their N-terminus. I hope this helps!
References:
 1. Touriol, C., Bornes, S., Bonnal, S., Audigier, S., Prats, H., Prats, A.-C. and Vagner, S. (2003), Generation of protein isoform diversity by alternative initiation of translation at non-AUG codons. Biology of the Cell, 95: 169–178. doi:10.1016/S0248-4900(03)00033-9
 2. Ivanov IP, Firth AE, Michel AM, Atkins JF, Baranov PV. Identification of evolutionarily conserved non-AUG-initiated N-terminal extensions in human coding sequences. Nucleic Acids Research. 2011;39(10):4220-4234. doi:10.1093/nar/gkr007.
 3. Sherman, F., Stewart, J. W. and Tsunasawa, S. (1985), Methionine or not methionine at the beginning of a protein. Bioessays, 3: 27–31. doi:10.1002/bies.950030108
 4. Post-translational modification - Wikipedia
 5. Liao, Y.-D., Jeng, J.-C., Wang, C.-F., Wang, S.-C. and Chang, S.-T. (2004), Removal of N-terminal methionine from recombinant proteins by engineered E. coli methionine aminopeptidase. Protein Science, 13: 1802–1810. doi:10.1110/ps.04679104
 6. Wolfgang Schumann; Wolfgang Schumann (Prof. Dr. rer. nat.) (2006). Dynamics of the bacterial chromosome: structure and function. Wiley-VCH
 7. Chaudhuri, T. K., Horii, K., Yoda, T., Arai, M., Nagata, S., Terada, T. P., & Kumagai, I. (1999). Effect of the extra N-terminal methionine residue on the stability and folding of recombinant alpha-lactalbumin expressed in Escherichia coli. Journal of Molecular Biology, 285(3), 1179–1194. doi:10.1006/jmbi.1998.2362

When ribosomes create peptides, Methionine is the starting amino acid. But, in many proteins, Methionine Aminopeptidases cut it off from N-terminus. This happens in cases when methionine is not required as starting amino acid (not required on N-terminus).
Source: https://en.m.wikipedia.org/wiki/Methionyl_aminopeptidase
I remembered the name of enzyme.


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How is sebum secretion regulated?
The principle of homeostasis in biology says that living organisms try to maintain some sort of equilibrium. Doing that requires the use of feedback mechanisms to regulate things like temperature, salinity, etc. Are there any feedback mechanisms the body uses to regulate the output of the skin's sebaceous glands? If so, what are they, and on what timescale do they operate?

Nice question! Unfortunately, the complete list of pathways involved in regulation of sebum production and secretion rate by sebaceous glands are not understood yet (Picardo et al, 2009). However, we know that sebum production is continuous and is not regulated by neural mechanisms (Thiboutot et al, 2004). Retinoids, hormones, and growth factors are known to influence sebaceous gland growth and differentiation (Zouboulis et al, 1998). Also, androgens and growth hormones are known to promote sebaceous gland differentiation (Deplewski et al, 1999, Rosenfield et al, 1998) whereas estrogens and retinoids, like 13-cis retinoic acid, inhibit their differentiation (Strauss et al, 1962).
In retinoids, isoretinoin is shown to have greater sebosuppressive action as compared to all-trans or 9-cis retinoic acid (Hommel et al, 1996). In androgens, androgen receptors have been localized to the basal layer of the sebaceous gland and the outer root sheath keratinocytes of the hair follicle, and testosterone and dihydrotestosterone are the major androgens that interact with these receptors (Liang et al, 1993). However, the molecular mechanisms through which androgens interact with these receptors and sebaceous glands are not understood yet (Thiboutot et al, 2004). Apart from this, insulin and Insulin-like Growth Factor 1 (IGF-1) also play a critical role here. Acne is considered as IGF-1 mediated disease, and high levels of sugar (caused due to diet) induce high levels of insulin and IGF-1. Both these hormones amplify the stimulatory effect of GH on sebocytes and augment mitogenic downstream signalling pathways of insulin receptors, IGF-1 receptor and fibroblast growth factor receptor-2b (Melnik et al, 2009).
Other (known) substances which are found to regulate sebum secretion include histamine (due to presence of H-1 receptor on sebocytes, Pelle et al, 2008), LXR ligands (due to presence of Liver X Receptor, Zouboulis et al, 2009), PPAR ligands (due to presence of Peroxisome Proliferator-Activated Receptor, Trivedi et al, 2006), vitamin D deficiency (Yildizgören et al, 2014), neuropeptides (Ganceviciene et al, 2009), etc. See the image below (from Makrantonaki et al, 2011) for visual representation:

In spite of this, elucidating the mechanism of regulation of sebum secretion by sebaceous glands is a difficult task since, although evidence suggests that nonendocrine factors may also be an important part for regulation along with endocrine factors, the nature of this secretion and the regulation of the secretory process seem to differ among the various types of glands which, in spite of being similar in structure, might be different in function and regulation (Thody et al, 1989).
References:
 1. Picardo, Mauro et al. “Sebaceous Gland Lipids.” Dermato-endocrinology 1.2 (2009): 68–71. Print.
 2. Diane Thiboutot, Regulation of Human Sebaceous Glands, Journal of Investigative Dermatology, Volume 123, Issue 1, July 2004, Pages 1-12, ISSN 0022-202X, http://doi.org/10.1111/j.1523-1747.2004.t01-2-.x.
 3. C.C. Zouboulis, L. Xia, H. Akamatsu, H. Seltmann, M. Fritsch, S. Hornemann, R. Ruhl, W. Chen, H. Nau, C.E. Orfanos
The human sebocyte culture model provides new insights into development and management of seborrhoea and acne
Dermatology., Volume 196, Issue 1, 1998, pp. 21–31
 4. D. Deplewski, R.L. Rosenfield
Growth hormone and insulin-like growth factors have different effects on sebaceous cell growth and differentiation
Endocrinology., Volume 140, Issue 9, 1999, pp. 4089–4094
 5. R.L. Rosenfield, D. Deplewski, A. Kentsis, N. Ciletti
Mechanisms of androgen induction of sebocyte differentiation
Dermatology., Volume 196, Issue 1, 1998, pp. 43–46
 6. J.S. Strauss, A.M. Kligman, P.E. Pochi
The Effect of Androgens and Estrogens on Human Sebaceous Glands
J Invest Dermatol., Volume 39, 1962, pp. 139–155
 7. L. Hommel, J.M. Geiger, M. Harms, J.H. Saurat
Sebum excretion rate in subjects treated with oral all-trans-retinoic acid
Dermatology., Volume 193, Issue 2, 1996, pp. 127–130
 8. T. Liang, S. Hoyer, R. Yu
Immunocytochemical localization of androgen receptors in human skin using monoclonal antibodies against the androgen receptor
J Invest Dermatol., Volume 100, 1993, pp. 663–666
 9. Melnik BC, Schmitz G. Role of insulin, insulin-like growth factor-1, hyperglycaemic food and milk consumption in the pathogenesis of acne vulgaris. Exp Dermatol. 2009;18:833–841
 10. Edward Pelle, James McCarthy, Holger Seltmann, Xi Huang, Thomas Mammone, Christos C. Zouboulis, Daniel Maes, Identification of Histamine Receptors and Reduction of Squalene Levels by an Antihistamine in Sebocytes, Journal of Investigative Dermatology, Volume 128, Issue 5, May 2008, Pages 1280-1285, ISSN 0022-202X, http://doi.org/10.1038/sj.jid.5701160
 11. Zouboulis, Christos C. “Sebaceous Gland Receptors.” Dermato-endocrinology 1.2 (2009): 77–80. Print.
 12. Nishit R. Trivedi, Zhaoyuan Cong, Amanda M. Nelson, Adam J. Albert, Lorraine L. Rosamilia, Surendra Sivarajah, Kathryn L. Gilliland, Wenlei Liu, David T. Mauger, Robert A. Gabbay, Diane M. Thiboutot, Peroxisome Proliferator-Activated Receptors Increase Human Sebum Production, Journal of Investigative Dermatology, Volume 126, Issue 9, September 2006, Pages 2002-2009, ISSN 0022-202X, http://doi.org/10.1038/sj.jid.5700336
 13. Yildizgören, Mustafa Turgut, and Arzu Karatas Togral. “Preliminary Evidence for Vitamin D Deficiency in Nodulocystic Acne.” Dermato-endocrinology 6.1 (2014): e983687. PMC. Web. 23 Apr. 2017.
 14. Ganceviciene, Ruta et al. “The Role of Neuropeptides in the Multifactorial Pathogenesis of Acne Vulgaris.” Dermato-endocrinology 1.3 (2009): 170–176. Print.
 15. Makrantonaki, Evgenia, Ruta Ganceviciene, and Christos Zouboulis. “An Update on the Role of the Sebaceous Gland in the Pathogenesis of Acne.” Dermato-endocrinology 3.1 (2011): 41–49. PMC. Web. 23 Apr. 2017.
 16. Thody, A. J. & Shuster, S. Control and function of sebaceous glands. Physiol Rev 69, 383–416 (1989)


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Toxicity of Zinc to fungi
I would like to know what are the mechanisms and overall effects of Zinc on fungi.
I know that Candida albicans is susceptible to Zinc deprivation and Zinc-infused paint is also used to repel mold.

http://goo.gl/sPhcyn and http://goo.gl/wrIX58 might be of interest to you

You might be interested in this (PDF) too. I couldn't find definitive reports on mechanisms of Zn toxicity on fungi, so it doesn't seem that the exact cause is known yet.


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Is the "freeze response" really a remain of our reptilian past?
I'm looking for any reliable sources relating the common-known human reaction on a stressful situation, humans sometimes freeze and can not move. From some materials found on the internet I got that it is supposed to be a remain from the bugs' playing dead. But it doesn't seem to be an advantageous reaction from the point of view of big mammals.
My explanation is that the brain just can't process the new complex signals. Are there any studies about this topic?

It would be helpful if you posted some of the sources that led you to this question. The "materials found on the internet" might be useful for better understanding your question.

While it's not a solid answer, this article might lead you in the right direction.  If you want a more substantive and scientific read, this article will be a good jumping-off point.

Freeze response is also a part of the fight or flight response. See this paragraph below from Wikipedia:

The fight-or-flight response (also called the fight, flight, freeze, or fawn response in post-traumatic stress disorder, hyperarousal, or the acute stress response) is a physiological reaction that occurs in response to a perceived harmful event, attack, or threat to survival.

This, being enough of a definitiin, does not explain the point in your question i.e. how could the freeze response help our ancestors in some dangerous situation (and thus become evolutionarily helpful)? Its actually quite simple. Let me first explain how the fight and flight responses would've helped us.

For the fight response, imagine a simple situation: a small animal (say, cat) runs towards you to attack you. Now, fight response immediately turns on. Hormones in your body tend to make you feel more powerful and aggressive, so that you easily fight off the cat and make it run away. This would be helpful for someone who would've otherwise done nothing and simply get a couple of injuries from a notorious cat.

In flight response, imagine a simlar situation: you are being attacked by a larger animal (say, bear). You know that you just can't fight with it, but if you run fast enough, you can outrun that bear. Now, flight response rapidly takes over. Hormones, like adrenaline and nor-adrenaline, tend to get more blood to your legs (so that you can run faster), dilate your pupils (so that you can see everything more clearly), etc., everything required for a faster sprint. This would be beneficial for someone who would otherwise not run away and reach a near-death situation.

So, how does the freeze response help? Consider another (last one) situation: you're being attacked by a lion. In this case, you know that you can neither fight with an angry lion nor outrun it. What should you do? One immediate idea would be to play a dead man's role in front of the lion so that (maybe) it will leave you. Of course, it doesn't pay off everytime, but surely it does, sometimes. And in such a case, this would be better for someone who would otherwise either try to fight with the lion or to outrun it. And, obviously, it is a better option for many other organisms too. So it indeed seems that this response developed much earlier in time, maybe even long before first chordates appeared.
With the above part explaining why it is beneficial, one part still remains i.e. how does it work? For this, see the paragraph below:

Studies show that particular connections from the periaqueductal grey (brain region located along the spine) to the pyramis at the base of your skull are integral to the freeze response. When these connections are activated, it causes the body to freeze. They can be activated by things that are actually dangerous and by things that aren’t, so even irrational fears can cause us to freeze. While giving a presentation, you might not actually be in danger, but your body responds like it is and causes you to clam up.

Below are images of the periaqueductal grey in spinal cord and pyramids in brainstem to help you understand their locations.

To conclude, freeze response is not a mere "remain" of our reptilian past, it is still beneficial for us.
References:

https://en.wikipedia.org/wiki/Fight-or-flight_response
https://www.psychologytoday.com/blog/evolution-the-self/201507/trauma-and-the-freeze-response-good-bad-or-both
https://joyable.com/blog/fight-flight-freeze/
https://www.slideshare.net/mobile/dr_ansari2000/the-brain-stem-ii
http://slideplayer.com/slide/4637165/


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Diploid cells and number of chromosomes
I'm struggling to get a hang on this. I'm getting confused by this sentence from one of my tests:
Each human diploid cell has two sex chromosomes and _____ autosomes.
I'm guessing they're meaning 46, but can someone tell me this in another way? Like in a really easy way, so that I can understand it?

if you think Alissa has answered your question, you can check her answer.

By definition, an autosome is a chromosome that is not a sex chromosome. Therefore, as a human diploid cell has a total of 46 chromosomes, including two sex chromosomes, I guess the answer to your question should be 44. I hope it's clear enough for you. :)

YES, that definitely cleared things up. I knew something wasn't right. Another one if you are up to it:
If the normal diploid number of chromosomes in an organism is 8, how many chromosomes are present in each of the daughter cells at the end of meiosis I?
Is the right answer half - 4?

Yes, the right answer is 4. ;)


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What is the Cordil that Edward Topsell describes?
In his "History of four-footed beasts and serpents", Edward Topsell describes a "serpent" called Cordil. Since he lists everything that crawls on the ground as a serpent, regardless of being a reptile, amphibian or even insect, there seems to be a wide array of possibilities.
So far, I couldn't find anything about what the cordil described here seems to be. Does anybody know more?

Your link says:

[...] whereof the Latines derive or rather borrow their Cordulus, and
  Cordyla [...].

Wikipedia says about this:

The genus Cordylus (Sauria: Cordylidae) includes a wide variety of small- to medium-sized spiny lizards from Africa, collectively called girdle-tailed or girdled lizards.

Tropical girdled lizard (Cordylus tropidosternum)
Source: Wikipedia


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Making Cupriavidus metallidurans in laboratory?
This is probably a stupid question but would it be possible to 'make' Cupriavidus metallidurans? And if so how? I'am guessing it wouldn't be possible without the use of expensive equipment for genome sequencing.

What do you mean by "make"? It is not possible to synthesize living organisms de novo. Also, according to Wikipedia, the genome has already been sequenced.

ok thank you my question then is where can I 'find' them?

I would expect places with high heavy metal concentration. Don't expect to go swabbing some tailings pond and get a viable, pure culture.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2168447/ They found a strain in "the sludge of a zinc decantation tank in Belgium that was contaminated with high concentrations of several heavy metals."

Wouldn't I be able to just buy a sample and then create more from those?

Potentially. This species may be hard to find and I don't expect many distributors would sell to private individuals.

You can buy Cupriavidus metallidurans from various culture collections.
See these links below:

Cupriavidus metallidurans (Goris et al. 2001) Vandamme and Coenye 2004 - DSMZ
Cupriavidus metallidurans (Goris et al.) Vandamme and Coenye (ATCC® 43123™) - ATCC

As canadianer has already explained, it will be next to impossible to "find" a pure, viable culture out there in the environment.


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What is meant by re-absorption?
It is said that PCT, DCT, Henle’s Loop reabsorb the filtrate. Does that mean they absorb the filtrate again? If it is actually reabsorbed to medulla then why it is said that PCT, DCT or Henle’s loop reabsorb the filtrate?

In the glomerulus of the nephron we have filtration occuring. The subsequent formation of an ultra-filtrate travels down the tubulus from Bowmans space; during this journey, the filtrate will be exposed to various transporters and forces such as solvent drags and diffusion gradients, which leads to the (re)absorption of this filtrate. Reabsorption occurs also in medullary tubules and later collecting ducts, until the filtrate (by now urine) reaches the calyces. (Note that secretion - that tubular cells permit the transportation of various electrolytes for instance to the tubulary lumen - also occurs in the nephron, giving it three ways to manipulate the its luminal contents: filtration, reabsorption and secretion)


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What makes delayed onset muscle soreness stop occurring?
If someone lifts weights or takes a long jog after not doing it for a while, they can experience delayed onset muscle soreness (DOMS).
However, when they return to the same exercise days afterwards, the chance of a new DOMS episode occurring diminishes.
I used to think that it was partly due to muscle getting larger. However, an individual who trains themselves to lift 100kg, stops for 2 months and still manages to lift the same 100kg can experience DOMS (assuming that little has changed in the muscle size and force it can exert).
This leads me to ask: are there other biological phenomena involved, rather than just muscle size?

Stopping for two months would result in muscle atrophy — are you trying to propose a hypothetical scenario in which muscle size wouldn't decrease?

I'm not sure what you are asking? When you stop training for two months your muscle size would decrease.


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What is the difference between Totipotent cells and Pluripotent cells?
I read the Wikipedia article about Cell Potency
(Article on Cell Potency)

Totipotency is the ability of a single cell to divide and produce all of the differentiated cells in an organism.

while pluripotency means

a stem cell that has the potential to differentiate into any of the three germ layers: endoderm, mesoderm, or ectoderm.

I don't quite understand the difference, then, between a totipotent and a pluripotent cell.

You might be interested in this.


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siRNA designing problem
I have a gene sequence with 15 alternative splicing forms. I want to design a siRNA for 1 isoform, I select the exon intron junction that is unique for this isoform, and I must design siRNA for this sequence or this unique isoform, but this sequence has a similarity with another sequence when I blast it, also this sequence doesn't have features for siRNA design. With this condition how can I design siRNA for my sequence?

Can you show how the sequences align? A rough illustration is sufficient if you do not want to share the details. Plus why are you targeting intron-exon junction? You can simply target the exon that is retained in the desired isoform.

i aligne these sequences with clustal omega, and also i have this schematic picture in the literature.my desired isoform is the smallest sequense between another isoforms with two exons,and all of the isoforms have both of above exons.therefore  i have to select exon intron junction , that its the uniqe sequence.

Have you extended the siRNA to 25 bases (usually considered the longest) and moved it up and down the junction to try to find a more unique sequence?  i.e. have at least 7 bases on each side of junction, but vary it from 7 to 18 on one side and see if you get more unique blasts. I assume you are blasting RNA and not DNA?

Can you show the alignment? siRNAs have to be perfectly complementary and the 5' pairing is the most crucial. There are other rules too. Also, please tell what were your BLAST parameters. Edit your question to include all necessary details otherwise it would not be possible for us to help you.


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Sections Of DNA
I know what major (2.2 nm) and minor (1.2 nm) groves are, but what is then name for:

a 360-degree rotation of DNA (3.4 nm)
the gap between each base pair (0.34 nm)?

The term for distance covered in a 360° rotation of helix is known as the pitch of DNA helix, though there is no special name for distance covered between 2 base pairs. It can be called as rise per base pair of DNA. See the table below from this article:

Reference: Nucleic Acid Double Helix

458 views :) wow !

It turns out that the gap between (heterocyclic nitrogenous) base pairs is called 'adjacent base pair width'. Also, the pitch (10 base pairs long) is also known as 'one helical turn'. Just a bit of additional information...

it is (kind of) mandatory here to give some references to your answer (even if its on your own question) so that other readers can have a source for more information.


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How does repair take place on leading strand in eukaryotes?
I am currently reading molecular biology of the gene by Watson to develop an understanding of the mechanism of replication and repair.
Under the topic mismatch repair of DNA, they mentioned that eukaryotes lack a homolog of MutH. The repair takes place from the nicks developed on the lagging strand before ligase acts on Okazaki fragments.
How then does the repair take place on the leading strand as there are no nicks on the leading strand?
And also, because eukaryotes lack Dam Methylase, how does the repair system recognize which nucleotide of the mismatched pair is incorrect?

I could be mistaken, but I think eukaryotic MutL homologous have intrinisc nuclease activity.

It does not mention so in the text so I am just confused about this.

I'll keep the answer to this as concise as possible. The major mismatch repair (MMR) pathway used by eukaryotes is the MutS$\alpha$-MutL$\alpha$-dependent MMR. See the diagram below for its mechanism:

The pathway initiates when MutS$\alpha$ (Msh2–Msh6) binds to a mismatch. This is followed by binding of MutL$\alpha$ (Mlh1 and Pms2). PCNA then activates MutL$\alpha$ to incise the nascent strand and the DNA ends are used for removing the replication error. After this, the repair is completed by correct DNA synthesis and ligation (note that this pathway works in both leading and lagging strands). DNA replication and MMR are temporally coupled in a manner that may be related to the regulation or appearance of the signals used for MMR. Also, pay attention to the point that the opposite strand is used as reference strand for repair and the strand to which MutL$\alpha$ binds is the one at which Pol$\epsilon$ (or Pol$\delta$) replicates as the DNA polymerase and the PCNA act as the signal for MutL$\alpha$ activity.
See this paper (also the image source) by Kunkel and Erie (2015), they describe this process and a lot of things related to it, including its regulation and signals, in much more detail. I haven't talked much about the details here as the paper is a much better source to understand them.
References:

Kunkel TA, Erie DA. Eukaryotic Mismatch Repair in Relation to DNA Replication. Annu Rev Genet. 2015;49:291–313. doi:10.1146/annurev-genet-112414-054722


text:
How does methamphetamine (meth) damage neurons?
Meth is considered to be neurotoxic by forming reactive oxygen species and oxidizing the neurons. But unlike dopamine, which, by the way, is neurotoxic due to ROS induced dopaminergic stress, meth does not have any oxygen atom, and thus cannot be the direct cause of ROS.
So, how exactly does meth exert its neurotoxic effects?

There are many possibilities, asking "how exactly" in biology is usually not possible to answer. It also isn't strictly true that the neurotoxicity of methamphetamine is via ROS. One possible mechanism is through methamphetamine's direct effects on dopamine, which is then metabolized including to ROS, another is through glutamate-based excitotoxicity, and there are other possible contributing mechanisms via effects on mitochondrial function.

Nice question! I will directly begin with the process through which methamphetamine causes damage to neurons, putting in as much details as are known, and adding appropriate citations wherever required.
Methamphetamine (METH) is known to act by increasing concentration of dopamine in brain1. When excess of dopamine is produced, it causes oxidative damage to axon terminals2. This is because direct oxidation of dopamine leading to quinone formation3, iron-catalyzed dopamine metabolism via Fenton reaction4, and metabolism of dopamine by monoamine oxidase-A5 contribute to production of superoxide and hydrogen peroxide.
Methamphetamine is known to increase concentration of glutamate. This (supposedly) happens as: high concentration of methamphetamine D1-mediated striatonigral GABAergic transmission, which in turn activates GABA-A receptors in substantia nigra pars reticulata (SNr), leading to increase in GABAergic nigro-thalamic activity which increases corticostriatal glutamate release6 (since I can't explain all those terms in a single answer). Now, excessive glutamate activates the glutamate-activated NMDA and AMPA receptors which, in turn, increases activity of nitric oxide synthase7. Activation of nitric oxide synthase generates reactive nitrogen species which create an oxidative stress8.
Oxidative stress is further increased because of depletion of antioxidant enzymes due to methamphetamine itself9. Now, the oxidative stress has to be manifested somehow. This is done by lipid peroxidation and protein carbonyl formation10, and also by specific nitration and nitrosylation of proteins important for monoamine synthesis and release, including VMAT-2 and tyrosine & tryptophan hydroxylase7,11,12. Oxidative modification of these proteins restricts their activity and contributes to their degradation, thus playing a major role in neurotoxicity. Researches substantiate the significant contribution of oxidative stress to the neurotoxicity of substituted amphetamines antioxidant treatments have also been shown to be neuroprotective against the damage produced by methamphetamine or methylenedioxymethamphetamine13,14,15.
P.S.: oxidative damage is not the only way through which methamphetamine causes neurotoxicity. Other possible ways include altered metabolism16, damage to mitochondria17, peripheral organ damage18 due to oxidative modification of hepatocellular mitochondrial proteins19, activation of microglia in striatum, cortex and hippocampus20, etc. Also, cannabinoids are known to suppress inflammatory processes and damage during methamphetamine exposure21. But since this is out-of-scope for this question, I won't go into their details.
References:
 1. Cadet JL, Brannock C, Jayanthi S, Krasnova IN (2015). "Transcriptional and epigenetic substrates of methamphetamine addiction and withdrawal: evidence from a long-access self-administration model in the rat". Mol. Neurobiol. 51 (2): 696–717. doi:10.1007/s12035-014-8776-8. PMC 4359351Freely accessible. PMID 24939695.
 2. Schmidt CJ, Ritter JK, Sonsalla PK, Hanson GR, Gibb JW. Role of dopamine in the neurotoxic effects of methamphetamine. The Journal of pharmacology and experimental therapeutics. 1985;233:539–544
 3. Graham DG. Oxidative pathways for catecholamines in the genesis of neuromelanin and cytotoxic quinones. Molecular pharmacology. 1978;14:633–643
 4. Yamamoto BK, Zhu W. The effects of methamphetamine on the production of free radicals and oxidative stress. J Pharmacol Exp Ther. 1998;287:107–114
 5. LaVoie MJ, Hastings TG. Dopamine quinone formation and protein modification associated with the striatal neurotoxicity of methamphetamine: evidence against a role for extracellular dopamine. J Neurosci. 1999;19:1484–1491
 6. Mark K. A., Soghomonian J.-J., Yamamoto B. K., High-dose methamphetamine acutely activates the striatonigral pathway to increase striatal glutamate and mediate long-term dopamine toxicity. J. Neurosci. 24, 11449–11456 (2004)
 7. Eyerman DJ, Yamamoto BK. A rapid oxidation and persistent decrease in the vesicular monoamine transporter 2 after methamphetamine. J Neurochem. 2007;103:1219–1227
 8. Imam SZ, Islam F, Itzhak Y, Slikker W, Jr, Ali SF. Prevention of dopaminergic neurotoxicity by targeting nitric oxide and peroxynitrite: implications for the prevention of methamphetamine-induced neurotoxic damage. Annals of the New York Academy of Sciences. 2000;914:157–171
 9. Jayanthi S, Ladenheim B, Cadet JL. Methamphetamine-induced changes in antioxidant enzymes and lipid peroxidation in copper/zinc-superoxide dismutase transgenic mice. Annals of the New York Academy of Sciences. 1998;844:92–102
 10. Gluck MR, Moy LY, Jayatilleke E, Hogan KA, Manzino L, Sonsalla PK. Parallel increases in lipid and protein oxidative markers in several mouse brain regions after methamphetamine treatment. J Neurochem. 2001;79:152–160
 11. Kuhn DM, Aretha CW, Geddes TJ. Peroxynitrite inactivation of tyrosine hydroxylase: mediation by sulfhydryl oxidation, not tyrosine nitration. The Journal of neuroscience : the official journal of the Society for Neuroscience. 1999;19:10289–10294
 12. Kuhn DM, Geddes TJ. Peroxynitrite inactivates tryptophan hydroxylase via sulfhydryl oxidation. Coincident nitration of enzyme tyrosyl residues has minimal impact on catalytic activity. The Journal of biological chemistry. 1999;274:29726–29732
 13. Gudelsky GA. Effect of ascorbate and cysteine on the 3,4-methylenedioxymethamphetamine-induced depletion of brain serotonin. J Neural Transm. 1996;103:1397–1404
 14. Sanchez V, Camarero J, O’Shea E, Green AR, Colado MI. Differential effect of dietary selenium on the long-term neurotoxicity induced by MDMA in mice and rats. Neuropharmacology. 2003;44:449–461
 15. Fukami G, Hashimoto K, Koike K, Okamura N, Shimizu E, Iyo M. Effect of antioxidant N-acetyl-L-cysteine on behavioral changes and neurotoxicity in rats after administration of methamphetamine. Brain research. 2004;1016:90–95
 16. Pontieri FE, Crane AM, Seiden LS, Kleven MS, Porrino LJ. Metabolic mapping of the effects of intravenous methamphetamine administration in freely moving rats. Psychopharmacology. 1990;102:175–182
 17. Burrows KB, Gudelsky G, Yamamoto BK. Rapid and transient inhibition of mitochondrial function following methamphetamine or 3,4-methylenedioxymethamphetamine administration. European journal of pharmacology. 2000;398:11–18
 18. Smith DE, Fischer CM. An analysis of 310 cases of acute high-dose methamphetamine toxicity in Haight-Ashbury. Clin Toxicol. 1970;3:117–124
 19. Moon KH, Upreti VV, Yu LR, Lee IJ, Ye X, Eddington ND, Veenstra TD, Song BJ. Mechanism of 3,4-methylenedioxymethamphetamine (MDMA, ecstasy)-mediated mitochondrial dysfunction in rat liver. Proteomics. 2008;8:3906–3918
 20. Pubill D, Canudas AM, Pallas M, Camins A, Camarasa J, Escubedo E. Different glial response to methamphetamine- and methylenedioxymethamphetamine-induced neurotoxicity. Naunyn-Schmiedeberg’s archives of pharmacology. 2003;367:490–499
 21. Yiangou Y, Facer P, Durrenberger P, Chessell IP, Naylor A, Bountra C, Banati RR, Anand P. COX-2, CB2 and P2X7-immunoreactivities are increased in activated microglial cells/macrophages of multiple sclerosis and amyotrophic lateral sclerosis spinal cord. BMC neurology. 2006;6:12

The king of referencing. +1

Mitochondrial damage turned out to be due to dopamine: https://www.ncbi.nlm.nih.gov/pubmed/12460681

@kirill2485 it is actually increased by dopamine. Dopamine activates NO synthase, same as what meth does. I didn't go into that point since it was out of scope here...

so meth + weed is saver than

@J.Chang (taking that as humor) I dont know much about weed, so I'd just say...two negatives dont really make a positive out of paper :P


text:
Preparation of dihydroxyacetone phosphate from glycerine by fermentation
I read on Wikipedia that
dihydroxyacetone (DHA) can be obtained from fermentation of glycerin. I would like to obtain dihydydroxyacetone phosphate (DHAP) for a science experiment but, since I'm 15, I cannot purchase it.
So I'm gonna have to make some if I want it.
With that being said, how do I properly ferment it, and how do I phosphorylate it? (I have phosphoric acid at home, maybe that would do the trick...)

I'm not convinced DHAP is easy to obtain by a fermentative process: it's an intermediary of glycolysis, so it's probably not accumulated.


text:
Why are my assay absorbance values very low?
I am culturing SH-SY5Y cells in 96-well plates at a seeding density of $1.2 \times 10^5$ cells/mL. I differentiate the cells with retinoic acid for 6 days before giving them treatments. The cells look okay under microscope after the treatment. However, every time I read the plates, I get absorbance values of less than 0.2 (including my control).
I have tried increasing the volume of MTT reagent (5mg/mL), increasing the incubation time, but in vain.
Increasing the cell density indeed increase the absorbance, but the outcome seems illogical. A seeding density of $2 \times 10^6$ cells/mL gives absorbance values of 0.4+ (less than 0.5).
I am pipetting the mtt reagent and media out one-well-by-one-well using a micropipette. Assuming no pipetting errors and loss of cells, what are the possible causes of getting these low absorbance values?


text:
Rosette formation: in which order are leafs created
From the picture below, it seems that new leaves are formed something like this (if you imagine the plant as a regular, 12 hour clock):
new leaf at 12 o'clock, then at 7 o'clock, then at 2 o'clock, then at 9 o'clock, and so on.
I imagine it could be some things as simple as 'always add 190 degrees'. Are the exact rules for this documented somewhere for various plants?


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Why arent mosquitoes found near neem trees?
I read an article yesterday that wherever neem trees or spices are cultivated mosquitoes are not seen there. So why arent  mosquitoes seen near these places (neem trees , spices, etc).
What is it that prevents mosquitoes from living near these places?

OK , I understand that , but what about spices??                  Do mosquitoes hate it ??

The growing accumulation of experience demonstrates that neem products work by intervening at several stages of an insect's life. The ingredients from this tree approximate the shape and structure of hormones vital to the lives of insects (not to mention some other invertebrates and even some microbes). The bodies of these insects absorb the neem compounds as if they were the real hormones, but this only blocks their endocrine systems. The resulting deep-seated behavioral and physiological aberrations leave the insects so confused in brain and body that they cannot reproduce and their populations plummet.

In case of a regular (house) mosquito, the effects of neem are as follows:
1. Retardation of growth
2. Inhibition of feeding
3. Eggs are unable to hatch
Apart from this, larvae of a number of mosquito species are sensitive to neem. They stop feeding (as mentioned above) and die within 24 hours after treatment.
Studies regarding your question are still in process so it's hard to narrow down to one exact reason.
Sources referred: The National Academies Press

sorry. Here it is: https://www.nap.edu/read/1924/chapter/6


text:
Can someone identify this ant queen?
I know it's kind of hard to see but can anyone tell what it is?

Sorry, but this is so blurry had a hard time to find the ant at first sight. Please try to get a better picture and add information about where you found this ant, otherwise it will be unlikely someone is able to identify it.

I found this ant in my backyard in North Carolina when I get home I'll get a better pic.

How do I add another pic?

You can edit your post.

[edit] to edit.


text:
Adding the Propionyl-CoA Pathway to E.coli
So I'm trying to simulate the production of 3-Hydroxypropionic Acid with E.coli via the Propionyl-CoA Pathway.
However I'm not really sure how the production in the pathway goes.
I got the following picture:

If I understand it correctly the pathway goes:
Acetyl-Coa--> Propionate --> Propionyl-CoA --> .... --> 3-HP
When adding these reactions in Cobra are the stoichiometric coefficients always just 1?

Source of the figure:
Luo H, Zhou D, Liu X, Nie Z, Quiroga- Sánchez DL, Chang Y (2016) Production of 3- Hydroxypropionic Acid via the Propionyl-CoA Pathway Using Recombinant Escherichia coli Strains. PLoS ONE 11(5): e0156286. doi:10.1371/journal. pone.0156286

If I understand it correctly the pathway goes: Acetyl-CoA --> Propionate --> Proprionyl-CoA --> ... --> 3-HP

Not exactly. The first reaction is:
$propionate + acetyl\textrm-CoA \rightarrow propionyl\textrm-CoA + acetate$
The CoA group is transferred from acetate to propionate. The following reactions are an oxidation to acryloyl-CoA and a subsequent hydration to 3-HP-CoA. Lastly the CoA group is transferred back to acetate.
Propionate is a 3 carbon molecule and so is 3-HP. So stoechiometric coefficients of 1 seem logical.


text:
This is the bone of which animal? And which bone?

so this bone was found on a construction site in Paris and I was wondering from which animal does it come from?

Not really a bone guy, but it does have a sortof tibial/carpal look to it. Some kind of ungulate maybe?

This looks quite large. I don't think it belongs to current french Fauna. Do you know in what geological layer this bone was found? Is it petrified?

It might be interesting to have information about the history of the site.

I don't really have any info about the geological layer and whether if it's petrified or not. My only guess is that it's a femur...I'm not really good with bones

looks like a femur to me. You can see the head and paired distal condyles

Related? https://biology.stackexchange.com/questions/62871/identifying-a-lone-bone-found-newar-rowena-crest-oregon-usa?rq=1

@LinuxBlanket. Thanks for bringing attention to that other bone ID question. However, the bone in your linked question is a forelimb bone (the humerus) while the bone in this post looks much more like a femur (a hind-limb bone). The sizes are also drastically different.


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Why does yawning trigger tears?
I'm just wondering when I yawned, there are tears coming out from my eyes, which makes me look like I'm crying.
So my question is how does yawning give out tears?

When you yawn, the muscles surrounding the glands which are responsible for bringing tears, i.e. the Lacrimal glands get squeezed leading to teary eyes. This is the location of Lacrimal gland (it's present at the top left corner in this image):
https://upload.wikimedia.org/wikipedia/commons/c/cf/Gray896.png

These glands actually work all the time as they've the responsibility to coat the surface of our eyes (that's the reason our eyes appear glistening). When they get squeezed, due to the tightening of facial muscles surrounding the eye, or maybe because your closing eyelids too tightly while yawning, they release a small amount of "tears" they would have otherwise used at a later moment.

Also, as a side note, there are more than one type of tears, this specific type of tears are called reflex tears. Quoting a Wikipedia article as a reference (https://en.wikipedia.org/wiki/Tears#Types):

$\ldots$ It can also occur with bright light and hot or peppery stimuli to the tongue and mouth. It is also linked with vomiting, coughing and yawning. These reflex tears attempt to wash out irritants that may have come into contact with the eye.

@GerardoFurtado I've come across that before concept before (New Scientist article a few years back I think. Did you also know Dogs catch human yawns?

I'm pretty sure I've passed on yawns to my Uromastyx before. Could have been a coincidence too though. Maybe I'll yawn at her today and see what happens.


text:
Do humans learn to distinguish different senses?
Does a human being learn to differentiate between its senses at some stage in their development? Is there a time when it, for example, cannot tell if an input is a taste or a visual image?
The question came to me because food may taste different when the sense of smell is impaired, although these are two separate senses with their own receptor organs. Is it possible for other senses to be mixed up in a similar way?

Taste is really not a separate sense.  Taste receptors on the tongue only react to a few things - sweet, sour, salty, bitter and umami, IIRC.  (And possibly chili peppers, though IMHO that probably involves pain receptors :-))  Everything else is really smell.

there may be another taste that responds to starches. https://www.researchgate.net/publication/306550362_Humans_Can_Taste_Glucose_Oligomers_Independent_of_the_hT1R2hT1R3_Sweet_Taste_Receptor

Short Answer: Though the concept of development of perception in children is known (Vernon et al, 1961), the process of differentiation between different senses is largely innate, though some disorders related to sensory processing may be acquired during infancy.
Background: The processes involved here are sensory processing and sensory integration. Sensory processing is a process that organizes sensation from one’s own body and the environment, thus making it possible to use the body effectively within the environment (Stein et al, 2009). It deals with how the brain processes multiple sensory modality inputs, like proprioception, vestibular system, auditory system, vision, etc. into usable functional outputs.
The second process is known as sensory integration. Sensory integration is the process through which the brain organizes different sensory informations. In short, it is the organization of different sensations for use by the brain (Ayres et al, 2005). The theory of sensory integration was put forward by Anna Jean Ayres.
As it seems obvious now, sensory integration is an innate process (Cronin et al, 2015). However, sensory integration disorders can be acquired by a child in the early stages of life. This can cause results similar to what you say. For example, according to a 2009 study, every 1 in 6 children has sensory issues which make it difficult for them to process different sensory stimuli. In fact, some symptoms which are common for children with sensory processing disorders are4:

They can’t sit still through a half-hour lesson and disrupt the class.
They often seem distracted and don’t pay attention to what teacher is saying.
They bump into kids in the lunch line, making them angry.
They can’t hold a pencil correctly, so they struggle with handwriting.
They get upset when asked to switch from one activity to another.
They melt down during assemblies and have to leave the gym.

Such activities are often seen as indications of problems with sensory processing and sensory integration i.e. they cannot differentiate between different senses or have problem organizing these sensory inputs to get meaningful output. However, I didn't find a case study where a person is unable to tell whether the input stimulus is touch or taste. This might be because (mostly) different senses are processed in different areas of the brain (Pirotte et al, 2008).
References:

M. D. Vernon, The development of perception in children, Educational Research 3 (1961),
no. 1, 2–11.
Stein BE, Stanford TR, Rowland BA (December 2009). "The neural basis of multisensory integration in the midbrain: its organization and maturation". Hear. Res. 258 (1-2): 4–15. doi:10.1016/j.heares.2009.03.012
Ayres, A. Jean (2005). Sensory integration and the child : understanding hidden sensory challenges (25th anniversary ed., rev. and updated / by Pediatric Therapy Network ; photographs by Shay McAtee. ed.). Los Angeles, CA: WPS. ISBN 978-087424-437-3.
A. Cronin and M.B. Mandich, Human development and performance throughout the lifespan,
Cengage Learning, 2015.
How Sensory Processing Issues Affect Kids in School - Child Mind Institute
Pirotte B, Voordecker P, Neugroschl C, et al. (June 2008). "Combination of functional magnetic resonance imaging-guided neuronavigation and intraoperative cortical brain mapping improves targeting of motor cortex stimulation in neuropathic pain". Neurosurgery. 62 (6 Suppl 3): 941–56. doi:10.1227/01.neu.0000333762.38500.ac

Mixing up input from different senses is actually a known neurological phenomenon called synesthesia. Synesthetes (ie. adults experiencing synesthesia) might see numbers in colors for example. Some may even "taste" colors as you say.
Now do all infants have synesthesia before some stage in development is another question. It is actually a rather old hypothesis called "neonatal synesthesia". One piece of evidence comes from this study which tested shape/color association in infants. I do not see any other study concerning this hypothesis though. I guess the main reason might be the difficulty to develop an objective experimental design on small infants who hardly communicate...

Nice answer, +1! According to Wikipedia, synesthesia is a neurological phenomenon in which stimulation of one sensory or cognitive pathway leads to automatic, involuntary experiences in a second sensory or cognitive pathway. which is IMO different from mixing up of two different sensory stimuli.

Thanks. That's true. I was meaning that signals "mix up" in the brain and stimulate two senses when it should only stimulate one. But that's not clear you're right.

Indeed the signals do not "mix up". As per one theory, when a stimulus activates a specific brain area, another area gets cross-activated by the first receiving area of brain. According to ideasthesia theory, synesthesia is fundamentally a semantic phenomenon. Don't misinterpret this, I just wanted to clarify it (all points from wikipedia).

To me, this would suggest that senses are not "learned", but are automatic and controlled by the brain. You can't, for example, choose not to feel something, there has to be a problem with the wiring in your body. This would suggest to me that a human can't mix up its sensory inputs through lack of learning on a basic level.

@another'Homosapien' I was saying that based on your answer I feel my response to OPs question would be that human's don't "learn" to distinguish their senses, the brain does it for them. Humans may have to learn what the feelings mean, but the feels themselves aren't confused naturally.

@sgr in a way, you might say so, though I won't say that thus view is completely correct or should be the primary view on the topic


text:
Why is methanol poisonous?
What should we do when someone is diagnosed with the methanol poisoning What harm does methanol cause on our body, such as the harm to some proteins? What first-aid measures should we take?

Are you asking for a real case? Seek help from a qualified medical doctor in a hospital immediately.

@gerardofurtado I counted you in my reopen vote ;)

Methanol is highly toxic in humans. As little as 10 ml of pure methanol can destroy the optic nerve and cause permanent blindness,  while 30 ml dose is fatal (Vale et al, 2007). However, its toxic effects take hours to come up after ingestion,  and antidotes are often helpful in preventing permanent damage.
Methanol exerts its toxic effects by two main methods:

Much similar to ethanol, methanol is also a CNS depressant since it enhances the activity of inhibitory neurotransmitter GABA and also interferes with excitatory neurotransmitters.
When ingested, methanol is converted in liver first to methanal by alcohol dehydrogenase, and then to methanoic acid (or formic acid) by aldehyde dehydrogenase (Schep et al, 2009). Under cellular pH,  formic acid exists as formate. Formate interferes with the mitochondrial enzyme cytochrome c oxidase, causing cellular hypoxia and metabolic acidosis (Liesivuori et al, 1991).

To prevent methanol toxicity, two kinds of antidotes are used:

Bicarbonate can alter the metabolic acidosis and potentially reverses the visual deficits.
Ethanol and fomepizole are also used as antidotes to methanol. Since the affinity of liver enzymes alcohol dehydrogenase and aldehyde dehydrogenase is about 10-20 times more for ethanol than methanol, ethanol can thus prevent (or at least delay) metabolism of methanol to formate. During this time, methanol can be removed from the body by kidneys or through dialysis. Fomepizole is also metabolized by the same enzymes, but ethanol is generally preferred due to high cost and low availability of fomepizole (Medscape). Thus, intravenous injections of ethanol can (under some circumstances)  serve as a first-aid measure (although consulting a physician is always the best option).

References:

Vale A (2007). "Methanol". Medicine. 35 (12): 633–4. doi:10.1016/j.mpmed.2007.09.014.
Schep LJ, Slaughter RJ, Vale JA, Beasley DM (2009). "A seaman with blindness and confusion". BMJ. 339: b3929. doi:10.1136/bmj.b3929.
Liesivuori J, Savolainen H (September 1991). "Methanol and formic acid toxicity: biochemical mechanisms". Pharmacol. Toxicol. 69 (3): 157–63. doi:10.1111/j.1600-0773.1991.tb01290.x
Methanol Toxicity Treatment & Management: Medscape


text:
Where to start understanding chemical principles of human body?
I have no background in chemistry.
What is a good way to start understanding principles of human body - how it works, determine which meals are good or bad for health. Maybe it is not just chemistry, but some other fields, too. I just want to know how human body works, lets say - improve health - but on my own. Knowing just that this is not good for health is not enough for me. I want to build deep knowledge.
I want to know how it is functioning at the lower level (based on chemistry).
Where to start?
(sorry for my incompetence)

If you want to start from the chemistry upwards I'd recommend you to either look into a biochemistry textbook (buy or borrow one/get a used one, since they are quite expensive) or look for some (online) courses in that field.
The textbooks I know from university studies are:

Biochemistry (Stryer, Berg, Tymoczko) [possibly downlaodable from here]

Biochemistry (Voet & Voet)
Lehninger Principles of Biochemistry (Cox, Nelson)

The MIT offers quite a few (free!) online courses and there seem to be quite a number of biochemistry ones (I haven't looked into any of them, but I reckon the MIT courses aren't too bad).

I did not find the prerequisities for Biochemistry (Stryer, Berg, Tymoczko). What should I know to start read this book?

@JúliusMarko If I remember correctly (I don't have anything at hand right now) the books contains a few chapters with basic information about the underlying chemistry. Maybe try the link I added to look into it.

Nicolai offered book (and other ressource) recommendations in biochemistry (+1). However, you might want to start with some very introductory general biology. For this purpose the Campbell Biology book is one of the best.
You can find the 11th edition here on Amazon.ca but it is quite pricy but if you can accept a slightly older edition (that will still teach you a lot) such as this one, then you can get away for much cheaper.


text:
Is there any database with RNA classification?
I am looking for a database that would provide classification of various types of RNA - information about its structure, function, etc.

Probably http://scor.berkeley.edu/

Rfam is a database about RNA families, similar to Pfam (wich is for proteins). I think it's what you're looking for.
http://rfam.sanger.ac.uk/search
You could also enjoy miRbase, a database for micro RNAs: http://www.mirbase.org/
There are tRNA databases, too, like this one: http://trnadb.bioinf.uni-leipzig.de/
And this tool for predict RNA secondary structure (However, this kind of tools aren't as good as they proteinic counterpart): http://mfold.rna.albany.edu/?q=mfold/RNA-Folding-Form