text:
Why are antibiotics prescribed with a viral infection like a cold?
I've heard both ways; people going to the doctor for a cold and then getting a prescription for antibiotics and those that go to the doctor and told they have ride it out because it's a viral infection.  Do antibiotics really help in true cases of a viral cold?

I have been told that in some cases patients will refuse to leave without some kind of prescription and rather unethically some doctors go along with it for a quiet life.

No, they don't. I'll return to this question if I have time with a full answer, but the largest reason people receive antibiotics if they have a viral infection is because they expect the doctor to give them antibiotics and will pester the physician about it. Sometimes the "prescriptions" are placebos to simply give the patients something, but physicians are well aware that antibiotics rarely do anything for viral infections.

And a recent german govt report states 50 per cent of AB prescriptions are inadequate.

@MCM Better cite sources for that since I know doctors who do prescribe antibiotics for the reason outlined in Bitwise’s answer. Can’t say I’m a fan of this wasteful use of antibiotics but there you go.

@KonradRudolph - So do I. I didn't say it was the only reason, nor practiced by all Doctors. But the reason I stated was the most common while I volunteered in my local E.D.

Isn't it the case that sometimes, the symptoms of a viral cold are hard to distinguish from a bacterial infection, so instead of playing playing guess the pathogen the doctor just hedges and treats for both?

Ultra-resistant bacteria are a real concern even to WHO. But anyway doctors keep on prescribing antibiotics as if it was tap water...

In general antibiotics don't help with viruses. However, sometimes a bacterial infection may follow a cold virus, so there might be some scenarios in which antibiotics would be needed. However in many cases it could be due to people demanding antibiotics from their doctor.
You can read more here (CDC site): http://www.cdc.gov/Features/getsmart/

You only forgot to comment on the third cause of deaths in the USA.

Antibiotics kill bacteria, not virus! So it's just plain wrong. If a bacterial infection appears after the cold, then the antibiotics should be prescribed because of the bacterial infection, not because of the cold. There is a serious concern about misuse of antibiotics promoting hyper-resistant bacteria through natural selection, but doctors keep ignoring alerts from WHO and prescribing antibiotics without even knowing the bacterial strain. It's absurd that a doctor should prescribe an antibiotic just because "the patient needs to get some medicine to be happy". In this case he/she should prescribe a placebo, not a real antibiotic (and there's still the point that killing most bacteria in our body destroy one of our defensive lines against pathogens). Confirming this point, according to American Medical Association, medical error is the third death cause in USA. So in many cases, yes, it might just be a medical error.

Now for those that think this is not an answer, explain me why?

"7000 deaths/year from medication errors in hospitals"

WHO alerts about misuse of antibiotics are not irrelevant. If a doctor don't know if an infection is viral or bacterial, how can a medicine be prescripted? And medical error as a "third cause of death" is irrelevant, in your opinion, really?

Man, IF doctors make SO MANY mistakes, then of course ONE OF THE REASONS they prescribe antibiotics for cold is "MISTAKE". Or is it almost impossible for you?

Have you READ the link I gave? "In any case, 225 000 deaths per year constitutes the third leading cause of death in the United States, after deaths from heart disease and cancer."

Please read the FAQ section on civility and keep comments on track.

Doctors are like the saints of today. Nobody can say they are there for the money, and not for the health. Even worse, we cannot even suggest they commit lots of mistakes. You can even point to solid statistics: not even this will allow you to tell many doctors are mercenaries. It would be laughable, if it wasn't tragic!


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Does the entire surface of the earth contain organisms?
Does the entire surface of the earth contain organisms?
My teacher mentioned that in some parts of the earth, there aren't any organism. Is this true?
Thanks in advance.

have you questioned their claims? can they tell you where these places are? Obvious place to start checking is hostile places, but there are a lot bacteria & other unicellular organisms that can withstand extremes, e.g. Thermophilic bacteria live in very hot places such as black smokers

That will depend on many things. How do you define surface? Is one meter underground still "surface"? How about a kilometer?
Also, how large an area are we talking about? You could probably find a square millimeter in, for example, Antarctica that has no organisms. I don't think you would find a square kilometer with no organisms though.
There are organisms (called extremophiles) that thrive in the most hostile environments we know, they can survive extreme heat, cold, acidity, salinity etc. I found this very nice list:

Cold – The McMurdo Dry Valleys in Antarctica are some of the coldest, driest deserts on Earth, with average annual temperatures of
  -20oC (-4oF) and less than 10 centimeters (4 inches) of precipitation a year. Scientists have found bacteria in liquid water pockets
  embedded about twelve feet deep in “solid” lake ice. Some of these
  bacteria use chemical nutrients from particles of dirt in the ice and
  use energy from sunlight for photosynthesis.
Hot – Large concentrations of microbes thrive in Yellowstone National Park’s Grand Prismatic Springs, a hot spring with water
  temperatures up to 90oC (188oF). Other hot springs in Yellowstone are
  extremely acidic, yet are home to many different kinds of bacteria and
  microbes. Many of these microbes use chemical nutrients in the waters
  and energy from sunlight for photosynthesis. Deep underground –
  Scientists have discovered bacteria living in ground- water 5
  kilometers below the surface in deep gold mines of the Witwatersrand
  Basin in South Africa. These microbes thrive in cavities and cracks in
  rocks. Scientists are also are investigating life within and below
  permafrost in north- ern Canada.
Bottom of the sea – Scientists have found abundant life clustered around hydro- thermal vents on the ocean floor, including bacteria,
  mussels, clams, shrimp, and giant tubeworms that can reach ten feet in
  length. Water pouring out of the vents in the complete darkness
  thousands of feet under the surface of the sea can reach temperatures
  of 113-120oC (235-248oF). The high pressures keep the water from
  boiling. Bacteria use chemicals in the vent’s water, primarily
  hydrogen sulfide, as their energy source instead of sunlight. Other
  creatures survive by eating the bacte- ria or each other.
High Acidity – The water in the Rio Tinto in southwestern Spain is very acidic, a result of chemical reactions between the water, and
  iron and sulfur minerals in the ground. The river has a deep red
  color, like wine, because of iron dissolved in the water. Microbes
  living in the water use chemical reac- tions with iron and sulfur
  minerals to generate the energy they need. Products from these
  metabolic reactions contribute to the low pH in the environment. Many
  algae and fungi also live in the acidic waters.

As far as I know, there is no evidence of life in molten lava. Apart from that though, just about every habitat you can find on the earth has been colonized by life. Ask your teacher what parts of the earth she is talking about, and report back here.
UPDATE:
MCM's very interesting answer prompted me to do some more research. It seems that life has now been found even in the Atacama (taken from Azua-Bustos
et al):

For a long time it was thought that regions of the Atacama could not
  uphold any type of life forms. However, recent culture-independent
  methods (metagenomics, transcriptomics, in situ hybridization, etc.)
  have improved the sensitivity for life detection. Thus, microorganisms
  have been found even in the driest areas of this desert, which makes
  scientists wonder about the true limit of water availability needed to
  sustain life as we know it. In this review, we summarize the efforts
  devoted to the characterization of microbial life in the Atacama
  Desert.

So, it seems that life can exist even in the Atacama. That leaves only molten lava...
Reference
Azua-Bustos et al, Life at the dry edge: microorganisms of the Atacama Desert, FEBS Lett. 2012 Aug 31;586(18):2939-45

The bottom of the sea is (relatively) crowded with life, even away from hydrothermal vents. http://en.wikipedia.org/wiki/Whale_fall

@JeremyKemball of course it is, my point was that an underground volcano spewing sulfuric acid and with the pressure found at half a kilometer underwater is hardly an environment that kends itself to life.

A fair point. I've gotten so used to hydrothermal vent = oasis I kind of forgot that they're toxic pressure cookers.

Barring the very obvious surfaces (the pits of active volcanoes), the only place I'm aware of that might not contain life is the Atacama Desert near the Andes Mountains in Chile and Brazil.
Whereas other places that seem inhospitable - Antarctic, Hot Springs, regular deserts, extremely high altitudes, etc. - the basic necessities for life still exist (carbon, water, nitrogen). In the Atacama, though:

The average rainfall in the Chilean region of Antofagasta is just 1 millimetre (0.04 in) per year. Some weather stations in the Atacama have never received rain. Evidence suggests that the Atacama may not have had any significant rainfall from 1570 to 1971...  Studies by a group of British scientists have suggested that some river beds have been dry for 120,000 years.

It's the driest place on the planet. It's drier than every other desert by a long shot, and is so dry that NASA occasionally uses it to simulate Mars.

In 2003, a team of researchers published a report in the journal Science titled "Mars-like Soils in the Atacama Desert, Chile, and the Dry Limit of Microbial Life" in which they duplicated the tests used by the Viking 1 and Viking 2 Mars landers to detect life, and were unable to detect any signs in Atacama Desert soil. The region may be unique on Earth in this regard and is being used by NASA to test instruments for future Mars missions. The team duplicated the Viking tests in Mars-like Earth environments and found that they missed present signs of life in soil samples from Antarctic dry valleys, the Atacama Desert of Chile and Peru, and other locales.

So while life might exist in the Atacama (signs of life do not always point towards currently-existing life), it's hiding extremely well. Probably beneath the topsoil, where no multicellular organisms have ever been spotted and unicellular organisms may not exist at all.
Ultimately your teacher is correct, although whether they meant the Atacama or erroneously considered other places on the planet you'll have to ask them.

A fascinating place - still I'd be suprised if a ribosomal rna PCR reaction showed up nothing - bacterial spores and simple animals like rotifers can survive for decades without water.  the volcano caldera and maybe the tops of mountains like K2 are good ideas though!

Heh, nice, +1. However, recent research has found life in the Atacama. See my updated answer.

@shigeta and terdon -  Yeah, I doubt there's any place on the planet that hasn't seem at least some biproducts or spores on it through dispersal and human activity, but as far as actively growing and consuming resources I don't think anything has been confirmed in some parts of the Atacama (though edges of it saw enough rainfall to briefly support wildflowers in 2011).

Sterile! Lake Vostok’s microbes elusive in first measurements of surface water
A first analysis of the ice that froze onto the drillbit used in last
  February’s landmark drilling to a pristine Antarctic lake shows no
  native microbes came up with the lake water, according to Sergey Bulat
  of Petersburg Nuclear Physics Institute (Russia). The very uppermost
  layer of Lake Vostok appears to be “lifeless” so far, says Bulat, but
  that doesn’t mean the rest of it is.   Bulat reported what he calls
  his team’s “very preliminary results” on Tuesday, at the 12th European
  Workshop on Astrobiology (ENEA 2012), in Stockholm, Sweden, at the
  AlbaNova University Center. Bulat and his colleagues counted the
  microbes present in the ice sample and checked their genetic makeup to
  figure out the phylotypes. They counted fewer than 10 microbes/ml —
  about the same magnitude they would expect to find in the background
  in their clean room. And three of the four phylotypes they identified
  matched contaminants from the drilling oil, with the fourth unknown
  but also most likely from the lubricant.   Bulat hopes to get clean
  samples from the ice frozen in the borehole below where the drill bit
  stopped. That won’t be until next May (2013), if all goes well after
  the next Russian drilling expedition in December-January. Even if the
  top of the lake ends up being empty, Bulat suspects microbes will come
  from lower water depths, or from sediment samples at the bottom of the
  lake.   Lake Vostok is a stand-in for icy bodies that might harbor
  life, like Jupiter’s moon Europa. Gerda Horneck of the German
  Aerospace Center (DLR) said that any result from Lake Vostok is
  important for astrobiology, and the search for extremophiles that
  could give hints of what life could be like elsewhere. “Let’s see what
  comes out next round,” she told me at the end of the meeting on
  Wednesday.

http://www.scoop.it/t/amazing-science/p/3031509753/sterile-lake-vostok-s-microbes-elusive-in-first-measurements-of-surface-water

More info on Lake Vostok:
http://earthsci.org/education/Lake_Vostok/vostok.html

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How long would it take for a change to the DNA would take effect?
I am not a Biology Student (sorry guys!) but I have thought about this question for a while and hope that maybe one of you can answer it. Lets say that I had my DNA changed so that I wouldn't be vulnerable to certain diseases or perhaps to make my body change so that I'd lose weight easier (Just a hypothetical here not sure if sci-fi have skewed my view on DNA).
From the change occurs to the DNA until the changes take effect, how long would that hypothetically be?

See http://people.umass.edu/bioch623/623/Second.Section/7.%20CoT.Web.2.08.pdf . Assuming that you've inserted desired gene (I don't think weight loss can be stimuulated by genes) in bone marrow and protein synthesis starts immediately, it shouldn't  take more than 5 minutes for protein to show effect. Of course, practical value would vary.

OK, let's set up a specific hypothetical situation so we have some details: A virus (we'll call it Human Nasty Virus 1 (HNV-1)) can infect T cells (a type of white blood cell in the immune system) by binding to a certain receptor on its surface, which we'll call the Nasty Virus Receptor (NVR). Scientists have found that HNV-1 absolutely needs a certain protein sequence in NVR to bind, as people with a certain mutation lacking that sequence are completely immune to HNV-1 infection.
You sign up for a clinical trial using gene editing to specifically remove that DNA sequence from the NVR gene. Once that changed gene is transcribed and translated into protein, it is expressed on the surface of the cell, and HNV-1 can no longer bind.
T cells are derived from stem cells that live in the bone marrow. In order for the gene therapy to work, doctors will need to perform a bone marrow transplant - they will remove a sample of bone marrow, give it to the scientists for the gene editing process, then reinject the edited cells back into you. The editing process involves subjecting purified stem cells to a process called CRISPR, allowing them to grow in culture for a while, then screening the cells to select only those where the editing was successful. The successfully-edited cells are separated, cultured some more to expand their numbers, then given back to the doctors, who put them into your body, either into the bloodstream or directly back into the marrow.
So now you have your edited cells back inside you - how long will it take to become immune to HNV-1? Well, the honest answer is that, in the absence of ablative chemotherapy (see the bone marrow transplant link above for more info) prior to reinjection of the edited stem cells, you may never become completely immune. Here's why: Unless all of the bone marrow stem cells in your body are destroyed before reinjecting the edited ones, you will still have fairly high numbers of what are called "wild-type" or un-edited stem cells and mature T cells in your body, and those stem cells will continue making new wild-type T cells. Additionally, there are already wild-type T cells in circulation and in secondary lymphoid organs such as lymph nodes and the spleen, and some of these cells can be very long-lived (months to years). If for some reason you decide to undergo complete ablative chemotherapy to essentially destroy your immune system, the reinjected stem cells will eventually repopulate everything and you'll be immune to HNV-1, although you will have potentially lost your immunity to everything else you've ever been exposed to, unless the chemo is done in such a way as to preserve your immune memory cells.

This is actually a best-case scenario, as we were working with cells that can (relatively) easily be removed from the body, edited, screened, and reinjected. If you were trying to cure a genetic disease that affected solid tissue like the muscles (see Duchenne muscular dystrophy for an example), you obviously wouldn't be able to remove all the muscles and edit them ex vivo, you'd have to do the editing in the body, most likely using a viral delivery system for the editing machinery. The viruses wouldn't infect every single cell, and the editing wouldn't work in every cell that got infected, so the best you could hope for would be a partial cure. For some diseases, this may be enough, and many companies are working on this from various angles. There are also other options besides CRISPR-mediated gene editing that have higher success rates in vivo.
Finally, getting back to your original question of how long it takes from DNA alteration to expression of the gene product, the answer is that it depends on the gene and the context. In the case of our hypothetical situation earlier, as soon as the NVR gene's DNA is edited, the new sequence begins to be transcribed and translated into protein. There is still some wild-type protein left over initially, so it depends on the transcription rate of the gene and the turnover of the existing protein. Some proteins have an extremely long half-life, on the order of years or decades (or more!), while some degrade within minutes to hours of being synthesized.

Well thanks for that! That was a very thoroughly explained answer and I learned a few things too. Thanks again! :) If you don't mind me asking, what is your background in biology?

Glad to help. I have a Master's degree in Molecular Medicine and over 10 years of experience working in various facets of industry, doing biochemistry, cell biology, and molecular biology in a few different fields (cellular signaling, rare diseases, immunology, oncology, etc.). I'm an immunologist by training, which explains all the T cell business in my answer :)

Thanks for answering! I'm just a lowly Professions Bachelor Programmer xD

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Are myosatellite cells myoblasts or do they differentiate into myoblasts?
Can satellite cells immediately fuse to a myotube/myofiber (meaning it is a myoblast already) or do they differentiate into a myoblast first and then fuse to myotubes/myofibers?

Where and how have you looked for an answer to this question already?

Why? I have looked at the (many, slightly different) definitions for what a myoblast is, which leads me to conclude (without certainty) that a myosatellite is a myoblast. I have searched this specific question but of course nothing has come up. I am doing a research project on cultured meat, and all the sources I am using do not mention specifically or imply what a myoblast is. Wikipedia says that myosatellite cells differentiate into myoblasts, from what the definition of a myoblast is it doesn't really add up.

Why -- so that potential answerers know how much you already know about the topic. It gives them a place to start with their answer. See http://biology.stackexchange.com/help/how-to-ask

I see, thanks. I am not at university yet, so I am a beginner when it comes to research. I don't know much about muscle fibres at all, or stem cells.


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Is the glucose produced from photosynthesis considered an aqueous solution when written as a chemical reaction?
In the very simplified reaction for photosynthesis, the states of the reactants and products are clear to me except for glucose. Inside a plant, it would be dissolved in water, so would it be an aqueous solution or be considered a precipitate in some way? In the reaction
$$\ce{6CO_2 {_{(g)}} + 6H_2O{_{(l)}} \rightarrow C_6H_{12}O_6{_{(?)}} + 6O_2{_{(g)}}}$$
what would I put in the place of the question mark?

Yes, immediately after synthesis, glucose is dissolved in water. However, it is later used by the plant to build more complex sugars as well as starches and celluloses, which are not necessarily water-soluble.

I’m curious as to why you ask this question — what you will do with this equation when completed. You do realize that what you have written is not ‘a reaction” but a partial summary of a whole series of reactions, which, in addition, involve other substrates that you have not included.


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Do all tumors form the same way?
Do all tumors - both benign and malignant - form when proto-oncogenes and/or tumor suppressor genes experience mutations? Were all malignant tumors once benign?

You might be interested in this.


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What is the actual size of a nucleotide?
I found in this website that the dimension of a nucleotide is 0.34 nm. Is there any experimental paper confirming this statement?

This site might be able to help you: https://en.m.wikipedia.org/wiki/Molecular_Structure_of_Nucleic_Acids:_A_Structure_for_Deoxyribose_Nucleic_Acid.  If you are collecting facts at Yahoo Answers, why not ask the people who posted there where they got their numbers?

What exactly do you mean by dimension? The molecule is not circular; do you mean the longest dimension? or the van der Waals radius?

I know it is not circular, rather a flattish molecule with different conformations; but a sphere is still a good approximation. Van der Waals is probably the best measure.

If you want experimental papers, we should be precise about what we're measuring. "The dimension of a nucleotide" is rather imprecise, as a nucleotide is a rather oblong, knobbly thing.
0.34 nm is a relevant measurement related to nucleotides, but it's specifically the distance between consecutive bases in a standard B-form DNA helix - that is, what's the spacing between the "rungs" on a DNA ladder.
This measurement can be confirmed by several experiments, primarily those involving X-ray or neutron crystallography or scattering. For example, both the Wilkins and Franklin papers that were published back-to-back with the famous Watson & Crick DNA structure paper referrence the strong 0.34 nm reflections from X-ray fiber diffraction which Watson & Crick reference as the spacing of the bases in their model of DNA structure. Other papers have confirmed the measurement. This 1983 Biomed Biochim Acta paper uses wide-angle X-ray scattering to find it. Additionally, there are a large number of structures in the Protein Databank which contain DNA structures - these have been determined by a number of different approaches (X-ray crystallography, neutron diffraction, NMR, electron microscopy, etc.) and all of which are consistent with the 0.34 nm average spacing of base pairs. (Modulo minor structure-to-structure variations.)

this is for a polymer of nucleotides, how big is an individual nucleotide though?

It's for an individual nucleotide within a polymer, yes. But if that doesn't work for you, how do you want to measure it? As mentioned, a nucleotide is a rather oblong knobbly thing - the size depends on which direction you're measuring it in. Additionally, molecules don't have well-defined surfaces, being made mostly of electron clouds. There's conventions for the standard surface, but if you want experimental references, you have to specify an experimentally measurable distance.


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Critical pO2 threshold for cell division?
I'm a physicist asking questions on an aspect of cellular metabolism, so excuse my biological ignorance! Hypoxia is a frequent complication of certain tumour types, and has quite an implication for treatment prognosis - at certain low oxygen levels, metabolic functions become massively reduced or even halted and eventually necrosis sets in.
My question is what kind of partial pressures will cell division typically be halted at? From this review paper, it indicates that below 8-10 mmHg, adequate metabolistic functions cannot be maintained. In this case, the critical parameter being measured is ATP production. However, I've seen quotes for Chinese Hamster Ovary cells of 0.5-1mmHg. In radiotherapy, "hypoxia" as a condition is defined as < 2.5 mmHg but this doesn't tell me much w.r.t cell division or lack thereof.
Does anyone know a ball park figure for the cessation of cell division, in a typical cell line, and where I might find information on this? Thanks!

Part of your problem is that while cell lines are often cultured in "normoxic" conditions, with atmospheric levels of oxygen (~21%), no tissue in the body (except maybe the lungs) actually experiences that; it varies, but most tissues in the body see something closer to 5%, with 1% being "hypoxic."  I don't think I could grow my cell lines in 5% oxygen.


text:
What will happen if a poisonous snake bites itself?
I wonder if in general snakes are immune to their own venom. I would like to know studies or references about times snakes bit themselves and got sick or the contrary.

Have you tried to google your question?

Homework questions and questions that show little or no prior research effort are off-topic on Biology unless you have shown your attempt at an answer. For more information see our homework policy.

“The conventional wisdom is that they have circulating antibodies in
  their blood,” says Stephen Mackessy, Ph.D., a Professor of Biological
  Sciences at the University of Northern Colorado and an expert in
  venomous snakes. “This would protect them from their own venom, as
  well of venom from another snake in their own species.”
Hypothetically, if a speckled rattlesnake bit another speckled
  rattlesnake, the immunity they’ve built from being exposed to low
  levels of their own venom—kept in glands behind their eyes and
  secreted when they bite—would protect them from a fatal wound. (Even
  though the glands are closed, they still contain blood vessels that
  allow the venom to circulate in their system, causing mild exposure,
  Mackessy says.) But a speckled rattlesnake that meets up with a cobra
  might have a different day entirely.

So in the case snake were to bite itself it wouldn't suffer as much from the poison compared to the actual bite it self-inflicted.

If you're quoting from a source, you should include the source in your answer so others can read the quote in context. Additionally, answers that are completely or almost completely made up of quotes from other sources are generally not good answers. Do research, find several sources, and synthesize a good answer in your own words. Make sure you include links and attribution for your sources, however.


text:
Question about microaerophilic parasite tolerance for oxygen
Does anyone know what is the maximal concentration of oxygen that can be tolerated by the parasite Giardia intestinalis?

Short answer: 50-60 µM O2 is ok; 80 µM is toxic.
Giardia lamblia (aka intestinalis) is a microaerophilic intestinal parasite.
According to:

Lloyd et al. (2000) The microaerophilic flagellate Giardia intestinalis: oxygen and its reaction products collapse membrane potential and cause cytotoxicity. Microbiology 146: 3109 - 3118

Giardia colonises the upper intestine, and the oxygen concentration there has been measured at 60 µM. At oxygen concentrations up to 50 µM the organism can scavenge oxygen; above 80 µM oxygen inhibits the oxygen-scavenging process. In this paper the authors used 10% air (equivalent to 25 µM oxygen) to characterise  oxygen toxicity.
The source of oxygen sensitivity was investigated by:

Li and Wang (2006) A likely molecular basis of the susceptibility of Giardia lamblia towards oxygen Molecular Microbiology 59: 202 - 211

These authors propose that the enzyme DT-diaphorase, previously suggested as a component of the oxygen detoxification system promotes the formation of reactive oxygen species which lead to death. Thus they found that overproduction increased sensitivity to oxygen, whereas a knock-down decreased sensitivity. This work does not, however, use controlled microaerophilic conditions.


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Is there a simple test that can differentiate menstrual blood " period blood" from spotting blood?
I have a simple question: If I give two samples of blood; one from a the menstrual period and one from spotting, is there a simple way to know which one is from the period and which one is from spotting " normal, non uterus " blood?
Thanks

Spotting is "normal, non uterus"? Where does spotting come from if not the uterus?

agree with above comment - menstrual blood and blood from "spotting" are likely both uterine (except in the case of trauma, vaginal laceration, etc)

@VanceLAlbaugh - in which case(s), it would not be "normal".

@anongoodnurse exactly

The blood during the period is from the enlarged lining of the uterus caused by estrogen. spotting may be from the uterus but not related to period

My instinct is that it depends on where it's coming from. Menstrual product, either from menstruation or an endometrial condition would probably show evidence of decidualized glands. Blood from something like a leiomyoma or a tubal rupture (from, say ectopic pregnancy) would probably not show as many glands and would look more like a regular peripheral smear. That's my guess, but I don't have sources, so comment and not an answer.


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Question about enveloped RNA virus viral genome
I am a newbie studying campbell biology. just a quick question about virus.
When viral genome(RNA) expose itself in the host cell, why does the host cell not eliminate the genome since it apparently not belong to the cell ? Is there any mechanism that the host cell can detect and eliminate the viral genome as in the step 2,3 in the figure below ?
Thanks in advance !

What research have you done before asking it here?

Your image illustrates the replication cycle of a negative-sense single-stranded RNA virus, where the viral genome needs to be "inverted" by an RNA polymerase into mRNA before being translated by the host. There are many examples of (-)ssRNA viruses, including filoviruses (Ebola, Marburg), paramyxoviruses (measles, mumps), orthomyxoviruses (influenza), rhabdoviruses (rabies), deltaviruses (Hepatitis D), and others.
These (and all) viruses evolved alongside their hosts, and consequently the hosts evolved various protection mechanisms. One primitive component of the so-called innate immune system in humans and other organisms (going back at least to plants) are proteins known as pattern recognition receptors (PRRs) which bind to conserved motifs found in microbes, including possible pathogens. The types of molecules recognized by these PRRs include certain types of carbohydrate moieties like LPS, peptidoglycans and other components of bacterial cell walls, fungal glucans, bacterial peptides, some types of microbial nucleic acids (such as single- and double-stranded RNA, more on this in a bit), chitin, and others.
One class of PRRs are the Toll-like receptors (TLRs), named after the Drosophila Toll protein. They recognize a wide variety of microbial patterns and activate downstream signaling to stimulate an immune response, including production of pro-inflammatory cytokines and anti-viral interferons. In our case, two of them are particularly important - TLR3 and TLR7. TLR3 recognizes double-stranded RNA, which occurs transiently during (-)ssRNA virus infection when the negative-sense genome is being copied to positive-sense mRNA. However, dsRNA is much more common in retroviral infections. TLR7 recognizes single-stranded RNA in endosomes, which would occur after macrophages, dendritic cells, or B cells consume dead virally-infected cells.
Unfortunately for the host cell, once it has been infected there isn't much that can be done to save it. Viruses evolved to hijack the cell's machinery and make more copies of themselves. This hijacking is generally one way, so the only way to fight the infection is to kill the cells producing the viruses. This is, for example, why you often get a sore throat during an influenza or rhinovirus (one of the most common causative agents of the common cold) infection - epithelial cells lining the throat get infected, and are killed by the immune system to prevent the spread of the infection. This leaves a "raw" area that must heal over time.

Hi, thanks a lot for replying and providing really clear explanations about the protection mechanisms for cells. This is my first time asking in the forum, and I am still newbie struggling in campbell biology. So..from your answer, protection or defense only comes from outside the infected cell, and put it bluntly, the infected cell can only wait to be kill since its interior can not do anyting to the viral genome or can not know whether to stop producing for the virusese ? (i.e infect cell has just no way to get back the cell machinery by itself ?)

@YaoHsiao yes, you are generally correct. These viruses have evolved alongside humans, and are extremely good at hijacking the host cell's machinery. Once the (-)ssRNA genome has been transcribed into mRNA, there really isn't a good method available to the cell to determine that those mRNAs are bad, while other self-produced ones are good. Yes, there are some sequence motifs that can be identified, but it's not enough for the infected host cell to clear the infection on its own. Instead, it tries to signal to the immune system that it is infected, allowing it to be killed for the good of all.

A common class of enveloped single-stranded RNA viruses are the Alphaviruses. They are typically spread through insect bites, usually mosquitoes. These viruses carry a single strand of "positive" RNA, which is 5' capped and has a 3' Poly Adenosine tail, making it appear like a normal mammalian messenger RNA, only much larger.
Because this RNA is positive, ribosomes in your cells can directly use this RNA to produce the enzymes needed to duplicate the RNA. These replicases use the positive strand to create many negative strands. Each negative strand can then be used to create additional copies of the positive strand as well many more copies of the subgenomic RNA, which is used to create the capsid and envelope proteins. Those proteins plus the positive strand RNAs are assembled into new viruses and bud off the cell.
The viral RNA protects itself by acting like a messenger RNA. This recruits host proteins that prevent degradation and promote translation to make the viral proteins. Most alphaviruses also shut down host-cell transcription and inhibit the interferon response. This prevents the cell from mounting a defense against infection, but also eventually kills the cell.
EDIT: I just noticed that your question is tagged "Retrovirus", but your image does not represent the retrovirus life-cycle. It looks more like an alphavirus life-cycle.

The image shown is of a virus with a a negative RNA genome - it must be copied to generate mRNA.

@MattDMo The image itself is labeled slightly wrong then. The caption says "Enveloped RNA virus", but the positive stranded RNA viruses are also enveloped. Too many types of viruses.

that is true, the image could be labeled more clearly. But, I think Step 3 indicates that the unnamed virus in question is negative stranded.

Depending on the nature of the viral genome there are multiple pathways (elaborated upon in previous answers and comments) that sense viral nucleic acids and trigger an interferon response. This can induce apoptosis and kill infected cells, or alternatively, it can set of a cascade of genes that induce replication arrest (which in the case of some viruses can be enough to thwart an infection because of viral dependence on host replication factors).
One byproduct of the induction of an interferon response is the induction of the APOBEC family of cytodine deaminases, which can hypermutate viral genomes (APOBEC1 hits RNA, multiple APOBEC3 proteins hit DNA/ssDNA that may potentially result from various phases of the replication cycle), and other related restriction factors.
However viruses have evolved to evade these responses, either by altering restriction factors themselves, or by evolving sequences that won't be detected by viral sensing molecules.
http://www.nature.com/nrmicro/journal/v14/n6/abs/nrmicro.2016.45.html
http://www.cell.com/trends/immunology/references/S1471-4906(16)30170-3
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3331687/

If you are trying to ask if the RNA can be destroyed, it is not likely unless you don't utilize siRNA.
SiRNA, a mechanism involved in the regulation of phenotype expression, plays a key role in avoiding lytic and lysogenic cycles that could potentially help the virus produce virions, helping the virus reproduce. This RNA, also known as small (short) interfering RNA, an RNA duplex, is able to target certain mRNA molecules, causing them to degrade.  This can eventually lead to gene knockdown.
Additionally, the lysogenic cycle, causing cells to lay dormant for some time before eventually releasing virions, contains a g0 phase.  The g0 phase is a period of the cell cycle in which the cell produces minimal proteins or undergoes little or no DNA replication.  Keeping the cell in this phase may help avoid virion synthesis.
Furthermore, being able to trigger immediate cell apoptosis would also help reduce the amount of viral replication.  However, this can be dangerous as the cell may be prone to undergoing the lytic cycle.
So yes, it may be possible without the use of siRNA, but it will be very unlikely.  Immune response can also help fight off the virions in the long run.

No, not all RNA viruses integrate into the host genome. Also, there are specific intracellular surveillance molecules looking for viral components like dsRNA, so that part of your answer is incorrect as well.

@MattDMo How does it look now?  I appreciate the feedback as I am new to this site.

There are still issues, mainly that you're talking about retroviruses, when the image in the original post clearly is not of a retrovirus at all. Second, lytic and lysogenic cycles are generally associated with bacteriophages, not viruses that infect eukaryotic cells like these, and the Wikipedia articles you reference are mainly about bacteriophages as well. Eukaryotic viral lifecycles have some similarities to bacteriophages, but there are many differences as well. Finally, you don't talk at all about the role of the immune system in surveillance and killing of infected cells.

@MattDMo Ok, I understand what you are talking about.  However, I still don't understand what's wrong about the siRNA part of the answer.


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Does drinking water affect oral thermometer accuracy?
According to various sources (including Mayo and Cleveland Clinics), one must wait a certain number of minutes before an accurate oral temperature reading may be taken. However, these two sources (and others) seem to disagree on the duration of this wait. In this case, the different is three fold.
When attempting to get an accurate reading of an oral temperature, what external forces play a part in the actual temperature of the tissue in the mouth, how long would it actually take for any small amount of residual tap water to assimilate its temperature to that of the mouth and body temperature, and how long does it actually take for the tissue in the mouth to fully return to normal after drinking room temperature water?


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What histological stain can I use for beta-keratin?
I'm trying to find a histochemical stain for beta-keratin, the type found in Reptilia which is organized in beta-sheets. It's different than alpha-keratin which is found in mammalian skin, hair, nails, etc., and is formed of alpha-helices.
Simple searches have produced results specific to mammals and alpha-keratin. Are there any good stains for beta-keratin?

After a quick search, it seems that many people working on beta keratin use specific antibodies. Yet it appears that you could use toluidine blue, but I'm not sure about the specificity regarding alpha/beta keratin.

Not sure if this is what you are looking for, but I did some searching around for histochemicals and reptilia.  I did come across a paper by L Alibardi, Dipartimento di Biologia evoluzionistica e sperimentale, University of Bologna, Bologna, Italy.  Now, that exact application doesn't seem to answer your question, it did open up a web page that contained numerous papers on reptilia and their beta-keratin structure and investigations into that (citations of the original paper, as well as papers by the same author).  I didn't see any that specifically spoke to the exact stain used, but then this is a little outside my area of expertise.  Perhaps this link will give you an avenue to pursue?
Wish I could help more.


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What is the mechanism behind "acquired" alcohol tolerance?
I can understand natural variation in alcohol dehydrogenase (ADH) in a population leading to variation in rate of inebriation (after controlling for other variables -- e.g., mass, food consumption, etc.).
But what physiological (adaptive?) process leads to increased alcohol tolerance over the long term in a single individual?

Are you asking about individual variability in alcohol tolerance or you mean the characteristical symptome of the Alcoholistm II: increase of alcohol tolerance?

[Untested] If I have 1-2 drinks per day 3-4 times a week. Assuming all other factors are equal, after some period of time (months?), I will be able to drink 3-4 on one day without feeling inebriated. How does this adaptive tolerance work?

The subject of alcohol tolerance is broader than it might appear. However, in most cases people refer to what is called metabolic alcohol tolerance. Based on your response to the comment made by Alexander Galkin, I assume that you also refer to metabolic alcohol tolerance.
Metabolic alcohol tolerance is the result of drinking significant amounts of alcohol over a period of time as you describe. Both the amount of alcohol and the duration that it takes to develop an increased metabolic tolerance towards alcohol differ from person to person.
When most people drink alcohol, the liver will responds by activating alcohol degrading enzymes that break down the alcohol molecules, which results in the elimination of the intoxicating effect. The activation of those enzymes occurs much faster with people who have developed metabolic alcohol tolerance and the concentration of those enzymes is generally higher. This means that those people can break down alcohol faster than you and me, that is, they can "tolerate" more alcohol in the sense that they simply get rid of it much quicker.
On a final note, being more alcohol tolerant is not exactly correct as metabolic tolerance doesn't necessarily mean that the organs affected/intoxicated (such as the brain) by alcohol aren't necessarily more tolerant. The alcohol is simply broken down much faster and can therefore have a limited impact.

So, judging by your answer to my comment you are most likely talking about so-called consumption-induced alcohol tolerance, that one might develop by regular drinking of alcoholic beverages.
We can group the reasons for increased tolerance to the following groups: better adaptation for the elevated concentrations (functional) or increased break-down (metabolic).
Functional tolerance.
This means that your body and its organs, especially your CNS, adapt to compensate for the increased alcohol concentration and manage to sustain its functioning despite the elevated blood alcohol concentrations (BAC). So, the dose of alcohol which previously led to trembling and disorientation now evokes only some coordinatory disturbances.
The physiological mechanisms involved here are:
1. Desensitization of the alcohol-sensitive (primarily GABA-ergic) receptors in CNS.
2. Changes in the neuron firing rates (to compensate for the deterioration of the GABA-ergic inhibition).
Metabolic tolerance.
This condition is characterized by the increased alcohol break-down by the liver, that slows down the increase of blood alcohol concentration (BAC) upon its consumption leading to the attenuation or complete disguise of alcohol intoxication (inebriation).
The main enzyme that is responsible for alcohol transformation is the so-called  alcohol dehydrogenase (ADH), that represents a group of substances catalyzing the alcohol oxidation to aldehydes. This enzymes are located in the liver cells (hepatocytes) and the increase in their activity (and most likely also the absolute amount) is not well understood. It happens, by the way, not only on alcohol consumption: the intake of barbiturates also leads to the increase of ADH and tolerance.
Here you can find much more information about acquired alcohol tolerance, but mostly from the behavioural viewpoint.


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The mechanism of cancer metastasis
Generally, EMT, Epithelial to Mesenchymal Transition is thought to be involved in the mechanism in which cancer cells metastasize in the early stage. EMT is an process in which epithelial cells depolarize and lose their cell-to-cell contacts, and gain mesenchymal morphology. The mesenchymal cells is capable of reaching distant sites through the blood vessels. So, EMT is thought to be a necessary mechanism for metastasis.
However, I found a surprising report from Nature article indicating that EMT isn't required for metastasis:
Fischer, Kari R. et al. "EMT Is Not Required for Lung Metastasis but Contributes to Chemoresistance." Nature 527.7579 (2015): 472–476.
They established an EMT lineage-tracing system in mice with the mammary tumors to monitor metastasis of the epithelial cancer cells to lung through EMT using epithelial-specific and mesenchymal-specific markers. This report showed that a small proportion of cancer cells underwent EMT and lung metastasis mainly consisted of epithelial cells which didn't undergo EMT.
I think this report is innovative and overthrows the commonly accepted thought that EMT is necessary for metastasis,
However, some questions come to me.
How the epithelial cancer cells gain the motility and metastasize without undergoing EMT？

This is an extremely broad question – there are several new theories on cancer metastasis even within the last few years. Do you think you could narrow your question down a bit to ask about one specific question about cancer metastasis? For example, like why do certain cancers metastasize to a particular tissue – that's still broad but much less broad than your current question.

I don't know much the mechanisms of cancer metastasis. All I know about it is EMT. I think epithelial cancer cells can't metastasize because they contact with the basement membrane and are lacking in the motility. So, what I want to know is why epithelial cancer cells can metastasize keeping their epithelial morphology.

It might be possible due to certain exosome secretions that prepare "pre-metastatic" locations in lung tissue.

I don't know an exosome is involved in the mechanism of the cancer metastasis !! However, do the exosome secretions have to do with getting the motility of the epithelial cancer cells？

This paper describes the mechanism for a different cancer metastasis: http://www.nature.com/nm/journal/v18/n6/abs/nm.2753.html

Basically, the secreted exosomes reach certain locations and cause the tissue to become more of a "tumor fostering" microenvironment.


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How exactly apoptosis starts?
I read article about apoptosis on Wikipedia, but didn't understand, how exactly the organism learns that it is necessary to launch process of apoptosis in certain cell. In other words, on what signs the cell is marked as "necessary to destroy"? How exactly at the chemical/biological level process of apoptosis starts?
Also I am misled by the fact that apoptosis occurs by a row of strongly differing reasons - not only aging, functionality losing, chemical/radiation affection, but also process of apoptosis can start in absolutely normal cells (including just newly created ones - for example, during formation of an embryo). How in that case the embryo knows what cells need to be destroyed, and how exactly it does it?

Unfortunately, this question is far too broad. From the [help/dont-ask]: Your questions should be reasonably scoped. If you can imagine an entire book that answers your question, you’re asking too much.

Too bad for me.


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Respiration of an animal cell media
I want to do respiration process of an animal cell media in laboratory environment.
I don't entirely sure how to supply it with Oxygen to the process because it is a gas, but not a liquid.

You want to grow animal cells in cell culture flasks?

@Chris I wanted to grow them in petri dishes, but I'll check it out!

That's basically the same.

@Chris so yes, I consider it as laboratory environment. I just look for a technique of supply.

Does this answer your question?

@Chris So are you basically saying I can just put Oxygen into container with a cell and it will absorb it by diffusion? I ask just to clarify.

@CubaQ it sounds as if you have little or no experience with growing animal cells in culture.  Be aware that there is a lot to know, and if you do things wrong (even slightly wrong) the cells will die very rapidly.  This isn't something you can improvise off the top of your head.

@CubaQ Yes, that's how it is done in the lab. If you have special requirements (higher or lower oxygen content) you will have to adapt this.

Supply of cells growing in adherent culture is unproblematic, as long as you don't fill too much media in the petri dish/cell culture flask.
Oxygen supply here work by diffusion which is getting more problematic if the layer of media covering the cells gets to thick. I usually follow the recommendations of Corning for the amount of media to be used in the flasks/dishes:

The complete information can be found here, other companies have similar data sheets available. With these amounts I do a lot of cell culture work and I have no growth problems.

I used to put 4ml of media in t-25 and 9ml in t-75, and change it in ~2 days. I mostly handled HeLa, HEK, Neuro2a and U87 cells. Worked fine for me.


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Geographical distribution of malaria and tuberculosis
Unlike malaria, tuberculosis (TB) is found across the whole world. Why and explain? I mean why are people affected with TB more than malaria and some say that in cold and developed countries malaria is less but TB cases are more.

Malaria is no longer found around the world because it has been eradicated from developed countries.  It was common in the USA until mid-20th century.

Both diseases have totally different dynamics. Why compare them?

@WYSIWYG Please tell me why this is not a 'good' answer?

The statement in the question about the current distribution of these diseases is not strictly accurate, as shown by the graphic below.

[Malaria graphic: Wikipedia user, Percherie (2006); TB graphic: Corbett et al. (2003)]
However there is no disputing that the contemporary and historical geographical distribution of these diseases differ. Why?
The crux of the answer is that this is because of the different agents that cause these diseases. Malaria is transmitted by certain mosquitoes and is therefore restricted to places in which these mosquitoes are found. TB is a bacterial disease, the geographical range of which is determined by human contact under conditions which favour its transmission.
To expand:
Malaria is transmitted by Anopheles mosquitoes, especially in Africa by Anopheles gambia together with the Plasmodium falciparum parasite. One of the factors determining the mosquito habitat is standing water and the elimination of malaria from Southern Europe followed drainage of the marches and swamps in which it breeds.
That is not to say that this is the only factor in the elimination of the malarial mosquitos from certain parts of the world in recent historic times. For example malaria has not been eliminated from Africa partly because of the cost and logistic problems of implementing programmes of eradication using drugs etc.
Tuberculosis (TB) in humans is caused by the bacterium, Mycobacterium tuberculosis. Its airborne spread was favoured by the crowded conditions in cities following the industrial revolution, and its elimination fostered by improved living conditions and the development of antibiotics in the twentieth century.
Footnote: Some Factors affecting Malarial Outbreaks in Africa
A section from an article by Tarekegn A. Abeku, entitled Response to Malaria Epidemics in Africa, is relevant:

In highlands, transmission is unstable due to fluctuations in temperatures that are normally low. Temperature affects duration of the sporogonic cycle of the Plasmodium parasite within the Anopheles vector, survival and feeding frequency of the adult female, and duration of the aquatic stages.

and

Semi-arid areas, on the other hand, have mostly warm climates, and epidemics are associated with anomalous rainfall, which causes increases in vector breeding and survival.

This is flat wrong.  Malaria was common in the USA before the 1940s.  It was transmitted by Anopheles quadrimaculatus in the east, An. freeborni in the west, and An. pseudopunctipennis along the U.S./Mexico border. All three are still prevalent; thus there is a constant risk that malaria could be reintroduced in the United States.

@iayork I was talking about Africa and Europe, where I believe malaria originated. That is why sickle cell anaemia and the thalasaemias arose. Malaria was wiped out in Europe by draining marches. I think your comment and down vote unjustified.

@iayork I have modified my answer. Biology SE exists to provide answers to biology questions. I have therefore tried to provide an answer to the question, which was about the restricted geographical distributiion of malaria. Is my first paragraph a correct answer to that question? If you think my amplification of that can be improved, please make constructive suggestions to that end and I will consider incorporating them. The risk of the recurrence of malaria in various parts of the world may be a global health concern, but it is not the subject of the question.

@iayork I have further modified my entry by adding some maps. This means that the one-line answer is no longer the first paragraph, as stated in my last comment, but the italicized sentence starting "The crux of the answer..."


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Gene sequence and DNA
can anyone help me with this?
It shows two gene sequences for a sheep and a goat.
   5’------C C T G A G G A G C A T G T T------3’
   3’------G G A C T C C T C G T A C A A------5’
               5         6         7         8        9
   5’------C C T G A G G G G C A T G T T------3’
   3’------G G A C T C C C C G T A C A A------5’
               5         6         7         8        9

I hope u can see it.
number 1 = goat
number 2 =sheep

what differences are there between the two gene sequences?
Decide the amino acids 5-9 for both gene sequence?

Look at the differences in the nucleotide sequences, and how those differences may change translation.

This question looks like it is from a homework assignment. What have you done to try to solve this problem on your own?

Thank you for replying. Well, as for question one, the goat has a AT meanwhile the sheep has a GC (under number 6) That may mean that there's a change in the sequence of the amino acid? Or is that thinking wrong?................. as for question 2) I find this difficult. I mean I have a table to see the amino acids, but what should i exactly do?

You're right. A change in nucleotide sequence 'may' change the amino acid sequence. To find out, use a standard translation table (https://en.wikipedia.org/wiki/DNA_codon_table) to see if a different amino acid results from the difference in codons. To translate, replace each three consecutive nucleotides (codons) with the amino acid in the table.

Amino acids can have different properties (ex. polarity) that can affect protein folding. If you find a difference in amino acids between the goat and the sheep, look up how the properties of the amino acids differ. If the properties are very different, then the resulting protein may have a different structure, and therefore may have a different function.

For translating, keep in mind that real sequences may be read by transcriptases in 1 of 3 different reading frames at a time. For each codon, you look at 3 nucleotides, but you may get a different amino acid depending on where you start.

Thank you indeed. I used the translate-table.  Now, I have to answer what difference there're between the enzyms of the organisms? How should I find that out?

As I mentioned in a previous comment, different amino acid properties can change the structure of a resulting protein, or enzyme in this case. The wiki page show some of the important amino acid properties. https://en.wikipedia.org/wiki/Amino_acid

Thank you. Now, when I'm going to use my "translate-table" to see which amino acids it's, let's take the goat, should I take the gen sequence from 5' to 3' or that from 3' to 5'  (i need to make the dna to rna)  thx

I recommend reading this article: http://www.ncbi.nlm.nih.gov/books/NBK22085/

Thank you indeed. The part with the difference between the enzyms of the organisms: I have translated my bases into amino acids, but now, when I have to find the difference, should I look at both amino acids from the goat and sheep and compare them? What should I focus on when I compare them? I find it difficult to find the difference between both enzyms.... Thx!

There is a one amino acid change, GAG encodes glutamate and GGG encode Glycine. the change from glutamate to glycine is a fairly substantial one, both in terms of polarity and also sterics, that likely effects the secondary structure of the polypeptide.


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Why can white hairs get dark again?
I have learned (probably in high school?) that hairs turning white is caused by the part of the folicle which produces the pigment dying and being replaced by an air bubble. This sounds very irreversible.
I have long dark brown hair, and since I turned 25, I have had a few white hairs here and there. It is not unusual to find hairs which have a dark tip but are white at the root, which fits the above theory.
But I also have hairs which are the opposite: the lower ten centimeters are pure white, but at some point, there is an abrupt transition to dark brown, and the hair is dark again up to the root. This is all a natural phenomenon, I haven't used dyes or bleaches.
So what makes white hair white, if it can turn back to dark? Why would a single hair turn back?

The pigmentation of hairs is achieved by the follicular melanocytes (specialized pigment cells) at the base of the hair shaft. These cells produce the pigment which is subsequently transported into the cells which produce the hair and integrated into the hair matrix.
Besides genetic reasons, there are two major ways of losing this pigmentation. First, as a part of the normal hair cycle, the hair grows for a while until it falls out and the hair follicle regresses. In this process the cells in the hair follicle die, including those which made the hair as well as of the melanocytes. In this step of the hair cycle the hair follicle changes its morphology. When a new hair cycle starts, the pigment cells in the hair follicle are replenished from a stem cell population called melanocyte stem cells. These cells are located in the hair bulge (marked in red in the figure below). The cells then start to proliferate to multiply their number. A few of these cells stay stem cells (to be able to repopulate the pigment cells after the next hair cycle.) Others differentiate into melanocytes which subsequently migrate towards the bottom of the hair bulb (shown in green in the figure).

Over time, the number of stem cells gets lower, and at some point there are none left. This leads to a situation where the pigment cells are not replenished at the beginning of a new hair cycle and the hair stays unpigmented. As this is a continuous process, the pigmentation gets weaker before it is completely lost. As far as this process is understood to date, this depigmentation is irreversible.
There are two very interesting papers about this topic:

Melanocyte Stem Cell Maintenance and Hair Graying
Melanocyte stem cells: biology and current aspects.

The other reason for losing pigmentation (temporarily or permanent) is the generation of so called "reactive oxygen species" (Hydrogenperoxide) in the cells of the hair follicle, which then destroy the pigment. This is basically the same reaction which is used to bleach hairs, but in this instance from inside. This reaction can have numerous causes, among them are vitiligo and stress. The reason for the build-up of the hydrogenperoxides is that enzymes, which usually break them down before they can cause harm are either mutated or downregulated. If the level of these enzymes (the catalases) goes back to normal, pigmentation is also getting back to normal. This has been tested experimentally with people who suffer from the pigmentation disease vitiligo.

Oxidative Stress in Ageing of Hair
Basic evidence for epidermal H2O2/ONOO−-mediated oxidation/nitration
in segmental vitiligo is supported by repigmentation of skin and
eyelashes after reduction of epidermal H2O2 with topical
NB-UVB-activated pseudocatalase PC-KUS

Can malnutrition cause temporary greying/whitening of hair?

@CRags If you lack tyrosine and cysteine, probably yes. Though I haven't read any reports on people changing their pigmentation levels upon a famine.

When you say "This includes dying of the cells" are you saying the hairs are "dyed" or they "died?"

@CayetanoGonçalves These cells actually die, I re-phrased the part. I hope it is clearer now.

One of the best answers I've come across, I find. With some basic knowledge, and speaking of dying - intrinsic pun - I think the answer just does not refer to any dying of the hair producing cell, as this is beyond this question. I wonder about related questions on StE about the dying of hair cells. Hair grows after death.

@PeterBernhard It is a myth that hairs and nails grow after death: https://www.snopes.com/fact-check/coffin-nails/

I think so, too, basically. Just let me know in case I am up to delete the comment or its final sentence. Great answer!

Hair colour is maintained by a pigment called Melanin which also affects skin colour too. When the melanin content in your hair decreases, it turns grey and eventually white. Multiple factors affect melanin levels in your body.
1) age
2) Genetics
3) Diseases
4) Cell Stress
You can read about them in a little more detail here. I cannot specifically pinpoint if you have deficiency in a particular mineral or the reason for your hair whitening is hereditary from your question. It could be a singular reason or a combination of different problems. Some solutions to treat hair can be found in this link (and plenty more if you Google it). If that doesn't work, I would suggest you meet a certified Dermatologist specializing in hair treatment.

A search of the Internet shows many anecdotal cases of people reporting their grey or white hair returning to their normal color.  Interestingly, many of these ancedotal cases begin by stating that their hair had turned grey or white at a young age (early 20s) before returning to it's natural color.  Finding a scientific explanation does not seem as easy.
Dr. Robert Graves reported in 1847 a case of a military field officer that had contracted dysentery, fever and other diseases. Prior to his illinesses, the officer's hair had turned white. After a few years of receiving treatment for his illiness, his hair had returned to its natural color.  This is consistent with a study by Bublin and Thompson (1992) which found that various drugs can cause sudden hair color changes. (The abstract does not say whether this includes a change from white to natural color.) Schaffrali et al. 2002) noted two people that had a disease called porphyria cutanea tarda regained their hair color.  Therefore, stress from disease or drugs may cause hair color changes.
Flesch (1949) found that the fur of black rats could be turned white when fed a diet deficient in copper. Restoring copper to the diet turned the fur color back to its normal color. Arthur (1965) found that excess molybdenum in the diet of guinea pigs can inhibit copper,  causing their hair to turn white. These results suggest that diet can also play a role in color loss and gain in mammals.  Vitamin B12 deficiency may also have affect hair color.
These studies show that regaining hair pigmentation has many possible causes. Of course, I have no way of knowing whether any of these apply to you, nor am I qualified to make such judgements. But, hopefully, some of this information will help you to understand some of the possible reasons for hair color change in humans.

In the case of drug induced pigmentation changes, there are two possibilities. Either the drug kill the melanocytes which produce the pigment and they are later replenished as I explained in my answer or that the drugs interfere with the signalling pathways which regulate the pigmentation. The case of the diet lacking copper is relatively easy to explain. The most important enzyme in the pigmentation process is Tyrosinase, as it is catalyzing the first step of the synthesis of melanin. This enzyme has copper in its active center, without copper it is not functional.

@Chris Thanks for improving the information contained in my answer.

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


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Are there cats with black skin?
Some mammals can have a black, pink or spotted skin, depending on race - see for example humans or pigs. But I recently learned that this is not the case with mice. Even black furred mice have pink skin, and there is a rare mutation which produces black skinned mice.
I was talking with a friend about cats and we got to wonder if (domestic) cats are the type of animal which can have dark skin, like pigs, or the type which doesn't, like mice. The tons of cat related sites on the Internet seem to all talk about black furred cats only, or about diseases presenting with skin discoloration, but they don't mention the skin color. So, which type of animal are cats?

A minor data point for you: look at the skin on the pads of the paws - our black and white cat has some black pads and some pink.  You might also look for pictures of cats that have been shaved for operations (e.g. spaying).

I have a black cat with white skin, so it doesn’t go hand in hand.

Easy: look at images of hairless cats. You will see they can be not only all black, but also grey, spotted, pink, and a few other rarer colors.

Also, take an average cat - and shave for surgery:

Note pigmented skin matching dark stripes.

This source seems to suggest that cats' skin colour is determined by their fur colour, as the same genes expressed in the fur which produce the colours (melanins) are also expressed in the skin.

The density of melanin can vary from one part of the body to another, down to patterns within individual hairs or gradients across skin, thus accounting for a wide variety of cat colors. Cats' skin appears strongly tied to fur pigmentation.
A cat who has darker fur probably has darker skin and vice versa on account of the melanin content of his skin and fur. Tortoiseshell cats and their white-stricken siblings, calico cats, have patches of both dark and light skin.

The color of mammals is determined by the pigment melanin. More specifically it is the mixture of the dark brown to black Eumelanin and the red to yellow Pheomelanin. These pigments are made a specialized cell type called melanocytes, which are located in the hair follicles (when they pigment the hairs) and in the skin.
Some animals (like mice) almost completely lack melanocytes in their skin (except for their ears, nose, parts of their feet and sometimes the tip of the tail), so they can only be pigmented when their fur is pigmented. For cats there is only very little data available and more, I haven't really found a good scientific article yet. From the descriptions (like here) I would say that the skin of cats is pigmented. Additionally they can get cutaneous melanoma which have their origin in skin melanocytes which would be possible if they weren't be there (this is the reason why mice cannot get cutaneous melanoma if they are not engineered).


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Why People have skin color between fair and dark?
According to Mendel's laws traits do not show any blending. So according to his laws people only with fair or dark skin should exist. Do the alleles in this case blend? And why?

There are several traits that do not follow the simplistic Mendelian rules. With skin colour, the trait is actually polygenic (and also quantitative).

Mendel also fudged his data. Traits blend all the time.

this question has been well addressed here: http://biology.stackexchange.com/questions/34565/skin-color-explanation
( so I guess it might be marked as duplicate ).

Mendel's laws were very basic to aid in the comprehension of genetics.  You think of Mendel's genes as an +- pair where + is dominant and - is recessive, making our +- gene produce offspring with the + trait but still being a carrier of the - trait.
However, when it comes skin colour, eye colour, hair colour, height, tendency to muscle growth, and a thousand other things, the gene is more like a series of ++-++-+++-, + is more recessive than -, but some of + will still show up over -.
In short, the colour of a person's skin is not a simple +- gene of dark and fair; everyone carries a certain amount of pigment genes and certain number of non-pigment genes.  The amount that one carries of each of the genes will determine his skin colour and his/her ability to pass on the dark/light characteristic.

To give a basic idea about the dimensions: if I remember correctly, from genome-wide association studies, height is currently known to be influenced by approx. 500 genes - that is 2-3% of all approx. 20000 protein-coding genes. However, studying these loci explain only about 20% of the variation seen in the phenotype height.

A minor suggestion: Instead of X and Y use some other symbols. X and Y can be confused for chromosomes.

Good point, @WYSIWYG .  Hadn't thought of that.


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Immunomic Microarray

"One can measure two or more signals simultaneously determined by a single feature, i.e.,
  epitope in immunomic microarray DNA microarrays measure one response value for each gene per sample; that is, mRNA concentration produced by the gene but a single epitope
  can generate different response values corresponding to different epitopes in peptide–MHC chips. In case of B cell epitope, it can be recognized by different isotypes of immunoglobulins, so here, one can measure both intensity and quality of antibody response."

These few lines are from the book:
http://www.springer.com/biomed/immunology/book/978-1-4939-1114-1
Chapter 3
What does measure of one response value for each gene per sample mean?
Different response value means??
how is intensity and quality both are being measured??

epitope in immunomic microarray DNA microarrays measure one response
  value for each gene per sample; that is, mRNA concentration produced
  by the gene but a single epitope can generate different response
  values corresponding to different epitopes in peptide–MHC chips.

The excerpt looks grammatically incorrect and is therefore confusing. I guess what it tries to convey is — like there can be several probes for a single mRNA in a normal gene-expression microarray, there can be several antibodies binding to different epitopes in the same protein. Different antibodies will bind to their cognate epitopes with different affinities. This is what is referred to as "response value"
By quality I guess what the authors mean is that for the same epitope it is possible to quantify the binding interactions between that epitope and antibodies of different classes (but same antigen binding site).
Having looked at this excerpt, I would not recommend this book to anyone.
You can also have a look at these two articles:

From Functional Genomics to Functional Immunomics: New Challenges, Old Problems, Big Rewards
Prospects for the Future Using Genomics and Proteomics in Clinical Microbiology


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Identification of proteins in this animation of a ribosome translating mRNA

This gif is from this page
After each aminoacyl-tRNA enters the ribosome, one blue thing comes and pushes the whole tRNAs whats that? I couldn't find it anywhere.(maybe some elongation factor?)
Also it seems that some thing is transporting the tRNA itself (maybe aminoacyl tRNA synthetase?)

The protein involved in "pushing" the tRNA and mRNA is the elongation factor EF-G. The protein involved in "transporting" the tRNA is the elongation factor EF-Tu.
Quoted from the Wikipedia articles:
EF-G:

When it binds to the ribosome A-site, EF-G causes the tRNA previously occupying that site to occupy an intermediate A/P position (bound to the A site of the small ribosomal subunit and to the P site of the large subunit), and the tRNA in the P site is shifted to a P/E hybrid state. EF-G hydrolysis of GTP causes a conformation change that forces the A/P tRNA to fully occupy the P site, the P/E tRNA to fully occupy the E site (and exit the ribosome complex), and the mRNA to shift three nucleotides down relative to the ribosome due to its association with these tRNA molecules. The GDP-bound EF-G molecule then dissociates from the complex, leaving another free A-site where the elongation cycle can start again

EF-Tu:

The tRNA anticodon domain associates with the mRNA codon domain in the ribosomal A site. If the codon-anticodon pairing is correct, EF-Tu hydrolyzes guanosine triphosphate (GTP) into guanosine diphosphate (GDP) and inorganic phosphate. This creates a conformational change in EF-Tu that causes EF-Tu to dissociate from the tRNA of the ternary complex (and therefore leave the ribosome). The aminoacyl-tRNA then fully enters the A site, where its amino acid is brought near the P site's polypeptide and the ribosome catalyzes the covalent transfer of the polypeptide onto the amino acid . The tRNA on the P site (without peptide) moves to the E site and is then released.


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Brainbow fluorescence labeling technique
I have this picture describing the Brainbow system here:

The paper I am reading says it uses Cre-lox recombination to express a certain color. If the cell in question was expressing a yellow fluorescence then what would the construct in that cell look like in terms of the picture given? Would it just be a single line with the UAS, EGFP, and mKO2 in that order or would it be two lines, wone with the UAS and EGFP and on with the UAS and mKO2?

I would suggest to also read the original Brainbow paper by Livet and colleagues, which goes in details in the genetics of the system and its variations. Transgenic strategies for combinatorial expression of fluorescent proteins in the nervous system - Livet et al., Nature 2007

Yellow would need the expression of red and green so that would mean the excision of the blue fluorophore. It would be one line with egfp and the other line with mKO2--- the order doesn't matter-- these represent chromosomes.

In the line expressing green wouldn't you have to excise the blue and red regions as well in stead of just the blue? Similarly for the line expressing red wouldn't you have to excise the green and blue regions? And also what about the STOP cassette?


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Why is the species-diversity of deadly parasites greatest in the tropics?
There are so many parasites living in tropical regions of Africa, South America, or Asia, but very few in Europe or North America.
Is this due to climate, or are there other reasons?
Many of the tropical diseases and parasites are transmitted by insects, such as flies and mosquitoes. Well there are flies and mosquitoes in Europe as well.
There might be malaria-transmitting mosquitoes in the very south of Europe, and there is encephalitis transmitted by ticks. But that's it. Why don't the hundreds of different parasitic species from Africa spread to Europe ?

Parasites aren't the only group to show this pattern. Many clades and ecological groups are more diverse in the tropics. This pattern is known as the Latitiudinal Diversity Gradient

Related Q/A: http://biology.stackexchange.com/q/14472/3624

The diversity of parasites shows a gradient with increasing diversity from the poles to the equator. Several reasons have been brought forth to explain the latitude-dependency of parasite diversity:

An increased diversity overall around the equator; species diversity in general is greater in the rain forests and hence more hosts are available and thus more parasitic species can develop that target specific hosts;
Larger amounts of precipitation and higher temperatures around the equator may favor the development and transmission of parasites (Nunn et al., 2005);
Increased available energy overall around the equator (Guernier et al., 2004).

References
- Guernier et al., PLOSone (2004): 0020141
- Nunn et al., Diversity and Distrib (2005); 11: 249–56

Nice answer +1 (and good post +1)! I have two questions: 1) Does "increased available energy" affect parasite diversity other than by increasing overall diversity (in which case the third bullet point would be the same as the first)? 2) I have a good intuition for what higher precipitation would favour parasite transmission but I fail to have a good intuition for high temperature. Can you explain? Thanks

@Remi.b - Thanks! 1) I think total energy has more to do with the gross number of animals present. Higher numbers of vectors and hosts will promote development of parasites overall. It's more of a general factor. 2) Most processes, including growth in general, goes faster at higher temperatures. Again, it's more of a general factor. The first bullet point has the strongest association, the 2nd and 3rd less so afaik.


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Was mammal body better suited for some type of the marine environment than the body of fish?
When some of the land mammals came back to the oceans, they seem to be successful in the competition with fish at least in some environment even though they seem to have a huge disadvantage in the need of breathing above the water. So how did they succeed in the competition with fish?

I think you have cause and effect reversed.  Marine mammals probably didn't start out competing with fish, they started eating fish.  A bear, for instance, isn't particularly adapted to marine life, yet can (in suitable environments) catch & eat them successfully.  Over time the more successful fishers might evolve to look like otters, say, and then seals...

Ok, so the main advantage was the size? I assume there were no bigger predators in the seas before. If you could link me any source, I'd consider this a nice answer ;)

Sharks can be pretty large - I think bigger than most land mammals, and a good many marine ones.  Other fish like tuna & swordfish can be pretty big, too.  These (or their ancestors) all existed for many milliions of years before marine mammals, but coexisted with ichthyosaurs, pleisosaurs, mosasaurs, &c.  It isn't necessary that mammals displaced prior predators, only that they could catch enough small fish to survive & reproduce.

By asking So how did they succeed in the competition with fish? you are making the false assumption that they had somehow to succeed at some form of competition. What lead you to this false assumption is I think either of the following two mistakes..

A misunderstanding of the principle of competitive exclusion.
A false assumption about the existing overlap between marine mammals ecological niche and fishes ecological niches

Competitive exclusion
The principle of competitive exclusion states that two species occupying exactly the same ecological niche cannot stably coexist. One must either become extinct or shifts its ecological niche (process that is known as character displacement).
A consequence of the above is that if two species have ecological niches that partially overlap, they can still stably co-exist.
Ecological niche of marine mammals
There are two independent lineages of mammals that evolve marine life (cetacea and sirenia). I don't know which one you have in mind when asking the question and a sensitive complete answer would depend on the lineage of interest. However, in any case, there is such a diversity of ecological niches in fishes that it is hard to really fully address the question.
Marine mammals occupy different ecological niches. There is no question of whether one has an advantage over the other as the species do not compete for the same ressources.
A typically important reason for why marine mammals and most fishes occupy different ecological niches relate to their size differences. Simply put, mammals to be quite big! For example a orca eat fishes (and other things) that had few predators before. There is therefore not much competition involved.
Just to reiterate... in your comment you say so the main advantage was the size?. Size was one of the biggest reason why they would be able to occupy previously unoccupied ecological niches. But it is not an advantage toward competition with fishes as you seem to be thinking as there probably little competition.


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Why does our body exhibit bilateral symmetry?
Externally, we (humans) look symmetrical. However, internal organs don't show the same patterns of symmetry (heart being on the left side while the liver is on the right side, etc.). It is a bit counter-intuitive to me that the exterior of our body seems to be mainly symmetrical while the interior is asymmetrical.

What is the advantage of having bilateral symmetry in our body?
Why don't all of our organs exhibit bilateral symmetry?

Welcome to Biology.SE. One cannot believe (or not) in evolution, one can only understand (or not) evolutionary biology.

The question is interesting +1, I am just afraid that there are two questions in the same post...we'll see if it is an issue. I'd guess that bilateral symmetry was under positive selection for mobility purpose but it is just a guess.

I don't wan't to be a bummer but I think you can just skip the I understand/believe evolution part. And the last sentence as well. I edited your question, feel free to roll back if you preferred your version. There are probably a few other edits to improve the question.

That's fine, the question gets more clear after the edition. I am thinking that internal asymmetry has something to do with improving biological functions like metabolism and absorption and assimilation, but I have no idea for our external bilaterally symmetry.

also Why are humans and almost every species on earth symmetrical?


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Why does all life use the same macromolecules in their genetic code?
There is no biochemical constraint of any sort, so why doesn't some other code work? Why is it specifically RNA/DNA?

possible duplicate of Why did abiogenesis only happen once?

You are asking two relatively different questions in your post. I'd suggest to restrict your post to only one (and expand on it).

I don't think it is a duplicate of "Why did abiogenesis only happen once?". The question above might be reformulated as: "Why hasn't any lineage evolve to use a different genetic code than the ancestor (or than the other lineages)".

"If it ain't broke don't fix it?" If there were organisms that used other genetic codes then it would seem they are now extinct; species that used this code had the most progeny surviving to reproduce. New, random mutations that modify some aspect of the translational apparatus, and that would yield a slightly different code, are presumably lethal.

There is an interesting biochemical question underlying this question: "Why are nucleic acids better than other polymers for our genetic code?" That's what I've answered anyway!

@GoodGravy "Why are nucleic acids better than other polymers for our genetic code?" There is no answer to it.. There can be many different polymers that can be equally good or even better. Good also is a very subjective term.

@WYSIWYG I try to address why RNA might have been originally preferred in my answer. I'll expand on that though. The main thing is that you're limited to abundant polymers, and of those RNA was preferable for early forms of life for some reason.

Preamble
Any answer regarding the origins of our biochemical evolutionary origin will be reasonably speculative given that this is a very hard question to scientifically test and this field is generally understudied to say it is pretty much the most fundamental biochemical question. But there are a few reasons why RNA makes sense as the prime genetic molecule compared to other established macromolecules present in the primordial soup, and also there are good reasons why DNA superseded it as genetic storage for most cellular organisms.
In summary, the alternative abundant polymer macromolecules that came from the primordial soup aren't as versatile as RNA, and over time DNA was used more over RNA due to it being a more reliable information storage molecule.
We must remember though that the conditions that lead to the genesis of RNA is a much tougher question. There are an unfathomable amount of combinations of chemicals that could have facilitated an evolutionary process. @WYSIWYG made an excellent comment regarding why this is an almost impossible question to answer definitively:

...Why is there a phosphodiester backbone used rather than
ether, amide, carboxyl ester or any other kind of linkage? Or why
purines and pyrimidines, why not naphthalene ring heterocycles? Why
imidazole, why not oxazole or furan? You cannot reason this out in a
reverse manner.

Therefor in this answer we will be discussing RNA and other bio-polymers that were established in abundance from the very early primordial soup, not the original genesis of such biochemicals. What made each of them good vessels for an evolutionary process?
A genetic code macromolecule needs the following features:

Stable.
Variable structure.
Expandable.
Replicable.

RNA has all these and doesn't rely on a biological system for reproduction of the RNA molecule.
RNA world.
Let's not forget that DNA is probably not the first one along and there was an RNA world before the cell as we know it. Even today many viruses particularly make use of ssRNA.
RNA was a good molecule because it was a polymer made of 4 base monomers that could bind with other polymers to make any array of compositions of the base components and was spontaneously replicable. This allowed a primordial form of molecular evolution as we know it today. It is able to carry more varied information than other abundant macromolecule polymers.
RNA can also carry out functions in a similar way a protein might, including catalysis. No known sugars or other macromolecules are able to demonstrate the same level of variability and versatility as RNA, although deoxyribosymes have been artificially designed in laboratories.
This probably gave it a good chance at establishing itself as the first molecule to trigger biogenesis, and this lead to nucleic acids being established as the fundamental molecule of molecular evolution.

DNA chemical structure.
Eventually RNA evolved into more complex structures and DNA broadly superseded RNA as a storage device for genetic information in cellular organisms primarily due to the increased stability DNA offers over RNA. If we take a look at DNA specifically we see a very good data storage mechanism for a couple of reasons.

Intra-strand hydrogen bonding and different chemically structured sugar group makes a more stable overall structure.
More rigid grooves allow proteins to bind at particular sites.
Again, it's a polymer of variable composition.

Alternative coding macromolecules.
What are our other options from the biological polymers?

Carbohydrates. The glycocalyx coats most cells in our body, and clearly sugars (specifically polysaccharides and glycoproteins) are an expandable, information rich molecule. However it relies on proteins for assembly in the same way proteins do, so it never really got the chance to be that prime molecule.
Lipids. A brilliant expandable polymer, and many are spontaneously expanding in the right conditions, but generally lipids cannot carry as much "information" in the polymer (pretty much just varying lengths of CH2 groups).
Proteins. Too complex and not spontaneously replicable. They rely on other systems for production (except in some rare examples, although they arguably still rely on a complex biological system).

There can be infinite comparisons. Why take only lipids and proteins for comparison. I can ask why phosphodiester bond as a backbone and not ether, amide, carboxyl ester or any other kind of linkage. Or why purines and pyrimidines, why not naphthalene ring heterocycles. Why imidazole, why not oxazole or furan.. You cannot reason this out in a reverse manner.

@WYSIWYG excellent point. I think we are talking about different things though, and my answer isn't clear enough. You're talking about the genesis of the primordial soup, I'm describing how RNA was a better vessel for evolution given other established bio molecules. I will edit later to tidy up this point.

One of the things that you left off of your list as to why DNA is more stable is the 2'-hydroxyl of ribose is reactive and can induce strand breaks where the 2'-hydride of deoxyribose is not a center of reactivity. RNA degrades more rapidly than DNA simply because of the chemical structure of the sugar it is made from.

That is an evidence that all the creatures share a same ancestor from evolution.
About the origin of the genetic code, scientists proposed some hypotheses to explain it.

Chemical principles: From the experiments, scientists found that some amino acid have a selective affinity to certain triplet codons.
Biosynthetic expansion: The original creatures may produce amino acids as by-products of metabolism, and then some of these function into the genetic coding. Evidences show that fewer different amino acids were used in the past than today.
Natural selection: The goal of the genetic coding is to minimize the mutation. Some scientists assume that ancient life may have longer codon than triplet codon, such as quadruplet codon, but quadruplet codon have more error that triplet codon, and then only the triplet codon can survive.
Information channel:  This hypothesis suppose that the process of genetic code translation is an error-prone information channel. The organisms wanted to inherent their genetic information accurately and efficiently and stay away from the genetic noise. Genetic code should be influenced by three evolutionary force: the needs for diverse amino acids, for error tolerance and for minimal cost of resource. Finally, the genetic coding amino acids become nonrandom.

I'm not sure how this answers the question of DNA and RNA being used to carry our genetic information. You're describing general theories about ribosomal translation. I think point 4 might be on point, but even in that point I don't quite understand what you are getting at entirely.

The interesting thing about evolution is that Mother Nature does not go back to the drawing board and start with a completely new design. Evolutionary changes happen in tiny increments. Faced with a problem like the appearance of oxygen in the atmosphere, evolution did not redo the whole genetic structure of plants. It tinkers. So we ended up with a wasteful and inefficient system. But it works.This kid does the most wonderful humorous video explaining this. Just google Rubisco tubes.


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What signals a ribosome to stop production when the cell is out of available amino acids?
In the production of a protein molecule, there have to be a ready supply of free-floating amino acids. When a given codon for adjoining, say, serine comes up, how are the serine molecules found out of a soup of 20 different types of amino acids?
For example,
Meleagris gallopavo (turkey) small muscular protein
NCBI Reference Sequence: XP_010724014.1  88aa GI: 733873411

 1 mskqpashvk aiqaninipm gafrpgaghp hkrkevtpee veesvpatee ekdkkhlpga
61 iklpgpavnl seiqniksel kfvpkaeq

has 9 alanines, 1 aspartate, 11 glutamates, 2 phenylalanines, 5 glycines, 4 histidines, 6 isoleucines, 11 lysines, 4 leucines, 2 methionines, 4 asparagines, 10 prolines, 4 glutamines, 2 arginines, 5 serines, 2 threonines, 6 valines, 0 tryptophans, 0 cysteines, 0 tyrosines.
So the cell would deplete glutamates much faster than aspartates and obviously infinitely faster than tryptophans. So, as the concentration of glutamates drops drastically with the production of each new turkey muscle polypeptide strand, getting diluted by the nonreactants tryptophan, cysteine, tyrosine, wouldn't the reaction rate get exponentially slow?
And when the last available glutamate residue gets attached, and if it happens before the polypeptide is complete, yet it needs one more glutamate to complete the chain, what signals the ribosome to "stop looking for more glutamates"?

Under normal conditions, it will not run out. Glutamate can be synthesized by the cell, so as long as there is a nitrogen and a carbon source, you can make it. Also the cell is degrading proteins all the time and those amino acids get recycled by the cell.

When cells run out of amino acids, more and more of their tRNAs remain uncharged. This elevated ratio of uncharged/charged tRNAs trigger complex signalling pathways that control amino acid biosynthesis, general reduction of translation, halting ribosome biosynthesis, autophagy (includes ribophagy - digestion of ribosomes) to recycle cells' components, etc. This can be clubbed into general amino acid control (GAAC) and involves the super important regulatory kinase protein called as Target of Rapamycin (TOR) and other transcription factors. The regulation of amino acids level is one of the most basic and important features of cellular metabolism and can be found conserved from yeast to humans. In addition to GAAC, there can be pathways for some specific amino acids as well.
There is not shortage of scientific literature. To start with you can read following article:
http://www.cell.com/trends/cell-biology/abstract/S0962-8924(14)00036-1
http://jcb.rupress.org/content/206/2/173.full

For the most part, there is no signal to a ribosome to "stop looking for more glutamates".  If there is a shortage of a needed amino acid that prevents a ribosome from continuing elongation of a polypeptide, the ribosome simply waits for the needed tRNA-amino acid complex to become available.
The main effect of a lack of amino acids for protein synthesis is to cause inhibition of new initiations of translation of mRNAs into proteins.  This form of translational regulation occurs when a protein called GCN2 senses the lack of an essential amino acid, which causes it to disable the initiation factor needed for a ribosome to start translating a new mRNA strand.

And what about the No-Go decay mechanism?