Extreme examples of protein translation/use coupling/decoupling? What are known extreme examples of protein translation/effect coupling/decoupling? For example, examples of proteins that are immediately used at the time the have been translated and vice versa, cases of proteins that are translated but then only used much later in time in/outside the cell?

Proteins that are membrane localized or secreted would take time to become active or even become poised for activity. Membrane receptors may remain inactive until triggered by the appropriate ligand. Nonetheless proteins won't remain (inactive or active) for a very long time as constant turnover happens in the cell.

One example, similar to what MarchHo mentioned in their answer (pre-proteins) is that of fibrinogen. Fibrinogen gets converted to fibrin when there is an injury and haemostasis reaction cascade is initiated. Fibrinogen has a biological half life (in its latency) of ~100 hours [ref].


Are there emotions that motivate pattern completion? If so, where in the brain are they located? I have been studying musical "tension." Musical tension essentially refers to the "expectations" one builds up in a melody that are then "released" when a stimulus matching the expectation occurs. For example, if you play the white notes on a piano in order CDEFGAB, you have a "tension" that motivates you to finish the scale and play C to complete the pattern.

I am aware pattern completion occurs in the brain and have seen a few biological models of this. For example, with attractor network models of human memory. So I am not surprised obviously that pattern completion occurs. But this example with musical tension highlights how there is an emotion (aka drive or motivation) that compels me to complete the pattern. When I hear the sequence CDEFGAB, I am compelled to finish the sequence.

My Question

Can someone provide me of examples of canonical models of emotions influence on pattern completion? I would like to learn example mechanisms as to how, on a circuit level, emotion would influence pattern completion.  I am particularly interested in examples relating to common forms of human creativity like visual art, problem-solving, etc., but any examples will do.

This "tension" is actually called anticipation in neurobiology and related fields. Whole purpose of this is to get higher reward. This is generally happens because of dopamine release. Many musicians have utilized this 'anticipation' technique in their compositions. Famous example is Led Zeppelin's stairways to heaven in which audience is 'anticipating' third part of song where Page's guitar in high tempo. Anatomically distinct dopamine release happens during anticipation and one will experience of peak emotion to music. You can read this paper for experiments related to this. This paper's introduction has given reference to many of such research papers. Go through it's references.


Should we induce fever to assist healing? I am currently reading "The Fundamentals of Anatomy Physiology" 10th edition, and have found it an incredibly interesting book. I have just been reading about the lymphatic system, and the various Leukocytes and their roles. When it mentioned fever as an immune response, I was familiar with the concept: Bacteria and viruses operate very nicely at our usual body temperature, but not so well at around 39 degrees Celsius.

What I wasn't aware of was "For each 1 degree Celsius rise in body temperature, metabolic rate increases by 10 percent. Cells can move faster, and enzymatic reactions take place quicker." (Quoted from page 828 of that book).

Now that seems like a massive benefit (though I believe you could only really push 1 or 2 degrees before you start getting into dangerous territory), but I notice that fever is not present in all illnesses. Inflammation seems to induce fever through the wounded area, which makes sense.

So now for my question: Could it be beneficial to artificially induce fever in a person who has an illness if they are not already experiencing fever? I believe a few things would need to be considered (more than likely a lot more than I can think to list):

Increased metabolic activity would surely need a higher energy intake would it not?
Are there cells that are actually going to suffer from the temperature increase?
I'm assuming this would actually be a rather poor technique to deal with cancer as from my currently limited knowledge, it is simply a cell that is producing abnormal proteins. If this is the case, the metabolic increase would likely apply to these abnormal cells, resulting in faster proliferation. Are there other such cells/infections that will benefit from temperature increase?

Finally, what are possible downsides of long term fever if energy intake is sufficient to maintain an increased metabolic rate at these higher temperatures?

Could it be beneficial to artificially induce fever in a person who has an illness if they are not already experiencing fever?

No, not really. Pretty much the only use of hyperthermia in medicine is in the treatment of cancer. If you google "use of hyperthermia in medical treatment", you'll likely only find two kinds of hits: those for cancer treatment and those for malignant hyperthermia (a side effect of some psychotropic drugs.) The hyperthermia used to kill resistant cancer cells is high enough to destroy proteins (~113°-114°) and very localized; your entire body raised to this temperature would result in death very quickly. Lower (i.e. physiological) levers of "hyperthermia" (or hyperpyrexia) would not kill the cells.

At the turn of the century, there were many who believed in the therapeutic use of hyperthermia in the form of hot baths, hot springs, and even injection of infectious agents to produce fever(!), but the practice has fallen into disuse, probably because there were no studies which supported it.

However, hyperthermia isn't good for you; it is something to treat seriously. When the cause isn't known, the efforts used to treat it can amount to many unnecessary tests and treatments (as seen in the accident victim in the fourth reference. When it's present in a moderate amount, it can still be dangerous:

  When fever occurs, many physiological stresses take place. Some of these include increased oxygen consumption as a response to increased cell metabolism, increased heart rate, increased cardiac output, increased leukocyte count, and an increased level of C-reactive protein. Oxygen consumption increases by 13% for every 1°C increase in body temperature, provided no shivering occurs. If shivering is present, oxygen consumption may increase by 100% to 200%. Some cytokines released during fever states also induce physiological stress. These cytokines can trigger accelerated muscle catabolism by causing weight loss, loss of strength, and negative nitrogen balance. Physiological stress can be manifested by decreased mental acuity, delirium, and seizures, which are more frequent in children.

It is likely beneficial in the presence of infection:

  Heat shock proteins are one of the more recently studied fever-responsive proteins. These proteins are produced during fever states and are critical for cellular survival during stress. Studies suggest that these proteins may have anti-inflammatory effects by decreasing the levels of proinflammatory cytokines. Fever also triggers other beneficial effects, including an increase in the phagocytic and bacteriocidal activity of neutrophils and enhanced cytotoxic effects of lymphocytes. Some bacteria become less virulent and grow slower at the higher temperatures associated with fever. Increased levels of C-reactive protein promote phagocytic adherence to invading organisms, modulate inflammations, and encourage tissue repair.

In the absence of infection, there is no benefit to systemic elevation of temperature. For the disadvantages of continued elevated metabolic rate, one need only look at hyperthyroidism to see the deleterious effects, the worst being cardiotoxicity, even in subclinical hyperthyroidism, as well as dementia, atrial fibrillation, ventricular hypertrophy, miscarriage, perinatal morbidity and mortality, decreased exercise tolerance, etc.

Years ago, one of the most common self-inflicted illnesses was hyperthyroidism - people taking thyroid hormone replacement unnecessarily - usually because of the weight loss that occurs with elevated metabolic states. Interestingly, efforts are underway to isolste and manufacture a thyroid-hormone like substance which will cause decreased weight without cardiotoxic effects.

Hyperthermia in Cancer Treatment
HYPERPYREXIA PRODUCED BY BATHS
ARTIFICIAL FEVER IN THE TREATMENT OF GONORRHEAL OPHTHALMIA
Thyrotoxicosis in a patient with multiple trauma
Metabolic Effects of Thyroid Hormone Derivatives


DNA methylation in different positions I'm trying to understand how does  DNA methylation and histone methylation status of promoters differs given their position in a gene? Does position affect whether they are repressive or activating?

For histone methylation , whether the marks are activating or repressive is determined predominately by which histone tail is modified at which position. DNA methylation by itself however is position dependent; in regulatory regions such as enhancers and promoters methylation tends to be repressive (at enhancers this is mostly mediated by being anticorrelated with the activation mark H3k27Ac) whereas within gene bodies DNA methylation is associated with increased transcription (Ref - http://www.cell.com/cancer-cell/fulltext/S1535-6108(14)00316-X )


How do catalase and other antioxidants neutralize free radicals? In learning about how cofactors are essential to proper enzyme function, my textbook mentioned catalase and its relation to the human body. According to my textbook, catalase is similar to hemoglobin in that it has 4 hemes which cradle an Fe (iron) atom; the iron atom is used to neutralize free radicals when it "pulls on the substrate's electrons, which brings on the transition state" after catalase is holding a substrate in its active site. I already know that free radicals have one or more unpaired electrons which make them dangerous as they "seek out" an electron to complete its pair on any molecule, atom, or ion it can find, perhaps causing significant tissue damage in the process. I also know that the transition state is a key point in a reaction in which the activation energy required has been met and the reaction will continue spontaneously until it ends.

My question is, what exactly is happening here that helps to neutralize a free radical, and what is the part after the transition state doing?

If I had to guess, based on that cofactors generally can be affected during a reaction, perhaps Iron somehow binds with the free radical and share its electrons, effectively neutralizing the unpaired electron as well as using up the Iron atom? I imagine the "pulling" in the book could fit a description of a weak chemical bond/attraction, but I'm still unsure.

Catalase (hydrogen peroxide oxidoreductase) does not actually quench free radicals. It catalyzes the conversion of hydrogen peroxide to water; the former is a source of a free radical, not a free radical in itself.

This is the proposed mechanism of action of catalase: First one of the oxygens is deprotonated by at the active site of the enzyme. Then the Iron atom that is bound to heme forms a co-ordination complex with the deprotonated oxygen and pulls it away from the other oxygen. As a result the O-O bond breaks.

Free radical quenchers/antioxidants react with the free radicals and form non-toxic products.


what kind of bonds join the okazaki fragments During DNA replication, the synthesized okazaki fragments adjacent to each other are joined up directly by DNA ligase-catalyzed phosphodiester bond formation. Can someone point out to me which part of this statement says it's false? All I know is that the fragments are joined together by DNA ligase, which can only mean the part about the phosphodiester bond is wrong, but arent the 2 nucleotides joined by a phosphodiester aka nucleotide bond?

I'm pretty sure the "phosphodiester bond" part is correct.

The only thing I can think of that might be questionable is the word "directly". If directly = immediately, then the sentence could be termed false, because they aren't joined immediately.

Even then, it seems like that's just grasping at straws, so I wouldn't worry too much about it. It sounds like you understand the concept, which is what matters.


Can fruit tissue be cultured and grown independent from the plant? Can fruit tissue be grown in a tissue culture as is done to other plant tissues? From the answer to this question, I learned that fruit is alive. Could it be possible to manufacture fruit products without plants, using this method?

Plants are not a strong suit for me, but in general the answer is yes.  What I know mostly comes from animal tissue, so someone may have a better answer than I...

Botanists have been cloning plants from cuttings for thousands of years.  More recently, propagation from cell lines around for much longer than for animals.  Entire plants can often be grown from a plate of cells.  So you can grow roots or an entire plant from cells right now, but I can't find any mention of anyone trying to grow fruit without the rest of the plant, and there might not be any research for this.  Let me explain why this may be...

Bioengineering animal tissue and organ growth has been an intensive area of research for the past 15 years or so.  In some cases, such as the growth of skin or liver, the technology has proven to be exceptionally valuable and useful.

Using plastics with biological growth factors attached and 3D printing, even more complex organs such as bladders and tracheas can be grown from the patients own cells, which avoids the problems of rejection and the complexities of donor matching.

More recently growing muscle tissue in an animal free culture has been tried, which would relieve some of the environmental and ethical problems of raising meat animals.

All this has been driven by a strong cost-benefit payoff.  A transplanted organ is highly valuable and improving that process and making organs more broadly available for patients has a high economic value.  The more often the structure is related to the tissue around, the more structurally complex, the more difficult it is to imagine growing that organ independently of the host organism (brain and eyes come to mind).  Other transplant worthy tissue cultures look quite promising.

Right now, it seems as if plant fruit like an apple or a kiwi might be difficult/expensive to grow in the lab as opposed to just picking them off the tree.  I think that growing a banana pulp or an apple sauce might be possible, though.  Who knows what we might be doing in 50 years or more though?


Why does hexokinase bond phosphate to the hydroxyl group on carbon-6 of glucose in glycolysis? When glucose enters the cell, it is phosphorylated by the enzyme hexokinase.

Why is this phosphorylation done at carbon-6? Why not at C-1 or C-2?

In other words, why is glucose-6-phosphate being produced rather than a different isomer of phosphorylated glucose?

First of all some nitpicking, but the actual phosphorylation happens not to the Carbon-6 but to the hydroxyl group bound to this carbon atom. The mechanism is a nucleophilic attack of the hydroxyl group on the terminal phosphoryl group of ATP. Schematically, this looks like this (image from here):

The main question, why the reaction happens on this carbon atom can be answered rather simple (although the explanation is a bit longer): Because only this is openly available for a chemical reaction and the others are inside the hexokinase and thus shielded.

Hexokinase exists in two forms: One relaxed, open when no substrate is bound and one closed with a changed morphology when the enzyme has bound its substrate. This mechanism is called "induced fit" and a quite common motif in enzyme catalyzed reactions and brings together the active center of the enzyme, possible co-factors and the substrate and excludes interfering other actions.

In the example of the hexokinase, glucose is brought into close proximity to the terminal phosphoryl group of enzyme-bound ATP to enable the chemical reaction. Because all other potential hydroxy groups are shielded by the enzyme, only the group at the carbon-6 can be chemically active. For more details, see the references.

Schematically, this looks like this, with the open form to the left (the arrow indicates the binding site for glucose) and the closed form right (image from here):

References

The Structure and Mechanism of Hexokinase
Mechanism of liver glucokinase.


What is the simplest way to demonstrate the germicidal property of UV light? This is intended for a high school project. I am familiar with the one that studies growth of e coli over time in a petri dish but I a bit concerned about as to how safe a demonstration of this nature might be. also no idea as how one may obtain such e coli sample safely.

You can make homemade bacterial growth medium.

https://www.madaboutscience.com.au/shop/science-extra/post/grow-bacteria-on-homemade-agar-plates/

Basically it is just nutrient jello: beef stock, sugar, gelatin to make a firm surface.  It would be nice to have all your cultures in uniform plates or cups.  You could order petri dishes or use what you have available.  I would consider an ice cube tray or you could cut off disposable Red Solo cups to make dishes.

Then forget e.coli.  Inoculate the dishes with random things in the environment.  Everything has microbial life.   Fingerprints from various people are fine. Tongueprints would be a good variation - the jello is not poisonous.   A paw print from an animal would be fun.  A stick from the yard.  A snail.  Label each one with a label you can see from above - maybe a piece of paper on the table next to it.

Each of these prints will grow a mixed bunch of germs and fungi.  You might want to keep them cool because they will grow fast.  Take pictures periodically over time.  Keep them covered so they don't dry out.

Each type of dish (for example, Ted's tongue print) will have one dish in the dark (under foil) one in the light and one under UV light.  If you make big dishes you could have a half and half: light side and dark side.

Count colonies that can be seen at each time period.  That is your hard number and you can graph it over time.  The lines will diverge which will be a great visual.

In addition to the inhibitory effect of UV you can discuss how it differs.  Suppose there are orange colonies which do not seem to be inhibited by UV in the same way as everything else.  You could smear some of the orange on a microscope and look it is.  Is it some resistant organism?  You could discuss the variety of colonies that appear depending on the inoculum.


Are viruses self-propelled? So obviously, viruses are nonliving. But when my teacher was teaching viruses in the video (we're doing "flip" learning this semester), the way he described it, it seemed like the viruses responded to their environment in that they moved around until they found a cell of the right type, and then they latched on and hijacked it.

I had always thought of it more like that they were just kind of floating around, carried by the host system (blood in animals for example), until they "bumped into" the right kind of cells and both sets of membrane proteins "docked". But my theory/idea doesn't really make sense because it doesn't account for how viruses would be able to infect bacteria.

But, the idea that viruses propel themselves doesn't make much sense either, because viruses are nonliving, and one of the characteristics of life that they do not meet is that living things acquire and use energy.

In summary my question is, how are viruses propelled? Do they move themselves, or are they moved by external forces?

All of your reasoning is correct - viruses are not motile (i.e. not self-propelled).

I don't understand why you think this would cause a difficulty in the case of bacteria.

Edit in response to comment @Remi.b

Some cursory research on estimating probabilities of collisions between particles engaged in random walks has revealed some very challenging maths. So I decided to simply look at some data.

Remarkably there is a fairly recent paper describing investigations of the kinetics of bacteriophage adsorption.

  Moldovan, et al. (2007) On Kinetics of Phage Adsorption. Biophysical Journal 93:303–315

I didn't realise it was still possible to publish papers like this, but in fact it is very interesting. For our current purposes we only need to consider the data presented in Figure 3, which show that when E. coli cells at a density of 108 cells ml-1 are mixed with bacteriophage λ at a density of 5 x 104 particles ml-1, then 90% of the phage have attached to a bacterial cell within less than 10 min.

Just to relate this to a real life situation, it is estimated that sea water contains bacteria at a density of 106 cells ml-1 and phage at 5 x 107 particles ml-1.


Why do men grow facial hair? Ancestral facial hair.
Our closest ancestors, the chimpanzee and bonobo, both grow facial hair around the mouth area. What is noteworthy is that this is the case in both males and females of the species.
Female chimpanzee with facial hair:

Dichotomy of facial hair in humans.
Our own species has a notable dichotomy in facial hair between males and females. I'm interested in what broadly speaking are the theories on facial hair. Could it be as simple as sexual selection over tens, or hundreds of millennia?
A previous answer eludes to a sexual selection direction, but my question is primarily why do human females not grow nearly as much facial hair as their male counterparts? Is this just a typical sexual dichotomy? I suppose here I am interested at a molecular level - is beard growth absent, or suppressed in women?
Speaking physiologically androgen is a hormone that drives hair growth and this hormone is more prevalent in males. Although females do have vellus hair coverage on their face, the thicker androgenic hair isn't typically present. A cursory search didn't reveal to me if this is due to less follicles in the first place so androgen would have little effect, or less hormone release.

To answer the question "Why do men grow facial hair" I think three smaller questions are raised:

What is the point of facial hair? (If there is any beyond sexual selection...)
What selected thick androgenic facial hair out of human females?
At a molecular level, have females lost the "facial hair gene", or gained a "facial hair suppressor gene"?

Hormones explain the sexual dimorphism.
Expose females to androgens and they develop masculine facial hair.  See hirsutism.  Also research:

... women’s intermediate facial follicles respond to men’s higher androgen levels by synthesizing more hair over several days ....


How mosquitoes get their food and survive? How do mosquitoes find and get their food? For how much time can they survive without food?

Only female mosquitos (of some, but not all species) need blood to reproduce, they find it by following cues that lead them to warm blooded animals. These include gradients of heat and CO₂. Pretty much all mosquitos feed on nectar and plants while they are adults...

As for how long they could survive without food, I don't know, but no longer than their normal lifespans of a few days to a couple of months as adult.


What is the length of the centromeric repeat sequence in a human? I'm looking for the lengths of the centromeres of human chromosomes.

The best I could come up with so far has been: The length of individual centromeric arrays was found to range from an average of 680 kilobases for the Y chromosome to 3000 kb for chromosome 11.

Here they say that "Human centromeres are located at repetitive alpha satellite DNA arrays that compose approximately 5% of the genome." Which unfortunately is not the same as saying the centromeres compose 5% of the genome. (Or maybe it is? Biologists to the rescue!)

Ideally an answer would contain the length of the centromere in each chromosome, but a precise percentage for the whole human genome would be good enough.

No specific length for centromeres. Actually in a real chromosome in a cell, centromeres are usually very condensed sequences of DNA, they are winded and folded (if you know about the DNA structure). Thus you cannot measure the length of the centromere unless you decondense the chromosome first.


Is there any use of CO₂ in human body? We all know CO₂ as a waste product of metabolism . Does CO₂ have any helpful role , apart from having a role in pH of blood ?

Before I restrict the answer to human metabolism, I recon it is important to mention that
CO2 is the source of the carbon atoms of glucose in photosynthesis (in the Calvin cycle). [In photosynthesis CO2 is 'fixed'].

Even with the above restriction, I am certain I  cannnot do justice to every helpful aspect of CO2 in mammalian metabolism, and I'll restrict myself to just one area that came to mind on reading your question: the requirement for carbon dioxide (in the form of bicarbonate) for fatty acid biosynthesis (FAS) and, in a bit more general sense, mammalian/bacterial biotin-dependent carboxylation reactions. Depeding on other contributions, I might be able to extend this a bit later.

Salih Wakil showed that CO2 is an absolute requiement for fatty acid biosynthesis, but carbon atoms from CO2 do not appear in the fatty acid product.

We now know that FAS begins with the carboxylation of acetyl-CoA to malonyl-CoA, catalyzed by the enzyme acetyl-CoA carboxylase. Acetyl-CoA, ATP and bicarbonate are the substrates for this enzyme, and malonyl-CoA is a key product. One of the many interesting properties of this enzyme is that it contains biotin, which (in this case) may be considered a carrier of 'active' CO2.

This explains the requriement for carbon dioxide but why no carbon from CO2 in the final product?

It is now known that in subsequent FAS reactions, a derivative of malonyl-CoA condenses with a derivative of acetyl-CoA (I am simplifying here) to give a four-carbon compound with loss of CO2.

Thus, carbon dioxide (in the form of bicarbonate) is an obligate requiement for mammalian fatty acid biosynthesis, but no CO2-derived carbon is incorporated into fatty acids.

Carbon dioxide is also required for oxaloacetate formation from pyruvate. This reaction may be though of a method of 'filling up' a key Krebs Cycle intermediate (a  so-called anapleurotic reaction).  The enzyme here is pyruvate carboxylase and the substrates for the reaction are pyruvate, bicarbonate and ATP, with oxaloacetate being a key product.  This enzyme also contains biotin and (like acetyl CoA carboxylase), CO2 becomes covalently bound to biotin during the reaction cycle.

Pyruvate-CoA carboxylase was discovered by Harland.G Wood and C. Werkman in bacteria (See here for a good reference on the early work on pyruvate carboxylase). Its discovery was very controversial because at the time it was thought that animal/bacterial cells could not 'fix' CO2; that is it was though that CO2 is only 'fixed' in photosynthesis.  This discovery disproved that piece of dogmatism.

A third enzyme that requires CO2  as substrate (in the form of bicarbonate) is propionyl-CoA carboxylase.  This enzyme occurs in mitochondria and functions in odd-chain fatty acid metabolism.  It also contains biotin.

I have concentrated on some biochemical aspects of your question.  The three enzymes mentioned, acety-CoA carboxylase, pyruvate carboxylase and propionyl-CoA carboxylase all require CO2 in the form of bicarbonate as substrate, all contain biotin, and (as far as I am aware) all play very central roles in mammalian metabolism.  (They also all require ATP as substrate).

Of the many interesting aspects of biotin, I'll mention just one.  Egg white contains a protein, avidin, which binds biotin very, very tightly.  In fact the biotin-avidin interaction is one of the strongest non-covalent interactions known.  As far as I am aware, no-one knows the function of avidin in egg white.  Some bacteria contain a similar  (but evolutionarily unrelated) protein called streptavidin. No one knows the function of steptavidin either (again, as far as I am aware).

The original Wood & Werkman paper: was published in the the Biochemical Journal in 1936

The utilisation of CO2 in the dissimilation of glycerol by the propionic acid bacteria.

Harland Goff Wood and Chester Hamlin Werkman.

Biochemical Journal, Volume 30, January 1936, pp 48-53


How is TB harmful in HIV patients? The mycobacterium of TB doesn't secrete any toxins. The cause of disease in the immunocompetent is the collateral damage due to the immune response against disseminated infection. But then, when HIV patients are immunocompromised, why should TB do any harm to them? There is an absence of the typical granuloma in HIV cases.

This is an interesting an useful question about host-pathogen interactions. For a general reference (for both hosts with and without a competent CD4+ T-cell response) see Cecil Medicine, Ch.332, and Murray Medical Microbiology, Ch. 28. There is also a decent review in Lancet Infectious Disease that discusses the pathophysiology in immunocompromised hosts.
Overview / tl;dr
Tuberculous mycobacteria may not secrete any toxins or replicate quickly, but they are clever and persistent. Without an effective immune response, they will eventually overwhelm the lungs, spread to other organs, and kill the host through organ failure and/or embolization.  In these cases, infection is universally fatal if not treated. This is what happens in HIV patients with a low CD4+ T-cell count.
In hosts with a competent CD4+ T-cell response, infection is sometimes fully resolved and sometimes held at bay for many years without major organ damage.  In other cases, the immune system's methods are too powerful for the infected organ. Tissue damage in these cases is the direct result of prolonged activation of large fused groups of macrophages. Importantly, this is not an overactive immune response, it just happens to be too much for the local organ. You cannot treat TB by shutting down this immune response. If you block TNF-$\alpha$, for example (a major player in the cross talk between CD4+ T cells and macrophages), you end up with disseminated TB. The solution here is elimination of the pathogen with direct anti-mycobacterial treatment.
Initial Infection
In either an immunocompetent or immunocompromised host, tuberculous mycobacteria enter, e.g., alveolar macrophages through phagocytosis and, initially, prevent fusion of the phagosome with lysosomes, while allowing fusion with other vesicles. This allows the bacilli to live, access nutrients, and replicate within the macrophage.
Immunocompetent host
In the immunocompetent host, the interaction between the infected macrophage and CD4+ helper T cells leads to formation of an activated macrophage and either elimination of the mycobacteria or compartmentalization of the infection. Either of these outcomes are generally good for the host. Clearance of a pathogenic bacteria is obviously good. Latency in a walled off compartment is a close second.
The typical disease syndrome of pulmonary tuberculosis involves a brief, often unremarkable respiratory infection, followed by a long period of clinical latency. In many cases where the primary infection isn't fully cleared, latency may be lifelong, only to be discovered incidentally at autopsy. The brief illness followed by clinical latency corresponds to the infection of alveolar macrophages with an immune response that successfully walls off the infection.
In a host with generally capable CD4+ T cell / macrophage cross talk, if disease develops, it typically occurs after years or even decades of latency, through reactivation. Reactivation may be the result of a temporary failure of the compartmentalization strategy, with short term or partial immunosuppression due to age, some other illness or drug. It is sometimes the result of re-exposure. In severe cases, the result is a massive and damaging, but relatively slow immune response. This is not toxic shock syndrome or gram-negative sepsis. It occurs over month to years, with night sweats and weight loss. Fever may or may not be present. Tb is a slow burn. The OP is correct here, that the tissue damage seen in these cases (caseous necrosis, cavitary lesions, sometimes followed by hemorrhage), as well as the night sweats and weight loss, are all caused by the immune response, not directly by any toxin produced by the mycobacterium.
This lung (image from wikimedia commons) was chewed up by giant, angry macrophages, spurred on by CD4+ T-cells:

Immunocompromised host
This lung (image from a public slide set through the University of Utah), on the other hand, was not chewed up by giant angry macrophages, but was lethally infected with M. tuberculosis all the same:

In an immunocompromised host, the clinical syndrome is different. For an HIV patient with a low CD4+ T cell count, alveolar macrophages are not sufficiently activated. There are no large cavitary lesions, but they are also unable to clear or quarantine the replicating bacilli. This results in disseminated tuberculosis, sometimes with spread through the bloodstream to the brain, kidney, and bone, and devastating illness that is universally fatal without treatment. Death may result from organ failure (e.g., of the lung), infectious or non-infectious embolism.
Interestingly, in an AIDS patient with disseminated TB, when you combine TB treatment with HAART (highly active antiretroviral therapy), you can sometimes see a paradoxical worsening of symptoms. This is called immune reconstitution inflammatory syndrome, or IRIS. It may look like worsening TB, with fever and worsening lung function. The solution for TB-IRIS is not immunosuppression, but supportive care and, again, direct treatment with antimycobacterial therapy. Here again, the problem isn't an overactive immune response, it is the pathogen.


How to determine genotype? In humans, the ability or inability to roll the tongue is a single
  gene trait.  The allele for tongue rolling (R) is dominant to the
  allele for not being able to roll the tongue (r).  Whether or not an
  individual can taste PTC is also an single gene trait.  The allele for
  being a taster (T) is dominants to the allele for not being able to
  taste PTC (t).

Claudia cannot roll her tongue but can taste PTC. Her mom also can taste PTC but her dad is not a taster. Claudia's grandparents were all unable to roll tongues.

1)  Based on the Info, what is Claudia's GENOTYPE?

I know she is "rr" because she cannot roll her tongue and it is recessive. However; I do not know the complete genotype for the PTC taster.  I know it for sure is a "T," but is it "TT" or "Tt?" How do we know? Do we have enough info to figure it out?

Claudia's dad is not a taster, so he is tt. He passes one allele on to his daughter. Since he is homozygous, he can only pass t. Claudia is a taster, so she must have the dominant allele from her mother, who is also a taster. Thus, Claudia is Tt.


What is the chemical process involved in human hairs changing colour after sun exposure? After a day at the beach, my skin tans due to Melanin.

But I also observe the black hairs on my arm turn a blond colour.

My question is What is the chemical process involved in human hairs changing colour after sun exposure?

Melanin is the main compound responsible for the color in hair. It is synthesized from the amino acid tyrosine. The absorption of tyrosine is around 280nm, which is a shorter wavelength than humans can see. Tyrosine can not absorb or preferentially scatter visible light in order to appear colored. It appears colorless as it scatters visible light equivalently. After tyrosine is synthesized into melanin, a pigment is formed which can be seen. Melanin scatters and absorbs light preferentially, it appears non-white.

The absorption of melanin is in the visible spectrum. This means it can absorb and scatter light in the visible spectrum differentially.

As your hair is exposed to sunlight, melanin begins to break down into lower molecular weight compounds which have their own absorbance spectra. The different forms of melanin and carotenoids in your hair can be oxidized by sunlight, giving hair a spectrum of possible colors.

Pigment in bleached hair has been oxidized into products absorbing light primarily outside the visible spectrum. White hair appears so because it lacks compounds which preferentially scatter and absorb light in the visible spectrum.


NMDA receptor mediated plasticity figure reference Because most of this research is over a decade old, finding a paper with a figure that clearly shows that (neuronal) synaptic plasticity (such as long-term potentiation/LTP) is NMDA receptor mediated has proven very difficult for me.

Is there a good reference for this?

One of the "Boss references" (nearly 11000 citations right now) for this is Bliss and Collingridge, A Synaptic Model of Memory: Long-Term Potentiation in the Hippocampus.
Being from 1993, it has references to some of the earlier work in this field (if that's what you're looking for).
It notes the different forms of NMDA-dependent and independent plasticity.
Another paper, also from 1993, on this topic is Malenka and Nicoll, NMDA-receptor-dependent synaptic plasticity: multiple forms and mechanisms

Some nice reviews with more recent work, focusing on the NMDAR itself include:

Paoletti et al, NMDA  Receptor Subunit Diversity:
Impact on Receptor Properties,
Synaptic Plasticity and Disease
Lau & Zukin, NMDA Receptor Trafficking in Synaptic Plasticity and Neuropsychiatric Disorders

and their references.


Have some humans evolved to be less attractive to mosquitoes? https://www.youtube.com/watch?v=38gVZgE39K8 at 10:10 minutes in the video.

It has been found out that single letter differences in people's genomes at specific locations have affected their attractiveness towards mosquitoes. This means there might be a possibility that some humans might have evolved to be less attractive to mosquitoes. Does any proof exist regarding that?

We now know based on a twin study that attractiveness to mosquitos is heritable (with a fairly high heritability of 0.62). Based on a genome-wide association study (GWAS) [which is probably the study referenced in the youtube video] we have found some of the genetic loci that control attractiveness; in particular, 15 single-nucleotide polymorphisms (SNPs) relating to (self-reported) attractiveness, were discovered in the latter study. These SNPs were in regions of the genome related to the immune system (which isn't surprising since immune system genes are closely linked to human odor profiles).

However, figuring out (a) whether these genes have been under selection (by looking for signs of genetic hitchhiking or unusual ratios of synonymous to non-synonymous substitutions) and (b) whether that selection is due to mosquito avoidance will probably a great deal more work - and may be very difficult given that the immune system is under selection for many different characteristics simultaneously ... the GWAS study says its results

  illustrate the complex genetic and immunological landscapes underpinning human interactions with mosquitoes ...


What is the difference between "gene delivery" and "gene therapy"? What is the specific difference between gene delivery and gene therapy?

As far as I understand, gene delivery is the first step of gene therapy, but where does gene delivery end and gene therapy begin?

Does gene therapy necessarily imply that the host DNA is itself changed, or is it just that there is "extra" DNA floating around with the host DNA that also gets replicated?

Citing wikipedia:

Gene delivery is the process of introducing foreign DNA into host cells.
Gene therapy is the therapeutic delivery of nucleic acid polymers into a patient's cells as a drug to treat disease.

In other words, 'gene therapy' refers to the use of 'gene delivery' for therapeutic goals.


Why are our muscles limited to 7 Hertz? I have heard from a (usually very knowledgeable) friend before, that a human can only tap his fingers 7 times per second.

I generalized this to "our muscles are limited to 7 hertz"

When my wife heard this she was like "no way, I'm faster" and we recorded a video of her blinking as fast as she could (her eyes hurt afterwards) and over 5 seconds she averaged exactly 7 blinks per second.

I can't find any articles on the subject, but I did find this video of a drummer doing 1208 beats in 60 sec, setting him up at 20.13hz, meaning 10hz each hand. However if you look at his hand, his muscles are not even really tapping, they are just in a vibration (like a spasm), while holding the drumsticks, which than do all the tapping...

Ussain Bolt sprinted 100m in 9.6 seconds, with 41 steps, that's a little over 4 steps per second.

Both these are very impressive. The drummer sticks out for coordinating his 10 taps per second on each hand, alternating with the other hand, while the motion is certainly faster then our eyes can see.

So what's up with the 7 Hz speed limit? Is it a thing, or did the drummer disprove it? Could the 100m world record be beaten by another 25% when we can find a tall guy capable of doing 7 or even 10 steps per second?

According to the book, Principles of Animal Locomotion by R. McNeil Alexander, oscillatory movements in animals are limited by an organism's nature in general to minimize metabolic energy costs. The energy capacity, inertial, compliant, and dissipative forces involved in the muscles, tendons, skeleton, and non-actuating load all enter into this cost equation.

Strictly speaking these structures are very difficult to model with any degree of fidelity, and so are often approximated by simple mechanical lumped parameter systems of masses, springs and dashpots. From these simple systems, differential equations can be written, and the frequency that minimizes cost turns out to be the natural frequency - since at the natural frequency the system has the greatest ability to trap, store and re-use energy for the movement.

Size and compliance are therefore the two parameters that matter most. Highest oscillatory speeds are able to occur in the smallest, stiffest muscles, assuming dissipative forces are small and input energy is available.


Do the organisms within a lichen communicate with each other? So you've got your fungus and your algae (or cyanobacteria) (and the multitude of other variations and additions to this two-species symbiosis that lichens present). Do the species that comprise the lichen communicate with each other via chemical or electrical signalling? For instance, could an algal cell "tell" the fungus that it's diseased, thus triggering the allocation of more resources toward pathogen resistance?

And if there is no communication, how have lichens been so successful?

Communication definitely happens, but I don't know of any research into response to disease.

One example are molecules known as lectins that help the fungal partner recognize the correct photobiont (algal or cyanobacterial) symbiont.

Another example are the physical connections between fungal hyphae and photobiont known as haustoria that appear to help the fungus extract sugars from the photobiont.

You should find this review by Piercey-Normore & Athukorala 2017 a helpful place to begin learning more.

Ref: Piercey-Normore, M. D., & Athukorala, S. N. (2017). Interface between fungi and green algae in lichen associations. Botany, 95(10), 1005-1014.


Are all carcinogens mutagens? I assume that all carcinogens must be mutagens, but I've read that this is not the case. However, I can't find any good examples or an explanation of why it is not the case.

How can a non-mutagenic agent be carcinogenic?

How can something lead to uncontrolled division of abnormal cells without changing the genetic material of the organism?

The only explanation I've found is that normal replication of genetic material during normal cell division includes occasional errors, so any physical or chemical agent that simply speeds up cell division will increase the number of errors per time and can therefore be considered a potential carcinogen even though it is not directly mutagenic.

But that example doesn't satisfy me because such a compound would not increase the number of errors created per cell division, but is that the only way something non-mutagenic can be "carcinogenic"?

I've also read in This Question that Alcohol is an example of a non-mutagenic carcinogen because Alcohol does not damage DNA, but I think that's not accurate because I've also read that Ethanol is mutagenic via its first metabolite, acetaldehyde, or are they just using wordplay to say that Alcohol is not mutagenic because only its first metabolite is?

How can a non-mutagenic agent be carcinogenic?
An agent that causes overexpression of oncogenes or inhibition of tumor suppressors, would be carcinogenic but not mutagenic.
HPV, for instance, produces proteins that cause inactivation and degradation of tumor suppressors, p53 and pRb[1].
Regarding alcohol. As you guessed, alcohol is metabolized to form acetaldehyde which is mutagenic as well as carcinogenic. Moreover, alcohol metabolism can lead to production of ROS which can also be mutagenic. Overall, alcohol is considered a potential carcinogen by IARC due to the observed effects. These classifications are not based on molecular mechanisms.
More recently, a study by Riva et al (2020) has found that only three out of the twenty carcinogens they tested had a mutagenic effect.
Thus, to conclude, not all carcinogens are mutagens.

Reference:
 [1] IARC Working Group on the Evaluation of Carcinogenic Risk to Humans. Human Papillomaviruses. Lyon (FR): International Agency for Research on Cancer; 2007. (IARC Monographs on the Evaluation of Carcinogenic Risks to Humans, No. 90.) 4, Molecular Mechanisms of HPV-induced Carcinogenesis.


What does vitamin B6 and B12 absorption depend upon? I'm looking at my question about homocysteine metabolism and am doing a followup inquiry into vitamins B6(Pyroxidine) and B12(Cyanocobalamin). I've found this interesting bit about vitamin B12 and am looking at its implications:

  Approximately 56% of a 1 mcg oral dose of vitamin B12 is absorbed, but absorption decreases drastically when the capacity of intrinsic factor is exceeded (at 1–2 mcg of vitamin B12)

Quote from vitamin B12 fact sheet

I'm trying to understand the implications of an intrinsic factor involved in B12 absorption. Lets say that a person gets vitamin B12 from both food and a single supplement pill. Will taking that pill "use up" the absorption factor and prevent food's vitamin B12 from being absorbed over time?

This is the first time I'm hearing of additional "factors" that may limit vitamin absorption in the human body. Is this common across vitamins, or is it B12 specific?

Thank you for your input!

Vitamin B12 (cobalamin) is a water-soluble vitamin required for homocysteine methyltransferase. In order to be absorbed, it must bind to intrinsic factor (IF), which is produced by the parietal cells of the stomach. The absorption of the vitamin B12-IF complex occurs in the terminal ileum (of the small intestine). The quote just means that if there isn't enough IF, then you can't absorb vitamin B12.

There are many things that limit absorption of vitamins, and even vitamin B12. Because vitamin B12 is found in animal products, vegetarians and vegans may need to supplement it. Pernicious anemia is an autoimmune disease that destroys IF or the parietal cells, Gastric bypass surgery can lead to vitamin B12 deficiency. Anything that affects vitamin B12 absorption in the terminal ileum, such as in Crohn's, celiac disease, or enteritis, can lead to deficiency.

To answer your question, no. Yes, it will use some IF (provided you have IF), but that would allow your body to absorb vitamin B12. For people who have diseases mentioned above, they can take vitamin B12 via injections, subligually (under the tongue), or intranasal gels, according to the fact sheet you cited.

Because all the B vitamins and vitamin C are water-soluble, they are easily absorbed through the intestinal wall. Excess amounts are usually excreted in urine. I believe vitamin B12 is the only vitamin that needs to be bound to a factor, due to its larger size. It can be stored in the liver for several years. Fat-soluble vitamins (A, D, E, K) are absorbed with lipids.


Help Finding Specific BlaZ Gene Type Sequences on Genbank I am doing an undergraduate research project that involves blaZ gene typing for different strain types of Staphylococcus aureus bacteria; for reference, here are some of papers on this topic that explore resistance abilities of the blaZ gene and four different beta-lactamases that can be produced:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3421557/
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC188454/
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC106017/
Right now, I need to be able to align blaZ gene sequences in plasmids (or chromosomal regions, when looking at type B blaZ genes) of different S. aureus strains to the four blaZ gene type (A, B, C, and D) reference strains as mentioned in the first paper. The first paper provides the following strains as "reference strains": type A, PC1; type B, 22260; type C, RN98; and type D, FAR19. However, I can only find the nucleotide sequence for PC1 and the partial sequence for 22260 on Genbank; when I search for RN98 or FAR19, no relevant results come up. Even though these gene type sequences should only be distinguishable by several SNPs, it's important that I have references for all four for the most accurate strain typing.
In the last paper, I noticed they provide some of the differences between all four blaZ gene type nucleotide sequences, but not in a "from start to finish" order (i.e. the numbering above the nucleotides is not sequential and the sequence comparison length overall is less than 846, which is the length of the PC1 coding regions). Please advise, as after countless searches on Genbank I still do not have the specific sequencing information I need for each blaZ type.

You might have already tried this, but how about doing a BLAST search using one of the sequences you do have, and perhaps limiting the organism to Staph a.
More info:
The below article did a similar comparison and mentions types RN9 and FAR10, perhaps these are related (or  misspelled originally)  See below.
"Real-Time PCR Assay for Detection of blaZ Genes in Staphylococcus aureus Clinical Isolates" at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3993521/
mentions:
"type A, PC1(pI254) and NCTC 9789; type B, 22260 and ST79/741; type C, 3804(pII3804), RN9(pII147), and V137; and type D, FAR10"
In any case I highly recommend going to your original article of interest, and use the "cited by" function to find more recent papers.


Woodland outdoor microscopy advice Let me start by saying I have never used a microscope outdoors, and in general I have never owned a microscope nor used one regularly.

However, I am currently developing and organising some activities for children, to be carried out in a woodland. I thought it would be really interesting to use a microscope to analyse and compare different samples: leaves, insects, etc. In a word, to do some "field microscopy" (I googled that, but doesn't seem to be a popular expression).

Is it possible?
Is it easy?
What type of microscope should I look for? We have quite a bit of funding, so feel free to suggest anything.

Thank you very much.

1: Yes it is possible

2: It's not as easy as lab conditions because of variable conditions, chances of equipment breaking, especially when small children are involved.

3: You can also look at a Foldscope. Its a small, but powerful microscope made with paper. It was developed by a scientist called Manu Prakash, and although it is still in its beta testing stage, I'm sure you would be able to obtain a few for your students. It is incredibly cheap, very customizable and really user friendly.

P.S.: With the amount I endorse the Foldscope, you would have thought they could have shipped one of the damn things to India for me.


How to edit/insert new gene after cutting with CRISPR/cas9 I'm a student started who has started learning about CRISPR/Cas9. As I understand it, CRISPR/Cas9 is an enzyme that is used to cut a gene at a specific sequence.  I would like to know how scientist do the next step to insert/edit a genome.

For example, say I have an original sequence ...AAATTT... Is it possible for me to insert a new sequence into the middle so it becomes like this: ...AAAGCGCGCTTT... ? Or is it possible for me to edit a single nucleotide of the sequence like this : ...AACTTT... ?

How is a new sequence inserted at the cut region? Is there any enzyme required to make them join each other?  How is it ensured that the sequence is not inserted or joined at the wrong position ?

Cas9 is used to create a double-stranded break (DSB) in genomic DNA. The cell can then use homology directed repair (HDR) to repair the break. The cell can also use non-homologous end joining (NHEJ) to repair DSBs, but this isn't useful for inserting specific sequences. In HDR, a sequence homologous to either side of the break site is used as a template so that the break can repaired error free. Naturally, the homologous template could be a homologous chromosome or replicated copy of the broken chromosome.

However, consider a situation where you introduce DNA into the cell with regions of homology to the break site and whatever other sequence(s) you wish to insert/delete/change. In this case, the break can be repaired using this exogenous DNA as a template and your changes will then be incorporated into the genome.

There are other methods of introducing site-specific DSBs to the genome, such as TALENs. The big advantage of CRISPR/Cas9 is that site recognition is performed by RNA rather than protein (it is much easier to synthesize small RNAs than to engineer large proteins).


Clatherin Mediated endocytosis is pinocytosis or phagocytosis? This was a question in a test. Clatherin mediated endocytosis is which of the two: pinocytosis or phagocytosis?

Precisely what is the difference between the two and CME?

My answer would be pinocytosis
Eukaryotic cells are also able to take up macromolecules and particles from the surrounding medium by a distinct process called endocytosis. In endocytosis, the material to be internalized is surrounded by an area of the plasma membrane, which then buds off inside the cell to form a vesicle containing the ingested material. The term “endocytosis” was coined by Christian de Duve in 1963 to include both the ingestion of large particles (such as bacteria) and the uptake of fluids or macromolecules in small vesicles. The former of these activities is known as phagocytosis (cell eating) and the latter as pinocytosis (cell drinking).

During phagocytosis, cells engulf large particles such as bacteria, cell debris, or even intact cells.In contrast to phagocytosis, which plays only specialized roles, pinocytosis is common among eukaryotic cells. The best-characterized form of this process is receptor-mediated endocytosis, which provides a mechanism for the selective uptake of specific macromolecules.The macromolecules to be internalized the first bind to specific cell surface receptors. These receptors are concentrated in specialized regions of the plasma membrane, called clathrin-coated pits. These pits bud from the membrane to form small clathrin-coated vesicles containing the receptors and their bound macromolecules (ligands). The clathrin-coated vesicles then fuse with early endosomes, in which their contents are sorted for transport to lysosomes or recycling to the plasma membrane.

For more information please see this link https://www.ncbi.nlm.nih.gov/books/NBK9831/

Hope this helps!


Do two compatible tRNA codons bond together? Can two tRNA with complementary anti-codons link together?  For instance UUU with AAA. If not, why not?

Yes, tRNA can form dimers. For example it was shown that E. Coli tRNA GCC forms homodimers, i.e. two identical molecules interact with each other. In this case the dimerization occurs between the anti-codon loops (what was probably meant with UUU and AAA).

References:

Sequence and structure of naturally-occurring tRNA transcripts and site-directed variants are significant barriers to forming oligomers beyond dimers.
(Harold S. Bernhardt, Warren P. Tate, Advances in Bioscience and Biotechnology, 2013, 4, 1-16 ABB)
Anticodon-anticodon interaction induces conformational changes in tRNA: yeast tRNAAsp, a model for tRNA-mRNA recognition.(D Moras, A C Dock, P Dumas, E Westhof, P Romby, J P Ebel, and R Giegé, Proc Natl Acad Sci U S A. 1986 Feb;83(4):932-6)

A naturally occuring mutation, A3243G in human tRNA(Leu(UUR)), causes dimerization via a motif which is not in the anti-codon loop.

Reference:

Wittenhagen LM1, Kelley SO., Nat Struct Biol. 2002 Aug;9(8):586-90.,
Dimerization of a pathogenic human mitochondrial tRNA.


Is it really detrimental to humans as a species to reproduce with one's own first cousin? Tired of hearing of these urban legends and popular opinions, I ask this question here to see if there really is scientific merit to this belief. My questions is, is it really "harmful" for a person to reproduce with his/her own first cousin? Everyone, at least in America, seems to think that this is incest which I completely dismiss because incest is purely a religious concept. The next argument I get is that we want more genetic diversity and having offspring with a first cousin is detrimental to our survival as a species. If you have any genetic weaknesses then your cousin is likely to be carrying them as well and then the chances of your offspring carrying them increase and so on.

I don't really believe any of this. It is rather well known (or may be not so well known) that only a very small percentage of a human individual is different from another human individual's genome. Differences due to skin color, race, ethnicity, and such are literally skin deep. So one reproducing with her cousin or someone half way across the globe is only negligibly different.

Forgetting about religion, has this been scientifically systematically tested and/or proven? Has any research been done on this? Is it true one way or the other? I don't mean to spark any debates here. Opinions are of course welcome. But if anyone can point me to any reputable sources or published results/references, that would be ideal.

Inbreeding depression, "the reduced survival and fertility of offspring of related individuals" (quoting the linked article), is a well-known and well-understood biological effect. It does, indeed, affect humans.

The problem is that recessive mutations become more likely to affect the survival of the offspring of relatives. Imagine that you have a mutation affecting, say, some gene that's critical to your metabolism, which is entirely possible. But, since you have two copies of the gene and only one of them is faulty, you are not affected by this. Nevertheless, you, by chance, pass the non-functional one on to a couple of your kids, who are also not affected due to only having one copy as well. They, in turn, pass it on to one or more of their kids. Now, two of them, cousins, have a kid. The kid gets both copies and can no longer properly metabolize something due to having two faulty copies of the gene. This can prove to be fatal or at least severely debilitating.

Now, lest you think this is improbable, there are on average 70-something mutations per generation. Some of those will be neutral in effect, others will be detrimental. Once an offspring gets two copies of those detrimental alleles, then there could be serious health effects. The likelihood of an offspring getting two copies decreases as the relatedness of its parents decreases. So, sibling or parent/child pairings would be the most likely to produce offspring with the problems. Pairing between 3rd generation (First-cousins) or any pairings between them and their siblings, parents, aunts/uncles or grand-parents would be the next most likely.

So yes, first-cousins marrying and having kids is a bad idea for very basic scientific reasons.

I missed the "as a species" part of your question. Inbreeding will only likely have an effect within small, closed populations, though it will continue to have a lasting effect even as those populations grow and open up. Two textbook examples are French Canadians and Ashkenazi Jews. Even now, there is continued elevated risk of certain rare genetic diseases in these populations. As for the species as a whole, it is likely to be really detrimental only if the effective population size of the species becomes really low: a general rule of thumb used by conservation biologists is that the effective population size should be at least 50 to avoid the effects of inbreeding (and 500 to avoid the effects of genetic drift) (50/500 rule).

Sorry about the confusion.


Would urination continue after death? If someone was urinating, and they were to hypothetically suddenly "fall dead" (the brain is unconscious and all muscles / organs are unfunctional), would they continue urinating or would it stop?

Yes. Moreover, even if they were not urinating at the time of death, they likely would at death, assuming adequate filling of the urinary bladder. There are two sphincters that close off the urethra. One is under control of the autonomic nervous system and the other is voluntarily controlled (somatic). At death, both sphincters will relax, releasing the bladders contents.


A simple question about amoeba (Naegleria fowleri) I have a very simple question about Naegleria fowleri amoeba. Some experts claim that boiling the water for 15 minutes kills Naegleria. However, I have studied somewhere that Naegleria can turn into cyst forms when the environment or the atmosphere becomes harsh to protect itself. So the question is that is it possible for Naegleria to survive boiling temperature if the water is boiled for 15 minutes at 100 degree celcius by converting into cyst form and enter the nose of human and kill the human?

I have studied somewhere that Naegleria can turn into cyst forms when the environment or the atmosphere becomes harsh to protect itself.

This is true, and can happen for a multitude of reasons, including extreme temperature (hot or cold), lack of food, and overcrowding.

  Is it possible for Naegleria to survive boiling temperature if the water is boiled for 15 minutes at 100 degree celcius by converting into cyst form and enter the nose of human and kill the human?

In short: no, this is not possible. According to a publication by the Environmental Research Center, & U.S. Environmental Protection Agency:

  At 51, 55, 58, 63, and 65°C, Naegleria survived about 30, 10, 5, 1, and <0.5 min, respectively.

That being said, just by going off the figures from the publication, there's no chance that Naegleria would survive for 15 minutes in 100°C boiling water.


Can virus survive dessication (and come back functional after rewetting)? I am thinking of ideas for disinfection that can be done by the average person. So, this is one question I have: Can a material/surface be effectively disinfected (I am more interested in virus) by drying using low/medium heat + wind (or any other less thermally-intensive means)? Would the virus be only temporarily inactivated and is able to come back functional?

Viruses that are protected by a protein shell (non-enveloped) like adenoviruses, rotaviruses, and hepatitis A virus can survive dessication for a while. This paper showed adenovirus remained clinically infectious after 28 days on smooth surfaces, and this paper found around 1% of human rotavirus and hepatitis A virus survived after 60 days.
Other viruses might survive dessication even longer, these are just the ones I looked into.
Regarding rewetting, any test for virus survival will re-wet the virus.


What is meant by `individuals do not evolve, populations do`? My university professor stated that "individuals do not evolve, populations do". But aren't populations made up of individuals? That's like saying when a compound changes in stability, none of the elements' properties change. If someone could clear this up, that would be great.

The statement individuals do not evolve, populations do is rooted in the (classical population genetic) definition of evolution. Here is this definition:

  Evolution is a change of allele frequency through time in a population

Evolution is defined for a population, it is not defined for an individual. And it makes intuitive sense once you get more used to how evolution works. For example, the so-called fundamental principle of natural selection states that at any given time, the rate of increase in the population mean fitness is exactly equal to the variance in fitness.

Indeed, evolution is all about phenotypic and genetic variance (for fitness or other phenotypic traits) and without a population to observe, there is no variance. It is within this framework that people say individuals do not evolve, populations do but you are correct that as populations evolve its constituents (the individuals) changes. The sentence has the advantage to reinforce the concept that evolution happens at the level of the population.


Primer Design With Primer-BLAST I am trying to design primers for sanger sequencing snp detection. In the past I have used Primer-BLAST, but I'm trying to pick up KRAS codon 12 mutations. The problem is that in Primer-BLAST you specify refseq gene ID and so it doesn't seem to design primers outside of the gene locus. This means that my primers will sit on the SNP. Is there a way to tell Primer-BLAST the exact locus I am trying to sequence? Or is there a better way of doing this? Thanks.

You can manually restrict the design ranges in Primer-BLAST screen.

First of all you should enter the targeted sequence. In this case, it will be NC_000012.12 which corresponds to chromosome 12 that has KRAS gene.
You should determine the position of variant that you interested in that chromosome. The KRAS G12D -or rs121913529- variant is in 25245350. position. You can find the position of specific variant on dbSNP.
For Sanger sequencing, the recommended size is 600-1000 bp. So, we should select ranges +/- 300-500 bp apart from the variant position.
For the left primer we choose From:25244850 To:25245050; for the right primer we choose From:25245650 To:25245850. And then submit.
Here are the primer-sets that you are looking for. :)


What is the largest species of polychaete? My Google searches seemed to avail no results. My question is: What is the largest living species in the class Polychaeta?

That's about it. I understand that there will be few accessible weights for these worms so length will suffice.

According to the Smithsonian:

The longest of all known polychaetes was found in Port Jackson, Australia. It was a member of the family Eunicidae, consisted of approximately 1,500 segments and was nearly 6 meters long when alive.

The Eunicidae consist of numerous species (including the super cool bobbit worm), many of which get fairly large.

Though, typically 3 m in considered quite large for worms in this group (e.g., see Uchida et al. 2009 for a description of a 3 m long Eunice aphroditois).
Polychaetes & Allies: The Southern Synthesis also suggests that members of Eucinidae can reach 6 m in length. From p. 94 of this report from the Australian Biological Resources Study:

Eunicids have many segments and may attain a length of up to 6m...
...Eunicids range from less than 10cm to 6m in length, and consists of up to 1500 segments (Fauchald 1992a).

Supposedly, according to Schulze 2011:

The Australian museum even holds a specimen that reportedly was nearly 6 m long when
collected (Fauchald 1992 and pers. comm.)

Salazar-Vallejo et al. (2011) also cite evidence of 3+ m long polychaetes in the genus Eunice as evidence that the genus is "the largest polychaete species and placing them among the longest benthic invertebrates."

None of these worms compare to a species of ribbon worm (phylum Nemertea) called Lineus longissimus that can reach 55 m in length! [Sources: 1, 2].


What is this type of diagram called and how to interpret? I'm just starting a project on neuroscience for sixth form. I have had no teaching in this area so had to teach myself entirely.

This is a "low-power image of a transverse section through
the telencephalon of an adult pigeon":

I understand the TH means tyrosine hydroxylase but I have no idea what the different colours mean.

Any information would be so helpful :)

thanks very much!

They used a stain that marks tyrosine hydroyxylase (most likely using an antibody to TH, followed by a secondary antibody tagged to an enzyme that then produces a dark precipitate in the presence of the proper precursor).

The dark regions are where more antibody bound, so you can infer this is where TH is highest. It's very difficult using these techniques to take anything quantitative from this, but you can use the technique to identify regions and possibly compare between them, given you have an appropriate control region.


Will a polyclonal antibody attach to proteins of different kDA? If I have a GST 26kDa polyclonal antibody, will it bind to the GST 28kDa protein as well?

If the sequence of the 26 kDa form is included within the sequence of the 28 kDa form then the answer is 'probably yes'.

However if the N- or C-terminus of the short form is an important/dominant epitope and it is masked in the long form (by being extended) then the activity of the serum against the long form could be significantly reduced.


Whole Genome Sequencing and Chromosome Counts In general, do standard whole genome sequencing techniques rely more on known chromosome counts, independently arrive at chromosome counts, and/or not directly address issues such as base number, aneuploidy, and polyploidy?

For example would have normal whole genome sequencing techniques detected that humans have 46 rather than 48 chromosomes?

Maybe a better way to put this question would be as follows:

Given the whole genome sequence for humans and a belief that chimpanzee had 46 chromosomes would whole genome sequencing of the chimpanzee most likely say

1) Here are the sequences for those 46 and by the way there was material left over.

2) Here is the best representation of all the chimpanzee's DNA mapped onto 46 chromosomes.

3) Here are the sequences for those 46 and chimpanzee's appear to have 48 chromosomes.

I'm pretty sure that it relies on a reference genome. As in, since the original human genome sequencing, most of the techniques used today rely on that original construction (with modifications).

That's how people use it to detect copy number variations (CNVs) and single nucleotide polymorphisms (SNPs) with these sequencing techniques (and aneuploidy as well).

The reads from the sequencing run are compared to the reference genome and if statistically significant differences in the number of reads are seen, then they are noted as differences in the genome. If there is extra unmapped DNA, then it would likely just not know where to put it and call it "extra material".

So #1.


Negative feedback in the fructose metabolism in liver What happens in liver when large amount of fructose is consumed?

I vaguely remember my biochemistry lecturer telling us that the enzymes that process fructose in the liver does not have negative feedback to control the rate of reaction. But I cannot find a reliable source. How is it regulated if it is?

The main reaction of fructose in liver is phosphorylation, catalyzed by ketohexokinase (UniProt P50053). In one paper with rats it was shown that fructose load can deplete the liver of nucleotide triphosphates (ATP, GTP) although ADP and GDP are inhibitors of the enzyme. This shows there is no effective regulation.

M. I. Phillips, D. R. Davies: The mechanism of guanosine triphosphate depletion in the liver after a fructose load. The role of fructokinase. In: The Biochemical journal. Vol 228, Nr 3, Jun 1985, p. 667–671, {{ISSN|0264-6021}}. PMID 2992452. PMC 1145036.


How is a very small quantity of poison able to kill a large organism? Take cyanide for example: it prevents mitochondria from producing energy in form of ATP but, in the process, it binds with it and hence it's spent.

It's theorized that half a gram of cyanide can kill an average adult human. How is this possible? There surely is more than half a gram of mitochondria in an adult human. So, if cyanide molecules bind and hence get spent so fast, how are they able to kill so many cells so fast and continuously?

Is it something to do with the amount of molecules in half a gram of cyanide being several times higher than the amount of cells in one gram of human tissue?

"Cyanide" doesn't refer to just one compound, but given the lethal dose you mention of "half a gram" you are probably referring to potassium cyanide, with a molecular weight of about 65g/mol, so 0.5 gram is about $10^{22}$ molecules. Potassium cyanide becomes hydrogen cyanide in the stomach, and hydrogen cyanide is the gas (at body temperature) that causes toxic effects.

The toxicity of cyanide containing compounds is because they bind with high affinity to cytochrome c oxidase, an enzyme that is part of the mitochondrial electron transport chain. The result is that electrons cannot be efficiently transferred to oxygen molecules. The effect is roughly the same as if oxygen was not present in the inspired air.

$10^{22}$ is a huge number. That's about 250 million molecules per human cell in an adult (taking # of human cells from Bianconi et al). Even so, it isn't likely that cyanide molecules be perfectly bound at every molecule of cytochrome c oxidase, just that there is enough to cause massive brain damage or stop the heart.

By comparison, cyanide is not even close to the most toxic substance. Toxins that target neurotransmission can be much more potent. For example, the IV LD50 for botulinum toxin is about 2 ng/kg, so something like 125 ng for an average adult, equaling only $5\times10^{11}$ molecules.


Are pheromones capable of activating changes to the Phenotype of a complex organism? I know that pheromones are means of communication between the same species, but are they capable of changing the phenotype of an organism, may be influencing the expression of the genes of a said organism.

Pheromones are means of communication between individual within a species, not between species.

  [A]re [pheromones] capable of changing the phenotype of an organism[?]

Yes! It actually necessarily does, by definition. If a chemical produced by an individual does not affect the phenotype any individual of the same species, then it is not a pheromone! You will note that behaviour is part of an organism phenotype.

Pheromones can have drastic impact on an organism phenotype. Most notable examples are from social insects, such as caste differentiation in termites (Matsuura et al. 2010).


Examples of things that are undefined in terms of living and non-living I'm putting together a class on basic biology for kids and I will discuss living and non-living.
I'm looking for examples of things which are undefined in terms of living and non-living, if there are any.
People expect viruses to be alive but they are defined as non-living. Other examples of things that go against intuition are also welcome. Or things which were once classified one way and later redefined.
I couldn't find anything online.

People expect viruses to be alive but they are defined as non-living.

This is actually one of the most widespread misconceptions I see. I think it's just one of those interesting but dubious factoids that spreads around in dinner party conversations. There certainly are some who take that position. But, after 11+ years of formal university education in biology, I can't think of a single professor or colleague who firmly embraced the position that viruses are non-living. Most (including myself) have been firmly in the camp that viruses are, in fact, alive. And the rest are more-or-less agnostic or ambivalent on the topic.
There's an intesting mini-debate between experts on the subject found here, I'll share this quote from one of the participants below because I think it's on point.

"In many ways whether viruses are living or non-living entities is a moot philosophical point."

There isn't one single, universally accepted definition of life. So ultimately, the answer to whether viruses are living or not will depend on ones chosen definition, and that's the case with most other controversial things.
However, viruses are unquestionably classified as biological replicators. There's a review on that topic (found here). It also includes discussions of other replicators which some experts also think of as living entities (but many don't). Examples include certain genetic elements like plasmid and integrons.
One notable exception that I didn't see mentioned in that review is prions. The first virology professor I ever had strongly advocated definitions of life that were inclusive of prions, but I haven't found that position quite as common among other academics. I'm a bit more agnostic on the prion debate, because it's hard to find prion-inclusive definitions of life that arean't also inclusive of something like an inorganic crystal.
The problem is that scientists like consistent definitions that don't have lots of exceptions, or require us to split existing categories. Between viruses, plasmids, and prions, there's a lot to talk about in terms of what characteristics they share with other life forms and what they lack that makes some question their classification. It's also interesting to consider whether any of the attributes common to living things occur in silico (or if they could in the future).


How do Streptococcus thermophilus and Lactobacillus bulgaricus precipitate the curd of swiss cheese? I learned in my food microbiology class that Streptococcus thermophilus and Lactobacillus bulgaricus precipitate the curd of swiss cheese. However, I was wondering what type of mechanisms do these bacteria use in order to accomplish this process.

lactic acid bacteria ferment the disaccharide lactose present in high amounts in milk to the three-carbon compound lactic acid, which acidifies the milk. this causes the proteins also present in milk to denaturate and coagulate, forming curdles. other causes/methods of curdling can be application of heat, salts or by adding the enzyme chymosin (rennin).


Do bald people not grow hair, or does their hair simply fall out immediately? This image is not directly related but it made me wonder if there was a relationship between the nature of the hair follicle and baldness, namely that the follicle cannot 'hold' the continuously growing hair, and it constantly falls out in. I wonder if this is the case or if the hair literally just does not grow out from the follicle at all.

I'm no expert on the whole matter, but I know that at least when it comes to male pattern baldness, it is caused by a hormone called dihydrotestosterone. As those men with the right (or wrong genes, however you choose to look at it) age, this hormone causes the hairs to progressively lighten and thin up until the hair stops growing altogether. The hair follicle dies out basically.


How much mass does a person lose in a day through breathing and perspiration? Water and carbon are lost through perspiration and breathing.

How much mass is lost in this way in a single day for a typical person?

The simplest route to your answer would be through the kcal consumed/expended equation.

1kg (2.2lbs) of fat has ~7700 kcal of energy. The average person requires roughly 2000kcal per day if they perform mild physical labor throughout their day - 25.9% of the total energy available in 1kg of fat. So you could say that if a person did not eat for a day they would lose ~1/4kg or 1/2lb of fat-mass.

I calculated the above in "fat" because it's the number I knew off-hand, but truth be told the amount of "mass" you'd lose also depends on density. Fat (9kcal/g) is more energy dense than alcohol (7kcal/g), carbohydrates/sugars (4kcal/g), and protein (4kcal/g). For the same energy expenditure of 2000kcal in a single day you would metabolise more than 1/2kg or 1lb of either carbohydrates or proteins.

In reality you will burn roughly equal amounts of fats and carbohydrates (assuming you're not forcing your body into a ketogenic state) at about a 55% fat/45% carbs ratio IIRC.

So, with the assumption that the person isn't on a keto diet, has sufficient fat reserves, and expends 2000kcal of energy in a single day while drinking enough water to replace what is used in the energy metabolism, you will lose ~.14kg of fat and ~.63kg of carbohydrates for a grand total of ~.77kg (~1.69lbs) of mass expended per day.

Since humans vary greatly, however, that is going to vary wildly. Personally speaking, it's easy for me to expend >3000kcal per day with an hour of moderate exercise since I'm simply bigger than the average person and require more energy to do anything. If you're shorter than average, do less work than average (i.e. - are sedentary), or hormonal conditions (which are rare and cannot be self-diagnosed) modify calorie expenditure, your numbers will be different.

Also worth it to note: Ghrelin, a major hunger-regulating hormone, changes its tonic behavior significantly if you go more than 2 days consuming less than 1200kcal. After 2 days fasting it will instigate changes that will result in more fat retained after you resume a regular eating schedule for up to 5 years... So starving yourself for a week to lose 5kg seems great until you realize you'll gain 10kg once you go back to a normal diet.

As always, if you're unsure of any diets please go to a qualified professional for consultation.


Why does azithromycin not affect human mitochondria? Drugs like tetracyclines, macrolides and aminoglycosides bind to prokaryotic ribosomes. It is interesting that our body too having mitochondria, which have prokaryotic ribosomes, there is little(?) effect seen. It can not be ruled out that the effect may be lesser due to them being organelles. Azithromycin's effect on parasites like Toxoplasma and Plasmodium is due to its effect on the plastid that these Apicomplexans have (Castro-Filice et al. 2014).

There are two general points that should be appreciated in relation to this question:

Your statement that mitochondria “have prokaryotic ribosomes” is a misleading simplification. Although mitochondria and plastids are thought to be derived from eubacteria — and their ribosomes have some similarities  in antibiotic sensitivity — the structures of their large rRNAs differ (as indeed do those of their small rRNAs and their ribosomal proteins). This is important because the large rRNA (the equivalent of 23S rRNA in E.coli) is the target of many antibiotics, including the macrolide antibiotics, of which azithromycin is a member.
Experiments in vitro have shown that human mitochondrial ribosomes are not sensitive to some of the macrolide antibiotics that inhibit eubacterial ribosomes, whereas those of some lower eukaryotes are.

Therefore it should not be particularly surprising that macrolide antibiotics do not affect human mitochondria, or that they do affect Toxiplasma etc., the ribosomes in the apicoplasts of which are sensitive to these antibiotics in vitro — presumably because of their rRNA structure in the specific target region.

An answer to the question in your title would seem to require an explanation of the molecular basis of these different sensitivities. It is thought (although not, I gather, definitely proved) that this is the identity of the base at the position equivalent to 2058 of E.coli 23S rRNA: those ribosomes that are sensitive to the antibiotics have the base A in that position, whereas those that are resistant have the base G.

References

Böttger, E.C. et al.(2001) EMBO Reports vol 21, pp. 318–323. Structural basis for selectivity and toxicity of ribosomal antibiotics.

Greber, B.J. et al.(2014) Nature vol 515, pp. 283–286. The complete structure of the large subunit of the mammalian mitochondrial ribosome.


How does the modern synthesis theory explain the evolution of birds from dinosaurs? The theory of evolution claims that birds evolved from dinosaurs only by mutation, genetic drift, migration and natural selection.

However, it seems to me that wings were not selectively advantageous for dinosaurs.

Would you show me a book or a paper which explains this point in detail with academic accuracy?
Level of the book or the paper should have detailed information for an advanced reader.

First of all, dinosaurs did not evolve to birds. A better way of saying it is that modern birds evolved from a particular type of dinosaur. That, however, is not the same as the blanket statement "dinosaurs evolved to birds". The latter implies that dinosaurs somehow morphed into birds and stopped being dinosaurs. What actually happens is that a species starts changing and, eventually, a sub-population of that species has changed so much that we call it a new species. It is a subtle distinction but important.

As for a specific paper, no we don't have anything like that for any specific examples. What we have is a huge collection of observations all of which point to the process of speciation occurring via the processes of mutation and natural selection. It's impossible to know the precise series of mutations that led to the creation of a new species for a variety of reasons.

All we have is the current species. If we know an ancestor, we can deduce a possible path that leads from the genome of the ancestor to the genome of the target species but we have no way of knowing whether that specific path was followed. For an analogy, consider computers. If I were to give you a modern desktop PC and one of the first computers:

You might be able to guess certain changes that were made to the old ones in order to build something like the new ones but would you be able to figure out every single step along the way? How would you detect all the attempts that failed? The ideas that didn't pan out? Would you be able to infer the existence of floppy disks, for example?

The same problem applies to species. It is essentially impossible to infer the precise series of mutations that led species B to split from species A. Especially since, usually, this happens through species A.1, A.2, A.2.1, A.3 etc, and all we have is species B.

Add to that the fact that evolution is not a linear process, there are many dead ends (way more than in computers), and the story gets even harder to understand. This graphic illustrates it quite well:

Obviously, if you have the first red dot on the far left and the last blue on on the far right, it will be impossible to infer the entire evolutionary history linking these species.

So, with this in mind, given that dinosaurs and birds share a common ancestor, it is essentially impossible to get the full, true, path that led from that ancestor to either dinosaurs or birds. More importantly, as shown in the image above, dinosaurs did not evolve into birds in the first place so the question is moot.


What purpose does the wax coating on blueberries serve? What purpose does the wax coating on blueberries serve? Is it some sort of protective layer?

A search on the web reveals that it is called "bloom". But the source is not a credible, scientific source. And it doesn't explain in detail what the coating does.

My uneducated guess is that the wax is called Epicuticular wax.

  The main functions of the epicuticular wax are to decrease surface
  wetting and moisture loss. Other functions include reflection of
  ultraviolet light, assisting in the formation of an ultrahydrophobic
  and self-cleaning surface and acting as an anti-climb surface.


Mechanism by which water flows through xylem I was doing a Cambridge iGCSE past paper when I came across the question:

  Describe the mechanism by which water flows through the xylem

I thought the correct answer would revolve around the xylem being composed of dead cells, thus allowing water to use capillary action to flow upwards, but it wasn't.

Instead, the mark scheme referred only to transpiration causing tension and so forth, not even mentioning capillary action.

Is capillary action not a valid answer? And if not, why not?

Thanks

-
NO,for capillary action 2 things are of importance 1) the radius of capillary tube[R] ,2)the tension force between molecules at surface of liquid [T] (for water=72.8 dynes/cm= 728 X 10^-6 N)

-
height to which the fluid will rise due to cap.effect, H=(2T cosα)÷(ρgR)

-
[ρ=density of liq,here water =1000kg/m³]

-
numer.=constant(for given liq) denomin.=variable R

-
so if capillary was in effect for trees 100s of meters tall the deno. wud have to be small while the ρg is a fixed value here for water = 10000 units the R wud have to be impossibly small

WHAT HAPPENS IS the transpiration of water droplets from the stomata causes a suction as no air can enter to fill in for the water lost the water as to rise up taking more of it from the soil


Are mutations a source of genetic variation? Here is a question from the book SAT II Success Biology E/M (where the SAT is the exam taken by the American high school students):

  Which of the following statements is true about mutations?
  (A) Rates
  tend to be very high in most populations.
  (B) generally lethal
  (C)
  irreversible
  (D) Only certain gene locations are affected.
  (E) source
  of genetic variation

In my opinion, we can definitely eliminate A, B, and D.
Then, I struggle between C and E since I think mutations are definitely a source of genetic variation but are as well generally irreversible (I've found evidence on different websites, including this http://hawaiireedlab.com/wpress/?p=154 where the author writes that only some mutations are reversible).
In the end, I think I should have probably gone with E because C can be seen as having some exceptions.
Then, here is the book explanation for this question:

  The correct answer is (C). These recent conclusions about
  mutations—recall that Darwin did not know of mutations—are all the
  reverse of those listed in the choices, with the exception of choice
  (C), the correct answer. Rates, in fact, tend to be below in
  populations, mutations are generally not lethal, any gene location can
  be affected, and they are felt to be the source of genetic variation.
  Darwin felt over-production of offspring was the source of potential
  variation.

The answer is C here. However, I didn't particularly understand why E wasn't considered a correct answer.
Could you please explain why C, and not E, is correct?

Going through the possible answers

(A) Rates tend to be very high in most populations.

This is a very unclear statement. What does "high" mean? In humans, the average mutation rate per reproduction per nucleotide is of the order of $10^{-8}$ (Rahbari et al., 2016) (hence of the order of 10 - 100 mutations for the whole genome). Whether someone wants to call that high or low is up to this person original intuition.

(B) generally lethal

No, that's wrong (Robert et al., 2018)

(C) irreversible

It is a little unclear. By "irreversible", do they mean that the function of the gene (or of any other functional element in the genome) cannot be restored or do they mean that a specific mutation cannot be exactly undone by a future mutation. In both cases, however, it would be wrong!
Mutations that restore the function of a gene (or any other genomic functional element) are called reverse mutations (aka. suppressor mutations; I personally don't know of any difference between the concepts of reverse mutation and suppressor mutation). Most reverse mutations are likely to act via a second mutation that restores the function of the gene rather than undoing the previous mutation. It does not mean however that it is impossible a mutation that perfectly undoes a previous mutation. Consider a substitution inverting A into T. A reverse mutation could do just the opposite.

(D) Only certain gene locations are affected.

Mutation rate varies throughout the genome but all of the genome is subject to some non-zero mutation rate.

(E) source of genetic variation

Yes, mutations are the ultimate source of genetic variation in populations, while genetic drift and directional selection removes variation.
As other users have highlighted in their answers, many mutations (incl. synonymous mutations but not only and soma mutations) do not bring up any the underlying genetic variance of phenotypic traits. These details are however mainly irrelevant; what matters is that it still remain true that (some) mutations increase genetic variance.
We could also add the complication as to wonder whether by "genetic variance", they meant "genetic variance underlying phenotypic variance" (which is its standard usage) or "genetic variance where one allele is given an arbitrary value and another (problem arising for loci with more than 2 alleles segregating). More information about the terminology and the math when it comes to quantifying genetic variance in the post Why is a heritability coefficient not an index of how “genetic” something is?
What I would have answered

The correct answer is (C). These recent conclusions about mutations—recall that Darwin did not know of mutations—are all the reverse of those listed in the choices, with the exception of choice (C), the correct answer. Rates, in fact, tend to be below in populations, mutations are generally not lethal, any gene location can be affected, and they are felt to be the source of genetic variation. Darwin felt over-production of offspring was the source of potential variation.

I disagree. To me, B and D are wrong, A is unclear, C is slightly unclear but wrong in both interpretations I can think of and E is correct. I would have answered E.
About the justification given

Rates, in fact, tend to be below in populations [..]

This piece of the sentence is not even grammatically correct. Below what? It highlights that A is unclear.

they are felt to be the source of genetic variation

The term "felt" is poorly chosen here IMO, but this piece of the sentence seems to rather give credit to answer E. I think, whoever wrote this answer mistakenly wrote C instead of E

Darwin felt over-production of offspring was the source of potential variation.

Really, who cares about Darwin thoughts on the subject here?! But in any case, this sounds like a misrepresentation of Darwin's ideas. More info can be found in Charlesworth and Charlesworth (2009) and also maybe this post


What is the last heavy atom of an amino acid? I'm a electrical engineer and I'm learning about bioinformatics. I was reading this paper that uses the last heavy atom to search for active sites of a protein but what would be a heavy atom? Is it all atoms but hydrogen? Atoms heavier than carbon? And how do I know which is the last heavy atom?

The article: http://bioinformatics.oxfordjournals.org/content/early/2014/11/08/bioinformatics.btu746.full.pdf+html

It talks about the last heavy atom under Materials and Methods 2.1.1 Individual Representation and Population Initialization

As mentioned in the comments by Roland, this term is not common and is first used by the authors of the mentioned paper (also the package mentioned by Roland in comments - STING).

From this link you can find the definition of the Last Heavy Atom which is possibly the most distal non-hydrogen (N, C, O, S) atom in the amino-acid side chain.

$$\begin{array}{|c|c|c|c|}
\hline
Ala\ :\ C_\beta & Asp\ :\ O_{\delta^2}  &Trp\ :\ C_{\eta^2}  &Asn\ :\ N_{\delta^2} \\
\hline
Lys\ :\ N_\zeta & Glu\ :\ O_{\epsilon^2}  & Ser\ :\ O_\gamma  & Gln\ :\ N_{\epsilon^2} \\
\hline
Cys\ :\ S_\gamma  & His\ :\ N_{\epsilon^2}  & Tyr\ :\ O_\eta  & Val\ :\ C_{\gamma^2} \\
\hline
Gly\ :\ C_\alpha  & Leu\ :\ C_{\delta^2}  & Met\ :\ C_\epsilon  & Ile\ :\ C_{\delta^1} \\
\hline
Arg\ :\ N_{\eta^2} & Phe\ :\ C_\zeta  & Pro\ :\ C_\delta  & Thr\ :\ C_{\gamma^2} \\
\hline
\end{array}$$

They have mentioned in the same link that:

  If in any of the PDB files (to be analyzed by the BLUE STAR STING components) that specific atom (LHA) is missing in the record, then our algorithms will search for the next closer atom in the side chain that would be considered as the LHA.

The exact location of some of the abovementioned atoms.

Some of the locations might be confusing. So I am just indicating what these are, for a few the amino acids (especially for the branched and cyclic side chains). [Images reproduced from here.]

Arginine

The terminal nitrogens $\eta^1$ and $\eta^2$ are symmetric and the atom that is actually (stereochemically) the most distal is considered the LHA, as inferred from the protein structure. The second choice, obviously is the $\eta^1$-Nitrogen.

Aspartic acid

The two terminal oxygens ($\delta^1$ and $\delta^2$) in the ionized form are equivalent (also otherwise because of resonance). The actual distal atom would be labelled as $\delta^2$

you can extrapolate the same for Glutamic acid

Histidine

$\epsilon^2$ refers to the pyrollic nitogen. .

Leucine

The last carbons ($\delta^1$ and $\delta^2$) are equivalent and the choice is based on the actual distance. Extrapolate for valine

Phenylalanine

$\zeta$ refers to the carbon in the para-position of the benzene ring. For tyrosine the LHA is the oxygen of the para-OH in the benzene ring.

Tryptophan

Proline

For Aspargine and Glutamine the LHA is the amide nitrogen of the side chain.