How much of what we eat ends up in the toilet? An awkward question. Bear with me...

In terms of mass, what percentage of the food that we eat do we end up excreting? Of course, it depends on a whole host of factors so lets assume a healthy average build/height male with a balanced diet in his 30s who doesn't drink or smoke.

I ask this because I am quite intrigued by my own bowel movements (typically 2 or 3 days apart and average in size - I have no problem passing them btw they've just never been that regular). I know my bowels are not excercised like most other adult males but what's more intriguing is that when I do finally "go", it looks like and feels like I've hardly eaten over the past few days! Take this weekend for example, it's fair to say I've been overdulging and overeaten but by the end of this week I will probably "see" only 10% of that in the toilet.

It very much depends on what specific kind of food you are taking.
Say, if we eat more green vegetables then we are supposed to excrete more compared to a highly meat-rich diet.
Also, it depends on the food-intervals, more the interval more the absorption by body so less amount going out(but giving extreme interval is not good either).
All depends on the need of body, if body needs more than what you are giving to your body it gonna obviously excrete more.
And always keep in mind to take sufficient water, because without it all things go malfunctioning in our body.


Primer Design with Primer-BLAST over specific site I am trying to design primers using Primer-BLAST such that the forward primer spans a specific base pair site.

I am looking at KRAS for which I believe the RefSeq ID is NG_007524.1 and the forward primer should span chr12:25398285.

However, I'm not sure how to restrict the design to accomplish this. Thanks.

I think various ways can be apply, but the easiest way could be to indicate the range to set a forward primer.

Decide the length of primer you are going to get.

Let's say you would like 25 mer.

You can set the range from chr12:25398261 to chr12:25398309.

When you identify where chr12:25398285 is in NG_007524.1, you are ready to design your primers.


Why aren't all infections immune-system resistant? It's been less than a century since the widespread use of antibotics started, and already we're seeing bacteria that have evolved immunities to the antibotics we use.

On the other hand, we've been using immune systems to to fight bacteria for millions of years, and bacteria evolve much faster than humans do.  Why have bacteria not evolved immunities that let them completely overwhelm our immune systems and kill us all?

First of, not all infections are mediated by bacteria and not all bacteria are infectious. Also, not all parasitic bacteria lead to a strong infection or important health problem that cause any non-negligible selection pressure. Following the implicit logic of your post I will talk about infectious bacteria which cause "noticeable harm".

The mistake in your thinking is in the sentence

  bacteria evolve much faster than humans do

While it is true that the mutation rate of base pair is higher and that the generation time is lower, the statement bacteria evolve much faster than humans do is made way too general and lead to your mistake here.

Infectious bacteria are selected to deal with the host immune system and the host is also selected to deal with the the parasite. Both virulence and penetrance evolve in this evolutionary arms race.

The evolution of host-parasite interaction is a very large field of study and it would take several books (and several books have been written on the subject; see this Amazon search) to summarize it. For some theoretical insights into the evolution of host and parasites, you might be interested in the book by Martin Nowak Evolutionary Dynamics: Exploring the equations of life

You will also note that a parasite does not have any "direct interest" in killing (or even harming) its host (thanks @jamesqf for his comment). You might want to have a look at the post Why do parasites sometimes kill their hosts?


How would one determine if an up regulation of one protein leads to an over expression of another? Again, I'm new to biology and have a bunch of questions.
Does it depend on the proteins involved? OR are there basic co expression procedures one could implement to determine exactly how much one protein upregulation leads to overexpression of another protein ?

To demonstrate a causal relationship where protein A leads to increase in protein B, you need to experimentally increase the level of A and measure if B increases. Over-expression is typically done with overexpression of protein A from a plasmid containing the coding sequence, driven by a strong promoter that causes high levels of protein synthesis. See this Wikipedia page for some pointers. Relative protein levels can be quantified by western blotting. The experimental details depend a lot on what cell type and protein you are studying, of course.


Purpose of EF1 alpha promoter Context: I have seen promoters used to have gene therapy viruses target specific cells, so I am referring to that apparent function of theirs.
As an example I have seen GFAP promoters used for targeting astrocytes (I have seen this in many more papers but this is the first one I found on google).
I am curious what the purpose of the EF1-alpha promoter in a lentil/retro/Adeno-Associated virus for gene expression is?
It would seem that it is often used for targeting embryonic stem cells, but then I had also seen else where that "The Lenti-X Expression System (EF1α Version) enables you to produce exceptionally high titers of recombinant lentivirus for expression of any cDNA in any cell type susceptible to lentiviral transduction." This made me think that perhaps since this promoter 'targets' stem cells which later turn into any type of cell, that this quote meant that the EF1-alpha promoter can be used to indiscriminately target cells? Is this true?
Please forgive any incorrect assumptions on my part, I am a novice in this field.

EF1-alpha is considered a ubiquitous/constitutive promoter; it is effective in all animal cells and tends to provide strong expression. Embryonic (and other) stem cells are more difficult to target than other cells because they don't express genes under the cell-type specific promoters that are often used for other populations of cells, which is why you're seeing it used specifically for that application, but that's not the only use.
You'll find a lot of the promoter information on individual commercial sites and rather than promoting specific ones I'd suggest searches like https://www.google.com/search?q=ef1+alpha+constituitive or https://www.google.com/search?q=ef1+alpha+ubiquitous - use of EF1-alpha isn't "owned" by anyone so when they say these things it's not just because they're trying to sell you on some special method of theirs, they are just using a field standard approach.


Is there any knowledge of physics can be applied in to evolution? I have asked a similar question in Biology.SE (What physics knowledge can be applied to biology of organisms and ecosystems?), but it just about organisms and ecosystems, not evolution. After watching a clip that Richard Dawkin talks about applying Darwinian evolution to physics, I would like to ask a vice versa question: is there any knowledge of physics can be applied in to evolution?

There's some. The basic idea is that entropy, as rigorously defined in statistical physics, can be equated to complexity. This is an idea that has been around since at least the 1957 paper by Jaynes. In a fairly hand-wavey way, one can then say that a system that is being fed a large quantity of free energy (as the earth is by the sun) tends to become more complex over time (i.e. evolve).

Thinking this through a bit, the above argument applies as easily to weather patterns as it does to living creatures. Recently, with the rise of computers and modeling there have been attempts to apply these kinds of general ideas (increasing free energy leading to increasing complexity) to living creatures in a more systematic way. Jeremy England is one researcher working on this problem, and this link goes to a pretty good pop-science-style writeup of his work on the topic.


Why does it hurt the next day after doing significant exercise? I think this is a fairly common observation that if one does some significant amount of exercise, he/she may feel alright for the rest of the day, but it  generally hurts bad the next day. Why is this the case?

I would expect that if the muscles have undergone significant strain (say I started pushups/plank today), then it should cause pain while doing the strenuous activity, or during rest of the day, but it happens often that we don't feel the pain while doing the activity or even on that day, but surely and sorely feel it the next day.

Another example - say after a long time, you played a long game of basketball/baseball/cricket. You generally don't feel any pain during the game/that day, but there is a good chance it will hurt bad the next day.

I am trying to understand both - why does the pain not happen on that day, and why it does, the next day (or the day after that).

Unlike the conventional wisdom, the pain you feel the next day (after a strenuous exercise) has nothing to do with lactic acid.

Actually, lactic acid is rapidly removed from the muscle cell and converted to other substances in the liver (see Cori cycle). If you start to feel your muscles "burning" during exercise (due to lactic acid), you just need to rest for some seconds, and the "burning" sensation disappears.

According to Scientific American:

  Contrary to popular opinion, lactate or, as it is often called, lactic acid buildup is not responsible for the muscle soreness felt in the days following strenuous exercise. Rather, the production of lactate and other metabolites during extreme exertion results in the burning sensation often felt in active muscles. Researchers who have examined lactate levels right after exercise found little correlation with the level of muscle soreness felt a few days later. (emphasis mine)

So if it's not lactic acid, what is the cause of the pain?

What you're feeling in the next day is called Delayed Onset Muscle Soreness
 (DOMS).

DOMS is basically an inflammatory process (with accumulation of histamine and prostaglandins), due to microtrauma or micro ruptures in the muscle fibers. The soreness can last from some hours to a couple of days or more, depending on the severity of the trauma (see below).

According to the "damage hypothesis" (also known as "micro tear model"), microruptures are necessary for hypertrophy (if you are working out seeking hypertrophy), and that explains why lifting very little weight doesn't promote hypertrophy.

However, this same microtrauma promotes an inflammatory reaction (Tiidus, 2008). This inflammation can take some time to develop (that's why you normally feel the soreness the next day) and, like a regular inflammation, has as signs pain, edema and heat.

This figure from McArdle (2010) shows the proposed sequence for DOMS:

Figure: proposed sequence for delayed-onset muscle soreness. Source:
 McArdle (2010).

As anyone who works out at the gym knows, deciding how much weight to add to the barbell can be complicated: too little weight promotes no microtrauma, and you won't have any hypertrophy. Too much weight leads to too much microtraumata, and you'll have trouble to get out of the bed the next day.

EDIT: This comment asks if there is evidence of the "micro tear model" or "damage model" (also EIMD, or Exercise-induced muscle damage). First, that's precisely why I was careful when I used the term hypothesis. Second, despite the matter not being settled, there is indeed evidence supporting EIMD. This meta-analysis (Schoenfeld, 2012) says:

  There is a sound theoretical rationale supporting a potential role for EIMD in the hypertrophic response. Although it appears that muscle growth can occur in the relative absence of muscle damage, potential mechanisms exist whereby EIMD may enhance the accretion of muscle proteins including the release of inflammatory agents, activation of satellite cells, and upregulation of IGF-1 system, or at least set in motion the signaling pathways that lead to hypertrophy.

The same paper, however, discuss the problems of EIMD and a few alternative hypotheses (some of them not mutually exclusive, though).

Sources:

Tiidus, P. (2008). Skeletal muscle damage and repair. Champaign: Human Kinetics.
McArdle, W., Katch, F. and Katch, V. (2010). Exercise physiology. Baltimore: Wolters Kluwer Health/Lippincott Williams & Wilkins.
Roth, S. (2017). Why Does Lactic Acid Build Up in Muscles? And Why Does It Cause Soreness?. [online] Scientific American. Available at: https://www.scientificamerican.com/article/why-does-lactic-acid-buil/ [Accessed 22 Jun. 2017].
Schoenfeld, B. (2012). Does Exercise-Induced Muscle Damage Play a Role in Skeletal Muscle Hypertrophy?. Journal of Strength and Conditioning Research, 26(5), pp.1441-1453.


How do normal cell division chance into a tumor forming cell division? Or its better to say what happens at molecular level that tumors are formed?

I tried normal google search and google books but couldn't find any appropriate explanation.
I am trying to understand why p53 or Rb genes are called tumor suppressor genes.I'm acquainted with the pathway through which p53 protein cause checkpoint arrest if the DNA is damaged and the pathway through which pRb protein cause G1 arrest.

In a word: mutation.

If you step back and think about it, multicellular organisms are really, really complex systems. Different cells have to do different kinds of things and interact with each other, they form organized tissues and organs and so on. That much is obvious.

For all of this to work in concert, cells have to grow and divide (to replace dying cells) in a nice orderly fashion/at a nice orderly pace. Since that's a complicated process, lots of the genes in any given cell play a role in managing how long that cell lives/how fast it divides (i.e., cell cycle regulation).

So now, if DNA in a given cell gets mutated, there's a chance that mutation will hit one or more of these genes that are involved in cell cycle regulation. And you can imagine there are two extremes of what might happen: On one extreme, the mutation could mess up the cell cycle in such a way that it's broken (the cell can't grow/divide, things get screwed up, and it dies off); on the other extreme, the mutation could instead destabilize the cell cycle in such a way that it's "kicked into overdrive."

In the first example, we wouldn't observe the effect; the mutated cell would just die off, no big deal. But in the second example, with the cell cycle in overdrive, that cell would barrel ahead, growing fast and dividing faster than the cells around it. And since each of its child cells would have the same DNA and thus have the same "kicked into overdrive" mutation, they'd divide too quickly as well, and so would their children…and eventually you'd have a crazy mass of out-of-control cells. That's a tumor.

p53 is a tumor suppressor because it effectively "sounds the alarm" when it notices DNA damage (mutation)—meaning, when it finds DNA damage, it initiates several processes to try and control/fix/stop it. This is important because if that DNA damage is like the second example above, it could lead to a cancer that harms or kills the whole organism.

If the p53 gene itself is mutated, then the cell has lost one of its major defenses against damaged DNA, and thus there's a much greater chance that a cancer-causing mutation in some other gene could go unchecked. That's why damaged p53 is found in lots of cancers: because the cell lost a big defense mechanism against cancer, and then cancer happened.


Why do birds that walk on the ground walk so "bumpy"? Why do birds that walk on the ground walk so "bumpy"? Most other animals walk quite smooth, doesn't matter if they are mammals, reptiles or insects or walk on two, four or more legs. Birds seem to be an exception and there is no difference between flying or non-flying birds.

If you mean the head bobbing displayed by many birds when walking: it is believed to help with visual stabilization.

  The term head-bobbing, used for the apparent back and forth movement
  of the head of some birds while walking on the ground (think pigeons),
  is a bit of a misnomer. These birds don't actually bob their heads
  back and forth – instead, they move their body forward, leaving the
  head behind, then thrust their head forward past their body (hold,
  high-speed thrust!). This innate behaviour is believed to help several
  key aspects of vision during locomotion and foraging. While the head
  is still, images are stabilized on the retina and moving objects
  become clear against the background, and during the thrust phase,
  depth perception becomes more accurate.

https://jeb.biologists.org/content/jexbio/217/11/1836.1.full.pdf

In this article you can find an stroboscopic photography that shows the particular bumpy walk.


What happens if there is a blood incompatibility during pregnancy? There are possible combinations of blood types with the rH factors:

Rh factors are genetically determined. A baby may have the blood type and Rh factor of either parent, or a combination of both parents. Rh factors follow a common pattern of genetic inheritance. The Rh-positive gene is dominant (stronger) and even when paired with an Rh-negative gene, the positive gene takes over.
If a person has the genes + +, the Rh factor in the blood will be positive.
If a person has the genes + -, the Rh factor will also be positive.
If a person has the genes - -, the Rh factor will be negative.

I am aware that an infant receives one gene from the father and one from the mother, but what happens when the mother's Rh factor is negative and the newborn's is positive? What happens if the mother is O and the infant is A or B?
What happens within the placenta and to the maternal blood poles which are connected by open ended arterioles into intervillous spaces? Will the chorionic villi be "demolished" and exchange of materials isn't as possible?

Little harm comes from ABO incompatibility (that would have been a major problem with reproduction.) Rh incompatibility is more dangerous, though.

If a fetus is Rh+ and the mother is Rh-, when there is mixing of maternal-fetal blood (at birth, but sometimes before that), the mother will form antibodies to the blood cell surface antigen. It doesn't usually affect the first baby (not sufficient antibodies), but if a subsequent baby is Rh+, there can be major consequences, which are multiplied with repeated exposure. Those maternal antibodies - which cross the placenta - can attack the fetal red blood cells and cause destruction of many of them (called hemolytic anemia) which, if severe enough, can be fatal to the fetus. It was a not-uncommon cause of fetal demise before Rhogam (Rh immune globulin) injections.

The immune globulin shots are given to women who are Rh- with Rh+ mates at a period before birth (before blood mixing), and immediately after birth if the child is Rh+. The antibodies bind with Rh+ antigens and "mask" the antigen from the mother's immune detection, so to speak, preventing the mother from making antibodies that can be used against subsequent pregnancies.

The major risk is to the fetal blood cells, not the placenta. The placenta isn't attacked. But with anemia, the fetus struggles, for example, without enough blood, the fetus can go into congestive heart failure and die.

It's also possible to form anti-Rh antibodies from blood transfusions. If an Rh- female has had a blood transfusion prior to her first pregnancy, maternal antibody levels will be drawn earlier during the pregnancy.

What Is Rh Incompatibility?


How do mosquitoes maintain telomere length? While the vast majority of eukaryotic organisms maintain their chromosome ends (telomeres) via telomerase, an enzyme system that generates short, tandem repeats on the ends of chromosomes, other mechanisms such as the transposition of retrotransposons (e.g. Drosophila) or recombination (e.g. Yeast) can also be used in some species.

I would like to know of your thoughts on the possible mechanisms that regulate telomere lengths in mosquitoes.

It seems that the current model is that recombination is the mechanism by which telomere length is maintained in the malaria vector Anopheles gambiae. Here is an exerpt of Roth et al paper that proposed the recombination mechanism:

  The insertion of a transgenic pUChsneo plasmid at the left end of chromosome 2 provided a unique marker for measuring the dynamics of the 2L telomere over a period of about 3 years. The terminal length was relatively uniform in the 1993 population with the chromosomes ending within the white gene sequence of the inserted transgene. Cloned terminal chromosome fragments did not end in short repeat sequences that could have been synthesized by telomerase. By late 1995, the chromosome ends had become heterogeneous: some had further shortened while other chromosomes had been elongated by regenerating part of the integrated pUChsneo plasmid. A model is presented for extension of the 2L chromosome by recombination between homologous 2L chromosome ends by using the partial plasmid duplication generated during its original integration.

You might also be interested in this paper: Genes required to maintain telomeres in the absence of telomerase in Saccharomyces cerevisiae and then look at whether there are mosquito homologs of the identified yeast genes that might be involved in telomere maintance.


Is reverse tonotopical organisation possible? In human cochlea tonotopical organisation is that higher frequency sounds are detected near the entrance whereas lower frequency sounds are deep inside the cochlea. Is this tonotopical organisation (high frequencies at the entrance, low - deep inside) justified by some physical or biological constraints or it doesn't matter and we could in principle have cochlea where low frequency sounds are detected at the entrance?

There are indeed constraints: in principle, low-frequency sound waves travel better in viscous media (look here for a simple explanation). The idea behind that is that being sound a vibration in the medium, it causes its molecules to move. The faster the movement (that is, the higher the frequency) induced by the wave, the more the particles will disperse their energy by crashing into each other. This leads to more loss of energy for high-frequency waves compared to low-frequency ones when travelling in a medium.

Now, all of this leads to the detection of high frequencies being better at the beginning of the canal. However, here is the law that quantifies the loss of amplitude of the wave with distance. As you can see, the damping is higher for high frequencies, as well as high viscosities. However, plugging in some sensible numbers (20 kHz for very high-frequencies heard by humans, 1500 m/s for the speed of sound in endolymph, 1 centipoise for its dynamic viscosity, 1 kg/liter for density) gives a negligible loss of intensity (something like 0.0001. I'm sorry for the poor formatting, but I'm on my phone right now and I hope you will try to run the calculation yourself).

Now, a possible need for the accurate detection of even higher frequency sound waves in water for the fish in which the cochlea appeared is possible. However, I neither know if that is the case, nor if the difference would be a significant one.


Does culling badgers restrict the spread of bovine tuberculosis? The British government has announced that it plans a large-scale badger cull which they argue are implicated in the spread of Mycobacterium bovis - so-called bovine tuberculosis. Any cattle that contract this disease need to be slaughtered under EU regulations.

However, the link between badgers and cattle doesn't seem that clear to me. What is the evidence that badgers spread tuberculosis to cattle? Also, what is the evidence that badger culling will have a significant effect on the spread of the disease to cattle?

This is apparently a debate since decades in the UK. As to the pathology:

  Eurasian badgers (Meles meles) are an important wildlife reservoir of
  tuberculosis (Mycobacterium bovis) infection in Ireland and the United
  Kingdom. As part of national programmes to control tuberculosis in
  livestock, considerable effort has been devoted to studying the
  disease in badgers and this has lead to a rapid increase in our
  knowledge of tuberculosis in this host.

L. A. Corner, D. Murphy, E. Gormley: Mycobacterium bovis infection in the Eurasian badger (Meles meles): the disease, pathogenesis, epidemiology and control.'' In: ''Journal of comparative pathology. 144, 1, January 2011, 1–24. doi:10.1016/j.jcpa.2010.10.003. PMID 21131004. (Review).

A summary of the pre-1997 debates is here:
http://archive.defra.gov.uk/foodfarm/farmanimal/diseases/atoz/tb/publications/krebs.htm

The up-to-date DEFRA informations are at:
http://www.defra.gov.uk/animal-diseases/a-z/bovine-tb/

For an alternative approach see:
http://www.ncbi.nlm.nih.gov/pubmed/19846226 (in short: educate them not to piss everywhere)

I have been asked to give also a summary. Tuberculosis is probably one of the nastiest bacterial infections in existence. It is a prototype of those diseases which are called latent: you can be infected for decades without symptoms, but when your immune system falters (or you have to take immune suppressants) it breaks out and kills you. One third of the human population has such a latent infection with Mycobacterium tuberculosis, and the HIV wave plus the high mycobacterial mutation rate with following extreme resistances make for interesting epidemiology. But this is also a result of our lifestyle, depending on huge cattle herds, as cattle can be cross-infected with human TB. In the west we have succeded to cut human infections by controlling cattle infection with human TB. Still, cattle can get bovine TB, and this may be economically disastrous. One of the pools of the infection is the badger population which can get bovine TB too and spread bacteria with their urine. It is unclear if protozoa may be an even more important pool. It is likewise unclear if culling of badgers would be successful for cattle TB control; the government bases its decision on a long-term study of regions where culling has happened. Alternative approaches include vaccination (which only affects uninfected animals), different cattle grazing regimes, habitat manipulations and badger latrine management. Physical exclusion of badgers from farm buildings is suggested as the simplest, and potentially most effective, method of reducing contact and opportunities for disease transmission between badgers and cattle. The government expert opinion clearly concluded that without such additional measures, culling won't be successful in reducing cattle TB.


Restriction enzymes, how are the recognition sequences determined? How were the recognition sequences (e.g. GAATTC of EcoRI, GGATCC of BamHI) characterised? Text books only list the recognition sites but never the methodologies used to determine the sequences.

This paper describes a simple method to determine restriction sites, which was used to determine the restriction sequence of the previously uncharacterised enzyme from Haemophilus gallinarum.

In short, a known sequence of DNA (from the phage $\phi \text{X174}$) is partially digested with the restriction enzyme, and the various digested fragments can be used to determine the relative distances between each of the restriction sites.

Then, the restriction fragments are extended using T4 polymerase and sequenced using $^{32}\text{P}$ labelled Sanger sequencing.

Once the restriction map of the enzyme on the known DNA sequence is completed, the individual fragments can then be checked for similarities. For example, HgaI has a recognition site outside of the restriction site. Therefore, when the individual restriction sites are compared, it can be seen that all of them have the recognition site GACGC.


Why are lipid-soluble substances harder to excrete? I understand why water-soluble substances can be excreted. However, why are they easier to excrete than lipid-soluble substances? Why can’t lipid-soluble substance be excreted just as easily in the kidneys?

Short answer
If you understand why hydrophylic compounds can be excreted, than it's kind of straightforward why hydrophobic ones can't - because they are not hydrophylic.

Background
The kidneys, through the production and excretion of urine, are the major gateway of clearing the body from toxins. Some toxins absorbed in the gastrointestinal tract can be excreted by the liver through the gall system.

Urine is watery and kidney's excrete water through ion homeostasis. Hydrophobic compounds do not dissolve in water and hence cannot be excreted by the kidneys. The liver has an important role in making hydrophobic toxins water-soluble. Often hydrophilic groups are attached to it in the liver, making them hydrophilic. If that can be achieved, they can be excreted through the kidneys. Hydrophobic compounds that are resistant to chemical modification tend to accumulate in the body in fatty tissues like the nervous system, for example the notorious polychlorinated biphenyls (PCBs).

Reference
- Chen. Activation and Detoxification Enzymes: Functions and Implications, Springer Science+Business Media (2012)


Lysis step during DNA purification I am currently studying DNA extraction from various bio-originated samples. I am new to this field, and have learned how commercial DNA extraction kits work for bacteria.

I understand that the very first step is called 'lysis', and that this is supposed to break cells to pull out all the stuff inside them, including DNA.

I am studying cell-free DNA extraction procedure from human blood, and I don't understand why the lysis step is necessary in this context.

If lysis is to break cells, and cell-free DNA is already out of the cell and freely circulating, such a step seems unnecessary.

Is my understanding about lysis right? Then, why is the lysis step necessary during cfDNA isolation?

You want to isolate the cfDNA, and leave anything else in the plasma out of your analysis — essentially, the lysis step is part of the purification.
(See here)
(I'll elaborate with edits shortly)
Edit:
Actually, it looks like lysis is not a good idea in cfDNA isolation — lysing cells in your sample will result in contamination by genomic DNA, as discussed here. It would be better to stabilize/fix cells to prevent them from lysing, to avoid this risk.
In other words, your initial instincts were correct!


How do biologists infect cells with viruses within a lab setting? I'm writing an experimental proposal as my final paper for my single molecule biophysics class. Part of the procedure I wrote involves intentionally infecting a culture of HeLa cells with SARS-CoV-2 in order to perform a series of tests on it. Are there any readings or articles that you guys can point me to which detail how biologists intentionally infect cells with viruses within a lab setting?

You'll probably want to consider whether HeLa cells are the optimal cell line for acheiving your objectives. This paper shows minimal change in cell viability of HeLa cells innoculated with SARS-CoV and SARS-CoV2, but it's probably a good resource for how cell-culture infections are performed. This paper claims that VeroE6 is the standard cell line for producing viral stocks of SARS CoV-2.

Best of luck with your proposal.


Refractory period in action potential I know that the part E in this graph is definitely the part of refractory period.

My question : Will there be any effect on B,C or D if a stimulus is given at  time B,CorD respectively ?

If there is a stimulus at E, there will be depolarization (membrane becomes relatively more positive). It is just that no action potentials are fired. Therefore, if a strong stimulus does arrive, it will depolarize the membrane to an extent depending on its strength. It will increase the height of the succeeding B phase or reduce the dip of the succeeding E phase. If it is strong enough, it might persist above the threshold till the refractory period is over, and then an action potential can be fired.


allogeneic organ transplant and the immune response What happens when an allogeneic organ transplant is performed on an immunocompetent recipient vs. when it is performed on an immunosuppresed recipient using a donated organ with immunocompetent cells?

The situation is just as you'd imagine. In an immunocompetant recipient, a host-versus-graft reaction occurs. This is called transplant rejection. Single episodes (acute rejection) are easy to treat and rarely lead to organ failure. Chronic rejection is the leading cause of organ transplant failure. The organ slowly loses its function and symptoms start to appear. This type of rejection cannot be effectively treated with immunosuppressants. Some people may need another transplant.[1]

In bone marrow and other transplants, T cells in the allografts reconstitute T-cell immunity in the recipient. Unfortunately, these T cells recognize the recipient as 'non-self' and employ a wide range of immune mechanisms to attack recipient tissues in a process known as graft-versus-host disease (GVHD).[2]

  Acute GVHD describes a distinctive syndrome of dermatitis, hepatitis, and enteritis developing within 100 days after allogeneic hematopoietic-cell transplantation (HCT). Chronic GVHD describes a more diverse syndrome developing after day 100. In addition to allogeneic HCT, procedures associated with high risk of GVHD include transplantation of solid organs containing lymphoid tissue and transfusion of unirradiated blood products.[3]

GVHD is increasing due to the increasing number of allogeneic hematopoietic cell transplantations (HCT). More than 25,000 allogeneic transplantations performed annually. Given current trends, the number of transplants from unrelated donors is expected to double within the next five years, significantly increasing the population of patients with GVHD.[4] Yet the major complication, GVHD, remains lethal and limits the use of this important therapy.

Long-term immunosuppressants are usually the treatment regimen for chronic GVHD. Fungal, bacterial, and viral infections are a major risk with this treatment since the immune system will be suppressed for a very long time.[5]

[1] Transplant rejection
[2] Graft-versus-host disease
[3] Graft Versus Host Disease
[4] Graft-versus-Host Disease
[5] Graft vs Host Disease: An Overview in Bone Marrow Transplant


Will a garter snake eat unusual prey if made to smell like something normal? I have noticed that my garter snake only eats after it has smelled it's prey to make sure it is a slug, and it doesn't matter whether it's moving or not. If I were to coat, say, a caterpillar with slug slime, would my snake try eating it?

Yes, changing the scent has been accepted by most snake breeders as a method to feed stubborn snakes (reference). For example, if your snake prefers chicken, and wont accept mice, rub a chick on a pre-killed mouse and this may trick it into eating the mouse (reference).  With regard to garter snakes, the diet may change based on its habitat, its age and even being kept in captivity can change its diet. This article should provide you information with feeding your garter snake if it is stubborn (reference).


Why do some animals and fungi prefer asexual reproduction? Animals like Sponges and Hydra and fungi like Yeast and Mushroom can reproduce both asexually and sexually. However, they only reproduce sexually if the 'circumstances' are 'bad'. Is there a specific reason for that?

Here is a quite intuitive and straight forward possible explanation:

The key is to rephrase "if the conditions are bad" into "if the focal individual don't fit its environment" or "if the genome of the focal individual is not fit" or "if the focal individual is not fit".

If an individual has a high fitness, it has better to create clones which will be fit as well.

If an individual is not fit, it has better to take the risk to reproduce sexually hoping that some of the offsprings will be fit thanks random recombinations and mutations (there are usually much more mutations during meiosis than during mitosis).

Note:

Sex allocation and evolution of sex is a very broad subject. Your question is linked with discussion on sex allocation. You might be interested by these books:

Eric Charnov
Stuart West
Perrin and Beukeboom

But you might simply have a first look through wikipedia sex allocation, Muller's ratchet or have a look to the diversity of reproduction. You could also have a look to specialized literature, the work of S. Otto for example. Usually introductory books on evolutionary biology contain a chapter on the evolution and diversity of sexual reproduction.


How do trees manage to grow equally in all directions? I was walking down a road with these beautifully huge trees when this question occurred to me.

Large trees with many thick branches have to grow equally in all directions, or they would tip over. Is there some sort of mechanism to ensure this uniform growth? Or is it just a happy coincidence arising from uniform availability of sunlight on all sides? If one branch of a tree becomes too heavy due to many sub-branches, does this somehow trigger growth on the opposite side of the tree?

I have seen that potted plants in houses tend to grow towards sunlight. My mum often turns pots around by 180 degrees to ensure that plants don't bend in any one direction. I assume that this is because sunlight increases the rate of photosynthesis, leading to rapid growth of the meristem.
For trees growing in open spaces, this wouldn't be a problem. But there are many large trees that grow in the shadow of buildings without bending away from the buildings, even though this is the only direction from which they would receive any sunlight. Is there any explanation for this?

There are some other good answers which provide part of the picture, but I think there is a fundamental organising principle which has been missed. Konrad has touched on it in his answer.

The reason trees, and most plants, tend to grow equally in all directions is that they have iteratively generated branching and radial symmetry which is controlled in a feedback loop of the growth promoting hormone auxin and auxin-sensitive auxin transporters. This is an elegant biological algorithm which explains all branching growth.

The things Konrad identifies (phototropism, gravitropism, etc.) serve as orientation cues which help the plant determine which axes to grow along, but fundamentally the process is about auxin gradients. There are exceptions, as others have pointed out in their answers, and they usually result from severe imbalances in the orientation cues.

I'll try to explain the growth process clearly (and it gives me an opportunity to try my hand at diagramming again ^_^)...

Auxin is a plant hormone (actually a class of hormones, but mostly when people say auxin, they mean indole-3-acetic acid) which promotes cell elongation and division. The basic principle which allows auxin to act in the organising way it does is that auxin is produced inside cells, and proteins which export auxin from a cell develop on the side of the cell which has the highest auxin concentration (see figure below).

So auxin gets transported up the concentration gradient of auxin! Thus if you get an area of high auxin concentration developing somehow, more auxin is then transported towards that area. An area of high auxin concentration relative to the surrounding tissue is called an auxin maximum (plural 'maxima').

For most of the life of the plant, auxin is produced pretty much equally in most cells. However, at the very early stages of embryo development, it gets produced preferentially along the embryonic axis (see figure below, part 1). That creates a meristem - a group of cells where cell division is taking place - at the auxin maximum at each end of the embryo. Since this particular meristem is at the apex of the plant, it is called the apical meristem, and it is usually the strongest one in the plant.

So by having a meristem at each end, the embryo then elongates as cell division is only taking place at those points. This leads to part 2 of the image above, where the two meristems get so far apart that the auxin gradient is so weak as to no longer have its organising effect (area in the red square). When that happens, the auxin produced in cells in that area concentrates in a chaotic way for a short time until another center of transport is created. This happens, as the first one did, when a particular area of the tissue has a slightly higher concentration of auxin, and so auxin in the surrounding tissue is transported towards it. This leads to part 3 of the figure, in which two new meristems are created on the sides of the plant (called lateral meristems).

Lateral meristems are where branches occur on plants. If you then imagine this process continuing to iterate over and over, you will see that the branches, as they elongate, will develop meristems at the tips and along the sides. The main stem will also continue elongating, and develop more lateral stems. The root will begin to branch, and those branches will branch, etc. If you can understand how this elegant system works, you understand how plants grow, and why they grow in repeating units as opposed to in a body plan like animals.

It also explains why, if you cut off the tip of a stem, it promotes branching. By removing the apical meristem, you get rid of the auxin gradient and enable the creating of multiple smaller meristems which each develop into branches.

So far I've explained regular branching, but the same system causes the radial symmetry which makes trees (usually) grow in all directions equally...

Imagine taking a cross section through a stem and looking down all the way through it (as depicted crudely above). Just as auxin gradients act to coordinate growth along the length of the plant, they also coordinate it radially, as the maxima will tend to space themselves out as far from one another as possible. That leads to branches growing in all directions equally (on average).

I welcome comments on this answer, as I think its so important to understanding plant growth that I'd like to hone my answer to make it as good as possible.


How does life change when you dig deeper? I've just realized that I have no idea what life / biotopes / soil looks like when you dig deeper than a few meters.

I know that in the first meter of soil you can find all sorts of live animals (like moles and rabbits), insects (like ants, but many more), plants, and single-celled organisms, of course.

But how does that change when you get to the depth of a metro station (below 30m)? When you plan to build a metro, do you have to consider that you might destroy a biotope?

I guess there is a point from which you will quite certainly not find animal/plant life in the soil anymore. This will, of course, depend on where exactly you are. But can you give a rough estimate of how deep we're talking? 50m? 100m? 1km?

Extremophile bacteria and archea are living very deep beyond our imaginations. This is what you need for general composition at different depths. And this and this is for the deepest living organism known ! Following is image from (Manson et al 2010) which shows at what depth you will get bacteria

Even more deeper, Wold's single species ecosystem, Desulforudis audaxviator which can be found 3 km below sea level.


How do signal transduction pathways utilize transcription factors to express a specific gene? I have an inquiry regarding the regulation of genes via extracellular signaling.

To my knowledge, in autocrine, paracrine, and endocrine cellular communication, large protein ligands that cannot directly diffuse through the plasma membrane of the target cell(s) use surface receptors to perform their desired action on the target cell(s).

I have learned that some of these ligands activate signal transduction pathways such as the MAPK/ERK and JAK/STAT pathway and drive the expression of specific genes by utilizing transcription factors (of course, in eukaryots). A simple example of this would be the action of epinephrine (adrenaline) on hepatocytes (liver cells), where the amino acid-based hormone uses the transcription factor CREB to express the gene coding for Glycogen Phosphorylase to engage in glycogenolysis.

Here I have two questions:

How does the transcription factor chemically indicate which gene to express? (Is there a gene indexing system like a computer filesystem?)
How does the transcription factor locate and bind to the promoter of the gene it is trying to express?

Thank you.

This is a combination of multiple regulatory systems. Most genes are not regulated by a single factor, but by many. Moreover in eukaryotic organisms there is also epigenetic, which "inactivates" permanently certain areas of the genome by compacting these zones forming heterochromatin.

Moreover, even when we are interested in a single function a TF might have, that does not mean that it only has this function in the cell. We view it as humans, and maybe for us it is logical that a response to a high metabolite in the environment simply leads to expressing the protein that metabolizes it. However, probably it is interesting for the cell to also activate other pathways and gene networks (i.e. anabolic pathways that feed off this metabolite, compensatory pathways to mantain homeostasis...). Because that normally TFs affect more than one gene naturally.

The mechanisms of action of the TFs are multiple, but they tend to simply allow or deny the access to the adequate RNA polymerase. For more information about this check the wikipedia article on TF structure

In this image we see a typical mechanism of action, DNA bending

Different domains interact in activating a gene, enhancers which are usually long distance, promoters which tend to be in the upstream region, though they can be downstream or in the gene sequence, and epigenetic factors that change the compaction of DNA, making it inaccessible to proteins.

Just as a last thing to point out, you should acknowledge that the biological systems are far from exact and yes, a single TF might activate 200 genes, even when its main objective in that moment is to activate one, but it won't really matter as long as the those 199 activated genes express at a very low rate (for example by not having the right RNA polymerase subunit accessible, being marked as inactive by epigenetic systems or having their own inhibitors).


Expanding the SETI initiative to seek intelligent data within DNA sequences? I've recently read a couple articles dealing with long term data storage, and DNA was suggested as one of the prime candidates for long term storage of digital data additionally, there is this article which deals with decoding of long storage data. These popular articles, though simple do mention important concepts- how packets are stored in DNA use addressing schemes, redundancy of storage, writing for a recipient who may be using a different language, etc.

This made me think - we have the SETI initiative which is looking for signs of (intelligent) life in the universe. That organization was created long time ago, and uses technologies of those days - radio waves. The modern science knows that we can store a lot of data in DNA, and that most organism DNA contains only a small fraction of protein coding sequences and a large amount of non-coding material. If I understand correctly, some of the non coding material is repetitive and highly preserved. Has anyone considered expanding the search for intelligent life to include examination of DNA for messages that might've been left by other intelligent species actually visiting earth?

Let's extend your idea a bit... Ok, there are conserved sequences that we may not know what their function is. Let's assume that they are indeed not functional and are some kind of message left by an ancient form of intelligence.

How would you go about detecting that? It is already given that they are highly non-random, but this is not surprising and many "non-message" sequences have this property. Also consider that these sequences are quite short, meaning that they will have low information content. This means that if you check enough conversion codes and use imagination, you would probably be able to find several "messages" which are "hidden" there (e.g. "bible codes" etc). In other words, as I am a scientist that deals with probability and pattern recognition frequently, you will have a very hard time trying to convince me that you found a real hidden message... Formally, you don't have a satisfying background model.

The main difference from SETI is that there they know that their background is essentially random noise, so it is much easier to detect "intelligent" messages.


What's the smallest organism that can produce voice? What's the smallest organism (animal, insect, or any living creature) that can produce voice. And not just make sound, but has an organ to specifically to create sound, like how us mamals have vocal chords.

I will go with lesser water boatman(Micronecta scholtzi).

The loudest of everything as well as small.

Size: 0.07-inch (2-millimeter)

Produces the highest sound by size ratio.
It's sound is almost equivalent to pounding jackhammer at two feet distance.

http://www.plosone.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pone.0021089.g001&representation=PNG_L

Source and Image Courtesy:

So Small, So Loud: Extremely High Sound Pressure Level from a Pygmy Aquatic Insect (Corixidae, Micronectinae)

Youtube: https://www.youtube.com/watch?v=i7-hREXmMFM

Update:

If we consider voice, I will go with Paedophryne amauensis

Smallest frog an known vertebrate
size: 7.7 mm (0.30 in)


When birds fly in V-formation, how is it decided which bird gets to be the 'lead bird'? I've read on Wikipedia and in other sources that the lead position alternates due to flight fatigue, but does it alternate between a small cabal of of leadership birds, or does (almost) every bird get to sometimes go first?

Is the process different across different species?

There is an advantage for birds to fly in a V-Formation as stated by Portugal et al, 2013:

  As a bird flaps, a rotating vortex of air rolls off each of its
  wingtips. These vortices mean that the air immediately behind the bird
  gets constantly pushed downwards (downwash), and the air behind it and
  off to the sides gets pushed upwards (upwash). If another bird flies
  in either of these upwash zones, it gets free lift. It can save energy
  by mooching off the air flow created by its flock-mate.

There is no advantage to the lead bird though, only the birds behind will get these free lifts by being in the upwash zones.

A study on Ibises determined that there was no clear lead bird and birds cycled between positions. Flying in a V-formation is a collective effort, there would be no benefit to always being in front, so the birds take turns. I would assume the same aerodynamics and the cycling of lead bird apply to all birds that generally fly in V-formations such as Geese. Otherwise the lead bird would just exhaust itself and not have enough energy to complete the migration, it would be the same situation as if the bird was flying alone.

  By carefully observing the flock, the investigators learned that the
  amount of time a bird is leading a formation is strongly correlated
  with the time it can itself profit from flying behind another bird.

  By working together, a flock of birds is greater than the sum of its
  parts. By not being selfish, individual birds can reap the collective
  advantage of aerodynamic wash-up, while also allowing for larger
  flocks, which result in yet more time for an individual to be in a
  backdraft situation.

Additional Reading:

http://phenomena.nationalgeographic.com/2014/01/15/birds-that-fly-in-a-v-formation-use-an-amazing-trick/

https://io9.gizmodo.com/why-birds-take-turns-at-the-front-when-flying-in-v-form-1683465294

References:

Portugal, Hubel, Fritz, Heese, Trobe, Voelk, Hailes, Wilson & Usherwood. 2013. Upwash exploitation and downwash avoidance by flap phasing in ibis formation flight. Nature http://dx.doi.org/10.1038/nature12939


Can humans distinguish light having the same color but different spectrum? Can humans distinguish light sources that have the same color in RGB space but having different spectral composition?

I know one method, that is when the light is producesed by monochromatic laser, it looks "grained" due to interference, but this is a shape-based indicator. What about indicators not based on the visible shape, just on color perception?

If by "same color in RGB space" you mean "activates human cones the same way" then the answer is no: color perception is based on the ratio that different cones are activated at. There is no difference between a spectrum that has a smooth distribution across wavelengths or one that is properly calibrated into three or more specific peaks.

This concept is why RGB monitors and TV screens work to produce just about every color (though there are of course limits to the spectrum that a RGB monitor can produce, but that is a technological limitation).


What is the number of species known through paleontological evidence? Essentially, this question could also be asked: how many species do all of the paleontological specimens in collections (or collections records) represent?

I recognize that species is a temporal concept when thinking about differentiation across time; but, natural history collection catalog specimens to species level, so there must be a reasonable basis to make this distinction.
Also, note that I'm not exactly interested in inferred species (i.e. if we have records of species A and species B, we might infer a last common ancestor, species C).

Very interesting question.

I remember reading about it in one of Stephen Jay Gould's great books (The Panda's Thumb? The Flamingo's Smile? Wonderful Life: The Burgess Shale and the Nature of History? Dinosaur in a Haystack? Probably in one of these).

He wrote exactly about this question, and the effort made by teams from many different countries to get to an "approximate" result. What really impressed me at the time (fifteen years ago) is that when Chinese scientists were invited to add material for a second analysis, the number of known fossil species doubled!

Please, if anyone find the exact source of this, I'll be glad to read it!

But maybe you can get an idea by looking at the number of fossil species for certain groups, and comparing with the number of estimated/known extant species. Keep in mind the rates of fossilization for each group, and also the fact that Nematoda and Acari might be the most overlooked groups in terms of species number (both seem to parasitize animals through most of the Animal Kingdom).


Guide to learning about Population biology / ecology / dynamics for a non-Biologist I'm an applied mathematician who works in the field of feedback control systems but has been becoming interested in looking at population biology (e.g. Lotka-Volterra, Mathusian growth,etc.) from a mathematical feedback and systems theory standpoint. Since I know almost nothing about biology save for a poor frog I nearly threw up on while trying to dissect in High School, I wanted to ask this community if anyone could provide me with some materials that give a good overview of the current state of this field.

There are three seminal works that will give you an excellent grounding in the study of dynamical systems in population biology.

The first details the foundations of population genetics:

Crow, James F., and Motoo Kimura. An introduction to population genetics theory. (1970).

The second deals with population ecology:

Maynard-Smith, John. Models in ecology. CUP Archive, 1978.

Finally, the field of evolutionary game theory has recently embraced a dynamical systems approach to studying populations under the guise of a new theoretical framework known simply as evolutionary dynamics:

Nowak, Martin A. Evolutionary dynamics. Harvard University Press, 2006.

I would probably read these in reverse order. The introduction to Maynard Smith's book has a nice discussion about some of the interrelations between population genetics and population ecology. Most of the original work was done by Fisher, but you don't want to read his stuff - it's famously inaccessible.

It is probably worth me telling you that a lot of mathematical biologists don't actually use dynamical systems approaches in their work. Instead, they favour optimisation models. A balanced discussion about the benefits of this approach, and some of the limitations of the dynamical systems approach can be found in these papers:

Smith, J. Maynard. "Optimization theory in evolution." Annual Review of Ecology and Systematics 9 (1978): 31-56.

Parker, Geoffrey A., and J. Maynard Smith. "Optimality theory in evolutionary biology." Nature 348.6296 (1990): 27-33.

As it happens, my soon to be submitted doctoral thesis is on dynamical systems in biology. Hopefully one day I will be able to add my own book to this list :)


Identifying whether amino acids are hydrophobic or hydrophillic How do you figure out whether an amino acid is hydrophobic or hydrophilic? (other than memorization) I know that it has something to do with the R groups of the amino acids, and that polar molecules are hydrophilic, while nonpolar molecules are hydrophobic, but that's about it. Please give a simple answer, I don't need too much information other than an easy way to tell.

Does the side chain contain any Nitrogen (N), Oxygen (O), or Sulfur (S) atoms?  If it does, then chances are high that this particular R-group is polar (although it may not be charged).

The converse is also true, if the R-group lacks any of those three atoms then chances are high that the side chain is polar.  There are exceptions; Methionine has a Sulfur, but is quite hydrophobic (non-polar).  Tryptophan has a nitrogen but is non-polar.


Is far Infrared heaters in the market truly producing healthy far Infrared and is it practical to install them at home? I read few blogs and websites about far infrared heaters and all are very possible about this new technology. I bought one of the heaters as a test and find quite impressive also.

However, I am concern about long term health effect. I know, there is no health effect of far infrared but the Heater that is producing infrared, is it truly producing only far infrared?

This business is not regulated so What Type of test (or certificate) the heater has to pass before coming in the market?

I am planning to install this heaters in my whole apartment, anyone has experience to live in a flat/house with far infrared heater? if then can you please share your experience? Is it medically healthy?

Thank you very much.

Far infrared is also known as thermal radiation. It is less harmful to the human body than red light and blue light. If you are under a cloudy sky and it is hot, say 30 degrees, that is how harmful thermal radiation is to the body.

The hight you climb up the electromagnetic spectrum, from radio waves to thermal waves to light waves to UV Xrays and Gamma rays, the more they can interfere with atoms and molecules, because they can disrupt bonds, ionize, and so forth.

So IR can only heat the body and can't ionize or disrupt the body.

Far infrared is the heat you feel when you are far away from a fire and the heat travels towards you without air transport. Near infrared is the heat you feel closer to the radiator, and that which causes convection nearest to the heat source, it gets absorbed faster by the air.

Insulation is most important for heating, as more than 50 percent of heating is lost through the ceiling. modern buildings in the west have high roof insulation standards.

oil heaters tend to absorb near infrared and reflect it back as far infrared better.

I think that the smaller and hotter the source, the nearer thermal wavs it produces, and the larger and less hot surfaces can make more far infrared.

It sounds like a lot of marketing terms.

Oil heaters are traditionally very efficient. I had one which i bought a bit rusty for 15 euros and it has lasted 5 years. the only issue with oil heaters is that they can eventually leak when very worn or less strongly welded.

microwaves are less HF than thermal, and they have not been associated with any health risks either even from phones used all day beside the ear.

You can think of far infrared as the warmth that is reflected from a hot wall heated by the sun. It is one of the least dangerous forms of radiation.

you may consider investing in a HPS lamp of 600 or 1000w because it produces 90 percent heat from that, and also vast amounts of light which are good for mental biology and good for growing tomatos and strawberries in the middle of winter. because they go in a ventilated area under a table in the house, the also radiate well. of all kinds of radiators, i prefer by far sitting under a hot lamp with a summer hat tending plants in the middle of winter, it's definitely hot. A 600W lamp can produce about 200 tomatos, 100 strawberries and 20 peppers and some melons/beans etc, in the winter months.


Is ATP produced in a different manner during glycolysis from that generated by the Krebs Tricarboxylic Acid Cycle? The ATP in glycolysis is produced in the cell cytoplasm but that from the Krebs Cycle is produced in the mitochondria. The mitochondrial membrane contains an ATP-synthase protein complex that harnesses a proton flow into the production of ATP from ADP and Pi.

Is the ATP made in the cytoplasm during glycolysis made in a similar or different way?

https://www.youtube.com/watch?v=mfgCcFXUZRk

The ATP in glycolysis is produced directly in certain reactions of the type:

  X-PO32– + ADP → Y + ATP

in a process is called substrate-level phosphorylation.

A key preceding reaction in the pathway is the one catalysed by glyceraldehyde 3-phosphate dehydrogenase, in which free orthophosphate is incorporated into a sugar phosphate in a reaction of the type:

  Z + PO43– → X-PO32–

(I have used X, Y and Z because other changes occur in the structures.)

This is totally different from the oxidative phosphorylation that occurs in the mitochondrion. In both cases the (free) energy driving the generation of ATP comes from oxidation of sugars involving cofactors such as NAD+ to NADH. In oxidative phosphorylation the reoxidation of NADH in the membrane (ultimately by molecular oxygen) is used to set up a proton gradient, which can then be used to drive the ATP-synthase. In substrate-level phosphorylation the chemistry of the intermediates is manipulated so that particular reactions involve sufficient free energy change to drive the conversion of ADP to ATP directly. (The anaerobic reoxidation of the NADH does not produce ATP in this latter case.)

You should read a text-book of biochemistry for the details, which are too extensive to present here. Berg et al. Section 16.1 covers this well, and is available on-line.


ID Request: What is this frog? Eastern Long Island, NY USA mixed hardwood forest Apologies for the potato quality photos, but can anyone ID this frog?
My son found a few frogs living under a porch at my father's house, which is situated in a mixed hardwood forested area of eastern Long Island, NY. I say "living" because he sees them sitting just at the edge of the low porch every day for a while now.

It is hard to tell exactly from the photos, but given the location and time of year, it is either a juvenile green frog (Rana clamitans) or juvenile bull frog (Rana catesbeiana).


What is the structure and function of chromosomes during interphase? Ok, it seems to be easy but I have probably ignored something by accident.

Interphase is the phase where things are growing and the preparation for cell division happens. Its stages G1, S and G2. DNA replication in S stage. So the DNA in some chromosomes must have the pieces of information about how to do the DNA replication. - I am not sure  about thing.

I would say to the part: structure that chromosomes are diploid at the given stage. - It does not feel right anyway.

What would you answer to the main question?

So the DNA in some chromosomes must have the pieces of information about how to do the DNA replication. - I am not sure about thing.

Genomes contain what is called the "origin of replication" - specific sequences in the DNA that tell DNA polymerase where to bind and to initiate replication.

As for your main question, I'm a little confused as to what you're asking. In a general sense, chromosomes function as carriers of genetic information. In eukaryotes, nuclear DNA is organized in the nucleus on linear chromosomes which carry most of the genetic information an organism needs to survive. In bacteria, the chromosome is a circular piece of DNA. In eukaryotes, the chromosome is also bound by histone proteins, which serves to regulate expression of certain genes and to help anchor the chromosomes to the inner nuclear membrane.


What percentage of DNA do people share? If you picked two people in the world at random, sequenced each of their entire genome, and compared their DNA, what would the expected percentage match be?

Based on fine scale mapping of human genome structural variation, which is expanded on here, according to this study, the amount of genome structural (nucleotide diversity) ranges from 0.1% to 0.4% (look under section "Fine-scale map of human genome structural variation"). Hence humans have an up to 99.9% nucleotide similarity. And according to this study the average proportion of nucleotide differences between a randomly chosen pair of humans (i.e., average nucleotide diversity, or pi) is consistently estimated to lie between 1 in 1000 and 1 in 1500.


Advantage of GCPRs over RTKs or other receptor protein kinases My book lists two important differences between GCPRs and receptor protein kinases:

GCPRs do not directly activate a signal transduction pathway. It only does so indirectly, via a G protein. On the other hand, RTKs directly activate a signal transduction pathway, bypassing the mediation of a G protein. (Any G proteins involved with RTKs act as relay molecules in  themselves and are part of the signal transduction pathway.)
GCPRs only activate one signal transduction pathway, while RTKs can activate many pathways.

From what I can tell, receptor protein kinases are faster and more versatile than GPCRs. They do not require as many intermediate steps and can activate many pathways at once. However, GPCRs make up the most largest class of ligand receptors in human cells. This leads me to think there is a great advantage GPCRs have over RTKs that I’m not seeing.

If RTKs are more advantageous than GPCRs, why are there more GPCRs than RTKs?

I think GPCRs are evolutionary more older since tyrosine kinase signalling is relative recent evolved system. This could be one explanation for why their is more diversity in GPCRs

By the way GPCRs can actually signal g-protein independent, for example via B-arrestin. Also their are many types of g-proteins witch can all induce signaling via different signaling pathways. So GPCRS are actually quite versitile.

And then their is also a lot of crosstalk between GPCRs and RTKs


Worm found inside of wahoo A fisherman from Hawaii wrote the following:

  This Fat juicy worm lives inside of every Wahoo that I catch. Inside
  the stomach. Right at the junction to the intestines. Sometimes there
  are two.

What is this parasite?

It is Giant Stomach Worm (Hirudinella Ventricosa).

It is a platyhelmith parasitic to Wahoo fish, feeding on its blood and found inside the stomach. It makes 98% of Wahoo's parasitic infections.

  It is a fleshy worm that varies in size and shape; with extended worms the size of a mans finger and contracted ones about the size of a walnut.

It requires two hosts to complete its lifecycle; a snail and a wahoo fish.

A picture from National Geographic Society

Source: lahaina news

Note: A youtube video shows this worm moving.


Are surface area or volume conserved during cell division? I am a student of physics of mathematics with very little knowledge of biology. Nevertheless, I am very keen on biophysics and I'm trying to learn the biological concepts that I need on the way.

I'm preparing now my bachelor thesis (regarding the physics of cell division) and my advisor has recommended me a paper of his where he studies some forces that are relevant in this process.

Under his analysis the constriction of the cell is independent of the area of the cell (the cells constrict on a similar fashion no matter which size they have, the only important parameter is the shape) and he considers several different scenarios. Two of those seemed plausible biologically speaking to me but I don't know if they happen or not in real life. They are to consider the surface of the cell constant during the process or to consider the volume to be constant (during the constriction of the cellular vesicle prior to the division in two new daughter cells).

Are any of these assumptions realistic? Does the area or the volume of the cell undertaking mitosis change drastically during the constriction of the cellular vesicle?

Another PLOS One article gives evidence of change both in volume and in surface area, but it is across mitosis phases. It could still be considered constant during cytokinesis only.

It seems that cell shape and size have important function during mitosis, according to this research. It would be interesting to investigate different models from your advisor's paper (constant maximum radius, volume or area) but starting from different shapes and sizes.


How do I tell whether a mass spectrum was made with ESI or MALDI? I was working through a previous exam and came across the following question (with reference to the picture shown below):

  "What MS ionization method was employed (MALDI or ESI)?"

I cannot seem to find the answer, so I'm guessing it is not possible to tell, but if there is a way to see which one was used, please enlighten me.

I am not an expert in this topic but from what I have heard ESI generates multiply charged ions but MALDI usually does't. It is possible to find multiply charged species in the spectrum.


What is the function of multiple nuclei in syncytial cells? What is the function of multiple nuclei in syncytial cells specially in protists with cilia? Is multiple nuclei a special characteristics of only ciliated cells?

A mononucleate's size is limited by its nucleocytoplasmic ratio, and protozoa like being big.

The solution? Multiple copies of the same genes in huge nuclei, or multiple individual nuclei.

Multiple nuclei are common in any large, complex cell. There is nothing specific to the presence of cilia that require multiple nuclei, and ciliates are not the only multinucleate protozoa (the amoeboid Chaos genus can contain up to a thousand). The reason large, complex cells require this is simply because they are so big. Such a huge size requires, in addition to more complex nuclear regulation, a high total protein turnover, which in turn requires a high transcription rate. Even with mRNA being translated by numerous ribosomes, the amplification factor is still limited. Having multiple nuclei increases the rate of mRNA production, which increases the total synthetic capacity of the organism. When only a specific gene is required to be transcribed at a high rate, that individual gene may be duplicated many times. This is often seen in the nucleolus, which contains many copies of the same genetic material required to create the huge amount rRNA needed for ribosome biosynthesis:

Many protozoa are large because they are packing as much complexity into a single cell as they can, even to the point of having a backbone-like structure or simple photosensitive "eyes" (though not all protozoa are large). Many adaptions are required to allow single-celled organisms to grow to this size, such as a more complex cytoskeleton, a dedicated feeding apparatus, a contractile vacuole, etc. Multiple copies of genetic material is just another required adaptation. This adaption can manifest itself in various ways. Some organisms have multiple copies of the same nucleus. Others fuse these nuclei into a single, large nucleus (a macronucleus), keeping a limited number of micronuclei around for sexual reproduction:

Multicellular organisms tend to have multiple nuclei in specific cells for the same reason. Many types of cells, for example, require an extremely high rate of protein turnover and are very large (such as skeletal muscles), so they have multiple nuclei. This occurs when a single nucleus is no longer sufficient, even at peak capacity.

I would like to point out that what you are describing is a coenocyte. A syncytium is a multinucleated cell which has arisen from the fusion of multiple cells and their constituent nuclei (karyogamy), whereas a coenocyte is a cell which had undergone multiple rounds of nuclear division, without accompanying cytokinesis.


Unknown Insect identification Found this bugger crawling across my laptop.  Any help identifying would be appreciated.  After a bunch of googling it appears to be close to a lady beetle larva.  I am located in north east USA.

It looks most like a common Green Lacewing larva - Chrysoperla rufilabris. Lacewings are considered a benefit in the garden because they effectively feed on aphids and other soft bodied garden pests. Here are some links that may be of further help.

https://bugguide.net/node/view/16103

http://www.uky.edu/Ag/CritterFiles/casefile/insects/lacewings/lacewings.htm

https://greenmethods.com/chrysoperla/


Fastest G protein coupled reactions As per few references, fastest G protein coupled reaction known is Drosophila melanogaster phototransduction which produces quantum bumps with average latency of 45 ms (and peak response around 200 ms). Another reaction is chemotaxis which is also in that order. I was wondering are there any known examples which are as fast as these responses?

P.S: Many ion channels are GPCR which triggers very fast but most of them takes long time (in order of seconds) to give peak ion concentration

P.S.S: By fastest I mean, minimum time required to give peak response after activation of receptor(s).

Update:

In abstract case, Let's say you got signal from outside at time t = 0. Now this will leads to reaction cascade which will take time 't1'. Assume output of this is opening of channel which will increase concentration of ion X. Now X will reach it's peak concentration at time t = t1 + t2. So I am looking for such reaction cascades with minimum time 't' (t1+t2).

Mammalian rod cells, the most numerous photoreceptor cells in the retina, reach a max depolarization after a single photon stimulus at 100-120 ms, implying a time constant (1/k) of about 25 ms (see Chen et al., Nature 404:557).  This is on the same order of speed as the fly eye, maybe a tad faster.  Non-photoreceptor GPCRs are probably slower, but few folks have tried to measure these effects. The m1 muscarinic acetylcholine receptor catalyzes Gq activation with a time constant of about 500 ms (Mukhopadhyay and Ross PNAS 96:9539), but there may be faster ones.


What type of wasp is this? I've been trying to match this wasp to photos, but it seems like every species has something that doesn't quite match up. I killed it in my home in Indiana, USA. My best guess is a Northern Paper Wasp (Polistes fuscatus). Does that seem right? I read they can sometimes be dark in color like this one.

It is hard to tell from the image, but using this species key for Polistes wasps, it is reasonable to conclude that your wasp is either P. metricus or P. fuscatus.

If you look at this image of a P. metricus female, you can see the dull reddish markings on the abdomen:

On your image, you can see the same markings on the abdomen, at a different angle:

Based on these markings, your wasp is most likely Polistes metricus. You can read more about this insect here and here.

Here is a link to the image I modified.


What is the perisomatic region of a neuron? In the scholarpedia page on interneurons I encountered the following passage:

  The perisomatic domain is responsible for the summation of postsynaptic potentials arriving from all dendritic branches [...]. Thus, the perisomatic region - and particularly the axon initial segment [...] plays a crucial role in the generation of output.

The page, however, does not define what the perisomatic region really is. What comprises the perisomatic region of an interneuron?

In cortical GABAergic cells with local axonal projections, the perisomatic region is defined as that part of the plasma membrane including the proximal dendrites, the cell body and the axon initial segment (Zabó et al., 2010).

Reference
- Zabó et al., Eur J Neurosci (2010); 31(12): 2234–46


Do beneficial viruses exist? If so, what examples are there? Typically, people call viruses some kind of organic compounds that cannot reproduce autonomously and which lower the fitness of their hosts. Even the word "virus" means "venom" in Latin.

But from the perspective of natural selection, one would expect those organic compounds that cannot reproduce autonomously, but which would increase the fitness of their hosts, to be more widespread. One can see an analogy with bacteria: people are more aware of harmful bacteria and even such words as "microbe" are perceived as somewhat harmful (among non-biologists for sure). But we know that an animal body contains many more useful bacteria than harmful ones, and animals have their own microflora, which are necessary for survival.

The same must be true for viruses: those viruses which were useful (or at least unharmful) to their hosts would be passed more easily to other organisms since their hosts would have a selective advantage.

So, do such beneficial for their direct hosts viruses exist? If so, what are they called? What are the examples?

Do they exist? Yes

What are they called? Marilyn Roossinck calls them viral mutualistic symbiotes. She has an excellent review here.

What are some examples?

My personal favorite is GB-Virus C, or Hepatitis G, which appears to slow the progression of HIV using a number of different mechanisms:

  Box 1. Summary of the effects of GBV-C infection in HIV-positive individuals

  GBV-C infection downregulates HIV entry co-receptors CCR5 and CXCR4, and increases secretion of their ligands RANTES, MIP-1α, MIP-1β and SDF-1.
  In vitro GBV-C NS5A and E2 proteins inhibit X4- and R5-tropic HIV replication, and NS5A protein downregulates CD4 and CXCR4 gene expression.
  HIV-infected individuals positive for GBV-C E2 antibodies have survival benefit over HIV-infected individuals with neither GBV-C viremia nor E2 antibodies; in vitro GBV-C E2 antibodies immunoprecipitate HIV particles and inhibit X4- and R5-tropic HIV replication.
  GBV-C induces activation of interferon-related genes and pDCs.
  GBV-C promotes Th1 polarization and the NS5A protein contributes to this effect.
  GBV-C infection reduces surface expression of activation markers on T lymphocytes, suggesting its role in T cell activation signaling pathways.
  GBV-C protects the T cell from Fas-mediated apoptosis and as a result of its effect on immune activation may also play a role in protecting lymphocytes from activation-induced cell death.
  GBV-C viremia reduces IL-2-mediated T cell proliferation suggesting a significant interaction between GBV-C, IL-2 and IL-2 signaling pathways.

Endogenous retroviruses

As @mbrig recalls in the comments, there are a number of retroviruses that have inserted themselves into the germ line. Those are called endogenous retroviruses, and they interact with the host genome in a number of ways. Some are even translated:

  Proteins produced from ERV env genes have also been demonstrated to function as restriction factors against exogenous retroviral infection


Why Do we close our eyes while sneezing? Google says germs  may fall on eyes from our sneeze but it happens all the time . Also it says it a part of contraction. What may happen if we sneezing wirh our eyes open ?

Mythbusters did this one!

The simplest response is that your eyes close as a reflex, because the nose and eyes are linked by cranial nerves which brings the sneeze signal to the brain and then to the eyes, making them blink. Would you eyes pop out if you managed to sneeze with them open? (a common urban myth) No! Your eyes are attached by strong muscles and it would take a lot more force than a simple sneeze to lose them.

Mythbusters article on the subject

I would love to give you a more scholarly article but this is the same one referenced on wikipedia on the subject, plus it's hard to find academia in the fluffiness of this question.


What is the secondary structure distribution per AA in the Human proteome? If one would classify each amino acid to either be in a Coil, Beta strand or Alpha helix what would be the distribution of these classes in the human proteome?

Is it 33%-33%-33% or is it biased? If it is biased why?

I thought it should be around equal, but I run the whole proteome through PSIPRED, and I found the distribution to be 60% Coil, 30% Helix, 10% Sheet. Why is it so?

The question asks why the distribution of coil, alpha-helix and beta-strand is 60:30:10 rather than 33:33:33. The answer is:

  “Why not”

This is because there is no reason whatever to expect that three types of structure (or in the case of coils, lack of structure*) should be present in equal amounts in proteins. It is like expecting that the percentage intron, exon and ‘junk’ DNA should be equal, or that the percentage of fuel reserves stored as glycogen and fat should be the same. Yes, they belong to the same category, but they are sufficiently different in each case for one not to be surprised if they are not required in equal amounts.

To understand this one needs to look a little more carefully at the occurrence of alpha-helix or beta-strand conformation in the three-dimensional structure of proteins. Three points may be emphasized:

Amino acids have particular conformations because they are part of an extended helix or sheet of strands the entirety of which leads to its structural stability — you don’t have a random mixture.
In many cases the helices or sheets are occur in particular combinations to give a family of proteins of similar overall structure. Again, the idea of random mixtures doesn’t enter into the equation.
These overall structures are suited to particular functions, so the abundance of proteins from a particular structural family will be determined by the requirement for antibodies or ion transporters or signal transducing proteins etc., not by some shake of the dice.

Images illustrating two such families are shown below:

(a) shows an ion transport proteins, predominantly alpha-helices, whereas (b) is an immunoglobulin domain with a distinctive pattern of beta strands (as well as some helix). For further examples and information I suggest the EMBL on-line course on protein classification and Berg et al. online, for example Section 7.3.

*Footnote 1: Situations where equal occurences might be expected
It is worth while contrasting the situation with protein secondary structure to some where the prior expectation might well be for equal usage, and the deviation from this could be regarded as bias and an explanation worth asking for:

The different proportion of the 20 amino acids in proteins (although a chemist would not expect equal proportions)
The different usage of synonymous codons of the genetic code in various species and mRNAs
The different usage of the similar molecules with a high phosphoryl group transfer potential: ATP, GTP, UTP and CTP (often loosely termed ‘high-energy’)

*Footnote 2: A coil is not a secondary structure

As is stated in the Wikepedia entry for Protein Secondary Structure:

  The random coil is not a true secondary structure, but is the class of conformations that indicate an absence of regular secondary structure.

It might be mentioned in regard to protein structure that there are smaller three-dimensional motifs that the analysis quoted does not consider. These do not occur in equal proportions either, to nobody's great surprise.


Why does methylation not occur in viral DNA? Why does methylation not occur in viral DNA? Can viral DNA undergo the process of methylation? If not then why does this process does not occur in viruses?

Contrary to the question title, viral DNA can be methylated.  See for example Bonvicini et al. 2012. (1) and Hoelzer et al. 2008 (2).

Hoelzer et al. give a review of the presence and role of cytosine methylation in DNA viruses of animals:

  To understand the impact of cytosine methylation on the viral life
  cycle and the evolution of base composition, the particularities of
  each virus will need to be considered. Differences will inevitably
  exist between actively replicating viral DNA and that which is
  integrated into the host genome. The type of viral persistence will
  also be of importance. The integration of adeno- or polyomavirus DNA
  into the host genome is usually a terminal process since the viruses
  cannot liberate their genomes and are therefore no longer infectious.
  The evolutionary roles of methylation in these cases will likely
  differ from those seen in other viruses, such as Herpesviruses, which
  can liberate their genome after periods of latency. But differences
  may also exist between large and small viruses—with many larger
  viruses encoding their own replication machinery and additional
  proteins which modify host cell processes and immune responses. The
  susceptibility of the viral genome to methylation and immune
  recognition will also be affected by other factors, such as the
  location of replication within the cell and the specific intracellular
  trafficking route.

Viral DNA methylation has mostly been studied in large DNA virii, and the extent of methylation may be related to repression of viral replication. Bonvicini et al. writes that

  Epigenetic mechanisms, and in particular the impact of cytosine
  methylation at CpG dinucleotides on the viral life cycle have been
  mainly studied for viruses that can establish latency and undergo
  reactivation, such as viruses in the Herpesviridae family, or for
  viruses that can integrate their genome into the host genome such as
  Retroviridae or Papillomaviridae. In general, a correlation has been
  found between the extent of CpG dinucleotides methylation of viral
  genomes and viral quiescence [24]. Scarce information is on the
  contrary available on the possible occurrence and role of methylation
  for actively replicating viruses


What is a genetic marker? In DNA sequencing and analysis, what is a genetic marker? I've heard that microsatellites are genetic markers? Those are repetitive strands of bases such as GCAGCAGCAGCA etc. Why are they markers and what defines a genetic marker?

There are many different KINDS of genetic markers as defined by wikipedia, RFLP, SNP and many more. But when you click these, you get a technique not a sequence. So I'm confused as to whether markers are techniques to find DNA sequences or if they are literally DNA sequences?
If they are literally DNA sequences, are they sequences that everyone has?
Example of RFLP:

  In molecular biology, restriction fragment length polymorphism, or
  RFLP (commonly pronounced “rif-lip”), is a technique that exploits
  variations in homologous DNA sequences.

As hello_there_andy (and also the Wikipedia page) has indicated, genetic markers are DNA sequences that can be used to distinguish individuals (can also be tissues, cells, etc.).

Linkage of a phenotype with genetic markers is used to identify regions of the genome that are likely causative for that phenotype, as hello_there_andy says, but there is nothing inherent to how a marker is chosen that says it has to be linked to any phenotype. Markers are typically chosen for an analysis because they are easy to measure and track, individuals differ at the locus (so you know that if your phenotype of interest segregates perfectly with the marker, it's unlikely to be chance), and they cover the genome (or the region of the genome you already know is linked) appropriately, among other things.


Is the activity of enzymes in the human body affected by the outer temperature? I have to do a research about the enzymes in the human body and the things that affect them. I know that the body temperature affects the activity of enzyemes but I'd like to know if the outer temperature of the air affects them, too?
When the temperature goes to 47°C or more we get tired and exhausted. Is this because the activity of enzymes decrease or is something else?!

Enzymes usualy have a relative narrow temperature optimum, for those of our body this is usually around 37°C. It is around 37,2°C in the morning and goes slightly up to 37,7°C in the evening (see reference 1 for details). The temparature optimum for most enzymes looks somewhat like displayed in the figure (from here, interesting to read):

Enzymes are relatively tolerant to lower temperatures (although their reaction rate is much lower), but generally they work. If you go too high with the temperature, the activity will soon be reduced to zero, as the enzymes are denaturated and are not able to catalyze any reaction.

The human body does quite a lot to control its temperature and to keep it within a pretty small limit. It does either excessive sweating (when it's hot) or shivering (when it's cold) to maintain its temperature within or at least near the optimum. For further details on the themorgulation have a look on the Wikipedia article on this topic or reference 2 and 3.

Although our enzymes work at slightly lower reaction rates when the body temperature is higher (think of fever), this is not a major issue. Slightly higher temperatures can thus be tolerated, although you don't feel very nice.

The effect of to hot temperatures is different, though. It is mostly due to not consuming enough water, so that the body has not the possibility to control its temperature via sweating. This condition will ultmatively lead to a heatstroke, see here for more details. Before you reach the temperature in which your enzymes reaction rate will go down drastically, you have long collapsed.

References:

A critical appraisal of 98.6 degrees F, the upper limit of the
normal body temperature, and other legacies of Carl Reinhold August
Wunderlich.
Skin blood flow in adult human thermoregulation: how it works, when
it does not, and why.
Thermoregulation: some concepts have changed. Functional
architecture of the thermoregulatory system


What kind of microorganism is this? It moves like a worm pretty much. I found it in a pretty big pond with brackish water. The water temperature was around 10 celsius.

Here's a video of it moving

Now  I cannot really tell the name of it without knowing more of its properties and characteristic features, e.g. size. (I am afraid I am not very good with faces, especially of microorganism :D)

But I am 90% sure it might be an
Oligochaete


Why don't antibodies generally bind to food and drugs? Are these excluded thru central tolerance?  What if you ingested something with a unique molecular structure that you hadn't ingested before?

B cells containing receptors against food's or drug's molecular structures may exists. However if the naive B cell binds the molecule without a second signal coming simultaneously from CD4 Tfh cells (linked recognition) the B cells recognizing this antigen will become anergic or will die by apoptosis. This occurs with antigens to which we are chronically exposed, like food.

Reference: Janeway's Immunobiology, 8th edition. Chapter 8 (The development and survival of lymphocytes). In particular section 8-26, p320-321.


What is the role of TATA box in transcriptional regulation? I know what is the TATA box, but I wish to know whether it has specific roles in transcriptional regulation.

TATA box serves as a binding site for the TATA-binding protein (TBP; and its associated factors, together comprising the TFIID).

TATA-box is one of the basic promoters present in many genes and therefore TBP is a general transcription factor i.e. TATA-box and TBP do not have specific roles. TATA-box is like a minimal promoter.


Deep diving in mammals Mammals like seals often dive and can remain under water for more than 70 minutes.

How do seals know when is it the time to come up?

I imagine that their breathing is controlled in the same way as ours. During a dive, oxygen will be used up and carbon dioxide will be produced, dissolving in the blood as bicarbonate and tending to decrease the pH of the blood.

Peripheral chemoreceptors in the circulatory system detect all of these changes and signal the need to breathe. This would tell the seal that it is time to head for the surface.

Diving mammals have various adaptations for prolonged diving, most importantly large reservoirs of blood containing haemoglobin which is oxygenated before a dive, as well as high concentrations of myoglobin in muscle which can also act as an oxygen reservoir.


For a luekemia patient - how does the chemotherapy fixes the bone marrow to not produce immature cells For ALL patient this link says 90% of the children are cured.   It has high survival rate. From what I understand is that - luekemia is type of cancer where the immature cells does not turn into mature cells. How does the chemotherapy with other drugs - fixes the bone marrow immature cells defect?

What are the survival rates for acute lymphoblastic leukemia?
About 98 percent of children with ALL go into remission within weeks after starting treatment.
About 90 percent of those children can be cured. Patients are considered cured after 10 years in remission.

Chemotherapy in general works by killing (hopefully all) cancerous cells, while leaving the patient / healthy cells alive.
The drugs used for this usually are in principle toxins/poisons, but are more deadly to cancer cells, since these cells are growing very quickly compared to healthy cells. This general strategy is true for a lot of different types of drugs (and cancers). However, because the drugs are still generally toxic they are hard to dose correctly and also the reason why chemotherapy often has quite strong side-effects.
Additionally cancer can quickly evolve to gain resistance to specific drugs, which is why nowadays often a combination of multiple drugs at once is used.

In leukemia - which is a form of cancer where the blood and immune cell precursor cells in the bone marrow become cancerous - additional ways of selectively killing the cancer are radiation therapy (of the affected bones) and in some cases complete bone marrow transplants (which have their own issues, so they are not usually  used as first option).


Cytokine responsiveness Why is it that cytokine responsiveness is less in progenitor cells than their ancestors(stem cells)?

What will be the benefit of such reduction in responsiveness?

My answer assumes you are asking about in-vivo effects of cytokine responsiveness.

It has to do with the regulation of the differentiation process. Cytokine responsiveness depends on other factors like cell-cell signaling. To be sure that the differentiation occurs in the right place, the progenitor cells need a signal feedback from the surrounding context (the actual tissue where the cells will differentiate). If the feedback matches, they differentiate.

Stem cells on the contrary, are physically distant from that context, so they lack all the feebacks needed and do not respond to cytokines stimulation as the progenitors do.

Here's some literature about it:

Developmental changes in progenitor cell responsiveness to cytokines.
Mechanisms regulating lineage diversity during mammalian cerebral cortical neurogenesis and gliogenesis.
Signal transduction pathways involved in the lineage-differentiation of NSCs: can the knowledge gained from blood be used in the brain?
Enhanced responsiveness of committed macrophage precursors to macrophage-type colony-stimulating factor (CSF-1) induced in vitro by interferons alpha + beta 1.

However, note that the whole process is still largely unclear and it may vary for different cell types, so consider my answer as a generalization of the concept.