How does most of lymph get back into the blood stream? (I don't mean the lymphatic system) I once read that it was because of osmotic pressure that it returns to the blood stream, by entering the venules. But why? If lymph originated as plasma how come that the solute concentration is higher in the venule? Doesn't plasma contain solutes such as salts, nutrients, oxygen, etc. ?

Technically 'lymph' is used to refer to the fluid found within the lymphatic system. If it's not in the lymphatic system, it is not lymph fluid. Thus, your question is really asking about interstitial fluid or the plasma that was filtered out of blood capillaries.

The answer to your question is based on the Starling equation. Normally fluid leaves a capillary due to a net pressure that favors the interstitium. This net pressure is based on the hydrostatic pressure within the capillary being greater than the interstitial pressure of the surrounding tissues, and the oncotic pressure of the capillary (that draws fluid in) being weaker than the hydrostatic pressure of the capillary (that pushes fluid out). At the venule end of this system, the capillary oncotic pressure is stronger than the capillary hydrostatic pressure, drawing fluid back into the circulatory system.

Remember that albumin is the most important component which establishes the oncotic pressure within a vessel, and that this protein is normally NOT released out of a vessel during filtration. Thus, it passes from the capillary into its corresponding venule directly.

Yes, plasma that enters the interstitium contains many of the same components as when it is in the blood, but the main difference is the protein content, losing the majority of proteins as it enters the interstitium.

Now, if you are asking how the majority of LYMPH fluid re-enters the blood stream, the answer is through the R lymphatic and L lymphatic (aka thoracic) ducts, at the location of the R subclavian or R internal jugular, and L subclavian veins, respectively. Once fluid enters lymphatic capillaries, it goes through a system of lymphatic vessels, trunks, and finally, the above mentioned ducts to rejoin blood.

References:

http://www.biog1445.org/demo/06/lymphaticsys.html
http://intranet.tdmu.edu.ua/data/kafedra/internal/in_mow/classes_stud/uk/med/medprof/ptn/англійська%20мова%20за%20професійним%20спрямуванням/2/№%2003.%20Heart...htm


What are some online databases that I can search to find the pathways for sythesis of Lignin, Cellulose, GAX? I am trying to obtain the pathway information for synthesis of Lignin,GAX and Cellulose in Sorghum. I am quite new to biology and genetics (EE background). I would appreciate it if y'all can provide me with some websites or books where such info maybe available. I have already looked in KEGG. Thank you very much.

The other big metabolic database site besides Kegg is MetaCyc which certainly responds to searches for lignin and cellulose.

The problem with lignin is that it is a very complex molecule, so in both Kegg and MetaCyc there are a many reactions involved in its synthesis. Cellulose is less complex and I have no idea what GAX is, despite an internet search. If you are so new to biochemical reactions and metabolic pathways that you cannot handle the results of a MetaCyc search on lignin you should easily be able to find articles devoted specifically to cellulose and lignin, perhaps using Wikipedia as a start.


fibroblast cells and fibers I am interested in fibroblast cells in human arteries. Here are the things that I am not clear at the moment and I could not find any answer from the literature:

What are the dimensions of these fibroblast cells? How big are they in terms of diameter and thickness? How big are they if they are comparing with the collagen fibers in the artery?
I think they have to attach themselves to the fibers in order to proliferate or differentiate. However, I do not know, do one fibroblast cell attach itself to one fiber and then "crawl" to another? Or do they "sit" on a network of fibers?

I will appreciate your help on this and will be even more grateful if you could provide me with some literature that I could find the answer to these questions.

Regarding dimensions:

As per this image the length and breadth seems to be ~30-50 μm (area should be roughly around 900 μm²). The third dimension (thickness) as per this article can be assumed to be around 3-7 μm.

Regarding cell attachment:

Cells attach to extracellular matrix via integrins, which attach to ECM proteins like collagen and fibronectin. The matrix is a net of fibres and the cell is not specifically attached to a single fibre but rather "sits"(as you said) on the matrix [see the below image]. A single cell also simultaneously interacts with two different types of ECM proteins such as fibronectin and collagen.

During migration they move along the matrix using lammelipodia (actin filament polymerization in the direction of motion).

Fibroblast express ICAM1/VCAM1 (Inter/Vascular Cell Adhesion Molecules) under certain conditions such as inflammation and bind to T-cells and endothelial cells.


In a vertebrate chimera, are particular organs homogenous genetically? I have read that a chimera is an organism with two or more sets of DNA, with every cell having one of the sets. Is it possible and common for the two or more sets to be present in the cells of a single organ? I'm confining my question to vertebrates because I don't remember much about the biology of invertebrates from high school, but please don't hesitate to add anything interesting about them.

Chimerism (or genetic mosaicism if the cells come from the same zygote) is possible in the same organ or tissue. I don't think you will see a homogeneous distribution of the chimeric tissue because the tissue in any vertebrate organ is rarely homogeneous to begin with. Microchimerism may occur in a small number of cells. That's about all I know.


Are peanut proteins similar to chicken meat proteins? I'm studying amino acids content in vegetable food. I was looking at peanut protein and noticed its similarity with chicken meat, as you can see in the table below (quantities are measured in grams). Third column is first column minus second column. Green amino acids are the essential ones.

The biggest difference (-1.11) happens for Lysine, but Lysine quantity (0.901) is still bigger than the lowest one, which is Tryptophan (0.2445). So in this case, is Tryptophan the limiting factor in protein synthesis? (Tryptophan amount is < than any other amount).

The table below lists the optimal profile of the essential amino acids (first column). Second column is obtained by dividing the values in table 1, first column, by 25.3055 and multiplying by 1000.

Notice that Lysine is the only one amino acid less than the reference (36<51).

So the questions are:

1) Have peanut proteins a limiting factor (if yes what is and why?) or can be considered a complete protein?

2) If the answer to 1) is "yes it has a limiting factor" what vegetable foods rich in lysine can be eaten with peanut in order to obtain all the amino acids? And how to calculate the ratio of peanut and the complementary foods to eat in order to get the proper profile of the essential amino acids?

Source for first table (first and second columns) https://ndb.nal.usda.gov

Source for second table (first column) http://nutritiondata.self.com/help/analysis-help

I'm not sure if biology is the correct site to post this question, so if you know a better one let me know, thanks.

I posted an answer to a similar question here: https://health.stackexchange.com/questions/9124/is-all-protein-the-same/9130#9130

  You're not using protein as it is to maintain your body. It's first
  broken down to the individual amino acids, which your body can then
  use to build new stuff.

  If you're lacking one of the essential amino acids, you can only build
  as much new protein until that runs out, and all the other amino acids
  are just excess. A protein that contains all the necessary amino acids
  is called a complete protein, and you could calculate the differences
  in the so-called quality of the protein.

  A perfect protein (i.e. from egg/milk/soy) will contain amino acids in
  exactly the ratio you need, some protein contains so little of a
  certain amino acid that you'd need to eat twice as much of that
  protein (for example rice or peanuts).

  In your case, if beef is making you recover fastest, you'd need to eat
  30*0.92/0.70 = 39g of peas for the same effect.

  You could get around this by combining different sources of protein.
  For example grains are limited in lysine, while beans are limited in
  cysteine/methionine.


Do humans sneeze or cough in their sleep? As far as I know, I've never seen anyone sneeze or cough while they're sleeping. Google wasn't very helpful either; a lot of contradicting claims.

So the questions remains: do humans sneeze or cough in their sleep? (a few other things I've never seen with sleeping people are yawning and vomiting) If they don't, why?

Sneezing does not occur during REM sleep, due to REM atonia.(1)

The coughing reflex is  also suppressed during sleep, but coughing may still occur occasionally during sleep. (2).


Confirming exon shuffling in a gene I'm trying to confirm that the sequence of a novel gene is derived by exon shuffling between several different genes. I have the promoter sequence, gene sequence, and mRNA (with defined exon/intro boundaries). I've tried performing several database searches with the sequences, but each search produces a set of different unrelated hits. How would one go about using this info to confirm the exon shuffling hypothesis? Any tips are appreciated. Thanks!

It's not clear what is 'several database searches with the sequences'. The most obvious solution is blasting your sequence so you can see which part can't be aligned and then blasting the rest. You can choose different implementations (megablast of blastn) and play with algorithm parameters because it may not work for you as-is. But it will work as-is if you'll blast exons separately. This way you can identify origin genes.


Is Behe's experiment (evolving the bacterial flagellum) plausible in the lab? [Warning: this question is motivated by a prominent proponent of "intelligent design": Prof. Michael Behe.  I'm not interested in debating creationism.]

According to Wikipedia[1]:

  In Darwin’s Black Box (Behe 1996) I claimed that the bacterial
  flagellum was irreducibly complex and so required deliberate
  intelligent design. The flip side of this claim is that the flagellum
  can’t be produced by natural selection acting on random mutation, or
  any other unintelligent process. To falsify such a claim, a scientist
  could go into the laboratory, place a bacterial species lacking a
  flagellum under some selective pressure (for mobility, say), grow it
  for ten thousand generations, and see if a flagellum--or any equally
  complex system--was produced. If that happened, my claims would be
  neatly disproven.

[emphasis mine.]

As far as I can tell, nobody has actually performed this experiment (although, my literature search was not comprehensive, so it is possible I simply haven't found the appropriate publications).  [However, there are arguments that the flagellum could have (or likely has) evolved from the type III secretory system, which shows similarity[2].]  This state of affairs strikes me as peculiar -- Behe's proposal sounds like an interesting experiment to perform (even disregarding any external debate).

  Question: Is the experiment proposed by Behe (or another experiment in the same spirit) plausible to implement in a laboratory experiment?

Experiments reproducing steps in evolution seem to turn out much easier than I would have expected a priori, e.g. reproductive isolation of fruit flies[3], experimental evolution of multicellularity[4], so perhaps Behe's experiment would also be surprisingly easy to implement.

References:

Wikipedia: Michael Behe
 Blocker A, Komoriya K, Aizawa S-I. 2003. Type III secretion systems and bacterial flagella: insights into their function from structural similarities. Proceedings of the National Academy of Sciences of the United States of America 100: 3027–30.
 Dodd DMB. 1989. Reproductive Isolation as a Consequence of Adaptive Divergence in Drosophila pseudoobscura. Evolution 43: 1308.
 Ratcliff WC, Denison RF, Borrello M, Travisano M. 2012. Experimental evolution of multicellularity. Proceedings of the National Academy of Sciences of the United States of America 109: 1595–600.

The experiment itself is technically feasible - but whether there is any point (as opposed to using the resources to perform a different experiment) is highly questionable. The problem is this: Behe's claim is that the mechanism is irreducibly complex, and that it could not have arisen by natural selection. This is theoretically falsifiable, but the experiment he proposed does not provide a good dichotomy - there is a very large chance that he is wrong but over the experimental term of 10,000 or 10,000,000 generations, the flagellum might not arise.

The absence of the flagellum in the experiment is the most likely scenario, and doesn't either support or falsify his claim. It took evolutionary time, something on the order of 1010+ generations, to arise the first time (according to the consensus claim); we could not expect similar complexity to arise for the same purpose under conditions of directed evolution. That's a terrible experimental design: huge resource input, huge likelihood of no result.

To be clear: it is technically feasible, but not a good experiment. He proposed it because he knew that nobody would do it (because it's a bad idea).


What factors are known to affect evolution? My understanding is that the possible mechanisms of evolution are:

Environmental changes
Cultural/mating preferences
Population Immigration
Genetic Mutation

Am I missing anything? I've heard that population shifts within a existing populaces will effect evolution, but imagining the most simplicity scenario, it's hard to see why the would make a difference.

Evolution is defined as a change in the allele frequency of population through time.  The Hardy-Weinberg model predicts that the allele frequency of a population will not change (i.e., evolution will not occur) if the following conditions are met:

no natural or sexual selection
no gene flow (immigration or emigration from the population)
no mutatation
no genetic drift (changes in allele frequency due to random events)

So we can conclude that if any of the above conditions are not met then there is a change in allele frequency and thus evolution, and thus that factor is the cause of evolution.


How can you stabilize enzymes in pellets made from microcrystalline cellulose? I want to make pellets consisting of mainly the following:

microcrystalline cellulose
saccharose
rice starch
ascorbic acid
glycerin

and an enzyme as active component.

Is it furthermore necessary to add protease inhibitors or other stabilizers to remain the activity of the enzymes for a periode of at least one year OR is the dry environment conservation enough?

The enzyme is called histaminase and is extracted from kidney cortex through a series of centrifugation, filtration and dialysation. To be more precise, it is a liquid protein extract containing small amounts of this enzyme. No buffer etc. is added to the protein extract so far. The whole purification process is done at 4°C. I don't know how long the enzyme is stable without further preparation. Probably not that long because some proteases should remain in the natural homogenate from porcine kidney cortex. The other components of the pellets are of pharmaceutical quality. The aim of this experiment is to feed the pellets to dogs with digestive complaints. For this purpose the pellets will get a enteric coating to survive acid environment of the stomach.

As you can probably guess from my comment, there are a lot of factors to take into account when thinking about protein stability. Here's what I would recommend you do.

First, make sure your extract is in a neutral buffer, like PBS, HEPES, or something similar. This is a fairly standard procedure when working with proteins. Next, since this is a kidney extract, there are likely to be gobs of proteases around, so I would strongly recommend adding broad-spectrum protease inhibitors, and keeping the extract as cold as possible to inhibit any enzyme activity. I would also add BSA at 10 mg/ml, both to stabilize the proteins and keep them from precipitating while in solution, and to lessen the chances that any proteases present will attack your enzyme of interest.

Once you have your solution stabilized, I would aliquot it and lyophilize it. Proteases are most active in solution, so once dried you'll reduce their activity even more. You can now add the inert ingredients (microcrystalline cellulose, etc.), mix thoroughly, press your tablets, and add the enteric coating. Finally, once everything is prepared, I would store the final product at as cold a temperature as is convenient. Again, this will inhibit any enzyme activity and prevent degradation.

I don't know if you have a functional assay to determine activity of the enzyme of interest, but if you don't I'd highly recommend developing one if at all possible. This way, you can test the activity of the fresh preparation of extract and compare it to various stages of processing into tablets, especially the finished goods, to ensure that you haven't lost much activity. I would also test random tablets throughout the year to make sure they haven't lost activity in storage, otherwise you won't be able to compare your experimental results.


How much percent of image does our eyes focus at any instant? I learned in highschool that even thought we have a wide view, we only observe a tiny fraction of that view through our eyes. So at any instant we are not really looking at all the objects infront of us, this is why we need to individually focus at each object at a time.
Question: What is the % of view that is in focus at any instant of time compared to the full view we observe thorough our eyes?

What you learned in high school isn't exactly true (or is misremembered). Human eyes get visual input across about 120 degrees of visual angle, and some herbivore mammals see near 360 degrees total between their two eyes.
However, the resolution is not constant. The fovea is an area of high-density receptors in the retina. When you look at something specific, you are directing light from that area of the visual field to the fovea. The fovea is limited to about 2 degrees of visual angle.
Additionally, your attention is often limited to a small section of the visual field. When viewing a scene, your eyes will naturally make saccades to bring various points into high acuity vision to get a good sense of the entire scene, but you are still seeing all the surrounding area, even if you aren't paying much attention to it. Importantly, you are still sensitive to surprising stimuli (especially those that are high-contrast or moving) in those areas that might cause you to redirect your attention, otherwise you would be very easy to sneak up on.


Life cycle of proteins I try to get a picture of the life cycle of a protein (considered as a specific molecule).

This is how I can imagine it:

After the cell is born a protein molecule is synthesized by gene expression for the very first time de novo. This happens at a specific point in time and in space, typically at an ribosome, which may be located anywhere inside the cell.
From the location of its generation (combination or recombination, see below) the protein travels to its final destination, e.g. as an ion channel in the cell membrane. (But possibly it was already synthesized very close to its point of use.) Or it just floats around in the cytosol. (Possibly, it gathers some other biomolecules around it.)
Whereever it arrives or not: the protein lives and works for some time.
Eventually, it gets damaged (= looses small functional units), but gets repaired in situ. Continue with 3.
Eventually, it gets marked by ubiquitin and destructed in a controlled manner. Continue with 7.
Eventually, it decays spontaneously (= splits into some larger fragments).
Its fragments are released (in case it was bound) and start again to float around in the cytosol.
Eventually, its (or other proteins') fragments are recombined (at specific points in time and in space, possibly at "re-factories" comparable to the ribosome-"factories"). Continue with 2.

Is this rough picture of the life-cycle of a protein essentially correct?

If so: What is known about the time ranges in which these processes take place? Especially: How long is the effective life and working time of typical proteins? Are there proteins that live and work only for minutes or hours, and others that live for months or years? (Specific examples are welcome!)

Protein half-lives range from less than 30 min (e.g., oxidoreductases) to more than 200 hr (e.g., some nucleic-acid binding proteins) and up to, at least, 2000 hr [Rahman & Sadygov, 2017, PLoS One 12(7): e0180428].

More ubiquitination sites, shorter half-life; more/larger intrinsically disordered regions, shorter half-life; more tightly coupled with the cell cycle, shorter half-life.

Note: Not all eukaryotic proteins are degraded via the ubiquitin-proteasome proteolytic pathway.

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0180428


What is a centrosome? I know that a centrosme is composed of two perpendicular centrioles, but the following sentences of Wikipedia confuse me:

Interestingly, centrioles are not required for the progression of mitosis.
Many cells can completely undergo interphase without centrioles.
Unlike centrioles, centrosomes are required for survival of the organism.

If centrosomes are essential then does this doesn't imply that centrioles too are necessary since centrosome is made of two centrioles, if not then what is it made of?

Reading the specified Wikipedia article about Centrosome, actually explains why centrioles are NOT IMPORTANT for the PROGRESSION OF MITOSIS.

To better understand what wiki meant, let us look at both centrioles & centrosomes.

According to Biology Pages for Centrioles and Centrosomes >>

Centrioles are built from a cylindrical array of 9 microtubules, each of which has attached to 2 partial microtubules.
The Centrosome

is located in the cytoplasm usually close to the nucleus.
It consists of two centrioles — oriented at right angles to each
other — embedded in a mass of amorphous material containing more than
100 different proteins.
It is duplicated during S phase of the cell    cycle.
Just before    mitosis, the two centrosomes move apart until    they
are on opposite    sides of the nucleus.
As mitosis proceeds,       microtubules grow out    from each
centrosome with their plus ends       growing toward the    metaphase
plate. These clusters of microtubules    are called spindle
fibers.

So, now we know that during mitosis, the nuclear membrane separates and the centrosome nucleated microtubules (parts of the cytoskeleton) can associate with the chromosomes to fabricate the mitotic spindle.

Understanding the conceptual working of centrosome, the Wikipedia article states >>

  Interestingly, centrioles are not required for the progression of
  mitosis.

  When the centrioles are irradiated by a laser, mitosis
  proceeds normally with a morphologically normal spindle.

  In the absence of the centrioles, the microtubules of the spindle are
  focused by motors allowing the formation of a bipolar spindle. Many
  cells can completely undergo interphase without centrioles.

Therefore, even in the absence of centriole, centrosomes develop Astral microtubules which just exist amid and quickly before mitosis. Astral microtubules are characterized as any microtubule beginning from the centrosome which does not interface with a kinetochore.

Astral microtubules are not required for the movement of mitosis, but rather they are required to guarantee the devotion of the procedure. The capacity of astral microtubules can be by and large considered as assurance of cell geometry. They are totally required for right situating and introduction of the mitotic spindle assembly, and are in this way required in deciding the cell division site in light of the geometry and extremity of the cells.

An important note from the the Wikipedia article >>

  Unlike centrioles, centrosomes are required for survival of the
  organism. Acentrosomal cells (i.e. cells without centrosomes) lack
  radial arrays of astral microtubules.

  They are also defective in spindle positioning and in ability to
  establish a central localization site in cytokinesis.


Genotypic distribution of a population with two characteristics and linkage I am currently doing some research into distributions and probabilities with Mendellian genetics. I came across this problem that I cannot seem to wrap my head around.

Given that the population has two characteristics, they are color and texture. Supposed two dihybrids reproduce (AaBb x AaBb) and if the dominant form of the
color gene is contributed, then the dominant form of the texture gene is three
times as likely to be contributed as the recessive form. If the recessive color gene is contributed then the dominant and recessive genes for texture are equally likely.

From this the geneotypic distribution has to be calculated.

I know the solution is:

[9/64   6/64   1/64   3/16   1/4   1/16   1/16   2/16   1/16]

 AABB   AABb   AAbb   AaBB   AaBb  Aabb   aaBB   aaBb   aabb

When I performed the punnett square I got the distribution of:

 [1/16   2/16   1/16   2/16   4/16   2/16   1/16   2/16   1/16]

 AABB   AABb   AAbb   AaBB   AaBb  Aabb   aaBB   aaBb   aabb

and did not know where to go from there.

My question is how did they incorporate the "times as likely" condition into the solution.

You are...  done. You fully answered the question; if I were you, I might just put it in ratio format instead of probability, just to be safe.

The three times thing is a bit weird, but I have seen it before. First, let's look at the phenotypic ratio of the progeny: 9:3:3:1 for Dominant Both:Dominant A Recessive B:Recessive A Dominant B: Recessive Both.

Let's find out how many dominant and recessive there are for each trait. For the dominant A trait, you add up the 9 and 3, because they are the only two types of dominant phenotypes, and find that 12 different organisms of the 16 possible are dominant for Trait A, so the probability of getting trait A is 3/4 or 75%. This means that 4 of the 16 orgamisms are recessive for Trait A, so the probability of being recessive for Trait A is 4/16, or 25%. Therefore, the ratio of Dominant Organism probability:Recessive organism probability is 75% to 25%, or 3:1. This means that it is 3 times as likely to get the dominant trait than the recessive trait. Make sense?


Current state of Gene Therapy I am interested in learning about attempts to treat adult individuals suffering from a genetic disease in which the underlying changes in the DNA of the gene are understood.

(i) Are there approaches that use drugs or do they use DNA corresponding to the normal DNA?

(ii) Are there attempts to reverse the condition or only ammeliorate it?

(iii) How near is such gene therapy to clinical use and for which diseases?

The scope of this question is too wide to be answered on Biology SE. However I will give you very brief answers to your questions (as I have rephrased them) and point you towards some sources of basic information on the Internet. After reading these you may wish to return with more specific questions. I have also briefly summarized some of the problems which it is useful to be aware of before reading details of specific approaches to gene therapy,.
Answers

(i) Some approaches involve attempts to replace a defective gene with
a functional gene or add the latter to the patient’s DNA. Others
involve drugs, often nucleic acid in nature.
(ii) Current efforts often have the more modest aim of ameliorating the disease, although there are also efforts to reverse the condition.
(iii) Gene therapy is not yet in general clinical use, although for some diseases (e.g. Severe Combined Immune Deficiency and Chronic Granulomatus Disorder) there have been reports of success in limited clinical trials.

General Reading
I am not an expert in this area, but by Googling for ‘Gene Therapy’ I came up with the following pages that you may find helpful.

Your Genome
University of Utah: Approaches to Gene Therapy
American Society of Cell and Gene
Therapy

You may also be interested to read about the currently controversial drug, Eteplirsen.
Problems in Gene Therapy
Rather than giving you details of technical approaches to gene therapy, for which you may not have the necessary scientific background, I draw your attention to some of the key problems and questions that have to be addressed in this area.

Does one need to counteract the harmful effect of a mutant gene product (e.g. sickle cell haemoglobin), or is it sufficient to produce a ‘good’ gene product to remedy a deficit?
Is it possible to target new cells or does one have to deal with existing mature cells?
(Some cells like blood and immune cells are constantly renewing themselves, whereas others like muscle turn over much more slowly. The latter are more difficult to deal with.)
How can the DNA (or drug) be deliverdd to the cell, and only to the appropriate cell. (A variety of delivery techniques have been employed in different circumstances.)
How can the therapeutic DNA be incorporated into the appropriate position in the genome, and how can one ensure that it is expressed, and that no other genes are affected. (Early attempts at gene therapy using in which DNA was inserted at the wrong position resulted in cancers. However technology here is moving rapidly.)


Carotene in Dracaena draco I'll keep this question straight and simple:

Some succulent plants produce carotene, a red pigment, in response to great heat, turning their leaves red. The dragon blood tree (Dracaena draco) is among the succulent plants. Does it exhibit this behaviour too?

Looks like they do.

What We Know and What We Do Not Know about Dragon Trees?

  Numerous phytochemical studies of resins from the Dracaena species
  resulted in the isolation and subsequent identification of sterols
  [135–138], steroidal saponins [110,138–141], lignans [138], and
  terpenoids [131,135,142–144], flavonoids (recently reviewed by Sun et
  al. [129], bioflavonoids [145,146], carotenoids [109,138], and
  aromatic compounds [107,147–151].

Citations are behind a paywall but apparently carotenoids are in the sap.


Do Cooper Hawks eat fish? I have seen a Cooper hawk sitting on a low branch above my small Koi pond 3 times in 4 months. The books and net say they eat birds and some mammals but I wonder if he is looking at my fish ? Or snakes or frogs ?  As I write this I had a thought, song birds come down to a shallow part of the pond, that may be what the hawk is after. But I still wonder about the original question.

Birds learn new tricks very often, using roads to crack nuts, opening foil milk bottles (tits), and Hawks are known to catch Koi.

These pages say that Cooper Hawks specifically do catch fish: http://forums.gardenweb.com/discussions/1997093/hawks-taking-koi
http://www.outdooralabama.com/coopers-hawk

Here is a cooper hawk catching a duck and swimming around with it: https://www.youtube.com/watch?v=A08jxYinAG8

if you put cooper hawk pond into youtube, you will find 10+ videos of them bathing in ponds, and 2 videos of them scouting at a pond.

My aunt saw a buzzard, Buteo Buteo 50cm tall, catching a yellow Koi right out of the water while I was out for the day. The Koi was 30cm long, 12", it dived on the water and flew away with a fish on the wing. The Koi had indeed vanished as my aunt had said.


How is the glycemic index computed from a blood sugar curve? The definition of the glycemic index is often given as the area under curve (AUC) of their two-hour blood sugar response. However, it's essentially meant to be a measure of whether food causes a fast or slow rise in blood sugar level. Why is the two-hour AUC a good measure of the speed of the rise?
When ingesting the "same" amount of sugar, no matter the form, the AUC should be the same, right? The only explanation I can find is that the two-hour cutoff means some carbohydrates are metabolized beyond that cutoff, so their AUC and hence their GI is lower, is that what's happening?
The reason I'm a bit confused is that all of the images of blood sugar curves illustrating low & high GI seem to show two curves with the same AUC, both going to 0 before the two-hour cutoff.

The AUC of identical dosages of sugar depends on digestion speed because of the rate at which sugar is removed from the blood stream. If sugar exponentially decayed in a first order rate, then the AOC would be the same, but it's save to assume some 0 order mechanisms contributing. E.g. alcohol is mostly metabolized in a 0 order reaction rate: A fixed amount per hour.
Edit: If you take up sugar slowly, it might never reach high concentrations in the blood stream and lead to lower AUC then if taken up fast. Each molecule has a longer lifetime if taken up faster.


Is there any mechanical digestion that occurs once food/chyme enters the small intestine? Does mechanical digestion occur in small intestines and, if so, how does it occur? I found some sources that say digestion happens mechanically and chemically in the small bowel, and others that say it only happens chemically? Also, does chemical digestion only occur with acids (e.g. HCl) instead of enzymes, or does it occur with enzymes?

I believe in small intestine peristalsis is sometimes counted as mechanical digestion as the food is moved along the digestive tract. Chemical digestion occurs with enzymes secreted from the pancreas.

https://www.smartlivingnetwork.com/digestive/b/mechanical-and-chemical-digestion/ - source


Why do we have an immune system? My daughter asked a question that I could not answer.

If you have a cold, you have symptoms such as fever, cold and sore throat. These symptoms, however, are the reactions of the immune system to bacteria, viruses and other germs.

So my question is: What would happen if the immune system did NOT respond? I know that bacteria can produce certain poisons. And viruses can capture human cells and make them produce more viruses.

Now to the naive part: But what's wrong with that?

Are Viruses dangerous because these cells would then no longer perform their function?
Without any immune system: Would a virus simply take over all human body cells?
Is it not the organism in the first place, who puts itself in mortal danger (such as high fever or inflammations) because of the defense reaction?

Thanx!

Basically you would rot from the inside out, as bacteria and viruses destroy your cells.

Fever is your body using heat to denature the viral proteins (viruses don't have chaperone proteins like us so they are more vulnerable to heat) Sore throat is you body killing infected cells before the virus can reproduce inside them, normally the virus will reproduce inside the cell until the cell bursts or simply runs out of resources and dies both release huge numbers of the virus.

Check out the virus life cycle. https://en.wikipedia.org/wiki/Viral_life_cycle


By what mechanism does Risperidone swell breast tissue? There has been much talk of the anti-psychotic drug Rispeirdone causing un-natural breast tissue growth as well as galactorhea (milk production). Especially in young men and boys.

What is the mechanism of this drug that is causing this? Is it actually introducing some amount of female hormones into the male's body or is just causing increased production of them?

Risperidone prevents dopamine from acting on the pituitary gland by blocking dopamine type 2 receptors. One of dopamine's effects on the pituitary is to suppress prolactin production. In patients taking risperidone, prolactin production thus increases and prolactin levels in the body are higher than normal. In younger males, this can result in abnormal growth of breast tissue and even milk production.

See e.g. Melkersson, K. I. (2006). Prolactin elevation of the antipsychotic risperidone is predominantly related to its 9‐hydroxy metabolite. Human Psychopharmacology: Clinical and Experimental, 21(8), 529-532.


Can Darkling Beetles Fly? I searched the internet on the question whether darkling beetles can fly, and I read mixed results to it. Some say they can, there are even videos about it, but then again they say that they cannot, due to fused wings or the like.

I am currently interested in mealworms, and plan to farm some myself, and some people show their containers without covers, even though the beetles should be able to fly out then, shouldnt they?

This is really confusing to me, thanks for the awnsers.

Short answer; It depends. Darkling beetles is a very large family of beetles (Tenebrionidae) where some species can fly and some do not. Looking more narrowly at the genus Tribolium (i.e. mealworms), which many people refer to when they talk about darkling beetles, it also differs. The common Tribolium castaneum (red flour beetle) as well as T. molitor are good fliers, while T. destructor does not fly. The same goes for the confused flour beetle (T. confusum), which is not know to fly from what I know.


What is the evolutionary cause for various finger lengths? Why are the lengths the way they are with middle finger the longest?

When you bend your fingers, they all arrive at the same height. I would tend to think that their lengths differ when you keep them straight because they need to have similar length when you bend them. And I guess that there is some optimal length (when bended) for fingers to grasp things.

It is nothing but a quick hypothesis. But it sounds quite plausible to me.

As @JordiZambrino commented, it is possible also that middle fingers evolved to be longer in reaction for the need for throwing things.


What is the name of this green plant with thin leaves? I've seen this in Scotland between Balmaha and Inversnaid:

A higher resolution is here: https://commons.wikimedia.org/wiki/File:Balmaha-Inversnaid-9.jpg

What is the name of this green plant with very thin leaves?
(I guess it was most of the time about 60cm high, but I don't quite remember)

This is a moss of the genus polytrichum, most likely it is P. commune or P. formosum


Horizontal gene transfer from humans It is known that some viruses embed themselves in the human genome. Is there a mechanism by which human genes can be transferred to other animals or plants by means of viruses shuttling them from humans to other organisms?

Yes, Horizontal gene transfer (HGT) can happen in both ways, from prokaryotes to eukaryotes and vice versa. So far less attension is given to from eukaryotes to prokaryotes HGT. It has played very important role in eukaryotic evolution also. Following figure from (Patrick and Palmer 2008) shows some potential cases in eukaryotic phylogeny.

You can find many such examples from above reference. Coming to human part, there are few cases like From Humans to Plasmodium vivax and From human to Neisseria gonorrhoeae , where researchers have shown evidence of HGT from humans to prokaryotes. Unfortunately , there is very little on mechanism by which they transfer. It is matter of speculation right now as these studies are controversial.


Why do people in the scientific community use terminology such as renal, hepatic, cardiac instead of kidney, liver and heart? Are there differences between renal, hepatic, cardiac and kidney, liver and heart? Is the "jargon" used more commonly because of tradition, or is there some definitive biological basis to it?

Medicine is not my field, but I want to point out two things:

The former words have latin (or greek) roots, and historically latin was the international language of science. Therefore, nomenclature in different scientific fields are often based on latin.
The former words describe tissues and the related functions/processes (e.g. renal = kidney + related tissues + processes carried out by the renal system), while the latter are names of organs. Therefore, the former words are more suitable and precise when you want to describe these processes. For instance (as far as I know), Hepatic disease can be be caused by problems outside of the liver as such, e.g. blockage in the hepatic vein.

Users more knowledgeable in medicine are welcome to fill in or correct me if I'm mistaken.


Why don't half of us have situs inversus? I don't see any possible evolutionary disadvantage in situs inversus(the condition where major organs are mirrored from their normal positions) when people with situs inversus can have a normal healthy life.

In the Wikipedia article linked to in the question, one will note that there are several medical conditions associated with situs inversus, including congenital heart disease, primary ciliary dyskinesia, and Kartagener Syndrome. These can easily lead to reduced fitness for reproduction, especially PCD/Kartagener Syndrome, as one effect is male infertility due to lack of functional cilia on sperm.

Therefore, there likely is a negative pressure on the alleles responsible for this condition, explaining why it is so rare.


What happens if both forward and reverse primers have same Tm? One of the key rules in primer designing is that Tm (melting temperature) of forward and reverse primers should be in the range of ±5°C. For example, if Tm of forward primer is 62°C, then reverse primer should be either 67°C or 57°C.

What happens if both the primers are having same Tm?

Is this to be considered as perfect score of finding correct primers set?

Thanks

It is actually good if both the primers have the same Tm (Melting Temperature) because you would basically want both primers to anneal at your Ta (Annealing Temperature) which is generally set as Tm-5. If the Tm(s) don't match, then your Ta should be set according to the lower Tm.


How many recombination events are there per generation in humans? I'm looking for a reference that tells me how many recombenation events occur in humans from one generation to the next.
Assuming that the human genome is a 3.3 GigaBases long DNA sequence, how many recombination events do you find, and what is he amount of DNA exchanged?
Is it in the order of 0.1%, 1% oder 10%?

Back-of-the-envelope calculation

The definition of the centimorgan is that it is the length of DNA in a chromosome corresponding to a 1% chance of crossover occurring.

In human chromosomes 1 cM  = approx. 1Mbp.

Your value for the length of DNA in the genome = 3.3 Gbp = 3300 MBp

Ignoring complications like the Poisson distribution:

1 cM corresponds to a probability of 1% chance of a detectable crossover. Detectable, because only an odd number of crossing over events between 2 genetic markers can be observed as a recombination, but even numbers instead go unrecognised. Therefore the actual chance of crossing over is doubled relative to the cM value.
If 1 cM = 2% actual chance of crossover, there will be on average 1 crossover per 50 cM or per 50Mbp

Therefore crossovers per human genome = 3300/50 = 66  or approx 2-4 per chromosome

This guess comes near empiric data:

Actual data

This Table, taken from here shows the number of chiasmata by chromosome for 8 human cells. (Note that it believed that there has to be at least one chiasma per chromatid pair since they have a structural role.)

The average chiasmata per chromosome for each chromosome can be estimated by dividing the number in the final column by 8. These vary from (rounding aggressively) 3.5 for Chr 1 and Chr 2, to 1 for Chr 20. So my back-of-the-envelope calculation seems to have produced a reasonable answer.

What is the amount of DNA exchanged? I'm not sure this question matches well with the picture that emerges from these numbers.


How many different kinds of polypeptides, each composed of 12 amino acids, could be synthesized using the 20 common amino acids? How many different kinds of polypeptides, each composed of 12 amino acids, could be synthesized using the 20 common amino acids?

The book's answer is $20^{12}$.

However, I disagree. This result distinguishes the following two polypeptides even though they are exactly the same polypeptide:

(Met)x11-Glu

and

Glu-(Met)x11

Am I right? How would I otherwise answer this question? My background in probabilities is very weak.

Judging from what you have said, I assume that combinatorics is not a problem to you.

I believe your problem is that you think Glu-(Met)x11 is equivalent to (Met)x11-Glu, just turned around. However, that is not a correct mindset. Amino acids are not symmetrical molecules, therefore reversed linear combination does not create a turned-around (be it chiral or not) form of a similar amino acid. My guess is that you write amino acid names in consecution when representing peptides. This method has a small problem that it does not incorporate directionality of molecules. Drawing the whole molecule may be a solution, but that is too much chore.

My solution is to add a small mark (perhaps an arrow, or a > mark) to represent a specific side of the amino acid molecule (amine group or carboxyl group), so that mirroring the sequence (so that the mark would be at the "other" side of each amino acid) would actually create a peptide molecule different from reversing the sequence (so that the mark is still at the "normal" side of each amino acid). If you think that doesn't look good, you can draw a frame around each amino acid, where one side of the amino acid has a dent and the other side has a bump (to represent the amine and carboxyl groups) so that only a bumped side can connect to a dented side. Mirroring the sequence would also reverse the positions of the bumps and dents, thereby creating a different peptide molecule than merely reversing the sequence while keeping the positions of the bumps and dents in place.


Osmosis and hydrostatic pressure I'm confused about the role of hydrostatic pressure compared to osmotic pressure.

Q1:If I have a U-tube with a membrane permeable only to water molecules and equal volumes of water on either side but only 1 side (side B) has NaCl, the osmotic pressure would cause water to move from side A to side B,correct ?

Q2.But then hydrostatic pressure would cause water to move back to side A.
So, the water would move from side A to side B until the effect caused by the hydrostatic pressure = effect caused by osmotic pressure ?

Q3. The last statement wouldn't be correct If I said that "water moves until the hydrostatic pressure=osmotic pressure" would it ?

and lastly, My friend said the water would move until the hydrostatic pressure on both sides was equal
Q4. If water is moving from side A to side B then the we have more water molecules at side B, how would side A ever reach the hydrostatic pressure at side B ?
Do I have a misunderstanding in the concept of hydrostatic pressure ? In this context, I understand that it is the pressure exerted by the water molecules on the selectively permeable membrane.

The more I google hydrostatic pressure the more lost I get because all sources seem to explain in terms of equations and physics and I'm only taking this for an introductory course in physiology.

Osmosis is defined as the flow of water/solvent molecules through a semipermeable membrane from a region of low to high solute concentration, until equilibrium is established.
To counter osmotic flow, some pressure must be applied to the solution in order to prevent pure solvent from going through the semipermeable membrane separating the two liquids; this is known as the osmotic pressure.
The osmotic pressure is the pressure required to counter, not sustain, osmosis.
The osmotic pressure can be approximated by using the following formula: $\Pi = i M R T$ .
U- Tube showing osmotic pressure. On the left side of the U-tube is an aqueous solution, and on the right side is pure water. The pure water is trying to dilute the solution by travelling through the semipermeable membrane. Eventually the added weight of the extra water on the left causes enough pressure to stop osmosis.
Osmotic pressure is the pressure that needs to be applied to a solution to prevent the inward flow of water across a semipermeable membrane. Osmotic pressure can also be explained as the pressure necessary to nullify osmosis. One way to stop osmosis is to increase the hydrostatic pressure on the solution side of the membrane; this ultimately squeezes the solvent molecules closer together, increasing their “escaping tendency.” The escaping tendency of the solution can be raised until it eventually equals that of the molecules in the pure solvent; at this point, osmosis will cease. The osmotic pressure is the pressure required to achieve osmotic equilibrium.
Osmotic pressure. Osmotic pressure is the pressure required to stop osmosis.
The osmotic pressure (II) of an ideal solution can be approximated by the Morse equation:
$\Pi = i M R T$
Here, i is the van ‘t Hoff factor, M is the molarity of the solution, R is the gas constant, and T is the absolute temperature in Kelvin. We can see from this equation that the amount of solute present in the solution will directly affect the osmotic pressure of the system.
Example
What is the osmotic pressure of a 1.35 M solution of NaCl at 25 $^\circ$C?
First, fill in all of the necessary information, and then solve:
i = 2 (NaCl breaks into two particles)
M = 1.35 $\frac{moles}{L}$
R = 0.0821 $\frac{L\times atm}{K \times mol}$
T = 25 $^\circ$C + 273 = 298 K
$\Pi = 2 \times 1.35 \times 0.0821 \times 298$
$\Pi = 66.1\ atm$


What is the meaning of 'state of nature' in On the Origin of species by Charles Darwin? I have started reading "On the origin of species" by Charles Darwin.
The beginning paragraph is:

When we look to the individuals of the same variety or sub-variety of our older cultivated plants and animals, one of the first points which strikes us, is, that they generally differ much more from each other, than do the individuals of any one species or variety in a state of nature.

What does he mean by state of nature here?
Note:
The term state of nature is very often used in this book, so for anyone reading this book my question would be helpful for greater understanding.
Edit: One user has requested for more context for better understanding...I would like to provide the next paragraph and also a related paragraph.

When we look to the individuals of the same variety or sub-variety of our older cultivated plants and animals, one of the first points which strikes us, is, that they generally differ much more from each other, than do the individuals of any one species or variety in a state of nature.
When we reflect on the vast diversity of the plants and animals which have been cultivated, and which have varied during all ages under the most different climates and treatment, I think we are driven to conclude that this greater variability is simply due to our domestic productions having been raised under conditions of life not so uniform as, and somewhat different from, those to which the parent-species have been exposed under nature. "

Another paragraph in which State of nature has been used:

Sterility has been said to be the bane of horticulture; but on this view we owe variability to the same cause which produces sterility; and variability is the source of all the choicest productions of the garden. I may add, that as some organisms will breed most freely under the most unnatural conditions (for instance, the rabbit and ferret kept in hutches), showing that their reproductive system has not been thus affected; so will some animals and plants withstand domestication or cultivation, and vary very slightly—perhaps hardly more than in a state of nature.

I would think that by "state of nature", he probably referred to any non-cultivated species. As @David suggested in the comments, the expression "in the wild" could also be a good replacement for "in a state of nature".

I think that the first paragraph you quote could be rephrased in the short sentence

  There is more phenotypic variation in cultivated species than in non-cultivated species.

My sentence is more concise but of course, is quite a bit less pleasant to read. Darwin was a very good writer after all.


Are viruses ever manufactured directly from viral DNA embedded in the genome? Some viruses can cause their genetic material to be pemanently stored in the human genome -- even getting passed on to offspring.

Endogenous Retroviruses, for example are thought to make up between 5~8% of the human genome.

Does stored viral DNA present in an otherwise uninfected human being's (a newborn baby for example) genome ever get used to spontaneously manufacture new virus bodies, thus infecting the host, and causing them to suddenly become contagious without ever having encountered an actual virus?

Put differently, is it possible that a human being harboring viral DNA and quarantined in a sterile enclosed environment (bubble, etc) preventing any contact with external contaminants (viruses), could ever spontaneously become infected with a virus, due to the stored viral DNA getting expressed?

It sounds like you're referring to the transition from the lysogenic cycle to the lytic cycle. The lysogenic cycle involves the viruses' DNA being integrated into the host's genome, such that the host has a dormant infection, the lytic cycle involves the virus' DNA being transcribed and translated to make the components of viruses, like capsid proteins, which then self-assemble to form many viruses which then leave the cell. The fact that this transition can occur means someone can experience an active viral infection, with proliferating virus particles, without exposure to additional viral contaminants. If it couldn't, then would there be much point (from a virus' perspective) to the storage of viral DNA in the genome which, as you've noted, retroviruses can do?

Transitioning from integrated DNA to phage particles:

To use the lambda phage (which is a bacteriophage and thus infects bacteria, not humans, but the underlying principles are the same) as an example, the expression of the viral DNA is controlled. But, the viral DNA is not a monolith - parts of the viral DNA of a prophage (the genetic material of the bacteriophage integrated into the bacterial host genome) are expressed but their expression prevents the expression of those parts of the viral DNA which would cause a transition from prophage an active infection, i.e a switch from lysogeny to the lytic cycle.

The lambda phage genome is shown below:

But an easier to deal with version which focuses more on the elements required for regulation would be:

There's lots of stuff going on here, but the key point is that lambda repressor, a protein coded for by the yellow cI gene, represses any transition to the lytic cycle. Aside: cI stands for clear I, because virus mutants which don't have c1 go straight into the lytic cycle and so produce clear spots on agar plates of bacteria since the bacteria are straight out killed rather than hosting the virus in the prophage form.
The lambda repressor prevents the transcription of the genes under those arrows in the top part of the diagram, and it's those genes which code for the things required for active virus particles, such as enzymes required to rupture the host cell's wall, and the proteins required to form the virus' coat.

So, to sum up, yes. Viruses existing as viral DNA embedded in the genome can cause infections, even in individuals not exposed to additional contaminants (but contaminants which cause damage to the host's DNA, like mutagens, will trigger the transition from lysogeny to lytic), and some of the viral DNA is always expressed (repressor genes) in order to prevent the expression of the parts of the viral DNA which would cause an active infection, were they to be expressed.


Why can't you taste food when you have a cold? It is a common observation that food is tasteless when we have a cold. Why is that so?
What is the cause of inability to taste when we have a cold? Are the nose and ability to taste connected?

This German review supports common wisdom that the sense of taste is predominantly informed by the sense of smell. For instance, common advice to children taking "nasty" tasting medicines is to plug one's nose. Any condition that blocks olfaction, such as sinusitis from flu or other sinus infections, or blocking nasal airflow, will decrease or block olfaction and as a result, the majority of taste.

Hüttenbrink KB. [Disorders of the sense of smell and taste]. Ther Umsch. 1995 Nov;52(11):732-7. [Article in German]


How is RNAse contamination in RNA based experiments prevented? Does anyone have any suggestions to prevent RNAse contamination when working with RNA?

I tend to have issues with degradation regardless of whether I use DEPC treated / RNAse free water and filtered pipette tips.

You need to be careful about everything that comes in contact with your samples. Every spatula, beaker and every magnetic stir bar need to be RNAse-free.

For metal- and glassware we usually put everything into a drying closet at 200-250 °C for a few hours. That should get rid of RNAses pretty efficiently.

The RNA chemicals should be seperated from other chemicals if not everyone in the lab is working with RNA. They shouldn't be weighed using spatulas, but just poured into an RNAse-free container to avoid contaminating the storage container.

Use disposable plastic wherever possible, you should be able to perform most stuff in falcons and Eppendorf tubes.

Be careful with performing e.g. a DNA-prep at the same bench as the RNA work. The first buffer for the DNA-prep contains RNAse.

Avoid keeping your Eppendorf tubes or falcons open for long, that should reduce the potential for contamination.

We've had pretty good experience with just using water from a Millipore system and autoclave it once, that seems to get rid of the RNAses. I know that this is not a sure thing as the RNAses can survive autoclaving, but it seems to work well enough.


What leads to the different types of navels? Obviously, there are "innies" and "outies" in the human belly button world.  Both are the result of a knot tied in the umbilical cord just after birth.

But why do some belly buttons become outies while others become innies?  Is it related to how the doctor ties the knot, or is it related to how the knot heals?

After childbirth, the umbilical cord is either tied (similar to a tourniquet - the cord itself is not tied into a knot) or clamped to cut off the blood supply. It is then cut distal to the clamp/tie, separating the child from the rest of the cord and the attached placenta. The remaining cells die and dessicate, and the stump eventually falls off, forming the umbilicus or belly button. The default result, barring any issues, is an "innie". However, an "outie" may form if the child was born with a tiny umbilical hernia, or there was a small unnoticed infection at the base of the umbilical cord. Either of these could lead to the formation granulation tissue, described colloquially as an "outie". People can also have combination navels, with the indentation of an "innie" but a small amount of protruding granulation tissue inside.


Do antisense transcripts have different names than their sense strand transcripts? I want to find which genes in the human genome can potentially be complementary to a transcript that could act as antisense transcript inhibtion? Are cis-NATs (naturally occuring anti-sense transcripts) considered different transcripts and named differently or do they have the same name as the sense transcript?

If the anti-sense transcript is correctly annotated and in the databases (a very very big if), then it will have a different name. For example, the mouse Msx1 anti-sense transcript has the RefSeq accession NR_027920 while the sense transcript of the same gene is NM_010835.

In general, each transcript that is transcribed from a given locus has a different accession. The same is true for alternatively spliced transcripts. If a given gene has 4 AS transcripts, each of these transcripts will have a different, unique accession. The human insulin receptor gene, for example, has two protein coding transcripts, each with its own accession: NM_000208 and NM_001079817.

You may be interested in a recent analysis of cis-NATs in 10 species[1] and also in NATsDB: Natural Antisense Transcripts DataBase[2].

Osato N, Suzuki Y, Ikeo K, Gojobori T. 2007. Transcriptional Interferences in cis Natural Antisense Transcripts of Humans and Mice. Genetics, 176(2): 1299-1306, doi:10.1534/genetics.106.069484.
Li JT, Zhang Y, Kong L, Liu QR, Wei L. 2008. Trans-natural antisense transcripts including noncoding RNAs in 10 species: implications for expression regulation. Nucleic Acids Research, 36(15):4833-44, doi:10.1093/nar/gkn470.


Surgical vs anatomical neck What is the significance of differentiating anatomical neck and surgical neck of a bone?

What could be criterias for differentiation?

I found an article here that says fractures to surgical neck are benign, could this be a criteria for differentiation?

Most of the time, I have heard this differentiation in context of Humerus bone only. In that context, have a look at the wiki pages on the anatomical and the surgical necks.

From this, and what I remember from anatomy class, this distinction is more a functional; practical distinction rather than that based on strictly defined criteria. Surgical neck denotes the most commonly fractured region of the bone, and also the region most likely to damage the axillary nerve passing nearby, and hence would have the greatest representation in an orthopedic clinic. The anatomical neck, on the other end, is the classical distinction based on the centers of ossification and the insertion of the capsular ligament of the adjacent shoulder joint, which gives a greater weightage to its origin and to the anatomical relations (insertions, etc).


What is the mechanism of transgene integration (from expression vector to the host genome)? How does a transgene (in vector) integrate to the host genome? (e.g. in glass bead method, neither biolistic nor agrobacterium).

I already cut some parts (NdeI-PciI) of the vector (pUC18) and wondering if it affects the integration procedure. Is there any recombination-like procedure same as gateway?

What is your host in this case? For integration into the genome of a bacterium, you would need to use an "integration" vector. Most commercial vectors (such as pUC18) will be maintained without integrating into the host genome.

Here is a description of an integration vector from the Bacillus Genetic Stock Center to give you an idea of how foreign DNA would be integrated into a Bacillus genome:

  Integration vectors are plasmids that feature conditional replication
  coupled with a selectable marker. If the plasmid is transformed into
  an appropriate host under conditions that select for the plasmid’s
  presence but restrict its replication, all transformants will have
  integrated the plasmid into their chromosome (or some other resident
  DNA capable of replicating under the selective conditions). In
  practice, the selectable marker usually specifies antibiotic
  resistance. Conditional replication usually means that the plasmid has
  replication functions that work in E. coli but not in gram-positive
  bacteria, such as B. subtilis. Sometimes a temperature-sensitive
  replication phenotype is employed instead. Integration is targeted to
  a particular locus on the chromosome by including identical sequences
  on the plasmid. If there is a single homologous sequence, a single
  crossover will integrate the entire chromosome into the target locus
  by a Campbell-type mechanism. If there are two homologous sequences,
  and they are relatively close together on the chromosome, then a
  double crossover will result in a cassette integrating between the
  chromosomal targets. (source)

For most routine molecular biology labwork, there is no need to integrate genes into the E. coli genome. Integration is usually used to generate "knockout" cell lines to study gene function in the bacteria of interest.


"Air sac" and "air cell" in a chicken embryo I need to translate the Russian term "воздушный мешок". It is part of the chicken embryo, marked by number 5 in the figure below.

I found the expression air cell but also found the expression air sac in English. On one site, "air sac" is described as a synonym to the "allantoic sac":

Just to make sure: is air cell the only correct translation for the structure marked by number 5?

My sentence goes roughly like this:

  ...  the injections are made from the direction of the naturally-occuring air cell (?) so as to apply the material onto the chorioallantoic membrane (CAM).

According to Atlas of Chick Development by Ruth Bellairs and Mark Osmond, a book I'm using for my developmental biology course :

  Air space  is the space between the two shell membranes at the blunt end of the egg. The chick pushes its beak into this space shortly before hatching and takes its first breathe of air.

Besides allantois is the extra embryonic membrane and the space enclosed by it is allantoic cavity.

Here label 2 is Allantoic cavity.


Identical twins' biological sexes Can identical twins have different genders (as in biological sex)?

I thought they should have absolutely the same genes. If they can, what caused it? I'd assume it MAY be because of errors in cellular division at conception.

Thank you.

Identical twins occur when a single egg is fertilized to form one zygote, which then divides into two separate embryos. Thus, identical twins are always the same sex unless there has been a mutation during development.

However, two identical twins expressing different sexual phenotypes does happen in some extremely rare cases due to environmental factors, deactivation of different X chromosomes in females, or aneuploidy. This is normally because an XXY Klinefelter syndrome zygote has split unevenly.

You are correct though, in that identical twins usually have hundreds of genetic differences early in fetal development which can be attributed to mutations in the DNA. But usually these differences do not result in twins with different sexual phenotypes, though it is possible.


The GUG start codon in E. coli: identity of initiating tRNA and efficiency of translation Translation in E. coli is usually initiated at an AUG codon, which encodes the amino acid methionine. In some cases, however, the start codon is GUG, which normally encodes valine. If GUG is used as the start codon, is a tRNA charged with methionine used or one charged with valine, and does the use of GUG as a start codon affect the efficiency of translation?

The NCBI translation table translates all alternative start sites as methionines. To my understanding, all translation is initiated by the fMet-tRNA. I don't know if there are any exceptions to this rule.

Regarding translation efficiency, I only found a 1985 paper in PNAS (Reddy et al, PNAS 82:5656-60), in which they compared the translation efficiency of adenilate cyclase's own UUG start vs GUG or AUG, obtaining a translation ratio 1:2:6 UUG:GUG:AUG, suggesting that AUG is the most efficient one, followed by GUG. Also, Romero and Garcia, FEMS microbiology letters 84:325-330 (1991) compared the efficiency of AUG vs AUC, AUA and AUU, showing a much lower efficiency for those codons, but they did not compare it to GUG.


Defining paper(s) in epigenetics For someone who is interested in learning about the discovery of epigenetics, which are the foundational defining papers in the area?

I understand that Robin Holliday was the first to discuss the possible role of DNA methylation
in the control of Gene expression. In his paper "The inheritance of epigenetic defects"
he presents what is one of the first modern formulations of what we now regard as epigenetics. The term "epigenetics" itself was coined by Conrad Waddington although this predated our modern understanding of heredity.

Holliday, R., The inheritance of epigenetic defects, 1987, Science, 238, 4824


Are all fusion genes somatic in origin or can fusion genes be germline? Fusion genes should have an origin.These are essentially hybrid genes that are translocated in its entirety. Eg. BCR-ABL, EML4-ALK are known to be implicated in cancer pathogenesis. Do these translocation events occur somatically or is there a possibility for it to be inherited?

There is at least one (possible) description of an inherited (aka germline) fusion gene:  KANSARL.  See the paper "Identification of KANSARL as the first cancer predisposition fusion gene specific to the population of European ancestry origin" by Zhou, Yang, Ning et al., Oncotarget. 2017; 8:50594-50607.

  KANSARL fusion gene is familially inherited and may be ubiquitously expressed in KANSARL-bearing individuals
  The presence of KANSARL fusion transcripts in normal and adjacent tissues in CGD and VPD raised the possibility that KANSARL fusion transcripts are derived from a germline-inherited fusion gene. To investigate this possibility, we performed RNA-seq data analysis for the lymphoblastoid cell lines derived from the families in the CEU population (CEPH/Utah Pedigree 1463, Utah residents with ancestry from northern and western Europe), which includes a three-generation family with 17 individuals [47]. Supplementary Table 9 and Supplementary Figure 8 show that KANSARL fusion transcripts were detected in 15 of 17 family members, as indicated by black squares and circles in Supplementary Figure 8, except son (NA12885), which is deviated from the first Mendel law. A reasonable explanation is that the grandfather sample (NA12889) might have been mixed with the son sample (NA12885). To prove this possibility, we performed analyses of the WSG data (PRJEB3381) and RNA-seq from 1000 Genome Project, and shown that both WSG and RNA-seq of grandfather sample (NA12889) are KANSARL-negative while WGS of the son (NA12885) is KANSARL-positive (Supplementary Table 10). Supplementary Table 10 shows the genomic breakpoint 1 and 2 of the KANSARL fusion gene (Supplementary Figure 5 and 9) identified by analysis of WGS data among some members of CEPH/Utah Pedigree 1463. Therefore, Both WGS and RNA-seq data support that the father (NA12877) and the mother (NA12878) have the genotypes of KANSARL-/KANSARL- and KANSARL+/KANSARL+ respectively and all their offsprings are the genotype KANSARL+/KANSARL-


Is there a formal definition of signature of natural selection? I’ve searched for a definition of signature of natural selection. Unfortunately, I haven’t found any formal definition of it.

The signature of positive selection on standing genetic variation. I found this post that links to an article measuring the signature with an Fst and a Linkage Disequilibrium test.

Are we looking at only some frequency of alleles in different populations? Is the signature only a fixation of alleles in a population where this allele was positively selected?

Another article says:

  A single beneficial substitution can be detected in polymorphism
  data, so long as it occurred recently. The fixation of a favorable
  allele in a population distorts patterns of variation at linked
  sites, thereby leaving a distinguishing signature that lasts up to
  about 104 generations in humans or about 106 in Drosophila
  melanogaster (Przeworski 2002). In principle, targets of positive
  selection can therefore be identified by searching polymorphism data
  for regions that harbor this signature (Nair et al. 2003; Wright et
  al. 2005).

Is it always in linkage disequilibrium?

Here is how I would personally explain what a genetic signature is:

A genetic signature of a certain type of evolutionary history (type of selection or demography) refers to the effect that this specific type of evolutionary history has on genomic properties of populations today.

We are interested in understanding such signatures because knowing the association between a number of evolutionary histories and their genetic signature allows us to reconstruct the evolutionary history of a population just by looking at the genomics of this population.

For example, recent selective sweep, population expansion after a recent bottleneck and/or linkage to a swept gene are all causing negative Tajima's D. Balancing selection and/or sudden population contraction are causing positive Tajima's D. In this example Tajima's D is a statistics that is used to measure this so-called signature of the different process.

The above was NOT a citation. I am NOT aware of any publications defining rigorously what a genetic signature is. I think it is not so uncommon for authors to use a term without strictly defining it. As long as the unclarity of the definition does not yield to limit cases and misunderstanding, then it is totally fine.


What is this crow eating, and is it a common part of the corvid diet? Here's a picture (by Rob Curtis) of a crow carrying and eating the corpse of what looks a bit like a small hawk or falcon:

Other pictures clearly show the crow is eating the dead bird. This image shows the underside of the head and beak; this one shows its legs, which are grayish.

What bird is being eaten?
Is this bird a usual part of the corvid diet? Or did the crow just opportunistically scavenge a dead bird?

Crows are omnivorous, and will eat almost anything they find or can kill.

In this case the prey looks like a Yellow-Shafted Flicker.


Can two arms-racing species be stabilized? I am trying to build an evolution simulator in which there is group A and group B, each group has 9 members each generation. Each generation, each member of group A will enter a competition (in the form of combat) with a random member of group B, and fitness will be calculated based on how quickly and with how little losses will one member's army destroy the other. The best few members of each group then becomes the parents of the next generation.

(Note that an "individual" of each group is in fact a genetically determine neural network that controls a swarm of robots, think of it as a swarm of ants sharing the same DNA and thus can be effective consider one individual)

Will this end up with both group A and B having phenotype/strategy that do not change very much over many generations, or will it result in strategies that gradually changes throughout generation, with each successful, significant change out-smarting the opponent's old strategy until the opponent develop a counter strategy?

To rephrase Cort Ammon. It depends on how you setup the system.

Imagine each combat strategy as a point on a landscape. Good strategies are on higher ground, poorer strategies are on lower ground.

A and B each have their own combat strategy and thus start at different points on this landscape. Mutations allow a species (say A) to explore the strategies around its starting point. Selection will cause the curtail that exploration.

If A find itself on a slop of a hill, selection (ie your combat and mating system) will cause the A population to drift upwards on this slop. However if A find itself on the peak of a small hill, it has no where else to go.

So how the scenario will play out will depend on the initial start conditions of population A and B. The mutation rate/genetic variability of the population (ie how many strategies population can explore around its initial strategy).

Additional factors is the genetic system that you have. If individuals of your species can only have one strategy (haploid), the species will be bound to its local hill. However if an individual can have more than one combat strategy at a time, (ie a diploid or gene duplication in RL), then the individual can have a combat strategy that work (local peak) and have a second strategy that is free to evolve... free to explore the landscape... going down valleys of bad strategies... and may eventually find the foot of a mountain... which a peak fitness higher than even the local peak it started.


Why does HIV belong to a group of retroviruses called lentiviruses? HIV is an enveloped retrovirus. Each virus particle contains two copies of an RNA genome. The virus also has a number of enzymes: reverse transcriptase, integrase and viral protease. But, once I also find that HIV also belongs to lentiviruses.
I am not very familiar with the relationship between retrovirus and lentiviruses. And does here have somebody know why HIV is a kind of lentivirus?

In Latin, lente means slow, so lentiviruses are retroviruses that are characterized by long periods of latency.

lentivirus A group of retroviruses that include human immunodeficiency virus, HIV-1. They cause disease after a long incubation period.
latency A state in which a virus infects a cell but does not replicate.

-Janeway's Immunobiolgy, 8th Edition, Kenneth M. Murphy
HIV-1 is characterized by long incubation periods. It can often take months before the virus is detectable on HIV tests.
It is also known that HIV reservoirs will exist in a patient, such that even if they have undetectable viral loads when on Antiretroviral Therapy, once they come off of the treatment, they will begin to produce virons again. The likely reason for that is that the immune cells that they infect can be very long lived, and as the viral genome has been incorporated into the host cells genomic DNA, it is incredibly stable. It will stay dormant for years until it is able to replicate again.


Ornithology related areas in Biology In relation to my work, I'm looking at ornithology as a field, and it would be interesting for me to know which areas in biology relate to ornithology.

Any help is much appreciated!

First of all, you can look at the papers published in the Journal of the Avian Biology, the Journal of Ornithology and the Auk. There you can see how bright is the field. It is about conservation biology, distribution of species, ecology of species, behavior, migration etc.


COPI/COPII proteins and kinesins/dyneins I am considering the transport of protein from ER to Golgi, and have read that this involves the COPII protein coat. I have also read that this is a form of anterograde transport, and elsewhere that kinesins are responsible for anterograde transport as they move from the negative to positive  (outside) poles of the microtubules.

Thus it seemed to me that the kjnesins carry the COPII vesicles carrying proteins from ER to Golgi.

However a Google search of the terms 'kinesins' and 'COPII' together did not seem to yield anything about kinesins carrying COPII.

On the other hand in this article it links COPII with dynsctjn, which I have not heard of before.

Does someone know the link between COPI and COPII transport, and/or retrograde and anterograde transport, with the microtubule motor proteins kinesin and dynein? Where do dynectins come into this? Do they bind the vesicle to the dynein or are they a different type of motor protein? If it is the first case, then why is this transport termed anterograde if it does not use kinesins? Are the terms anterograde and retrograde not directly related to kinesin/dyneins use?

Interesting question. The term anterograde refers to movement in the forward direction. In the context of vesicular trafficking, anterograde refers to (1) movement from the site of protein synthesis in the rough endoplasmic reticulum (RER) towards the Golgi and then (2) movement from the Golgi towards the final destination in the cell.

Both processes rely on microtubules for transport. Microtubules are polar and radiate from the microtubule organizing center (MTOC) with their (+) ends directed towards the periphery of the cell:

There are two broad classes of molecular motors that facilitate directed movement along microtubules. Kinesins are generally (+)-end directed motors whereas dyneins are (-)-end directed:

These images should already give you a hint. Your question may have arisen due to the assumption that the ER is centrally located near the MTOC with the Golgi somewhat peripheral. This is incorrect. In reality, the Golgi complex is actively clustered near the MTOC by movement on microtubules. Furthermore, the ER extends along the microtubule network towards the (+)-end periphery. Taken together, it is evident that microtubule (-)-ends are located near the Golgi and transport to it from any part of the cell, including the RER, requires the (-)-end directed motor dynein. Subsequent anterograde transport from the Golgi to a specific destination in the cell, or through the secretory pathway, requires the (+)-end directed motor kinesin. Retrograde transport from the Golgi back to the ER would also use kinesin:

The article cited in the question (which I also reference in this answer), mentions that COPII vesicles are coupled to microtubules via dynactin. Dynactin is a protein complex that is used to both activate and adapt cargo to dynein (ie COPII vesicles are coupled to microtubules via a dynein/dynactin complex):


What limits the speed of human perception? I'm writing a novel in which the main character's perception and thought processes are sped up considerably, in essence slowing down the world around him. To others, it seems like his reactions are far faster than normal. Of course, there's a fantasy explanation for this in the story, but it led me to wonder exactly what limits the speed of human perception and reasoning in the real world.

From what I know, the speed at which we perceive events appears to be a constant. What exactly determines that rate? Is it possible to change it? Is it possible that different people perceive things at different speeds?

Flicker Fusion Threshold:

The wikipedia definition:

  It is defined as the frequency at which an intermittent light stimulus appears to be completely steady to the average human observer.

Background

In 1824, Peter Mark Roget (who also wrote the famous Thesaurus) first presented the concept of "persistence of vision" to the Royal Society of London, as the ability of the retina to retain an image of an object for $\frac{1}{20}$ to $\frac{1}{5}$ second after its removal from the field of vision.

A second principle - the $\phi\ phenomenon$ or stroboscopic effect is closely related to flicker fusion. It was first studied by Max Wertheimer and Hugo Munsterberg between 1912-16. Wertheimer and Munsterberg found that subjects can perceptually bridge the temporal gap between two consecutive displays, so that a series of static images appear as continuous movement. The discovery of flicker fusion became the perceptual basis for moving pictures, television, and all media based on stroboscopic presentation of stimuli.

The minimal frequency at which flickering stimuli appear continuous is called the critical flicker frequency.

Perceptual factors affecting the critical flicker fusion threshold

This critical flicker fusion threshold depends on the stimulus’

Luminance (the Ferry-Porter law),
Size (the Granit-Harper law),
Color,
Retinal eccentricity,
Background Luminance, and other factors.

Biology Behind it:

  Physiological evidence in humans and monkeys shows that flicker rates
  above the perceptual critical flicker frequency threshold can
  nevertheless generate cortical and subcortical visual responses.  Thus
  the temporal integration underlying flicker fusion does not occur at
  the level of the retina,  but must take place later in the visual
  hierarchy. Single-unit recordings in the primary visual cortex of
  primates suggests that,  for two brief-duration targets presented in
  close succession, the after-discharge to the first  target interferes
  with the onset-response to the second target (Macknik, 2006) (see
  Figure 5). The onset-response to the second flash is absent for
  inter-stimuli intervals of 30 msec or shorter (equivalent to 17 Hz
  periodic). If the flashes are separated by more than 30 ms, the
  after-discharge to the first flash and the onset-response to the
  second flash begin to recover (i.e. equivalent to <17 Hz flicker).
  These intervals roughly coincide with the critical flicker fusion
  threshold in humans for 100% contrast stimuli in the fovea .

  This suggests that perceptual flicker fusion may be due to the lack of
  robust transient responses to the flickering stimulus.

http://images.scholarpedia.org/w/images/thumb/8/8b/Flicker_fusion_fig5.png/360px-Flicker_fusion_fig5.png

Source:

Bartley (1939). Some effects of intermittent photic stimulation. Journal of Experimental Psychology 25, 462-480.
Bloch, A. M. (1885). Experience sur la vision. Comptes Rendus de Seances de la Societe de Biologie, Paris 37, 493-495.
Brücke, E. (1864). Über den Nutzeffect intermittierender Netzhautreizungen. Sitzungsber k Akad Wissensch Math-naturw Cl, Wien 49, 128-153.
Di Lollo, V., and Bischof, W. F. (1995). Inverse-intensity effect in duration of visible persistence. Psychol Bull 118, 223-237.
Ferry, E. (1892). Persistence of vision. Amer J Sci 44, 192-207.
Fukuda, T. (1979). Relation between flicker fusion threshold and retinal positions. Percept Mot Skills 49, 3-17.
Flicker Fusion

What is the Different speeds of Visual Perception?

First-order motion

Experiment: A moving sinusoidal grating with bright peaks and dark troughs is seen through a window.

Result: Even when its velocity is so high that 30 of its bright peaks pass each location per second (30 Hz), observers still perceive its direction of
motion.

Depth from binocular disparity

Experiment: Two identical gratings, one in each eye, are viewed through identical windows.

Result: One is spatially shifted relative to the other, introducing a binocular disparity that is perceived as depth.
Even when they move at a 30 Hz rate, the depth is still perceived.
If the input to depth mechanisms were blurred at a >30 ms timescale, detecting the depth would be impossible at this rate.

Edges and texture boundaries

Experiment: Against a gray background, a field of white dots is adjacent to a field of black dots.

Result: Both fields are set in rapid alternation between white and black, but out of phase – when
one is white, the other is black. The conspicuous boundary between them is perceived even at fast
rates of 30 Hz, whereas at faster rates the black and white are averaged by the brain into the same color as the background.

http://ak.picdn.net/shutterstock/videos/3139525/preview/stock-footage-retro-geometric-dot-background-in-black-gray-and-white.jpg

Binding of color and orientation sharing a spatial location

Experiment & Result: If a red, right-tilted patch is alternated with a green, left tilted patch,
it is easy to distinguish from the complementary pairing of red left alternating with green right, even at
fast 20 Hz rates.

Binding of form and color across space

Alternating color-shape pairings can only be reported at rates below ~3 Hz.

source: http://www.psych.usyd.edu.au/staff/colinc/HTML/dynamics.htm

Binding of global form with color

Two specially constructed dot patterns that form distinct shapes alternate, with all the dots of one red and all the
dots of the other green.

At alternation rates faster than several a second it is very difficult to determine the shape color pairing even though the shapes and colors themselves
are easily identified.

Direction change and acceleration perception

A moving stimulus alternates between two speeds (acceleration) or two directions. When the alternation occurs
faster than several per second, these changes are unperceivable.
Its limit is 8-10 Hz.

Word perception

Certain pairs of words (such as ‘jump’ and ‘pink’), when alternated in the same location, cannot be distinguished
from another matched pair at rapid rates as one perceives only the sum, which is the same for both pairs.
They can be distinguished only at rates slower than several items per second.

Source: http://www.psych.usyd.edu.au/staff/alexh/research/words/

Source:

Holcombe AO (2009) Seeing slow and seeing fast: two limits on perception. Trends Cogn Sci 13:216 –221.
http://www.psych.usyd.edu.au/staff/colinc/HTML/dynamics.htm


Why does K+ have more concentration inside of the cell compared to outside of the cell? Why is Na+ and Cl- the opposite? Can someone tell me the fundamental reason why K+ has low concentration outside of the cell and more inside of the cell?

Why nature has done it this way around is difficult to explain. What is certain, however, is that the membrane potential which results from the imbalance of these ions across the membrane is used for a variety of purposes, such as transport of other ions and molecules, action potential generation in neurons among many other things.

How it is accomplished is mainly through the Na+,K+-Atpase pump and secondarily through Cl- channels that exchange Na+ for Cl- to lift the amount of Cl- outside the cell.


how much can changing light enter the eye shap what you see? Does it change the shape and how objects are seen or does it just stop you from seeing certain things?

I'm interpreting your question to be: "How much can changing the light entering the eye change the shape of/how objects are seen? Would manipulating that light just stop you from seeing certain things?"

Manipulating the light entering the eye is the exact premise of a virtual retinal display (VRD):

  From Wikipedia –  A VRD is a display technology that draws a raster display (like a television) directly onto the retina of the eye. The user sees what appears to be a conventional display floating in space in front of them.

Google Glass and other technologies (virtual reality headsets, heads-up displays) operate through relatively similar projection mechanisms. Light defines everything the eye sees (outside of hallucinations, and even those can be induced by flickering light). Also, the way your brain processes visual information (photons received by your eyes) can be "tricked," which is discussed in this BBC article. Finally, your brain's ability to process visual information can be altered by external forces (e.g. drugs, motion, or even strong magnetic fields).


B cell clones and affinity maturation As B-cells undergo affinity maturation, their BCR sequences change. Are they still considered to be part of the same clone?

I couldn't find a clear answer in response to this very similar question:

What is meant by clones of B-cells?

There are different opinions on this, since it's about usage. You could make an argument that, if you're talking about a B-cell clone, it is the product of a specific VDJ recombination (a mature, but naive B-cell), and refers to B-cells that produce antibody to one antigen. However, the term was originally proposed in this context:

  ...the expendable cells of the body can be regarded as belonging to clones which have arisen as a result of somatic mutation or conceivably other inheritable changes. Each such clone will have some individual characteristic and in a special sense will be subject to an evolutionary process of selective survival within the internal environment of the body.

In this case, I'd argue that, when the BCR sequence changes in progeny from that original naive B-cell (as in affinity maturation), you end up with different clones.

You do have to be careful, though, because people use this term differently.


Are there differences in DNA between humans of today and humans from 2000 years ago? Are there any significant differences in our genome compared to the genes of our ancestors from 1000-2000 years ago?

And if there are significant differences, do they result in significant differences in phenotypic traits?

The larger differences are most likely in epigenetic marks on the DNA. The environment is a lot different today than it was 2000 years ago and those differences are stronger determinants of epigenetic change than sequence change.

2000 years is only about 40 generations and that is not very much to see great differences in DNA sequence or allele frequencies - once founder populations are removed from the analysis.

Height is highly influenced by genetics, but can be masked by environment - notably diet. Diets higher in protein content are more likely to elicit the expression of the "height alleles" but only to a point as too much protein is also unhealthy.

Added in Edit 4 Apr 2012: I should add that my response is written from the perspective of frequency of alleles or epigenetic marks across a population.


Why/how does exposure to noise cause cochlear hair-cell loss? I am trying to understand why listening to loud music - e.g. concerts or earphones at high volume damages hearing.

According to the National Institute on Deafness the cause is physical.

  Most NIHL is caused by the damage and eventual death of these hair
  cells. Unlike bird and amphibian hair cells, human hair cells don’t
  grow back. They are gone for good.

But I don't understand why/how would noise - which should basically lead to higher amplitude waves in the basilar membrane, induce damage and death of these hair cells?

There are a number of pathophysiological mechanisms that are thought to underlie noise-induced hearing loss:

Mechanical damage to the delicate cells and supporting structures of the organ of Corti;
Reduced blood flow to the inner ear;
Intense metabolic activity, which increases mitochondrial free radical formation.

Reactive oxygen species (ROS) are highly reactive. They are essential for mitochondrial function to generate energy. However, too many of them damage cellular lipids, proteins, and DNA, and upregulate apoptotic pathways. The observed impaired blood flow to the cochlea can enhance the toxic effects of ROS. Mechanical damage to the delicate hairs and membranes of the hair cells reduces their ability to converge acoustical energy into potential differences.

References
- Le Prell et al., Hear Res (2007); 226(1-2): 22–43
- Kurabvi et al., Hear Res (2017); 349: 129-37


Which fish will have more developed gills? A fish lives at the depth of 1000-2000m and another at the depth of 200-700m. Which of them would have a more developed gill system ?

200m is still pretty deep...

However, I'd give my money for the surfacers. Oxygen concentration decreases with the depth, and so abyssal fishes have very low metabolism, mainly focused on anaerobic muscles. This is also true for fishes that live in the bottom (benthic), which probably also applies for those living in a few hundred meters. If not, they will probably be active swimmers and then they will probably need bigger gills in order to maintain aerobic movement. Even if we're talking about abyssal and non-abyssal benthic species, I think the abyssal ones would probably be even more anaerobic.


Which mushroom could be this? Collected in northern West Europe in autumn 2017

By a hint from a FB forum, it should be meripilus giganteus and I have to agree.


Why don't antibiotics affect mitochondria? Given that mitochondria are evolutionarily closely related to bacteria, and antibiotics kill bacteria, why don't antibiotics also kill mitochondria?

The short answer is, as you found, that mitochondria are wrapped in a double membrane and are thus harder to penetrate with antibiotics.

The long answer is some of them do.  Good antibiotics target structures widely found on and conserved in bacteria that are not found in human bodies.  Some antibiotics are a little less specific and can indeed interact with other molecules.  The allergy to penicillin, for example, is caused by the immune system reacting to a "novel" protein formed when penicillin binds to the surface of red blood cells.  Some antibiotics can indeed harm mitochondria, but we tend not to use those and in fact wouldn't even call most of them antibiotics since we wouldn't use them because of their harmful effects.  Here is a very recent report looking at some of the anti-mitochondrial effects of some antibiotics.  To quote from the abstract:

  We show that clinically relevant doses of bactericidal antibiotics—quinolones, aminoglycosides, and β-lactams—cause mitochondrial dysfunction and ROS [reactive oxygen species] overproduction in mammalian cells. We demonstrate that these bactericidal antibiotic–induced effects lead to oxidative damage to DNA, proteins, and membrane lipids.