What are the risks of elevating the legs too regularly and when tired? I started to to think the pathophysiology of elevating legs high next to the wall too often and when you are tired.
I think possible manifestations

some damage to valves of the veins (No!)
because of collateral circulation, rhombus, heart damage, ... (No! Only in pathological situation but cannot be considered here. I think here that the risk of thrombus leaving legs is higher when you elevate your legs.)

Other side is when you should do this.
To do regularly like every evening - may not be the right way to go.
If you are tired and you do this, the vasomotor tonus is already lower so smooth muscles can less help to keep the blood so much more stress to the valves.
Cardiac output is also less because of tiredness so lymphatic drainage is less.
Elevating legs will move more lymph and blood to the middle of the body.
So less lymph and blood can be moved back to legs when you tired.

What are the risks of elevating legs for too long time in Short time and Long time?
Is there any advantage in elevating legs like increasing blood circulation of our body?

In what manner would elevating legs harm valves?

There should be no damage to valves because the direction of the blood circulation does not change.
Blood is only going from legs to heart.
I think the vasoconstriction of smooth muscles occurs first in the legs.
This returns some blood to the legs.

How is lymph made - -?

Lymph is made in lymph nodes.
After leaving the node, it is rich in lymphocytes.
After leaving digestive system, it is rich in triglycerides so called chyle.
I think after leaving legs it is also rich in triglycerides.

[W]hat is the danger of lymph leaving the legs?

I think the effective lymph (that one used in legs) is coming from the lymph nodes of the legs.
Some lymph can be made in lymph nodes of legs so no danger of lymph leaving legs.
However, some may come from the region of coxa.
How long distance can lymph travel as effective unit of immune system?

If all lymph nodes are working, there is no danger of lymph leaving the legs, I think.
If there are problems with lymph nodes of legs, then there may occur some constitutional symptoms of legs - but not sure about how fast.

Does the heart get tired like your head does, or like muscles after exercise?

No.

To answer your questions, one needs to address certain issues one at a time.

Veins do have valves, but they function to hold blood from settling in the legs. When you flex muscles, the blood flows towards the heart. Valve failure occurs when people stand (especially if they stand relatively still) for long periods of time every day over many years, dilating veins. You can see this on the surface of the legs as varicose veins. One way to treat varicose veins is with elevation. So, elevation does not harm vein valves.

Lymph is made at the arterial end of capillaries and is part of the interstitial fluid of tissues. It bathes cells, and returns to the circulation via the lymphatic system (which also has one-way valves), goes through lymph nodes, and returns to the blood via connections with the subclavian veins. The treatment for too much lymph in the lower extremities (also known as edema) is to elevate the legs. So, elevation does not harm the lymphatics system.

The heart was made to pump all day, every day, for many, many years. It doesn't get "tired" during a tiring day, and doesn't need to rest like we do. But it can get weak and pump inefficiently if injured (e.g. myocarditis, myocardial infarct), or if it pumps against high arterial pressure (hypertension).

As long as you have healthy arteries to the legs, I can't see how your legs can suffer by elevation.

The main effect that I can think of is on baroreceptors. The increased volume of blood in your upper body will cause an increased stroke volume from the heart, sensed by baroreceptors, and may cause smooth muscle dilation of the vascular system. In the short term, that means you will experience more pronounced orthostatic hypotension on standing (you will be dizzier). The long-term effect from elevation for a couple of hours a day are basically nil.

Since you asked about these parameters only, I won't elucidate on other possible effects.


Why are protein-coding regions rich in GC? I have been searching for an answer for this question and have some possible solutions, but I am not sure. GC regions are more stable as there are 3 hydrogen bonds instead of 2 with AT, however I am not sure if this would influence the number of protein-coding genes in GC regions? Protein-coding regions would have to be less condensed than noncoding regions so transcription factors could access them. Would a high GC content influence this as well?

Transcription factors generally bind to promoters, enhancers, silencers, and other regulatory regions that lie outside coding regions, through there are "duons" which code for amino acids and also bind TFs to regulatory effect. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3967546/
One paper suggests GC content helps balance recombination events with genetic stability, and so there may be an evolutionary benefit from organisms that undergo sexual reproduction having GC-rich coding regions. https://www.frontiersin.org/articles/10.3389/fpls.2016.01433/full

In eukaryotes, meiotic exchange of genetic information, or recombination, between homologous chromosomes is a critical step in generating genetic diversity required for adaptation. Recombination is also a crucial tool in plant improvement efforts. Local genome architecture is sculpted by the recombination process, and genome architecture, in turn, drives recombination. This interplay helps to create variability in genomic space, defining relatively stable and plastic genomic regions. This fluctuation in genomic stability is critical for balancing adaptation and stability on the phenotypic level.
Recombination has direct implications for GC patterns and vice versa. GC content refers to the percentage of guanine and cytosine bases in a DNA sequence, as opposed to adenine and thymidine bases. There have been many studies substantiating the positive correlation between recombination and GC content (Ikemura and Wada, 1991; Eyre-Walker, 1993; Fullerton et al., 2001; Galtier et al., 2001; Marais et al., 2001; Duret and Arndt, 2008; Haudry et al., 2008; Escobar et al., 2010; Muyle et al., 2011). Crossovers have been found to be correlated with high GC content in rat, mouse, human, zebrafish, bee, and maize at a broad scale (Jensen-Seaman et al., 2004; Beye et al., 2006; Gore et al., 2009; Backstrom et al., 2010; Giraut et al., 2011), while other studies detected strong correlation only at a fine scale (∼5 kb for yeast, ∼15–128 kb for human) and rather weak correlation at a broad scale (∼30 kb for yeast, ∼1 Mb for human; Gerton et al., 2000; Myers et al., 2006; Marsolier-Kergoat and Yeramian, 2009).

GC-richness may offer the ability for organisms to create offspring that evolve to changes to the environment and fend off parasites, while also being viable enough to procreate, themselves.


What is the transmembrane 'Positive-Inside Rule' nowadays? Has the definition changed over time? First definition.
Two publications by von Heijne in 1989 and 1992 coined the 'Positive-Inside rule' and showed it's practical value in topology prediction of transmembrane helices. It was clearly defined and evidenced that in bacteria the positively charged residues more commonly were found on the "inside" of a membrane (the cytoplasm rather than the periplasm).
Recent Literature.
However it seems the field has moved away from the idea of "inside the compartment" to "inside the cytoplasm" as more data became available. In a 2006 review even von Heijne describes some transmembrane helices as abiding to the positive inside rule because their positively charged residues were inside the cytoplasm, although never explicitly backtracks on the original definition. A similar review in 2007 by von Heijne offers a more definitive refinement of the rule, however removes the concept from being applicable to subcellular membranes.

...the loops connecting the helices differ in amino acid composition, depending on whether they face the inside or outside of the cell (the “positive-inside” rule).

We are now faced with an awkward rule that doesn't account for proteins elsewhere in the secretory pathway or in the other organelles. All those proteins are inside the cell.
More recently still large-scale analysis of transmembrane helices from different biological membrane surfaces, Sharpe et al., 2010 and Baeza-Delgado et al., 2013, show the clustering of positive charge being cytosolic rather than discussing it in terms of the inside of the compartment. Both of these papers still say that they corroborate with the positive inside rule.
Question.
To me it seems that the definition is somewhat sloppy and can broadly be used to say "inside the cytoplasm", despite publications being reluctant to define the rule clearly. Has the definition ever explicitly been changed, or has the field silently changed what "inside" means? ... Or have I completely misinterpreted something? How do the organelles fit into any of these definitions?

I think you have misunderstood the "inside" part of the "positive-inside rule". Perhaps because "inside" is indeed an imprecise term (but now it is history and cannot be changed ;) ). In order to understand it a bit better it helps to think about the topology of the membrane. During synthesis most membrane proteins (ignoring peroxisomal and mitochondrial proteins, which are a whole other topic) are inserted into the ER membrane by the Sec translocon. The parts of the membrane protein that are exposed to the lumen are matured by the ER and Golgi apparatus to be presented on the extracellular surface. Secretory proteins (those that will ultimately be exported from the cell) are made in similar way except they pass entirely through the translocon and end up in the ER lumen. Therefore, the lumen of the ER (and consequently the lumen of other endomembrane compartments) are topologically consistent with the extracellular space, "outside", and not the "inside" of the cell. Perhaps is is easiest to see in a picture (borrowed from here: http://www.bioon.com/book/biology/mboc/chapter12/figure12-4.gif)
Coloured in pink are compartments whose topology is consistent with the "outside" and coloured grey are compartments whose topology is consistent with the "inside". So, for membrane proteins found in the endosome, for example, amino acid residues in the lumen are actually "outside" not "inside". It is true that this may not be immediately clear to those not steeped deeply in the field. As the initial studies used bacteria, which do not have membrane-enclosed subcellular compartments, "inside" was simple and made sense. Perhaps "positive-in-the-cytoplasm rule" would have been more accurate. Hope this helps!


How do platelets produce proteins (if they do)? I'm aware that platelets don't contain a nucleus, but do contain mitochondria (so have mtDNA) and rough endoplasmic reticulum / Golgi. Since platelets require many important cell surface proteins (such as aIIb b3 for ECM binding), are these proteins (1) synthesized de novo in the mitochondria using mtDNA, and then somehow shuttled to the ER / Golgi for secretion, (2) remnants from proteins that were synthesized in their megakaryocyte precursors and not actually created anew, or (3) synthesized via some other mechanism I'm not aware of? Online sources weren't clear on this question. Thanks!

it seems that megakaryocytes, while nucleated, create a large dormant reserve of mRNA and ribosomes, which can be used by platelets later, upon their activation. So platelets can synthesize only certain proteins already transcribed by their megakaryocyte predecessors. The reserve of mRNA decline with the platelet age.


Storage DNA Condition It is possible to store a digestion of cells with lysis buffer several days at -20 degrees and then proceed with the phenol chloroform isoamyl purification?

Should be fine, but if I were you, I'd spare a few more minutes and carry on until ethanol precipitation (15 min of work at worst). Here's the protocol:
https://www.thermofisher.com/pl/en/home/references/protocols/nucleic-acid-purification-and-analysis/dna-extraction-protocols/phenol-chloroform-extraction.html

You can store it in -20 degrees for several days (extend the overnight incubation, that is the second step of ethanol precipitation) and you'll have the certainty that it will stay ok. In fact, freezing in most buffers, whether lysis buffers or extraction buffers shouldn't significantly hurt any nucleic acids. From my personal experience: I've frozen plant material in extraction buffer for RNA isolation (TRI-zol method) in -80 for a few days and got very high concentrations in most samples in the end. I was told freezing in -20 would impact quality but RNA is generally less stable than DNA.

If you had little to none material, you're better of doing the precipitation procedure and then freezing it. If those are minuscule amounts and/or you work with something sensitive like forensic evidence, following through with the procedure will be the most reasonable solution.


Fruit colour related to the dissolving of pectin What does the dissolving of pectin have to do with the colour of a fruit?

During ripening, pectinases are produced which break down pectin and render it soluble. Color change is also associated with fruit ripening.

Hence the correlation.


How are cardiac cells stimulated by an action potential? Why, and how, does the action potential of one cell in the heart stimulate an action potential in the next cell? I'm interested in an answer with citation.

If you go to probably any physiology textbook and look at the chapter on cardiac action potentials, you'll find a number of diagrams of the different ion permeabilities and channels in the heart (e.g. fast sodium channels, calcium channels, etc) that lead to the depolarization of the cardiac myocyte. As you alluded to in your question, there is one cell, or group of cells, that is part of the sinoatrial node (or SA node) that is referred to as the "Pacemaker of the Heart". It is these cells in the SA node that have the leakiest ion channels and thus most frequent spontaneous depolarizations that set the rate of contraction for the heart.

For the cells in the atrium, the depolarization of the sinoatrial node spreads almost instantaneously across the atria because of gap junctions (see that link for more info...Michela et al. Role of connexin 43 in cardiovascular diseases. European Journal of Pharmacology, 2015) between the cardiac myocytes. Gap junctions are small communicating junctions that link all the cells of the atrium and "electrically-couple" the cells to contract in synchrony. There are typically no gap junctions between the atria and the ventricles, which is why the atria contracts before the ventricles. However, there is the bundle of His that slows the electrical conduction just enough before it rapidly spreads through the purkinje fibers and then to the remaining ventricular myocytes through gap junctions in those cells as well.

**For more information on gap junctions go to any basic cell biology text or Wiki. The picture below is a simplified diagram of gap junctions. For this question all you really need to appreciate is that the electrical depolarization (i.e. the positive charge) spreads quickly across cells connected by gap junctions because they are 'sharing' a common cytoplasm due to these channels. When ions flux during depolarization that current flows through the gap junctions and nearly instantaneously depolarizes the next cell... and so on, and so forth.


Can the dietary fibres as chemical compounds be regarded as polymers? At the level of molecular structure, can the dietary fibres be regarded as polymers?

Dietary fibers are the indigestible portion of food derived from plants.

Most of these are indeed polymers of sugars (that is, a chain of repeated basic unit of carbohydrate), for example cellulose, alginate or pectin. They have glycosidic bonds that cannot be broken down by enzymes found in humans, and are thus indigestible.

But there are exceptions, for example raffinose, a trisaccharide found in beans & cabbage, is also categorised as a dietary fiber, as it is not breakable by human enzymes.


How do legs of tiny insects/spiders like mosquito/Opiliones work? I think I understand how legs of humans work. We have bones to which muscles are attached. Muscles can only contract / relax. By the combination of many different muscles we can make complex movements:

Image source: https://commons.wikimedia.org/wiki/File:1015_Types_of_Contraction_new.jpg

However, I have no idea how this works for insects / spiders. On the one hand, I'm not sure where the muscles should be attached to due to the exoskeleton. On the other hand, I have difficulties imagining that the same system works for legs which are this tiny:

Image source: https://commons.wikimedia.org/wiki/File:Spider-IMG_1630.jpg

Arthropods use basically the same system to operate their legs. Yes their legs are tiny, but so are their muscles.(Is it so hard to imagine everything is downscaled? Their digestive system is also much smaller, but they don't need to eat the same amount as we do either...)
In general it's just a kind of smaller-sized mechanism that is based on the same principles: use a muscle to create tension over a joint, and so move the appendages. The big difference is off course that in mammals the muscles work against an internal skeleton, and in arthropods the muscles attach to the inner surface of an external skeleton.


Why is sugar absorbed very fast into the blood stream? Recently, I heard from a pregnant person I know that immediately after she eats something sugary/sweet, the baby starts kicking and moving around, as if reacting to the sugar. She told me (unscientifically) that sugar gets absorbed fast into the bloodstream (and then into the baby), faster than protein for example, which takes a couple of hours to be digested.

However, I know that both sugar and protein must go through the digestive system until the small intestine to be absorbed into the blood. This is done through mechanical action (peristalsis), as well as chemical digestion. Yet I was wondering how there is such a big time difference between the digestion of sugars versus proteins if the path to the bloodstream is the same.

I did a little bit of research and found that there are some glucose transporters in the cheeks, which could explain how glucose is absorbed so fast (in the same way alcohol is also absorbed fast through the cheeks too).

I wanted to ask if theres any other reason or way in which sugar is given so fast to the foetus when ingested by the mother?

In short, sugars are absorbed quicker than proteins and fats because they pass through the stomach quicker and their digestion is simpler.

Sugar can be absorbed through the mouth mucosa when applied as a sublingual gel, as discussed here on Biology SE: Is sugar absorbed into the bloodstream through the walls of the mouth?, but probably in much smaller amounts during usual eating/drinking followed by swallowing.

SUGARS

Not all sugars are absorbed at the same rate.

Glucose and galactose do not need to be digested and can be quickly absorbed in the small intestine via sodium–glucose linked transporters (SGLTs) - sodium acts as a cofactor that stimulates glucose and galactose absorption (Lumen Learning).

Fructose also does not need to be digested but is absorbed much slower than glucose via GLUT5 transporters without the help of sodium (Lumen Learning).

Sucrose needs to be digested in the small intestine with the help of the enzyme sucrase to glucose and fructose, which are then absorbed. Glucose stimulates the absorption of fructose (Food and Agriculture Organization). This means that glucose and fructose from sucrose will be absorbed slower than glucose alone, but faster than just fructose alone.

Lactose needs to be digested to glucose and galactose, which prolongs the time in which they can be absorbed.

The absorption rate of various sugars is reflected in their glycemic index (the rise of blood glucose levels after ingestion): GI for glucose = 100, sucrose = 65, lactose = 46, fructose = 19.

STARCH

Starch is not digested in the stomach, so it can pass through it quickly, and is then, in the small intestine, quickly digested to glucose with the help of the enzyme amylase. The glucose from plain starch is absorbed almost as quickly as when ingested as glucose alone and faster than fructose, sucrose or lactose. This is evident from high glycemic index of foods made mainly of plain starch: cornflakes (81), instant oats (79), potatoes (78), rice porridge (78), white wheat bread (75).

FIBER

Foods high in dietary fiber slow down gastric emptying and thus absorption of nutrients (Faseb).

PROTEINS

Proteins need to be digested in the stomach by the enzyme pepsin (which slows down gastric emptying) and then further in the small intestine by peptidases into amino acids, which can be absorbed. Slow gastric emptying is the main reason for slow absorption of proteins (Diabetes Care, Experimental Physiology).

FATS

Fats are not digested in the stomach but they slow down gastric emptying, so they are absorbed slower than carbohydrates (JCEM, Vivo Colostate).

LIQUID vs SOLID MEALS

Liquid meals pass through the stomach quicker than the solid ones, so glucose from sweetened beverages will be absorbed quicker than from whole fruits (Vivo Colostate, JCEM).


Why does Stereology use Systematic Random Sampling? I am a student of Neuroscience and in all my textbooks and lecture notes it is written that in Stereology, Systematic random sampling (SRS) is used to obtain sections.

Why it's that and not any other type of sampling? For example, why do we not use completely random sampling? What are the advantages of SRS over any other type of sampling when applied to stereology?

Systematic sampling refers to a method where all samples have an equal probability of being chosen but the spacing between samples is constant. That is, although each individual section is equally likely to be chosen, the combination of samples is not. The Wikipedia article on systematic sampling provides a good overview.

Stereology refers to the analysis of a three-dimensional structure using two-dimensional slices. Such an approach is common with histological techniques. A block of tissue is sliced into thin sections that allow for examination of the tissue with light microscopy, usually with the aid of stains.

If you sampled purely randomly, by chance, you are likely to obtain "gaps" in your analysis by random chance. For example, imagine you section a 3mm block into 40um sections. This process gives you 75 sections. It is too time-consuming to analyze all 75 sections, so you want to choose just 15 of them.

Let's try generating 15 random numbers from 1 to 75 and look at the maximum gap. I do this by taking the first 15 numbers of a random permutation of 1 to 75. In MATLAB, one can do: x=randperm(75,15), max(diff(x));

Here are some results:

23    26    33    34    35    37    44    54    55    58    60    69    72    73    74

Max diff: 10

12    14    15    16    17    20    22    27    28    34    44    47    58    59    73

Max diff: 14

 8    14    15    18    19    20    29    32    40    41    47    67    70    71    72

Max diff: 20

 3     7    16    19    30    32    33    34    38    39    50    57    61    65    75

Max diff: 11

 3     7    17    18    21    26    29    37    42    46    49    52    60    61    69

Max diff: 10

If we were to instead use systematic sampling, the difference between sampled sections would be fixed at 5: you skip 4 sections to get 15 evenly spaced sections out of 75 total. But with purely random sampling, the largest gaps are bigger, sometimes much bigger! 20 skipped sections means there is a 800um gap with no data! Even worse, I noticed later that in the first draw, the lowest number was 23! So the first 22 sections are completely omitted from analysis! There can be major morphological changes and entire brain nuclei missed within a gap that size, whereas 100um gaps are no problem.

I didn't print out the minimum gaps, but you can look at my examples to see the other side of this problem: in the first set, numbers 33, 34, 35 and 72, 73, 74 are right in sequence! There is likely little or no morphological difference on those short intervals and yet with random sampling one can waste time analyzing those adjacent slices. Because these draws are completely random, you can notice similar adjacent stretches in all of these random draws, even though I made no effort to select particular examples: these are just the first 5 results I got from MATLAB.

References

Gundersen, H. J. G., & Jensen, E. B. (1987). The efficiency of systematic sampling in stereology and its prediction. Journal of microscopy, 147(3), 229-263.

Gundersen, H. J. G., Jensen, E. B. V., Kieu, K., & Nielsen, J. (1999). The efficiency of systematic sampling in stereology—reconsidered. Journal of microscopy, 193(3), 199-211.


Which is better against genetic mutations? Asexual or Sexual Reproduction? In terms of genetics, which type of reproduction is better against adverse mutations? I understand a bit of Muller's Ratchet—in which asexual organisms accumulate a number of deleterious mutations in their genomes. However, doesn't the crossover process and corresponding genetic diversity in sexual-reproducing organisms make them more susceptible to these mutations?

Mutations can be caused by much more than just recombinatory events--polymerase fidelity, DNA damage repair, even environmental factors can have a huge impact on DNA damage. While most DNA polymerases have an error rate of around one mutation per billion, there are different levels of fidelity among different polymerases (McCulloch and Kunkel, 2008).

Regarding the fidelity of crossover/recombination events, it is true that these events increase the likelihood of a lethal or detrimental mutation. However, recombination is not a random process. Recombination hotspots are chromosomal locations where the rate of recombination can be hundreds of times higher than other locations. These hotspots are generally in "safe" locations, not in the middle of a crucial gene, etc. There are also recombinase enzymes specific to certain sites of recombination.

As to "which is better", I don't think the answer is as straightforward as you might think. You might think a sexually-reproducing eukaryote with a very high-fidelity DNA polymerase and safe, specific recombination hotspots would be ideal. That situation is generally what we find in nature, so you're (probably) correct. However, at the other extreme, think of a virus*. Viruses have a much, much, much higher rate of mutation than eukaryotes--orders of magnitude higher. This is how a virus survives, basically out-evolving the host's defenses. A high rate of mutation works for a virus, and a low rate of mutation works for a multicellular eukaryote.

*Of course, there is always debate about whether or not viruses are alive. However, they definitely reproduce.


Is a "Fact" any theory for which there is overwhelming evidence in any field other than biology? Evolution is often described as a fact, and a theory. Evolution is a heavily overloaded term, with one definition being the fact that, "changes in the frequency of alleles in populations of organisms from generation to generation." This is a measurable fact, but not the usage of the word evolution that I am in interested in.
Wikipedia has several quotes on the matter, including the Webaters definition used in this questions title, but also includes clearly observational facts like the Earth revolves around the sun.

A fact is a hypothesis that is so firmly supported by evidence that we assume it is true, and act as if it were true. —Douglas Futuyma
There is no sharp line between speculation, hypothesis, theory, principle, and fact, but only a difference along a sliding scale, in the degree of probability of the idea. When we say a thing is a fact, then, we only mean that its probability is an extremely high one: so high that we are not bothered by doubt about it and are ready to act accordingly. Now in this use of the term fact, the only proper one, evolution is a fact. —H. J. Muller
Scientists most often use the word "fact" to describe an observation. But scientists can also use fact to mean something that has been tested or observed so many times that there is no longer a compelling reason to keep testing or looking for examples. The occurrence of evolution in this sense is fact. Scientists no longer question whether descent with modification occurred because the evidence is so strong. —National Academy of Science

Do scientists refer to any theories for which there is overwhelming evidence as a "scientific fact", other than in biological sciences?
Note: Good answers will include quotes from scientific organizations or prominent scientists using the term fact to describe the theory, and will include references to the theory itself.

Your question really applies to any scientific theory, not just evolution.

The problem is that, outside of the scientific world, a theory is often thought as something unproven, an unproven guess if you wish. This is not true for scientific theories, which, instead are confirmed by experimental data.

The OED defines theory as:

  A scheme or system of ideas or statements held as an explanation or account of a group of facts or phenomena; a hypothesis that has been confirmed or established by observation or experiment, and is propounded or accepted as accounting for the known facts; a statement of what are held to be the general laws, principles, or causes of something known or observed.

and fact as:

  Something that has really occurred or is actually the case; something certainly known to be of this character; hence, a particular truth known by actual observation or authentic testimony, as opposed to what is merely inferred, or to a conjecture or fiction; a datum of experience, as distinguished from the conclusions that may be based upon it.

So, essentially we start with an unproven idea, we corroborate it with facts (=experimental data) and we define our theory accordingly to facts.

So, why don't we say that evolution is true or that it is a dogma or that it is a fact?

Well, that is not how science work. Evolution is a scientific theory, and it always will be. Maybe (hopefully, dare I say) in 50 years from now new evidence will have make us change the theory of evolution, at least some bits of it.
Luckily evolutionary biology is not stuck at the time of Darwin and genetics is not stuck at the time of Mendel. Many new pieces of evidence have made us improve the theories that they initially defined.

Does that mean they were bad scientist or that they experiments were faked? Not at all!  Simply as their knowledge was more restricted than ours, they could not formulate a more advanced theory. Mendel's experiments still hold true, but now we know that transmissions of characters is not as simple. He was just looking at a special case. And his experiments still fit in our current theory, and will have to fit in any future one.

A scientific theory is defined by its falsifiability, that is

  the trait of a statement, hypothesis, or theory whereby it could be shown to be false if some conceivable observation were true. In this sense, falsify is synonymous with nullify, meaning not "to commit fraud" but "show to be false".

The famous black swan example by Karl Popper (see e.g. Conjectures and refutations, 1963, chapter 11.6), can be exemplified by (source: Wikipedia):

  One notices a white swan. From this one can conclude:
      At least one swan is white.
  From this, one may wish to conjecture:
      All swans are white.
  It is impractical to observe all the swans in the world to verify that they are all white.

  Even so, the statement all swans are white is testable by being falsifiable. For, if in testing many swans, the researcher finds a single black swan, then the statement all swans are white would be falsified by the counterexample of the single black swan.

So, our theory of the white swan is accepted as "temporary true", as long as a black swan is not found. Obviously the more white swans we count (i.e. the more experimental evidence we have), the stronger our theory will be. But it will never be true.

I would like to finish quoting Richard Feynman:

  It is scientific only to say what is more likely and what less likely, and not to be proving all the time the possible and impossible.

and

  We never are right, we can only be sure we're wrong

I suggest to watch the full video of his fantastic lecture on scientific method on YouTube.


Could homoplasy occur within a clade? Consider the below phylogeny. taxon1 and 2 are sister taxa but:
- share a brown color coat
- differ from their closest common ancestor (light color coat)

Is this a case of homoplasy (Analogous trait)?

According to Furtado and Pessoa (2014):

Homology: A similarity due to common ancestry.

Homoplasy: A similarity not due to common ancestry.

And, according to Futuyma (2006):

Homology: Possession by two or more species of a character state derived, with or without modification, from their common ancestor.

Homoplasy: Possession by two or more species of similar or identical character state that has not been derived by both species from their common ancestor

Therefore, the answer is quite clear: the trait here is an homoplasy, since it's not present in the common ancestor of A and B.

PS: Homoplasy and analogy are not, technically speaking, synonyms. Analogy is a special case of homoplasy.

PPS: A clade is just a monophyletic group. For instance, the hominids form a clade, Mammalia is also a clade, Vertebrata is a clade, even Animalia is a clade. Therefore, a clade can be very exclusive or very inclusive. Because of that, I'm skipping the title of the question ("Could homoplasy occur within a clade?"), whose answer is obviously yes1, and focusing only on your second question: "Is this [image] a case of homoplasy?"

PPPS: Furtado is me, and that quote was translated from the original.

Sources:

Furtado, G. and Pessoa, F. (2014). Liçoes sobre sete conceitos fundamentais da biologia evolutiva. Brasília: Editora UnB. (translation: On seven fundamental concepts of evolutionary biology)
Futuyma, D. (2006). Evolutionary biology. New York: W.H. Freeman.

1For instance, my metamery and the metamery of an earthworm is an example of homoplasy. Both myself and the earthworm belong to a clade called Animalia. Therefore, there is homoplasy within a clade


What type of Insect Egg is this? Can you please tell me what type of insect eggs these are? I found them in the corners of my office kitchen behind boxes and cardboard. Found them in between the broom bristles. Found them along the edge of the wall. There are quite a few of them.
If you could please provide me some tips on how to avoid getting these eggs or killing off the main insect would be helpful.

These are probably cockroach cases, or oothecae, that may contain up to 50 eggs, depending on species.

It looks like they are oothecaes of German cockroaches.

You can read more about baby cockroaches here.


Do metastatic cells still have their parent's identity? If a liver cancer, for example, gives metastases. Will metastatic cells still have liver identity? I mean, if we mark liver cells, will we see the cancer cells too?

Thanks a lot!

Welcome to stack. This is a good question.

To answer your question: Generally, yes.

Howeve like @user137 stated below it can depend on many factors most notably how many division cycles they go through, and also where they metastasize to. The immediate environment of a cell is very effective at altering gene expression.

I use Hepg2 cells regularly. These are hepatocellular carcinoma cells that can be cultured. These cells are known to express 3-hydroxy-3-methylglutaryl-CoA reductase and hepatic triglyceride lipase, two enzymes characteristically highly expressed in liver cells. If we want to do a quick quality control typing we will perform rtPCR for those enzymes. I have seen the expression drop off after about 4 months (~35 passages).

Looking at gene expression (ideally through microarray) is a very valid way to identify/type a cells tissue of origin.


Does urine therapy really work? I heard a lecture from a supporter of urine therapy and he claimed that urine is not only good disinfection but also as rich source of minerals. To me, these two advice seemed contradictory.

In addition, the supporter emphasized one should use his own urine - and yet, as an example of the magical effect of urine therapy we got a story of a boy who was hooked by jellyfish but was saved by a nearby doctor who used urine of his own. Apart from that I see no reason why urine should work against toxins better than a water or a disinfection (they don't).

Though, I know a very qualified doctor who advocated this treatment. What do you think?

This is at best anecdotal evidence. First of all, urine is, although it has been thought otherwise for decades, not sterile. The bacteria in it just don't grow under the conditions used in the lab which are used to proof bladder infections. See these two articles:

Evidence of uncultivated bacteria in the adult female bladder.
Urine is not sterile: use of enhanced urine culture techniques to
detect resident bacterial flora in the adult female bladder.

When you take into account that bacteria grow on almost all surfaces which have a connection to the outside (like mouth, stomach, gut and so on) this is not really surprising that this is true for the bladder as well.

Urine might be a relatively low risk solution of choice to rinse a wound when nothing else is available, but otherwise I wouldn't recommend it.

Then think of what urine is used for: it is the way our body excretes all the water soluble stuff it doesn't need any more. The body makes a lot of effort here to concentrate the primary urine in our kidneys to recover all the stuff which is still needed and to save water. I wouldn't drink it and make my body go through the whole process of excretion again.

About the doctors: is there any hard evidence for that or is this only an anecdote? I get highly skeptical when I hear about such stories.


Are lactic acid and prolactin rise after exercise connected? I've been reading about prolactin, a human hormone. Apparently it's levels within the brain can raise after exercise, although the mechanism is not clear to me. I'm interested of there is any connection between lactic acid build up in muscles during anaerobic exercise and prolactin levels in the days following exercise. Both of these sound similar, which may be a coincidence.

Prolactin (PRL) is a pleiotropic hormone. More than 300 different functions have been described for it (Bole-Feysot et al., 1998), although probably the most well known/studied1 is the maturation of the mammary gland during pregnancy and subsequent stimulation of milk production.

One of the fairly well known situations when PRL increases is after an acute stress (Neill, 1970; Seggie and Brown, 1975; Kant et al., 1983). Although the details of this are still a bit foggy, the reason seems to be connected to the anxiolytic properties of PRL (Torner et al., 2001, Donner et al., 2007).

Anaerobic excercise is considered as a stressor, and therefore the PRL response may be important to avoid hyperactivation of the stress pathway. This has been suggested before (Ohiwa et al., 2007) and the rise in PRL may be triggered by lactic acid, as administration of lactic acid alone can stimulate PRL secretion (Sculthe et al., 2013).
Note that this does not exclude that there may be other factors involved in this response.

1 at least in female mammals, but bear in mind that PRL is present in all vertebrates, males and females alike.


Can adenosine be cleared? I've been thinking about this question for awhile, since reading this question: What causes adenosine build up in the brain when awake?

We know that a couple of things will block adenosine receptors: caffeine and hops. If you're overloaded with adenosine and it's early in the day, coffee (or other caffeine sources) make you feel alert by tricking your brain by blocking the adenosine receptors. The dubious downside is that when it finally quits blocking the receptors, you've got a much bigger load of adenosine. Which might not be a downside if it means you fall asleep more easily and deeply.

But what about just clearing the adenosine?

In order to do this you would need to find a compound that does all of the following:

Crosses the blood-brain barrier. Many pharmaceuticals are not able to do this.
Binds strongly to, or has some metabolic effect on adenosine. The resulting product must also cross the blood-brain barrier, and be excreted.
Not bind or react with other molecules that are similar to adenosine and cause side effects.
Not cause some sort of immune response - along with the blood-brain barrier issue, this rules out any sort of protein, and really limits the potential specificity for items (2) and (3): there simply isn't a lot of chemistry outside of biochemistry that is that specific.
Not cause systemic effects via depletion of adenosine and products of adenosine. There are several problems caused by a failure of the enzyme that metabolizes adenosine but it seems like most of the primary symptoms are due to an accumulation of adenosine rather than an absence of inosine, so I am not certain how much of a problem this would be.

And probably numerous other issues I haven't thought of yet. The point is, adenosine is a useful biological molecule, not just junk to get rid of, and developing something to "clear" just one specific compound is actually really complicated. If the main concern is the sleepiness caused by adenosine build-up, caffeine is widely available and relatively safe compared to some novel way of actually clearing adenosine.

In fact, I can't really think of many pharmaceuticals that work by actually "clearing" something, but feel free to leave any suggestions in the comments. Chelating agents come to mind, but those are only used in some very specific circumstances.


What are the different types of helices in protein secondary structures and how do they differ? What are the different types of helices in protein secondary structures and how are they differentiated?

In the DSSP docs, types of helices mentioned are: Alpha-Helix, Helix-3, and Helix-5.

In the STRIDE docs, types of helices mentioned are: Alpha-Helix, 3-10 Helix, PI-Helix.

Why does DSSP have Helix-3 and Helix-5, while STRIDE has 3-10 Helix and PI-Helix - are they different expressions for the same thing?

What are the differences between these types of helices, what are their full scientific names so that I could read more about them, and are there any other types of helices not mentioned here?

This DSSP page makes it clear that:

Helix-3 = 3-10 helix
Helix-5 = π-helix

The α-helix is described in every biochemistry text book and widely on the web. It has 3.6 residues per helical turn and has 13 atoms in the ring formed by the hydrogen bond and so can also be called a 3.6-13 helix.
The 3-10 helix is less common than the α-helix, but is still widespread. By analogy with the alternative nomenclature just described for the α-helix, it has 3 residues per helical turn in a 10 atom ring.
The π-helix is even less common. It is a wider helix with 4.6 residues per turn.
A comparison of the three can be found in this proteopedia article, from which I have taken the illustration below.

There is also the collagen triple-helix, but that is specific to collagen, whereas the others are general examples of secondary structure found in many proteins.
Standard Nomenclature
There is no such thing as a “full scientific name” in this area of molecular biology. Names tend to get standardized by unofficial agreement when ambiguity becomes a problem. Helices other than the α-helix are not very well known, but the terms 3-10 helix and π-helix are certainly more common than Helix-3 and Helix-5, which I suspect may have been a computational convenience. However, an internet search indicates that for scientific journals 310-helix is generally preferred to 3-10 helix or 3(10)-helix, these latter perhaps reflecting work in a plain text environment or the word-processing or HTML limitations of writers.


What kind of big bird is this seen walking around Taipei? I've seen this humorous sign warning drivers to keep an eye out for birds many times, but today I finally realized what it's talking about!

This is a large bird and I've seen it all around Taipei in gardens and green areas. It's not shy of people unless you get too close.

I'd guess it's about 30 cm tall when standing upright, but it often is bend down looking for things to eat. It takes one step at a time, sometimes very slowly, and it's head moves out-of-synch with its body as it hunts for food. I am not sure if it can fly, I've only seen it on the ground, and I've never heard it make a sound.

It's various shades of brown and tan, and just like the cartoon on the sign it has long feathers projecting backwards from its head. That can be seen in the center top of the photo montage.

Any idea what kind of bird this is?

These are cell-phone photos from the closest I could get without it getting nervous.

"Life imitates Art far more than Art imitates Life" Oscar Wilde

I am fairly certain that this is a Malayan Night Heron (Gorsachius melanolophus).

Taiwan is listed as one of the countries where the Malayan night heron can be found. Its diet consists of small reptiles, snails, chilopods, arachnids, crabs and insects. This would explain why you have observed it bend down a lot to look for food.

Needless to say you can find more information in the corresponding Wikipedia article.

Here a photo with better resolution:

Photo by: Pete Morris/Birdquest

In addition, here is a link to a video taken in Taiwan. Does this remind you of the bird that you saw?


How are behaviors genetically coded in animals? I am curious as to how complex behavior is passed down genetically? For example, how is the building of a web genetically coded in a spider? And how is the complex behavior of constricting prey coded into a boa? As these critters do not get raised by their parents, and hence cannot learn to copy these behaviors, it has to be genetically imprinted. How?

I will focus my answer on the evolution of orb web spiders (Fig. 1), because arachnids, like insects, are relatively non-complex creatures with an obvious systematic behavior (the weaving of highly symmetric, repeating structures). Hence I reasoned this would be a good approach of investigating the answer to this question.

The orb-weavers (Orbiculariae, an informal name for the taxon containing the superfamilies Deinopoidea and Araneoidea) are among the most diverse lineages of spiders (Hormiga & Griswold, 2014).

Fig. 1. Orb web. Source: Encyclopedia Britannica

Bond et al. (2014) report that according to various estimations the date of the origin of the orb web was somewhere around the Lower Jurassic 201 million years ago and 52 million years ago, and the authors support the view of a monophyletic origin of the orb web.

Despite this excellent opportunity to elucidate the (monophyletic) genetic underpinnings of the evolution, and hence the passing down of orb weaving, are largely unknown. Not only is the evolution of orb weaving unknown, even the evolution of the intricate physical properties of the silk are largely unknown. For example, how the sticky glue araneoid orb web evolved is a mystery. This complex multicharacter trait is hypothesized as a key innovation to explain the increase in diversity of araneoidea. For example, araneoid orbs contain viscous adhesives and they have low UV-reflectance and are hence less visible to insects. There exists one proposed evolutionary pathway from the dry, cribellate orb web of deinopoids to the sticky glue orb web of araneoids, but that's about it (Hormiga & Griswold, 2014).

In all, physical properties of silks contained in webs are hardly explained in evolutionary terms, let alone the behavioral profiles necessary to make a web out of it.

References
- Bond et al., Curr Biol (2014); 24(15): 1765–71
- Hormiga & Griswold, Annu Rev Entomol (2014); 59:487–512


Dominance and recessive relationship of alleles You can find easily in textbooks that definitions for dominant and recessive alleles as follows:

Dominant allele: produces working protein and shows its effects in hybrid state.

Recessive allele: produces defective protein and remains suppressed in hybrid state.

But I have these confusion:

Defectiveness or benefit is relative thing.
There are many genetic diseases which are caused by dominant genes, for example short toe fingers. The protein related to it is also defective.

Another definition includes dominant as wild type most circulated while recessive as mutant allele. But even this seems to be unsatisfactory as every mutation cannot be recessive or defective.

Then, finally, what determines dominance of an allele over others?

Phenotype determines dominance. The "rules" you state are just general possibilities that are most likely; they are not correct definitions. "dominant as wild type most circulated" is just completely totally false.

It's common to have mutations that cause loss of function. These often end up as recessive alleles, because the second copy still makes a functional protein. It's not about the allele being suppressed necessarily, and doesn't have anything to do with benefit or not, it's just that the other copy is able to do the job, so you don't see much effect. Because there are often feedback mechanisms for gene expression, having 1 less copy in the genome often means much less than a 50% reduction in protein.

It's also common to have mutations that cause negative gain-of-function: these are often dominant, because you only need one copy for that negative effect to be observed.

However, as you point out, these aren't always the case. You could have an allele where loss of a single copy causes a deleterious phenotype. Sometimes these might more appropriately be considered "incomplete dominance."

I think it's important to note that these terms are really labels based on phenotypes, they are not biological realities. An allele could be thought to be completely dominant, but under further study actually demonstrates a form of incomplete dominance or co-dominance.

The Wikipedia page on dominance has some better definitions for you.


why do marine organisms orient with their bellies facing downwards? why do marine organisms orient with their bellies facing downwards (like most creatures) given that they have relatively fewer constraints on their orientations than land or air organisms?

I'll address fish here. It's hard to tell which way is up with many sea-dwelling invertebrates, e.g. sea cucumbers. Sea urchins often are oriented "sideways" if you count their mouths as "down".

All animals normally orient themselves in the most advantageous manner dependent on their situation. Probably the most important determiners are field of vision and the inner ears, which work much like those of humans (who walk upright even if blind.) Unlike land vertebrates, the ear of fish is thought to have evolved as a vestibular organ for balance and orientation in space rather than as an auditory organ. Fish (and other sea creatures) also have other sensory apparatus which orient them, such as lateral lines.

Pipe fish swim in a horizontal manner like other fish, but rest vertically, swaying with the sea grass around it. Flatfish start "normal" but as the eye shifts position to the other side of the head, it will assume a bottom dwelling "sideways" position, with a contorted mouth and a fin squashed against the sand.

  “Flatfish are the most asymmetrically-shaped vertebrate to ever live on earth,” says Alexander Schreiber, a flatfish expert at St. Lawrence University. “It sounds likes a really dramatic thing to say, but as far as vertebrates go, it’s true.”

Apparently flatfish brains start to receive stronger signals from one inner ear than the other.

  Two organs — the eyes and inner ears — work together to keep typical fish in an upright swimming posture... If the eyes are not receiving the same amount of light on each retina... retinal neurons trigger the brain to tilt the entire animal and set it straight. ...As a fish’s vertical orientation in water changes, the brain combines information from the eyes and ears to figure out which way is up. ...[f]latfish larvae that are deliberately blinded adopt a sideways swimming posture.

When snorkeling, it is not at all uncommon to see any of a number of fish flip to their sides side to get a good look at you (floating above) with one eye, as opposed to maneuvering itself to face you. I imaging they assess the threat; since I wasn't a threat, they would just reorient themselves normally and go about their business.

Whatever aids survival within the parameters they are confined to (were born with) in that niche will be what you see.

The Improbable—but True—Evolutionary Tale of Flatfishes
The Vestibular System and Sense of Equilibrium in Fish


Can stress echocardiography show coronary blood flow difference before and after exercise? Stress echocardiography means a pair of cardiac ultrasound imaging examinations, before and after exercise. I assume that coronary blood flow is increased after exercise. Is cardiac ultrasound technology capable of showing this blood flow difference?

Update: I emphasize that my question concerns stress echocardiography, i.e. two echocardiography sessions before and after exercise (or pharmacological stress test) - not simply echocardiography.

No, echocardiography is not sensitive enough to do so. For tracing coronary arteries directly flow angiography is the choice.


Inexperienced divers damage coral, but parrot fish eating coral doesn't do damage? I've been learning about life on coral reefs. Recently I've become aware of the damage to coral reefs caused by tourism and inexperienced divers:
1) Corals have a thin membrane which keeps them healthy. Touching them could break this membrane, causing infection which can lead to death.
2) Stepping on, leaning on, and sitting on coral could smash their polyps.

I am not against being responsible as a diver, respecting nature, arriving and leaving without a trace. I'm just curious what the difference is between human and animal contact. Parrot fish eat coral, taking bites out of it, leaving exposed areas and this damages the coral. I've seen footage of sharks having feeding frenzies on reefs, where they smash into the reef during the commotion and while trying to catch their prey. Fish rub up against coral and peck at them to get algae, and crustaceans walk on the coral with legs that seems like it would break the thin protective membrane on the coral.

Obviously, as humans we technically do not belong in their world, so I'm sure there are reasons for damage with that alone; but why does marine life causing damage not cause actual damage? Or does it, and it just repairs differently or faster somehow?

You are absolutely correct in regards that marine life does cause damage to corals. In particular, parrotfish have been found to play an important role in regulating the biodiversity of coral reefs through their feeding behavior. Certain species of parrotfish feed on certain species of coral, typically faster growing species that branch out into easier access bits of corals that the fish can consume. This has the effect of allowing slower growing species that may also be harder corals to consume (in terms of hardness, shape accessibility, or other factors) to grow and compete in the coral reef and prevent the reef from being overgrown with the faster species. A similar process is seen on the land with grazing herbivores which help propagate biodiversity by consuming certain plant species thereby giving increased chances for other species to grow. These ecosystems and the relationships between corals and species like parrotfish have had an extremely long time to come to shape through evolutionary pressures on both sides of the organisms, consumer and producer.

The problem with divers who cause damage to corals is that it is an introduction of artificial stress and arbitrary damage to the coral reef in a short time without much time to adapt, placing additional stress on the environment which is already stressed. Unlike the parrotfish, divers may not discriminate on what corals they damage. Additionally, areas where inexperienced divers damage coral generally will see more inexperience divers often at the same diving site, so from the standpoint of protecting the coral reef, minimizing the damage caused by divers becomes an important priority to the stewards of those areas and the diving shops which bring divers to those areas.


What is the most heat-tolerant organism? What is the most heat-tolerant (or heat loving - hyperthermophile) organism so far identified? What adaptations does this organism have in order to endure such high temperatures?

Methanopyrus kandleri has been able to grow and proliferate at temperatures of up to 122°C when under around 20atm (Takai et. al. 2008).  This was achieved in the lab but the theory should hold true for deep sea thermal vents.  Another strain of M. kandleri survived incubation to 130°C however was unable to reproduce at this temperature.

One of the key adaptions for thermophiles is the selection towards an extremely thermo-stable copy of the enzyme DNA polymerase.  This allows DNA replication at high temperatures and is similar to the 'Taq' polymerase used in the polymer chain reaction in labs, derived from another thermophile, Thermus aquaticus.

References

 Takai K, Nakamura K, Toki T, Tsunogai U, Miyazaki M, Miyazaki J, Hirayama H, Nakagawa S, Nunoura T, Horikoshi K. 2008. Cell Proliferation at 122°C and Isotopically Heavy CH4 Production by a Hyperthermophilic Methanogen Under High-Pressure Cultivation. PNAS 105: 10949–10954.


Is household ammonia okay for plants? My father-in-law claims that since plants need nitrogen to produce proteins, and since ammonia is NH3, that Ammonia should be fine for the plants, since it's just nitrogen and water and hydrogen, according to him. We were cleaning a rusty chain and a bunch of spilled into our garden. I'm talking about household ammonia.

Is that true?

I'm thoroughly convinced he is an utter idiot but then again he could be right since he does say he minored in Chemistry in his college days.

Okay, he's not wrong, technically speaking. Practically speaking never ever fertilize your plants with ammonia.

The ammonia you spilled will be converted into nitrates eventually, so it's not like you spilled lead into your garden. On the other hand the populations of nitrifying bacteria take a fairly long time to adapt to a bounty like "a bunch" of household ammonia (their idea of a banquet beyond their wildest dreams is 2-4 ppm ammonia) but they will eventually eat it all.

(Fishkeepers should know about the nitrogen cycle, because you have to set up a complete yet tiny version of the real thing, which takes at least a week to establish)

So your plants will be fine... next year. This year they might have a little bit of trouble considering ammonia is a base and can burn plants directly or indirectly. Don't fertilize your plants with ammonia. They will probably die.


What is solid-phase bridge amplification? During Illumina sequencing there is a step called bridge amplification by which DNA is amplified by isothermal enzymes. What is this stage, and how does it work?

This stage is after the adsorption of the adapter-ligated fragments on the flow cells.
The fragments are isothermally amplified to generate clusters [1]. The exact nature of the enzyme mix that catalyses this step is not disclosed by Illumina. I assume it must be similar to Helicase mediated isothermal amplification, which uses helicase and single strand-binding proteins (SSB) to denature the template. The polymerization is catalysed by a mesophilic DNA-Pol such as Klenow (E.coli).


Identification of a plant (in a pot) I have in my flat a plant which sometime make strange flowers. When the start it looks like plastic stars:

Then the flowers are opening after few days and looks like this:

The smell is a bit strange (I cannot say bad but definitively not good as other flowers). In general this plant does not need many watering and even I am in Switzerland, I guess it is living normally somewhere else.

For the size, mine is quite small (30 cm high but many wires) but my mother have a very long one along the wall (few meters).

Many picture with higher resolution are in my flikr gallery.

Anybody can tell me what is the name of this plant and where it lives normally?

It is a Hoya Carnosa Krinkle Kurl flower. It is native to Australia and East Asia. Hoya Carnosa links to wikipedia and Krinkle Kurl links to plant rescue in case you want to read more on it.


How only one follicle develops into graffian follicle? I've studied that one out of many follicle develops into mature or graffian follicle. The fact which confuses me is that, since all follicles are in same ovary, close to each other with equal supply of nutrients. What causes the other follicles to give up the race? Why our body cannot develop mature follicle from a single one?

It doesn't mean only one follicle maturates within a lifetime of a woman. For every ovulation only one follicle maturates from the batch of primary oocytes stored within the ovary. Before a female is born, all the primary follicles are arrested in the diplotene stage of prophase I. Still, we do not know exactly the mechanisms that let only one follicle to release a mature egg cell, but studies have shown why it possibly happens.

Granulosa cells surrounding the oocyte have receptors for FSH (follicle-stimulating hormone), FSH activates the production of aromatase, which transforms testosterone produced under the influence of LH (luteinizing hormone) in cells of theca interna into estrogens. Estrogens activate expression of LH receptors on the surface of granulosa cells and further stimulate the production of LH. The more LH activates thecal cells, the more estrogens are produced in granulosa cells and that at the same time increases production of LH receptors on granulosa cells.

FSH also stimulates granulosa cells to proliferate, providing the whole follicle with a large number of FSH receptors and increased production of aromatase and at the same time stimulates the follicle to finish meiosis I. Eventually one of the growing follicles will have enough FSH and LH receptors on the granulosa cells to become able to respond to large surge of LH, which results in ovulation. The rest of the follicles that started to develop degenerate due to insufficient number of FSH and LH receptors. The fact that FSH and LH concentrations drop rapidly after ovulation also halts the development of remaining follicles.

The follicles that did not receive enough FSH, won't grow to the point, where granulosa cells start expressing LH receptors and they won't pass through the 1st meiotic block, therefore they still may be activated in the next month. Those that did pass the 1st meiotic block but couldn't be ovulated, will degenerate.

It is still unclear whether there are some additional mechanisms that help the atrophy of underdeveloped oocytes.

Sources:

Larsen's Human Embryology
https://kjcscientific.wordpress.com/project-excalibur/


By what mechanism does elevated homocysteine level cause endothelial dysfunction and damage? It has been stated that elevated homocysteine level causes endothelial dysfunction and damage. By what mechanism does this happen? Why is it the endothel where elevated homocysteine causes problems?

In addition Alan Boyd's answer homocysteine interferes with Glutathione synthesis by reducing the catalytic efficiency of GCL (Glutamate–cysteine ligase), the enzyme which performs the rate-limiting step in GSH synthesis.

  http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2267299/

  Results of the present study are the first to suggest that the relatively high levels of homocysteine that accumulate during aging can interfere with de novo GSH synthesis. Although the precise nature of the underlying mechanism is at present unclear, our results demonstrate that physiological concentrations of free homocysteine can inhibit the efficiency of cysteine utilization by GCL in a competitive manner. Homocysteine has been shown to bind GCLc at the active site in vitro [25] as well as in vivo [35], forming γ-glutamylhomocysteine [36], which is then rapidly degraded enzymatically. An additional mechanism by which an age-related increase in free homocysteine can inhibit the catalytic efficiency of GCL in a competitive manner is described in [35]. It is possible that an aging-related increase in the competition between cysteine and homocysteine for the cysteine binding site of GCL might lead to a decrease in GC synthesis.

Low glutathione means a reduced ability to detoxify and deal with oxidative stress and a more oxidised redox state which has many implications

Further reading:

Inhibition of glutathione synthesis in brain endothelial cells lengthens S-phase transit time in the cell cycle: Implications for proliferation in recovery from oxidative stress and endothelial cell damage
http://www.sciencedirect.com/science/article/pii/S2213231713000244

Glutathione reverses endothelial dysfunction and improves nitric oxide bioavailability
http://content.onlinejacc.org/article.aspx?articleid=1125915


neural genes expressed in nasopharyngeal specimens Is it possible in a nasopharyngeal specimen genes of neural system to be expressed? For example, genes about neural differentiation?

This paper mentions using a cytology brush (not the usual NP swab) to obtain cells from the olfactory epithelium. They obtained and cultured neural precursor cells. Have a look.
Trends in molecular medicine.
"The Olfactory Neural Epithelium as a Tool in Neuroscience"
Joëlle Lavoie, Patricia Gassó Astorga, [...], and Koko Ishizuka
from:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5399677/


what kind of insect is this It has what appears to be antennas in both front and back and legs front and back orange coloured dots ob front and rear of a blackish brown body

Those are two mating "love bugs". Flies (Diptera) in the family Bibionidae. https://en.wikipedia.org/wiki/Lovebug


How do we perceive weight? How do we perceive weight of our own body or something we are holding?

It might turn out that we don't perceive weight so is it subjective? Is it similar to pain, or something different?

This would most likely come under the category of Proprioception - the sense of how our bodies are arranged in the world, and how much effort each part of our body is expending.

From Wikipedia, 'In humans, it is provided by proprioceptors in skeletal striated muscles (muscle spindles) and tendons (Golgi tendon organ) and the fibrous membrane in joint capsules. '.

So our brain receives signals from muscles, tendons and joints, and integrates these into an internal sense of how we are arranged and what our bodies are busy doing.


Effect of sex-ratio on the effective population size As stated on this wikipedia article, the effective population size $N_e$ when the sex ratio differs from $\frac{1}{2}$ is

$$N_e = \frac{4N_mN_f}{N_m+N_f}$$

I understand the biased sex-ratio decreases the effective population size and the formula is quite simple. However, I would fail to prove that this formula is right.

Can you demonstrate to me that $N_e = \frac{4N_mN_f}{N_m+N_f}$ is true?

The reason that an unequal sex ratio affects the effective population size is because offspring are produced by one male and one female parent, and an unequal sex ratio increases the rate at which genetic drift will occur.

  "...the smaller number of males still contributes half of the genes in the next generation..."

In other words, assuming the male population is smaller, the genes passed on by the males/fathers are sampled from a smaller population than that of females/mothers. As you know, smaller populations are more prone drift.

Imagine the classic drift example with a bag of blue and red marbles, but have the parental generation with an unequal number of marbles in either bag.

Hartl & Clark illustrate (see figure 4 here) the relationship between sex-ratio and effective population size, where a sex ratio of 1:9 gives an effective population size of around 36% the actual size (given by $100 \times (N_e/N)$). This means that the rate of inbreeding and drift in the focal population is equivalent to that of an idealised population which is 0.36 times the census size of the focal population.

$$N_e = \frac{4N_mN_f}{N_m+N_f} = \frac{4 \times 1 \times 9}{1 + 9} = 3.6$$

The population is diploid and dioecious; each parent carries two genes, and each parent must be replaced within the population so each pair must produce two offspring. Consider the case where $N_m = N_f = 1$ (and thus $N = N_e = 2$). The number of genes in this population is four. Therefore, to maintain the same population size, four genes must be drawn from the ancestral population.

Further reading:

Hartl & Clark (Page 123-124, Random Genetic Drift: Unequal Sex Ratio)
Conner & Hartl (Page 62, Chapter 3)

While (personally) I can't prove this mathematically, I can demonstrate it using simulation. I've written up a simulator of genetic drift in R, which can cope with unequal sex ratios.

The first four graphs are populations with $N_E = 360$ at various sex ratios ($N_M / N_F$ = 0.11, 0.33, 0.67, 1.00), for 100 replicate populations simulated over 80 generations, with an initial allele frequency of 0.2. The four simulations have different census population size, but equal effective population size, because of the sex ratio. The four groups of populations behave similarly (rates of drift are similar for the simulated populations under the various conditions).

These four use larger populations ($N \times 15$), at the same sex ratios, where $N_E = 5400$ in all cases simulated over 400 generations. Again the groups of simulations behave similarly.

Update:

I've added histograms to ease viewing of the pattern, using $P = 0.5$, for 1000 populations simulated over 25 generations, where $N_E = 360$ and census population size/sex ratio varies between simulations. This distributions are similar despite the different census population sizes.


Separation of closely-sized isoforms I have to separate two proteins of 86kDa and 80kDa respectively, however, I just cannot get a decent separation even in 6% polyacrylamide gel. To make matters worse, these two proteins are isoforms and there is no commercially available antibodies to differentiate either one. I am pretty sure raising an antibody against one of the isoform is not an option for me.

I am tying with the idea of reducing the gel to 4% (I am pretty sure I am pushing it already) or a 2D gel (both isoforms seem to have the same IP though).

6kDa are usually enough to seperate two proteins in my experience. Try the other way, use a 7 or even 8% gel. They run longer but have a higher separation capacity. If you look at this figure from the LabFaQ, you see that you can use a higher percentage gel:

The other thing are the antibodies: Where are your isoforms different? 6kDa are 55 to 60 amino acids more for the long form, so there should be enough possibilities to make specific antibodies.


Is the structure of human brain white matter fixed at/near birth? I have been reading that, with exceptions for a few parts of the human brain, no neurogenesis occurs, so no new neurons are created.  I have also heard that no new axons are formed through the white matter of the brain after birth as well.  I also know that the axons are myelinated, minimizing crosstalk and other interesting structural effects that might occur.

Between those, does that imply that the structure of the white-matter of the brain is fixed at a very young age, and never changes through our life?  It seems like a natural conclusion from the data, but it feels counterintuitive when contrasted with the continuous creation and destruction of synapses which happens so close nearby.

No, white matter structure is not fixed at a very early age. Although a person is born with most of the neurons they will ever have, those neurons must form connections between each other, via axons and synapses, and many of the axons become myelinated during this period. Although the number of neurons remains relatively constant, these processes lead to a substantial increase in overall brain volume. After a few years, there is then a period of synaptic pruning (https://en.wikipedia.org/wiki/Synaptic_pruning), in which many of those connections are rationalised. These processes explain many of the characteristics of human development.

For example, mammalian species can be characterised as precocial or altricial. A precocial species is one in which much of the brain's development has been completed in utero. This allows for a relatively sophisticated behavioural repertoire to be immediately available (think precocial = 'precocious'). For example, a foal is born and almost immediately is able to walk, follow its mother, and so on. Meanwhile, an altricial species like a human is born in a relatively helpless state, incapable of independent locomotion and with even very limited perceptual processes. It is the development of axonal and white matter pathways, with associated synapses, that allow learning and development of new skills in the post-natal period.

During this process, the brain is extremely flexible. For example, a baby can initially distinguish between the phonemes of any language. As its white matter connections develop in response to a lot of exposure to the language(s) in its home environment, the brain becomes more specialised. Eventually, past the pre-teen period, it becomes much harder to perceive and articulate subtle phoneme distinctions from other languages, and the acquisition of new grammars shifts from effortless and rapid, to slow and requiring formalised instruction rather than being spontaneous.

This shift to relative inflexibility reflects the second phase of white matter development (i.e. large-scale synaptic pruning). That is, in the first phase, there is widespread growth of connections between neurons via axons and synapses, along with myelination. In the second phase, the flexibility of this system is traded for the efficiency and focus of a brain that has learned what specific abilities it needs to have. This continues up until about age 10, at which stage 50% of the synapses present at age 2 have been lost (https://link.springer.com/referenceworkentry/10.1007%2F978-0-387-79061-9_2856). Learning is then no longer so rapid, but with specialisation and development, an adult is able to focus attention explicitly and maintain discipline towards achieving goals, where a child might get more easily distracted and seek novelty.

Synaptic formation and loss then continues throughout life, as the underpinning of learning processes, but no longer on the mass structural scale seen in earlier development.


How do Proteins migrate in MES vs. MOPS My gels look significantly different in MES (2-(N-morpholino)ethanesulfonic acid) and MOPS (3-(N-morpholino)propanesulfonic acid). That is to be expected. What I don't understand is why the simple presence of the counter-ion significantly changes the velocity of certain proteins.

Is this due to the different pH (MES is usually run at pH 8.0, MOPS is usually run at pH 7.0) or is the charge distribution on the counter-ion responsible for everything?

Well, to rationalize everyone's comments, I think @leonardo is right.

This is a denaturing SDA PAGE gel.  The migration of the SDS Micelles which are negatively charged, depends upon the shielding of the solution around it.  The difference in mobility is because the SDS micelles will experience a slightly different field at pH ~6.2 (MES) vs 7.2 (MOPS).

The thought that these have the same charge would be right at exactly the pH corresponding to the pKa.  For these two ions the proportions will not be the same when running 0.8 pH units from their respective pKas. the ion concentration goes as +/- log ([BH]/[B-]) and the charge environment of the buffer should not be the same.  I think that the higher pH for MOPS running will tend to create more negative charge in the solution from MOPS- but also OH- in solution, slowing the mobility of the micelles and favoring the resolution of the larger proteins with MOPS.

This is all given even if the buffering ion concentration is the same.

I'm sure the gory details are buried in the musty tomes of some physical biochemistry journals deep in the library, but this is how it sounds to me.


Can supplements affect DNA? (Could 10,000% Methylcobalamin affect MTHFR genotype) Originally titled "Could B12 supplementation affect dna test results for B12 need?" - B12 just seems like a good example question to frame the more general question of "Can supplements affect DNA?"

I recently got a DNA test done from DNAFit and found out I do not have a raised need for B12 - however - I've been supplementing with about 10,000% B12 (as methylcobalamin) for quite some time now. Been taking 10,000% every day for 5 months and like 1,000+% B12 for another 5.5 months before the increased dosage. I actually am quite dependent on my supplements, and think it's quite possible that my DNA has adapted to them, if DNA does such things. (Just looking briefly, it appears there is some disagreement as to whether DNA can change due to supplementation: google.com/search?q=CAN+SUPPLEMENTS+CHANGE+DNA )

So there's the root of the question - can supplements affect DNA - more specifically - could B12 supplementation affect the result of my MTHFR genotype (which is CC, just FTR)

What the DNAfit test does is analyse some of your genes for common variants (called SNPs - single nucleotide polymorphisms). These are hard-written in your genetic code, they won't ever change (you could in theory have mutations in some individual cells, but we can ignore that).

Taking supplements or any other environmental influences will therefore not affect these tests.

The environment can affect certain markers on the DNA, that control how active a given gene is (how strong its expressed) - this is called epigenetics. Since these markers are written on the DNA they are also potentially heritable and the two effects (the genetic code itself and the markers on it) are often thrown into one pot when some news report about 'changes to your DNA'.


Why is ATP synthase sometimes referred to as ATPase? Quite a few times I have seen the term ‘ATPase’ used for what I would consider ATP synthase. For example, my text has:

  “The phosphorylation of ADP to ATP is also catalysed by the enzyme ATPase.”

I don’t understand this. Surely the enzyme that catalyses the synthesis of ATP should be entitled ‘ATP synthase’, so why is ‘ATPase’ used in this case?

The way we were

To understand why you may encounter ATP synthase referred to as ATPase, you need to be aware of the historical context — the experimental work that preceded the knowledge of the structure and function of the enzyme complex that we have today. In a nutshell:

  Original studies of the components of what we now know to be a complex capable of synthesizing ATP could only be assayed by their ability to hydrolyse ATP. Even though these components (F1 and F1FO) were derived from a mitochondrial system that coupled electron transport to ATP synthesis, and the authors believed these components were responsible for ATP synthesis, they were obliged to refer to them by the activity they had assayed: hence F1 ATPase and F1FO) ATPase.

History lesson

It is instructive to consider a paper by Kagawa and Racker, published in 1966, and entitled:

  Partial Resolution of the Enzymes Catalyzing Oxidative Phosphorylation
  VIII. PROPERTIES OF A FACTOR CONFERRING OLIGOMYCIN SENSITIVITY ON MITOCHONDRIAL ADENOSINE TRIPHOSPHATASE”

This work demonstrated that a mitochondrial ‘fraction’ (FO — ‘F’ stood for ‘fraction’) when added to another ‘fraction’ (F1), previously shown to have ATPase activity, could confer sensitivity of the ATPase to inhibition by oligomycin, a compound that inhibits oxidative phosphorylation in intact mitochondria. The title shows clearly that they were aiming to understand ATP synthesis, but were at the stage where all they could measure was the ATPase activity of fractions. It was not until 1973 that Racker and Stoeckenius were first able to  synthesize ATP, and for that they had to use a different system — the light-activated purple membrane of Halobacterium halobium. The key was the incorporation of the membrane — without it there could be no proton gradient to drive the synthesis of ATP, and this was why the isolated F1FO) complex could never catalyse synthesis of ATP on its own.

Those days are gone now

The structure of the components of the ATP synthase finally started emerging in the 1990s, after which no doubt remained that the F1 and FO fractions were part of a synthase.

  Therefore, in describing the enzyme complex as we now know it to be,
  there is no excuse to refer to it as anything other than ATP synthase. Moreover there is a particular need to avoid confusion with a membrane ATPase (below).

In my opinion, any textbook that refers to ATP synthase as ATPase is severely out of date and should be burned.

Of course, I exempt historical accounts, as long as the context is made clear.

The acid test

In some cells there are transmembrane complexes, structurally related to the mitochondrial (or bacterial membrane) ATP synthase, that are ATPases. These are the Vacuolar-type H+-ATPases (V-ATPase) which use the energy of ATP hydrolysis to transport hydrogen ions across the membranes of certain tissues and organelles. Another reason not to refer to the ATP synthase as ATPase!


What is the latency between paired neuronal responses in the brain? Is there any data on how long it takes for signals to propagate from one neuron to its neighbors in complex networks, such as the brain (particularly the neo-cortex)?

If not, is there any reasonable way to estimate at least the order of magnitude (for example by considering synaptic delay, which is in the order of 0.5 ms and the firing delay)?

Short answer
A rough indication of the delay in monosynaptically connected cortical neurons is 6 - 14 ms.

Background
As @Jonathan correctly states, there are many variables involved in neuronal delays. However, because you ask for an estimate of the order of magnitude of the neuronal delay between two coupled neurons in the neocortex, I will suffice by providing the latencies reported form one study that seems to meet your demands very well. In this study the latency data on horizontally connected neurons in monkey prefrontal cortex in layer III were reported González-Burgos et al (2000).

The authors inserted stimulating electrodes to evoke action potentials and used distant recording electrodes to measure the responses in cells located distally from the stimulation site (Fig. 1).

Recording setup used in González-Burgos et al (2000).

They report that delays between monosynaptic connections range between 6 - 14 ms. Fig. 1 shows that these latency estimates depend on the position of the stimulating and recording electrodes, i.e., which part of the presynaptic cell is stimulated and which part of the postsynaptic cell is recorded. Most notably in the recording setup used, longer axon collaterals will have resulted in longer latencies. The authors conclude that the conduction velocity of the horizontal axon collaterals was 0.14 ± 0.04 m/s and the synaptic delay was estimated at 2.29 ± 0.49 ms.

Reference
- González-Burgos et al., Cereb Cortex (2000); 10(1): 82-92


Association of shorter telomeres with heart disease From this paper

  Those with shorter telomeres in blood DNA had poorer survival,
  attributable in part to a 3.18-fold higher mortality rate from heart
  disease (95% CI 1(.)36-7.45, p=0.0079), and an 8.54-fold higher
  mortality rate from infectious disease (1.52-47.9, p=0.015).

What is the connection between shorter telomeres and heart disease ?

This seems a bit like a hen and egg problem. Telomere length is both associated with age and with heart diseases, but heart disease is also associated with age. The question here is, is one really causing the other here (short telomeres heart problems) or do they occur simultaneously? The other problem with heart disease is that it is a multi-risk disease, with many risks accumulating with age. The figure below sums this up, it is from the first paper:

Have a look on these articles:

Telomere biology in heart failure
Aging, telomeres and heart failure.
Telomeres and Cardiovascular Disease


Can twins that develop in separate sacs but share the same placenta be identical? I have two younger non identical twin sisters. When my mum was pregnant she was told they were both in different sacs when developing but shared the same placenta.
We have done hours of research on the topic, as we have reason to believe they could after all actually be identical.
After all this research we’ve just found a load of fancy names for twins and no information on non identical twins that share the same placenta and are in different sacs.
Another thing that may help is that they are mirror twins.

they were both in different sacs when developing but shared the same
placenta

This suggests that they were monochorionic diamniotic twins, which would mean they are monozygotic, i.e. identical.


How to interpret the breeders equation? The univariate breeders equation is defined as,

$\ R = h^2 s$

where $\ R $ is the response, $\ h^2 $ is the heritability (additive genetic variation), $\ s $ is the selection differential. The multivariate equation is similar to this in principle but includes a multiple trait variance-covariance matrix and multiple selection differentials.

Essentially the breeders equation tells us how strong the response to selection will be as a result of the additive genetic variance within a trait (and between traits in the multivariate) and the selection applied to that variation ($\ s = cov (w,x) $ = the covariance between fitness ($w$) and the trait $x$).

For example, in trait $x$, $s$ = 0.8 and $h^2$ = 0.5 the value of the response for $x$ is $R$ = 0.4. Compared to another trait, $y$, where $s$ = 0.8 and $h^2$ = 0.1 and thus $R$ = 0.08.

My question is, if we look at a trait in a population, measure it's population mean and define $h^2$ and $s$ values, can we then predict the change in the population? IE. can we predict (with the values of $s,  h^2$  and the population mean) what the mean population mean trait will be in the next generation directly from the result of the breeders equation? Does the value of $R$ give us anything of use?

Following from the example above, I examine a trait (wing length in chickens) and find the mean to be 24 cm. I select birds to start my next generation in a way that causes $s$ = 0.8. The additive genetic variance for the wing length is quite high, $h^2$ = 0.5. The predicted response is $R$ = 0.8 x 0.5 = 0.4. What does this tell me about the next generation?

The breeder's equation as you wrote it:

$$R = h^2S$$

The heritability that is the ratio of additive genetic variance over the total phenotypic variance is called the heritability in the narrow sense and is noted $h_N^2 = \frac{V_a}{V_P}$, where $V_A$ and $V_P$ are the additive genetic and phenotypic variance respectively. In contrast the heritability that consider the total genetic variance is called the heritability in the broad sense and is noted $h_B^2 = \frac{V_G}{V_P} = \frac{V_A + V_D}{V_P}$, where $V_G$ is the total genetic variance and is equal the sum of the additive genetic variance $V_A$ and the genetic dominance variance $V_D$. We can rewrite the breeder's equation using the standard notation for the heritability in the narrow sense:

$$R = h_N^2S$$

The so-called response to selection $R$ is the mean deviation of the trait in the next generation. In other words, $R$ is the difference between the mean trait of the parents and the mean trait of the offspring, So to answer your question, yes, the breeder's equation gives the value of the mean trait in the following generation. It does not give any information about the frequency and number of alleles though.

$S$ is the the mean trait of the individuals which reproduce weighted by their reproductive success minus the mean trait of the parents. In other words, it is

$$S=\frac{1}{\bar w}\sum_{i=1}^{\text{nb inds}}m_iw_i - \bar m$$

, where $m_i$ is the trait measurement and $w_i$ is the fitness of this individual, $\bar m$ is the mean trait of the parents and $\bar w$ is the mean fitness.

The mean trait of the parent generation does not appear in the breeder's equation but only their mean trait weighted by their reproductive success. In the standard case of truncated selection (common in artificial selection programs) all $w_i$ are equal and $S$ becomes the mean trait of the individuals that we allow to reproduce in the parent population. And it is exactly the same thing for the multivariate case except that the variance-covariance matrix should be taken into account.


Confused at what is happening with these action potentials Ok so for a bit of a background, I am doing a science project looking at the action potentials of the earthworm. I anaesthatized the worms then hooked them up to a spiker box (http://backyardbrains.com/products/spikerbox) and stimulated them.
This is an average result:

What I am confused about is why the action potential goes negative first before then going back up. From my readings online, I thought that the action potentials were meant to go up first then travel down and then continue on its course. If it helps I used a program called audacity to record the action potentials.

Thanks very much guys. Sorry if I'm not being clear. Just ask anything if you need more information!

Nice graph. What happens when you reach the top of the potential (when you depolarize the membrane) that you need to go back to a resting potential to be able to stimulized again. The membrane gets "neutralized" and this reaction often over-shoots and goes below the resting potential, which is quite normal. Before reaching the normal resting potential there will be no further activation. The Wikipedia article on the "Action Potential" contains a more complete explanation.


How can I tell if a certain marker is useful to date a phylogeny? If I have a phylogenetic tree for a genus, how can I tell if a certain protein would be a good phylogenetic marker to use if one wanted to use a molecular clock to date the age of some speciation event in that a genus? How can I look for it on a tree?

Speed of Sequence Divergence

You need to use a sequence which diverged only little among most closely related lineages in your tree and diverge quite a lot among most distantly related lineages. In other words, you need a sequence that diverge at a rate that is convenient for your needs.

If you investigate a young tree (a tree which MRCA of all lineages lived recently) you need a sequence that diverge quickly through time. If you investigate an "old tree" (a tree which MRCA of all lineages lived a long time ago) you need a sequence that diverge slowly through time.

Selection

Selection is affecting how fast two sequences diverge. But because selection is specific to the environment experienced by the individuals in each lineages, it can be more difficult to use sequences under selection as a molecular clock (exception of highly conserved selection which are under purifying selection used for very large trees). So we use neutral sequences.

Rate at which mutations fix

Let $u$ be the mutation rate for the sequence of interest and $N$ be the population size. The number of new mutations per year is equal to $2Nu$ (assuming a diploid population). Now, knowing that the sequence is not under selection, the probability of reaching a single mutation to fix (=to reach a frequency of 1 in the population) is $\frac{1}{2N}$ (see this post for a very introduction to why the probability of fixation is inversely proportional to $N$). As a consequence, the rate at which mutations fix is $2 N u \frac{1}{2N}=u$. In other words, the rate of mutation fixation is the mutation rate (for neutral sequences).

Rate at which mutations fix and sequences divergence

The term, sequence divergence is not clearly define. Typically, one would mean "average number of pairwise differences". Assuming that each new mutation that fixes occurred at a new locus (infinite allele model), then the number of pairwise differences between two lineages is the addition of the number of mutations that fixed in each lineage, that is $2u$. Always under the infinite allele model, the probability of the average number of pairwise differences to equal k is given by a Poisson distribution.

Wrapping up

  how can I tell if a certain protein would be a good phylogenetic marker

The sequence

has to be neutral (it makes things easier)
has to have a mutation rate of the right order of magnitude (it improves accuracy of the estimate and therefore improves statistical power)


What is a reflex pathway? I know that the pathway of nerve impulses during a reflex action is called a reflex arc. However, I want to know whether the term reflex arc can be called either a reflex path or simple reflex?

A reflex arc is sometimes called the reflex pathway. While there is no involvement of the brain in the output/response to stimulus, it does receive signals via the spinal cord informing it of the action. In other words, the reflex action is registered in the brain as soon as it occurs.


What determines when twining plants twine? Some climbing plants, such as clematis and honeysuckle use their leaves like tendrils. Others, like Aristolochia use their stems. The young leaves of these plants are able to twist around slender objects. Twining stems twist around whatever they touch, be it a pole, branch, wire or chair leg. The stems will wind clockwise or counterclockwise, depending on the species of plant.

AFAIK, plants can't see or feel, but the way they climb clearly shows they have some way of knowing when to twine. How does this work?

Thigmotropism

This is a special case of tropism, called thigmotropism. In botany, tropism is a modified growth in response of an environmental stimulus. The most famous tropisms are:

Phototropism: plant growth in response to a light stimulus
Gravitropism: plant growth in response to gravity

In the case of thigmotropism, the growth is modified in response to touch (from the greek θιγμός). Curiously, this phenomenon was studied by Darwin in his late life: Darwin, C. (1865), On the Movements and Habits of Climbing Plants.. Journal of the Linnean Society of London, Botany, 9: 1–118. doi:10.1111/j.1095-8339.1865.tb00011.x

The mechanism of thigmotropism can be compared to that of phototropism: in phototropism, the shaded side of the stem apex has a higher concentration of auxins compared to the sunny side and, therefore, grows more quickly, and the result is that the plant grows towards the light source (positive phototropism).

In thigmotropism, there are mechanic receptors in the epidermis which detect touch (mechanoreceptors), possibly membrane proteins. Then, after detecting touch, there is a signal transduction somehow, which "informs" the cells opposite to the touching side about the stimulus, and those cells exhibit an increased rate of growth.

The mechanism may be similar to that of phototropism, also depending on auxins. According to Scorza et al. (2011):

  Ultrastructural studies revealed that most thigmotropic and thigmonastic movements are caused by differentially changing cell turgor within a given tissue. Auxin has emerged as a key molecule that modulates proton extrusion and thus causing changes in cell turgor by enhancing the activity of H+ATPase in cell membranes. (emphasis mine)

The actual details regarding the mechanism are not well understood, and they are way less understood than those of phototropism or gravitropism, for instance. The result, however, is that the touching side grows less that the opposite side:

If you combine thigmotropism and negative gravitropism (the growth against gravity), the result is that the climber grows up going around the support, in an upwards spiral:

A detailed explanation can be found here: Plant tropisms. 1st ed..

Sources:

Scorza, Livia Camilla Trevisan, and Marcelo Carnier Dornelas. “Plants on the Move:  Towards Common Mechanisms Governing Mechanically-Induced Plant Movements.” Plant Signaling & Behavior 6.12 (2011): 1979–1986. PMC. Web. 14 May 2017.
Gilroy, S. and Masson, P. (2008). Plant tropisms. 1st ed. Ames, Iowa: Blackwell Pub


What is this plant, and is it edible? After I planted some spring mix lettuce a couple of years ago, nothing survived except for this plant.  It doesn't look like any of the leaves that I am used to.  Does anyone know what it is?  Is it edible?  I am located in East Tennessee.

Thank you for any help you can give!

I just posted some more photos with measurements. The total length from base of the plant to the end of the leaf is about one foot. These plants have no flower growing from the base, however there is a separate plant nearby in the mix that does have flowers. I included a photo of it in case it is related. The original plant in question has leaves that are mostly smooth (some have tiny white or clear hairs on the backside or stem...some are smooth). They are almost as thick as spinach leaves.

This is a leaf vegetable called Cichorium, Endive in English. There are several closely related species, Cichorium endivia (also called endive), Cichorium pumilum (also called wild endive), and Cichorium intybus (also called common chicory). I think it looks most like common chicory, but if it comes from your seeds, Cichorium endivia is more likely.

Flower from Cichorium intybus

Flower and leaves of Ch. pumilium

https://en.m.wikipedia.org/wiki/File:Cichorium_pumilum.jpg
(source pictures:wikipedia)