Why can't we always create a vaccine against a virus when an ELISA test to detect it is possible?

I found the question quite interesting and will to provide a concept and a speculation although I could not answer the question to my own satisfaction (edits to this regard are welcome)

Currently (2020), the advanced form of ELISA tests for HIV are designed to simultaneously detect both the HIV P24 antigen (produced by the virus) and anti-HIV igG and igM antibodies (produced by the body in response to the virus). Refs (CDC: What kinds of tests are available, and how do they work?)(HIV Diagnostic Testing: 30 Years of Evolution)

While it is easy to detect known viral antigens like the p24 capsid protein in a diagnostic, it is not straightforward to use the same antigen as a vaccine and expect the host to mount an immune response that neutralizes the viral infection, although attempts have been ongoing. Possible scenarios could be that the binding strength of the antibody to P24 might be good enough for detection, but not enough for immunity or that recognizing and binding to P24 does not inhibit the infection. Coming to the evolution/mutation question, since both the p24 antigen and a few antibodies are being detected, it is unlikely the virus would mutate so as to evade the ELISA for all the targets.

The first point in Charlie's answer might be getting at this but it did not come through clearly.


At what point during an action potential are the sodium potassium pumps working?

The Sodium-Potassium Pumps are always at work. One can think of them as a continuous process that maintains the equilibrium potential for the individual ions. They always are grabbing internal sodium and exchanging it with external potassium at the cost of ATP.

However a neuron's rest state (in your example -60 mV) is a combination of the equilibrium of the Sodium, Potassium, Chlorine, and other ions. Thus when the membrane hyperpolarizes beyond the rest potential, it is actually the leak potential that brings the membrane potential back up, not the Sodium-Potassium pump.

Leak potentials arise from ions (usually chorine) that pass through the membrane via channels that are always open. Furthermore, sodium channels reactivate and a small amount open to  sodium to enter. (Recall as a population there is usually a small amount of sodium channels open at rest. Another contributing factor is as the potassium channels close the other to factors dominate and slowly bring the membrane back to rest state. Remember that rest is defined as the balance of currents, there will always be small amounts of currents flowing. So even though the neuron is rest small amounts of sodium leak in and less potassium out. The sodium potassium pump maintains the equilbrium potential that allows these currents to flow.

The Sodium-Potassium pump is a slower process, so it usually can be ignored over a single spike. But If there is a high frequency spike train then the small amount of sodium that enters the cell and potassium that exits the cell can add up and effect the equilibrium potentials of the individual Ions. This of course changes the firing properties of the neuron.


Does the renal vein have a greater glucose concentration than the renal artery?

The kidneys use glucose from the blood as a nutrient, so, this is the reasoning behind your source saying there is less glucose in the renal veins than in the arteries.

If the renal vein contains both less of water and glucose than the renal artery, the concentration of glucose in the renal vein still be lower. This agrees with Bioninja.com.au:

  Blood in the renal vein (i.e. after the kidney) will have:

  Less urea (large amounts of urea is removed via the nephrons to form urine)
  Less water and solutes / ions (amount removed will depend on the hydration status of the individual)
  Less glucose and oxygen (not eliminated, but used by the kidney to generate energy and fuel metabolic reactions)
  More carbon dioxide (produced by the kidneys as a by-product of metabolic reactions)

On the other hand, an article in Scielo.br says:

  Unlike the proximal nephron, cells in the distal nephron are fully
  capable of glucose utilization. In physiologic conditions, the amount
  of glucose utilized in the distal segments of the nephron equals that
  derived from the renal gluconeogenesis in proximal tubules. This is
  confirmed by the common finding that the arterial-renal vein blood
  glucose concentration difference in the post-absorptive state is near
  zero.

In conclusion, your source can still be right.


Wikibooks claim that it is difficult to find two texts that agree on the definition of an animal

Definition of Animal

Animal is typically defined phylogenetically (just like any other monophyletic taxon; see here for intro to phylogeny). Any lineage part of the taxon Animalia (aka metazoa) is an animal. This is the definition given by wikipedia > Animal. You can find the animals here on the tree of eukaryotes.

Issue with the claim

  It is surprisingly difficult to find two texts that agree on a precise definition of an animal.

This claim is pretty clumsy in my opinion. It sure can be hard to find a set of phenotypic traits that would group all animals together but it does not mean it is hard to define 'animal'.

IMO, what they meant is

  It is surprisingly difficult to find a set of phenotypic traits the are shared by all animals and by none of the living organism that is are not animal.

This claim would make more sense. It is indeed true that it is hard to make such set of phenotypic traits. There are plenty of non-animals that are heterotrophic eukaryotes (such as fungi), there is at least one animal that is (at least partially) autotroph (Elysia chlorotica), not all animals have a nervous system, etc...


The structure of skin (epidermis) can change with damage, when the skin is broken the body repairs this partly by recruiting cells called fibroblasts. These fibroblasts lay down collagen fibres to repair the skin. These fibres a normal component of skin are not as neatly arranged as the original fibres and may also higher in number leading to 'denser' skin. This is essentially what a scar is. In some cases the above process can go awry forming what is known as keloid scars.

The other thing that can happen with repeated pressure exposure the skin can become callous, this is when there is thickening of the outer layer formed of cells called keratinocytes increase in number due to recurrent damage. These form typically on pressure points such as balls of feet.


Chromosome position mismatch for SNPs in dna tests

Most or all consumer DNA companies doing autosomal SNP tests deliver their raw data (at least by default) based on human reference genome build 37 (GRCh37).  This is effectively the standard for this arena because it is compatible with existing files and other companies, allowing matching and other processing.  dbSNP and SNPedia have changed to use the next major genome update, build 38 (GRCh38).  The major genome builds can be expected to have different position numbers for most all comparable places in the genomes, including of course all SNPs which are defined in both builds (most of them).

So the differences in positions shown in your raw data files and dbSNP/SNPedia are due to this difference in the reference builds they are based on.  I don't know a way of getting build 37 positions on SNPedia, but on dpSNP one way of seeing the build 37 position is to scroll down to "Genomic regions, transcripts, and products", "Choose placement" of GRCh37, and then hover over the blue highlighted SNP name, which will show a drop-down list with the (build 37) position, among other things.


Sulfate-reducing bacteria are everywhere, one spoon of soil contains several different species of them. The problem is how to isolate them from the other bacteria.
This old paper explains how to do it, I am sure there are newer techniques to do the same, it's up to you to dig into the literature to find the one you prefer if you want to isolate them by yourself.

Otherwise, just buy it from a collection.


How are Mono and Diglycerides metabolized without the Free Fatty Acids of Triglycerides?

Inside the intestinal lumen, di- and triacylglycerol are hydrolysed to free fatty acid and monoglyceride by lipase.

These diffuse through the plasma membrane of enterocyte where they will   used to resynthetize triacylglycerol, and ultimately the lipoprotein chylomicron for transport into the general circulation.

Contrary to what your question seems to imply, the glycerol to which the free fatty acid are affixed is not necessarily coming from the food: glycerol is routinely produced by glycolysis. (This notably also happens in the adypocytes). There is no requirement that food contain a ratio three fatty acid to one glycerol to be fully absorbed - if the weight loss property of DAG are true, it may be through  a different mechanism.


Biopython - Big Discrepancy Calculating RNA melting Temperature over Literature

Comparing Biopython MetlingTemp to other calculators.

I have written the recent version of MeltingTemp in Biopython's SeqUtils.  I have extensively tested the Tm calculations against other programs like MELTING and Primer3Plus and other online Tm calculators with consistent results, thus I'm pretty confident that there is no gross error in the module. The simple answer in this case is: the calculation of siDirect is wrong.

Sources of discrepancy.

One minor thing: Many programs calculate k as k = total Oligo/4. MeltingTemp uses k = Oligo1 - (Oligo2/2). Thus to mimic this behaviour, you have to use

dnac1=50, dnac2=50

instead of

dnac1=100

And now the major thing: Oligo concentration is usually given in nanomolar. However, if you look at the calculation in the Perl script, siDirect seems to use micromolar!

my \$tm = ( 1000 * $dH / ( -10.8 + $dS + 1.987 * log(0.0001/4) ) - 273.15 + 16.6 * log(0.1)/log(10) )

The critical part here is:

log(0.0001/4)

which should be:

log(0.0000001/4)

Thus, you have to pass 1000-fold higher oligo concentrations to Biopython's MeltingTemp to get the same result as siDirect:

>>> from Bio.SeqUtils import MeltingTemp as mt
>>> print mt.Tm_NN('GGAUUUG', dnac1=50000, dnac2=50000, Na=100,
                  nn_table=mt.RNA_NN1, saltcorr=1)
20.1472140567
>>> print mt.Tm_NN('CUCAUUG', dnac1=50000, dnac2=50000, Na=100,
                   nn_table=mt.RNA_NN1, saltcorr=1)
18.1074422939

This is of course wrong if your primer concentration is 100 nM, but that's the result you get from siDirect.


Which lipoprotein has the highest protein content?

LDL has the higher protein content than HDL. LDL consists of Apo B48 and Apo B100. These are proteins with higher molecular weights between 250 kDa to 550 kDa as compared to other apoproteins. And these apoproteins are not present in HDL.

And if lipoprotein (a) is included in comparison then it has highest protein content.

(Via:  https://lipidmaps.org/resources/lipidweb/index.php?page=lipids/simple/lipoprot/index.htm)


Introductory biology text for an outsider

I found the Campbell Biology textbook to be quite comprehensive and approachable. I think many introductory biology courses use it.

http://www.amazon.com/Campbell-Biology-Edition-Jane-Reece/dp/0321558235


Online phylogenetic tree of human lineages

Trees for haplogroups

See

https://www.eupedia.com/genetics/phylogenetic_trees_Y-DNA_haplogroups.shtml
https://www.eupedia.com/genetics/
focus on Europe: https://www.eupedia.com/europe/origins_haplogroups_europe.shtml

and many pages linked therein such as https://www.eupedia.com/europe/Haplogroup_J2_Y-DNA.shtml#subclades

and so on.

More detailed for mtDNA (female lineage):

https://en.wikipedia.org/wiki/Human_mitochondrial_DNA_haplogroup

and many links therein

More detailed for the Y chromosome (male lineage):

https://en.wikipedia.org/wiki/Human_Y-chromosome_DNA_haplogroup

and many links therein

https://en.wikipedia.org/wiki/List_of_Y-chromosome_haplogroups_in_populations_of_the_world and links therein
https://isogg.org/tree/index.html
and the Google Sheets linked therein
https://www.yfull.com/tree/

"Trees" for populations

Note that the trees are for genes/haplogroups, whereas such a "tree" for populations actually also has gene flow across branches. Imagine overlaying the tree for mtDNA (female lineage) with the slightly different tree for Y-DNA (male lineage).

Geography of migration

Migration and geographical distance played a key role in the emergence of distinct populations. See

maps of migration by haplogroups: Human migration by haplogroups, World map of Y-DNA haplogroups, Early human migrations, Simplified interactive map, And so on.
maps of distribution of haplogroups: mtDNA in Europe, Y-DNA in Europe, many of the links listed here, and so on

Also check out how theories about migration are changing. For example about mutation M174: theory around the year 2010 vs. theory since at least 2016.


I will argue that yes, it is POSSIBLE. It is possible on earth like on other planets. Given enough time, matter, and energy, "something" that resembles life will emerge. The problem I see, however, is that life has already conquered our planet, so any "new living thing" will have to compete with other long-time adapted living thing, in practice, no chance of survival. The right conditions you refer to are the ones that allowed "life as we know it" to emerge. Given other conditions (other chemicals, other energy forms, etc), something completely different will form.

Of course, without final proves, this is still speculation.

Some speculative links:

http://speculativeevolution.wikia.com/wiki/Alternative_biochemistry

http://www.dailygalaxy.com/my_weblog/2015/05/alien-life-habitats-nasa-brainstorms-alternatives-to-water.html

http://www.nature.com/news/2009/090513/full/news.2009.471.html


Micelles have a hydrophobic core and a polar, hydrophilic surface. This surface will preferentially associate with water molecules and become solvated, rather than sticking to lipids.

Negative charge on phospholipids at the micelle surface mediate electrostatic repulsion to other micelles, keeping them from sticking together.


Understanding genetic similarity in humans

Yes, these are different measures, and agreeably confusing. The "more than 99%" figure refers to pairwise distance. This figure (actually 99.9%) means that if you were to line up the 3 billion nucleotides of DNA from of any two people, on average, 1 in 1000 of these nucleotides would be different. Among siblings, this number would be even smaller. The 50% figure refers to the origin of DNA stands in a diploid organism: you get one exact copy of each of your genes from your mother, and an exact copy from your father. So half your DNA comes from each parent. But the DNA from each parent is still nearly identical. Siblings will get all their DNA from their parents, but for any particular section, they will get either their maternal grandmother's or grandfathers gene from their mother, and either their paternal grandfather's or grandmother's gene from their father.
For reference, you often hear that humans and chimps share 98% of our DNA. This is the not exactly a pairwise difference value, because it only counts changes in amino acids (http://humanorigins.si.edu/evidence/genetics). The amino acids between chimps and humans are about 98.8% identical to humans. The DNA across the whole genome is about 94% identical. There are about 50 genes present in humans that are absent in chimps https://www.genome.gov/15515096/2005-release-new-genome-comparison-finds-chimps-humans-very-similar-at-dna-level


Why does this oxygen duration chart have increased times above 30,000 FT MSL?

This is related to the diluter demand system, O2 present in the cabin, and tracheal pressure.

The diluter demand system is designed to compensate for the
short-comings of the continuous flow system. It   gives the user oxygen
on-demand (during inhalation) and stops the flow when the demand
ceases (during exhalation). This helps conserve oxygen. Additionally,
the incoming oxygen is diluted with cabin air and provides the proper percentage of oxygen, depending on the altitude. This system
is typically used at altitudes up to 40,000 feet.

Source: Oxygen Equipment: Use in General Aviation Operations - Federal Aviation Administration
When you get at altitudes higher than 35,000 feet you're more or less totally reliant on the oxygen provided by the diluter, that's why the diluter demand is very close to the cruise time. If there's low air pressure in the cabin above 35,000 feet there won't be enough oxygen for normal body function, and you run the risk of becoming hypoxic within half a minute.

Toe of Useful Consciousnees (TUC) per Effective Performance Time (EPT)

Look at the chart below:

Tracheal oxygen partial pressure starts at 149mm. Hg for sea level and can drop to 20 at 40,000 feet. If oxygen is given according to the % supplement O2 required for inspired air, the tracheal pressure stabilizes back to what it is at sea level. Above 30,000 feet, tracheal oxygen partial pressure cannot be maintained at 149mm. Hg. Therefore you need to use the diluter longer to at least maintain it close to 149mm. Hg. Or at level where the mm. Hg. isn't extremely low.
The required mean tracheal oxygen partial pressure can be different at the same altitude depending on the liters of O2 per minute BTPS (Body Temperature and Pressure Saturated) being inspired.
Source: Introduction to Aviation Physiology
Fore example, according to 14CFR 23.1443:

(ii) At cabin pressure altitudes above 18,500 feet up to and including
40,000 feet, a mean tracheal oxygen partial pressure of 83.8 mm. Hg
when breathing 30 liters per minute, BTPS, and with a tidal volume of
1,100 cc. with a constant time interval between respirations.
(2) For each flight crew member, the minimum mass flow may not be less
than the flow required to maintain, during inspiration, a mean
tracheal oxygen partial pressure of 149 mm. Hg when breathing 15
liters per minute, BTPS, and with a maximum tidal volume of 700 cc.
with a constant time interval between respirations.

So, at above 30,00 feet you will use most of the diluter demand oxygen to preserve tracheal pressure until the plane has stabilized. At lower altitudes the diluter demand is lower because you can reach safer altitudes faster.


Do the standard curve once for each primer pair to determine efficiencies. You can use the efficiency values for any number of replicates with any template.

I think we have somewhat discussed this issue in your previous post.


For starters, you can just google "confluent".  It means that there are no colonies, but that the cells cover the whole plate.

So when you provide all three amino acids, the cells fill up the whole plate.  If you leave His out, but keep the plate at 25 degrees, the plate still fills up with cells, so the His- allele isn't hurting the cells at all at 25 degrees, but it's pretty nasty at 37 degrees.  That makes it conditional; the mutation only impairs His metabolism at some temperatures.

There is not a single cell which is surviving a lack of Leu, but there are some which are surviving the lack of Trp, and the lack of His at harmful temperatures.  Presumably, those are the small number which are lucky enough to acquire mutations which compensate for the original deleterious alleles, but NO cells were able to overcome the problem with the Leucine metabolism.  This suggests that the Leucine mutation might be a total deletion.


Let's do some math.

Also, let's ignore your examples, and use a clearer one - instead of fingernails, let's look at the cells that line the intestine.  Intestinal epithelial cells are shed and replaced constantly and very rapidly, roughly every 5 days.  So that means about 50-70 cell generations per year.

Each time the cell replicates, it loses a little bit off the end of its telomeres.  How much does it lose?

We know that for lymphocytes, adults lose roughly 30 base pairs of telomeres per year.  Lymphocytes don't replicate as fast as the colonic mucosa, though.  The estimate for these rapidly-dividing cells is about 44 bp/year. We can say 50 for a round number.

That doesn't tell us much unless we know what we're starting and stopping with.  Humans start life with about 10,000 bp of telomeres.  At least in cultured cells, once telomeres reach 1000-2000 bp, cells become senescent and stop, or greatly reduce, their growth rate.

So we start at around 10,000, we can lose up to 9000, and we lose around 50 per year. That means that the intestinal epithelium, which have about the most rapidly-dividing cells in the body, are good for about 180 years of life, assuming that the loss remains constant.

(I don't know if loss does remain constant in these cells, but in lymphocytes, the loss of telomeres accelerates in elderly people, from about 30 to about 60 bp/year in people over 60. However, it's likely that reflects increased lymphocyte turnover in older people, not something intrinsic to the age per se.)

So bottom line, we're good for it.

More generally, keep in mind that the popular media have seized on telomeres as a simple answer for everything related to aging.  Obviously, that's not reality.  Telomeres certainly reflect aging; in some cases, perhaps many cases, they may be one influence on aging; but in most cases, telomere shortening is probably only a minor aging factor, and many other causes are more important.


How do plant cell divide without centrioles?

There are many different ways to make a spindle in plant cells:

  Mitotic spindles may be organized at centriolar centrosomes (only in final divisions of spermatogenesis), polar organizers (POs), plastid MTOCs, or nuclear envelope MTOCs (NE-MTOCs).

Of these, only the latter has been observed in angiosperms (flowering plants). For more info (and the source of the quote), see Brown & Lemmon, "The Pleiomorphic Plant MTOC: An Evolutionary Perspective"


To determine no beating cardiomyocytes from ECG or video recording

A number of cardiomyocytes is lost during an infarction. Instead, fibrous tissue forms, but it only preserves structural integrity, having no contractile function [1]. Myocardial infarction is an uncommon condition in pediatrics, happening very rare, when embolization occurs due to blood coagulation affections or heart congenital defects [2].

The fibrous tissue has different properties, thus modifying:

MDE-MRI images [3]
ECG: deep Q wave [4]
echocardiography: hypoechoic and hyperdense echoes inside the fibrotic material (the latter compatible with calcium) [5]

That video record is probably about 3D Echocardiography (look here at Video 2 and figure 2).

References:

Yao Sun, Myocardial repair/remodelling following infarction: roles of local factors
Nicola Carano et al., Acute Myocardial Infarction in a Child: Possible Pathogenic Role of Patent Foramen Ovale Associated With Heritable Thrombophilia
Harikrishna Tandri et al., Noninvasive detection of myocardial fibrosis in arrhythmogenic right ventricular cardiomyopathy using delayed-enhancement magnetic resonance imaging
ECGpedia - Pathologic Q Waves
Berenzstein CS et al., Usefulness of echocardiography and doppler echocardiography in endomyocardial fibrosis


What would cause bands to appear lower on a nonreduced SDS-PAGE gel?

The major effect of changing the redox environment of a protein is the formation or breakage of disulfide bonds. Under sufficiently reducing conditions no disulfide bridges will be present, while under oxidizing conditions your protein will form disulfide bridges if it has the ability to do so.

Disulfide bridges can significantly change the tertiary structure of a protein and change the behaviour of the protein on a gel that way. Generally, disulfide bridges should make the protein more compact and make it run faster on a gel.

It is therefore plausible that your faster band is the protein with disulfide bridges, which will appear to run like a smaller protein as it is more compact. The slower band then is the protein without disulfide bridges which can adopt a more extended conformation.

I'm assuming you're talking about native gels here, as denaturing gels usually contain DTT or beta-mercaptoethanol in the sample buffer to reduce any disulfide bonds and avoid this effect altogether.


Which hydrophobicity scales are best for detecting transmembrane regions, and why?

This has been studied by some of my labmates in Why is the biological hydrophobicity scale more accurate than earlier experimental hydrophobicity scales? I am not involved in their research, but here is the gist of the paper:

Different scales are, as you say, developed based on different criteria. In particular, Eisenberg scale is one of the consensus scales, that is hopefully at least as good as all of its components. It was believed that there were no big performance differences between scales. This could be why Uniprot doesn't specify their choice of scale: at the time, it didn't matter too much. A study in 2009 showed that the new UHS scale was actually better than others.

The results of the benchmark are that the differences are indeed not so big: roughly $\pm2\%$ in difference in prediction accuracy. The overall winner? Hessa, scoring $1.29\ \sigma$ over the average of the scales, but closely followed by UHS, PM1D and PM3D. Eisenberg performance, by the way, is average.

Final note: they found that a near optimal window size for all the scales was 21 with double the weight in the central third.


Is it plausible that eukaryotic organelles like flagella and cilia are the result of endosymbiosis with spirochetes?

Well, since all cells in a multi-cellular organism originally come from the same precursor cells, it’s hard to argue that some of them have endosymbiotic compartments that are missing in others, and notably their precursor.

Notably, there are species which possess both ciliary and rhabdomeric photoreceptor cells, and their precursor is non-ciliary. This is incompatible with Margulis’ endosymbiosis hypothesis.

PZ Myers has a good summary of the relevant papers [1, 2].

[1] D. Arendt, K Tessmar-Raible & al., Ciliary photoreceptors with a vertebrate-type opsin in an invertebrate brain, Science 306, 2004.
[2] D. Arendt, Evolution of eyes and photoreceptor cell types, Int J Dev Biol. 47, 2003.


Sure, flowers can be sign that the fruit is underway as @JonathanMoore said and viewing any trait as a result of selection is probably what the OP was waiting for. Thinking that if an organism produces a behaviour, then this behaviour must have been selected is wrong though.

The reality is that specific behaviours are affected by evolution of other behaviours and other traits as well as an by our environment (incl. social environment). It will be particularly difficult to hypothesize as for the different selection pressures that may have existed on a specific behaviour especially in animals with such high cognition as humans. Maybe we like flowers because we like colour contrast and maybe we like colour contrast because face with stronger colour contrast is more attractive because it is a sign of health. Maybe we like sunset because we like flowers. Maybe we like colour contrast because we like fresh fruits. Maybe, we like complex design because it makes us think about the possible complexity of shapes. Maybe we like complex shapes because we like to explore. Maybe we like simple design because we like clear skins. Maybe we like flowers because of the diversity of shapes. Maybe we like flowers because they are a sign of the end of the cold winter. Maybe we like flowers because we are being told that they are pretty things. Maybe we like flowers because it symbolizes abundance and reproduction. Anyone could formulate loads of hypotheses. Maybe we like flowers because we like any smell that is not the smell of something that is rotting. Maybe we like flowers because we like trees, leaves, mountains, rivers, lakes and pretty much anything else in our natural surrounding. Maybe we like flowers because flowers is a sign that there is not no pests in our garden or simply that the plant we are growing is healthy.


Is the amount of dNTPs rate limiting for very long PCR products?

200uM dNTPs in 50ul reaction mix could produce more than 10ug DNA if all dNTPs were consumed whatever the length of PCR products is. You could detect as low as 5ng DNA fragments by conventional electrophoresis using EtBr. You probably could see a clear band when you load more than 100ng of a DNA fragment. Therefore I am not worried much about the dNTP concentration.

The longer PCR products you amplify, the more difficult it is to amplify. Then you may not get enough efficiency to detect your PCR products. You might want to try lower annealing temp if you do not get any none-specific bands with/without some additives such as DMSO, betain, etc., or use more stronger enzymes. Also touch down PCR may be useful to get specific bands efficiently.

When you increase dNTP concentration, Mg++ effects may be muted because dNTP could chelate Mg++ as Chris mentioned in the comment column.


What are the differences between Trachinotus and Bramidae species?

Pomfrets comes from the order Perciformes (the largest order of fishes) and are part of the Bramidae family. They strictly live in marine environments, mainly the Atlantic, Indian, and Pacific Oceans. They have a dorsal fin extending over the length of the body in some and anterior dorsal fin spines unbranched.

http://www.fishbase.org/summary/FamilySummary.php?ID=319

Pompano comes also comes from the order Perciforme and are part of the Carangdide family which includes jacks, mackerels, scads, and runners. Most are fast-swimming predatory fish that hunt in the waters above reefs and in the open ocean. They also mainly live in marine environments such as the Atlantic, Indian, and Pacific Oceans, and are rarely found in brackish waters. Their body is generally compressed, although body shape extremely variable from very deep to fusiform.

Quote about Pompanos from Fishbase.org:

  Most species with only small cycloid scales. Scales along lateral line often modified into spiny scutes. Detached finlets, as many as nine, sometimes found behind dorsal and anal fins. Large juveniles and adults with 2 dorsal fins. Anterior dorsal fin with 3-9 spines; the second having 1 spine and usually 18-37 soft rays. Anal spines usually 3, the first 2 separate from the rest; soft rays usually 15-31. Widely forked caudal fin. Caudal peduncle slender. Pelvic fins lacking in Parona signata. Vertebrae 24-27 (modally 24).

Unfortunately, I can only post one link due to my rep, but it fairly easy to search fishbase.org for information on both species.


Disclaimer: there is a very large amount of literature on the subject and I am in no way expert enough to properly review it here.

In any case, here's a few papers that review the issue and may serve as a basis to look up other references

Evolution of consciousness: phylogeny, ontogeny, and emergence from general anesthesia - Mashour and Alkire, PNAS 2013

  We propose that the stepwise emergence from general anesthesia can serve as a reproducible model to study the evolution of consciousness across various species and use current data from anesthesiology to shed light on the phylogeny of consciousness. Ultimately, we conclude that the neurobiological structure of the vertebrate central nervous system is evolutionarily ancient and highly conserved across species and that the basic neurophysiologic mechanisms supporting consciousness in humans are found at the earliest points of vertebrate brain evolution.
  [...]
  The distinction between phenomenal and access consciousness was noted, but phenomenal consciousness itself reflects the dissociable neurobiologica processes of awareness and arousal. Awareness refers to the content of consciousness (red apple vs. blue sky), whereas arousal refers to brain activation and level-of-consciousness (alert vs. drowsy vs. asleep vs. anesthetized). A number of current theories about consciousness propose that the cortex is the primary site containing the neural correlates of awareness, whereas midline subcortical brain structures provide ascending arousal influences to the cortex

This is also reviewed in this paper:

Subjective experience is probably not limited to humans: the evidence from neurobiology and behavior. - Baars, Conscious Cogn., 2005

  Thus consciousness is not a metaphysical absolute, but a scientific construct like any other. In humans, the standard behavioral index of conscious cognition is accurate or verifiable report. It has been used scientifically since the beginning of psychophysics in the 1820s. Accurate report is highly reliable, but of course it is subject to limitations like any other empirical measure (Baars, 1988).
  [...]
  In humans the thalamus and cortex are crucial for supporting the contents of consciousness (Edelman & Tononi, 2000). Thalamus is often considered to be an extension of cortex, an added sandwich of interacting layers that controls most traffic to and from cortex. Local damage to cortical sensory regions, like the fusiform gyrus for face perception, results in a loss of conscious knowledge about faces but not about other visual features like color, location, or size. If the intralaminar nuclei of the thalamus are lesioned bilaterally, the conscious state is lost. By comparison, large lesions to cerebellum, basal ganglia, and spinal cord do not impair either conscious contents or state. Cerebellar damage can cause paralysis but not loss of consciousness. Lesion evidence on these points is supported by stimulation experiments using electrodes, transcranial magnetic stimulation (TMS), and microdialysis. It is also reflected in functional brain imaging. The evidence is therefore very strong that the T-C system supports consciousness. That is why many neuroscientists consider the T-C system to be the “seat” of conscious experience, and have done so for at least a century.

Again, citing from the first paper:

  The recent experiments with general anesthesia in humans suggest that phylogenetically ancient structures in the brainstem and diencephalon—with only limited neocortical involvement—are sufficient to support primitive consciousness. Where, then, does consciousness arise on the evolutionary timeline? One might be tempted to conclude that consciousness commenced as our mammalian ancestors evolved just beyond reptiles and their predominantly subcortical brains. However, paleontological findings suggest that the synapsid line that gave rise to mammals and the sauropsid line that gave rise to reptiles and birds both diverged from the primitive anapsid line at a single point ~315 million years ago. Furthermore, there is significant evidence that avian species are capable of higher cognition and even consciousness itself. For example, birds demonstrate evidence of explicit episodic recall (i.e., conscious memory of an event) and theory of mind (i.e., attribution of subjective mental events to another being). Thus, it would be misguided to try to identify a single point at which consciousness emerged because evidence suggests that consciousness evolved along two independent lineages.


What is the difference between sieve cells and sieve-tube elements?

All plants have sieve cells, but not all plants have sieve tube elements because they evolved after the plant family tree had started to branch. Only angiosperms have sieve tube elements.

Sieve tube elements are more specialized for their job as transport cells, and can transport more nutrients faster than sieve cells. During their development, the meristem cell divides into two cells: the sieve tube element and the companion cell. The sieve tube element loses its nucleus, vacuoles, and ribosomes when it matures in order to make it easier for its cytoplasm to flow, and so it relies on its companion cell for proteins and carbohydrates. The porous plates between sieve tube elements provide little resistance to water and nutrient flow, and so flow through the sieve tube is more rapid than it would be if there were cell membranes or small pores for it to pass through. The sieve tube elements are wide to make wide tubes, which provide less resistance to fluid flow.

Sieve cells evolved before sieve tube elements, and are a bit less specialized for their job. They still have all their organelles, and are long and thin. Some plants, such as seedless plants and gymnosperms, don't have any sieve tube elements and rely solely on sieve cells for nutrient transport.

References:
Organelles present in sieve tubes
https://en.wikipedia.org/wiki/Sieve_tube_element


Is glutamate always involved in the deamination and amination of the other amino acids?

For most amino acids, the removal of the α-amino group involves α-ketoglutarate and glutamate. The amino group is first transferred to a-ketoglutarate by transaminases, and the resulting glutamate is then deaminated (via glutamate dehydrogenase) to yield ammonia.

The same is true for amination. Glutamate and glutamine are the two major amino group-donors. Most ketoacids are converted to their respective amino acids by transamination involving glutamate or glutamine. Glutamine can be synthesized by amination of glutamate with ammonia without transamination (via a synthetase enzyme) and glutamate can be aminated with ammonia too.

Exceptions do exist, of course. For example, Not all transaminations involve glutamate/glutamine (as this user has replied), and serine and threonine can be directly deaminated (via dehydratase enzymes, as opposed to the dehydrogenase used for glutamate).


How mosquitoes get their food and survive?

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

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


Is Sanger sequencing still used in labs, and therefore worth learning?

Sanger sequencing is still used in the labs today - and not only on the side. Next-generation sequencing has its strength when it comes to sequencing very large amounts of DNA (basically whole genomes or exomes).

Sanger sequencing is used when you want to sequence smaller regions or portions of a genome/plasmid. Typical read length is (depeding on the machine and the skills of the operator) 600-900bp. This is enough to verify site directed mutagenesis, the presence of inserts you cloned as well that they are correct (if the insert is longer you will typically nest the single sequence reactions to cover the whole sequence) or look for a polymorphism. There are endless possibilities.

Additionally it is relatively cheap to sequence single samples (which is not really working on the next-gen machines), one sample comes between 8 and 10$ (at least the last time I sent this out). And you don't even have to do it yourself as there are a lot of service providers available. The technique itself is not hard to learn either.


Do we know if RHEB is more sensitive to some amino acids than other amino acids?

RHEB does not sense amino acids. See the abstract of this paper.

  Activation of this pathway requires inhibition of the tumor suppressor
  complex TSC1/2. TSC2 is a GTPase-activating protein for the small
  GTPase Ras homologue enriched in brain (Rheb), GTP loading of which
  activates mTOR by a yet unidentified mechanism. The level at which
  this pathway senses the availability of amino acids is unknown but is
  suggested to be at the level of TSC2. Here, we show that amino-acid
  depletion completely blocks insulin- and TPA-induced Rheb activation.
  This indicates that amino-acid sensing occurs upstream of Rheb.
  Despite this, amino-acid depletion can still inhibit mTOR/S6 kinase
  signaling in TSC2-/- fibroblasts. Since under these conditions
  Rheb-GTP levels remain high, a second level of amino-acid sensing
  exists, affecting mTOR activity in a Rheb-independent fashion.

RHEB also doesn't have any amino-acid binding (or any small molecule binding) domain.


It looks like a species of Megachilidae family of bees, solitary and leaf eaters, covered in pollens.
It could be from Genus Megachile.
All its identifying features are hidden though:

T1 segments have 2 “sides”, one that faces forward or faces the thorax and one that faces the top.$^1$
In Megachile, the “corner” where the forward side and the top side meet is severe. It creates a flat or concave appearance like a circular shelf.$^2$

This genus it comparable to Lithurgopsis which

has a more gradual transition to the "sides" of T1.$^3$

(Source: bugnet)


What are the most important differences between HSP70 and HSP90?

Hsp70 and Hsp90 are not single proteins, but entire protein families. And those two protein families are not the only ones of their kind. There are different groups of heat shock proteins, Hsp70 and Hsp90 are molecular chaperones that assist in protein folding. There are five major families of molecular chaperones: Hsp100, Hsp90, Hsp70, Hsp60 and Hsps.

Hsp70 binds to nonnative, unstructured segments of proteins and helps folding them. Hsp90 doesn't bind to unfolded proteins, but to native-like proteins. Some substrates are also handed over to Hsp90 by Hsp70.

The whole area of chaperones and heat shock response is a very, very large and interesting field. I recommend to you to read the reviews below.

Vabulas, R. M., Raychaudhuri, S., Hayer-Hartl, M. & Hartl, F. U. Protein folding in the cytoplasm and the heat shock response. Cold Spring Harb Perspect Biol 2, (2010).
Richter, K., Haslbeck, M. & Buchner, J. The heat shock response: life on the verge of death. Mol. Cell 40, 253-266 (2010).


Antibody production in secondary immune response

1)  The secondary response requires CD4+ T cells to activate memory B cells.  That first paper actually gives some evidence that some of the rapidity could arise because T cells and memory B cells are in very close proximity to each other in germinal centers.

2) Yes.  The affinity of antibodies increases during the initial infection, both through isotype switching and affinity maturation, producing far superior antibodies.  Upon reactivation, memory B cells can undergo further somatic hupermutation.


Why there are no plants that offer salt fruits as opposed to sweet fruits?

Soil salinity and sodicity cause severe problems in agriculture worldwide, and salt tolerance in crops is an extremely important trait and a major focus of research. Detrimental effects of high salinity on crops are multifaceted and affect plants in several ways: drought stress, ion toxicity, nutritional disorders, oxidative stress, alteration of metabolic processes, membrane disorganization and reduction of cell division and expansion (Hasegawa et al. 2000; Munns 2002; Muscolo et al. 2007, 2013; Zhu 2007; Sidari et al. 2008). As a result, plant growth, development and survival are reduced (Muscolo et al. 2011; Schleiff and Muscolo 2011). Two major stresses affecting plants under salinity are osmotic and ionic stresses. Osmotic stress, occurring immediately in the root medium on exposure to salts, can result in inhibition of water uptake, cell expansion and lateral bud development (Munns and Tester 2008). Ionic stress develops when toxic ions (e.g. Na+) accumulate in cells causing increase in leaf mortality, chlorosis, necrosis and decrease in the activity of cellular metabolism including photosynthesis (Yeo and Flowers 1986; Glenn and Brown 1999). In fact, excess Na+ and Cl− have the potential to affect plant enzymes, resulting in reduced energy production and other physiological processes (Larcher 1980; Morais et al. 2012a,b). Ionic stress results in premature senescence of older leaves and in toxicity symptoms (chlorosis, necrosis) in mature leaves due to high Na+ and Cl− which affect plants by disrupting protein synthesis and by interfering with enzyme activity (Munns and Termaat 1986; Hasegawa et al. 2000; Munns 2002).

Source: Effect of saline water on seed germination and early seedling growth of the halophyte quinoa

Salt is really good at inhibiting enzymes and biochemistry, which translates into not being great for seeds. So to have a fruit that has a high concentration of salt is really risky and not likely to be successful. Sugars on the other hand attract a multitude of other organism that would help move seeds around or create an ideal growth environment. To have crops that are resilient to salt would be useful but would require a lot of wasted energy to maintain osmoregulation. So it's not so much that animals wouldn't eat a salty fruit but more that it would be harmful to the seeds.


Repair wrong DNA pair after ending replication?

DNA mismatches and indels can be repaired after replication through an aptly named mechanism called DNA mismatch repair.

I'll briefly describe the mechanism in Escherichia coli, but it's similar in other organisms. A protein called MutS scans DNA for lesions caused by mismatched nucleotides incorporated during replication that escaped DNA polymerase proofreading. These are detected by the kink they produce in the DNA backbone. MutS recruits MutL and MutH; the former activates the latter, which is an endonuclease. MutH cuts the DNA backbone near the lesion in the newly synthesized strand (the one containing the misincorporated nucleotide). This strand can be identified because it has not yet been methylated, while the parent strand contains the original methylation. After cleavage, UvrD helicase unwinds the strand and an exonuclease digests it. The gap around the former lesion can then be filled by DNA polymerase III and DNA ligase.

[ image adapted from ]

Here's an interesting review in a Nature publication that discusses it in more depth, as well as the mechanism in humans:
Guo-Min L. 2008. Mechanisms and functions of DNA mismatch repair. Cell Res 18:85-98


Why is the heart not in the middle of the body?

First of all, let me make it clear that the heart is at the vertical centre of the body -- it is not shifted towards left (or right). However, it is slightly tilted towards the left in most cases.

In some cases, it is tilted towards the right, and the condition is called Dextrocardia. For why it is so, lets look at what the heart does. Below is a diagram of double circulation (from here).

As you see, the highest pressure needs to be generated for pumping oxygenated blood into the body. Thus, the left ventricle needs the thickest muscles for this purpose. And due to these extra muscles, the  heart appears extended and seems shifted towards left.

Coming to the evolutionary perspective, it is important to mention that humans are not the only organisms with this feature. Indeed, displacement of the heart towards the left is a conserved feature in all vertebrates (Fishman et al, 1997). See this answer for more information.

Coming to genes, bending of the heart towards one side is actually controlled by the NODAL gene during development. See this diagram (from Jensen et al, 2013):

Tilting occurs in two phases, one during the first four and a half months of intrauterine life and the other, which is actually a 45° rotation to the median plane, later. During the early development of the heart, a process called cardiac looping happens and the straight heart tube develops a bend (see diagram). The NODAL gene, along with the Lefty1 and Lefty2 genes, regulates the speed and direction of cardiomyocyte movement during the development of the heart, leading to this asymmetry. To confirm it, researchers knocked out the spaw/nodal gene from a zebrafish and found randomized development of heart, even symmetric heart, as the result(!) (see Walmsley, 1958 and Rohr et al, 2008).

Now, talking about why this happened in the first place, and why it is so conserved among vertebrates, we need to ask ourselves a basic question: what good would a symmetrical heart be? External symmetry is preferred (probably) because it helps in locomotion; it would be quite difficult to move with your two legs placed away from your center of gravity. But when we talk about internal symmetry, conditions drastically change. We get a major restrictive factor here: space. And limited space always dominates other factors. Seeing that the structure of the heart is necessarily pointed towards one side, it becomes difficult to make it symmetrical. (The only option IMO is to have another pointed end at the right side.) In this case again, what advantage would a symmetrical heart provide? None. And it might even be harmful since having an even bigger heart would mean making both lungs smaller. Thus, a symmetrical heart would only prove to be a liability rather than an asset. See this question for more information.


That looks like a type of "robber fly" — compare with this image:

BugGuide is a great resource for identification of insects, spiders and their ilk.


This is an interesting question, and there are a number hypotheses available to explain this phenomenon. The short answer (as far as I can say after my literature search) is that we don't know the answer for sure. The long version follows below.

The main problem with all these hypotheses is that though they may have a valid point, a definitive hypothesis hasn't been demonstrated yet. All these hypotheses are listed in the first reference, with a ton of additional references in the paper. I will summarize the different hypotheses only briefly here; for details please read the paper. The second reference is also interesting.

The point when this process started was after the last common ancestor of chimpanzee and humans when our two lines diverged. Chimpanzees are our closest relatives and still have hair coats, so this process must have started afterwards. Analyses of MC1R mutations (which affect pigmentation) suggest that human have been hairless for at least 1.2 million years. See reference 3 for details on this.

Aquatic ape hypothesis (also known as aquatic ape theory): This hypothesis states that modern humans spent some time semi-aquatic. In this lifestyle fur does not insulate very well and this led to an evolutionary disadvantage.

Cooling hypothesis: This hypothesis states that the modern humans lost their hair when they left the forests and started to live on the savannah. There they got too warm with their fur and finally lost it. This hypothesis sounds logical at first thought, but has a few problems. Naked humans have two problems: during the day they collect quite some heat via their skin, which requires them to have a cooling system (we sweat to cool us), and during cold nights we need a lot of internal energy to keep our temperature stable. Insulation however works both ways (not only keeps the warmth in, but also can keep heat out), and indeed some savannah monkeys have denser fur than their relatives in the forest. The cooling system will also lead to water loss and potential dehydration.

Hunting hypothesis: This hypothesis states that humans started becoming carnivores and therefore had the need to run for extended periods of time to hunt for meat. This leads to thermal overload; without a fur they can release this heat much faster to avoid overheating.

Bipedality hypothesis: This hypothesis assumes that modern humans, walking on two feet, have a lower direct influx of solar radiation. This lowers the chance for overheating.

Allometry hypothesis: Allometry states that species which get bigger during evolution, do not have all their organs getting bigger at the same rate. The hypothesis states that humans got bigger, the number of hairs stayed the same, and finally got lost.

Clothing hypothesis: One of the more illogical hypotheses, this assumes that hair loss wasn't critical for humans as they managed to make themselves clothes.

Vestiary hypothesis: A mix of the cooling and the clothing hypothesis: Here it is assumed that hair loss is beneficial due to more cooling and that the negative effects of too much loss of heat were counteracted by the invention of artificial insulation.

Neoteny hypothesis: Neoteny denotes the retention of of juvenile physical characteristics in adults. Humans are characterized as retarded in development (compared to the apes) and mature more slowly. Additionally, it is assumed that some characteristics (here loss of hair) of juvenile or fetal apes are maintained.

Carrion-eating hypothesis: Another strange hypothesis, this assumes that man as a messy eater (like vultures and condors, which have naked necks) have an advantage of being hairless.

Sex-related hypothesis: This hypothesis assumes that hairless skin is more sensitive to stimuli like touch, temperature and pain. This would allow more sensitive social contacts, especially between man and woman, but also between woman and child. Pubic hair is not explained by this hypothesis.

Adaptation-against-ectoparasites hypothesis: Here it is assumed that naked humans are less prone to harbour ticks, fleas and other parasites which hide and live within fur. Apes have great social rituals of removing these within their group.

References:

Evolution of nakedness in Homo sapiens
The Hairless Mutation Hypothesis Explains Not Only the Origin of
Humanization from the Human/Ape Common Ancestor but also Immature
Baby Delivery
Genetic variation at the MC1R locus and the time since loss of human
body hair.


Needleman Algorithm for Optimal Alignment of two Amino Acid Sequences

Needleman-Wunsch does an end-to-end (global) alignment (BLAST uses Smith-Waterman). Needle from the EMBOSS toolkit performs Needleman-Wunsch alignment. It will report the highest scoring alignment. I am not sure which alignment it reports when there are two of them with equal scores (I don't think it is random).

I just tried your case: replaced B with W as the former does not denote any specific amino acid (it is ambiguous). It does give:

     1 ----------AW-DE      4
                 || ||
     1 AAAAAAAAAAAWCDE     15

Note that you can change this behaviour by altering the gap-open and gap-extend penalties. You can also change the end-gap penalties (gaps in the beginning or end of the alignment; not in the middle) in Needle.

In this case gap-open=10, gap-extend=0.5, end gap penalty=false and matrix=BLOSUM62

For performing a local alignment you can use Smith-Waterman. It just aligns the highest scoring region and does not do an end-to-end alignment. You can change gap-open and gap-extend penalties in Smith-Wateman and BLAST too, but these algorithms do not begin or end an alignment with a gap.

This is the output of Smith-Waterman with gap-open=1 and gap-extend=0.5 and BLOSUM62 as scoring matrix.

     1  AW-D  3
        || |
    11  AWCD 14

For more information see What is the difference between local and global sequence alignments?


Does a reproductively successful male have the same genetics as a reproductively successful female?

Evolutionarily, using humans as an example, it would make sense that a successful female would produce successful male offspring. If a successful female produced male offspring that weren't successful, the female also wouldn't be successful by definition and would, through evolution, stop being desired by males. Therefore, females are selected for by their ability to produce successful males and thus successful male genes must be the same as successful female genes?

That assumption is wrong. Of course the best thing for an individual's reproductive success is to have as many successful offspring as possible regardless of gender, but in the real world there are sometimes tradeoffs. If an individual had a trait that made, say, their female offspring a lot more successful but mildly impaired their male's offspring's success, the advantage to the female offspring might outweigh the disadvantage to the male and the trait might get passed on, even though it produced male offspring that weren't very successful.

Here is a paper apparently exploring the concept in seed beetles:
http://rspb.royalsocietypublishing.org/content/early/2009/12/21/rspb.2009.2026

  However, I've heard that in humans today, males don't like rich females while females like rich males.

You've heard that of humans, have you? Are you sure what you heard actually applied to all humans, and not the humans in one specific society? You say "humans today", do you mean "anatomically modern humans" or "people in the 21th century"?

You really ought to investigate this kind of thing you hear before drawing all-encompassing conclusions about biology or evolution from them. Maybe you were assuming that "in humans, males don't like rich females while females like rich males" was consensus biology; if so, well, it isn't. And given that it isn't, we can't answer your questions based on such a vague claim; you should give a source that explains more precisely what exactly is being said there.

  Also, from what I've read, lascivious females used to be looked down upon in the past while lascivious males weren't.

Same thing; I'll also highlight the "in the past" when your previous sentence talked about "today". Evolution works on the scales of hundreds and thousands of generations. Why would you assume evolutionary explanations for social trends that, by your own words apparently, have changed recently?

  This suggests that successful males are genetically different than successful females?

In order for those things suggest that, you would need: 1) to establish reliably that the differences you talked about exist, 2) to establish that they have a probable biological basis; one way of establishing this could be to show that they are universal across human cultures, geography and history. If they aren't then it's more likely the explanation is cultural than biological, and 3) to establish that the biological difference is related to individuals being successful, as opposed to being random variation (which happens a lot in evolution).


What are the coverings of femoral hernia?

Femoral hernia coverings (from inside out):

Peritoneum
Femoral septum (extraperitoneal fatty, connective and lymphoid tissue)
Tranversalis fascia
Cribriform fascia
Superficial fascia
Skin

Image source: SurgWiki, Creative Commons Licence

Sources:

SurgWiki: Hernias
SlideShare: Femoral hernia, p. 12
EarthsLab: Femoral canal
Textbook of Anatomy Abdomen and Lower Limb;, Volume 2, By Vishram Singh, p.45


How is the rate of transcription influenced by temperature?

If your looking at transcription then your talking about RNA POLYMERASE.

And there are many variants. Here's a good Nature paper that discusses temperature and RNA Pol

http://www.nature.com/ncomms/journal/v1/n6/full/ncomms1076.html

And another:

http://www.ncbi.nlm.nih.gov/m/pubmed/12729734/

I couldn't get full access to this JBC paper but I think the answer would be clearly in here, prob worth a look

M. Chamberlin and J. Ring. Characterization of T7-specific ribonucleic acid polymerase. 1. General properties of the enzymatic reaction and the template specificity of the enzyme. J Biol Chem. 248: 2235-44 (1973)


agglutination test using blood of the donor and the recipient

Disregarding Rh factor for a moment: when you add A-antibodies to a blood sample and agglutination occurs, this means the blood contained A-antigens (A-type). The same can be said for a sample of blood to which B-antibodies are added (B-type). If agglutination for both antibodies occurs in separate assays on the same sample of blood, it means the sample contains both A and B antigens (AB-type). If the sample is said to be O-type, this means neither A or B antigen would be present in these cells. It's safe to transfuse O-type blood into any recipient due to this fact. What you also want to watch out for, is attack on the recipients RBC's by antibodies in the donor's plasma. This can result in a hemolytic transfusion reaction (HTR), but it's noted in the following text:

  Red blood cell incompatibility may also occur when the patient's RBC antigens are attacked by antibodies from the donor's plasma. This tends to be a minor problem because of the small amount of antibody present in the donated plasma, which is further diluted on transfusion into the recipient's circulation.

If you're in the lab doing a Coombs test, for example, you're checking to see if there are any extraneous antigens present that might results in a HTR. In a normal result, ergo there aren't any antibodies to RBC's in the sample mixture, you wont see any agglutination. This is for considerations outside of ABO antibodies, generally. If you're adding to B-type RBC's a plasma with known antibodies to B antigen, like O-type plasma, you can probably expect an event. To my knowledge, O-type plasma wouldn't be safe to give to anyone but an O-type recipient.

additional source


HELP! How will pH 14 affect enzyme structure?

This is a very chemical explanation. Here goes.

$\ce{pH = -log[H+]}$

$\ce{pOH = -log[OH-]}$

$\ce{pH + pOH = 14}$

Therefore, at a $\ce{pH}$ of $14$, $\ce{pOH}$ is zero, so there is 1 mole of $\ce{OH-}$ and $10^{-14}$ moles of $\ce{H+}$ in a liter of your substance.


Is there an optimal composition and length for protein linkers in FRET?

I am also about to undertake some FRET studies (this week in fact). FRET linkers are a thing of tinkering, unfortunately. Förster resonance energy transfer, or FRET, is a phenomena that decays with $ 1/{r^6} $, the radius between the donor and acceptor. When constructing FRET reporters, there are a few things to keep in mind:

Length of linker. The length of the linker (including any cleavage sites), follows an concave optimization curve. A linker too long (> 18 amino acids) or too short (< 5 amino acids) and the FRET signal rapidly diminishes. When considering a FRET reporter in which no cleavage site is introduced, I've seen reporter an optimal linker length of 7-8 amino acids. When including a cleavage site, I've seen optimal liker lengths reporter of 18 amino acids. TO my knowledge, there is no theoretical way to predict the FRET efficiency based on linker sequence, and from scientists I've talked to, they conduct a trial-and-error approach using purified protein products to screen for an optimal length if it appears necessary to do so.
Type of FRET reporter. Cleavable FRET reporters fall into two classes. Positive reporters, in which signal appears after cleavage, must use longer linkers to separate fluorophores enough to reduce the FRET phenomenon. Negative reporter, in which FRET signal is lost after cleavage, must necessarily employ both short cleavage sites and linkers, to maximize the FRET phenomenon prior to cleavage. Since you mention the cleavage site itself is 15-18 AA, I would certainly expect very little FRET when uncleaved, assuming that the linker and cleavage site are unstructured, as the distance between the two fluorophores is quite large for the FRET phenomenon. Alternatively, intramolecular FRET reporters are usually designed as positive FRET controls, using short linkers to maximize the FRET phenomenon. When tagging two proteins seperately for FRET, short linkers are also chosen, relying on some external interaction to bring them together, however, this requires a lot of optimization of linker length for both fluorophores for maximum efficiency.
Choice of linker amino acids. This part here is somewhat subjective. The choice I often see in the literature are the tiny and small amino acids (especially Ser, Ala and Gly). The choice of these is mostly because they will likely have the least interaction among the linker structure and adjoining proteins and will be the most flexible. The linker should be chosen to avoid use of putative sites for modification (e.g., phosphorylation, glycosylation), rigid geometry (Pro, or bulky aromatics) and excessive charged amino acids.

I should note that I have found no comprehensive review of these three parameters for FRET construct design, and I have gleaned them from the literature. In my opinion, linker length is more critical to optimize than its amino acid sequence, provided that the linker does not lend itself to stable/rigid geometry and modification.

I would also suggest seeing if FRET constructs have been made using your cleavage site of interest already, and perhaps use the same linking sequences. From this, you could construct a slightly shorter and longer construct to see if one is more optimal over the other.


Species identification - What is this "bug"

After conducting a small investigation, it would appear most likely that the spider captured in the attached photograph is an arachnid in the family 'Thomsidae' or 'Crab Spiders'.

Although the proposed genus of Araniella proposed above by user137 shares a superficial similarity to this family, thomsids generally do not construct webs to ensnare prey - I might hazard that the web on your car does not hold the same structure, as shown below, to that of an Orb Weaver Spider (Araniella).

From the available information it is challenging to propose a genus, let alone a species. Based on the location of the car, I may propose the sub-family Misumenoides or genus Thomisus.

The general characteristics of crab spiders are the ambush of prey as opposed to trapping prey; the inverted V-shape under the cephalothorax; and the sideways movement of certain species in the Thomsidae family. It is of interest to note that any member in the population could vary appreciably in colour.

Wikipedia article concerning Crab Spiders available from: https://en.wikipedia.org/wiki/Thomisidae
Britannica regarding Crab Spiders available from: https://www.britannica.com/animal/crab-spider
Information regarding Misumenoides is available from: https://en.wikipedia.org/wiki/Misumenoides


What is this black insect (wasp-like?) South America?

Actually I took photoshop to help me find this little guy, Ensign Wasp(Evaniidae)

Google Images:

My Photoshop research:


How should you choose from the various methods of constrained ordination?

You might want to check out Mike Palmer's webpage on ordination, specifically the constrained ordination section: http://ordination.okstate.edu/

The main difference between constrained ordination techniques is the distances that are preserved. Redundancy analysis (RDA) preserves Euclidean distances, so in order to use it, you need to transform your OTU table with an appropriate transformation (e.g., Hellinger), after which a Euclidean distance calculation is appropriate. It also works best identifying linear relationships between environmental variables and species responses. Canonical correspondence analysis (CCA) preserves the chi-squared distance, which tends to emphasize common taxa, and looks for unimodal responses to environmental gradients. Distance-based redundancy analysis (dbRDA) accepts any distance matrix, allowing you to use non-metric distances, and then looks for linear relationships with distances and environmental variables.

Before applying these metrics, you'll need to understand their advantages and limitations, and then you'll need to make a decision about which combination of constrained ordination techniques and distance metrics are best for answering your questions. This is something you'll need to justify yourself, based on your own question, because different approaches are better at emphasizing different aspects of your data. I strongly suggest you study a copy of Legendre and Legendre (2012) for more information about these methods.


How deep underwater could you breathe using a tube which breaks the surface until the water pressure makes it impossible to inhale air?

First, a sanity check.  Snorkeling isn't generally done at much depth, and this question reflects some subjective sense of that.
My guess (after much confusion) is the table they're providing is apparently the pressures that the subjects were able to apply, when striving to breathe in or out at various levels of "Lung Volume".  But what is "Lung Volume"?  Not Total Lung Capacity - is it Tidal Volume, Expiratory Reserve Capacity, something else?
If I read it that the person, at 22-54% "Lung Volume", can apply only 53 cm H2O of pressure differential while inhaling, that implies that at this depth of external pressure, they can't inhale.  (Oddly, if they lose the battle and go to 1%, the data says their ability to inhale is reduced!) In theory the fluid pressure of water or air on the body should be similarly positioned.
Even so, there are two things that make me doubt this.  First, the inability to inhale should be coupled with a greater ability to exhale.  So I still wonder if sort of shallow breathing might still be possible at the limit of the expiratory reserve, or even in the range of "residual volume", as the external pressure is opposed by connective tissue.  Second, the diaphragm and the external intercostal muscles are, well, muscles, so it should be possible that someone could train those muscles well and resist more pressure.


Note: Since my area of expertise is with peptide hormones, I will offer a partial answer.

Steroid hormones are carried through the circulation by binding to globular proteins. When these hormones are released from binding proteins, the classical route of action is by free diffusion through the cell membrane. This diffusion is due to their aromatic structure. You rightly point out that the classical receptors of these hormones are found in the cytoplasm or nucleus. For example, estrogen signalling as a classic signalling template which has genomic (DNA) and non-genomic (protein) targets to exert its effects.

Non-canonical signalling can occur through at least one G-protein coupled receptor (GPCR). Unlike most GPCR's which are localized to the cell membrane, GPR30 appears to be localized to the endoplasmic reticulum, which means steroid signalling still occurs through canonical means and also this newer pathway.

Then again, there are also steroid effects that modulate ion channels, for example GABA receptors. These are not specific receptors where only a steroid hormone can have an effect, yet they can activate or inhibit the effects (along with other drugs).


Can you detect if a mutation is spontaneous or induced?

Here's a quick answer; hopefully someone will give a more complete one.  But meanwhile you've got something.

Some genotoxic agents have predictable results.  For example, they cause Gs to substitute for Cs, or they cause mutations at specific spots on the genome.  So if you had a bunch of mutations in a single cell (or collection of related cells) that matched the modus operandus of a known genotoxic agent, then it would be reasonable to conclude that the mutations were induced.  But not all genotoxic agents are like that.  And if you only have 1 or 2 mutations, that's not enough to prove they were induced.  Also, of course, it depends on your sample size and your controls.


GnRH is found in very low concentrations (2-10 pg/mL)

Options:

  A highly sensitive analytical method (e.g. radioimmunoassay)
  To sample directly from the hypophyseal-portal system
  A surrogate measure

This abstract: http://www.ncbi.nlm.nih.gov/pubmed/9749566 describes direct measurement.
Direct sampling could only be done under general anaesthesia and in a short window, so I'd avoid that altogether unless you're talking about using an animal model and can surgically impact a cannula.
This abstract: http://www.ncbi.nlm.nih.gov/pubmed/21646369 describes use of the $\alpha$-subunit as a surrogate of GnRH (the $\alpha$-subunit is the same for FSH, LH, and TSH and is released under the control of GnRH).

By the way, GnRH does not promote secretion of hCG so much as it does LH and FSH (LH is fairly homologous to hCG).  For the most part hCG is secreted by trophoblasts (in the placenta) and is quite low except in pregnancy or the presence of certain germ cell tumors, so wouldn't be worth measuring in non-pregnant women or males anyway.

The bigger point is why do you want to measure GnRH pulsatility?  This has been done and the you know that it is pulsatile is because it has been done.


Why are the walls of the bronchioles folded?

Those foldings are called as mucosal folds, formed by the contraction of smooth muscles , are also present in trachea, and in many other organs such as gallbladder etc.

Physiologically: This folding causes an increase in area for better action of mucus which protects the body from entry of dirt, pathogens and loosing the moisture.

Anaomically: as @Bryan pointed out that the folding permits the  contraction and relaxation of smooth muscles around the bronchioles.

Source 1

Source 2


What kind of Brazilian Arthropoda is this?

I was fooled by the red marks in its back, that made me believe they were each pair of marks in a segment. Looks like they're distributed in one pair of red marks for each 2 segments. Maybe that's a mimic of some similar Diplopoda (which usually have such colored marks, see for instance Rudiloria)?

Looks like it's some species of Scutigera or some related group.


Pectoralis muscles as push muscles vs pull muscles

The pectoralis major is not just an adductor and medial rotator of the arm. Its clavicular fibres also flex the arm at the glenohumeral joint. This is the action useful in performing push-ups and bench presses.
And yes, its adductor action also plays a role in pull-ups and climbing (along with that of the latissimus dorsi, another adductor).

References and further reading:

https://www.kenhub.com/en/library/anatomy/major-pectoralis-muscle

https://www.kenhub.com/en/library/anatomy/the-shoulder-joint

Romanes GJ. Cunningham's manual of practical anatomy. 15th ed. Vol 1, Upper and lower limbs. Oxford: Oxford University Press; 1986. (ELBS edition, 1989 reprint). 263 p.


This small hexapod appears to be a species of Springtail (or Collembola).  It is similar to the one below, with slightly different markings.

From the University of Florida:

  Springtails are minute insects without wings in the Order Collembola. They occur in large numbers in moist soil and can be found in homes with high humidity, organic debris, or mold. Homeowners sometimes discover these insects occurring in large numbers in swimming pools, potted plants, or in moist soil and mulch. They feed on fungi, fungal spores, and decaying, damp vegetation, causing organic material and other nutrients to return to the soil; these nutrients are later used by plants. Occasionally, springtails attack young seedlings and may damage the roots and stems.

More information can also be found at NC State University Entomology Website:
http://www.cals.ncsu.edu/course/ent425/library/compendium/collembola.html

It is hard to say what species it could be, but it looks most similar to:

Isotomurus plumosus:

or Isotomurus tricolour from Rick Cowen:

It is hard to tell but it seems to be part of this genera, or is at least in the family Isotomidae, if not the exact species.

Their taxonomy is actually under debate, and they are in a group of hexapods that are no longer considered insects.


What is the difference between spidroin-1 and spidroin-2?

I've looked into literature on this. Wow, there is a lot of research on this. Here's a quick summary:

Functionally they are very similar. Both are fibrous proteins. Together they constitute spider silk. Sp-1 and Sp-2 are two different genes, often present in multiple copies in the genome, depending on which spider species you consider. They differ in amino acid content and are post-translationally modified differently. Sp-2, for instance, is heavily modified. There also exist different transcriptional isoforms of these proteins. It seems quite complex.

There are also different types of silk. You may be referring to major ampullate silk, which is only one of six different types of silk fibres spun by the spiders of the genus Nephila. Only this one contains major ampullate spidroin-1 (MaSp1) and major ampullate spidroin-2 (MaSp2).

Excerpt from one paper on the subject, which lists some differences:

  MaSp1 and MaSp2 are large proteins of about 250 to 350 kDa that share
  a general domain architecture. Both proteins contain a large, central, repetitive domain that
  consists of approximately 100 tandem copies of a 30 to 40 amino acid
  repeat sequence. The consensus repeat sequences for both MaSp1 and
  MaSp2 are glycine-rich and end in poly-alanine motifs (usually four to
  seven residues long). For MaSp1, the consensus repeat includes (GGX)n
  motifs (where X = A, L, Q, or Y) and very low proline content. In
  contrast, the MaSp2 consensus repeat has significant proline content
  and characteristic motifs such as GPG and QQ.
  The repetitive domains of different spidroins display a relatively
  high level of amino acid sequence variation that has been implicated
  in providing the elasticity and toughness that is characteristic of
  the different fibers.

It is possible that different amounts of Sp-1 and Sp-2 are combined to tune the elasticity and toughness of the silk. I have no idea whether the mechanical properties of silk are changed by the spider to suit the context (e.g. elasticity in windy conditions, or whether the content changes seasonally in response to temperature differences). That would make for a cool research hypothesis.


Do all plants grow roots when separated from parent?

Dear respected person,

I am not a professional botanist, but I adore gardening, and would like to help you as much as I can from my humble garden experience.

As far as I have experienced, not all plants have stems which root when put in the ground. For instance, I have a plant called Bouganville Tom Thumb (I apologise for any spelling error). I once decided to clone this Tom Thumb variety by cutting its stem off and then burying its base in potting soil. I even tried rooting hormone powder (from a gardening store) but it did not root, even after a whole month.

On the other hand, I had a plant called Petunia whose stem I cut off on purpose to maintain the plant's shape and threw the stem into the soil. The stem shriveled, and I thought it died and left it there. However, to my surprise, I found the stem all fresh after 2 weeks only to find that it had rooted into the soil from side of its stem. Another plant called Jade Plant can be cloned by putting its leaf in soil.

I think it really depends on the type of plant whether its stems will root or not and how long the stem will retain its rooting potential after being cut.

If possible, you can try the following. Put the cut stem in a small plastic pot (they are very cheap) with soil and see if it roots (leaves will begin growing). If it does, transfer it into a larger pot later once it has grown. Wait for it to grow big enough to spread its roots thoughout the pot, then shift it into a big pot.

I believe if a plant roots, then all stems of that plant will root. Plus, congratulations on your first plant.


Concentration of degenerate primers should you dilute to?

You can just add 2µl from each working stock (10µM) to your PCR mix of 20µl.

You can check this protocol.
Caution: The author has used $l$ instead of $\mu l$

He uses 5µl of each primer (20µM) in a 50µl reaction. This is double of what I mentioned. IMO it is best to try with a lower concentration and then increase it if necessary. Excess primer concentration can give rise to some nonspecific binding and amplification if the primers are not perfectly designed.

From this site:

  Using degenerate primers

  Because a degenerate primer is really a mix of different primers, only
  a fraction of the degenerate 'primer' will actually work in the PCR.
  One would therefore need to increase the primer concentration in PCR,
  sequencing reactions, etc. If a primer is 8-fold degenerate, the
  concentration should be raised 4-8-fold, and so on. However, for
  higher degeneracies, e.g., 64-fold, one cannot increase the primer
  concentration 64-fold and would have to try their luck with a
  5-10-fold increase only.


Molecules like complex lipids and carbohydrates are all synthesized by a special class of proteins that catalyze chemical reactions, called enzymes. Since the information of these proteins is coded for in the nucleus, you can imagine that ultimately the synthesis of these molecules does boil down to the genome.

The basic building blocks that the enzymes use to synthesize complicated molecules come from things you eat. Of course, we eat things that were once alive, and so the molecules that we get have been built up through enzymatic processes in the organisms we eat.

Ultimately, the "pre-organism" source of most of our molecules is CO2 from the air. Plants and photosynthetic algae have proteins that allow them to use the energy of the sun to reduce the carbon, making useful compounds such as glucose.


How can toddlers expend seemingly boundless energy when they eat so little?

They don't eat little. Consider the volume of milk / food they consume as a ratio of their weight. Quite the contrary they are ravenous machines and their consumption is much higher than an average adult. All cellular energy comes from the hydrolysis of ATP, and the production of ATP comes from the breakdown of glucose. The glucose comes from a sugar found in breast milk, called lactose.


The veterinarian in our group offers this: For humans, who choke much more frequently than other mammals, it is likely to be a cognitive problem. We talk and eat at the same time and so give ample opportunity to allow food passed the epiglottis and choking. Animals do choke - dogs can, cats can. Not all animals can vomit and this is particularly a problem for horses, whose stomachs will rupture instead of releasing contents through the mouth.


How do red blood cells survive without a nucleus?

As explained in the previous answer, the RBC loses its nucleus only at maturity. The nucleus contains the DNA and which can in turn produce protein. No nucleus means - no protein/ mRNA synthesis. Also, obviously, the cell loses its capability to divide.

Hemoglobin too is a protein. Knowing that it would lose its nucleus, hemoglobin is synthesized in the precursor stages of RBC. A mature RBC can not synthesize new Hb. Hence, the RBC keeps ready its store of enzymes and structural proteins (not only Hb, all proteins it would need for normal functioning) since it can not form new stuff once it has lost its nuclues.

The lack of a nucleus also limits the cell's repair capabilities. So human RBCs are cleared from circulation once they are about 4 months old. Damage (mostly from oxidative stress) to their structural proteins leads to loss in membrane flexibility. Since, the RBC can't replace the stuff, it gets gulped in by macrophages.

It is not surprising that the cell doesn't have a nucleus. The loss of a nucleus renders it better oxygen carrying capability. Even platelets donot have a nucleus. There too, enzymes are prepared and stored beforehand.

Hope that helps!


What is the significance of cysteine in a protein sequence?

What can I infer if I get a high percentage of C from a protein
  sequence?

A highly stable structure that is likely found in the extra-cellular space.

Cysteine can form a disulphide bond with another cysteine. Cysteine can be found as a lone cysteine, but is often paired with another cysteine in the tertiary structure to form these bonds.

Disulphide bonds play important roles in protein folding and stability (60 kcal/mol compared to around 1 and 5 kcal/mol for a hydrogen bond depeneding on the environment). Notably though, cysteine disulphide bonds are usually only used in extracellular secreted proteins, as they are unstable in the cytoplasm.

As an example, take the structure 2ksk. Look at how the structure is held together by cysteines that are distant in the sequence. If you see cysteines in a sequence, expect interesting folding!

The cartoon is going from blue to red, whilst cysteines are shown with sticks and the S-S bonds are in yellow.

Side note, they are annotated as SSBOND in the PDB.


What specific markers does a Covid-19 PCR test look for?

The SARS-CoV-2 diagnostic tests that are currently in use, both serological and nasal swab, are binary tests - they either are positive or negative, like a pregnancy test. They do not (yet) report viral titre, like the first image you linked, or look at restriction enzyme "gene fingerprinting" patterns, like the second. They simply tell you if either a part of the virus is in the sample (RNA or capsid protein in the two nasal swab tests) or if your immune system has seen enough of the virus to mount an antibody-mediated immune response (the IgM/IgG blood tests).
It's worth pointing out that all of the current tests in the US are available under emergency use authorizations from the FDA, meaning they haven't gone through the usual (and time-consuming) process of full qualification and validation. That type of work needs to be done in order to develop quantitative testing ("You have a viral titre of X, compared to an average range of Y through Z."), which will likely appear in the coming months and years as the proper development work is done to support their validity.


What are "primary amino acids and secondary amino acids"? Context: analysis of amino acid content using reversed-phase HPLC

I would guess that 'secondary' refers to amino acids that have been derivatized in some way, possibly by reacting with o-phthalaldehyde. (To measure the fluorescence of an OPA-derivatized amino acid, you excite at 340 nm, so I presume the derivative will absorb at this wavelength?).


This question is waaaay too broad, but I'll give some short and simplified answers to the hypothetical you asked at the end. First, let's reformulate your example a little bit:

How does the ribosome move along a strand of RNA?

How would it do it?

By hydrolyzing GTP and somehow coupling the free energy associated with that reaction to forward motion. Keep in mind that both ribosome and RNA are constantly undergoing random-walk Brownian motion (ie jiggling), so it's more a matter of biasing the ribosome's motion in a particular direction than it is of moving the ribosome in the first place.

What forces would move it along this strand?

The current understanding of molecular biophysics, which is by no means complete, says that the primary driver of this sort of protein activity is electrostatic forces.

Is it electromagnetism?

There are no electric currents, per se, so magnetism does not play a role.

Would gravity be involved to a significant degree?

At these scales gravity does not have a significant effect.

What effect would shape have?

Shape has an enormous effect. One of the fundamental axioms of molecular biophysics is that function follows form. The 3D configuration of those electrostatic forces I mentioned is determined in turn by the 3D configuration of the involved macromolecules.

If you want to know (a lot) more about this specific question, and if you have access to journals, check out this review: How Should We Think About the Ribosome?


How many centrioles/basal bodies are there in multi-ciliated cells throughout the cell cycle?

It seems that there is one basal body per cilium in multiciliated cells. Centriole duplication (as far as I understand, a basal body is just a different name for a centriole that is attached to a cilium) is tightly coupled to the cell-cycle. There is always one pair of centrioles that are at the base of the primary cilium (of which there is exactly one in most cells).

But not in multiciliated cells. These cells are differentiated and can no longer divide, and their centriole duplication process is decoupled from the cell cycle. In fact, they aren't, strictly speaking, "duplicating", since many procentriolar bodies may form around one cylinder. Indeed, each cilium has its own basal body; thus a cell with hundreds of cilia has hundreds of basal bodies.

Ishikawa 2011 is a review that examines the structure of primary and motile cilia, and ciliogenesis. It does not spell out how the basal body gets there.
Anderson 1971 describes the formation of new cilia in monkey oviduct. They first remove the ovaries of these monkeys to prevent cells from differentiating (this apparently requires estrogen), then administer estrogen and look at EM images of the cells over the following 6 days. They describe at length the processes of basal body formation.
Dirksen 1991 is another review focusing specifically on basal body formation during ciliogenesis. From their introduction:

  In order for the 200-300 cilia to form that the fully differentiated cell will need, production of that many centrioles is required first.
  The cell, after the last division, has usually retained a pair of
  centrioles. To what extent these mature centrioles are involved in the
  earlier stages of centriole formation, in which centriole precursor
  structures of varying sizes and shapes are generated and proceed to
  undergo transformational changes of great complexity, is largely
  unknown..

Sorokin 1968 is apparently a classic text which goes over EM images of ciliogenesis at various stages, and proposes a series of events describing what is happening. This is probably what you want, re: where are the other basal bodies coming from.
Bettencourt-Dias 2007 reviews the research on the formation of new basal bodies. This is another publication that answers your question very directly:

  Many ciliated cells, such as those in vertebrate respiratory and
  reproductive tracts, can have 200–300 cilia per cell. This requires
  the generation of multiple centrioles during ciliogenesis. Here,
  centrioles are generated by two pathways, a centriolar and an
  acentriolar mechanism. In the first one, a parent centriole usually
  produces one daughter at a time; however, in certain cases several
  centrioles have been observed to develop simultaneously around one
  parent centriole, with the daughter centrioles being released into the
  cytoplasm to mature. The acentriolar pathway is the major pathway for
  basal body production. In this pathway, fibrous granules 124 that are
  70–100 nm in diameter first appear in the cytoplasm and subse quently
  move to the apical cytoplasm. Deuterosomes appear within the area.
  (...) Multiple procentrioles can grow out from deuterosomes, and
  mature daughter centrioles travel towards the apical region where they
  form ciliary basal bodies.


You're talking about the difference between "taste" and "flavor." In common speech we use these words synonymously, but they actually mean different things.

Taste refers to the five sensations your tongue can detect -- sweet, sour, salty, bitter and umami. There's growing evidence for a sixth taste, "fat."

Flavor refers to the combination of several factors:

1) taste, as just described,

2) the aromas of esters, flavinoids, ketones, and other compounds in your food, detected by the nose. This happens a) before you take a bite, and b) as you chew and swallow, releasing different compounds and higher concentrations into your nose through your retronasal passage,

3) physical sensations such as texture, heat and cold, visual appearance and even sound (for example, the crunch of celery or potato chips)

4) chemesthetic effects, like the astringency of tannins or the "artificial" heat of chili peppers. (The compound responsible for chili heat actually down-regulates physical heat receptors so they're more sensitive. Menthol up-regulates them to create a cooling sensation.)

5) Emotional and social factors, like the memory of your grandmother's homebaked bread, or many people's aversion to raw fish.

All of this put together is why blackberries and strawberries are both sweet and tart, yet blackberries taste like blackberries and strawberries taste like strawberries.

Hope that helps!

References:

-- The collected works of Karen Page & Andrew Dornenburg

-- "Tastebuds And Molecules," Francois Chartier

-- LOTS of personal empirical evidence (I'm a chef)


What are the typical values of probabilities for nonspecific binding to an antibody?

TL;DR Specificity of antibody can be not superb. It can give false-positive results in up to 90% of experiments. However, some essay are 90% specific.
That is an interesting question and there sure a lot of research done to understand specificity and strength of binding of antibody to its target.
First of all, let me say that antibody-epitope interaction is, as many biological processes, probabilistic process, which means it can go either way, however, after binding antibody need a lot more energy or time to "fall off". Direct contact is always required for establishment of non-covalent bond between antibody and epitope, because characteristic length of that interaction is very low (order or angstroms, 0.1nm and less). Point here is that you don't need to run antibody in stream, rather let is sit in solution with your sample or mix gently, random thermal motion will take care of them finding each other. In flow you will waste a lot of antibody, which is expensive.
I think that you can estimate probability of given antibody binding given molecule from their 3D structures, but this is extremely burdensome calculation. What you can do experimentally, I suppose, is label "right" epitope with red fluorescent tag, and every other molecule in your solution with green tag. Then run solution through column with antibody sitting on beads (as in chromatography), elute everything and compare green to red signal. Measuring accurately, this will tell you how much "junk" antibody picked out of solution.
Now, to numbers. Here Abcam talks about its antibody for progesterone. Molecules, closely related to progesterone, are recognized with 40-90% efficiency, compared to true-positive target (progesterone). But this is absolute-worst case scenario, because those molecules are so closely related.
On other note, antibody specificity is very important when essay is used, e.g. for HIV diagnosis. Here is nice page from U Penn, that discusses issues with specificity:

For example, in one study of 290,000 asymptomatic Minnesota blood donors donating 630,000 blood units, the false positive rate when both the screening and confirmatory assays were positive was was 0% per donation (95% confidence interval 0% to 0.0006%).
...
For example, in one study of asymptomatic Italian blood donors, only about 13% of donors with repeatedly-reactive EIA tests were confirmed to be HIV-infected on the basis of positive immunoblot. However, in a high risk population the false-positive rate can be much lower, as low as 1-3%.

I couldn't find any more precise data or studies. In biological imaging (my field) antibodies are split into "works" and "don't work, drop it" (aka high background) groups.


Can ncRNA convert to coding RNA/mRNA by mutations?

Answers

Possibly, but with such a low frequency as to be unimportant and undetectable. (Monkeys with typewriters producing Shakespeare’s Hamlet comes to mind.)
No. Because it would be extremely difficult to detect, it would seem to be of no importance if it did occur at a very low frequency (you make no suggestion of why it would be of interest) and therefore there would be no reason for anyone to try.

Why would it be difficult to detect?

The difference between mutations that occur in DNA and any that might occur in RNA, is that a mutation in DNA can give rise to a population (e.g. of bacteria, or offspring) all of which carry the mutation. Thus, even though the chance of the particular mutation may be very low (say 1 in a million or less), a situation can arise in which the whole population is producing the RNA transcribed from the mutated gene and the protein encoded by the RNA. If RNA mutation occurs with the same frequency and managed to change a non-coding RNA (perhaps a pseudogene with a frameshift) to a coding RNA, only 1 in a million transcripts would be changed. Therefore if one sequenced the RNA the incidence of such changed RNA would be too low to detect, or if detected would be below the error margin in such experimental work.

Why has nobody looked for it?

Experimental science costs time and money. Scientists explore theories that have an importance and probability of success that attracts competitive funding. If there is no particular reason to look for something and the chances of seeing it are minute, nobody will waste their time on it, and they would certainly not get funded to do so.


Presumably this means that at least some grey haired humans have
  noticeable reproductive advantage, or maybe they had it in the recent
  past.

No it doesn't.  Natural selection is not that strong, it doesn't optimize every single possible physical trait towards maximum reproducing.

And as others have mentioned, having lots of grey hair usually happens after reproduction is over.  Historically, lots of women did a lot of reproducing before they had any grey hair.


What happens when too much sodium flows in the cell due to a faulty voltage-gated sensor? What about too little?

To answer the OP directly: You may be interested in looking at diseases that abnormally increase or decrease the activity of sodium channel proteins, changing the degree to which sodium ions cross the cell membrane. Some diseases are genetic in basis, which means they are inherited. This lends them to characterization and study.

This review paper by George summarizes some of the genetic diseases associated with sodium channel mutations, which might give you some direction for further research:

Muscle sodium channelopathies (SCN4A)

Hyperkalemic periodic paralysis
Paramyotonia congenita
Potassium-aggravated myotonia
Painful congenital myotonia
Myasthenic syndrome
Hypokalemic periodic paralysis type 2
Malignant hyperthermia susceptibility

Cardiac sodium channelopathies (SCN5A)

Congenital long QT syndrome (Romano-Ward)
Idiopathic ventricular fibrillation (Brugada syndrome)
Isolated cardiac conduction system disease
Atrial standstill
Congenital sick sinus syndrome
Sudden infant death syndrome
Dilated cardiomyopathy, conduction disorder, arrythmia

Brain sodium channelopathies (SCN1A, SCN2A, SCN1B)

Generalized epilepsy with febrile seizures plus
Severe myoclonic epilepsy of infancy (Dravet syndrome)
Intractable childhood epilepsy with frequent generalized tonic-clonic seizures
Benign familial neonatal-infantile seizures

Peripheral nerve sodium channelopathies (SCN9A)

Familial primary erythermalgia

Generally, you might search on the term "sodium channel mutant" or "mutations" to see what kinds of health problems are caused by under- or over-activity of these proteins.