Identify these two large, colorful dragonflies in Taiwan? Here are two dragonflies that I photographed today in Hsinchu county Taiwan. They are both quite large, with a body length of about 5 or 6 cm.
I often see them in the same pond or nearby marshy area. They seem pretty confident and are easy to photograph as long as you don't make a big commotion.
The arrows were drawn for my other question Why do dragonflies have these special little spots on their wings?
Is it possible to identify these two species? I can break them out as separate questions if necessary; I don't want to flood the site with "identify this dragonfly" questions.
The first is jet-black everywhere except for a robins-egg blue powdery coloration along the top side of the first two-thirds of it's abdomen. It's wings, like most but not all dragonflies, are transparent.
The second has some amount of red almost everywhere; its eyes and thorax are dull red and it has bright red patches on each segment of its abdomen. Notably its wings are solid opaque red, except for the furthers 1 cm which is transparent. The tiny "special spots" on the tips of each wing are a particularly bright shade of red!

Looks like this species is Orthetrum triangulare commonly known as blue-tailed forest hawk. It is an Asian fresh water dragon fly species.
As you mentioned that the dragonfly had a bluish hue, it became clear.

The other one looks like Neurothemis ramburri, commonly known as red perch Reference

Neurothemis is a genus of dragonflies in the family Libellulidae. Most Neurothemis species are red in color.
Neurothemis ramburii (Brauer, 1866) is distributed from Sundaland to New Guinea. There are records from Peninsular Malaysia, Taiwan, the Andaman Islands, Sumatra, Java, Borneo (Sarawak, Sabah, Brunei and Kalimantan), the lesser Sunda islands, the Philippines, the Bismarck islands and New Guinea. It is a widely distributed and common species that thrives in disturbed habitats.


Can potassium ions depolarise neuron membranes? I am reading a journal paper about the cell adhesion molecule NCAM2 and I have come across the following statement:

To confirm the functionality of the reporters, neurons were time-lapse
recorded before and after application of 90mM K+ used to depolarize
membranes and induce Ca2+ influx via VDCCs.

I know that depolarisation is when the membrane potential of a neuron becomes more positive. I have read that the opening of channels that let positive ions flow into the cell causes depolarisation, such as the opening of channels that let Na+ into the cell.
However, the above statement in the paper seems to imply that extracellular K+ ions can also cause membrane depolarisation. I am not sure what the relationship between potassium ions and membrane depolarisation is and I have not found anything about it online. Any insights are appreciated.

Yes, this is a very basic neuroscience question, something that would probably come up in the first week of a neurophysiology class or unit.
The polarization of the membrane at rest is due to cells being primarily permeable to potassium at rest, and due to a concentration difference of potassium inside vs. outside the membrane. Inside, potassium is high, outside potassium is low.
Therefore, there is a concentration gradient such that if a cell were at 0 mV, potassium would be flowing out of the cell. There is a membrane voltage where this net flow would stop. We refer to this as the "reversal potential" or "equilibrium potential" for an ion. For potassium in a typical cell, this tends to be around -90mV. The larger the ratio of concentrations in versus out, the larger the potential. You can calculate this potential with the Nernst equation if you know the concentrations (image from Wikipedia):

From this equation you can see that the reversal potential is negative for a positive ion if [outside] is small compared to [inside]. By applying higher potassium outside than usual, the ratio of [outside]/[inside] gets closer to 1, so the reversal potential for potassium is closer to 0mV, and typical neurons that are mainly permeable to potassium at rest will depolarize.


What is the difference between phylogenetic tree "construction" and "reconstruction"? When I look through papers, there are two terms

Phylogenetic tree construction
Phylogenetic tree "Re"construction

What is the difference between phylogenetic tree "construction" and "reconstruction" ?

There is no difference! In both cases, they refer to the building of a phylogenetic tree from data.

The expression 'phylogenetic tree construction' is less common.


Identifying an insect in Cambridge UK I have come across an insect in Cambridge UK that I could not identify.
I tried to find this in various catalogues of local insects without success. The insect was about 1-2cm in length and didn't move at all until it was disturbed. I found it around 11am. We are currently experiencing high temperature variations (8C-20C).
Could someone please help identify it and point me at any useful resources I can use in the future?

It's a greater bee fly, Bombylius major, a nectar feeder and generalist floral pollinator which pollinates hundreds of species of flowers. It lays eggs near real bee nests and it's larvae feed from the bee larvae.
https://en.wikipedia.org/wiki/Bombylius_major


Do plasma B cells express the BCR or only produce soluble antibodies? Is the B cell receptor still expressed on a B cell once it has begun to produce soluble antibodies? Is there a gene change that prevents the membrane-bound form from being produced anymore?

B cells can secrete antibody before they are terminally differentiated into plasma cells, so there is a phase during which both membrane-bound and secretory antibodies can be produced by the same cell:

  When a naïve or memory B cell is activated by antigen (with the aid of a helper T cell), it proliferates and differentiates into an antibody-secreting effector cell. Such cells make and secrete large amounts of soluble (rather than membrane-bound) antibody, which has the same unique antigen-binding site as the cell-surface antibody that served earlier as the antigen receptor (Figure 24-17). Effector B cells can begin secreting antibody while they are still small lymphocytes, but the end stage of their maturation pathway is a large plasma cell

--Molecular Biology of the Cell. 4th edition.

Plasma cells, generally speaking, have little or no surface immunoglobulin, but it's been claimed that some subsets of plasma cells do have surface Ig:

  Surprisingly, although IgG PCs downregulated surface IgG expression, IgA and IgM PCs expressed their respective isotype both intracellularly and on the plasma membrane (Figure 1A, lower panel). Importantly, concordant Ig’s were also detected on the plasma membrane of IgA and IgM, but not IgG, PCs isolated from BM or colon LP indicating that this property is a characteristic of PCs present in their physiological niches

--A functional BCR in human IgA and IgM plasma cells


Can you identify this bee? Found on the ground on dried cottonwood leaves in southern Utah.

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)


How do I prepare a solution? (Calculation) I have to make 100mL of 400mM NaOH. How do I go about calculating what I need to prepare this?

This is relatively easy. First: Look up the molecular weight of sodium hydroxide: Wikipedia gives a molar weight of 39.997 grams/mole (lets round this to 40 g/mole thats easier to calculate and the error in this is marginal).

So when you dissolve 40 g of it in 1 l of water, you have a 1000 mM (or 1 M) solution. Since you only want to have a 400 mM solution, you need to multiply the final concentration with the molar weight to get the amount of NaOH for one litre:
40 g/mole * 0.4 mole/l = 16 g of NaOH per litre. Since you only need 100 ml, you only need 1/10th of the NaOH (1.6 g).

So to prepare 100 ml of a 400 mM NaOH solution you dissolve 1.6 g of NaOH in 80ml of water and fill up to 100ml in a appropriate messuring cylinder.


Why were dinosaurs not as smart as humans are? According to http://en.wikipedia.org/wiki/Dinosaur, Dinosaurs were the dominant terrestrial vertebrates for 135 million years.
They had a lot of time to evolve. My question is: why were dinosaurs not smarter than us, and why was their society not complex like ours is?

We are all equally evolved

All life that exist on earth today had the exact same amount of time to evolve (3.5 billion years). Therefore, one cannot say that one species is more evolved than another one. It just makes no sense (at least if "more evolved" means "have evolved for more time").

Being a dominant species/clade for some time (whatever dominant may mean to you) doesn't make this species/clade more evolved than any other one.

Your question need not be specific to intelligence

You can think of any other phenotypic trait (wings, toxins in the skin, good eyes, good smell, strong leaves, etc...) and ask this same question. You seem to assume that being smart should be some kind of goal or necessary direction toward which species should evolve. Following your reasoning I would rather ask why the hagfishes, the oyster, the lampreys or the turtles are so dumb although they exist for so long (once again remember that this notion that some lineages have existed longer than others is flawed).

You might also want to have a look at: Why evolution should not be equated with progress?

Being clever is not a goal of evolution

Most of these trait have associated cost to the benefice they might bring. For example having a big brain asks for much energy (20% of ATP in humans) and it also has a cost due to its weight. The sperm whale for example has a brain that weights 7.8 kg. Obviously it is not a big cost for such a big animal to carry heavy organs while it would be impossible for a migratory bird to carry such a brain.

taking different evolutionary path This part is not complete!

Now the question of why Homo sapiens are smart while Tyranosaurus rex are not or why wings evolved in bat and not in mice is rather interesting and hard to answer. I can think of 2 main causes:

1) The newly arising trait (which is usually not the trait you can observe today. Big brain did not appear suddenly, first there were individuals they had slightly bigger brains than the other individuals in the population) is not beneficial over the wildtype trait. There are so many parameters that will affect if a trait is beneficial or not. You can think of the predators, the humidity in the environnement, the social structure, the population size, the type of reproduction, the genetic background etc...

For example, think of a species that is fixed, has no social contact, has nothing it can really predict in the environnement. What would an individual from this species do with a brain? Think of a bird that needs to make food stock for the winter. This bird needs to remember where it hide something. It has been found by the way that some birds have an awesome spatial memory, way better than humans.

2) The trait never happen to occur (or never in a strong enough individual, or never in a population big enough to not suffer from to much drift while the trait is at low frequency) just because the necessary mutation never happen. Mutation is just a random process.

For example. It seems rather hard for a tree to have the necessary mutations to have develop a brain! But we don't need to go to such a extreme example. If you split a population of clone mice in two, the two subpopulation will evolve differently (even in absence of genetic drift (infinite population size)) just because  some mutations occur on one side while some others occur on the other side. Or maybe the same mutation might occur but once in an individual that has low fitness and once in a very fit individual.

Evolution of human cognition abilities

So what are the factors that drive humans to evolve big brains? This question is not solved yet. We have many models to explain this but I don't we have much solutions to test these models. The 2 most common models explain big brains

for social purposes (understanding relationship between other individuals, being able to coordinate the movement for a hunt, etc...)
due to sexual selection. Being intelligent would be a proxy for having good genes.

For more information concerning the evolution of human cognition, this wikipedia article might be a good start.

UPDATE

  Why do you think mutation is a random process?

Our genetic data are encoded into a succession of 4 types of nucleotide bases (A,T,C and G). A mutation results from a modification of this sequence such as a replacement of a T by a C. These mutations are due to mistakes usually while duplicating the DNA. Most of these mistakes do not affect the fitness (survival + reproduction ability) of the individual, very often these mutation are deleterious and rarely these mutations are beneficial. Some mutations are more probable than others but nevertheless some individuals have a higher mutation rate than others. In order to make things slightly more complicated, some sequences have a higher mutation rate than others. For example, the sequence AAAAAAAAAAAA is more likely to mutate than the sequence ATGTGCATCTA. But even if some mutations are more likely to occur it is still a random process (we couldn't talk about likelihood otherwise!). Two clones living in the exact same environment that both have a baby at the exact same time wil not create babies with the exact same genome given the randomness of mutations. One baby might have a very bad mutation that will make him die, while the other baby might synthesize (=construct) a new enzyme that increases its digestive capacity.


Why do rabbits often have white hindquarters? There are several species of herbivores that have a very visible white hindquarters: several kinds of deer, rabbits, antelopes, etc.

Does the white fur serve a functional purpose, or is it purely random?  Is it defensive enabling them to escape predators, or is it for intraspecies communication?

Examples photos to clarify:

deer

Notice that otherwise relatively well camouflaged animals have visible white fur.

Apparently the most noticeable research on this subject of a rabbit's white behind has been done by Dr Dirk Semmann of the University of Goettingen. He proposes that

  these spots actually confuse predators because of their very
  noticeable nature. By focusing on the bright spot, the would-be
  predator ignores the larger body of the animal. Then, when the rabbit
  executes a sharp turn, the spot disappears and the predator has to
  readjust to focus on the camouflaged coat, losing vital seconds
  (reference 1, reference 2).

It could be the same reason for the white behind of a deer. As to why deer flag their tails, there is a paper on the subject which lists 4 possible reasons for the behaviour.

1) Flash behaviour

2) Alarm Signal

3) Cohesive signal

4) Detection signal

More can be read about it in this paper.


HPV. How do viruses persist outside the body? The main route of transmission of human papillomavirus (HPV) is generally believed to be sexual. While fomites have been postulated for inexplicable infections, sexual health professionals regularly counter that lying respondents are the more likely explanation.
Research into HPV seems to have mostly stalled and there are few in depth in-vitro studies into viability of the virus outside the body, the infectivity of fomites or their infective dose that I could find.
There are some footnotes and references to animal models, with claims that HPV can remain infective at least 7 days after desiccation but no upper limits. There is some more precise research but understanding the significance is difficult for layman.
For example research published in Nature stated HPV-16 "can remain viable and capable of transducing the reporter construct upon stimulation of cell cycle re-entry for at least 2 weeks, but most likely for no longer than 4 weeks."
How can one understand the viability and limits of viruses, and HPV in particular, outside the body?
To clarify: Despite the fanciful language of the bounty I'm not looking for certainty, but general principles of environmental virology and an overview of statistical observations in regards to HPV in particular.
Note: The various aspects which influence the persistence of viruses in the environment spoken of below are summarized with some additional detail in a literature review published in 2010 in Food and Environmental Virology.

bob1's answer is good, but I was already working on this one so I'll go ahead and post the parts that aren't redundant:
What does it mean for a virion to lose infectiousness?
To be 'infectious' a  virus particle perform a set of tasks that result in more virus particles. A simplified list for HPV could be: attach to receptor on host cell > enter cytoplasm > enter nucleus > make proteins > copy DNA > assemble new virions from protein and DNA > exit cell. The first four tasks must be performed by proteins in the virion; if enough of these are degraded, the corresponding task cannot be completed, and the virion cannot infect a cell. This means that there are many different routes by which any particular virus might be inactivated. One of the references in the question suggests HPV can be inactivated by gunk from dead cells sticking to the otherwise-viable virions:

The greater inactivation of the virions in the extracts at 56 C may be due to denatured cellular protein, which visibly aggregated at 56 C and above, interfering with infection.

Viruses are not metabolically active on their own!
This means that damage cannot be repaired, and also that a functional protein cannot be 'reset' after it changes shape. To use the SARS-2 spike protein as an example, the spikes have energy stored in them like a mousetrap. If the transition from open to closed is triggered while the spike is bound to ACE2 on a host cell's membrane, the motion of the spike protein changing shape will bring the viral membrane in contact with the host membrane, fusion occurs, and the virion contents enter the host cytoplasm. If the transition is triggered before the spike is bound to a host receptor, that spike is 'dead'. SARS-2 virions have many spikes, but if all of them trigger prematurely, the virion as a whole becomes uninfectious. The transition from the high energy 'prefusion' state to the lower energy 'dead' or 'postfusion' state has to be energetically accessible in order to be triggered by the new host cell. This means that the risk of premature triggering is inescapable. Therefore, damage or premature transition of all copies of some viral protein that changes shape to allow cell entry is a likely candidate for inactivation for any viral species. This hasn't been investigated systematically, though, so there's no reference I can cite for this.
In papillomaviruses:
Unlike coronaviruses, HPV doesn't have a membrane that can fuse with the host's for cytoplasm entry. Instead, it is absorbed by endocytosis, then the capsid disassembles, and L2 disrupts the endosome membrane. The details of how this happens aren't known, but it's likely that L2, which is protected inside the capsid most of the time, becomes exposed by structural changes to L1 which occur in the endosomes. This suggests to me that degradation of L1 is the main cause of viral inactivation outside of the cell. That hypothetical structural change of L1 would need to be identified before you could start to investigate if it's present in inactivated particles.


What is the statistical relationship between radioactivity and mutation rate? This question tries to narrow down the scope of that question.

What is the statistical relationship between radioactivity and mutation rate? By how much would the mutation rate be lowered in a idealized world were radioactivity is absent?

According to this wiki page , the average background radiation is 3.01 milli-Sievert per year (including natural and artificial sources). This equals 0.301 rad.

I found a short letter to nature that says the average forward mutation rate in human is 2.6 * 10^-7 per locus per rad = 2.6 mutations per ten million bases. Also it say that this mutation rate is quite uniform among species. The size of the human genome is approximately 3.2 gigabases.
So doing a quick maths: (2.6*3.2*100)*0.301 = 250.432 mutations per year per human. This is an approximation because I rounded the size of the human genome to 3.2 gigabases. Also this doesn't mean that we actually acquire this amount of mutations because we have repair mechanisms.


Is an Eidetic Memory (or other unusual forms of memory) less susceptible to anterograde amnesia? I'm a physicist, so as a fellow scientist I want to apologize because this question will be entirely based on anecdotal inferences and I am well aware how irritating that can be.

I have an eidetic memory and I've never experienced any of the common forms of anterograde amnesia. No blackouts from rapid consumption of alcohol (and believe me, I've tried. That was the fun part. But not for kids; then it's not fun), not from extreme fatigue, head trauma, I even went in for surgery once and the anesthetist said at one point "Well since you asked, the amnesiac should be setting in right about now" and I vividly recall another couple minutes of conversation while we waited for the general anesthetic to knock me out.

So, naturally, I just assumed it must have been because of my eidetic memory. But I've always had an interest in neuroscience and now my curiosity has gotten the better of me. Surely the memory systems of all people are similar enough that amnesiacs and the like should work on everyone. So I ask, are eidetic memories (or perfect, or photographic, or other unusual forms) actually less susceptible to anterograde amnesia? Or perhaps have I just been the victim of probability; this is more a matter of luck not neuroscience?

Please don't spare the gory details, neuroscience is cool (Neuroscientists are brainy guys. Sorry, I couldn't resist that pun). That said, I am physics, not biology; I'm probably under-specifying the question. Let me know if it's too broad and I'll try to focus.

This question is more of a medical question than one of the underlying mechanisms of biological function.

The formation of long term memories is related to long-term potentiation. There are multiple neurotransmitters involved in this process. Ethanol primarily affects NMDA receptors. Drugs used to specifically induce anterograde amnesia, like propofol, primarily affect other others, like GABAA.

The process of memory formation relies on a variety of factors including the orchestration of multiple neurotransmitters. Anterograde amnesia can be induced by many factors and does not have a single known mechanism of action. It is not possible to conclude any single person will react identically to all inducers of anterograde amnesia. It is often the case that people have unique responses to drugs within a distribution of possible reactions.

The individual nature of responding to drugs is why side effect lists are lengthy, and usually only a few out of this list are observed in any individual.

My hypothesis is, as a regular consumer of alcohol, your liver function is elevated and responsible for your high tolerance. The cytochrome p450 family of enzymes are responsible for much of the metabolism of drugs in the body.

Liver function tests are cheap and interesting, I find. You might have some blood work done at a local lab to check out those stats as well as your cholesterol, etc., if you have an interest in such things.


Why don't dragonflies wings collapse? How do dragonflies manage to fly at such high speeds without their wings collapsing? Their wings are thinner than paper, but they do not even flutter. What gives them their strength?

Wootton (1992) reviewed the anatomy and biomechanics of insect wings. Basically the wing is a lightweight but strong scaffolding of veins, supporting a thin membrane. The veins are composed by a sandwich of cuticle with a potential space in between. The membrane is also a double-layer but without the space.

In the venous space are is circulating hemolymph and often nerves and tracheae. The wikipedia image is pretty good:

The nerves carry sensory information and the tracheae oxygen.The hemolymph is continuous with the body and thus is able to circulate and hydrate the wing (important for maintaining flexibility). As Wootton says:

  desiccation destroys both compliancy and toughness, and a dry cuticle would be mechanically disastrous

So by maintaining a flexible tissue, insects have strong and tough wings that remain light enough.


How many mice are on the Earth? We are 7 billion human beings on the Earth. But how many mice are there? How would you estimate such a number?

Mark-recapture is the most frequently used method for small mammals. It's best when combined with uncertainty estimates and population dynamics models (e.g. projection matrix).

The fluctuations of small rodent populations have long fascinated scientists, and various models have been developed. Logistic regression models can be used to estimate likelihood of mice outbreak based on local rainfall data.

Estimates vary.

Rat population in New York city, for example, was thought to be 1 rat to 15 humans in the mid 40s, 1:36 in the late 40s (Davis ratio), 12:1 in 2002.

The population of mice is often estimated per hectare - 0.25-60/ha in buildings and 1-200 in the field, over 1000/ha during outbreaks. 10^9-10^10 hectares of habitable land means
that populations of mice and men are, probably, of the same order of magnitude.


Data on Recombination rate and Gene Positions in Humans I am looking for estimates of per base pair recombination rate in humans and indication on gene positions. The goal is to be a able to plot recombination rate in the y-axis and position (in bp) along all chromosomes in x-axis. Then add the genes on the graph.

I have never had to search for this kind of data. Can you give me some hints of where I could find these data into a simple format like the simple table presented below?

> Gene Positions
from       to
1145146    1147112
1568742    1570012
...

> Recombination rate
from   to       r
1      156787   1.2*1e-9
156788 256888   2*1e-8
....

A good baseline for this type of research in human genetics is Standards and guidelines for the interpretation of sequence variants from ACMG. It is a guideline for clinicians, and it gives a good sense of good variants data, bad variants data and setting up confidence level.

Try to consolidate data from:

Population databases

GWAS databases

Exome Aggregation Consortium
1000 Genomes Project (there is data in vcf format which is pretty much what you need)

SNV databases

dbSNP (it is uncurated so you got to be hypercritical)

Disease databases

ClinVar (be aware "12% of interpreted variants have ≥2 submitters in ClinVar , and 21% are interpreted differently")
OMIM
HGMD (it is a gold standard as it is curated, but you could only search for variants but not collect data because you could not download it unless you pay for it)


Why do some women have menstruation-like spotting throughout their pregnancy? An interesting question that was asked during a lecture about human reproduction: what is the biological mechanism behind some pregnant women getting monthly spotting that they mistake for a regular period? I've found articles and research papers about bleeding during zygote implantation, ectopic pregnancies and problems with the placement of the placenta, but nothing regarding menses-like bleeding during otherwise unproblematic pregnancies.

Here are some causes of bleeding during pregnancy:

early pregnancy (first trimester):

implantation bleeding [1]
infection [1]
after intercourse [1]
miscarriage [2]
ectopic pregnancy [2]
cervical changes [3]

second part of pregnancy:

abruptio placentae [1, 2]
placenta previa [1, 2]
miscarriage [2]
vasa previa [2]
preterm labour [1]

References:

American Pregnancy Association. Bleeding During Pregnancy. Available from http://americanpregnancy.org/pregnancycomplications/bleedingduringpreg.html (accessed 29.07.2014)
U.S. National Library of Medicine. A.D.A.M. Medical Encyclopedia. Vaginal bleeding in pregnancy. Available from http://www.ncbi.nlm.nih.gov/pubmedhealth/PMH0003748/ (accessed 29.07.2014)
WebMD, LLC. Bleeding During Pregnancy. Available from http://www.webmd.com/baby/guide/bleeding-during-pregnancy (accessed 29.07.2014)


Effective population size when the population sizes varies from season to season Let's think of a species which has four generations per year and which population size changes from season to season so that the population size is 100 in summer, 200 in spring, 50 in autumn and 20 in winter for example. In such case, the effective population size $N_e$ can be calculated by:

$$N_e = \frac{n}{\sum_{i=1}^n\frac{1}{N_i}}$$

where $n$ is the number of generation per year (4 in my example) and each $N_i$ correspond to the population size in one season.

My question

Can you please provide an explanation of why this formula (based on the harmonic mean) holds true to define the effective population size?

source

This is derived from studying how heterozygosity changes over time. The standard equation for change in heterozygosity ($H$) with constant population size ($N$) is:

$H_t = \left(1 - \frac{1}{2N}\right)^tH_0$

When $N$ varies between generations you use the product of this formula:

$H_t = \left(1 - \frac{1}{2N_0}\right)\left(1 - \frac{1}{2N_1}\right)...\left(1 - \frac{1}{2N_{t-1}}\right)H_0 = \prod_{i=0}^{t-1}\left(1 - \frac{1}{2N_{i}}\right)H_0$

To get the overall $N_e$ you need to find the population size that gives the corresponding decrease in heterozygocity over t generations i.e:

$\left(1 - \frac{1}{2N_{e}}\right)^t = \prod_{i=0}^{t-1}\left(1 - \frac{1}{2N_{i}}\right)$

Rearranging gives:

$N_e = \frac{1}{2\left[1-\left[\prod_{i=0}^{t-1}\left(1 -\frac{1}{2N_{i}}\right)\right]^{1/t}\right]}$

This expression can be approximated by the harmonic mean, which is easy to verify with some toy data (you get small deviations if yearly population sizes are very small). The explanation given above can also be found in Hedrick (2009, p217ff), along with some nice examples that integrates the effects on effective population size from several factors.


How can P450 distinguish between foreign and native compounds? It is my understanding that P450 enzymes are capable of selectively degrading compounds that enter the cell from the outside (e.g. synthetic drugs) without damaging compounds that are metabolic intermediates normally found in cells. What is the mechanism that provides these enzymes with the ability to distinguish the foreign compounds that are substrates from the normal metabolic intermediates that are not substrates, if they are structually similiar?

False Premise

The false premise in this question lies in the end of the last sentence:

  …the ability to distinguish the foreign compounds that are substrates
  from the normal metabolic intermediates that are not substrates,
  if they are structurally similar

The assumption here would seem to be that the similarity between normal metabolic intermediates and foreign compounds is too great for discrimination to occur. There is no reason to assume this.

Explanation

  The substrate specificity of those P450 enzymes that metabolise
  xenobiotics is such that they will not metabolize normal cellular
  constituents.

There is a wealth of evidence that enzymes can have substrate specificity that is either extremely narrow or relatively wide. This obviously depends on the structure of the substrate binding site — its shape and size and the chemical nature of the amino acid residues there. Thinking in these terms one can envisage an enzyme that will discriminate against substrates with a single substituent at a particular position, but metabolize a variety of similar compounds that lack this. The evolution of P450 enzymes can be imagined as a process whereby mutations that allowed metabolism of toxic environmental compounds would convey an advantage and be selected for, but mutations that disrupted normal metabolism would be lethal (or disadvantageous) and be selected against.

The Broader context of P450 Enzymes

The question is posed in terms that might suggest that the only function of P450 enzymes is in removal of xenobiotics, and perhaps that they are only a feature higher organisms. In fact neither of these are true. Details of their occurrence in bacteria can be found in the Wikipedia article. However, a paper which I, as a non-expert, found interesting in this respect was published by Kawashima and Satta in PLOS ONE in 2014. This makes the point that there are two classes of P450 genes — those involved in normal cellular biosynthesis (e.g. steroids, cholesterols, vitamin D3 and bile acids), and those active against xenobiotics (e.g. plant alkaloids, aromatic compounds and fatty acids). Comparison of the genes for these in a variety of (mainly) vertebrates implies those involved in the metabolism of xenobiotics evolved from those involved in normal cellular metabolism, and such detoxification genes have arisen not just once, but on several occasions.


Can skeletal morphology change in adults? I'm just a curious layman, so be gentle. I read around that things like the cranial1 and pelvic2 morphology change with age, but I also read seemingly contradictory information that bones are 'completely ossified' around age 25 (can't post a third link for reference) and that's often cited as meaning "done changing."

Wikipedia (my trusty friend) also describes 'bone remodeling' as a lifelong process, yet also describes ossification (not a lifelong process) as a key component.

So I'm confused. What actually changes in terms of bone morphology throughout an adult's life? Does bone tissue continue to form in adults? Do bones "bend" and flatten ever so slightly into new forms? Additional reading would be appreciated as well.

Thanks

Bone never stops changing.
Your bones are constantly being broken down and reformed on a microscopic level. Your bones are done growing at a certain point but they continue to be reshaped. Remember bone exists to supply calcium (and to a lesser extent phosphorus), to your muscles, Your body needs to break down the surface of the bones for this calcium.*  So bone is dissolved and redeposited constantly, this regulated mineral levels but also allows the bone to slowly reshape itself.
Bone will slowly reshape itself to resist any stress it experiences, for instance if you build muscle the attachment point for the muscle will become more rugged to strengthen the attachment. A runner's leg bones will get thicker and denser to resist the greater stresses. Joint surfaces can even reshape with repetitive motion.
*bone originally evolved as armor but this has been lost in modern vertebrates. Vertebrate muscle requires calcium to function, Vertebrates have lost the armor but not the need for a calcium store, and have repurposed into a structural support. Vertebrates without structural bone need to have massive calcium levels in their body tissue instead.
for continued reading there is a whole series of books by R. Mcneill Alexander that cover bones in fascinating detail.


Mass spectrometry versus western blotting for validation I have mass spectrometry data (LC-MS/MS) from rat cortices under either drug or control treatments. The results were performed in triplicate (three pairs of rats, drug or control per pair). In addition to some of the bioinformatics analysis I am doing, I will have to validate some of the fold-changes from the mass spectrometry by Western blot in order to have my results published.

Some of the proteins I have chosen to to validate work very nicely by Western blot which captures the same trend as the mass spectrometry. However, other proteins that I have attempted to validate go in the exact opposite direction.

My questions:

In general, how accurate is mass spectrometry compared to Western blotting?
Is it unusual to have a lot of variability between the results of the two methods? I am worried that I might have to try multiple proteins before I see the results replicated and this seems problematic to me. That leads me to the third question.
Which result should I trust?

Other information - Some of the proteins I have chosen for validation come from lower in the list where not as many peptide fragments were detected. In some cases, fragments were detected in only 2 of the 3 biological replicates. I did not chose to validate proteins where the 2 or 3 replicates varied widely in normalized spectral count values so I would expect these readings to be accurate. Additionally, the mass spectrometry part of the experiment was performed by a reputable lab that has filtered erroneous data using FDR cutoffs. There is a high correlation overall between all three replicates for a particular treatment and low standard error between samples across the population so, statistically, I trust the mass spec results.

If you need more information please ask - I don't know what exactly will be useful to answer my questions.

EDIT :

This article discusses the justification for using western blotting to validate mass spec results. It suggests using selected reaction monitoring assays as an alternative. Some of the points made by commenters in this thread are reiterated in this article.

It is a common practice to prove a result using an orthogonal technique. Like RNAseq followed by qRT-PCR etc.

Western blotting is not a robust technique and cross comparisons are difficult because of difference in the avidities/affinities of different antibodies. So comparisons can be made only with one protein-control pair in different conditions.

LC-MS is more sensitive and less biased(IMO). So the general trick is- don't do westerns for all proteins just report the ones that behave well (say that you "chose" these because they are important). I know this is a wrong practice and I should not be advocating it. For your own scientific validation try it with another MS technique; if you used ESI-Quadrupole/ion-Trap etc then try with MALDI-TOF or iTRAQ. Some luddites will continue to cling to westerns.

I think it is better to not test the proteins that have low peptide counts. See what is known as MA plot. This is frequently used for microarrays. Here M denotes fold change and A denotes total expression in both samples. Don't pick proteins that are low in expression in both samples; they might not be meaningful. For example if you have 2 molecules of X and 100 molecules of Y in control condition and 5 molecules of X and 200 molecules of Y in test; then the fold change in X would seem important; however this change may not be relevant and can be a result of stochastic fluctuation/measurement error. If you have many samples you can see if something is stochastic or not but the limitation is the number of samples.

Note: I am not saying that 2→5 molecule increment should be meaningless. But to know if they have a meaning or not you would require more complex models; better avoid them at this moment.


How to do a whole genome analysis of Multidrug-resistant Mycobacterium tuberculosis I'm looking for tutorials and software that can help me study whole genome sequence data is and genome wide associations. I have Matlab and Bioconductor R so anything involving those packages would be preferable.

You've picked a fascinating and very important organism to study. Unfortunately there are many many steps with many software packages that you'll need and each next step will depend on what you find making any particular tutorial nigh on pointless. I'm sorry to say that I don't think anyone will dump an entire project proposal or workflow as an answer. I'll give you an answer to get you started on your research.

Example

An excellent example of such a study is Fellay et al., 2007 and you can find their materials and methods supplement here.

An introduction to this kind of research

First you need to find the sequences of proteins that you think are significant. There are a bunch of ways of doing this, but I suggest standing on the shoulders of giants and scouring the literature (regardless, find an example where this has been done elsewhere). If there isn't much out there or for an entirely new viewpoint on something, this answer might help for finding proteins in the DNA sequence.

Sequence alignments against other strains is your best bet of identifying mutations (and possibly an indicator of resistance, which is what I guess you're after). There are plenty to choose from, but BLAST is a good tool to start with. You should compare your resistant strain with non resistant strains. Be very careful when analysing the data, not every mutation will be significant.


When you have your gallbladder removed, how does it affect bile flow into your small intestine? Cholecystectomy, or surgical removal of the gallbladder, is an extremely common operation around the world. The gallbladder is typically viewed as a storage organ for bile produced by the liver, but is not necessary for life.

The classical teaching from digestive physiology is that bile is stored in the gallbladder and then released in a pulsatile fashion from the gallbladder in response to nutrients/hormones in the intestine during a meal. The major function of bile for digestion is to solubilize dietary fat so it can be digested by digestive enzymes in the small bowel.

When you don't have a gallbladder and there is no storage of bile, how does that affect bile flow into the intestines? Has anyone ever examined the effects of gallbladder removal on the release of bile from the liver? Is bile continuously released by the liver or is there still pulsatile release in response to intestinal nutrients?

Bile is stored, concentrated, and acidified in the gall bladder. Schwartz Principles of Surgery ch. 32 has a good section on this. After recovery from an uncomplicated surgery, the loss of the gall bladder does surprisingly little (other than, usually, resolve the symptoms of gallstones). This was a bit of a surprise to the medical community when the first cholecystectomy was performed in 1882, and it remained a controversial procedure for some time.

There are a number of studies on the effects on bile flow and the overall cyclic release, reabsorption, and return to the liver of bile via the portal vein called enterohepatic circulation.  Animal and human studies demonstrate compensation by the liver, bile duct, and the sphincter of Odie. Overall bile flow is reduced, there appears to be greater release into the intestine during fasting states, and there do appear to be changes in the composition of bile, but, most importantly, enterohepatic circulation is still pulsatile, in response to a meal, as you can see in the figure below.

Both solid lines are subsets of bile acids, measured in the serum of cholecystectomized patients in a classic 1978 study. The shaded areas represent control (not cholecystectomized) patients. These measurements suggest that enterohepatic circulation still follows a pulsatile pattern after cholecystectomy.


What light intensity starts melatonin release in humans? I'm interested in whether any studies have determined the intensity of light at eye level that starts melatonin release in humans.

I know that:

melatonin release is suppressed by blue light with peak suppression
occurring at 420-480nanometer range.
This light is registered by Melanopsin, a photopigment in the
eye.
Melanopsin signals the Suprachiasmatic Nucleus, the master clock of the human body.
The suprachiasmatic nucleus makes a decision to suppress melatonin
release in response to blue light observed.

What I need to know is how much light is "enough" to trigger the suppression by the mechanism described above. I've seen a mention of as little as 200 lumens of white light, but do not have any reference to verify that. Additionally, the figure of 200 lumens was given for a typical smartphone screen, not necessarily translating to 200 lumens at eye level.

I'm aware of this experiment involving rats, where the light intensity at eye level was quantified. I'm looking for a similar measurement in humans.

Here's my original question on the subject, but I've learned quite a lot since then to refine the question

I appreciate your input!

The question piqued my interest, but after hunting through the literature for a bit, I hadn't found any direct answers.  Then I went back and read the mouse study you cited a bit more carefully. The mouse study only made a reference to mice being affected at 4 lux, ~100x more sensitive than humans.  However, for that number it cited a paper in Science that has a direct answer.

http://www.sciencemag.org/content/210/4475/1267

    Melatonin concentrations decreased 10 to 20 minutes after the subjects were exposed to 2500-lux incandescent light and reached near-daytime levels within 1 hour (Fig. 1). After the subjects resumed sleeping in the dark, the melatonin concentrations increased immediately and within 40 minutes were at the levels measured before exposure. The fluorescent light (500 lux) did not reduce melatonin, and there was no change after the return to darkness. In the two subjects who were exposed to 1500-lux incandescent light, melatonin concentrations decreased to levels intermediate between those measured during exposure to 500 and 2500 lux (Fig. 2). The return to normal nighttime concentrations after subjects were exposed to 1500 lux was similar to that occurring after their exposure to 2500 lux. The concentration of melatonin in subjects awakened and exposed to 500-lux fluorescent light did not differ significantly from that measured while they were asleep in the dark.

Since that was the granddaddy study of the subject, I just checked the recent citation list on that page for modern articles.

Using pure blue LED lights at 446-477 nm wavelengths, West et al. measured light intensities necessary to induce melatonin suppression. Table 1 of that study converts LED irradiance/lux into retinal irradiance (uW/cm2) based on mean pupil size.  Figure 2 shows plasma melatonin falling (p<0.05) at 20 uW/cm2 of corneal irradiance (then curve fit to 14.19 uW/cm2). It's at least twice as powerful as white light, which didn't show significant suppression at 40 uW/cm2, but was "numerically similar" to 10 uW/cm2 exposure.  If I've got the conversions right, 20 uW/cm2 is about 136 lux, which is about the brightness of an overcast day or half the brightness of typical office lighting.

http://jap.physiology.org/content/110/3/619.full

As for the discrepancy between the two studies (1500 lux vs. 136 lux), I would blame it mostly on technological advances since 1980.  The original study used gas chromatography. You can see the huge error bars and noisy data in the Figure.  The modern study uses a radioimmuno assay using antiserum, and is presumably far more sensitive.

I was also going to mention a nice review paper that summarizes more findings, but apparently I can only post 2 links as a new user.  So I'll just paste the abstract and citation.

    Light is a potent stimulus for regulating the pineal gland's production of melatonin and the broader circadian system in humans. It initially was thought that only very bright photic stimuli (≥ 2500 lux) could suppress nocturnal melatonin secretion and induce other circadian responses. It is now known that markedly lower illuminances (≤ 200 lux) can acutely suppress melatonin or entrain and phase shift melatonin rhythms when exposure conditions are optimized. The elements for physical/biological stimulus processing that regulate photic influences on melatonin secretion include the physics of the light source, gaze behavior relative to the light source, and the transduction of light energy through the pupil and ocular media. Elements for sensory/neural signal processing become involved as photons are absorbed by retinal photopigments and neural signals are generated in the retinohypothalamic tract. Aspects of this physiology include the ability of the circadian system to integrate photic stimuli spatially and temporally as well as the wavelength sensitivity of the operative photoreceptors. Acute, light-induced suppression of melatonin is proving to be a powerful tool for clarifying how these elements of ocular and neural physiology influence the interaction between light and the secretion of melatonin from the human pineal gland.

Photic Regulation of Melatonin in Humans: Ocular and Neural Signal Transduction
Brainard, Rollag, and Hanifin
J Biol Rhythms December 1997 vol. 12 no. 6 537-546

If you need more information, I'd start by checking the papers cited by the second paper. Alternately, there's probably more historical information available by looking at papers which have cited the first one.


The origin of molecular machines DNA holds genetic information and holds the key to the evolution of living organisms. Transcription and translation mechanisms enable living cells to process information encoded in DNA. To that end, transcription and translation are fundamental mechanisms needed to enable the evolution of organisms. Molecular machines (enzymes) carry out these mechanisms by reading the information in DNA and using it to construct proteins.

Did the first living cell contain the machinery needed for translation and transcription? or  Did they evolve over time?

EDIT: Edited the question to narrow the scope.

The main hypothesis is that all starts from RNA. "The RNA world". There was no DNA and no proteins. Both function was performed by RNA. Now there are no living organism that carrying information in RNA (only viruses...), but there is "enzymes" from RNA - ribozymes.
The evolution to DNA was later, according to this hypothesis.
There is really good article in wiki.
http://en.wikipedia.org/wiki/RNA_world_hypothesis
or if you want something more look here
http://www.ncbi.nlm.nih.gov/books/NBK26876/

Summary

  From our knowledge of present-day organisms and the molecules they contain, it seems likely that the development of the directly autocatalytic mechanisms fundamental to living systems began with the evolution of families of molecules that could catalyze their own replication. With time, a family of cooperating RNA catalysts probably developed the ability to direct synthesis of polypeptides. DNA is likely to have been a late addition: as the accumulation of additional protein catalysts allowed more efficient and complex cells to evolve, the DNA double helix replaced RNA as a more stable molecule for storing the increased amounts of genetic information required by such cells.


Why do sneezes come out the mouth? As anyone who's ever sneezed can tell you, it's caused by irritation in the nose.  And the answer to a question on this very SE attests that "sneezing is a reflex, partially autonomous, to clear the nasal cavity of particles that don't belong there."

That being true, the sneeze mechanism is a little bit strange: if you hold your hand up in front of your face when you sneeze, you'll feel that all of the rapidly-expelled air that ought to be cleaning out your nasal cavity is coming out your mouth, not your nose.  In fact I don't think I've ever felt air coming out my nose when I sneeze.

So what's going on there?

I've pondered this question too.  It's very clear that when we sneeze, the expelled air comes mostly from our mouths.  However, at least as far as my own sneezes are concerned, some of the air comes from my nose as well.  I know that if I pinch my nose closed as I sneeze, my ears hurt and pop.  If my nose is sniffly, I usually notice mucus come out.  Our soft palate partially lowers and our tongue rises as we sneeze, in order to divert a portion of the air up into our noses.  That position of our tongue is why our sneezes make a CHHH sound. If people intentionally keep their mouths wide open as they sneeze, that could explain why nothing comes from their nose, as there's nothing to divert the air.


Evolution: Can the genotype frequencies change, but the allele frequencies remain constant? If a population isn't evolving because it's in Hardy-Weinberg (HW) equilibrium, then I know that both genotype and allele frequencies must stay constant.
My question is, can evolution still not occur even if Hardy-Weinberg conditions aren't met? In all of my books, the conclusion seems to be that if HW conditions are met, then evolution doesn't occur. However, they don't clarify if HW conditions being met is both a necessary and sufficient condition for evolution to not occur (they only imply that it's sufficient).
Any thoughts?

Where do you get that populations aren't evolving?
A population might be in HWE for a particular trait if there is no selection on that trait, but that doesn't mean that there is no selection or drift happening on any trait!


When there's a wound, the end result is a thrombus or thrombosis? When there's a wound, the blood vessels are damaged. To stop the loss of blood, the clotting cascade starts off and forms a clot. This clot is a thrombus, right? Seems like perfect physiology. Where does the clot occur? As in, if we consider the vessel to be a pipe, the clot is formed at one end to block the flow or is attached to the wall of the vessel on one side?

This doubt arises because thrombosis (considered pathological) is defined as a clot within a blood vessel. Is the same not happening when there is an injury? If we consider the clot formed at one side of the vessel wall, doesn't it become thrombosis? Even if the clot is like a plug, it has to be attached to the wall, right?

In short, what is the difference between a clot due to a wound and one thrombosis (due to the Virchow's triad)? Where are the clots attached in either cases?

Here are a couple of distinctions,

1) The thrombus is the actual blood clot

2) Thrombosis is the condition of having a clot form in the blood vessel.

3) If the thrombus breaks away and becomes capable of traveling to some distant site, we refer to that as an embolus.

4) If the embolus lodges somewhere disrupting blood flow, we call that embolism, or in the case of a thrombus, thromboembolism.

So referring here, a protein called tissue factor is expressed on the outside of blood vessels, and when ruptured, is exposed to the blood stream that carries Factor VII. This initiates the coagulation response, and through the action of these factors you get platelets sticking to the endothelium, thrombin cleaving fibrinogen to fibrin that sticks to the platelets, and the fibrin/platelet plug forming over the wound is like a gel and RBCs become mired in it. So really, the thrombus is stuck to the endothelial wall.


how do macrophages have the capacity to digest pathogen in opsonization how do macrophages  have the capacity to digest pathogen in opsonization but not in the            first time when the pathogen is new  and they play the role of antigen presenting cells(APCs) first they digest polypeptide of antigen and then let the plasma cells first secrete an antibody and after that they can destroy antigens?

It's a simple matter of ionic charge

Opsonization works because it is masking negative charge with positive charge. Phagocytosis works on positively charged things.

Your right though, the sequence seems odd.

First something is phagocytosed (by a macrophage or another monocyte-derivative, these are the APCs... but neutrophils, which are not APCs or monocyte-derivates also perform phagocytosis but they dot not have the MHC-II to be described)
then digested in endosome/lysosomal,
then presented on the MHC class II,
recognized by TCR on T-cell,
then much more complicated stuff to get to B cells to convert to plasma cells
plasma cells secrete the antibody, in order for opsonization of the pathogen to be phagocytosis more easily.

Yet it was the initial phagocytosis that led to this. A bit of a circle.

Here are three answers:

one is cytokines
another one is about how the TLR receptor mediates phagocytosis
a third is how complements act as opsonins

local presence of cytokines (ex. interleukins, interferon, TNF) from either innate or adaptive "immune system" (by "immune system" I mean immune cells other than macrophage, but also epithelium which secretes types of interferons) that lead to "signal transduction" ("signal transduction" is the intracellular chain reaction in response to the activation of the cytokine (or other ligand) binding to the receptor, too complicated for me to explain) that alters the behavior of macrophage to enhance phagocytosis.

On the other hand, PAMPs activate the TLR which could permit phagocytosis without prior activation from sources "other" than the thing being phagocytosis.

By "other" things I mean opsonins and cytokines.

PAMPs (pathogen associated molecular pattern) are things on the pathogen that are distinctively foreign to the host, like flagella or LPS [which is the outer membrane from gram (-) bacteria]

TLR is the receptor on the macrophage that recognizes PAMPs. I think that TLR simply enhances phagocytosis via signal transduction much like cytokines. As an interesting side note, the TLR is quite ancient in kingdom animalia, having it's origin in sponges  as close to the beginning as you get). Other aspects of the immune system evolved later on specifically in vertebrate. In fact the lymphocytes is unique to jawed vertebrate (aka absent in agnathans and invertebrate) and i don't know much about antibody production in non-mammals. Also in lower vertebrate and invertebrate, phagocytosis is done by hemocytes. In other words, the TLR is pretty fundamental as far as immune stuff goes, more so than cell types doing their things (ex. plasma cell making antibodies, macrophages doing phagocytosis).

But there is also complement mediated opsonization, primarily C3b but other complement proteins as well. Finally there are yet more (less important) opsonins, Mannose-binding lectin and C-reactive protein (CRP). all of these things are "Acute phase reactants" that are secreted by the liver under inflammatory conditions, mediated by cytokines. Complement is not always activated by the immunoglobulins.

Complement is activated by

classical pathway, again Fc region of antibody (IgG/IgM), just like antibody mediated opsonization. In addition, classical pathway can be activated by CRP binding to microbial polysaccharides

alternative pathway, which is the spontaneous hydrolysis of C3. Under normal (non-infected) circumstances, this is normally prevented by a variety of mechanisms.
activation by mannose binding lectin. MVL recognizes certain sugars that are found in certain positions that are unique to bacteria, fungi, viruses.

I'm saying all these things as explanations of human immune system. It's probably different in different animals, the more different the further away from human. The complement system has been discovered in primitive vertebrate (agnathans) and invertebrate (specifically in deuterostomes like protocordates and echinoderms) but there are variations.


When was it determined that Type 1 Diabetes is an autoimmune disease? I just found out today that type 1 diabetes is an autoimmune disease.  When was this discovered?

This question has two answers: The difference was first described in 1936 by Harold Percival Himsworth, which described it in this article.
At this time it was established that there are two forms of Diabetes, one sensitive to insuline while the other is not.
The terms Diabetes type 1 and 2 where established somewhere between 1974 and 1976, for details see the review "The discovery of type 1 Diabetes".


Why is competitive inhibition reversible? My Biochemistry book mentions that 'competitive inhibition' is a reversible form of inhibition. But given that the inhibitor is blocking the active site and prevents an enzyme-substrate complex to be formed, how can it be reversible?

A competitive inhibitor typically competes for the active site with the substrate. In this textbook case, binding of a competitive inhibitor is reversible, because it binds to the active site of the enzyme, but is also released, making way for the substrate to bind. The affinity of the substrate, as well as its concentration determine the amount of inhibition (Berg et al., 2002).

An irreversible inhibitor may covalently bind to the active site, permanently disabling the enzyme (McDonald et al., 2012).

References
- McDonald et al., Enzymes: Irreversible Inhibition. In: eLS. John Wiley & Sons Ltd, Chichester (2012)
- Berg et al., Biochemistry. 5th ed. New York: W H Freeman; (2002)


Where is pollenkitt secreted? Where is the pollenkitt material secreted? I think the tapetum would be a good candidate, since it provides nutrition to the pollen grains.

The correct name of the coating is "pollenkitt", not "pollen kit" (I edited your question accordingly).

From the book "Biology of pollen" (Shukla, Vijayaraghavan and Chaudhry, 1998):

  The term pollenkitt is used for the oily, pigmented and sticky coating deposited on the pollen grain surface during the final stages of maturation. (emphasis mine)

That may explain why you and others struggled to find an answer in Google/Google Scholar.

Back to your question: there are two types of adhesive coats in pollen grains:

Pollenkitt
Tryphine

Pollenkit is the most common one and, as tryphine, it is secreted by the tapetum.

According to Pacini and Hesse (2005):

  Two types of sticky pollen coat material exist in angiosperms, both produced by the anther tapetum. Pollenkitt is the most common adhesive material present around pollen grains of almost all angiosperms pollinated by animals, whereas tryphine seems to be restricted only to Brassicaceae. (emphasis mine)

Sources:

Pacini, E. and Hesse, M. (2005). Pollenkitt – its composition, forms and functions. Flora - Morphology, Distribution, Functional Ecology of Plants, 200(5), pp.399-415.
Shukla, A., Vijayaraghavan, M. and Chaudhry, B. (1998). Biology of pollen. New Dehli: APH Publ. Corp.


What determines whether I will have any dream or not? Sometimes I have many consecutive "dreamfull" nights but sometimes there is no dream during week. Why? What determines whether I will have any dream or not?

According to the DreamResearch.net of UCSC, typically, we dream up to 10 times a night (sometimes more, sometimes less), and it is likely that on those nights when you feel that you have not dreamt, you may have forgotten the dream.

Dream amnesia is very common, where we forget most of the dreams (an any instances of sleep walking etc), this article Dreaming: A Neurocognitive Approach has more of the study.


What are the advantages of heterologous expression systems? I am doing research in a lab and I am relatively new to wet lab work. Many experiments that people are doing in my lab include overexpressing a protein of interest from another species (e.g. mouse) into CHO cells via transfection. I have learnt that these are examples of heterologous expression systems.
I was wondering in general, what are the advantages of heterologous expression systems? I have read that you can use them to study the function of a protein in a well-defined, controllable environment. However, I was wondering what other benefits/uses are there to these kinds of experiments?
Any insights are appreciated.

It takes significant resources to establish a cell line. More efficient to use existing lines.

Often cell lines used for expression grow faster. This is why so many proteins are expressed in E coli - they only take a day to grow vs the week or two for mammalian cells, meaning you get a much faster learning iteration in your research.


What are the physiological effects of wine? I have read that alcohol in general and wine in particular can have advantageous as well as detrimental effects on human health. Is this true? What are the physiological effects of consuming wine in moderate quantities?

It is undisputed that heavy alcohol consumption (of any variety) leads to many deleterious effects on health.

It has also been claimed, however, that low to moderate alcohol intake can in fact be protective against some medical conditions (in particular, cardiovascular and cerebrovascular events). That is, there is often said to be a 'j-shaped' curve relating alcohol consumption to mortality and morbidity: low to moderate intake actually slightly reduces risk of adverse events relative to people who abstain completely from alcohol, but the risk increases markedly as consumption becomes heavy. See Plunk et al (2014): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3872245/

Sometimes the protective association is attributed to the alcohol content itself (i.e. the ethanol), and sometimes to non-alcohol compounds (often specifically those found in red wine). The existence of such a possible protective effect at moderate doses is not a controversial position but it is also not settled science as yet. You should make up your own mind by reading reviews and ideally meta-analyses in the area. As a starting point, this 2013 review by Chiva-Blanch et al. in the journal Alcohol & Alcoholism has been well-cited by other researchers and is available to read in full here: https://academic.oup.com/alcalc/article/48/3/270/244770


Why is glycine considered a nonpolar amino acid but a polar molecule? Glycine has a dipole moment, so why is it considered a nonpolar amino acid when discussing its occurrence in proteins?

Also, is the backbone of a protein nonpolar?

The first part of your question illustrates a common confusion of beginners between the physiochemical properties of free amino acids in solution, and the properties of that part of an amino acid that remains after it has participated in a condensation reaction to form part of a polypeptide. They are different. (It was for that reason that I modified the question to make it clear that the ‘consideration’ of glycine as nonpolar applies to it in its protein context.)

I have prepared a diagram to clarify.

As can be seen on line 1, all free amino acids at physiological pH are charged because of the pKa of the  α-amino and α-carboxyl groups (proline, as an imino acid is the exception). The chemical features common to all amino acids are shown in blue, for the second amino acid, and the unique feature — wherein amino acids differ — is shown in red.
To show amino acid 2 in the context of a polypeptide chain, I have condensed it with two other amino acids (1 and 3) to produce a tripeptide (line 3). (This is the situation most amino acids in a long polypeptide chain will be in, as there are only two that will be at the ends.)
You can see from the colouring that what is left of the amino acid in the protein — the amino acid residue — has lost the charges of the α-amino and α-carboxyl groups, which have become parts of peptide bonds. (A molecule of water is removed in a condensation.)
The properties that a particular amino acid endows to a protein are those of the ‘R-group’— R2 in the diagram. In the case of glycine, R is H, so that in the context of proteins we regard glycine as a non-polar amino acid (The C-H bond has a negligible dipole.)
Don’t confuse R with residue. It is a side-chain, designated using a common chemical abbreviation.

The second question was “is the backbone of the macromolecule nonpolar?”.

No. The backbone of a protein has partial charges on the oxygen and nitrogen atoms of the peptide bond, as shown below. This is because it has a partial double-bonded character. These partially charged atoms can (and frequently do) form hydgrogen bonds, either with another part of the backbone (secondary structure such as α-helix or β-sheet) or with polar side-chains.

Reading

Berg et al. Section 3.2 covers the basics (although it fails to emphasize the difference in properties of amino acids and amino acid residues) and Section 3.3 covers the role of the peptide bond in protein secondary structure.


How does boiling water revive cut flowers? A classic tip to revive wilted cut flowers is to plunge the stem into boiling water for some period of time, and then back into cold water.

What process is occurring that causes the flower to be "revived"?

I could not find any scientific papers that have done research into this phenomenon but the general reason given for wilted flowers to being resuscitated is given as the hot water being absorbed faster and I quote

  Florists use warm water only for resuscitating wilted flowers, because
  warm water is absorbed quickly. For restoring wilted stems, hot water
  (110 degrees Fahrenheit) is recommended. For woody or badly wilted
  stems, very hot water (180 to 200 degrees) is better. Florists then
  move them into a refrigerator (reference).

The reason for absorbtion faster is given as

luke warm water in a vase arrangement because warm water is “thinner” (has fewer air
bubbles) and moves up the stem faster than cold water (reference) and Warm water molecules move faster than cold water molecules and so can be absorbed by flowers with greater ease (reference).


How to determine if two mutations in a gene are on the same or different alleles? I would like to know, except a familial study, is there another way to determine if a mutation/variation is cis or trans (i.e. on the same or different alleles)? For example by sequencing technique or other molecular biology procedure.

CIS               TRANS

+  +              +  +
|  |              |  |
A  |              A  |
|  |              |  |
B  |              |  B
|  |              |  |
+  +              +  +

Thanks

Yes, it can be determined by sequencing but the sequencing read has to be long enough to span both the mutations. PacBio sequencing allows long reads but it also has higher error rate than the short read sequencing platforms like Illumina. If you know the gene locus then you can amplify the region using PCR and use Sanger sequencing too (for this the amplicon has to be cloned in a plasmid, transformed into bacteria and then single colonies must be sequenced; see Why does one combine PCR and cloning as ways for amplification of sequences?).

Another possibility is to look at the RNAs from this gene. If the two alleles have different expression then comparing the number of reads for each mutation might tell if they occur together. However, as I said it already depends on the two conditions: expression and dissimilar expression.


What chemicals and structures control the *direction* of plant growth in leaves, stems and roots? If you want a specific plant, let's say the snap peas I am growing that I bought at Agway. I noticed that they grow towards the light source through the nearby window. Also I think roots work the same way for water/minerals. also don't various kinds of ants find food conceptually identically?

How much of this is true? Please correct:

I think analogous to ant colonies, plants will attempt to grow every which way initially, and will only continue growing in directions that give the most/enough light/water/minerals. If a direction is or becomes unfruitful, that section withers. After the initial state the plant will start branching in directions off of locations on still growing sections of plants and that cycle continues until none of the plant can be supported and the whole thing withers (perennials) or slows its metabolism down to the point where it could survive those conditions until they picked up again (such as winter seasonal survival of tree species). Also, it is not as if they decide which direction to go in. that type of decision would forgo going in another direction. And not sure, but I don't think plants have decision capabilities anyways. they grow in directions they grow best.

PART 1 : Phototropism

The movement of plant shoot towards light is called phototropism. This process is mainly stimulated by the blue light. The photoreceptor involved is called Phot1 (Phototropin 1) or JK244.

Auxins such as IAA (indole acetic acid) are plant hormones, expressed highly in meristem, which cause shoot growth. On illumination this phototropin, through currently unknown messengers, causes inhibition of polar Auxin transport in the illuminated side. This causes the non-illuminated side to grow more and thus bending the plant towards light.

The image represents an older model which proposed lateral movement of auxin. The mechanism mentioned in last paragraph is the currently accepted model. The below figure illustrates 'polar auxin transport'

For details refer to this nice review on phototropism.

PART 2 : Geotropism and Hydrotropism

Geotropism or gravitropism is movement of roots towards earth (gravity) and hydrotropism is movement of roots towards water. Both phenomena interact with each other and share some common pathways. But hydrotropsim can inhibit geotropism and it is evident in conditions when root goes towards an adjacent water source.

Ethylene and Auxin signaling is involved in root growth both in geotropism and hydrotropism. In geotropism the auxin is stimulated by statoliths (clustered and membrane bound grains of starch) in the amyloplasts- the organelles which store starch. The model suggests that amyloplst sediments under the influence of gravity and thereby affect auxin polar transport (the second figure co-incidentally illustrates polar auxin transport in geotropism).

The exact moisture sensor is unknown but Abscissic acid (ABA), which is well known for its involvement in drought tolerance, is known to affect hydrotropism.

MIZ1/2 are some proteins uniquely involved in hyrdotropism.

Both pathways are dependent on Calcium as a secondary messenger.
To conclude, these pathways are not as clear as those of phototropism.

Reference:

http://www.academicjournals.org/ajar/pdf/Pdf2006/Nov/Dexian%20and%20South.pdf
http://www.sciencedirect.com/science/article/pii/S1360138504002717
http://www.plantphysiol.org/content/133/4/1677.full


What is happening at the electrode interface when the electrical field is modified due to the change of ion concentration after an AP? I have been working for quite a while now on electrophysiology and electrode fabrication.

I studied what is happening at the neuron level during an action potential (polarization/depolarization, change in ion concentration inside/outside the cell membrane) as well as the interface electrode/electrolyte (double layer, electrical model of an electrode, etc...), but I am still struggling to tie all of those principle together.
My question is, what is actually happening when an electrode is recording an AP (extracellular recording). To my knowledge, this is what is happening:

AP triggered, change of ion concentration outside the cell membrane.
As the ion concentration is modified, electrical field is modified around the cell

My question is now, how does the electrode record this change of electrical field? In almost all of the literature, a simple, but unexplained, shortcut is usually done: the authors usually speak about the change in ion concentration and then directly link it to a "change of potential at the electrode", but how can we explain this change of potential? What is happening at the electrode interface when the electrical field is modified due to the change of ion concentration after the AP? Is there any current flowing inside the electrode?

Thank you in advance

There is an art to expressing the nature of any kind of uncertainty in writing, and especially in experimental literature, to stating no more than has been empirically shown.  An electrode interface only measures a one dimensional trace of what actually happens during an action potential cycle or spike, and it could be that in most of the literature, the precise mechanism by which the spike is measurable takes lower priority than the existence (or non-existence) of a particular signal.
According to Hodgkin-Huxley theory, the action potential is controlled through changes to the ionic permeability of certain membranes.  The precise mechanisms by which this happens depend on the molecular structure of channels through which sodium and potassium ions flow.  However, it is not hard to explain how a change in the permeability of a membrane can cause changes to an electric potential gradient (over 'large' length scales); the "deep concept" at work here is the second law of thermodynamics.
Let's suppose that you have two ions, one positive and one negative, confined to one side of a box as shown:

You might notice that there are more negative ions than there are positive ions, so there would be a nonzero electric potential gradient between the left and right hand sides of the container.
Now let's suppose that the confining membrane is replaced with one that allows only negative ions to pass (through the purple or tapered channels.)  You might expect a fraction of the negative charge to flow over to the other side of container where the potential is slightly higher (as shown):

The result is that the original potential gradient (from left to right) is dampened slightly.
The OP is probably aware of this, but it turns out that replacing the membrane with one that allows positive charge to pass through results in a fraction of the total positive ions moving to the left side of the chamber (even though it would be attracted to the right hand side by the net negative charge)*.  The reason for this is that the entropy gained by the first positive charge to move into the (log-macroscopically large) empty chamber vastly outweighs the (microscopic) entropy cost of leaving the occupied chamber with fewer positive ions to offset the negative ones.

This results in a slightly larger potential gradient than in the first (impermeable) case, as there are now positive charges in the region of higher electric potential.
The electrode can pick up on changes to the potential gradient by "grounding" the circuit at several points.  In particular, this requires a circuit that is soft or sensitive enough that it does not disturb the ambient potential significantly (a tape measure or height rod adapts to your height, not vice versa.)  That is, whatever current flows between the electrodes should be weak enough that it does not completely drain or equilibrate whatever local potential difference might exist, and other circuit elements should be weak enough that they do not cause flooding or, in a sense, drought of the natural electrodynamic state.  Beyond this, the complex and densely packed environment of neurons would make it a challenge to place electrodes to isolate a single action potential, or even a potentially useful signal across several action potentials.  Also, there is inevitably a certain amount of excessive unnatural current flow below a certain length scale (the scale at which the electrode starts to look like a bulk conductor.) Because of this, neuroscientists probably care more about the presence or absence of noise at this point than about the precise physiological origin of the signal, except insofar as the disturbance from the electrode is correctable and within tolerance.
*If the experiment is performed at nonzero temperature, which seems to be unavoidable.


what is the modern, molecular explanation of independent assortment of alleles? in case it isn't obvious i'll begin by stating that i'm a layman, trying to understand something about this subject from reading books. the books i've looked at so far give murky and confusing accounts of meiosis (example: a schaum's outline refers to chromosomes that are "identical, but not the same"), and they always seem to duck the questions i most want answered. what i'm reaching for right now is a coherent, schematic understanding of meiosis. i'm aware that the real world is messier than that, but there clearly is a simple schema that accounts for the most typical cases of meiosis in an approximative fashion. in particular, there must be some way of deriving the approximate correctness of mendelian independent assortment of alleles from the molecular process of recombination.

here's what i think i can make out so far: if two chromosomes x1...xn and y1...yn get paired together then some number of interstices (spaces between successive loci) get picked and each chromosome gets broken at each interstice. after crossover each of the two resulting chromosomes have x-segments alternating with y-segments. for example if only one interstice is picked, and it's between the k-th and (k+1)-th loci, then the chromosomes that are there after crossover are x[1]...x[k] y[k+1]...y[n] and y[1]...y[k] x[k+1]...x[n]. it also seems clear that all interstices are equally likely to get picked. have i got at least this much right? and if so, how many interstices get picked?

also, if anyone knows a book that might suit my needs i would obviously be glad to hear about it. thanks if you can help

peace
stm

Parts of your general idea are correct, others need some refinement. To skip ahead to the conclusion: I'm going to recommend that you read up about linkage disequilibrium. Everything else is background information that will hopefully help you understand why linkage disequilibrium is what I think you're looking for.

Background: Meiosis Basics

Firstly, in the bare principle, meiosis is quite simple. Let's consider meiosis in a human cell, i.e. the division of a primary spermatocyte (the only other example is division of primary oocytes). That's this one we're talking about: http://en.wikipedia.org/wiki/File:Figure_28_01_04.jpg In simple terms, the ready-to-develop primary spermatocyte contains 46 chromosomes, two (2n) each of chromosomes 1-22, an X and a Y chromosome. Two chromosomes of the same type (e.g. "chromosome 4") are called homologues. Homologues contain different versions (= alleles) of the same genes. During Meiosis I, homologues align in pairs, recombine, and then separate into two new cells (which are now 1n). The following Meiosis II is basically a mitosis, meaning that the two (identical apart from previous recombinations) chromatids of the chromosomes are separated and packaged into separate cells.

Recombination and Interstices

During the alignment of homologues in Meiosis I, the attraction between the two chromosomes depends on their homology - i.e. similarities in DNA sequences that end up being close to each other in this setting. This attraction is on the molecular level, so the tightly-condensed neighbouring DNA double-helices actually physically stick to each other because the polarities/charges across relatively large stretches of the molecules complement each other. I don't think how this exactly works is well understood yet, but what is clear is that homologues attract each other at this point because they contain mostly the same DNA sequence, apart from small differences (which make the different alleles).

How exactly recombination occurs at this point isn't entirely clear either on the molecular level (http://en.wikipedia.org/wiki/Homologous_recombination#In_eukaryotes). Just to get an idea of how it could work: while the two chromosomes are aligned, it's not difficult for them to actually tangle up and break, leaving the repair machinery with the potential to fuse the wrong chromosome ends together. The breaking and exchange might also be a programmed process with dedicated cell machinery (quite probably so I think personally).

In any case, not all locations are equally likely to recombine. It depends on levels of homology (i.e. "stickiness") between individual stretches of DNA and other unknown factors. Just in the same way, the number of break points in each chromosome isn't pre-determined.

Mendelian Inheritance

First of all, the concept of loci is arbitrary and has no molecular basis. A locus is simply "a place on a chromosome" and could refer to an individual base(-pair) or a whole stretch of DNA. The concept is however useful when talking about inheritance, as it illustrates the principle of linkage, or rather linkage disequlibrium.

As far as I am aware, it comes from a time before we began thinking in chromosomes. One could study whether there was linkage between two traits (or more generally loci), i.e. a higher-than-random chance to inherit the two together. We now know that linkage simply means that the two loci are on the same chromosome (for example, chromosome 6). Thus, if no linkage exists, the chance to inherit both loci together is no larger than expected by random Mendelian inheritance (which makes sense as there is no molecular mechanism that makes offspring e.g. more likely than 50/50 to inherit chromosome 6 and 19 together from the same parent). If linkage exists , the loci are on the same chromosome, and any case where the two are not inherited together must be caused by recombination.

The idea of linkage disequlibrium is that loci that are close to each other on a chromosome are more likely to remain together (and be inherited together) than far-apart loci. This is obviously due to the increased chance of a recombination event occurring between them with increased distance. This actually seems to be what you are looking for as a pointer for where to go next, so I recommend using your preferred internet search engine to learn more about that :)


How are dental cavities different from body injuries? I always had this question why dental cavities cause pain. I stumbled on this question on the reasons why dental cavities are painful. I have a followup question on how dental cavities are different from bodily injuries. I was under the impression that pain causes inflammation which in turn triggers something like mitosis that causes healing. Why does the same not happen with the dental cavities? Why are they not treated like the bodily injuries?

I disagree with some of these statements. Dental cavities are injuries and are treated like injuries warrent.

Unlike maybe trauma or cancer, dental cavities are a injury caused by decay of the enamel (the protective hard shell of the tooth). The decay is a result of the proliferation of bacteria, streptococcus mutants which releases an acid and breaks down the tooth.

When you have perforated enamel, other particles like food can get caught in the tooth and give rise to the growth of other bacteria. At this point you have a cavity.

Infection, the presence of certain toxins, and trauma all causes inflammation, a type of non specific immune reaction characterized by increased blood flow to the site of injury (which causes swelling, pain, redness).


Identify the caterpillars These are the two caterpillar I found at Taipei, Taiwan. Can anybody help me identify the species. The first caterpillar is about 6-7 cm long and the other one 10-12 cm. Thanks in advance!

This is actually not easy - for the first one I am sure that is a caterpillar from order Orgyia and the family Erebidae, but since there is a vast number of different caterpillars on all continents, I am not sure which one it is exactly.
If you look at this image (from here), you will see a striking resemblance:

A lot more information on these moths can be found here.

The second one is most likely Trabala vishnou ssp. guttata, see the image (from here) for comparision:

There seems to be very little information available, some on the Wikipedia page.


Extra-mitochondrial conversion of Acyl Carnitine to Acyl CoA Normally fatty acids in the form of acyl CoA are converted to acyl carnitine in a reaction catalysed by carnitine palmitoyltransferase I (CPT1), which is also known as carnitine acyltransferase I. This allows them to be transported across the inner mitochondrial membrane by a translocase when the acyl CoA is regenerated in a reaction that is chemically identical but catalysed by a different enzyme, carnitine palmitoyltransferase II (CPT2).

As a result of observations I have made (detailed below) I wish to known whether acyl carnitine that has not entered into the mitochondria — either present in the cytosol or blood/plasma — can be converted back into acyl CoA without entering mitochondria?

Essentially, does a reaction like that catalysed by CPT2 occur outside of the inner-mitochondrial matrix?

Elaboration

I'm studying plasma metabolites. During fasting there is an increase in plasma acylcarnitines due to increased fat utilization/beta oxidation. If the fast is broken, acylcarnitines are typically supposed to drop. Oddly, some people experience an increase in plasma acylcarnitines 0-30 minutes following eating - but then they drop after the 30 minutes. I'm confused as 30 minutes after food ingestion, elevated circulating insulin levels are still present and should be still working to inhibit the majority of fatty acid oxidation - yet the odd increase and then drop in acylcarnitines after 30 minutes of food intake still exists.

So it leaves me with the question, is there another pathway in which acylcarnitines are converted back to acyl CoA outside of the mitochondria? In short, how does the cell recall fatty acids that are destined for the mitochondria?

The introduction to Ann N Y Acad Sci. (2004) 1033:17–29 lists the various carnitine acyltransferases and mentions CPT-1a, CPT-1b, CPT-1c (tissue specific) but states there is only a single CPT-2 in humans. It does not appear that there is any other variant, so extra-mitochondrial conversion of acyl carnitine to acyl CoA would require a post-translational variant of CPT-2, or CPT-1 working in the reverse direction.
The discussion of carnitine metabolism in Berg et al., Section 22, implies the reaction is near equilibrium. Hence, if the concentrations of substrate and product were appropriate it would be thermodynamically possible for CPT-1 to operate in the reverse direction.
Thermodynamically possible does not necessarily mean enzymically possible. I am not familiar with kinetic studies on CPT-1 and CPT-2, but imagine that CPT-1 has a higher affinity for acyl CoA and carnitine than for the product acyl carnitine, and that the reverse situation holds for CPT-2. I imagine that the ability of CPT-1 (or one particular isoform) to catalyse the reverse reaction in physiological circumstances would depend on its Km for acyl carnitine and the concentration of the latter. It might be worth seeing what kinetic analysis has been done.
The ‘appropriate’ situation for (2) might be if something were preventing utilization of acyl carnitine in the mitochondria of ‘target’ cells.
If you work in this area you will know better than me that there are various clinical conditions and sub-clinical conditions (e.g. obesity) that result in abnormal utilization of acyl carnitine. Could the abnormal instances you observe be for such individuals?


What is this plant, and should the lowermost leaves be curling up? We've got a couple of these plants but have no idea how to look after them. Watering them regularly (every 2-3 days, or when the soil seems dry) seems to help. The pot rims are about a foot at their widest part.
However, we're concerned about the lower leaves drying up. Is this a normal part of this plants growth process and does it continue this way and produce a 'trunk' of sorts?
As a follow on question, do we need to re-pot these plants?

I may be wrong, but I believe these are two Foxtail Agaves (Agave attenuata). These resources may help you take care of them.
Foxtail Agave Care Information
And for the wilted leaves:
How to Save a Dying Agave Plant
Also, the Gardening SE may be able to help more.
Hopefully this helps!


What is a good identification key for European mushrooms? I live in the Netherlands, and I am looking for an identification key for mushrooms.
Are there any keys you could share?

There are various types of Mushroom identification Sites. you can take help from:

Mushroomexpert
Rogersmushrooms
MycoKey 4.0

Source: MycoKey 4.0


How much does hearing deteriorate with age? For the average person, what is the lowest volume of a pure tone at each frequency they can hear as a function of age?
I know some people lose hearing faster than other people, because they are exposed to loud sounds. So I am also interested in hearing loss induced by loud sounds as a function of frequency.
The brain can adapt to the hearing loss, thereby creating the illusion that a sound is just as loud as if nothing happened to their hearing. For that reason, I also wish to know what volume the ear transmits to the brain as a function of frequency and age.

Hearing sensitivity deteriorates with age, which is called age-related hearing loss, or presbyacusis. Presbyacusis is characterized by elevated hearing thresholds. Especially the high frequencies are affected by age, but eventually even the low frequencies may deteriorate substantially. Hearing sensitivity is typically expressed in an audiogram, which depicts the hearing threshold as a function of acoustic frequency. To express hearing loss as a function of age, however, it is more convenient to plot the threshold at various frequencies as a function of age (Fig. 1).

Fig. 1. Hearing thresholds at various frequencies plotted as a function of age. source: Handbook For Acoustic Ecology.

Exposure to loud sounds may be detrimental to hearing, referred to as noise-induced hearing loss. Typically this results in a loss of sensitivity at the moderate frequencies (3k to 4k); a mid-frequency dip (Fig. 2). Old age will add a high-frequency hearing loss on top of that.

Fig. 2. Typical audiogram associated with noise-induced hearing loss. source: American Hearing Research Foundation

The brain will not adapt to elevated thresholds. A threshold represents the minimal intensity level a sensory system can detect. Elevated hearing thresholds due to old age and noise-induced hearing loss are caused by sensori-neural hearing loss, meaning the hair cells in the inner ear (the cochlea) are dying. The brain can never detect a signal that is not transmitted via the auditory nerve and can hence never compensate for elevated thresholds. In turn, when thresholds are elevated substantially, a person suffering from such a hearing impairment may ask you several times kindly to repeat what you were saying, but a little louder. Then, when you start screaming after the third time, the hearing-impaired person returns the dreaded "You don't have to scream at me!". That is because the brain does not adapt to the elevated thresholds; once the sound is transmitted by the degenerated cochlea, it is transmitted at that loudness and perceived at that loudness by the brain. Moreover, a process of recruitment can occur in the hearing impaired, where the perceived loudness is exaggerated. Recruitment may occur at the hair cell level, but it is a not well characterized phenomenon.


What effect does vortexing have on a fluid sample that simple mechanical shaking does not? Some protocols call for fluid samples to be mixed with a "vortexer" on the high setting.  What effect does the vortexing have on fluid samples that mechanical shaking does not?  Does it shear long molecules like DNA, for instance?

A friend is setting up a new lab and asked if vortexers were strictly necessary.  I am aware they are often called for in various protocols, but I actually don't know what specific effect the vortexing has that makes it better than manual shaking.  What do you think?

In my experience, shaking and mixing have different "dead spaces". Supposed you had an eppendorf tube and you stirred it around with a pipet tip for thirty minutes. You would have great convective mixing in the radial direction but virtually no mixing in the Z-direction. Supposed you had a very viscous fluid like PEG. If you set the tube on a shaker for an hour it will virtually not mix. The vortexer provides a very different profile of mixing.

Instances where I wouldn't use the vortexer would be for sensitive objects like DNA and cells.

(update)
We had some interesting suggestions from the FDA (since the FDA pays attention to these type of discussions). To get proper mixing, it is often not considered enough to merely swirl a tube a bunch. Their actual recommendation is to train technicians to perform a 90 degree angle arc with their forearm to generate proper force in mixing.


Concept of mean systemic filling pressure Mean circulatory filling pressure (MCFP) in humans was defined by Guyton as "the pressure that would be measured at all points in the entiere circulatory system if the heart were stopped suddenly and the blood were redistributed instantaneously in such a manner that all pressures were equal".
Now according to many physiologists, there must be a location in the vascular network where the pressure is completely independent of the cardiac activity, and this pressure must be equal to the MCFP. Apparently, this was already noted by Starling in 1897. The entire point is well explained in this article.
I have read this article and some others introducing the concept of MCFP to medical students; many of them report the same observations made by Guyton, Starling, etc., but a point which is never addressed is why there must be a location in the vasculature where the pressure is independent of cardiac activity.
I feel like getting a satisfactory answer to this question would greatly improve my understanding of hemodynamics, so I would be very grateful if you could explain the concept to me.

You've misread the linked article if you take this to mean there is some place that is unaffected by cardiac activity. It's just that there must be some place that is equal in pressure to the MCFP. The actual position fluctuates throughout the cardiac cycle.
The reason, though, that some place must be equal to MCFP is that pressure is continuous. Somewhere in the vasculature (i.e. proximal arteries) is definitely greater than the mean; somewhere else (i.e. proximal veins) is definitely less than the mean. Because the pressure varies continuously the function must pass through the mean at some point along the vascular path. This isn't anything special about biology, just mathematics.