How large are the inner ear hairs? I was always under the impression that the auditory hairs located deep within the ear, past the ear drum, are microscopic.

After taking a shower today, I was softly padding my outer ear with some tissue paper to dry any moisture, when some wax just got attached to it. What was unusual was that there were some hairs on it (3-5 perhaps, overlapping) that were about half a centimeter in length.

Are these just regular hairs that grow in the inner/outer ear? Or are they the ones that actually aid in hearing (the ones I thought were microscopic).

My question is to verify whether or not these hair shafts I observed are used in auditory perception. Either way, are these supposed to fall off?

Those are just ordinary hairs growing in your ear, like the kind you find in your nose and, if you are fortunate, on the top of your head. The "hair cells" of the inner ear aren't really "hairs" at all, they are totally different, and you would never find them falling out of your ear.

Hairs like on your head are protein filaments produced by follicles in the skin.

Hair cells in the inner ear, on the other hand, are sensory epithelial cells with stereocilia, which are protrusions of the cell membrane. Those membrane protrusions have mechanically gated channels which are coupled to nearby protrusions; when the whole cell is pushed one way or the other, that influences the mechanical stress on those channels and they open and close, which produces an electrical signal that can be sensed by the auditory nerve.

These special 'hair cells' are way way deep in your ear, past your ear drum, past three little bones that conduct sound into your cochlea. If you are touching those, you are in bad shape indeed - this is very very unlikely under normal circumstances.


Molecular biology - fundamental questions Basic Gene, Chromosome, Genome, Protein - how are they ordered?

Genes make up Chromosome, and Chromosomes make up a Genome...

So, where does Protein come into play?

What do you call Genes that are spliced together to form something new?

What do you call a variable inside a Gene?

Thanks.

where does Protein come into play?

A Gene codes a protein.
DNA is transcibed into messenger RNA (mRNA). mRNA is translated into protein.

What do you call Genes that are spliced together to form something new?

Genes are not spliced together. One single gene can consist of introns (intervening sequences) and exons (expressed sequences). Transcribed introns in the RNA are spliced out and the exons glued together to form a functional mRNA.

What do you call a variable inside a Gene?

Genes are made up of DNA. DNA is made up of nucleotides.


Breathing faster to lose (more) weight? I understand that when the human body loses weight, the vast majority of that weight is lost as $CO_2$ (and a small bit is lost as water). I expect the predominant way $CO_2$ exits the body is through exhaling.

So, let's take a human with no influx of carbon (they are not eating); I expect such a person is slowly losing weight, a near infinitesimal amount with each breath (correct me if I'm wrong).

If the person breathes faster (more breaths per minute), that causes an increase in the rate at which $CO_2$ is expelled, correct (more mass per minute)? Is this rate expected to decrease, i.e., as one breathes faster, less $CO_2$ is contained in each subsequent breath? Or, does perhaps the body mobilize and oxidize carbon fuels (carbohydrates first and eventually lipids) to generate $CO_2$ in an attempt to restore homeostatic equilibrium?

Could breathing quickly and heavily possibly cause an increase in the $CO_2$ content of exhaled breaths? That is, would voluntary hyperventilation cause an increase in heart rate (and thus increase in carbon catabolism)? How much $CO_2$ is in a typical exhalation during exercise?

I realize that without exercise, the amount of $CO_2$ being lost during normal breathing is nearly negligible. But perhaps laying down and breathing quickly could cause a measurable increase in the net rate at which mass leaves the body. What do you think?

Thank you for your time.

The rate of CO2 production is normally set by the rate of metabolism and breathing rate is determined by the level of CO2 in the blood.  What you are suggesting is known as hyperventilation. Because blood CO2 plays an important role in maintaining the pH of the blood, hyperventilation can lead to a dangerous increase in blood pH, referred to as respiratory alkalosis.

Apparently one response to respiratory alkalosis is an increase in metabolic rate as the body tries to compensate for the increased rate of loss of CO2. However, respiratory alkalosis is dangerous so I don't think hyperventilation is a viable strategy for losing weight.


Why do many fruit trees have five-petaled flowers? Peach, pear, apple, cherry, and many other fruit trees seem to have flowers comprised of five petals. Assuming there is no evolutionary advantage to confusing students of trees, is there a plausible reason (evolutionary or otherwise) the morphology is so regimented? Are the trees related? Do they like the same pollinators?

Thanks for any insight.

Peach, apricot, plum, pear, apple, cherry trees are plants of the same family, Rosaceae, so they are closely related. They share many more aspects than the five petals. In fact, other plants in this family, and even many other dicots have five petal, simply because their share a common ancestry.


How does BH2 reduction to BH4 need only one NADPH molecule? Dihydrofolate reductase (DHFR) reduces dihydrobiopterin (BH2) to tetrahydrobiopterin (BH4). Someone told me that this reaction needs only one NADPH molecule (I am not sure if this is correct), namely, NADPH provides one hydride atom and becomes NADP+.

Could someone explain to me how is this possible? How can BH2 -> BH4 conversion be done with one NADPH molecule, while I am expecting two (to give two hydrogen atoms)?

The short answer is that in reduction of BH2 to BH4 by dihydofolate reductase not only is a hydride ion (a proton plus an electron) transferred from NADPH to BH2, but the product also picks up a proton from the solvent: N5 of BH4 is protonated.
$$\ce{BH2 + 2e- + 2H+ <=> BH4\tag{1}}$$
Enzymically (see EC 1.5.1.34):
$$\ce{NADPH + BH2 + H+ <=> BH4 + NADP+\tag{2}}$$
Thus the reduction of BH2 to BH4 involves 2 electrons and 2 protons. NADPH donates 2 electrons and 1 proton (as a hydride), forming a new carbon-hydrogen bond. The solvent accounts for the other proton. The situation is very similar to the alcohol dehydrogenase reaction (discussed below).
The reduction of biopterin all the way to tetrahydrobiopterin by dihydrofolate reductase is a 4-electron reduction, and requires 2 NAD(P)H.
Background
There a couple of points about NADP-linked enzymic oxido-reduction, and about oxido-reduction in general, that possibly need clarification.

NAD(P)-linked enzymes, almost invariably (and perhaps always), catalyze the direct, stereospecific transfer of a  hydride ion (a proton plus two electrons) as a single entity between the nicotinamide cofactor and acceptor.

This statement probably needs some explaining.  The fact that NADP-linked oxidoreductase reactions are consistent with the transfer of a hydride ion is one of the great contributions of Westheimer to enzymology (see here). In many cases, this results in the formation of a carbon-hydrogen bond.
Secondly, hydride transfer is stereospecific. Amazingly, NADP-linked oxido-reductases distinguish between the two hydrogens at C4 of NAD(P)H.  This is an example of prochirality (the Ogston effect in the Krebs cycle is another).
For simplicity, the two hydrogens at C4 are called the HA and HB.  The work of Westheimer,  Vennesland and co-workers showed that NAD(P)-linked enzymes can be divided into two classes: those that transfer HA from cofactor to substrate (A-sterospecific dehydrogenases) and those that transfer HB (B-stereospecific dehydrogenases).
It is now known that sterespecificity of hydride transfer is one of the most evolutionary conserved traits of NAD(P)-linked oxido-reductases. Enzymes that may be shown to be descended from a common ancestor by amino acid sequence analysis invariably display the same stereospecificity of hydride transfer (Yeast and horse liver alcohol dehydrogenase is an example) 1†.
In addition hydride transfer displays apparent absolute stereochemistry fidelity: the 'wrong' hyride is never transferred.  Transfer of HB by lactate dehydrogenase, which is A-stereospecific, could not be detected experimentally, for example (see here).
A great review of this aspect of dehydrogenase biochemistry has been published by You (1985), available as a a pdf from here. (An earlier review may be found here)
Finally, a brief word on oxido-reduction in general. Oxidation is the loss of electrons, reduction is the gain of electrons.  An ionization is neither an oxidation or a reduction, and neither is hydration/dehydration. This, of course, is 'basic stuff', but seems to sometimes cause confusion.  When dealing with oxido-redution reactions we can add in as many protons as we like, or take out as many protons as we like, and this may be important stoichiometrically, but  ionization does not change the oxidation state of a molecule.
An Illustrative Example - Alcohol dehydrogenase
Alcohol dehydrogenase (EC 1.1.1.1) catalyzes the following reaction, the 2-electron reduction of acetaldehyde to ethanol with NADH as hydride donor:
$$\ce{Ethanol + NAD+ <=> Acetaldehyde + NADH + H+ \tag{3}}$$
This very nice diagram, taken from Cornforth's nobel lecture, Asymmetry and Enzyme Action, illustrates all the points made above.

The hydrogen labelled with the asterisk it HA. Stereospecific transfer of hydride to acetaldehyde results in the formation of a new carbon-hydrogen bond.  If the asterisk represents deuterium or tritium, the result is deuterated or radiolabelled ethanol.

If, instead, HB is deuterated or tritiated, the result is deuterated or tritiated NAD+, with no transfer of label to product.

Formation of the alcohol involves 'picking up a proton' (from the solvent).

Transfer of hydride acetaldehyde is also stereospecific. The hydride is stereospecifically transferred to one of the faces of the planar carbonyl group.  I am ignoring this aspect here (but see Cornforth's lecture) 2†.

To be very pedantic, HA is more correctly called the pro-4R hydrogen, and  HB is the pro-4S hydrogen.

(In Cornforth's original diagram the H+ was left out).
The Specific Question Posed by the OP

How can BH2 -> BH4 conversion be done with one NADPH molecule, while I am expecting two (to give two hydrogen atoms)?

As stated above, BH4 (tetrahydrobiopterin) contains one more pair of electrons than does BH2 (dihydobiopterin), but (like the alcohol dehydrogenase reaction) there are two protons involved. The fact that reduction involves hydride transfer accounts for one. The other is picked up from the solvent.
This is illustrated in the diagram below, where the key point is that the carbon atom at C6 now has a new carbon-hydrogen bond.  This bond accounts for 2 electrons plus 1 proton. But the nitrogen atom at C5 has also picked up a proton.
(We must be very careful when dealing with reduction of the pteridine ring because of the quininoid form (see here).  This is why I first picked  alcohol dehydrogenase as an illustrative example, and I am ignoring such complications here).

The OP chooses an interesting substrate for DHFR, an unconjugated  pteridine. The 'more usual' substrate, of course, is the conjugated pteridine, dihydrofolate (FH2). Although DHFR does catalyze the transformation of BH2 to BH4 , the enzyme usually associated with this transformation is dihydropteridine reductase (EC 1.5.1.34).
One final point.  Both chromosomal and plasmid dihydrofolate reductase, although unrelated from an evolutionary point of view, are both A-stereospecific with respect to hydride transfer from NAD(P)H.
(The above diagram was modified from one found on the internet. The original may be found here)
Four-Electron Oxidoreductases
Most NAD(P)-linked oxidoreductases catalyze a two-electron reduction that involves just one molecule of nicotinamide cofactor.
A few, such as dihydrofolate reductase can catalyze two sequential 2-electron reductions, where the  first 2-electron product is released into solution before it is reduced to the final product by a second encounter with enzyme. (In the case of DHFR,  the reduction of folate to dihydrofolate is a two-electron reduction, and the reduction of dihydrofolate to tetrahydrofolate is another 2-electron reduction).
Some oxido-reductases, however, catalyze a four-electron oxido-reduction where the intermediate product is not necessarily released into solution. Such enzymes are called four-electron oxido-reductases, and are very rare.  They have been reviewed by Feingold & Franzen, (1982).
One example is histidinol dehydrogenase (EC 1.1.1.23), that catalyzes the reduction of an alcohol to an acid (the aldehyde being the intermediate 2-electron reduction product).
$$\ce{L-histidinol + 2 NAD+ + H2O = L-histidine + 2 NADH + 3 H+ \tag{4}}$$
Another example is HMG-CoA reductase (EC 1.1.1.34), a key enzyme of cholesterol metabolism (that is inhibited by statins).  In this case, the enzme reduces a substrate formally at the oxidation level of a carboxylic acid (but 'activated' by thiol ester linkage to coenzyme A) all the way to the alcohol.
$$\ce{Mevalonate + CoA + 2 NADP+ = 3-hydroxy-3-methylglutaryl-CoA + 2 NADPH + 2 H+ \tag{5}}$$
A third example is UDP-D-glucose 6-dehydrogenase (EC 1.1.1.22), which catalyzes the reduction of the C6 alcohol group of UDP-glucose all the way to the acid.
$$\ce{UDP-D-glucose + 2 NAD+ + H2O = UDP-D-glucuronate + 2 NADH + 2 H+}$$
So, a four electron NAD(P)-linked oxido-reduction is possible.  But such reactions are relatively rare. The key to the biochemistry of the NAD(P)-linked enzymes, IMO, is to realize that a hydride is transferred as a single entity (and that hydride transfer is stereospecific).
Footnotes

Alcohol dehydrogenase from Drosophila is unrelated to the yeast and horse liver enzymes from a evolutionary perspective, and is B-stereospecific.
The same Cornforth that reputedly said that if the β-lactam structure of penicillin was correct he would give up chemistry and grow mushrooms (see here).


What is this insect in Southeast Idaho? This thing ran out of the wall of my dorm hallway. It had a lot of what look like antennae, and it's very fast.

(click to enlarge)

That is a silverfish, order Zygentoma (also known as Thysanura). Likely genus Lepisma (family Lepismatidae). Zygentoma are insects, and are the sister taxon to Pterygota (winged insects)


How do you determine the length of an annelid? I'm currently studying a horse-leech, and would like to know if it is fully grown or not. When I read about different annelid species a maximum length is often given, so I wonder if there is some standard way of measuring these elastic animals?

For example, my leech varies from 2 to 10 cm, but often seems to prefer to stretch out to about 6 cm when not moving.

(Possibly I should modify this question to be just about leeches, but I also wonder about earthworms, and probably other soft and difficult worms as well...)

Leeches:
According to Taube (1966)$^1$:

The adults of American leeches range from about 1/4 inch to 12 inches in contracted length.

Because leeches can bloat to more than 10x their "normal" size after a meal (and can undergo up to a 300% change in length), it seems that measuring a leech at anything but their contracted state would lead to wildly too variable of measurements. Therefore, it seems likely that only contracted size would prove to be truly useful.

However, see Klemm (1982)$^2$ (or Klemm,1995 $^3$) for comments about preferred preservation for identification purposes:

[Leeches] have a soft, highly contractile body. Therefore, if leeches are dropped alive into preservatives such as 70% alcohol (ethanol)...they contract strongly and sometimes such features as the eyes, general body shape, and the genital pores become distorted and difficult for the non-specialist and occasionally even for the expert to discern. When leeches are properly anesthetized prior to fixation, there is usually less muscular contraction. the body shape remains more uniform, and there is less variability of the anatomical structures. ... The preserved leech should be straight, moderately extended and undistorted.

However, Klemm does not use body length as an identification feature in his key, and therefore his directions seem to be more concerned with preserving other anatomical features (not to ensure accurate length measurements). He does provide "average size" for species in his key but notes that "contraction during processing" can lead to variation in measured length.

Other Annelids:
Interestingly, naturewatch.ca provides the followign instructions for measuring earth worms:

1.Allow the worm to freely extend itself as if it was crawling.
2.Measure the maximum distance the earthworm covers when completely stretched out.

Similarly, a Ph.D. dissertation by Cynthia M. Hale (2004)$^4$ measured earthworms by preserving them and then

measur[ing] on the longest axis of the straightened individual.

Takeaway:
It seems as though ranges of body length are almost always provided for each species. Although this is not uncommon for any taxa, many sources (including those cited) mention that variability in preservation methods/ body orientation  can lead to variation in lengths recorded (as can age, vitality, gut content, moisture content, etc.). Klemm, in particular, suggests using numerous museum specimens to make conclusions about species because of these variability issues.
As a result of these discrepancies/inconsistencies, I would guess that you're best off citing a methodology source (e.g., Taube 1966) and explicitly indicating your measurement methods.

Lit Sources:
[1] Taube, Clarence M. 1966. Leeches. Institute for Fisheries Research Report No. 1713. http://quod.lib.umich.edu/f/fishery/AAG2862.1713.001?rgn=main;view=toc.
[2] Klemm, Donald J. 1982. Leeches (Annelida: Hirudinea) of North America. EPA-600/3-82-025. Cincinnati, OH.
[3] Klemm, Donald J. 1995. Identification guide to the freshwater leeches (Annelida: Hirudinea) of Florida and other southern states. Florida Department of Environmental Protection. Tallahassee, FL. http://publicfiles.dep.state.fl.us/dear/labs/biology/biokeys/leeches.pdf
[4] Hale, Cynthia M. 2004 Ecological consequences of exotic invaders: interactions involving European earthworms and native plant communities in hardwood forests. PhD dissertation. University of Minnesota.


how do microtubules polymerize? given that micro tubules are involved in so many processes in cells, it seems that such a complex "highway" would require some advanced underlying mechanism to orchestrate its assembly in a direction needed for the cell, such as towards a kinetochore. multiple search results on google and textbooks simply just state polymerization as is without explaining how these events happen. so how are microtubules polymerized and how is this polymerization oriented directionally ?

Microtubules are made up by $\alpha$- and $\beta$-tubulin units, the wiki page for this will link you to a short section on microtubule dynamics, which is the basis of how the growth & shrinking of microtubules is controlled:

Microtubules grow (by addition of $\alpha\beta$-units) and shrink (by dissociation of these units) primarily at the '+ end', which is the one in the cell periphery not at the centriole. Actually both of these reactions (growing/polymerisation and shrinking/de-polymerisation) usually happen at the same time but with different speeds. These speeds depend on whether GDP or GTP is bound by the $\beta$-tubulin at the + end, the (relative) concentration of GTP-bound free monomers and other structural proteins. Except for the GTP/GDP bound state in the mircotubule all of these factors can be controlled (or altered) by the cell through various mechanisms (some are listed on the 2nd wiki page I linked; I may add some specific ones if I have more time).


What are these black masses floating on my pool? I've been cleaning them for some time. At first I thought it was some kind of synthetic material, but when I took one with my fingers it disintegrated into filaments. I placed another under my usb microscope and they appear to be an aggregate of green tubular bodies.

They grow (appear) from one day to another, only 1-2mm diameter. My best guess is that they are some kind of algae, but I'm lost to find exactly what. I live in the south of Spain, the pool is treated with chlorine, in a well illuminated zone. There are no other algae growing, and the area is urbanized.

I was looking in the wrong kingdom. After much searching I asked myself: are those eggs? Silly me, of course they are. I should have thought it from the start. Mosquitoes plant their eggs on water over night. I was confused because in the past I've never seen the eggs, only the larvae and the pupae in the water. So, that's what I have every morning floating in my pool, groups of mosquito eggs.
http://animalia-life.club/other/mosquito-eggs.html


Using catalase-test to determine if Staphylo- or Streptococcus If the microscope clearly shows bacteria of cocci morphology but it is difficult to determine if they are Staphylo- or Streptococcus, are catalase tests a good way to differentiate between the two since Staphylococcus are positive and Streptococcus are negative? Are there any traps/exceptions?

Thanks!

Generally yes: streptococci are catalase negative while staphylococci are catalase positive.

  The catalase test is important in distinguishing streptococci (catalase-negative) [from] staphylococci which are catalase positive.

  Unlike Staphylococcus, all streptococci lack the enzyme catalase.

However, there are exceptions to every rule:

Catalase negative Staphylococcus aureus.

Catalase positive Streptococcus sp.


What type of moth is this? What type of moth is this that was on my wall in Spain

It looks very much like Manulea palliatella, Family Erebidae, Subfamily Arctiinae.
https://commons.wikimedia.org/wiki/Category:Eilema_palliatella
These are present in Spain.


Why are mammals unable to produce Essential Fatty Acids? Why do we have to get them from our diet, and if they aren't taken in our diet we will face disease? Then why we don't have the enzymes which are require for EFA synthesis?

Well, the essential fatty acids that humans fail to produce are not the same ones that other species fail to produce. For example, while cats produce their own Vitamin C and will therefore never develop scurvy, they can't produce their own taurine and will become sick if they don't consume enough of it.

To answer why a species might lose the ability to produce an essential amino acid, you have to consider what that species is eating most of the time. If its diet is rich in the amino acid anyway, individuals who lose the ability to synthesize it either feel no cost or--possibly more likely--even benefit by not wasting resources synthesizing compounds that may be abundant already in the diet and must be excreted if unused.

Turns out that this loss of ability to synthesize your own fatty acids is a particularly common consequence of evolving parasitic lifestyles, which makes sense: if you're just stealing someone else's acids, why bother to produce your own? Even outside of parasites, there's some interesting discussion on why the nine amino acids essential to all animals might have evolved from a genomics paper here, discussing which amino acids you really do have to make on your own and which you can get away with consuming depending on your species' lifestyle and dietary habits.


How can I fit the A595 of my unknown samples to the data? While I was conducting the Bradford Assay experiment to determine the concentration of my unknowns, I ended up by having an A595 for my unknown samples that is higher than the A595 of the standards. How can I resolve this issue?
wishes.. Micheal.

You could, depending on what you are doing, extrapolate your standard curve to include the absorbance of your samples. This, however, is not recommended since absorbance is linear only within a certain range. It's best to dilute your samples so that they fall within the range of the standard curve while also ensuring that your standard curve is, in fact, linear.


Good source that explains the evolution of single-celled organisms "from scratch" Are there any books or sites that detail, step-by-step, the evolution of the first single-celled organisms (bacteria, archaea) from a Miller-Urey-like beginning? That is, assumes only amino acids, then from there to self-replicating proteins, until culminating in the formation of a basic cell?

Origin of Life: Chemical Approach is an edited volume by Piet Herdewijn and M. Volkan Kisakürek.

here is the book's description from the webpage:

  Dedicated to the fond memory of two great pioneers of this science, Leslie E. Orgel and Stanley L. Miller, this compilation of reviews and original manuscripts provides an overview of the current state of the art, written by some of the eminent "players" in this creative domain of "explorative chemistry".
  Since we are still far from finding a definitive answer to the most fundamental of questions in science, "chemistry" here is defined in its broadest sense. It is against this background that the contributions cover such a wide range of theories, including chemistry and selection, evolution of the pioneer organism, chemical aspects of synthetic biology, ribozyme catalysis of metabolism in the RNA world, intractable mixtures and the
  origin of life, the chemical etiology of nucleic acids, interstellar amino acids, and even the chemistry that preceded life's origin.


Trying to identify an insect Toady a friend saw an insect in his garden, in the UK (England).

It looks like a combination of a hover wasp, a wasp and a dragonfly. Whist flying, I'd describe it more similar to a dragonfly.

I've used Google images to try and identify it, and come close, but the creature was about 3 inches long and up to 1 inch wide. I thought it was a broad-bodied chaser but he assures me (possibly incorrectly) it wasn't big enough

I would agree with you on this one - looks like a female or young male Libellula depressa (the 'broad bodied chaser') to me. It has the characteristic broad, flattened abdomen and the distinctive brown-yellow abdomen with bright yellow patches and the dark wing bases are both visible (the latter only just, to be fair). The broad abdomen differentiates it from the other Chaser and Skimmer dragonflies while the colour is quite distinctive (the species is sexually dimorphic; mature males have a blue abdomen while females and young males have a yellow abdomen). Not sure what you friend is talking about regarding the size; 3in long is about right for L. depressa. It's in the right geographical region too.

(thanks to @RHA for pointing out to me that young males also have yellow abdomens!)

Citation from Wikimedia Commons: By No machine-readable author provided. Bogdan assumed (based on copyright claims). - No machine-readable source provided. Own work assumed (based on copyright claims)., CC BY-SA 3.0, https://commons.wikimedia.org/w/index.php?curid=754252


Is DNA from more parents (than two) better for the fitness of the offspring? I'm designing a system (a computer system actually) and (a whole while ago) I spoke with a friend about it and he had this opinion:

  If you combine DNA of more parents (than 2) it's better for the
  offspring.

It's a bit of a theoretical question but is this true?

I'm using genetic algorithms where you can choose the number of parents,
if this were to be true I'd take 4 parents, if not I'd stick to 2.

I saw here a question about the occurrence in nature but it remains unanswered.

(2 parents are easier - in this system - so maybe that's the reason it is not observed in nature)

About the system: it needs to produce 'fit' offspring (as fit as possible and as fast as possible), where fitness is measurable (this part is already covered...) and the most fit individuals in the population are selected to pair.

The only limitation set on this kind of systems is that the offspring has to have a chance to be fitter than the parents (so children are allowed to be less fit than parents (being it 4 or 2).

(Of course this lowers the importance of the question but still: does offspring of more than 2 parents have a higher chance to be fit? (my friend mentioned: the more diversity in the DNA the better...))

If you need more information about this bit I'll try to answer comments (if I do know the answer or can give more information about it).

There are very many details to address in this question. I will try to keep it brief and keep the scope of your question in mind, which is rather narrow. I also think your friend is over-simplifying and misleading you, assuming he is honest about the explanation he gave you.

We are talking about sexual reproduction, correct? Firstly, with 3+ parents:

it's not obvious that you will have "more diversity" in the DNA, nor that
"more diverse" DNA will be a cause for increased fitness.
Additionally, it would take a whole lot of machinery and evolutionary happenstance at the cellular and molecular levels to recombine DNA from 3 or more parents to make a stable, recombined genome, and this itself may introduce more problems than solutions.
More so, you're implying that a sexual organism that requires mating between 3 or more individuals will be fitter than an organism born of fewer parents. This is subject to whether the gain in fitness of having more genetic parents will outweight the cost of maintaining such a system. This would certainly be dependent on the environment, the population, and all the nasty little details of life, such as how mate choice would work, whether a backup for 2-individual mating would exist, etc.

Remember that fitness is a probability of obtaining a number of offspring rather than the number of offspring. I think it is self-evident that the requirement for more parents, rather than less, lowers the probability (i.e. fitness).

This is quite a hypothetical discussion. In nature, for all its ever-experimenting and ever-diverging forms of life in the last 4 billion years, we find no organisms with more than 2 sexual parents. Take this as a sign that the natural occurrence of this kind of system is probably not favorable to survival and reproduction.

And I realize we could discuss this topic on many fronts (I have a few more ideas that I omit here), it's a rich question to digest.


How do I efficiently grow bioluminescent algae? I have 6 vials of Pyrocystis lunula that I would like to grow. What would be a more suitable container, a tank or a clear jar? Also, I would like to know what kind of nutrient solution to use. Is it possible to get them to reproduce at a rate that eventually there can be a whole tank full of them?

I have no experience with that particular species but dinoflagellates are often slow growing, very tricky to get to high densities and hard to maintain for a long time without proper experience and lab conditions.

If you still want to have a go I would recommend the following. Growth conditions are rather similar for most dinoflagellates: use a rotary shaker (gentle rotation) in a 12:12 day night regime, don't dilute to hard when subculturing and use standard F2 medium (see link for recipe). If you cannot get hold of seawater you can use saltwater aquarium salts such as Instant Ocean.

Most hate temperature changes so best to keep them at 18-21C


Can you tell the sex of a white willow when it's not flowering? Can you tell whether a salix alba tree will produce male flowers or female flowers by looking at it, touching it or generally using your unaided senses? If not, is there any way to do that without specialized equipment or lots of expertise?

I remember overhearing a botanist some 10 years ago, that he cannot tell male poplar from female when they are not flowering or producing seeds. Poplars and willows are related, so it is a weak indication for you, you will likely not find any visible features in willow neither. But it is an old information, too.    (Are you interested in DNA sequencing evidence or not ? I can look it up for you, but it seems your statement in comment question was ironical.)
EDIT: have just found an article which says: "In Salix viminalis, the sex of plants cannot be confirmed until the first time they flower." At that time, 1997, there were no DNA markers for plant sex determination, but it is apparent, they did not know how to differentiate the sex of this willow just from morphology. This example is even closer to Salix alba than poplar. I find it even more likely now, that you will not find the morphological features.
I took the suggestion of Oreotrephes. This is what to look for under the tree - fruit and seeds:
.
Source.
( C. Alström-Rapaport, M. Lascoux, U. Gullberg. Sex determination and sex ratio in the dioecious shrub Salix viminalis L. Theoretical and Applied Genetics 1997, Volume 94, Issue 3-4, pp 493-497).


Unknown plant, can anybody identify this plant? Location: Western Germany
Can anybody identify this plant from Germany ?

This is Phytolacca esculenta, Asian pokeweed. Because the flower stalks (berry) are standing upright, and not hanging. The berries are also closer together compared to P. americana.

Despite the name 'esculenta', this plant is also poisonous.

https://m.wikidata.org/wiki/Q17244662


Has there ever been a published experiment to take a viral "census" of a human subject's blood? Has there ever been a published experiment to take a viral "census" of a human subject's blood?

By a "census", I mean to identify every active virus in the subject's blood with some probability.

So, for example, we can imagine taking different samples of blood, diluting them, then taking the dilution and using it to innoculate a lawn of hemocytes. Presumably, different viruses would make different plaques, so they could be separated, isolated and identified. By doing different combinations of dilutions, one could I suppose make a table or curve that would show the probability of detection of a given virus based on its concentration in the blood. Thus, at the end of the experiment the researcher could state, "I have isolated all the viruses in the subject's blood having a concentration above X with a probability of Y." Obviously, this would require hundreds of samples and thousands of innoculations to achieve an accurate census.

Has anyone published a study like this?

You wouldn’t try to isolate viruses, this being the 21st century.  You’d perform metagenomics analysis, which is much more sensitive.

That’s been done several times.  Two examples:

  Anellovirus and pegivirus C (GBV‐C) were detected among these donors. None of them were found solely in donors with abnormal liver enzyme. Anellovirus was highly prevalent (93.3%) and the co‐infection with multiple genera (alpha, beta, and gammatorquevirus) were more common in the donors with normal ALT values in comparison to those with elevated ALT ...

—-Full annotation of serum virome in Chinese blood donors with elevated alanine aminotransferase levels

  Anelloviruses were detected in each of the 10 plasma pools. Human pegivirus A (HPgV; GB virus type C) sequences were identified in eight of the 10 pools, more than 90% of which belong to Genotype 2. The recently described human HPgV2 in Flaviviridae was not detected. A small number of sequence reads of human papillomavirus were also detected in three pools. In one pool, two different gemycircularvirus genomes were identified and fully sequenced.

—-Viral nucleic acids in human plasma pools


How many cells should be seeded for passaging? Do you count cells when you passage them?
I found that many people will according to a ratio (maybe 1：2 or 1：3，etc.) to subpackage. It is so indistinct!
What is the optimal seedling density or optimal original confluent in various sizes of cell culture dishes and flasks?
that's all, thank you!

This answer is relevant in case of cell lines and not so much for primary cultures

When I first started doing cell culture, I used to count the cells before passaging. The idea is to seed enough cells to keep the population viable but not so much that you have to re-passage within 2 days. However as I became good with the technique I stopped counting as I would have a decent estimate of how much to seed. For seeding cells for some experiments (transfection/drug treatment etc) it is crucial to count the cells.

How much to seed depends on what the division time of the cell type is and how much you need after a given duration of time. You have to calculate it accordingly. For example a fully confluent well of a 6-well plate will approximately have 1 million Hela cells (this number would vary for different cell types because of the difference in sizes). Hela cells have division time of ~17h (see this post). If you need ~70-80% confluency after 17h then you should seed ~0.3 million cells.

Likewise, a T-25 flask would have ~3 million cells in full confluency. So, if you need a confluent flask in 3 days you can calculate how much cells to seed.

See this table in Nunc website for number of cells at confluency and optimal seeding density for different culture vessels.

Note that some cells (mostly primary cultures) may need to be seeded at high densities because they may need contact with other cells for survival. So, I cannot give any authoritative answer for primary cultures. Moreover, since it depends on the cell type, all examples cannot be listed here.


Common Errors For Low R Value in Bradford Assay I've recently started doing Bradford Assays for my samples and my standard curve has been non-linear and I have been getting low R values (.90-.95). I initially thought the error was in pipetting, most likely in adding BSA while establishing the standards but I have repeated in care and somehow still get low R values. Are there any other possible sources of error?

You could be measuring outside the dynamic range of the assay (you can only add so much / so little BSA to a certain amount of reagent).
You could be outside the linear range of your spectrophotometer, usually under 1 is fine, although some old/crappy ones might not even be reliable over 0.5.
If you're fast you're measuring your different concentrations also at different times. Bradford is a little bit time-dependent, so waiting the recommended time before measuring your standards is not a bad idea.

Probably it's still pipetting though, try pipetting at least 20 uL in every dilution step and see if you're still off.


Is there such thing as Animal non-verbal body language? Have there been any studies done on the animal use of their bodies to signal, communicate or express their emotions, particularly to members of other species (ex: humans)?

I've been observing a very intelligent indoor-outdoor cat who has been doing the same sideways stretching posture every day he met me. There has been a number of other postures that the cat has been using - tearing at a carpet with claws, or dragging himself against the carpet by using claws that I've repeatedly observed.

Another cat was thumping her head against a door to "knock" and indicate that the cat is outside.

To me, these gestures appeared as clear expressions of intent or emotional state.

Other experiment involved "trained" geese at a local pond who would indirectly approach humans to ask for food. Their body, neck and head position appear to indicate intent (is the animal grazing towards the human or away from the human).

Yet another experiment involves nesting birds who start to clearly express their displeasure at me located near their nesting area. They repeatedly produce high pitched screech until I move away.

For example I repeatedly see geese assume this gesture to intimidate other geese.

As a human, I'm very conditioned to vocal and eye related coordination, and this "non-verbal" language is fascinating to me.

Have there been any studies in how indoor/outdoor - partially domesticated animals communicate with humans?

Is it true that this communication uses their entire body and not just the vocal cords?

Is there some "foundation" language that would be similar among members of the same species, or is it entirely a learned skill that has nothing to do with evolutionary adaptation?

Finally, is there some sort of a brain complexity cut off at which level the animals can no longer understand if they are being communicated with?

The closest reason that I know of for such behaviour is simple conditioning!

B. F. Skinner conducted some fairly famous experiments with pigeons, where he put hungry pigeons in cages, and randomly administered the food. The pigeons associated the foods arrival with whatever they happened to be doing at the time (be it looking to the right, or bobbing their heads). They would then keep trying this until more food came out (randomly), and the pigeons 'superstition' was confirmed. See the wiki.

I realize this is not concrete, but it seems to me that they are not 'communicating' as such, they are simply repeating what has worked before. It is your anthropomorphication that has meant this seems like deliberate communication in my opinion. Although I'm sure it could be argued that all communication is having been 'conditioned' to use words/gestures to get your meaning across.

Update (14.6.12)

Just read the abstract for this paper (published yesterday) that finds that experts in dog behaviour can interpret the ('socially relevant') posture of a dog in a similar way to that of a human. We can therefore interpret the body language of an animal (in this case, dog), if we are familiar (you do not even have to have owned a dog necessarily) with the kinds of postures adopted. So the dog does not have to consciously 'communicate' for us to interpret their emotional state (happy/sad/angry/...).

In terms of human-pet communication then, there seems to be more emphasis on the human interpretation of the natural postures adopted by animals, than the animals themselves. Pets may behave very differently to animals in the wild, but it comes back to what the specific human is used to. If you have had a lot of contact with pet dogs you are in a better position to associate the current behaviour of a pet dog with the correct emotional state. No doubt the animal with subconsciously adjust their behaviour to achieve the 'correct' human interpretation, and thus get fed, or whatever.


Can a drug induce specific mechanism of resistance in tumors? For example, can a drug that targets a given protein induce overexpression of that protein or increase the copy number of the gene coding that protein?

I strongly suspect that antineoplastic resistance happens due to natural selection alone but I was wondering if there are examples that suggest otherwise.

Yes.

There is a lot of literature on cancer evolution and now several countries have genome sequencing programs for "pharmacogenomics", for example Genomics England, specifically to see which cancers are likely to evolve resistance to which drugs.

One small detail is that mutation exists before treatment in a subset of the cancer population —as happens with evolution normally. That mutation is neutral for the fitness of the cancer before, but is advantageous during treatment.


What is the most critical step of plasmid purification? During the process of plasmid purification and quantification, which step is the most critical to the success of the process?

There are a few critical steps (which sounds horrible if written together, but the method per se is robust and usually without problems):

Resuspension of the pellet: Make sure it is really resuspended and not floating around as a big blob. If it is not resuspended properly your yields will go down dramatically.
NaOH/SDS-Lysis: Don't lyse for too long as you may end up with low quality DNA. This denatures the plasmid and makes it often useless for subsequent enzymatic reactions.
Mixing: Don't mix too harsh once you lyse the cells, otherwise you may break up genomic DNA of the bacteria which subsequently stays in solution and is not precipitated during neutralization.
Neutralization: Make sure you mix good here (by inverting the tubes 4-6 times) but not too harsh. It is critical to neutralize the whole lysate, otherwise proteins may stay in solution.
Drying: Overdrying of pellets can cause problems when you try to dissolve them again.


Are the proteolytic enzymes in syconiums and nettles identical to those in rennet? I would like to compare rennet capability under various conditions. The issue is, I don't want to use calf rennet, but I can't figure out if nettle and syconium, which also coagulate milk, contain regular rennet or other enzyme? If so, what is its name? It's quite important.
Thank you.

Rennet is not an enzyme, but rennin is.

Any protease enzyme should be capable of causing milk to coagulate, or prevent gelatin from setting. Examples such as papain and bromelain are all cysteine proteases, and all of them will cause milk to coagulate.

The example of fig protease that you mentioned is a cysteine protease (no specific name found, referred to in scientific literature as fig protease). Nettles are a highly polyphyletic group, and the specific enzyme cannot be named without a more specific phylogenetic group being identified.


When comparing oral infection v IV infection in mice, why would the CFU given be different volumes? In the paper, orally infected mice are given 1x10^9 CFU of C. Rodentium and IV infected mice are given 5x10^7 CFU of the pathogen. Does anyone know if there is a generic reason for this? Thanks in advance.,

Intravenous delivery of pathogen produces infection more efficiently than transmucosal delivery.

10^7 is 2 orders of magnitude less than 10^9.  It is not the volume that is different (although it may be), it is CFUs or "colony forming units" which is a proxy for viable pathogens in the inoculum.  The oral dose is 100x that of the IV.

Getting germs directly into the bloodstream bypasses the built in protections that our mucosal surfaces have.  The GI and GU tract have a lot of defenses.   For example an experimental SIV infection produced intravenously in monkeys requires an order of magnitude less virus than an infection established rectally or vaginally.

I would suspect that the CFUs of a given pathogen via a given route is something established empirically as producing the desired outcome.  If you used the same CFUs for an IV route as were required for the oral route, you might have a fair number of mice that just died from septic shock from the huge number of bacteria suddenly in the blood.  Given the 2 order of magnitude difference of inoculum (IV vs PO) to produce infection you might conclude that the stomach kills 99% of any inoculum.


Is it possible to identify the wasp species/family by the nest? I've seen a weird looking wasp nest recently.
Here's the picture:

I'm saying weird because it's the first time I see a nest that isn't a ball made of grey paper. Although this one is also made of paper, I don't understand where does the colour come from.

Is it possible to say, what species or family does it belong to?

(location is the North-West of Russia, close to Saint-Petersburg)

Ok, my bad. Should've googled better.
It seems that it might be a common wasp aka Vespula vulgaris. It's said that the colour of the nest is caused by material being collected from the rotten tree trunks.

See the identified sample:

It's said that they don't make nests in houses too often that's why I'm not accustomed to the look of the nest.


Usage of the taxonomic classification "Pinnipedia" According to ITIS the classification Pinnipedia is  invalid, and it is proposed to rather use Caniformia. The later group however includes a range of terrestrial animals as opposed to the pinnipeds (the seals), which only include marine mammals.

Is the term Pinnipedia nevertheless still accepted and used in scientific media? Is there any debate whether to use one and not the other?

The Comments section of that page has the explanation:

  Wilson & Reeder (eds., 1993) note that "the pinnipeds (otariids,
  odobenids, and phocids) are included within the suborder Caniformia;
  placing them in a separate Order would make the Carnivora
  paraphyletic." This arrangement continues to be followed in Wilson &
  Reeder (eds., 2005)

If both Carnivora (Bowdich, 1821) and Pinnipedia (Illiger, 1811) are orders in the traditional Linnean taxonomic sense, then one cannot be nested within the other. If this were to happen, then Carnivora would be paraphyletic because it would exclude some of its members. The same argument is made when discussion birds as dinosaurs (you can't talk about Dinosauria that doesn't include Aves).

The problem arises when phylogenetic systematics (clade names) meets traditional Linnean systematics (orders, suborders, etc.). Phylogenetic systematics does not distinguish these higher taxonomic groups. Clades are just nested groups of monophyletic taxa.

So then to answer your last question, Pinnipedia does appear to be in common usage (Google Scholar reports several hundred citations in the past few years). The key is to distinguish Pinnipedia as a traditional Linnean order (not valid) and Pinnipedia as a monophyletic clade that includes seals, walrus, and sea lions (perfectly fine). Seals, walrus, and sea lions are all more closely related to each other than to other Carnivora, so they are monophyletic, and the name for that grouping is Pinnipedia.

Here's the Tree of Life page that has all the clade names.


Is there an optimal illumination level for human habitats/workplaces? I know of melanopsin, a photo pigment in mammal eye that helps regulate circadian rhythms. It responds most strongly to blue spectrum light. There have been experiments that demonstrated that intensity of light is proportional to the impact on circadian rhythm regulation/ melatonin suppression.

This is why I'm interested if there is some optimal illumination intensity that has been demonstrated to result in better health/cognition in humans. I heard anecdotal reports of full spectrum lighting improving attention in classrooms, but is there some chart or figure which says how much is "too much light".

It seems there has been some work done on too much light affecting human health, but in regards to lack of darkness at night, rather than too much during the day. Without the appropriate amount of darkness at key times melatonin production and the major clock regulator or SCN can be disrupted and lose sync with the peripheral clocks. See here [1] for a comprehensive article with loads of information and other links to studies done on this topic.

This part in particular illustrates some of the problems associated with too much light:

"Overexposure to sun-mimicking light is also believed to play a role in the increase of insulin resistance, type 2 diabetes and obesity in developed countries (where round-the-clock illumination is more prevalent). Some research also shows that too much sun-mimicking light ups our craving for carbohydrates.

Before humans started cultivating grains, carbohydrate energy was available only from spring to fall. In response, our bodies evolved to stock up on carbohydrates during the growing season to prepare for winter, when no carbohydrates were available. In turn, we didn’t crave carbohydrates in the winter. All that changed with the light bulb, write T. S. Wiley and Bent Formby, PhD, in Lights Out: Sleep, Sugar and Survival (Atria, 2001)"

This might be a bit off topic but check out http://www.lightingdeluxe.com/workplace-lighting-ergonomics.html and the HSE has some info on what the required lighting conditons in the workplace should be [2]. They only mention lighting conditions with reference to reducing levels of stress in the workplace though.

Also not directly related but pretty cool; an article in Science from 1998 found that light shining on the back of the knees may be able to regulate circadian rhythms [3].

[1] http://experiencelife.com/article/light-rhythms/

[2] (scroll to the lighting section) http://www.hse.gov.uk/humanfactors/topics/lighting.htm#lighting

[3] Wright, K.P. Jr. & C.A. Czeisler. Absence of circadian phase resetting in response to bright light behind the knees. Science 297, 571 (July 26, 2002).

or if you don't have access http://www.genomenewsnetwork.org/articles/08_02/bright_knees.shtml


Does covariance and phenotypic variance have to be for the same trait to calculate narrow-sense heritability? I'm working on a problem where I'm given that the phenotypic variance of the parent, $p$, for trait $A$ is $175.2$ and the phenotypic variance of the offspring, $o$, for trait $A$ is $146.1$. However, I'm also given that the covariance between parent and offspring of a different trait, $B$, is $14.6$.

Can I still calculate the narrow-sense heritability of $A$ using
$$\begin{eqnarray}
\frac{h^2(A)}{2}&=&\frac{\text{Cov}(p,o)}{\text{Var}(p)}=\frac{14.6}{175.2}\approx0.0833 \\
h^2(A)&=&2\times0.0833\approx0.167
\end{eqnarray}
$$
even though they're different traits?

I'm also told that any resemblance between parents and offspring is completely due to genetics, ie. without environmental effects. I've read that if this is the case, then $h^2$ is $0.50$, but I'm a little confused with it.

Does covariance and phenotypic variance have to be for the same trait to calculate narrow-sense heritability?

Yes. See below for more information.

  Can I still calculate the narrow-sense heritability of AA [..] even though they're different traits?

No, you can't. A measure of heritability makes sense only for

a given trait
a given population
at a given time
in a given environment

  [I'm also told that if any resemblance between parents and offspring is completely due to genetics, ie. without environmental effects, then $h^2$ is 0.5, but I'm a little confused with it.]

The above is not a exact quote from you but the original sentence made no sense. I rephrase what I suppose you tried to say.

The formulation is inaccurate and could therefore be misleading. It is wrong to say that any covariance between parent and offspring is only due to genetics. In reality, environments between parent and offspring often covary. There might also have covariance due to epigenetic reasons and potentially many other reasons.

You cannot make any claim about what value should $h^2$ takes for the special case where covariance between parent and offspring is solely due to genetic variance (or any other special case considering only genetic variance). You still need to know the relative importance of the genetic variance to the total phenotypic variance. If any of this is unclear, then you should keep on with the recommended reading below.

Reading Recommendation

I recommend that you have a look at Why is a heritability coefficient not an index of “how genetic” something is? for an overview of the concept of heritability and common misconceptions.


Why aren't leaves black? I s'pose this is a variant of the age-old question, "Why are leaves green?"  It's fairly easy to ask teh internets and find plenty of answers for that one.

I have a different but related question: why aren't leaves black?  That is, chlorophyll varieties in leaves' cells mostly absorb red and blue wavelengths.  Why isn't there a pigment in photosynthesis that absorbs green?

Instead, the green gets reflected back to the atmosphere.  Its energy is otherwise lost to the plant.  Nature is awfully well optimized to so many niches; why would this band of light be wasted?

There are some plants that do absorb green (and have dark leaves).  These pigments -- such as anthocyanins, betalains, and carotenoids -- don't have any role in photosynthesis, and play other roles (such as protection against extreme temperature, or acting as an anti-oxidant).  Am I missing some pigment in my list that is green-absorbing and participates in photosynthesis?  If there were such a plant with a pigment like that, why wouldn't these plants dominate?  Is there a large cost to producing the green-absorbing pigment that mostly negates the advantage of the extra energy gained?

After a little more searching on SO, I found the top answer to this question.  In slightly different words, it says that light arrives in quanta, the chemistry in photosynthesis is driven by a certain threshold of energy, and any excess energy from a photon goes to waste heat (that tends to denature some of the proteins involved).  The answer points to another answer with similar reasoning.  However, their explanations don't account for the fact that chlorophylls strongly absorb blue in addition to red, where blue photons have nearly twice the energy of red ones.

Moreover, the answer goes on to say:

  Of course, this is still no explanation why leaves are not simply black — absorbing all light is surely even more effective, no? I don't know enough about organic chemistry, but my guess would be that there are no organic substances with such a broad absorption spectrum and adding another kind of pigment might not pay off.

Are there nothing other than educated guesses at an answer?  And why not use a combination of pigments, instead of a single, broad-spectrum absorbing pigment?  For example, some metabolic pathways use parallel processes.  Quoth the Wackypedia:

  Sometimes more than one enzyme can catalyze the same reaction in parallel; this can allow more complex regulation: with, for example, a low constant activity provided by one enzyme but an inducible high activity from a second enzyme.

Evolutionary answer: I like to go one step before green plants and consider the humble alga. Algae were historically classified as green, red, and brown, based on the wavelengths that their characteristic pigments absorbed. It is believed that land plants evolved from a common ancestor of algae, so you might wonder why we don't have similar broad categories of green, red, and brown plants.

Our best guess is that the organisms we call "plants" came from a single evolutionary event and share a common ancestor with green algae, rather than a different group. These green plant-like beings were probably the first big land organisms to try photosynthesis and happened to do well enough to out-compete any other plant-like being that might arise in their environment. Being green was "good enough" to for photosynthesis, allowing these organisms to survive and thrive.

Meta-answer: "Why" questions in biology often have probabilistic (and intuitively unsatisfying) answers. It's very hard to collect data that can "prove" why certain things evolved the way they did. Plus, evolution is not an engineering or design process. It leaves dead ends and doesn't always find the right solution. Founder effects can be very strong. But organisms which last long enough for us to study tend to be "good enough" at what they do. Here, the most parsimonious explanation for why leaves aren't black is that land plants came from green algae and didn't need to produce more of other pigments to take over the world.

Biochemical side-note: Plants can suffer from photooxidative stress when exposed to intense light due to the generation of reactive oxygen species, which disrupt metabolism. Therefore, some non-green pigments, like xanthophylls, are actually responsible for quenching chlorophyll and dissipating energy away from light-harvesting complexes. More energy is not always a good thing.


Could someone help me identify this insect? Does anyone know what this insect is? I put a rubber ball on my lawn, and within seconds a bunch of these insects (maybe 15 or 20) landed on it. I took a look around and saw that there were lots of them flying low near the grass or sitting on the grass (they were not as obvious on the lawn as on an orange ball :).
Location: Massachusetts (USA).

Looks like a Bibio, sometimes referred to as "March flies" and one species in particular known as "St Mark's Fly". Yours seems unlikely to be that one because it is found in England and it seems like nowhere else.

Most likely I think yours is a Bibio vestitus from the picture below (unfortunately I wasn't able to find multiple sources corroborating this, though, so take it with some caution), and although I had trouble finding definitive distribution data, it looks like the one in your picture has the copper-colored legs, and in addition the first image below claims to be from Massachusetts. There are many many species of Bibio though so I can't be certain of species.

Bibio vestitus
Reference


Difference between clonal and subclonal mutations I'm a physicist writing a proposal that has to do with cancer as a disease driven by evolutionary selection. As far as I understand, all tumors start with a single precursor (single cell or group of cells), and the other cells derive from this precursor by cycles of alterations and selection processes.

Reading recent articles, such as this, I learned that the derived cells include both clones and subclones. Since I'm not sure I understood things correctly, I have a few questions on the difference between the two words:

Is it OK to call clones the cells derived from the precursors?
When should I use subclones?
In the case of heterogeneity, is it fine to call clonal population a group of clones with the same characteristics?

clones means when a cell has the same DNA characteristics as his predecessor so in that case of yours you could say that those cells are clones while for sub-clones I am not that sure, the difference of clone and sub-clone is that a sub-clone is basically a clone who is then remade with a different characteristic(an upgrade if you will) , since cancer are mutated cells you could call them like that but only if you study its DNA, meaning you have to study deep to find out if there are sub-clones in there. AS for the 3 question I didn't quite understood what you meant cuz you just used 2 words with opposite meaning because heterogeneity means a group of organismes with different characteristics and clonal population means organismes with same DNA ( much like a colony of bacteria).


What material fills the synaptic cleft? Is it water? The synaptic cleft is the gap between the pre-synaptic and post-synaptic neurons, and neurotransmitters are transferred between the neurons within this region. What substance exits in this space, is it water? If so, what force makes the neurotransmitters move toward the receptors despite colliding with water molecules?

There are two types of synapses namely Electrical synapse and Chemical synapse. In electrical synapse there is physical contact between two cells through gap junctions. In chemical synapse there is a small gap between two cells which is termed as synaptic cleft.

The presynaptic and postsynaptic membranes at chemical synapses are separated by a synaptic cleft that is 20–50 nm wide, 10 times the width of the separation at gap junctions. The cleft is filled with a matrix of fibrous extracellular protein. One function of this matrix is to serve as a “glue” that binds the pre- and postsynaptic membranes together.(reference 1)

The same reference also states Water is the main ingredient of both the fluid inside the neuron, the intracellular fluid or cytosol, and the outside fluid that bathes the neuron, the extracellular fluid. Electrically charged atoms, ions that are dissolved in this water are responsible for the resting and action potentials.

Reference 2 mentions, The synaptic cleft is not simply an empty space, but is the site of extracellular proteins that influence the diffusion, binding, and degradation of the molecules, including neurotransmitters and other factors, secreted by the presynaptic terminal

If we think in this direction, of course holding together two neurons at synapse position is important. Moreover, the presence of several dissolved ions (in water) are necessary. If you remember, for the release of neurotransmitters into the synaptic cleft, influx of Ca2+ ions through voltage gated ion channels is essential.Thus, from above all points we can conclude that, the extracellular fluid in synaptic cleft is mainly aqueous in its composition with several ions, released neurotransmitters and several proteins that constitute a matrix.

What force makes the neurotransmitters move toward the receptors?

An essential role of astrocytes is regulating the chemical content of this extracellular space. For example, astrocytes envelop synaptic junctions in the brain, thereby restricting the spread of neurotransmitter molecules that have been released.(reference 1).Thus, it helps to confine the neurotransmitters in the small region, thereby increasing the probability of getting in touch with the target receptor.Also, as reference 2 says, there are several proteins present in the synaptic cleft which influence the diffusion.It means movement of neurotransmitter is by diffusion and above mentioned various factors can influence their movement towards receptor efficiently.

References:

Bear et.al, Neuroscience, exploring the brain, 2015
Neuroscience, textbook by Dale Purves.


Why aren't all strongly self-recognizing T cells made into regulatory T cells? Negative selection in T cell development is often simply described as preventing effector T cells from recognizing self-antigens. This is complicated by regulatory T cells developing from T cells with moderate affinity for self-antigens. If recognition of self is useful for immune tolerance, why don't T-cells with strong affinity for self-antigens also become regulatory T cells?

The selection is based upon the strength of the binding. A strong bond causes a signal in the T-cell to self destruct (apoptosis).

Wikipedia has a post on T cells. Perhaps the moderate bonding become regulatory cells, because these cells have to recognize those T cells that survive negative selection, which are most likely to cause autoimmune responses over a long period of time.

Strong affinity to self means the immune response will become a danger to the host.


Localization of Protein Kinase-A Is protein kinase-A located in the cytosol/cytoplasm of cells or in the plasma membrane?  Also, is it considered a receptor molecule since it is dependent on cAMP?

Any and all help is appreciated. Thanks!

The localization of the protein kinase A (PKA) cannot be explicitly answered, since the localization depends on the activation state of the protein. Lets have a look at the protein itself first, as this is important for the activation.

PKA consists of four subunits, two catalytic subunits and two regulatory subunits. See the image from the Wikipedia article on PKA:

Each regulatory subunit R is binding two cyclic AMP (cAMP) molecules and dissociates then from the protein complex. This sets the catalytic subunits free, which can then transfer phosphate groups from ATP to serine or threonine residues of target proteins. Among the target proteins is also the Phosphodiesterase (PDE) which gets activated by phosphorylation from PKA. Activated PDE hydrolyzes cAMP into AMP which reduces the amount of free cAMP which is necessary for PKA activation. PKA is also inactivated by phosphorylation.

In the cell you will find PKA almost everywhere. The traditional belief is that the protein is activated in the cytosol and enters the nucleus where it phosphorylates targets like CREB which then subsequently binds the the CRE sequence in gene promoters and activates this genes. Reference 1 shows that PKA is also activated in the nucleus, meaning that also the inactive form is present there. Reference 2 gives a nice summary of the article.

The regulatory subunit of inactive form of PKA binds to a special class of proteins: The A-kinase anchor proteins (AKAP). These are membrane bound and allow the association of PKA to membranes, although the protein itself is not directly binding to the membrane. The AKAP family is rather big (at least 50 family members are known today), which probably allows the localization of PKA at different membranes. Have a look at references 3-5 for details on the localization and the anchoring.

References:

Regulation of nuclear PKA revealed by spatiotemporal manipulation of
cyclic AMP.
Protein kinase A activated in the nucleus as well as the cytoplasm
The where's and when's of kinase anchoring
Localization of A-kinase through anchoring proteins.
The biological functions of A-kinase anchor proteins


At which step should I apply a detection filter when preprocessing microarray data? (Before/After normalization, batch effects removal) What is the best practice when preprocessing microarray data using a detection filter (on scanner p-value)?

Suppose I have a microarray dataset that I have to normalize with Loess and correct with ComBat. When should I apply a detection filter, relative to the other steps in the process?

In my experimental design, I have two pipelines to test:

Normalize per sample between 0 - 1
ComBat
Loess normalization between samples

and

Loess normalization between samples
ComBat

Is there any best practice for the timing of applying a detection filter?

My comment above still stands; provided your detection filter doesn't rely on your data being normalized, your detection filter can exist anywhere.

However, since it seems you know that you want to run a PCA, and know all the normalization's you'd like to try already, it is simplest to run all of your normalization first, that her than having to filter out high scoring vectors that appear to be caused by inter-sample variation.


Does using animal models for medical research also promote veterinary research on these animal types? I have been reading about mouse models for studying inflammatory bowel diseases such as Crohn's disease and Ulverative Colitis. For example, according to this publication, a widely used mouse model for colitis is the Dextran Sulfate Sodium (DSS)-Induced Colitis.

This got me thinking: when we induce disease in mice (or monkeys, fish etc.), is that somehow beneficial for veterinary research of these animals when they get sick (unrelated to medical research focusing on humans)? Are the data from pre-clinical trials used for that purpose in any way?

Short answer is no. Human disease take a long time to develop naturally, far longer than the lifespan of animals models used (mice, rats or fish).

Also the cost of the drugs far exceed the cost of the animal. There is little point in spending $40k to make a non-commercial anti cancer drug to save the life of a pet mouse who has developed the rare cancer.

Longer answer... some... a bit. Not quite what you expect. There are a few labs that are re purposing anti cancer drugs that failed animal (mouse) trials to treat dogs. It appears that people are willing to spend a fair amount on experimental drugs to save the life of the family dog.

Mice have increasingly been shown to be a poor model for human anti cancer drugs. Their cells grow to fast, their immune system is subtly different from humans. Stuff that work in mice often times are too toxic in human or just don't work. A longer lived animal model is needed. However dogs as experimental animals is too costly to maintain, too much red tape to use and takes too long for cancer progression (You cannot wait 2 years for a cancer experiment to finish).

However a sick family dog with cancer is another matter.


Fibrinous inflammation, exudate and scarring in monotonous movements and ageing I have palpated many hard organs during my work and studies.
I have seen many young and old people who have hard organs, like very hard shoulder - very common.
I have interviewed some of them, some points

only one type of weight lifting
no running
no stretching
no stretching before training
no stretching after training
not age dependent only - very old can be healthy
dynamical movement dependent

There are two mechanisms of fibrinous inflammation

trigger the release of fibrinogen
trigger release of fibrinogen-to-fibrin reaction

which both result in the production fibrin in the interstitium:

The area may also be mixed with serous so two variations of fibrinous inflammation

serofibrinous
fibrinous.

I am interested in the mechanism that leads to this hard tissue throughout the organ.
This raised to me an idea about Fibrinous inflammation in the shoulder.
Robbins say that if the exudate cannot be sucked out, it leads to scarring.
I think this is what is making the organ feel hard.

What is the pathogenesis in such monotonous movements without stretching?

I would now say that the hardening is just local acute venous congestion if in the short term.
Without stretching after practice, it just takes more days to recover.
So lymphatic drainage is the one which helps the muscle get its needs and nutrients.

If this happens during years, it is difficult to say what is the causal factor.
It depends on many factors.
One key factor is how well the lymphatic circulation can recover the body back.
So genomics of the patient comes in the picture.
Many other factors too like anatomical structure of chest.
Then, depending on these factors and other pathological processes may happen many processes like

accumulation of fibrinoid
accumulation of calcium deposits
shorter diffuse distances
smaller total area of cells

which are some adaptation processes to the ageing (also of prolonged monotonous weight lifting).
They can lead to

acute lymphangitis (reddening of the skin)
Chronic lymphangitis
Chronic Granulomatous Lymphadenitis (fibrosis happening between muscles and connection points - not in all cases granulomatous - rare only)
lymphadenopathy (very, very late - after many years)

during ageing (adaptation).

Better question would probably be: what are processes happening during ageing?
And then cover pathologies of ageing separately and also the physiological processes on the weight lifting separately.


Complementation cloning: what, why and how? I get that you're cloning a whole cDNA library, but why does E. coli need a complementary gene to allow the gene expression?
Why is that complementary gene considered to be a mutant?
AND how does one detect the gene of interest after cloning?

What is this kind of cloning used for?

I figured it out. You're complementation cloning when you know the function of a mutant sequence but not it's sequence. For example, your organism (human) gets skin cancer from too much UV light exposure.

With complementation, two mutants can restore the wild type phenotype (well functioning UV repair).

We know E. coli has a well studied UV repair gene so you transform the cDNA library from your human into an E. coli which we know has the mutation, then grow them all under intense UV light. The  E. coli with the human mutant allele (the right cDNA fragment) will survive, so you can amplify that colony, sequence it, and then use it as a diagnostic tool in humans.

I'm wondering why that was vague. Is "complementation cloning" not a well used name for that technique? Was the question too broad or elementary? It's the first time I've used Stack and it seems I may be a little too undergrad for this crowd.


What Makes an Afrothere an Afrothere? The mole-like golden moles.

The hedgehog-like tenrecs.

The shrew-like sengis.

The rodent-like hyraxes.

The anteater-like aardvarks.

The whale-seal-hybrid-like sirens.

The tapir-like proboscideans.

All these mammals, diverse in appearance, actually belong to one superorder, called Afrotheria.  Which raises the question — what are the anatomical characteristics common to all afrotheres?

The word "Afrothere" comes from Latin Afer (referring to Africa) and Ancient Greek θηρίον (thēríon, meaning “beast”). In other words, "Afrothere" etymologically refers to animals with origins in Africa.
So really, Afrotheria and it's members are referred to based on their origins and not their physical characteristics. In other words, they needn't share morphological characteristics, but rather they all evolved from the same common ancestor from Africa.
From the Afrotheria Wikipedia page:

Afrotheria is a clade of mammals, the living members of which belong to groups that are either currently living in Africa or [are] of African origin...
They share few anatomical features but many are partly or entirely African in their distribution

These animals are all chordates of the class Mammalia, and therefore do share the common "basal" characteristics shared among all members of these higher taxanomic levels -- for example, a notochord (and backbone), hair, three middle ear bones, mammary glands, etc.


Relationship of RNA-binding proteins to peptidyl-prolyl cis-trans isomerase I am studying a Plasmodium gene, known to encode an RNA-binding protein. However a BLAST search brings up mainly peptidyl-prolyl cis-trans isomerases from other species. Why would this be so?

Without seeing the sequence of the RNA-binding protein it is impossible to be sure, but the obvious conclusion is:

  The RNA-binding protein is a peptidyl-prolyl cis-trans isomerase.

It has been known since 1989 that peptidyl-prolyl cis-trans isomerase is a multiple-function protein, also exhibiting properties of the cyclophilins, proteins which bind cyclosporin A. The post raised the possibility that it may have other activities and a literature search reveals several more recent papers that indicate cylcophilin A can bind certain RNAs. I list some of the titles:

A nuclear RNA-binding cyclophilin in human T cells (1996) FEBS Letters 398 201–205

Molecular cloning, structure and expression of a novel nuclear RNA-binding cyclophilin-like gene (PPIL4) from human fetal brain (2001) Cytogenet Cell Genet 95 43–47

Cyclophilin A Binds to the Viral RNA and Replication Proteins, Resulting in Inhibition of Tombusviral Replicase Assembly (2013) J. Virol. 87 13330–13342

Structure of RNA-interacting Cyclophilin A-like protein from Piriformospora indica that provides salinity-stress tolerance in plants (2013) Scientific Reports 3 : 3001, DOI: 10.1038/srep03001


Skeletisation in space A space pod containing an astronaut drifts out to space and cannot be rescued. The space pod contains no insects, and the only bacteria present are those originally brought in by the astronaut. There is plenty of oxygen (assume 20%) and the interior is heated in the long term to 20 degrees C by a radioisotope heater.
The astronaut eventually dies through lack of food or water. His body is found many years later. What will the rescuers find? A body or a skeleton?

First I assume many years equals 10 years or more, although the presence of oxygen may drastically speed this up or it may interfere it is hard to say. Nobody was tried to figure out how something will rot in sealed but consciously oxygenated container since is basically does not exist without a custom built chamber.
Your main factor is humidity that is whether the pod has humidity control, if it keeps a human comfortable humidity you will have a skeletal mummy since skin and hair will survive but much of the body will desiccate. If you just treat it like a sealed container the body fluids breaking down will ramp up the humidity and you will just a have a pile of bones and rather disgusting soup. A sealed container is one way to rot down an animal carcass to get bones, it is called maceration and something that has been well studied. I have done it many times and a few years is more than enough to reduce a carcass down to a skeleton.  Note depending on how long you wait even the bone may be damaged or destroyed although the restricted biota may prevent the final stages of this leaving you with extremely fragile skeleton remains.
I must emphasis the smell will be disgusting, as in even seasoned investigators will be tossing their cookies if they smell it. Almost nothing can describe the disgust of the smell of a human body rotting in a sealed container. Our brains have evolved to find human rotting flesh as disgusting as possible.
for additional comparison  a a paper comparing decomposition of several pig carcasses sealed in concrete.
Source link addresses
https://pubmed.ncbi.nlm.nih.gov/2738563/
https://onlinelibrary.wiley.com/doi/10.1002/9781118953358.ch33
https://journals.lww.com/amjforensicmedicine/Abstract/2013/03000/Burial_of_Piglet_Carcasses_in_Cement__A_Study_of.13.aspx


Do corresponding areas in the two hemispheres arise from the same stem cells? After having asked this question about the connectivity between clonal cortical neurons, I'd like to know:

  Do corresponding areas in the two hemispheres arise mainly from the same stem
  cells, such that these areas connect to each other more strongly than to others?

No, they don't. The stem cells of each cortical hemisphere are located far from each other, in the subplate below the developing cortex.


How do ion channels transport only specific ions? Ion channels, such as $Na^+$ channels and $K^+$ channels, are higly specific for ion permeability. But how do these channels achieve and maintain this specificity? Like how does a $K^+$ channel transport only $K^+$ ions (same for other channels like $Na^+$, $Ca^{2+}$, $Cl^-$, etc. channel)?

I am restricting the answer to only $Na^+$ and $K^+$ channels, assuming similar mechanism for other channels. In these 2 channels, such high level of specificity is achieved because of two main differences between $Na^+$ and $K^+$:

difference in size of $Na^+$ and $K^+$ ions.
difference in chemical properties of $Na^+$ and $K^+$ ions.

Lets discuss these points one-by-one:

Difference in ionic size: the ionic size of $Na^+$ ion is 0.96$\overset{\circ}{A}$ while that of $K^+$ ion is 1.33$\overset{\circ}{A}$. How this size difference of 0.38$\overset {\circ}{A} $ is exploited by channels will be discussed in later section.

source

Difference in chemical properties: the property we are concerned here with is hydration enthalpy. $Na^+$ ion has hydration enthalpy than $K^+$ ion, meaning $Na^+$ has higher tendency to remain bounded by water molecules than $K^+$. How this enthalpy difference is exploited by channels will be discussed in next section.

source

I will discuss different methods used by these channels one at a time.

$Na^+$ channels: $Na^+$ channels are less studied than $K^+$ channels, but some of the mechanisms used are known and explained below:

$Na^+$ ions pass through channels in partially hydrated form1, and these channels have 2 rings of selection filters2 in mammals.
The first (outer) ring contains amino acids EEDD (or EEMD)3 while second (inner) ring contains amino acids DEKA4. How these amino acids bind to specifically $Na^+$ ions is not completely known yet, but it is hypothesized that the inner ring, being more conserved, is more important as a filter than the outer ring. Also, it has been shown that by changing the amino acid K in DEKA makes the channel more permeable to $K^+$ and $Ca^{2+}$ ions, and by changing sequence from DEKA to EEEE makes the channel more selective towards $Ca^{2+}$ ions5.
$K^+$ ion, in hydrated form, cannot pass through inner filter due to larger size and presence of negatively charged D and E of DEKA, whereas $Na^+$ easily passes through due to smaller size and higher hydration enthalpy6.

Negative charge in channel is such that it mimics the hydration shell (regular octahedron) of $Na^+$ from side

source (1)           source (2)

$K^+$ channels: $K^+$ channels have been studied more intensively, so their mechanism is much more understood. The main points to ponder are:

The filter of $K^+$ channel contains amino acids TVGYG 7 and is present in the narrowest region of the channel.
To pass this channel, $K^+$ ion needs to be completely dehydrated i.e. without any water molecule bound to it. The amino acids in the filter replace water molecules with polar oxygen atoms. On the other hand, $Na^+$ cannot get rid of water molecules so easily and hence, its passage through the channel is thermodynamically unfavorable8, partly also because dehydrated $Na^+$ is so small that it cannot even bind with all of the polar oxygen atoms of amino acids.
Here nature shows some clever techniques. The amino acids, TVGYG, having their electronegative carbonyl oxygen atoms aligned toward the center of the filter pore, form a square anti-prism similar to a water-solvating shell around each potassium binding site. The distance between the carbonyl oxygens and potassium ions in the binding sites of the selectivity filter is the same as between water oxygens in the first hydration shell and a potassium ion in water solution, providing an energetically-favorable route for de-solvation of the ions9.

This is how the passage of a $K^+$ ion through $K^+$ channel looks like:
source

The carbonyl oxygens mimic this configuration as this is how a $K^+$ looks in hydrated form (square antiprism):source

P.S. as more deep studies are made, more mechanisms may be revealed. Also, above mentioned points are just theories and not conclusive proofs.

References:

Hille, B. The permeability of the sodium channel to organic cations in myelinated nerve. J. Gen. Physiol. 58, 599–619 (1971).
Guy HR, Seetharamulu P. Molecular-Model of the Action-Potential Sodium-Channel. Proc Natl Acad Sci USA. 1986;83:508–512.
McNulty, M. M., Edgerton, G. B., Shah, R. D., Hanck, D. A., Fozzard, H. A. and Lipkind, G. M. (2007), Charge at the lidocaine binding site residue Phe-1759 affects permeation in human cardiac voltage-gated sodium channels. The Journal of Physiology, 581: 741–755. doi:10.1113/jphysiol.2007.130161
Favre I., Moczydlowski E. & Schild L. On the structural basis for ionic selectivity among Na+, K+, and Ca2+ in the voltage-gated sodium channel. Biophys J 71, 3110–3125 (1996).
Calcium channel characteristics conferred on the sodium channel by single mutations.
Heinemann SH, Terlau H, Stühmer W, Imoto K, Numa S 1992 Apr 2;356(6368):441-3.
Mechanism of Ion Permeation and Selectivity in a Voltage Gated Sodium Channel. Ben Corry and Michael Thomas
Chemistry of ion coordination and hydration revealed by a $K^+$ channel–Fab complex at 2.0 Å resolution, Yufeng Zhou, João H. Morais-Cabral, Amelia Kaufman & Roderick MacKinnon
Mechanism of potassium channel selectivity revealed by $Na^+$ and $Li^+$ binding sites within the KcsA pore.
Ameer N. Thompson, Ilsoo Kim, Timothy D. Panosian, Tina M. Iverson, Toby W. Allen, and Crina M. Nimigean
A comparison between two prokaryotic potassium channels (KirBac1.1 and KcsA) in a molecular dynamics (MD) simulation study; Mikko Hellgrena, Lars Sandberg, Olle Edholm, 1 March 2006


What is the acceleration profile of the greyhound? I'm interested in the acceleration curve over time that's typical of an adult greyhound prior to attaining this peak velocity. My curiosity is motivated by a desire to understand the biomechanical reason why land mammals run so fast.

I'm going to try to break this up a bit to address your sub-questions. Most of it is summarized from Williams et al 2008--and almost all of the work I'm referencing comes from the Royal Veterinary College Structure and Motion Lab.

Acceleration Profiles:

So, I can't find an acceleration curve over time for these, but we do know about the potential acceleration range for greyhounds and cheetahs. Greyhounds can reach a max speed of about 17 m/s (Usherwood and Wilson 2005), cheetahs can reach up to 29 m/s (Hudson et al. 2010). Cheetah stride-averaged accelerations have been measured up to 120 W/kg --they can speed up by 3 m/s over a single stride, and slow down by up to 4 m/s (Wilson et al. 2013). Racing greyhounds have achieved 60 W/kg (Williams et al. 2009).  Maximum acceleration decreases with increasing speed

How Land Animals Can Be Fast

Augmentation or hypertrophy of proximal musculature. More than a fifth of a greyhound's limb muscle mass is associated with the proximal portion of the hindlimb (Williams et al. 2008). Muscle power (work/time, important for acceleration) is roughly proportional to muscle volume, so bigger muscles are better in this case.  In cheeetahs, a similarly large muscle mass is devoted to hip extensors (though different specific muscles; Hudson et al 2010). Big muscles = high power and high force production.  In addition, sprinting mammals tend to have longer muscle moment arms than non-sprinters--so they can produce greater torques for a given force.
Longer muscle fascicles. This may also be an adaptation for power output. Greyhounds have longer fascicle lengths in their hamstrings than your average domestic dog (Williams et al 2008), and human sprint athletes also have longer fascicle lengths than endurance runners (Abe et al. 2000).
Long limbs and flexible spines: Longer limbs w/ spinal flexion = greater stride length--and cheetahs have particular elongated hind limbs. A long hind limb also lets cheetahs maintain foot contact with the ground for longer, so lower peak forces are required.

These aren't nearly all of the things involved, but I suppose this is a start.

References:

Abe, T., K. Kumagai and W.F. Brechue. 2000. Fascicle length of leg muscles is greater in sprinters than distance runners. Med. Sci. Sports. Exerc. 32: 1125-1129.
Hudson, P. E. et al. 2010. Functional anatomy of the cheetah (Acinonyx jubatus) hindlimb. J. Anat. 218: 363–374.
Usherwood, J. R. and A. M. Wilson. 2005. No force limit on greyhound sprint speed. Nature. 438, 753-754.
Williams, S.B. et al., 2008. Functional anatomy and muscle moment arms of the pelvic limb of an elite sprinting athlete: the racing greyhound (Canis familiaris). J. Anat. 213:  361–372.
Williams, S. B. et al. 2009. Pitch then power: limitations to acceleration in quadrupeds. Biol. Lett. 5: 610-613.
Wilson, A. M. et al. 2013. Locomotion dynamics of hunting in wild cheetahs. Nature. 498: 185-189.


How can I save bacillus strains on filter paper without an -80 degree freezer? I want to save my bacillus strains but I don't have access to a -80 degree freezer.  What are possible alternatives?

Use agar stubs: pour some Nutrient agar (or any suitable agar medium) in a test tube (~10% of the tube volume) and punch your inoculum halfway into it using a pipette tip or inoculation loop. Store it in 4⁰C.

Glycerol stocks can be made and stored in -20⁰C also.


Can you help identify this bird in Louisville Kentucky? This bird shows up in my back yard every night.  It is calling and sometimes I hear a bird in the distance calling back.  I think its an owl but I haven't seen it yet.  Any ideas what it is?

To me that sounds like the distinctive "who cooks for you" call of the Barred owl.

Compare with the recordings available from the Audubon Society, Cornell's All About Birds, and many others such as this YouTube video from a Cornell Lab Bird Cam of a Barred owl calling from its nest.


What flower is this? I received this flower as a gift.

So far, I couldn't identify what flower it is. My family thinks it may be either some sort of Clematis or an Ipomoea purpurea.
The main reason I want to identify this flower is to know if it can live outside most of the year (I live in France).

The leaves are most similar to this Mandevilla

It may be a hybrid periwinkle, in France and UK there are blue ones in wild and there are pink ones i.e. in Madagascar. If it's a periwinkle you can tell by the fruit and veins of the leaves. It can be a variant of Vinca minor. It has evergreen type leaves, it may be tropical. It is also similar to the Oleander family. Clematis and Ipomea have new foliage every year.

Also see this.


Cationic lipid mediated transfection optimization for 150mm dishes I need to optimize a transfection protocol to transiently express a plasmid encoding a chimera of  eyfp attached to the c term of a Golgi apparatus signaling molecule) in hela cells and hepg2 cells and get as high expression as I can get.

I need enough protein for about 100 wb's. I've seeded hela cells to 12 150mm dishes. And the same with the hepg2. I've prepped mg's of plasmid.

I'm using invitrogens original lipofectamine reagent; not the 2000, or ltx or any of that stuff.

Any suggestions on a protocol here for hela and hepg2 plasmid dna and lipofectamine mediated transfection on such a large plate size.

I figure just scaling up should work but there's some pitfalls here. Look at this table for example when you go from 60 to 100 mm you about double the area, so you also about double the culture volume. However when you go from 100 to 150mm you triple the area, but only increase the culture volume two fold about. This is making my scale-up calculations for transfection look really off:

So, for every row on the dish protocol, the entire process is scaled up a discrete value. In the case of 100mm to 150mm, the values are scaled up by about 2.76 across all values:

(a) 152/55 = 2.76, (b) 1.52e7/5.5e6 = 2.76, (c) |avg(30.4-45.6)/avg(11-16.5)| = 2.76

(as answered in comments)


HOW is the Gallbladder attached to the liver The gallbladder’s function is to store bile from the liver which is delivered through the cystic (bile) duct.  The cystic artery is also connected to the gallbladder to deliver blood.  (Correct me if I am wrong about any of this.)

However, when I was watching a gallbladder surgery video on YouTube, in the process of removing the gallbladder the surgeon clips the bile duct and artery which I understand but he/she also cauterises the gallbladder off the liver.  I also understand that The cauterisation is to prevent bleeding.

BUT the question is WHY is the gallbladder attached to the liver in the first place?  WHAT purpose does being attached to the liver serve? Does it provide stability? Because I always thought the gallbladder just sits beneath the liver.  Most importantly, HOW is the gallbladder connected to the liver?  (This maybe be more of a chemistry question), what bonds is it connect through, what/which biomolecule connects it and why is it that biomolecule/ bond that is used.

As watching the video,  I also noted that the surgeon didn’t clip the cystic vein, or even mentioned it.  Maybe I am wrong and he/she did clip the cystic vein but I didn’t see, would you also be kind enough to explain to me why the surgeon didn’t clip the cystic vein or if he did why it wasn’t pointed out.  Also tell me more about the cystic vein where is it located because it’s very hard to find clear diagrams with them...(is it because it’s small)

1. Gallbladder attachement to the liver

In this video (check from 55 sec on), you can see that the gallbladder is covered by a thin sheath that wraps the gallbladder; the sheath extends to the liver and intestine and thus keeps the gallbladder in place. The sheath is a part of the abdominal membrane (peritoneum) that covers most of the abdominal organs. You can see that the surgeon is cutting the sheath.

2. The Cystic Vein: The Significance of a Forgotten Anatomic Landmark (PubMed Central)

  ...there is no cystic vein per se, but the venous drainage is
  through the bed of the liver [between the attachment surfaces of the
  gallbladder and liver]...however..Gray's
  Anatomy of the Human Body...describes cystic veins which join at the
  neck of the gallbladder to form either single or double cystic veins
  which flow along the cystic duct and upward along the hepatic
  ducts.


Cholesterol and fatty acids role in bile? The composition of gallbladder bile is 97% water, 0.7% bile salts, 0.2% bilirubin, 0.51% fats (cholesterol, fatty acids and lecithin)1. Bile's role is mainly help for digestion of lipids via bile salts and acids (emulsification) but i dont understand what is cholesterol and fatty acid role in bile. What is cholesterol and fatty acid's function in bile?

The main function of bile is to emulsify large fat molecules into small fat droplets. You must have heard about micelle formation by soaps. Well, bile acids perform quite similar function. Bile acids, having both hydrophobic and hydrophilic parts, form micelles and trap fat molecules and form emulsion, hence naming the process emulsification. Similar function might be performed by fatty acids. See this article:

  Bile acts to some extent as a surfactant, helping to emulsify the lipids in food. Bile salt anions are hydrophilic on one side and hydrophobic on the other side; consequently, they tend to aggregate around droplets of lipids (triglycerides and phospholipids) to form micelles, with the hydrophobic sides towards the fat and hydrophilic sides facing outwards. The hydrophilic sides are negatively charged, and this charge prevents fat droplets coated with bile from re-aggregating into larger fat particles.

Now lets have a look on bile acids. The principal bile acids are cholic acid, chenodeoxycholic acid, glycocholic acid, taurocholic acid, deoxycholic acid and lithocholic acid, all of which are synthesized from cholesterol (see this). Now this partly explains why a small amount of cholesterol is released along with its derivatives; it might be the 'unprocessed' cholesterol which 'leaked out' from liver. But, in fact, it seems to do a bit more. Actually, cholesterol secretion into bile needs to be carefully controlled; too less secretion may lead to accumulation of cholesterol in blood vessels, leading to cardiovascular diseases (this is why cholesterol secretion is the final stage of elimination of cholesterol from reverse cholesterol transport), while too much secretion into bile may cause gallstones (see this). Hence, cholesterol secretion into bile also serves as a way to maintain cholesterol homeostasis (see this). In fact, bile acids serve as hormones in cholesterol homeostasis in the body. Similar reason may cause fatty acid elimination through bile.

Cholesterol and fats are hydrophobic, so they cannot be released as it is into GI tract. This is why they are released with bile. Bile acids are amphiphatic i.e. have both hydrophilic and hydrophobic parts. Hydrophilic part helps it in dissolving in chyme (containing HCl) while hyrdrophobic part helps it in dissolving fats and cholesterol (and lipids of course) into itself.

source