How statistically significant was the "sweaty T-shirt" experiment? An Overview of the Experiment.
In 1995 there was an experiment that involves young people smelling T-shirts worn by another gender and rating their preference. The researchers found that people preferred shirts belonging to people with a dissimilar Major Histocompatibility Complex (MHC). Another interesting finding was that this preference reversed for the women 'sniffers' that were using oral contraceptives.
Here is a link to the wikipedia entry.
These findings were reiterated by a study in 2005.
My Question.
I'm very ignorant in the subject of pheromones, particularly in humans. For those of us not 'in the know' a result like this seems like magic! I want to get a better grasp on how set in stone pheromone preferences like this are.
Unfortunately I do not have access to these articles at the moment. The actual statistical difference in populations isn't mentioned in the abstracts  (the cynical sceptic alarm bells are ringing!) other than the 2005 one stating that the total sample size was 58, which sounds low given that the total population is split into two.
Generally I'm looking for any supporting or opposing critiques of the study, specifically I want to know more about the statistics of the studies.
My question is:

What statistical validations and scores appear in these studies?

I also am willing to accept answers discussing validation in similar studies. I'm after a number or quantification for how consistent pheromone preferences are.

First, let's consider the original Wedekind et al (1995) study.

Sample sizes seem reasonable, if the effect is not very noisy:

  [...] 49 female students (average age: 25.2 years, s.d. = 4.0) and 44 male students (average age: 24.7 years, s.d. = 2.6) [...]

... and the statistical design accounts for individual differences in a fairly robust way:

  [...] women were asked to rate the odours of six T-shirts each, three of them worn by men who were dissimilar to the rating woman's MHC (average number of dissimilar HLA-antigens = 5.9, s.d. = 0.26), and three worn by men who were more similar to it (average number of dissimilar HLA-antigens = 2.7, s.d. = 0.74). We tried to present every T-shirt as often to MHC-dissimilar women as to MHC-similar women (average difference of presentations to thc two groups: -0.02, s.d. = 0.73). The presentation was random in every other respect [...]

Rather irritatingly, although the study design involved asking women to rate at least three attributes of the smells (sexiness, pleasantness, and intensity) the study performs a bait-and-switch in its results:

  The scores for sexiness are not shown in the figures as they were highly correlated with pleasantness (all scorings: r = 0.85, n =  294; for women who do not take the pill: r = 0.87, n = 186; for women who take the pill : r = 0.83, n = 108, p always << 0.001)

This is a bait-and-switch because even if A correlates with C, and B correlates with C, we do not know that A and B correlate with each other. Of the three measured attributes, 'sexiness' arguably has the most direct bearing on mate-choice. Because analysis for 'sexiness' is not presented, the paper ends up telling us much less than it could have about the relationship between MHC relatedness and mate choice.

The results for 'pleasantness' and 'intensity' look like this:

One further piece of analysis is presented: some number of the female subjects seem to have reported that particular smells reminded them of their partner or ex-partner; or reminded them of family members. Mentioning that a shirt smelled like a partner or ex-partner happened more frequently for MHC-dissimilar shirt smells (~17% vs ~9%; p = 0.038, two-tailed Fisher exact test). Oddly, no written response-collection is described in the methods, so I can only assume that these assessments were ad-hoc.

If this was all of the analysis that had been done on the topic, my assessment would be: this is amongst the many published research findings that are probably false. My main concerns would be that

Not all of the collected data are presented;
The most directly-informative contrast is not shown;
No adjustments for multiple comparisons are made on the statistical tests;
The data that are shown are very noisy, and sample sizes are not huge, raising concerns that the tests are underpowered;
The authors conduct tests based on data-collection which is not detailed in their methods, raising concerns about p-hacking.

And now, the 2005 paper!

Right off the bat, this paper cannot possibly replicate the findings of the Wedekind (1995) paper, because Wedekind et al found significant preferences for dissimilar MHC odours in women not taking the pill, and significant preferences for similar MHC odours in women taking the pill. In this study:

  [...] we did not distinguish between, in our statistical analysis, women who were taking oral contraceptives from women who were not.

  [...] Nine female participants (31.03% of female subjects) were taking oral contraceptives.

Sample sizes are smaller than Wedekind 1995 in terms of number of participants, but larger in terms of number of contrasts, because this experiment had two different sample types (sweat odour and urine), and had men smelling women as well as women smelling men. Within-individual effects are not modelled, so there is a potential for (e.g.) a small number of generically good-smelling individuals with rare MHC alleles at the population level to bias the analyses - whereas this potential bias was accounted for in Wedekind by performing within-individual correlations. The sample-sizes look like this:

The analysis was a series of Chi-squared tests, for data collected in four different sessions: one with men smelling female urine, one with men smelling female body odour, one with women smelling male urine, and one with women smelling male body odour. All chi-squared tests returned non-significant results with the exception of women smelling male body odour, for which the Chi-squared table looks like this:

So, this study didn't find the same result as the Wedekind study, but then, it couldn't find the same thing as the Wedekind study because of the way the analysis was performed, so that is no surprise. The authors claim that they found a significant effect of MHC relatedness on odour perception, but only in the proportions in the hard-to-interpret 'indifferent' response category. I am inclined to disagree. The authors presumably conducted 16 contrasts (a test of independence and three goodness-of-fit tests in each of four treatment types), and found one instance of p < 0.05. I would argue that the one 'significant' result is best explained as a failure to account for multiple comparisons.

Ending notes

If these two papers were the only things that had been published on MHC-directed mate preferences in humans, I would be far from convinced that the claimed effects were real.

however...

These are far from the only papers on the subject of MHC-driven mate-choice in humans. Wedekind and Füri (1997) conducted an analysis with very similar experimental design to Wedekind et al (1995), but arguably better statistical analysis, and found the same direction of association as Wedekind et al (1995), albeit still with a fairly high noise-to-signal ratio. Subjectively, this goes a reasonable distance towards making me think that the findings of Wedekind et al (1995) were not just a statistical fluke. I'm still not utterly convinced, but certainly more convinced than I would be if Wedekind's final paper on the topic had been the 1995 publication.

MHC-driven mate-choice has also been investigated using facial preferences and mate choice surveys. The combined evidence (across odour preference, facial preference, and mate choice surveys) is reviewed in Havlicek and Roberts (2009).


Why are certain aneuploidies more common? Certain aneuploidies such as trisomy-21 (Downs syndrome), trisomy-18 (Edward syndrome), Turner syndrome (XO) etc are more common than others.

I had a vague thought that it is related to chromosome size: the chromosomes which are towards the extremes of size will be affected in an improper segregation event.

Chromosomes 13, 18, 21 and Y are among the smaller chromosomes in humans, and are commonly associated with aneuploidy (but 22 which is also small is not affected). The larger ones are unaffected (X is an anomaly).

I thought that longer ones should be more affected because more cohesin bridges have to be broken, but it seems that is not the case.

Is there any association of chromosome size and frequency of aneuploidy?

EDIT

If the difference is because of differential lethalities then does the length correlation still hold true? Smaller the chromosomes, lesser the genes and hence lesser would be the effect of extra copy on the cellular biochemical networks.

I thought it was just that the other aneuploidies were fatal. They occur as often but miscarry earlier in the term therefore you don't see them. So basically there are only three that are viable 21,18 and the sex chromosome with a number of combinations: XO, XXY, XYY and XXX.

More information here:
http://www.nature.com/scitable/topicpage/chromosomal-abnormalities-aneuploidies-290

With regard to the frequency for each chromosome:

For males (i.e., sperm; source):

  The mean disomy frequency is 0.15% for each of the autosomes and 0.26%
  for the sex chromosomes. Most chromosomes analyzed have an equal
  distribution of disomy with the exception of chromosomes 14, 21, 22
  and the sex chromosomes, which display significantly higher disomy
  frequencies.

Size of the chromosome is frequently reported as a factor in the frequency.

For females (i.e., eggs; source):

  The data is obviously harder to attain. One study from IVF treatments
  show differences in the frequency of different chromosomes at
  different stages in meiosis.


number of chromatids seen in karyotype The karyotype is performed on a cell whose cycle has been stopped in metaphase or pro metaphase, using colchicine or by other means. In the textbooks I read that during the S phase each of the 46 chromosomes is duplicated, giving, again, 46 chromosomes, but, and here I am deducing, 92 chromatids. When we perform the karyotype, we only see 23 pairs of chromosomes (46, that is), and, it looks like to me, the same number of chromatids (46 as well). What am I missing? Why can't we see 92 chromatids in the karyotype?

Thanks a lot for your attention.

As you noted, karyotypes are prepared from cells halted in metaphase or prometaphase.  In either of these phases, the chromosomes will have two chromatids bound together at the centromere with the chromatid arms lying parallel to each other.

The difficulty in seeing the chromatids in most karyotypes is due to the way they are prepared. Most karyotypes are prepared using Giemsa staining which causes contrasting bands to appear on the arms.  These bands have patterns characteristic for each chromosome type and thus allow the chromosome images to be identified and sorted into pairs.  Between the stain, lighting and exposure used to show the banding, the images don't show the separate forms of the chromatids well.

With alternative staining and lighting, the chromatids can stand out (all images from commons.wikimedia.org):

Still, in typical karotype photographs of sufficient resolution you can at times make out the separate forms of chromotid arms, or perhaps the "pinched waist" shape where the centromere draws the chromotid arms together:

So, yes, a normal human karyotype has 92 chromatids present; they just tend not to be apparent due to the preparation done to show banding.


Can E. coli make pyruvate from acetate? What pathway would E. coli use to make pyruvate from acetate? I have found several papers that refer to a possible mechanism that could move acetate to pyruvate via a three-step process:

Step 1: Acetate Kinase (EC 2.7.2.1)

Step 2: Phosphate acetyltransferase (EC 2.3.1.8)

Step 3: Ferredoxin oxidoreductase (EC 1.2.7.1)

Is this the pathway that would be used in an E. coli system?

Summary

Several pathways/metabolic reactions are required for bacteria to convert acetate to pyruvate — or more pertinently to the gluconeogenic pathway — but the key is the glyoxylate cycle or shunt. The sequence of reactions is:

2 acetate → 2 acetyl CoA (acetyl CoA synthetase)
1 acetyl CoA + oxaloacetate → citrate → isocitrate (entry to Krebs TCA cycle)
isocitrate → glyoxylate + succinate (glyoxylate shunt)
succinate → oxaloacetate (Krebs TCA cycle)
1 acetyl CoA + glyoxylate → malate (glyoxylate shunt)
malate → oxaloacetate (Krebs TCA cycle)

Thus, the two molecules of acetate replenish the original molecule of oxaloacetate used for one of them to enter the tricarboxylic acid (TCA) cycle, with — in addition — a second molecule of oxaloacetate. This is available for:

oxaloacetate → phosphoenolpyruvate (PEP carboxykinase of gluconeogenesis)

The phosphoenolpyruvate (PEP) could, in principle, be converted to pyruvate:

phosphoenolpyruvate → pyruvate (pyruvate kinase of glycolysis)

Although this sequence of reactions would normally be used to generate glucose etc via gluconeogenesis.

The link betweeen the TCA cycle and glucose metabolism

In addition to oxidizing acetyl CoA, the Krebs tricarboxylic acid cycle (TCA cycle) can act as source of certain metabolic intermediates for other pathways. As shown below, oxaloacetate (OAA) can be converted to phosophoenol pyruvate (PEP), in a reaction that is part of the gluconeogenic conversion of pyruvate to PEP.

Although certain bacteria can convert acetate into acetyl CoA in a reaction catalysed by acetyl CoA synthetase  the TCA cycle per se does not perform a net conversion acetyl CoA to OAA, because a molecule of OAA is needed for acetylCoA to enter the TCA cycle and must be regenerated. The TCA cycle, in effect, oxidizes acetyl CoA to carbon dioxide. The TCA cycle, per se, can only convert to OAA and PEP those intermediates that enter the cycle directly after the acetyl CoA stage.

The glyoxylate shunt

The foregoing explains why most animals cannot convert fat to glucose. (Acetyl CoA cannot be converted to pyruvate by pyruvate dehydrogenase is this reaction is effectively irreversible.) However plant and certain bacteria (including Escherichia coli) can overcome this limitation by means of the glyoxylate shunt. A text available online that explains this is Berg et al., in a section entitled ‘The Glyoxylate Cycle Enables Plants and Bacteria to Grow on Acetate’. To help clarify this I have prepared my own diagram, below.

This involves the conversion:

oxaloacetate + 2 acetyl CoA → 2 oxaloacetate

i.e. the net conversion of

2 acetyl CoA → oxaloacetate

The glyoxylate shunt reactions are imposed on the TCA cycle with a pink overlay. One molecule of acetyl CoA condenses with OAA to enter the TCA cycle in the normal manner. However the isocitrate formed from citrate, instead of being decarboxylated, is converted to glyoxylate and succinate. The succinate — a dicarboxylic acid — regenerates the original molecule of OAA used to allow acetyl CoA to enter the TCA cycle.

What of the glycoxylate produced in the isocitrate lyase reaction? It reacts with a second molecule of acetyl CoA to produce the dicarboxylic acid malate in a reaction catalysed by malate synthase, the second unique enzyme of the shunt. This TCA cycle intermediate is converted to OAA. This second OAA is a net gain from the metabolism and can be converted to PEP, as indicated in the first diagram.

The poster asks about production of pyruvate from acetate. This is technically possible through the pyruvate kinase reaction. However I do not quite see the point of this. I would normally expect PEP to be channeled allong the gluconeogenic pathway towards glucose.

Coda: Pyruvate:ferredoxin oxidoreductase

The poster suggests a series of reactions to convert acetate to pyruvate, the final one being that catalysed by pyruvate:ferredoxin oxidoreductase. Although the pyruvate:ferredoxin oxidoreductase (EC 1.2.7.1) reaction is reversible, it generally functions to oxidize pyruvate to acetyl CoA. It is used as an alternative to pyruvate dehydrogenase by bacteria under anaerobic conditions (as it does not require NAD+), and this is regarded as its role in E. coli, and to an even greater extent in obligate anaerobes such as Clostridium.

The reverse reaction suggested by the poster, involving the synthesis of pyruvate from acetyl CoA, is restricted to autotrophs


What insect is this? Found in Russia Found in Russia in the kitchen. Its about 15 mm long.

Common name: Stonefly completely harmless!
(the terrestrial adult does not have mouthparts) and is an indication that the stream nearby is somewhat healthy.
Below is great info from online site. I just now joined Biology Stack so not sure if we can post links but I’ll try it at the end.

Neither a stone nor a fly, the stonefly is in an order of insects called "Plecoptera," which means "braided-wing", due to the prominent network of veins in its wings. The common name “stonefly” refers to the fact that the larvae live among stones in rivers and streams, and the adults fly.
Like most insects, the larvae and adults live radically different lives.
By far the majority of the stonefly’s life, two to four years, is spent as a larvae or naiad (the term for larvae that live in water). The naiads are entirely aquatic, living secretive lives in cool streams where they feed on plants, algae and decaying matter.
Giant stoneflies are the largest stonefly species, with adults reaching nearly two inches long. They emerge from the water in late May to early July and live only a few days — just long enough to mate and lay eggs. To attract a mate, the males drum their abdomen on the substrate or surface on which they're resting. The female feels these vibrations and moves towards it, sometimes drumming a response call. Adults have no mouthparts so they do not eat or bite. As large and imposing-looking as giant stoneflies are, they're completely harmless.
While most people would find the giant stonefly to be an interesting-looking insect, fisherpeople get particularly excited about them because they indicate good water quality — and possibly trout. Like trout, stoneflies need fairly cool, stable water temperatures and a high amount of dissolved oxygen. Stoneflies are also a favorite food of trout, so they can be used as lures. Finding these critters in the Mississippi River is another indicator of how water pollution has greatly improved from historical conditions in the early and mid-1900’s.

https://www.fmr.org/news/2017/12/27/nature-notes-its-sign-giant-stonefly-found-downtown-st-paul


What is full form of r and K in r-selection species and K-selection species? What is full form/ meaning of 'r' and 'K' in r-selection species and K-selection species? Does this 'r' means "Random" and the 'K' means "constant"?

This article discusses the origin of the terms. They come directly from the equation used to describe population dynamics. As Canadianer mentioned the Wiki also covers it quite well.

"r" stands for "rate" {growth rate}, r strategists have a high r value and a low K value. They grow fast but most die.

"K" stands for Kapazitätsgrenzen which is german for capacity limit, now called carrying capacity, K strategists have a low r and a high K. They grow slow but more survive.


Purple Mushroom Identification I found a purple mushroom that looked like this on a nature walk in South Carolina, USA today. This is not my picture, but one that looks exactly like the mushroom I saw. I have searched the internet, but I could not identify it. Does anyone know what this could be?

The image you used is from a Reddit Thread, where the mushroom is identified to be Cortinarius violaceous. More information on Cortinarius violaceous can be found here.

Although it could be a different mushroom, as the picture you provided is not a picture of the specific mushroom you saw.

Another picture of Cortinarius violaceous

Source: velutipes.com

All credit goes to Reddit user tubergibbosum for the identification.


What could cause sudden deafness and deliriousness on a boat adrift? I'm reading a completely nonfiction book  called In the Heart of the Sea, and in it, the characters are lost at sea without food and they are starving. They cast lots to see which crew member will be eaten, and it lands on one of them. He asks for the night to resign himself to his fate, and the other members accept. However, by midnight, he'd become deaf and by morning he was delirious. Why would this happen? It wasn't starvation-induced because they'd used up the very last of their rations that night in a large meal. So why did the threat of death induce deafness and deliriousness?

Edit: And it was 100% true: not only was the book nonfiction, there are accounts from the surviving crew members of the event.

He probably had hypernatremia: salt toxicity from drinking seawater.  That definitely can cause delirium.  It was harder to nail down that hypernatremia could cause deafness specifically but I found that for pigs.

http://www.merckvetmanual.com/toxicology/salt-toxicity/overview-of-salt-toxicity

  Affected pigs may be blind, deaf, and oblivious to their surroundings;
  they will not eat, drink, or respond to external stimuli.

It would be easy to think a person was deaf if he were altered / delirious / encephalopathic.  His brain does not process what he hears and so he is oblivious - like these pigs.


Arm at Heart Level when Measuring Blood Pressure How come that one's arm has to be at heart level so that the blood pressure can be measured accurately. I've tried researching this question, but most answers to it were just "if the arm is above the heart level the blood pressure is too high and vise versa," but I want to know why this is so.

This page (and many others) explain the idea rather well. This is more of a physics than a biology question, but the fundamental concepts are the same.

In fact, contrary to what you wrote in the question, the measured blood pressure should be lower than expected if the arm is elevated above heart level.

When you reduce the pressure on the bent pipe, the water level on the side where the pressure is reduced rises.

Similarly, When the arm is elevated, it is equivalent to the right hand side of the image, where the right hand tube's water level is higher than the left hand side. Raising the arm above heart level, with the pressure of blood at the heart level remaining constant, will result in a lower pressure being measured, due to the heart effectively having to pump the blood up the distance.

For the same reason, giraffes have very high blood pressures (double that of humans) due to their long necks. If their blood pressure was at the level of humans, they would faint when raising their necks, due to the blood pressure falling to zero at their brains.


Does vitamin D form crystals in the blood with calcium and magnesium? I read on a vitamin-D product (2000NE) that I should not use calcium and magnesium with it, because it can result crystal formation in the blood. I googled, but find anything about this. Is it true?

(Somehow I doubt it, but I don't know the exact mechanism how vitamin-D works by building bones. Afaik. there are osteoblasts and osteoclasts which constantly build and degrade the Ca-Mg-PO4 depos, and I assume vitamin-D is just a cofactor of an enzyme or it is required to produce a hormone. I never heard of Ca/Mg - vitamin-D cross-reactions...)

Vitamin D does not bind to Calcium. It is a pre-hormone which is converted to calcitriol. Calcitriol has an intracellular receptor (VDR) that, as a heterodimer with Retinoid-X receptor, regulates gene expression.

I guess the "should not be had together" is because of possible over-absorption of Calcium. There are commercially available supplements (e.g. 1, 2) that have Vit-D + Ca + Mg.


Concept and analysis of Pedigree Pedigree analysis is a process of establishing a virtually correct inheritance pattern of a genetic condition in a proband's family. I call it virtually correct because in many a cases we assume the genotype of a parent to be something by weighing the genotypes of the offsprings.

Now in a given problem like in this one where the trait follows autosomal dominant inheritance pattern I have problem deciding the genotype of I-3.

My opinion:

The genotype of II-6 is AA'. (Obtained from a calculation which I have decided to not to mention as it will make it lengthy and complicated)

(here A=Normal allele on autosome and A'=Mutant allele on autosome)

II-6 receives allele A from mother I-4 (who is obviously AA) and allele A' from father I-3. Now the genotype of the father could be either AA' or A'A'.Since the probability of having a AA' female child becomes 100% if we assume the genotype of the father to be A'A' so the genotype of the father I-3 is A'A'.

But one of my instructor says that it cannot have a genotype A'A' because it is fatal and I am not convinced with his reasoning.

In Huntington's disease presence of one HTT gene is enough to cause death of the person. It is a dominant lethal allele. While in achondroplasia, an autosomal dominant disorder the mutant allele when present in two copies is fatal.It is a recessive lethal allele. A heterozygous person survives with symptoms of Achondroplasia.

So death is not always caused by two copies of a mutant gene of a dominant autosomal trait. It may be caused by only one copy of gene as in Huntington's disease or may not be caused at all(I've no proof of this. Its my assumption).

So in a pedigree where nothing has been mentioned about the lethality of the genes concerned we shouldn't assume them being recessive lethals. This is all I think. Am I correct?

Finally: Should the genotype of I-3 be A'A'?

I-3 can be either A'A' or AA'. In Huntington's disease or Achondroplasia, the father could still survive to adulthood and reproduce. If the father had a chromosomal disorder such as Kallman's syndrome, he would be unable to reproduce. However, this is not a simple mutation, and it is not heritable. You should ask your instructor to clearly define the problem.


Where are the ATP synthases synthesised? The nano-machinary of energy production ATP synthase is well known to exist on mitochondrial inner membrane and chloroplasts. But how and where are they formed or synthesised ?

The interesting thing is that the mitochondrial ATP synthase consists of many subunit proteins, both encoded by nuclear DNA and mitochondrial DNA. It has long been unclear exactly how these synthases are assembled, and what differences exist between bacteria, yeast, and humans - where ATP synthase formation is normally studied. Regardless, each of these proteins is translated on ribosomes from mRNA transcripts of genes, just like regular proteins. However, these must come together correctly (in the right order) and end up in the correct location.
There are recent publications that answers your question rather directly.
Assembly of the membrane domain of ATP synthase in human mitochondria
In short:

We have shown that the assembly of human ATP synthase in the inner [mitochondrial] membrane involves the formation of a monomeric intermediate made from 25 nuclear-encoded proteins into which the two mitochondrially encoded subunits are inserted and then sealed by association of another nuclear-encoded protein, thereby dimerizing the complex. Association of a final nuclear protein oligomerizes the dimers back-to-face along the cristae [inner membrane of the mitochondrion] edges.

A commentary on the paper is also available, which provides insight into the historical and biological context and difficulties which the paper addresses and overcomes. It may be worth reading their synopsis first. You can find it here:
Assembling the mitochondrial ATP synthase


Does electrotonic spread/conduction occur in saltatory conduction? Even as textbooks, and almost all web pages I've seen so far, explain electrotonic spread/conduction as the passive current flow along an axon, they do so with continuous conduction only. Apart from myelin sheaths which enwrap axons leaving only the Nodes of Ranvier exposed, and of course, the energy requirement and speed of conduction differences, I can't see how else continuous conduction differs from saltatory.
My question then is why electrotonic spread is never mentioned in saltatory conduction.

Generally textbooks take the following pedagogical flow in basic neurophysiology:
Ions flow, so voltage changes propagate
This is the "electrotonic part". The key concept is that if you add some ions or change the voltage of one part of a neuron, adjacent areas will also change in voltage as current flows 'passively'. The further away you go, the longer it takes the signal to arrive and the smaller it will be as the charge spreads out.
A more advanced course might also talk about the sources of those charges, like sensory receptors or neurotransmitter action, and might talk about the ways that polarizing pulses integrate over space and time. Or these may be saved for later.
(side note: in reality, neurons aren't all that passive, there are lots of conductance changes occurring even in this supposedly "electrotonic" scheme, but the electrotonic equations tend to work pretty well, and in a simplified experimental system they are sufficient. Biology is almost always too complex to try to include everything at once)
Action potentials
The key concepts here are that if the voltage changes enough, it stops being possible to think about just the passive flow, you now have to think closely about voltage-gated channels that create a positive feedback loop response to voltage. Above threshold, voltage-gated channels cause sufficient depolarization that adjacent areas of the membrane are also depolarized beyond threshold, and we call this propagating signal an action potential.
At this point, you are supposed to remember and understand that what is driving this active response is still a somewhat "passive" flow of charge that you understood from the "electrotonic" part of the course. That part is the physics and is always present, you can't get rid of it. However, you're in a new scheme where you can't use the electrotonic equations to understand what happens anymore.
Saltatory conduction
Myelination and saltatory conduction comes next. In this section, you're supposed to be thinking about the way action potentials spread, but to add one extra little wrinkle. What if, instead of transmitting piecemeal to the next adjacent segment of membrane, axons were more insulated? In this scenario, the flow of charges will extend much further. You should still be applying the concepts you learned in the "electrotonic" part, though: if you add some ions/change the voltage of one part of the neuron, adjacent areas will also change in voltage as current flows. The further away you go, the longer it takes the signal to arrive and the smaller it will be as the charge spreads out.
Therefore, even though insulation lets the signal travel further, it still decreases in amplitude over long distance, and you need to "boost" the signal again. That's where nodes of Ranvier come in.
Back to your specific question...
"Does electrotonic spread/conduction occur in saltatory conduction?" - No, but not because the "physics" part is different: saltatory conduction is necessarily active (involves voltage-gated channels), not electrotonic, even though all the electrotonic principles still apply.
The "electrotonic" part of the lesson contains important concepts that you are supposed to remember and carry through the other sections, even if it's not discussed explicitly. I think making that active/passive distinction is possibly a bit misleading, but the concepts you are supposed to grab from the electrotonic section in terms of the physics of how charge/voltage moves around in a neuron applies to everything.
Additionally, you should gather that the nodes of Ranvier are spaced in order to conduct action potentials. These are big voltage changes. Smaller voltage changes that are subthreshold will of course also travel down the axon (this is the physics part - nothing stops physics!), but if they aren't strong enough to open voltage gated channels at the next node of Ranvier then the voltage change isn't of any consequence and just decays with distance. If it was strong enough, then by definition it is superthreshold rather than subthreshold, and we are talking about an action potential.

All the content in this answer is material like you would find in a basic undergraduate neuroscience textbook. The ones I usually recommend are Purves or Kandel.


How EGDS (endurance genetic distance score) is calculated? Can anybody please make me understand how EGDS5 has been calculated to 40.8 in this paper at page#31?

The formula has been described in this paper but when i tried the same, I am not getting the same results.

According to paper describing the formula:

$EGDS = 100 - \frac {100\cdot d} { n \cdot w }$

where

$n =$ number of studied polymorphisms

$w =$ score given to worst genotype

$d =$ euclidean distance calculated as follows

$d = \sqrt{ \sum_{i = 1}^{n} (2 - x_i)^2}$

$x_i =$ genotype score of corresponding polymorphism

$2 =$ optimal genotype score

here is what I tried. Given below is the genotype score of 5 genes:

$ x = (1,1,1,1,0)$

$d = \sqrt { (2-1)^2 + (2-1)^2 + (2-1)^2 + (2-1)^2 + (2-0)^2 }$

$= \sqrt { 1 + 1 + 1 + 1 + 4}$

$= \sqrt 8 \approx 2.82$

Now, $EGDS5 = 100 - \frac{ 100 }{ 5 \cdot 4 } \cdot 2.82$

$= 100 -  5  \cdot 2.82 $

$= 85.9$

which is not equal to 40.8.

In my opinion, there must be something wrong with the formula given in the paper. The rationale behind the conversion of $d$ into the range 0-100 is stated in the papera as follows:

  An EGDS9 of 100 represents an “optimal” endurance genetic profile,
  that is, all GS’s are 2. In contrast, an EGDS9 of 0 represents the
  “worst” possible profile for endurance genetic profile, that is, all
  GS’s are 0.

So what they are basically saying is that they want

$d_{max} = \sqrt{\sum_{i=1}^n(2-0)^2} = \sqrt{4n} = 2\sqrt{n} \Longrightarrow EDGS_n \stackrel{!}{=}
 0$

$d_{min} = \sqrt{\sum_{i=1}^n(2-2)^2} = \sqrt{0} = 0 \Longrightarrow EGDS_n \stackrel{!}{=}
 100$

So let's just define EGSD as the percentage of reaching the minimum possible distance:

$EGDS_n =100 \cdot \frac{2\sqrt{n} - d}{2\sqrt{n}} = 100 \cdot \left(1 -\frac  d {2\sqrt{n}} \right) = 100 - \frac {100\cdot d}{2\sqrt{n}}$

Which gives us a formula very similar to the given. (Actually their formula is just missing the squre root in the denominator).

Let's apply this formula now to the case of the other paperb in discussion:

$EGDS_5 =100 \cdot \frac{2\sqrt{5} - \sqrt{8}}{2\sqrt{5}} \approx 36.754$

Not quite 40.8, but closer. Now, what if we assume the people in the other paper used this formula but made a mistake when calculating d, getting $d = \sqrt{7}$?

$EGDS_5 =100 \cdot \frac{2\sqrt{5} - \sqrt{7}}{2\sqrt{5}} \approx 40.839$

Interestingly, the other score 33.8 comes from apparently calculating

$EGDS_4 =100 \cdot \frac{2\sqrt{4} - \sqrt{7}}{2\sqrt{4}} \approx 33.856$

In their table, there are actually five rows but the last row has no value in its column?

I would say these are just bad papers, IMHO.

References

a Meckel, Yoav, et al. "Practical uses of genetic profile assessment in athletic training–an illustrative case study." Acta Kinesiologiae Universitatis Tartuensis 20 (2014): 25-39. (http://ojs.utlib.ee/index.php/AKUT/article/view/11961)

b Ben-Zaken, Sigal, et al. "Genetic profiles and prediction of the success of young athletes’ transition from middle-to long-distance runs: an exploratory study." Pediatric exercise science 25.3 (2013): 435-447. (https://www.ncbi.nlm.nih.gov/pubmed/23877193)


Killing microorganisms on agar plates? If I grow microorganisms on agar plates and I expose them to UV light. How exactly will I know that the microorganisms have been killed? I was watching a video that showed spots in the petri dish where the microorganisms were killed when viewed under microscope but will this be visible to the naked eye? If not, is there any way that I can show without the use of a microscope the fact that the organisms have been killed?

Looks like this is a follow up to this question on this forum.

The short answer to your question is you will not be able to indicate that a cell or colony on an agar plate is dead even with a microscope unless you are using fluorescent dyes (i.e., some form of live/dead staining). There are quite a few ways to do this, but they will all require that you have access to a microbiology laboratory.

Now, if your objective is to simply show that UV light kills microorganisms, this is easily done as an experiment with one target microorganism (i.e., one species). I'm going to obfuscate details aplenty here, but I'll offer you a description anyway.

You'll need replicate plates of agar colonies inoculated with the same quantity of the microorganism--this is typically achieved by propagating the microorganism in liquid medium and depositing equal quantities of the medium onto multiple agar plates. Once your plates have been incubated to obtain some colonies, retain one plate as control (this will not be exposed), and expose the remaining plates to your UV source. [Ensure that you've counted the number of colonies in every plate--including the control--before you subjected them to UV irradiation.]

Now comes the hard part. You will need to re-suspend the colonies from your plates in liquid media and re-plate them on agar. You can either choose a single colony from each plate (ideally, colonies that are similar in size across plates) for re-suspension, or you can re-suspend all colonies visible to the naked eye. Either way, re-suspend your colonies in liquid media, and deposit them on agar thereafter, and incubate the agar plates.

If everything went right, the number of colonies you would observe in the re-plated control plate should be higher than the number of colonies in the UV-exposed "re-plates." What that indicates is that at least some of the colonies that were exposed to UV irradiation died, and thus did not show up as colonies upon re-plating. This would loosely "prove" that exposure to UV irradiation kills microorganisms (with many, many caveats).

All that being said, I would not attempt this at home. To the best of my knowledge, this shouldn't even be doable at home without spending a significant amount of money to obtain some of the necessary equipment (which I have not described here). Further, doing this experiment in the format I described would likely yield very noisy results--the way I've described it is more back of the envelope experimentation than something proper.

If you are keenly interested in this topic, find the nearest microbiology department, and talk to a subject expert. They might even let you try this experiment out for yourself in their lab.

Edit - the core methodology I've described here is CFU counting (CFU - colony forming units).


What is a starter cell? I am reading the paper Cooperative Subnetworks of Molecularly Similar
Interneurons in Mouse Neocortex and a term "starter cell" apears there (page 6):

  This yielded tissue sections where SOM or
  VIP starter cells carry both nucleus-localized GFP and cytoplasmic mCherry

Does anyone know what a starter cell is?
(I couldn't find it on the web)

Nice question - this terminology isn't referring to a special type of cell or anything, but to a peculiarity of the technique they are using.

They are labeling a subset of cells with rabies virus; rabies then travels in retrograde fashion to presynaptic cells, and labels those as well.

The "starter cells" are those initially infected cells, where the tracing "starts." This reference more explicitly states this terminology, and talks about the technique extensively, I would strongly recommend it for helping to understand the paper you are reading.


Why are the neurites from hair cells to spiral ganglion cells called axons? In Kandel's Principles of Neural Science I found the following figure which shows the innervation of the organ of Corti:

From the legend to this figure (30-10, p. 602):

  "The great majority of afferent axons end on inner hair cells, each of
  which constitutes the sole terminus for an average of 10 axons.[...]
  Efferent innervation of inner hair cells is sparse."

BUT: The depicted axons that "innervate afferently" hair cells seem to go into the wrong direction (downwards, not upwards). What do the (red) bulbs touching the hair cells represent. I guess synapses, but which one is the presynaptic and which one is the postsynaptic neuron? (I guess: The hair cell is the presynaptic neuron - it's a sensory neuron! But then the neurites emanating from it would be afferent dendrites of the ganglion cells, not axons. I'm lost. Might it be the case that transport along these neurites is active - like in axons, not passive like in dendrites? Or are they called axons because they are myelinated? Or is it because in bipolar cells it is not distinguished between axon and dendrite?)

Question: Why are these neurites called axons?

I believe to understand now, thanks to @AliceD's answer to this question:

Why are Merkel cells innervated by an axon, and not a dendrite?

The axon seemingly emanating from the cell (hair or Merkel) is just by coincidence not a physiological part of the cell (hair or Merkel), but its functional axon. The tactile meniscus (in the case of the Merkel cell) plays the role of an "out-sourced" axon hillock of the cell (hair or Merkel) which possesses no axon hillock (and axon) on its own.


Is there a DNA analogue to ribozymes? If not, is it impossible for DNA to have enzymatic activity?

Not very common, and not found so far in nature, but they exist and are called deoxyribozymes.

Additional information:

Deoxyribozymes are the equivalent of ribozymes in the DNA world and can function as catalysts for different biochemical reactions, such as DNA cleavage. While DNAzymes (short name) were synthesized in a laboratory context (In-vitro) and proved to be active, no observations were made of DNA molecules having an enzymatic activity In-vivo which is of course not a definitive proof they don't exist in nature.

The latter point is a major difference compared to ribozymes which were proved to be active and functional in living cells.


Is the blastopore imaginary? I've been told in my zoology class that the blastopore is an imaginary pore found in gastrula, from which mouth develops first in protostomes and anus develops first in deuterostomes. But we've also been told about the famous blastopore grafting in newts experiment by Spemann-Mangold. So how can you graft something which is imaginary? Is the blastopore really an imaginary pore?

From Merriam-Webster:

Definition of pore
1 :  a minute opening especially in an animal or plant; especially :  one by which matter passes through a membrane

The blastopore is a real thing, it is not imaginary. It is the point where the mouth or anus eventually develops. I'm guessing the reason your zoology class referred to it as imaginary, however, is probably because it isn't really a pore (and especially it is not a pore into the blastocoel). It sort of looks like a pore, but it's just a little indentation (and may even be considered a blastopore before the indent forms); it doesn't really become an opening until later, and the process of gastrulation doesn't actually involve anything going inside the blastopore, it's just a folding in of the cells on themselves.
In summary, I think your understanding is sound, good job, and I just wouldn't get too hung up on the "imaginary" part.


DIY extraction and long term storage of human DNA sample? What is the recommended DIY way of extracting and long term storing of human DNA samples to store at home and send for sequencing in years time? Considerations:

Sample material: cheek swab, hair, blood?
Extraction: which detergent, alcohol?
Storage: freezer? what temperature?

Any ideas?

If you have access to a centrifuge, either spin columns or phenol:chloroform will give very pure, high-quality DNA. Even with dirty methods, you can re-extract the product several times, to sacrifice yield for purity. Just be very clean. Whatever method you use should remove salts and proteins, which are the major contaminants. I won't go too much into how to extract DNA, as that's a whole separate question - but the most important thing is that purer is better.

You should resuspend in Tris-EDTA. Tris buffer maintains pH at slightly acidic (best for DNA) and EDTA chelates metal ions which can catalyze oxidative damage of DNA. Very pure distilled water works too, but if you get contaminants they will do more damage.

Afterwards you can store the DNA for quite some time provided it's frozen. At -20C you can store DNA for years. It may not be perfect quality when you pull it out a decade later, but most of it will be good, and I'm sure it will be okay if you use a good sequencing method (and I'm sure sequencing technology will advance more in 10 years than the degradation of your DNA). The good news is that you can simply store it in your freezer, and it will be okay. -20C particularly is not hugely important, you can probably get away with -10C or so - the crucial thing is for it to be frozen, not liquid (this vastly reduces diffusion).

If you want to do it like a pro, you would put it under -80C. This is considered very safe for multiple years. You can do even better by precipitating it with ethanol, and then storing at -80C. In my opinion, this -80C is overkill - DNA is fine, for the most part, stored at -20C and even 4C, especially if you work reasonably clean and contamination-free. If you had some extremely valuable, very sensitive DNA, sure, do the -80. But just personal sequencing/genotyping? Just extract a bit extra DNA  (a couple micrograms).

The really safe method is liquid nitrogen, which stops practically all chemical activity. Higher temperatures are too cold for most DNA-damaging reactions to proceed at a significant rate, but the molecules still move around. At -200C, they stop dead. But, once again, overkill unless you are saving very critical DNA for centuries later.

Source.

Three simple things I can recommend that are less obvious: First, do not handle your sample with hands, even gloved. Use some kind of plastic tweezers. Hands are warm and will locally warm up the sample. I would go as far as to put the sample tube in another box so that there is no direct contact. Second, avoid freeze/thawing. Whatever your storage system is, make sure it is very reliable. Third, wrap it in something opaque, to minimize light exposure.

Note as per Chris's comments: Always consult the MSDS of the substances you work with and take appropriate safety precautions! Always make sure to receive proper training before working with hazardous materials, and never purchase illegal contraband without appropriate authorization!


How come degraded eyesight still holds with a mirror? When you use a mirror to look at something, you can position it at an angle arbitrary to your face and still look at an object far away. My question is, for degraded eyesight, how come the picture is still degraded in the mirror? Is it because of an imperfect mirror? Is it theoretically possible to have a mirror that when looked at an angle with perfect scattering to give you better vision than without the mirror, just looking regularly with degraded vision? I am just wondering, it seems like a photonic process, but i don't know enough about the eyes to turn them into any sort of functional system

It's been too long since physics to have a good answer, but I know that if you look at an object in a flat mirror, the light coming off the mirror would be identical to light coming a real object in the same position. The angles of the light rays are the same. Therefore, no matter how close the mirror is to your face, your eyes treat the image as if it's coming from 10 feet away, or however far the object in the mirror is away from the mirror. Bent mirrors will change this, that's why you get the "OBJECTS IN MIRROR ARE CLOSER THAN THEY APPEAR" warning.

I made a diagram to to try and explain it better.

The eye is looking at a mirror, the light from the arrow on the left of the mirror reflects off the mirror and toward the eye. The eye sees an image that appears as if it were behind the mirror, on the right.


What part of the body holds the most pain receptors? What part of the body holds the most pain receptors or is likely to cause someone to feel the most intense pain?

I thought it was the eyes but I can't find that source anymore.

There is anecdotal evidence that the cornea is indeed the most sensitive tissue. Just think of it: our eyes well up with tears when slicing an onion. A tiny insect who flew into our eye feels enormous, and a corneal injury, say a scratch, can leave us severely compromised for a number of  days. Luckily, the cornea has rapid healing powers.

The cornea is so sensitive that part of determining the amount of brain injury one has sustained is by measuring the corneal reflex. The way this is done is to take a cotton swab and pull off some cotton fibers and twist them into a tiny tail (so to speak), and tough the cotton fibers to the cornea. If there is no reaction, that's a bad sign.

The Sensitivity of the Cornea in Normal Eyes
Evidence-based guideline update: Determining brain death in adults
Report of the Quality Standards Subcommittee of the American Academy of Neurology


For Penicillin Binding Proteins, why is the enzyme-peptide complex less stable than the enzyme-β-lactam complex? I'm trying to figure this out. I cannot find any publications that go into good detail about the chemistry of PBP inhibition by β-lactam antibiotics.

PBPs cross-link adjacent pentapeptides to form peptidoglycan. My understanding is that, in most bacteria, this pentapeptide has a terminal D-Ala-D-Ala dipeptide. The enzyme removes the terminal D-Ala and forms a D-Ala-Enzyme complex, where the enzyme is linked to the rest of the peptide via ester bond to the D-Ala.

However, when PBPs bind to β-lactams, they also form a β-lactam-ester-enzyme complex. However, this complex is more stable so the β-lactam remains in the active site. Why?

Any good publications are also very welcome.

I would also like to ask, is there any reason the "β-lactamoyl-enzyme" complex can't be hydrolysed?

According to Foyes Principle of Medicinal Chemistry, the significant difference is the crowding of the active site by the cycle next to the lactam ring, which prevent attack on the ester and release of the drug from the PBP.

Reversing the reaction to the beta-lactam is unfavorable given the resulting ring strain.

I would personally expect the ester to be hydrolysable (water being much smaller), but not very rapidly given the active site somewhat shields the complex from water. Foyes disagrees on that. ("Water is also an insufficiently effective nucleophile and cannot hydrolyze the complex either.")


Expected number of SNPs in a sample of size `k` Consider a Wright-Fisher population of constant size N. We sample k haplotypes in this population. What is the expected number of SNPs?
I think the answer should be in Watterson (1975) but it looks like my institution does not pay for access to this journal.

Let $\theta = 4n\mu$, then $E(S) = \theta\sum\limits_{i=1}^{k-1}\frac{1}{i}$, assuming infinite sites model. This is indeed given by Watterson (1975).


Why does snow not stick to the fur of wolves and some breeds of dogs? This question made me wonder, why for example wolves don't suffer from these "paw snowballs"?

  (...) but after a few miles on the trails in soft snow, he often develops snowballs between his paw pads - usually one big one right in the middle. (...) I have heard really bad snow buildup can lead to raw/bleeding paw pads.

I couldn't find scientific references, but regular web searches basically indicate that long fur as well as webbed toes promote formation of ice and snowballs in certain breeds.

From Hubpages:

  The snow attaches to the dog's long hair, melts from the body heat, and forms ice balls that grow larger, stretching your dog's toes apart and causing cracking, bleeding, and hair pulling.  This is painful and distressing for the dog, who may then try to remove them by licking them, which then causes even more ice to build up.

And among the solutions:

  Clip the fur between your dog's toes. [J]ust trim off the excess fluff.

A typical breed thriving in icy conditions is the Siberian husky. A comparison to to an airedale terrier breed shows the difference in fur length quite clearly, especially around the areas most suceptible to come in contact with snow (legs & chest areas):

And both breeds in the snow:


Do bisexuals have any evolutionary advantage over straights and gays? Do bisexuals have  any evolutionary advantage over straights and gays? Bonobos exhibit bisexuality extensively. Why so?

Like many things, whether bisexuality is advantageous for an individual's reproductive success or not depends on the environment. The fact that a wide variety of sexual systems and behavior exists in the animal kingdom suggests that. Also, "advantageous for an individual's reproductive success" doesn't necessarily imply "will spread via the processes of evolution"; for a trait to spread via natural selection+random mutation you need the trait to promote the individual's reproductive success, and for it to be reliably passed down to its offspring. And as the causes of sexual orientation in humans aren't well understood there is always the possibility it isn't strongly or genetically inherited.

As far as bonobos go, I am given to understand they use sex as a social tool, much more so than we do. In that context it does seem like bisexuality would be advantageous; it's silly to only be able to use your most powerful tool for conflict-resolution and social bonding on half of your community. This particular advantage won't be true, or will be much reduced, in species that don't use sex in the same way, i.e. all or most other species that we know of.


Pichia pastoris and ornithine Can Pichia pastoris (species of yeast used for recombinant protein) produce the non-protein amino acid Ornithine? Or does it express ornithine at all?

Yes, it contains arginase. Thise enzyme converts arginine to ornithine and is probably part of the urea cycle.

You might notice the arginase is listed as coming from Komagataella phaffii GS115, but this is just another (new?) name for Pichia.


Speed of protein conformational change? Although the speed may vary a lot based on factors like protein size/scale of conformational change/type of changes (small block change/arm movement,etc), are there examples of experimental results of time scale of such processes? (Only a single conformational change is considered i.e. the time delay between the begain and the end of a single conformational change event of a single protein (or subunit to be more precise?) )

This paper uses "ultrafast 2D-IR vibrational echo chemical-exchange spectroscopy" to track switching between different protein conformations and finds that they take place on the order of 50 pico-seconds ($ 1 \times 10^{-12} $ seconds). Another paper finds something similar but notes that full equilibriation can take on the order or nanoseconds:

Although the main conformational change of the backbone is completed after only 20 ps, the subsequent equilibration in the new region of conformational space continues for times >16 ns.


Any good fish books out there? I recently read "What a Fish Knows: The Inner Lives of Our Underwater Cousins" by Jonathan Balcombe. The first part was the best where the author explained how fish are very advanced creatures because they have been around a lot longer than other vetebrates.

Are there any other books out there similar to this one? There seem to be tons of bird research books. Of course, birds are relatively easier to study than fish. (Their size and ability to fly makes them difficult to track. But, at least they are not underwater and sometimes stay in one area for awhile. Fish are pretty much constantly on the move.)

I am not really looking for a text book unless you know of one that is interesting to read and not just a list of facts...unless a text book would be a good place to start.

I have read Colin Tudge's books on trees and birds. I wish he would write one on fish.

As a fisheries biologist these are what I would recommend to read.These are all science entertainment books(i.e., factual, but fun to read).The first 2 are more fish biology. The second  2 is more fisheries ecology.

Your Inner Fish: A Journey Into the 3.5-Billion-Year History of the human body.
Neil shubin
Demon Fish
Juliet Eilperin
Four Fish: The Future of the Last Wild Food
Paul Greenberg
Cod: A Biography Of The Fish That Changed The World
Mark kurlansky


How can the pressure during contraction vary between the left and right ventricles? After reading this passage from my physiology textbook (Vanders Physiology p. 384), I'm confused about how exactly the right and left ventricle can create markedly different pressures as they pump blood even if they have the same stroke volume, i.e. they push out the same amount of blood.

Typical pulmonary arterial
systolic and diastolic pressures are 25 and 10 mmHg,
respectively, compared to systemic arterial pressures of 120
and 80 mmHg. Therefore, the pulmonary circulation is a
low-pressure system, for reasons to be described later. This
difference is clearly reflected in the ventricular anatomy—
the right ventricular wall is much thinner than the left.
Despite the difference in pressure during contraction, however,
the stroke volumes of the two ventricles are the same.

How can two ventricles push the same amount of blood but at different pressures? I always assumed that pressure was created by a change in volume of the ventricles, and so I expected that if both ventricles have the same "change in volume" as they contract, they should also push out blood at the same pressures. Why is this not the case?

The key is vascular resistance.
Pumps like the heart don't move fluid, they exert force ("push") on it, increasing the pressure. The movement happens subsequently because there is somewhere for the fluid to go, so it moves down the pressure gradient from a place of high pressure to a place of lower pressure. If you clamped their outputs (increased resistance to infinity), neither ventricle would push any blood out.
We can say that the flow rate is proportional to the pressure difference and resistance:
Flow ~ ${\Delta}$P/R
If we assume that the two ventricles push out over the same time frame, you could easily get equal "Flow" with different "${\Delta}$P" if RLungs is different from RBody, and this is exactly the case: pulmonary vascular resistance is much lower than systemic vascular resistance. It's easier to pump the same volume through the lungs than through the rest of the body, so less pressure is needed.


Is a one ventricle heart feasible? So this is derived from a lesson at Khan Academy.

The mind activity assumes that the one ventricle heart pumps blood to the lungs for oxygenation then rest of the body. However, the problem is that there is too much pressure at the lungs leading to bleeding.

This problem, however, can be solved if the lungs come before the one ventricle heart. This way, most of the pressure is used going through the body and pressure would not become a problem.

Thus, is a one ventricle heart that connects to body tissues first then lung feasible? If so, why have organisms not developed this way?

Alternative Heart Morphologies

Amphibians and some reptiles have a three-chambered heart, with 2 atria and a single ventricle. There are still separate circulatory pathways for the lungs and the rest of the body, but the oxygenated and oxygen-depleted blood mix in the ventricle, and are pushed at the same time to the lungs and body.

The disadvantage of this system is that it is less efficient at providing oxygen to the body than a four-chambered system, because the blood pumped to the body is a mixture of blood that has recently been to the lungs and blood that has not.

You seem to be suggesting another system, where there is just one serial pathway from heart to lungs to body, or from lungs to heart to body. This is more like the two-chambered heart of a fish: blood is pumped from the heart through the gills, and then to the body.

Lungs and body in series, and fluid dynamics

So why wouldn't this work for a mammal? It could, but gills and lungs are very different. The vasculature of the lungs requires a lot of pressure to get through, which is generated by the right ventricle.

Pressure is required to push fluids through a constriction (note that even a straight pipe is a constriction). After a fluid passes a constriction, there is always a pressure drop. That pressure drop is a function of the rate of flow and size of the constriction. If you give less pressure at the start, there is less pressure to "drop", and so you get a lower flow rate (note that this is nearly a perfect analogy with electricity, where flow is current, pressure is voltage, and the size of the tube is the conductance).

If you want to pass through a second constriction, you have to use pressure that is "left over" after the first drop: you can't use the pressure you started with because that was lost getting you through the first constriction. In reality, in a closed system, the total flow rate will be determined by the summed series resistance, so adding a second constriction slows the flow rate for the whole system, and you get a partial pressure drop after each.

If you put the lungs and body in series with each other, no matter which comes first, you need to have enough pressure left over when you pass one to get you through the next one, otherwise the flow will slow down. Blood in a human aorta has a mean pressure around 100mmHg, whereas back in the vena cava it is close to 10mmHg. That suggests you need about 90mmHg to get enough flow through the body's circulation. The lungs use a little less, but you still have a pressure drop of around 50-60mmHg. Therefore, you would have to increase the blood pressure by 50%-75% to get circulation through both lungs and body.

Higher pressures lead to more turbulent flow and take more effort to achieve. The four-chambered heart, with 2 ventricles, is simply more efficient.


calculate elimination rate constant A patient diagnosed with cancer takes antiproliferative drugs. Suppose the intake of drug(dose) is 250mg and excreted amount 125 mg. Amount of excreted drug as metabolites 1 and 2 are 75mg and 50mg. T1/2 is 4 hours. Calculate its elimination rate constant (K).

My idea is : amount actually used from the body is 250(dose) - 125mg amount excreted= 125mg. Which means that we are at steady state. Steady state is reached after 4 half lives (t1/2). Taking this into consideration we calculate 4 k respectively: K=0.693/4 ; K=0.693/8 ; K=0.693/12 ; K=0.693/16

You can use this equation to very generally describe the one-compartment pharmacokinetics of a drug:

Cplasma = (Dose*F/Vd)e^(-kt)

Where F is the fraction that is bioavailable and Vd is the volume of distribution of the drug.  These values can be obtained from the Lexi-comp monograph.  If a drug is administered i.v., F = 1.  k in this equation is your elimination rate constant.

Your description of steady state is not correct.  Steady state is reached with multiple administrations of the drug after 3-5 half lives.  We usually assume steady state is reached in 5 half lives.  Here you are only dealing with one administration of the drug and a steady state is never reached.  The drug will be continuously cleared from plasma until Cplasma = 0.  The time that this takes is usually 5 half lives (50% of initial plasma concentration excreted after 1 half life, 75% after 2 half lives, 87.5% after 3 half lives, 93.75% after 4 half lives and 96.875% after 5 half lives).

Without any plasma concentration data, a route of administration, volume of distribution and bioavailability, a proper elimination rate constant cannot be calculated.  Consider the case where an oral drug is only 75% bioavailable.  This means that 75% of the administered dose reaches the plasma and systemic circulation while 25% is cleared initially by stomach acid, digestion, poor absorption from the GI tract, etc.  The elimination rate constant for this drug will be different than for one that is 100% orally bioavailable.


Can fruit fly larvae eat plastic? I highly doubt that fruit flies or their larvae can digest any plastic used in everyday products. But are there any documented cases where they attempted to eat plastic? I ask this because last Sunday I was setting up a Wii U at my grandparent's house. It had been in this plastic bag that has been sitting in the same room for about three weeks because I only use it at other people's houses and is never set up in my house. This plastic bag was similar in shape and size to many re-suable grocery bags that supermarkets distribute, example Whole Foods. But this bag was made entirely out of plastic. Of course I don't know what type because it wasn't recyclable. It was also more rounded on the edges. Okay, here comes the biology part. I took the Wii out and there were light-brown, rice-shaped and approximately rice-sized "things" on some of the controllers, the power adapter and on the inside of the bag. There were a couple of fruit flies flying around when I took everything out. This immediately led me to believe that the "things" were fruit fly larvae, or dead larvae. I came to this assumption because in the past few weeks there have been more fruit flies than normal in my house, probably because of compost staying inside for too long (in a container in the kitchen sink) and a few too many rotting bananas that weren't eaten or disposed of for a while. And after seeing two or three live flies flying around the controllers I assumed that's what it must be. When searching for fruit fly larvae on Google Images the best picture that represents what I'm describing is this. There were also smaller brown dots where the larvae were and in some places they were not. I don't know what these are. They are smaller than 1mm in diameter. I understand that the flies probably thought that the bag was a dark and safe place to reproduce, but there are two things that I could not figure out, and they seem to be related. One of the Wii remote controller's strings (handles?) was dark brown and slightly wet. It looked like it had been soaking in muddy water. I was very confused by this. I took the bag outside to try and empty it but the supposed larvae were stuck to the inside of the bag. What did fall out of the bag that I missed before was a black ball about two inches in diameter that was also slightly wet upon touching it and was apparently plastic. There were a couple larva on it as well. The bottom of the bag looked like it had some plastic removed from it. This led me to believe that larvae had eaten some of the bag and detached it from the bottom. And somehow this ended up in the form of a ball. (Not a perfect sphere, but round.) I really wish I had taken more time and examined it more to confirm that it was from the bag. I don't have pictures of any of this because everyone was pressuring me to throw out the bag and clean off the equipment, apparently not caring about what actually happened. I also don't have pictures of the Wii remote string because I cut that off and threw it away as well. I later realized that I should have taken pictures because it is so difficult to describe. I began thinking of explanations for each part of what happened. My hypothesis is: Fruit flies in our house reproduced until there were too many to be sustained by the amount of food that was available. This probably happened when there were no bananas left or compost had just been taken outside. Some found the bag which was dark and safe, so they reproduced there. There wasn't any food for the larvae so they tried to eat the plastic that they were on but couldn't digest it, so they died.

This is way longer than I wanted to it to be...
So it comes down to these questions:
1. Would fruit flies lay eggs where there is no food?
2. Would fruit fly larvae attempt to consume something that clearly wasn't food?
3. What are the small dots on the adapter?

As someone commented, it seems likely that this was just caused by a piece of fruit that had been accidentally left in the bag. It attracted fruit flies and for weeks they were reproducing.


Protein diet composition I have read that non veg food are better for proteins while veg food is deficient in either one or other protein. If it is so are herbivores protein deficient always in case of animals as well as humans?

Link from VonBeche is good.
Proteins vary in amino acid content.  Humans can make some but we need 9 of them in our diets.

from https://www.ncbi.nlm.nih.gov/books/NBK234922/
    Nine amino acids—histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine—are not synthesized by mammals and are therefore dietarily essential or indispensable nutrients.

This guy http://michaelbluejay.com/veg/protein.html
is clearly a vegetable enthusiast but he makes a good point (and provides a nice table): just about any vegetable can provide enough amino acids if you eat enough of it.  Getting your entire caloric requirement from iceberg lettuce would a project, it is true.  But until I did the back reading for this answer I thought it would be impossible to take in the calories it would require to get all necessary amino acids from some of these plant foods.  Thanks michaelbluejay.

I here assert that animal foods have more amino acids per calorie than vegetable foods.  So, if you wanted to limit calories but meet your amino acid requirement it would be easier to do with animal proteins than with vegetable proteins.

But even all calories from potatoes can get you your amino acids.  The people who get into trouble are people who are not getting all the calories they need because they are starving, and the calories they do get are from low protein source foods like yams or bananas.  That is protein-calorie malnutrition.


How do beneficial features evolve in species without progressing through detrimental stages? I'm thinking in particular of wings on birds that would - I'm guessing - have to progress through stages during which they confer no particular advantage. Or is it that all evolved features must have followed a path of incremental benefit therefore imposing a fundamental limit on what evolution through natural selection can "achieve"? (features that are not beneficial while gradually appearing cannot be evolved)

There are some interesting hypotheses that wings initially evolved for display, not flight.  Then at some point, the winged dinosaurs also had a locomotive advantage, at which point the wings could further evolve with selection for even better locomotion and eventually full flight.

Here is an article about Darla Zelenitsky's work on this:  http://phenomena.nationalgeographic.com/2012/10/25/bird-mimic-dinosaur-hints-that-wings-evolved-for-show-not-flight/

There is also an article by Richard Prum in a recent Scientific American that mentions this.https://www.scientificamerican.com/article/dinosaur-feathers-came-before-birds-and-flight/


Is it possible to stop yourself from going into shock? https://en.wikipedia.org/wiki/Shock_(circulatory)

I was helping someone move a refrigerator down steps and it slipped while I was holding a sharp corner and it sliced my finger and there was continuous blood flow. Soon after, I started feeling light-headed and was shaking and felt like I was about to pass out or have an attack, but I could not allow myself to appear weak, so I fought against it mentally and I got past it without anyone observing any signs. Did I avoid circulatory shock? Did pure mental dedication allow me to surpass such a thing?

Is it possible to stop yourself from going into shock?

There are different types of shock: hypovolemic, cardiogenic, anaphylactic, septic, neurogenic, etc.

Can you prevent yourself from going into shock by virtue of pure willpower? No. You cannot override the body's reactions to decreased oxygen to the brain any more than you can will yourself out of the flu.

The early signs of hypovolemia (blood loss), though, can be confused with those of vasovagal syncope (simple fainting). Both involve dizziness/lightheadedness, cool or clammy skin, and a decrease in blood pressure. However, with hypovolemia, your heart rate increases to compensate for the lowering of blood pressure (which eventually leads to shock), whereas with vasovagal syncope - which can occur with sudden fear - your heart rate drops, which is what causes your blood pressure to fall.

Passing out due to blood loss depends in part on how rapid the blood loss is (the more rapid, the earlier on might pass out) and the volume lost. To lose enough blood to pass out, a healthy, normally hydrated person would need to lose about 2 liters of blood (or 20% of one's blood volume); maybe 1.5 liters if it happens quickly enough.

Regardless of whether it happens slowly or quickly, if enough blood is lost, shock will ensue. No amount of willpower will stop it.

Interestingly, the sight of blood or having your blood drawn are frequent triggers of vaso-vagal syncope.

What you experienced is commonly called pre-syncope: the feeling of lightheadedness as though one might blackout, but consciousness is preserved.

Vasovagal syncope
Hypovolemic shock
HEMORRHAGIC SHOCK


Sweating at all temperatures Is sweating possible if surrounding temperature is below the body temperature? How the sweating occur due to the combustion of food?

Most people most of the time live in the environments that have lower temperatures than it is their normal body temperature (36-37 °C). And most people sweat sometimes at these temperatures.

In the summer, when it is 30 °C and you wear only swimming trunks, even light walking can make you sweat. The same can occur in the winter when the ambiental temperature drops below 0 °C and you wear warm clothes. This is because the muscles, when working, can generate more heat than you need and sweating is the way to get rid some of it.

When you eat food and the food is broken down to release energy, some of this energy will be released as heat. If the food generates more heat than your body needs, eating foods, especially ones high in protein, can make you sweat.

Some people get sweaty after eating certain spicy foods. This is called gustatory sweating, which is not related to food combustion, but it is a neurological phenomenon.

Capsaicin in red hot chili peppers can also trigger heat generation and sweating.

Drinking alcohol dilates the blood vessels in your skin, which results in increased flow of warm blood through your skin, which can signal the thermoreceptors in your skin to trigger sweating.


What made this small light weight bee hive-like structure? This structure was photographed in mid December in Eastern Iowa, USA along a path within a public use area with tall grasses framed by small to medium trees.  It is approximately 5 cm (2 inches) long and 10 cm (4 inches) in diameter.  It had the light airy appearance of honeycomb but was one solid ribbed structure attached to a small branch.  I'm not sure if this was something used over the summer by an insect or if something will come out of it in the spring - winter temperatures often go below -18 degrees C (0 degrees F) in this area of the country.  Any help would be appreciated.

This is a mantis (Mantodea) egg sack, or ootheca. The female mantis makes it in the fall and it will remain over winter until (juvenile) nymph mantises emerge from it in the spring.

The following site introduces how to raise mantises from eggs but also has some general background information including on how seasonal temperature changes can affect the ootheca:

https://www.keepinginsects.com/praying-mantis/caring-for-mantis-eggs/


When designing primers how important is the GC clamp? I'm designing a set of primers and reading about the principles of primer design one of which is:

  GC Clamp: The presence of G or C bases within the last five bases from
  the 3' end of primers (GC clamp) helps promote specific binding at the
  3' end due to the stronger bonding of G and C bases. More than 3 G's
  or C's should be avoided in the last 5 bases at the 3' end of the
  primer.

From here.

My question is how essential is it to have a GC clamp?

It's hard to provide an objective answer. If you have a decent length and good complexity, even a single terminal 3' G or C would do. Of course, one has to take into account the primer's overall GC:AT ratio and things like annealing temperature.

Here's a link to diverse opinions on the topic and it has this nugget (which I subscribe to when possible):

  FWIW, my preferred offerings to the PCR gods are primers with a single
  G or C 3', FWIW. Seems to keep 'em happy most phases of the moon.


Which Papaya (Lechosa) plant (male or female) bears fruit? I will be planting Papaya fruit seeds and I understand that there is a female and a male plant, so how can one distinguish which are the ones that will bear fruit and which I should just rip up by its roots as I have limited planting space?

Male flowers have no ovary and do not produce a fruit but females need to be pollinated or the fruits will be aborted falling off when they are about golf ball size (1). Therefore, you will need at least one male or hermaphrodite plant with your female plants so you can manually pollinate the female plants. Also, note that hermaphrodites can pollinate themselves so you will not need another one or a male for fruit.

The article goes on to say that hermaphrodites are the preferred type but under certain circumstances a hermaphrodite can shift to a female.

  Cool winter weather or high soil moisture can lead to a shift toward femaleness, where the stamens fuse to the carpels or ovary wall. The re
  sulting fruits become severely ridged (carpelloid, or “cat faced”) and hence are deformed and unmarketable (1).

  Home gardeners should take steps to avoid having only a single papaya plant, in case it turns out to be a female. One way to accomplish this is have several plants in the garden, to ensure the possibility that at least one will be
  a hermaphrodite with pollen. If space is limited, allow several seedlings to grow to flowering stage in the same planting spot, and then remove all but the healthiest hermaphrodite plant (1).


Is the "Manhattan Ant" a new species; still only found in Manhattan's Upper West Side? I've stumbled upon the viewing.nyc article Upper West Side Has Its Own Ant Species Dubbed the "ManhattAnt" which says:

Columbia University biologist Rob Dunn has discovered a unique species of ant living between 63rd and 76th streets along Broadway on the Upper West Side of Manhattan. Dubbed the "ManhattAnt", the ants have a higher concentration of carbon in their bodies, indicative of a high corn-syrup diet, likely from eating trash and discarded street food.

Biologists stumbled upon a new species of ant in the Broadway medians at 63rd and 76th streets […] The ant looks like it hails from Europe, but so far the scientists have not been able to match it with any of the approximately 13,000 species of known ant. “It’s new to North America, and we believe it’s new to the entire world,” biologist Rob Dunn, whose team discovered the insect, told the Post. The ant doesn’t have a scientific name yet, but it’s fondly nicknamed the “ManhattAnt.”

and references the Simthsonian Magazine article NYC Has Its Own Ant, the “ManhattAnt” with the subtitle:

A new ant species joins a menagerie of other creatures cut off from their kind in isolated patches of urban green in NYC

A "new species" is not the same thing as a "creatures cut off from their kind in isolated patches of urban green in NYC"
Question: Has the "Manhattan Ant" or "ManhattAnt" turned out to be a new species, and is it still only found in Manhattan's Upper West Side?

Rob Dunn is a professor at North Carolina State University (though apparently taught at Columbia University at some point). I recall him mentioning this specific NY ant discovery to me 4-5 years ago. A better pop-sci article can be found here that suggests this discovery was circa 2012. Another related article can be found here.

You can find a few other papers regarding urban ant populations by Dunn and collaborator Amy Savage and others via Rob Dunn's website, (Ex: Savage et al. 2014 and Penick et al. 2015).

However, I could not find evidence in the few relevant papers I skimmed for the the so-called "Manhattant" or evidence of any publications formally introducing this as a new species.

Pećarević et al. 2010 ("Biodiversity on Broadway - Enigmatic Diversity of the Societies of Ants (Formicidae) on the Streets of New York City") lists a number of species found by Dunn and others in Manhattan, but again makes no mention of this specific discovery.

My conclusion is that since Dunn has not listed this as one of his many publications on his website it's either burried in another paper as an ancillary artifact, or, more likely, has not been formally described...

You could reach out to Rob directly [email | twitter], I suppose, and update us all on this question!


What is the mIU unit as used in hCG hormone levels? My girlfriend is in her very early pregnancy, and has provided several blood samples by now where the doctors measure her hCG levels.

The hCG hormone level is measure in a unit called mIU/ml which I figure is milli-something per milliliter blood. But what is that something? What is the IU?

IU stands for "International Units" and it is an arbitrarily chosen unit of measure used mostly to quantify hormones, vitamins or various substances found in the blood.

The idea is well explained by the Wikipedia article on international units)

  Many biological agents exist in different forms or preparations (e.g. vitamin A in the form of retinol or beta-carotene). The goal of the IU is to be able to compare these, so that different forms or preparations with the same biological effect will contain the same number of IUs. To do so, the WHO Expert Committee on Biological Standardization provides a reference preparation of the agent, arbitrarily sets the number of IUs contained in that preparation, and specifies a biological procedure to compare other preparations of the same agent to the reference preparation. Since the number of IUs contained in a new substance is arbitrarily set, there is no equivalence between IU measurements of different biological agents. For instance, one IU of vitamin E cannot be equated with one IU of vitamin A in any way, including mass or efficacy.

For hCG, in the 55th report for of the WHO Expert Commitee on Biological Standardization, you could find:

  The Expert Committee on Biological Standardization, after consideration of this issue (11), concluded that the choice of unit should be made on a case-by-case basis and reflect, and be based on, the biological and medical as well as the physicochemical information available.
  Many biologicals exist in both active and inactive states, and the clinically relevant form of the analyte may depend on the diagnostic aim. For example, the active state of the placental hormone chorionic gonadotrophin (hCG) is the relevant molecule to measure in the diagnosis of pregnancy, whereas the biologically inactive free beta subunit (hCG-beta) is measured to diagnose choriocarcinoma. Generally, a measurement of biological activity is expressed in IU, whereas measurement of the amount of a protein or of a specific protein structure is expressed in SI. In this case there would be a compelling reason to relate the measurement of hCG to a unit of biological activity, and the measurement of hCG-beta to an SI unit of quantity. Accordingly WHO has established a reference preparation for hCG (currently the fourth International Standard, with an assigned content of 650 IU/ampoule) (7) and a reference preparation for hCG-beta (currently the first WHO Reference Reagent for immunoassay of hCG beta subunit, with an assigned content of 0.88nmol/ampoule) (18). The former preparation was assigned a value based on bioassay, whereas the latter preparation had been extensively characterized by physicochemical and
  immunological methods and calibrated in nanomol by amino acid analysis. Applying these considerations of the properties of biological analytes, and their measurement in the clinical situation allowed the WHO biological reference standard for hepatitis B surface antigen, assigned a value in arbitrary IU rather than in SI units, to be adopted by the medical devices sector of the European Commission as the standard required for the fulfilment of the so-called Common Technical Specifications (CTS) for in vitro diagnostic devices. The Common Technical Specification document supporting the European (IVD) Medical Devices Directive 98/79 EC is a legally binding document within the 25 countries of the European Union.
  Where it is appropriate for a WHO biological reference standard to be calibrated in SI units, the principles outlined in ISO 17511 (8) should be followed. This will necessitate the existence and use of an appropriate single reference method and an assignment of uncertainty, derived from calibration data. Such a reference method should not be a biological assay because the factors that affect the results of such assays are not fully understood. Where they are used, SI units assigned to biological reference standards should be derived from, and traceable to, physicochemical procedures.

Note that IU are not the same as enzyme units (U) which is a measure of enzymatic activity


Should I use RNAseZAP on my bench and pipettes before RNA extraction? Should I spray RNAseZAP on my bench and pipettes before working with RNA? I am regularly using RNase at my bench and would like to work with RNA as well. Could traces of RNase on my equipment degrade my RNA?

The common practice in my lab is to work in a laminar flow cabinet and clean it with alcohol, then spray it with the RNAseZAP. I've always heard from my professors that, while DNAses are more uncommon, "RNAses are everywhere". So, zap it early, zap it all.


How fast do we fall asleep? When looking at the process of sleeping, most research I find point to a group of mutually inhibitory cells which form a sort of biological "flip flop."  There's cells that promote awakenness and cells that promote sleeping.  The process we typically think of as "falling asleep" is getting to the point where this transition can occur, but I'm interested in the transition itself.

How fast is this transition? In engineering, we'll typically measure the speed of such a transition as a 10-90 measurement: the time it takes to go from a 10% signal to a 90% signal.  Is there a similar measurement made in such biological systems?

Our ability to maintain sleep or wakefulness is because of "mutual inhibition" between the wake-promoting neurons and the sleep-promoting neurons. The areas in brain which regulate wakefulness by activating the cortex also inhibit neurons present in ventrolateral preoptic nucleus (a cluster of neurons situated in the anterior hypothalamus). And when VLPO neurons are activated, they induce sleep, and this also inhibit activity in the arousal centers like neurons in tuberomammillary nucleus (TMN).

Transitions between these states of wakefulness and sleep is very rapid, usually in seconds. Various researchers have reported this neurological mechanism for "flip-flop switch" in form of electrical circuit.

The mechanism  for mutual inhibition is regulated by sleep drive or the circadian signal. When one of this body signal is sufficiently strong, it transits to the opposite state from wakefulness to sleep or vice versa. This mechanism is analogous to mechanism involved in  transition between rapid eye movement (REM) sleep and non-rapid eye movement (NREM) sleep.

Humans require some time to relax and then fall asleep, and deep sleep needs 20 or more minutes after sleep onset. Sleep onset and associated loss of consciousness is related to one another and occurs instantly.

Many intrinsic and extrinsic factors  regulate sleep cycle. Adenosine is one of the chemical which accumulates during wakefulness and later induces sleep by inhibiting wake-promoting neurons. And caffeine inhibits adenosine activity and helps in wakefulness.

The time needed for transitions between sleep and wakefulness  is  maintained by biological clock located in the suprachiasmatic nucleus. This is small structure consisting of about 50,000 brain cell. And it receives light signals from eye  via  optic nerve. Light controls the day-night cycle and which in turn regulates various biological functions including temperature, hormone release,  sleep and wakefulness. The SCN stimulates wakefulness by producing a  alert signal which inhibits sleep. The SCN also helps in inducing sleep by turning off alert signal.

(Via:  http://healthysleep.med.harvard.edu/healthy/science/how/neurophysiology)


Does the necessary Carbon Dioxide need to be in the atmosphere for mammals? In the answers to this question, we've learnt that carbon dioxide is necessary for mammalian life, but is it necessary in the atmosphere/to breathe it in?

Or does the act of respiration give a human (or other animal) enough carbon dioxide to fulfill all of the functions that carbon dioxide is needed for?

Or, phrased another way, if you put an animal in a carbon-dioxide-free atmosphere, and continually removed the carbon-dioxide that they generate upon respiration/exhalation, would they get enough carbon dioxide to fulfill these requirements:

fatty acid biosynthesis (FAS)
mammalian/bacterial biotin-dependent carboxylation reactions.
blood pH regulation

No it isn't necessary to breathe in CO2 from the atmosphere. For the buffer system your brain detects the amount of CO2 (H+ which is an indicator of excess or too little CO2) and adjusts your breathing automatically to compensate so that your blood's pH stays normal. No outside CO2 is needed. Your kidneys also play a similar role but the lungs are what provide a rapid response.


Does methanol fixation deform cultured cells? I use methanol fixation (@ -20⁰C for 10 minutes) when performing immunofluorescence assays on cultured cells. Generally speaking, this results in very good antibody staining. However, the cells tend to look markedly different than they did under phase contrast microscopy prior to fixation. This has my PI worried about how these images will be received by reviewers.

How does a methanol fixative work, and why does it cause a change in cell morphology? Are there parameters that can be adjusted to mitigate this effect?

Yes, fixation of almost any kind can have effects on morphology.  When you take a free flowing, protein spiked fat-blob (ie cell membrane), and make it rigid, you are going to get some differences.

A fun visualization of this can be done by wrapping cellophane/shrink wrap around a serological pipette and dipping it in a dry ice and methanol bath.  It's something I show students all the time before getting into histology work.

Back to what you need.  What cells are you using and what are you growing them on?  Have you tried acetone fixation and you know it destroyed your plastic?  The amount of time and concentration needed for acetone fixation is low enough that most modern chamber slides can handle it.  Do you need the membrane to be permeabilized in fixation?

I don't know the main effect you are measuring, but assuming you have good controls, you should be able to see it past the fixation.  The effect in your controls should be similar to your treated groups, unless the treatment is specifically effected by your fixative.

Moving to some more general recommendations.  I think you should reconsider the fixative’s you’ve ruled out, because I am unconfident about their application.  The base source I always recommend students to turn to is the Wiley "Current Protocols in X" book that is relevant to the task at hand.  In this case, I think the most relevant text is Current Protocols in Immunology, and the appropriate unit is 21.4 "Immunohistochemistry."

I think a particularly useful, and relevant to this question if you are concerned with formalin masking, is Table 21.4.3.

That is for human antigens, but the “antigen retrieval” process works for murine cells in most cases.  You are right that you antigen could be blocked by formalin, but the solution is often unmasking as MtOH are often more harsh to morphology.  To support protocol 1:

  Formalin or paraformaldehyde fixation cross-links protein, often
  making antigens inaccessible to specific antibodies. The antigen
  retrieval protocol, which combines high temperature with buffers at
  different pH, has been very effective in unmasking antigenic
  determinants which may be masked in fixed tissue or fixed cell
  preparations, particularly determinants within the nucleus or
  cytoplasm (Taylor and Shi, 2013).

My modification of the protocol is:

Sodium citrate buffer: 0.1 M citric acid/0.1 M sodium citrate, pH 6.0

Wash sample on a liner rocker for 5 min w/2x culture volume of d.i. H2O
Place your slides in 1mM citrate buffer in Coplin jars with the lid slightly off
Weigh the jar in final state so you know how much water to add back
Microwave 4-7 min.  You don’t want it to go to a boil, and you need to remember to allow for venting
Weigh the jar again and add back water
Microwave another 4-7 min, again you don’t want a boil
Take out of the oven and allow it to come to room temp by sitting it on the bench.  If you do it too fast you’re going to disrupt the membrane.
After it’s back to room temp, wash 2x PBS+0.05% Tween20 for 10 min each
Try your IHC again, it will probably work now.


Has anyone attempted to add extra senses to a creature through a BCI/Neural interface? Basic BCI's (Brain computer interfaces) have been available for quite a while now and allow users to preform rudimentary tasks such as moving prosthetic limbs with force-feedback or moving a mouse on a screen through only neural impulses.

I'm interested if anyone has performed experiments in the direction of adding non-native extra senses to a creature using a neural interface/BCI. For example, feeding a magnetometer's sensor reading or clock data into a BCI and using that to give the person/creature a "sense" of magnetic fields or exact time.

Short answer
Yes

Background
This subject touches upon a related technologie, namely sensory substitution, where a lost sense is replaced by a still functional sense, for instance:

The BrainPort developed by Wicab that lets blind people taste light (Fig. 1) (Stronks et al., 2016).
The, now discontinued, yet still highly popular Optacon device developed by Telesensory Systems that allows blind folks to scan a normal printed book page with a camera and read it back through braille input via this device (Stronks et al 2016).

However, you are specifically asking for devices that add novel sensory information, referred to as sensory augmentation, or sensory enhancement. The technique of sensory substitution can,quite obviously, be easily extended to add novel sensory perceptions, simply by using a sensor capable of sensing stimuli that the human sensory systems cannot, for example magnetism, infrared light and what not, for instance:

Mapping the magnetic North on the human body through auditory or tactile actuators (Schumann & O'Reagan, 2017).
Electrically stimulation of the brain in response to otherwise invisible infrared light (Thomson et al., 2013).

References
- Schumann & O'Reagan, Sci Rep (2017); 7: 42197
- Stronks et al., Brain Res (2015); 1624: 140–52
- Stronks et al.., Exp Rev Med Dev (2016); 13(10): 919–31
- Thomson et al., Nature Communications (2013); 4: 1482

Fig. 1. BrainPort V100 vision substitution device. source: Plaid Zebra


Plant anatomy, what are these stem like filaments growing under the flower The picture below shows what I am talking about. Each flower has one and I am just wondering what they are?

These are "floral spurs" – they usually contain nectar, and are part of the variety of complex flower shapes that orchids and other flowers, like columbines, have co-evolved with their pollinators.

Essentially, in order for the pollinator to reach the nectar down in the base of the spur, it must move into a position where pollen is deposited onto it; then when it moves to another flower, it can transfer that pollen and the plant is able to reproduce.

Of course, long tongues are good at getting nectar from long-spurred flowers, so there is both species filtering for long-tongued species, and presumably also selective pressure within a species for long-tongued individuals. This, in turn, drives selective pressure on the spurs.

Spurs are a classic example of a "key innovation": they have evolved separately in different types of flowers, and when they evolve, they often lead to rapid speciation (because a small change in spur architecture can constitute a barrier to reproduction). (See, for example, publications of Scott Hodges)


Which spider species is this, and is it dangerous? Sorry for a quite bad picture. I was afraid to get closer!

Seen in Croatia, inlands, not near sea. As he is on the picture there with the legs stretched out, I'd say he was about 8-10 cm in length.

It is a female, the males of this genus are quite distinct. The genus is Argiope, and the specific epithet most probable is bruennichi. It is not a clinically important spider.