Left-handedness and Right-handedness - Are they genetic? I have a biology book that states that whether a person will be left-handed or right-handed is determined by the genetic constitutional makeup.

Is this true? As far as I knew, these traits depend on how a person is trained as a child: every child has a tendency to use the left hand first when he starts to write, but if the parents teach him, then it will change to the right hand.

What is the truth?

Handedness has, like many traits, a non zero heritability. You now should read the post Why is a heritability coefficient not an index of how “genetic” something is? to understanding what heritability mean.

In short, yes part of the variance in handedness seen in the human population is due to genetic variance.

You will note that footedness is highly correlated with handedness (wiki > footedness).

Note also that today, in the western world at least, it is generally considered unhealthy for the kid to force him/her to use its other hand (as the catholic church used to do). I am not sure what are the evidence for that but it is a totally different question.

References

McManus et al. 2013
Brandler and Parachini 2013
Harmour et al. 2014


How to measure bacterial content I´m using water container placed on a radiator to humidify room air. Someone might argue that it is a perfect nest for bacteria. I have to put copper coins into the water to kill the bacteria.

I would like to do an experiment, have two similair containers filled with water one with copper coins, the other without them.

I would like to compare how many bacteria are living in those containers, how can I do that? (in home conditions)

There is evidence that copper pots have antibacterial effects when used for storing drinking water (Sudha, et al. 2012), so the copper coins will probably have a similar effect.

The easiest way to test this at home would probably be to buy a test kit from an online vendor - these are relatively inexpensive.

Some Googling produced this website [appslabs.com.au], which has some tests for common types of bacteria. There are undoubtedly others too, if these don't sound suitable


What kind of creature is this? I saw this on Facebook today and have tried researching it myself, but I have had no luck.

This actually looks like a Gaudy Sphinx caterpillar (Eumorpha labruscae). It only mimics the appearance of a snake!

You can find more information about this species here.

Range: Argentina north through Central America, Mexico, and the West Indies to Florida, Mississippi, South Texas, and Arizona. Strays to Missouri, southern Michigan, Pennsylvania, Maine, and southern Saskatchewan.

You can find more pictures here or videos here and here. Also the below gif (see whole video here) demonstrates the ability of this caterpillar to vibrate its tail end to -- as far as I can tell -- imitate a snake's rattle:

Below is a picture of an adult moth from UC Berkeley:


Why does high pH result in the denaturation of DNA? In the Southern blot method, for example, a solution of NaOH is used to denature the DNA in the sample.
I find this counterintuitive since I expected that $\text{Na}^+$  cations would neutralize the negative charges of phosphate groups, hence stabilizing the double helix.

The pKas of (neutral) guanine and thymine are 9-10 (ref). At high pH (>~10), those bases will be deprotonated and exist as negatively charged conjugate bases. As the deprotonated species, part of the G/C and A/T hydrogen bonding networks are eliminated. In the figure below, green dotted lines represent the hydrogen bonds that explain the observed base pairing. Red dotted lines represent disrupted interactions.


Meaning of "f.a." in the species name What does "f.a." stand for in the name of the "Wickerhamomyces menglaensis f.a." yeast species mentioned in this article https://ijs.microbiologyresearch.org/content/journal/ijsem/10.1099/ijsem.0.003350 ?

"Forma asexualis" as explained in another paper

  The authors favor the use of the expression forma asexualis (f.a.) in the
  description of anamorphic species of the genus
  Cystobasidium and this decision follows the current
  practice of reclassification of asexual yeast taxa (see
  e.g. Lachance 2012; Groenewald and Smith 2013;
  Daniel et al. 2013; Selbmann et al. 2014)

  Lachance MA (2012) In defense of yeast sexual life cycles: the
  forma asexualis: an informal proposal. Yeast Newslett
  61:24–25


Can a lack of sleep degrade balance? For years, I've noticed that the day after a night of poor sleep (4 hours or less), my balance noticeably degrades. For instance, while walking 20 feet to the coffee maker, I might stumble into the fridge. Is this a shared experience among humans, and is there a physiological explanation for it?

I have noticed that other functions of my body degrade as well (e.g., my ability to focus), but I am particularly interested in the change in my ability to balance.

Short answer
Sleep negatively impacts attention, which in turn impairs balance control in cognitively challenging situations.

Background
Schlesinger et al. (1998) argue that under normal conditions, postural control appears to be automatic, and to require little or no attention in young, healthy adults during quiet standing with full sensory input. However, postural control appears to require increased attention when sensory integration or motor coordination are required. Examples of such challenging conditions where increased attention is required are situations during reduced or conflicting sensory input conditions, or when one is subjected to balance perturbations. The regulation of attention, in turn, is dependent on sleep, because sleep deprivation causes deficits in attention. Hence, although sleep deprivation per se has little or no effect on standing postural control, it can impair postural balance when one has to perform a cognitive challenging task.

Reference
- Schlesinger et al., NeuroReport (1998); 9(1): 49-52


What is the function of nodes of Ranvier in axons? In a neuroscience class I'm taking, it was explained that myelin covers axons in sections, the uncovered sections are called nodes of Ranvier, and signals propagate much faster in the covered sections.

But if it is faster for signals to propagate along myelinated regions of the axon, why doesn't the entire axon get covered by myelin? Wouldn't that make it faster?

Every signal rapidly fades out with distance if it is not amplified. So if the whole axon were covered with myelin, action potentials wouldn't reach their target. Each Ranvier node can be seen as an active signal repeater.


Why humans have the temperature they have? It is obviously very onerous to generate heat at all, although it has advantages. We don't have to lie on the sun like a crocodile to get warmer. And we avoid the freezing of our body water by out own means. But wouldn't just a little of heat be enough?

Why do humans go as far as 37 C? Couldn't we just have a temperature of 10 C to avoid freezing but stay at it?

It's simply not possible for humans to live with an absolute body temperature below 20 C for the simple biophysical reason that it would prevent flux of protein through the Golgi and therefore biosynthetic and secretory pathways, as well as endocytosis. The lipid membranes become too "stiff" to correctly function.

My own sense is that the nominal 37 C body temperature is a result of all of the ATP hydrolysis reactions that happen all the time. The chemical reaction is not efficient, and some of that energy is absorbed, heating the tissue.

There are various grades of hypothermia, from mild (33–35 °C) to severe (< 28 °C). Death from hypothermia results only from prolonged exposure, for example, being in ice-cold water results in death after 50-100 minutes. The basic mechanism is that the body dies from a combination of decreased electrical conductance of pacemaker nerves in the heart, and a slowed heart rate incompatible with sustaining life. Ultimately, hypothermic death is a dysregulation of the body's thermoregulatory mechanism, rather than an immediate biochemical problem as I've pointed out above. For a detailed review, there is an open access article detailing hypothermic etiology and pathophysiology.

M.L. Mallet. Pathophysiology of accidental hypothermia. QJM (2002) 95 (12): 775-785.


Human anti animal antibodies issues in blood testing Do people have to be exposed to animals to get HAMA antibodies? Can these antibodies impact blood tests with false negatives as well as false positives?

You do not need to be exposed directly to animals to get human anti-mouse (or human anti-animal) antibodies; you can also be exposed to animal products in various ways.

  Circulating anti-animal antibodies can arise from iatrogenic and noniatrogenic causes. The former is the result of the normal response of the human immune system to an administered “foreign” protein antigen. Currently available diagnostic and pharmaceutical agents derived from an animal source are extensive and range from rodent immunoglobulins to hormones isolated from fish. In addition, some recombinant proteins are affinity purified on immobilized monoclonal mouse antibody columns, and the possibility exists for some of the mouse monoclonal antibody to detach and copurify with the protein

You can also get anti-animal antibodies from blood transfusions:

  Blood transfusion is also associated with an increased incidence of anti-animal antibodies. A study of 2829 participants in a population health survey revealed that 14.4% of the participants who had been transfused were anti-animal positive, compared with 10.4% of the participants who had never received a blood transfusion. This difference was presumably attributable to infusion of preexisting human anti-animal antibody or as a result of infusion of a foreign antigen present in the unit of blood

or through vaccination:

  Vaccination against infectious diseases is another route by which animal protein antigens may be inadvertently presented to the immune system and trigger antibody formation. In the US, chick embryo or egg cultures are frequently used in vaccine production, and residual chicken protein may be present in vaccines, whereas in Europe, some vaccines contain rabbit serum, e.g., rubella vaccine in France, and multimicrobial vaccine (Bruschettini vaccine) in Italy

or "unconventional therapies":

  The administration of unconventional therapies is also a route to immunization with animal protein. For example, a patient developed anti-rabbit antibodies following injections of “antireticulocytoxique”, which is a lyophilized serum obtained from rabbits injected with homogenates of human bone marrow and spleen and is intended as a tonic to improve senescence and to reduce fatigue and debilitation

Other routes:

  Noniatrogenic causes of anti-animal antibodies include maternal transfer across the placenta to the unborn child (37)(38), animal husbandry or the keeping of animals as pets (39), and the transfer of dietary antigens across the gut wall in conditions such as celiac disease (40)(41). Anti-animal antibodies are also more common in multiparous females (36), and a high incidence of human anti-animal antibodies has also been observed in association with certain disease states, e.g., idiopathic cardiomyopathy

All quotes from Human Anti-Animal Antibody Interferences in Immunological Assays, by Larry J. Kricka (1999).


Expression of eukaryotic ribosomal DNA The Wikipedia page for rDNA says "Ribosomal DNA (rDNA) is a DNA sequence that codes for ribosomal RNA" Also, the figure next to it says "The gene segment of eukaryotic rDNA contains 18S, 5.8S, and 28S tracts and forms a tandem repetitive cluster". So, it gave me the impression that rDNA codes for both rRNA and the structural proteins of ribosome. Is that right?

As well as messenger RNA (mRNA) that encodes protein, there are a variety of RNAs that have structural or regulatory roles and do not code for protein. Ribosomal RNAs (rRNA) are one such structural RNA. Like mRNA, rRNA (and other stable RNAs) are  specified by genes in the chromosomal DNA, although the details of their transcription (the RNA polymerase employed and the nature of the promotors) may vary.

The mature eukaryotic ribosome contains three species of rRNA that are analogous to those in prokaryotes — 18S (cf. 16S), 28S (cf. 23S) and 5S (sizes for mammals). However there is an additional 5.8S species in eukaryotes. The questions addressed in the article are: 1. What genes and what transcripts give rise to these mature RNA species? and 2. Is there a single gene for each species or multiple repeated genes? A third, implicit, question is whether the situation in eukaryotes is similar to that in eukaryotes.

The answer to question 2 is given in the phrase “forms a tandem repetitive cluster” — there are multiple copies of the genes for 18S, 28S and 5.8S rRNA, clustered together one after another. These genes are separated (‘spaced apart’) by regions of the genome that are not transcribed, and are termed non-transcribed spacers (NTS).

(There are also multiple copies of the 5S rRNA gene, although these are only clustered in some species.)

The answer to the first question is that the 18S, 28S and 5.8S rRNA are transcribed from a single gene and are initially present in a single transcript. This is processed by ribonucleases to generate the three mature species. If one compares the sequences of the mature species with that of the gene/transcript one can identify portions of the initial rRNA transcript that are not present in any of the three mature species. These are termed transcribed spacers. The one at the 5′ end of the transcript is termed the external transcribed spacer (ETS), and those that are between the three mature species are termed  internal transcribed spacer (ITS).

The situation in prokaryotes differs from eukaryotes in so far as the 5S rRNA gene is part of the gene/transcript containing the 16S and 23S rRNAs, lying at the 3′ end of this. This is mentioned in the Wikipedia entry for Ribosomal RNA, rather than that for ribosomal DNA, quoted in the question, and illustrated in the figure below taken from the teaching web pages of Ross Hardison at Penn State University. Notice the transfer RNA gene in the transcript between the portions resulting in the mature 16S and 23S rRNAs.


Is most of the human genome functionless “junk DNA”? In January 2012, David Icke published a book (ISBN: 9780955997334) entitled “Remember where you are and where you come from” in which he challenged what he claimed to be the view of mainstream science that 90–97% of the human genome was “junk DNA”, serving no function. He implied, instead, that it must have a function, but that this was unknown.

Is it still true that we do not know what all this DNA does? I see that we consider this DNA to be non-coding, but does that mean it is “junk”? I find it hard to believe that it can serve no function, otherwise why would the DNA be there? Is it possible that it is used for things we don't yet understand?

What is junk DNA?

The term junk DNA is not used that often in the scientific literature and when it is it is often used very generally, often early in the introduction. It generally refers to any non-coding DNA.

In humans, about 25% of the non-coding DNA is introns and regulatory sequences. These sequences are highly essential for the working of the organism. There are many cases of adaptation from these regulatory sequences (see this answer).

The term junk DNA is very loaded and may make it feel to people that this DNA is not important for the organism survival but this is not quite what was first meant by the term junk DNA. It is true though that repeated DNA such as those in  transposable elements are thought to have little impact on the organism phenotype. Transposable elements can however have important role on the evolution of a lineage.

IMO, the claim is false and insulting

By saying things like They do this because they gave no idea what it does and, from their version of reality, it appears to serve no function., it feels to me that David Icke is using the loaded side of the term junk DNA to insult all geneticist in general.

D. Icke is 1) doing a strawman by suggesting that geneticists think that regulatory sequences are of no use and 2) he is suggesting that geneticists are biased and will invent whatever theory in order to match with a pre-conceived opinion of the reality.

About David Icke

I don't mean to make an intentional fallacy but I would like to note that David Icke is a famous conspiracy theorist who has been illogical and obviously opinion based many times. For example David Icke claims that the moon is actually a spaceship and not a natural satellite (see here). He has made many other fantastic claims of the kind. Scroll down the wikipedia article to enjoy some non-sense!


Can iGEM distribution parts be directly PCR'd? The iGEM DNA Kit Plate Instructions say that there is only 2-3ng of DNA per well, which is already miniprepped and in plasmids.  Then it says that "there is not enough DNA in each well to perform anything but transformations".

Couldn't PCR be performed on an amount of DNA that small, given appropriate primers?  Is transformation truly the only thing that could be done with that DNA?  If PCR could be done on the DNA, why might they suggest otherwise?

You probably could do PCR on that amount of DNA, but if you screw something up you don't get a second chance. Transforming bacteria and doing a miniprep turns your 3ng into a few micrograms, which is enough to tolerate a few mistakes.


Do the simplest bacteria have ribosomes and helicase? I find it interesting that all life on earth use DNA. I've seen video on how helicase and ribosomes work together to copy DNA sequences (to RNA) with helicase then recreate them using ribosomes. Does this process work the same way in the simplest life forms? Bacteria and other unicellular life that reproduce through mitosis, for example?

I've had a direct look at Carsonella rudii, which is I believe is the bacterial genome with the smallest number of genes so far - 184 as well as being only 160 kb in length.   It has a putative DNA helicase encoded in it.  37 of those genes encode for ribosomal components as well.

If there was ever a bacterium or any living cell (non virus that is) discovered without a ribosome, you would have heard about it.  nobel prizes all around.

So I would say that your answer is yes.


Which part of the genome are the developmental sequences of embryogenesis located? Which part or parts of the the genome are the sequences located. Are they spread across the chromosomes? If so how are they accessed sequentially with precision during embrygenesis?

This is a very general question. The "developmental sequences" are just genes like any other. Like all genes they are semi-randomly distributed through the genome. While there are gene-rich and gene-poor areas in the genome, with some exceptions --notably the homeobox genes--, genes are not grouped by function.

As to how they are accessed sequentially, that is a huge question but it is not specific to embryogenesis. Genes will always need to be turned on/off at specific times and in response to specific stimuli. This is particularly obvious during development but is not exclusive to it.

The basic way this happens is through feedback and control loops. Gene A activates the transcription of gene B which activates gene C which then deactivates A. If you manage to turn on A, the rest will follow. One of the ways this can happen in developing embryos is through maternal mRNA. These are mRNA molecules that are present in the fertilized egg and which begin to be translated. This gives us a starting point to activate gene A, which then turns on B etc.

This answer is a huge simplification but a full answer could take up a couple (or 40) of PhD projects.


What are the exact differences between stereocilia and microvilli? This is a question in an old exam of Histology. I tried to answer the question, and I've made many searching attempts, but without resulting in any fixed/exact information. In some articles on the web, I've read the stereocilia and microvilli have both actin core, and this website states that stereocilia doesn't have actin filaments! I'm just feeling lost at this point. And now, I'm just searching for an exact answer for that question.

Note : It may be a super easy question for you. So please note that I'm a novice self-learner at Histology.

Stereocilia are basically modified microvilli. They are much longer than microvilli, and lack the villin protein.

According to Ross histology textbook, they both contain actin filaments.


Why do membrane proteins at lower temperatures contain more alpha helices than beta sheets? Why do organisms found at low temperatures have membrane proteins with a higher percentage of alpha helices compare to beta sheets?

The reason could be the greater motility of the alpha helix, compared with the more rigid beta sheet.
This allows the enzyme to remain functional at low temperature.
The proteins of such organisms tend also to have less hydrophobic regions and covalent bonds.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1692995/pdf/12171655.pdf
Molecular basis of cold adaptation
Salvino D’Amico, Paule Claverie, Tony Collins, Daphne´ Georlette,
Emmanuelle Gratia, Anne Hoyoux, Marie-Alice Meuwis, Georges Feller
and Charles Gerday*

This doesn't refer to alpha helix explicitly, however alpha helix are known to allow more flexibility than beta sheets, so it's reasonable to argue that the increase in alpha helix could be one of several strategies used to obtain more flexible enzymes, as well as other means cited in the paper.

This point is also made by Brock-Biology of microorganisms(2015) pag.161

  Several cold-active enzymes whose structure is known show a
  greater content of α-helix and lesser content of β-sheet secondary
  structure ( Section 4.14) than do enzymes that show little
  or no activity in the cold. Because β-sheet secondary structures
  tend to be more rigid than α-helices, the greater α-helix content of cold-active enzymes allows these proteins greater flexibility
  for catalyzing their reactions at cold temperatures.

However unfortunately no reference is provided about this claim.


Which hydroxyl from either the phosphate or the glycerol is taken during synthesis of a phospholipid head? The oxygen anion in the phosphate group is likely to be bonded with a hydrogen cation and thus forming a hydroxyl.

When the phosphate group is condensed with glycerol to make a phospholipid, is the hydroxyl from the glycerol molecule taken or the hydroxyl from the phosphate group taken?

I believe it's related to the difference of electronegativity of oxygen and phosphorus which causes unequal sharing of electrons between atoms, thus making a hydroxyl from one side easier to get taken off than the hydroxyl from the other side is.

In all phosphorylation reactions, the oxygen of the hydroxyl group in the substrate attacks P of phosphate. This is because of high partial positive charge on P which is bonded to four highly electronegative oxygen atoms. When the bond forms between the substrate oxygen atom and phosphorus of terminal phosphate, electrons are transferred to the O that bridges the ester bond between 2nd and 3rd phosphate. Therefore the O of the substrate is retained and that of the terminal phosphate (of ATP) becomes the part of the 2nd phosphate (now terminal phosphate of ADP).

See this


Can COVID-19 affect a person a second time? I keep hearing people are recovering from COVID-19 virus. Is there any chance that same person can become infected with COVID-19 for a second time?

Short answer: Although there are some reports on this, it is pretty unlikely. It is more likely that patients where released too early from hospital, developed further symptoms later on and got worse, was re-hospitalized, tested again for SARS-CoV2, which was positive and counted as re-infected.

Another possibility is that a false negative test happened, when people got re-tested later the test was positive again and the patient was counted as re-infected. Given the rising number of cases worldwide this should become evident pretty soon, if this is a real problem and not an artefact. For the moment, I don't think there is enough evidence for the re-infection of the same patient in such a short time period. If this holds, future will tell.

Long answer: There is now an experimental paper, which infected rhesus macaques with SARS-CoV2, tested if the infection was similar to humans happening in the upper airways (which it was), and re-infected the animals after 28 days with a really high dose of virus (which is much higher than what comes around in our environment), with none of the macaques getting re-infected or showing pathological signs of the infection. See reference 1 for details.
This article has its limitations with small sample size and the general questions if the chosen animal model is really comparable with human.

Additionally it looks very much like that patients who are recovering don't shed infectious virus anymore. The PCR test however does not discriminate between infectious virus and plain virus RNA, so it is most like much longer positive than people are infectious. They also show the rapid appearance of specific antibodies, which would at least temporarily protect against a re-infection. See reference 2 for a nice summary and reference 3 for the original article.

References

Reinfection could notoccur in SARS-CoV-2 infected rhesus macaques
People ‘shed’ high levels of coronavirus, study finds, but most are
likely not infectious after recovery begins
Clinical presentation and virological assessment of hospitalized
cases of coronavirus disease 2019 in a travel-associated
transmission cluster


Can life occur from a fertilised egg cell, in which both the egg and sperm possess an extra copy of a chromosome? Patau, Edward, and Down Syndrome are all the result of either the egg or sperm cell possessing an extra copy of chromosome 13, 18, and 21, respectively. However, what would be the outcome if both cells possessed an extra copy? That is to say, if the fertilised egg cell is left with not three, but four copies of a chromosome?

There are many ways to answer your question, I'll try a couple.

First, extra chromosomes in humans are commonly deleterious. However, there are known rare forms of tetrasomy that are not lethal, see Wikipedia on tetrasomy. Note that the causes of tetrasomy are rare events, so they are typically occurring in just one of the original gametes, not both; for it to happen in both would require a rare event paired with another rare event - not saying this is impossible, just less likely.

Polyploidy in other organisms, particularly plants, is both common and normal, see Wikipedia on polyploidy.


Drinking soda triggers tingling on a tiny spot on my upper back... but how? The title pretty much says it all.  Yes, I know it doesn't make sense. That's why I'm baffled.

For the past week or two, I've noticed that drinking soda seems to cause a tingling/stinging sensation on a very tiny spot on the skin of my upper-left back. It happens within a second or two after I swallow. This has been happening pretty consistently since I first noticed it. (I've noticed it at least a dozen times; I'm pretty sure I'm not hallucinating...) I think it also happened once or twice when I was drinking plain water, but not enough for me to be sure whether or not I actually felt it or if I was just imagining things...

I've been otherwise healthy and there's nothing particularly special about that spot on my back, so I'm pretty baffled at the moment. How/why could this possibly be happening?

The skin is a very richly innervated organ, and minor strange sensory phenomena are not exceedingly uncommon.

The thing about sensory nerves is that they can misfire and you seem to feel something when there's nothing there. This actually happens all over our bodies all the time (mostly our brain blocks them out, like it blocks out background noises after a while): an itch for no reason whatsoever (no bug, no bite, no reason) is the most common manifestation of this phenomenon.

Sensory nerves start their journey out of the central nervous system as relatively large bundles coming off the spinal cord, and keep on branching becoming finer and finer as they reach the periphery.

since there's a lot of muscle under the skin, most of these sensory nerves have to come up through muscle.

Sometimes an inflamed bundle of muscle fibers (aka a "knot") will entrap a small branch of a sensory nerve, and the pressure on the nerve will cause it to "misfire", causing a sensory illusion, if you will. If this is the case (if it's in the exact same spot every time) and a slender nerve branch is being squeezed by a muscle knot in your back, you can do a little test on yourself: have someone run a fine sharp object (say the end of a toothpick) softly over an area starting away from the spot going through it. If the sensation changes right on that spot - going from sharp to dull, for example - and does so consistently, that's what's going on. If you have the person map the change of sensation with a pen, the spot will be about the size of a quarter or smaller.

If, however, the sensation is only associated with swallowing, and there's no change to light touch, I have no idea what's going on.

Anyone reading this should know, though, that strange neurological symptoms can be an early sign of MS.


DNA content in plant seeds vs. fruit flesh Is there a publication comparing DNA yield and/or PCR-amplifiability after extraction from fruit flesh (like apples, oranges, cherries etc) in comparison to seeds of the same fruits?

I would prefer a reference, but your unpublished experience is also interesting to me.

It depends on the seed and fruit you're talking about.

The amount of DNA in your crushed up sample of plant matter depends on only one thing--how many cells are in your sample. Look at this diagram of a kernel of corn (U of Indiana):

There are different cell densities in each area--in the endosperm, the cells can be huge (and therefore have a lower density of DNA when compared with the embryo).

Let's look at a stained mustard seed (U of London):

As you can see, the cells here are very dense. More dense means more DNA per unit sample.

As far as fruit is concerned, the same rule of thumb applies. Verner, 1938 shows some cool apple tissue histology that might give you an idea of cell density in fruit tissue (again, it will be different in different fruits--search for "fruitname histology" if you're interested).

However, now that we've talked about density, we need to actually think about getting the DNA out. The extraction process is actually much more important in terms of your final yield.

Many plant seeds contain polyphenolics, which can cause DNA degradation. This protocol (Cornell U) details many of the possible shortcomings:

  These compounds have also been reported to cause difficulty in DNA purification in other plant species; polysaccharides (Murray and Thompson, 1980; Fang et al., 1992); polyphenolic compounds (Katterman and Shattuck, 1983; Couch and Fritz, 1990; Howland et al. 1991; Collins and Symons, 1992); and sticky and resinous materials (Webb and Knapp, 1990).

These contaminants can degrade DNA, but also render it unusable in PCR amplification and endonuclease digestion (Kim et al. 1997, Cornell U, EPICENTRE Biotechnologies).

Overall, there are definitely species-specific differences in fruit/seed plant DNA content. Practically, however, the most important factor in DNA yield and viability for future experimentation is sample purity and contamination. Specific fruits and seeds may contain one or more of the above contaminants, so the answer to "Seeds or fruits?" definitely depends on the species of plant you're working with.


Should hydrogen peroxide be applied on a bloody nose? When I was a kid, my parents taught me to apply hydrogen peroxide on my nose whenever it bled. It's a rare event, but my nose bleeds from time to time, and when it does, I always go through the same procedure of dipping a cotton bud in hydrogen peroxide, and applying it to the inside of the bleeding nostril. It always stops the bleeding immediately and I get on with my day.

It happened right now, and since I always just go through the motions without thinking about it, today I was curious about the principles at stake here. In looking for an answer about why it does what it does, I found only references to the effects of drinking hydrogen peroxide, which looks like a controversial subject whose benefits may be non-existent; but I didn't find a single mention about the application of hydrogen peroxide directly on a bleeding nose, which made me worried if what I'm doing is even recommended or if I'm doing something potentially dangerous.

So my question is: is this practice beneficial, and why?

Update: This question mentioned oxygenated water, which is the literal translation of "água oxigenada" (PT), but apparently that's only the commercial name for "peróxido de hidrogénio" where I live, which translates to hydrogen peroxide (H2O2); and since that returns many more hits on google, I've renamed all instances of oxygenated water to hydrogen peroxide in this question.

No, I don't think oxygenated water does anything to stop bloody noses. But holding a wet cotton swab with pressure to the inside of the nose might.

The vast majority of bloody noses in healthy individuals arise from one specific area in the nose (on either side):

In the mucosa of the nasal septum (the cartilagenous structure separating the nose into two sides), there is an area where several arteries "meet", giving it an exceptionally rich vascular supply, called Kiesselbach's plexus. It is on the anterior surface, and exposed to dry air and trauma (even such as might be sustained by a bad cold). Bleeding typically occurs when the mucosa erodes for any reason, and the capillaries and venules (and sometimes arterioles) become exposed and subsequently break. The result is the familiar bloody dripping of a nosebleed.

The most common treatment is direct pressure (squeezing the sides of the nose together) for 5-10 minutes. This works because putting direct pressure on any bleed stops the blood flow long enough for a clot to form and the arteriole to close down.
If needed, more aggressive control can be achieved by a professional.

If you happen to apply pressure with the wet cotton swab to a large enough part of the plexus (or somewhere near the spot from which your nose is bleeding), your nosebleed will stop. But it really doesn't matter what you use to wet the cotton swab (plain water, oxygenated water, carbonated water (ouch!), or other. (Noted: OP added that the liquid is hydrogen peroxide. This is not a good idea as it is an irritant and actually can cause mucosal damage.) Sufficient pressure and clot formation (and subsequent tenderness with the nose) is all that is needed.*

What doesn't work:

icepacks to the neck
leaning your head forward (increases blood flow) or back (may cause the blood to flow into your throat)
lying down (increases blood flow)
frequent 'peeking' to see if bleeding has stopped
a dry object placed against the area of bleeding (it will break up the clot when pulled away from the septum)

Aftercare and prevention is another subject.

Note: The safest way to end a common nosebleed is by squeezing as much of the 'rubbery' portion of the nose together for up to 30 minutes if necessary. Putting something into your nose poses the risk of infection.

*more serious or recurrent bleeding needs medical attention


Why do animal cells lack a contractile vacuole? I was asked why animal cells do not have contractile vacuoles. Other than the lack of need, I don't know what else to say.

Lodish et al. (2000) explain that animal cells rely on the Na+,K+-ATPase to pump Na+ out of the cell. Exporting electrolytes decreases the hypertonicity of the cell, thereby preventing too much water from entering.

Plant, algal, fungal, and bacterial cells are surrounded by a rigid cell wall. Any osmotic influx of water in a hypotonic solution leads to an increase in intracellular pressure, but not in cell volume. hence, the cell wall effectively prevents the cells from lysis.

Protozoans do not have a rigid cell wall and these organisms sometimes contain a contractile vacuole that permits them to avoid osmotic lysis. A contractile vacuole takes up water from the cytosol and periodically discharges its contents through fusion with the plasma membrane. Thus, even though water continuously enters the protozoan cell by osmotic flow, the contractile vacuole prevents too much water from accumulating in the cell and swelling it to the bursting point.

Reference
- Lodish et al. Molecular Cell Biology. 4th ed. New York: W. H. Freeman (2000)


What are null cells? My histology textbook says the following:

  The pluripotential hemopoietic stemm cell (which resembles a lymphocyte) is a member of the null cell population of lymphocytes.

It then goes on to add:

There are three types of lymphocytes:

T cells
B cells
Null cells:

Pluripotential hemopoietic stem cells
Natural Killer cells

However, this is the only text I find that classifies Pluripotential hemopoietic stem cells as null cells.
My question is: what are null cells? (and is this textbook accurate)

Thank you,
jsx

Null cells are a "slang term" for cells of the lymphocyte progeny that are not APC (antigen presenting cells) and lack T and B cell receptors - therefore they are the natural killer (NK) cells.


Is it possible to create an experiment in house conditions to prove the existence of germs? I realise that the best way to prove the existence of germs or single-celled organisms is by looking at them through a microscope.
But I don't have a microscope at my home, how can I design an experiment in a normal house environment to show the existence of germs (or other single-celled organisms) without spending too much money?

By "house environment" I mean that I have access to normal stores and the internet. If it's something that can be bought in a "normal" store or on-line without getting me into trouble, and doesn't cost a lot then I can have access to it. I don't have access to lab grade equipment or conditions, so no sterile rooms or special growth environment.

I thought about the following experiment, inspired by the mythbusters pyramid power episode. In the episode they cut an apple in half and put one half under a pyramid and the other not under a pyramid. In the first attempt one of the halfs rotted quicker than the other, they concluded that it happened because the saw they used to cut the apples wasn't sterile.

So I thought about taking 3 apples, contaminating a knife (by rubbing human saliva on it). Cutting one apple with the contaminated knife, one apple with a sterile knife (using rubbing alcohol to sterilize it) and one apple by a knife that has 1 contaminated side and one sterile, which is a contaminated knife, that had only 1 side sterilized with rubbing alcohol. Then leaving the 6 halves in separated sealed containers (some tupperware) for a few days and then looking examining the rott. The expected result is that the "contaminated apple" will have a lot of rot on both halves, the "sterile" apple will have no (or close to no) rot, and the half and half apple will have one rotten side and one not rotten side, and the sides will coincide to the contaminated/sterile sides of the knife touching them.

Will this experiment work?

You could use Jell-O for growing bacteria if you don't have access to agar ! (I have never tried this but I think it should be possible because the gelatin in Jell-O is like agar.)

You should first sterilize a small knife on a gas stove or with alcohol and then gently rub it on any surface (where you think bacteria are likely to be found ) and then rub it on Jell-O taken in a dish. You should then place it in an environment similar to the one from where you isolated the bacteria. After one or 2 days the bacteria should grow.

For control : You could simply put a plate of Jell-O in the same place but without inoculation of bacteria.

Disclaimer : I am not a microbiologist and I am not sure this would work but you could give it a try as it will not be really expensive :)


What controls Fructose regulation in plants? Sugars are found ubiquitously in plants and are regulated.

For sucrose it's pretty straightforward - it's basically kept at a low ish level, and put into storage or other intermediate compounds. These act to inhibit or promote other parts of the calvin cycle of sugar production (fructose 2,6 bisphosphate especially iirc).

Fructose is a bit more obscure. What are the regulatory feedback loops involved?

Preamble

In short, fructose kinases (like Fru6P,2-kinase) and fructose phosphotases (such as Fru2,6bisP) regulate and are in turn regulated by fructose (specifically Fru6P)  levels in plants. There are also several metabolites that regulate the rate at which those fructose enzymes function creating quite a complex fructose regulatory network. This phosphorylation can make fructose unavailable or available to proteins as well as providing energy in the process (and aparently the rate of this can be controlled effectively in vivo (Stitt, 1990)).

I haven't come across any cell uptake regulation, but remember plants are physiologically very different to humans and there may not be a like for like system in this case. Although I suspect there will be since in plants fructose can be concencentrated in fruiting bodies. Perhaps another answer, or a major edit to this answer can explain that.

Fructose is often referred to as a regulatory metabolite in plants i.e levels of fructose affect other pathways due to its phosphorylated state. However, there are lots of sugar regulating systems in plants. Although this article focuses more on glucose and galactose, it emphasises the idea of a regulatory web rather than a cycle when it comes to plants and sugar regulation. Below the studies are based on plants such as spinach and other leafy vegetation, not fruiting plants I'm afraid!

Kinase Control

3PGA, 2PGA, PEP, dihydroxyacetone P, and the 2-carbon intermediate glycollate-2-P are all metabolites that control phosphorylation that inhibit the kinase, whilst Pi activates the kinase. Interestingly PPi also inhibits the kinase by competing with ATP. As one can imagine, this causes sigmoidal ATP saturation kinetics and is clearly indicative of regulation.

Phosphorylation

Fru6P and Pi both inhibit Fru2,6bisP hydrolysis by FRU2,6PASE.

This article from 1996 has a figure showing just how complex sugar pathways can be. To expand on your question, we can see how fructose phosphorylation plays a role in regulating in Sucrose and Starch glycolysis (Plaxton, 1996).

Disclaimer: I haven't studied this since undergraduate level, so constructive comments are welcome and I encourage people to edit this answer to improve it and help it more aptly answer the question!


Why do birches have a white bark? Several species of the tree genres Betula have a white bark,especially when they are young. This is quite peculiar to trees - at least in central Europe; so I'm wondering if there is a ecological reason behind it.

The first idea I have is that they protection against the sun. But normally protection of nature against the sun is to make the opposite: put more pigments in the skin, so that the sun does not damage the underlying DNA.
If this is the explanation, how do other tree species protect against this?

It is protection against rapid warming of the cambium layer. A lot of far northern timber has light colored bark which reflects sunlight. The rapid heating from very cold after sunrise can actually damage or even split the bark of dark colored species. This is called sunscalding.


Help needed in fish identification Please help me identify these fish. I looked around but wasn't able to determine its species.

It looks like southern platyfish (Xiphophorus maculatus) to me.

Courtesy: http://aquaticszone.blogspot.in/2011_04_01_archive.html


How are drugs distributed in regards to bone marrow? I know that as volumes of distribution increase they correspond to the blood, then the vascular rich group (heart, kidneys, liver, brain if BBB permeable), then muscle then adipose. But things like flow should also be taken into account. So are drugs usually distributed in a similar manner to blood, vascular rich group, etc?

How are drugs distributed into any tissue, and what affects it?
Note that there are no general answers, and that this is highly dependent on the drug in question.
Active or passive transport
Is your drug a substrate for any uptake or efflux transporters that may affect the distribution?
Solubility
Lipophilic drugs will generally have a greater volume of distribution, as there is more passive diffusion into tissue.
Blood flow
How much drug is presented to the area in question? Tissue with greater perfusion (e.g. kidneys) will have a greater exposure to the drug. Look up the well-stirred model.
Relating this to the blood marrow
So what should you research in order to answer your question?

What are the physiochemical properties of the drug in question? How are these compared to other drugs where the bone marrow is a target?
Is the drug a substrate for any relevant transporters in the tissue of interest?

You should also look up if there are any physiologically-based pharmacokinetic (PBPK) models for your drug or drugs with similair physiochemical properties. Some of these are free, and allow you to make general assumptions about the distribution of the drug.


What is the number of synaptic vesicles in an axon terminal? Is there any research as to the average number of synaptic vesicles per axon terminal in a human neuron's axon? On top of that, what percentage of those vesicles are used in a single action potential cycle i.e. membrane depolarization, hyperpolarization and return to resting potential?

Short answer
Several to thousands of vesicles per synapse. In the cortex, 0-1 are released per typical synapse. At neuromuscular junctions or specialized CNS synapses there can be more.
Longer answer
It doesn't make much sense to talk about an "average", since there are different types of synapses with very different properties, but we can talk about some examples from synapses used as models. In Rosenmund & Stevens, 1996 they estimate about 10 readily releasable vesicles at one synapse in hippocampus. Rizzoli & Betz, 2004 count hundreds at a frog neuromuscular junction.
In hippocampus and neocortex, for a typical synapse there are from 0-1 vesicles released per spike. Higher release probabilities to activation of single cells are achieved by making multiple synaptic contacts; in a typical cortical synapse, there's really just one active site so a max of one vesicle released (Silver et al 2003; Auger & Marty 2000 and Abbott & Regehr, 2004 also discuss this a bit).
Short-term plasticity can strongly influence release probability (Abbott and Regehr 2004 is a good reference to thinking about synaptic computations like this). Multiple action potentials occurring quickly can cause a sustained increase in calcium concentration in the presynaptic cell, increasing release probability at otherwise low-probability synapses (short-term facilitation). Alternatively, many spikes over a longer time period or at higher probability synapses can exhaust the pool (short-term depression). Rosenmund & Stevens used this to estimate the readily releasable pool size of about 10: they triggered a ton of rapid-fire spikes and counted release events, finding only 10. Rizzoli & Betz mention that 10 seconds of 30 Hz stimulation (300 pulses) depleted the available vesicle pool.

Abbott, L. F., & Regehr, W. G. (2004). Synaptic computation. Nature, 431(7010), 796-803.
Auger, C., & Marty, A. (2000). Quantal currents at single‐site central synapses. The Journal of physiology, 526(1), 3-11.
Reyes, A., Lujan, R., Rozov, A., Burnashev, N., Somogyi, P., & Sakmann, B. (1998). Target-cell-specific facilitation and depression in neocortical circuits. Nature neuroscience, 1(4), 279-285.
Rizzoli, S. O., & Betz, W. J. (2004). The structural organization of the readily releasable pool of synaptic vesicles. Science, 303(5666), 2037-2039.
Rosenmund, C., & Stevens, C. F. (1996). Definition of the readily releasable pool of vesicles at hippocampal synapses. Neuron, 16(6), 1197-1207.
Silver, R. A., Lübke, J., Sakmann, B., & Feldmeyer, D. (2003). High-probability uniquantal transmission at excitatory synapses in barrel cortex. Science, 302(5652), 1981-1984.


What type of bug cocoon is this? My question is about these cocoon like things that are all over my house and fence in Florida (USA).

That is a bagworm. Order Lepidoptera, family Psychidae. You can read about them here https://en.wikipedia.org/wiki/Bagworm_moth


Why are Excavata called "Excavata"? The explanation given in my textbook is:

  Some members of this diverse group also have an “excavated” feeding
  groove on one side of the cell body. (Campbell Biology)

This still isn't clear, though. What does it mean that this groove is "excavated"? Is it hidden inside the organism and then dug out?? Several websites just say the same thing.

This is just a reference to the feeding groove - a morphological feature that groups these organisms. The presence of the term in quotes as "excavated" is an indication that the word is not meant to be taken literally. Quotation marks used like this are referred to as scare quotes - they are meant to alert the reader that the phrase in quotes is not to be interpreted by its standard meaning.

Instead, you could read the sentence as meaning:

  Some members of this diverse group also have a feeding groove on one side of the cell body, as if part of the cell was excavated.

One should not take the etymology of species names too literally - they are really just names. This is also true of common names of organisms.


What effect does taking antibiotics unnecessarily have on future bacterial infections? I have been told by my biology teacher that you shouldn't take antibiotics unnecessarily because "the body gets used to them" and it reduces the effectiveness of antibiotics against future bacterial infections, which can be dangerous.

I can't understand how the body could "get used to" antibiotics. How does prior use of antibiotics affect their effectiveness against future infections?

Every time you expose a population of bacteria to an antibiotic, you select for organisms with resistance-granting genes.

Bacteria can pass plasmids full of genes back and forth.  So if you get a nasty E.coli infection, do you really want one of your usual bacteria with a resistance-granting gene sitting right next to it?

Let's say you are so sick you go to the hospital.  Do you think the hospital wants your antibiotic-resistant E-coli around?


Does the Miller-Urey experiment explain the origin of life? According to the Miller-Urey experiment, the early earth atmosphere could have supported the formation of amino acids - and the experiment is hailed as being important in the explanation for the origin of life. However, I do not understand how life could have started from amino acids (or proteins) which do not self replicate. Certain types of RNA do self-replicate, and it is plausible how life could have evolved from there.
Does it matter if amino acids came before RNA if they did? Is it correct to assume that in the RNA world, life somehow learnt how to use amino acids?

This is a common question. I think the experiment and its conclusions are often misunderstood.
Originally, the null hypothesis was that the ingredients for life could not have come about spontaneously, from inert, inorganic molecules. There was no evidence of strictly physical, non-biological processes being able to produce compounds that were necessary for the proteinaceous life as we know it. In other words, abiogenesis was therefore not supported by any line of positive evidence... until the Miller-Urey experiment. The experiment showed that the ingredients could arise through plausible, natural conditions prior to the existence of life! It bridges the gap between inert, inorganic, non-biological, and the rich soup of complex molecules that would - arguably - be necessary for anything like abiogenesis to even be a consideration based on empirical observation.
Of course the presence of amino acids is not evidence for the abiogenic origin of life. Life is not protein nor amino acid alone. But demonstrating that complex biological ingredient chemistry occurs spontaneously in large abundance - that sounds like a great take-off point for an abiogenic origin of life! That's really all the experiment achieved. In its historical context, it is a very impressive discovery, but it is certainly not a complete explanation, merely something that makes myriad biochemical explanations possible (and perhaps even plausible!). Perhaps you can now better appreciate why it excited and continues to excite biochemists working on trying to understand the chemical origins of life. The Miller-Urey experiment is foundational.
As for the transition from RNA to an RNA-protein origin of life, I quote briefly from another answer elsewhere here:

Regarding the transition from RNA-only to RNA-protein world, peptides
function as cofactors for some ribozymes. Amino acids and peptides are
known to have existed in the prebiotic environment and have been found
in space (glycine has been found in comets, along with other 70 amino
acids).


Mechanism by which hypokalemia reduces insulin secretion Is there any known mechanism by which hypokalemia reduces insulin secretion?

This video explains a mechanism, but its inherently wrong because ATP dependent K+ channels will allow movement of K+ from inside of cell to outside.

tl;dr
Hypokalemia hyperpolarizes membranes by increasing the $K^+$ gradient, making $\mathcal{E}_K$ and consequently $\mathcal{E}_m$ more negative. This makes any signaling event controlled by depolarization less responsive.
It's complicated, but we can understand the effect by looking at $K^+$ alone
Good catch. Yes, the video (and diagram) are incorrect. The electrophysiology of pancreatic $\beta$-cells is still an area of active research. Your textbooks (e.g., Costanzo Chapter 9, under Regulation of Insulin Secretion) will tell you that an increase in the $\frac{[ATP]}{[ADP]}$ ratio closes ATP-sensitive $K^+$ channels, which depolarizes the membrane. This is, in large part, correct, but not thoroughly understood, and not only by decreasing the $K^+$ conductance of the membrane. Further work in the years since that linked article supports the importance of a $Cl^-$ gradient and anion current, but $K^+$ conductance is still involved, and probably still underlies the mechanism through which hypokalemia reduces insulin secretion.
Membrane potential is determined by the concentration gradients and permeabilities of ions
The membrane potential of the pancreatic $\beta$-cell, as with the neuron, is determined by both concentration gradients and permeabilities of the membrane to ions. I'm sure the OP understands this, but for the general reader, you can read about this basic principle in any neuroscience or physiology textbook. You can calculate the membrane potential using the Goldman equation or chord conductance equation. Both are representations of the same principle, but I think the chord conductance equation is more intuitive. We'll simplify for our purposes to.
$\mathcal{E}_m  = \frac{g_{i}}{g_T} \mathcal{E}_i + \frac{g_{j}}{g_T} \mathcal{E}_j + \frac{g_{k}}{g_T} \mathcal{E}_k + ... $
Here, for ions i, j, k, ..., the membrane potential is equal to the sum of a series of terms for each ion, with each ion term being a product of the equilibrium potential of that ion ($\mathcal{E}_i$) and the portion of the total conductance across the membrane that the conductance of that ion represents. Conductance can roughly be understood as permeability. More open ion channels means a greater permeability/conductance to that ion.
Short term changes in membrane potential used in signaling are accomplished by changing the conductance of the membrane to specific ions. If the $\frac{g_i}{g_T}$ increases for ion i, the membrane potential moves closer to the equilibrium potential for ion i.
The concentration gradient determines the equilbrium potential
Each ion has an equilibrium potential, a membrane potential at which the net current of an ion across the membrane is 0. From the Nernst equation, we can say:
$\mathcal{E}_i \propto log_{10}\frac{[I]_{out}}{[I]_{in}}$.
Here $[I]_{out}$ is the concentration of the ion outside the cell, and $[I]_{in}$
is the concentration inside the cell. We've eliminated the proportionality constant because, in physiological conditions, it's constant, it's different for pancreatic $\beta$-cells (vs. neurons), and it's not relevant to our discussion (since we're not going to make any calculations with real numbers. If you are very careful, you'll notice the log term has outside concentration on the top, inside concentration on the bottom. You may find the Nernst equation written with a negative proportionality constant and with the inside concentration on top. These are equivalent because of how logs work.
Changing conductance, or permeability, changes the membrane potential
When you increase the conductance of a membrane to a particular ion, the membrane potential moves closer to the equilibrium potential for that ion. This is why in the neuron, for example, increasing the conductance of the axon membrane to $Na^+$ causes depolarization. The equilibrium potential $\mathcal{E}_{Na}$, is positive. The resting membrane potential is negative. Higher permeability to $Na^+$ moves the membrane potential closer to $\mathcal{E}_Na$.  Similarly, increasing the conductance of the axon membrane to $K^+$ (after the membrane has depolarized) repolarizes and then hyperpolarizes the membrane. $\mathcal{E}_K$ is negative (more negative than resting membrane potential). Higher permeability to $K^+$ moves the membrane potential closer to that large negative $\mathcal{E}_K$.
Increasing the permeability of pancreatic $\beta$-cells to $K^+$ hyperpolarizes the membrane
I'm using examples of the neuron because this is typically where these concepts are most thoroughly taught, but lets try to apply our understanding to the pancreatic $\beta$-cell. Concentrations, permeabilities, and membrane potentials are a little different, but not that much. Resting membrane potential for a $\beta$-cell is about -60mV. Threshold potential for $Ca^{++}$ release (which leads to insulin secretion) is between -50 and -40 mV. (Refer to my earlier linked articles). I don't have an exact number for $\mathcal{E}_K$, the equilibrium potential of $K^+$ in $\beta$-cells, but it is more negative than the resting membrane potential of that cell. We know this because (as is demonstrated in the linked studies), the OP is correct, increasing the conductance of the membrane to $K^+$ causes a net $K^+$ current out of the cell, rather than in, moving the membrane potential to a more negative state (hyperpolarizing the membrane), similar to what we see in neurons.
Decreasing the permeability of pancreatic $\beta$-cells to $K^+$ DEPOLARIZES the membrane
As discussed in Constanzo Chapter 9, ATP-sensitive $K^+$ channels close (not open) in response to an increase in the $\frac{[ATP]}{[ADP]}$ ratio. This decreases the $K^+$ conductance of the membrane, allowing the membrane potential to move closer to other equilbrium potentials (e.g., $\mathcal{E}_{Na}$, which is positive). With $\mathcal{E}_K$, which is more negative than the prior membrane potential, contributing less, the membrane potential becomes less negative, or depolarizes.
You can use a less mathematical reasoning to work out what happens when the $K^+$ conductance decreases as well. Close a $K^+$ channel and positive ions that would have moved out of the cell stay inside the cell, making membrane potential less negative, depolarizing the membrane. This is effectively the same as bringing positive ions inside the cell.
When the membrane depolarizes, $Ca^{++}$ is released, which causes secretion of insulin.
Hypokalemia
In hypokalemia, outside concentrations of $K^+$ decrease. This has an effect on the equilibrium potential, $\mathcal{E}_K$. From the Nernst equation above, we can look at the log term to see how $\mathcal{E}_K$ changes when $[K^+]_{out}$ decreases. The fraction $\frac{[K^+]_{out}}{[K^+]_{in}}$ is less than 1 in all human cells (there is more $K^+$ inside the cell than out), so the log term is going to be log(some number between 0 and 1). You can work this out using a calculator, but in this domain (0-1), the log is negative. It is larger and negative the closer you get to 0, smaller (but still negative), the closer you get to 1. If this behavior is unfamiliar to you, I encourage you to explore it with a calculator.
If you decrease the numerator in the log term ($log_{10} \frac{out}{in}$), as we do in hypokalemia, you get a larger negative number. This doesn't change the net direction of flow, or current for $K^+$ at levels that occur in the cell. It's still net out. $\mathcal{E}_K$ is more negative than it would otherwise be, so why doesn't decreasing conductance/permeability by closing the ATP sensitive $K^+$ channels do the same thing and depolarize the membrane?
Closing ATP sensitive $K^+$ channels in the setting of hypokalemia does cause depolarization, but not enough. You have to go back to the chord conductance or Goldman equation and consider the effect of $\mathcal{E}_K$ on the membrane potential before the ATP sensitive $K^+$ channels are closed. With a more negative $\mathcal{E}_K$, the chord conductance term $\frac{g_{K}}{g_T} \mathcal{E}_K$ is more negative, and the overall $\mathcal{E}_m$ is more negative. Global hypokalemia effectively hyperpolarizes the membrane, not just in the pancreatic $\beta$-cell, but everywhere. This is an important principle for understanding the consequences of hypokalemia, not just in insulin secretion, but in all settings. As a rule, excitable membranes are sluggish in hypokalemia (except Purkinje fibers). This is why, for example, it causes muscle weakness.


How do disulphide bonds in hair cause curling? I understand that there are several characteristics of curly hair which differ from straight hair (such as an asymmetrical distribution of disulphide bonds in curly hair), but really am struggling to understand the root cause of inherent curl on the macroscopic level.

My current understanding of the hair structure is based mostly upon this website

The most relevant part of the hair for our discussion is the cortex, which is made up of many axially aligned macrofibrils, or macroscopic keratin fibers, which are in some filler essentially of lipids/proteins. Inside these macrofibrils are microfibrils. These are also aligned axially and in some filler of lipids/ proteins. Inside the microfibrils are the protofibrils, even smaller fibers which are twisted around each other like a yarn. These protofibrils are made up of 4 keratin chains which are essentially twisted together and connected by disulphide bonds and hydrogen bonds. While hydrogen bonds are easily broken, the disulphide bonds are not. In curled hair, the macrofibril isn't symmetrical but I am unsure as to how this, or what other effects, actually lead to the curling.

I had previously assumed that the reason for curling is that in an asymmetrical configuration of the hair(IE not cylindrical but more oval in cross section), some residual stresses are formed by the disulphide bonds between the keratin, If this is true, it would lead me to believe that it would cause increased buckling of the protofibrils. But, even with straight hair and more symmetrical disulphide bonds, you already have some curling and buckling of the protofibrils, but the hair doesn't curl on a macroscopic level.

As such, it doesnt seem like this buckling due to asymetrical disulphide bonds would necessarily lead to a curled or organized structure on the macroscale, with the macrofibrils. This leads me to believe I am missing something.

Nice question. I must say it took me many hours to get satisfactory answer.
Hairs are made of keratin molecules, which contain cysteine. Cysteine has thiol (-SH) group, by which it can form disulfide (-S-S-) bond with another cysteine of another keratin, causing bending of hair. See this image from here:

Curling of hair can be justified on both microscopic and macroscopic level.

Microscopic level: See this post from here:

Curly hair has to do with the chemical bonds in the protein that makes up hair - $\alpha$-keratin. Keratins, particularly $\alpha$-keratin, have long sequences of amino acids (often more than 300) which forms a helical structure.
Pairs of these helical structures then coil about each other in a left-hand coiled-coil structure. These are then attracted to another coiled coil so two keratin helices will stick together. These four-chain structures then associates with another four-chain structure to form the hair filament. One of the amino acids which make up these chains, is cysteine which has a sulpher group which is able to make connections with other sulpher groups on other coiled coils.
The more interactions a filament has with another filament, the more tightly coiled the coiled-coil becomes. Hence, curly hair has more interactions than straight hair. The process of `perming' hair introduces more accessibility of the sulpher on the amino acid, cysteine, to make these connections. Finger and toe nails have many many bonds between filaments and are thus, very hard.

For example, see how hairs are curled artificially via perming.

Source
This change in location of bonds is what causes curling of the hair (look again at the first diagram and notice the orientation of disulfide bridges). Those vertical strands now get curled due to change in these bonds. Here, the required mechanical tension for bending is provided artificially.

Macroscopic level: Shape of hairs is also determined by its macroscopic structure. Look at this article:

All hair, whether curly or straight, has two major components: the shaft and the follicle. The shafts are the visible, flowing strands that we see on our heads. The follicle is the part of our hair that resides within the skin, or dermis, of our scalp. Each of these structures plays a role in determining our overall hair shape.
Let’s start at the root of the issue (pun 100 percent intended): the follicle. It turns out that the shape of our follicles is a major determinant of our hair texture. If you were to look at the follicle of straight hair, you would find it is perfectly round. The follicle of curly hair adopts an oval shape. The flatter the oval is, the curlier the hair will be.
Another contributing factor to a hair’s curl is the way the follicle tunnels into the scalp. Follicles of straight hair tunnel vertically down from the skin’s surface into the dermis. If the follicle angles into the dermis then the hair will curve as it grows causing it curl. Although, this curving of the follicle can lead to gorgeous curls it causes one major drawback that all curly-haired persons can attest to, dryness. Within the dermis, special glands line the follicle to secrete oil, called sebum, to lubricate the hair. Unfortunately, when follicles curve sebum isn’t able to travel the length of the hair as well leading to dryness of hair that doesn’t get lubricated.

Source
Although how shape of follicle determines structure of hair strand is probably not known, the major contributing factor likely is how hair emerges from the scalp. When it emerges in a bent shape, it faces a lot of tension from the scalp, which causes it to bend in the shape of the follicle to form curls. Since straight-emerging strands don't face such forces, they do not lead to curled hairs.
In this way, hair curls are a consequence of large number of disulfide bridges between keratin molecules and how the hair emerges from the scalp.


Can any one reaction in a cell be at equilibrium? I know that metabolism as a whole can never be at equilibrium (otherwise the cell is dead !) but I wonder whether a few reactions in the cell could be at chemical equilibrium at a  given point of time.

Is it possible theoretically ? Is there any real example ?

I think there are a few principles that we need to consider before answering your question.

(a) When a reaction is at equilibrium, the rate of any elementary reaction is exactly balanced by that of the reverse process.  This is an important one.

The above principle follows from transition-state theory, which holds that the activated state for the reaction in one direction is that same for that in the reverse direction.  It also follows from the principle of microscopic reversibility at equilibrium or, more correctly, the principle of detailed balance at equilibrium, which states that “in a system at equilibrium each collision has its exact counterpart in the reverse direction, and that the rate of every chemical process is exactly balanced by that of the reverse process” (my emphasis) [Laidler, 1987, p 130]. It is important to realise that these two points of view are equivalent.  To again quote Laidler (p130), if one is working within the framework of TST “the principle of microscopic reversibility presents nothing new”.

To put it bluntly: a system where any elementary reaction, either explicitly or implicitly, is not exactly balanced by the reverse process is not at equilibrium. By this criteria, the actin example alluded to above cannot, even loosely, be considered at equilibrium.

This principle has many important consequences, even when a system is not at equilibrium.  One is that the the product of the ratios of rate constants around a cycle (closed loop) equal the equilibrium constant for the cycle (see Cornish-Bowden, 2004, p 104). [see Addendum for an example of where this consequence was not adhered to].

(b) When a species is in a steady-state, the rate of formation equals the rate of breakdown. The steady-state concentration may differ markedly from the equilibrium concentration.

(c) As @WYSIWYG has pointed out, an enzyme (catalyst) does not change the equilibrium constant for the uncatalyzed reaction.

(d) When we are dealing with equilibria, we are usually interested in Gibbs free energy changes.  For example (Silbey & Alberty, 2001, p 277).

ΔGo' = -RT ln K’

(In the above equation K’ is the apparent equilibrium constant, that is the equilibrium constant at specified pH, and ΔGo' is the standard transformed Gibbs free energy of a biochemical reaction.  More on this distinction, if you are interested, in the Silbey and Alberty reference quoted above).

The important point is that there is a relatively simple relationship between Gibbs free energy and the equilibrium constant. The Gibbs free energy, of course, gives a measure of the spontaneity of a reaction and also its capacity to do work.

When the transformed Gibbs free energy is of a reaction (ΔG') is zero, the reaction (at specified pH) is at equilibrium and cannot perform useful work, and reactions with negative ΔG' may be considered ‘spontaneous’.  It is also important to realize that equilibrium is a dynamic state: chemical bonds are continuously being broken and energy is continuously being redistributed (with no loss of energy). [I am dealing here with the transformed free energy, ΔG', that is the free energy change at specified pH, rather than ΔG (the pH independent value), as this is the most useful when considering a biochemical reaction.  However, similar conclusions apply to ΔG].

Having got those out of the way, I can now attempt to answer your question (slightly rephrased). Can a reaction in a metabolic pathway be at equilibrium?

To be extremely pedantic, if there is a flux through the pathway (net conversion of first substrate to end product) then the answer is no (Newsholme & Start, 1973, p 11). That is, if there is a flux through the pathway, ΔG' cannot be exactly zero for any individual reaction.   However, reactions in a metabolic pathway may be very close to equilibrium (Newsholme & Start, 1973, chapter 1).

Let’s (once again) rephrase your question.  Are there any examples of reactions in metabolic pathways that are close to equilibrium, and how can we determine this?

To again quote Newsholme & Start (1973, p11)  “In a series of reactions that constitute a metabolic pathway, a few may be displaced far from equilibrium, whereas the majority of reactions may be close to equilibrium”.

So how can this be determined? One way would be to measure the ratio of products to substrates (or the ratio of product to substrate pairs) in the cell, and compare this with the equilibrium constant.  Note that it is only the ratio of substrate/product pairs we are interested in, not the absolute concentrations. We might be interested in the NAD+/NADH ratio in the cell, for example.

That is, we measure the mass action ratio and compare this with the equilibrium constant.

Such measurements are fraught with difficulties, but let’s agree that they can be made. We could rapidly freeze the tissue sample to -190°C (using liquid nitrogen), for example, and then measure the ratio of metabolites.  Finally, it should be pointed out that comparison of mass-action ratio with the equilibrium constant is not the only way of deducing that a reaction is near equilibrium, and agreement between alternative methods is highly desirable before any firm conclusions are drawn.

Let’s consider glycolysis as an example.  It is generally agreed that the reactions catalyzed by phosphoglucoisomerase, phosphoglycerate mutase and enolase are all close to equilibrium: the mass action ratios and the equilibrium constants are about the same (see Newsholme & Start, 1973, p 98).

It is also generally agreed that the reactions catalyzed by phosphofructokinase and pyruvate kinase are far from equilibrium (see Newsholme & Start, 1973, p 98).

What is the rationale? In general, it is control reactions catalyzed by regulatory enzymes that are displaced from equilibrium. (A key property of a regulatory enzyme is that the activity is controlled by factors other than substrate concentration).

The enzyme phosphofructokinase is a good example.  This enzyme plays a key role in the regulation of glycolysis. Measurement of the mass-action ratio for this enzyme gives a value of 0.029, where the equilibrium constant for the reaction is about 1000 (see Newsholme & Start, 1973, p31). It is clear that physiologically this enzyme catalyzes a reaction that is far from equilibrium.

In conclusion, many reactions in metabolic pathways may be close to equilibrium, but regulatory enzymes almost always catalyze reactions that are displaced from equilibrium.

Finally, if anyone wishes to provide more recent references or to otherwise improve the answer, feel free to edit.

Addendum

For a well-known controversy in the enzyme kinetics field where the requirement that product of the ratios of rate constants around a closed loop equal the equilibrium constant for the cycle was not adhered to, see Selwyn (1993) and Topham & Brocklehurst (1992).  These authors were critizing the work of Varon et al (1992), who made a bit of a hash of things. If you are interested in this area, you may wish to read up on this controversy, which is very informative. (Selwyn’s paper is a great start). [All the above papers are freely available in PubMed Central].

References

Cornish-Bowden, A. (2004) Fundamentals of Enzyme Kinetics. 3rd Edn. Portland Press.

Laidler, K. J. (1987) Chemical Kinetics 3rd Edn. Harper & Row.

Newsholme, E.A. & Start, C (1973) Regulation in Metabolism. John Wiley & Sons.

Silbey, R. J. & Alberty, R.A (2001) Physical Chemistry. 3rd Edn. John Wiley.

Eric Arthur Newsholme (1935–2011) Obituary


Why is the separation of biochemical synthesis pathways safer and more economical? During our first lecture of plant physiology, our teacher told us that the separation of biochemical synthesis pathways was advantageous because it was safer and more economical. The problem I got, while studying this back at home, was that he didn't explain why it is so.

I can understand why it is safer (for example, a lysosome could break down a lot of major components of the cell if that lysosome was not restricted to its area), but it's quite difficult for me to understand why it's more economical, in terms of energy. Any clear/simple explanation about this would be greatly appreciated.

False Economies?

Goodness knows what the poster’s teacher meant by saying that the separation of biochemical pathway is “more economical”! This is not a term usually applied to metabolism and, anyway, in life people who are economical do not always get value for the money they do spend, never mind obtain a better quality of life.

Most treatments of the separation of biochemical pathways justifiably emphasize the advantages of being able to regulate forward and reverse reaction sequences independently. However let us have a look at the separation of pathways in terms of energy, as the poster requested.

Some basic thermodynamics

The poster also requested the explanation be clear and simple. The following is simple, as long as you are familiar with the some basic ideas of chemical thermodynamics. If you are not, I suggest you read the three pages in  Section 8.2 of Berg et al. online. (Whether it is clear or not I leave others to judge.)

What determines whether a chemical reaction proceeds is the overall
(Gibbs) free energy change (ΔG). If it is negative, the reaction is
thermodynamically favourable.
The actual free energy change depends on ΔG0, the standard
free energy change (reflecting the chemistry of the reaction(s)),
together with the actual concentrations of reactants and products.
Enzymes are necessary to catalyse reactions in living organisms,
but do not affect the position of their equilibrium.

Argument

For simplicity, let us consider a series of reactions interconverting compounds M and P:

  M ⇄ N ⇄ O ⇄ P

No separation between pathways

Consider a situation in which the forward (M➞P) and reverse biochemical transformations (P➞M) involve the exact same chemical changes catalysed by the exact same enzymes, i.e. no separation between pathways. In order for this to work the overall ΔG0 must be near zero, otherwise reaction in one direction will be very difficult to achieve (require a very high concentration of starting reactant). For a ΔG0 near zero there will be equilibrium (no net reaction) at equal concentrations of M and P. In order to cause a flow of metabolites, say in the forward direction, there must be an increase the concentration of M relative to P.

There are two problems with this.
First, quite a large ratio of M to P, say, would be required to achieve net flow through the pathway, and this would involve having a large pool of unreacted M. (Section 8.2 of Berg et al., cited above, has some calculations that illustrate this.) This may or may be regarded as economical use of thermodynamic energy, but is not particularly economical in the  use of resources. However, a ‘pathway’ in which it is employed is glucose transport in the liver (actually a single transport process).
Second, the direction of overall reaction is controlled solely by the ratio of M to P, a situation that lacks flexibility.

Separation between pathways

If separate pathways are involved, the first problem of a single pathway mentioned above is overcome in the following way. Each overall reaction can have a high negative ΔG0, so that it does not require such a large pool of reactant and is essentially unidirectional. One might ask how this can be, as the value of ΔG0 for the chemical reaction, M ⇄ P is fixed. The answer is that separate pathways will involve  other reactants, so that the overall forward reaction might be
M + X ➞ P + Y
whereas the reverse reaction might be
P + A ➞ M + B
This is considered for glycolysis and gluconeogenesis in Section 16.3.6 of Berg et al. — with actual equations. The ΔG0, for glycolysis is quoted as – 84 kJ/mol, and that for gluconeogenesis as –38 kJ/mol.

Of course, if both reactions have a thermodynamically favourable values of ΔG0, it is necessary for the cell to prevent the uneconomic cycling of P back to M after it has been formed. However the fact that the pathways are different means that different enzymes will be involved, which are the targets of regulatory molecules that can switch them off and on. These regulatory molecules usual reflect supply and demand, but need not be intermediates in the reaction sequences, and they can act as far more sophisticated ‘switches’ for the enzymes. The particular details of this for glycolysis and gluconeogenesis can be found on the first page of Section 16.4 of Berg et al.

…the price of everything, the value of nothing

So are separated biochemical pathways energetically more economical? The large free energy change that drives these reactions is ‘lost’ as heat, so one could argue that the reverse is actually true. Or, then again, one might say that “you get what you pay for”.


What's the purpose of segregating a virus from the blood and growing it in the lab? I heard that the scientist in Australia found a way to segregate the 2019 NovCoronovirus from the blood. Does this mean they are one step closer to the cure? Why is virus segregation crucial in finding a cure for a viral infection?

2019-NCoV was first cultured by a Chinese group, as published here on January 24. China has not shared samples, but did share sequencing data in the linked paper and via GISAID. The Australian group at the Doherty Institute hasn't published yet, but did put out a press release today (January 29), and appears to be the first group outside of China to have cultured 2019-NCoV.

Viral isolation, and in particular, culture, is an important, and often difficult step in characterizing a novel virus. Once characterized, viral culture serves as a gold standard for diagnosis. Generally speaking, the ability to grow virus in cell culture allows for a broad range of pre-clinical studies that can lead to clinical advances including prevention, diagnosis, and treatment. Consider how difficult it may be to study a pathogen if you are not able to manipulate it in a living culture. You can read about this in Murray Medical Microbiology, Ch 50. This article, which does not require a subscription, may also be of interest. The article describes a variety of historical and modern methods, but also includes some discussion about the use of viral culture.


What exact characters determine an animal's Genus? I do know that if two animals cannot naturally reproduce, they are said to be of two different species. But what determines the genus?

Just for example, the African elephant belongs Loxodonta but the Indian counterpart belongs to Elephas , despite the fact that they are so similar, as opposed to say, the fact that, the Bengal Tiger and the Snow leopard despite being so different , are placed in one genus, Panthera ?

I don't think there is any non-arbitrary concept being used to tell whether two species belong to the same genus or not. The same goes on with any other taxonomic rank. Systematicists build some intuition within each clade about what a genus could mean and use it to argue what is the most strategic grouping but the concept of genus may well vary a lot from clade to clade (from spiders, to mammals or to flowering plants, ...).

Note that even the concept of species is not as nicely defined as you may think. Have a look at How could humans have interbred with Neanderthals if we're a different species? for discussion on the concept of species.


Is it possible to feel pain in some part of a body, but the pain "feeling" is introduced somewhere else? Is it possible to feel pain in some part of a body, but that the cause of the pain is situated elsewhere in the body? For example, somebody feels pain in his toe, but it turns out that this pain is not signaled by nerves in his toe, but caused by a damaged nerve in the spinal cord, or somewhere in the brain.

Yes, this is pretty common.  Examples include

sciatica, pain felt down the back of a leg to the foot, from irritation to components of the sciatic nerve but commonly at the level of the sciatic nerve roots
angina pectoris, pain from myocardial ischaemia felt in the throat (Latin angina "infection of the throat"), arms, chest etc
shoulder tip pain from a subphrenic abscess

The clearest possible example of this is phantom limb pain, where pain is perceived to be arising from an amputated limb indicating that the pain is arising from central mechanisms.


clades on a tree - biopython Suppose we have an alignment. When a phylogeny tool (PhyML in this case) is used on this alignment, a tree consisting of 5 clades is returned.

The thing is: suppose we have this alignment on a web site, and some user uploads a new sequence to add to this alignment. After realign with the new sequence, phylogeny inference is applied, and then, a tree visualizer.

I'd like to know which one of the 5 clades contains the new sequence (if any), without the need of looking at the tree.

How should I approach this issue? I think that first of all, I should define my clades (how to?), and then, measure distances from my new sequence, to all clades, and keep the one with the shortest distance...But I'm not sure if this is a good strategy (not to say I'm not sure how to accomplish this..)

This is maybe more of a concept question...

I'm working with biopython.

You could decide to just insert the new clade next to some "closest" one ("closest" being defined in a clever way that remains to be devised), but it is possible that the result will be different from what you would obtain by reconstructing the phylogeny from scratch. The reason is that the information that the character combination in the new clade brings may alter the relationships between the other groups present in the data in a newly optimized phylogeny.

An example of application is that one typically wants to add more taxa in a phylogeny in oder to prevent long branch attraction.

As an aside remark: When one speaks of a "clade", one usually thinks of a bunch of terminal taxa (leafs of the tree): do you want to insert an whole bunch of taxa forming a monophyletic group, whose internal topology is already known, or just one terminal taxon?


Large scale reverse transcription? I need to make RNA:DNA duplexes. I can make 100 to 200 ug of mRNA through in vitro transcription, and I know how to use reverse transcription to make a cDNA library, but I have questions with this.

The mRNA I make with IVT is all poly A RNA, and the reverse transcription kit I have says to use 5ug of total RNA or 500ng of poly A RNA. I need to make at least 10ug of RNA:DNA, which is 20 times the suggested limit for poly A RNA, so a direct scale up probably isn't practical.

I can't find a literature precedent for making such large amounts of DNA through reverse transcription, everything I have found that uses RNA:DNA duplexes used short strands that were chemically synthesized and combined, my mRNA is 1800 bases long, so I can't just order an oligo, I have to make it.

EDIT : I can't comment on my own question.

The duplexes will be about 1800 bases long, it's for firefly luciferase.

Trying to make the DNA for the duplex from the original DNA template presents other issues. While it would be easy to cut it out from the plasmid, it would be double stranded, and I would have to mix with the RNA and heat it up to dissociate everything and hope that the RNA bound before the DNA strands reassociated. I also think it would complicate my controls, because it would be harder to say that any expression I see after delivering these duplexes came from the RNA and not the DNA. Of course synthesizing the DNA from the RNA could also introduce that problem.

Some crude calculations suggests that the dNTPs are the limiting reagent for a transcript this size, and that even with 5ug of mRNA I should have enough oligo dT primer for the reaction. I right now I am running reactions from 0.5 to 5ug of mRNA, 1uL of primer, and 4uL of dNTPs, to make sure I have enough. Hopefully the gel will turn out ok.

EDIT: I got the results. So far it looks like 3.0ug of mRNA works the best. It has the darkest band, and looks like the right length. Less mRNA gives fainter bands that appear too short, and more mRNA gives slightly fainter bands that appear slightly too short. Also, I ran the reaction for 2 hours instead of 1.

The best way for scaling up these kinds of reactions is to set up many reactions. Prepare a mastermix for lets say 20 reactions. You can pool them together, precipitate the RNA and dissolve to appropriate concentration in nuclease free water. Also, use gene specific primer instead of oligo-dT and don't add poly-A tails (poly-A does not affect the in-vitro stability of RNA).

As Mad Scientist already indicated, you would not need to make DNA again from RNA. Simply take 1:2 molar ratio of your IVT template dsDNA (restriction digested) and the RNA (post IVT). Heat and anneal slowly. DNA-RNA hybrids are stronger then DNA-DNA hybrids and the former is more likely to form after annealing. You can digest the unpaired strands using enzymes like mung bean nuclease.


Does carbon dioxide from carbonated drinks enter the bloodstream? When drinking soda or any other carbonated beverage, does some of the CO₂ find itself in the bloodstream? And if so, how long does it take until the carbon dioxide levels in the blood return to normal?

Is there enough CO2 to matter?

A can of soda contains about 2.2 grams of carbon dioxide (see this question from Chemistry.SE).

A human outputs about 1 kg of CO2 daily from respiration, though the rate can be much higher during physical activity. So, even if all of the CO2 content of a can of soda was absorbed into your blood, that's only 0.2% of your ~resting daily CO2 output.

A normal range for [partial pressure of CO in blood] is about 38-42 mmHg.

Gas exchange

The surface area of the lungs is something like 50-75 m2.

The surface area of the stomach is much smaller, closer to 1 m2.

Therefore, gas exchange is going to be much more efficient in the lungs than at the stomach.

Result

Any CO2 is going to be fairly efficiently cleared from expiration if it gets into the blood from the stomach. It's unlikely that you could detect any appreciable change in CO2 levels beyond what happens naturally as blood travels through the circulation and picks up CO2 from the periphery, and it's even less likely this difference would be greater than the difference between rest and exercise. That isn't even accounting for the buffering capability of the blood and diffusion into other tissues (both would smooth out any rise of CO2 over time) as well as not all of the CO2 will even make it to the stomach, and the gases that make it there can also leave via the esophagus.

As a sidenote, the Mythbusters partly addressed this issue in their episode on Mentos+coke. One of the factors they discussed is that much of the CO2 doesn't even make it to the stomach because it is released in the process of drinking, though they didn't quantify it. Therefore, CO2 is likely to have even less of an effect than described above.


What determines the size and shape of a cell? What determines the size and shape of a cell? They differ at different tissues / organs/ species

This is quite a hard to answer question.
There are different cell cycle molecules that, if mutated or knocked out, have shown to cause the cell to have a different shape or "overgrow" in size or not grow at all...

You might find some insight here.

There are lots of factors that influence cell size and shape, thus it is a very complex system to study. For example, cell shape is influenced by the cytoskeleton but also other factors.


Vaccines against bacterial endotoxins Today in class, there was a discussion going on about what part of pathogens(which can act as an antigen) can be used to make vaccines.
There was this point where our teacher said that bacterial exotoxins can be used for making vaccines.

My questions are-

Can bacterial endotoxins be used in making of vaccines?
If not,  then why is it so? What are the problems we face ?

There are several papers that use alkaline hydrolysis to delipidate or "detoxify" the endotoxin for use as a vaccine (1, 2, 3). The point of many of these papers is to develop a detoxified LPS (dLPS) vaccine to protect against sepsis in the pathogenesis and treatment of gram-negative infections. The detoxification is important, as the lipid-A portion of the LPS contributes significantly to sepsis. In this case you would be targeting the O-antigen or core oligosaccharide.

So one of the problems that I can see is that there are many bacterial serotypes, comprised of many different O- and core groups. I'm not aware of any vaccines with that sort of breadth. Issue two is you get an infection and you need to administer these vaccines quite fast, if not prophylactically, as adaptive immunity takes a number of days to come to speed.

It's also not clear to me whether a prophylactic vaccine to E. coli is useful to the populace at large, epidemiologically (just as an example).

The field also seems to lack clinical data on tolerability and efficacy, which is what I'd be more interested in, e.g. is it safe for humans and does it work?


How is ligand binding modeled? I have the following exercise to solve:

To be honest, for both parts, my only idea so far would be to divide the rate expression by the sphere area and multiply by the new available areas (that of a circle for part a and that of many circles for part b). But if I do this, I will have an "a" parameter always, which makes no sense because it is representative only of the sphere.
Any ideas on how to approach this?
All help is greatly appreciated.

don't use the perfect square model. You will keep getting Pi but it's not a real life formulae only used for theory. Try to use a Cartesian graph but three dimensions to take into account curve flexibility. Integral calculus is similar too or better.


How does human body deal with inert solid material in the bloodstream? How does human body deal with inert solid material in the bloodstream? For example, if there is a powder of glass injected into our bloodstream, will the white blood cells do anything or will kidney excrete these materials? Thanks.

Non-opsonized particles (Particles that can't be coated with opsonins like antibodies or complement proteins) can be engulfed by macrophages which could end up, for example, in the lung secretions and be coughed up one day. Note that a cell can only engulf a particle so large, so you'll not feel yourself coughing up anything out of the ordinary. Only tiny particles can be dealt with like this. Bigger particles can become trapped in fine vasculature (small veins; venules, and small arteries;arterioles). This can lead to abscess formation necessitating amputation of the affected limb.


How can I tell if a protein has been denatured? So i recently done an experiment using egg albumin, and we had 5 test tubes. the goal was to see if they have been denatured.
1- heat
2-acid (HNO3)
3-base (NaOH)
4- Alchol (ethanol)
5- heavy metal ions (AgNO3)

So some of the test tubes became cloudy/milky and some clear. Is it the clear ones that has been denatured? I don't know how to tell.

Thanks in advance :)

In my experience, when protein denatures, it typically aggregates and precipitates from solution. I would expect a denatured protein to create a cloudy solution, or actual precipitates in the form of little globs or fine wisps. A solution where protein is correctly formed and solubilized in the solution should be clear.