Blood cells penetration Is there a type of blood cell that can reach all other body cells? By "reach", I mean to "touch" the surface of the target cell.

If we look at the red blood cell for example, that moves in blood vessels, there are cells close by - after the wall of blood vessel - that get oxygen by diffusion and not by direct contact, as far as I know.

No, there is not. Cells in the bloodstream reach most areas in the body, but there are certain privileged areas which stop cells, drugs and macromolecules from leaving the bloodstream and entering the tissue. These privileged areas are thought to exist in sensitive or important areas for their own protection:

  Immune privilege is thought to be an evolutionary adaptation to protect vital structures from the potentially damaging effects of an inflammatory immune response. (Wikipedia)

The most common example of such an area is the blood-brain barrier, but there other barriers to privileged areas, including the blood–testis barrier, the blood-retinal barrier and the blood-ocular barrier. Cells do not pass from the blood through these barriers, except in disease (Larochelle et al. 2011).

Related reading:

The first chapter of Blood Groups and Red Cell Antigens has a decent high-level overview of different types of blood cells and their roles in the bloodstream and the immune system.

How do immune cells overcome the blood–brain barrier in multiple sclerosis? Larochelle et al. 2011


What is the difference between myopia and hyperopia? In myopia the lens is bending the light too much even in the most relaxed state. Thus the image is produced in front of the retina. If the object comes closer  the lens just adjusts a bit less than a healthy eye and the myopic subject is able to see clearly.

Why is the hyperopic eye not able to do that? If the object is far away, could the lens not just bend a bit more to elicit normal vision? So, why is the Myopic eye able to adjust its focus, but the Hyperopic not?

Short answer
Myopic eyes can still focus on nearby images as the lens needs to relax a bit more than in a normally-sighted person. However, objects far away cannot be focused, because in a complete relaxed state (for distant objects), the lens focuses the image in front of the retina. Hyperopic eyes cannot focus on nearby objects as, at a certain close distance, the lens reaches maximum accomodation (maximum roundness) and objects cannot be focused any longer.

Background
Myopia or near-sightedness is a condition of the eye where the light that comes in does not directly focus on the retina but in front of it, causing the image that one sees when looking at a distant object to be out of focus, but in focus when looking at a close object. Often the eye ball is too long, or the cornea has too much curvature (Web MD).

Hyperopia ("over-measured sight") or farsightedness, is a defect of vision caused typically by the eyeball being too short, or a lens that cannot accomodate/become round enough. It causes difficulty focusing on near objects (wikipedia).

Source:Monroe Publishing


Background correction when reading ELISA with TMB substrate I'm doing some ELISA development, and I'd like some justification/best practices for background correction. I'm using a horseradish-peroxidase (HRP) detection system along with a TMB substrate and an acid-based stop solution, which is quite common. When TMB is cleaved by HRP, it produces a blue (maximum absorbance (Amax) of 650 nm) product. The addition of the acid not only stops the reaction for endpoint detection, but it amplifies the signal two- to three-fold, and turns the solution yellow, so that it should be read at its Amax of 450 nm. The acid itself supposedly has an Amax of 540 nm, which is why you should use that wavelength for background correction, subtracting it from the A450. Other sources claim the A540 reading is supposed to correct for "optical imperfections" in the plate.

Using either of these explanations, one would assume that the A540 would be relatively uniform across the plate, independent of the A450 of the same well. However, in my experience, that is not the case at all. My blanks and negative controls are averaging about 0.041 absorbance units (AU) at 540 nm, with an average A450 of about 0.065. However, an A450 of 0.9 gives an A540 of 0.051, 1.4 gives 0.6, 2.0 gives 0.73, and 3.5 gives about 0.14. The absorbance spectrum (Fig. 2) of the substrate appears to be quite minimal at 540 nm, so why am I seeing this dose-dependent increase as the A450 increases?

More practically, how should I do background correction? Currently, I'm subtracting each individual well's A540 from its A450. Should I continue this practice, or should I determine an average plate background at 540 nm using my blanks and negative controls, and subtract that value from each individual A450?

Using different wavelength for reference give some advantages. You can measure a baseline of each well. All well might not have the same baseline because each well might not be the exactly same as others. In addition, you could make scratches on it, you might touch the bottom, or you get some dirt from your bench. And this can be corrected by A540 in your case. So, variations at a lower range are not much concerned. Sometimes, even if you choose a wavelength where the absorbance seems not to change after reaction, there might be a small change. This is not concerned ether, because both absorbances are concentration dependent unless states in solution do not change (froming complexes or something like that).

But still, you get high background from samples showing 1.4 or more at A450. I do not have experiences for this substrate, but you might want to think several possibility:
1)You might get bubbles on the top of your solution in the wells,
2)You might not get accurate values because OD is too high,
3)The solution might get precipitates
4)This may be a very less possibility, but some secondary reaction occurs.

For 2), 3), and 4). You might want to check linearity by drawing a standard curve, and avoid to use the range deviating from the liner relation.

PS
I should've mention that you would check the specification of your plate reader. OD=3 could be way to high to measure it. Because light intensity decreases to one thousandth though 1 cm light path at OD=3. It is very hard to measure such weak lights exactly. Probably many specifications of plate readers say you could measure ODs up to around 2, but some people think it is ideal to measure ODs up to around 1.


What is the known maximum ranging distance of a bat's sonar? Bats are known to navigate by using echo-location.

How far away can a bat detect an object by its sonar?

This paper finds some species can detect as far as 67 meters, but the range varies between species.

Note that the bats can actively change their range of detection and trade off range for resolution (low range with high speed resolution for hunting in closed, cluttered spaces or high range with low speed resolution for hunting in open spaces), as explained in Wikipedia's article on Animal echolocation.

Cool stuff.


When did animals begin to "parent"? After having a fun conversation with a friend regarding parenting, I actually had the general question arise in my mind of when did parenting actually start to take place?

But, first, I think we need to define what I mean by "parenting".  Specifically, what I am talking about is when animals decided to give birth to their young and not abandon them to immediately fend for themselves.  Instead, parenting is taking care of, and protecting children for a period of time (even a brief one) until they are grown enough to take care of themselves.

Also, I think it's worth not counting the actions of a mother or father hovering over eggs of unhatched offspring until they hatch.  True, this is a form of parental watching but I'm more interested in the general timeframe of when parents started watching over the general actions and "shenanigans" of their offspring in order to protect them from harm and to give them a better chance of survival.

Parental care

What you call "parenting" is called "parental care" and "parental care" is any investment of the parent to improve the fitness of their offspring. Parental care can take many forms from niche building for the offspring to parental feeding passing by placing plenty of ressources in the egg.

Issue with the definition of parental care

Given the vastness and eventual lack of a strict enough definition of the concept of parental care, it will likely be difficult to really know what you would consider as being parental care. Below I am suggesting two possible cases. If you were expecting to another answer, you will need to provide a nice and strict definition of parental care.

Mutation rate

Under a very broad definition of parental care, one could argue that first examples of parental care would be found in very early organisms (bacteria/archae, eventually viruses) that would at some point (for a given lineage) reduce its mutation rate to ensure transmitting a good genome to its offspring cells.

Nutrients in eggs

If you feel unhappy with me using such a broad definition, you might want to consider the first examples of parental care as being the existence of anisogamy (see here), where females (by definition) produce large eggs filled with nutrients, proteins, mRNA and other things. I doubt we know what lineage first evolved but it could be an ascomycota eventually.


DNA base pair heading Does it make ANY difference to which strand of DNA double helix base pair heads? I mean, could base pair AT and base pair TA makes any difference when interpreted by biochemical mechanisms which use DNA?

Double helix has two strands, right? So does pair Adenine on the first and Thymine on the second strand make any difference with Adenine on the second and Thymine on the first?

I am a novice in biochemistry, so please excuse me my ignorance if the question is ridiculous.

Absolutely yes, is the short answer.

All genes are encoded in a  5-prime $\rightarrow$ 3-prime manner on each of the 2 DNA strands of the double helix.

Here's an example of a stretch of the genome from a bacteria that I work on in my PhD:

Each of the blue boxes is a separate gene. You can see they're able to be encoded on both strands, and run in opposite directions.

Consequently, whether a base pair is AT or TA changes the overall sequence, and would affect any gene which happens to span that base pair.

When reading the DNA during transcription, the strand that the gene resides on is called the Template (sometimes "Sense") strand.

The strand is separated by RNA polymerase enzymes, and it then uses the opposite strand of the DNA, known as the "anti-sense" strand, to create a copy of the gene sequence, but in RNA instead of DNA (and Thmidine bases are substituted for Uracil, as in the diagram).

Thus, the polymerase creates a mirror image of a mirror image, restoring the sequence of the original strand, but in it's RNA representation.

Flipping the bases round in the helix would change the sequence in the DNA molecule, and this would be propagated by the enzymes etc. which rely on it for transcription and replication.


How do retroviruses exit the cell Do they just pass through the membrane? Is there some specific transporter or mechanism? Does it vary?

I've seen pictures if retroviruses outside the cell but no details

Retroviruses, like many other enveloped viruses, exit the cell by a process called budding. The virus uses the host machinery for producing transmembrane proteins to enrich areas of the host cell membrane in viral transmembrane proteins, and co-opts a host process for releasing vesicles.  You can see budding illustrated in the context of the life cycle of HIV in this figure from Murray Medical Microbiology.

The process has been studied in some detail in HIV and other retroviruses.


Is there a timeline for the frequency of evolution of any species? Evolution is traditionally spoken of as an inherited change over generations.

Does evolution happen one change at a time - or are there multiple changes occurring between two successive generations? Is there a known timeline for the frequency of such changes in any species?

Something like ...

20 Million years ago - Species X showed A, B, C.. Z characteristics

19 Million years ago - Species X following characteristics changed A'

17 Million years ago - Species X following characteristics changed B', C', Q', M'

16 Million years ago - Species X following characteristics changed A''

There can be multiple changes at the DNA level generation after generation, however most of these changes are insignificant (doesn't contribute for any specific character). But rarely, there can be a significant trait/change gained by an individual because of such changes in DNA level. Unfortunately such changes gets 'lost', unless it is fixed in the population (i.e., the gained individual should be successful in breeding and passing the trait/change to large number of progenies. Those progenies should further continue to pass on the trait till about every one (or most of them) in the population has those trait/change). Only such changes contribute for the species development (continuous accumulation of such changes, over time will result in the novel population that is very different from the original population).

Most of the timelines that we know are reconstructed from the DNA/protein sequences. Usually, DNA or protein sequences from the closely related species will be compared and looking at the differences they have, using suitable models, ancestral state of those sequences are determined. Once the sequence for the last common ancestor is known, mutational rate per unit time can be used to estimate the evolutionary time for those species.

A simple example would be the blue eye color in humans: it occurred about 10,000 years ago and it is still not fixed in the population.


Preservation of human tissue At my med school we have human samples (body parts, organs, etc.)

They are soaked in some sort of solution for long term storage. I'm quite sure that it's not formaldehyde as that would be really toxic and we're allowed to pick them up from the tubs.

What sort of solution could this be?

Embalming solutions for cadaver study differ from institution to institution (and are reportedly somewhat different from embalming for funerals, but I'm not sure of those details). Typically embalming solutions for cadavers meant to be stored indefinitely consist mostly of water with lesser but roughly equal amounts alcohol (usually methanol), gylcerin, phenol, and a smaller percentage of formalin/formaldehyde to prevent mold.

A document from Albert Einstein College of Medicine lists:

Methanol: 11.1%
Glycerin: 11.1%
Phenol: 9.3%
Formaldehyde: 1.9%

If you want to know what your institution uses, you should just ask, and they should be willing and able to tell you.


Can ants survive a plane ride? I just came back home a few hours ago from the airport and my aunt had peaches in her car full of ants. This made me wonder if the ants had joined us from the plane?

This leads to the question can ants can survive at high altitude?

It depends on the altitude of the plane, species of ant, flight length, location in hold, and more, but generally yes, they should be able to survive. At such locations that a plane flies at, the temperatures range from 0 to -50 degrees Centigrade. At such extreme temperatures the ant's entire body system is brought to an almost complete stop, where their heart is barely beating, and nervous system barely functioning other than to tell the heart to beat, and other normal involuntary actions. This means they won't need to consume as much oxygen (because their slowed brain won't need as much) allowing them to survive with the minimal oxygen in the atmosphere.


Pitch perception - why is the missing fundamental not directly detected in the cochlea? I'm learning about pitch perception, and learned about the case of the missing fundamental.

In the main image in that wikipedia page, it seems like the bottom graph, with the fundamental frequency and its second harmonic removed, that the wave is still very periodic at 100 Hz. Since the Organ of Corti has some area which should be excited when there's a sound wave of frequency 100 Hz, why does this sound wave, which seems periodic at 100 Hz, not directly excite that region of the organ?

Can someone explain the workings of the inner ear and detail on why the missing fundamental does not activate the cochlea? Reversely, how can 100 Hz be heard when the cochlea is not even activated at that frequency?

The basilar membrane in the inner ear (cochlea) is a place-dependent Fourier transformer (Fig. 1). This means that there is an orderly tonotopic map projected on the basilar membrane (BM). Traveling waves imposed on the BM via the ossicle chain and the oval window start of at the base and travel all the way to the apex. Along the way the resonance frequency of the BM gradually decreases, as the BM gets wider and more flexible (like piano strings).

Now, if a certain frequency is missing, the BM is not moving at that frequency location, and hence the hair cells do not become activated, and the neurons with that specific characteristic are not activated either. How on earth can you still hear that frequency?

It is the harmonic structure that determines our perception of pitch, rather than the lowest harmonic alone. Our brains are sensitive to the frequency difference from one harmonic to the next and base the "real" pitch of the tone on that difference. This is referred to as the "difference tone". When you hear two pure tones, the ear and brain subtract one frequency from the other, and you "hear" a tone with a frequency of this difference (source: National Taiwan University).

Fig. 1. Frequency tuning in the cochlea. source: New York University


How can we tell which direction sound is coming from? Pretty self descriptive, without being able to view the source of the noise how can we tell the difference between a sound in front of us and a sound behind us if pitch, volume and distance are all the same.

Also assume that it is not biased to one side more than the other, e.g its not to your left or right but directly in front or behind.

I'm interested in knowing if it is a part of the ear that makes this distinction, or a function of the brain.

The head-related transfer function. Sound coming from front, and from back differ because of the human body's asymmetry in the vertical direction where the biaural cues such as inter-aural timing and intensity differences are identical. The shape of the ear, and body is necessary for this perception, but eventually, the signal must be analyzed by the brain for localization.


How do archaea relate to eukaryotes and bacteria? I've read that they all share some genes, internal structure, and behaviour with each other, but with different degrees of overlap depending of what the function is. E.g., archaea have some eukaryotic and some bacterial function, and eukaryotes have bacterial function in the form of mitochondria and plastids.

However I'm finding the nitty-gritty of all this rather confusing. Could anyone please explain some of the detail for me as I can't seem to make any sense of this from reading Wikipedia, etc.

The relationship between the three is so overly complicated because of horizontal gene transfer, i.e. cells sharing parts of their genome with others instead of the normal passing-down to the next generation. This works between eukaryotes, archaea and bacteria and causes the mixing of the three.

An overview (originally proposed by Woese et al):

Bacteria are simplest considering cellular organisation. They have no nucleus or other internal membranes and no cytoskeleton. Their DNA is generally "junk-free"* (i.e. no introns), not bound by histones ("organising" proteins) and the organisation of regulatory sequences is relatively straightforward, typically with one 'operator' sequence before a gene.
Eukaryotes are complex cells in comparison. They have a nucleus and are full of internal membranes (ER, golgi, vesicles,...). Their complex cytoskeleton allows them to grow very large in comparison. Their DNA is usually full of more or less "junk"*, organised into tight bundles by histones and they tend to have a ridiculous amount of regulatory sequences way before, just at the start and even inside genes. Very importantly, they possess endosymbionts as you mentioned - mitochondria or plasmids, derived probably from some protobacterium.
Archaea at first appear to be a mixture between the two. A nice way to sum it up (though not very accurate) is "eukaryote in a bacterium's clothing". Their cells look a lot like prokaryotes because they are similar size, have no nucleus, endomembranes or cytoskeleton. However, some archaeas' DNA is bound by histones and they use similar machinery as eukaryotes for DNA replication, transcription and translation.

One possible explanation for this (theory by Margulis & Schwartz as explained by my tutor) is: From the last universal common ancestor, first prokaryotes and archaea diverged. After this branching, the differences in genetic machinery evolved. Archaea then branched, producing a protoeukaryote line which went on to endosymbiosis with some protobacteria. That would explain the similarities I outlined above: similar cell structure between archaea and prokaryotes but similar genetic machinery between archaea and eukaryotes.

It gets a bit more complicated though, because archaea and bacteria can exchange genetic material, and eukaryotes incorporated a lot of their endosymbionts' DNA in their own genome, so you end up with all of them having a huge mix of genes from the others.

Edit: Genetic machinery refers to the enzymes used for DNA replication and transcription (DNA and RNA polymerase and the transcription initiation factors) and translation (ribosomes and several other translation factors involved). For example: Prokaryotes only have one type of RNA polymerase which uses sigma factor to bind the initiaion site. Eukaryotes and archaea both have three types of RNA polymerase which use TATA-binding protein for initiation. Or: In Prokaryotes, the translation start codon codes for formyl-methionine while in eukaryotes and archaea it codes for "normal" methionine. (Source)

*) Unrelated to your question, but in my own defence: I am aware that the usage of the word "junk" is somewhat unaccepted nowadays, because it supposes that there is "useful" and "unuseful" genetic material. Also, some of what was thought to be junk has been identified to have regulatory function etc. However, it's also a fact that a lot has been identified to have no function to the cell whatsoever, most of it parasitic DNA which is dead or still happily replicating away (LINEs and SINEs). That is, "junk" to the cell.


Is there a difference between drinking water straight from the tap compared to leaving it to sit? An idle question - if a glass if filled from the tap and consumed immediately, it contains some dissolved oxygen from the physical process of moving through the pipes & tap. If left out (unrefridgerated) and then consumed later the bubbles are gone and there is presumably less dissolved gases.

I'm wondering whether this might have the effect of changing the relative levels of oxygen available to microbiota in the gut, and hence have some effect on the human host?

If you are speaking especially of the stomach, it actually makes no difference because the extremely low pH of the stomach allows very few bacterial organisms to survive. Often, Helicobacter pylori can however be present. Whether dissolved oxygen makes a difference to it is, to my knowledge, unknown. However, pure water does not stay long inside the stomach and passes almost immediately through to the intestines in most cases, so I doubt it would make that big a difference.

Now, it seems you are actually referring to the intestines in your question. Well, in fact the bacteria that inhabit the gut are almost exclusively limited to the colon and to a limited extent to the distal part of the ileum (small intestine). The stomach and almost all the length of the small intestine are sterile. Water absorption takes place in the jejunum (proximal part of the small intestine), which is a sterile region proximal to the locations colonized by bacteria. In conclusion, the oxygen content of tap water will not influence the bacterial flora simply because it does not come into contact with those bacteria.

BTW, the major difference between tap water that you leave sitting and the one that just came out of the tap is the chlorine concentration (decreases with time). Of course this will favor microorganism development, since it is precisely one of the reasons why we put chlorine in the water in the first place...


4DGenome or another comprehensive database of chromatin interactions I'm searching for the most comprehensive source of chromatin interactions to support enhancer targets (data such like Hi-C, ChIA-PET, IM-PET, 5C, 4C, 3C, etc.) and my question according that could be split into two following parts:

On page http://epigenie.com/epigenetic-tools-and-databases/ I've found out links to two databases, but the reference to 4D Genome doesn't work. Does anybody know whether this database
http://4dgenome.int-med.uiowa.edu was moved somewhere else or maybe its only internally available for U Iowa community? (I'm asking about probably exclusive access, because on Tan's lab page http://www.healthcare.uiowa.edu/labs/tan/software.html only the 4DGenome has the trailing part of the link int-med.uiowa.edu (presumably this int-med strands for internal/general medicine or maybe in the sense of internal/intranet access), whereas all other services like IM-PET has its link starting with http://www.healthcare.uiowa.edu/labs/tan/.
Maybe you know even better database for chromatin interactions covering as much as possible cell lines/tissue types for GRCh38 assembly or any other whose coordinates could be easily converted, e.g. by liftOver? I need data only for human and mouse, but I would be grateful also for solely human data.

Thank you in advance for your answer.

This problem has been finally solved with help from prof. Kai Tan.
It occurred that his lab has been moved from University of Iowa to Children's Hopspital of Philadelphia, so has been this service.
Now, the working link is:
http://4dgenome.research.chop.edu


Making penicillin using animals - specifically, a goat In the scifi novel Lucifer's Hammer, one of the characters (a biologist, if I remember correctly) finds himself in a post-apocalyptic world and tries to make penicillin to save his own life. To do this, he repeatedly states that he needs "a goat" - for some reason which is never explained.

I know that penicillin (in its various forms) is a byproduct of some types of fungi (see Wikipedia), but I can't make sense of the statement "I need a goat to make it". Assuming you don't have a chemical lab at your disposal (think "post-apocalyptic world"), does this requirement make any sense to any of you (apart from "I need to eat the goat to stay alive long enough to find a deserted biochemical lab" :-) )?

If not, how would you go about finding or making penicillin in such an environment?

Here is a link to a survivalist blog with a protocol for making penicillin. (I'm not recommending this by the way.)

Is it possible that the reference to the goat in Lucifer's Hammer is for the extraction of insulin (from the pancreas)? Have a look at the Wikipedia entry for Eva Saxl - in Shanghai during WWII her husband kept her alive with insulin extracted from water buffalo pancreas.


Do single nucleotides spontaneously bind to ss DNA? Do single nucleotides spontaneously bind to ss DNA? AT. GC. I realize the rhibisome is usually needed for making a strand, but what about randomly hbonded base pairs? Does this occur?

I am no expert on the topic, but single stranded DNA is commonly found during DNA replication, when DNA helicase splits apart the DNA strands so that the DNA can be replicated. When this occurs, the two DNA strands naturally have a high affinity for each other, bearing complementary base pair sequences, and another molecule must be present in order to prevent the two DNA strands from re-binding. These are single-stranded binding proteins, and they bind to ssDNA to prevent re-binding from occurring. As this prevents the DNA from binding to the antiparallel strand, I would imagine it has a role in preventing single DNA nucleotides from binding to the DNA strand as well.


Why would a mother reject her offspring if it has been "interfered" with by humans? There was a recent incident at Yellowstone National Park in which tourists placed a bison calf in their vehicle, and that eventually led to the calf being euthanized.

The National Park Service issued a statement in which they said:

  In addition, interference by people can cause mothers to reject their offspring. In this case, park rangers tried repeatedly to reunite the newborn bison calf with the herd. These efforts failed.

Why would a mother reject her offspring if it has been "interfered" with by humans?

Several ungulates and other species such as seals and primates are known to initially use odour to discriminate their offspring. Most relevant work to study this has been done in sheep; sheep are ideal for studying attachment because there are ethical and logistic difficulties that limit laboratory and research use of most other species known to develop selective mother-young social relationships. In addition domestic sheep are common worldwide, easily bred and handled, and well-understood in terms of behavior and natural history, providing a solid base for more intricate study (more information here).

According to this paper ewes are attracted to amniotic fluid for a few hours after birth, which stimulates nuzzling, sniffling and licking behaviour; after a relatively short time she becomes familiar with the lamb's unique odour. Thereafter, lambs without this odour are almost always rejected. After some time the ewes learn to use visual and auditory cues to identify their lambs and smell becomes less important. The Wikipedia article on the subject gives some information about the neurobiology of the process.

From a selective advantage point of view, I would speculate that this would evolve to reduce the risk of being exploited by 'free-loader' genotypes that engage in behaviour similar to brood parasitism in birds (i.e. leaving their offspring to be cared for by other ewes).

This can work both ways; in addition to the risk of disrupting the smell of a lamb by excessive handling, shepherds have recognised for centuries that lambs which are rejected by their own ewe, or whose ewe has an inadequate milk supply, can be fostered by other ewes who have lost lambs using a technique historically called skin-grafting, where a dead lamb is skinned and the skin tied around the foster lamb. The odour is thus transferred to the foster lamb for long enough for the ewe to accept it and become familiar with its visual and auditory identifiers, after which the odour is no longer important. The paper I cited above above describes a study that found that cloth 'stockinettes' could be used in place of a skin to achieve the same outcome.

edit: Interestingly, the responses to this question at skeptics.SE suggest that the popular notion that odour-based attachment results in abandonment following human interference with birds is probably untrue.


What is the difference between Leloir and Non-Leloir glucosyl transferases? The following questions were on the slides for my biotech course and I haven't been able to find any information on what the answer is.

What is the difference between Leloir and Non-Leloir glucosyl transferases?

LeLoir glucosyltransferases use uridine-diphosphate (UDP) 'activated' sugars as substrate, for example UDP-glucose, where 'LeLoir' refers to the LeLoir pathway, the metabolic pathway that inter-converts glucose and galactose (or, more strictly, the inter-conversion of UDP-glucose and UDP-galactose)
Non-LeLoir glucosyltranserases use sucrose as substrate and do not require the sugar to be be conjugated to UDP (or to be 'activated' in any way), and as such are very useful in the biotechnology industry.
See
A new pathway for the synthesis of oligosaccharides by the use of non-Leloir glycosyltransferases)

LeLoir was an eminent Argentinian biochemist.
For the enzymes of the LeLoir pathway,
The Leloir pathway: a mechanistic imperative for three enzymes to change the stereochemical configuration of a single carbon in galactose
by Perry A Frey is IMO definitive (and the pdf is freely available).
(Glucose and galactose are epimers: they differ only by the configuratation at C4. A key enzyme of the LeLoir pathway is UDP-glucose 4-epimerase, which contains a tightly bound NAD(+) and epimerization proceeds by oxidation/reduction (strictly, hydride abstraction/addition) at C-4, where the tightly bound NAD(+) is transiently reduced during catalysis: ie, NAD acts a (transient) hydride 'repository'! To the best of my knowledge, no enzyme has ever been found that directly catalyses the epimerization of glucose to galactose (although there appears to be no thermodynamic reason why this is not possible): the sugar must be conjugated to UDP in order to be a substrate for UDP-glucose 4-epimerase)


Why is this the equation for the fitness of cooperators? This paper gives the equations as:

The fitness of cooperators and defectors is respectively given by fC = b(i − 1)/(N − 1) − c and fD = bi/(N − 1).

c - cost
b - benefit
i - number of cooperators
N - population size
For the equation fC, does this mean
(b(i − 1)/(N − 1)) − c, i.e.:
$$
\frac{b (i-1)}{N-1}-c
$$
or b(i − 1)/((N − 1) − c), i.e.:
$$
\frac{b (i-1)}{{N-1}-c}
$$
Guessing the former but I just want to check.
While we're at it, could someone explain why this is how fitness is modeled?

As Bryan Krause points out in the comments, looking at the units gives you the answer. The correct form of the equation is $f_{c}=\frac{b(i-1)}{N-1}-c$, where $f_{c}$ is the fitness of cooperators, $N$ is the total population size, $i$ cooperators, $b$ is the fitness benefit of cooperating and $c$ is the fitness cost of cooperating. It doesn't make sense to subtract $c$, which is a kind of relative cost in terms of offpsring production, from $N$, which is population size. It would be like subtracting the cost of a car from the speed of an aeroplane. It also makes sense from the viewpoint that we expect the the fitness of cooperators, $f_{c}$, to reduce as the cost of cooperating increases, but independently from the number of defectors in a population.
Also, in the paper, it gives the equation with square brackets:

then the fitness of cooperators and defectors, respectively,is given
by fC=[b(i−1)/(N−1)]−c


Why do we use cRNA instead of initial extracted RNA in the microarray technique? I am recapping for the exam in transcriptomics and stumbled into a question about microarray. So, our regular workflow is to

extract RNA from cells
generate cDNA from the initial RNA using reverse transcription
transcribe cRNA from cDNA
label cRNA with biotin
fragment biotin labeled cRNA
hybridize to a plate, scan and quantitate

So the question is - since we use RNA for the further quntification steps why should we perform reverse transcription+transcription to produce cRNA while we could just use the initial RNA?

Is the cRNA more stable than RNA? Or we already make labeled cRNA using labeled nucleotides?

After clarification via the comments of the OPs question:

1) The procedure you describe is not for standard RNA microarray experiments, it for olgionucleotide microarray. This type of chip is special because it has multiple probes for each gene to allow detection of special features (i.e. mutations, alternative splicing, ...).

2) The reason for the generation of cDNA with subsequent reverse transcription and biotinylation is not explicitly stated in the source of the OP, but there are some possible advantages:

Amplification of material: cDNA can easily be amplified, which would make it easier to analyse samples whit low RNA yield, genes with low expression levels or to analyse the same sample on multiple chips.
Sensivity: oligonucleotide arrays may use very short (10-25 bases) probes, for which fluorescence readout may not be sensitive enough. Biotinylation of a given RNA base (by the use of pre-biotinylated NTPs during reverse transcription) can give multiple 'marks' on each fragment, which can be read with out streptavidin coupled signals. Additionally this would allow the signal strength to change in respond to certain SNPs/mutations.


Rosetta - What score does RosettaDock use for I_sc? I want to get a score using Rosetta for how well a protein binds to a ligand. I understand RosettaDock has a score called I_sc which will give me a number to indicate that.

I found documentation in https://www.rosettacommons.org/demos/latest/tutorials/scoring/scoring about how Rosetta scores structures, but not sure what scoring function RosettaDock uses and whether it is the talaris2014 score.

So the question is what scoring function is used in RosettaDock for calculating I_sc.

Cheers

Unless you (a) ran some absolutely ancient version of Rosetta or (b) explicitly specified a different score function, your protocol should have used the current default ref2015. This will be the default until a few years when the next major update is released.
You can verify this by checking your log file, which should have a line like
core.scoring.ScoreFunctionFactory:  SCOREFUNCTION: ref2015


How are testosterone levels distributed among men and women? Wikipedia tells me that men have 7 to 8 time higher levels of testosterone than women, on average.

Since the hormone is linked with performance in certain athletic events, my hypothesis, which I presented to a disagreeing friend, is that female top athletes in certain fields will have levels above the average male.

I found Why do endocrine profiles in elite athletes differ between sports? (Clinical Diabetes and Endocrinology 2018) which in Figure 10 presented testosterone levels for men and women in a number of olympic athletes:

As you can see in the plot it seems that even in the cohort of olympians there is an overlap, even if small, between men and women. Am I misinterpreting these result? I noticed that the units (nmol/L) are different from those used on Wikipedia (ng/dL), is this somehow important?

So:

Are there information about the distribution of testosterone levels among the general population to help answer the question of the share of women exceeding the average male level?
Am I interpreting the above results correct, are there indeed female olympians with higher testosterone levels than male olympians?

(The mapping between numbers and sport)

  Power Lifting (18 M and 1 W)
  Basketball (27 M and 14 W)
  Football (Soccer; 37 M)
  Swimming (100 M and 91 W)
  Marathon (1 W)
  Canoeing (7 M and 1 W)
  Rowing (36 M and 25 W)
  Cross Country Skiing (8 m and 9 W)
  Alpine Skiing (11 M and 12 W)
  Weight Lifting (10 M and 7 W)
  Judo (26 M)
  Bandy (19 M)
  Ice Hockey (38 M)
  Handball (23 M and 29 W)
  Track and Field (95 M and 49 W)

To the first question we can look at a paper such as "Estimating age-specific trends in circulating testosterone and sex hormone-binding globulin in males and females across the lifespan" from Handelsman et al.  The figures they provide are:

The top image is of females, the bottom of males.  We can see throughout a lifetime that the top 2.5% of females and bottom 2.5% of males seem to have approximately the same amounts of testosterone.  If we went to the top and bottom 1% there would likely be consistent overlap between the male and female distributions.

I believe you are interpreting the figures correct, although it is important to keep in mind these figures do not include any information on age and are a single point measurement.  To facts that may limit the depth of inference you can make about testosterone levels among the sexes.


Why do doctors still advise HIV+ couples to wear a condom during sex? HIV infected people already have HIV, but why do doctors still advise condom use for HIV+ couples?

Doctors would recommend the use of barrier protection for couples where both partners are HIV+ because the virus can mutate. Mutated forms of the virus can become resistant to Highly Active Antiretroviral Therapy (HAART) treatments, rendering them ineffective.

The use of barrier protection reduces the risk that a resistant mutant strain of HIV is transferred into the population.

Also a child conceived by a couple that is HIV+ is at high risk of being born with the infection.

This link explains some of the risks and ways to attempt to prevent mother to child transmission of HIV.

Edit

In retrospect, I have been thinking about the answer I gave, and while I still think that what I said above is relevant, I feel that I left out an import aspect of why a medical doctor would recommend the use of barrier protection during sexual activity, even if both partners are HIV+.

One thing that we should remember is that a person with HIV, even when the virus is suppressed by HAART is immunocompromised to some extent and they will likely be more susceptible to secondary pathogens and cancers initiated by oncogenic viruses.

An HIV+ person will be more vulnerable to sexually transmitted diseases such as human papilloma virus, herpes, hepatitis, chlamydia, gonorrhea , or simply opportunistic pathogens such as C. albicans than they would have been had they not been HIV+. Cells that mediate innate immune response are affected by HIV as well as cells of the adaptive immune system, so any dysregulation of the immune system creates an opportunity that a pathogen would not normally have.

Not only will these diseases have an easier time infecting an immunocompromised patient, but these infections will also be more difficult to cure once they have taken hold, as the person's immune system will likely not be able to mount as robust a response as it would have if the person was not HIV+. So barrier protection provides a means to help protect a person from secondary infections as well as for the reasons given previously.

Use of barrier protection during sexual activity to prevent the transmission of sexually transmitted diseases is just as relevant for people who have HIV as for those whose HIV status is negative.


Are there any organisms, extant or extinct, that have only one neuron? Nervous systems are useful in one way because they allow for integration of complex information. They are also useful because they transmit information very rapidly, over a large distance.

However, that last function can be done without an actual nervous system; presumably, all you need is one cell. Some individual sensory neurons can transmit an impulse at 120 m/s, which in and of itself would be useful in many circumstances.

So, are there any species that have only one neuron? There may have been many one-neuron creatures in the early days of animal evolution, but it's also possible that nerve nets appeared together, as a unit. I also suppose there are some small multicellular organisms that have a single excitable cell, but it's up for debate whether we should call those "neurons" or not.

In evolution things don't just pop into existence. So, it's unlikely that a single neuron originated by itself. The question is, what would that neuron do? It would communicate to at least one other cell, right? Otherwise the transmitted signal would be lost and useless. And where is the signal coming from? Neurons generate signals either by receiving signals from other neurons or, for specialized sensory receptors, through some changes in the environment. The receiving cell could be a muscle cell, so your minimal network would consist of a sensory neuron and a muscle cell. Upon a detected change in the environment, the neuron would signal the muscle to contract.

In evolutionary basic organisms we can find action potential like excitability and synapse-like cell-cell contacts in non-neuronal cell types. This hints towards a step-wise development of these functions before actual neurons arose (wiki, paper). Even one-cell-organisms have neuron-like features (sensory input dependent polarization, intracellular signal propagation, coordinated movement). If cell-cell communication or excitability are not limited to neurons, what makes a neuron a neuron? This is also a matter of definition, as discussed in the paper mentioned above.

What makes neurons unique is their property to propagate signals in a network. That's why the neuronal nets of jellyfish are usually seen as the first appearance of neurons in the evolutionary tree. While organisms without a nervous system are able to respond to their environment by signal transmission between non-neuronal cells, I am not aware of any organism that possess only a single cell which we would now call a neuron. At the stage where neurons arose, animals were already a more complex arrangement of specialized cells for different functions. You would therefore assume, that also the neuronal predecessors were a group of cells within the organism.


What are the main differences between tubers and taproots? From reading accessible information about tubers and taproots I recognize that the main differences between tubers and taproots (as well as a fibrous root system) are:

Shape
Different nutrient synthesis: Tubers contain less complex sugars than taproots

A possible third difference

As one who prefer a vegan diet in general I read a lot about B12; in many places (for example) Wikipedia, something like this was written:

  In the past, humans got Vitamin B12 from eating the roots of "short plants" that absorbed
  the vitamin from bacteria which produced it near to their roots.

This led me to assume that either tubers or taproots (as well as a fibrous root system) have Vitamin B12 absorption by dedicated receptors and if one has it and the other doesn't here is yet another difference.
An interesting side note: Tubers are always under soil while roots in general, aren't necessarily; as with aerial roots.

My question

What are the main differences between tubers and taproots?

They are actually completely different plant parts: a taproot is the central root of a taproot-system plant while a tuber is an engorged modified underground stem called a rhizome.

A morphological and functional difference between rhizomes and roots are that rhizomes (being modified stems) have nodes, while roots never do.

Note: a node = the location on a plant stem where buds (leaves, flowers, stem branches) initiate

According to "Plant Identification Terminology: An Illustrated Glossary" (Harris & Harris, 2001)1:

  Taproot. The main root axis from which smaller root branches arise; a root system with a main root axis and smaller branches...Figure 1273

  Root. The portion of the plant axis lacking nodes and leaves and usually found below ground.

Compared to...

  Tuber. The thickened portion of a rhizome bearing nodes and buds; underground stem modified for food storage. Figure 1366

  Rhizome. A horizontal underground stem. Figure 1052

See here for a photo of a potato plant showing a young tuber and an older tuber growing on the end of a rhizome.

According to here:

  Tubers-are swollen regions of stems that store food for subsequent growth. The potato is an example. It is a stem because it has many nodes called eyes with spaces between eyes known as internodes. Potato tubers develop at the end of swollen underground stem structures, rhizomes.

  Eyes of potatoes are really axillary buds which contain several small buds at each site. These buds can expand to form shoots which grow on to make whole plants.

You can explore histologic, anatomic, and physiologic differences of stems vs roots more generally to understand broader differences between the two plant parts.

Examples:

Proença & Sajo (2008)2 discuss root and rhizome anatomy in select bromeliads.
Figure 1 from Hernán et al. (2014) shows how the vascular and various tissue layers can differ quite a bit between roots and rhizomes on the same plant.

Notes:

Some structures characteristics of roots (e.g., casparian strips) can also occur in rhizomes. (E.g., see Lersten 19974.
Unlike potatoes (which are tubers), sweet potatoes (Ipomoea batatas) are actually a modified root called tuberous roots

Works Cited:

1 Harris, J.G. and Harris, M.W., 1994. Plant identification terminology: an illustrated glossary (No. QK9 H37 2001). Utah: Spring Lake Publishing.

2 Proença, S.L. and Sajo, M.D.G., 2008. Rhizome and root anatomy of 14 species of Bromeliaceae. Rodriguésia, 59(1), pp.113-128.

3 Hernán, G., Varela, B.G., Fortunato, R.H. and Wagner, M.L., 2014. Pharmacobotany of two Valeriana species (Valerianaceae) of Argentinian Patagonia known as “Ñancolahuen”. Lat Am J Pharm, 33(6), pp.891-6.

4 Lersten, N.R., 1997. Occurrence of endodermis with a casparian strip in stem and leaf. The Botanical Review, 63(3), pp.265-272.


How do plant cell vacuoles form? Does the plant cell vacuole form by the invagination of the cell membrane?

Does the plant cell vacuole form by the invagination of the cell membrane?

Yes, in part, but the complete answer is way more complicated than that.

Endosomes (the vesicles formed by "invagination" of the cell membrane, as you said) are responsible for (part) of the biomembrane of the cell vacuole. However, some biomembrane comes from the Golgi-ER system, and almost all proteins come from ER (having passed by the Golgi apparatus).

Have a look at this image (Marty, 1999):

Its legend says:

  Seven basic pathways are used for the biogenesis, maintenance, and supplying of vacuoles. Pathway 1: entry and transport in the early secretory pathway (from ER to late Golgi compartments). Pathway 2: sorting of vacuolar proteins in the trans-Golgi network (TGN) to a pre/provacuolar compartment (PVC) via an early biosynthetic vacuolar pathway. Pathway 3: transport from PVC to vacuole via the late biosynthetic vacuolar pathway. Pathway 4: transport from early secretory steps (ER to Golgi complex; pathway 1) to the vacuole via an alternative route with possible material accretion from Golgi (indicated by the asterisk). Pathway 5: endocytotic pathway from the cell surface to the vacuole via endosomes. Pathway 6: cytoplasm to vacuole through autophagy by degradative or biosynthetic pathways. Pathway 7: transport of ions and solutes across the tonoplast. AV, autophagic vacuole; E, early endosome; ER, endoplasmic reticulum; PVC, pre/provacuolar compartment; TGN, trans-Golgi network.

According to the same paper (Marty, 1999):

  Experimental evidence suggests that material within the vacuolar system in plants derives confluently from both an intracellular biosynthetic pathway and a coordinated endocytotic pathway. (emphases mine)

Source: Marty, F. (1999). Plant Vacuoles. THE PLANT CELL ONLINE, 11(4), pp.587-600.


How to calculate the effective population size ($N_e$) with overlapping generations? From this Source: If generations are overlapping, then the effective population size $N_e$ does not equal the population size $N$.

I know mathematical formulations in order to find the effective population size $N_e$ when the sex-ratio is biased $\left(N_e = \frac{4N_mN_f}{N_m+N_f}\right)$ or when the population size varies cyclically through time $\left(N_e = \frac{n}{\sum_{i=1}^n\frac{1}{N_i}}\right)$.

What is the effective population size in a population with overlapping generations?

There are many different ways to do this, depending on what assumptions you make on e.g. stable age structure, distribution of offspring, haploidy/diploidy, population growth etc. As you probably know, there are also two main approaches to effective population sizes, namely ones based on:

the rate of inbreeding ($N_{e,i}$)
the increase in variance of allele frequencies ($N_{e,v}$), and they can sometimes differ a bit from each other.

An early attemp to calculate effective population size with overlapping generations comes from Felsenstein (1971), which is based on life table information. This paper includes several derivations, both on inbreeding $N_e$ and variance $N_e$. As an example, the formula of inbreeding $N_e$ for a diploid population is:

$N_e = \frac{N_1T}{1 + \sum_i^\inf l_i s_id_i v_{i+1}^2}$

Here, $T$ is the generation time, $l_i$ is the survival up to age i, $s_i$ is the survival from age i, $d_i$ is the probability of death at the end of age i (i.e. 1-$s_i$), and $v_{i+1}$ is the reproductive value of individuals in stage i+1. However, this is assuming a constant population size and a stable age distribution, so some rather restrictive assumptions. The paper also includes models for haploid populations, and I haven't gone through it carefully.

A couple of more recent papers that calculate $N_e$ for overlapping generations are Engen et al. (2005) and Engen et al. (2007). These papers use diffusion approximations to derive several formulas for $N_e$ under different assumptions, for age-structured density independent populations. One model for a haploid population in a fluctuating environment is:

$$\begin{align}
N_e & = \frac{N}{\sigma_d^2T} \text{, with} \\
\sigma_d^2 & \approx \sum_{i=0}^k \frac{\lambda^{-2}}{u_i} \left[\left(\frac{\delta\lambda}{\delta b_i}\right)^2\sigma_i^2 + \left(\frac{\delta\lambda}{\delta s_i}\right)^2 s_i(1-s_i) + 2\left(\frac{\delta\lambda}{\delta b_i}\right)\left(\frac{\delta\lambda}{\delta s_i}\right) c_i \right]
\end{align}$$

where $T$ is the generation time and $\sigma_d^2$ is the demographic variance. In the lower equation, $\lambda$ is the deterministic growth rate (dominant eigenvalue), $u_i$ is the proportion of the population in stage i (a component of the stable age distribution), $b_i$ is the expected number of offspring with variance $\sigma_i^2$, $s_i$ is the survival rate of stage i (with binomial variance), and $c_i$ is the covariance between reproduction and survival. You really need to dive into these papers to fully understand how these equations are derived and how the variables are defined (will take up far to much space here). However, at its core, it is using a diffusion approximation on an allele at a selectively neutral locus.

There are many other papers out there deriving effective population sizes, under different assumptions and restrictions, but the ones cited above should be a good starting point, and by looking at citations to and from these you should get a decent overview of the topic. Many textbooks also cover ways to calculate effective population sizes with overlapping generations, e.g. Hedrick (2011) and Felsenstein (2013, free pdf).


Which direction are wild beehives combs oriented? Is it on the North-South axis, the East-West axis or some other orientation?

I've usually observed wild Indian Bees (Apis cerana) orient their hives in an East-West direction. The entrances are usually oriented towards the Sun.

This is purely from my own observation (in South India) and not from any research.


What is the minimum population size that Hardy-Weinberg calculations can be applied to? I'm trying to find out if a particular allele is in Hardy-Weinberg disequilibrium, but the data is poor. What's the minimum population number that you can use to get any sort of respectable conclusion?

I've heard it's 5 individuals minimum for each genotype but can't find a source on that.

You can use power analysis to work out answers depending on the specifics of your data. The things you need to consider are:

The power of the test. This is the probability that the test will
fail to reject the null hypothesis even if in truth it is false
(Type II error). If the population is not in equilibrium, what is
the probability that the test will fail to detect this? This will largely depend on the costs of a Type II error. If the experiment is expensive in terms of time/money/animals used etc. you would want to make sure it will give a sold answer at the end.
The significance level. 0.05 is commonly used. The probability that
the null hypothesis is rejected even though it is true (Type I
error). If the population is in equilibrium, what is the probability
that the test will erroneously say it is in disequilibrium.
The degrees of freedom. The number of alleles.
The effect size. This is how far away from equilibrium you expect
your samples to be. The largest effect size would be extinction of
one allele. However, if two alleles are in a ratio of 100:101 across
the full population, this is a small effect size.

For the Pearson's Chi-squared test we can use (in R)

library(pwr)
pwr.chisq.test(w = 0.3, N = 40, df = 4, sig.level = 0.05 )

A rough guide for effect size (w) is 0.1, 0.3, and 0.5 for small, medium, and large effect sizes. There is more detail here. N is the total number of data points, df is the number of alleles. This function will give us a value for 1 minus the power of our test. A value of 0.9 means there is a 10% chance of failing to detect an effect that truly exists.

If we want to work out a suitable number of data points to collect we must decide what power we want. Say we decide that a 0.01 chance of doing the test, but failing to detect disequilibrium if it exists is acceptable.

pwr.chisq.test(w = 0.3, df = 4, sig.level = 0.05, power=0.99 )

tells us that 280 data points are needed.

Without estimates of effect size or a number of genotypes it is hard to give a straight answer to your question, but 5 per genotype seems very small.

If you have only two genotypes, you might choose to use the Fisher Exact Test in which case you can use power.fisher.test() in the statmod package. The definitions of effect size and degrees of freedom are slightly different but the idea is the same.


What are the stretch of amino acids? I found the words "stretch of amino acids" in a newspaper article.

"This lipopeptide matches the stretch of amino acids in the spike protein of SARS-CoV-2 exactly."

What is the "stretch of amino acids"? Is this different from "amino acid sequence"?
I looked for a definition of the word but could not find it.
From the usage, I guess it means something similar to "sequence", am I right?

Yes, stretch means sequence in this context.  See definition #5 for stretch (noun) on Wiktionary:

A segment or length of material.

So, the "stretch of amino acids" in the article refers to the peptide sequence portion of the lipopeptide prophylactic.


What is the effect of exendin on beta-cells? Do you know if exendin, an analog of GLP-1 (glucagon like peptide-1), can be toxic for beta-cells? For example, what is the effect on INS1 or Min6 cells at a certain concentration or after 90 mins of incubation. And what is the impact on insulin secretion?

I recently tested exendin on INS1e cells in an Edu incorporation assay (similar to BrdU incorporation) to observe if this compound induces proliferation of the cells.  Compound incubation was for 24 hours.  I saw no incorporation of EdU with this compound over untreated levels.  In addition, during the assay I look at overall cell number with a DNA stain, but I did not see any effect on total cell number with exendin (ie, if it were toxic the total cell number should go down which I have observed with other compounds).


Is the empty GI tract a hollow tube with air inside, or is it generally collapsed until food is eaten? I have heard that "air in the GI tract" results in flatulence and burping etc, however I initially assumed that the "empty" GI tract was a hollow tube filled with air anyway.

So on an empty stomach (or "empty" GI tract rather), does the GI tract collapse due to the pressure in the surrounding cavities, or is the GI tract normally a hollow tube filled with air, and flatulence merely a result of "excess" air?

Under normal circumstances the stomach and GI tract have very little "gas" in them - whether it be flatus, air, CO2, or anything else - and so are essentially collapsed with the walls against each other. However, gas is continually being produced by the microorganisms that inhabit our gut, and can also come from swallowing small amounts of air, fizzy drinks, etc., so the environment is never 100% gas-free. A typical person produces on the order of 500-1500 ml (0.5-1.5 liters) of gas per day.

If you're interested, the Wikipedia article on flatulence is a good introduction.


What portion of the electromagnetic spectrum do cats see? I have seen numerous articles and various information about how cats and dogs see into the ultraviolet spectrum with interesting artistic renderings such as this:

http://www.livescience.com/40459-what-do-cats-see.html

But I have been unable to find any specific parameters of what wavelength boundaries actually exist for cats.

We know that humans see from around 750 to 400 nm, but what would a cat's range be?

Short answer
Spectral sensitivity of cats indeed ventures into the UV, but not beyond ~320 nm. Their maximum is likely similar to ours, i.e., ~750 nm.

Background
The spectral sensitivity of blue cones (photoreceptors detecting low wavelengths) of many species, including humans and cats, extends into the UV range (Fig. 1).

Fig. 1. Human cone absorption spectra. Source: University of Kentucky

However, the various structures in the eye, most notably the lens, filter out UV in humans (Fig. 2). Indeed, surgical removal of the lens in humans results in enhanced sensitivity to UV light below 420 nm (Griswold & Stark, 1992).

Fig. 2. Human transmission spectra. Source: Columbia University

In the cat, however, the lens transmits a large portion of the UV light in the range of 320 - 400 nm, while primates transmit virtually no light of these wavelengths. Figure 3 shows the lens transmission spectra of various species. At 50% transmission the second (dotted) line from the left is the cat (50% transmission at ~340 nm), while a primate (squirrel monkey, species representative for humans and other primates) in this graph is line number 7 from the left with (50% transmission at ~410 nm). Hence, cat lenses absorb less light in the UV region, but transmission is virtually nil at 320 nm (Fig. 3). Given that their cones, just like humans, are sensitive to UV, we can reasonably expect that cats can see in the UV region including wavelengths of 320 nm and up. Cats also have the 560 nm (red) cones, like we do, so their maximum wavelength is expectedly similar to ours (~750 nm).

Fig. 3. Lens transmission spectra of various species. Source: Douglas & Jeffery, 2014

References
- Douglas & Jeffery, Proc R Soc B (2014); 281: 20132995
- Griswold & Stark, Vis Res (1992); 32(9): 1739-43


Why sperm count matter for pregnancy? In order for a woman to become pregnant, sperm is needed. Why is sperm count so important for pregnancy?

http://en.wikipedia.org/wiki/Sperm

It's more than just sperm count that matters for a pregnancy if you are considering normal methods of insemination such as intercourse or assisted methods such as artificial/intrauterine insemination or in vitro fertilization. For couples having trouble getting pregnant, most OB-GYNs and/or Reproductive Endocrinologists/Infertility physicians do a semen analysis. This involves checking several things:

Ejaculate Volume (>1.5mL)
Sperm Concentration (>15million/mL)
Motility (>40%)
Morphology (>4%)

(and a host of other factors including rapid progressive motility, pH, etc). Why? Because there is no point of there being high numbers of sperm, if their motility is poor, because they won't be able to reach the oocyte. There's no point if they can reach an oocyte, if they are poorly shaped and cannot penetrate it. There's also no point in there being a high concentration of sperm, if the ejaculate volume is so low that it thins out before reaching the cervix. All these factors matter.

Total Motile Sperm Count (TMSC) is the most common way that physicians determine what route is best to increase chances for getting their patients pregnant.

TMSC = Concentration x Ejaculate Volume x % Motile (in decimals). Thus if, the value is:

greater than 10 million = normal male factor; check anatomy, check female causes
less than 10 million = low male factor; consider intrauterine insemination (IUI)
less than 5 million = severe male factor; consider in vitro fertilization (IVF) with intracytoplasmic sperm injection (ICSI)

Sources:

Paper 1
Advanced Fertility


does the amount of blood circulate in a body is same before and after amputation? if a person loose his hand in an accident do the blood flows through his body is equal to the volume of blood before accident? how human body manage with that blood which is deserved by the missed body part? if human body have such a mechanism. does it effect other body parts? or is there any change in the proportion of blood flows through different arteries?

The kidney regulates the amount of blood being produced and removed from/recycled in the body. Even if somehow the body lost no blood when it lost the limb, the kidneys would remove the excess blood as it filters.

I think the misconception in asking this question is that the body knows how much blood to produce for the body. Yet, that isn’t the case, it just regulates the amount based on different signals it gets from the blood.

More info: https://www.ncbi.nlm.nih.gov/m/pubmed/17630596/


What would happen if one eats silica gel? What happens if one actually does go about eating the beads in those "do-not-eat" packets?

Usually, nothing happens if you eat silica gel. In fact, you eat it all the time. Silica is added to improve flow in powdered foods. It occurs naturally in water, where it may help confer resistance against developing senility. Silica is just another name for silicon dioxide, the main component of sand.
Mayby you think if silica is harmless to eat, why do the packets carry the warning? The answer is that some silica contains toxic additives. For example, silica gel beads may contain toxic and potentially carcinogenic cobalt(II) chloride, which is added as a moisture indicator. You can recognize silica containing cobalt chloride because it will be colored blue (dry) or pink (hydrated). Another common moisture indicator is methyl violet, which is orange (dry) or green (hydrated). Methyl violet is a mutagen and mitotic poison. While you can expect most silica you encounter will be non-toxic, ingestion of a colored product warrants a call to Poison Control.


Insertional inactivation using pBR322 I have questions regarding "selection using insertional inactivation".

In a typical DNA recombination experiment using plasmid pBR322 where a new gene in inserted in the place of tet gene, it is said that entities with the recombinant plasmid can be selected by growing all the bacteria in two different medium: one with tetracycline and one with ampicillin.

I know that pBR322 contains two genes that make it resistant to both tetracycline and ampicillin, and also that the newly created plasmid will only be resistant to ampicillin, since its tet gene is no longer functional.

So in the plate with tetracycline, only entities with the original plasmid will grow. In the plate with ampicillin, however, entities with the original plasmid and the modified plasmid will grow.

How can this be a selection when two different types of entities are growing in one plate?

Am I misunderstanding the meaning of "selection" in this case?

My explanation above seems very immature, so it would be great if someone can provide me with deeper understanding.

The ampicillin plate is selecting for bacteria transformed with the plasmid, either the original or recombinant, whereas the tetracycline plate is selecting only for bacteria transformed with the original plasmid. Since you are only interested in the recombinant plasmid, you need to do some form of replica plating and compare the two plates to infer which colonies contain the recombinant plasmid (those which grow on ampicillin but not on tetracycline).


identification of species of tree I just want to confirm the species of the tree in the middle of the picture. Is it the "Flame of the Forest"? This is taken in my school campus. Thanks in advance!

It looks like a Royal Poinciana tree with the scientific name Delonix regia..

Please refer to this link for more info


What limits the maximum spacing of Nodes of Ranvier and which organisms tend to have the widest gaps? Assuming that a longer distance between gaps in the myelin sheath is beneficial for an organism due to the increased propagation speed, what is the limiting factor in determining the maximum spacing between nodes?  I have previously encountered the analogy of the Nodes of Ranvier as forming a circuit between themselves and the previous node in order to pass on the action potential, which leads me into thinking that it is simply electrical resistance that is the cause however I assume the analogy is an over simplification and would be very interested in any alternatives.

Also, is there a significant variation in node separation between organisms?  Which organisms have the greatest gaps?

This is best answered via something called cable theory.  Basically, as the action potential (AP) propagates along the membrane of the axon, it's tripping voltage gated channels that "renew" the flux of ions into the stream at the nodes. There are no ion channels under the sheathing (or they are there anatomically and inactive, but I don't remember), so the current is able to zip through that area.  There's no renewal of AP, but there's no loss due to leak of ions either.  Since there's no influx of ions from outside of the membrane until the next node, the capacitance and resistance of the membrane is exponentially decaying the voltage.  So, if the distance between the nodes was too long, the voltage would just die off and the AP wouldn't propagate.

I don't have any anatomical data about individual species, but know that only the smaller diameter axons require sheathing to compensate for the slower ion flow due to higher resistance (e.g., the squid giant axon(not to be confused with the "giant squid" axon) has no myelination due to its large diameter).


For the human head, which direction is anterior, and which direction is ventral? I read the wikipedia entry and I am sort of confused.

In dog, the nose is toward the front. That's anterior. So I conclude that human nose is anterior.

In dog, the head is on the back. So that's dorsal. So I concluded that humans' top head is dorsal.

Yet that's not how things seem to work on anatomy.

We call humans' top head anterior. We also call human nose direction as ventral.

How could that be?

The whole system of anterior, dorsal, ventral, posterior is there so we can see humans like we see dogs (at least anatomically).

Yet it changes again.

So which one is right?

Let me put it this way

Dog's chin is ventral from the eye
In humans, is humans' chin ventral from the eye too? or posterior?

What about the nose? Dog's nose is it's anterior most organ.

In humans, is the nose anterior too?

I mean, if we're going to have different terms for humans and dogs, might as well use words like up, down, front, back right?

Humans are are upright in their anatomical position - fig. 1 - from which all directions and terminology stems.

Figure 1: Anatomical Position

Because of this, anterior is normally the same direction as ventral and posterior normally the same as dorsal - fig. 2.

Figure 2: Normal directions in humans

Cranial anatomy is a special case, however, as the entire axis of the body bends round during embryonic development as seen in fig. 3.

Figure 3: Bending of the developmental axis

This leads to the cranium being a little odd, where dorsal is equivalent to superior and ventral to anterior in this area of the body only

Figure 4: Resultant difference in neuroanatomy conventions

However, for convenience, anterior and posterior retain their original directions even in this area.  Therefore you could eliminate a large amount of your difficulties by just using these terms instead for most of the body.

To answer your specific questions:

  So I conclude that human nose is anterior

Yes

  So I concluded that humans' top head is dorsal. Yet ...We call humans' top head anterior

The top of the head is technically dorsal, however in practice would never really be referred to as such, instead being superior.

  In humans, is humans' chin ventral from the eye too? or posterior?

The human chin is both inferior to the eye (looking straight at the face in the coronal plane) and anterior to the eye (but only marginally).  It's more obvious if we look at the tip of the nose instead, which again is both inferior and anterior to the eye.

  In humans, is the nose anterior too?

Yes, the nose is anterior.


3 flaws of genes from the perspective of a programmer Having a double helix structure seems like a waste of space. In programming you would have a single array and just before mitosis you would double the single helix.
Having an exact copy of a cromatid. As long as a cromatit exists, there is always a possibility of errors, for example if something attacks the chromosome. So why isn't the cromatid just before mitosis, just like in 1? Then you are 100% certain, you have an exact copy. Again, a waste of space, but additionally vulnerability now.
Having 2 nucleobase (adenine, thymine, guanine, cytosine) seems like it makes more room for errors. Why aren't there just two of them? They are complementary anyways, so adenine for example can only be on the opposite side of thymine. Is it so that splitting is easier? In programming, if you only have to deal with a boolean value, you would always take it over having to deal with 4 values.

So, what does nature do different than a computer and why does it behave so differently?

Your individual questions here are reasonable enough - although you could do a bit better at knowing some more details of the systems you are dismissing as 'flawed'. However, I think the bigger problem is your overall approach, which seems to be to make analogies between human-made computers and biological systems and then critiquing the 'missing' parts from biological systems.

Analogies like this are necessarily limited. Take the idea of DNA as 'like' a hard-drive of a computer. The nucleotides = bits, genes = contiguous segments of memory, promoters = pointers, etc. Where does this model go wrong?

Well, hard-drives are not (currently!) self-assembling structures that read themselves by coding for more, smaller fragments of hardware that additionally compress or expand parts of the structure of the hard-drive according to which part needs to be read. Moreover they don't do this while floating in liquid and self-repairing from chemical and radiation damage.

There is an excellent book called "Cats' Paws and Catapults: Mechanical Worlds of Nature and People" by Steven Vogel that covers this kind of flawed analogical reasoning between biological and human-made systems. It's not that such analogies are useless, but it is very important to recognise the limitations and fully understand why certain design choices are made by biological systems due to the particular environmental and evolutionary constraints that they work under.


Do cells communicate only in binary levels? In modern communication we generally have various schemes to communicate the given signal, one of them is to convey information with different levels. does cell signaling too have levels apart from binary 'Yes' and 'No'.

For instance if a cell 'A' wants to communicate with another cell 'B'. I know it can do that by varying the concentration of molecules in the given media and 'B' will decide in favor of 'Yes' or 'No' based on the concentration sensed. But my question is does this sensing always happens in binary levels or is there some thing like:

If nothing sensed do operation 'a'
If moderate concentration sensed do operation 'b'
If high concentration sensed do operation 'c'

I mean communication not done in binary levels but may be quaternary levels. If yes can any reference be provided?

Binary responses are associated with switches, which in turn are associated with bifurcations in the steady states of the biological system in question. Varying some system's parameter (such as a cell's signalling strength) cells can switch from 'on' to 'off' (or viceversa) states. As an example, check out Gardner's toggle switch
(https://www.nature.com/articles/35002131), in which this property is exploited in a synthetic system.

However, cell-cell interactions can be much more complicated, allowing behaviours other than binary responses, such as multistability or oscillations. Thus, upon varying a parameter, a cell's state can, for example, go from a particular 'off' state, chango to an oscillating state and then change again to an 'on' state. Thus not only binary responses operate in cell communications, but many intermediate responses are also possible. For a review in multistability in biological systems, check out: http://m.pnas.org/content/101/7/1822.long

Hope it helps!


Can I use commercial DNA loading dye for my RNA samples without degrading them? I was wondering if I have to use special RNA loading dye or can I run RNA samples with regular loading dye that is used for DNA?

Handling of RNA requires extra care, especially using RNase-free pipette tips, tubes and reagents, to prevent RNase contamination. Common labware and reagents usually indicate whether they are RNase-free certified. If there is no such mention written on the box or label, then you should assume it is not RNase-free and you should not use it to handle your RNA.

Check whether your loading dye is certified RNase-free (this should be written on the tube, or easy to find out on the manufacturer's website using the product reference number). If it is, and you exclusively used RNase-free certified tools and reagents all the way, then maybe the loading dye tube or something else got contaminated by one of your co-workers.


Can multiple overt/covert intentions produce identical EEG readings? With sophisticated techniques likes ERP, it is possible to correlate certain EEG activity with certain overt/covert actions.

What I'm wondering is: is there a risk for 2+ overt/covert actions producing identical EEG activity? Meaning:

Perhaps when I go to open/close my right hand, I produce certain neural activity (lets just summarize this as A1); where A1 is a specific set of wave signatures
Perhaps when I go to open/close my left hand, I produce neural activity A2 (a specific set of wave signatures that is distinctively/mathematically different than A1)
Perhaps there are 10,000 other movements I could make that produced their own distinct set of wave signatures (A3 - A10002), etc.
But perhaps when I think of sea turtles and pat my stomach at the same time, I produce the same set of waves as A2 (opening and closing my left hand)

My question is: is this a concern/possibility with EEG/ERP? In other words, can multiple overt/covert intents produce identical wave activity (hence, identical EEG readings)?

To curtly answer your question: given the sheer amount of different thoughts possible (billions I guess) and the limited spatial resolution of the standard EEG as well as the restricted number of characteristic parameters to describe EEGs (frequency, amplitude, latency) it is safe to say EEG is not suitable to characterize all of the brains processes. In fact, no state-of-the-art technique can do so, as far as I can see.


What is the purpose of gluconeogenesis? The gluconeogenesis pathway seems quite pointless to me. I don't understand why an organism would want to spend energy to create a molecule that can then be metabolized again for less energy? The pathway seems only to serve as a complete waste of energy?

Can someone explain why we have gluconeogenesis and when it is used?

Gluconeogenesis is not the reversal of the glycolysis, but the generation of glucose from non-carbohydrate precursors (like odd chain fatty acids and proteins). The reason why we have this process is because some organs and tissues can only use glucose as their energy source. These include the brain (although ketone bodies can be used here as well), erythrocytes, testes and the kidney medulla.

Usually the glucose for the supply of these tissues comes directly from carbohydrates in food or storage carbohydrates as glycogen or starch, but when these are not available, the body has another way to get around this problem and to avoid the starvation of these tissues. See for example here and here.


Growth factors vs. mitogens According to Campbell Biology,

  A growth factor is a protein released by certain cells that stimulates other cells to divide.

and according to Wikipedia,

  A mitogen is a chemical substance that encourages a cell to commence cell division, triggering mitosis.

What’s the difference between them? I suppose a mitogen specifically refers to mitosis, but if something is stimulating mitosis, isn’t it stimulating growth? Are mitogens all growth factors? Are all growth factors mitogens?

You can find a great article about this here.

basically, these two groups are very similar in their effects, however they work through different pathways.

Mitogens directly promote cell to get through G1 checkpoint through highering the activity of cyclin D/cdk4 (the complex needed to get through the checkpoint.) and according to the article above, also the cyclin E/cdk2 complex (which helps cell to get into S phase). By activating the MAPK (mitogen-activated protein kinase) pathway leading to production of transcription factors (Elk-1, jun, fos), which then promote specific transcription of proteins needed to get through cell cycle.
The mitogen pathway also causes phosphorylation of Rb (Retinoblastom) protein, which then dissociates from E2F transcription factor. This activates the E2F, which in turn helps synthesise proteins needed to promote S phase.

Growth factors usually stimulates mTOR receptor, which is a "serine/threonine protein kinase that regulates cell growth, cell proliferation, cell motility, cell survival, protein synthesis, autophagy, and transcription." Source

mTORC complex generally promotes translation. It plays role in "cell growth via the modulation of protein synthesis in yeast and mammals, it and its yeast homologs strongly stimulate transcription from all genes involved in ribosome biogenesis, transcription of rRNA genes by RNA polymerase I (Pol I), transcription of ribosomal protein genes by RNA polymerase II (Pol II), and transcription of tRNA and 5S genes by RNA polymerase III" and many other effects. Source.

Although all of this, in practice, I've seen many people use this categories interchangeably or referring to mitogens as a subgroup of growth factors.

I hope this helps.


Are there limits to drug resistance? It's well-known that indiscriminate use of a drug leads to resistance. My question is what the limits on resistance are. It seems obvious that there must be limits: for example I can hardly imagine a tiger evolving "resistance to bullets", and similarly I can hardly imagine a microorganism evolving resistance to heat treatment @ 1000 degrees celsius (surely its proteins must long denature before then).

Are there methods of killing microbes that cannot be resisted? If so, can we make similar cannot-be-resisted drugs?

There are physical limits to the existance of life forms, wether temperature, pressure, osmolarity, etc. But these are usually physicochemical fields acting over a wide spatial structure. In the case of drugs, they are physically localized molecular entities. They are usually very tiny, even compared to the smallest microbes. Even though the genome of any microbe is finite and they could not, in theory, recognize the infinitely many drugs we can synthesize (assuming the simple case they need one gene per drug resisted), they can just evolve very generic mechanisms like preventing these molecules to get into the microbe, pumping them out of the cell, or other generic mechanism; with the same overall effect: preventing the drug from acting in the desired way.

The question you ask is very interesting, and it is the focus of some recent efforts and discussions among academics. Here you can find a recent article discussing the possibility of "evolution-proof" drugs. As you can see, the subject is not trivial.

Cheers,

Pedro


Save endangered parasitic species? It seems to be an important issue the parasitic control and even some pursue the eradication of some species. Most of the researchers in parasitology are focused on the host damage and population regulation. How do we perceive and value the function of parasites? Is it really needed a change in paradigms and views of dependent species? How important is to conserve them?

Although we think of parasites as harmful and tend not to consider them for conservation, they do peform valuable functions including population regulation and the development of immune systems. More philosophically, under the 'intrinsic value' argument sometimes used for conservation, every species should be considered to have an intrinsic right to existence, regardless of its ecosystem function, harmful effects on other species or appeal to humans.

Conveniently, this article has just been published on this very subject. :)


Polar bodies fertilization Suppose a sperm fertilized a 2nd polar body( haploid) is there a chance of somewhat normal development?

The 2nd polar body contains almost no cytoplasm, so if only this body is fertilized it contains no maternal genes to guide the development and moreover not enough nutrients. So this wouldn't work. "Source"
Moreover, there wasn't reported even any case of "twin" resulting from the fertilization of 2nd polar body according to this article

There was reported case of twins formed by a mass of fertilized ovum and fertilized (diploid) first polar body. Source

What could happen is that if both polar body and oocyte are fertilized, these two cells merge and form tetraploid embryo. Which is sometimes able to form fetus (sometimes just ends as mola hydatinosa), but definitely not able to produce a viable child in humans.


Measuring optical density with/without re-suspending cells When measuring absorbance using a plate reader, is it necessary (or better) to resuspend the culture if the plate has been sitting still for 1-2 days?

While this could be a good physics question, I am more interested in the correct biological assay technique.

--

The two options are:

1) growing microbes in a plate inside a static incubator and then put the plate in a plate reader without agitating the liquid

2) growing microbes in a plate inside a static incubator and then put the plate in a plate reader after agitating the liquid

In option 2, the agitation could be achieved by gently pipeting the liquid up and down a few times...

Definitely (2). Clumps of cells will cause a lot of noise in your absorbance measurements (depending on whether the light beam hits a clump or some empty space).

I don't know what your microbe is or what growth medium you're assaying on, but typically it's very important to maintain the culture well-mixed at all times, not just during measurement. If your cells clump to the bottom, you will not get the same aeration as you will if they're well-mixed, and accessibility of other nutrients could potentially be limited as well. Generally the most controlled condition is to maintain good mixing at all times, but certainly this is organism- and medium-dependent.


How does sequence independent single primer amplification work? I'm having difficulty finding an explanation of how single primer amplification of DNA works in the literature available to me, can anyone explain the methodology and what it accomplishes?

This process is called sequence-independent single primer amplification (or in short SISPA). Its used to amplify unknown sequences for amplification, for example in unknown viruses.
The primers used for this process contain random sequences which should bind to the DNA to be amplified and also known sequences, which can be used a adapters. In the first rounds of PCR only the random primers give rise to specific products, which are amplified exponentially in the later rounds of PCR since the primers fit perfectly then. This is described in detail in this publication:"Random priming PCR strategy to amplify and clone trace amounts of DNA"
Another interesting paper describing the method is:"Sequence-independent, single-primer amplification (SISPA) of complex DNA populations."


Did I understand the definition of "gross primary production" correctly? According to wikipedia

  Gross primary production (GPP) is the amount of chemical energy as biomass that primary producers create in a given amount of time.

So if a plant creates 6g of biomass in 1 second for example, then the amount of chemical energy stored in the 6g increase in weight is the GPP?

Yes, you more or less got it!

If you have only 3 primary producers (say 3 plants) in a given ecosystem.

Plant A produces 2g of organic carbon per second
Plant B produces 5g of organic carbon per second
Plant C produces 1g of organic carbon per second

, then the GPP is 8g per second.

This produced organic carbon can be in the form of leaves, root or whatever tissue these plants are growing.

Note: the numbers chosen are irealistic both in terms of production per second and in terms of number of plants in an ecosystem.

  gC (grams of carbon assimilated) m-2 (m squared) year-1", what is meant by "grams of carbon assimilated" ?

The whole point of primary producers is to fix carbon. That is to take inorganic carbon (such as $CO_2$) and make it organic (such as $C_6H_{12}O_6$ aka glucose). This is why we are typically particularly interested in carbon and not so much in water.

For more info, you should have a look at an intro course to respiration and calvin cycle.

Note that if you remove water from an organism you are roughly speaking left with 75% of carbon, 10% of Nitrogen and the rest made of different elements.


What species is this orange mushroom in Romania? So I've found these mushrooms near a ditch on a field a few days ago in Romania. Can anyone help me with identifying what species of mushroom is this? The size of a mushroom is about 3-6 cm in diameter. Thanks and a happy new year.

This is most likely Kuehneromyces mutabilis or sheated woodtuft. It is quite common in Romania where it is named Gheba ciobanilor.

Quote from Wikipedia about the diagnosis:

  The clustered shiny convex caps are 6–8 cm in diameter. They are very hygrophanous; in a damp state they are shiny and greasy with a deep orange-brown colour towards the rim; often there is a disc of lighter (less sodden) flesh in the middle. In a dry state they are cinnamon-coloured.
  The gills are initially light and later cinnamon brown, and are sometimes somewhat decurrent (running down the stem).
  The stipe is 8–10 cm long by about 0.5–1 cm in diameter with a ring which separates the bare, smooth light cinnamon upper part from the darker brown shaggily scaly lower part. This type of stem is sometimes described as "booted".
  This species always grows on wood, generally on stumps of broad-leaved trees (especially beech, birch and alder), and rarely on conifers.
  It is found from April to late October, and also in the remaining winter months where conditions are mild. It is often seen at times when there are few other fungi in evidence.

Further details can be found here in English

or here in Romanian


What's the distinction between a tetrad and a synaptonemal complex in meiosis? What's the distinction between a tetrad and a synaptonemal complex in meiosis?  Are they synonyms?

I ask because the concepts seem very closely related, but it seems like there may be a subtle distinction.  Unfortunately, none of the sources I've been consulting use both terms.

As far as I can tell there is a distinction.

A tetrad refers to the entire group of four chromatids after they have come together for crossing over in Prophase I (synapses).

A synaptonemal complex as you would expect is formed in synapses.  This is a protein-RNA complex that connects the intervening regions of matched chromosomes in some circumstances - it is not required. Mutated yeast that can not form this complex has still been shown to be able to exchange genetic information.

In other words, you can have a tetrad without a synaptonemal complex, but not vice versa.


Recombinant protein fraction in E. coli If a protein is heterologously expressed in E. coli under the T7 promoter, what fraction of the total protein concentration in the cell is the heterologously expressed protein? What could be its concentration at most? Does it strongly depend on the size of the protein or are there certain size thresholds for low/high expression?

Miroux and Walker (1996) Over-production of Proteins in Escherichia coli: Mutant Hosts that Allow Synthesis of some Membrane Proteins and Globular Proteins at High Levels. J Mol Biol. 260: 289–298

The authors report on problems of over-expressing membrane proteins in E. coli using a T7 (pET) system. They isolate mutant strains which show improved levels of expression compared to the parent strain, BL21(DE3). In their Table 1 they document levels of expression of 17 proteins including, as a control, GFP. GFP was found as a combination of soluble and inclusion body protein at a level of 37 mg L-1 in BL21(DE3) and 140 mg L-1 in one of their mutant strains (C41(DE3)). The highest level of expression that they observed was 300 mg L-1 for bovine OSCP.

Unfortunately the authors document neither the total protein content, nor the cell density of the cultures that they analysed.

Let's assume that the cultures were 10e9 cells mL-1 = 10e12 cells L-1.

According to this source (citing Neidhardt F.C. Escherichia coli and Salmonella: Cellular and Molecular Biology. Vol 1. pp. 14, ASM Press 1996), the dry weight of an E. coli cell is 2.8e-13 g

The generally accepted figure for protein as a fraction of dry weight in E. coli = 0.55

I calculate from these numbers a value of 1540 mg protein L-1. For the three protein expression levels described above this means:

GFP in BL21(DE3) = 2.4%

GFP in C41(DE3) = 9.6%

bovine OSCP in C41(DE3) = 19.4%

I conclude (from these numbers, and from personal experience) that overexpression levels are highly variable, and are going to be strain and protein-dependent. Values in the range of 1-20% total cell protein may be anticipated.


Can a novel protein domain arise de novo in nature or did all protein domains evolve from a single ancestor? I know there is extensive research into the taxonomy and evolution of protein domains and many connections are, and are continuing to be, found between numerous domains. However, as far as I can see, new domains always arise from preexisting ones. I have seen no paper, in any field, showing the development of a new protein domain from a random piece of DNA which just mutates a start codon and synthesizes a new protein with no apparent function. I know this is theoretically possible but has anyone seen any evidence it has happened in any form of life in any geological period of time? OR are there some other mechanisms that could generate novel domains from non-coding DNA that I have overlooked when searching the journals?

My thinking is that, if de novo protein domain generation doesn't occurr, does it mean that all protein domains are a kind of "progeny" of a single domain that arose at the onset of life as we know it (or maybe even was the first lifeform on Earth). It seems very strange to me that this hasn't been pointed out by now since it's a relatively simple deduction. Thus, I'm asking either for a reference paper showing evidence for the evolution of de novo protein domains from a random piece of DNA that somehow managed to turn into a gene or for a reference to a paper discussing the idea that all proteins originate from a common ancestor existing at the onset of life and even, possibly, a single domain as old as life itself?

Yes. Novel protein domains can arise de novo in nature. The evidence is quite solid as those new domains show all the expected mutation patterns and statistical properties (expected for something evolving from DNA that doesn't yet encode for a domain). E.g.: see the following meta-analysis, which also describes how those new domains behave relative to older ones, and how they integrate into proteins: Toll-Riera et Mar Alba 2013, BMC Evolutionary Biology, "Emergence of novel domains in proteins":  https://bmcevolbiol.biomedcentral.com/articles/10.1186/1471-2148-13-47

If you are additionally interested in new genes, the following mini-review: http://www.sciencedirect.com/science/article/pii/S0960982214001547#bib20 .

If you are additionally interested in in-vitro evolution, which is directly observable within the life-span of single humans, the following review: http://www.sciencedirect.com/science/article/pii/S0022175904001309