One flybase gene number (FBgn), many Affymetrix Id's I am trying to convert a set of Affymetrix ID's, like this one 143053_at_3745, to Flybase Gene Numbers (FBgn) like this one FBgn0000015. I have downloaded the Flybase file required to do so (as described here) but I have noticed that most of the FBgn's have more than one associated Affy id.

My question is, how do I know which to assign to my data? From the list of affy-ids that I have, how do I label each one with the appropriate FBgn? I am using data from the Ayroles et al 2009 (DGRP) which has a column of AffyID which look similar to the ones in the Flybase file but shorter (1638273_at). Perhaps I don't grasp why there would be more than one.

Some have one affy id which is repeated across 15 columns in the file, whereas some seem to have several affy id's associated with them.

Some questions this problem raises:

Why does a singular FBgn identifier have more than one associated affy identifier?

Why do some datasets, such as the dataset I have, have shorter versions of the affy identifier?

Where can I find an up to date and appropriate list matching these Affy id's the FBgn identifiers correctly?

I can answer this - I may not have time to dig though the file you are pointing to... but here's some explanation - lmk if you need more.

The shorter names (123456_at) are the original names for the probe sets that Affymetrix gave.  The file you area asking about has been extended for FlyBase's purpose and I'm only dimly aware of its existence. It looks like Flybase has tried to rename the probe set to a minimal gene list and create less ambiguous mappings.  I'm not familiar with it.  If I have time Ill try to look at it and put something here, but I'm fairly slammed this week.

In general you should know, there is a many to many relationship between probe sets from arrays and genes.

There are a few reasons for this.  The most common reasons:

More than one probe set per gene
1) More than one start sequence per gene. The IVT arrays such as you are looking at read only the 3' end of the gene.  If there are  more than one such terminii, you will have more than one probe set.
2) Duplicate genes.  If the 3' end of the gene has been duplicated recently, then a probe set may read more than one gene and not be able to distinguish them, so it will have both gene references in its annotation files.
3) Duplicate probe sets. For older arrays, this did happen where the probes in two probe sets will be mostly or entirely the same.
4) formerly separate genes are now joined into a single gene.  This is similar to (1) above, but with the added reason that two neighboring transcripts seen separately at the time of the array design are currently known to be part of the same transcript.  This is something we often don't think about, but the array may have been designed before your current gene of interest had a full length sequence.

In several cases the transcription behavior of the two probe sets will be quite different and you can decide which one to take based on how it behaves experimentally.  for example one of the probe sets may never respond while another one may register large changes with biological sample conditions.  Sorry I can't be of more help here. There are too many possible scenarios to consider to write about cogently.

More than one gene per probe set
1) a single stretch of DNA, even on the same strand, may simply be associated with more than one gene and the probe set will read both of them.
2) Even if they are not exactly the same, some genes resemble each other in nucleotide sequence that is impossible to choose probes which do not read both of them.

Since they have similar read length to a probe set, all this is also true to some extent for short read NGS sequencers in RNASeq data.

As you can hopefully see, ambiguity is something you have to expect to some extent when deciding to work with a biological system.  In many cases (~ 80%) you will have a single gene read per probe set, but with those odds you'll be looking at the genome browser for a half dozen of your favorite experimental results.


Teens concerned about impregnation through clothes Dry Humping, is:

  dry humping is the process of two people repeatedly moving up and down and back and forth on top of each other fully clothed( or missing various pieces, but the penis must not come in contact with the vagina with out some sort of fabric separating them ex: boxers,panties, or even sheets!!)

We all know that the basic rule for impregnation is that the sperm must come in contact with the egg, and even be able to fertilize it. While sperm can get through clothes, semen (but this is yet been proven or disproved) gets stuck, thus the sperm dies.

What is your opinion about this? If two people are on top of each other, fully clothed, and the male comes to ejaculation, is there any chance that pregnancy can happen, in the realistic and biological look at it (and not some probability or statistical way)? What advice should be given to teens on the matter?

I am a computer scientist with no biology knowledge, and am very interested in getting the opinion of biologists.

But since I know that the stackexchange community likes to see work done before asking questions, I did my own research (I am used to googling code and algorithms):
Very few research has been done on the subject. There is one shining research that  concluded, as I recall, that:

  If the underwear is completely saturated with semen, and is in direct contact with the woman's vagina, pregnancy is possible statistically, but highly unlikely.

If there has been an ejaculation by the male, and semen is present, there is a chance of getting pregnant. Period. Teens really need to know that.
I think you may have your terms confused - semen is the overall fluid released during an ejaculation, sperm are the cells with tails that are produced in the testes and fertilize the egg. At any rate, according to the WHO, a normal sperm count is over 15 million per milliliter, with some counts much higher (>50e6/ml ), and an average between 20 and 40 million. The volume of the ejeculate tends to be anywhere from 1-6 ml. If you take a healthy young male at the peak of his reproductive capabilities, this equates to a very large number of sperm being released during a sexual encounter. All it takes is for one to reach an egg and fertilize it. Sperm are very very small, much smaller than the pore size of average fabric, so clothing will do very little to stop them. The female is likely sexually aroused during this activity as well, and produces additional fluids and lubricants that promote the survival and motility of sperm, among other things.
So, it depends on many factors. If both parties are fully clothed (at least 4 layers of clothing between their respective reproductive organs) and there is a minumum of soaking through, the chances of pregnancy are correspondingly quite low. On the other hand, if only one partner is wearing just their underwear, it's essentially like there is no clothing present at all, and the relative chances go up significantly.
Safe sex practices can't be emphasized enough to young people, as education and awareness is so much better than ignorance and myths. Even aside from pregnancy, if condoms are not utilized properly to contain all the semen there is the chance of sexually-transmitted diseases, ranging from herpes and gonorrhea to AIDS. None of these require penetration to be passed along, and one might argue that the additional presence of potentially irritating fabrics could open up raw areas or cuts and enhance their transmittal.

Take home message
Now, all this being said, the chances of impregnation through clothing without direct penetration of the penis into the vagina is quite low compared to "typical" unprotected fully-penetrating intercourse, especially depending on where the female is in her fertility cycle. According to this study, a woman's most fertile day is two days before ovulation (as had been postulated before), and the chances of pregnancy on that day are about 25% (assuming penetrating intercourse). Overall, the chance of pregnancy throughout the month is about 5%.
I don't have any hard numbers on the pregnancy chances when one or both partners have at least some clothing on, as obviously it will vary greatly depending on who is wearing what, the volume of ejaculate, contact time after ejaculation, etc. Just for fun, let's assume it's 100 times lower. That means the chances of impregnation two days pre-ovulation would be 0.25%, or 1 in 400. While rather low, this is still a non-zero chance.
Condoms are about 98% effective if used properly during penetrative vaginal intercourse. Various other birth control methods such as contraceptive pills, intrauterine devices, implants and injections are quoted as being 99% effective on their own, although they do not protect against sexually transmitted diseases. I'm certainly not one for preaching abstinence, but done properly it should be 100% effective. Ultimately, it is up to both partners to decide what their risk tolerances are, together. It is much better to seriously talk about it beforehand than to be panicked and unsure afterwards.

Hopefully this addresses your concerns, please leave comments if you have additional questions.


How specimens are organized in a large biological specimens archive In a library, (and I'm not totally sure about this, but from experience) books are organized by category/theme into sections, and then they are given a number so that, globally, the numbers are ordered sequentially. This way you can easily just look up a number and go right to it, but then you can also browse entire sections by a common theme. I'm not sure how exactly they do this, but this is roughly what I've seen how it works.

So I'm wondering how biological specimens are organized in a gigantic specimen archive like at a large museum or university collection, with hundreds of thousands or millions of specimens. I'm wondering if they just give them a random number, and then place them wherever that number falls in the sequence. Or if they do like the libraries and group them by category/theme, then by number. Or something different.

Biological specimens are ordered in museums phylogenetically. So all the birds are in one place, and the insects in another. Fossils are generally kept in their own place. Different museums may have their own standards, but most sort specimens phylogenetically as well. But alphabetical sorting also happens. So that all the members of a family are in one place, and then the genera within the family are organized alphabetically. So all the Trichoptera (Insecta), for example, at the Smithsonian are together on one of the floors with other insects, curated by a Trichoptera specialist. Within Trichoptera, the first drawers are Apatanaeidae, and the last are Xiphocentronidae. Individual specimens are often given a unique number, usually sequential, with the time of accession into the museum.


How many Watson-Crick + Hoogsteen triple base pair combinations are there? Are these triple base pairs the only Watson-Crick + Hoogsteen triple base pairs possible? Furthermore, are TAA and TAT mixed up? This image is from Wikipedia, so it's possible that it's erroneous.

You are correct in assuming that the image labeled TAA should be labeled TAT and the second one labeled TAT should be labeled AAT. The image should be removed from the Wiki page until it has been corrected (even so I find it unclear).
Only some of these images show Watson-Crick/Hoogsteen combinations. To answer your question of how many such combinations there are, let us first recall what a Hoogsteen base-pair is. As stated in the first diagram on the Wiki page, this is a non-standard AT or GC base-pair formed by purine rotation about the glycosidic bond and base-flipping. In the diagram I have produced by canabilizing the above I show W-C and Hoogsteen base-pairs with the difference in the glycosidic link shown in yellow overlay. Because the pyrimidines A and C in a W-C base-pair have no groups left to hydrogen-bond, the only way you can theoretically make a W-C/H combination is by ATA and CGC as shown in my diagram. Therefore there are only two such possibilities.

I am not quite sure why you want to know about WC/H combinations, other than to understand the diagram in the article, because they are not particularly important. The author of the diagram shows such combinations because they apparently occur in triple-helices of artificial copolymers, however his diagram also shows some non-Watson-Crick base-pairs, e.g. CGG and CGA (which are not examples of WC/H combinations). The molecule where most Hoogsteen base-pairs are found naturally is RNA, not DNA: e.g. tRNA and ribozymes, in regions which do not have a standard double-helical structure. In these case they can occur in combination with both WC base-pairs and non-WC base-pairs (e.g. the GG illustrated above), so there is nothing special about Hoogsteen base-pairs being combined with WC base-pairs.

What I would consider important to realize is that in the context of the DNA double-helix WC base-pairs give the most thermodynamically stable structure, but outside this context, especially in RNAs that have protein-like structures, a variety of alternative base-pairs and base-triples are structurally and thermodynamically possible, including but not restricted to Hoogsten base-pairs.


Which turtle species was on board the Iranian Space Agency launch in 2010? They are seen briefly in this video:

https://www.youtube.com/watch?v=nZoNdf6hlII

The launch made international news, but there was no mention of the species.

Here's the entirety of Wikipedia's description of the launch:

  On February 3, 2010, ISA launched a Kavoshgar-3 (Explorer-3) rocket with one rodent, two turtles, and several worms into sub-orbital space and returned them to Earth alive. The rocket was enabled to transfer electronic data and live footage back to Earth. The Iranian Aerospace Organization (IAO) showed live video transmission of mini-environmental lab to enable further studies on the biological capsule. This was the first biological payload launched by Iran. Iran is the sixth country to send animals in space.

The Farsi language Wikipedia entry on the launch (کاوشگر ۳) does not appear to contain any more information on the species.

I've tried searching Google Scholar for papers, but my search turned up nothing. I also tried asking Reddit on the day of the launch, also without results.

Bounty Note: I appreciate all answers, especially from herpetologists. However, the bounty will only be awarded only for a reliable, third-party, published source (i.e. acceptable for use on Wikipedia).

Sorry, too big for comment!
It's actually hard to tell, as there is no official claim on this one.

Photo Link: http://youtu.be/nZoNdf6hlII?t=17s
Al I guess is, it can be:

Native breed of Iran like, Spur-Thighed Tortoise (Testudo graeca)

or something like this

(source: deserttortoise.org)
Trachemys scripta elegans


Why darwins, a measure of evolutionary change, is calculated on the log scale? In a famous paper, Haldane is describing the idea of rate of changes in "darwins". Here below is the excerpt where he introduces the math about the concept.

Haldane, J. B. S. 1949. Suggestions as to quantitative measurement of rates of evolution. Evolution 3:51–56.

  Now suppose that in time $t$ the mean length of a structure has
  increased from $x_1$ cm to $x_2$ cm, the mean value of the
  proportional rate of change

  $\frac{1}{x}\frac{dx}{dt}$ or $\frac{d}{dt} (\text{log}_ex)$ is

  $\frac{\text{log}_ex_2-\text{log}_ex_1}{t}$

I don't understand why he is arguing that the difference should be logged. Why can't you just use:

$\frac{x_2-x_1}{t}$?

What justifies this line below?

  $\frac{1}{x}\frac{dx}{dt}$ or $\frac{d}{dt} (\text{log}_ex)$

Why not just using:
$x\frac{d}{dt}$?

There are several purposes for log transformations, but one of the most common that occurs in biology is when changes are relative aka multiplicative. See for example this answer from CrossValidated.

If I told you that one lizard has a tail 5 cm longer than another lizard, that doesn't actually tell you much about how different it is. If the first lizard had a tail 1 cm long, that's a pretty massive difference! If the first lizard had a tail that was 100 cm long, the 5 cm difference is pretty minor.

Taking the log shows this:

Big (relative) change:

$log_e(6) - log_e(1) = 1.8$

$6 - 1 = 5$

Small (relative) change:

$log_e(105) - log_e(100) = 0.049$

$105 - 100 = 5$

The simple differences are both 5, but the log differences show you a big change versus a small one.

Logarithms are also more convenient than ratios for rates of change because they are easy to manipulate to predict change over any time interval assuming a constant relative change over time.

Taking the 6cm vs 1cm example above, lets say we want to guess the change when only half of the time is elapsed. If we take half of 1.8 = 0.9 and solve the following for X:

$log_e(X) - log_e(1) = 0.9$

$X \approx 2.5$

So we'd expect after only half the time, the length would have been about 2.5 cm.

$2.5/1 \approx 6/2.5$ meaning that the relative change for each subdivision of time is equal.

You could try this for any dt, too, and plot out X as a function of time with any dt when you use logarithms. You can't do this directly with a ratio like "6/1" because you can't directly subdivide that "6/1" into smaller time intervals (trying to do so would take you into the world of logarithms again :) ).

test <- function(time,x1,x2) {
  out = exp(log(x1)+(log(x2)-log(x1))*time)
  return(out) }
time = seq(0,2,0.01)
plot(time,test(time,1,6),
     xlab = "Time",
     ylab = "X",
     type = "l",
     main = "Change in morphology through time")
points(x = 1,
       y = 6,
       pch = 21,
       bg = "black",
       col = "black")

Ultimately, what matters most is what thing you are measuring and how you want to interpret a particular type of change. For things like lengths or average counts, often a relative multiplicative change makes the most sense.


What causes the line patterns in the palm of the hand? The line patterns on the hand are unique to each individual, but what causes these lines and re they advantageous in anyway?

The lines on the hand are known as flexion creases, and they exist because in their absence, the skin will stretch outwards when the palm is closed due to the decreased surface area of the closed palm, causing problems with gripping.

Developmental disorders such as Down Syndrome often cause there to be only one palm line, known as the simian crease, as shown on the left.


Are brain cells replaced over time? You know how your cells die all the time and new ones are made to replace them, so you practically have a new body every maybe 5 years?

Many people say you become a completely different person every several years, but what about neural cells, do they get replaced?
I believe it would cause a lot of information to get lost if this happened.

By brain cells, I'll assume you mean neurons (the other type are called glial cells). Yes, new neurons arise in a least certain parts of the brain, and yes, they do cause memories to weaken or disappear. This has been shown in mice, guinea pigs and degus.

It would be wrong to assume that neurogenesis occurs with the frequency of, say, gastric cell or skin turnover. Up until recently, it was not thought to occur at all.

Learning and remembering use various cortical structures, including the hippocampus.Throughout life, new neurons (neurogenesis) are continuously added to the dentate gyrus. These additions remodel hippocampal circuits, and when this occurs after memory formation, this neurogenesis leads to degradation or forgetting of established memories. This was shown in adult mice. Conversely, decreasing neurogenesis after memory formation decreased forgetting.[1]

It is not only plasticity that makes the brain adaptable to continuous changes in environmental demands. Adult-born neurons integrate into preexisting neuronal networks and participate in information processing. Adult neurogenesis itself is a type of circuit plasticity required for hippocampus-dependent learning and memory recall. Adult hippocampal neurogenesis may also promote forgetting.[2]

The more neurogenesis there is, the more memories are broken down. Since we retain many memories over our lifetime, it's pretty safe to say out brains don't "turn over" every five years (or even over longer periods); some parts of our brain don't seem to undergo neurogenesis at all.[3]

[1] Hippocampal Neurogenesis Regulates Forgetting During Adulthood and Infancy Science 9 May 2014
[2] A Price to Pay for Adult Neurogenesis Science 9 May 2014
[3] Neurogenesis in the Adult Brain The Journal of Neuroscience February 1, 2002


Resting membrane potential: K+ concentrations and charges on inside and outside of the neuron According to this site, there is a greater concentration of K+ ions inside the cell than outside. The following screenshot, taken from this website, supports this statement.

However, I don't understand how the inside of the cell can have a net negative charge if there is a greater concentration of K+ inside the cell. This seems like a contradictory statement to me. (1) Why is the interior negative despite the fact that there are more K+ ions inside than outside, and (2) What exactly causes the net negative charge?

Why is the interior negative despite the fact that there are more K+ ions inside than outside, and (2) What exactly causes the net negative charge?

It's because K+ isn't the only player in the game. Yes, there is a bigger concentration of K+ inside of the cell, however, there is also a higher concentration of Na+ outside of the cell, and also, there are other charged ions, such as Cl- or proteins.

One of the main reasons for the gradient is Na+/K+ ATPase, which transports 2 K+ ions to the inside of the cell, while 3 Na+ ions are pumped to the exterior of the cell. This generally yields in a higher concentration of + charge on the outside of the cell.

The final membrane potential depends on the permeability of the membrane to these ions. Higher the permeability for an ion, the closer is the actual potential to the equilibrium potential of this ion. (you can read about its calculation here.). Since the membrane in a normal state is not permeable to Na+ to a big extent, but is permeable to K+, the resting potential is similar to the equilibrium potential for K+, which is negative (the actual value depends on the specific cell type, generally we can say -70mV in neurons). (The K+ is driven to exit the cell because of the chemical and electrical gradient, which results in negative charge inside of the cell). The approximation of final potential can be calculated by using Goldman equation.

The principle is therefore in selective opening and closing of specific ion channels and functioning of transmembrane pumps.


What kind of fish is on the picture? I saw these fish in a video at an art exhibition, I'd like to find out what kind they are.

This is an Atlantic wolffish (Anarhichas lupus). It's a very characteristic fish, with the teeth, the long dorsal fin and the small back fin.

https://en.m.wikipedia.org/wiki/Atlantic_wolffish


Can a bacterium survive without GroEL protein? In prokaryotes, GroEL protein (together with GroES) is required for protein folding.

Question: Can a bacterium survive without GroEL protein?

In E. coli, GroEL/GroES is found to interact with about 10% of all soluble proteins (Kerner et al. Cell 2005) and is the only chaperone essential to the bacterium under all tested conditions (Horwich et al. Cell 1993).


What would EEG recordings reveal if their resolution was better? 1. Temporal resolution

Of course, we would see higher frequencies. But would these be informative? Aren't the frequencies measured today near the border to noise?

2. Spatial resolution

I guess LFP measurement goes in this direction (closer to the sources of the signals being measured). But what would we learn by that? Finding small-scale regions (below Brodman area size) which behave phase-locked/synchronously?

3. fMRI

The same questions could be asked with respect to fMRI. But I guess, as long as temporal resolution is as poor as it is today (and which cannot be much better), we don't have to ask for spatial resolution, or do we?

The temporal resolution of EEG is already considered to be very good. The problem is spatial resolution. Even the loss of very high frequency activity, like individual spikes, is really a problem of spatial rather than temporal resolution: the spiking cells are too far away, so it is only possible to detect them if they are very synchronized (in which case they still show up as lower frequency signals).

Because EEG recordings are so far from the sources they are recording from, and because even structures deep in the brain can contribute to surface potentials,the signals end up as complex averages over a large space. There is an entire field called EEG source modeling that tries to use signal processing methods to improve this spatial resolution.

However, you don't really have to ask this as a hypothetical question, since we already have methods that have better resolution than EEG. Electrocorticograms (ECoG) are the most similar, and most applicable to human studies. ECoG arrays are very similar to EEG, but they are placed directly on the dura, under the skull. They increase spatial resolution because they cut down distances dramatically by not having to record through the skull.

As you mention in your question, local field potentials (LFP) get even closer to where the measured currents are occurring, by recording from within the brain itself. The spatial resolution of LFPs themselves can also be improved by recording from multiple electrodes and computing a current source density. This also helps mitigate the effects of volume conduction.

fMRI is a completely separate issue. Often, EEG and fMRI results can act in conjunction, using EEG to determine time and fMRI to determine space (note that although there are limits to the spatial resolution of fMRI, for a human subject it is dramatically more spatially precise than EEG, especially for any structures not at the very surface of the brain, including any of the sulci of neocortex). fMRI spatial resolution can be improved by using stronger magnets, but eventually there are technological (and expense) limitations, but as you say the temporal resolution is fixed, and even the spatial resolution has some practical limitations.

To generally answer your title question: if the spatial resolution of EEG is improved (practically, this means either source modeling or using ECoG or LFP), one is better able to identify the brain structures that are producing the signals observed in the EEG, and able to be more confident that the signals observed are "real" rather than an artifact of filtering over space. For example, a higher-frequency traveling wave could appear as a lower-frequency signal on an EEG, or a localized, high-intensity event could appear like a generalized, low-intensity event; higher spatial resolution would allow you to distinguish between the two in both cases.


Does the Parasympathetic Tract of Colon Sigmoideum Travel with Nervus Vagus and its Nucleus Dorsalis Nervi Vagi? I have the following tractus now:

  nucleus parasymphaticus sacrales -> nervus splanchnic -> ganglion
  terminalis -> colon sigmoideum

The tract is parasympathetic.
It suggests me that it should travel along CN 9 or CN 10, most likely with CN 10.

Does tractus colon sigmoideum travel with CN 10 and its nucleus dorsalis nervi vagi?

I found the following from Wikipedia:

  Pelvic splanchnic nerves are the primary source for parasympathetic innervation [for Sigmoid colon].

The non-cranial nerve is extending the scope of the cranial nerve by a synapse between the two neurons. The neurons are transmitting the electrical impulse from one neuron to another.
So this way the splanchnic nerve does not need to be with CN 10 in the region of impact.

The parasympathetic tract of colon sigmoideum can travel with nervus vagus by having a synapse between pelvic splanchnic nerve and CN 10. I verified this from my professor.


Confusion related to gene expression I have a set of gene expression data downloaded from http://www.ncbi.nlm.nih.gov/geo. I have two sets of data, one is the raw probe intensity data set in the form of CEL files. Another is processed txt file.

Here is a link for example
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE7904

I don't know what kind of processing is done to generate the processed data from the raw CEL files. For example in the above link, I have processed data like

SOFT formatted family file(s)
MINiML formatted family file(s)
Series Matrix File(s)

I don't know what sort of processing is done to generate those files. Any suggestions? I can read the raw CEL files in matlab but what sort of preprocessing am I supposed to do?

I also want to map these probe its to gene ids and get the corresponding gene. How can I accomplish this? I know matlab. But I am bit confused about the terminology and all. Any suggestions?

If you click through to some of the samples in the study, eg. GSM194397, GSM194398, etc. it mentions under the "Data processing" section that "The data were analyzed with dchip with default normalization settings".

You can learn more about dChip over at the dChip website.


Reversal of cross-linking in ChIP-seq Chromatin immunoprecipitation (ChIP) is a type of immunoprecipitation experimental technique used to investigate the interaction between proteins and DNA in the cell. A summary of the protocol for ChIP is here. Briefly, the steps are:

DNA and associated proteins on chromatin in living cells or tissues are crosslinked;
The DNA-protein complexes are  sheared into ~500 bp DNA fragments by sonication or nuclease digestion;
Cross-linked DNA fragments associated with the protein(s) of interest are selectively immunoprecipitated from the cell debris using an appropriate protein-specific antibody;
The associated DNA fragments are purified and their sequence is determined.

After step 3 (immunoprecipitation of the protein-DNA complex), it is my understanding that the protein–DNA cross-link is reversed and proteins are removed by digestion with proteinase K.

Can anyone tell me if during this step the DNA at site of cross-linking is included in further sequencing step or is washed away with the protein itself?

After the crosslink reversal step, you still have some DNA connected to protein fragments.

So at that step, instead of doing a normal DNA purification, we also need to use a phenol-chloroform extraction or special columns to seperate DNA from protein fragments.

Thermofisher usually gives really good explanations too.

Please let me know if I didn't understand the question correctly! :)


Can anyone identify this beetle? Fruit Chafer found in Zambezi valley at Victoria Falls on the Zambia/Zimbabwe border

That is a flower beetle in the family Scarabaeidae, subfamily Cetoniinae.
Derby's flower beetle (Dicronorrhina derbyana)
https://en.wikipedia.org/wiki/Dicronorrhina_derbyana


How many genes does D. melanogaster have? Obviously there is no 100% exact number, but I came across this on flybase, the gold standard for annotation. I am confused now. "Genes located to the genome", is that what I am looking for? If so, what does "Genes not located to the genome" mean?

EDIT

Personal correspondence to representative at FlyBase.org

  In FlyBase we have been gathering information about genes and phenotypes for over 20 years including information from papers and resources older than that.  We annotate gene models on the Drosophila melanogaster genome assembly and when possible associate those annotations with other information (eg. phenotype, function etc) that is known about the gene.  However, in some cases, especially for genes and phenotypes that were described in the older literature before the genome was sequenced we still have some information about those genes but have been unable to associate that information with a genome annotation.   Those are what we call unlocalized genes (i.e. those without a annotation on the genome).


Does sperm weight causes sex ratio? Chromosome X in female sperm is heavier than male Y chromosome. Does it causes difference in fertility of sperm and heavier female sperm is unable to fertilize better than male sperm?

This is given in AK Jain of physiology, chapter on reproduction.
I doubt this explanation.

Probably not! There are certainly some physical reasons to doubt it. Looks like the mass difference between X and Y sperm is on the order of 0.1 picograms: X chromosome "weight"?

First, mass differences are not likely to affect swimming and motility of sperm, because sperm are at low Reynolds number -- the forces of fluid drag vastly overwhelm inertial forces. See, e.g. Purcell's lecture "Life at Low Reynolds Number" (http://aapt.scitation.org/doi/abs/10.1119/1.10903 but also available online). For this reason, even much larger differences in mass are not likely to matter to swimming.

If motility is not the issue, you could imagine that, during the fertilization or insemination process, sperm might be under the force of gravity, leading to different sedimentation rates. A sperm's sedimentation speed is equal to the force on it divided by its friction coefficient $\gamma$,
$$v_{sperm} = \frac{(m_{sperm}-m_{displaced}) g}{\gamma} $$
where $g$ is the gravitational acceleration and $m_{displaced}$ is the amount of mass displaced by the sperm. You can estimate $\gamma$ with Stokes' law (https://en.wikipedia.org/wiki/Stokes%27_law) as about $6\pi R \mu$ with $R$ being the sperm size and $\mu$ the fluid viscosity. We're interested in the maximum possible difference in speed, so we'll choose $R$ to be at the small scale of sperm size, $5$ microns and $\mu$ to be that of water $\mu \approx 0.01 \frac{g}{cm s}$. This gives us $\gamma \sim 10^{-4} g/s$. The difference between $v_X$ and $v_Y$ is then
$$v_X - v_Y = \frac{(m_X - m_Y) g}{\gamma} \approx 0.01 \,\textrm{micron}/s$$

This means, for there to be a significant difference between X and Y sperm you'd have to keep them sedimenting under force for quite a while. This can be used (especially in a centrifuge, where you can increase the gravitational force) to select between genders - but it seems unlikely to happen in vivo.

To see why this is a small speed in practice, you have to ask whether the sperm would also have diffused a larger distance or managed to swim while it was sedimenting. Sperm velocities are on the order of tens of microns per second, so anything that changes the sperm swimming speed by even 0.1% is more important than the mass difference in sedimentation.

Putting this together, it suggests that mass differences are not a likely origin for sex ratios slightly deviating from one - if they are tuned, it would make more sense to change sperm length or swimming stroke. In fact, I believe there are some small geometric changes between X and Y sperm - but could those geometric changes happen simply because there is less chromosomal material in the Y? That, I'm not sure.


Blood pressure difference while seated and laid down My blood pressure readings differ a lot when I read them while seated and while I lay down on a bed.

I tie the strap in both cases to my left bicep and rest for a minute before noting the readings down.

For example, one reading I took was:

Seated: 130-85
Laying on bed: 115-75

These were noted down one after the other.

I am not sure if there should be this much difference in the readings and is this something to be worried about.

I can't offer specific advice as to your personal readings, but it is normal to expect a difference in blood pressure between sitting & supine (lying down) positions.
I have taken this quote from the Department of Health Care Sciences at Wayne State University website.

Effects of body position on blood pressure
Blood pressure is commonly measured in the seated or supine position; however, the two positions give different measurement values. With that in mind, any time a value is recorded, body position should also be recorded. It is widely accepted that diastolic pressures while sitting are higher than when a patient is supine by as much as 5 mmHg. When the arm is at the level of the heart, systolic pressure can be 8 mmHg higher, such as when a patient is in the supine position rather than sitting. A patient supporting their own arm (isometric exercise) may increase the pressure readings. If the patient’s back is not supported (i.e., when a patient is seated on an exam table instead of a chair) the diastolic pressure may be increased by 6 mmHg. Crossing the legs also may raise systolic pressure by 2-8 mmHg. Arm position plays a dramatic role in value errors as well. If the arm is below the level of the heart, values will be too high; if the arm is above the level of the heart, values will be underestimated. For every inch the arm is above or below the level of the heart, a 2 mmHg difference will be found (Pickering et al. Circ 2005;111:697-716).

So if you are comparing your own blood pressure day-to-day, make sure you keep a consistent position.
Additionally, if you are reading guidelines for healthy/risk blood pressures, make sure you take this into account.


Why are vertebrae, specifically, so important in classification? A fundamental level of animal classification is the distinction between vertebrates and invertebrates.  The vertebrata are, arguably, often classified as higher life forms than the invertebrata.  But why is the presence of the spine so important?  Why not use the simpler concept of internal bones as a classifier?

I might be missing something, but I can't think of any creature that has an endoskeleton but no spine.  Do any such creatures exist?  If not, why does classification focus on the spine and not the endoskeleton?

Short answer
The term vertebrata stems from grouping animals according to obvious gross anatomical distinguishing features as typically used in the early days of taxonomy. However, from a phylogenetic point of view, the presence of the neural crest during embryonic development, which is unique to this subset of animals in the phylum chordata, is a much more important distinguishing feature than the presence of vertebrae.

Background
Vertebrates belong to the phylum chordata, but share some characters that make them unique. Chordates, with a few exceptions, are active animals with bilaterally symmetric bodies that are longitudinally differentiated into head, trunk and tail. The most distinctive morphological features of chordates are the notochord, nerve cord, and visceral clefts and arches.

Vertebrates feature neural crest cells, which sets them apart from any other group. These cells appear early in development, and only vertebrates have them. Neural crest cells form the skull and jaw bones.

The neural crest has sometimes been called the fourth germ layer because of its importance (Fig. 1). The neural crest cells produce a variety of  cell types, including (1) the neurons and glial cells of the sensory, sympathetic, and parasympathetic nervous systems, (2) the epinephrine-producing (medulla) cells of the adrenal gland, (3) the pigment-containing cells of the epidermis, and (4) many of the skeletal and connective tissue components of the head (Gilbert, 2000).

Fig. 1. Regions of the neural crest. The cranial neural formt the bones and cartilage of the face and neck. It also produces pigment and cranial nerves. The vagal neural crest (near somites 1–7) and the sacral neural crest (posterior to somite 28) form the parasympathetic nerves of the gut. The cardiac neural crest cells arise from the neural crest by somites 1–3. Neural crest cells of the trunk (about somite 6 through the tail) make the sympathetic neurons, and a subset of these (at the level of somites 18–24) form the medulla portion of the adrenal gland. Source: Gilbert (2000)

In all, the term vertebrates is just a reflection of an apparent and obvious marker of this group of animals, namely the presence of vertebrae, but their distinguishing most important feature is the presence of the neural crest during development.

Reference
- Gilbert. Developmental Biology, 6th ed. Sunderland (MA): Sinauer Associates (2000)


Importance of Double Helix DNA Structure Gene expression involves transcribing only one strand of DNA molecule. So i was wondering what are some biological advantages of the double stranded DNA?

The structure allows for the DNA to be tightly packed into chromosomes. It also provides an extremely stable backbone with the negatively charged phosphates pointing to the outside of the molecule. This charge aids in the attachment of other molecules to the strand of DNA.

DNA double helix allows it to be stable and it won't easily destroyed.


Can some colours be processed faster/more accurately than others? Is the human visual / motor system able to track, and move in response to, objects of certain colours more quickly and reliably than for others?  By more reliably, I mean with greater accuracy in judging position and velocity, and with greater accuracy when moving in response.

Which colours are "most visible" in that sense, as a function of background and illumination?

This interests me specifically in the context of juggling: I like to juggle, and I wonder whether there's a difference in my response time and accuracy with different colours of balls/clubs.  Usually I'm indoors, and ceilings are usually white, sometimes black or brown, with strip lighting.  My only personal observations are rather obvious: dark colours can be hard to see against dark backgrounds, and white can be hard to see against white.

The answer is yes and yes. Firstly, motion cannot be processed at equiluminance. In other words if you have clubs that are equally as bright as their background you will not be able to see them move even though they are clearly visible because of a different color. It's a remarkable effect (demo link below), as you become in effect motion-blind. Obviously you notice after a while that things moved, but you don't see them move smoothly as you are used to. This is similar to what people with akinetopsia experience (had lesions to brain areas involved in motion processing). So have clubs that have clear luminance contrast to the background (very dark, or very bright).

Then there are known difference in processing latencies for different colors. More specifically yellow is processed faster than blue. And black is processed faster than white (if you consider them colors). These effect are massive, a few hundreds msec in some cases which is very long. There is also a known relationship between stimulus intensity (here color contrast) and response time, called Piéron's law. However that effect saturates at fairly low contrast so as long as you can see the clubs clearly it's unlikely there will be a difference in response time for more contrasted colors.

Finally there are discrimination differences for colors. For example yellow and orange are more easily discriminable than blue. But that's only true if you have to perceive a low contrast color difference (a yellow club on a yellow background). Here again as long as you see your clubs very clearly, it's unlikely the specific color of the clubs will make a difference.

So overall I would recommend to use clubs as contrasted as possible to the background (which is common sense). Then prefers darks to lights colors, and prefers yellows to blues. The ideal color is brown, which is in facts a dark yellow.

http://visionlab.harvard.edu/Members/Patrick/Demos/index.html

http://www.michaelbach.de/ot/col-flicker/index.html

Komban, S. J., Alonso, J. M., & Zaidi, Q. (2011). Darks are processed faster than lights. Journal of Neuroscience, 31(23), 8654-8658.

Wool, L. E., Komban, S. J., Kremkow, J., Jansen, M., Li, X., Alonso, J. M., & Zaidi, Q. (2015). Salience of unique hues and implications for color theory. Journal of vision, 15(2), 10-10.

Witzel, C., & Gegenfurtner, K. R. (2013). Categorical sensitivity to color differences. Journal of vision, 13(7), 1-1.


How is RNA of retrovirus converted into cDNA? The retrovirus (oncovirus) contains RNA. It also has a molecule called reverse transcriptase. This molecule transcribes RNA into cDNA. This cDNA is the DNA copy of viral RNA genome

RNA has Uracil instead of thymine and DNA has thymine instead of uracil. So, how can RNA be converted into DNA? Where does Uracil go and where does thymine come from?

RNA has Uracil instead of thymine and DNA has thymine instead of uracil. So, how can RNA be converted into DNA?

I think you may want to ask a more basic question.  DNA and RNA are extremely similar, with only an oxygen being the difference.  This has vast consequences for organisms, and life as we know it uses DNA and RNA for very separate purposes.  DNA stores the genome providing the instructions for life, and RNA in a nutshell is how that message gets converted into protein for a useful action.  RNA is generally less stable than DNA, so this arrangement works out well.

DNA is regularly and constantly transcribed to RNA, so Thymine is regularly used in favor of Uracil.  There is a fantastic answer here on Biology.SE already dealing with why so I suggest reading that.  The how is pretty straightforward, there are different molecules used!  DNA polymerases incorporate Thymine whereas RNA polymerases incorporate Uracil.  The reverse transcriptase that is encoded by the retrovirus does just this: it transcribes RNA to DNA, using Thymine instead of Uracil.  Both Uracil and Thymine are present in the cell and are thus available for use.


Non-ribosomal peptide synthesis: why Glutathione cannot be produced by the ribosome? Case: I am writing a summary for a class in protein structure and function, and was asked to describe some different ways that peptides are synthesized (that does not involve the ribosome). I understand that glutathione is a tri-peptide consisting of L-cystine with a "gamma" bond to L-glycine which is then bound to glutamic acid.

Problem: Why is it that the ribosome cannot produce this peptide? What is special about the peptide-gamma-bond?

My reasoning: The peptide is too short, meaning that the large ribosome complex cannot bind to mRNA of this length as it need many different binding spots in order for the large and small subunit to come together. Also, the "gamma" bond is very special, and the ribosome can only produce peptides with the "Standard" peptide bonds.

Is this correct, and is there something else I am missing?
Does the "gamma" bond relate to the fact the glutathione is not that easily degraded by peptidases in the cytosol?

It's definitely not the length. Although ribosomes can't make really really small peptides because they need something to hold onto and in any case proteins start with methionine(usually), there are workarounds. There's no reason why a tripeptide couldn't be coded for by a gene directly.

The 'traditional' method of producing very short peptides is producing a longer protein and cleaving off a chunk of it, which works great for signal peptides and a number of other systems. Very small peptides are more efficiently made by enzymes like this but in principle there's no reason to besides efficiency and complexity. (You need a special protease for each small peptide etc etc etc)

However, this gamma bond is a different beast entirely, and no ribosome could ever produce it, even in the middle of a longer protein. Amino acids 'snap' together in a very specific way. The amino group bonds to the carboxyl group of the previous amino acid, making a chain. The side groups of an amino acid aren't involved. Like Legos that snap together only one way and can be any color or have any designs on the side. The difference here is glutamate has a carboxyl group as part of its side chain. It's like a Lego with holes on two sides. The NRPS here connects the cysteine to the side chain of the glutamate instead of the 'bottom' where it would go if a ribosome-synthesized glutamate-cysteine bond.

This gamma bond also explains the increased longevity of the product. Proteases aren't designed for things that look like this. The gamma bond doesn't 'fit right' in the protease active sites and therefore activity is slower.


At what levels of muscle energy intake does catabolism start? From my own reading, there are three ways used by the body to produce energy:

Alactic anaerobic (direct degradation of ATP and creatine phosphate for regeneration of ATP)
Lactic anaerobic (breakdown of muscle glycogen with lactic acid production)
Aerobic (breakdown of carbohydrates and fats primarily and secondarily of proteins)

My questions are:

1) Knowing that the anaerobic mechanisms (alactic and lactic) are triggered when the effort is intense and / or greater than body oxygenation capacity, it seems logical, at rest, the body uses mainly aerobic way for producing energy. Am I right?

2) If 1) is true, what are the conditions (trigger elements, trigger events) which lead to muscle catabolism (so protein degradation) in order to produce energy? ? Is it well the last resort used by the body to produce energy that is to say after degradation of total carbohydrates and lipids?

1) Yes, most cells in the body derive energy from oxidative metabolism, unless oxygen is not available for some reason. There are some exceptions, for example red blood cells lack mitochondria and so have no respiration, and various types of rapidly proliferating cells such as activated immune cells have high glycolysis and lactate production (for reasons that are still not well understood).

2) The main fuel of exercising muscle is glycogen, which can account for 60-80% of energy requirements (article). Triacyglycerols (fat) stored in muscle tissue may account for most of the remainder (artice). Normally, muscle protein is not a major energy source during exercise. Some muscle protein breakdown has been observed after 2-3 hours of intense exercise (think marathon runners), when glycogen stores are depleted. See this review article.

If glycogen is not synthesized and stored normally while resting, then muscle may be more likely to catabolize protein during intense exercise. This can happen to some extent in diabetes, see for example this paper. There are also severe genetic disorders that disrupt glycogen synthesis, but those are very rare. I would guess fasting also makes it difficult to replenish muscle glycogen stores (and muscle triglycerides as well), so strenuous exercise combined with fasting might result in muscle protein breakdown, but I don't know of a study on this.


Could an annual plant be genetically modified to be a perennial? My chives, asparagus, oregano, and rhubarb come back every year like clockwork.  Suppose I want my bok choy to join the party - is there an "I'll be seeing you next year!" gene that can be modified to be turned on to be like my hardy chives, or is it more complicated than that?

Researchers at Ghent University have made a discovery that downregulation of the proteins CONSTANS 1 (SOC1) and FRUITFULL (FUL) lead to the development of many perennial traits in annual plants (in the study Arabidopsis thaliana is used) (reference).

The CONSTANS gene controls flowering in Arabidopsis thaliana (reference).

FRUITFULL (FUL) is an MADS box gene that functions early in controlling flowering time, meristem identity and cauline leaf morphology and later in carpel and fruit development in Arabidopsis thaliana (reference).

The process is complicated and would need many genes to be manipulated but this research proves that it is possible. Another article of interest.


Are there any mutagens that can undo the mutations they cause? I was reading a section from my textbook about tautomeric shifts, and it seems to suggest that there are some mutagens that can be directly responsible for the phenomenon. The section is mainly describing spontaneous mutations as opposed to induced mutations, and examples of mutagens are mentioned. However, the author explicitly states that the sort of changes made to DNA due to spontaneous mutations also occur at a higher rate during induced mutagenesis.

If a tautomeric shift can occur due to mutagenic activity, is it possible for the mutagen to undo and "correct" the mutation by reversing the shift? If so, what kind of chemicals or physical mutagens (e.g. radiation) would be involved?

It is possible but extremely unlikely.

When a base undergoes tautomeric shift the DNA does not contain a mutation yet, just an unmatched pair. The mutation will only becomes inscribed into the DNA permanently after the DNA is replicated or wrongly repaired.

In order to reverse the mutation you would need to provoke a chemical change to that specific base using the same or another mutagen and as most of them are unspecific the likelihood of obtaining both the correct mutation to reverse the effect AND at that specific location is extremely low. Just for the location itself (i.e. that base pair), in human you have ~0.000000033%  chances (1/3 billions) to mutate that base. This is assuming equal probabilities across the genome and a single modification event which is of course not true but shouldn't modify much the conclusion. I am not even speaking about provoking the chemical modification that will reverse it which will even further reduce that probability.

Such induced or natural mutations will actually only rarely appear in the genome permanently as the cell has multiple DNA repair mechanisms (see this wiki). So in this case the modified base does not need to be reverse as the cell will make sure to repair it directly but using mechanisms not based on mutagenesis.


Anti malarial drugs and g6pd deficiency Why does antimalarial drugs causes hemolysis in g6pd deficiency patients?
I know that g6pd protects the cell from oxidative stress by maintaining glutathione in reduced state but how does the antimalarial drugs cause the deficiency of gsh? I came across this(https://malariaworld.org/blog/hemolytic-anemia-and-antimalarials) site and it says:

  The antimalarial activity of quinine and compounds vicine and convicine present in broad beans eventually follow the same path. In the gastrointestinal tract they are hydrolyzed to form unstable pyrimidine aglycones. They reduce red blood cell GSH and generate hydrogen peroxides and free radical species.

I highly doubt the last line, how does gsh produced not prevent the cell from hemolysis?

Antimalarials, fever, age (of the RBC), other drugs, and a host of other things increase oxidative stress in RBCs (which results in the production of H2O2.)

The line you point out as a problem is a bit confusing, but it is entirely correct. It helps to keep in mind that 'glutathione' exists in two forms in the cell: glutathione disulfide (GSSG) and glutathione (GSH). GSH is the reduced form. So a reduction in GSH (the reduced form) does lead to an increase of H2O2.

Another way to say it is that in the absence of G6PD, the amount of reduced glutathione is decreased.

Glucose is used by RBC's as food, and G6PD is needed to metabolize it. G6PD reduces a molecule of NADP to NADPH + H+, which then reduces glutathione disulfide into GSH (reduced glutathione). That molecule is used in the reduction of H2O2 to H2O.

If there is a deficiency of G6PH, there will not be enough NADPH to reduce GSSG, leading to decreased levels of GSH; H2O2 levels rise, and oxidative damage to proteins in the RBC occurs.

  Glutathione metabolism consists, in large part, of its oxidation to the disulfide and recycling to the reduced form by the co-enzyme nicotinamide adenine dinucleotide phosphate (NADPH) by mediation of glutathione reductase (Figure 1⇓). Reduced glutathione is important in the detoxification of free radicals. In normal cells, NADPH is regenerated by G6PD during oxidative stress. Impairment of this step prevents reduced glutathione recycling, exposing the cell to oxidative damage. Alternative pathways to G6PD-dependent NADPH production exist in most human cells but not in erythrocytes, and the lack of protein synthetic machinery deprives the erythrocyte of the opportunity to replace enzyme that has been lost. For these reasons, these cells are uniquely vulnerable to oxidative stress in G6PD deficiency.

These damaged proteins bind to the red cell membrane, which is then processed in the spleen; the spleen removes the damaged part of the RBC membrane. A few passes of this, and the RBC can no longer maintain the integrity of its cell membrane, and it breaks up (hemolysis).

Glucose-6-Phosphate Dehydrogenase Deficiency and Antimalarial Drug Development


why a testosterone pill can't be effective? Why estrogen, progesterone etc. in the contraceptive pills survive the acid environment of the stomach and all the digestive enzymes, while testosterone needs to be injected or spread with a gel on skin?
I have no idea of why this difference in assumption, because I know testosterone and "feminine" hormones have the same steroid based structure...so I can't pick up why testosterone differently from "feminine" hormones can't resist the digestion.

As stated in the comments by Eliane B., testosterone can actually be administered orally when an undecanoate ester is attached. The reason regular testosterone cannot be adminstered orally is because it undergoes extensive first pass metabolism (oxidation of the 17b-hydroxyl group to a 17-keto group, catalyzed by 17b-hydroxysteroid dehydrogenase enzymes, which are active in the liver). The undecanoate ester makes the substance lipophilic enough to be transported by the lymphatic system to the circulation after absorption by the intestines. Without the ester it will first reach the liver via the portal vein, thus exposing it to first pass metabolism. Nevertheless, bioavailability of oral testosterone undecanoate is estimated to be less than 10% [1].

Besides that, there are also derivates of testosterone which have a high oral bioavailability. These derivates have an alpha-oriented alkyl group, usually methyl, at position C-17, which retards hepatic metabolism. However, this can lead to hepatotoxicity [2].

https://www.ncbi.nlm.nih.gov/pubmed/3770015 (note, the subjects were women, but in the literature it is assumed that similiar bioavailability is obtained in men)
https://www.ncbi.nlm.nih.gov/pubmed/27372877


Can an organism process H₂O into H₂O₂? In an answer to a recent question on Worldbuilding, I suggested that an organism convert $\ce{H2O}$ into $\ce{H2O2}$. I suggested a few processes that yielded the desired final result ($\ce{2H2O \rightarrow H2O2 + H2}$ and $\ce{H2O + O3 \rightarrow H2O2 + O2}$). I noted that both were mere guesses. The feasibility of it was debated because hydrogen peroxide is a rocket fuel and contains a lot of energy (I heavily modified the answer and set it on an entirely different track after another mistake was pointed out).

Could some process similar to this ever happen in an organism?

Hydrogen peroxide as a reactive oxygen species (ROS) is a highly problematic molecule for the processes inside of cells (it can spontaneously oxidize and damage cellular components). With Catalase, organisms have a very effective enzyme which degrades the peroxide into water and oxygen.

However, although the molecule is problematic, it is still produced by organisms in traces. For its production by the NADPH oxidase, first NADPH is oxidized and superoxide is formed. The reaction looks like the following:

$NADPH + O_2 \rightarrow NADP^+ + H^+ + O_2^-$

In a second step the superoxide dismutase uses two molecules of superoxide and H+ to generate H2O2, the total reaction (which is divided into several steps) looks like this:

$2O_2^- + 2 H^+ \rightarrow H_2O_2 + O_2$

H2O2 is then usually degraded by the catalase (or used in immunological processes like the respiratory burst).


What happens between making a DNA library and screening by nucleic acid hybridization? I understand how a plasmid library is made and how each clone is put on the nitrocellulose membrane and nucleic acid hybridization is done. What I don't understand is how each clone is "identified" and separately put on the membrane?

The library is 'created' during a ligation reaction: plasmid vector + insert (e.g. cDNA). That DNA is used to transform E. coli, and, after plating out the transformation mixture, single bacterial colonies are obtained. Each colony contains, to a first approximation, a single plasmid species (i.e with a single insert). So each colony represents a clone, in the terms that you use.

I don't know if anyone really does things like this any more, but originally each plate would be transferred to nitrocellulose, for probing, and to a fresh plate for archiving. This way, any colony identified as positive after nucleic acid hybridisation could be picked from the archive plate for further characterisation.

This screening can be done on large format Petri dishes to reduce the number of plates needed. I know of one lab which in the 1980s used to screen λ libraries after plating out for plaques on cafeteria trays. That was the heroic era of molecular biology.


Sequence analysis software suites I have used DNAStar laser gene and VectorNTI in the past for cloning, primer design, sequence alignments, etc but no longer have access to these. Are there any comparable replacement suites or what stand alone packages would you now recommend?

I would strongly recommend benchling https://benchling.com

This is an awesome web based tool for cloning, primer design, multiple sequence alignments and everything else you are used to doing with the other tools. It is very user friendly, and most importantly you can share designs with your collaborators. Also, the graphics are very beautiful. I recently started using it and I am really impressed with the technical support they offer: you can chat with them and they would reply within minutes. Also, if there is a feature you would like to have implemented they would definitely consider it. Benchling is free, open source and you might be even able to code up some features yourself.


How straightforward is in vitro compartmentalization? in vitro compartmentalization (IVC) is one of those technologies that everyone knows about, talks about, but never actual does due to the rather technical difficulties in setting the system up. I was wonder if anyone not named Tawfik, Griffiths or someone who did a post-doc with them have been successful in making IVC work? Details in how stable emulsions and a homogeneous mixture of cell-free components in the droplet are made would be wonderful.

It is actually surprisingly easy and reproducible to make emulsions with defined components. We do it routinely in our lab:
http://www.sciencemag.org/content/332/6026/209.full - CBT protocols
http://www.sciencemag.org/content/336/6079/341.full - CST protocols


What shape is the pupil of squirrels? In the animal kingdom there is a striking variety of pupil shapes, with great variety among relatively close relatives. Cats have vertical slits. Siberian tigers have round pupils. Cuttlefish have a W shape. Goats have what I would call a horizontal bar. Many foxes have vertical slits, many dogs have round ones.

I just started paying attention to it and I was looking at some good pictures of both Japanese and European squirrels. I sometimes feel that I see a round irregularity at the centre, but can never be sure.

Here's a good photo of a squirrel eye showing the pupil being round.

Source: https://www.treklens.com/gallery/photo390926.htm

Also, these acrylic squirrel eyes for taxidermy show a round pupil.

Source: https://www.mckenziesp.com/Squirrel-Eyes-Acrylic-C3837.aspx


Is there a practical upper limit to ploidy? In my AP Biology class, we were discussing polyploidy, specifically, its deleterious nature in mammals and its prevalence in plants.  We also learned that commercial crops, especially fruit, are often selectively bred for high magnitudes of ploidy.

Fascinated, I googled the subject and ended up reviewing the Wikipedia article to get a little more background info, where I read this:

  Polytene chromosomes of plants and fruit flies can be 1024-ploid.[44][45] Ploidy of systems such as the salivary gland, elaiosome, endosperm, and trophoblast can exceed this, up to 1048576-ploid in the silk glands of the commercial silkworm Bombyx mori.[20]

From this, I have three questions. The first is, is there an upper limit to ploidy that can occur in nature? I understand that polyploids can "lose" ploidy by haploidisation, but is this as common as increases in ploidy? I believe that the answer to this would imply the answer to my first question, however, I could not find much literature in the way of this area.

My second question is, is there an upper limit to synthetically induced polyploidy? Is the Bombyx mori's ploidy arbitrary, or is it at the max that technology can produce? Can it's ploidy be expanded further?

Lastly, does arbitrarily high ploidy serve any purpose in agriculture or science? Is there a threshold where utility is no longer maximized?

Thank you in advance.

Note that it is customary to restrict posts to a single question, which is easier to answer for these complex topics. I'll do what I can here. I'm going to deal with everything at once and then reference pieces in direct reference to your 3 questions.

MECHANISMS OF CONSTRAINTS ON PLOIDY

I think that it's worth separating out some of the different mechanistic ways in which a practical limit can be set for how many chromosome copies you could have.

Another point is that the examples you give in flies and silkworms are organs with high ploidy, rather than whole organisms. It's a lot easier for an organism to have a few weird snippets of tissue with weird ploidy than to maintain that ploidy in the germ line.

Ciliates are weird and instructive:

As another totally insane example of how some organisms have evolved to reconcile this somatic desirability of lots of DNA with a stable germ line, you should look into the nuclear organization of the ciliates, which have a germ-line micronucleus (which is just passed on to future generations) and a somatic macronucleus (which is generated by amplification of the micronucleus and does all the cellular work of DNA). The macronucleus is of extremely high "ploidy" (it's more complicated than that but that's close enough), but the germ line is of a more sensible ploidy.

Some constraints I could think of:

Physical limits:

DNAs are basically huge polymers. Packing polymers into a cell imposes a physical constraint, in the sense that you need to 1) fit all that polymer into the cell/nucleus, and 2) need to still be able to use the DNA for all of the necessary cellular processes. These constraints will vary vastly from organism to organism, based on cell volume, plasticity, morphology, etc.

Metabolic limits:

DNA is expensive to make, energetically and physiologically. It ties up a lot of sugar and nitrogen that you could use to do other more interesting things, like the rest of cellular metabolism. Silkworm silk glands are obviously eye-popping, but I assume that there is some theoretical limit above that million-ploid amount (for silkworms) that would be too much DNA to support. For a little more information see this Mike Lynch paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4697398/

Chromosome segregation limits:

Moving homologous chromosomes to daughter cells is not a perfect process; cells mess it up frequently, leading to aneuploidies and cancers. Some ploidies such as triploid, and presumably higher numbers with 3 as a smallest common denominator, are particularly unstable in meiosis. However, any high ploidy leads to errors at a higher rate than lower ploidies. Look at the ciliate example also. This is I believe the main reason for the "collapse of high ploidies into lower ploidies that you mention.

UPPER LIMIT TO PLOIDY IN NATURE

See all above answers.

UPPER LIMIT TO SYNTHETIC PLOIDY

See all above answers. Synthetic increases should behave the same as natural ones, as we are honestly much worse at getting making things happen than nature itself. Nature will have gotten higher already than we ever will, in all probability.

PURPOSE OF HIGH PLOIDY

See the cost/benefit of ploidy article from above.


TSS of a gene vs TSS of a transcript I have an annotation from gencode.vM1.annotation of a mouse. Exons, genes, transcripts and UTR are listed there. For each feature a start and end positions are present.

I need to find a TSS for each gene. Will it be wrong to define one TSS for all transcripts belonging to one gene? So, I want to define a TSS for each gene as a minimum start UTR from all transcripts.

Example:

gene id, transcript id, feature, start, end

gene A, transcript A1, UTR, 102, 205
gene A, transcript A1, UTR, 506, 520
gene A, transcript A2, UTR, 78, 205
gene A, transcript A2, UTR, 502, 512

So, for gene A I would define a TSS on position 78 (minimum start UTR). And the gene body end on the position 520 (maximum end UTR).

There is no TSS of a gene. Geneic region will be a union of all the transcripts arising from that locus (including introns).

Sometimes two variants of a gene can have different TSS. You can define a 5' boundary of the geneic region which would be the most 5' TSS amongst all variants. You can also give scores to the TSS based on the expression of the different transcripts.

Nevertheless, I am not sure why you want this.


Liebig's law of minimum I was reading from Odum about Liebig's law of minimum.

It said that

  the law is appicable in steady state condition i.e. when the inflow of energy and material balances out the outflow.

I got two questions:

1.Here what is actually in steady state? Photosynthesis? or Plant community? or Biotic community?

2. Inflow of energy and material balances out the outflow.

What is the net material/energy that is flowing in an out of a system? Could it be amount of light absorbed and amount of glucose and O2 produced respectively? He used the word balances which means they are not equal actually but proportionate I suppose.

Your question is not directly related to Liebig's Law of the Minimum. Instead you ask about a conditions under which the Law holds according to your quote.

From the quote it is clear what is in steady state: it is the total amount of energy and material. If the the amount of energy and material flowing into a system equals ("balances out") the amount of energy and material leaving the system, the total amount in the system does not change, that is, it is in steady state.

This does not mean that other quantities in the system are necessarily in steady state. For instance, the species composition of a bacterial community may fluctuate or evolution may cause the community to change.

An example of the sort of systems we are talking about here is the chemostat. A chemostat is a device for culturing microorganisms. It consists of a culture vessel connected to a feed bottle. A solution of nutrients (the growth medium) literally flows from the feed into the chemostat. Microorganisms in the chemostat will grow and reproduce (if the concentration of nutrients is sufficient). A mixture of microorganisms, unused nutrients, and byproducts of growth leaves the chemostat in the effluent flowing out of the outflow of the vessel. The rate at which this happens is the same as the rate at which medium flows into the vessel. Typically, after a while the concentration of microorganisms and the concentration of nutrients in the chemostat and effluent do not change anymore (if the inflow is constant, that is). The chemical conditions in the chemostat have then become static (hence "chemostat"). The concentration of nutrients and microorganisms are then at steady state.

In the case that the microorganisms are phototrophic, the nutrients may be inorganic and energy is added to the system through light. The light absorbed may then be considered as the energy flowing in, and the energy flowing out is then the chemical bond energy in the organic material that make up the microorganisms and the byproducts, and heat.

Chemostats are culturing devices, but are also models of natural systems such as lakes or ecosystems.

Liebig's Law of the Minimum says whichever resource (nutrient of light) is in short supply determines the growth rate of an organism. For instance, if nutrient concentrations are in ample supply but light levels are low, changing the nutrient concentrations will not change the growth rate of the organisms, however, changing the light levels will. The quote of Odum suggests the Law only holds under steady state conditions, but I do not understand very well why this would be so.


Does THC excretion increase if urine volume increases? In regards to the body metabolizing and excreting THC: if urination is increased as a result of drinking lots of fluids, does that mean that more THC is leaving the body? To rephrase the question, is metabolism required for urination? Or can you simply urinate as a body process without metabolizing toxins from your body?

This question asks about the urinary excretion of THC. Before answering the question I think you're getting at, I'll first note that cannabinoids (of which THC is one) are primarily metabolized by hepatic cytochromes rather than being excreted directly. This article is a classical pharmacokinetic paper on the topic if you’re able to access it; this one is a more recent general review accessible on Pubmed Central.

Cannabinoid metabolites are excreted both renally (via kidneys) and in the feces, so I’ll understand your question to refer to the renally excreted portion. When considering renal excretion of any substance we think in terms of glomerular filtration rate, which refers to the volume of blood filtered through the glomerular capillaries per unit time, often estimated as creatinine clearance. The question then boils down to:

  Does excess hydration increase GFR?

And the basic answer is: no. The  kidneys control both volume and osmolality more distally, i.e. after the event of glomerular filtration.1

In the scenario you posit – drinking a lot of dilute fluid – osmoreceptors in the hypothalamus will sense the decreased plasma osmolality and suppress ADH (antidiuretic hormone, a.k.a. arginine vasopressin), the hormone that acts on the distal nephron to control water reabsorption. If ADH is completely suppressed, the kidneys can produce up to 25 L/day of urine with an osmolality as low as 60 mOsm/kg.2,3 This huge volume of urine, however, reflects water homeostasis achieved at the distal tubule rather than increased glomerular filtration. It does not correlate with increased excretion of THC metabolites or anything else at the level of the glomerulus.

Notes and References

1. If this makes no sense to you, you may want to check out this basic introduction to renal physiology that is available online. The referenced textbook in #3 below is more comprehensive but requires a library or purchase for access.

2. "Normal" urine osm ~300-800 mOsm/kg; plasma Osm ~280-290 mOsm/kg.

3. Christopher Lote. (2012). Principles of Renal Physiology. Springer New York.

P.S. If the question you really wanted to ask was, "Will drinking lots of water make my tox screen negative faster?".... I'm not answering that question. For reasons largely unrelated to the discussion here (but see references in paragraph #1), I suggest assuming that THC metabolites will be forever detectable via tox screen. ;-)


Bird ID (greenish passerine, Sacramento, CA) Can anyone identify this small, greenish bird I saw in Sacramento, California, in May 2016?  I tried using whatBird.com but wasn't able to come up with anything convincing.

It looks a little like a willow flycatcher (Empidonax traillii) or dusky flycatcher  (E. oberholseri), but their heads don't seem so strongly two-coloured.

(Photo: own work; sorry about the not-great quality)

You probably found a Yellow Bellied Flycatcher, which is weird because they are mainly midwest.


Is an egg classified based on the species inside it, or by the species that laid it? Basically what I'm asking is if an animal of species x were to lay an egg, and the animal inside that egg happened to be the first member of a genetically new species y, would the egg be considered an x egg or y egg?

Species are generally defined in terms of populations (see e.g. the wikipedia page), and it is therefore relatively meaningless to talk about individuals as species. That species is defined in terms of populations is true for many species concepts, e.g. as groups that can produce fertile offspring (biological species concept) or as a evolutionary distinct lineage (phylogenetic species concept). The question is therefore somewhat ill-posed, since it is only framed in terms of individual parents and offspring.

A possible exception could be speciation in apomictic species or speciation events following a change in ploidy level, but this is mostly relevant for certain types of asexual species and probably not what you are after since you are talking about egg-laying animals.


Is a wet-mount needed to use Immersion Oil? When I prepare my slide to use immersion oil, do I really need to wet-mount the specimen?  Can I do it with just the coverslip?

I am preparing fungus spores.

Using water for the wet-mount gives you a sort-of time limit.  You have to do your work before the water evaporates else you get little rivers at x100.

When I prepare my slide to use immersion oil, do I really need to wet-mount the specimen? Can I do it with just the coverslip?

Ideally you shouldn't use either with immersion oil. You should match the mounting media index as closely as possible to the immersion oil index, otherwise you'll reduce the resolution and contrast of your image. See:

http://www.microbehunter.com/the-importance-of-mounting-medium-refractive-index/

  Using water for the wet-mount gives you a sort-of time limit. You have to do your work before the water evaporates else you get little rivers at x100.

There are lots of options for higher index mounting media that will also preserve your specimen at least as well as air.


How much energy we get from oxygen? During a whole day breathing, how many kcal or watts do we get from the oxygen we breathe?

I know that you already picked an answer, but I found an alternative answer for you. On average a person consumes 550 litres of oxygen in a day. Now, our body could burn carbohydrates or fats or proteins to produce energy. Each litre of oxygen can produce 5.04 kcals if it burns carbohydrates, produce 4.68 kcals if it burns fats or produce 4.48 kcals if it burns proteins (reference). That being said, if I consider that all 550 litres were used to burn carbohydrates, a total of 550 x 5.04 kcals will be produced which is 2780 kcals.


Size of Mamenchisaurus sinocanadorum In most books the size of long-necked sauropod Mamenchisaurus is stated as about 26 meters. Recently, a huge specimen of Mamenchisaurus sinocanadorum was discovered.
However, Gregory S. Paul estimates its size in length of 35 meters and weight of more than 65,000 kg, rivaling Argentinosaurus and Patagotitan, the largest known dinosaurs. However, many doubt these estimates and say they are exaggerated. What are the current and most reliable esimates of the size of Mamenchisaurus sinocanadorum?

The holotype specimen originally discovered in 1993 is described as being 26m in length:

  An articulated neck of a large, mature sauropod, with enormously elongated cervical ribs, was discovered in strata of Late Jurassic age in the eastern Junggar Basin, Xinjiang, People's Republic of China. The animal is estimated to have originally measured 26 m in length, but was lightly proportioned relative to Brachiosaurus and Apatosaurus.

  ...

  In the present specimen, one rib from the midregion of the neck was seen to be at least 3540 mm long in the field, and after preparation measures 4100 mm in length.

  "A large mamenchisaurid from the Junggar Basin, Xinjiang, People Republic of China", Russell, D.A., Zheng, Z. (1993) Canadian Journal of Earth Sciences

The larger measurements come from additional remains attributed to this species, but not yet formally described. Here is the relevant section from Paul's book:

The Princeton Field Guide to Dinosaurs, Paul, G.S. (2010), Princeton University Press.

Paul's figures are echoed in the following papers:

  2006 年，中科院古脊椎所在新疆昌吉奇台（原中加马门溪龙标本发现地附近）发
  掘出一具巨型蜥脚类恐龙，经初步鉴定应归入马门溪龙。从发现的部分颈椎长度推测，
  这具马门溪龙长度可达 35 m 以上，成为了中国乃至亚洲目前发现的个体最大的恐龙。

    [Google Translate]

    In the year, the ancient spine of the Chinese Academy of Sciences was located in Changjiqitai, Xinjiang (near the original site of the discovery of the Jiamamen brook specimen).

    A giant sauropod dinosaur was excavated and the initial identification should be attributed to Mamenchisaurus. From the length of the cervical spine found,
    This [Mamenchisaurid] can reach a length of more than 35 m, becoming the largest individual dinosaur ever discovered in China and Asia.

  马门溪龙化石研究综述, (2008)

  Mamenchisaurus sinocanadorum (体长26~35 m)

  Advances in research on dinosaur gigantism, X XU, Q ZHAO (2016)

Though the first paper does not cite a source, and the second paper cites only Russel and Zheng's original paper describing the 26m specimen.


Distinguishing Father from Brother Given the (non-identical) DNA sequences of two men and the knowledge that the second man is either the father, brother, or son of the first man, is the DNA useful in determining which of these three he is?  Even the slightest probabilistic indicator would be useful.

I will clarify your question a little. We start with two men, Dave and John. We know Dave and John are related, either as brothers, or parent-child. Can we use genetics to work out their relationship?

If Dave and John are brothers they will have the same mtDNA, the DNA in the mitochondria, because mitochondria are maternally inherited. They should have the same Y chromosome, because they have the same father (the Y comes from the father, and males have one Y to pass on, therefore they each received the same Y).

If Dave (John) is John's (Dave's) father, then they should have different mtDNA because they have different mothers (assuming that Dave (John) didn't have a child with his mother or sister, and that mtDNA is variable within the population). They would have the same Y chromosome, because that is paternally inherited.

If Dave and John have the same X chromosome it would be indicative of the same mother (there is a 50% probability that two male siblings will have the same X chromosome, while the probability of a father and son having the same X chromosome would be determined by variability of the X chromosomes within the population).

For the autosomal part of the genome, each parent carries two copies of each gene. This means that, in each gene, there is the potential for four different alleles, with two of those being passed to the offspring. For example, at gene $A$ the mother may have alleles $A_1$ and $A_2$, while the father has $A_3$ and $A_4$. The offspring receives one copy from each parent, with equal probability. The probability that a son receives $A_3$ from the father is 50%. The probability that a second son receives the same $A_3$ allele is 50%. Therefore, both father-son and brother-brother relationships have a coefficient of relationship of 0.5.

In summary, the mtDNA will liekly be the best indicator, but it is only indicative, it is possible (but highly unlikely in most modern societies) for father and son to share the same mtDNA.

You could, in principle, work out whether Dave is John's son or his father. For example (a really over simplified example), look at the diagram below. You first look at Dave's sequence and one chromosome in a pair has the sequence AAAAAAAAAA (Red chromosome) while the other has GGGGGGGGGG (Yellow chromosome). You then look at John's sequence and find one chromosome with the sequence TTTTTTTTTT (Green chromosome) and one with the sequence AAAAGGGGGG (Red & Yellow Chromosome). John could have received the AAAAGGGGGG chromosome from Dave after Dave's red and yellow chromosome recombined, while it is not possible that John is the father of Dave. John's green chromosome came from his mother.


What is the preferred way to abbreviate amino acids? Amino acids are often denoted using either a 3-letter abbreviation or a 1-letter notation, e.g. Glutamine  is denoted via $\mathrm{Gln}$ or $\mathrm{Q}$.

When one notation should be preferred over the other and what are the reasons behind?

P. S. This is a follow-up to my question on Chemistry.SE Proper common notation for a ligand, where the problem of distinction between $\mathrm{L}$ notation for "ligand" and for "leucine" occured.

In my experience neither is preferred.

When simply presenting a protein sequence, e.g. in the context of a database of proteins encoded by a genome, then the one-letter code tends to be used.

When showing an alignment of a DNA sequence with the encoded protein sequence both can be used, although personally I prefer the one-letter code for this too because I don't like squished-together text like LysAlaTrpLeu.

In papers referring to an individual residue in a protein I would say that the three-letter code would be more likely to be used.

When referring to a mutation (or,  rather, an amino acid substitution) you might see Leu129Gln or L129Q.

And, by the way, I use L for ligand and have never found it to be confusing. If the reader of your text is sophisticated enough to know that L is leucine then I think they would be able to tell from the context that you were using L for ligand.


Why does allele linkage cause disproportionate phenotypic ratios? I was learning about allele linkage in Biology class and I got confused by the resultant phenotypic ratios.

Say you have a dihybrid cross BbGg x BbGg.

The Punnett square would look like the following (sorry for bad formatting):

     BG...... | Bg.... |  bG.... |  bg

BG   BBGG       BBGg      BbGG      BbGg
---  -----------------------------------
Bg   BBGg       BBgg      BbGg      Bbgg
---  -----------------------------------
bG   BbGG       BbGg      bbGG      bbGg
---  -----------------------------------
bg   BbGg       Bbgg      bbGg      bbgg

So:

This would result in a a 9:3:3:1 phenotypic ratio. (Dom/Dom : Dom/Rec : Rec/Dom : Rec/Rec)

However, if the alleles B/b and G/g were on the same chromosome, the ratios turned out to be around 4:1:1:4 in an example (still Dom/Dom : Dom/Rec : Rec/Dom : Rec/Rec)

The stated reason was that there would only be Dom/Dom and Rec/Rec, and the Dom/Rec and Rec/Dom only showed up due to crossing over. However, this begs the question: Why could Dom/Rec and Rec/Dom not have occurred prior to recombination? My reasoning is that just because the alleles are on the same chromosome does not mean that they must both the autosomal chromosomes for the allele must have either a dominant genotype or recesssive phenotype. That is, before crossover, there should still be a 9:3:3:1 random distribution between phenotypes represented by genotype sets (BbGg/BBGg/BbGG/BBGG):(Bbgg/BBgg):(bbGg/bbGG):(bbgg).

Note: when I say dom/rec for example, I mean that for the first allele the character represented by BB or Bb was expressed, and the "rec" means that for the second allele the character represented by gg was expressed. I am assuming autosomal dominance for simplicity.

If anything is unclear, don't hesitate to comment. I'm pretty tapped out right now. Thanks, hob

I found the explanation at this site helpful:
http://www.ndsu.edu/pubweb/~mcclean/plsc431/linkage/linkage1.htm

I don't have a clear sense of what you mean when you ask about assorted phenotypes occurring before recombination ("crossover"). All of your examples deal with diploid organisms. If they are multicellular then the cells that can undergo meiosis are highly specialized, and eventually become haploid. As the chromosomes are prepared they tend to become compact, and are often not expressed. So it is difficult to assess the phenotype of those haploid cells. The rest of the cells in the organism are diploid  and at least some of them can express the alleles that give rise to the phenotypes that you are scoring.

At the moment of fertilization there is no further recombination, as the zygotic cells undergo mitosis.  There is no segregation, no independent assortment, no linkage (that you can measure--the genes are still arrayed along their chromosomes). Each mother cell divides to give two perfect copies of itself. Then the daughters divide, etc. Even in the cells that are going to become germ cells, they divide by carbon copy mitosis right up until they enter meiosis.

So there is no mechanism that would lead to genotypes different from the genotype of the zygote (until meiosis).


Counterintuitive action of Vitamin D? Vitamin D acts in a way which to me is counterintuitive. It functionally supplemets Parathormone. It in the intestinal tract steps up calcium absorption by altering nuclear gene expression and also prevents calcium excretion in kidneys. All of this is understandable. But it also, like parathormone, steps up osteoclast action in bone (actually steps up both osteoclast and osteoblast, but the osteoclast action is increased more to result in net bone resorption). This means that Vitamin D increases blood calcium level by increasing bone resorption.

Then how does Vitamin D help in improving bone density, bone strength and prevent rickets or osteoporosis? All of these would require bone deposition rather than resorption.

There are two pieces to this question:

a) How does bone resorption (movement of Ca/Phos out of bone into the blood) result in net improvement in bone structure?

Bones are constantly remodeling, primarily in response to mechanical stressors. Although you clearly already realize this, I will make it explicit: osteoblasts are the cells that create new bone; osteoclasts break down (resorb) bone.

Quoting Harrison’s Internal Medicine1:

  Radioisotope studies indicate that as much as 18% of the total skeletal calcium is deposited and removed each year. Thus, bone is an active metabolizing tissue.…The cycle of bone resorption and formation is a highly orchestrated process carried out by the basic multicellular unit, which is composed of a group of osteoclasts and osteoblasts

Bone mineral density (BMD) can not be equated with bone quality. (This is the difference between osteoporosis – deficient bone density – and rickets – poor bone architecture.) Thus, vitamin D’s stimulation of both osteoblast and osteoclast activity is beneficial to bone structure.

b) How does vitamin D lead to overall increased bone density?

In addition to the effects above, you mentioned that vitamin D increases serum calcium by several mechanisms. This is true. Both this increased serum calcium as well as the direct effects of Vitamin D on the parathyroid gland suppress PTH production.* As PTH has powerful actions to increase bone resorption by mobilizing calcium and phosphorus to move from the bone into the blood, the suppression on its excretion applied both directly and indirectly by Vitamin D results in a net increase in bone density.

Thus, both by its effects on bone quality and quantity, vitamin D is a net boon for the bones.

*Parathyroid hormone, a.k.a. parathormone. There is a paradox here, because drugs such as teriparatide (a.k.a. Forteo, recombinant PTH) are anabolic for bone and are used to treat osteoporosis. Although the mechanism is unresolved, intermittent administration (as in the case of drug treatment) increases BMD while chronic sustained elevations decrease BMD.2

References

1. Bringhurst F, Demay M.B., Krane S.M., Kronenberg H.M. (2012). Chapter 352. Bone and Mineral Metabolism in Health and Disease. In Longo D.L., Fauci A.S., Kasper D.L., Hauser S.L., Jameson J, Loscalzo J (Eds), Harrison's Principles of Internal Medicine, 18e.

2. Rosen CJ. The cellular and clinical parameters of anabolic therapy for osteoporosis. Crit Rev Eukaryot Gene Expr. 2003;13(1):25.


When does the brain stem appear in humans? This article states:

  Once the neural tube closes, at around week 6 or week 7 of pregnancy,
  it curves and bulges into three sections, commonly known as the
  forebrain, midbrain and hindbrain. Just to the rear of the hindbrain
  sits the part that will soon turn into your baby's spinal cord. Soon,
  these areas bubble into those five different regions of the brain that
  we're most familiar with: the cerebrum, cerebellum, brain stem,
  pituitary gland and the hypothalamus.

How "soon" after 6 - 7 weeks is this soon the article talks about? When does the brain stem appear in humans?

Fetal Brain Development

To correct the article you referenced the neural tube closure normally occurs by the fourth week of pregnancy (28th day after conception). https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279093/

The Brainstem is comprised of three parts:

Medulla (Melincephalon)
The Pons (Metincephalon)
The Midbrain (Mesencephalon)

  During fetal development
  the brainstem is formed by:

  the myelencephalon (fifth vesicle) which will develop into the medulla (Melincephalon)
  the metencephalon (fourth vesicle) which will differentiate into the pons and cerebellum
  and the mesencephalon (midbrain)(third vesicle)

  An outline of the development of the brain stem is depicted in the image below:

  Pansky, B. 146. Introduction to Brainstem Development. Retrieved from https://discovery.lifemapsc.com/library/review-of-medical-embryology/chapter-146-introduction-to-brainstem-development

    By the end of the sixth week the rudimentary development of the five brain vesicles is complete. The cerebral hemispheres have grown and now cover the diencephalon, the mesencephalon and the cerebellum, which has only just begun development.

    Montfort, G. J., & Boon, R. Stages of Brain Development. Retrieved from https://www.bondingandbirth.org/uploads/5/4/1/5/5415260/06_stages_of_brain_development.pdf


How does 2-mercaptoethanol lead to shift of the band to a higher molecular weight? I have a project to isolate a protein with biological properties from a plant. The purified protein forms four bands with similar molecular weight on SDS-PAGE (30–35 kDa) in the presence of 5 % 2-mercaptoethanol, and two bands with lower MW (27–30 kDa) when 2-mercaptoethanol is omitted.

How can these results be explained? What is the easiest and lowest cost method to separate closely related proteins (if that’s what these are, and not just subunits of a single protein)?

2-mercaptoethanol (2ME) reduces the disulphide bonds in proteins. If disulphide bonds are connecting two polypeptide chains ("intermolecular") then 2ME would cause them to separate and therefore instead of a higher molecular weight (MW) band you would get one or more lower MW bands.

However, if there are disulphide bonds in the same polypeptide chain, they may cause the chain to fold up. This results in the polypeptide chain to effectively have a smaller hydrodynamic radius compared to the fully denatured chain. In such cases reducing the disulphide bonds using 2ME would cause the band to shift to a higher MW.

  What is the easiest and lowest cost method to separate closely related proteins

This is a different question altogether and there are several techniques depending on how "dissimilar" or "similar" the closely related proteins are. 2D PAGE (with isoelectric focussing) is one technique that can offer higher resolution compared to a normal SDS-PAGE. There are many other chromatographic methods.