Why we utilize dextro glucose and levo amino acids?

Our body digests only certain type of enantiomers like L amino acid and D sugars because enzymes are specific for their substrates stereochemistry meaning they will only recognize a particular enantiomer.So I hope this answers to your first question.
Now, why we only see L amino acids and D sugars, there is some interesting hypothesis listed in this article.Here is the link
http://guava.physics.uiuc.edu/~nigel/courses/569/Essays_Fall2006/files/Rajan.pdf

I am adding some answers I found from research gate here, which includes
1)I think the prevalence of L-amino acids in biological systems is a quirk of our evolutionary history; there's no reason D-amino acids wouldn't work chemically, but once early life forms started building proteins out of L-amino acids, L-amino acids became abundant an it became selectively advantageous to use L-amino acids because then you could use the amino acids you obtained by eating someone else. It's a matter of compatibility; if you use D-amino acids, you have to build them all from scratch, because you're not going to find them in your environment. As long as you use L-amino acids, you don't even need to maintain the de novo synthetic pathways; you can just eat something that has those pathways (hence the 'essential' dietary amino acids).
2)There are a couple of reasons for biological homochirality.
One, our galaxy has a chiral spin and a magnetic orientation, which causes cosmic dust particles to polarize starlight as circularly polarized in one direction only. This circularly polarized light degrades D enantiomers of amino acids more than L enantiomers, and this effect is clear when analyzing the amino acids found on comets and meteors. This explains why, at least in the milky way, L enantiomers are preferred.
Two, although gravity, electromagnetism, and the strong nuclear force are achiral, the weak nuclear force (radioactive decay) is chiral. During beta decay, the emitted electrons preferentially favor one kind of spin. That's right, the parity of the universe is not conserved in nuclear decay. These chiral electrons once again preferentially degrade D amino acids vs. L amino acids.

Thus due to the chirality of sunlight and the chirality of nuclear radiation, L amino acids are the more stable enantiomers and therefore are favored for abiogenesis.
3) Morozov, L. 1979. Mirror symmetry breaking in biochemical evolution. Origins Life Evol Biosphere 9: 187-217

But I think we have D amino acids also, as this paper says https://www.hindawi.com/journals/scientifica/2016/6494621/

Hope this helps!


What is the role of various immune cells in demylinating neuropathy?

Hi I don't think there is a simple way of describing the way the immune system works. However I'll give it a rough go. The immune system can be broken into two major categories, The innate immune system which does not need to learn about what foreign bodies are and works via physical systems such as the skin and molecular structures on cells such as PAMP-receptors (Pathogen associated mollecular pattern receptors) on Phagocytic cells (such as macrophages, neutrophils, ...) which innately recognize the bad guys which have characteristic non human molecular structures.

The other half of the immune system is called the adaptive immune system in which specialized cells T-cells and B-cells, rearrange their own DNA to create new and varied receptors which are specific for foreign antibodies.
T and B cells work together to recognize different sides(epitopes) of foreign mollecules (foreign peptides) and have to agree that the mollecule is foreign. A process of clonal selection and deletion of T-cells and B-cells in the thymus and bone marrow respectively can sometimes go wrong and this leads to auto-immunity. For example some B-cells which recognize self antigens might escape clonal deletion during their maturation process, and become later (many years ?) activated by a T cell which recognizes an adjuvant (close by aggravating molecule, such as a viral surface molecule).
Once the B-cells matures they can secrete self anti bodies.

Finally the innate and adaptive immune systems work together and shouldn't be thought of as separate. For example the complement system is part of the innate immune system as a molecular cascade amplifying immune system signals and works with both the adaptive and innate systems.

It would help if you can describe the specific type of autoimmune condition that you are investigating as there may be several ways that the immune system can become directed towards self.

There is a great online course from UC IRVINE and whose videos/lectures on the immune system available on youtube, you'll need at least 27 hours of good concentration, the autoimmune lectures are towards the last ones.

https://www.youtube.com/watch?v=gVCfC8WW4eU&list=PLIHnZ4fK_IyJaH2WNHIk2cFsnR2UM4z7t

My understanding is still evolving, however I hope this helps.


Can a rotten egg actually hatches to a real life?

A chick can't develop outside of it's egg, so you won't see an embryonic chick growing and wiggling in a pool of substance leaked from a cracked egg.

Centuries ago, people believed in spontaneous generation: that life can arise from non-living things. A common example of this was the fact that maggots would "arise" from rotting meat if left to rot.

Although this theory was disproved, it is not rare to find someone that still believes it, because they seem to see it happen.

In the 1800's, before DNA was discovered, it became accepted that "like gives rise to like" - that is, chicken eggs will hatch chicks (not peacocks or mice), pea seeds will always give rise to peas, etc.

DNA was 'discovered' in the late 1800's by Johann Friedrich Miescher. He extracted a new king of organic moleculr out of cell nuclei, which he called "nuclein". Although Miescher did develop some hypotheses about how "nuclein" might be involved in heredity, he ascribed to the view at the time that any one type of molecule would be too simple to account for all the variation seen within species.

It would be about 75 years before the magnitude of Miescher's discovery would be fully understood, and that DNA is the basis for heredity.

Chicken eggs, if they give rise to anything (which will depend on if it is fertilized and properly incubated) can only give rise to chickens. Whether they are fertilized or not, they can't give rise to worms. A chick can't develop outside of it's egg, so you won't see an embryonic chick growing and wiggling in a pool of substance leaked from a cracked egg.

If you buy bananas and let them ripen and rot on your kitchen counter, you will suddenly find a lot of fruit flies in the house. The fruit flies did not spontaneously arise from the bananas; they came from eggs laid on the bananas before you bought them.

If you buy bananas and wash them well when you get home, and let them rot, you will not find fruit flies buzzing around them.

That is why your rotten egg didn't give rise to those little worm things.


What's the difference between morphospace expansion and packing?

You're almost there--both terms concern the relationship between increases in species richness and morphological diversification. They're two opposing patterns:

Morphospace expansion indicates that a lineage is occupying new areas of morphospace with increasing species richness. (The slope is more or less relating density of morphospace occupation to speciation rate--so > 0 means new species tend to go farther away in morphospace.)

Morphospace packing indicates that a lineage is not expanding its morphospace with increasing species richness, so the existing region of morphospace that it occupies is getting more densely filled, instead of expanding.

The relationship between functional/ecological diversity and morphological diversity isn't always clear cut, though, so you have to be careful when relating the two. If you're going to use these concepts, especially if you're going to use morphological diversity as a proxy for functional diversity, it's best to state that assumption outright.

This paper includes a nice discussion of the two concepts (and is cited by the one you list): http://rspb.royalsocietypublishing.org/content/283/1822/20152013


Human bones grow in length due to the effects of human growth hormone on the epiphyseal plates near the ends of the bone. Over time these two growing margins decrease in size, or width, until those special cells are either gone, or can no longer respond to hGH. At that point the body has no mechanism to increase the size of the skeleton, and growth stops. In females this tends to happen earlier than in males; approximately 2 years after the onset of puberty for females.


Klenow seems to lack exonuclease activity ("proof-reading"), but otherwise works like normal DNA polymerase, so I wouldn't expect anything different from PCR. On each step, as long as there is enough template and primers, you'll get doubling of current template.


How much electrical energy is required for intracellular stimulation of a neuron?

I think this question is somewhat ill-posed, but I'll try to answer it:

None.

All you have to do is to short the inside of the cell to the outside/ground. Of course in reality this means expending some energy somewhere, but at that point it's an engineering problem, not one of biology, and it has nothing to do with the neuron itself.

Action potential firing is a completely passive process. The only part that requires energy (besides protein synthesis) is for the sodium-potassium ATPase that maintains sodium and potassium gradients.


Protein that exit from the cell - as marker

You can always express GFP or your favorite protein in a secretory vector like pSecTag or pSecTag2 from Invitrogen/Life/ThermoFisher/SuperUltraBioMegaMart. There are probably others, but those were the first ones I came across. They contain the mouse Igκ signal sequence for efficient secretion (so the website says, I've never used it).

I don't know the details of your experiment, but are you sure you want to use a secreted protein as a transfection marker? Remember, it's possible that only a small fraction of your cell population will take up the vector (or mRNA, if that's what you're using, but there are issues with that), but you will see secreted protein regardless of the number of cells that take it up.


Can dish soap really be used to kill ticks and fleas?

First part of the answer - Yes fleas (Siphonaptera) can be drowned. But not as easily as the internet would lead you to believe.

There are many claims on the internet (and printed works) expounding on how simple it is to drown fleas.  The best science I found so far on the topic is in Forensic Entomology: An Introduction By Dorothy Gennard; John Wiley & Sons, Apr 30, 2013; section 4.3 which reflects a 1985 work by Simpson K. (Journal of the New York Entomological Society 76: 253-265, not finding this online). Gennard is using the fleas present on a human body at death to determine how long the body had been submerged.  Findings -

A flea submerged for up to 12 hours will appear to dead, but can revive in about 60 minutes after being removed from the water
A flea submerged for 18 - 20 hours will appear to dead, but can revive in  4- 5 hours after being removed from the water
It takes 24 hours of full submersion to fatally drown a flea

Side note; lice (Phthiraptera) can be fatally drowned in about 12 hours.

Second part of the answer - Yes soap can facilitate the death of fleas in bathing

So far the best I have is Medical and Veterinary Entomology by Gary R. Mullen, Lance A. Durden Academic Press, Apr 22, 2009

This work suggests the process of washing the flea (and the pet) removes integumental waxes on the fleas body and they die from desiccation (dehydration).

More Research

I have been unable to find solid research specific to fleas (Siphonaptera) and soap (surfactants), so I had to reach in to the general insect works for answers.  There are a number of pesticides which include surfactants in their make up to increase effectiveness but these seem to be to an aid in the delivery of the pesticide not because the surfactant has any additional killing power.

  a surfactant may affect the efficacy of an insecticide by its influence on wetting, spreading and run-off rather than by its influence on cuticular penetration

The Physiology of Insecta, Volume 6 edited by Morris Rockstein

There is some science suggesting soaps can help break down cell membranes but they seem to be most effective on soft bodied insects (which fleas are not)

  Soaps... kill insects by disrupting the exoskeleton and breaking down cell membranes.  Soaps generally work best against small soft bodied insects such as aphids, scale crawlers, meatybugs, and young caterpillars as well as spider mites.

Destructive Turfgrass Insects: Biology, Diagnosis, and Control By Daniel A. Potter

Summary

There are multiple online reports of "drowning fleas" and killing them with soapy water.  After looking for the science there does not seem to be much support for these fatal claims. There is little doubt that giving your pet a soapy bath in the tub will help remove the fleas, they may even appear dead.  But in all likelihood these fleas are just waiting to dry out and be revived, hopefully in the city sewer.  If you bath your pet in the yard, and than let the dry pet in the yard again the next day the clean pet and clean revived fleas will likely reunite. Soapy water is more likely to facilitate removal of the comatose flea from the pet and carry it down the drain. So it is reasonable to have noticeable decrease in the flea population after a bath.  But excessive bathing has it's own risks and given the life cycle of a flea soapy baths alone are unlikely to be a final solution.


Are nucleotides at the ends of DNA stripped on aging?

The Stanford article that you read is correct, in the sense that telomeres do not need to be completely removed by cell division before deleterious effects occur and cells start undergoing senescence.

This Nature article describes an experiment in which the minimum length of telomeres (beyond which chromosomal fusion occurs) was determined:

  The critical telomere length was 12.8 repeats (of six base pairs)
  long, they found — any shorter and the chromosomes began to fuse
  together at their ends (R. Capper et al. Genes Dev.
  doi:10.1101/gad.439107; 2007). Baird suggests that without
  sufficiently long telomere caps, the cell may perceive the chromosome
  ends as broken strands of DNA and attempt to piece them together.

Therefore, we can conclude that while it is not impossible for non-telomeric nucleotides to be stripped from chromosomal ends, this generally does not happen, since cellular defense mechanisms such as non-homologous end joining (NHEJ) and microhomology-mediated end joining (MMEJ) would activate before that point, and start joining chromosomal ends together. This would then lead to issues during mitosis, which would likely halt further cell divisions.


I'll amend this answer as I get details from you.

What is your cytometer, and how are the optics set up? You typically have 1-5 lasers: UV (355nm), violet (405nm), blue (488nm), green/yellow (~561nm) and red (~633nm) lasers. Your FL number, FL1-4, typically refer to a particular PMT (photomultiplier tube) and filter combination. For example, a typical FACSCantoII has a 4-2-2 setup with 4 PMT on the blue laser, 2 on the violet laser and 2 on the red laser (if you bought the device that way, there are other configurations). These fluorescence channels are set up to detect a particular fluorophore or equivalent with a bandpass filter. The base filters on FACSCanto II red laser are 660/20 and 780/60. These filter light emitted by the stained cells at a particular range of wavelengths, and you read them as 600nm +/- 10nm and 780nm +/- 30nm, for example.

You can set your software up to be FL numbers or fluorophores, but what you need to know is what filter is FL1 and so forth? Typical cytometers like FACSAria, these are FL1 = FITC, FL2 = PE, FL3 = 7AAD, PerCP/Cy5.5, etc., FL4 = APC.

So you used a live/dead thermofisher kit, please provide us also the catalog numbers.

What we want to do is take the information about your dyes and about your cytometer and reconcile them to determine what channel they should fluoresce in. 488nm looks like FITC or FL1 and 570nm looks like PE or FL2, but these look like lasers, whereas you want to tell me the dye emission to match it to a channel, using the information about your device configuration!

As for software, there are a number of good, expensive options like FCS Express and FlowJo but they're costly. See if your core or what have you has these available for you to use on-site. Otherwise, the on-board cytometer software like FACSDiva may need to suffice, and often does. I've used some of the "free" ones but they're very clunky and/or terrible to use.

R has some usefulness for high-dimensional analysis, but you need to be able to use R fluently, and you can't draw manual gates. There do exist helpful packages with good documentation like X-cyt (broad institute), though. And for visualization like PCA and t-SNE, R has a lot of documentation for flow data. Also consider R loads everything into RAM so on a slower 2-4GB computer it might have lackluster performance.

To start with your analysis, I'll ask why did you use two dyes? The LIVE/DEAD product line are reactive with free amines which present inside and outside the cell. Dying cells have more permeable membranes and take up more dye. So when you analyze the cells, everything is positive, but the dead and dying cells are 1-2 logs higher intensity of staining compared to the live population.

So the first thing any flow experiment needs are controls. You have unstained controls, FMO controls and compensation controls. The unstained just gives you an idea your morphology by light scatter, but for low-dimensional experiements can act as an FMO. The FMO or fluorescence minus-one is a cell stained with everything in your antibody/dye panel except one marker, so that you can compare against the fully-stained sample and see where to draw your gate. Compensation controls help the cytometer correct for the fact that filters pick up emission from other fluorophores than the target. You also have a biological control, which is good, because for analysis you always want to see where a clear positive and negative population lay on your dotplots or histograms. Live cells help you see where the positive and negatives are but may have a weak positive signals, and unstained cells will have a negative population that is shifted down 1/2 log or so because they dont have any dye at all. The dead stained cells will show you a strong positive signal and potentially a weak negative signal. Use these to draw your gates.

So then compensate the data electronically with your software (follow the manual), and create a dotplot with FSC-A and SSC-A on the axes. Only experience will tell how your cells look on this plot, but for reference, a blood or leukocyte sample would like like this:

You want to draw a gate around your monocytes and then create a plot based on your monocyte gate (at least gate out debris). It's also useful for further experiments to stain with a monocyte marker so you can dump everything but your target cells, so use CD14, for example, which is specific to monocytes.

On the next dotplot, make the axes FSC-A and FSC-H. This is a doublet discimination step where laser area scaling done before a cytometer run helps a lot (see your core expert). The principle here is to gate out (get rid of) cells that are stuck together:

Then you would want to look for your target cells. If they're both live/dead dyes you're going to have the same signal on two different channels, so you can probably just pick one, like live/dead green.

You can do a histogram of FL1 based on the cells kept in the doublet plot. You should see two discrete peaks on a log or bi-exponential transformed intensity axis (width basis -10 is good to use, but FACSDiva does it automatically). Width basis is a co-factor that compresses the data around 0, so negative populations get smaller and you get better resolution among the positive populations.

You would draw a bifur gate between the positive and negative peak or a range gate around the positive, and select tell the software to generate statistics to get your percentages. And you can repeat for the FL2/red dye to get those percentages, too, but both markers are looking at the same thing.

Then, apply those gates to all your samples and adjust the gates based on what the data looks like.

Please try this presentation: https://www.slideshare.net/richardhastings589/kumc-introduction-to-flow-cytometry


To what extent do gonads affect differences in gendered behaviour?

Yes

During embryonic life,there is formation of new synapses by a process termed as exuberant synaptogenesis.
Their differential formation in the males and females could be due to the effect produced by the gene PCDH11X/Y located in the allosomes.

  PCDH11Y is a gene unique to human males that encodes Protocadherin 11Y, aprotein that guides the development of nerve cells. PCDH11X, located on the X chromosome, is common, in both sexes, to humans and our nearest relative, thechimpanzee; however, PCDH11Y, located on the Y chromosome, is unique to males.[3]
  ...PCDH11X/Y are cadherin family genes. They make proteins, involved in signalling, that attach to the surface of nerve cells.[4] PCDH11X and PCDH11Y, respond in different ways to Retinoic acid, a chemical involved in the development of embryos. The acid stimulates the activity of PCDH11Y but suppresses PCDH11X. This is likely one of the explanations for the differences between the brains of men and women.[3]
  [source]

About the parts of the brain which are deemed"sexually dimorphised" a few of them are:

1.hemispherical differences due to which inter hemispherical functioning is better is females
 whereas intra hemispherical functioning in males

2.hippocampal and amygdaloid laterisation

  on average males had larger grey matter volume in bilateral amygdalae,hippocampi, anterior parahippocampal gyri, posterior cingulate gyri, precuneus,putamen and temporal poles, areas in the left posterior and anterior cingulate gyri
  ...females on average had larger grey matter volume at the rightfrontal pole, inferior and middle frontal gyri, pars triangularis, planum temporale/parietal operculum, anterior cingulate gyrus, insular cortex, and Heschl's gyrus; bilateral thalami andprecuneus; the left parahippocampal gyrus and lateral occipital cortex
  Source:Neuroscience of sex differences

Furthur,since synaptogenesis may occur throughout one's lifespan perhaps not as greatly as during embryonic life and as receptors for gonadal hormones are present in the brain it can be said that the gonads may affect the phenomenon,though mainly after puberty when their concentrations are higher than during childhood.


Why is cold water more refreshing than warm water?

Short answer: Cold is pleasant only when your are not already freezing and cold might satiate thirst better because it acts as enhancer of the "water intake flow meter".

Is cold water more tasty than warm water? No, it is actually the reverse as detailed in my footnote.

Cold is pleasant when your body is over-heating and definitely not if you live naked in the North Pole. Over-heating means sweating which means you loose water and therefore feel thirsty faster. Yet drinking cold water will not rehydrate the body more than warm water and drinking water has only a very small impact on the body temperature. So why do we like it?

A study was actually conducted on the subject and answers most of your questions. Here the reference.

The temperature of the body will indeed not change.

  cold stimuli applied to the mouth
  (internal surface of the body) do not appear to impact on body
  temperature and are not reported to cause any reflex shivering
  or skin vasoconstriction that influence body temperature.

As you pointed out, the temperature of the ingested water will not affect the overall hydration of the body as cells are rehydrated mostly via the blood  stream and the blood temperature will not be affected. Someone could argue that, at identical volumes, cold water (above 4C) contains more molecules (i.e. is denser) than warm water but this difference is likely very slim.

In this paper they also define "thirst".

  Thirst is a homeostatic mechanism that regulates blood osmolarity
  by initiating water intake when blood osmolarity increases

The problem is that it takes some time before the water reaches the blood stream, and therefore you need a feedback mechanism that tells you to stop drinking independently of the blood's osmolarity. This is where cold might play a role.

  The cold stimulus to the mouth from ingestion of water may act
  as a satiety signal to meter water intake and prevent excessive
  ingestion of water

The picture would then be the following

In essence, a cold sensation is pleasant in warm weather, both on the skin and in the mouth, and it apparently helps in reducing thirst by being some kind of an  enhancer of the "water intake flow meter".

Footnote

Reading the comments I just want to clarify some points.

The 5 basic tastes (sweet, salty, bitter, sour and umami) are very distinct from taste sensations (pungency, smoothness, cooling to name a few). The main difference is that taste and "sensation" signals use completely different paths to reach the brain - namely, the facial and glossopharyngeal nerves for the former and the trigeminal nerve for the latter.

Is the temperature affecting basic taste perceptions? The answer is yes. How this happens is quite simple if you understand the fundamental concepts of molecular taste perception. Essentially the temperature affects the response of the receptor TRPM5 which is the main player in depolarizing taste receptor cells in the papillae. To put it simply, higher temperatures provoke a greater perception for taste, and this is not only in term of perceived taste but really modifies the amplitude of the response at the molecular level. As an example this is why ice cream does not taste sweet when frozen but only after it melted in the mouth or on the tongue.


I interpret your question as: Given a stretch of DNA sequence, can we determine if it encodes a gene? My summary of the answer would be: "Sometimes".

The problem you ask about is called "Gene prediction" and is described in some detail by Wikipedia:  http://en.wikipedia.org/wiki/Gene_prediction

The most basic indication that a gene may exist is the presence of an "Open Reading Frame" (ORF). An ORF is a stretch of DNA from which a single protein may be produced.  However, an ORF is not strictly required for a gene (as not all genes encode proteins), and not all ORFs are genes. There are many software tools for gene prediction available which use different rules to predict if a given region of DNA is functional (contains a gene or a regulatory element). They may be usable on any kind of DNA sequence, or on sequences from certain organisms only, depending on the program.

Two commmonly used gene prediction tool are GLIMMER (http://www.ncbi.nlm.nih.gov/genomes/MICROBES/glimmer_3.cgi, used for microbial genomes) and GeneMark (http://opal.biology.gatech.edu/gmhmm2_prok.cgi). See also http://en.wikipedia.org/wiki/Gene_prediction

As a quick check, you may also use NCBI BLAST (http://blast.ncbi.nlm.nih.gov/Blast.cgi) to see if your sequence aligns to a known gene.


Have there been studies done to test Immortality of cancer cells in culture?

The HeLa cell line is undoubtedly the most used and investigated human  immortal tumor cell line. Extracted from a cervical tumor from Henrietta Lacks in 1951 at Johns Hopkins hospital, Baltimore, MD these cells proved immortal and are still used in many, many labs worldwide today. It is the oldest human cell line in use and, therefore, the oldest human tumor cell line (Callaway, 2013).

In terms of senescence of immortal cells; HeLa cells are immortal, and hence do not grow old as such. However, they are subject to mutations and the genetic profile of HeLa cells does change over time. Hence, although they may not be growing old, they do age in the sense that mutations are accumulating in continuous cell lines.

References
Callaway, Nature (2013); 500: 132-3


Location of microbes causing eliminated diseases

Whether a disease can be eradicated or not depends on its reservoir. To be eliminated it needs to be eliminated in all places and organisms it can thrive in and spread from. This makes diseases like rabies for example hard to eradicate altogether because it can exist and spread in many different animal species.

Polio and smallpox however both have no non-human reservoir, which makes it possible to eradicate them. There is no "in the wild" for them to persist in because humans are "the wild" for them. So smallpox the disease has indeed been made extinct like the dodo; polio we're not quite there yet but we seem to be close.

I said "smallpox the disease" because "smallpox the virus" still exists in two laboratories in the US and Russia.

Polio, as I said, isn't an "eliminated disease" yet (as of May 2017), but since you mentioned it, the main places it persists now are Afghanistan and Pakistan.


Our food mostly gets spoiled by bacteria and / or fungi. There are 2 main reasons for sugar crystals not getting spoiled.

1- Lack of sufficient amount of water to sustain metabolic processes by microbes.

2- Even if sufficient amount of water is present , then due to high osmolality of the fluid formed, will cause plasmolysis or cell shrinkage.

Some technical data:

  Microorganisms differ widely in their ability to resist salt- or sugar-induced reductions of aw. Most disease-causing bacteria do not grow below 0.94 aw (roughly 10 percent sodium chloride concentration), whereas most molds that spoil foods grow at an aw as low as 0.80, corresponding to highly concentrated salt or sugar solutions.

Source: https://www.scientificamerican.com/article/how-do-salt-and-sugar-pre/


Strange white strings on cherry tree leaves

This sort of thing happened to one of my plants.  When I took a closer look at the plant, it was a group of white aphids.  The brown coloration of the leaves of your cherry tree was relevant because aphids can sometimes kill the entire plant that they feed off of.

I did not take a picture of the plant, but I found one online: https://entnemdept.ifas.ufl.edu/creatures/trees/shivaphis_celti03.jpg


Can any gas other than nitrogen cause decompression sickness (the bends)?

Yes, it is possible to get decompression sickness with other gasses, such as the "oxygen bends" or oxygen decompression.  For instance, in this study, they demonstrated that oxygen decompression sickness in mice.  Another study demonstrates a more common non-nitrogen decompression sickness - helium bends.
Undoubtedly you will be wondering at this point why breathing pure oxygen would diminish (or, in certain circumstances, completely remove) the risk of bends as compared with nitrogen.  The reason is simply that oxygen, unlike nitrogen gas, is constantly being metabolized by the body tissues.  Consequently, even if the oxygen levels in your body fluids become elevated, they would have to be way higher than normal levels (like in the first study linked) before you would start to have it accumulating enough to form bubbles.
The body is designed for the shipping and handling of oxygen (think haemoglobin & myoglobin).  Nitrogen, on the other hand, is relatively incidentally present - so long as atmospheric pressure remains relatively constant (which it did until we devised technology allowing us to radically change it), it's present in low levels in all the body tissues without causing any trouble.


A phosphoester bond is in fact a bond between the phosphorus atom of a phosphate group and an oxygen atom. Your confusion comes from the fact that electronpusher's statement is inaccurate.

Instead, electronpusher should have said:

  Each nucleotide contains one phosphodiester bond (between a phosphate O & a 5'-C on one sugar belonging to one nucleotide, and then another bond between a phosphate O & a 3'-C on another sugar belonging to another nucleotide).

More elegantly put, "a phosphodiester bond occurs when two of the hydroxyl groups in phosphoric acid react with hydroxyl groups on other molecules to form two ester bonds" (source).

The resulting bond is between O-C because the hydroxyl groups react with each other and transesterification occurs. The OH from the phosphate interacts with the OH (attached to the carbon) from the sugar, transesterification occurs, thus leaving only 1 oxygen, of which is the oxygen in the P-O-C bond sequence, exhibited in the following image.

The next image is a simplification of the reaction mechanism. Dehydration does not actually occur (transesterification does, as mentioned), but instead, this image is provided as to more easily identify which entities are involved in the reaction, as to more directly address the concerns expressed by the OP. The true reaction mechanism can be found here.


How does the Pectoralis Major work when doing a bench press?

The pectoralis muscle attaches to the top to the inner half of the clavicle, just underneath the biceps on the inner part of your arm and the breastbone (a.k.a the sternum) which is found in the middle of your ribs. See below:

So taking that in account the pectoralis muscle helps bring your arm closer to your body (adducts your arm), pulling it forward in front of you (flexes the humerus) to push up like you would when you bench press. This action can be seen below.


It said to be an eagle.

It looks like a Ptolemy V (204–181 BC):

http://www.bonanza.com/listings/-DD-G-068-Ptolomy-V-Octadrachm-COPY/16293418?gpid=21297750541&gpkwd=&goog_pla=1&gclid=CMWBpbOaxrUCFYx_Qgod6TsA9w

it looks to be a pretty standard motif of that era:

From: http://www.worthpoint.com/worthopedia/alexander-iii-great-336bc-greek-coin-150614256

I agree that this is not really a biology question.. but what the hey.


Edible by whom? Lets assume humans.

Yes all quadrpeds are edible though you may not want to eat every part.

For example, the scent glands of a skunk, or the quills of a porcupine are repulsive or impossible to eat. Also, some organs, like the liver of a polar bear, which accumulates vitamin A to toxic (to humans) levels.

It's impossible to say why this is so, since we can't prove why evolution occurs one way or another. What you suggest about mobility is reasonable, but not universal, since the poisonous puffer fish is able to move.


How much mass does a person lose in a day through breathing and perspiration?

The simplest route to your answer would be through the kcal consumed/expended equation.

1kg (2.2lbs) of fat has ~7700 kcal of energy. The average person requires roughly 2000kcal per day if they perform mild physical labor throughout their day - 25.9% of the total energy available in 1kg of fat. So you could say that if a person did not eat for a day they would lose ~1/4kg or 1/2lb of fat-mass.

I calculated the above in "fat" because it's the number I knew off-hand, but truth be told the amount of "mass" you'd lose also depends on density. Fat (9kcal/g) is more energy dense than alcohol (7kcal/g), carbohydrates/sugars (4kcal/g), and protein (4kcal/g). For the same energy expenditure of 2000kcal in a single day you would metabolise more than 1/2kg or 1lb of either carbohydrates or proteins.

In reality you will burn roughly equal amounts of fats and carbohydrates (assuming you're not forcing your body into a ketogenic state) at about a 55% fat/45% carbs ratio IIRC.

So, with the assumption that the person isn't on a keto diet, has sufficient fat reserves, and expends 2000kcal of energy in a single day while drinking enough water to replace what is used in the energy metabolism, you will lose ~.14kg of fat and ~.63kg of carbohydrates for a grand total of ~.77kg (~1.69lbs) of mass expended per day.

Since humans vary greatly, however, that is going to vary wildly. Personally speaking, it's easy for me to expend >3000kcal per day with an hour of moderate exercise since I'm simply bigger than the average person and require more energy to do anything. If you're shorter than average, do less work than average (i.e. - are sedentary), or hormonal conditions (which are rare and cannot be self-diagnosed) modify calorie expenditure, your numbers will be different.

Also worth it to note: Ghrelin, a major hunger-regulating hormone, changes its tonic behavior significantly if you go more than 2 days consuming less than 1200kcal. After 2 days fasting it will instigate changes that will result in more fat retained after you resume a regular eating schedule for up to 5 years... So starving yourself for a week to lose 5kg seems great until you realize you'll gain 10kg once you go back to a normal diet.

As always, if you're unsure of any diets please go to a qualified professional for consultation.


Relaxing Eyes when using Virtual-Reality-Glasses?

The eyes cannot focus on something a few centimeters away. The average maximum distance where the eye can still focus is 14 Diopters in young people (Duane, 1922) (approximately 7 cm in 8-year olds). The distance to the eyes of the display in a head-mounted display (HMD) is often less than this and hence the eyes cannot possibly focus on this. Instead, with the use of lenses, a virtual image is created at a virtual distance approximately a meter away (Fig. 1). In the Oculus Rift DK1, for example, the virtual screens were infinitely far away; in the Oculus Rift DK2, they are about 4.5 feet (1.4m) away (source: Immersive Computer Graphics). One meters is a comfortable viewing distance with minimal accommodation needed and hence little eye strain (source: Immersive Computer Graphics). At around 6 meters the eye is unaccommodated.

Fig. 1. Virtual image in a HMD. Left: eye failing to focus on a very close real screen. Right: eye able to focus on the virtual image of the same real screen created by an interposed lens. source: Immersive Computer Graphics

Reference
- Duane, Trans Am Ophthalmol Soc (1922); 20: 132–57


What is the biological name of this plant?

This is Ageratum conyzoides, a flower of Asteraceae family.

The common Bengali name of this plant is Uchunti.

Other than this purple colour a white colour of this flower is also observed.


Blood group A expresses A antigens and anti-B antibodies etc etc, see the next figure:

Taken from the wikipedia entry on blood groups.


Why does the pH decrease, when adding pancreatin to different types of milk (cow milk, soy milk etc.)?

the pancreatic fluid contains lipase which breaks down the fat in the milk in to fatty acids and glycerol. The fatty acids produce lower and create a more acidic pH.


What could cause individual false positives in ELISAs, while the rest of the plate looks fine?

Is your detection or secondary antibody aggregating? I've done extensive clinical ELISA development in the past and when this problem inevitably crops up for these assays the most likely culprits in order were:

Plate washer acting funny
Antibody aggregates binding nonspecifically to the plate
Inefficient blocking reagent/not enough time spent blocking
Person running the samples is mixing things up

Even if your false positives predate the platewasher malfunction, you could still have a leaky/clogged dispensing nozzle. Try rotating the plate 180 between wash steps or hand-washing and see if that helps.
For aggregated secondary/detection ab, give them a brief spin and pipette off the top, and for blocking increase volume/time.


The expected value is what the values would be if the tested conditions had no effect on the sample distribution. In your case, you are testing the effect of herbicides on butterfly populations. If the presence of herbicides wouldn't matter you would expect an equal number of butterflies on fields with herbicides as without.

So, the total number of butterflies being $37 + 3 = 40$, you would expect $\frac{40}{2} = 20$ butterflies on fields without and $\frac{40}{2} = 20$ on fields with herbicides.


Question: What is CINWntUp and CINnormL?

From the paper:

  The dataset contains six colon cancer subtypes: class 1 = CINImmune-Down (116 samples), class 2 = dMMR (104 samples), class 3 = KRASm (75 samples), class 4 = CSC (59 samples), class 5 = CINWntUp (152 samples), and class 6 = CINnormL (60 samples).

CINWntUp and CINnormL are therefore two classes of colon cancer. You are correct, CIN is for chromosomal instability; WntUp refers to upregulation of Wnt, a signalling pathway involved in some cancers and named for a Wingless/Integrated phenotype in fruit flies and the homologous gene in vertebrates. normL stands for "normal-like."

See the original paper describing these classes:

Marisa, L., de Reyniès, A., Duval, A., Selves, J., Gaub, M. P., Vescovo, L., ... & Kirzin, S. (2013). Gene expression classification of colon cancer into molecular subtypes: characterization, validation, and prognostic value. PLoS medicine, 10(5), e1001453.


Should we induce fever to assist healing?

Could it be beneficial to artificially induce fever in a person who has an illness if they are not already experiencing fever?

No, not really. Pretty much the only use of hyperthermia in medicine is in the treatment of cancer. If you google "use of hyperthermia in medical treatment", you'll likely only find two kinds of hits: those for cancer treatment and those for malignant hyperthermia (a side effect of some psychotropic drugs.) The hyperthermia used to kill resistant cancer cells is high enough to destroy proteins (~113°-114°) and very localized; your entire body raised to this temperature would result in death very quickly. Lower (i.e. physiological) levers of "hyperthermia" (or hyperpyrexia) would not kill the cells.

At the turn of the century, there were many who believed in the therapeutic use of hyperthermia in the form of hot baths, hot springs, and even injection of infectious agents to produce fever(!), but the practice has fallen into disuse, probably because there were no studies which supported it.

However, hyperthermia isn't good for you; it is something to treat seriously. When the cause isn't known, the efforts used to treat it can amount to many unnecessary tests and treatments (as seen in the accident victim in the fourth reference. When it's present in a moderate amount, it can still be dangerous:

  When fever occurs, many physiological stresses take place. Some of these include increased oxygen consumption as a response to increased cell metabolism, increased heart rate, increased cardiac output, increased leukocyte count, and an increased level of C-reactive protein. Oxygen consumption increases by 13% for every 1°C increase in body temperature, provided no shivering occurs. If shivering is present, oxygen consumption may increase by 100% to 200%. Some cytokines released during fever states also induce physiological stress. These cytokines can trigger accelerated muscle catabolism by causing weight loss, loss of strength, and negative nitrogen balance. Physiological stress can be manifested by decreased mental acuity, delirium, and seizures, which are more frequent in children.

It is likely beneficial in the presence of infection:

  Heat shock proteins are one of the more recently studied fever-responsive proteins. These proteins are produced during fever states and are critical for cellular survival during stress. Studies suggest that these proteins may have anti-inflammatory effects by decreasing the levels of proinflammatory cytokines. Fever also triggers other beneficial effects, including an increase in the phagocytic and bacteriocidal activity of neutrophils and enhanced cytotoxic effects of lymphocytes. Some bacteria become less virulent and grow slower at the higher temperatures associated with fever. Increased levels of C-reactive protein promote phagocytic adherence to invading organisms, modulate inflammations, and encourage tissue repair.

In the absence of infection, there is no benefit to systemic elevation of temperature. For the disadvantages of continued elevated metabolic rate, one need only look at hyperthyroidism to see the deleterious effects, the worst being cardiotoxicity, even in subclinical hyperthyroidism, as well as dementia, atrial fibrillation, ventricular hypertrophy, miscarriage, perinatal morbidity and mortality, decreased exercise tolerance, etc.

Years ago, one of the most common self-inflicted illnesses was hyperthyroidism - people taking thyroid hormone replacement unnecessarily - usually because of the weight loss that occurs with elevated metabolic states. Interestingly, efforts are underway to isolste and manufacture a thyroid-hormone like substance which will cause decreased weight without cardiotoxic effects.

Hyperthermia in Cancer Treatment
HYPERPYREXIA PRODUCED BY BATHS
ARTIFICIAL FEVER IN THE TREATMENT OF GONORRHEAL OPHTHALMIA
Thyrotoxicosis in a patient with multiple trauma
Metabolic Effects of Thyroid Hormone Derivatives


This is a wasp spider (Agriope bruennichi)

See here: Wasp spider

The link leads to a German Website showing the belly side of a wasp spider

Or see here: Wasp spider II


How does BH2 reduction to BH4 need only one NADPH molecule?

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

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

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

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

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

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

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

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

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

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

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

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

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


It means the software has 4753 genes it has labeled with "biological regulation" and the short list you gave has 45 of those genes.  That is a little higher than you might expect by chance if you'd given a random gene list of the same size.


Does breath-holding cause permanent brain damage?

In order to reply to your question I (*) need to dissect it into 3 parts.

1 - Can you voluntarily hold your breath so long that damage actually occurs?
There is evidence that apnoe-divers damage their brains while diving. In the above, the marker protein S100B, representing brain, damage was elevated. This marker had been found previously to be increased in stroke and other forms of brain damage. Therefore, it appears that brain damage occurs when trained freedivers hold their breath on average 335 s (range 281-403 s). I could not find published data on whether this results in cognitive changes. Another really interesting study I found was also on US Navy divers but with oxygen supply. Their cognition was tested and transient alterations in affect, visual focusing, and physical activity were temporarily seen for 10 days after diving. Pressure changes might have an impact on top of the lack of oxygen.

2 - To summarize a study from a good previous post, researchers measured oxygen saturation in the blood while subject were holding their breath. Oxygen saturation dropped as low as 75% (see original paper).

3 - Additional studies. A blood oxygen level dependent functional-MRI study in adults and children showed similar activated regions while holding their breath. Breath holding in childrens’ brains causes stronger alterations. Their brains seem to be more vulnerable than adult brains. The insular cortex was identified as a specific region in the brain, being responsible for breathing again after holding breath. These findings originate from a positron-emission study which was able to localize air hunger to the insular cortex. The insula is part of the limbic system which regulates essential tasks in humans including temperature, nausea, and pain. Feeling shortness of breath is important for survival and therefore as shown with PET also located in the limbic system.

(*Note that I'm submitting this well researched answer for Tim, an MD, who took the time to write the text but doesn't have the time to sign up or reach the required reputation limit to post. I only filtered out some medical lingo and streamlined the text. The kudos are his.)


How to learn and memorize animals classification to get an intuition about them?

Another alternative is the Tree of Life web project, which includes species richness information in the lower levels of the tree and allows reasonably easy navigation of subtrees. You can find the animal portal here.

EDIT -- another alternative, which is in active development, is this integration of Wikipedia and the Open Tree of Life Hyperbolic Tree.


I think the first possible answer is wrong because maybe by "set" they mean the total number of autosomes. Where as in the figure below it states that the autosome is only responsible for a repressor(Dpn), and that in normal conditions (in pairs i assume) they product equal amounts for females and males.

If the chromosome 2 was not in a proper pair, then I assume the dosage of the Dpn repressor would be off.

The gene dosage is with the activators produced also, sis-a, and sis-b. So I guess in females they produce twice as much activator for the Sxl protein, which later on allows for the repression of male genes and activation of female genes.


What are known methods of non-surgically disabling neural tracts/pathways (esp. Corpus Callosum)?

I was able to find one non-invasive method to sever the corpus callosum (callosotomy). This method is referred to as gamma knife radiosurgery (Mathew et al., 2007). Basically, 201 beams of gamma beams are focused on the corpus callosum and where the beams intersect, the energy is high enough to permanently damage the tissue. I doubt this technique is available for routine use in animals, though.

Another interesting technique is photothrombosis. This method is based on the systemic injection of a photosensitive dye named Rose bengal. Subsequent focal illumination of the brain with a cold light source through the intact skull leads to focal cortical infarcts of reproducible size, location and geometry (Schroeter et al., 2002) . Brain damage is induced due to photo-activation of the dye and subsequent endothelial damage with platelet activation and thrombosis, resulting in local blood flow interruption. The light source can be applied on the intact skull with no need of craniotomy, which allows targeting of any cortical area of interest in a reproducible and non-invasive way (Labat-Gest & Tomasi, 2013). However, although the light source penetrates the skull, I don't think the method is useful for the induction of deep-brain lesions, as I was able to locate only studies using it to model cortical lesions.

Having not answered the question, I'd like to say that either surgical sectioning, or chemical ablation using micro-injection of neurotoxins are the most commonly encountered methods to perform a callosotomy.

References
- Labat-Gest & Tomasi, J Vis Exp (2013); 76: 50370
- Schroeter et al., J Neurosci Methods (2002); 117(1): 43–9
- Mathew et al., J Neurosurgery: Pediatrics (2007); 106(4): 312-5


How are the various classes of E coli genes determined?

I read through the paper. The author starts by stating that as of the time of writing, two different classes of codon usage profiles were known (or at least putatively so). All 782 unique CDS sequences used were subjected to a two-step classification method. In step one, each CDSs was broken down into a 61-dimensional vector representing each of the 61 possible codons. A factorial cluster analysis (the categorical, multi-variate equivalent of principle component analysis) was run on these vectors, condensing 61 dimensions down to 2 dimensions. Now that the data complexity has been reduced to 2D, it is more manageable for a k-means algorithm to partition the data. In the end, the genes were clustered into 3 orthogonal groups (classes I, II and III, with 502, 191 and 89 CDS, respectively).

Only after the authors clustered the gene set were they able to go back and look at the canonical definitions of each gene. It so happened, fortuitously, that each class of the genes had a strong bias for subsets of cellular function (eg, metabolism, protein biosynthesis, transport). They did not use proteome data, but they were able to define the role for a large number of these genes based on the body of literature at the time.


Signaling through G protein Coupled Receptors?

EDITED ANSWER

Based on comments and responses my original answer to this question received I have decided to edit the answer and respond to some questions.

Since I work on proteins, I tend to favour protein based approaches specially when wondering about the presence of a protein. This is simply the case because protein is what is important functionally (purely talking about protein based problems/questions here and not talking about RNAi stuff here) so what I have experienced editors require for majority of papers, they want to see some sort of protein work. Now I'm aware that is not always possible since the antibody (Ab) might not be very specific or sensitive specially for low expressing proteins. If a protein is highly transient that makes the problem even worse, which is why many people resort to mRNA expression to make deductive reasoning for the presence of proteins although that makes a number of assumptions about how the mRNA is processed and whether the relationship between mRNA expression and protein expression level is linear but thats another discussion. So all I'm trying to say is that it's important check for the presence of a protein using Ab based techniques, which are immunohistochemistry (IHC) and western-blot (WB).

So my primary recommendation is to use Gi and Gs species specific (non-cross reactive) antibodies to check for the presence of your proteins of interest and always use Ab heavy chain control for IHC and a negative control for your WB using a sample that you know doesn't express your proteins of interest, if thats available. IHC also tells you some spatial information and whether Gs and Gi are both present in the same cell line or not and if they co-localise etc etc! Obviously check for Ab availability and if its compatible for IHC or WB procedures.

The other method that is feasible is if you know your two different cells express only one of the Gs or Gi exclusively, you can look at their specific inhibitors and add it to some of your cells and the chances are if the dose is high enough it will cause the cells to die since Gs or Gi are crucial for cell function. You can probably get away with an experiment like this using wells in a 24 well dish so you don't have to use that much media or drugs. But with stuff like this it might not work and you might get off-target effects so just do this as a complementary test. For your drug test always do a DMSO control since the chances are that's what the drugs are dissolved in and if not just use whatever solvent the drugs are dissolved in and add them to your cells in your control experiments.

Now the other possible and commonly used method to check for the gene expression of protein and subsequently infer its presence as a protein is to use a reverse transcription based PCR, such as RT-PCR although it doesn't have to be real-time as correctly mentioned in the comments. Please note that I'm not at all an expert in this and do check my answer in this section since I haven't personally done reverse transcription based PCR. As far as I'm aware, the basic procedure is to extract cellular mRNA, which can be performed using kits such as RNeasy or a similar product (I'm not promoting any products here and these are just what I have came across!). The protocols come with the kits and available online, and tells you exactly what min/max cell number/RNA levels should be present and how your cells should be (pelleted) before processing. Another method for RNA extraction is CsCl but thats pretty messy and complicated and requires high expertise to get it right but I know its inevitable for certain situations but for cell processing, a kit will do. At least RNeasy protocol states it enriches for mRNA and selectively exclude other types of RNA. Once you have your cellular mRNA you can proceed to reverse transcription using the appropriately designed primers for your gene of interest using a thermocycler. Again I'm not sure what tools to use for designing the primers for making cDNA from mRNA and what to look for (apart from the fact that make sure your primers are specific) as I only do regular PCR but would welcome any edits! Once you get from mRNA to cDNA, you can then run them on your (Ethidium Bromide or whatever DNA staining based) agarose gel and see if your amplicon is present and is the correct size (again based on the primers you have chosen you would know what the correct size is) and hence whether your gene is expressed or not. At least RNeasy kit says you do not need to use DNase digestion to get rid of any DNA before reverse transcribing your mRNA as most of it gets cleaned up when using the kit but you have that option. Now regarding the next-generation RNA sequencing I do not know anything about them so would again welcome any edits but seems unnecessary since you only want to know if the gene of interest is expressed so don't need any sequence info but thats an option too (although I imagine a little expensive?). Just to mention something very obvious, it's important that the species, which your lines have been generated from are sequenced or you have good sequence information about the Gs and Gi genes in your lines otherwise designing primers would be guess work. Its always best to see if anyone has done what you are trying to do and ask for their primers as most people are happy to share reagents.

Now you have probably noticed so far that my methods are quite biased towards molecular biology approaches and that's simply because that's what I know more about, however a great suggestion was to use cAMP levels as an indicator for Gs or Gi expression. Again I'm not an expert in this since I haven't ever analysed small molecules but I imagine that involves something like a HPLC, which you need to discuss with a chemist/biochemist how to extract and clean up your cells from everything and leave only the cAMP. There is probably a procedure/kit/biosensor for it but I will avoid getting into it as I know virtually nothing about this. However I have a note of caution for these types of indirect experiments. I have no idea what your cell lines are and how well they are characterised but since lines have all sorts of mutations and deletions and insertions in them, it's not a good idea to make inferences from cAMP levels. Since considering cAMP presence is quite important for cellular function, their absolute levels in a cell line is not necessarily a good indicator of whether one cAMP production regulator is present or not and I'm sure if you do something like this you open yourself to major criticism by any journal editor/referee. What will be a good idea though in any future experiments you do with these cells is to over express Gs or Gi and see their effects on cAMP production but I just don't recommend using cAMP levels as a sole indicator as to whether Gs or Gi is expressed or not.

If everything else fails and you got tired and wanted to wash your hands off this identification task, you can always lyse your cells and send them for mass spectrometry (MS) if there is such a facility at your institute. It's crucial that the species, which your lines originate from are characterised in terms of their global protein sequences since programs such as Mascot query the raw spectral data against databases such as UniProt to get protein coverage and subsequently protein hits. Also before you go ahead with you MS experiments, just speak to the facility manager and ask for guidance as to what lysis buffer is best to lyse your cells in and what components should not be in your lysis buffer and how sensitive their machines are and how likely you are to get detection and what your protein concentration should be. I think the best machine to use is Orbitrap and as a general rule, the higher the protein amount, the more likely you are to detect it. Since cell lysate is pretty messy and the MS machine columns can get saturated by abundant proteins such as actin, it would be best to run your lysates on an SDS-PAGE gel under reducing conditions (you can even do multiple loads by running your samples in the gel, switching off the WB machine, loading more samples and running them in the gel and continue doing this a few times. It works, I have done it myself but for pulled down samples which are a bit cleaner (less contaminants/unwanted proteins) in general). Once your gel runs through just cut the region of the gel corresponding to the molecular weights of Gs and Gi and send that for MS identification. This method (running your lysate through SDS-PAGE gel) gets rid of unwanted proteins that can interfere with the identification process. But MS is very expensive!

Again I would highly welcome any edits to my own edited reply! I'm here to help and learn.


Does double stranded RNA (dsRNA) exist in eukaryotic cells?

Yes, dsRNAs are present in eukaryotic cells and regulate various biological processes.
These nucleic acids are also present in the nucleus and regulate mitosis. Altering this nucleic acid could even lead to cell death.
(Reference: https://pubmed.ncbi.nlm.nih.gov/25504323/)


The first one is dyer's polypore or rusty gilled polypore.
https://en.wikipedia.org/wiki/Gloeophyllum_sepiarium
The second one looks a bit like orange peel fungus, although it could be something different.
https://www.wildfooduk.com/mushroom-guide/orange-peel-fungus/


After getting fully vaccinated for HBV why does the antiHBs titer last for so long?

There is such a thing as memory plasma cells, discovered only relatively recently. Here is a review from 2010 discussing them, here is another review from 2012, and here is a pre-publication manuscript of an upcoming review in Leukemia (I apologize if any are behind paywalls, let me know if you can't access any of them).


Here is a quick drawing of how BamHI cuts the DNA:

As you can see, after cutting, the two ends are actually the same (always read sequences from 5' to 3').


Effect of extracellular molecules on membrane potential

The absolute answer would depend on a lot of factors, but the basics of it would be that - Yes, the volume does change and Yes, it would have an affect on the membrane potential.

By adding mass to any liquid solution, you are changing the volume. Plain and simple. Liquids are not compressible, and the only way to maintain volume while adding mass would be to increase the density of the liquid. [Edit] I'm wondering if you don't mean increase the volume of the cell - in which case, in extreme conditions where the cell cannot maintain water and salt concentrations, the cell would lose volume as water and salts move out. In a hypotonic solution (much more water than solutes), the cell would lyse as osmotic pressure favors water moving into the cell

The membrane potential would change, but how much depends on a lot of factors. It would most likely change due to the movement of ionic solvents down their concentration gradients. Osmosis would move water out of the cell and into the extracellular environment, and ultimately reduce the membrane potential as more water outside the cell would essentially decrease the molarity of the solution. The cell would have to pump more ions out in order to regain the membrane potential.

The exception might be if you added so many hydrophobic molecules outside the cell that you basically saturate the environment, which could prevent exchange of all charged or partially charged atoms and molecules.


How does the NAD+/NADH ratio affect lifespan in vertebrates?

This study found a statistically significant decline in NAD+:NADH ratios and in intracellular NAD+ with age in the organs of rats.

They discuss that the activation of  PARP - the  NAD-dependent enzyme Poly(ADP-ribose) polymerase-1 instrumental in DNA repair - increases in aging organs (heart, liver, kidneys). This depletes cellular NAD+ levels via poly(ADP-ribosylation) of proteins. This reduced cellular  NAD+ then reduces the effectiveness of Sirtuins (Sirt1) which can deacetylate tumor-suppressor proteins such as p53.

Here's schematic showing the basic idea from their figure 10:

So, the inference is that oxidative stress in vertebrates increases with age due to lowered cellular NAD+ - i.e.,  consistent with the free-radical theory of aging.  This could mean that lowered cellular NAD+, NAD+/NADH in any given individual may well decrease said individuals lifespan.

The authors of the first study (Braidy et al 2011) suggest that therapies involved in maintaining high NAD+ levels may alleviate age-associated disorders.

Braidy N, Guillemin GJ, Mansour H, Chan-Ling T, Poljak A, et al. (2011) Age Related Changes in NAD+ Metabolism Oxidative Stress and Sirt1 Activity in Wistar Rats. PLoS ONE 6(4)
Smith, J., (2002) Human Sir2 and the 'silencing' of p53 activity, Traneds, Cell Biol. 12, 404


Question about alternative polyadenylation

According to a 2011 review1 alterntive polyadenylation sites can be located upstream of the 3'UTR (i.e. within introns or exons).  When these sites are used it results in transcripts missing exons at the 3' end and can force alternative splicing.  This alters the final protein product.

This figure from that paper may help make this clearer.

  Figure 1. Schematic Representation of CR-APA and UTR-APA

  CR-APA produces mRNA isoforms with distinct C-terminal coding regions,
  resulting in distinct protein isoforms. UTR-APA produces distinct mRNA
  isoforms with different-length 3′ UTRs but encodes the same protein.
  Longer 3′ UTRs usually contain cis-regulatory elements, such as miRNA
  and/or protein binding sites, which often bring about mRNA instability
  or translational repression. CR-APA, coding region-alternative
  polyadenylation; UTR-APA, 3′ UTR-alternative polyadenylation. Light
  green boxes, untranslated regions; light blue boxes, shared coding
  regions; dark blue and yellow boxes, unshared coding regions; lines,
  introns.

Reference:
1: Di Giammartino, D. C., Nishida, K., & Manley, J. L. (2011). Mechanisms and consequences of alternative polyadenylation. Molecular cell, 43(6), 853-866.


This is not a yes / no question. Many tortoise eat plants (veggies and fruits) while some turtles eat fish too. Snakes are basically predators and do not dwell on plants neither do most of the lizards. I think if a reptile is capable of digesting plant food in general, then it should be able to digest preprocessed grains as well.

Edit:  As for whole intact grains I'm unsure, as canadianer pointed out in comments section, intact grains are hard(er) to digest. /end of edit/
I found this article where scientist fed alligators with a mixed diet in various setup. The diet included corn too and the 'gators responded well in terms that they could use carbon-hydrates.

  Recently, we (3) have demonstrated that hatchling alligators benefit from and apparently do utilize some dietary carbohydrate.


Welcome to Biology.SE!
I am not aware of any book that talks extensively about the evolution of dominance. It is a very interesting field of research. You can probably search for papers on the subject that will go much further than my below answer. For example, you may want to read Mayo and  Burger (1996), Bourguet (1999) and Billiard and Castric (2011) I hope that my answer below can provide the ground for more searching by presenting the two main (and of historical importance) hypotheses.

There are several hypotheses about the evolution of dominance. It is important first of all, to note that empirical observations show that beneficial alleles tend to be more dominant than detrimental alleles. There are a number of hypotheses and I won't be able to make a complete review. Among the two main hypotheses to explain the evolution of dominance, one has been formulated by Ronald Fisher and one by Sewall Wright (and J.B.S Haldane).
Fisher's hypothesis
According to Fisher's hypothesis, between two equally beneficial alleles, if one is more dominant than the other than it's heterozygote carrier will have higher fitness. In consequence, beneficial alleles evolve to become more dominant while detrimental alleles evolve to be recessive (so that they can hide from selection in heterozygotes). The main criticism to this model is that selection for dominance is possible only when the locus is polymorphic. This means that the strength of selection for dominance is of the level of the mutation rate, seemingly way too weak to explain the observed pattern of dominance.
Wright's hypothesis
According to Wright's hypothesis, beneficial alleles are more dominant because of the kinetic of biochemical reactions. The rate of a biochemical reaction is a function of the concentration in the substrates of interest. The function is called "Michaelis-Menten function" after the name of the authors. The Michaelis-Menten function looks like this:

Think about a knock-out mutation. Such mutation will decrease by half the concentration of protein the gene in question produce in heterozygotes. Imagine, the concentration of proteins in the wildtype homozygote was 3 (see above graph). The rate of reaction of this homozygote is therefore about 3. The heterozygote would have a concentration of 1.5 and the rate of the reaction is therefore about 2.5-2.75. Assuming that the rate of this biochemical reaction is directly related to fitness, then a the locus of interest, benefical alleles are necessarily dominant and detrimental alleles are necessarily recessive. Selection for dominance is not involved in Wirght's model.
In addition to that, if you have a series of biochemical reactions, you will likely have one reaction that is causing a bottleneck. One reaction that is the limiting factor of the speed of some biochemical pathway. Let's call this reaction process A. If a mutation occurs on a gene coding for any other reaction process B that is not the limiting factor (process A), then this mutation will have no effect on fitness as long as it is not important enough to make process B slower than process A. This may lead to pattern of dominance. I am not quite sure by how much of this has been formulated by Wright and Haldane though.
Is Fisher's or Wright's hypothesis correct?
To my understanding, current state of the art is to consider Wright's model to be correct and Fisher's model to be wrong. In reality, the truth probably lies somewhere in between these two extremes. There exists more detailed (and more mechanistic) models of the evolution of dominance that and the above dichotomy might not be very representative of the current debate on the subject. For example, I (vaguely) remember that during my undergrad, Sylvain Billiard gave a talk at my university in which he reported that some alleles actually have some domain that are directly responsible for decreasing the expression of the other allele on the sister chromosome suggesting that Fisher's hypothesis might sometime be quite a good explanation as well.

This answer was recycled from what I wrote here. But it is a much better fit to your question than to where it was originally posted.


Is it possible to estimate tree height from stump/breast diameter and species?

This is an interesting question for me because my first research internship centered pretty much entirely around this.  It got pretty deep into the weeds as this was a CS, rather than biology, internship and we were mostly analyzing the math behind the allometry (e.g. Log-transformed linear vs. nonlinear regression for fitting the curve, OLS vs. RMA regression, traditional vs. monte carlo methods for comparing curves with different numbers of parameters, etc.) but much of the work we did is applicable here.

So, what you have here is DBH, or Diameter at Breast Height, which, lucky for you, happens to be the most common method for estimating the biomasses of trees.  Here is the way that it works.  Basically, a research team will go out and measure the diameter of a bunch of trees.  Then they will cut down those trees and weigh them.  What they will end up with is a graph with a bunch of points that give you the weight of trees of particular diameters.  Then you fit a curve to this graph and, next time you want to estimate the biomass of a tree, you plug that tree's diameter into the equation for your curve.  There are a bunch of databases containing allometric equations for different tree species.  You just need to find one that contains the trees that you are interested in.  Given that you are working in New York, this might have what you need:

https://www.fs.fed.us/psw/publications/documents/psw_gtr253/psw_gtr_253.pdf

Though you are better off figuring out the species of the trees you are looking at and seeking out allometric equations for those specifically.  There might even be allometric information included with the data you are being provided.  One thing that may be an issue is that correlations between DBH and biomass are much more common than correlations between DBH and height.  Though both exist, you may have more trouble tracking down the latter for specific cases.  Additionally, these numbers are very rough estimates that vary a great deal depending on the techniques used to collect the data, fit the curve, and extract the equation.  In my own research, I found that log-transformed linear regression tended to be more successful over all (oddly enough) but that nonlinear regression was more effective on young forests dominated by stands of small trees.  We also had a rather odd finding that log-transformed linear regression of two lines with a breakpoint tended to be less accurate in both situations but more accurate overall (i.e. it did better on big trees than nonlinear regression and better on small trees than linear regression) but we weren't able to come up with a mechanism to explain why this would be the case so we scrapped the findings.  At any rate, all of this should illustrate that these numbers are very rough estimates that can be heavily influenced by environmental biases and that different research teams may even disagree on the proper allometric equations to use on a given species.  This is why databases are helpful, as they tend to average out a large number of allometric studies rather than relying on a single one, but even these should be taken with something of a grain of salt.

If you are expected to actually come up with these equations yourself, then you need to actually measure the diameter and heights of a bunch of trees, plot them, and fit a curve to them.  But from the sounds of it, you are only expected to estimate tree height based on diameter.  If that is the problem you are being asked to solve, chances are that there are allometric equations available to help solve it, perhaps even ones that were provided to you.


Brain wave and motor movement correlation

As said by MG_MD:

  You would be thinking about moving, actually moving, and perceiving the movement. These affect different areas of the brain and as such, the electrical output would increase.

Also, it is very rare that the brain produces only one type of waves as it is continuously processing millions of information, though we know the basic functions of all of those types (from here).

As to how EEG works:

  The billions of nerve cells in your brain produce very small electrical signals that form patterns called brain waves. During an EEG, small electrodes and wires are attached to your head. The electrodes detect your brain waves and the EEG machine amplifies the signals and records them in a wave pattern on graph paper or a computer screen.

Source

Source of image

If you look at the image, th EEG has captured many waves of different types at the same time, which proves the staement of MG_MD.

For the "overlapping frequencies..." part:

  For example there is the “mu rhythm” (which is actually alpha activity in the relevant sensory and motor cortical areas that happens when the arms/hands are not doing anything)...

Source


Yes, the individual number of exons/introns will vary in a transcript, but what you can do is just count all possible exons of a gene
For example, lets say you have an alternative exon in these two isoforms. The XX's are exons

XX---XX---XX---XX

XX--------XX---XX

We would say this gene has 4 exons and 3 introns, even though one isoform only has 3 exons. Its the transcript that varies in number of exons, the gene remains constant.

Heres a slightly more complex example. Mutually exclusive exons

XX---XX--------XX

XX--------XX---XX

We would still say it has four exons. Pretend that every exon of every isoform is included and thats how you get the number of exons in gene. So for the above example, just pretend both mutually exclusive exons are included

XX---XX---XX---XX

According to this old paper there are 8.8 exons per gene (7.8 introns). Their gene number count is high because its older, but they estimate that there are 207,344 introns in the human genome.


Does the DNA sequence of a butterfly match that of the caterpillar it used to be?

The genome (entire DNA sequence) of the butterfly would be identical to that of the caterpillar in all somatic cells.  A caterpillar has the genes to produce wings, for example, however at that stage in it's development they are not 'switched on' to make the necessary proteins.

If you were to sample the mRNA produced from transcription of the DNA in the caterpillar and butterfly stages, there are likely to be many differences.  As in the example I previously used, the mRNAs that are translated into wing-forming proteins are more likely to be apparent in the butterfly than the caterpillar.  When saying this, please be aware that I'm assuming that the regulation of these genes is pre-transcriptional - I'm not an expert of butterfly physiology!


Why does the structure for cellular retinol binding protein show interactions with cadmium ions?

As far as I am aware, there is no known requirement for Cd in mammalian systems, but it is extremely toxic (Waalkes & Goering).

It would seem that cadmium is required to get crystals of RBP, and its presence is an artifact of the crystallization process (ref):

  Pig holoRBP crystals were obtained at 277 K by the sitting-drop vapor- diffusion method, at a final protein concentration of approximately 8 mg ml ~ and in the presence of 8%(v/v) 2-methyl-2,4- pentanediol, 3mM cadmium acetate, 0.1 M Tris-acetate, pH = 6.8

The only mammalian Cd-binding protein I am aware of is metallothione (ref), which was originally isolated as a Cd-binding protein (ref), and allows safe transport of a highly toxic metal.

Carbonic anhydrase from the marine diatom Thalassiosira weissflogi can use Cd  as active-site metal (typically when Zn is low) and this may explain "the nutrient-like behaviour of cadmium in the ocean" [ref and ref]


Why don't all male animals kill a rejecting female?

The simple answer is most animals females can fight back. Its similar to the reason male to male fighting often evolves to become more and more ritualized. Fighting is risky, and the closer in size and capabilities the fighters are, the riskier it becomes. Behavior that tends to get you injured for little to no benefit tend not to get passed on. and there is little to no benefit in killing females for a male. Plus a female who is alive can change her mind later, so there is a direct benefit to the male for not harming her.

Now there are animals where a female will be bullied into mating to the point of risking injury or death. Those animals are very rare and have high dimorphism, they have males that are MUCH larger and more dangerous than the females, to the point the female is incapable of being a significant threat to the male. It is most common in animals that express harem polygyny. It also tends to carry the risk of inbreeding.

One horrifying example is hamadryas baboons. Males maintain a harem and threaten any female that even strays too far from the male. They even bite disobedient females.


How many organisms have ever lived on Earth?

it is impossible to know the exact number so here is my gross ballpark estimate of an upper bound -  i.e. the maximum number of organisms that could have lived on earth in the extreme best case scenario. in practice it is probably much less, but this is to get an idea of what kind of numbers we are dealing with.

The earth's volume is about 1.08321 * 10^12 cubic kilometers =  1.08321 * 10^21 cubic meters

The crust of the earth is 4-8km and the radius is about 6,353km giving around 1% of the total volume available for life.

Hence, the volume available, i.e. the volume of the crust is about 1.1 x 10^19 Meters.

An average-size bacterium such as the rod-shaped E-coli is about 2 micrometers long and 0.5 micrometers in diameter. Hence, the volume is roughly:

(2*10^-6)*(0.5*10^-6)*(0.5*10^-6) = 0.5*10^-18 meters

Hence, if the entire volume of the crust of the earth were entirely filled with e-coli bacteria, there would be:

(1.1 x 10^19 meters)/(0.5*10^-18 meters) = 1.3*10^36 bacteria on the earth.

Bacteria take time until they reproduce. If they reproduce faster than they grow, they will become reduced to zero size, so there must be a balance between growth and reproduction.

Under ideal conditions the E-coli bacterium would divide every twenty minutes. source

Let's say we have the maximum number of bacteria on earth dividing every twenty minutes. Somehow, they divide and then one dies so that the population is stable. (hypothetically)

The age of the earth is roughly 4.5 Billion years. Much of that time, it was not colonised, but just to give an upper bound let's assume it was colonized the whole time.

There are 525600 minutes in a year so this give

4.5 ^ 10^9 * 5.3* 10^5 = 2.385 * 10^15 minutes

Dividing by twenty minutes gives 1.1925 * 10^14 total reproductions.

Hence, the number of organisms that ever lived if the entire volume of the crust of the earth were entirely filled with e-coli bacteria reproducing at the maximum of every 20 minutes would be:

(1.2*10^14) *  1.3*10^36 bacteria = 1.56 * 10^50 bacteria

This is an highly exaggerated gross estimate of the maximum number of organisms that ever lived in the extreme best case scenario. In practice it is probably 5-15 orders of magnitude less than this but we get an idea of the kind of numbers we are dealing with.

UPDATE: A more realistic number

The number of bacteria currently on earth is about 5*10^30 forming a biomass which exceeds that of all plants and animals. source.

According to this source cited by the previous wikipedia article:

  Most of the earth’s prokaryotes (bacteria) occur in the open ocean, in soil, and
  in oceanic and terrestrial subsurfaces, where the numbers of cells are
  1.2 × 10^29, 2.6 × 10^29, 3.5 × 10^30, and 0.25–2.5 × 10^30, respectively. The numbers of heterotrophic prokaryotes in the upper
  200 m of the open ocean, the ocean below 200 m, and soil are
  consistent with average turnover times of 6–25 days, 0.8 yr, and 2.5
  yr, respectively. Although subject to a great deal of uncertainty, the
  estimate for the average turnover time of prokaryotes in the
  subsurface is on the order of 1–2 × 10^3 yr. The cellular production
  rate for all prokaryotes on earth is estimated at 1.7 × 10^30 cells/yr
  and is highest in the open ocean.

Hence we have about 1.7 x 10^30 New Cells/year

Multiply this by the estimated 3.5 Billion years (3.5*10^9) when the earth was colonized and we get

  5.95 * 10^39 Bacteria that ever lived. of course there were other organisms, but as above even the biomass of bacteria exceeds that of
  all plants and animals combined so their effect on this number is
  negligible. Likewise, the life conditions were surely not ideal at all
  times, so this number may be lower still.

For some perspective, the estimated number of atoms comprising all of planet earth is about 1.33 * 10^50 according to this source.

ESTIMATE OF NUMBER OF MAMMALS THAT EVER EXISTED

The upper bound for mammals is as follows.

The surface area of the land of the earth is 149 million square kilometers.

Let us consider if the entire land area of the earth was completely covered with mice.

A mouse is typically 10cm from nose to base of tail and about 5 cm wide=0.1*.05=0.005 square meters. So we get 200 mice per square meter.

Hence, if the entire land area of the earth were covered with mice the world population of mice would be:

149*10^12 square meters * 200 mice per square meter = 1.788 * 10^15 mice

Mice typically produce a litter of 6-8 young and a female can have 5-10 litters per year. source

Let's say we have this maximum population reproducing in a stable manner. i.e. for every new mouse, an old one dies.

Hence the total number of new mice per year would be:

1.8 * 10^15 * 8 young * 10 litters = 1.44*10^17 new mice per year.

Mammals appeared around 200 million years ago (source), so that makes

1.44*10^17 new mice per year * 200 million years

= 2.88 * 10^25 total mice.

In practice mice need space and resources and compete with other mammals which take up space and which reproduce less frequently. Likewise, deserts and polar regions are less inhabitable, and sometimes there are periods of droughts, and they don't always reproduce at the maximum rate etc. so the total number is probably about around 4-10 orders of magnitude less than this.

So it is probably something like 10^20 total mammals ever existed.


Are multi-chain proteins synthesized as one biological unit?

Sometimes yes but mostly not.

Some proteins are synthesized as one long polypeptide pre-protein which is cleaved by some proteases to yield multiple chains. After cleavage the intramolecular interactions become inter-molecular or inter-chain interactions. Insulin is a good example of this (See the figure below).

In other cases the chains are synthesized as different polypeptides which (with or without processing) subsequently associate with each other. In case of homo-multimeric proteins, the polypeptides are made by the same mRNA.


You are on the right track.  This is an example of microchimerism (the maternal part is a bit off), and the key issue at hand is central tolerance.
Background:
A good definition of microchimerism is:

Microchimerism is existence of an allogeneic DNA in a living creature. (1)

Scientist do this on purpose for all kinds of reasons, but mostly to ether is study the immune system directly or to get a near-transgenic model.  It should be noted that this isn't perfect, and that when you try to do this, you often can lead to auto-immune problems and often death of the mouse (30-50% survival in early work).  If you go back to one of (if not the) pioneers of immunology, Peter Medawar, you can see when how this was done:

Mice and chickens never develop, or develop to only a limited degree,
the power to react immunologically against foreign homologous tissue
cells with which they have been inoculated in fetal life. Animals so
treated are tolerant not only of the foreign cells of the original
inoculum, but also of skin grafts freshly transplanted in adult life
from the original donor or from a donor of the same antigenic
constitution. (2)

If you would prefer a visual layout of the experiment, Starlz put together one in his review of transplantation (Pubmed):

After looking over the section you quoted from Alberts, I'm pretty sure he was in fact referring back to these early experiments.  But that was all the way back in the 1950's, what have we learned as the mechanism in 60 years?
Possible Mechanism:
The truth is that we don't have an absolute grasp on how this works when it doesn't cause an autoimmune problem and abort the fetus or even neonate pup.  It's import to note that it probably does cause auto-immune problems and various other side effects (like sex differentiation) in mammals.
But when and how it is tolerated is likely mediated by central tolerance, and the ability to get the foreign MHC molecules tolerated by early lymphocytes.  Essentially, the cells have to get incorporated into the AIRE machinery at an early enough stage that the T-cells are selected against the foreign cells.
There is enough biology here that an in-depth answer could be a dissertation, so I only want to touch on a few more points.  You should note that this was done with relatively genetically similar animals, and most modern researchers use cells modified from genetically pure mouse breeds.   We also know a lot more on how the cells "recognize self" and the HLA types of the population.
You are most likely to succeed when the MHC molecules are very similar (ie from a direct family member).  This happens when the host and foreign cells have an HLA type match.
TLDR:
The lymphocytes, mostly T-cells in this case, of fetal mammals seem to be able to look at very similar MHC molecule on a foreign cell and decide "eh.. close enough," and build negative selection (part of β-selection) against lymphocytes that would kill the foreign cells.  This requires that the cell be in the right place at the right time, and of course, be "close enough."
Do let me know if something is not clear or needs to be expanded upon.  As someone who works in Immunology, I have difficulty determining where the detail line should be.


Was Darwin aware of the difficulties behind the concept of species?

The whole point of Darwin's theory was that transition from one species to another is extremely slow and gradual. There are plenty of quotes in "Origin of Species" stating this, and also affirming that there is no clear boundary between species and subspecies, or "races".

Quotes from Origin of Species > Variation under Nature (Chapter 2)

Quote 1

  Nevertheless, no certain criterion can possibly be given by which variable forms, local forms, sub species and representative species can be recognised

Quote 2

  Several experienced ornithologists consider our British red grouse as only a strongly marked race of a Norwegian species, whereas the greater number rank it as an undoubted species peculiar to Great Britain. A wide distance between the homes of two doubtful forms leads many naturalists to rank them as distinct species; but what distance, it has been well asked, will suffice if that between America and Europe is ample, will that between Europe and the Azores, or Madeira, or the Canaries, or between the several islets of these small archipelagos, be sufficient?

Quote 3

It is here the most definitive quote I managed to find and partially answers to your second question.

  From these remarks it will be seen that I look at the term species as one arbitrarily given, for the sake of convenience, to a set of individuals closely resembling each other, and that it does not essentially differ from the term variety, which is given to less distinct and more fluctuating forms. The term variety, again, in comparison with mere individual differences, is also applied arbitrarily, for convenience sake.