Is brain transplantation possible? Many organs can be transplanted nowadays, including the liver, lungs and kidneys.

Can the brain be transplanted?

Short answer

Yes, brain transplantation is technically possible, but only for short periods of time, and only in experimental settings.

Background

In terms of a full-brain transplant there has been only one group that have made serious attempts in doing this (according to wikipedia and a literature search on my end). In the 1960's White and colleagues transplanted canine brains from one animal to another (White et al., 1965). In total 6 brains were transplanted. However, the recipients' brains were not removed and the brains were merely surgically transplanted into the neck region of the recipient animal, and connected to the recipient's cervical vasculature (carotide arteries and jugular vein). Hence, the recipient canines ended up with two brains. The authors, however showed with these experiments that the transplantation of brains was feasible, and that the transplants survived and remained functional, which was evidenced by EEG activity. The brains survived from 6 hours up to two days.

Later, White and colleagues worked out a way to keep an isolated (but blood-perfused) monkey brain alive outside the skull, potentially allowing for a primate brain to be transplanted (White et al, 1975). The procedure could include longer-term 'storage' of the brain by cooling it, making the possibility of transplantation more feasible. However, White realized the difficulties with this approach, since, and I quote:

  [...] by definition the brain must be isolated before the transplantation, and thus requiring all nervous tissue connections to be severed (e.g. cranial nerves and spinal cord), the isolated transplanted monkey brain is without a mechanism to receive or transmit information.

To address this issue White et al. set out to transfer  the entire cephalon (head) of a monkey to the body of a recipient whose own cephalon had been removed at a mid-cervical
level. Under these circumstances the brain, being within its own cephalon, still connects to the cranial nerves:

source: University of washington

White et al. succeeded in transplanting a head, but the preparation rarely survived longer than three days due to haemorrhagic shock (White et al, 1975). Basically the recipient was quadriplegic, as the face was fully functional and White comments, and I quote:

  Observe the wakeful appearance of the cephalon and the obvious movement of the facial musculature with open mouth and eyes. This preparation gives every evidence of being in intelligent contact with its environment. [...] Cortical [EEG] activity in this preparation demonstrates awake recordings.

Hence, with the current available technology it does not make much sense to perform a brain transplant, as the transplanted brain cannot be functionally (neurally) connected to recipient body. However, strides are being made in re-connecting a severed spinal cord (Canavero, 2013), endeavors that could bring head transplants a little closer.

Quadriplegic people obviously face extreme psychological challenges (Sane Australia). However, even when they have become quadriplegic due to an event later in life, they are not mentally changed, in that they are still 'themselves'. Therefore, although human transplants never have been done, I dare to say that the transplanted head will determine the psychological 'self' of the recipient body, which includes memory and personal traits. At least, assuming the brain can be transplanted without inflicting neuronal damage.

References
- White et al. Science 1965;150:779-81
- White et al. Resuscitation 1975;4,197-210
- Canavero et al. Surg Neurol Int 2013;4:S335–S42

Further reading
- CBS News


Does anyone know what marsupial this is? I know what this is a marsupial, but i'm not quite sure which one. Any thoughts?

I've been told it is the marsupial 'Myrmecobius fasciatus' commonly known as the numbat.

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


Allele-specific bisulfite sequencing When evaluating methylation status at various CpG sites after sequencing, how much consideration should one give to random single base pair insertions and deletions. Suppose there is a CA dinucleotide; can we assume that the CA is native to the sequence or results from a G deletion especially when the latter is suspect once comparing to other sequences. Is there really a set standard sequence to compare it?

I agree with Vance, we need a little more detail to better answer your question. From what I can tell, you are asking whether a single nucleotide polymorphism (SNP) that results in the addition of a cytosine base to your sequence is of concern when examining the methylation signature of that sequence.

I would first determine whether the polymorphism is common in the population using NCBI. The more common the polymorphism, the less likely it is to have a serious effect. However, that is not to say that it doesn't have any effect.

I would then examine how much the methylation of that one site varies compared to samples without the additional cytosine base.

Finally I would determine the importance of the location of the SNP. Is it located in a CpG island? Or is it located on the shores, shelves or 'open sea'? (see work by Sandoval et al.)

Without knowing all the above it is hard to make a call on how important/unimportant the SNP is in your methylation analysis.


Bacteria without plasmid I am currently working on antibiotic resistance and I would be very interested to know which bacteria has no plasmid, in a similar way than M. tuberculosis.
This would help me a lot for my work and I did not succeed to get that much information online.

Thank you very much for your answer !

You might want to take a look at Bacillus subtilis. Most of the lab strains don't contain plasmids, though they have been found in some environmental isolates.

https://academic.oup.com/femsre/article/21/4/337/490925

All this depends on exactly what you're looking for: a species with no known plasmids in any isolates, or some commonly used lab strains with no plasmids?

M. tb is a pretty unique case. Most of the other species in the Mycobacterium genus do contain plasmids.


Liquid that comes out raw mangoes What is the composition of the liquid that comes out of a raw mango when you break it off from its stem? It oozes out some sort of juicy liquid. Any idea what that is?

Also, is it edible?

It is the sap; you can see the composition of the sap (of Indian mangoes) in this article. Some plants also produce latex from injury sites. The mango sap is not supposed to be eaten as it can irritate the skin; a condition referred to as Mango Dermatitis.


Why are tardigrades so rare? If tardigrades are so resilient and nearly immortal, why are they so rare when looking at samples of a pond or lake, where tardigrades should thrive?
I've met people who've been studying protozoa and metazoa in nature all their life and have only seen tardigrades once or twice!

From wikipedia > tardigrade

[Tardigrades are] considered cosmopolitan and can be located in regions all over the world.
Tardigrades are often found on lichens and mosses. Other environments are dunes, beaches, soil, and marine or freshwater sediments, where they may occur quite frequently (up to 25,000 animals per litre). Tardigrades, in the case of Echiniscoides wyethi,[20] may be found on barnacles.[21] Tardigrades can be often found by soaking a piece of moss in water.

Tardigrades are, in fact, very common. See the simple video how to observe tardigrades. If the people you've met have rarely seen tardigrades, it is probably because they are not looking for them.


What is the animal in this video? I made some research however there seems to be a conflict with this animal's translation to my language and the original. So I couldn't find it. Do you mind helping me out ?

https://static.59saniye.com/videos/2018/04/21/20180421080742-6014_720.mp4

Some resources say pufferfish or Porcupinefish. Are these the same thing ?

This is a Northern pufferfish. It is called Sphoeroides maculatus.

  Source: https://www.flickr.com/photos/vims_photos/3570935564

You can confirm this on FishBase.


How would constantly growing nails have aided early human? Nails grow rapidly and constantly, such that without constant artificial trimming they would reach lengths difficult to manage. How did this benefit early humans, say 200kya? Were they used like claws? Did physical activity keep them at a short length?

I can't say anything for sure (and, with questions like this, it's rare that anyone can), but my guess would be that human nails grow constantly for the same reason as the (analogous) claws of most mammals do: to keep them from accumulating damage.

Your bones, if they suffer mild to moderate damage, are capable of healing through the concerted action of several specialized cell types in your body.  This healing process, however, is only possible because the bones are inside the body, surrounded and permeated by living tissue.

Your nails, however, are simple sheets of keratin, and contain no living cells that could heal them, nor any blood vessels that could keep such cells alive.  Being exposed to the outside of the body, outside the skin barrier, they cannot really support living tissue that could heal them.

Instead, the way human nails (and animal claws, more generally) "heal" is by growing.  Since the nail itself cannot contain cells that would rebuild it, those cells are instead located in the nail matrix, which is located under the nail and from which the exposed part of the nail continually grows out of.

(Indeed, the same is true of most of the exposed parts of your body: your hair and even the surface of your skin itself are also composed of non-living keratin constantly growing from an underlying matrix.  This is necessary to maintain the skin barrier between the interior and the exterior of the body.)

The reason human nails must keep growing all the time is that they do continually wear down and suffer damage from various causes (and would surely have worn down much faster yet for our primitive ancestors, who had to sustain themselves through hard manual labor with few or no tools).  If your nails just stopped growing after you reached adulthood, they'd be in horrible shape even just a few years down the road, not to mention decades later.

While the rate at which human nails do grow is pretty slow — it takes several months for a damaged fingernail to fully regrow, and up to a year for a toenail (a fact I can confirm from personal experience, having broken my toenail last summer) — it's still enough to ensure that your nails will only bear less than a year's cumulative damage at any moment, rather than every nick and scratch and cut they've suffered during your entire lifetime so far.

In a relatively sheltered modern lifestyle, it's quite likely that even this moderate growth rate may exceed normal wear on your nails, requiring them to be clipped regularly.  Still, the fact that you can clip your nails (or, in a pre-modern society, just bite or scrape or cut them down) reduces the selection pressure against excessive nail growth.  On the other hand, not having your nails grow back as fast as you wear them down through hard manual work could be quite bad for your fingers, and could easily reduce your working ability or even lead to harmful infections.  Thus, it makes sense that evolution has optimized out nails to grow at a rate that, on average, tends to somewhat exceed the typical rate of wear.


What is the total number of rounds of cleavage during mammalian embryonic development? That for frog is 12, but what about mammalian embryos?
I cannot find the exact number anywhere.

It's not a totally answerable question, since some types of cells are going to divide more times than others.  But for an estimate, take as a starting proposition that there are 1 trillion cells in the adult human body. [1]  The average weight for a human is 62kg. [2] Average birth weight is about 3.4 kg.  [3]

So that implies roughtly (3.4/62)* 1 trillion = 55 billion cells in a newborn.

You then take the log base 2 of 55 billion, which gives you the exponent you have to hang on 2 in order to get 55 billion, which is about 35.  Then add one for that additional cell division to get from one to two cells == 36 divisions.

Of course I'm just using math, not biology, so your actual reality may vary.  Certainly some cells will reproduce more often than others, maybe cells actually grow in mass instead of dividing (i.e., baby cells might have less mass than adult cells) so the baby-cell-count could be off, lots of possible sources of error.

[1] http://www.nichd.nih.gov/publications/pubs/fragileX/sub3.cfm

[2] http://en.wikipedia.org/wiki/Body_weight#Average_weight_around_the_world

[3] http://en.wikipedia.org/wiki/Infant#Weight


What is the recommended PPM when foliar feeding L-amino acids It is said that L-amino acids such as histidine, methionine, aspartic acid, glutamic acid, asparagine and glutamine can revert plant stomata closure, increase quality of fruits and assist maturity. It is also said that the best way to apply is through foliar feeding.

I would like to start experimenting with different amino acid foliar feeds but would first like to know if there is a recommended maximum/minimum/recomended Parts per million(PPM) , for foliar feeding of these compounds.

I know that some of the amino acids you listed are commonly found in fish fertilizer. I haven't read any studies on the use of these amino acids individually and not sure where you would purchase them separately. If you're just experimenting in your own garden I would just use fish fertilizer according to the label directions. If you look for fish fertilizer studies you'll probably find more info.

Also, I've never heard of these opening up the stomata of the plants. The only references I've read indicate that foliar sprays are best applied in the early morning or late day when the stomata is already open. This is how the nutrients get absorbed from the leaves.

I don't know that I would want to intentionally manipulate stomata closure. The plant knows when it needs to breath.

Where did you read the above info? I'd be interested in seeing it.


Normal Frequencies in Heart I am trying to visualise possible ranges of frequencies from different structures of heart:

different valves and their possible frequencies
heart sounds I - IV and their normal frequencties
what can frequencies be in healthy situation for adult
what can frequencies be in healthy situation for children 4-9 years old

I searched meta-analysis, clinical trials and reviews in PubMed unsuccessfully.

Is there any review article or book about the frequencies from different structures of heart?

Search terms used

frequency heart
frequency heart valve

This is a part answer (as this is outside of my field), but the article Self Regulation of the Heart: Natural Frequency and Damping of the
Heart Contractions  (Bahramali et al. 2009) imply that 'normal' frequencies may not be possible to precisely define, due to:

  ECG frequency analysis is complicated by the fact that ECG signals are non-stationary, that is, their activity
  patterns change slowly or intermittently as a result of variations in a number of physiological and physical influences.

The article extensively reviews the general frequency analysis, divided into P, Q, R, S and T components.  However, they define 'optimal conditions' (i.e. 'normal and healthy) as:

  optimal conditions of the heart contraction as those under
  which the dynamics of contraction shows the best
  agreement with underdamped harmonic oscillation

An example of this is visualised in the diagram below:

this example is provided on the University of Pennsylvania tutorial site ECG Tutorial

In the article Comparison of Power Spectral Density (PSD) of Normal
and Abnormal ECGs (Das and Chakraborty, 2011), note comprisons for the QRS component, as

  QRS complexes are chosen because
  it shows distinct differences for different heart diseases

In other words, distinguishing healthy from not-so-healthy.


gene transformation from plant to plant - transgenic plant I want to know if the expression of a transfered gene depends on source of the gene, if e.g.:

1] I isolate a gene from plant and transfered it to the same plant?

2] I isolate a gene that is highly expressed in plant, and transfer it to another plant ?

3] I isolate a gene that is lowly expressed in plant and transfered it to another plant

Is there a difference between the expression of the transferred gene in these three cases? What does the expression of the transfered gene depend on?

There are many factors that could influence in the level of expression of a gene, but the two most important are the promoter and the place where your gene has introduce in the genome of de recevier plant.The first one, the promoter depends of the original expression of the original plant, if the expression was high in the original plant, it will be in the receivier plant (if you include the promoter in the construction of the transferred gene and both plant are close in filogenetically).The second one,the place where your gene has introduce in the genome of de recevier plant is a matter of luck, if you use a Agrobacterium, if you gene was introduce in a heterochromatin region it won´t express.

Sorry for my bad english, hope I was useful


How are mitochondrial diseases like MERRF inherited? I am doing a project on the disorder MERRF in Mitochondrial DNA. I have to make a pedigree and explain how it is transferred on from generation to generation. I know that it is inherited maternally, but I am confused about how it is inherited. Would it be inherited inherited like autosomal DNA in a Mendelian fashion? If so, would this gene be dominant or recessive? Or would the children just automatically inherit whatever gene their mothers have? Also, how would the genotypes for Mitochondrial DNA be displayed? Any other useful information on Mitochondrial DNA or MERRF would also greatly appreciated. Thanks.

Mitochondria are primarily thought to be inherited from the mother but there is evidence now that the father can also contribute mitochondria (Schwartz and Vissing, 2002; Luo et al., 2018).

Even if the mitochondria were purely maternally inherited, a cell (including oocyte) typically contains many mitochondria and not all of the mitochondria may have the (deleterious) mutation. This phenomenon is called heteroplasmy.

MERRF is associated with a loss of function mutation in mitochondrial tRNAs (See NIH, Genetics Home Reference). The extent to which a cell will be affected would depend on number of mutated mitochondria it contains. Therefore different cells would be affected differently.

The trait inheritance would therefore not be in the typical Mendelian fashion.


Why is a mosquito feeding on human blood not a parasite? I recently read in my Ecology course notes that a mosquito feeding on human blood is not considered as a parasite. However, since it sucks blood from the human body, shouldn't it be regarded as a parasite, just like lice and ticks?

A mosquito is a biological parasite, it is not a medical parasite.

There are two definitions of parasite. A biological/ecological definition and a medical/physiological interaction definition.

A parasite in biological terms is an organism that benefits from a parasitic relationship; a parasitic relationship being a non-mutual relationship between species, in which one species benefits at the expense of the other. Generally the host is not killed by a small number of parasites. When the host is killed the organism is usually called predator or parasitoid.
A parasite in medical terms is an organism that lives on or in a host and gets food from or at the expense of its host.

The difference is small but important; only the medical definition requires the parasite to live in or on the host for prolonged periods. It is a much narrower definition.

Biologically, a female mosquito is an indirect ectoparasite, it can be facultative or obligate depending on the species. It harms its host to benefit itself, that is all that is needed to be a parasite by the biological/ecological definition. And just like a leech or vampire bat it is hemophagic and leaves the host as soon as it is done feeding. Brood parasites are another great example of a biological parasite that does not live on or in the host. So a cuckoo would be a biological parasite but not a medical parasite. When you consider the function and practice of medical science the more narrow definition makes sense, they are not concerned with parasites that are not going to stick around or not affect the host organism's physiology directly. By the narrower medical definition, none of these organisms are parasites even though by the biological/ecological definition they are.

Consider the wiki or a paper on parasite evolution vs say the CDC to see the difference.


Which way to run BLAST? I have a set of scaffolds from a genome assembly, and I want to align a collection of proteins from various species to it. I can do this using BLAST in two ways:

Create a BLAST database of the scaffolds, and run tblastn on it with
the proteins as the query.
Create a BLAST database of the proteins, and run blastx on it with
the scaffolds as the query.

Should both of these produce the exact same hits? Will there be any significant difference in running time between them?

Quick answer: use tblastn.

As a general rule, when comparing two datasets using BLAST, it is recommended to use the larger of the two sets as the database and the smaller as queries. The main difference is one of computational time. Blast is optimized for large databases.

You are also likely to get different hits. Blast's e-value is calculated based on the size of the database, among other parameters. Roughly, the e-value answers the question: "How many high scoring sequence pairs with X% of sequence identity and Y length would I expect to find in a database of size X by chance?". Your e-values could be artificially high if you use the protein sequences as a database. I am not sure about this, but there may also be differences in the way gap penalties are dealt with by tblastn and blastx.

That said, I would first try doing this using a tool specifically designed for the task. BLAST has no model for dealing with splicing and it is a pain to build gene models from BLAST results. To align protein sequences against genomic DNA I would use either exonerate (with the p2g model) or genewise. Both programs incorporate splicing models and will give you a decent prediction of the gene structure of your target genes. The following are extracts from each program's man page:

GENEWISE:

  Genewise2 compares a protein sequence to a genomic DNA sequence,
  allowing for introns and frameshifting errors.

EXONERATE:

  exonerate is a general tool for sequence comparison.

  GAPPED ALIGNMENT OPTIONS

  -m | --model

  protein2genome

  This  model  allows  alignment of a protein sequence to genomic DNA.   This is similar to
                       the protein2dna model, with the addition of modelling of introns and intron phases.  This
                       model is simliar to those used by genewise.

In general, genewise gives slightly better results but is much slower and cannot deal with multi fasta files. It is best when you know that your query protein will align against a specific nucleotide sequence.

Exonerate is fast but uses some heuristics that can give slightly worse results in some cases. Personally, I use exonerate to get my hits and then, if necessary, refine the gene model using genewise. In most cases, exonerate should be enough though.

EXAMPLES:

exonerate -m p2g -q proteins.fasta -t scaffolds.fasta > output.txt

genewise -pretty -pep -gff single_prot.fasta single_scaff.fasta > output.txt


Fine permanent fluorescent marker for blue light I am looking for a fine- (or small-)tipped permanent marker to write on Petri dishes that is visible under a blue light or a transilluminator. It would seem obvious, but it is a nuisance.

The Sharpie Neon series are too thick.
Highlighters and all the arts pens I have tried rub off the polycarbonate.
The red colour from Staedtler lumocolor (black body) shows up faintly —none of the other do— but too faintly.
The Neon series from Staedtler triplus fineliner (gray body, triangular) rub off

So I would like to find what solutions other have come up with or if there is a brand that works well.

EDIT. This is how the Sharpie series look:

I have had this problem before... this is what I ended up using:
https://www.amazon.com/Invisible-Blacklight-Marker-Blue-Yellow/dp/B004C89M9Q

You may have to write on a tape or something so that the ink doesn't come off. (Ink may come off if you incubate plates)


Are tuna fish present in the Baltic sea? Yesterday my grandmother ate fresh tuna at a friend's party. She swears it was fresh and bought at a local fishmonger. The problem is, that we live in Gdańsk, by the south-eastern side of the Baltic sea and I have never heard of tuna in the Baltic. I told her that the fish couldn't have been local and therefore couldn't have been fresh but frozen and thawed. But the thought still bothers me, maybe tuna fish can reach the Baltic?

I did search a bit and found that tuna may be sometimes found in the Northern sea, so maybe it actually can travel so far east as to reach the Baltic? But the water in the Baltic is hardly saltwater (6-8‰), so would it be able to survive?

Indeed tuna are present in the Baltic sea, and they can also grow in the Pacific and Indian oceans. A lot of the tuna we see in tuna cans in supermarkets comes from the stocks in the Indian ocean, but it is possible to have fresh tuna from the Baltic.

Sorry, I only found a French answer from a famous French news paper: http://sante.lefigaro.fr/mieux-etre/nutrition-aliments/thon/dou-vient-thon


How prevalent is Taq polymerase in adding 3' A overhangs to the PCR product? I am conducting a mutagenesis on a gene in vivo of which I need to ligate into an expression vector.  The primers I have designed overlap restriction sites of which I plan to use to ligate into the expression vector.  The parts between the primers I will try to create mutants with error prone PCR.

My concern is the 3' A overhangs that are created from Taq polymerase.  How prevalent is this?  If it is highly common, what is the best way to account for these additions when trying to ligate my PCR product into the vector?

I am not sure of a case where Taq doesn't add 3' A overhangs.

You could use TA cloning to clone your PCR product.  The basic principle is to use a vector with 3' T overhangs.  If you have a vector without these overhangs, you can use a terminal transferase + dTTPs to create them (or even Taq, but this is not as great because it adds a purification step to isolate the vectors with overhangs; terminal transferase is much more efficient).  You can then ligate your PCR product that has a 3' overhang.

Protocols for adding the 3' T overhangs to your vector are given in Zhou and Gomez-Sanchez 2000.


Hydrogen Ions — Common, right? The Wikipedia entry for Ion states "A positively charged hydrogen ion (or proton) can readily combine with other particles and therefore is only seen isolated when it is in a gaseous state or a nearly particle-free space."  Cells pumping ions across membranes is very common so can someone help me understand what context might be implied by the quote?

I'm still not entirely sure what specifically you're asking about, but I have a guess. It is true that positively-charged hydrogen ions, or bare protons, are typically only observed in gaseous/plasma states and hard vacuums, and it is also true that cells routinely pump positively-charged hydrogen ions across membranes. This is not a paradox because in aqueous solutions, hydrogen ions exist as $H_3O^+$, also known as hydronium or hydroxonium.

Image from Wikimedia Commons


Cell state and cell function I have read many papers that refer to cell type, cell state and cell function, but I haven't found an explicit definition for each of these terms.

For example this paper (Brown et al. 1994. J General Virology 75: 2367-2377) refers to cell type and cell state without providing an explicit definition of both terms.  I have a vague idea of what these terms mean but a more explicit definition would help me greatly in understanding them.

Mainly cell type refers to the differentiation degree to form a cell population whose characteristics are identifiable by using simple microscopy, stains or immunological methods. Examples of cell types would be T8 lymphocytes, peripheral astrocytes or hepatocytes. Cell types can be pathological too, like tumor cells.

Cell state makes references to the current physiological condition of a given cell. A given cell type can be found in different proliferation states, metabolic conditions (i.e: An adipocyte or a hepatocyte will have different metabolic profiles depending on the insulin and glucagon balance), electrophysiological state (The human oocyte rapidly changes its membrane potential once a spermatozoid has entered) or even degree of differentiation (The typical example are B lymphocytes, which can be in a "naïve" state if they haven't found an antigen, or into a mature state. Once they have matured, thay can be subdivided into cells that actively produce antibodies and cells that divide actively).

A cell function usually refers to a process that occurs inside a cell, or to the physiological function that cell type has in the whole organism. Cell functions could be metabolism, signaling, cell division, etc.; while also could be the likes of detoxification (hepatocytes), hormone production (Langerhans cells) or contraction (myocytes).


Resolution of gel electrophoresis My professor mentioned the resolution of the gel in gel electrophoresis. He stated that agarose has large pores and thus low resolution whereas polyacrylamide has the opposite.
I don't understand what resolution has to do with this. Can someone explain?

Resolution size of the gel simply means the distinction that can be made between molecules very close in size.

If you were looking to distinguish between a 100bp fragment and a 200bp fragment, then agarose will give you that level of differentiation.

But if you were looking to distinguish between a 190bp fragment and a 200bp fragment then you would likely want to us polyacrylamide. The PA gel has a higher resolution because you can distinguish between smaller differences on molecule length.

Think of it in terms of a simplified idea of a microscope, at 100X, you can probably distinguish between cells, maybe make out a well stained nucleus. where as at 1000X you can start to discern other organelles. You are seeing a finer degree of detail at the higher magnification. There are many factors that go into the resolving power of a microscope and the example based on magnification is simplistic and doesn't really address optical resolution, but it is an illustrative example of resolution in a gel. You can think of agarose as the 100X and PA as the 1000x, if that helps.


Do we know how animals refer to us, humans? In human languages, we have "sounds" (or words) to refer to animals. For example, in English, we denominate a dog using the vocal sound dɒɡ. So, from the perspective of dogs, if they knew that the sound dɒɡ refers to them, then they "could deduce" that a human emitting the following collection of sounds is referring to them:

  lʊk, ðæt ɪz ə kjuːt dɒg. aɪ ˈwʌndə ˈwɛðər ɪt ɪz lɒst?

Now, what about the reverse? Do scientists know of a particular sound (or maybe a sign, a movement, or related form of communication) used by any animal which signifies "human"? In case the current answer is no, is this ever possible to know? Maybe for animals where studies are more advances, like primates?

The question seem to assume that animals (as a weirdly inclusive group) have a "word" to refer to humans. The vast majority of animals species do not use any specific signal to refer to humans. Very few species has the social intelligence needed to communicate about the the presence of individuals of a difference species and among them few have important enough direct relationship with humans to have do so.

Consider vervet monkeys as an example. Vervet monkeys make sounds to indicate the presence of a flying vs terrestrial predators. If a human shows up, then the sound should be the one associated to terrestrial predator but that would not qualify as a sound to refer to humans. See Seyfarth, R.M.; D.L Cheney; Peter Marler (1980). "Vervet Monkey Alarm Calls: Semantic communication in a Free-Ranging Primate". Animal Behaviour. 28 (4): 1070–1094. doi:10.1016/S0003-3472(80)80097-2

Outside of a very small zoo population of some vertebrate species, I doubt (but might be proven wrong, who knows?!) there is any species that would have a term for "human". If you have any reason to think the opposite, can you please try to focus on this specific species for which you think individuals might vocalize (or signal in any way) to convey the concept of "human" to its congeners. Likely the only species that has a "word" for "humans" are humans!

  Do scientists know of a particular sound (or maybe a sign, a movement, or related form of communication) used by any animal which signifies "human"?

It is not a matter of knowing what sound they use. Excluding humans, animals likely don't use any sound to refer to the concept of "human".

  In case the current answer is no, is this ever possible to know?

The answer is not "no, we don't know" but rather "there is nothing to be known here as animals just don't do that."


Can a person die instantaneously from internal damage to the brain? Given the human heart is autonomous, can a person die instantly from internal damage to the head/brain? I would expect the heart to continue to pulse until it ran out of energy ...

My contention is whether brain-injury can cause death, albeit Memming raised a deeper question - What is the biological definition of death?

Please consider this only as a starting point (although a lengthy one), and a race against an acute onset of  tl:dr ...

A person cannot die instantaneously from internal brain damage (under everyday circumstances). The reason is the non-centralized architecture of the brain and that consciousness is a global phenomenon which underlie the activity of many brain structures.

These brain structures are themselves comprised of a cellular hierarchy, with each cell being self-sufficient for at least a time regime in the order of minutes. As such the brain underlies to some extend the study of networks and robustness thereof. The brain also maintains a scale-free organization . Actual Scale free networks in nature are known to be robust.

Instantaneous in this context means a consciously discernible difference in time, which is on the order of tens of milliseconds (See: Inspection time, mental chronometry).

Also I narrow the medical cause of death down to a intracerebral haemorrhage, systemic shock or hypoxia. I definitely leave out all (rare) CNS-immunological phenomena (e.g. explosive brain death, Immune reconstitution inflammatory syndrome related,... )

But, effects that can mimmick instantaneous brain death are very plausible.

Notably, this question can be answered despite there being no rigorous consensus model of consciousness.

Consider the following just as pointers, but not as qualified, thoroughly sourced information, - contrary to a paper or review ( I will gladly include your resources, or turn this post into a community wiki if demand to do so exists):

**** Consciousness**:

The brain weighs only 2% of the human body mass, yet consumes 20% of the total energy at rest. Crucially the brain can deplete oxygen at a great rate, which is proportional to the brain activity in various regions, giving rise to indirect measurements of brain topology and images like these:

"Visualization of a DTI measurement of a human brain"-2006,
author: Thomas Schultz, DOR: 25/09/2012

Humans have different states of consciousness which show different overall patterns of brain activity. As such the result a scientist would witness through an high-resolution fMRI/PET scanner in a stroking-individual would differ during sleep, sleep/wake transition or various levels of awareness during the days. Stroking and the effects on the brain is studied quite extensively with rats(See: rat, fMRI, stroke).

Moreover the brain activity, fine-anatomy and orchestration of brain utilization differs from individual to individual. In short the brain is what neurologists call "plastic" Neuroplasticity is the change of entire brain structures, and the brain itself from experience and physical stress/trauma (on the brain).

We are biologial enetities which have evolved to be in-sync with the planetary rotation and solar energy influx. As such brain activity changes during the day, in accordance with our circadian rythm or biorhythm, and if it weren't for artificial lightning brain activity would change over the seasons as well.

Connecting all the dots: Describing brain death in a seconds-regime comes down to which areas in an individual brain consume the most oxygen and "shut down" first, and which processes steer brain activity till organic shutdown.

Since Stackexchange has a strong programmatic background, to put it in a somewhat programmatic analogy:

The output of a memory dump and its analytic result depend on the hardware, the software and the state of the application. Unfortunately the software is spread across processors, has multiple threads and applies a genetic algorithm with dynamic recompilation.

Death Definitions:

The notion of instant death is a cultural meme (which one can witness in child's play) and is further propagated in the media.  Additionally "death" is a highly political matter...
"Death" has numerous legal definitions (throughout various cultures) medical definitions and biological definitions depending on the context. Legal definitions depends on the culturally dependent legal corpus, medical definitions on the state of (pragmatic) technologies. The medical definition of human death is influenced by the legal definition. The legal definition in turn is influenced by politics.
The biological definition of death depends on the context and a threshold thereof, which in turn describes the level and and of hierarchical systems or one large system comprised out of systems such as organs. An organ is the collection of units in one structural one to serve a common purpose.

Finally to answer more accurately, a person cannot (under everyday circumstances) shutdown brain activity within the time-interval of one reaction time-unit or 'cycle', but may transition between discernible states of global brain-activity. Such states may only be measurable with functional Imaging techniques and classifiable using computer algorithms.


What is the best way to make a phylogeny from a list of genera? All I have is a list of about 500 eukaryotic genera, and I need a neighbor-joining tree to show their relationship.  I want to cast on top of this tree the loss of a particular enzyme.  Is the best way to do this to make a 16S phylogeny?

16S phylogeny would only work for bacteria and archaea unless you are talking about mitochondrial or chloroplast 16S rRNA. Your phylogenetic marker choice should depend on which phyla you are looking at. I suggest you try using Ef-tu if your genera are highly diverse
http://www.scs.illinois.edu/schulten/tutorials/ef-tu/eftu_tutorial.pdf

Once you have a tree in Newick format, iTOL has some nice web tools for overlaying data on trees
http://itol.embl.de/itol.cgi


Why are nitrogenous bases of DNA hydrophobic if they can hydrogen bond? Why are nitrogenous bases of DNA hydrophobic if they can hydrogen bond?

Is it that they are only relatively hydrophobic?

This forum explains it but does not give an example of the structure.

These two concepts are not mutually exclusive. You have constructed a false dichotomy.  Both of these facts are true:

The electrons in the pi orbitals of the conjugated double bonds in the planar rings are hydrophobic and can "stack" on each other as shown in this drawing of a DNA helix where the bases are shown as planar rectangles:

The nitrogen and oxygen molecules (either in the rings, or as substituents on the rings) can participate in hydrogen bonds (H-bonds):

There are other examples of hydrophobicity and H-bonds co-existing.  For example on the interior of proteins.


How to detect Zika in mosquitos I'll keep this as brief as I can. I am an engineer and I have an idea for an early detection system for the Zika virus. I want to build it. However, first I need to do research on how one detects Zika in mosquitos.

I am under the impression that to detect it in a human you would wait for the appropriate antibodies to appear in the blood. I am assuming that I would need to culture anything I get from a mosquito.

Can someone point me at any research material they can find? All of the search terms are to ambiguous for mere non medical mortals like myself.

The gold standard would be the isolation of infectious virus from mosquito saliva. Extraction of saliva from mosquitoes is fiddly if you have to do it in containment and the survival of mosquitoes collected from the field may be low. Alternatives, in roughly declining order of strength-of-evidence, would be

identification of virus from dissected salivary glands,
identification of RNA from saliva/salivary glands,
identification of virus or RNA from heads,
virus or RNA from whole bodies of insects that are not visibly
engorged with blood (and we're getting
into not-very-reliable-at-all territory at this point).
detection of viral RNA from pooled field-collected (unsorted) insects, possibly including those which have recently blood-fed.

There are also other technologies that are beginning to be used for field surveillance of arboviruses in vector populations, such as sugar-coated or honey-coated Whatman FTA cards (mosquitoes sugar-feed on the cards which preserve RNA).

Two other things are worth emphasising here. One is that not all mosquitoes which ingest infectious virus will develop a transmissible infection even if they survive to complete the necessary incubation period. Some will clear infection completely, others may develop a disseminated but non-transmissible infection due to the existence of barriers to replication within the vector's tissues (see this paper for a nice review).
The second is that the importance of a vector is not determined solely by its competence (the probability that a mosquito ingesting an infectious dose and surviving the extrinsic incubation period develops a transmissible infection) but also things like vector:host ratio, biting preferences, and typical lifespan. Vectorial capacity is more important (this is a recent paper pointing out the differences).


Is Melanin a PCR Inhibitor? I have been growing B16F10 Mouse Melanoma cells. I need to extract the genomic DNA and do PCR to amplify a specific region. However, no matter what temperature or magnesium concentration I use, I have no luck.

I obtained mouse DNA from someone who was genotyping mice. I tested the PCR oligos with that DNA, and the reaction worked, so it's not an oligo problem.

The genomic DNA had poor 260/230, about 0.6. I thought the EDTA levels may have been high, so I did an isopropanol precipitation to clean it up. This made the 260/230 ratios about 2.1. But the PCR still didn't work.

What I had noticed during the precipitation however was that the DNA pellets were gray to black. I assume this is melanin, because the cells are melanoma cells, and turn black.

Could this melanin be a problem in PCR?

Melanin is a potent inhibitor of PCR - when you use B16 cells (or any other cell line that produces melanin) you have to purify your sample from it. Unfortunately a simple Phenol-Chloroform extraction or an ethanol precipation won't do the magic, since melanin co-precipitates with the nucleic acids.

I recommend following the following paper: "CTAB–Urea Method Purifies RNA from Melanin for cDNA Microarray Analysis".

The protocol derived from the paper can also be found here.


Different Mutations Leading to Same Allele? Can different mutations lead to the same allele? In my genetics books, I always see alleles referenced as, eg. Aa where A = dominant and a = recessive, but are these strictly binary phenotypes? Since there are an infinite number of mutations that could theoretically take place, wouldn't there be an infinite number of alleles? Eg (not an actual biological phenomenon but just as an example) A1C on chomosome 3 leads to allele a1, A1T leads to allele a2, etc.

You are looking at high school biology books. if that.  I'd be shocked if a high school text didn't mention blood group genes, for instance.
The simple genetics that Mendel elucidated only applies to a very small number of situations.
In real life, very few situations are explained by the interactions of only two different alleles, one of which is classically dominant to the other, within a single gene.
So sure, you could have many alleles which break a gene, but where the presence of one working allele is enough to be functionally indistinguishable from having two working copies.  You could also have slight sequence differences that are functionally identical.
Here's a random example; all the variants ensembl knows about for a random gene.  Note that these are only variants which have been found, obviously private individuals and families might have their own variants that are not documented
http://uswest.ensembl.org/Homo_sapiens/Gene/Variation_Gene/Table?db=core;g=ENSG00000280165;r=13:61409685-61415522;t=ENST00000409204
Most of these are in the 3' UnTranslated Region, and likely have no functional significance.


Nervous system : Nerve signals If the electrical signals from all the various organs throughout the body eventually connect to the nerves in the spinal column traveling up to the brain, how does the brain differentiate the different signals.  Is the nerve in the spinal column like an electrical conduit with many wires inside?

Yes is the simple answer. A nerve will go up to a specific part of the brain which the brain knows corresponds to a certain region of the body. It isn't perfect though e.g. pain in the diaphragm confuses the brain which doesn't recognise that pain must be coming from there so instead tells the body there is shoulder pain, however this is useful in medicine. Another infamous example is pain from heart disease (angina) which causes pain in the jaw and arm. Perhaps even more interestingly, if a nerve is cut and then grows back linking to the wrong nerve it may lead to the completely wrong part of the body being identified when touched. Also if the brain itself is stimulated in these corresponding areas, a person will feel he or she is indeed being touched in a certain part of the body.


How do I compare bacteria growth curves? I have bacteria growth curves for 5 different temperature conditions and these were created using %red-light transmittance. How do I compare these growth curves? Should I calculate the growth rate and if so how do I do that?

1) A Bacterial growth curve:

When we provide a favorable medium for bacteria to divide regulary and increase in number, we get what's called a "growth curve", measuring the concentration of cells against time as time passes.

2) Phases:

A) The first phase is called the "lag phase", in this phase bacteria are adapting to the new medium, preparing enzymes etc, to start dividing. Therefore little to no growth is observed.

B) The second phase is the "Exponential growth phase", bacterial cells are well adjusted to their medium and ready to reach full potential, "maximum division and growth" happens here.

C) The third phase is the "stationary phase", bacteria are no longer able to grow or feed, they run out of nutrients, and growth is stationary/zero again. It can persist for a long period of time. (Cell growth=cell death, no actual increase in cell number=stationary)

D) The final growth phase is the "death phase", no nourishment is available and toxic metabolites have been accumulating during the stationary phase, death occurs (death here means that an increasing number of bacterial cells are dying, unlike the stationary phase where the number of cells dead equals the number of cells viable), following cell death (which now happens at a faster rate than cell growth), the cell concentration starts to decline. However, it doesn't really reach zero and bacteria might be able to regenerate again when the conditions are healthy again.

3) Recording bacterial growth using transmittance or spectrophotometer:

As bacterial cells increase in number, the turbidity of their medium increases (depends on the concentration of cells), and the incident light (if you shoot a beam of light across the medium) is more deflected away from the receiving detector (to detect the intensity of light), which makes spectrophotometer a reliable and accurate method to measure cell growth (proportional to the intensity of light detected).

4) How to compare growth curves?

Looking at the growth curve will give some idea of the rate of growth in relation to a standard growth curve or some other available growth curves (compare phases and their durations, the exponential phase, etc). However there is a way to calculate growth curve and generation time (doubling time) from a growth curve.

The difference in cell concentration/difference in time = growth rate constant. Or dN/dt = kN or you may use this advanced equation: log10N2 – log10N1 = k(t2 – t1)/2.303

Simply plot any two random points of time on your curve: the first point is t1, the second point is t2, N1 is the number of cells (cell concentration) at t1, N2 is cell concentration at t2.

Or you can simply use dN/dt = (N1 – N2)/(t1 – t2) and compare the resulting k between curves.

I hope this answers your question, please know that I am by no means an expert on the subject and you may search further or get expert advice if you need to.

References:

Textbookofbacteriology.net

Miller-lab.net/MillerLab

biotek.com/

Academic.pgcc.edu

Web.mst.edu


What are the differences between the margins of the lateral and medial condyles of the tibia? During an osteology lecture about the bones of the leg, the professor mentioned that the posterior (i think it was the posterior at least, I didn't write my notes down very well) margins of the lateral and tibial platues at the articular surface are different; the medial one's is sharper, and the lateral one's is smoother, rounder, or, as he put it, "sloppier", and this helps give more motility to the lateral meniscus and makes its injuries less likely. It also apparently helps the motion range of the knee joint.

I can't seem to be able to find any article or book that talks about this (I've checked Snell's, Gray's and Grant's anatomy books), so I was wondering if this is really a thing.

The proximal end of the tibia is broad and flat known as tibial plateau. The intercondylar region crosses through the midline of this plateau, separating the medial and lateral condyles of the tibia.

The two condyles are in form of flat and broad surface for articulation with the medial and lateral condyles. The medial surface  is convex and subcutaneous. The lateral surface, also known as articular surface is smooth surface and somewhat concave, and articulates with the talus.

[Sources:
https://www.physio-pedia.com/Tibia
http://en.wikipedia.org/w/index.php?title=Medial_malleolus&oldid=240146811
http://www.bartleby.com/107/61.html ]


What is the difference between tonic and phasic firing? I am reading about dopamine, and I have realized that dopaminergic neurons can fire phasically or tonically. What is the difference between these two modes of firing?

Tonic firing typically occurs without presynaptic input and can be viewed at as background activity. Tonic activity is often characterized by a steady action potential firing at a constant frequency. Note that not all neurons may have tonic activity at rest. It may serve as keeping a steady background level of a certain neurotransmitter or it can serve as a mechanism where both an inhibition or increase in presynaptic input can be transmitted. When a neuron is silent at rest, only an increase in presynaptic activity can be transmitted postsynaptically.

In contrast, phasic firing occurs after a neuron is activated due to presynaptic activity and it incurs activity on top of any background activity a neuron may have. It is typically restricted to one, a few, or a short burst of action potentials, whereafter the activity quickly returns to the resting state.

Reference
Tsai et al., Science (2017); 324: 1080-4


What is the purpose of requiring two separate binding systems for the antibody response? I've read that in most cases, B-cell activation requires helper T-cells.  This requires antigen binding by both antibodies and T-cell receptors, using two different antigen-binding proteins, recognizing two different epitopes.

Why is this so complex?  Would the overall antibody system still work if B-cells required only antibody/B-cell receptor binding?

Immunity can be a double edge sword. It is aimed to detect and destroy invading pathogens but it can also target the self, as exemplified in autoimmune diseases. To avoid this, many failsafe mechanisms exists.

For example, imagine an innocuous foreign antigen gets into your body and reaches the lymph node. There it may find a naive B cell that has a receptor that recognizes it. Without a double check mechanism this B cell will mature and begin to produce antibodies against this antigen, triggering an immune response that is not beneficial (e.g. in allergy) and is not necessary (the antigen is harmless).

Because of this, activation of the adaptive immune system requires usually two signals. In the context of B cells the other signal usually comes from effector CD4 T cells (of the type T follicular helper Tfh) and is called linked recognition, because both the naive B cell and the Tfh cell have to be specific for the same antigen.

So a possible scenario may look something like this: a pathogen's antigen is taken by DCs. If there is an ongoing inflammatory response this DCs will get fully activated (a process called licensing) and migrate to the lymph nodes. There they present the antigen to naive T cells. Naive T cells specific for the antigen mature and become effector T cells that may include CD8 and several classes of CD4 T cells, including CD4 Tfh cells. The antigen is also transported to the lymph nodes and presented to naive B cells. Naive B cells that recognize the antigen AND also are stimulated by Tfh specific for the same antigen then mature into plasma cells that secrete antibodies.

For harmless antigens, even though DCs may phagocyte them they will not get fully activated in the absence of an inflammatory response. So the activation chain is broken. This system fails somehow in the case of allergy.

Another point is that this mechanism is related to the generation of antibodies against microbial protein antigens. Animals lacking T cells cannot produce them and so they are called thymus-dependent (TD) antigens. Other microbial antigens like bacterial polysaccharides can induce antibody production without the help of T cells. This so called thymus-independent (TI) antigens provide the second signal by direct recognition of the antigen (e.g. through TLRs) or by inducing extensive crosslinking of B cell receptor (BCR). TI antigens include LPS and bacterial DNA. TI antigens appear earlier than TD antigens and although provide some protection they are less efficient than the TD ones because TI-specific B cells do not undergo affinity maturation and isotype class switching as TD antigens do.

Reference: Most of what I describe is found in Janeway's Immunobiology, 8th edition. Chapter 10 (The humoral immune response). In particular the section 10- "B-cell activation by helper T-cells".


Differences Between Protein Motifs and Protein Domains? I am in a 300-level molecular biology class and am unclear about this concept and how to delineate motifs versus domains of proteins.  Any suggestions would be much obliged.

These are completely different concepts, which sometimes may be connected.

A motif in biology is a mathematical model, typically of a sequence, that predicts which sequences belong to some defined group. For example, a DNA sequence motif can characterize the binding site of a transcription factor, i.e. which sequences tend to be bound by this factor. For proteins, sequence motifs can characterize which proteins (protein sequences) belong to a given protein family. A simple motif could be, for example, some pattern which is strictly shared by all members of the group, e.g. WTRXEKXXY (where X stands for any amino acid). There are also more complex motif models.

Protein domains, on the other hand, are a structural entity, usually meaning a part of the protein structure which folds and functions independently. So, proteins are often constructed from different combinations of these domains.

So how are motifs and domains related? Well, when you think about protein families, it makes sense not only to look at the whole sequence but also to focus on individual domains. Since they are a elementary functional-structural units, it makes sense to find sequence motifs for individual domains. So, you often find that a protein contains multiple domains, each domain characterized by having a sequence that matches the motif of its family.


Why is the ability to drink salt water so rare in land-animals? Apparently, some species are capable of drinking salt water, like the sea lion and otter.

But given how rare fresh water is, and how abundant salt water is, why have more land animals not evolved to drink it? Why are kidneys capable of handling such a thing so uncommon?

I understand that evolution doesn't necessarily always do what's most efficient on a macro scale, but this drives me nuts.

So many animals live less than a five minute walk from the shores of an ocean, and such water is so abundant that they'd never be thirsty.

According to an answer here there is around 356,000 km of coastline on the planet. If we take an average human walking speed of say 5 km/h then our 5 minute walk takes us 0.417 km inland - giving approximately 150,000 km^2 of land conveniently supplied with sea water.

Now according to this page the total amount of land area is around 150,000,000 km^2 which according to this page is covered by somewhere in the vicinity of 117 million lakes [I'm certain a large portion of them are more accurately described as puddles but well go with that number for now], that gives on average a fresh water body every 1.3 km^2.

If we simplify things and imagine dividing the land area into 1.3 km^2 grid with ~1.14 km the distance separating each watering hole meaning the furthest distance to a watering hole across all the earths land area (ON AVERAGE) is around 0.570 km or just under 7 minutes walk (using our previous 5km/h)

So according to my very very rough calculations only around 0.1% of the land area is located within 5 minutes of sea water while 100% is located within 7 minutes of fresh water! I don't think that extra two minute walk is going to be that much of an evolutionary drive for any species.


Where exactly is 'Colloid' with regards to synthesis of thyroid hormones? I've researched colloid and it seems to be a substance of microfibres and thin films in which thyroid hormones may be synthesised, but I was wondering where this exactly is... I think it could be in the inter membrane space but I have no evidence of that, or is it just surrounding all cells?

Colloid is found in thyroid follicles and is composed of the protein from which thyroid hormones are made.

This link below states: "Follicles are filled with colloid, a proteinaceous depot of thyroid hormone precursor."

That precursor is called thyroglobulin.

The image below shows micrographs of the thyroid.

In the image, the colloid is surrounded by thyroid epithelial cells, which collectively form a follicle. The lower mag on the left shows many follicles filled with colloid.  The image on the right shows one follicle. The white areas inside the follicle near the epithelial cells show uptake of colloid by the epithelial cells, which are activity synthesizing thyroid hormone.

http://arbl.cvmbs.colostate.edu/hbooks/pathphys/endocrine/thyroid/anatomy.html


Identify bee in photo (found in Utah, USA) A friend took this photo of a bee in his back yard in central Utah (© Jon Mott, CC-BY 3.0). I have no formal training in systematics or entomology, so to me everything looks like the bees' poster child Apis mellifera. Can someone with a bit more experience confirm or refute this?

Yes, this looks like Apis mellifera, which is also one of the most common bees you'll run into. If you have other pictures, you could check the identification tips at the bugguide page for the species.

As a side note, in general to really confirm an identification a specialist would need to see a collected specimen (that is, a live or pinned bee) as the distinctive characters (things like size, wing veins, or in this case, long hairs on the eye) may not be visible in photographs.


How much variation in the human genome for humans We are currently learning about the Human Genome Project in high school biology. Wouldn't the human genome that was mapped be different from, say, mine if it was mapped? How much variation is there between individual humans in our genetic sequencing? I'm assuming there is not that much difference since multiple volunteers were used in the project. I did see another question that talked about mutation rate, so I'm not sure if that's the same thing.

You are correct in saying that the human genome sequenced in the project was contributed by a dozen anonymous volunteers. However, the final sequence that is used as a standard reference is a somewhat arbitrary construct that represents a collection of consecutive segments taken from one or other of the contributors. It is a haploid sequence, plus a Y and an X chromosome.

Now you ask how different are the genomes of any two subjects, taken at random from a population. Imagine for simplicity looking at your own genome. For each of the 22 autosomes, you know you have two copies, one transmitted from your father, the other from your mother (for the X chromosome you have two copies, if you are a girl). Now imagine comparing the sequence of each of your pair of homologous chromosomes side by side; remember that they are derived from very different individuals (unless your parents are close relatives), so that they will not be identical, as they represent independent evolutionary histories.

Then, the question becomes: how much variation is there between the sequences of your paired chromosomes? And the answer is known: approximately every 1,000 base pairs your chromosomes show a base pair in one chromosome and a different base pair in the other; otherwise they are identical. The sites where this variation occurs are called SNP, for Single Nucleotide Polymorphisms (many other kinds of variation exist, but SNPs are the more common). We can generalize this observation, as it remains true for any pair of chromosomes chosen at random from any pair of subjects. Therefore, we can say that humans are identical for 99.9% of their genomes, whereas the genetic variation responsible for the differences that allows us to recognize ourselves as unique are limited to 0.1% of our genome.


Regulation of chromatin structure Recently, I reviewed the different levels of chromatin structure. The primary level is nucleosomes, where DNA is bound to histones, and has structural similarity to "beads on a string." The secondary level is a 30nm fiber, and the tertiary level is formed by radially looping the fibers.

I've also been learning about the histone code and how different modifications to the core histones relate to transcriptional regulation. Are these modifications the primary regulation mechanism for chromatin structure? In other words, does chromatin assume the most compact structure possible until histone modifications are made to enable transcription? Or have other regulatory mechanisms unrelated to transcription been discovered and characterized?

"Are these modifications the primary regulation mechanism for chromatin structure?"

It depends on how you define primary, we might currently think of histone modifications as primary because other regulatory mechanisms have not yet been well studied. Something else you can think of are the various regulatory proteins that interact with histone marks to modify chromatin.

I don't think you should imagine chromatin as assuming "the most compact structure possible until histone modifications are made to enable transcription" but rather histone modifications being a dynamic process with various transcription factors (a class of proteins) coming in and adding/removing histone marks as well as 'remodeling chromatin' (adding/removing nucleosomes)

As a sidenote, I don't believe much is known about the tertiary stage you initially mentioned so maybe that could play a huge role in the regulatory mechanisms of chromatin structure, it has just not been well explored.


How do nuclear membranes form during Telophase of Mitosis/Meiosis? During Telophase, homologous chromosome pairs reach the poles of the cell with the help of microtubules. From there, nuclear membranes form around each new set of chromosomes.

My confusion originates from a single question: How did these nuclear membranes form around the chromosomes?

According to this book, during disassembly of the nuclear envelope, the nuclear membranes are broken down into vesicles. The nuclear membranes reform at the end of mitosis as the vesicles bind to the surface of chromosomes and fuse with each other to form a double membrane around the chromosomes (how this happens is not clear, except that integral membrane proteins and lamins may be involved, but physical contact is supposedly the first step).


Can we produce sugar using chlorophyll dissolved in ethanol? I can't find anything about this on the net.
I read in my (high-school) textbook that if plants get sunlight, water and carbon dioxide, and the catalyst called chlorophyll, they can make sugar.
I'm just thinking... We CAN extract chlorophyll by dissolving the boiled leaf in ethanol! So can't we just bubble CO2 in and let the sun shine on it and add some water? Shouldn't that make sugar in the solution?

The mechanism of photosynthesis proceeds via light-dependent reactions and light-independent reactions within the chloroplasts (organelles in cells which house the photosynthetic machinery, and indeed chlorophyll itself).
To produce glucose via photosynthesis, you certainly need the pigment chlorophyll - it is necessary but not sufficient by itself. For that, you need the Calvin cycle, which is part of the light-independent reaction within photosynthesis.
The light-dependent reaction requires chlorophyll and uses H2O and sunlight to produce ATP and NADPH, with oxygen as a byproduct. ATP and NADPH are necessary for the Calvin cycle to proceed, which takes atmospheric CO2 and produces glucose and other sugars. This is simplified into basic photosynthetic equation which you are familiar with.
     6 CO2     + 6 H2O  -->  C6H12O6 +  6 O2
carbon dioxide + water  -->  glucose + oxygen

Here is an illustration:

The red arrows point to the light-dependent ("light"), and light-independent ("dark") reactions.
Take a look at this slideshow, which answers all your questions with illustrations.

We CAN extract chlorophyll by dissolving the boiled leaf in ethanol! So can't we just bubble CO2 in and let the sun shine on it and add some water? Shouldn't that make sugar in the solution?

Unfortunately you destroy the chloroplast structures during the extraction you describe. These structures, and especially the membranes, are necessary for photosynthesis in its entirety to proceed.


Gaps in FASTA formatted genome? I'm just getting interested in genetic structure and I decided to find a FASTA formatted genome (human) and I found one here. However, I'm confused. I know that A can only match up to T and C to G but it appears as though T is matching up to T, A to A, C to A, and etc. How is this possible? Can there be gaps where T,A ,C ,or G is connected to nothing? Small part of genome: ATTTAGAAATGACTAACAATTATGTAGGTTTATTTCTCTCAGTATAGAATGTTCATATAGAATT

Your question is based on a misunderstanding. You have a single strand, lets assume it's the red sequence in the image. The linear sequence along this strand is not limited by base-pairing rules.

The base-pairing rules (A-T, G-C) apply to the complimentary strand, given in blue in the image.

It's convention to only give the sequence for one strand because the base-pairing rules allow us to infer the complimentary sequence.


Sources of Mutations I'm looking for a reference that gives some information quantifying sources of mutations that occur within cells. These can be general, but I'm interested in some percentage of mutations caused by external vs internal sources (like mutagens vs replication errors).

An extensive collection of the various mutation rates (from which you could reverse-engineer their fraction on the total share of mutations):

http://www.bionumbers.hms.harvard.edu/search.aspx?log=y&task=searchbytrmorg&trm=mutations&org=&rpp=100


Modeling population growth - Variance I've been studing population growth models, but there's something I can not find that's fustrating. That's a formula for the variance in population growth. I know that other models can be aplied, but I want to start with the simplest case.

Let's assume a population is growing exponentially as defined by:
$N(t) = N(0)W^{t}$

The parameters $W$(absolute fitness in my definition) tell us that the time for division (if the species reproduces binarally) is given by an exponential distribution with $\lambda = \dfrac{\ln W}{\ln 2}$

So I see a model for $N(t)$ and a random variable associated with this model. What is the pdf, expected value and variance of $N(t)$? The expected value I expect it to be given by the first equation (or the value to be the same) but what about the variance?

If $W$ is a parameter, I'd expect (in the simplest case) that $W$ itself is a constant (i.e. it doesn't have a distribution). (By the way, I would normally use $T_{1/2}$ to denote the doubling time, $\ln 2/\ln W$, and would use $\lambda = \ln W$ for the exponential rate, i.e. $W^t= \exp(\ln W)^t = \exp(t \ln W) = \exp(\lambda t)$. I don't normally see people express rates scaled by $\ln 2$.)

In the case of a continuous-time birth-death process (the technical jargon for your model), I believe the analytical answer will be that the standard deviation of the population size at time $t$ will grow at the same exponential rate as the mean population size, and that the variance will grow twice as fast (because it has units of $\textrm{population size}^2$), i.e. $\propto \exp(2 \lambda t)$)

I don't have a derivation/reference handy, will dig around for one. This is fairly basic stochastic-process math, but stochastic-process math also gets pretty hairy-looking (to a biologist) quickly. Bartlett 1960 (Stochastic population models in ecology and epidemiology) is one place to look for basic results, although I'm sure there are many others. This recent PhD thesis gives a thorough introduction to the math of birth-death processes ... although, not to my disappointment, a canned derivation of the variance result I'm too lazy to derive for you.


Apoptosis vs necroptosis I understand that apoptosis and necroptosis share the same upper part of the pathway, but I cannot seem to distinguish when is each one activated? From my readings, it seems that when procaspases 8 or 10 are unavailable, the cell will shift to necroptosis. What makes these procaspases unavailable and why does a cell second the necropotosis?

From my readings, it seems that when procaspases 8 or 10 are
  unavailable, the cell will shift to necroptosis. What makes these procaspases unavailable and why does a cell second the necropotosis?

This seems to be right.

  Mice with a conditional deletion of caspase-8 in the intestinal
  epithelium (Casp8ΔIEC) spontaneously developed inflammatory lesions in
  the terminal ileum and were highly susceptible to colitis. Casp8ΔIEC
  mice lacked Paneth cells and showed reduced numbers of goblet cells,
  indicating dysregulated antimicrobial immune cell functions of the
  intestinal epithelium. Casp8ΔIEC mice showed increased cell death in
  the Paneth cell area of small intestinal crypts. Epithelial cell death
  was induced by tumour necrosis factor (TNF)-α, was associated with
  increased expression of receptor-interacting protein 3 (Rip3; also
  known as Ripk3) and could be inhibited on blockade of necroptosis.

  Caspase-8 is a cysteine protease critically involved in regulating
  cellular apoptosis. On activation of death receptors, including
  TNF-receptor and Fas, caspase-8 is activated by limited
  autoproteolysis and the processed caspase-8 subsequently triggers the
  caspase cascade that finally leads to apoptotic cell death.
  Caspase-mediated apoptosis is important for the turnover of IECs and
  for shaping the morphology of the gastrointestinal tract 4.

2011 - Caspase-8 regulates TNF-α-induced epithelial necroptosis and terminal ileitis

  Caspase-8 has both prodeath and prosurvival roles, mediating apoptosis
  and/or preventing RIPK1-mediated necroptosis depending on cell type
  and stimulus. We found that inflammatory stimuli (LPS, lipoteichoic
  acid, or TNF-α) caused an increase in caspase-8 IETDase activity in
  primary rat microglia without inducing apoptosis. Inhibition of
  caspase-8 with either Z-VAD-fmk or IETD-fmk resulted in necrosis of
  activated microglia. Inhibition of caspases with Z-VAD-fmk did not
  kill non-activated microglia, or astrocytes and neurons in any
  condition. Necrostatin-1, a specific inhibitor of RIPK1, prevented
  microglial caspase inhibition-induced death, indicating death was by
  necroptosis.

2013 - Caspase inhibitors protect neurons by enabling selective necroptosis of inflamed microglia.

  Necrosis has long been described as a consequence of extreme
  physicochemical stress, such as heat, osmotic shock, mechanical
  stress, and freeze-thawing, which kill cells quickly and directly.
  Therefore, this cell death has been described as uncontrolled and
  accidental necrosis characterized by loss of plasmamembrane integrity
  and cellular collapse, though nuclei remain largely intact during this
  process (Krysko et al., 2008a,2008b; Vanden Berghe et al., 2010). Loss
  of membrane integrity and release of intracellular content grant
  necrotic cells the ability to induce an inflammatory response. These
  immunogenic endogenous molecules fall under the umbrella term
  ‘‘damage-associated molecular patterns’’ (DAMPs) (Garg et al., 2010;
  Kryskoet al., 2011). They include, in the case of accidental necrosis,
  HMGB1, IL-1a, uric acid, DNA fragments, mitochondrial content, and ATP
  (Tables 1and2)(Eigenbrod et al., 2008; Kono et al., 2010; Krysko et
  al., 2008a; Sauter et al., 2000). Because the nomenclature of DAMPs in
  the literature is confusing, here we define DAMPs as a family of
  molecules that are intracellular in physiological condition

2013 - Necroptosis: The Release of Damage-Associated Molecular Patterns and Its Physiological Relevance

Based on the articles above, I would say that capsase-8 is a signal that apoptosis works finely, and so the cell can kill itself whenever it wants. So if that signal is lost because of an infection, mutation or extensive cell damage, the cell has no choice, but to activate the necrotic pathway.

Figure 1 - cell survival and programmed cell death - source

  During tumorigenesis, significant loss or inactivation of lead members
  in the caspase family leads to impairing apoptosis induction, causing
  a dramatic imbalance in the growth dynamics, ultimately resulting in
  aberrant growth of human cancers. Recent exploitation of apoptosis
  pathways towards re-instating apoptosis induction via caspase
  re-activation has provided new molecular platforms for the development
  of therapeutic strategies effective against advanced prostate cancer
  as well as other solid tumors.

2012 - CASPASE CONTROL: PROTAGONISTS OF CANCER CELL APOPTOSIS

  These findings reveal that, although apoptotic/drug resistance is a
  formidable “stronghold” of cancer against chemotherapy, necroptotic
  susceptibility is an intrinsic “weak point” of cancer.

2007 - Targeting the Weak Point of Cancer by Induction of Necroptosis

  Playing a central role in cell death, caspases are targeted by
  different viruses in the aim of prolonging cell survival. For
  instance, viral IAPs (inhibitors of apoptosis) interact with and
  inhibit the processed active caspases, either by blocking the
  catalytic part of the enzymes, or through E3 ubiquitin ligase activity
  from RING domains, targeting caspases for rapid degradation via
  proteasome. Baculoviruses, asfiviruses or irridescent viruses encode
  such IAPs. Another class of caspase inhibitors frequently found among
  poxviruses include the serine proteinase inhibitors serpins:
  CrmA/SPI-2. Crma targets cysteine proteases such as host Caspase 1 and
  Caspase 8.

viralzone - Inhibition of host caspases by virus

  Pathogens specifically target both the caspase 8-dependent apoptotic
  cell death pathway and the necrotic cell death pathway that is
  dependent on receptor-interacting protein 1 (RIP1; also known as
  RIPK1) and RIP3 (also known as RIPK3). The fundamental co-regulation
  of these two cell death pathways emerged when the midgestational death
  of mice deficient in FAS-associated death domain protein (FADD) or
  caspase 8 was reversed by elimination of RIP1 or RIP3, indicating a
  far more entwined relationship than previously appreciated. Thus,
  mammals require caspase 8 activity during embryogenesis to suppress
  the kinases RIP1 and RIP3 as part of the dialogue between two distinct
  cell death processes that together fulfil reinforcing roles in the
  host defence against intracellular pathogens such as herpesviruses.

  The MCMV protein vICA prevents caspase 8 activation, and this
  sensitizes cells to death receptor-induced necroptosis. In addition,
  the MCMV protein vIRA blocks necroptosis and MCMV-induced programmed
  necrosis by inhibiting RHIM (RIP homotypic interaction
  motif)-dependent interactions.

2012 - Viral infection and the evolution of caspase 8-regulated apoptotic and necrotic death pathways

  One potential explanation for this is that this form of death evolved
  to provide a “backup” pathway. Indeed, cowpox virus produces the
  factor CrmA, a potent apical caspase inhibitor capable of blocking
  apoptosis (Ray et al., 1992; Gagliardini et al., 1994). Several viral
  encoded genes are similarly produced to prevent apoptosis, and thus it
  is clear that inhibition of apoptosis is an important means viruses
  have exploited to avoid immune clearance. Interestingly,
  cytomegalovirus induces RIP3-mediated necroptosis via the interferon
  regulatory factor DAI (Upton et al., 2012). This virus also produces a
  protein called viRA, a protein that disrupts assembly of RIP1/RIP3
  necrosomes and consequent necroptosis. Thus, while the physiological
  function(s) of necroptosis remains to be fully elaborated, it is clear
  that this cellular process has been around for a long time during
  evolution. It is likely that necroptosis may serve as an “Achille's
  heel” in tumor cells, and thus greater understanding of the process
  may reveal novel therapies for cancer therapeutics.

2014 - Grand challenges in cell death and survival: apoptosis vs. necroptosis

It seems like there is a 3rd pathway too, it is called ferroptosis.

  TNF-induced necroptosis depends on receptor-interacting protein-1
  kinase, mitochondrial complex I and cytosolic phospholipase A2
  activities, whereas H2O2-induced necrosis requires iron-dependent
  Fenton reactions.

2009 - Necroptosis, necrosis and secondary necrosis converge on similar cellular disintegration features

  The transition metal iron is essential for life, yet potentially toxic
  iron-catalyzed reactive oxygen species (ROS) are unavoidable in an
  oxygen-rich environment. Iron and ROS are increasingly recognized as
  important initiators and mediators of cell death in a variety of
  organisms and pathological situations. Here, we review recent
  discoveries regarding the mechanism by which iron and ROS participate
  in cell death. We describe the different roles of iron in triggering
  cell death, targets of iron-dependent ROS that mediate cell death and
  a new form of iron-dependent cell death termed ferroptosis. Recent
  advances in understanding the role of iron and ROS in cell death offer
  unexpected surprises and suggest new therapeutic avenues to treat
  cancer, organ dam
  - age and degenerative disease

2013 - The role of iron and reactive oxygen species in cell death
2012 - Heme induces programmed necrosis on macrophages through autocrine TNF and ROS production

Not just a 3rd, there are many more pathways (pyroptosis, MPT-RN, parthanatos, ferroptosis, NETosis).

Figure 2 - Signalling pathways of regulated cell death.
2014 - Regulated cell death and inflammation: an auto-amplification loop causes organ failure


Cell targets of Glybera So we know that there is a first gene therapy drug in the market out there called Alipogene tiparvovec to address  lipoprotein lipase deficiency (LPLD) at a genetic level. Does this genetic drug target all cell types (except germline) that expresses the LPL gene in the human body or simply the parenchymal cells that process fat? I have not been able to find information specific to Glybera.

Glybera doesn't target all cells, and doesn't target fat processing cells. Glybera is adeno-associated virus 1, which normally infects skeletal muscles. Glybera is delivered by intramuscular injection, so the virus easily infects the muscle tissue. The infected muscle cells produce a variant of lipoprotein lipase that has better activity than normal LPL and secrete it into the bloodstream. Once in the blood LPL can interact with chylomicrons and make them smaller.

Here is a paper about viral gene therapy for LPL deficiency, specifically about glybera, but I don't think it's open access.


At what point is a picked flower considered dead? Let a flower be picked from the ground such that its stem is cut and the flower is separated from the root system (as in figure).

Questions:
1a. At what point is it considered dead?

Does the flower and attached bit of stem continue to live for some time before dying?

Is this like asking when an limb that has been chopped off an animal dies - should we considered not the flower, but the root system?

1b. How does one define death for an organism without a nervous system?

This is very much analogous to your "limb" suggestion, or, since the flower is a reproductive organ, one can ask,

  At exactly what point is the uterus considered dead after a hysterectomy?

or,

  At exactly what point are the testicles considered dead after a male dog is castrated?

The organism (woman and dog respectively) does not die. Tissue dies. Tissue dies all the time. Red Blood cells die after about 120 days, give or take. Skin cells die faster than that.

It depends on the definition of death. If one of the requirements for "life" is the ability to reproduce, are both the woman and the dog now dead? Of course not. They had the potential, or perhaps they already reproduced.

If one of the requirements for "life" is the ability to grow, well, the uterus and the testicles are dead immediately upon removal. But we stop "growing", and we don't die.

If one of the requirements for "life" is the ability to respond to its environment, the uterus and the testicles are not dead. They are "alive" for a time, though the environment is toxic to them if thrown away. If placed in nutritious media, they will "live" a bit longer.

Common sense, which often isn't reliable in science, would dictate that the flower dies when it can no longer maintain cell turgor, i.e. can no longer absorb fluids. But the argument can be made that it is only "dying" at that point.

Basically your question depends entirely on the definition of life. And that has not been agreed upon.


Why are there more stomatal openings on the lower surface of a dicot leaf? This causes more transpiration to occur from lower leaf surface. What's the exact reason for why are there more stomatal openings on the lower surface of a dicot leaf?

Firstly, it is not necessary that all dicots have stomata on their lower surface of their leaves. The lotus Nelumbo nucifera has its stomata on its upper surface, due to the lower surface of its leaves being in contact with water, and therefore unable to transpire effectively.

The reason that stomata are usually on the lower surface has been analysed in this paper, which rejects the commonly held hypothesis that stomata appear on the lower surface of leaves (hypostomatous) as a response to dryness, by citing that hypostomatous leaves are relatively less common in dry environments.

The paper then analyses the correlation observed between parameters of leaves and their stomatal locations.

By using a number of computational models (which conclude that given the set of assumptions in the paper, leaves should not generally be hypostomatous), the paper addresses the faults of the model and concludes that there is no one single reason why leaves are usually hypostomatous, and then brings up a couple other possibilities that may help in explaining the majority of plants being hypostomatous.


Did humans evolve the ability to swim? Or is it just luck that we are able to swim? Many animals like ducks have evolved features to be able to swim. Even not so aquatic animals like a tiger evolved so that its feet can act as paddles. In humans I don't see any direct feature that has specifically evolved for the purpose of swimming. So is it just luck that we are able to swim and some of our cousins like gorillas are not able to swim? Or did we evolve in some way to be able to swim

The Jane Goodall website says: "You’ll rarely see a chimp paddling about in the water as they don’t like to swim. Their low body fat ratio causes them to sink and their top heavy body composition makes it difficult for them to keep their heads above water.  However, some chimpanzees do enjoy a good splash around in shallow water."
Some monkeys have been taught to swim, see this video: https://www.youtube.com/watch?v=q2vekGuV8xA
So, the answer is, it's just luck that humans are quite good swimmers compared to other monkeys, because strong bipedal running and legs also gives humans good stability in water. After us the best swimmer is the proboscis monkey. Many other monkeys do play in water and swim: https://www.youtube.com/watch?v=sn-M1kCvzLg
There are many studies that theorize that modern humans have evolved beside seas and rivers.
Here's a massive infographin on the subject: https://visual.ly/community/Infographics/science/possible-aquatic-adaptations-human
Humans crossed the open ocean at least 50,000 years ago, i.e. to colonize Australia, the oldest evidence of fishing is currently from East Timor, 42,000 year old fishing hooks: https://www.livescience.com/17186-oldest-fish-hooks-early-humans.html#:~:text=Their%20discovery%20uncovered%20fishing%20hooks,%2C%22%20O'Connor%20said.


How do animals lose heat? I remember being told as a child that dogs stick their tongue out to stay cool, because they can't sweat like us. This made sense to me.

But only a couple of days ago I suddenly thought: What about all the other animals?! I mean, I don't see a cat or a horse putting their tongues out, and yet I don't see them sweating either. How do they lose heat? How do different kinds of animals lose heat?

There are a number of ways, which are briefly summarized here. I also recommend reading this nice Scitable article on thermoregulation. It is not too technical. Felines do pant when they get hot. Horses do sweat. Jackrabbits can enlarge the blood vessels in their large ears to eliminate excess heat. Bird use a process called gular flapping, which is similar to panting of dogs and cats.  Animals can move into shaded areas.  The possible mechanisms are many.


Which are the last cells of the human body to die? When somebody dies, which are the last surviving cells of his/her body? Those of hair, nails, or some other obscure but resilient cells?

Shedding light on why and how they are so vital might boost our knowledge of survival pathways.

They found live skeletal muscle stem cells in human corpses 17 days after death (LiveScience, 2012).

They isolated live stem cells from the bone marrow from human fingers 5 days after death and transformed them into cartilage, bone and fat cells (NewScientist, 2013).

The survived cells were in a dormant state with very little metabolic activity.


How is protein cavity centre related to binding? I am confused and I have the following questions:
1. What are (in the context of article below) protein cavity centres?
2. How are they related to binding?

(Automated identification of protein-ligand interaction features using Inductive Logic Programming: a hexose binding case study, Santos et a. 2012)

As you can find under the table with cavity centers in pdf version of this article:

  The table lists the protein’s PDB ID, the ligand considered and the specified cavity center. 22 ligands are similar to hexoses in shape and/or size. The cavity center is the centroid of the reported PDB atom numbers.

And a little later:

  The binding-site center is computed as the
  hexose pyranose ring centroid for the positive examples,
  and as the ligand or empty pocket centroid for the negative
  ones. The hexose pyranose-ring atoms are located up to
  2.9
   ̊
  A away from the ring’s centroid. Since some atomic
  interactions can be important up to 7
   ̊
  A [22], we consider
  the binding-site as all protein atoms present within a 10
   ̊
  A radius sphere around the binding center. All other atoms
  are discarded.

So basically @aandreev is right. You can read about centroids here


Are bacteria incapable of producing cytokines such as interleukins? As far as I understand, bacteria cannot produce cytokines such as interleukins. However, I have not read an explanation as to why they cannot. Perhaps it has to do with an evolutionary limitation. Yet, if this is the case, why would bacteria be incapable of acquiring new functions such as cytokine production during their evolution, especially intracellular bacteria which reside within immune cells. If bacteria have not been able to acquire this function, then maybe it has to do with a biological constraint (size of the proteins, amino acid composition, machinery or bioenergetic capacity). If anyone knows the exact reason or has a knowledgeable explanation I would really like to read it. Thanks.

It seems especially pertinent to point out from the start that many cytokines are anti-inflammatory/immunosuppressive. The immune system has evolved to remove pathogens from the body, and normally these cytokines act to deactivate the immune response once an infection has been cleared. It should not be surprising that pathogens have co-evolved defences to the immune system, including interference with cytokine networks and even production of anti-inflammatory cytokine homologs, ostensibly to subvert the immune response. Below are but a few examples of this.

Viruses
Kotenko SV, SAccani S, Izotova LS, Mirochnitchenko OV, Pestka S. 2000. Human cytomegalovirus harbors its own unique IL-10 homolog (cmvIL-10). Proc Natl Acad Sci USA 97(4):1695-1700.

Many viruses exploit the strategy of using homologs of cellular cytokines or cytokine receptors to shield virus-infected cells from immune defenses and enhance virus survival in the host. The presence of virus-encoded homologs of cellular proteins may be an indicator of the importance of these cellular components in immune mechanisms for combating this virus in vivo. A number of herpes viruses harbor homologs of IL-10. Epstein–Barr virus (EBV)-encoded IL-10 (ebvIL-10), the first viral homolog of IL-10 identified, shares many but not all of the biological activities of cellular IL-10 and may play an important role in the host-virus interaction. In addition to EBV, another virus, the Orf poxvirus (OV), which can infect humans, has its own IL-10 homolog, ovIL-10.
...
IL-10 has several immunosuppressive activities that would be favorable for CMV, such as down-regulation of MHC class I and II expression, inhibition of production of inflammatory cytokines, and interference with antigen presentation. Murine CMV infection induces transient early expression of IL-10, which plays an essential role in MHC class II down-regulation. EBV infection causes expression not only of ebvIL-10, but also of human IL-10. We demonstrated here that human CMV encodes its own functional IL-10 homolog, which is expressed by CMV-infected cells. Thus, it seems likely that herpes viruses acquire many advantages by using IL-10-specific biological activities either of virus-encoded or host IL-10s.

Parasites
Ouaissi A. 2007. Regulatory Cells and Immunosuppressive Cytokines: Parasite-Derived Factors Induce Immune Polarization. J Biomed Biotechnol 2007(4):94971.

Another intriguing aspect in the parasite relationship is the fact that parasites could release factors that mimic host cytokines. For instance, (1) hydatid ﬂuid fractions mimicked IL-1, IL-2, and IL-6; (2) an IFN-γ homolog that binds to the IFN-γ receptor and induced change in lymphoid cells has been identiﬁed in an intestinal nematode; (3) two homologs of the human macrophage migration inhibitory factor (MIF) have been characterized in the human parasitic nematode Brugia malayi and termed Bm-MIF-1 and Bm-MIF-2, both having functional properties similar to the MIF human counterpart; (4) Toxoplasma gondii releases cyclophilin-18 (C-18) that signals through the chemokine receptor CCR5 leading to the IL-12 synthesis by dendritic cells and a strong protective response; (5) the tapeworm Hymenolepis diminuta has been shown to express an IL-12-like peptide, one of the suggested hypothesis being that the peptide could act as a competitive antagonist for the IL-12 receptor, thus contributing to the general immunosuppression.

Bacteria
I have not found such explicit examples of bacteria producing cytokine homologs. However, their ability to produce immune modulating, paracrine signalling proteins, which is essentially the definition of a cytokine, is well known. The following reviews are quite extensive and provides numerous examples:
Wilson M, Seymour R, Henderson B. 1998. Bacterial Perturbation of Cytokine Networks. Infect Immun 66(6):2401-2409.

In recent years it has become apparent that bacteria produce many molecules which have profound effects on the capacity of leukocytes and tissue cells to produce selected cytokine networks. Thus attention will have to switch from the current view of the host cell as the only controlling factor in cytokine biology, once the bacterium has stimulated this cell, to one in which the bacterium, by modifying its exported or structural molecules or by direct interaction with the cell, can directly modify cytokine networks.

Henderson B, Poole S, Wilson M. 1996. Microbial/host interactions in health and disease: who controls the cytokine network? Immunopharmacology 35(1):1-21.

Recent cytokine transgenic knockouts demonstrate that the normal benign response to commensal gut microflora becomes a lethal inflammatory state in the absence of the cytokines interleukin 2 or interleukin 10... We propose that the ability of the multicellular organism to live harmoniously with its commensal microflora must depend on mutual signalling involving eukaryotic cytokines and prokaryotic cytokine-like molecules. Such interactive signalling sets up non-inflammatory cytokine networks in tissues which form the background on which responses to infectious microorganisms must be built and related... It is now clear that bacteria contain and produce a large number of diverse molecules which can selectively induce the synthesis of both pro-inflammatory and immunomodulatory/anti-inflammatory cytokines.

Finally, the mechanisms by which bacteria can co-evolve such cytokine-like molecules is discussed in this review:
Stebbins CE, Galan JE. 2001. Structural mimicry in bacterial virulence. Nature 412(6848):701-705.

Recent studies have begun to reveal that many bacterial pathogens mimic the function of host proteins to manipulate host physiology and cellular functions for the microbe's benefit. This is in contrast with the strategies used by some pathogens that involve microbial products with activities lacking clear counterparts in eukaryotic cells. Here we consider recent structural work that provides unique insights into the mechanisms of host mimicry by bacterial virulence factors. In some cases, these factors are homologues of host proteins that have been incorporated into the genome of the pathogen and subverted for its benefit. In others, convergent evolution has produced new effectors that have no obvious relationship to host factors. However, although hidden at the sequence level, the determination of the crystal structures of several bacterial factors and bacterial–host protein complexes has revealed the presence of mimicry at the molecular level.


What's in a Name: Statistical Genetics The novice often performs population calculations using
what is referred to as Mendelian Genetics. Soon after the
publication of Mendel's results; Hardy and Weinberg presented
their results after the interjection of a collection of axioms.

Is there a difference between Medelian genetics and the
Hardy-Weinberg model?

Mendel published his results 1866 but they were rediscovered only in 1900. The Hardy-Weinberg model is an application of Mendel's rules to a population that is not under selection forces. So the one builds on the other, and Hardy-Weinberg is a simplification model-wise, and Mendel's rules are not detailed enough either. It's the same relation as with a physical law like gravitation and a mathematical model of its consequences applied on many entities, like models of a solar system's gravitational behaviour.