text:
definition of tempo and mode in evolution
I am reading Punctuated Equilibria: The Tempo and Mode of Evolution Reconsidered, which mentions the "tempo" and "mode" of evolution. I'm not familiar with the related literature and when I google the concept, what I got is something like:

One general topic, suggested by the word "tempo," has to do with "evolutionary rates..., their acceleration and deceleration, the conditions of exceptionally slow or rapid evolutions, and phenomena suggestive of inertia and momentum." A group of related problems, implied by the word "mode," involves "the study of the way, manner, or pattern of evolution, a study in which tempo is a basic factor, but which embraces considerably more than tempo''

This is as elusive as a definition can be. A clear definition should be something like "tempo is ...."
So what are the definitions of mode and tempo in evolution?

Actually, we can go right to the source on this: George Gaylord Simpson's Tempo and Mode in Evolution (1944).
Tempo is the rate of evolution. Simpson was a paleontologist, so he was trying to answer questions like "what is the percent change in the size of this tooth per million years?" He has a chapter estimating these rates for various characters in horses, which have a very good North American fossil record.
Mode encompasses the mechanisms responsible for evolution and their patterns. Simpson was working at the time of the Modern Synthesis (the wikipedia page is decent and brief enough on the topic, about which books are written), coming from the perspective of a paleontologist trying to reconcile genetic evolution with the macroevolutionary patterns he was seeing in the fossil record.
Simpson was really the first paleontologist to look at fossils in a quantitative way, trying to understand of connections between microevolutionary processes and macroevolutionary patterns. He even co-authored one of the first quantitative and statistical methods books for "organismal" biologists: Quantitative Zoology.
Specifically, of tempo, he says (p. xvii):

"...evolutionary rates under natural conditions, their acceleration and deceration, the conditions of exceptionally slow or rapid evolutions, and phenomena suggestive of inertia and momentum."

Of mode, he says (p. xviii)

"...the study of the way, manner, or pattern of evolution, a study in which tempo is a basic factor, but which embraces considerably more than tempo. The purpose is to determine how populations became genetically and morphologically differentiated, to see how they passed from one way of living to another or failed to do so, to examine the figurative outline of the stream of life and the circumstances surrounding each characteristic element in that pattern."

Mode basically encompasses all the processes of evolution. Tempo is the subset of mode that concerns how fast evolution is (or is not) happening.
The great thing is that 70 years after Simpson's book, biologists are still trying to understand tempo and mode of evolution.

It's great that you clarify tempo IS the rate of evolution. However, I'm still not clear about the relation between mode and tempo. Since tempo is a "rate" of evolution, in the context of dynamics, it is a rate of the underlying process, or generally speaking, a property of the process. How should I understand "mode ... encompasses all ... processes .... Tempo is the subset of mode..."? The sentence seems to suggest tempo is also a process.

Does it help to think of mode as all the processes involved in evolution? The rate of evolution is one of those processes, but there are additional processes (e.g., classical modes of speciation: allopatric, parapratric, etc.). So an "evolution" textbook probably has a chapter on rates. The rest of the book would be classified as "mode".

the textbook metaphor is a nice one.


text:
Could super-caffeinating somebody's bloodstream be dangerous?
I'm currently planning out an RPG based on Misfits. Basically young offenders get super powers. I want one of the villains to have a really lame power that they use to become incredibly dangerous. I thought about using a power to caffeinate drinks. If someone used that to super-caffeinate somebody's bloodstream, could that hurt or kill somebody? Or would it not cause any real damage?

In extreme doses, caffeine can - like almost any substance - cause death. Wikipedia has this to say on the subject:

Extreme overdose can result in death.[59][60] The median lethal dose
  (LD50) given orally is 192 milligrams per kilogram in rats. The LD50
  of caffeine in humans is dependent on individual sensitivity, but is
  estimated to be about 150 to 200 milligrams per kilogram of body mass
  or roughly 80 to 100 cups of coffee for an average adult.[61] Though
  achieving lethal dose of caffeine would be difficult with regular
  coffee, it is easier to reach high doses with caffeine pills, and the
  lethal dose can be lower in individuals whose ability to metabolize
  caffeine is impaired.

You may wish to consult the references mentioned in the Wikipedia article for further details (As we all know, one should not trust Wikipedia too much). Note that caffeine administrated directly to the bloodstream will be more dangerous than the same amounted ingested.
Information on caffeine toxicity can also be found at Medscape. I you need concrete examples, Holmgreen, Norden-Petterson and Ahlner have published case reports on four recent cases of coffeine-related fatalities. (3)
To cover all bases, it should be said that none of the information mentioned should be used to estimate a safe level of caffeine intake.

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text:
Breakpoint resolution for copy number variation analysis
I am reading [1].
One limitation of the Read Depth approach is that "the breakpoint resolution is often poor". Which is the meaning of low-resolution breakpoint in this case?
Breakpoint is defined as the sequence breakpoint:

Examples of a structural variation include a large deletion, insertion, duplication and inversion. Each requires the DNA duplex to be broken and rejoined, and this creates a new sequence of bases at the rejoined sites, i.e. the breakpoints.
Sequencing the new breakpoint regions is a good way (perhaps the only way?) to demonstrate an inversion, which does not increase or decrease the amount of DNA.
Original sequence: 123456789
Sequence with inversion: 123765489
Breakpoint sequences are at 37 and 48

[1]: C. Alkan, B. P. Coe, and E. E. Eichler, “Genome structural variation discovery and genotyping,” Nature Publishing Group, vol. 12, no. 5, pp. 363–375, Mar. 2011.

It means that it is hard to tell the precise location on the chromosome where the structural variation event starts and finishes using only read-depth information.
Read depth is measured by counting the number of mapped reads that overlap targeted regions aka bins. These bins are typically many basepairs wide and are used to normalize coverage with respect to various parameters (e.g. GC content). Smaller bins can give better breakpoint resolution but have noisier statistics. Large bins have better statistics but can't be used to precisely call the SV boundaries.
The CNVnator paper discusses the topic
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3106330/

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text:
How copy number variation thresholds are defined in GISTIC
I am having trouble trying to understand how GISTIC discretize copy number variation to values -2, -1, 0, 1, 2. I am using TCGA copy number variation for ColoRectal Adenocarcinoma.
In cBioPortal FAQ it is written that:

For TCGA studies, the table in all_thresholded.by_genes.txt (which is the part of the GISTIC output that is used to determine the copy-number status of each gene in each sample in cBioPortal) is obtained by applying both low- and high-level thresholds to to the gene copy levels of all the samples. The entries with value +/- 2 exceed the high-level thresholds for amps/dels, and those with +/- 1 exceed the low-level thresholds but not the high-level thresholds. The low-level thresholds are just the 'amp_thresh' and 'del_thresh' noise threshold input values to GISTIC (typically 0.1 or 0.3) and are the same for every thresholds.
By contrast, the high-level thresholds are calculated on a sample-by-sample basis and are based on the maximum (or minimum) median arm-level amplification (or deletion) copy number found in the sample. The idea, for deletions anyway, is that this level is a good approximation for hemizygous given the purity and ploidy of the sample.

The low-level thresholds are quite clear, while the high-level threshold not (the ones used to label +/-2 values).
I tried to reverse engineer the discretization function (the cutoffs are not available on firebrowse). The best solution I found is, for each sample, to:

split the copy number values in two groups (amplified - positive values, deleted - negative values)

for each group (amplified - deleted)

compute the median copy number value inside each chromosome arm
take the maximum (minimum for deleted group) median value across arms and use it as higher (lower) threshold

I tested it using the files:

all_data_by_genes.txt
all_thresholded.by_genes.txt

trying to get the correct discretized value (-2, -1, 0, 1, 2) of the second file from the first. However, a small part of the values are not correctly mapped. Am I missing something?

The best solution is to use only the broad alterations, using the file broad_values_by_arm.txt.
In particular, for each sample, the highest threshold is computed as the sum of the noise (low-level) threshold (e.g. 0.1) plus the maximum value of copy number variation for the sample over all the arms. Similarly, the lowest threshold is the minimum value for the sample over all the arms plus the negative noise (low-level) threshold (e.g. -0.1).

if: Total copy number (major + minor allele copy number by SCAT R) for SMAD4 in a sample = 4
Th estimated ploidy by SCAT for this sample = 4.043696
So, the segment mean (required for GISTIC) for SMAD4  = log2(2/4.043696) =  -1.015675
If I put -td threshold in GISTIC as 1.25, do I miss this loss for SMAD4 in GISTIC output because this is > -1.015675?
In the other word, does -td = 1.25 is the same when I ignore any segment mean < -1.25?

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text:
Does immunity to CRISPR proteins limit their effectiveness?
The use of crisper-cas systems is currently applied to cells cultivated in vitro. As control of the ‘off target’ effects of Crispr improves and Crispr is used in vivo, why won’t the immune system neutralize it?

Usually not.  the Crispr/Cas proteins can be delivered to the cell as DNA/RNA and the proteins will only exist inside the cell in low numbers.
Even in systems that deliver the protein from the outside in vivo almost always the proteins would be encapsulated in a delivery system to ensure they and any necessary accompanying nucleic acids get into the cell. Getting Crispr/Cas into a cell is difficult to do and they don't just pop in by themselves. They also require guide RNA, which will not easily stay whole in the blood stream and tissues for long.
if you want to just inject a fluid into the blood with unprotected CRISPR/CAS proteins, an immune reaction might stop them.  Not all proteins produce an immune reaction. Sometimes just 2-3 proteins of an entire bacterium produce an immune reaction (antibodies).   But then again its unlikely the proteins would have edited any genomes in any host cells even so.

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text:
Is this a valid definition of independent assortment?
"Allelic combinations separate randomly. I.e. a parent might be Aa and Bb for two traits but that doesn't necessarily mean the gametes will strictly be AB or ab but any of a number of combinations. I.e. blue eyes does not imply short height or something."

That's a valid explanation, but not definition. Mendel's law of independent assortments states that during the formation of gametes, the alleles for one trait segregate independently of the alleles of another trait.

The Law of Independent Assortment:
Alleles for different traits are distributed to sex cells (& offspring) independently of one another.

This one is like written on the stone in my mind!


text:
How does X chromosome monosomy occur
I want to understand how Turner syndrome - monosomy X - occurs at the molecular level. The NIH mentions that there are cases of both complete monosomy and of mosaicism.
I’m particularly interested in the monosomy case, as this really confuses me. How does a fertilized egg end up with only one sex chromosome (an X, in this case)? Is an empty egg fertilized by an X-bearing sperm? Is an X-bearing egg fertilized by an empty sperm?
The case of the mosaicism is easier to imagine - say through X chromosome nondisjunction at a very early point in some cells of the embryo. NB: unsure this is actually how mosaic monosomy X happens.
I haven't found a source that doesn't begin from the point at which monosomy has already occurred.
How do things get to that point? Where and how is a sex chromosome lost, such that a human can develop with only the one?
Thanks so much for any pointers!

Most often, it seems that Turner syndrome is due to fertilization by a sperm cell lacking a sex chromosome. I wouldn't describe such a cell as "empty": it still has the other 22 chromosomes, but in meiosis the sex chromosomes failed to segregate appropriately.
Monroy et al 2002 note that of 10 people with complete monosomy X, 9 had their single chromosome from the mother.
Monroy, N., López, M., Cervantes, A., García‐Cruz, D., Zafra, G., Canún, S., ... & Kofman‐Alfaro, S. (2002). Microsatellite analysis in Turner syndrome: parental origin of X chromosomes and possible mechanism of formation of abnormal chromosomes. American journal of medical genetics, 107(3), 181-189.

Thank you! I hadn't found that reference earlier. Definitely helps me to understand it better.


text:
What is the adjective for PHAGE?
if the adjective of the noun BACTERIUM is 'bacterial' and that of VIRUS is 'viral', what is the adjective for (BACTERIO)PHAGE? Is 'phagial' accepted?
Thank you

Bacteriophages are viruses so what's wrong with viral?

@Cell "Bacteriophages"!? Not to be a grammar-nazi, but bacteriophage is an unchanging irregular noun. The plural of bacteriophage is bacteriophage. The plural of phage is phage.

@MikeyC If it's good enough to be acceptable on Nature's educational website, it's good enough for me: https://www.nature.com/scitable/definition/bacteriophage-phage-293/#:~:text=A%20bacteriophage%20is%20a%20type,surrounded%20by%20a%20protein%20structure Not to mention it is also found in published work: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3109452/

Have you done a Google search for "phagial"? You might try and see what you find. (And there is no need to use capitals. On the internet that is considered to be shouting.)

can you give a context in which you want to use it?

The context would be: "there were 32 phagous species in our samples". (as opposed to 50 bacterial and 12 viral species).

@Cell. I learned something today. Thanks for supporting your usage. It seems both are acceptable. The invariant form was just drilled into me for 5 years of undergrad and 6 years of grad school. Seriously, my PhD advisor would interrupt a research talk to correct something like that.

It is bacteriophagous as given in wiktionary.

From bacterio- (“bacteria”) + -phagous (“eating”).

Reference

This is what I found by googling it and hence shared with the reference. Why downvote then?

I didn't downvote, but this would seem to me to be an adjective modifying "virus" (e.g. a phage is a "bacteriophagous virus") rather than an adjective modifying something associated with a phage "phagial(?) population growth", "phagial(?) biochemistry", etc.)

I downvoted this answer for 2 reasons: (1) a search for "bacteriophagous" on PubMed yields very few results (only 25), and (2) from the context of those results, "bacteriophagous" means a "bacteria-eating" or "bacteria-engulfing"; not bacteriophage-like.

In the literature, it's most common to see hyphenated compound adjectives, like "phage-mediated," "phage-dependent," or "phage-encoded" where "bacterial" or "viral" might be analogous. For example, "Phage‐mediated selection and the evolution and maintenance of restriction‐modification."
Sometimes "phage" seems to be used as a standalone adjective, like in "Phage antibodies: filamentous phage displaying antibody variable domains." Although I'm not sure that it would be correct to use "bacterial antibodies" or "viral antibodies" in this case, so maybe that one is an anomaly.
I would suggest following one of these trends, unless you want to do a lot of explaining to reviewers.

so something like "pagial/phagous species" should become phage-species, right?

In that case, you would probably not use the hyphen. There's some discussion of naming conventions in this article on PubMed, and they do use the phrase "phage species." https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5408676/.

I read the article, but the space is related to naming the phage itself, not the adjective for phage...

I only referenced it to give you an example of how "phage species" might be used appropriately. Sorry for the confusion.

I asked the author of that paper and she replied: "I have never in my career heard anyone use the terms phagial or phagous." Probably "phage-species" of "phage species" is the more accepted way, 'phage' being (I presume) a modifier more than a real adjective.

From the University of Wyoming (courtesy Prof. Suess) I got: "I would go with phagial.   Following the Latin ending for viral, bacterial: -ial - (Latin: a suffix that forms English adjectives from Latin adjectives ending with -is or -ius with meanings about "pertaining to, relating to", or "characterized by")"


text:
Is there a database for immunoglobulin domain structure?
is there a database where I can find the sequences of the hypervariable domain of immunoglobulins and the sequences of the related antigens? Thank you

There are a number of databases that exist, though the one you would want to use will likely depend on what you need it for. The one that's recommended at my university is IgBlast, associated with The National Center for Biotechnology Information (NCBI), however I've seen IMGT as a recommended source, as well; it seems to have a wider array of tools. That being said, I can't say which you might find more beneficial, as I'm uncertain as to how you'd be using the resource.

essentially I am interested in the primary sequence of the variable regions of the immunoglobulins (let's say GALMF) and the corresponding antigenic primary sequence (let's say CHYR), this sort of association. Thank you, I will have a look at those databases.

actually, these databases are blasting tools to search for patterns. I am looking for a list of sequences hits with both TCR of Ig and related antigens, if any.


text:
Co-culture models of bacterial invasion: where to find them?
I am interested in models showing how pathogenic bacteria (namely Escherichia coli O157) can overcome commensal species (thus, causing a disease). This is a basic concept in biology but I can't find a proper article describing it.
I am looking, essentially, for a co-culture experiment with a pathogenic and a non-pathogenic bacteria that shows how the former can outcompete the latter. Is there a reference to such experiments?
Thanks

Are you sure you know what a commensal species is because the Wikipedia definition is incompatible with one member overcoming another: "Commensalism is a long-term biological interaction (symbiosis) in which members of one species gain benefits while those of the other species neither benefit nor are harmed" ? And which species do you maintain Escherichia coli O157 outcompetes — could you cite references on this point?

@David, I believe Gigiux is using commensal with respect to the hosting organism (e.g. human), contrasting those species with E. coli O157, which is not commensal with the host.

@mgkrebbs OK. But does the O157 strain have to complete with the commensal strain? For what? There are dozens of different bacteria in the gut managing to share resources.

@David, This usage of commensal is pretty consistent with the usage in most gut microbiome literature. Although I agree with you that it is probably used incorrectly most of the time, it seems like a fair enough label to apply until a specific harm or benefit for the host has been empirically demonstrated.

@MikeyC OK I misunderstood the OP with regard to commensal, but — and I am asking with skepticism but out of ignorance — does  O157 compete with K12 (or whatever) as his question implies? Because this is the crux of the viability of what he proposes. To do competitive growth experiments it would have to be established that the two strains complete for some nutrient, and what that nutrient is to be able to construct a growth medium. If this is true/know one would imagine it is also known what O157 does better — induce some enzyme, or whether its toxin affects K12. I think the OP should clarify.

I do not consider a request for a reference as question about biology and therefore will vote to close this. I found an answer by a simple internet search resulting from the comments above. Vet Sci 2018 5 93 https://www.mdpi.com/2306-7381/5/4/93#.

@David you are right: I meant commensal in terms of the interaction with the human host. I read already the article you indicated. But I am looking at a system describing how a bacterium pathogenic for human outgrows (I used outcompete because grows more than  the harmless species) one that (1) is not pathogenic and (2) that was initially present at a density higher than the pathogenic form.


text:
Is it possible to re-align of SAM/BAM files?
I am carrying out some metagenomic comparison using whole genome sequencing approach. I would like to filter out reads from my files in a sequential manner, thus I would like to align to a first reference genome, then use the generated SAM/BAM file to extract the mapped reads with samtols view -F4, re-generate fastq files and align those to another reference genome. This decreases the size of the input and speeds the procedure.
Using BWA, though, I get an error of file synchronization when doing the second alignment:
[mem_sam_pe] paired reads have different names:
"HISEQ:90:C3UNJACXX:1:1107:16388:61141",
"HISEQ:90:C3UNJACXX:3:1303:2008:58095"
[mem_sam_pe] [mem_sam_pe] paired reads have different names:
"HWI-ST1437:64:C3UM1ACXX:4:1214:3833:62731",
"HWI-ST1437:64:C3UM1ACXX:4:1202:18519:45906"

This is weird since the fastq files were generated by the filtered BAM file, samtools should have known how to keep the synchronization of the files.
My question is: is it possible to realign a BAM file? maybe not with BWA, at least with another tool?
Thank you.
The procedure I carried out is:
# align
bwa mem -R <read_group1> <ref.fa> <file1_1.fq> <file1_2.fq> -o <file_aln.sam>
# convert
samtools view -Sb <file_aln.sam> > <file_aln.bam> # sort samtools sort <file_aln.bam> -o <file_alnSRT.bam>
# select mapped
samtools view -h -F 4 <file_alnSRT.bam> -o <file_alnMAP.bam>
# convert to fastq
samtools fastq -1 <filemap_1.fq.gz> -2 <filemap_1.fq.gz> <file_alnMAP.bam>
# re-align
bwa mem -R <read_group> <ref2.fa> <filemap_1.fq.gz> <filemap_1.fq.gz> | samtools sort -o <file_realign.bam>

Looks like I solved it by using PICARD: extracting the aligned reads but without sorting, I used
java -jar picard.jar SamToFastq I=<file_alnMAP.bam> FASTQ=<filemap_1.fq> SECOND_END_FASTQ=<filemap_2.fq>
bwa mem -R <read_group> <ref2.fa> <filemap_1.fq> <filemap_1.fq>

From samtools flagstat the output looks fine.


text:
How is the carrying capacity of a logistic growth model calculated?
I am reading a book in epidemiology where the carrying capacity for a standard logistic growth rate is given by
K = (b - delta) / gamma

where:
K is the carrying capacity
b is the birth rate
delta is the death rate

but what is gamma?
Thank you

Your equation is not a difference equation (discrete time) nor a differential equation (continuous time). It therefore cannot describe a population growth. I don't know what the authors may have intended with this equation but we would need more information to address that question (book reference, page number, full description of the equation, etc...)

@Remi.b is correct that you haven't given us very much information, but I think we can reconstruct what's going on. Suppose the population growth rate is written out as
$$
\frac{dN}{dt} = N ( b - \delta - \gamma N)
$$
then the equilibrium (carrying capacity) occurs when $N>0$ and $dN/dt=0$, i.e. $b - \delta - \gamma K = 0$.  Solving this for $K$ gives $(b-\delta)/\gamma$ (as you stated).
So what is $\gamma$?  It is the decrease in the per capita growth rate per unit of increase in population density, or more biologically speaking it's the decrease in the birth rate or the increase in the death rate per unit of increase in population density. This could be due to increased competition for resources, or decreased environmental quality, or attraction of predators, or ...
Another, vaguer way to say this would be to call it the "effect of density-dependence".
Given the equations you list in the comments, with a $-\gamma N$ term included in the per capita growth rate for each compartment ($S$, $E$, $I$), we can say more specifically that $\gamma$ determines the rate of density-dependent increase in the ("natural" or disease-independent) death rate per unit population density. This parameter would not typically be broken down into lower-level processes.

sorry, I thought it was a standard measure, thus no information needed -- and in fact, you reverse-engineered. K was mentioned in a SEIRD model. Is gamma a constant or is it derived itself from more basic data? Thank you

Can't really answer that question without more context.  Can you give a link to the source, or post a screenshot of the relevant part of the text, as part of your question?

the context is a SEIR model with:

the context is a SEIR model with: dS/dt = (b-delta-gamma * N)*S - beta * S * I; dE/dt = beta * S * I - (sigma + delta + gamma * N) * E; dI/dt = sigma * E - (delta + deltaI + gamma * N) * I; with b = birth rate, delta = death rate, 1/sigma = latency, gamma as you said, N = total population.

I'm curious: can you say what book you're using?

It's actually a kind of pre-print/internal manual from the ETH Zurich. I could not add yesterday this: "this model assumes that the population dynamics of the host in absence of infection are governed by the standard logistic growth model... in absence of infection it equilibrates to a carrying capacity given by K = (b - delta) / gamma".

It's actually a kind of pre-print/internal manual from the ETH Zurich. I could not add yesterday this: "this model assumes that the population dynamics of the host in absence of infection are governed by the standard logistic growth model... in absence of infection it equilibrates to a carrying capacity given by K = (b - delta) / gamma".

I think it's also important to note two things. 1.  as a "capacity" is not very useful concept. Although the disease-free equilibrium can be calculated as (−)/, that's not interesting or useful because you are trying to model disease. 2. It's important to note, as was pointed out in this answer, that the units for  and  are different:  has in units of individuals and  has units of per-capita.  is used in the SEIR model to include a negative effect of crowding/density-dependent effects, and 's "relevance" is vestigal.


text:
Who creates first nitrogen compounds in the food supply chain
As I understand the food supply chain, organic compounds have to be created from a unlimited source (air, water...).
For instance, I figure that plants transform CO2 from air to organic carbon compounds, mainly carbohydrates, which are then the main source for most other life forms.
But I never heard about a plant turning atmospheric N2 to nitrogen compounds.
Where nitrogen compounds come from, and from which source ?

There are nitrogen fixing bacteria who turn N2 into NH3.  Some are free-living in soil, others live symbiotically with plants.
https://en.wikipedia.org/wiki/Nitrogen_fixation

Also some is fixed by inorganic processes, e.g. lightning converting nitrogen into various oxides.


text:
Are hens and roosters the same species?
I know that one is a female chicken and the other is male chicken. Are the chickens laying eggs considered the same species as those that we use for poultry meat? Or, are they different sub-species, analogous to how there are multiple breeds of dogs?

The main difference between a rooster and a hen is that the former is male and the latter is female. Their appearance differs in several ways [1].
A rooster also known as a cockerel or cock, is a male gallinaceous bird. The term usually refers to a male chicken [2]. The hen or the chicken (Gallus gallus domesticus) is a domesticated fowl, a subspecies of the Red Junglefowl [3].
And yes, the chickens laying eggs could be the same as the chickens that we use for poultry meat.
References:

Anjus Chiedozie. Rooster Vs. Hen on eHow.com
Wikipedia. Rooster
Wikipedia. Chicken

There are probably different breeds that are commercially preferred for egg laying versus eating.

Actually, this is partially correct.  I disagree with the downvoting.  Yes hen = female, rooster = male of same species.  But although basically all chickens can be used for meat and for eggs, there are some breeds that are better for prolific egg-laying and some for fast growth of thick meat.  See here: https://www.extension.purdue.edu/extmedia/as/as-518.pdf

Yes, they are the same species. Meat birds and layers are the same species, they have just been bred differently to produce a certain result. (Along these lines, you may wish to picture a tomato, there are many different shapes and colors. However, they are all the same thing.).
As with humans, certain chickens have certain characteristics. And to an extent "personalities".
It does appear, based on this link, that chickens are a subspecies of Red Junglefowl. However, chickens themselves do not appear to have an subspecies within them. Sorry I had to use Wikipedia.


text:
Was the Okazaki fragment experiment ever replicated?
Prof said that the experiment "proving" the existence of Okazaki fragments was never replicated.
Is this true? I tried looking on Google Scholar and I cannot find any experiments talking specifically about the existence of such fragments. Wikipedia also doesn't list any other researchers "finding" Okazaki fragments.

You mean replicated in another lab?

Yes that's what I mean

Are you sure your professor wasn't talking about the STAP cell retraction The first author on that paper was Obokata.

It seems that many people have done experiments based on the results of Okazaki fragments and published positive data. This means they suggest existence of Okazaki fragments directly or indirectly. When you say an experiment is never replicated, you have to mentioned what actually they did. Because we never know if the articles mentioning Okazaki fragments show the exactly same experiment or take other experimental approach. http://www.ncbi.nlm.nih.gov/pubmed/?term=Okazaki+fragment%5Btitle%5D

Formation of Okazaki fragments in polyoma DNA synthesis caused by misincorporation of uracil - Brynoff, et.al. Cell; Volume 13, Issue 3, p573–580, March 1978 one of many, but you only need one to disprove your professor.
You do not always need to replicate the exact same assays in order to validate a model. Replicate means reproduce the same experimental results in which to draw the same conclusion. Another person need not reproduce your work exactly, so long as your results were the results of experiments that you were able to reproduce on your own. Standards for Replication in Science

In addition to the wealth of work done on Okazaki fragments, it's important to note that the original work in the 1960s showed how both lagging and leading strands of DNA can be replicated despite the 5' to 3' direction of DNA polymerase. Work starting with the identification of Okazaki fragments underlies much of what has been learned since about replication forks. That might be the best "replication" of all: forming the basis for decades of continued research.


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Kinetics and de novo protein prediction

De novo conformation predictors usually function by producing candidate conformations (decoys) and then choosing amongst them based on their thermodynamic stability and energy state. Most successful predictors will have the following three factors in common:
1) An accurate energy function that corresponds the most thermodynamically stable state to the native structure of a protein

This is an excerpt from Wikipedia. I have a very, very limited understanding about de novo protein prediction so here goes.
I asked the post-doc I'm working with about whether there are kinetic barriers to protein folding. Yes, everything wants to be at an energy minimum, but sometimes that just can't happen due to kinetic barriers (the reason your diamond ring doesn't turn into graphite/pencil "lead"). So, why does protein prediction software look for energy minimums? Do they also consider activation energy barriers? Do they take into account the presence of chaperonins? Are there examples where the thermodynamically most stable protein conformation is not the biologically active protein? The post-doc told me that perhaps most proteins do reach their thermodynamically most stable state. True?

Generally speaking, structure prediction programs look only at the thermodynamic minimum, without consideration of the kinetic trajectory of folding.
The main reason for this is mostly time considerations. It's very difficult to accurately model the true folding pathway of even a moderately sized protein. With special tricks and a bunch of computing power, we're barely able to simulate a folding trajectory of small, simple proteins. We aren't (yet) able to do so with anything of reasonable size.
Instead, what protein structure prediction programs do is take a shortcut, skip the physically-realistic folding simulation, and instead look for low energy models, with the assumption that these low energy states will look like the natively folded proteins.
(One such program I'm familiar with - Rosetta - effectively takes small backbone structures already seen in crystallized proteins, stitches them together and asks if that looks like a reasonable structure for the sequence. If not, it tweaks which backbone fragments it uses, repeating until it gets something it thinks looks good.)
This assumption - that the native structure of the protein is the global energy minimum - is called Anfinsen's hypothesis. One rationale is related to Levinthal's paradox: unlike simple chemical reactions, a protein folding trajectory has too many degrees of freedom for even nature to exhaustively sample all conformations. This implies that stably folded proteins evolved with well defined "energy funnels" - that is, the energy landscape of well-folded proteins is such that the folded form is "downhill" from a large number of potential states. Since a large number of potential states need to point toward the folded form, this implies that the local minimum of energy which is the folded form is also likely the global minimum of folding.
The energy differences in protein folding also tend to be small - it's relatively easy for proteins to climb back up of local minimums and go elsewhere. Without the strong, global energy funnel to direct them toward a stable state, it's difficult to keep proteins from unfolding and refolding. This is why kinetic considerations like controlling the trajectory of folding from a ribosome, or having special chaperonins don't really work. Because chaperonins are catalysists, they change the rate of the reaction they're involved in, but not the equilibrium. Microscopic reversibility means that any protein which randomly collect enough energy can use the chaperonin to escape the dead end it was put in: it's not a one-way gate.
Now having the kinetic minimum be the thermodynamic minimum doesn't have to be the case - it's just the case for the vast majority of proteins we've seen. There are certain systems where we're pretty sure the normal folded form is in a local kinetic trap, and with time it can escape into a more stably folded version. Amyloid fibrils and prion proteins are thought to be one such instance. The normally produced version is in a low-energy kinetic minimum, but over time or through various interactions with amyloid or other prion proteins those proteins can relax into an alternative, lower energy conformation.
The keyword here for future literature searches is "kinetic trap". Some kinetic traps are very short lived (microseconds), but other may be longer.
Finally, I'll point you to the paper "The Protein Folding Problem" by Dill et al., which is a good review on the topic of protein folding.


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How are Maggots Sterilized (Disinfected)?
For maggot therapy, how are maggots disinfected? I'd imagine there's a limited scope of measurements that can be taken to sterilize the maggots - i.e. we don't want to sterilize them and kill them too.

Speculation : Maybe they are grown in laboratory settings, preventing them from any microbe infection...Something like germ free mice.

Of course, but what about the first generation? They have to have come from the wild.

They are grown in the same way that "clean" mice that don't have any gut flora are grown - originally they came from the wild, were cleaned, then kept in specific conditions after that. The first couple generations may be iffy, but dirt isn't inheritable...

How is gut flora taken care of? I thought gut flora was necessary for digestion.

History
Ambroise Paré is credited with being the first to note his observations on Maggot Debridement Therapy (MDT) in the 1500 though it is a technology that has been used for centuries (reference). It wasn't until the 1920's that therapeutic experimentation with maggots was instigated by William Baer, a clinical professor in orthopaedic surgery at the Johns Hopkins University in Baltimore, Maryland, whose unorthodox methods were successful in the treatment of osteomyelitis and pyogenic wounds. He is also considered the father of modern MDT since he was the first to devise a way to sterilize maggots (reference).
Procedure
In addition to removing necrotic tissue from the wound (a procedure known as debridement) maggots have also been proven to disinfect wounds, promote healing, and inhibit a pesky substance known as biofilm from forming on the wound bed. Maggots are nature’s cleansers, showing up to remove dead tissue and promote healing (reference).
Currently Lucilia sericata, or the greenbottle blowfly larvae is preferred for MDT because

Firstly, larvae have been shown to debride wounds with extremely low
probability of myiasis upon clinical application. Larval secretions
have been shown to help in tissue regeneration. L. sericata have also
been shown to lower bacteremia levels in patients infected with MRSA (reference).

Sterilizing maggots
In early applications, sterilizing the larvae was a major problem. Doctors had to first bathe the eggs in bleach and then soak them in mercuric chloride or formaldehyde. The bandages, gaudy and cumbersome for the patients, were held in place with either surgical tape or Unna’s paste—made of zinc oxide, gelatin, glycerine, and water. Other problems that doctors faced included the maggots escaping during the application process and the leakage of toxic waste secreted by the maggots into the wound, which led to infections such as tetanus. Today, commercial and research laboratories produce sterile larvae. And instead of the bulky gauze bandage, a form-fitting cast with a nylon net to corral the larvae is placed over the wound. An absorbent pad put on top of the netting soaks up the larvae’s toxic waste products. The number of larvae used has also changed. Early prescriptions ranged from 5–6 maggots for a fingertip injury to 500–600 for a more serious wound. Today, the scientific standard of 10 larvae/cm2 is used (reference).
William Baer proposed a method to produce sterilized maggots and it is understood that sterilization has to start from the egg stage in itself (reference). The sterilization solution that he proposed was.

Stock Solution of bichloride of mercury, strength one in 1,000 parts.
Stock Solution of fifty per cent. ethyl alcohol. Take equal volume of
each Solution, mix, and add one-half of one per cent. chemically pure
hydrochloric acid. The final Solution will contain bichloride of
mercury, strength one in 2,000 parts, twenty-five per cent. alcohol,
and one-half of one per cent. hydrochloric acid.

He did not sterilize the maggots as such but took care to feed it sterile food. His work can be read here. Another solution used for sterilization was  5 per cent solution of formalin plus 1 per cent sodium hydroxide (reference).  Sterilization of maggot larvae in itself was found to be hard with some success being reported (reference). Current maggot sterilization techniques include.

UV Sterilization
Rapid washer sterilization
Egg to maggot sterilization (reference)

There is no first generation that has been detailed as such. Mostly sterilization starts from the egg stage. As far as bacteria in the gut is concerned, if sterilization is carried out well, it has been found that there is a significant decrease in any harmful bacteria present (reference). Most details of sterilizing maggot larvae is given in this paper. Consider reading this paper as well.

Medical maggots are FDA approved. Their use for wound debridement of bullet wounds was recommended in the US Army Special Forces Medic handbook back in the 80's. I assume it is still there.

How could sterilized maggots cause tetanus? Or was it case with un-sterilized maggots?

@abukaj That is in the case of un-sterilized maggots

There is an interesting and authoritative paper on rearing of larvae of blue bottle flies for debridement purposes, cited below.

Essentially the eggs are disinfected (rinsed) using .25 % chloramine solution (NH2Cl), then the larvae are hatched and reared in aseptic conditions and fed sterilized food. There are some additional controls after initial disinfection (eggs are placed in agar and the resulting growth is compared to non-disinfected eggs). The procedure is detailed on page 127-128.

Whether the eggs are perfectly germ-free may be somewhat moot. Historically this was done without disinfecting the eggs (or anything else). Secondary infections were probably not uncommon but the advantages of the technique far outweighed the disadvantages until the advent of antibiotics. Apparently these things are great at debridement of wounds (but shouldn't be used too close to organs or blood vessels).
See Wolff and Hansson, Rearing Larvae of Lucilia sericata for Chronic Ulcer Treatment--An Improved Method, Acta Derm. Venereol. (2005) 85: 126-131.


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Feeling warm and cool breezes - how does it work?
As you travel with your hand sticking out of a car the sensation you have is one of cooling: even though molecules are transferring energy to your hand, you interpret it as being colder. Now, at a certain speed your hand would actually melt down, and I'm assuming you'd be feeling warmth by the time that happened.
I'm wondering how this works: how can your body sense warmth and cold from a phenomenon that, physically speaking, is just about molecular collisions?

You feel cool because of the evapoative cooling of the thin layer of sweat that exists. There must be a tipping point where the sweat evaporates altogether and air friction takes over. Ya, im just guessing. Sure for the first part.

@Polisetty Pretty solid guess in my opinion. As you said, sure for the first part, good guess for the second part.

This is the same principal behind the wind chill factor. Your body makes heat. This heats up the air around your body. If that air is quickly replaced by unheated air, you have to spend energy to reheat that air, which is again quickly replaced; your body is working a lot harder to warm up the air around you, which makes you sense that it's cold.

You have many different types of sensors in your skin; you probably feel the pressure of the air moving past your hand in addition to the temperature.
The temperature increase in your hand due to collisions isn't very significant, you have to be going at really high speeds to encounter that phenomenon (spacecraft reentry would be an extreme example, for example see this wikipedia page).
Temperature changes due to evaporation are probably most significant (this is why even warm air blown from a fan can feel cool, especially if you are perspirating), as well as the temperature of the outside air around your hand compared to the air inside the car.

Does that mean I will not feel the wind as cool if I'm not sweating? Because that doesn't really look obvious to me.

If the air is colder than your body, you feel it as cold because it is actually cooling your hand; this will be enhanced by evaporation, which will be greatest if you are sweating but even if you aren't sweating your skin still contains water that can evaporate.

@QuantumBrick Sweating is a physiological mechanism to cool down anyway, why would the brain want to actively feel water evaporating as much as it wants to actively think about heartbeats.

The few points mentioned in the threads are correct. Physical collision do not transfer that much heat when it comes to air. Multiple temperature sensors can also be activated simultaneously. For example you could be in a cold room and feel conducted cold, and have the sun shine at you through a glass panel with radiated heat. But this almost never happens with friction with air of course.

@Liu Tianyi: I have to disagree.  It's quite normal to feel a breeze as hot, if for instance you're in Las Vegas in the summertime.  Or think of warm air blowing from central heating vents...  Though of course it's not air friction doing the heating, but convection & conduction.

The collisions result in heat loss because the air molecules bounce off your skin with more energy than they impact with. You have to be moving a tremendous speed before the friction heating is greater than the heat loss through transfer. By moving the air (or moving through the air) each molecule is new and at a lower energy state than your hand and there are more collisions. this cools it faster than standing still where the air around you becomes slightly heated by the collisions and have to diffuse away, so many of them get bounced back now at higher energy states when they contact again resulting in less heat loss. your hand is cooled and thermoreceptors in your skin detect the lower temperature. these sensors just detect specific temperature ranges, warm or cool past these ranges and your body can't detect the temperature.


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Could all mammalian receptors be described as allosteric?
Allosteric regulation in enzymes is where a molecule binds at a site other than the active site and thus changes the tertiary structure of the active site, hence altering the binding of substrate and formation of enzyme-substrate complexes.
As I understand it, if this is extended to receptors, for example G protein-coupled receptors, which effectively causes a conformation change which is transmitted across the membrane and 'activates' a G protein which is associated with the receptor. The Gα subunit swaps a GDP for a GTP which causes the dissociation of the alpha from the beta-gamma coupled subunits and from the receptor. The dissociated Gα and Gβγ subunits then take part in a cascade process interacting with other molecules.
However, photoreceptors such as rods/cones in the eye respond to light. These photons tend to cause changes in the structure of the rhodopsin/iodopsin pigments and not the actual 'receptors' themselves. G proteins do seem to be involved in this process too.
Therefore, are photoreceptors allosteric? And if not, are they an anomaly in mammalian receptors, or are there many other examples of receptors that do not rely on allostery?

"Allosteric" refers to an alternate site of action, but it is not limited to a discussion of enzymes. For a protein that is a receptor, allosteric modulation refers to modulation of that receptor away from the binding site or "active site" of the endogenous ligand.
Although it is true that the receptor may have enzymatic activity when a ligand is bound, it would be non-standard to use the term "allosteric" to refer to the normal ligand binding site, even if this terminology is technically correct with respect to the enzymatic activity.
There are many receptors which are not enzymes at all: a great example would be ligand-gated ion channels - all of the activity of these proteins is due to their conformational changes, and not due to any catalyzed reaction.

So would ligand-gated ion channels not be described as allosteric since they are not enzymes? Or they would because they rely upon conformational changes?

I think you have to be careful of how you attribute the word "allosteric" - in the canonical case, an enzyme itself is not allosteric - the modulation of the enzyme by some other factor that binds outside where the substrate binds is allosteric. "Allosteric" literally means "other site". I suppose you could consider ligand binding on an ion channel to be "allosterically" changing the protein structure at the pore, therefore allowing ions to pass.

I think you recognize a very important concept in biology: changes in protein function result from conformational changes. You are wanting to call this "allosteric" - you can probably twist the concepts to say that (most) proteins' conformation changes somewhere when something binds elsewhere on the protein, therefore an allosteric effect. Does that really get you any further than the initial statement that changes in protein function result from conformational changes?

To me, it makes more sense to reserve the term allosteric regulation for a) modulation of enzyme function at a site that is not the normal substrate binding site, or b) modulation of receptor function by changing efficacy, promoting or preventing ligand binding, etc, at a site that is neither the endogenous ligand binding site nor the site of enzymatic or other functional activity (e.g. an ion pore).


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Photoreceptors and light with mixed frequencies
I am interested in how the activation of a, say, blue cone depends on the incident light. Wikipedia tells me this:
 ,
which describes how strong the activation of the blue cone is for light with a single wavelength and a given intensity. But what happens if the incident light has several frequencies?
My question is: given the intensity i(f) of the incident light at frequency f, what is the activation of the blue cone?
(A natural guess would be that if b(f) is the activation curve in the figure, then the activation of the blue cone should be the integral of b(f)*i(f) over f. But I have not found any confirmation of this guess. For example, in the reference for the picture above, only pure light was used in the experiments.)

I'm confused. Your question seems to ask for a simple reading of the graph at a particular frequency but your comment implies otherwise. Also, what do you mean by pure light? I gather the vertical axis is fraction of maximum possible? If so, would integrating under the curve make sense?

Yes, current color models assume a linear response in the spectrum.
Given a light with mixed spectrum $\Phi(\lambda)$, the response of a cone with spectral sensitivity $\Psi_i(\lambda)$ is a (nonlinear) function of the L2 inner product:

This is how CIE XYZ color space is defined.
Reference:

M. D. Fairchild. Color Appearance Models, 3rd edition. 2013 (p.63)
https://en.wikipedia.org/wiki/CIE_1931_color_space


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Will a vasectomy prevent genetic engineering of a child?
Making the assumption:

Within 10 years, an adult will be able to genetically engineer (modify, enhance, clean, etc.) a child from their own DNA (and the DNA of a non-related partner).

then would getting a vasectomy today preclude this?

From the wording of your question the 'genetic engineering' that you are envisaging will involve sperm. So the question is really, does vasectomy affect sperm production?
The answer is that it does, but it doesn't abolish it. For example:

McVicar et al. (2005) Effects of vasectomy on spermatogenesis and fertility outcome after testicular sperm extraction combined with ICSI. Human Reproduction 20: 2795-2800

These authors found that sperm yield fell to about 35% > 5 years post-vasectomy.

Thanks, but I didn't mean to imply that sperm or an egg need to be involved, just DNA.

DNA from which cells?


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A question about IPTG induction
I have found the information: `In the absence of lactose, the lac repressor binds to the operator sequence on DNA and bends the DNA by 40 degrees. This blocks access of T7 RNA polymerase to the promoter site and thus prevents leaky transcription of your gene before induction.'
I am confuse about one fact.
When I add IPTG,  the lac repressor protein (from E.coli chromosome) can no longer bind the operator and native E. coli RNA polymerase begins transcribing, the T7 RNA polymerase gene engineered into its chromosome.
So if there is IPTG and lac repressor protein (from E.coli chromosome) can no longer bind the operator standing in front of the T7 RNA polymerase gene, why lac repressor protein still can bind to operator standing in front of the target gene from plasmid?

What makes you think that the lac repressor will still be bound at the target gene?
In strains with this type of regulatory configuration (usually with DE3 in the genotype) the idea is that IPTG induction turns on expression of T7 polymerase from a lac promoter on the chromosome, and then this T7 polymerase then transcribes the target gene on the plasmid. The presence of IPTG ensures that repressor will bind at neither site.
Supplementary:
I think that I understand why you are confused now. Your picture of the way this works is based on the idea that the repressor is locked on to the operator until an inducer such as IPTG comes along. In fact there is an equilibrium between bound and unbound:

repressor/operator <=> repressor + operator

and, in the brief periods when the repressor isn't bound, the E. coli RNA polymerase can bind and transcribe the operon. This is referred to as 'escape synthesis' and it is generally assumed that it is functionally relevant in ensuring that there are low levels of lac permease expression at all times so that lactose can be taken up. If this wasn't the case, how would the natural inducer (a derivative of lactose) ever be able to induce the lac operon?
In protein expression systems it is generally considered desirable to keep escape synthesis of the foreign protein to a minimum so that there is no selection acting on the gene to negate any deleterious effects of its expression. The use of T7 polymerase as an intermediate level of regulation helps to achieve this. Even if there is a low level of escape synthesis of T7 polymerase, the concentration of T7 polymerase will be so low in the uninduced state (compared to the endogenous RNA polymerase) that the amount of escape synthesis of the target protein due to T7 polymerase gaining productive access to the T7 promoter on the plasmid will be negligible.
Read more here.

As I wrote before I have found the information: `In the absence of lactose, the lac repressor binds to the operator sequence on DNA and bends the DNA by 40 degrees. This blocks access of T7 RNA polymerase to the promoter site and thus prevents leaky transcription of your gene before induction.'

Because the T7 RNA polymerase is expressed after IPTG induction, there is no possibility that the T7 RNA polymerase is before the IPTG induction. Right? so how lac repressor protein  blocks access of T7 RNA polymerase and leaky transcription of the gene before induction if there is no T7 polymerase then? I do not understand the second sentence of passage that I quoted

@gucio I have expanded my answer - hope this helps.


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What is the derivation of the rules of proportionality between axon conduction velocity and diameter?
We have been told that in myelinated fibres, conduction velocity is proportional to the diameter of the axon. In unmyelinated fibres, velocity is proportional to the square root of the diameter.
Can this be derived from use of the length constant? The length constant being the distance over which the voltage drops to 37% (1/e) of its original value.
length constant = sq.root(transmembrane resistance/longitudinal resistance)
I understand that longitudinal resistance would (if analogous to electrical resistance in a wire) be inversely proportional to the cross-sectional area, which would lead to being inversely proportional to the square of the diameter (from area = pi.r^2).


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Does the vagus nerve supply the human thoracic diaphragm?
The vagus nerve (CN X) passes through the oesophageal hiatus of the diaphragm at the vertebral level T10.
But does the vagus nerve actually offer any nerve supply to the diaphragm?

No, it doesn't supply thoracoabdominal diaphragm.

Sensory and Motor Innervation of the Crural Diaphragm by the Vagus Nerves https://www.sciencedirect.com/science/article/pii/S001650850901511X?via%3Dihub


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Why do bananas turn black after some time?
Why do bananas turn black after some time? Please don't just give hypotheses but concrete references to experiments

Banana skin consists of plant cells and cellular tissue. This tissue contains phenolic compounds. On getting old, the cell membranes of the banana get weak. When the membranes weaken, the phenolic compounds mix with polyphenol oxidase (an enzyme present in the cells cytoplasm). As a result of this interaction, the phelonic compounds oxidize and produce a brown compound called melanin which results in the colour of the peel turning black. Also, the green skin of banana contains a gaseous plant hormone, ethylene, which diffuses into the fruit and hastens the process of ripening. It is yellow when the fruit is ripe and turns black with the production of more and more ethylene.

Good one potterbond007

@speedoheck Thx. I added some more details btw.


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Why do our eyes close when we sleep?
Why do our eyes close when we sleep? Is it to relax our eye muscles? How can it be explained from an evolutionary point of view?

The human optic nerve connecting an eye to the brain has about 1,000,000 or 10^6 fibres, each with a response time of about 1/100th of a second. In computer terms that accommodates a bandwidth of about 100 Megabits per second. We are awake in general for about 16 hours per day which is 57,600 seconds, so the brain receives from the eyes about 10 trillion or 10^13 informations bits per day. Under extreme conditions the the human brain can stay awake for longer than this, but its performance degrades significantly and becomes unusable at a week (168 hours) of wakefulness. During a week of wakefu

There's definitely something to the fact that eyes work better when they are closed periodically and don't work well when they are open constantly, but there is another angle to this topic.
I think its worth adding that not all animals sleep with their eyes closed.
This is because some animals sleep with only half of their brain at once.  Ducks, some birds, aquatic mammals like whales dolphis and seals engage Unihemispheric sleep.  In Unihemispheric sleep, half the brain is asleep and the other is awake.  Not necessarily fully awake, but enough that one eye is open and watching for predators or other threats.
One might ask - didn't we all have predators and threats?  Why don't we all sleep half the brain at a time?  The answer is not clear, but it appears that unihemispheric sleep is not a trait that is maintained easily.  Very few animals really have the ability.  As such there must be some advantages physiologically to closing both eyes at once and experiencing total sleep.  Once the threat is not so great from being sleeping prey, animals start to close both eyes pretty quickly.

is it necessarily the case that full sleep confers an advantage? Couldn't it also be true that unihemispheric sleep is advantageous but the requires very complex adaptations that have simple only happened in a few species? Or is the likelihood/difficulty of a mutation taken into account when biologists use the term "advantage?"

Great comment.  I think its the case the unihemispheric sleep is definitely an advantage!  Keeping one eye open must be very helpful.  You have hit the nail on the head.  the advantage of an adaptation must be large enough to eliminate the mutants that don't have it efficiently.  that is pretty much how I understand 'advantage': 'advantage' means an adaptation will stay around...

Through psychology, It shows that proper sleep aids in memory retention and learning. It could be possible that evolution led some animals/organisms to better retain information by allowing for full sleep compared to unihemispheric sleep. Just food for thought.

Tears contain an important hormone that kills bacteria. Closing eyelids during sleep allows a prolonged contact between the cornea and tears killing resistant bacteria in the process. The action of the tears during blinking is not sufficient to completely get rid of the foreign bodies in the eyes. Closing eyelids gives the tears a capacity to accumulate forming a film of moisture above the cornea and acqeous humour. This has many important uses. It allows dust particles to dissolve and be eradicated when the tears flow out of the eyelids. This partially explains the residue that is seen on the cheeks when people wake up in the morning in addition, of course, to the sodium and potassium salts in the tears. The other importance of the film of tears accumulated on the eye is to help keep the acqeous humour moist. This has a great effect on how the lens receive light and also on the overall refractive index  of the eye as system.

Any references to add to allow for background reading?

"an important hormone that kills bacteria" ... which is?

@AliceD One reputable source is: "Antimicrobial Compounds in Tears" (Jul 20 2013), by Alison McDermott, published on the US National Library of Medicine website. There are similar articles about lysozyme elsewhere.

@Rob - in that source I've searched for hormone and it's not mentioned anywhere in the paper. Please adapt answer and include the reference in the answer and not in the comments

I agree that hormone isn't there (or in relevant information elsewhere). Pride Chigs only used the word once in their answer. Whether they found something that I wasn't able to, confused hormone with enzyme, or confused the types of tears their properties and function, is unknown to me and will have to await a reply from the OP. I'm reluctant to make edits where the meaning (premise) of the question or answer is altered as reviewers are keen to reject such edits, and then I must successfully appeal (increasing the effort). So I suggested an improvemnt


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What nutrients do I lose in the water when I boil vegetables?
What nutrients do I lose in the water when I boil vegetables. Has to be some water-soluble and heat labile ones right? Which ones?

Vitamin C and the B complex vitamins are water soluble.   Thiamine and folate are also heat labile.
Overall there are hundreds or often thousands of kinds of small molecules (not protein or DNA) in the cell and many of them are water soluble or heat labile.  Plants especially have many unusual small molecules.  Its not known how many of them affect human health, but may affect factors like the gut microbiome quite a bit and have an effect on well being if not mortality.
Some people think that live uncooked vegetables have enzymes and other proteins which are good for you since cooked proteins are denatured and may be taken in differently.  At the very least they are probably easier to digest when they are not heat denatured.

Why would non-denatured proteins be easier to digest? Got any links on that?

I could site a couple of papers, but it would still need some explaining because its common sense.  thoroughly cooked protein is a lot like a fried egg - its a solid.  The same can be said for cooking a prep of tissue or bacteria - the protein tends to aggregate.  As such, proteases or even acid can't diffuse as readily into the matrix of glop as well as through a solution of soluable protein.

Interesting. But then, why do we prefer to eat protein-rich food, such as meat and eggs, cooked? Any idea?

Jarlemag Why do you want to eat Salmonella and E coli from uncooked meat and eggs

what @speedohack is saying is that meat rots quickly and cooking is more necessary when eating meat.  that's more a preference of appetite.  We eat protein when we can get it but our dietary requirements as adults are not as much as many people in industrialized nations eat.


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Activity of DNA glycosylase
I am wondering how DNA glycosylase works from the chemical point of view. Sometimes in papers I can see that they are doing activity assays with 1M NaOH and I am trying to understand why using 1M NaOH is more factual? Thank you for any help.

DNA glycosylases bind to dsDNA, flip a base out of the base-paired double-helical structure and cleave it off, leaving the sugar-phosphate backbone intact. This base removal renders the DNA susceptible to alkaline cleavage.
In this recent paper:

Miyazono et al. (2014) A sequence-specific DNA glycosylase mediates restriction-modification in Pyrococcus abyssi. Nature Communications 5: #3178

the authors monitor the activity of a DNA glycosylase using this phenomenon: after treating an oligonucleotide with increasing amounts of the enzyme R.PabI they treat the DNA with NaOH so that the oligo is cleaved, allowing detection of the result of enzyme action on a polyacrylamide gel, as you can see from this image, taken from their Figure 3.

Incidentally the same phenomenon is exploited when DNA is transferred to a membrane for Southern blotting. After electrophoresis the gel is soaked in acid which causes depurination (analogous to DNA glycosylase). It is then transferred to an alkaline solution. Although protocols often refer to this as a neutralisation step it actually breaks the DNA at the apurinic sites and separates the strands. This cleavage is important for effective transfer of larger fragments from the gel to the membrane.


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Ni-NTA purification, problem with the chaperone protein
I'm trying to purify the protein by Ni-NTA affinity chromatography. It seems that my protein (size about 54 kDa) is co-purified with chaperone protein (probably GroEL  - as the band is around 57kDa).
I tried the method where 4M glycerol and ATP is added to the wash buffer 1 and then I incubated this with the resin for 2 hrs in 4C, but it did not help.
Has anyone met such a problem before? I will be grateful for any advices.

If chaperone proteins are not an expected binding partner to your protein/peptide fragment then you need to use imidazole in your lysis and wash buffer ranging from 1 to 10 mM depending on how stringent you want but 1 mM worked for me. Can go higher than 10 mM if the problem does not resolve but don't go too high since imidazole is also used to get the purified proteins off the nickel beads as an elution buffer!

My lysis buffer and first wash buffer contained 10 mM Imidazole, then I made second wash with 10% buffer B in A, and eluted protein with buffer B contained 250 mM imidazole. The band of chaperone protein appear in 'second wash' fraction  and 'elution' fraction but mostly in 'elution' fraction.

The go higher, try 25 or even 50 mM in your wash buffer (and maybe lysis buffer). I know someone had this very exact problem and increasing imidazole concentration solved it! I can't remember the exact conc they used but it was between 20-50 mM (that I remember for sure!). However it might effect your purification yield, but thats the compromise you might have to make. If you have high amounts of purified protein, then it shouldn't matter!

Also try increasing your wash numbers since two is far too low! Try 5 perhaps. I do 3-5 washes.

Also in what system are you over-expressing your protein since what you are seeing at 47 could be the result of post-translational modifications (http://www.embl.de/pepcore/pepcore_services/cloning/choice_expression_systems/comparison_expression_systems/index.html), which can increase the MW of your protein from 54 to 57 kDa! i.e. what I'm saying is how do you know you are co-puryfying a chaperone?

I did western blot, so I know which band is my protein - it is below the bigger band. It is T7 expression system which is started by adding IPTG to medium in final concentration of 0.1 mM.

ah, so you did an Ab based assay of your protein after pulldown with Ni beads and the second protein did not produce any signal? or you just did a coomassie stain in a SDS-PAGE gel? Although it's commonly said in science that in E. coli you don't get post-translational modifications but it does happen! (http://www.sciencedirect.com/science/article/pii/S1874391913004533) so my question is what have you done to exclude the possibility that the higher MW band is not your protein?

I don't see how "did a western blot" would not involve antibody-based staining, though.

I was confused as to whether at which stage (coomassie stain or WB) the OP was observing the extra bands when referring to WB (as commonly done) was not referring to commassie by mistake. This was just for clarification purposes.

Is it possible to clone your gene of interest onto a new plasmid (preferably with a GST/avidin/alternative tag)? If all else fails, this would probably remove the problem with elution.


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What is the evidence that plants and animals had a common ancestor?
According to the theory of evolution (which I don't dispute), plants and animals evolved from a common ancestor, probably a eukaryote. I'd like to know how we know that to be true.
Specifically how did scientists come to that conclusion, and what verifiable facts did they rely on? It would also be interesting to know who (and when) was the first to propose that plants and animals had a common ancestor. Was it Darwin himself?
Note that I'm not asking for the details of when and how that happened (the diversification/evolution of eukaryotes into plants, animals and other types), but rather the evidence we have to support it.

Darwin did propose that all extant organisms have a common ancestor:

Therefore, on the principle of natural selection with divergence of character, it does not seem incredible that, from some such low and intermediate form, both animals and plants may have been developed; and, if we admit this, we must likewise admit that all the organic beings which have ever lived on this earth may be descended from some one primordial form. But this inference is chiefly grounded on analogy, and it is immaterial whether or not it be accepted. No doubt it is possible, as Mr. G.H. Lewes has urged, that at the first commencement of life many different forms were evolved; but if so, we may conclude that only a very few have left modified descendants. For, as I have recently remarked in regard to the members of each great kingdom, such as the Vertebrata, Articulata, etc., we have distinct evidence in their embryological, homologous, and rudimentary structures, that within each kingdom all the members are descended from a single progenitor.

--Darwin, Origin of Species
He probably wasn't the first one; Darwin cites a previous suggestion:

From a circular lately issued it appears that Dr. Freke, in 1851 ("Dublin Medical Press", page 322), propounded the doctrine that all organic beings have descended from one primordial form. His grounds of belief and treatment of the subject are wholly different from mine; but as Dr. Freke has now (1861) published his Essay on the "Origin of Species by means of Organic Affinity", the difficult attempt to give any idea of his views would be superfluous on my part.

--Darwin, Origin of Species
As you can see, he offers no real evidence for this; he explicitly says it's speculation. Of course, nothing from Darwin is necessary for modern evolutionary theory, and other groups have tried to make this more concrete. Several lines of evidence provided increasing evidence for a universal common ancestor (UCA):

For a century after the publication of Darwin's bold proposition, before the advent of molecular biology, the UCA hypothesis remained an untested and hardly testable speculation. However, first the universality of the genetic code and later the demonstration of the (near) universal conservation of approximately 100 RNA and protein-coding genes among cellular life forms provided ample evidence in support of the UCA. Although generally considered compelling, this evidence fell short of a rigorous, formal test of the UCA hypothesis.

--The common ancestry of life
A relatively recent approach has tried using information theory to formally test a UCA:

Here I provide the first, to my knowledge, formal, fundamental test of UCA, without assuming that sequence similarity implies genetic kinship. I test UCA by applying model selection theory to molecular phylogenies, focusing on a set of ubiquitously conserved proteins that are proposed to be orthologous. Among a wide range of biological models involving the independent ancestry of major taxonomic groups, the model selection tests are found to overwhelmingly support UCA irrespective of the presence of horizontal gene transfer and symbiotic fusion events. These results provide powerful statistical evidence corroborating the monophyly of all known life.

--A formal test of the theory of universal common ancestry
Formal positive proof of theories in science, outside of math, are rare to non-existent (what actually happens is that competing theories are disproved) and I don't think that this approach is different. It's not a formal proof, it's yet more powerful evidence that theories not involving a UCA suck.

A formal demonstration of the Universal Common Ancestry hypothesis has not been achieved and is unlikely to be feasible in principle. Nevertheless, the evidence in support of this hypothesis provided by comparative genomics is overwhelming.

--The common ancestry of life

Thank you for the detailed answer and references. I understand that most of the evidence comes from analysis of DNA/RNA, combined with knowledge of the evolutionary mechanisms at play. And we have concrete evidence for evolution at different levels (species we can observe), which I guess is extrapolated to the level of eukaryotes evolving into the different kingdoms, right? And before genetic evidence was available, it was just a speculation.

I was wondering if there's any other kind of evidence, such as from (micro)fossils, if there are any that can provide usable information. Either way, I'm not expecting an absolute/formal proof.

Would not another piece of supporting evidence be the commonality of basic cell mechanisms, such as ion channels and the like?  It would seem that either there was a common ancestor, there's only one way for life to work, or plants and animals happen to have developed the same mechanisms.

It is also interesting to note that one of your references ("The common ancestry of life") is basically a criticism of another one of your references ("A formal test of the theory of universal common ancestry"), addressing the alternative hypothesis of convergent evolution, but still coming to a similar conclusion in favor of a UCA.

@jamesqf I guess that could also be counted as evidence, maybe you can explain it more and post it as an answer? It would be nice to find some references about that too.

the UCA hypothesis has not been achieved and is unlikely to be feasible in principle. - because the fossil record doesn't go back far enough?

@mazura because other hypothesis can be made less and less likely, but can't be formally disproven because they come down to statistical arguments; there might be only a 0.000000000001% chance that observations arose through paths other than a UCA, but that's still not zero.

"...what actually happens is that competing theories are disproved..." No, what actually happens is the predictive power of a theory is tested. New hypotheses are developed based on what the theory implies, and those are tested. If the hypothesis is false (and the assertion that the theory implies it is true), the the theory can be rejected. If the theory is not subjected to such tests, it is untested and there's no reason to believe it. There would also be no value in believing such a theory, since it has not been demonstrated as an accurate predictive model. Anything less is not science.

@aditsu it was not speculation before genetics, biochemistry and cellular anatomy also points to a common ancestor, plants ans animals share several organelles not seen in many other branches of life, (like mitochondria , golgi, and nucleolus).


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Blosum matrix with probabilities instead of the positive and negative scores
I am trying to find a version of the BLOSUM matrix that has the frequencies instead of the scaled log-odds. i.e. instead of the common version that tells us that the score LEU/ASP is -4, I would like to know the probability of LEU replaced by ASP.

Download the BLOSUM data and source-code from here. Unzip the archive which has several files.
The file called blosum'XX'.qij will have the co-occurence probabilities, and the subsitution probabilities can be calculated from them.
Also have a look at this article.

Thank you for the answer and the link. For the benefit of anyone reading this: the frequencies in .qij files still need to be normalized before they can be used as substitution probability since they don't add up to 1 for each column or row (they add up to 1 for the entire matrix). i.e. If I want to know the probability  of ALA being replaced by HIS, the table will say it is 0.0011 but actually it is 0.0011/0.0741 (the sum of the frequencies in the ALA column) = 0.014844804318488529

So perhaps they are more called cooccurance probability than substitution probabilities. The probability of ALA substutited by HIS is p('His'|'Ala') but the table gives the joint probability p('His', 'Ala'). So we get the conditional probability p('His'|'Ala') = p(His,Ala)/p(Ala) and p(Ala) is basically p(Ala,x) for all x. so it is the sum of the Ala column.

oh yes you would need the $p_i$ for the calculation. I have not checked if that file exists in this archive.


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Dark veil when getting up too fast
I was asking myself this weird question.
When you get up or stand up too fast, sometimes, you see something like a dark veil, and you aren't able to see anything distinctly for 2 or 3 seconds, then it come back to normal.
Do you know what causes this weird phenomenon (biologically speaking), or am i the only weird person feeling this sometimes?

If your interest is academic then you may wish to look further into orthostatic hypotension. I don't know why this causes visual disturbances however.

It's caused by a sudden shift in the pressure needed to circulate blood to your brain which your body fails to respond to sufficiently quickly. This results in a sudden loss of blood pressure termed Orthostatic Hypotension which, in turn, results in a transitory reduction in the blood supply necessary for brain function. You experience a momentary loss of vision for the same reason that you would if someone strangles you.

Are other brain functions also affected when this happens?

Other brain functions may indeed also be affected. Dizziness is another possible effect, as one example.


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What if Staphylococcus Aureus are extinct?
What if Staphylococcus Aureus are extinct?
Can it be good for human or bad for human?
Thanks for your answer in advance.

thats a homework question isnt it.

Of course not. I have nose infection and it was caused by my razor. I am curious how I can prevent bacteria in this kind of situation (when I am not protected by skin).

It is almost entirely parasitic and has not physiological or ecological effects that could not be replaced easily by another bacterium. It is responsible for immeasurably more infections that protections of humans, therefore it is a disease vector, not a beneficial bacterium.
If it went extinct, humans may suffer from increased population pressure, that would be the only worry.

I know this has been closed already, but could you please provide a reference?

There are millions of references, i.e. A large proportion of the population (60%) harbours S. aureus intermittently, and the strains change with varying frequencies. Such persons are called intermittent carriers. Finally, a minority of the people (20%) almost never carry S... it's not possible to find a study about benefits of aureus, it's always benefits of treatments of the desease.

So this is a very helpful answer. It means scientists don't have to hesitate to kill S.aureus as many as they can.

thanks, the over use of antibiotics is what creates super resistant variants. excess and low hygiene and un-natural human cities and social structures probably cause most S. aureus problems.


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What kind of leafy house plant is this?
I was given the plant as a gift.  Started out small and has grown to almost 6 1/2 feet tall and has sprouted off spring.
Original

Offspring:

Google reverse image search resulted in "Houseplant".  Not very helpful.
I have since removed the dead leaves from the plant.

Future visitors might appreciate for reference the somewhat similar (though different) species found in this post: What is difference between “Syngonium” & “Pothos”?

I believe it's a Dieffenbachia, see also this question & answer from Gardening.SE:
https://gardening.stackexchange.com/questions/9765/what-is-this-thick-stemmed-houseplant-with-variegated-leaves
though I am not sure of the species, it could be Dieffenbachia seguine which shows a similar coloration and is one of the taller species (I believe some of the others stay bushy).
On the linked answer, @TeresaMcgH warns:

By the way, one of the common names for this plant is "dumb cane" because the sap can cause numbness and swelling in the mouth and throat if ingested. So watch pets and small kids around it if you have such at home.

Bryan is correct: this is a Dieffenbachia. Also, I would like to emphasize the warning: it may not only cause numbness, but can be dangerously toxic. If you search scientific literature, several serious cases are documented. Those include necrotic tissue (fingers, to the bone!) and other severe systemic health issues.


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Interesting Insect, possibly a beetle (Northern Indiana)
I happened across an interesting looking insect, that I've never seen before.  In Northern Indiana, late spring around 5 PM CST.  I tried a reverse image search, with no luck.  It is approximately 3/4 inch long.
Any ideas?

That is a carrion beetle. Family Silphidae, in the genus Necrophila
https://www.insectidentification.org/insect-description.asp?identification=American-Carrion-Beetle

Ugh.  After reading the linked page, I'm sorry I asked.  ;)


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Why is assembling paired end illumina without any input parameters an important problem?
In one of the comments in this question about multiple sequence alignment, it was stated

@5heikki: btw if you want a good bioinformatics problem, come up with an assembler that assembles any paired end illumina run optimally de novo without any input parameters.

What is a paired end illumina? How is optimally defined in this context? What are the usual input parameters?

The Next-Gen sequencers cannot sequence a very long stretch of DNA with good reliability (~150 for the recent model- HiSeq2000; even less for older models such as GA (40), GA-II (70), GA-IIx (90)). For increasing the confidence in a certain hit, it was sequenced from both the ends.
For example, if you have selected 500bp DNA fragment, then after ligating adapters to both the ends, it is sequenced from both the direction up to 150bp. This would leave an unsequenced "insert" region of 200bp. (In the example image below, they have sequenced up to 40bp [case of old GA] )

During assembly you stitch together the fragments of DNA to find out the larger DNA from where the fragments arise. In case of RNAseq, these arise from a transcript, and your assembly should give you the complete transcript (mRNA or ncRNA etc). There are two basic types of assembly: reference guided assembly and de-novo assembly. In the former you use a sequence such as the genome as a reference to assemble the transcripts. If such a reference is not available then you have to go for de-novo assembly.
The assembly algorithms use several parameters and since these are computer algorithms and not some kind of magic, their output depends to an extent on the different parameters.
In case of paired end data there are some parameters that are important. Most important is the size of the insert. In case of a 500bp fragment, you'll end up with an unsequenced region of 200bp. This is not much of a problem with reference guided assembly because you can figure out the sequence of the insert based on where the sequenced region align to the reference. The average insert length is important to remove discordant reads (aligning too far apart in the reference). In case of de-novo assembly, the insert will remain unsequenced even if you know that the final transcript looks something like:
frag1-frag6-frag3-frag9-frag4
So, to get the sequence of the assembly, you need to sequence the insert regions. This is not a problem if you at least know the order of fragments in the assembly. However you should know the insert size to get the assembly size correct and as skyminge said, in scaffolding. Obtaining this insert length is not that difficult (You need not provide it as a parameter. Most algorithms can calculate it automatically).
Another parameter in de-novo assembly is k-mer length (the sequence reads are broken down into k-mers for better assembly). I cannot explain the algorithm of assembly here in detail. You can check the manuals/papers of common assembly algorithms like Velvet, SOAPdenovo, Euler [de novo]; cufflinks [reference based]
I have mentioned transcriptome sequencing here but the principles are same for genome sequencing too.
Back to your main question:
Why is assembling paired end illumina without any input parameters an important problem?
Because it is less effort; but tweaking may be difficult. I won't consider it as an important problem. There are other important algorithmic optimizations that are required with de-novo assembly.

Another important wrinkle in this kind of data, it's relatively error prone.

@swbarnes2.. There is some level of error but when you say "relatively error prone", what are you comparing it with?

@WYSIWYG You wrote: "if you have selected 500bp DNA fragment". Does this guarantee that the fragments would be 500bp each? If yes, then how does the NG sequencer do that? (If I understand correctly, https://emea.illumina.com/content/dam/illumina-marketing/documents/products/illumina_sequencing_introduction.pdf says that the DNA is fragmented randomly)

@OrenMilman I was just giving an example; not saying that DNA would be of this precise length. The DNA is sheared randomly but the library is constructed from DNA pieces in a selected size range.

In Illumina sequencing, the DNA is (usually randomly) sheared into fragments. For paired end sequencing, fragments of a specific size range are selected and then sequenced from both sides.
This results in two reads for each fragment. As read length is fixed, also the remaining "middle part" of the fragment is in a specific size range. In some cases there is no middle part, because the fragments have been chosen so small, that the reads overlap.
The information about the size of the fragment and/or the "middle part" as well as read length are some of the most important parameters you need for de novo assembly. Your could get away with not taking read size as a parameter, if you need it you can still run over all reads and check. But fragment size or insert size is important to place the reads, especially in scaffolding.
This blog entry also has some nice information about the often upcoming discussion what is meant by insert size (fragment size, the size of the middle part) and what can happen with overlapping reads and read-through.
There is lots more to say about this. Illumina also provides some nice videos available on youtube.


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How are PPI networks constructed?
I am a CS graduate working in Computational Biology. While the theoretical aspects of both AP/MS (and the various types) and Y2h are quite clear to me, the actual technical aspect of building large-scale PPI networks is not. Is there a machine that can do these experiments? How long would building a network take for say, 2000 proteins? Is there a company that can provide this service?
I would appreciate any help. I have searched a lot but was unable to find an answer for this question.

Welcome to Bio. Could you explain all the acronyms perhaps and give some background info?

Hiya @Christiaan! I am sorry, it might not have been clear. When I say PPI I mean protein-protein interaction networks. AP/MS Affinity Purification/Mass Spectrometry, Y2H: Yeast two-hybrid. It is not clear to me what do you mean by background.

It depends on the PPI network. Some, like DIP are exclusively experimental, depending on high-throughput robotic AP/MS, Tandem Affinity Purification, Y2H, cross-linking with formaldehyde, clever things involving half-fluorophores, etc. There are a lot of different methods, is what I'm saying. Y2H has a high false-positive rate, immunoprecipitation is expensive (antibodies cost money), others have other drawbacks.
You can also exploit the existing huge body of research using text mining, even though that's really crude. (It boils down to: protein A and protein B or their pseudonyms are often mentioned in the same sentence, they must be related somehow). There are also RNASeq methods, where you just do hundreds of RNASeq experiments and two genes that correlated(or inversely correlated) are probably interacting in some way. If two proteins interact in organism A and they have closely-related homologs in organism B, the proteins probably interact in organism B too.
In short: In a lot of different ways. It would be wise to check the provenance of a link in such a network and handle it differently depending on what kind of link it is if you're working with big networks like this.
I don't know that there are any companies that do this commercially, but the Max Delbruck Center will talk to you about screening something custom. I don't know how long it would take but 2000 proteins would not take a long time, relatively speaking. The human genome has tens of thousands of proteins, so 2000 proteins would only be a few percentage points of the effort. However if they're totally novel there's probably library setup times and overhead, but I don't even have a good guess how long this would take. Depends on who you talk to, I expect.

Dear @Resonating, thank you very much. This was very interesting to read, I really appreciate your help.


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Coagulation of blood in small intestine due to trypsin
Trypsin is secreted in the small intestine to convert proteins into dipeptides i.e. to carry out digestion of proteins. However, it is also a coagulating agent which coagulates blood by hydrolysing fibrinogen into fibrin. My question is, why doesn't the blood in the small intestine coagulate?

Remember trypsin is an intraluminal enzyme, and is not normally in contact with blood.


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Distribution of sodium–potassium pumps
How are sodium–potassium pumps distributed over the membrane of a neuron? Where are the most, where are the fewest? Or does this dependent on the type of neuron?
Are there known and understandable correlations between the local densities of  sodium–potassium pumps and other membrane molecules (like ligand-gated or voltage-gated ion channels)?


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Spatial distribution of axons connecting distant groups of neurons
It would help me to shape my picture of the brain, if I knew the following:
Consider two specified groups of neurons A and B in the brain that are well-located but quite distant from each other (e.g. two roughly spherical nuclei, or two Brodman areas corresponding across hemispheres), and which are (more or less) directly connected synaptically, i.e. axons of the first group build synapses with dendrites of the second, the distance being mainly bridged by the axons. I assume there are lots of examples on different scales.
My question is: Is there a preferred way how the axons are organized, i.e. spatially distributed in the brain? Do they run  mostly parallel to each other in bundles, or are there (maybe exceptional) cases, where the axons (or small subsets of axons) take individual routes, possibly quite far from each other?

I am aware that with intermediate groups of neurons, there are different and non-parallel pathways of one group of neurons to the other. So my question is explicitly about directly connected groups.
(Are there too many simplifying assumptions in my question that make it vacuous?)


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The human brain in numbers II: synaptic connections
The overall number of synapses in the human brain is roughly 1,000 trillion, i.e. 10,000 synapses per neuron.
My question here is three-fold:

I assume that each structural type of neuron (basket, pyramidal, ...) has a somehow characteristic average number of in-coming and out-going synaptic connections, i.e. not every type of neuron will have about 10,000 in-coming and 10,000 out-going synaptic connections. I am looking for a thorough overview of these characteristic numbers by structural type.
I assume that for some functional groups of neurons (see The human brain in numbers I: neurons) there are characteristic average numbers of in-coming and out-going synaptic connections per neuron. I am looking for a thorough overview of these characteristic numbers by functional group.
Finally, for some functional groups there are presumably characteristic ratios of inner and outer synaptic connections: "x % of the in-coming synaptic connections of a neuron in group X come from other neurons in this group, the rest comes from the outside. y % of the out-going synaptic connections of a neuron in group X go to other neurons in this group, the rest goes to the outside".  I am looking for a thorough overview of these characteristic ratios by functional group.

Woah, that's just too broad a question! Divide it into (at least) three questions, lest even a bounty of +500 points is not very likely to get you a complete answer for such a big question...

Yes, incredibly incredibly too broad. You might look into projects like the Blue Brain Project in Europe and the BRAIN initiative in the US.

I'd like to, but these are real huge projects with vast web sites. And I am not sure if I would find thorough and concise overviews of the kind I'm looking for. So if anyone knows...

@hansstricker honestly, if you ain't sure you'd get all that you want even on such vast websites, how do you expect somebody here to pack all of it in a little answer?

The little answer might be a link that would be hard to find.


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How are fMRI responses to auditory stimuli measured?
How can fMRI experiments be conducted which measure the response to auditory stimuli (e.g. music) when the apparatus makes such loud, nasty, and distracting noises? Are there quieter MRI tomographs in the meanwhile, or must the stimuli (transfered by earphones) be louder than the noise of the machine? How to measure the effect of a whishper then?

I could have found this article earlier, but as things go, I didn't. But possibly it contains most of what can be said to this question:
Jonathan E. Peellej, Methodological challenges and solutions in auditory functional magnetic resonance imaging, Front Neurosci. 2014; 8: 253


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Is dextrocardia congenital?
Dextrocardia is displacement of human heart to the right side. Does it occur during the life span of a human being or right from birth?

A simple google search gives your answer "Dextrocardia is a rare heart condition in which your heart points toward the right side of your chest instead of the left side. Dextrocardia is congenital, which means people are born with this abnormality."

Oops... never knew this.... thanks for telling me....

As the comments pointed out, this is not a hard question to answer with some research, but I'll add a few more details.
Dextrocardia is congenital. The human heart normally actually isn't so much on the left side - it's more pointed towards the left. In dextrocardia it points more towards the right side. This develops within the first few weeks of embryonic development, as the heart is one of the first organs to develop.

Source
It occurs in about 0.7 percent of live births and 2.7 percent of stillbirths, indicating that there are health problems in the fetus associated with it. After birth, it's possible that the heart functions perfectly fine, but often there are other heart defects associated with dextrocardia.
Dextrocardia with situs inversus is a condition in which the heart and visceral  organs are reversed. As for the cause, it's genetic and follows a recessive inheritance pattern, meaning both parents need to be carriers, but don't necessarily have the condition.


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is it possible for Cougars and Cheetahs to reproduce
I know that many big cat hybrids exist ie ligers, but I always thought it these hybrids were limited to members of the Panthera genus till I came across a cross between a leopard and a cougar. Now since cougars and cheetahs are more closely related to each other than to leopards could these two successfully reproduce?