text:
Why don't antibiotics affect mitochondria?
Given that mitochondria are evolutionarily closely related to bacteria, and antibiotics kill bacteria, why don't antibiotics also kill mitochondria?

Just found this interesting information from the wikipedia article about ribosomes: "Even though mitochondria possess ribosomes similar to the bacterial ones, mitochondria are not affected by these antibiotics because they are surrounded by a double membrane that does not easily admit these antibiotics into the organelle"

And so how do they get into bacteria?

I think many bacteria only have one membrane instead of the two on mitochondria.

Gram-positive bacteria have no outer membrane, but gram-negative bacteria (from which mitochondria are thought to derive) have a double-memberane. Gram-negative bacteria are susceptible to aminoglycosides, so I am afraid that your explanation (and the first statement in the accepted answer) is inadequate.

I think this answer by David should provide further insight. Macrolides do have an effect on protozoan plastids. http://biology.stackexchange.com/a/48004/20449

The short answer is, as you found, that mitochondria are wrapped in a double membrane and are thus harder to penetrate with antibiotics.
The long answer is some of them do.  Good antibiotics target structures widely found on and conserved in bacteria that are not found in human bodies.  Some antibiotics are a little less specific and can indeed interact with other molecules.  The allergy to penicillin, for example, is caused by the immune system reacting to a "novel" protein formed when penicillin binds to the surface of red blood cells.  Some antibiotics can indeed harm mitochondria, but we tend not to use those and in fact wouldn't even call most of them antibiotics since we wouldn't use them because of their harmful effects.  Here is a very recent report looking at some of the anti-mitochondrial effects of some antibiotics.  To quote from the abstract:

We show that clinically relevant doses of bactericidal antibiotics—quinolones, aminoglycosides, and β-lactams—cause mitochondrial dysfunction and ROS [reactive oxygen species] overproduction in mammalian cells. We demonstrate that these bactericidal antibiotic–induced effects lead to oxidative damage to DNA, proteins, and membrane lipids.

Absolutely fascinating stuff. Thanks for sharing the article.

Also note the fluoroquinolone group of antibiotics (Cipro, Levo, etc) are very good at damaging mitochondrial DNA, causing long term, sometimes permanent, debilitating effects. https://www.ncbi.nlm.nih.gov/pubmed/8913349

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text:
Effect of alcohol on parasites
I recently came across an article saying that fruit flies use alcohol to deter parasites. The researcher was quoted as saying there have not been any studies on the effect of human alcohol consumption on parasites. Is there any research being done on this? Another related question I have is whether the fruit flies can tolerate higher alcohol concentrations than mammals/humans.

Drosophila is seen as a highly alcohol tolerant species which is mainly dependent on the environment it lives in. So are flies, which are captured in the cellar of a wine yard more tolerant to alcohol than flies which are captured outside (see first reference).
The environment in which the flies grow up and live does not influence the activity of the alcohol dehydrogenase enzyme but seems to influence the expression (amount) of it. The more alcohol is present, the higher the expression is (see reference 2).
I haven't seen explicit data on the comparison between humans/mammals and drosophila, but since drosophila is seen as a good model organism to study alcoholism, I would think it is not too different. (see reference 3).

Micro-differentiation in a Natural Population of DROSOPHILA
MELANOGASTER to Alcohol in the Environment
Alcohol tolerance, ADH activity, and ecological niche of Drosophila
species
Functional Ethanol Tolerance in Drosophila

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text:
Last-ditch efforts to maintain thermal homeostasis
I was in the gym's steam-room today and a thought occurred to me: have I truly thwarted all possible mechanisms for maintaining thermal homeostasis?
There's sweating, which is thwarted because the steam-room's atmosphere is as close to 100% humidity as possible, so there's almost no evaporative cooling.
There's convection, which is thwarted because the ambient temperature is above normal body temperature.
And I can't get rid of heat by exhaling, because every lungful of air I inhale is already above normal body temperature.
I think that, eventually, I should go into hyperthermia, but beside the above, are there any other last-ditch attempts to lower core temperature that my body could take?

Thermotaxis? :)

Another factor at play here is the cardiovascular system.  Biro, Masudo, et al (2003) wrote an article about the benefits of the induction of systemic vasodilation for those with congestive heart failure.  This may be a short-term adaptation of the body stemming from the reduced ability to sweat in those conditions, or it may be a harbinger of the more serious circulation changes below.
Epstein and Roberts (2011) explain how the eventual results of heatstroke (which isn't the phenomenon that you are describing, but a sauna might induce some of the features of these same pathways) can cause a circulatory collapse due to an initial overtaxing of the circulatory system to compensate as well as the activation of certain heat shock proteins.
There are a lot of other references out there on sauna physiology, but many are not in evidence-based journals, so you can make your own decisions on those.
One factor that I didn't find mentioned explicitly was the basal metabolic rate.  It's probably safe to assume that the body will limit its own processes and reactions which produce heat.  I'm not clear on the extent to which factors such as the level of interleukins, etc. would play a role as they do in fever regulation.


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Atomic force microscopy: depth penetration?
What depth penetration can  one typically get with atomic force microscopes? (i.e. how far into the tissue can one image?). I have found numbers on acquisition times (minutes) and spatial resolutions (~nm), but what about depth?
Also, what is the sensitivity of AFM? (e.g. in moles)

AFM is a surface technique, it has no depth. Spatial resolution can be far in excess of nm - there are publications wherein bonds -ewven hydrogen bonds- are shown.
Here is a popularized article which is not behind a paywall
https://www.chemistryworld.com/news/new-afm-tip-reopens-hydrogen-bond-imaging-debate/3008878.article
The sensitivity of AFM would not be measured in moles at all. How to measure it depends entirely on the mode you work with. Are you imaging the surface topography? Are you measuring the friction between the tip and the sample? Are you measuring magnetic domains? Surface hardness?

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

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

The authors report on problems of over-expressing membrane proteins in E. coli using a T7 (pET) system. They isolate mutant strains which show improved levels of expression compared to the parent strain, BL21(DE3). In their Table 1 they document levels of expression of 17 proteins including, as a control, GFP. GFP was found as a combination of soluble and inclusion body protein at a level of 37 mg L-1 in BL21(DE3) and 140 mg L-1 in one of their mutant strains (C41(DE3)). The highest level of expression that they observed was 300 mg L-1 for bovine OSCP.
Unfortunately the authors document neither the total protein content, nor the cell density of the cultures that they analysed.
Let's assume that the cultures were 10e9 cells mL-1 = 10e12 cells L-1.
According to this source (citing Neidhardt F.C. Escherichia coli and Salmonella: Cellular and Molecular Biology. Vol 1. pp. 14, ASM Press 1996), the dry weight of an E. coli cell is 2.8e-13 g
The generally accepted figure for protein as a fraction of dry weight in E. coli = 0.55
I calculate from these numbers a value of 1540 mg protein L-1. For the three protein expression levels described above this means:
GFP in BL21(DE3) = 2.4%
GFP in C41(DE3) = 9.6%
bovine OSCP in C41(DE3) = 19.4%
I conclude (from these numbers, and from personal experience) that overexpression levels are highly variable, and are going to be strain and protein-dependent. Values in the range of 1-20% total cell protein may be anticipated.

I also had a feeling that the protein concentration should be more uniform, especially for the same protein (GFP in this case). I also imagined it would not be lower than 40%.....

Well, the % estimate is clearly a little uncertain because of the assumptions that I had to make about the cultures, but the protein yields in BL21(DE3) range from 2-65 mg L-1 (and expression was undetectable in four cases). I have added a link to the paper.


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Resources for interesting facts about biology
Are there resources for interesting or fun facts about biology, for example:

fastest animal/bird/insect
largest organ in human body
largest virus
largest genome
largest de novo synthesized genome
largest protein
longest experiment done so far
most expensive experiment done so far
biggest discovery by luck
...

You get the idea. It would be nice if these is a curated "database" for all these interesting facts that might be fascinating to lay people as well.

Well I think that jarlemag's answer is pretty good and important for the community. Too bad that others can't post other sources if they stumble upon them. I actually disagree that the answer will be opinion-based, as I would expect people to provide resources, not what they would consider to be "fun or important". If you have any suggestions how to change my question to reflect this, let me know.

Whether you find the content interesting or not I can't say, but you might want to check out the BioNumbers database. It has a category for "Amazing bionumbers" and a "BioNumber of the Month" section.

That's cool! Yeah, that's what I am talking about. And this is not just for me, but for the community. So whatever I don't find interesting, I am sure others will :) Your 'BioNumbers" link is not working.


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Does yeast grow on LB agar plates?
I would like to grow E coli cells on cellophane on top of LB plate, and then grow yeast cells on the same LB plate. Does (or how well) yeast grow on LB plates? Is there a composition media that can be good for both E. coli and yeast? Has anyone done this experiment?

not sure if LB is a good medium but yeast does contaminate bacterial plates often. Fungi also grow easily. May not be the most optimal medium but nonetheless fungi seem to be quite robust.

Not well, they need  dextrose. Use YBT:
20 g Casein Peptone Tpe-M
10 g Yeast Extract
20 g Dextrose
17 g Agar
q.s. to 975 mls in di-water.
pH to 6.2 w 5M NaOH
q.s. to 1L with di-water.
Autoclave for 45 min at 121C
Aseptically dispense in Petri dishes.
Store at 4C for up to 12 weeks.
If you want to grow Co-culture do so in LB supplemented with 20g/L Dex.


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Why is PEG important for efficient yeast transformation?
One way to do an yeast transformation is by using lithium acetate, a single-stranded carrier DNA, and PEG (1). I was wondering why is the polyethylene glycol important for the efficient transformation. How does it affect the take-up of the foreign DNA? Yamakawa et al (2) showed that PEG is essential for the recovery of the cells but I couldn't access that paper to read more about it.
1. R Daniel Gietz & Robert H Schiest (2007). High-efficiency yeast transformation using the LiAc/SS carrier DNA/PEG method
2. Yamakawa, M., Hishinuma, F. and Gunge, N. (1985). Intact cell transformation of Saccharomyces cerevisiae by polyethylene glycol. Agric. Biol. Chem. 43, 869-
871.

It is more of a comment, but I can not add one due to my rep points. In addition to what others have already added, I was also told that PEG helps in stabilising the yeast cells, thereby increasing their recovery. I can not share the Nature Protocol paper from Gietz et al, but this is a book chapter from the same authors on the same topic:
https://www.researchgate.net/profile/R_Gietz/publication/11302160_Transformation_of_yeast_by_lithium_acetatesingle-stranded_carrier_DNApolyethylene_glycol_method/links/0f31753c6bfdf40dc4000000.pdf

http://www.protocol-online.org/biology-forums/posts/26634.html
I found this link - it says 'we don't really know'.  It says PEG binds DNA, I assume shielding the membrane from its negative charge and allowing internalization to happen.
I would guess that the amphipathic nature of PEG, being partly hydrophobic, also helps soften up the membrane.  Interestingly, if you increase the PEG concentration beyond the limits, it decreases the efficiency of the procedure.

I assume it has an analogous function in ligation buffers. There it apparently takes up a large proportion of the volume and thereby increases the chance of interaction between bits of DNA.
In a transformation buffer it should increase the chance of DNA getting into a cell. Unfortunately the only reference I found for this was at Bitesizebio: http://bitesizebio.com/20/5-dna-ligation-tips/


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Co-transformation of plasmids from the same incompatibility group
Can two plasmids with the same origin of replication (for example pBR322 ori) and thus from the same incompatibility group be successfully co-transformed in E. coli? What are the mechanisms that would prevent the two plasmids from co-existing together? Does it matter what is the dual resistance selection? How would the efficiency of co-transformation compare to the efficiency of a uni-transformation?

It turns out that there doesn't seem to be a specific mechanism to prevent multiple incompatible plasmids from coexisting.  Velappan et al put in more than one incompatible plasmid with different selection genes in them and put the bacteria on a single antibiotic and periodically checked for the second vector (by testing for  second antibiotic resistance).  It apparently took weeks for the second vector to disappear - many generations.
Higher copy number plasmids did better, with longer times to lose the second plasmid.  They seem to conclude that its just the natural rate of loss of plasmids that will cause the bacteria to lose the second plasmid without selection.  I imagine with two antibiotics in the culture it would take some months and you could potentially store the bacteria at -80C indefinitely.  Still in most experiments its going to be an additional headache where compatible origins of replication seem to have a more typical half life for retaining the plasmids.
They also state that the frequency of double transformations is more frequent than is usually appreciated, which seems to imply that you will get some colonies from a typical high efficiency transformation from plasmid preps.  However, they introduced the multiple plasmids by phagemid infection rather than transformation in this study.

Thanks for your answer. I actually co-transformed and I got twice as many colonies compared to a uni-transformation. I think there might me something wrong with the plates or the cells, but perhaps the co-transformation is more efficient. Which I still don't understand why would that be....

That is interesting.  I take it that both plasmids have different selection markers?


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How can I fetch nucleotide sequences based on ENA accession numbers and positions?
I have a list of ENA accession numbers and a start and end position in each sequence. In the end I want to align all those sequences, but first I have to fetch them and the list is too long to do that manually.
Is there any existing tool or script that can fetch all those entries from a database and extract the correct subset of the sequence?

Could you show us a sample of the file? What's the format like? What operating system are you using? You will probably need to download each sequence and then extract the subsequence, all of which is easy enough but the details depend on how your information is formatted and the system you are using.

I will edit this if you update your question with more information, but for the moment I am assuming you have access to a Linux/Unix system and that your file of accessions looks like this:
A00145.1 123  456

Where the first column is the accession and the next two are the start and end of the region of interest. So, using the same basic approach as WYSIWIG's answer, you can combine this with fastasubseq from the exonerate suite of tools (on Debian based systems, which include Ubuntu and Mint, you can install by runnning sudo apt-get install exonerate). Just copy/paste this into your terminal:
while read acc start end; do
  wget -q -O "$acc".fa "http://www.ebi.ac.uk/ena/data/view/$acc&display=fasta" &&
  fastasubseq "$acc".fa $start $end > $acc.$start-$end.fa
  rm "$acc".fa
done < list.txt

With the example above, this command will create a file called A00145.1.123-456.fa which contains the subsequence of A00145.1 from positions 123 to 456. Since it first needs to download the entire sequence, it also creates the temporary file A00145.1.fa which is deleted by rm "$acc".fa. If you want to keep the file, just remove the rm line.
If you can't install exonerate, you can also extract the subsequence manually but that's a bit more complex:
while read acc start end; do
 wget -q -O "$acc".fa "http://www.ebi.ac.uk/ena/data/view/$acc&display=fasta" &&
awk -v st=$start -v end=$end '{
                               if($1~/>/){print}else{s=s$0}}END{print substr(s,st,end)
                          }'  $acc.fa |
 fold -w 60 > "$acc.$start-$end.fa" && rm "$acc".fa
done < list.txt

I think explaining these scriptlets in detail is not in scope here but I'd be happy to do so if you post a question over on unix & linux.

From ENA

To retrieve results by a single identifier for all records other than
  Taxon and Project please, use the following URL syntax:
http://www.ebi.ac.uk/ena/data/view/
For example, the following URL returns the EMBL-Bank entry with
  accession number A00145 in HTML format:
  http://www.ebi.ac.uk/ena/data/view/A00145

Check this.
If you use a *nix system (such as Linux, Unix, or OSX) then you can do this:
[ if list.txt contains all your ids ]
for i in `cat list.txt`; do wget -q -O $i".fa" "http://www.ebi.ac.uk/ena/data/view/"$i"&display=fasta"; done

OR ELSE
Download the entire database and pick up sequences based on your identifiers, offline. You can use your favourite programming language to retrieve sequences. [I prefer awk but python is also good]


text:
Have there been any positive public health effects due to UV lights?
Occasionally, in hospitals and in eating establishments in the US, they have industrial grade UV lights in sconces attached to the wall (though they seem to be less prominent as the years go by).  I understand the anti-microbial properties of UV light, but are these devices anything more than show pieces?
Have there been any lasting, significant public health gains that have been correlated with the use of UV light in public places?

Regarding UV lights attached to walls going out of fashion - I'm seeing them more and more over washbasins used on wards, particularly on specialist units.

There have been some studies regarding the use of intensive UV light installations in surgical wards or other settings as a anti-microbial tool. Generally speaking, these are part of a general interest in non-cleaning based anti-microbials in hospitals, such as UV light, O3-based machines, and copper/silver coated surfaces.
The answer to your question will depend on what you consider "lasting" and "significant". They're a relatively new technology, and haven't had a huge penetration into the market yet, so the only evidence you're likely to find is hospital-sized non-randomized trials.
So basically, the answer to your question, as I read it, is "No, but..."
There hasn't been an opportunity for these technologies to show any sort of lasting, significant reduction in hospital acquired infections. But there is some promise that these types of technologies, and those like them, may help reduce the burden of infections when they're used appropriately. The current state of research is figuring out just how workable they are, how to best use them, and what they can and cannot be expected to do. That kind of evaluation is actually what I'm doing as part of my dissertation work, though my focus is on the general concept, rather than a specific device.


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What is the difference between naive and adjusted p-values in a GWAS study?
What is the difference between a naive p-value and an adjusted p-value in the results of a GWAS study? See from this paper:

After Bonferroni adjustment, a single gene, DCTN4 (encoding dynactin 4) on chromosome 5q33.1, was significantly associated with time to chronic P. aeruginosa infection (naïve P = 2.2 × 10−6; adjusted P = 0.025; Supplementary Fig. 1).

Why did they even report it? Because the adjusted isn’t below their significance level? Well, tough luck!

Agree, including the unadjusted p-value is just waving around a big red herring.

Hummm, do you think they included the unadjusted p-value because the adjusted p-value is not very good?

No idea. For the normal 5% threshold, the adjusted p-value is actually still significant. I’ve seen several times that an unadjusted p-value was reported in papers without any explanation why that was done. Maybe the researchers just report what the software gives them without questioning whether it makes sense.

I suspect one of the reasons to report the unadjusted value is, as I allude to in my answer, many papers are now simply using a non-0.05 cutoff point instead of using some sort of multiple comparisons adjustment (which have their own issues). The unadjusted answer allows for comparison with those studies - I don't actually think its a red herring.

There’s an XKCD comic which explains the problem. Unfortunately, that comic is too big to post here. Briefly, a p-value of 0.1 says (roughly) that there’s a 10% chance (0.1) of the observed result being as extreme1 as it is simply due to chance (sampling variation from a population), assuming the null hypothesis is true.
Often, 5% is more or less arbitrarily chosen as “cut-off”: results with p-values below that (which occur by chance 1 time out of 20) are called significant – results above are insignificant.
However, this directly implies that when doing multiple studies, say 20, there’s a very high chance of getting a “significant” result by pure chance, without there being a real effect.
GWAS studies essentially perform experiments on many (hundreds or thousands) of factors simultaneously. Therefore, reporting the pure p-values would be very misleading since there would be a lot of spurious results with “significant” p-values. The probability of getting one or more spurious hits is called the familywise error rate (FWER).
The FWER can be reduced by adjusting the p values, for instance by performing the Bonferroni correction. The resulting p-values are quite a bit higher, which reflects the reduced certainty that the result is due to chance, i.e. the reduced significance.
It doesn’t generally make sense to report the unadjusted p-value. It was probably reported here because correcting for FWER is quite conservative (i.e. it trades a low false-positive rate for an increased false-negative rate) and the authors feared that the adjusted p-value looked less impressive than it should. This involves a fair bit of interpretation.

1 extreme = different from the expected result under the null hypothesis

I would have liked to +2 this: +1 for an excellent, precise answer and +1 for xkcdification.

I'd argue this actually belongs on CrossValidated.
Essentially, the problem is one of how a GWAS study is conducted. By looking over an entire genome for associations, you're actually conducting thousands or millions of experiments, not the single experiment most statistics were designed to handle. As such, you're going to find many results that meet the traditional threshold for "significance" purely by chance.
Early genomics studies had this problem - they'd generate tons of false-positives, and because of the numbers involved, their very small p-values would give an incorrect perception of the precision of their results. One way to handle this is to adjust for multiple comparisons to essentially penalize the p-value to enable you to still use the p < 0.05 threshold.
Another very common choice is to recognize that 0.05 is something of an arbitrary boundary, and simply choose a much, much stricter criteria for significance. This is, as far as I'm aware, what most state of the art GWAS epidemiology studies do.

Indeed. Bonferroni p-value correction simply divides the desired confidence (usually 95%: 0.05) by the number of independent tests performed - this gives you an adjusted 95% cut-off for significance. Alternatively, the Benjamini-Hochberg method actually adjusts the individual p-values after you have performed all your tests (see the "False discovery rate" wiki http://en.wikipedia.org/wiki/False_discovery_rate)


text:
Modularity of transcription factors
I attended a seminar about neurogenesis that presented results for PAX6 as an important TF that contains 3 domains with very distinct patterns of downstream expression. The speaker ended up saying that PAX6 can be considered as 3 TFs in one protein, acting independently in different situations:
Relative roles of the different Pax6 domains for pancreatic alpha cell development
Does anybody know of more examples like this?

interesting - I have heard of 'generic' transcription factors that act on many genes via common sequence motifs (the CCAAT-enhancer-binding-proteins, for instance), but not factors that actually have different motifs with different downstream effects. I'm also interested in this.

The NF-κB family of transcription factors is very modular, with different combinations having different effects. The active (nuclear, DNA-bound) TF is a dimer, composed variously of RelA/p65, RelB, c-rel, NFKB1/p50, and/or NFKB2/p52 subunits. For example, the "canonical" p65/p50 dimer is activated in response to stimulants like TNF-α (tumor necrosis factor alpha, released in response to inflammatory signals like the presence of pathogens) and LPS (lipopolysaccharide from the cell walls of Gram-negative bacteria), while the RelB/p52 dimer plays an important role in the development of B cells (the immune system component that produces antibodies). The AP-1 transcription factor is also heterodimeric, containing proteins from the Jun, Fos, JDP, and ATF families, and there are numerous other examples of multimeric transcription factor complexes. This recent article in Nature Immunology (disclaimer: I was not involved in that research, but my old lab did similar work) shows DNA sequence-specific binding by different NF-κB dimers.
Polymerism in general, and dimerism in particular, are quite common modes of transcriptional activation and regulation. The large number of ways in which a relatively small number of transcription factors can be combined allows for the exquisite control of genes, responding to a huge variety of cellular situations. Unfortunately, it also means that mutations in key, common components can result in transformation, unrestricted growth, and the generation of tumors.

There was a paper published in Cell last year that has shown that the binding motif of a Hox transcription factor will change depending on whether there's a co-factor bound to the Hox.

Slattery et al. (2011) Cofactor Binding Evokes Latent Differences in DNA Binding Specificity between Hox Proteins. Cell, 147(6) 1270-1282. doi: 10.1016/j.cell.2011.10.053 (pdf)


text:
Can the excessive consumption of mineral water lead to kidney stones or other health issues?
I heard that drinking too much mineral (bottled) water could lead to problems such as kidney stones because of the high amount of minerals in it. Is it true? If so, what is considered to be excessive?

I suffer from calcium oxalate stones.  My doctor pointed me to this study:
http://www.ncbi.nlm.nih.gov/pubmed/9096270
tl;dr;  For calcium oxalate, drinking Mineral Water high in Calcium and Magnesium may reduce the risk of forming stones.

It is unlikely that drinking too much mineral water will cause kidney stones. One of the chief causes of kidney stones is dehydration. I can't imagine the calcium content of mineral water could be that high as to cause kidney stones (please correct me if I'm wrong) unless you drink ridiculous amount by which stage you will probably start to have electrolyte abnormalities and perhaps seizures.
Consumption of excessive amount of water can cause various health issues (even life threatening). These include seizures, rhythm disturbances in the heart (all usually secondary to acute electrolyte imbalance in the blood).
I've never come across drinking too much mineral water as a cause for kidney stones-most people who get kidney stones usually aren't drinking enough water. The more water you take (in moderation), the less the likelihood for stone formation in your kidneys.


text:
Why don't individuals with sickle cell trait suffer from sickle cell anemia?
Ostensibly, in people with sickle cell trait, half of the hemoglobin in their body would be defective.
Is it actually the case that sickle cell hemoglobin is produced in equal amounts?
If not, how is that regulated? If so, how does that still not cause anemia?

This could be a very long answer, but I'll try to keep it brief.
The first thing to understand is what causes the anaemia. I'm going to refer to defective haemoglobin found in a sickle cell patient as HbS and normal haemoglobin as HbA. Under certain circumstances (low O2 concentrations) the HbS protein is prone to aggregating into long filaments. Here is an image of a lysed erythrocyte releasing some of these filaments.

The presence of these filaments in the erythrocytes causes them to become misshapen (sickle-shaped) and this in turn causes them to get filtered out for destruction in the spleen which is continuously monitoring for defective erythrocytes (which could cause blockages in the circulation). This causes the anaemia (specifically a haemolytic anaemia, due to erythrocyte destruction, and nothing to do with a lack of iron).
The appearance of the ability to form filaments is due to a single Glu>Val mutation in the two β subunits of the haemoglobin tetramer. The new amino acid can fit into a pre-existing hydrophobic pocket on the surface of another subunit and so the molecules can daisy-chain to form the filaments.
The normal HbA can also bind on to a growing filament (it has the binding pocket) but that terminates the filament (because HbA doesn't have the Val residue). In this way people with sickle cell trait are protected from the anaemia by their normal haemoglobin.


text:
Is there a difference between pig and cow anatomy that makes religious slaughter of the latter less painful?
This question is not for the squeamish. I was told that non-Kosher animals like pigs have a different anatomy in their neck compared to kosher animals like cows such that the Shechita method of religious slaughter (a very sharp knife held on the neck only by the weight of gravity rapidly going back and forth in a single cut that drains blood and results in an "instant" drop in blood pressure in the brain), while causing pain in the non-Kosher animals, doesn't cause pain in the Kosher animals. Is there such an anatomical difference and thus difference in pain?
(If this would be more on-topic at Skeptics.SE, let me know.)

This could be extended as well to other religions, such as Islamic dhabīḥah

@nico Possibly. That's how I had an earlier version of this question before I edited it. But the original claim was in context of Kosher/shechita and I'm not familiar enough to know if there's a practical difference with the Islamic method.

Difference between kosher and non-kosher animals
Rabbi Zamir Cohen, in his book The Coming Revolution - Science Discovers the Truths of the Bible, quotes modern day scientists that have made an incredible discovery of a major difference in the way the blood flows in the species that are kosher and those that are not. In non-kosher mammals, the vertebral arteries flow directly to the brain through the rete mirabile. However, in cloven-hoofed, cud-chewing mammals and permitted foul, the vertebral arteries drain into the carotid artery and do not have any direct flow to the brain. There will therefore be an immediate drop in blood pressure at the time of shechita that causes the animal to lose consciousness, thus feeling no pain.

It was my understanding that the vertebral arteries bring blood to the brain even in cattle, and are not severed, and keep them conscious far longer than any kosher bird. Do you have a source other than a rabbi?

The technical details on this are a bit muddled. The wording "drains into" doesn't seem to fit with what an artery does. Could we get a more biologically precise description of what is alleged to be happening here?


text:
Do fish break a water molecule to absorb oxygen?
How do fish separate oxygen from H20 & consume it? Do they break the water molecule and absorb  the oxygen only?

The answer to this, I reckon, is that they don't.
They use molecular oxygen (O2) dissolved in the water for respiration, where it acts as a terminal electron acceptor, just as we use molecular oxygen in the air for respiration. We can speak of the water as being oxygenated.
Water is split in photosynthesis, where reducing equivalents from water are used to reduce NADP+ (giving NADPH).
One of the great discoveries of biology, IMO, is that the oxygen formed in green-plant photosynthesis comes from water, not CO2.
Tricarboxylic Acid Cycle (Krebs Cycle) Rant
Despite claims to the contrary, most infamously by Racker (1976, pp 28 - 29) and Wieser (1980), but also by Madeira (1988) and Mego (1986) for example, water is not split in the tricarboxylic acid cycle (Krebs Cycle). Banfalvi (1991) also sails pretty close to the wind on this one.
That is, reducing equivalents from water are not passed down the respiratory chain, or in any way used to make ATP, or are in any way a 'source' of free energy.  Such claims, IMO, are nonsense.
The definitive answers to the Wieser (1980) paper are given by Atkinson (1981) and Herreros & Garcia-Sancho (1981). Both of these articles are models of clarity, and categorically refute the claims of Wieser (1980).  Nevertheless, as shown by the references above, the controversy surfaces periodically.
The only sources of reducing equivalents in the TCA cycle are carbon compounds, and the only electrons passed down the respiratory chain are those 'held' in C-H and C-C bonds (Herreros & Garcia-Sancho, 1981).  An ionization is neither an oxidation nor a reduction (see Atkinson, 1981) and neither is a hydration. Adding water to (say) a double bond does not make the compound any more oxidized or reduced.  As far as oxygen and electrons are concerned, and to generalize from a biological point of view, what is has it holds - except in photosynthesis.
As you may have guessed, the splitting of the water in the TCA cycle is a pet rant of mine.  Thanks for the opportunity of airing my views!
Edit 3
Found this one when searching Google (Brière et al, 2006).  In an invited review for the American Journal of Physiology (Cell Physiology) at that!

Finally, TCA cycle should also be considered as a water-splitting process generating oxygen for acetyl-CoA oxidation [they quote Wieser]

So now the TCA cycle is producing oxygen from water.  Wonders will never cease!
(end edit)
(end rant)
Edit 2
As rwst and Alan Boyd have drawn attention to, the concentration of dissolved oxygen in water is all important, and varies with (for example) temperature.
In air-saturated buffer at 25oC the concentration of oxygen (O2 molecules) is about 0.24 mM (0.24 μmoles/ml, or about 0.474 μg-atoms of oxygen per ml). [Chappell (1964)]. This figure decreases with increasing temperature.
Great question, BTW.
References
(Apologies for the incomplete Atkinson and Herreros & Garcia-Sancho references. I have a photocopy of these papers but have been unable to trace the full source. They are both in the 'Letters to the Editor' section of the February 1981 edition of Trends in Biochemical Sciences. They do not appear to be in Pubmed, or anywhere else on-line.  Has anyone ever seen these references quoted, or can provide me with a full source?.  I'll update if I find anything)

Atkinson, D.E. (1981) TCA Cycle Confusion.  Trends in Biochemical Sciences (February 1981 edition; full ref to follow)
Banfalvi,G. (1991)  Conversion of Oxidative Energy to Reductive Power in the Citrate Cycle. Biochemical Education, 19, 24 - 26  [see here] (pdf apparently free to all)
Brière, J.J., Favier, J, Gimenez-Roqueplo, A.P. & Rustin, P (2006) Tricarboxylic acid cycle dysfunction as a cause of human diseases and tumor formation.  Am J Physiol Cell Physiol, 291, C1114-20. [Pubmed]  [pdf]
Chappell (1964) The oxidation of citrate, isocitrate and cis-aconitate by isolated mitochondria. Biochem J., 90, 225-237.[pubmed]  [pdf]
Herreros, B. & Garcia-Sancho, J. (1981) TCA Cycle Confusion.  Trends in Biochemical Sciences (February 1981 edition; full ref to follow)
Madeira, V.M.C. (1988) Stoichiometry of Reducing Equivalents and Splitting
of Water in the Citric Acid Cycle.  Biochemical Education 16, 94 - 96 [pdf] (apparently free to all.)
Mego, J.L. (1986)  The Role of Water in Glycolysis Biochemical Education,  14, 130 - 131. (see here)
Racker, E. (1976) A New Look at Mechanisms in Bioenergetics.  Academic Press, New York.
Wieser (1980) Textbook Errrors: The splitting of water by the tricarboxylic acid cycle.  Textbook error or textbook omission? Trends in Biochemical Sciences, 5 (Issue 11), 284. [see here].  [pdf], apparently free to all.

Edit 4
I have not been able to locate the exact reference for the incomplete Atkinson and Herreros & Garcia-Sancho references cited above but, in response to this great question, I have put a copy of a very bad scanned version here
Another great reference to this controversy which I should have quoted is the
following:

Losada, Manuel
. (1978) Energy-Transducing Redox Systems and the Mechanism of Oxidative Phosphorylation. Bioelectrochemistry and Bioenergetics, 5, 296-310 [Science Direct].

The following is the relevant section, for those who do not have access:

A more complete version of the Racker reference quoted above by Losada (1978):
However, pyruvate has only 4 hydrogens to donate to 2 oxygens and with a P:O ratio of 3 should therefore yield only 6 molecules of ATP (Table 1.2). Where are the other 6 hydrogens coming from so that 15 ATP can be formed? The answer to this question gives us what I think is the key to the puzzle why nature has designed the complex acrobatic scheme of the Krebs cycle. Its major purpose I believe is to increase the energy yield by catalyzing cleavage of water.
There are three steps at which water enter the Krebs cycle. - one at the transformation of fumarate to malate an the other two somewhat more indirectly during the utilization of acetyl-CoA and succinyl-CoA. In the course of the Krebs cycle the hydrogens of these water molecules are separated from oxygen and are donated to DPN or to a flavoprotein (e.g., succinate dehydrogenase) and then transported via the oxidation chain of mitochondria as electrons and protons as we shall discuss later.
[Racker, E. (1976).  A New Look at Mechanisms of Bioenergetics, pp 5-6, Academic Press].
IMO, the last sentence of this quote is complete rubbish. (For DPN, read NAD. DPN, or diphospo-pyridine-nucleotide (or something close), is an old name for NAD)

It would also be worth noting that if the fish absorbed ONLY the oxygen, then all of the H2 would be racing out of solution in a gas before entering the atmosphere, implying that the water breathed by fish would eventually run out. :-)

Yes, and to emphasize it: gases can be dissolved in liquids like salts. They escape when the liquid is getting hotter (water bubbles when boiling) or when you put sugar into soda water, for example

@MCM, & rwst.  Yes, very good points.  I'll incorporate later, but feel free to edit

In the Antarctic Ocean the temperature of seawater can fall as low as -1.9 C. Because of the resulting high levels of dissolved oxygen in Antarctic seawater, fish of the family Channichthyidae (icefish) can survive without hemoglobin, relying entirely upon oxygen dissolved in plasma. They have numerous physiological adaptations which increase blood volume and blood flow to support their low metabolic rate.

@TomD This answer is a little research paper in itself. Thanks for taking the time in compiling such a comprehensive reply!!

Great answer (+1), but remove 'I reckon' from the first line; this isn't just a personal opinion!

so your answer could begin with "no, they don't break the water molecule plants do, fish don't"?

authors: ʇolɐǝz ǝɥʇ qoq


text:
When giving blood, what is the specific Iron measurement they take?
I went to give blood the other day, and they take an "iron" measurement prior to actually drawing the blood. My level was 16.4 -- but what specific type of iron were they measuring?
I've heard of ferritin, transferrin, iron binding cap, total, etc., but when I asked what the upper limit was, she said 19, which didn't really fit within the healthy ranges I can find for the above types.
Thoughts?

Most likely they were measuring the hemoglobin concentration, in units of g/dL (i.e. 101 kg/m3). Assuming by your username you are male, the reference range for [Hb] is approximately 13.8 to 18.0 g/dL (sources vary somewhat), which roughly matches the "19" you were told was the upper bound.
Wikipedia also notes that [Hb] "is typically tested before or after blood donation", making it likely that that was what they measured.
Calling it "iron" isn't strictly correct. The human Hb tetramer's molecular weight is about 65 kDa, yet it contains only 4 iron atoms, so the actual concentration of iron in your blood is actually much less.
Useful resource: Wikipedia's list of reference ranges for blood tests has a very detailed chart of commonly cited reference ranges for many substances, with citations.


text:
Is there a gene that starts meiosis 2?
Yesterday I thought about a question and asked it to my friend.  The question was
which gene is completely the same for a male cell that made meiosis 1 recently.
My answer was the gene that starts meiosis 2, but he said he thought that there is no such gene - only a gene to start meiosis and meiosis 1 and 2 are just parts that scientists named.
My question is is there any gene that starts meiosis 2?


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SPINAL CORD: Do the axons from white matter synapse with the cell bodies in grey matter?
After wading through a sea of information, I understand the main differences between the white matter and grey matter of the spinal cord.
I know that white matter contains myelinated axons in the ascending and descending nerve tracts from the brain to the spinal cord. I know that grey matter contains somata which contribute to sensory and motor functions from and to the peripheral nerve fibers.
With the differences in mind, I am confused about the relationship between the two.
The main question being: What signaling, if any, takes place between the myelinated axons of white matter and the somata of grey matter? More pointedly, do the myelinated axons from the nerve tracts in white matter ever synapse with dendrites from somata in grey matter?
My guess is yes, that this is a key aspect in how the brain and the spinal cord communicate. But I haven’t yet found any definitive source that addresses this question directly.

This is kind of a big question, as there are lots of different pathways that synapse at different levels and some of the cell bodies send axons over long distances.  Is there a particular tract that you are interested in?

I am studying Excercise Physiology, for the purposes of personal training, from that vantage point I am trying to solidify a big picture understanding mostly. So no i don't have to know the nitty gritty of a particular tract, my texts and resources have illustrated the big differences between the white and grey matter and thier main functions but do not really address what if any signaling takes place between each other. I was guessing and take it from your answer they do. Is there a typical pattern or does each pathway feature a unique setup between the white and grey matter?

That should give you a start.  You can read up on these and some of the other tracts and see if you have specific questions on them.

Here is a great diagram (from here) that outlines all of the different white matter tracts running up (blue) and down (red) the cord.

The portion in the center, as you have found in your research, is the gray matter.  In there are the different interneurons (cells that exist in the network to integrate information from descending controls and do further processing on it) and all of the different motor neurons.  The corticospinal tract descends to the appropriate level (for example, a neuron in charge of moving your arm, to keep it simple, will have a cell body in the brain, and descend to the thoracic level), enters into the gray matter and either synapse on an interneuron or directly onto a motor neuron).
The sensory neurons are a slightly different animal.  Some (pseudo-unipolar cells) have what are basically two "legs", one that runs out into the periphery, which will take the signal from something like a Pacinian corpuscle in the skin, propagates a signal to the cell body, which is outside of the spinal cord in the dorsal root (see below), and the other "leg" runs all the way up the dorsal column into the medulla of the brainstem.

from here
So that should give you some idea of the two major tracts.  To see some of the finer detail, you can look into the different layers (laminae) that the gray matter is composed of, so that you can trace the connections all the way in.


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Why do we squint?
Recently, I was having an eye exam and admitted to squinting my eyes to sharpen blurred edges. Later, while waiting for the dilation to set in, my brother (a would-be pharmacist fresh off an anatomy course) was telling me about how vision works.
As a non-scientist, here's as much as I gathered:

The pupil allows light into our eyes.
The lens bends and shifts to focus that light against our retina.
The retina translates this light-information into signals via the optic nerve.
Something about brains, and then sight!

So, my question is, if the lens being bent and shifted inside of our eye by muscles is how our eyes focus, why do those of us with poor vision squint? Surely it can't be that by narrowing my field of vision I'm consciously bending my lens.

When I was younger (before I got glasses), I sometimes used to pinch four fingers together to make a tiny square hole and look through it. Same principle as squinting; you decrease the aperture size.

Actually it's a bit physics and biology,
It works, all right. In fact, the word "myopia" (near-sightedness) comes from the Greek words myein (shut) and ops (eye). When you squint, it's like reducing the aperture of a camera lens: You reduce the diameter of your visual lens. This gives you a longer depth of focus.
Shortly you can say, Yes by squinting your eyes you actually bends the eye lens with the help of Ciliary Muscles present in your eyes which reduce it's focal length and helps you to see with a better vision


text:
What are the different ways an exon gets spliced?
Exons are produced by more than one mechanism, e.g. splicing out introns after transcription, if I remember correctly. Please list all mechanisms.

When voting to close a question please take the time to explain your reasoning in a comment, particularly if you are the first to cast a vote :)

Is this homework?

Exons are not "produced" by splicing. What exactly are you asking here?

There are several ways splicing can occur, which depends on the RNA molecule to be spliced and the catalyst that performs the splicing:

mRNA splicing is carried out by spliceosome, which consists of small nuclear RNAs. There are sequences at the end of the introns and branch sties which indicate the splice sites. The so called lariat structure is formed when the 2'OH group of an adenosine residue in the branch site attacks the 5' splice site.
self-splicing of ribosomal RNA precursor - it is performed with the absence of spliceosome.
tRNA splicing - it requires three enzymes and ATP hydrolysis.

References:
Biochemistry, L. Stryer, 5th eddition
J. Abelson. tRNA Splicing


text:
What is a cortical circuit?
I have read about cortical circuits in the context of connectomics (e.g. any example here) and computational neuroscience (e.g. any example here), but a simple Google/Wikipedia does search not show an exact definition.
What exactly is a cortical circuit?

Could you maybe give an example of one or two places where you read about them?

I may be simplifying this, but I think it's just a fancy schmancy way of referring to the electrical "circuits" found in the brain, in this case the cortex (overall, or more specifically motor, visual, etc., as the case may be).  Connectomics tries to map the connections between neurons, mainly in the brain, building what is, in some sense, a circuit.  For some sentences in context:
http://www.jneurosci.org/content/32/31/10562.short

These results indicate a tight correlation between the effects of sensory drive and maturation on cortical neurons and provide a new set of cellular mechanisms engaged in the postnatal refinement of cortical circuits.

http://www.jneurosci.org/content/32/32/10982.short

...spontaneous cortical activity provides a recurring template of functional cortical circuits within the developing cortex and could contribute to the maturation of integrative connections between sensory and motor cortices.

+1 as it is correct, although I don't really see how it is fancy... a series of cortical neurons connected between each other forms a cortical circuit. Doesn't seem too fancy to me :P

Thanks Amory and @Nico. So does the term "cortical circuits" refer to circuits found anywhere in the brain, or in a specific place?

"the cortex (overall, or more specifically motor, visual, etc., as the case may be" I meant to imply that "cortical circuit" appears to broadly refer to the cortex, but there are instances of more specific uses.  Visual cortex circuits, motor circuits, etc.

@user815423426: In general you can speak of a "circuit of neurons" anywhere in the brain. For instance you can talk about hypothalamic feeding circuits, in reference to the circuit of neurons controlling feeding in the hypothalamus (a region at the base of the brain).

Thanks nico. I think I understand that "circuit of neurons" refers to circuits anywhere in the brain, my question was more about "cortical circuits. I guess that refers to circuits within the neural cortex (grey matter), probably excluding circuits in the white matter. Is that correct?

@user815423426: I don't think a distinction between white and gray matter is really necessary in this case. The fibers that compose the white matter come from neurons, so they can still be part of a circuit. "Cortex" refers to the outer layer of the brain, which is connected to many other parts of the brain (for instance connections between neurons in the cortex and neurons in the thalamus will form cortico-thalamic circuits, and so on). Of course you can also have purely cortical circuits (i.e. connection of neurons in the cortex between each other)

The term "cortical circuit" refers to the generalization that the neocortex is a uniform structure. For the most part, the outer sheet of the brain (the neocortex) is the same structure of neurons all the way around the brain.  It consists of the canonical six layers and it generally looks something like this.  Different research will emphasize different aspects of the circuit.
Anyway, it's quite an interesting evolutionary step for mammals.  The neocortex.. or "associative cortex" as it's sometimes called... is a very dexterous structure.  Someone born without sight will still make use of their occipital lobe to process nonvisual sensations.
Of course, as a I qualified above, it's not strictly true that the neocortex is uniform all the way around; there are exceptions.


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Cell growth conditions for preparing electrocompetent cells
Usually the protocol for preparing electrocompetent E. coli cells calls for growing the cells at 37deg and 225rpms until they reach OD of 0.3. I was wondering, is there any reason they should grow at optimal conditions for growth, instead of at suboptimal, for example at 30 degrees? Also, what is the physiological/epigenetic difference between a culture of OD 0.2 vs 03. vs 0.3?

I don't know for sure, so I won't post as a formal answer, but my guess is that you want to maximize cell health and viability. Transformation of electro competent cells kills a lot of them, and you want to maximize the chance some of them survive.

I'm new so I can't make this a comment, and I don't think the other commenter addressed your questions so here it goes: I don't think there will be much difference, if any, between 0.2 and 0.3 OD. Once you get higher and the cells start transitioning into a stationary phase is a different story. Did you mean to ask about 0.03 OD as well (you wrote 03.)? I'm not an expert in E. Coli, but they would probably be less likely to produce proteins that are contact inhibited. Sub-optimal temperatures may have a minor effect on growth, but I don't believe this will initiate much change or induce production of large amounts of cold shock proteins.

I did electroporation of E.coli before using common protocol "growth at 37oc until OD 0.4-0.6, and pellet cell and dowstream works at cold condition". Recently, some publications gave different protocols with much higher efficiency. Briefly, (i) they growth E.coli at 18oC and did the same procedure; or (ii) they growth E.coli at 37oC and pellet cell, transformed at 24oC..
The references tittles are shown: "Growth of E.coli at low temperature dramatically increases the transformation frequency by electroporation" and "Room temperature electrocompetent bacterial cells improve DNA transformation and recombineering efficiency"
You may try and find out protocol suited to your works.

Welcome & thanks for your answer. Can you add those references?


text:
T7 promoter leakiness
Can a gene be expressed under the T7 promoter in an E. coli strain (e.g. DH5 alpha), which does not have the T7 polymerase gene encoded in its genome? In other words, is T7 promoter leaky?
To be more specific, how is it possible that a regular E. coli strain, which does not encode for the T7 polymerase, can grow on kan selective media if it was transformed with a plasmid that has the kanR gene under T7 promoter?

I know I'm digging this up, mostly b/c I'm running into some T7 issues, but if you are referring to a specific experience, are you sure plasmid has the kan resistance under T7 promotion, not just the insert?

Apparently not, leakiness can be controlled by tightly regulating the T7 polymerase with a tight promoter (in this case lacUV5).

Isn't it possible that a regular E. coli strain that does not have T7 polymerase, has other polymerases that can recognize the T7 promoter?

The reference points to BL21.  I took a look at the MG1655 genome to see how many copies of the alpha I or II subunit, which with sigma subunits, defines the sequence specific binding affinity of the native polymerase.  That should reveal any variations in the RNA polymerase binding. There is only a single copy of RNA polymerase alpha (which along wg of RNA Polymerase).  Its hard to say that something like this is impossible.  Its true that DH5alpha isn't a B or K12 derivative I think, so its always possible, but there is not rnap component mentioned in the strain description.

@GerganaVandova I've been thinking about this, and it seems to me that phage gene transfers might be relatively rare in bacteria because their genomes have so much genetic flux.  a new polymerase would not affect any of the native genes - it would require quite a few mutations for a second polymerase to take hold in the genome given how trim bacteria tend to make themselves.


text:
What is the tRNA gene copy variation between different yeast strains?
I just started working on predicting steady-state protein levels from different codon usage bias measures. I have whole-genome sequences (it's NGS data) from different strains of S. cerevisiae and S. paradoxus and I began to wonder if it's possible that different strains of the same species could have different copy numbers of tRNA genes? If so, would this be detectable in the sequencing data (presumably the reads were mapped onto a reference genome so maybe this copy number variation would be lost)?

What type of sequencing data do you have? Are we talking about RNA-seq or DNA?

I would reask this question on BioStar. They may have better ideas than we mere experimentalists.

I'd take that computational angle and run the sequence data through tRNAscan-SE (Lowe & Eddy, Nucl Acids Res 25: 955-964). Ideally, you'd install this locally. This tool is what the UCSC folks use and it has been the best known, most widely used tRNA predictor for years. It's what we all used on Arabidopsis thaliana genome annotation back in the late 1990's.
There is also a genomic tRNA database that may have many of the predictions you seek, at least for some of your species/strains.

I don't think this will work since it's NGS data assembled against a reference genome. In fact I ran tRNAscan-SE and all strains have exactly the same tRNA GCN as the reference strains but this is a consequence of the assembly process.

It sounds like you should try a De Novo assembly. That might be tricky since you don't have any paired-end data but that might be able to discover any novel contigs.

I like @bobthejoe 's suggestion. I never intended that tRNAscan-SE would be run against an assembled genome. Depending on the size of your reads vs. the size of a typical tRNA gene, you may be able to input the reads themselves into tRNAscan-SE. If coverage of each genome is deep enough, try that de novo ass0embly. Also run the unassembled reads from each strain through tRANscan-SE - perhaps these are indeed those extra copies of the tRNA genes you're searching. Lastly, are there any gaps in an assembly where known tRNA genes are? I still think my suggestion would work.

I don't think the coverage is deep enough (1-4x) for de novo assembly but I'll try running tRNAscan-SE on the unassembled reads and maybe try to see if there's a difference in coverage of some tRNA genes which would suggest that duplicated genes have been mapped on the same locus.

I would use an RNA microarray to look at those difference instead of sequencing. To delicately amplify your tRNAs in an unbiased manner would be a tricky molecular biology endeavor. I wouldn't be surprised if there were detectable and significant differences. Those experiments will be able to confirm your hypotheses regarding codon usage bias.

The data I have is for over forty Sc strains so it wouldn't be possible to do those experiments within my timeframe/budget. I'm limited to computational approaches and my best guess was that some copy number variation detection algorithm could be applied to the raw read data.


text:
How old does a baby have to be before it can retain memories?
For most people (my earliest memories are of perhaps when I was 2 or so) their earliest memories would be when they were over a year old.
How old does the average baby have to be before it can retain memories?
Are there any preconditions that need to be fulfilled?

I wish I had the time to do some research and give you a proper answer with references, but exams... As far as I know, the brain starts working completely even before birth (including memory function - think about it, a newborn remembers who its parents are), and you can't remember anything from before aorund age 3 because of radical rearrangements while shaping personality. If nobody answers in two weeks, I'll get back to you ;)

I'll wait. What you mentioned there about the brain working completely even before birth was where I was headed myself - Why do we seem to remember nothing from our period as a foetus? My guess was that it is a sterile environment - nothing new ever happens. Anyway, regardless of whether anybody else replies, please do post your thoughts after the exams. All the best for them!

Surely an important question. But there are different kinds of memory (classified mainly as declarative and procedural) which you don't specify exactly in your question. Wikipedia and Scholarpedia list here many known facts. I will give you some short hints and links for introduction and overview instead of pasting that stuff here.
You are probably referring to autobiographical or episodic memory, that is memorizing consciously particular events within one's own life within a context. And for this type of memory researchers agree that self-awareness seems to be a necessary precondition. The existence of this cognitive ability can be checked by the mirror test. Human infants pass this test normally around a age of 18 months (also some animals). The cognitive self develops between 21 and 24 months and marks the end of infantile amnesia.

I did indeed mean episodic/autobiographic memory, albeit the terms were not in my dictionary earlier. During the period between birth to when this self-awareness is exhibited, would it be fair to state the baby still acquires knowledge ? E.g. Self/body control (movement of limbs), cause-and-effect (crying to convey discomfort) etc. At some point such knowledge as is already acquired triggers (for want of a more appropriate word) self-awareness?

This seems like a funny interpretation to me: if self-awareness is a precondition, we're forced to conclude that many animals never retain memories (e.g. dogs). Under one definition of memory this may be true, but as I read the question it's not the definition the OP is working with.

@Everyone Your further questions are answered in the first paragraphs of the given link http://en.wikipedia.org/wiki/Memory_development, e.g. recognizing mother voice or language acquisition. What triggers self-awareness is one of the trickiest questions in science, you should open another question for this.


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Could Junk DNA be used as a Turing Machine by nature?
In what ways has DNA been studied to see if there a "programmable" aspect to it?
Has nature produced anything resembling a Turing machine within the cell, perhaps using the "junk DNA" as its code? I expect nature's way would probably be very round-about and not compact.
NOTE: I am not asking about building DNA computers, as this question had recently been contorted to become.

What evolutionary disadvantage would it give if it did not encode for anything? (not saying it doesn't, I am just not a fan of the "Nature must have thought of xyz in all these years" questions)

@nico If it didn’t code or regulate, it would be garbage which the cells have to drag around with them. More expensive to replicate and maintain, more material cost (just because it’s longer and requires more material to form), requires more space in the cell. There are evolutionary disadvantages to having a large, partly non-functional genome.

@Konrad: one could argue, however, that our body is all but efficient, and has plenty of redundant mechanisms. That said, it is known that certain mutations on ncDNA can have visible effects so, as I was saying, it may have a function, and it probably does, but from there to saying it encodes for some sort of Turing machine...

@nico Redundancy is required for a fail-safe system, it provides a direct evolutionary advantage. And while our bodies aren’t particularly efficient in many aspects that cannot be controlled by evolution (laryngeal nerve …), most isolated systems under evolutionary control have been highly optimised. For instance, a eukaryotic cell’s energy turnover is orders of magnitude more efficient than any engine or generator ever created by humans (intelligently designed).

@Konrad Rudolph: sure, but cells are far from being 100% efficient. An interesting book that touches the subject of how our brain is inefficiently built, for instance, is "The accidental mind" by David J Linden. But I am digressing. My point was only that "Nature must have thought of that in 4 billion years" is NOT a good excuse for a question. I was NOT saying ncDNA is useless.

Can one consider living (biological) cell to be Turing Complete?

Perhaps this question is whether the regions between genes sometimes known as 'junk DNA' has any function.
In the human genome, out of ~5 billion bases there are something like 20-30,000 genes which take up perhaps 10s of millions of base pairs, depending on how you count it. 1% of all human DNA is the common figure.
It is sometimes asked as if biologists commonly think of it as having no use, but in fact this is a researched topic, and few feel that it has no evolutionary or biological function at all.
Some of the most common uses for intergenic DNA in eukaryotes (bacteria are an entirely different topic with very different responses.

Transcriptional Regulation

Outside the coding sequences of the gene, there can be an extensive set of binding sities for proteins which regulate the gene.  In this paper in Figure 1 the celebrated regulatory sequence of ENDO16 is can be seen in Figure 1. As you can see for almoat 2000 bp there are numerous binding sites for many sorts of promotors and inhibitory factors, as well as factors which may splice the gene in various ways.
As I recall, ENDO16 only  turns on for a brief period in the development of the sea urchin and so its very tightly controlled, which means that its got a lot of regulatory elements upstream of it, controlling transcription. Its one of the most exhaustively studied genes ever and the believe they have most of it.  Other human genes ive seen perusing medical literature have seen 20kb are necessary to reproduce the regulation of a gene. Still all this might at best only triple the amount of DNA actively involved.

Centromeres and Telomeres
The physiology of the chromosomes have large regions as Deniz mentions are necessary for cell reproduction and for development.  In animals (like humans) the regions are devoid of transcribed genes and might be 10-15% of the genome length (I'm eyeballing this from the UCSC genome browser on chr21 - in some organisms like yeast the centromere can be just a few hundred base pairs.  So anyway we are getting somewhere now!
Non translated genes.
There are lots of pieces of DNA that might be copied into RNA and then do not function as templates for proteins.  some folks say there is a lot of this stuff.  The typical view is that there are a few thousand of these sorts of beasts known, and humans are currently thought to have about 1500 of them.  A small tweak in the number of genes, but they are there nonetheless.
Chromatin binding and organization sites
Although Centromeres are places where chromatin binds, the several families of proteins which bind DNA and wrap them into organized coiled coils thought to be like spools of telephone wire to form the Nucleosome which makes the chromosomes look like the little stick men you see in text books.  Chromatin can spool up just about any sort of DNA but seems to have a preference for regions which are at the ends of genes.  They can be modified by enzymes (acylated, methylated) to modulate their affinity for some classes of DNA sequence.  This is a hot topic of research.  The ability for RNA polymerase to find transcribe a gene is not good if its wound onto chromatin and though its not a precise binding like a transcription factor, chromatin binding and regulation must be affected greatly by changes in the distance between genes and the DNA sequences which surround a gene for thousands of base pairs, which is one of the main differences between species.

Of all biological systems (at least that I know of) this one accounts for the most bulk DNA sequence and is probably as related to the difference between different species as transcription factors and almost certainly is an older system of gene regulation, if you think about it.

Copy Number Variations and repetitive regions
just a side note, but small and very long repeat sequences can show up in the intergenic regions as well as inside a gene boundary to account for some of the differences between individuals.  they can be quite short or quite long.

Well hope this helps?

Just to be more accurate, about 1.5% of the human genome is coding DNA (Nature 409, 860-921 (15 February 2001))

wow - thanks for the bounty vote.  I'd like to add that the mathematical Turing machine would involve using the DNA as memory and sequences over long distance affecting each other in a systematic way.  chromatin sort of behaves like this, but the analogy is a stretch...

just found this nice blog post with some hot links on 'Junk DNA' and how its being studied recently. http://phylogenomics.blogspot.com/2011/06/selfish-dna-symbionts-and-parasites.html

Depends on what you mean by "non-coding".
There are structural elements in telomeres & centromeres -- although the DNA there does not code for proteins, it contributes to the three dimensional structure of the chromosome.
"Non-Coding" DNA can also act as a binding substrate for many proteins: transcription factors,  enhancers, histone proteins; and thus control regulation indirectly through these intermediaries.
Promoter regions upstream of transcribed/translated regions are the combinatorial control switches/dials of our genome, and have tremendous regulatory importance.
Non-Coding DNA also acts as repertoires of mobile DNA elements, which enable fast evolution / "plasticity" by copying&pasting exons around (L1 transductions) or by copying into coding regions & interrupting them.
Lastly,  they can act as the sandbox of evolution: Non-coding regions not genetically linked to functional regions are very likely to not suffer from  purifying selection, so they can act as templates of random evolution - where the vast majority of mutations won't have any impact positive or negative.  This enables exploring brand new combinations, which may then become new exons / miRNA / regulatory regions or get shuffled into other regions to enable new functionality.

You may wish to expand on the 'sandbox of evolution' point =)

@Rory Good point, will do.

By programmable, I suppose you mean that it contains information or can be altered in response to some input or stimulus.  The answer is "no" for both.  Well, sort of.
Does noncoding DNA contain information?  By definition, no.  There are probably many regions of the genome that appear to have no information, only later to be found to contain introns, regulatory elements such as enhancers, boundary element, MAR/SARs, targeting sites, etc.  Even functional tests (such as removing the region) may not reveal anything because the effects could be minor, or only evident under special conditions.  But arguably, if you remove a region and it has an effect on the organism, then it's not really a noncoding DNA, it's just you didn't see the coding before hand.
As for the latter, can it altered, the answer is again "no," or at least "apparently not."  Intergenic regions (those stretches of DNA that do not contain obvious or characterized transcribed regions or their control elements) are very stable between organisms and even between species.  They seem to have a mutation rate expected for having no information, and thus free to mutate slowly without being swept away.  There is no evidence (as far as I know) of any region of the genome being purposefully altered, with the exception of a handful of specific genes whose regulation is controlled by DNA nicking or some such.
Perhaps I am missing your question, being a biologist and not really knowing what a "Turing Machine" is.  If I misunderstood, please clarify.

I don't have a reference to give right now, but mutations in introns can, for instance, affect splicing.

Nico, that's not necessary.  I'm well-aware that mutations in introns can affect splicing (as well as expression should the gene have intronic enhancer elements).  However, I was talking about mutations outside of transcribed regions.  Part of the problem with the question is divining what he or she means by "noncoding DNA."

Sure, mine was just an example

@KAM Noncoding DNA does contain information, it just doesn't encode for protein sequences.

@Gergana Vandova, OK.  I guess it's a difference of definition.  If you define "coding" as open-reading-frames, then you're right. I look at "coding" as carrying useful information.  Overall, though, I think it's a vague term.  I've heard some describe rRNAs as coding, since they code for structural information.  It's a semantic argument.

@KAM I think that this is the common definition of noncoding DNA. Tried to find a reference, but couldn't find any except wikipedia and some dictionaries. Would be nice if people don't spend time trying to infer what the asker meant....

Nature has done pretty well in the subject of formal computation. So much that we are still trying to keep its pace.
As about your question, it depends on your definition of "non-coding DNA".
In general, DNA together with the machinery in charge of its maintenance is Turing-complete in several senses. Take a look, for example, to the existence of mobile genetic  elements: some of them are "subprograms" coding for reverse transcriptases which in turn are able to reproduce the original program. I must note that for doing this with a Turing-complete formalism like the lambda-calculus, well, you need to do a fairly long and complicated program: http://crpit.com/confpapers/CRPITV26Larkin.pdf .  And the lambda calculus is "easier" than bare Turing-machines, meaning that you can write shorter programs than with Turing machines for doing the same thing. So, my (somehow specious) argument is that any real-world information machine capable of self-replication is with high likelihood Turing-machine equivalent.
It just happens that the essential feature of mobile genetic elements is to ensure its survival, so, that's probably the reason we haven't found a fragment of DNA able to do something as interesting as calculating square root.
If you refer to the part of DNA that can not do anything at all, well, for talking about Turing-machines and computation you need a way in which some "data" can be "interpreted"  as a program. A totally inert piece of DNA does not fill that role, by definition.

Unfortunately, it can be shown trivially that self-replication isn’t sufficient for being Turing complete (imagine the programming language “Rep” which has a single command, “rep”, which prints “rep”; clearly this language allows to write self-replicating programs and clearly it isn’t Turing complete).

@Rudolph: that's what I meant by "specious". So, it is not a formal proof, and you will need to do some more work to have one. However, it would surprise me that a machine more complex than anything we have invented (including our beloved computers) would be not Turing-complete.

The problem is not that the proof is specious, it’s that the proof is impossible since the assertion is provably wrong. I agree with the more specific point that cells in particular are Turing complete – but not all self-replicating information machines are.

@Rudolph: Agree, my mistake.

Let me answer your question by splitting it into two parts:
Can DNA be used as an programmable medium (=band) for Turing machine?
The answer is YES.
Starting from the breaking paper by Shapiro et al. in Nature, followed by another great article by Parker, there are many scientific publications about how to use DNA for computing. Unfortunately, these findings are still not applicable for classic computations and DNA computers will hardly substitute the normal ones in the nearest future.
Can a junk DNA work as Turing machine?
There is a known principle in Computer Science called "Junk In, Junk Out". Same in the case of DNA -- there is a way to use junk DNA for computing, but the result of the computation will mostly be junk too: as long as we don't know what this DNA is for, and this doesn't seem to operate as Turing machine on its own, there is hardly possible to get something reasonable by running this DNA on a turin machine...

"Junk" here has a specific meaning. And by the way, its usually written "Garbage in, garbage out"

Thank you. I am aware of what "junk DNA" means, just wanted to play around with the word a little bit to make my point clearer.

My question wasn't so much using a dna strip in place of the paper for a turing machine. That's not very interesting. I am asking if nature already has computation machines in a cell, which might help explain some of the non-coding DNA

Oh, I see. I misunderstood your question then. Maybe you try to re-formulate it to clarify your point, because other answerers might have understood it wrong way too.

You understandably misunderstood the question because some moron has hijacked my question and changed it into something completely different. If you look at the comments under the question and the high rated answers you see they are discussing my original question, not the one you saw. I've tried to edit it back to what I asked.

Indeed, I noticed the mismatch between the question and the comments, but I thought that it is because the question was improved in reply to comments. Now it is much more clear, thank you for your efforts!


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Reproduction and defecation
In mammals and birds the external reproductive organs and waste removal organs see to be the same. Is this always the case with other animals such as insects etc...? Are there any good reasons for it?

Birds are animals too.

@Kevin You're right, fixed it

I guess I'd also add "some mammals."

The cloaca, which is the common opening of the urinary, excretory, and reproductive systems, is present in birds as well as in non-avian reptiles (and thus presumably dinosaurs), amphibians, and monotremes (e.g., duck-billed platypus). To answer your first question, yes, this condition does seem to be universal for those groups mentioned above.
To answer your second question, evolutionary history is as good a reason as I can think of. The cloacal system has worked well enough for >350 million years (in the case of amphibians).

Another nice showcase that we weren’t designed (or that the designer just hated sex …).

Or perhaps the designer was lazy, extremely short sighted and had no long term plan. Just ship it out as fast as you can before an impossibly short deadline. The designer was overworked, underpaid and had boss that only cared about short term profit.


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Does AMP/ATP ratio affect lifespan in vertebrates?
The reference below says that a higher AMP/ATP ratio is associated with lower lifespan in C. elegans.
Is this finding also generalizable to vertebrates as well?

Reference:
Apfeld, J., O’Connor, G., McDonagh, T., DiStefano, P. S. & Curtis, R. The AMP-activated
protein kinase AAK-2 links energy levels and insulin-like signals to lifespan in C. elegans.
Genes Dev. 18, 3004–3009 (2004). PMCID: PMC535911.

Interesting, but I am not sure how useful studies into many of these processes  which shorten lifespan actually are. There are many drugs/poisons which have deleterious effects on organisms, but they don't tell us much about  longevity or the aging process. Better to focus on drugs/interventions which extend lifespan?

There are many papers suggesting a link between AMPK (the major cellular sensor of the AMP/ATP ratio) and lifespan.  As with most of these sorts of experiments, I think it is currently unclear precisely what the mechanism for this is, but AMPK regulates TORC1 and autophagy, both of which are also important for lifespan regulation.  Here is a PubMed link to search results.


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How do dopamine agonists like amphetamine/methylphenidate affect acetylcholine signalling?
Do they increase it, or is the effect mostly neutral?

In its current form, this question can be answered in one sentence by a simple Google search. Can you be more specific and expand your question?

Amphetamine and methylphenidate are not (direct) dopamine agonists.
Dopamine agonists are the substances that would specifically bind to dopamine receptors and activate them, thereby mimicking the effects of dopamine release.
Amphetamine/methylphenidate are so-called indirect sympatomimetics. This means that they stimulate the simpatyc nervous systems (with neurotransmitters noradrenaline and dopamine in CNS), but in indirect way: they don't bind to the receptors. Rather, they promote the massive neurotransmitter release from the presynaptic part. The released transmitter (DA, NA) then just diffuses to the postsynaptic membrane and binds to its own receptors.
There are some works done on investigating the effect of these substances on parasympatic system with acetylcholine as neurotransmitter.
Sympatomimetics like amphetamine generally lead to increase of acetylcholine release throurout the nervous system: in hippocampus and caudate nucleus, nucleus accumbens and generally in forebrain and cortex.
This effect of amphetamine is indeed in many cases mediated through dopamine receptors. Same time some direct dopamine receptor agonists were found to supress ACh release in some brain regions.


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Is the protein in teardrops still attached to cells, or is it released and free-flowing?
A ScienceDaily article says that the protein in teardrops can kill bacteria.
But how does it reach the bacteria?

I am not sure I understand your question.
According to the article you mention the proteins in teardrops kill the bacteria which are invading the eye (e.g. also present in the teardrops):

"Those jaws chew apart the walls of the bacteria that are trying to
  get into your eyes and infect them,"

EDIT: These proteins are enzymes called lysozymes. Those are free-flowing proteins of the human tears. These proteins are actively produces in the lacrimal glands and actively secreted into the lacrimal liquid.

Basically, I'm wondering: are these proteins in teardrops free-flowing? Or are they still attached to cells in the teardrops?

I added information about these proteins into the question.


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What was the reason for some plant and animals to become giant in course of evolution?
The dinosaurs, mammoths, giant plants etc are known to be bigger than modern animals. I wonder why they had been lived and why they are not living now? I really don't know much but is it something about oxygen balance or something similar?

The wording of your question is somewhat obscure. Do you mean "what was the reason for some plant and animals to become giant in course of evolution?" or probably "What are the advances and drawbacks of being a giant plant or animal organism?"

Sorry for my bad English. I mean "what was the reason for some plant and animals to become giant in course of evolution?"

Your English is not at all bad, I just wasn't sure what you mean and wanted to ask before I correct the title of your question. My native language is Russian, by the way, so don't take my English for "granted"  :-)

You might find the following question helpful, but (replying to the duplicate flag) I don't think that these questions are exact duplicates...

But note that the largest animal ever to have lived (blue whale) is alive right now!

consider the current era is also a time of giants, the largest whales, the largest cephalopods, and the largest trees all all alive right now. Basically you can find something giant in every era.

Thanks for asking an interesting question which made me think.
The short answer is that something evolves if there is an advantage to the genes involved, and, by 'advantage' I mean it produces more copies of the genes in the next generation so more individuals with that characteristic will be present in the population.
As to what particular advantage increased body mass had to any particular species that would depend on the particular species and its environment at the time.  There is almost certainly not a 'one-fits-all' answer.
Most very big land mammals are herbivores and there is an advantage in having a large digestive tract when you eat a lot of plant material with a fairly low nutrient level.  However, when there are also predators around, getting big and slow might be more of a disadvantage than staying small and fast. With evolution there is often a balance of competing forces which are traded of against one another.
Where large mammals have become isolated on islands with no predators, such as a species of now-extinct elephant on the Flores Island, they tend to become smaller so this suggests avoiding predators by simply being too big for them to kill might be an important factor.
And of course with many species we have the effect of sex-selection. If females select for the biggest males, there will be a selection pressure towards greater size.
With plants it could be something else entirely. Trees, for example, have long trunks basically for one of two reasons.
Firstly to put their leaves and seeds out of the reach of herbivores, so we have a kind of arms race like that between giraffes and acacia trees in Africa.
Secondly, when they grow in close clumps like woods and forests, there will be competition for sunlight and soil resources like water. A species which can reach higher and put it's leaves above those of it's neighbours will win the competition and there will also then be pressure on it's neighbours to evolve longer trunks.  Long trunks mean that water must be pumped a long way to the leaves so the tree with the longest trunks will also need bigger root systems.  Again a trade off between making a long trunk and dominating the water supply underground.
Many trees are also believed to have formed symbiotic associations with fungi in their root systems which help them take in the nutrients and water required to 'service' a long trunk and high-up leaf crown so they may be the only types of plants capable of doing this anyway.
One thing you might like to think about is why some whales are very big and some are relatively small (dolphins, porpoises, killer whales). What is the difference in their life-style, food, habitat, and so on, which could drive these evolutionary differences.

Getting big is not necessarily disavantageous when there are carnivours arounds. If you are big enough there needs to be a big number of predators to bother you, especially if you travel in big groups (think about elephants, for instance).

another big advantage is resource and environmental fluctuation , a big animal can survive sudden changes in the environment or resource availability better than small ones, https://pubmed.ncbi.nlm.nih.gov/16701331/

to expand on Rose's answer, certain environmental factors are what people cite with unusual size changes in an animal over time as it diversifies into new species.
Gigantism (and dwarfism) on islands are a particular example.  In this case an animal may arrive on an island and some of the predators or competitors that it is used to will not be there.  Then a single species will spin off many species, each one will fill one of the niches that are unfilled on the island - eating bugs from bark, breaking open nuts.  The lack of large carnivores will allow a nice juicy herbivore to get larger without fear of being eaten.  Similarly the Moa was a bird that became an aggressive carnivore in its island habitat, where it's very rare to see an aggressive land bird when a big cat or other carnivore is already present.  Such large changes in environment can also result in dwarfism - smaller species as smaller animals like squirrels or mice might not be present to consume all the food that are available.  The Hobbits recently discovered in Indonesia are an example of island dwarfism.
That being said, selective pressure can probably make many animals larger or smaller - lots of the dog breeds are smaller than wolves that they descended from.  I think steers are as large as we can make them and are larger than native cattle stock.
As far as the environment that caused dinosaurs to be so large, the higher levels of oxygen on the planet at the time is a common theory for why they were so large.  I also think that at least early on, the selection conditions that favored larger animals were probably put in place as animals evolved without any competitors whatsoever (first animals on land or sea).  If this were to happen again, its not clear whether dinosaurs would have been so large - perhaps we could have had gigantic mammals or descendants of trilobites.

It needs to be recognized that this is an outstanding question in biology, i.e., there is no certain answer.
This review considers the various theoretical and empirical evidence for phenotypic selection on body size:

Blanckenhorn WU (2000) The Evolution of Body Size: What Keeps
Organisms Small? Quarterly Review of Biology 75: 385-407.

Some have hypothesized a connection between body size and the evolution of endothermy:

Clarke A, Portner HO (2010) Temperature, metabolic power and the
evolution of endothermy. Biological Reviews 85: 703-727.

And others have suggested a link to oxygen in the atmosphere:

Harrison JF, Kaiser A, VandenBrooks JM (2010) Atmospheric oxygen
level and the evolution of insect body size. Proceedings of the Royal
Society B: Biological Sciences 277: 1937.

And I'll throw this hypothesis into the ring.  The large dinosaurs only went extinct 65 million years ago.  That's basically yesterday in terms of the geological time scales across which body size may evolve - they (dinosaurs) originally evolved 230 million years ago.  That means we've got at least 165 million years to go before you can see if our current diversity of life on earth can evolve similarly large organisms!


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What is the morphological difference between Leydig cell in human and pig?
The pig is only an example, just an animal. Leydig cells have protein inclusions (Reinke crystals) that are mostly made of crystallised lipofuscin. They are secretory inclusions i.e. cells formed in secreting cells.
An example of Leydig cell in pig's testicle:

My teacher told me that there is a difference in the existence of some cells between humans and animals.
However, I cannot find such a difference. I have not been provided a slide of human Leydig cell so I have not been able to compare.
What is the morphological difference between Leydig cell in human and pig?

Perhaps what your teacher meant was not so much a difference in Leydig cell morphology, but in interstitial tissue morphology, ie. tissue which occupies the space in between seminiferous tubules. Leydig cells are its most interesting component, others being small blood vessels (a lot of them), nerves and connective tissue (mostly fibroblasts, mastocytes, lymphocytes and macrophages). In different species interstitial tissue looks differently, for example:

Leydig cells form clumps around blood vessels, and are surrounded by fibroblasts (which makes them more difficult to isolate) in guinea pig, but not in mice or rat;
in human a lot of interstitial tissue is extracellular matter, Leydig cells are not so frequent, but more active;
and, last but not least, in pig, there is little extracelluar matter and a lot of Leydig cells that are very easily isolated (and produce large amounts of estrogen).

I found all this in some old lecture notes; I couldn't dig up any sensible reference, though.

I have studied all available (via University library) literature on the Leydig cells and I think your teacher might have this article summarizing the morphological studies on Leydig cells in different animal models in mind.
To put it straight, the most common animal models for studying Leydig cells are rats, mice and pigs.
The development of Leydig cells in rats was shown to be bi-phasic: development of the Leydig cell population in fetus and its degradation while transforming into the mature cells. It has been believed for quite long that this is also true for human Leydig cells. However, some studies performed on pigs and monkeys delivered an evidence for an additional phase of cell degradation sometimes between the fetal and neonatal development shifts. These data are summarized on the following Figure (taken from the referenced paper):

So, by comparing the Leydig cells of rats and humans from the same fetus age or shortly after the birth (neonatal time) you might see the degradation of Leydig cells -- they decrease in size and many of them eventually die -- compared to normal state of these cells in rats.


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Do humans have Coelom?
Kimball Biology 5e says

Coelom is the main body cavity of many animals. It is lined with an epithelium derived from mesoderm.

Gilbert Embryonal Biology 9e says

Coelom is the space between the somatic mesoderm and splanchnic mesoderm that becomes the body cavity. In mammals, the coelom becomes subdivided into the pleural, pericardial, and peritoneal cavities, enveloping the thorax, heart, and abdomen, respectively.

Then my lecture materials and the research site say

Coelom is the secondary body cavity.

Finnish Wikipedia says that Coelom is only with invertebrates.
Again the Wikipedia page about peritoneum suggests that human has abdominal cavity and no coelom, and other mammalians coelom.
Does human have Coelom?
The confusing thing is the use of the word "OR", since I am not sure whether people are using it in different pages like "XOR" or like "AND" in normal speaking.

Wikipedia actually covers this:

Most bilateral animals, including all the vertebrates, are coelomates.

Now, some coelomates have subsequently lost their coelom but primates (actually, I believe, all vertebrates) are not among them. In humans, the coelom forms, amongst others, the pleural cavity.
So, yes: humans do have a coelom that partitions into different, unconnected body cavities during development.

So the coelom is not any specific cavity of human adult. It just a cavity in the embryonal stage which divides to other cavities. - So if you see the preparat of human adult, you cannot show that the thing here is coelom.

I read the following definition somewhere: "Coelom is the fluid-filled body cavity that separates the digestive tract and the outer body wall and is completely lined with mesoderm." - The clause may be wrong, at least for adult human, since it suggests me that you can see such a cavity in adult human. - It may be the case for other vertebrates where you can see in the adult species. - Thinking better definition. So probably it is better to say "Cavity that separates the digestive tract and the outer body wall at some point of development of vertebrates." - What do you think? Is it better?

@Masi Well, where is the mesoderm in an adult human? Or any other adult animal? As far as I know, all of these definitions apply to (some stage of) embryo development. Not only for humans and not only for vertebrates but in general.

I need to find a general definition for humans. - Is the following any better? "Coelom is the lateral cavity between parietal and visceral mesodermal layers. Coelom forms at the time of primary neurulation (formation of neural groove etc)."

I think so that you cannot really see mesoderm in an adult human. - It is a developmental layer between ectoderm and endoderm. You can see it after gastrulation, probably during gastrulation too its development. It forms finally for instance muscles and bones during organogenesis.


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Do eye muscles relax when you close your eyes?
I wonder whether the eyes muscle relax when you close them. Common knowledge told us the eyes muscle get tense when you stare at nearby object. If you close your eyes, you eye lids have 0 distance with you eyes. Would the eyes muscle relax in this case?

Related: http://biology.stackexchange.com/questions/968/what-is-the-eye-muscle-status-when-you-stare-at-distant-view-through-a-glass-wal

I would guess that the eye muscle relaxes when the eye is closed. After having the eyes closed, just in the moment after opening them, it seems that the focus is in the distance. It takes a fraction of a second before you can read some text on your computer screen for example . This focusing-duration seems to be shorter when looking into the distance after opening the eyes.
Another effect is when you look at an object in short range for quite a moment and then close your eyes. You can feel the relaxation.

Certainly noticed what you mean when closing eyes and then attempting to immediately focus on a near-to object.  I wonder if it could be due to it being dark when the eye is closed - this could I suppose result in the relaxation (as there is nothing to "see" if you do this in a pitch black room).

I can confirm the eye muscles relax. Not just intraocular muscles, but also the extraocular muscles. I've recovered from chronic eye strain. I know.