text:
Based on which criteria should i choose the control sample to calculate delta_delta_Ct
I want to calculate the gene expression of an experiment with the Delta delta Ct method.
I have these results from two runs of a real time PCR (one for the GOI(Gene of Interest) and one for the reference gene ($\beta$ actin) )
Samples | GOI CT | reference gene CT |

1         16.52         16.24
2         18.58         18.47
3         14.55         20.56
wt        23.06         24.17

So to calculate the $2^{-\Delta\Delta CT}$ for my GOI I've done this :
1st - Normalize CTs of GOI to CTs of reference gene
$ΔCT = CT_{sample's} - CT_{reference's}$
This new table then occurs:
Samples | ΔCTs

1         0.28
2         0.11
3        -6.01
wt       -1.11

After this i normalize these ΔCTs to a control sample. And here is where the question was born. On which criteria should i choose the control sample ?
What i've done was to choose the sample with the bigest CT from the first table. And that was the sample No. 2.
2nd - Normalizing all samples to the control sample
$\Delta\Delta CT = \Delta CT_{sample} - \Delta CT_{control}$
and the final results are
Samples | ΔΔCTs

1         0.17
2         0
3        -6.12
wt       -3.08

Is that method correct ? If yes, let me write once more the question.
On which criteria should i choose the control sample for the last normalization ? Should i choose the sample with the highest Ct or the lowest one ? And why ?
I hope now be more clear.
Question edited to be more clear.

What do you mean by calibrator sample? Standard curve??
See these posts- 1 and 2

No. I don't mean standard curve. In the video above, they choose a calibrator sample from target gene samples to normalize later on the ΔCT to it. Here is the video link: http://youtu.be/tgp4bbnj-ng?t=34s

But what do you mean by calibrator sample.. I have never heard this term.. You have a reference gene which is $\beta$-actin in your case.

In the video they use the term calibrator sample to mean control case. Nobody uses the term calibrator. Follow good references. Check the link to a paper on RTPCR analysis, provided in the posts that I mentioned in previous comments.


text:
It's right to say coding sequence is part of exon sequence?
Some basic ambiguities making me confused. I downloaded 5'UTR, CDS, 3'UTR, and exon sequences, separately from Biomart for a gene P4HA2 (Homo sapiens) and found some simple sequence repeat (SSR) on them. While there is a repeat x on the exon sequence, it was not located on the 5'UTR, 3'UTR, and coding sequence (or CDS) of gene. As I remember, exon sequences is the same with coding sequence, except for the first and last exon, which are parts of 5'UTR and 3'UTR, respectively, am I right?. Could you please help me out to find how the mentioned event is possible?
Thanks

Are your comparing the same splice variant?

As @canadianer said, remember that almost all human genes are interrupted. There are long intronic sequences in the gene that can interrupt your coding sequence. Also alternative splicing can cut out exons that make up the mature mRNA. If you do an alignment you should be able to pick up where the exons are in the splice variant of your gene.

Yes Canadianer, I compare the same splice variant.

As I remember, exon sequences is the same with coding sequence, except
  for the first and last exon, which are parts of 5'UTR and 3'UTR,
  respectively, am I right?

Not necessarily. The UTRs can be composed of multiple exons and there can be an exon that spans both sides of the start codon i.e it is both a part of the 5'UTR and CDS. Similarly, an exon can span both sides of the stop codon.
A reason for why you are not able to map your repeat to any of the regions of the mRNA could be that your repeat falls in an exon that spans the start/stop codon. The repeat itself might span these sites. You need to provide additional details such as the location of the repeat, size of the repeat and which exon it maps to. Also mention which reference genome file are you using.

The coding region is that region of the DNA coding strand that is translated into a product. This is synonomous with the exon region. The 5' untranslated region and the 3'untranslated region are just that and though they may serve some little understood function in replication, they are not translated into a protein. "coding region" is not a term that I have heard widely used although I am a neophyte as a molecular biologist.

source: Stack Exchange

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/

sort: votes


text:
Marker validation using transcriptome and genomic sequences derived from a single cell
I conducted a SSR marker analysis using bioinformatic tool on some RNA-seq data of human tissues. Now, my supervisor believed that we have to validate these SSR on a transcriptomic and genomic sequences derived from single cell.
My question is: why I should do validation on sequences from single cell? Thanks for sharing your idea and experience here.

SSR=simple sequence repeats ?

I think your supervisor wants to see if there is inter-cellular variation in the repeat length and if so, calculate the variation. This may be compared with inter-tissue or inter-individual variation.
Usually when you take a pool of cells for any assay, you would average out the properties of individual cells.
Using sequencing you may actually be able to find the variability in the repeat length if your reads are long enough. According to wikipedia, the SSRs are 2-5bp long motifs that are repeated 5-50 times. So the max length would be 250bp, sequencing which, is an easy task. So you would be able to know the fraction of the SSRs with a certain length from a pooled sample and obtain a length distribution. This is quite easy if you know the locus of the repeats and use specific primers for sequencing.
However, if you do not know the exact locus of your SSRs and you are doing random RNA/DNA fragmentation and total RNA/DNAseq, then you may not be able to do that so easily.
In any case I think that it is easier to determine the locus and do targeted sequencing in pooled sample, than doing single-cell RNAseq (At least if the objective is to obtain repeat length distribution).

all_licenses: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/


text:
Safe level of chlorine in water
Chlorine is usually mixed in water to make it safe for consumption. What is a safe quantity of chlorine that can be consumed? What are the side effects of chlorine and does this include hair loss? What are some common chemicals utilized for water purification? Thank you.

What has this got to do with governments?

You are asking many questions here. Q1 is in any case off-topic. Question 5 is too broad.

Chlorine is a reactive substance and an oxidizing agent. It can cause damage to surfaces exposed to it such as eyes, skin etc but it cannot penetrate deeper. Chlorine can damage your hair by oxidation — hair becomes rough and brittle. This is not same as hair loss — chlorine doesn't cause hair to fall out because it cannot penetrate to the follicles. See here
EPA has set maximum residual disinfectant level for chlorine (as Cl2 and other chlorinating agents such as chloramine [NH2Cl] and chlorine dioxide [Cl2O]) beyond which it is considered unsafe.
Chloramine       :  4.0 mg/L or 4 ppm
Chlorine         :  4.0 mg/L or 4 ppm
Chlorine Dioxide :  0.8 mg/L or 800 ppb

thanks for the answer, I mentioned "govt", as different countries have different standards.


text:
Ants eating bark
Was out walking in the park today, came across a tree, and me being me I thought "Hey lets try climbing this thing for fun." But something strange struck me, the tree was completely devoid, as in COMPLETELY, of any bark. On the trunk, on the branch, no bark anywhere, pure albino. Well, I reasoned, maybe it's just born that way. But then I look down, and I see the remnants of some bark wrapping around the tree's base. (Greyish colour). Huh. And I also saw approximately 7 massive slightly orange ants tumbling through an ant hole. I'm not a large fan of ants, especially since I had pretty much been standing on their nest for a couple of minutes, so I hastily backed off.
Here's where my mind kicked in though, how did the tree become barkless? For some background, I live in Sydney, NSW, Australia, and it's pretty darn hot here, nearly Summer. MAYBE the wind blew it off? (but there hasn't been any wind lately) Only logical explanation was THE ANTS DID IT. Do ants really eat the bark off trees like this?

Dang that's a big picture. You can sort of see if you look closely the remains of the bark at the bottom. Been to this park before, and I'm 75% sure the tree was not albino back then.

This question appears to be off-topic because it is about diagnostic tree care, not biology as defined in the Help Center. It should be on Gardening & Landscaping beta.

Is there like a general stack exchange where I can ask questions like these because I didn't know where to put it? I knew it was slightly different to biology, but I had 0 clue there was a gardening and landscaping site

There isn't a general site like that. This can be moved to gardening.se, but generally it's good to look around here, and try to find the closest fit.

Trees have different kinds of bark. If your tree was not moist and seeping, it had bark. Since that tree is clearly alive, it's likely that it has a smooth, light-colored naturally peeling bark.

Japanese Stewartia (Stewartia pseudocamillia) has a beautiful bark that is constantly shedding in patches of tan, green, orange and brown. It always has bark, however.
Crepe Myrtle is also used in landscaping for it's beautiful, peeling bark.
To know if this condition is normal for that tree, identification (using range, habitat, bark, leaves, twigs, and sometimes flowers, fruits and seeds) is needed.
Eucalyptus grandis is native to your area. Eucalyptus species also shed bark and the picture in your question definitely looks like eucalyptus.

When it is finished peeling, it's very light. This might be your tree.

Perhaps you can put up a pic of eucalyptus which also sheds bark. It is eucalyptus in the OP's picture

@WYSIWYG - thanks! I had just done a search when your coment popped up and confirmed it. :) If you know how to reduce a picture's size, please feel free.

Size is fine. I just think it should generally not exceed 500px


text:
Taste of salt water
I had a question relating to chemistry and biology, so please tell me if this is suited better for the Chemistry website.
My question was, if water dissolves salt by separating the two ions, the Na+ ion and the Cl - ion, then why do we still taste salt in the water? The ions in the salt are still separated, so wouldn't the water not taste like salt?
(Any help on fixing this question would be appreciated)

We taste things in solution, either in liquids, in saliva, or a combination of both. Salt also separates into ions in the saliva on our tongues, the water in our mashed potatoes, the juice on our steaks, etc. If our tongue was perfectly dry, salt would not taste salty (nor would it "dissolve" on our tongues, as it does). That's what we are tasting: salt in solution as water, Na+ and Cl-. Like seawater.

Perception of saltiness is because of the sodium ion. At concentrations ≤ 100mM, sodium ions elicit a taste response pathway which is inhibited by a small molecule called amiloride. Other monovalent cations do not elicit this "amiloride-sensitive" response.
At higher concentrations sodium ions elicit a non-amiloride sensitive response; other ions like K+ also elicit this response.
The Epithelial sodium channel — ENaC, is responsible for sodium taste perception (amiloride sensitve) and there are distinct population of taste receptor cells that express this channel (Chandrashekar et al., 2010).
So other sodium salts like NaNO3 would also taste salty (the anions can surely have some role in the difference of taste)


text:
Folding of bulliform cells
How do bulliform cells cause a leaf to fold in half when the leaf looses water? Also, how would these bulliform cells be arranged to cause the cell to instead curl up?

This is a really well written paper which answers at least your first question. As long as the curling up is concerned, they curl up when there is insufficient water and they curl in order to avoid excessive transpiration. There is something about this in the Discussion part, check it out. http://www.bio.uaic.ro/publicatii/anale_vegetala/issue/2010F2/01-2010F2.pdf

Curling up is due to turgor pressure. Quoting from wikipedia

Loss of turgor pressure in these cells causes leaves to "roll up" during water stress

More scientific reference , on morphology,  on mechanism, on development, some genetics and on physics.

Can I get a deeper explanation of the mechanism in layman's language?

In layman's term, According to this paper, these cells loose their water and reduces their volume in water scarcity. This osmotic flow of water creates pressure which pushes plasma membrane of cell to cell wall (which I think is causing 'curl up' phenotype') However same paper has also mentioned other hypothesis for this mechanism like use of 'pectin' as water reservoir.


text:
Polymorphism in number of chromosomes?
The answer to this question, saying that Down Syndrome - a trisomy of human chromosome 21 - is caused by de novo mutation (rather than resulting from standing variation) made me think about polymorphisms in the number of autosomes (not so much for sex chromosomes because of dosage compensation). The reason for this question is that I would never have thought that an aneuploidy, in theory, could be a segregating trait because of meiotic barriers.
I found evidence of ploidy polymorphisms in plants (especially their hybrids) that occurs when plants with different karyotypes hybridise [see, for example, Vandenhout et al. (1995) and Husband (2014)]. Additionally, I also found that this also applies to some aquatic vertebrates, however, 'fish' are also known for karyotype diversity (see Zhou et al. (2007) and Zhao et al. (2016)).
In rather sharp contrast to that, mammals are (almost) strictly diploid and most mammal species are characterised by fixed chromosome numbers, even though exceptions exist, i.e in mice and other rodents that exhibit intraspecific variation in diploid numbers - these are created by Robertsonian translovations [Graphodatsky et al. (2011)].
However, all of these are diploid and variation always needs to be expressed as a chromosome number of the form $2n$ because of meiosis. The karyotype of a human with trisomie 21 cannot be expressed in that form as this person has $2n +1$ chromosomes. All cases of aneuploidiy in autosomes I am aware of cause disease. My (related) questions now are:
(1) Are there described cases of non-deleterious aneuploidies in autosomes?
Those cannot be segregating in the populations as aneuploidies are not inherited to children, so more importantly:
(2) Are there indirectly segregating aneuploidies in autosomes (i.e. some sort of heritable trisomy that e.g. result from a trisomy followed by chromosomal rearrangement)?
If so, do any of these also exist in mammals, particularly in humans?

There is definitely long lasting variation in copy number (CNV) where the number of copies is not a multiple of 2. I don't know about whole chromosome number variation. I guess sexual chromosome would not count as long as there is a pseudo autosomal region (PAR) unless for XXX individuals.

According to Wikipedia, XXX and XYY snydrome cause no or little symptoms. https://en.wikipedia.org/wiki/XYY_syndrome https://en.wikipedia.org/wiki/Triple_X_syndrome

@adjan, sorry, I should have clarified that I was not asking about sex chromosomes because of dosage compensation.

I suppose XXX individuals would still qualify as an answer, wouldn't it? It is a "unusual" (unlike the standard XY) case of a chromosome number that is equal to 2n + 1.

Good questions, but you make a claim that isn't necessarily true:

However, all of these are diploid and variation always needs to be expressed
  as a chromosome number of the form $2n$ because of meiosis. The karyotype of a
  human with trisomy 21 cannot be expressed in that form as this person has
  $2n+1$ chromosomes.

The emphasized text isn't necessarily true - there are certainly more involved ways to describe the karyotype of a given individual or cell line. For instance, take the GM12878 cell line, likely the most well-defined cell line in terms of genetics, epigenetics, and chromatin biology today. It's karyotype is listed as:

46,XX[23].arr[hg19] 9p13.1(38,787,480-40,911,212)x3

This is a fairly common way of representing changes known as copy number variation, wherein only a small region of a given chromosome is duplicated or deleted. For this cell line, which relatively closely mimics lymphoblastic B cells, the genome is nearly normal (46 chromosomes, XX) with only a small amplification on chromosome 9 (9p13.1(38,787,480-40,911,212)x3). This is a mild example, but smaller copy number variations like this are quite common and can amplify or delete both large chunks or very focal regions of genomes.
But to answer your first question, no, there are no known non-deleterious trisomies in autosomes. Trisomy 13 (Patau's syndrome) and trisomy 18 (Edward's syndrome) children can live to birth, but die within the first few months of life. Unsurprisingly, these chromosomes are also the smallest chromosomes with respect to the number of transcripts that they encode 1. This suggests that the additional amount of genetic material determines the severity of the defects, and this trend also holds true in mice. From a figure caption of the cited paper (which is likely behind a paywall for those without institutional access):

A correlation between degree of aneuploidy and organismal fitness in humans and >mice. (A) The number of known human transcripts/chromosome in humans. Trisomies >below the line develop to birth. Trisomies above the line are embryonic lethal. Only those chromosomes containing the least amount of transcripts survive birth. (B) In mice, survival of the embryo is inversely correlated with the size of the chromosome that is present in three copies. Linear regression analysis fits the data with an R2 of 0.71.

I was unable to find any examples for your second question. Cancer cells can get very messed up in terms of copy number, but I've never seen anything about heritable aneuploidy.

Fascinating, thank you very much for your answer! This is a very interesting way to think about CNV - actually these large CNV chunks are already examples for my second question. I will have a deeper look into that.


text:
Why can't ciliary muscles in the human eye relax like other muscles?
I had laser eye surgery a decade ago, but in recent years my eyesight has become significantly myopic. I consulted an ophthalmologist to see if this was eye strain because I work at computers a lot, or part of a natural degradation of the eye over time, or both. My ophthalmologist seems to believe that in my case I'm youngish enough that the natural degradation with age is minimal, and that it's mostly eye strain that is my problem. She believes I can get my eyesight back to roughly 90% of my post-surgery sight ability, if I can reduce eye strain. She gave me some eye drops to help with dryness, and recommended various ways to for me to help my eyes recuperate.
I decided to look into eye strain to learn more about what conditions cause it and what can alleviate it. What I learned is that the lens of the eye needs to be flatter to accommodate focusing on far objects, and rounded to focus on near objects. The way the lens becomes flat is by using spring-like connective tissue called choroids that pull it taught. Attached to these choroids are muscles called ciliary muscles that stretch the choroids out when they contract. This action causes the choroids to stop pulling on the lens, and the lens will retract into a more rounded shape. So, when the ciliary muscles are relaxed, you can see far. When the ciliary muscles are contracted, you can see close up. This diagram from the York University website was the clearest explanation I have come across:

Thus, the reason for my current inability to focus on far objects is that so much focusing on close objects, mainly computer monitors, is straining my eyes. In order to regain the ability to focus on far objects, I need to reduce strain and allow the muscles to relax. If they relax, the choroids can pull the eye to the flatter shape needed to see far.
However, I can't reconcile that model with how I understand the mechanics of the other muscles in my body. If I go to the gym and run or lift weights, or in any way expose my muscles to work, they respond by getting stronger without sacrificing the ability to stop contracting. The muscles in my body don't lose the ability to relax, no matter how much I train them. I have never heard of anyone who worked out too hard or too long such that their bicep would remain in a permanent state of contraction.
In fact, in my experience, after a hard workout, it's impossible to prevent my muscles from relaxing and resisting doing more work. When I do a bicep curl at the gym, and I do it to the point that I can't lift the weight anymore, my muscle gives up and I drop the weight. Similarly, if I've spent a long time looking at close up objects, shouldn't my ciliary muscles give up, allowing the choroids to take over, making clear far vision the unavoidable outcome?
The idea that my ciliary muscles need to relax in order to see far also seems to contradict my personal anecdotal experience. Sometimes I am able to see far away, but I can't hold it for more than a few seconds. If I try to maintain focus on far objects for too long, I get an uncomfortable feeling in my eyes that is hard to describe, but it's a form of pain that forces me to give up. My vision goes blurry, and I can only see close objects again. If my bicep worked the same way, it would be as if it hurt to let my arm hang straight down with a weight, and the only way to alleviate it would be to raise the weight, which makes no sense. I feel like the effort is in seeing far, and that when I'm tired, I can only see close up.
It's not that the case that I think that all medical research on the eye has it backwards, it must be that there is some aspect of this that I am not seeing (pun intended).
How can it be that the ciliary muscles, unlike other muscles, lose their ability to relax?
Why is it that my ciliary muscles don't become exhausted and allow the choroids to take over by default?

Regarding focusing on far away objects - perhaps that is unrelated to the distance? I imagine you would "stare" at the objects with intense concentration, rather than gazing casually, and would probably blink less and move your gaze direction less, fatiguing the retina.

First of all, I should correct some points that were misunderstood.
Don't change the question because this will lead to confusion.
"The way the lens becomes flat is by using spring-like connective tissue called choroids that pull it taught."
In classic ophthalmology you don't need to think about choroid in direct relation to accommodation: choroid is a sponge-like layer between the sclera and retina and in general it is consisted of blood vessels. The anterior part of the choroid continues anteriorly to became a ciliary body which in turn contains ciliary muscle - one circular muscle per eye. From the ciliary body/muscle spread zonules (zonule fibers) and they are fixed on the lens equator.
Physiology: contraction of ciliary muscle causes zonules to became loosen and "free" the lens to became more convex and move the focus anteriorly (not choroid contracts itself). If the ciliary muscle relaxes then zonules are tighten up and the lens consequently becomes more flat (less convex) moving the focus posteriorly. In other words you can say it in the terms of depth of focus - convex lens gives less depth, less convex gives more depth of focus.
Thus, the classical choroid layer does not perform any action (look at your choroid related link - there are almost nothing about accommodation).
"Permanent state of contraction" can be physiological (=normal) as well as abnormal one, and it is very common in some conditions (muscles spasms). One example is priapism, where corporal smooth muscle contraction causes permanent and dangerous penile erection which can be medical emergency (priapism is by far more complex, so take the explanation like a metaphor).
If we refer to "accommodation spasm" there is analogy to "muscle spasm" (and partially to priapism), but I should state we believe that spasm of ciliary muscle exists - since we don't see it directly. Probably (and take this sentence as speculation, since I cannot give you reference right now) the causes of this is not a muscle spasm itself, but the state of zonular fibers which cannot come back to their base state. I like the example with iron rod - if you will contract it fast and many times, at some point it can be "loosen" as well as fractured (and probably it does happens to zonules too). Probably (I say "probably" to underline the point we do not exactly know this), the "accommodation spasm" is partially misname and in future the investigations will clarify that.
Probably, you will learn some interesting facts from definition of "pseudoexfoliation" syndrome, but I do not explain it here because it is not related directly to the question. From wiki "has been known to cause a weakening of structures within the eye which help hold the eye's lens in place, called lens zonules"
Another example for analogy for continued "spasm" is the situation when one should care something heavy for a long distance without releasing the grasp - finally one can get not only spastic contraction but also severe ischemic damage to the fingers.
Considering your case, you should know about pathological (degenerative) myopia where the eye expands posteriorly and consequently the focus is before the retina which should be corrected by minus lenses. It is well known fact that myopic eyes have longer axial length then normal eyes. Probably, it is your case.
So, as you can see, the answer to your question is not a clear cut, but assumption. The ciliary muscle does can relax, but probably the problem is more complex then only ciliary muscle related issue.
PS The image you reposted is a little bitconfusing one and is not exact. This one is classical and gives better understanding of the anatomy -

I'm not a eye doctor but I do workout. I would like to say something about your metaphor or comparison from the ciliary muscle to the body muscles.
Let's look at a workout. In a workout, you strain the muscle then relax the muscle repeatedly until you exhaust the muscle.  Another part of the exercise is stretching. If you don't stretch, you will lose full range of motion. For instance, if I were to do a regiment of bicep curls for the first time, and I slept that night with my arm cocked, it would be a painful effort to straighten it the next day. If I don't stretch it my arm would stay in that position having limited motion. The muscle is relaxed but it's range has changed. Another example would be, when I was a teen, I did karate and could do the splits. Now-a-days I can not do the splits no matter how much my muscles are relaxed.
Looking at the computer all day isn't comparable to working out a muscle because you don't contract and relax repeatedly. You only contract.
Now let's look at the body muscles in a more relevant metaphor - Tension. Tension is an involuntary reaction. Because you hold the muscle in a contraction state for such a long time, it tends to want to stay contracted without you making the effort. A lot of people hold tension in their neck and shoulders and no matter how much pain it causes them, they can't relax it voluntarily.
Muscles have a mind of there own (muscle memory). To assume you have complete control over them is wishful thinking. I assume that the ciliary muscle is no different.

Can you please add some references to your answer?

There are a few more things that need to be considered to get a better understanding of the physiology.
The ciliary muscles are not skeletal muscles (voluntary muscles that you can control) but smooth muscles (involuntary muscles which are under the control of the autonomous nervous system, which is self regulated by the parts of brain not under the conscious control). This has several deep implications.

Smooth muscles do not hypertrophy - grow and become thick like skeletal muscles - They are more or less constant and their growth/strengthening is more related to hormones than regular contraction/relaxation exercises
Smooth muscles are supplied by autonomic nervous system - Parasympathetic system is the main supply. Recently evidence for sympathetic innervation of ciliary muscles has been found.

Generally, there is a balance between the sympathetic and parasympathetic, the balance being driven by the need brain perceives. An imbalance in these systems can cause accommodation problems

This point is speculation based on proved biological laws: Law of tension-stress: This states that if under constant tension, the biological systems grow.

Gradual traction on living tissues creates stress that can stimulate and maintain the regeneration and growth of certain tissues. Slow, steady tension of tissue causes them to become metabolically activated, resulting in an increase in their proliferative and biosynthetic functions. These processes are dependent upon two main factors:

The quantity and quality of blood supply to the tissue being mechanically stressed and
The stimulating effects of tensile forces acting along the lines of muscular contractions because collagen fibers are generally aligned parallel to the vector of tension-stress.
  source:http://jontristermd.com/for-physicians/the-tension-stress-effect-on-the-genesis-and-growth-of-tissue-2

This may cause changes in the choroid that may reduce the tension on the zonules causing a semi-permanent/permanent myopia.

Thank you for responding. I think there's some interesting and useful information here in your answer. However, you've used a lot of deeply technical terminology that makes it very hard to follow and understand. If you could rephrase your answer with a non expert audience in mind, I think it would be a lot more informative and helpful.

After reading various theories of how the ciliary muscle body works, I came across a convincing new theory by Dr Goldberg, one of reciprocal action. In other words, the lens is only under posterior (rear-inner side) tension when focusing on near objects, but anterior (front-outer side) tension when focusing on distant objects. In both cases the lens is under a form of zonular tension. The ciliary muscle moves forward (near focus) and backward (distant focus), actuating the zonular strings and circular apparatus accordingly. As I have witnessed how I sometimes have to force myself to focus in the distance, I am inclined to believe that relaxation of the ciliary body only leads to a medium focus, and while contraction, either forward and backward, for near and distant focussing respectively. In other words, the ciliary body would also contract slightly for a distant focus, but this contraction would be in opposite direction. There's a video illustrating Dr Goldberg's theory: https://www.youtube.com/watch?v=1yIpyitm6eE
I must add that there are theories saying that the zonular fibre gets stretched (permanently longer) when using too much near-vision, so that when ciliary muscle body relaxes, the lens is not held taut enough, causing it to be always convex (nearsighted).

The ciliary muscle is made of smooth muscle rather than skeletal muscle.  These two types of muscles have different mechanisms for contraction and relaxation.  Skeletal muscle is relaxed unless it is stimulated by a nerve.  Smooth muscle is able to lock itself into a contracted state through a chemical reaction (phosphorylation).  It then does the reverse chemical reaction (dephosphorylation) to relax.  This is important because smooth muscles do things like keep the urine in your bladder (urinary sphincter), and you don't want that muscle getting tired and giving up.

Can you add references or other credible sources to allow others to background read on your answer?


text:
What's the minimum distance of focus for the lens of a human eye to reach maximum flatness?
According to the Wikipedia article on eye accomodation, the range in which a human eye can focus is from 7 centimetres away up to essentially an infinite distance. Of course, people can't see things an infinite distance away, but at a certain point the light reflected off an object will come at the eye in effectively parallel paths.
As an eye focuses on objects progressively farther away, it seems to me there would be a point when the lens hits maximum flatness, after which it everything will be equally sharp in focus. Looking at an object 500 metres away or 1000 metres away probably doesn't require any change in the lens. However, going from one metre away to seven requires the ciliary muscles adjust to just the right amount.
My question is, what is a normal minimum distance from the eye at which the lens will reach maximum flatness? Everything else in this question is just for context, so an answer to this, stated in metres from the eye, is all I am seeking.
The article I linked to above mentioned the human eye seeing "13 dioptres", and I have tried to understand dioptres, but it's a little confusing for me. If I understand correctly, the higher the dioptre, the closer you focus, so the 13 dioptres refers to how close the human eye can see. If I have this backwards, please let me know.
In any case, my purpose in asking is to determine the range in which ciliary muscles would be required to do more nuanced work in order to hold the lens at in the right shape. Focusing on something 7 centimetres away, the ciliary muscles are at maximum exertion, and at a certain point and beyond the ciliary muscles are completely relaxed. To hold somewhere in between would require more subtly nuanced, and, I suspect, more difficult work on the part of the ciliary muscles.
At least, I assume that to be the case because I am hypothesizing that the act of contraction for the ciliary muscles would be similar to other muscles. For example, it is easier to do a bicep curl with weight when going from full resting position to maximum contraction, as opposed to stopping at a particular spot somewhere in the middle of the motion. To stop mid-motion requires more muscle control, and, depending on how fast you wanted to do it, can be difficult to be exact.

I'd like to answer your question but as usual in one question you have at least three: what is the diopter, what is the range of accommodation, what is the amplitude of accommodation, near point of convergence etc. In such a scenario (as we saw in previous question) you cannot get acceptable answer, so, probably, you should focus your question more...

@Ilan pun intended?

@Michael could u elaborate?

@Ilan "you should focus your question more"

There are practical questions in ophthalmology and you've asked someone that has a common theoretical answer: 6 meters.
However, you should know that from the same theoretical point the far the object the less accommodation we need, so the second answer is - infinity.
What is the difference? From the practical point the accommodation between this two points is negligible and does not have to be taken into account when we correct the refraction error.
Small theory - to see an object placed at a distance of 1 meter we need 1D of accommodation power (1/1meter=1D), to see an object placed at a distance of 30cm we need 3D of accommodation power (1/0.3meter=3D), for an object at a distance of 10cm we need 10 diopters and finally for an object at the distance of a 6 meter we need accommodate 0.16 diopter.
Thus between 6 meter and infinity the accommodation is very low and this is why the distant visual acuity is checked at this distance. Consequently, the lens convexity difference between 6 meters gaze and infinity is negligible and this is why the answer to your question is between 6 meters and infinity (zero accommodation).
From this explanation you can calculate the dioptric add for any reading distance  and understand how the reading spectacles correct the loss of accommodative power (=presbyopia, the vision of older people).
If you want to know how much the crystalline lens changes its dimensions during accommodation, the answer is near 7% for diameter and near 10% for thickness, so the lens as was convex, stays convex and the visible changes are minimal.


text:
What is the blood ejection speed outward from human body vein?
At what height blood can eject from human vein ?
I see, sometime there is direct blood transfer from one person to patient.
So sometime blood bottle is kept at certain height and blood is transfered from person to upper bottle and then from that bottle to patient directly.
At what height blood can go ?
EDIT
For example, I had not mentioned before,
What would be the blood pressure outside from body after cutting certain nerve or vein or whatever which carries blood-speedily, when we go inside vacuum chamber ?
Consider any chamber where you will be able to remove air/atmosphere inside it and a person is provided with oxygen cylinder. Now what will be the blood ejection speed outward from the body ? At what height ? You will have to consider atmospheric pressure also when we leave normally on earth. So question is, at what height in vacuum (where there is no pressure from outside world) ?

I'm a little uncertain based on your title and wording, but are you asking how elevated a human donor has to be, vs. the recipient, for an unaided (no pump) blood transfusion?

@AtlLED At what height blood can go if one's vein got cut by knife or something ?

This question appears to be off-topic because even though it presents a biological scenario it is about basic principles of physics.

You can use Bernoulli's equation and the equation of continuity to measure velocity of blood from the cut site. Then add the effect of gravity of calculate the distance covered.

@WYSIWYG If people want to close, I have no objection.  I couldn't tell if it was on topic here because it needed to look up average venous pressure, but that's such an easy task, it doesn't on topic ether.  I had a hard time deciding whether or not I should answer. I'm at least willing to say it's not a good question, but not sure on close.

@AtlLED I edited my question.

@AtlLED.. There is no problem in answering.. In one or two instances I have answered and then closed the question. I guess the purpose of closing is to avoid long discussions and also to encourage the OP to ask the right question or ask elsewhere. I don't know if this is a right thing (to answer and close); I try to answer in the form of a hint.

@AmitG.. your question still has got very little to do with biology per se. It is more of fluid mechanics (just veins instead of the pipes). So I suggest that you reformat your question and ask in physicsSE.

This question appears to be off-topic because it is about physics.

Does this question have anything to do with needle "blow-out"?

No. This is random question as a curiosity. This question is related with Biology along with Physics. Doctor must be knowing what is the speed of flow of blood from the human body when injection is injected to take the blood from the body in the vacuum chamber. Normally we have atmospheric pressure on our body. Looking for answer in vacuum. I didn't understand why this question was closed. There must be some answer.

Ah, I'm afraid there are a near infinite number of variables that will make a general answer impossible.  Factors such as: age, sex, weight, which vein, additional damage, heart condition, cholesterol level, body position, body temperature, and how the vein was cut and exposed will all lead to different answers.
A general answer from someone with lots of trauma experience, not very far.  Rarely if ever greater than 10cm.  Veins just don't have the pressure that arteries do.

Central venous pressure is something like 5 mm of mercury.

@kmm I'm not so sure a chest/back wound required to expose the venae cavae would spurt, even at it's higher pressures.  You simply have to go through so much to get there that it seems unlikely.  Also at that point you almost assuredly have arterial if not aortic damage.  That average of 5mm for a healthy adult [caucasian] male at room temp has to pass a lot of tissue.  There are a lot of ways to get blood splatter, but neatly cutting through a vein isn't a particularly good one.

For a further point of clairification, the CVP is normaly limited to the blood pressure in the proximal SVC, not the more distal portions that would be more exposed to puncture.  The pressure change would make more of a pulsing uzze than big spirts.  If the punture was small enough to take full advantage of the pressure changes, you could get some distance from the body, but nothing like an artery.

Agreed. The OP was asking about veins, which have almost no pressure even where their pressure is highest.

@AtlLED I edited my question.


text:
Evolution of protein and protein efficiency
Suppose we have a bacterial protein that performs a function and let's say we can measure the efficiency of the protein. Let's say we have two species, species A and B, both of which have this protein. One of these species, species A, is close to the common ancestor of A and B, in terms of evolutionary distance, while B is farther although for both cases, it took two speciation events to end up with species A and species B.
Let's say for both for species A and species B, we measure the protein efficiency in different environments. The species A protein has the efficiency highest in an environment most similar to its own and the same is true for the species B protein. But let's say we have two situations:

When species A protein has best efficency, it has a lower efficiency compared to species B best efficiency
Species B protein best efficiency is lower than the species A best efficiency

In these two cases, what conclusions can we make in particular about the evolution of the protein itself? Can we show that the protein evolved to a degree to suit the different environment of species B compared to species A?

A few details

One of these species, species A, is close to the common ancestor of A and B, in terms of evolutionary distance, while B is farther although for both cases, it took two speciation events to end up with species A and species B.

I have two issues here.

I don't understand why this information matter for your question.
There are several metrics of evolutionary distance. In terms of time to common ancestor and therefore, in terms of number of neutral substitutions (it is ok if you don't understand why I talk about neutral substitutions) species A and species B are at exactly the same "evolutionary distance" to any of their common ancestor. However, you may want to talk about evolutionary distance in terms of "By how many standard deviations of a quantitative trait did the mean trait value shifted since the common ancestor (in haldanes unit by definition)", then one species might be more closely related to the ancestor indeed. But in such case, you need to talk about the quantitative trait resulting from protein changes and not directly at the discrete, non-ordinal (nominal) nature of proteins.

And a third general issue I have

As I understand the question, I don't think the question is specific to proteins at all. The question seem rather to relate to "environment specific adaptation in comparative genomics and reaction norms" and would be completely legitimate to look at that at the level of a protein or of a quantitative traits.

To answer your question
You are interested in the measure of fitness as a function of both environment and the protein under consideration. The relationship between the fitness (and other quantitative traits) and the envrionment is referred to as the reaction norm.

Here the graph display the quantitative trait (could be fitness) in the Y axis and environment in the X axis (as it is usually represented).There are two lines, for two different genotypes (the two different proteins in your case).

Can we show that the protein evolved to a degree to suit the different environment of species B compared to species A?

Well, looking at the graphs it looks like indeed one protein has been under selection in one environment while the other has been under selection under the other environment. Testing this is just a matter of statistics. Basically, to test for this, you run a linear model with the quantiative trait (eventually fitness) as the response variable and the environment, the genotype and their interaction as explainatory variables. If the interaction term is significant (and if the directionality of the interaction is the one you would expect, that is genotypes are more fit in the environment where they live and if each genotype outcompete the other in at least one environment), then the genotypes are locally adapted.
EDIT

what counts as significant?

You can chose the level of significance that you wish (0.05 for example). If this is unclear, you'll probably want to learn more about stats before.

can you provide an example of when this method you have described was used the literature to show the evolution of a protein?

If you want example from the literature you can just type Genotype by Environment Interaction on google scholar and will get tons of hits. Here is a paper discussing this methodology specifically and here is a (old) book on the subject. I am not sure why you're still talking about proteins. Most often those studies are done at the level of the gene (or directly on the phenotypic trait). But you can find the gene and get the protein sequence from it or even play around to visualize it with various biophysics softwares.

could you explain the stastics further, and give an example? other thstn that, great answer!

Sure. Can you point to what exactly is unclear/incomplete? If it is the very end (what follows "To test for this"), then you'll probably read a bit by yourself on wikipedia (linear regression, interaction) and eventually ask questions on stats.SE.

When you mean the interaction terms are signficiant, what counts as significant? Also, can you provide an example of when this method you have described was used the literature to show the evolution of a protein?

Please see the Edit section in my answer

In these two cases, what conclusions can we make in particular about
  the evolution of the protein itself?

It's not clear to me that it is right to make any evolutionary conclusions based on function alone.  DNA sequence would be a FAR better way to estimate evolutionary relatedness.


text:
Stretching and compressing bones
The Young's modulus of elasticity when a bone is stretched is : 16×109 and when it is compressed, it is 9×109 N/m2. That means, change in length will be more if you compress a bone as compared to stretching it.
What is the biomechanical reason behind this ?

I really don't know anything about this but it doesn't seem surprising that a material would have different tensile and compressive properties. I don't think there necessarily needs to be a biological reason for this difference in bone, though it's likely because of my naivity on the subject.

@canadianer hi ! In my textbook, they have cited different values of Y (tensile and compressive )only for bones ,for other materials - there is only one Y.

Citing your source would help to answer.
In order to test an elastic modulus, you need to apply some non-zero strain. If the strain is infinitesimal, then compression and stretch modulus will be equal. But if it is finite, then there can be a difference due to the structure of the material.
In bone, I believe porosity will provide most of the dissymetry between compression and extension: at small scales, the material can rearrange using the pores without much deformation. Whereas in extension, there has to be some deformation of the osteons.
In other living tissue, the difference can be due to filamentous proteins: if you compress them, they buckle (form loops) without much resistance. If you exert extensive stress, once they are stretched tight they will resist any further extension. (Think of what a piece of string would do, it's very similar)


text:
Cytoplasmic determinants - protostomes and deuterostomes
Cytoplasmic determinants are spread unevenly in the egg, and so when embryo starts forming (cells start dividing), the determinants are also unequally divided between cell. This unequal distribution later plays a major role in differentiation and gene regulation.
Protostomes undergo determinate cleavage. Their cells' fates are determined very early in development, whereas deuterostomes undergo indeterminate cleavage. So, if you take away a cell at early stage of development, it can be replaced.
Now if we compare the division of cytoplasmic determinants in protostomes and deuterostomes, what I said in the first paragraph seems true (to some extent) for only protostomes.
My questions:

Do deuterostome oocytes have even distribution of cytoplasmic determinants initially and  divide unequally only after certain number of divisions?
Are there any studies showing correlation between the stage at which determination happens in deuterostome and beginning of unequal division of determinants?

I dont have a definitive answer but the axis of cleavage can determine the nature of the daughter cells. Imagine an antero-posterior (AP) gradient of some determinant X. If the cell undergoes a division along AP axis the resultant daughter cells are identical. However, if the division is perpendicular to the AP axis then two different types of cells are produced (whose fate is in a way sealed).

The two distinct types you have mentioned in your question (determinate/indeterminate cleavage) are actually called autonomous specification and conditional specification, respectively.
In the case of the former one, if we were to remove a blastomere, it would still produce the previously determined type of cells, while in the case of conditional specification the cells, which are going to be produced, depend entirely on the neighbouring ones. The latter's ability to alter their fate is called regulation.
As for answering your questions, cytoplasmic determinants are spread unevenly in deuterostomes as well, as otherwise no axis could be developed.
You might be interested about this answer as well.
I've used the following book as source: Gilbert, S. (2000). Developmental Biology [ online version ]


text:
How does guanidium denature DNA?
Guanidium salts like (G-isothiocyanate) disrupt the hydrophobic interactions inside a protein or nucleic acid and denature it. What happens when hydrophobic interactions in DNA are broken? (I don't think it should get ssDNA because guanidium doesn't break hydrogen bonds within molecules)

Guanidium is a chaotrope i.e it increases the entropy in the solution. It doesn't disrupt hydrophobic interactions. Guanidium and urea act by forming hydrogen bonds. They can bond with both the dissolved macromolecule and water. The water molecules are arranged as a shell around the hydrophobic regions so as to contain it, which leads to the reduction of entropy. This containment causes hydrophobic regions to come together and give rise to a pseudo-interaction (hydrophobic interaction. See the figure below). Guanidium interacts with the water shell and disorders it, thereby reducing the hydrophobic effect.
Guanidium can also interact with macromolecules directly, by forming hydrogen bonds. In this process they can disrupt the normal H-bonds in the macromolecule.

So what would its effect be on dna ?

Just think about it: a molecule which can disrupt hydrogen bonds and increase water entropy. What can it do? :)

DNA becomes single stranded ?

yes it would...

It is important to realize that the hydrophobic effect is largely due to the exclusion of water from non-polar surfaces, which increases entropy. This effect is a major contributor to the helical structure of DNA, which effectively brings the bases closer together and excludes water from contacting their hydrophobic rings. Chaotropic agents like guanidine thiocyanate increase water entropy by disrupting its hydrogen bonding network (decreasing it's order) and this makes it more favourable for hydrophobic surfaces to be exposed to water, thus denaturation can occur. Implicit in that process is that GITC is a hydrogen bond competitor, which is also evident when looking at its structure. So, in fact, GITC can disrupt the hydrogen bonds between base pairs and denature dsDNA at high enough concentrations.
That all said, we're ignoring a major component of aqueous solutions that can also form hydrogen bonds with the bases: water itself! So we must ask ourselves that if a compound capable of hydrogen bonding (water) is present, what exactly is it that holds helical DNA together? While base pairing certainly does contribute, the major factors are the hydrophobic and base stacking interactions.


text:
Is there any evidence that a virus can modify human evolution
I was just reading Evolution of lactose tolerance, and in it one line says "But there was a time in human history when our diet and environment conspired to create conditions that mimicked those of a disease epidemic".
Something I've always wondered is rather than natural selection occurring and survival of the fittest and so on, is that a viral epidemic caused a mutation in the survivors, i.e. DNA was inserted from the virus that modified the survivors genome. There is some evidence that a significant percentage of the human genome comes from viruses. Probably a naive question - so is there any evidence that this has occurred? From my lay perspective this is what attempts at genetic engineering use, so it's possible nature already did this?
It's always seemed to me that natural selection and point mutations, and the chance meeting of two people with the same mutation would be too slow and viruses would be a more efficient method to evolve a large population at the same time. Things like punctuated evolution might support this? not really sure.

Why would two people with the same mutation have to meet unless the allele was recessive?

those viral elements are still being evolved and altered into useful things by point mutations why would it e less effective? viral segments don't come into the genome useful they have ot mutate into something useful afterwards.

There is some nice work from Pardis Sabeti in this broad area (not just viruses but pathogens in general). Her colleagues have found polymorphisms in SLC40A1, encoding an iron transport protein, that influence susceptibility to tuberculosis. She's also looked at human genetic variation and susceptibility to Lassa fever. And this paper talks about CD36 and malaria in sub-Saharan African populations (no association). Look at her work from 2009 onward, as there is a lot there. They're also looking at variation in the pathogen because it is a two-way interaction.

The simplest example, that I can recall are the flu pandemics. The 1918 pandemic is the first to be described because of its severity, but quite possibly not the first in human history (see for example the Black Death - Yersinia pestis is a bacterium, but in the 15th century in just a few years it covered almost all of Europe, sometimes killing up to 40% of population in a given area).
Influenza pandemics appeared quite regularly during the 20th century, usually every 20 years and killed suspiciously many people compared to yearly influenza strains. Additionally, a person who survived one pandemic, was unaffected or only mildly affected by the next pandemic.
All this suggests, that the pandemics "clear" the population from susceptible individuals, and regularity of pandemics (notice, that 20 years is more or less the time of one human generation!) assures that the new generations also go through this kind of selection. The surviving individuals are more resistant to all strains of influenza then those, who never suffered from a pandemic. Maybe the influenza didn't mutate our DNA, but it could be a major force of natural selection.
And one more note: did you notice the great noise in media every time a new potentially pandemic strain is discovered? Actually, it's not just hyperboly of the danger. Last pandemic was in the '70s, so it's high time for a new one. And, since the last one was  almost 40 years ago, the new one (when it happens) will probably be very severe.

indeed, but the selection there is can this virus/bacteria kill me. You could argue that certain personality traits/intelligence etc was a byproduct of this - e.g. a fear of rats from the plague, and perhaps an intelligent person would be more inclined to notice patterns and adjust their behaviour to avoid infection. I was wondering if there was a more direct result - fragments of dna inserted into genomes that altered organisms, certainly possible I'd imagine - was wondering if it ever actually happened - that anyone knows about anyway.

I think it did, but right now this is just a vague memory of an Evolutionary Genetics lecture. I'll find more time tomorrow, and try to locate my notes and the actual data.

"[...] the new one (when it happens) will probably be very severe.". You were right about that.

all_licenses: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/


text:
Up to date B cell review
Where would I find an up to date (last 6-7 years max) review on B cells? I've tried searching through pubmed with filters, cochrane library, medline and various other resources including searching old questions. A textbook would be fine too, but I'm not sure which one would give me detailed information. I'm a BSc student studying immunology. I'm not trying to create a war of "best" answers, any answer that fits these criteria I will accept.

what specifically about B cells are you interested in? The possible subject matter is so broad that I doubt you'll find reviews covering all of B cell biology and function. A recent immunology text might be better.

@MattDMo Essentially a standard textbook on immunology level detail but more up to date like novel knowledge on how BCR are activated (for example I read that the cross linking model is widely disputed) etc. Not something that just focuses on the concrete but delves a little further and includes up to date research

Do you have any references for the BCR cross linking model dispute? I'm not working directly in the field now, so I'm not as up to date as perhaps I should be...

Cellular and Molecular Immunology by Abul Abbas et al. is pretty good, and you can't beat Charlie Janeway's Immunobiology either. Both will give a good introduction to B-cells, antibodies, BCR signaling, and how they fit in to the immune system's structure and function. I own earlier editions of both, and their different perspectives are good for getting a more holistic understanding of the field. Good luck in your studies, it's a fascinating subject!

looking into these! Thanks. And totally agree I love it like anything

@AndroidPenguin If you're looking for reviews on specific subjects in journals, some of the journals I turn to include Annual Reviews in Immunology, Trends in Biochemical Sciences, Cell, Nature Reviews, Nature Reviews Immunology, and Trends in Immunology, among others. It's quite possible to find great reviews in lower-impact journals like the Journal of Immunology, and you'll often find more esoteric reviews there as well, but for now I'd stick with the real biggies like the ones I mentioned.

I agree entirely with Matt, Abbas and Janeway's books are the standard for even graduate-level introductory Immunology. Both are easy to read and well organized. Definitely start here.
However, depending on what you have access to and the depth of reading you want to do, there was an Annual Review of Immunology issue some years ago (maybe 2003?) that discussed a number of B Cell topics (signaling, fate decisions, etc). I also see that there is a newer article:
"B Cell Signaling and Fate Decision"
Annual Review of Immunology 28: 21-55 (Volume publication date April 2009)
Tomohiro Kurosaki, Hisaaki Shinohara, and Yoshihiro Baba
that might be pretty general if you have access through a university.
Good luck.
By the way, I think the disagreement about BCR crosslinking is for survival/development (i.e., are 'tonic' signals sufficient to allow cells through development?) As for activation, B cells are triggered either by antigen-specific BCR crosslinking or more general TLR activation (e.g., LPS).

could you post Pubmed/DOI links so others can find the article you're referencing? They're more likely to be "permanent" (long-lasting) than are direct journal URLs, which can and do change.

Good point. Done.


text:
Ill effects of urea and NH₃ on metabolism
What exactly does urea do that harms our body? Does it interfere with our cellular processes or disturbs the colloidal onchotic pressure of our blood?
I have heard that NH3 damages the brain. What does it actually do?

Urea and ammonia are two very different molecules, except for the fact that urea is a metabolite of ammonia, they have almost nothing in common in a chemical sense. I would suggest that you restrict your question to one of those molecules, and maybe add some more detail about what exactly you are interested in.

The denaturing effect of Urea is mostly at very high concentrations.   (~Molar levels)!
Physiologically, urea, a product of the breakdown of retired amino acids, will build up rather quickly if it weren't secreted in the urine. Looking into this, it doesn't seem as there is a clear understanding of why this causes a disease, though the buildup of a waste product definitely is a unifying concept.
Uremia - kidney failure - causes a build up of urea in the blood as the kidney eliminates urea from the blood into the bladder.  The specific effects of Urea on cell metabolism are probably numerous as the symptoms:  anorexia and lethargy, and late symptoms can include decreased mental acuity and coma. Other symptoms include fatigue, nausea, vomiting, cold, bone pain, itch, shortness of breath, and seizures.
Being a metabolic waste product, it certainly would interfere with and inhibit any enzyme that produced urea - the Urea cycle in particular.  Its clear that uremia is ultimately associated with cell death, oxidative stress, some cell signalling and proliferation.
I'm just googling around here, but I don't think there is any one single answer as to what goes wrong when the cells are exposed to too much urea.

@SatwikPasani you may be interested in this answer in relation to one of your questions.


text:
Why deoxyribose for DNA and ribose for RNA?
Why is DNA made out of deoxyribose and RNA made of ribose? Why can't they both use ribose or deoxyribose? I think that the deoxyribose gives an advantage in storing genes, the job of DNA and ribose is better dealt with outside the nucleus...but why?

The vast majority of RNA in most cells is found in the ribosomes, where it is largely double-stranded and quite stable (and ribosomes are not typically in the nucleus), so answers about relative stability, sub-cellular localization, and strandedness are not germane.

The nucleus is irrelevant. DNA and RNA arose in non-nulceated organisms (prokaryotes).

Nice question which leads to the fundamentals of DNA and RNA.
DNA (Deoxyribonucleic acid) is the core of life in Earth, every known living organism is using DNA as their genetic backbone. DNA is so precious and vital to eukaryotes that its kept packaged in cell nucleus, its being copied but never removed because it never leaves the safety of nucleus. DNA directs all cell activity by delegating it to RNA. RNA (Ribonucleic acid ) have varied sort of biological roles in coding, decoding, regulation, and expression of genes. RNA carries messages out of the cell nucleus to cytoplasm.

The structure of RNA nucleotides is very similar to that of DNA nucleotides, with the main difference being that the ribose sugar backbone in RNA has a hydroxyl (-OH) group that DNA does not. This gives DNA its name: DNA stands for deoxyribonucleic acid. Another minor difference is that DNA uses the base thymine (T) in place of uracil (U). Despite great structural similarities, DNA and RNA play very different roles from one another in modern cells.
http://exploringorigins.org/rna.html

RNA has three main characteristics that differs it from DNA

RNA is very unstable and decomposes rapidly.
RNA contains Uracil in place of Thymine
RNA is almost always single stranded.

DNA and RNA use a ribose sugar as a main element of their chemical structures, ribose sugar used in DNA is deoxyribose, While RNA uses unmodified ribose sugar.
Ribose and Deoxyribose

From the fig above we can see that the principal difference between
  the two molecules is the presence of OH in ribose (2' tail) and absence
  in deoxyribose. There is a difference in one Oxygen atom as the name
  stands de-oxy ribose. Both Ribose and deoxyribose have an Oxygen(O)
  atom  and a Hydrogen (H) atom (an OH group) at their 3' sites. The OH
  groups are very reactive in nature, so the 3' OH tail is required for
  phosphodiester bonds to form between nucleotides in both ribose
  and deoxyribose atoms.

Answer
DNA is such an important molecule so it must be protected from decomposition and further reactions. The absence of one Oxygen is the key for extending DNA's longevity. When the 2' Oxygen is absent in deoxyribose, the sugar molecule is less likely to get involved in chemical reactions( the aggressive nature of Oxygen in chemical reactions are famous). So by removing the Oxygen from deoxyribose molecule, DNA avoids being broken down. In an RNA's point of view the Oxygen is helpful, unlike DNA, RNA is a short-term tool used by the cell to send messages and manufacture proteins as a part of gene expression. Simply speaking mRNA (Messenger RNA) has the duties of turning genes ON and OFF, when a gene needed to be put ON mRNA is made and to keep it OFF the mRNA is removed. So the OH group in 2' is used to decompose the RNA quickly thereby making those affected genes in OFF state.
Finally, the ribose sugar is placed in RNA for easily decomposing it and DNA uses deoxyribose sugar for longevity.

References
Flesh and Bones of Metabolism -  Marek H. Dominiczak
Genetics For Dummies -  Tara Rodden Robinson

Do you have a reference for the claim that the 2'OH is important for regulating mRNA? My intuitive guess would be that active degradation by RNAses would be far more important than the chemical instability by the 2'OH.

@MadScientist: References are attached on the bottom of the answer. It must be  the selective advantage of DNA over RNA as the genetic material.

As far as I know, the hydrolysis of RNA via the 2'OH doesn't play any role in regulating mRNA levels, there are lots of active RNA degradation mechanisms that are responsible for that.

"RNA is very unstable and decomposes rapidly.".. this is not a correct statement... it is not thermodynamically unstable.. It is chemically unstable given the physiological or alkaline environment.

@WYSIWYG: I meant it is chemically unstable

@MadScientist: As mRNA is unstable due to the presence of 2' OH and degrading enzymes(ribonucleases) involvement. But the question is related to the usage of ribose & deoxyribose in RNA & DNA. The 2' hydroxyl in mRNA is frequently methylated, so I think the instability of OH in RNA is reasonable for the degradation.

"DNA is so precious and vital to eukaryotes that its kept packaged in cell nucleus, its being copied but never removed because it never leaves the safety of nucleus." You do realize that in most Eukaryotes, the Nuclear Envelope breaks apart during Mitosis and Meiosis? Prokaryotic bacteria and Archaea also use DNA, but don't have nuclei. Mitochondria have their own DNA and genome, yet they are organelles inside the majority of Eukaryotic cells. Red Blood Cells discard their genomes when they terminally differentiate, and those are kind of important to the life of most land animals.

"RNA is almost always single stranded." Nope. RNA forms double strands frequently, and needs to be straightened out when entering the ribosome. RNA that is not formed into some kind of secondary/tertiary structure is unusual, not the other way around.

Then why do many viruses use RNA?

I am obviously biased, but find this a very poor answer to have been accepted. It is puffed out by unedited quotes of basic information and empty statements about molecules being 'important'. It contains factual inaccuracies  "every known living organism is using DNA" (RNA viruses?) and sloppy expressions such as "genetic backbone". There are no links to original literature. No links are given to the listed references, but the citing of "Genetics for Dummies" does not engender confidence in them. Oh well, @Tanmath, you pays your money...

Another importance of RNA (specifically tRNA) is also its responsibility for the transcription of information from codons in protein synthesis

Addition to Jvrek's answer based on the comments. Most RNA degradation mechanisms catalysed by different RNAses (RNAse-A and RNAse-S, for example), involve the 2'-OH. Therefore the repertoire of RNAses is selective towards RNA and not DNA because of the 2'-OH.

Why DNA for the genetic material?
I think the correct and sufficient answer to this is the one so frequently repeated that it is difficult to find the original source. For example, G.F.Joyce wrote in a 2002 Nature review article:

The primary advantage of DNA over RNA as a genetic material is the greater chemical stability of DNA, allowing much larger genomes based on DNA.

To expand, RNA is unsuitable for large genomes because the 2'-OH of ribose (obviously absent from the 2'-dexoyribose of DNA) renders the phosphodiester bond susceptible to alkaline hydrolysis (see illustration adapted from Wikipedia article).

This will occur slowly at pH 7.6, but at a rate calculated to be sufficient to degrade a 1000 nucleotide RNA in about 70 days. This explains why all RNA viruses have small genomes (and why some, like flu virus, are segmented).
Why RNA for other informational functions?
There are a variety of ad hoc arguments here, but none as conclusive as the argument above for DNA. This is partly because there are a variety of functions RNA performs — one can make different arguments for each. Before making a point that I don’t think has been made above, I would say that RNA most likely preceeded DNA (whether or not one believes it preceeded protein) and that there would have had to be a selective advantage for organisms to switch from RNA to DNA. One can see that for the genome, but not for the other functions.
This argument also applies catalysis, but in a slightly different way. If RNA enzymes (ribozymes) preceeded protein enzymes, most ribozymes have been dumped because protein enzymes are more efficient and organisms which developed them were at an advantage. Those that are left are so intimately involved with RNA that replacement by proteins would have been difficult. So answers to this question about DNA not being able to replace catalytic RNA, though correct, seem to me peripheral the general question of RNA function.
The central function of RNA is surely in protein synthesis — mRNA, rRNA, tRNA. One thing that these perhaps have in common is a three-dimensional structure that differs from an extended double helix. (Yes mRNA has tertiary structure too.) RNA lends itself more readily to such structures because the chemical difference between ribose and deoxyribose leads to a different helical structure (A-helix) from that of DNA (B-helix). To quote Fohrer et al.:

The presence of the ribose 2'-hydroxyl group in RNA engenders a preference for the C3'-endo puckering, thereby providing the decisive factor for the differences in conformation, hydration and thermodynamic stability between canonical RNA and DNA helices.

(Image from Niel Henriksen showing C3'- and C2'-endo pucker of ribose. C2'-endo pucker is found in deoxyribose in the B-DNA helix.)
The RNA A-helix involves less stringent base-pairing than the DNA B-helix (hence the greater error frequency in replicating RNA virus genomes), which is also reflected in non-WC base-pairing in rRNA and tRNA. (The presence of U in RNA, rather than T in DNA should also be mentioned — GU base-pairs are found frequently in rRNA.)

+1 for the RNA hydrolysis point. Could you mention what the half-life of RNA in water is? Would help to judge how serious the RNA hydrolysis issue is.

@Roland - According to J. Am. Chem. Soc., Vol. 121, No. 23, 1999 (p.5371) the rate constant for RNA hydrolysis is 1.4 × 10-7 min-1 at 37C and pH 7.4, which works out as a half life for a 1000 nucleotide RNA of 70 days. (The paper quotes half lives for the much greater rate constant at 100C, in relation to thermophiles).

Excellent! That definitely shows RNA is too easily degraded to be viable as genetic material.

If the degradation mechanism is alkaline hydrolysis... does that mean RNA is more stable in acidic environments?

@LoganR.Kearsley —  Yes, I think that is so, and I seem to recall it is one of the arguments used against the RNA world theory. I'm just off for a week's vacation and will check and answer more fully when I get back. Oh, just found the type of paper I was thinking of. Haven't had time to read it though: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3372908/


text:
How to get Population Genotype Frequency from 1000 genomes Perl API
Posted a similar question on Biostars but got no response. Not sure if I'm allowed to link to it? Basically I want to pull genotype frequency data for a population group (such as CEU) instead of allele frequency data, via the Perl API for 1000 genomes. I have tabix and perl API installed. This is for 100,000+ SNPs so the solution should hopefully not involve manually downloading genotype and calculating the frequency manually in a for-loop. My understanding also is no solution exists in BioMart (according to the Biostars answer).
Following the instructions here, I can see how to get specific genotypes for all individuals as a list.
Eg: Input -> Some snp, CEU... Output -> G/G 0.87, G/A 0.13 (frequency of some snp for CEU population).
I need to do this for 100,000+ SNPs, so I imagine manually pulling all genotypes for each SNP and calculating the frequency manually in a loop would not be practical.

Please add a link to the data repository and show a dummy example of the data format. Questions about a specific programming language are considered off-topic. So you should edit the question to make it "Language-neutral", focussing only on the methodology rather than the actual script.

Hi, I think Perl is the only way to access the 1000 genomes data genotype frequency, according to this post: https://www.biostars.org/p/153923/#153929 Unfortunately I got no further answer there on how to actually do this.

Can you add a link to the actual repository? You may be able to simply download the entire data (from here perhaps) and parse for the desired data. Moreover, the API mentioned in your link would allow you to customize the data that you want to download. You may have to do it one by one using a loop.

I'm new to 1000 genomes so not sure how to access the data directly, I've just been following the perl API tutorial for homo sapiens as per the link. That link you provided seems helpful but it looks like I'll need to manually iterate through the hundreds of genomes and calculate the frequency in the loop as you suggest, rather than there being an actual functional call like there is for allele frequency? I think if that's the case I'll just stick with the HapMap genotype frequency data.

You don't have to manually do it. Get the VCF or GVF file.  A small script will parse the desired co-ordinates in a few minutes (or less than that).

At the very bottom of the Ensembl link you provided it explicitly suggests using their mailing list if you have further questions. That might be more productive then hoping someone in Biology SE has experience with the API.

If you want population specific allele frequencies you have three options: * For a single variant you can look at the population genetics page for a variant in our browser. This gives you piecharts and a table for a single site. * For a genomic region you can use our allele frequency calculator tool which gives a set of allele frequencies for selected populations * If you would like sub population allele frequences for a whole file, you are best to use the vcftools command line tool.
This is done using a combination of two vcftools commands called vcf-subset and fill-an-ac
An example command set using files from our phase 1 release would look like
grep CEU integrated_call_samples.20101123.ALL.panel | cut -f1 > CEU.samples.list
vcf-subset -c CEU.samples.list ALL.chr13.integrated_phase1_v3.20101123.snps_indels_svs.genotypes.vcf.gz | fill-an-ac |
    bgzip -c > CEU.chr13.phase1.vcf.gz
Once you have this file you can calculate your frequency by dividing AN (allele number) by AC (allele count)
Please note that some early VCF files from the main project used LD information and other variables to help estimate the allele frequency. This means in these files the AF does not always equal AC/AN. In the phase 1 and phase 3 releases, AC/AN should always match the allele frequency quoted.

Another possibility is to use glactools. I will show this by using data from the 1000 genomes.
First, we download the chromosome names and length for the reference:
 wget ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.fai

We then require information on the panels from the VCF file:
  wget https://personal.broadinstitute.org/armartin/ginger/integrated_call_samples_v3.20130502.ALL.panel.txt

 grep -v ^sample integrated_call_samples_v3.20130502.ALL.panel.txt  | cut -f 1,3  > panel.txt

You can run the following to transform VCF into allele counts format (ACF):
 tabix -h ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr2.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz 2:136486829-136653337  |glactools vcfm2acf --onlyGT --fai human_g1k_v37.fasta.fai  -  |glactools meld -f panel.txt -  | glactools view -h -

This will print the allele counts:
#chr    coord   REF,ALT root    anc AFR AMR EAS EUR SAS
2   136486850   G,T 0,0:0   0,0:0   1322,0:0    694,0:0 1008,0:0    1006,0:0    974,4:0
2   136486967   C,T 0,0:0   0,0:0   1321,1:0    694,0:0 1007,1:0    1006,0:0    978,0:0
2   136487007   C,T 0,0:0   0,0:0   1322,0:0    694,0:0 1007,1:0    1006,0:0    978,0:0
2   136487181   C,T 0,0:0   0,0:0   1322,0:0    693,1:0 1008,0:0    1005,1:0    978,0:0
2   136487214   G,A 0,0:0   0,0:0   1321,1:0    694,0:0 1008,0:0    1006,0:0    978,0:0
2   136487246   G,A 0,0:0   0,0:0   1282,40:0   693,1:0 1008,0:0    1006,0:0    978,0:0
2   136487336   G,T 0,0:0   0,0:0   1322,0:0    694,0:0 1008,0:0    1006,0:0    977,1:0
2   136487417   G,A 0,0:0   0,0:0   1321,1:0    693,1:0 1008,0:0    1006,0:0    978,0:0
2   136487504   A,C 0,0:0   0,0:0   1316,6:0    694,0:0 1008,0:0    1006,0:0    978,0:0


text:
Difference between null and recessive allele?
I get that in a single gene locus, an individual can have RR, Rr, or rr as the two alleles for that gene. R is "wild type" because it is the allele occurring most frequently. r is the allele that is not WT.
RR and Rr show dominant phenotypes, whereas rr shows the recessive phenotype.
But what's the difference between r and a null allele (allele generated by a loss of function mutation outputting the complete loss of the WT phenotype)? Where _ is a null allele, my questions are below:

R _ would produce the same as Rr, correct or not?
r _ would produce the same as rr, correct or not?
_ _ would produce the same as rr, correct or not?

Good question +1. Unfortunately, the mechanisms by which dominance work is relatively poorly understood and it is likely that the mechanism differs from one locus to another.
You might want to have a look at the posts

Why are some genes dominant over others? What is the mechanism behind it?
Evolution of dominance

or some papers such as

Llaurens et al. (2009)

I don't think one can make any general prediction about the phenotype of R_, r_ or __ without having a priori knowledge of the biological pathway (incl. allele interaction (see Llaurens et al. (2009)) and gene interaction network) by which this particular locus is affecting the phenotype. It is tempting to say that R_ is alike Rr or RR, and r_ is alike rr but this is not necessarily true.

To add to Remi b's answer - this question is confusing because 'null' and 'recessive' are terms emerging from two very different levels of analysis. The concept of 'recessive' existed before we knew what genes were, or how they worked. It just describes the patterns of inheritance you see in a gene's effects.
The concept of a 'null' allele however came later, and explicitly describes how an allele works - by destroying gene activity. So 'null' is molecular concept, 'recessive' is an abstract genetic concept. It so happens that null alleles are very often recessive, because usually one working copy of a gene is fine. But the two terms are describing genetics at very different levels.

That makes sense. Why scientists don't change the nomenclature?

Because both levels of genetics are still very much in use. We often want to talk about molecules, but if we have a family tree, or an association study, or a mathematical model of inheritance, we also want to talk about the effects of mutations while remaining agnostic about the molecules.

Basically, a recessive allele leads to formation of a product that has a low activity or no activity, which is complemented in the presence of the dominant allele (there can be effects related to dosage, in some cases). This can be easily understood in terms of an enzyme; a dominant allele would code for an enzyme with full activity whereas the recessive allele codes for one with a reduced activity. There are further complexities but this is a simple example.
A null allele however results in zero activity of the gene. This may be because of many reasons:

The allele may produce a non-functional protein (for e.g. an enzyme
with mutated active site such that it cannot carry out the catalysis)
The geneic region of the allele may be transcribed but not translated (loss of ORF)
There may be no transcription at all (deletion of DNA sequences
critical for transcription)

In cases where there is no dosage effect, a null allele is always recessive but the converse is not true.

R _ would produce the same as Rr, correct or not?
r _ would produce the same as rr, correct or not?
_ _ would produce the same as rr, correct or not?

The first two these assumptions are true for a simplistic case (no dosage effects). Since, r is a hypomorphic allele (by assumption) i.e. it has a reduced activity whereas _ has zero activity, _ _ may not have the same phenotype as rr. Only in cases where there is a threshold on the activity leading to phenotype, can a low activity allele/genotype (activity below threshold) lead to same phenotype as the null allele.
If we add further complexities, R _ or r _ may not be functionally equivalent to Rr or rr respectively. Even RR may behave functionally different than Rr. This would happen because of altered gene dosage (expression level) and reduced expression level of the functional product can cause a change in the net activity. (Also see: Can difference in the expression potential of alleles lead to dominance?)

It is not true that a null allele is always recessive. R_ can have a different phenotype from RR if gene dosage matters.

@JackAidley True. I have mentioned gene dosage. I also clarified that when dosage matters then even heterozygotes would behave differently from the homozygotes. Basically the concept of dominant/recessive alleles somewhat breaks down when dosage is important. I have clarified all these exceptions. However, the null allele may still be considered recessive because the presence of R will at least partially complement it. I added a statement to explicitly mention this.


text:
How do CO₂ and carbonic acid (H₂CO₃) work in buffering the blood?
Been struggling with this for the past few days even after reading half of the acid base tutorial here, if someone could help me that'd be great.
What I don't understand is how HCO3- is supposed to buffer the blood. I know that HCO3- is a base and can accept H+, but the way that the HCO3- came to fruition is by donating a H+ to the surrounding water, so there's a net zero change in H+ thus no buffering action took place. Let's say a HCO3- accepts a H+, now the CO2 produced by H2CO3 → CO2 + H2O leaves the blood because the PvenousCO2 gets higher than the CO2 pressure in the air in the lungs, and you exhale. Now you're in the exact same situation as before the CO2 got attached to H2O.
Still the text calls it as an buffer, with a very large buffering capacity as well. How does this work?
To me it seems that buffering blood using HCO3- makes as much sense as using HCl, Cl - can accept H+, right? Nevermind that HCl is a very strong acid.. Surely no one would think of using HCl to buffer blood.

I just have one question for you. If the body could regulate the amount of HCO3-, in effect generating new buffer, would that help you to understand how it is the major buffer that it is?

maybe, not sure if I understand it now

Wish you had answered me days ago.

What do you mean by "there's a net zero change in $\ce{H+}$ thus no buffering action took place"? The property of a buffer system IS to prevent drastic change in pH.
Buffer capacity, a measure of how much a buffer system can sustain a change in $\ce{[H+]}$ (aka. pH), (mostly) depends on two parameters -- the concentration of that buffer, and how close the desired pH is to its pKa. $\ce{H2CO3}$ has pKa's of 6.4 and 10.3. Given that the pH of blood is about 7.4 and better to stay that way, the base/acid pair, $\ce{[HCO3_^{-}]/[H2CO3]}$ (pKa=6.4) (plus a whole bunch of various proteins such as albumins in blood, all of which has its own pKa) does provide a good buffer capacity around that pH.
True, $\ce{CO2}$ is constantly removed through respiration, but it is also constantly generated by cellular respiration, making $\ce{H2CO3<=>CO2 + H2O}$ a "volatile equilibrium" and keeping both $\ce{HCO3_^{-}}$ and $\ce{H2CO3}$ in high enough concentration to sustain its buffer capacity.
HCl has a pKa of about -7 so it would make a good buffer around pH of -7. In an aqueous environment, all HCl molecules will 100% dissociate, and no $\ce{H+}$ will ever bind to $\ce{Cl-}$ because water itself will first "hijack" the proton as  $\ce{H3O+}$ (pKa=-1.74) before $\ce{Cl-}$ by about five order of magnitude.
---EDIT---
You may be thinking that when cells release $\ce{CO2}$ to the blood, $\ce{H2CO3}$ would be the first product, and in order for $\ce{H2CO3}$'s conjugate base to work as a base to absorb any extra $\ce{H+}$, first it must release a $\ce{H+}$, resulting in no net change in free $\ce{H+}$ and hence no capacity in balancing extra or insufficient $\ce{H+}$ to maintain the pH. Indeed, if $\ce{H2CO3}$ is the ONLY chemical species in the blood when it would not be a buffer. A buffer requires at least two species -- a potential proton donor and a potential proton acceptor, both of which in high and comparable concentration. pH is a measure of external free $\ce{H+}$, a result of final proton balance of all the acid and base in the blood, dictated by the Henderson–Hasselbalch equation. Thus when $\ce{H2CO3}$ is released in the blood, the blood's basic pH will causes most of $\ce{H2CO3}$ to become $\ce{HCO3_^{-}}$, releasing free proton. Again IF that's all the $\ce{HCO3_^{-}}$ in the blood after being made from $\ce{H2CO3}$, the blood's pH will drop, but there is already abundant amount of $\ce{HCO3_^{-}}$ in the blood, helping the system to reach new equilibrium. Of course, the buffer capacity of blood is not infinite. If there is so much metabolic acid being produced that it shifts the ratio of $\ce{[HCO3_^{-}]/[H2CO3]}$ toward excessive acid, acidosis would occur.

I'd hate to see what it takes to get water at pH of -7.

@user137 it need not be water.. It can be any solvent. Base/acid/salts etc are defined with respect to a solvent (which is water in most cases). If H₂SO₄ is the solvent then K₂SO₄ will be a base, not a salt. You can also imagine what if ammonia is the solvent.

What do you mean by "there's a net zero change in H+ thus no buffering action took place"? I mean that the H+ absorption is nice and all, but it's only made possible by producing a H+ at an earlier step. It's like saying glycolysis produces 4 ATP - it does of course but there's 2 ATP needed for glycolysis, so the net gain in ATP is only 2. I accepted your answer btw, thanks for the help (and commenters) but I'm not sure if I understand it any better now.

I think I have better understood your difficulty. You may be thinking that when cells release CO2 to the blood, H2CO3 would be the first product, and in order for H2CO3's conjugate base to work as a base to absorb any extra H+, first it must release a H+, resulting in no change in free H+ and hence no capacity in balancing extra or insufficient H+ to main the pH. Please see Edit.

I don't personally understand how you can discuss this buffering system without discussing the role of the kidneys.

Isn't that like saying 'glycolysis produces 4 ATP, we can ignore the 2 ATP that are needed for glycolysis because cells are bursting with ATP'? The net effect is +two ATP, like here it's +zero H+. Anyway thanks for the help I'll go back to review basic buffer/law of mass action and the role of the kidney in acid/base balance, I think that'll help. Sucks that I can't find a source that describes the big picture, everything I found so far separately describes all the systems (lungs, kidneys, red blood cells) involved without drawing a lot of connections with the others systems.


text:
Effect of the health of the male parent at the time of conceiving
Does it matter at all in determining the traits of a baby what the current health of the father is? For example, let's say I got diabetes at the age of 40 because of the poor lifestyle choices. Will the baby be any different from how it would be if it was when I was say 26?

It can matter, though at this point we are just starting to understand how much.
Men can typically have children much later in life than women, but there are costs as time goes on.
Epigenetics has shown us that what happens to the parents in their lifetime can affect his offspring.  Obesity especially has been shown to affect the offspring, producing a higher risk of diabetes for two generations.
It is thought that this is not going to affect fathers who develop diabetes at a later age, but primarily those who are obese around 9-12 y.o. when the spermatogenic cells are produced in the testes.
What happens to men as they get older though is that their ability to produce healthy sperm starts to degrade.  They can lose fertility and produce more birth defects typically as early as age 35.  Given this there are probably a lot of habits or events that can adversely affect fertility.
Lifestyle choices as simple as tight underwear which might block blood flow to the testes is sometimes cited.
Given all this DNA or cellular damage from chemicals or diet or poor health certainly would also affect male fertility.


text:
What’s this bug? Sign of an infestation? Found crawling up the side of my washing machine. [WA]
Just spotted this bug on the side of my washing machine after putting some dirty clothes in the hamper and transferring a damp load to the dryer. I’m hoping it came in from outside somehow, and isn’t some type of vermin (I live in an apartment and I’m probably the cleanest resident in the building. I’m also paranoid about household pests.) It’s very small, photographed against a damp paper towel. Please tell me this is not a baby roach?

Rob Dunn's lab at NCSU does all kinds of neat projects looking at the diversity of organisms living in people's homes. Possible household organisms includes over 1000 possible insects, and often times more than 100 invertebrates living in single home -- and cleanliness has nothing to do with it! (source: Michelle Trautwein).

Don't worry, it is definitely not a roach. It is a true bug, Hemiptera. Not a household pest.

Can you say a few words how you know this? What sorts of features allow you to characterize it as Hemiptera? Mostly for those of us (me) who know nothing about insect phylogenetics.

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/


text:
Telomere and its effect on aging
The cloned sheep, Dolly, was said to have died very soon because the cells used to create it were taken from an adult sheep with an aged telomere. Why doesn't this happen with humans? Why aren't we born with 25 years less lifespan?

Our telomeres shorten as well with every division, except for stem cells (which have an active telomerase). The maximum number of divisions is called Hayflick limit.

Broadly speaking there are two classes of cell in an organism:

Somatic cells

These are by far the most numerous in your body, and are the differentiated cells including everything from retinal cells to liver cells to neurons.

Stem cells and germ cells

Stem cells reside in tissues and replenish the somatic cells as they are damaged or removed, or as the organ grows,
Germ cells - in particular oocytes in women's ovaries - are pools of immature eggs that are generated when a women is still a foetus in her own mothers womb!

The difference between these two types that relates to your question is that somatic cells have a limited replicative lifespan - a limit to the number of times they can divide - because their telomeres (caps to the ends of chromosomes) erode during cell division, whereas stem cells are able express the enzyme telomerase which extends the telomeres and allows cells limitless replicative potential (excluding other factors). Replenishing telomeres is a major step in cancer progression [1].
Embryonic cells have 'complete' telomeres when they are fertilised and begin to proliferate into a new organism. Interestingly the telomere length of the germ cells is not at all related to fertility [2], suggesting to me that telomerase is expressed for a while post-fertilisation, so the length prior to fertilisation is not important.
Dolly was produced by a process called Somatic Cell Nuclear Transferase, where the nucleus from a somatic cell from an adult organism is transplated into an embryo with its nucleus removed [3]. A study found that she had consistently shorter telomeres corresponding to the fact that the original donor was 6-years old already [4]

You might also be interested in my answers to these questions

Are human bodies programmed to die?
Cell proliferation limit and senescence of embryonic stem cells and fibroblasts
Do trees age on a microscopic level?
Difference In Telomeres Between A Thale Cress Plant And A Methuselah Tree

Shay, 2001, Human Molecular Genetics. Telomerase and cancer. http://hmg.oxfordjournals.org/content/10/7/677.full
Turner, 2013, Mol Hum reprod. Telomere lengths in human pronuclei, oocytes and spermatozoa. http://www.ncbi.nlm.nih.gov/pubmed/23519357
http://learn.genetics.utah.edu/content/cloning/whatiscloning/
Shiels, 1999. Cloning. Analysis of telomere length in Dolly, a sheep derived by nuclear transfer. http://www.ncbi.nlm.nih.gov/pubmed/16218837