text:
if sperm contains only 50% of someone's DNA how can it be used to identify someone?
Is DNA so unique that 50% of it is enough to identify a single person?

any single sperm cell contains half the DNA, but a typical sperm sample has many millions of cells, so in total, the entire DNA is available.

You make one mistake: The set of chromosomes in sperm and egg cells is haploid, this means that there is only one copy available in each cell instead of two.

@user137 Every sperm cell has the complete set of genes. But only one copy instead of two. So each sperm cell is enough to identify its owner.

@Chris It's way late here, I'm tired. And how often does someone ID a person based on a single cell?

@user137 For forensics this happens.

@Chris In a forensics example, are they finding a single cell, isolating its DNA, then running PCR, or do they just run PCR on a sample and hope that at least a single cell's worth of the suspect's DNA is in there?

@user137 I know a case from Germany where terrorists left one or two hairs at the crime scene. These were sucessfully used to identify the person who lost them. I am not too much into crime forensics, but here you have to amplify the DNA first. And make sure you have no contaminations.

Your both wrong- there is no guaranteed 100 percent proof to ID someone from DNA. look into the numbers generated to give the 99 percent chance. They say million to 1 in that persons ethnicity group.There is no way to identify a humans ethnicity either.

@TheVoid There are issues with DNA identification, especially if the lab is doing a sloppy job, but DNA has to be more reliable and objective than fingerprint identification or eyewitness reports.

The comment from @User137 pretty much gets it: the mix of all sperm cells in even a small sample will contain the whole genome on average. So in the hair example in the comments above, there are probably a good number of dead cells hanging onto the hair, enough for analysis. Meiosis will redistribute the DNA sequences inherited from mom and dad randomly, so each sperm is in theory a unique patchwork of that person's genome, but overall the genome will be covered well. Single-cell work, on the other hand, is technically very challenging.
[edit: here is an article describing methods for low-input analysis of forensic samples. Unfortunately paywalled.]
To directly answer the OP on uniqueness: absolutely a single sperm is that unique for each person, in principle. There are lots and lots of genetic variants in each human, and everyone represents a unique mix. It is estimated that 1/1000 places in the genome of each person differ from any other person, on average (for substitutions). there are 3*10^9 places in the genome for this to be the case, which gives you a very large number of differences, ASSUMING that you can actually ascertain all those differences. [edit: for a discussion of these stats see here.]
The technical problem with forensics is that often they only look at a few places in the genome (microsatellites usually), because it is relatively expensive and hard even with recent technology to look at more than that in any detail. This leads to the non-trivial possibility of misidentification with the standard battery of loci. This possibility never goes away entirely, but it becomes very small with more data. I am not a forensic scientist, possibly they have gotten more comprehensive or the methods have changed in recent times.
[edit: here is a document that has what appears to be a readable introduction to DNA forensics, including technical discussions of some drawbacks of marker panels used by for instance the FBI of the USA.]

It would be more difficult to identify someone from a single sperm cell, rather than other cells contained in their semen.
However, if we are just comparing the DNA from any diploid cell in the body, you run electrophoresis to compare DNA samples.
For example, if you wanted to establish the paternity of a child. You would collect a sample of the child's DNA, the mother's DNA and the possible fathers' DNA (usually all from cheek or hair cells).
PCR would be carried out to replicate each sample into a large quantity.
You would then use the same restriction enzyme in each sample to cut the DNA in specific places along the sample.
Each sample is placed in an individual well at one end of agarose gel, immersed in a buffer solution, and a current passed through (cathode at the well-end, anode at the opposite end).
As DNA is negatively charged due to phosphate groups, it travels towards the anode, through the gel. Shorter fragments of DNA travel faster in the set time the electrophoresis is run for.
Southern blotting is then used to establish a banding pattern of the fragments of DNA - you rule out the bands that the child and the mother share. To establish paternity, you identify bands that the child shares with each possible father. The father whom the child shares the most bands is the most likely father.

Welcome to Bio. Isn't DNA profiling done with PCR and detection of SNPs? I'm not an expert here, but your answer reads like an undergrad biochemistry assays handbook. The question is not so much how it's done, but if it can be done given the properties of the DNA in gametes and diploid cells.


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Germ layer and platyhelminthes
Some introductory biology textbooks state that sometimes the body cavity is formed from pouches pinched off from the endoderm. So, I am interested in understanding  what 'pouches pinched off' actually means? Also, are platyhelminthes triploblastic or diploblastic (my professor says that they are diploblastic but books write that they are triploblastic).

Could you split this into two questions? Since the two don't seem to have a relation as platys dont have a coelom itself. I get it that they are 2 separate things you talk about but still!

@polisetty you can answer both qs: What does 'pouches pinched off' means and the other one is whether platyhelminthes are triploblastic?

planarians seem to be triploblastic. There is a reference to three germ layers in this paper https://www.researchgate.net/profile/Jose_Martin-Duran/publication/221982471_Planarian_embryology_in_the_era_of_comparative_developmental_biology/links/00b4952ea46adccee6000000.pdf skip to the embryology part. I guess the other two classes too should turn out to be triploblastic

source: Stack Exchange

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

sort: votes


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Can aptamers be used to identify the terminal amino acid residue of a peptide?
Suppose there were DNA or RNA aptamers that bind specifically to a certain terminal amino acid residue. Let's name it aaSA (amino acid specific aptamer). For example, the aptamer binding to terminal methionine residue is named as MetSA.
If such 20 aaSA all existed, then they could be applied to identify the terminal amino acid of a peptide. Concretedly, the peptide sample is immobilized to a solid surface, then all 20 aaSA are introduced and bind to the terminal residue. Extra unbinding aaSA will be washed away, and the binding aaSA will be separated later by another approach (like heating). And by sequencing the binding aaSA we can know the terminal residue of the peptide.
Either N-terminal or C-terminal is OK.
I know mass spectrometry is much more powerful in this task than the method I have supposed. But I still want to know if such aptamer exists or not.
I have searched in Google and Google Scholar, only to find aptamers binding to some intact proteins (rather than short peptides with terminal exposed). The binding site is unknown, possibly not in the terminal.

I'm not quite sure what you're asking about. If you're just talking about peptides, then N- or C-terminal sequencing is much easier and more accurate than the method you describe. For large proteins, they're still easier, as the terminal peptides may not even be available to an aptamer in the protein's native conformation.

@MattDMo Thank you for your comment. I have learned many well-developed N- or C-terminal analysis method in biochemistry class such as DNS, PITC, hydrazinolysis and amino/carboxy peptidase. I'm not proposing the first peptide terminal analysis method but just an alternative. Despite this, I think the method by aptamers may still have some advantages. For example, if the peptide is in trace amount, the signal produced by other methods may be too weak to be detected accurately. But for aptamers, they are nucleic acid and can be amplified.

@MattDMo And after searching in the Google, I found it seemed that nobody had done it. So I'm wondering if I have read enough paper or someone already did it.

Two places I'd definitely recommend looking are the US and EU patent and trademark office websites. If someone has developed something like this, they almost surely have filed for patent protection. If you end up doing it, you should get a lawyer and patent ASAP.

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


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Do you know what type of insect this is?
I found these in my appartment (we live in a half basement). It's been three so far and I can't find the thing anywhere in insect lists, etc. Could you tell me what type of insect this is?

There are 900 different species of Crickets but I would say it is a Camel Cricket based on the info provided.

As camel crickets often live in basements, you are probably right. It might be good to add a reference, for example Some hilarious info on how to get rid of then can be found here

@RHA Why would anyone get rid of such harmless insect?

This is a camel cricket (family Rhaphidophoridae); T. H. Hubbell's 1936 monograph on the genus Ceuthophilus has a key to the North American genera then known (and those added since are not found in Canada).  The photograph does resemble specimens of Ceuthophilus that I have collected and may well be that genus.


text:
Are Young Girls Stronger than Young Boys?
According to "common wisdom" the average man has, as a proportion of his body weight, 50% more muscle mass than the average woman. This is in addition to how the average man is several inches taller than the average woman and thus has a larger body mass to take that proportion out of.
Notice the above is phrased in terms of men and women as opposed to boys and girls. I am interested in how strength compares at a younger age. If we took the average ten-year-old boy and the average ten-year-old girl $-$ before the first growth spurt of puberty $-$ and compared their proportional muscle masses, how would they compare? Have any studies been carried out?
Looking for information online about this nets me a hundred accounts from men who remember how, as children, they lost every fight with their older sister. The problem here is that in any contest between siblings (twins excluded), the older sibling most likely has a height and mass advantage. So it's hard to say much about proportional muscle masses.
My guess is that if we took twins Bill and Roberta then they would have similar muscle-mass proportions up until about age 10. From then Roberta would have a growth spurt and increase proportional (as well as absolute) muscle mass due to extra testosterone (in addition to extra estrogen). A few years later Bill would have a growth spurt and increase proportional muscle mass to exceed Roberta's. But she would still be stronger than him, until he caught in terms of height.

Why is this VTCed as opinion based? It is clearly possible to do studies like this, similarly to other types of studies on the average development rates in children (as well as sex-differences), and I assume that there are data out there that could answer this question.

Here's a study comparing performance in swimming. Before age 8, there's no difference; from age 11-12, there's some small difference, after age 13, there's a large difference.
https://www.eurekalert.org/pub_releases/2012-05/iu-wsg052512.php


text:
What happens when our muscle tense?
Is the tensing of muscles equivalent to stretching them? I am trying to understand what tensing of the muscles means.

Do you mean to ask the sarcomeric state of the muscle while maintaining posture?

Stretching of muscle means muscle getting relaxed while "if you tense your muscles, or you or your muscles tense, they become tight and stiff, especially because you are not relaxed" (http://www.oxfordlearnersdictionaries.com/definition/english/tense_3). So, tensing can be called a consequence of stretching of muscle.

The course-work tag is nonexistent.  Please don't put it back.  Edits made by hi-rep users are often made for a reason.

@WYSIWYG et al; what is not clear in this question?

@Christiaan "Is the tensing of muscles equivalent to stretching them" What kind of equivalence is the OP referring to is unclear. Tensing is a standard English term and nothing specifically biological.

@WYSIWYG true, it's all about terminology. OP is likely trying to grasp what a regular word means in terms of the biological mechanism behind it. At least, that's what I understand and that's what I've answered. I don't think it should be closed. If it needs closure than the unclear what you are asking seems invalid to me.

@Christiaan That's the point. This question can have multiple interpretations. 1. what you said 2. whether tensing/extending involve same molecular mechanisms 3. whether they are mechanically equivalent... and many more so. That's why I VTCed this as unclear. Plus OP did not respond to comments requesting clarification, for more than a week. Moreover "What happens when our muscle tense" is basically a homework type of question.

Muscles are designed to contract i.e., when they tense they get shorter. Their stretch is a passive process, typically facilitated by antagonist muscles in case of skeletal (striated) muscles. Consider the biceps and triceps antagonists in the upper arm in Fig. 1:

Fig. 1. Left: The biceps actively contracts to bend the arm and is called the agonist. The triceps is inactive and is passively stretched by the biceps, called the antagonist. Right: To stretch the arm, the reverse happens, i.e. the triceps contracts and is now called the agonist. The biceps is now inactive and is called the antagonist and it is passively stretched by the triceps. Source: Pilates Studio
At the molecular level, the tensing of muscles can be readily seen as contraction, as opposed to stretching (Fig. 2):

Fig. 2. Muscle fibers contract actively and stretch passively. The passive stretched state is depicted in the upper panel. Under the influence of ATP (active part) the muscle fibers condense and the muscles contracts. source: Emaze Presentations.
Further Reading
- Do both ends of a muscle contract?


text:
Doesn't the sarcomere contract during isometric contraction?
During muscle contraction, the lenght of the sarcomere changes, length of myocyte changes and so does the length of muscle. However, if the length of muscle is not changing length as in isometric contraction does it mean that the sarcomeres are not contracting?

Yes, sarcomeres do contract during isometric contraction, they just don't change the overall length of the muscle. This is due to the tension being transferred to elastic filaments within the muscle that maintain the same muscle length but increase the muscle tension. Thus, this is how sarcomeres can contract while the muscle does not have an overall change in length. (See this link for a paper discussing these elastic elements within the muscle itself; also, this is discussed at this wikipedia link as well).
In an isometric contraction the sarcomere is increasing the tension in the muscle, but without an overall change in length. (Isometric Contraction = No change in length, but INCREASE in tension)
Once a muscle overcomes the tension needed to lift a weight/load, then the tension ceases to increase but the sarcomeres begin to shorten which moves/lifts the load. When the length of the sarcomeres change and the tension remains the same, that is called isotonic contraction. (Isotonic Contraction = No change in tension, but DECREASE in length)

The picture below is from a website discussing these muscle physiology principles and is freely available on the web.

I vaguely recall having studied that even though there is sarcomeric contraction, there is no reduction in length in isometric exercise due to equal compensatory relaxation of sarcomeres elsewhere.. is this true? If not how is the length maintained despite contraction?

so, contraction (in the sarcomere context, not the muscle) need not mean decrease in sarcomere length right?

I learned something new... looks like the sarcomeres can contract during an isometric contraction, though this doesn't mean the muscle contracts. What appears to happen is that the sarcomere contracts but the tension is transferred to elastic filaments in the muscle which maintain the same muscle length but increase the tension - this is how sarcomeres can contract while the muscle does not (see http://jcb.rupress.org/content/105/5/2217.full.pdf+html for more info) - I will add this to my answer


text:
Is natural selection still at work in humans in the 21st century?
There has been some disussion on this site about some aspects (e.g. evolution of eye sight, or height, or the effect of medicine, or evolution the past $\sim10000$ years). My question is really more general regarding evolution and more specific regarding the current age. I'm looking for answer with references to original research if possible.

@Remi.b Thanks for finding this. The question is indeed similar, but the answers are not what I'm looking for, as they consider recent evolution (in the past 10000 yrs). I'm wondering about the today. Our cultur today is very different from that 10000 years ago and this might strongly effect natural selection.

You really cannot view evolution today.. But it is definitely happening..because humans are no more segregated populations but as a famous TV personality said a global community. But two hundred years from now when we have put colonies on Mars and then a thousand years from then you can expect Martian populations to carry traits that are a bit different from Earth humans.... I think you get my point.... That one of things required for viewing evolution is a niche population which has no exterior generic pressure...and lots of time....these are just my thoughts based on what i know till now...

Selection is still occurring because there are many genetic effects on reproductive output - some die before being able to reproduce, there are effects on fertility, behavioural traits (including those making one more or less prone to wanting children)... it is a duplicate as that is covered in the linked question which also focuses on very modern humans

@DavidBlomstrom Selection is most certainly occurring in all populations of humans. The modern cultural and social advances have altered the adaptive landscape, not flattened it. In some genes, net selection may even be stronger now. We also have continued evolution of the meta population, along with selection, by drift and mutation, as well as migration among populations leading to further evolution within sub populations.


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Why do typical acetylcholinesterase inhibitors (like carbamates) have a greater parasympathetic effect than a sympathetic effect?
I understand that the post-ganglionic neurones of the sympathetic system are adrenergic, but surely these neurones will be excited to the same extent as the parasympathetic post-ganglionic neurones (due to the ganglionic synapses being cholinergic), and thus target organs/tissues will be receiving equal and opposite sympathetic/parasympathetic stimulation, or rather equal and opposite activation of the muscarinic/adrenergic receptors. (Sub-question: Why does caffeine, a perhaps atypical acetylcholinesterase inhibitor have a greater sympathetic effect than parasympathetic effect?).

We were taught that ganglionic receptors have very high thresholds. So we need a very high concentration of the drug to produce the sympathetic effects. We even solved a hypothetical problem in class, where a patient presented with a pinpoint pupil (typical insecticide poisoning) and increased secretions but an increased heart rate (usually they present with bradycardia). We would still treat the patient with atropine since the combo of pinpoint pupil and increased secretions would be exclusively explained by insecticide poisoning (either organophosphate or carbamate). The increased heart rate could be explained by ganglionic action leading to sympathetic activation of the heart.
But as said this was only a hypothetical case and patients of organophosphate or carbamate poisoning always present with bradycardia. To elicit ganglionic responses the person has to consume a dose way higher which would certainly lead to sudden death.
Hope that helps :)

I guess why ganglionic receptors have high thresholds would be the actual answer to your question. Ya, but this is what I have!

Thanks! Yeah that helps a lot, should put me on the right track for some further research - I'll have a further look about the ganglionic thresholds & the caffeine.

It's worth mentioning that, despite both neurones in your question being cholinergic, they aren't exactly the same: the pre-ganglionar neurones are nicotinic, while the parasympathetic post-ganglionar ones are muscarinic. And carbamates have more muscarinic activity than nicotinic activity.
PS: this is not a good answer because it simply leads us to another question: why do carbamates have more muscarinic activity than nicotinic activity? And the answer to this last question may be Polisetty's hypothesis.

These drugs are Acetylcholinesterase inhibitors. They just increase the ACh. How does that have an relation with the receptor? When the ligand is the same and you're effecting the ligand, why should the receptor come to play?

Read my last paragraph again, I'm referencing your answer: why the thresholds are different? It has to do with the kind of receptor. The Ach are all the same, the cholinesterase are all the same... only the receptor is different. And that's the key.


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Why does protein kinase C activated by different means have different effects?
I could be way off base but I think I remember learning that Protein Kinase C has some effects when activated by one pathway and other effects when activated by another. How does this happen? Is it just phosphorylated differently or what?

Can you provide some background? Protein kinase-C would do the same job (in a molecular sense) irrespective of the upstream pathway.

It's good to take a step back sometimes and look at a bigger picture: PKC got activated, but what else is being activated or deactivated by other signals at the same time?

You probably remember correctly — at least in part. The part that is missing is that protein kinase C isn't just one enzyme, but perhaps a dozen different isoforms that fall into three different classes, differing, among other things in their requirements for activation (e.g. whether they require calcium ions as well as diacylglycerol). It would be theoretically possible for protein kinase C activated by one pathway to have different effects from that activated by another if the different isoforms involved had different properties. This has indeed been suggested, although it has been difficult to establish experimentally.
The following two reviews that deal with this are about 20 years old, but may allow easier general access (and are easier to read):
Dekker, L.V. and Parker, P.J. (1994) Trends in Biochemical Sciences vol 19 pp 73–77.
Jaken, S. (1996) Current Opinion in Cell Biology, vol 8, pp 168–173.
The following quotation from the summary of a more recent and more extensive review article (Steinberg, S.F. [2008] Physiol. Review. vol. 88 pp. 1341–1378) may be pertinent:

"There is growing evidence that individual PKC isoforms subserve unique (and in some cases opposing) functions in cells, at least in part as a result of isoform-specific subcellular compartmentalization patterns, protein-protein interactions, and post-translational modifications that influence catalytic function."

One other feature of protein kinase C is relevant to this question. Most other protein kinases (which tend not to have multiple isoforms) have a more or less restricted substrate specificity determined by residues of a particular type at particular positions with respect to the phosphorylation target residue (Ser, Thr or Tyr). This limits the proteins the kinases act on to specific targets. In contrast, protein kinase C can phosphorylate target residues in a wide variety of contexts. The current model (above) allows specificity of protein kinase C for target proteins to be obtained in a different way — by the specific proteins that each activated isoform binds to, i.e. by protein–protein interaction rather than target-site context.


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How does an excessive amount of beta carotene affect skin colour?
How much is the daily need of beta carotene and how many carrots have to be eaten in order for one's skin to turn "orange".
I found 2-4 mg/ day as basic need, 30 mg daily over three weeks turns white skin orange. Is this correct? And what is the reason behind this?

How much beta carotene does it take to change someones skin colour?
To turn the skin yellow, rather than orangish, a person would have to eat about 10 carrots a day for a period of at least two weeks, consuming at least 51 grams of beta-carotene each day. The average carrot contains about 5 to 6 milligrams of beta-carotene

What is the reason behind this?
A very high diet of food which contain carotenemia (such as carrots, squash, sweet potatoes and others) can cause skin discoloration. The skin, and especially the palms of the hands, turn yellow, rather than orange. This change in skin colour fades and eventually disappears when the individual's diet changes back to normal.

Carotenoderma is deliberately caused by beta-carotenoid treatment of certain photosensitive dermatitis diseases such as erythropoietic protoporphyria, where beta carotene is prescribed in quantities which discolor the skin.

What does an excess of carotenoids do?

An excess of carotenoids, being eliminated via sweat, may cause a marked orange discoloration of the outermost skin layer. This benign and reversible condition – which is most easily observed in light-skinned people and may be mistaken for jaundice – is known as carotenosis or carotenoderma.

sources:

https://en.wikipedia.org/wiki/Carotenosis
http://www.webmd.com/vitamins-supplements/ingredientmono-999-beta-carotene.aspx?activeingredientid=999&
http://umm.edu/health/medical/altmed/supplement/betacarotene
http://emedicine.medscape.com/article/1104368-overview


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Restriction enzymes, how are the recognition sequences determined?
How were the recognition sequences (e.g. GAATTC of EcoRI, GGATCC of BamHI) characterised? Text books only list the recognition sites but never the methodologies used to determine the sequences.

This paper describes a simple method to determine restriction sites, which was used to determine the restriction sequence of the previously uncharacterised enzyme from Haemophilus gallinarum.
In short, a known sequence of DNA (from the phage $\phi \text{X174}$) is partially digested with the restriction enzyme, and the various digested fragments can be used to determine the relative distances between each of the restriction sites.
Then, the restriction fragments are extended using T4 polymerase and sequenced using $^{32}\text{P}$ labelled Sanger sequencing.

Once the restriction map of the enzyme on the known DNA sequence is completed, the individual fragments can then be checked for similarities. For example, HgaI has a recognition site outside of the restriction site. Therefore, when the individual restriction sites are compared, it can be seen that all of them have the recognition site GACGC.

Wonderful, the paper is also openly accessible without a subscription! Wonder if this is still the method of choice nowadays for sequence determination given the advances of next generation sequencing platform...

@Green Presumably for restriction enzymes, Sanger sequencing (albeit with improved methods, such as the BigDye-based sequencing technique) is likely to be still superior to high throughput sequencing, as the number of sequences required to determine the restriction recognition site is very small and not sufficient to make high throughput sequencing worthwhile.


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What are unmapped reads?
I am mapping some reads to a reference genome (hg19). I used bamtools to have the percentage of mapped vs unmapped reads.
Total reads:       1150004
Mapped reads:      1052983  (91.5634%)
Forward strand:    624067   (54.2665%)
Reverse strand:    525937   (45.7335%)
Failed QC:         0    (0%)
Duplicates:        0    (0%)
Paired-end reads:  1150004  (100%)
'Proper-pairs':    1046208  (90.9743%)
Both pairs mapped: 1049400  (91.2519%)
Read 1:            575002
Read 2:            575002
Singletons:        3583 (0.311564%)
Average insert size (absolute value): 534.479
Median insert size (absolute value): 215

My question:
What represent exactly these unmapped reads? What information do they tell us? How can we analyze them?
Thanks

In transcriptome (RNA-Seq) libraries, unmapped reads are reads that fail to map to known exons. More often than not, they represent genomic DNA. RSeQC has tools to help identify genomic (also sometimes called intergenic) sequences.
For the most part, the percentage of unmapped reads just provides you with QC information, like how much gDNA you purified along with your mRNA. It's unlikely to be very useful beyond that, but it really comes down to what you're looking for in those sequences.
If you're doing DNA-Seq, then unmapped reads generally represent reads that failed to map unambiguously to known sequences. This will depend on a threshold (usually provided by the user) for alignment stringency.


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Difference of coverage between amplicons
I have 2 fastq files and I generated BAM file (indexed and sorted) of some reads. I aligned them to a reference genome (hg19).
I am working with different primers.
FORWARD
1. TTGCCAGTTAACGTCTTCCTTCTCTCTCTG
2. CCCTTGTCTCTGTGTTCTTGTCCCCCCCA
3. TGATCTGTCCCTCACAGCAGGGTCTTCTCT
4. CACACTGACGTGCCTCTCCCTCCCTCCA

REVERSE
1. GAGAAAAGGTGGGCCTGAGGTTCAGAGCCA
2. CCCCACCAGACCATGAGAGGCCCTGCGGCC
3. TGACCTAAAGCCACCTCCTTA
4. CCGTATCTCCCTTCCCTGATTA

Therefore I have different amplicons. How can I plot the coverage of these different amplicons. And what could explain big difference between them?
Thank you very much for your help.

I answered before about things which will effect coverage in NGS http://biology.stackexchange.com/a/57169/990

Well, to plot the coverage I would use something like Python Matplotlib. Take a look at this example:
import matplotlib.pyplot as plt
import matplotlib

amplicons =  ('TTGCCAGTTAACGTCTTCCTTCTCTCTCTG',
      'CCCTTGTCTCTGTGTTCTTGTCCCCCCCA',
      'TGATCTGTCCCTCACAGCAGGGTCTTCTCT',
      'CACACTGACGTGCCTCTCCCTCCCTCCA')
countAmpl = (1635, 4734, 2156, 3085)

fig = plt.figure(figsize=(10,8.5))

subplt = fig.add_subplot(111)
subplt.set_ylabel('Count')
subplt.set_xlabel('Amplicons')
subplt.plot(amplicons, countAmpl,  linestyle='-', marker='o', color='blue')
for tl in subplt.get_yticklabels():
    tl.set_color('blue')

plt.savefig("amplicons.eps")

Check other types of charts in Matplotlib if you think you need something else.
You can also try to open and visualize the BAM in IGV from the Broad Institute.
Regarding the difference in coverage, I would say that some are from a repetitive region. Or the amplification depth of a region is greater than for the others. Or maybe the aligner found similar regions and decided that the amplicon aligns well in all those regions.

These amplicons are all of coding exons, so repetitiveness is not likely to be a problem.  Unless the read is quite short, it won't align to the wrong place.

BEDTools, among other software suites, will give you a coverage histogram.  Biggest source of bias in PCR efficiency is just that some primers work better than others, there is sequence bias in the PCR amplification stage of the library prep too.  GC content contributes to this.


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Explanation of the ‘cherry red spot' in Tay Sachs disease
In Tay Sachs disease, a hallmark symptom is a cherry red spot in the macula of the eye surrounded by a halo of white.
I understand that the ganglion cells, which are higher in numbers around the macula rather than in the macula, accumulate gangliosides due to the hexosaminidase deficiency, and thus cause the surroundings of the macula to appear white, but I don’t understand why the macula is red.
It is said that in Tay Sachs disease, the macula is the only normal region of the eye, but isn’t the macula supposed to be yellow, as it is referred to as the yellow spot?
Moreover, I’ve read that the red color comes from the choroid blood vessels, but isn’t the choroid black? It contains blood vessels, yes, but it is pigmented. The hindmost layer of the retina also happens to be a pigmented epithelium. So what is the explanation of a cherry red spot?

Short answer

The fovea centralis is colored red in both the healthy retina and Tay-Sachs affected retinae. The macular region around the fovea has a yellowish hue. You are confusing fovea and macula in your question.
The reddish hue from the fovea comes from the well-vascularized choroid layer below. The choroid is not black, it is colored red due to the presence of many blood vessels. You are confusing choroid with the retinal pigment epithelium, which is indeed black.

Background
The macula includes the fovea at the center, also called the fovea centralis, which forms the very center of the retina. The macular region around the fovea includes the perifoveal and parafoveal areas. The macular region around the fovea has a slight yellowish appearance to it due to yellowish pigments present in the cone axons (Fig. 1) (Kolb, 2012).

Fig. 1. Healthy retina. The macular region is seen in the center, The parafoveal region has a slight yellow/orange hue to it. Note that the landmark yellow circle at 4 o'clock, with the vessels sprouting from it, is the optic nerve head. source: Webvision.
Below a Tay-Sachs affected retina showing the hallmark cherry red spot (Fig. 2):

Fig. 2. Tay-Sachs affected eye. The fovea centralis appears red. source: Prezi
The only normal part is the fovea centralis, appearing in its native red color, i.e. the cherry red spot.
The choroid plexus is well-perfused and is, therefore, red. You are confusing it with the pigment epithelium, which is pigmented (Fig. 3).

Fig. 3. Layers of the eye. RPE = Retinal Pigment Epithelium. source: Retina Eye Specialists
Reference
- Kolb (2012), Simple anatomy of the retina. In: Kolb et al. (eds.), Webvision. The organization of the retina and visual system. Salt Lake City, UT, Moran Eye Center

But is the RPE is present in the fovea too? I don’t understand why the fovea doesn’t appear black when the rest of the eye’s interior does.

The retina does not appear black. See the images above. Note that the black borders are outside the eye.

But where does the black appear then in the eye? Isn’t it important for the eye’s interior to be black to absorb backscattered light? You mentioned the RPE is black, but this should be visible, should it not?

It's a very thin structure.

So the RPE is so thin that you can’t really see the black? But what about the whole part where the pigmentation helps absorb scattered light? I’m just thinking that if, upon hitting the RPE, light is absorbed and not scattered, then there is no light reflecting back into the observer’s eye and the eye’s interior would appear black. If the eye’s interior doesn’t appear black then that does mean that light is being scattered about in the eye.

The black RPE contributes to the "normal" color of the eye fundus in photos of the retina. Albinism is a condition of absence of black pigment, and then you can see the eye fundus without pigment. Compare the two images below

Welcome to Biology.SE! It isn't clear that this answers the original question, which was about Tay Sachs not albinism. In addition, answers are much more likely to receive a favorable response if you include supporting references (primary literature is best). Without that support, your answer is indistinguishable from opinion. ——— Please take the [tour] and then consult the help pages for additional advice on [Answer] effectively on this site and then [edit] or delete your answer accordingly. Thanks!

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


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

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

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

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

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


text:
Difference between Fragmentation and Budding
I have heard about two terms stating similar things - Fission and Fragmentation . I know Amoeba undergoes fission and Fragmentation is done by spirogyra. So what's the main difference between them?

Welcome to Bio. Could you add context to your question? Are you talking about cellular processes?

Yes, i am talking about asexual reproduction.

As far as I remember yeast undergoes budding (in fact even hydra does). Have never heard of amoebae budding. Wasn't the amoeba thing plain old binary fission?

I am sorry for the mistake. See the edit


text:
How do I measure genetic distance?
I'm not sure how to measure genetic distance. There seems to be many different equations out there, and all the ones I found are rather old.
In my specific problem I want to see if the twist in collagen differs if the species are different. (I have a program to predict collagen twist according to amino acid sequence)
I therefore want an objective numerical value to base my comparaison on. "Nei's standard genetic distance" seems good, but it is very old so I was wondering if there was a modern alternative. Is there an R package or something like that to calculate it automatically?

There are a few answers here, it is a little unclear which is closest to what you want.
[edited to be more complete and direct]
1) Nei's distance is mostly for comparing populations of the same species, so it should be fine if that is what you are doing. I am guessing that based on your post, you are more interested in cross-species comparisons. Of course, the logic is the same, it's just the math is different. For among-population divergence, Fst (fixation index) is also commonly used. But if you are using a sequence alignment or some such data to compute genetic distances, there are lots and lots of metrics. Some of them are very simple- for instance you could use Hamming distance and just count the number of residue differences between each sequence.
As for computing these metrics, there is a webserver called GenePop online that will compute Fst for you if you plug in a dataset. I don't know of R packages that compute these things, I would guess just by looking at wikipedia that coding functions to do this would be relatively trivial (if you are comfortable with r).
2) If you are truly looking among species, a somewhat more appropriate approach might be to model your species in a phylogeny, rather than to use distance methods (though the two are attempting to solve sort of the same problem). There are lots of easy-to-use online programs for this, for instance: FastML. You can just copy-and-paste a seq alignment in there. After you have the tree in for instance newick format, there are good tools for visualizing trees both online at iTOL, and through R with APE.
APE also has good utilities for modeling phylogenetic processes, so you could in principle directly model changes in protein folds through evolutionary time (assuming you have a meaningful summary of protein folding, either continuous or discrete).
I don't have enough reputation to link to more of the resources I mentioned, sorry.

I've already worked with SeaView for making phylogenetic trees but I am looking for a good numerical value I could use to do some data analysis (and very basic machine learning) Since time of divergence and simply counting different bases seemed a bit basic I am looking for something more accurate... I'm using amino acid sequences of collagen taken from PDB.  Thank you, your answer gives me a few pointers.

ah- i see. my naive guess is that all of the distance metrics will tell you similar things. nonetheless, since you are working with different species and want a more sophisticated distance metric, you might try something like protdist from [phylip] (http://evolution.genetics.washington.edu/phylip/doc/protdist.html), which has various substitution models available. Again, I would recommend trying to model the problem phylogenetically, which is preferred in the field. Distances can be tricky because observations are non-independent. But probably most methods will give the same. Good luck!

I think my approach would be to make a phylogenetic tree and color the tips by collagen twist. There are several R packages to help with this, including APE, ADE4, and poppr. To make a phylogenetic tree, you first calculate a distance. You mentioned Nei's, and that's actually still used pretty commmonly. I know you're not doing population genetics, but check out this tutorial: https://grunwaldlab.github.io/Population_Genetics_in_R/Pop_Structure.html. They calculate Gst (mentioned in the other comment), talk about a few different distant metrics (including Nei's), make phylogenetic trees, and it's all in R. They even color the tips by population - in you're case, your populations would be types of collagen twist with your samples named by species (Lizard-1, Lizard-2, Chimp-1, Chimp-2, etc.). You also could color the tips by species and name your samples by twist type (forward-1, forward-2, reverse-2, etc.). I know this question is old, but hopefully someone else who stumbles here will find this answer helpful.


text:
RNAse activity review
I was searching for any review unravelling the structure-function motifs responsible for RNAse activity. Or at least a well-composed review of RNAse superfamilies that are described nowadays (with linkage to their functional activity). My PubMed search performed didn't give any valuable results for that.
Any specialists to comment?
Thanks in advance!

Not a specialist but was wondering whether your interest and expectation was motifs related to catalysis or to substrate specificity.

@David I'd rather say both. But mainly focusing on the catalytic sites.

I did a few searches, just for fun, but all I came up with was:

Yuhong Zuo and Murray P. Deutscher "Exoribonuclease superfamilies: structural analysis and phylogenetic distribution"
  (2001) Nucl. Acids Res. 29 (5): 1017-1026. doi: 10.1093/nar/29.5.1017

Not very recent, but it's open access. It might be possible to search for more recent papers that have cited this. Although I haven't tried it myself, I found suggestions for doing this at https://www.bc.edu/libraries/help/howdoi/howto/pubcitation.html.


text:
Why are minor introns bounded by nucleotides AT-AC, where T is not normally in RNA?
Major intron boundary nucleotides are GU-AG. Minor intron boundary nucleotides are AT-AC. Why does the former use RNA Uracil and the latter use DNA thymine? Since introns are in the primary RNA transcript, shouldn't both be RNA and use U rather than T?

It is not unusual for RNA sequences to be reported with T instead of U; the writer is reporting the cDNA sequence instead of the RNA sequence.  In RNA at the boundary of the minor intron, there is a uracil.  In the following page, the writers follow the oft-used convention of describing RNA with T instead of U (writing the cDNA sequence).  https://en.wikipedia.org/wiki/Minor_spliceosome


text:
Why do fetuses have membranes between fingers and toes?
Are the membranes present between the fetal fingers and toes a remainder of the phylogenetic evolution, or just a way organs do grow most easily?

It seems difficult for me to define "easily" in the context of organ development. In any case, the way organs develop is mostly inherited from our ancestors, so "it's easy to do so" and "it's inherited" are not necessarily contradictory statements.

Short answer
The transient membranes between the fingers and toes in embryos are a myth.
Background
The presence of transient membranes in developing embryos supposedly points to our fishy evolutionary origins. However, I couldn't find any credible sources to support this myth. In fact, I couldn't find any source mentioning the presence of webbing between the fingers and toes at any stage during development.
To support this lack of evidence, I have posted several photos of embryos and fetuses in various developmental stages. None show any signs of the "swimming webs". Note that the age mentioned is the developmental age, counted from the moment of conception (add 2 weeks to have gestational age):

Fig. 1. Five-week embryo. source: Palm Reading Perspectives

Fig. 2. Seven-week embryo. source: Wikipedia

Fig. 3. Eight-week embryo. source: WemMD

Fig. 4. Fourteen-week foetus. source: WemMD

Fig. 5. Eighteen-week foetus. source: WemMD
Fig. 2 may seem to show some webbing, but if we look at some close-ups of the hand and feet at week 7 in Fig. 6 below, we can see that there is no real webbing; fingers and toes are simply budding from the primordial hand and foot structures.

Fig. 6. Developmental stages of the hand and feet around week 7. source: I am Pregnant
Note that an embryo is called a fetus only after the first trimester, i.e. after some 12 weeks. There is certainly not any sign of webbings in healthy fetuses.
Also note that webbings may be the result of birth defects, such as syndactyly and pseudosyndactyly (Fig. 7):

Fig. 7. Infants with Syndactyly (left) and Pseudosyndactyly (right). sources: Wikipedia & University of Columbia
Original photographic image source (Figs 1 & 5)*
- Nilsson, Ett Barn Blir Till
* Credits go to rg255

Figs. 1 + 5 at least come from Lennart Nilsson's Ett Barn Blir Till (ISBN: 9789174242751) - just thought that deserves proper credit because it's a beautiful book (and has English versions I think)  :)

@rg255 - thanks! - ref added + acknowledgement :-)

There is some "webbing" in very early stages. These cells between the digits undergo apoptosis. At least that's what I have read in the dev bio textbooks.

@WYSIWYG - yes, that's what I thought too. I just couldn't find it. I'll look into some text books and try to find out. Thanks for this.

Thanks. So (if there's apoptosis of the cells between fingers) the second option (it is the easier way to "grow a hand) is correct, isn't it (but yeah, I understand your point, why no "membranes" exist?

@Probably - thanks for accepting. I'm still working on your answer though. I'll try to get back to you asap. The answer as of now is OK, but I'm going to add another line of reasoning. In due time, promised. I've not forgotten about this!

@Christiaan Yeah I realised that it is pretty clear from your answer, thx.


text:
How are physiological reversal potentials (or ion concentrations) of neurons measured?
Patch clamp electrophysiology experiments typically use an intracellular solution that mimics the ionic concentrations of neuronal cytosol. At the same time, the extracellular solution is meant to mimic cerebrospinal fluid. If these two sets of ion concentrations are similar to their in vivo physiological values, then one might expect a patch-clamped neuron to also have physiological ionic reversal potentials. If, on the other hand, they are dissimilar, then we might expect the behavior of the patched neuron (for example its intrinsic excitability or synaptic currents) to be different from the behavior of the same neuron in vivo. In principle, one would like to use solutions that are as close as possible to physiological for this type of experiment.
My question is: how do we know what these physiological values (concentrations or reversal potentials) really are? It is easy to find these values in a textbook, but I would like to know what original research was performed to determine these values in the first place.
In many patch clamp experiments, the solutions are designed to set the reversal potentials to non-physiological values, or are otherwise constrained by the practicalities of the experiment. Let's consider these issues to be outside the scope of this question.

There are various methods to determine the intracellular ionic concentrations. One method is to register action potentials by the fowling method: inject a Voltage Active dye VAD (something like a -2di Anepp or s similar dye) into the cell or tissue and using an Optic Mapping System register the Action potentials and then determine the intracellular ionic concentrations by Nernst equations.
We could also register Action potentials by "ion-sensitive glass electrodes method" by introducing ion-sensitive glass electrodes directly into the interior of the cells. The problem with these electrodes is that they cannot register very low ionic concentrations especially of Calcium. And so the above method is superior using  VAD.

Given that multiple ionic currents set the behavior of the cell during an action potential, it seems infeasible to determine ion concentrations from only a voltage recording. Can you point to an example of this method being used to determine ion concentrations?

Sorry for the delayed response! Busy with routine.I recommend to read the information posted on http://www.utdallas.edu/~tres/microelectrode/microelectrodes_ch11.pdf for understanding how ionic concentration is measured inside the cell.

Thanks for the review! That is an excellent seed for digging through the ion-selective electrode literature. So far I have been able to find measurements in oocytes, epithelial cells, photoreceptors, neuroblastoma cells, purkinje fibers, muscle, etc. No measurements, however, from neurons in anything resembling a physiological preparation. From your reference, it seems like it would be very difficult to make such measurements in cells as small as most neurons, as this would lead to excessive cell damage.


text:
How can a tongue-biting parasitic arthropod become a fully functional tongue?
From wikipedia:

The parasite Cymothoa exigua [consumes a fish's tongue and] then replaces [it] by attaching its own body to the muscles of the tongue stub. The fish is able to use the parasite just like a normal tongue.

Wikipedia says that it replaces the host's tongue and becomes fully functional. But how does the arthropodic parasite reattach the nerves of the fish, such that the fish can assume control of it? Am I misunderstanding something?

Short answer
There is no evidence whatsoever that the parasitic arthropod Cymothoa exigua develops itself into a functional tongue. Instead, it consumes the fish's tongue and occupies the freed buccal space to continue feeding onto the fish's blood or mucus.
Background
The linked wikipedia page that states that Cymothoa exigua arthropods form fully functional tongue-replacements refers to Brusca & Gilligan (1983) to back up that claim. While the journal is credible, the article itself is a theoretical work. The authors base their conclusion that the tongue replacement is functional on the relatively healthy condition of just 2 specimens of fish. They reasoned that, because the parasitic arthropods were relatively large, the fish had to be hosting them for quite a while. In turn, given the relatively healthy condition of the fish, the authors reasoned the arthropodic tongues may actually have had functionality. In the figure below taken from Brusca & Gilligan (1983) the parasite does indeed look much like the normal tongue.

Source: Brusca & Gilligan (1983).
However, there is no mention whatsoever that the parasitic tongue taps into the nervous system and I have not found any literature supporting such a claim. Further, Brusca & Gilligan (1983) specifically say that:

[...] we propose [that] a fish with an 'isopod tongue' [is] not feeding as efficiently  as a non-parasitized fish, [but] feeds more efficiently than a fish with no tongue at all [...]

The authors' claim is much more nuanced than the blunt conclusion as drawn in the wikipedia page that it is a fully functional tongue; while the effects on its host may be relatively mild, it may not replace all, or even any, physiological functions of the normal tongue.
Reference
- Brusca and Gilligan, Copeia (1983); 3:813-6

Just to add to Christiaan's excellent answer: The authors of his cited study state:

[the tongues] replacement by a parasite would not appear to be a complex phenomenon.

Implying that this is a very basic process, according to what they observed.
To answer your question as it was posed:
Wikipedia states the tongue becomes fully functional. The authors of the study quoted by Christiaan also state two further pieces of information which may be of benefit to you.

It [the tongue] is primarily a mechanical device to hold prey ... in the roof of the mouth while being processed.

[the parasite] attaches to the remaining tongue stub.

I suppose that with 'fully functional' you mean innervated. However, the parasite merely has to perform a basic mechanical function, and may be directed by the remaining stub (though that is my own inference).


text:
Why do Kupffer cells not attack malarial sporozoites?
During malaria, why don't Kupffer cells (hepatic macrophages) attack  the Plasmodium sporozoites and stop schizogony, thus saving us from the disease?

I assume the parasite has developed some coating to prevent Kupffer cell uptake, but I don't know what. Of course, once it enters a blood cell, Kupffer cells uptake won't be an issue anymore. This might be interesting to look at in more detail, people doing nanoparticle research are also interested in making particles avoid Kupffer cell uptake while getting hepatocyte uptake.

I know only tardigrade is only being capable of creating bio-glass coating to prevent itself being dessicated.I didn't know sporozoite having same capability.

Indeed the process is even more interesting than thought: sporozoites actively attack Kupffer cells and let themselves get eaten! In a 2001 research, Pradel et al found that sporozoites pass through a layer of Kupffer cells in order to enter hepatocytes for the next stage of their life cycle. They observed that in rat liver cells, Plasmodium berghei and Plasmodium yoelii sporozoites attach to and enter the Kupffer cells, but not the sinusoidal endothelia. During experiment, the number of intracellular sporozoites kept increasing for upto 12 hours, unlike hepatocytes and other non-phagocytic cells which were invaded in vitro for only the first hour of parasite exposure. The sporozoites entered the Kupffer cells via endocytosis in specialized vesicles which did not interact with lysosomal markers. From Kupffer cells, sporozoites traversed to hepatocytes where they developed into exoerythrocytic schizonts. In another 2015 research, Cha et al concluded that the sporozoites interact with CD68 receptor on the surface of Kupffer cells for endocytosis. In short, sporozoites literally pass through Kupffer cells without letting Kupffer cells doing any harm to them. See this diagram for illustration:

EDIT: What happens in Kupffer cells during traversal of sporozoites remains unkown to some extent. However, Frevert et al, 2008 has shown that sporozoites render Kupffer cells insensitive to pro-inflammatory stimuli and force them towards apoptosis (aka programmed cell death or "cell suicide"). This happens as sporozoite-exposed Kupffer cells are stimulated by lipopolysaccharide or IFN-$\gamma$, causing down-modulation of TNF-$\alpha$, IL-6 and MCP-1 and upregulation of IL-10. Nuclear factor NF-$\kappa$B is also activated, which causes apoptosis in Kupffer cells (Punsawad et al, 2014). However, if Kupffer cells are activated, in particular by immunization caused due to high antivody levels, they may phagocytoze the sporozoites and thus prevent their traversal (Krzych et al, 2015).
References:

Pradel, G. and Frevert, U. (2001), Malaria sporozoites actively enter and pass through rat Kupffer cells prior to hepatocyte invasion. Hepatology, 33: 1154–1165. doi:10.1053/jhep.2001.24237
Cha, S.-J., et al. CD68 acts as a major gateway for malaria sporozoite liver infection. J. Exp. Med., July 2015 DOI: 10.1084/jem.20110575
Klotz C, Frevert U. Plasmodium yoelii sporozoites modulate cytokine profile and induce apoptosis in murine Kupffer cells. International journal for parasitology. 2008;38(14):1639-1650. doi:10.1016/j.ijpara.2008.05.018
Viriyavejakul P, Khachonsaksumet V, Punsawad C. Liver changes in severe Plasmodium falciparum malaria: histopathology, apoptosis and nuclear factor kappa B expression. Malaria Journal. 2014;13:106. doi:10.1186/1475-2875-13-106.
Frevert U, Krzych U. Plasmodium cellular effector mechanisms and the hepatic microenvironment. Frontiers in Microbiology. 2015;6:482. doi:10.3389/fmicb.2015.00482.

Does the Kuppfer Cells get affected while letting sporozoites pass through them?  @another 'Homo Sapien'

Does the Kupffer cells get affected while letting the sporozoites pass through them?

@swastik I've that part in the answer. If you have any further queries, please ask them here or add them in your question with an "EDIT" :)


text:
How to improve DNA extraction
I am using the following protocol to extract chromosomal DNA from bananas:

Cut up one banana into small pieces, approximately (1 cm3)
Add ½ a cup of warm salt water and the banana pieces into the blender and set to max for 5-10 seconds
Poor into a beaker and add 1 teaspoon of detergent to the beaker
Stir for 5 mins with a spoon to break down the plasma membrane
Place the mixture into a centrifuge for 30 seconds
Pour the mixture through a gauze with a beaker catching the liquid underneath
Smoothly pour cold ethanol into the mixture at a 1:1 ratio so a clear layer of liquid will form on top of your mixture

Why is the centrifuge step (5) needed? Why would that increase the yield of DNA?

There are some pharmaceutical companies that sell kits for DNA extraction.

In a protocol like this, a low centrifugation is typically used to separate DNA in solution from larger, heavier components of the mixture. By lightly pelleting the banana slurry at the bottom of the tube, the DNA in solution is less likely to stick to that fraction of the mix when you pour it through the gauze. That's where your increased yield will come from.

Yes. that is correct.

@Rob - do you mean that this answers your question? Don't forget to vote an answer up, if it solves your question. :-)


text:
Can the dendrites of sensory neurons be a meter long?
The typical textbook structure of neurons is a cell with a short dendritic tree and a long axon. The dendrites receive information and send it to the axon via the cell body (soma). The axon is a long structure designed to send the information to distant parts.

A neuron. source: ASU School of Life Sciences
In sensory neurons of skin receptors, however, the dendrites are considered to receive information about the outside world, i.e., the dendrites are the receptive parts of sensory neurons. They generate action potentials that are sent to the soma. But I've been told that the soma of sensory neurons are located in the dorsal root ganglion of the spinal chord?
Does this mean that the dendrites of sensory neurons are exceptionally long? Suppose I feel a prick in my finger, do the pain receptors really have dendrites a meter long all the way to the dorsal root?

I made some extensive edits to your excellent question. I think it still contains your initial question and my answer still addresses your problem. However, I've added a dimension to it to make it interesting for this community at large. I hope you can agree. +1

Absolutely... Thanks for taking the time to do it.. #christiaan

Short answer
Axons can be over a meter long, but dendrites are never that long. Distance in the body is covered by axons. The dendritic part of skin receptors is generally considered to be the receptor part and the receptor part only. The elongated structure leading to the soma, as well as the axonal part to the spinal cord are generally considered to be one and the same axon, the soma being attached to the axon in this case.
Background
The sensory receptors in the skin have their cell bodies located in the dorsal root ganglia situated adjacent of the spinal cord (Bourinet et al., 2014). In the case of pain receptors it is shown in Fig. 1. The same basic structure holds for the touch receptors in the skin.

Fig. 1. Signaling of pain receptors in the skin. source: Bourinet et al. (2014)
The cell bodies are located in the dorsal root ganglia of the spinal cord. Action potentials are sent from the dendritic region in the skin to the cell body in the ganglion. From there on it is transmitted to spinal interneurons in the spinal cord and up to the brain.
The nomenclature of these sensory neurons is generally as follows: in the cell body the axon splits in two. The afferent part that transmits the pulses from the skin to the cell body and the part that transmits the signal from the soma away from the cell body to the spinal cord are both considered as a part of the axon. The dendritic region is generally considered to be the nerve ending (Fig. 2C). So the axons of peripheral sensory neurons, as well as motor neurons for that matter, can indeed be over a meter long (Lodish et al., 2000).

Fig. 2. Types of neurons. Arrows indicate the direction of conduction of action potentials in axons. (A) Multipolar interneurons. The dendrites receive signals at synapses with several hundred other neurons, and there is a single long branching axon. (B) A motor neuron innervating a muscle cell. Typically, motor neurons have a single long axon extending from the cell body to the effector cell. (C) A sensory neuron in which the axon branches just after it leaves the cell body. The peripheral branch carries the nerve impulse from the receptor cell to the cell body, which is located in the dorsal root ganglion near the spinal cord; the central branch carries the impulse from the cell body to the spinal cord or brain. Both branches are structurally and functionally axons, except at their terminal portions, even though the peripheral branch conducts impulses toward, rather than away from, the cell body. source: Lodish et al. (2000)
References
- Bourinet et al., Physiol Rev (2014); 94(1): 81-140
- Lodish et al., Molecular Cell Biology, 4th ed. New York: Freeman (2000)

there are axon's in giraffe that are 15ft (4.5m)long.

Great answer -- the visuals are key. worth briefly mentioning "unipolar", though? You describe it, but never use that "vocab" word.


text:
Bioinformatics basics
What are the basic differences between genbank, NCBI and entrez gene?
And please tell some books and webpages where I can get more about the databases .(currently I'm using Bioinformatics and functional Genomics by Pavsner)

Unfortunately, this is not a "please hold my hand and walk me through this paper/concept/idea" site. I strongly suggest you take the [tour] and carefully read through the [help] to learn more about the site, including what is on-topic and what is not, and how to ask a good question. Use Google to find websites, that's what it's there for. Go to the databases themselves, they all have help pages.

are you a university student or perhaps a graduate student? there are resources to help with this sort of thing - but it depends on what your status is - but I completely agree with MattDMo, though - this site is not what you need

Genbank is a database of nucleotide sequences that are public.
NCBI stands for "National Center for Biotechnology Information" (in the US).
Entrez is NCBI's retrieval system.
You can find more information in this article
I don't know which kind of databases you are looking for, but there are hundreds of them!
In this wikipedia article there are some of them.

This is probably what the OP was after. This answer answers the question correctly and succinctly so I'm not sure why it received a downvote other than you were setup to fail because of the off-topic question.


text:
Multiplication of bacillus subtilis
I have a supplement for use in horticulture.  It is a powder that contains mostly subtilis with smaller amounts of a few other strains.
Prior to horticultural application I would like to "multiply" them so as to get to most out of the product.
Is water and a drop of molasses sufficient? (that seems to be accepted in cannabis culture)
How fast do these guys replicate? Without high tech lab equipment is there anyway I can tell that they are in fact multiplying?

You need to add some protein to your media. Use yeast extract if it is available or just boiled commercial baking yeast.

I am basing my answer on this document issued by one of the departments of the Ludwig Maximilian University of Munich.
Bacillus subtilis:

Doubling time: 30 minutes
Incubation temperature: 37°C
Growth conditions: strictly aerobe

Recommended media:

Luria-Bertani (LB) broth/plates - (for everyday use)
Difco Sporulation    Medium (DSM) - (for long-term storage)

You can find the formulations for the aforementioned media by following the link above.
With regards to the latter part of your question, the easiest way to tell (and doesn't require any "high-tech" lab equipment) whether your cells are multiplying or not is to inoculate a broth and see whether there is turbidity after a certain time of incubation. However, please be aware that you may have cross-contaminated your broth so unless you do further testing you cannot know for certain if it is Bacillus subtilis in your broth.


text:
Pooling already extracted dna?
I had ethanol precipitated a large amount of DNA (2ml) and had to split the sample in half to spin down because only the microcentrifuge has the correct rotor to spin that fast. I want to get as concentrated of a DNA sample as possible. Is it possible (correct) to combine the resuspended DNA? I wanted a total of 30 ul of extracted DNA. Could I resuspend each of the two sample in 15 ul and then combine them?
What is the best way to go about this. I realize just keeping them separate might be the best option. I also realized I could've lost DNA when transferring the sample to a smaller tube. I did this because I don't believe it is correct to spin for longer at a lower speed...

Assuming you are using standard 1.5ml microcentrifuge tubes, it is completely possible to resuspend a dried DNA pellet from an ethanol/isopropanol precipitation. I have resuspended RNA pellets in 10µl water frequently with no issues.

But then can I combine the resuspensions?

I see no reason it will cause any issues.

If it were me...

You can resuspend the two separate pellets (A and B) in 10ul each.
Collate in one tube (add A to B).
Use the remaining 10ul  from your desired volume to 'wash out' tube B and add the wash to tube A.

So long as the DNA is from the same sample this is a perfectly reasonable step that should not result in a substantial loss.


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Identification of proteins in this animation of a ribosome translating mRNA

This gif is from this page
After each aminoacyl-tRNA enters the ribosome, one blue thing comes and pushes the whole tRNAs whats that? I couldn't find it anywhere.(maybe some elongation factor?)
Also it seems that some thing is transporting the tRNA itself (maybe aminoacyl tRNA synthetase?)

The protein involved in "pushing" the tRNA and mRNA is the elongation factor EF-G. The protein involved in "transporting" the tRNA is the elongation factor EF-Tu.
Quoted from the Wikipedia articles:
EF-G:

When it binds to the ribosome A-site, EF-G causes the tRNA previously occupying that site to occupy an intermediate A/P position (bound to the A site of the small ribosomal subunit and to the P site of the large subunit), and the tRNA in the P site is shifted to a P/E hybrid state. EF-G hydrolysis of GTP causes a conformation change that forces the A/P tRNA to fully occupy the P site, the P/E tRNA to fully occupy the E site (and exit the ribosome complex), and the mRNA to shift three nucleotides down relative to the ribosome due to its association with these tRNA molecules. The GDP-bound EF-G molecule then dissociates from the complex, leaving another free A-site where the elongation cycle can start again

EF-Tu:

The tRNA anticodon domain associates with the mRNA codon domain in the ribosomal A site. If the codon-anticodon pairing is correct, EF-Tu hydrolyzes guanosine triphosphate (GTP) into guanosine diphosphate (GDP) and inorganic phosphate. This creates a conformational change in EF-Tu that causes EF-Tu to dissociate from the tRNA of the ternary complex (and therefore leave the ribosome). The aminoacyl-tRNA then fully enters the A site, where its amino acid is brought near the P site's polypeptide and the ribosome catalyzes the covalent transfer of the polypeptide onto the amino acid . The tRNA on the P site (without peptide) moves to the E site and is then released.


text:
Which is the proportion of metagenomics reads that cannot be mapped in any genome?
I was wondering if anybody knows how many reads from metagenomic or metatranscriptomic data do not map to known sequences and are therefore unidentifiable?
I found a figure for viromics, which seems to indicate that only about 6% of the sequences correspond to known virus (http://www.pnas.org/content/111/29/10714.full). But I couldn't find a more general percentage.

I think this will vary greatly depending on the source environment. Your example (marine viruses) is probably due to the large diversity of ocean viruses of which most have no reference genome.
Referencing the Human Microbiome Project:
A total of 57.6% of the high-quality microbial reads could be associated with a
known genome (ranging from 33–77% for anterior nares and posterior fornix, respectively).

Other papers describing more recent k-mer based approaches for classification report between 40-90% classified to a known reference. See:
http://www.nature.com/articles/srep19233
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4401624/


text:
Unwanted E. coli product in plasmid product
Using a TOPO XL Cloning kit, our lab took some amplified human DNA, inserted it into the vector, and attempted to clone it in E. coli. However, upon sequencing the purified plasmid product, the sequence we got back was E. coli rather the human we had amplified. The primers sat down in the plasmid as intended, just the sequence between the primers appears to be from E. coli (as implied by BLASTing it against a human, getting no results, and then blasting it against E. coli and getting a hit).

Is it from the E. coli genome, or from the plasmid itself?

Genome. So it's like (M13F Primer)(E. coli)(M13R Primer)

So you need to troubleshoot.  Is the "amplified human DNA" what you think it is? Are you confident in the insertion before the amplification in E. coli? Are you certain you're actually sequencing plasmid? Is there any chance your primers are incorrectly designed, mixed up, or produced wrong by the synthesis company?

The root cause turned out to be a lying spec. Using a different one, it was revealed that there was next to no template DNA in the initial amplification. No DNA, no good plasmids.


text:
What is this creature?
I found this small creature in my water bucket which i filled from my water tank. I would like to know what kind of creature I have found here.
Features which ought to help for identification:

Size = 1 cm
2.Transparent or semi Transparent
4 thread like legs
6 tentacles
2 black dots possibly eyes
It can swim
Triangular tail (Fish Like)
Found in Karachi City, Pakistan.

I think I see 6 legs in the picture. Could that be?

I looks a bit like a shrimp (Caridea)

The triangular "tail" is actually the tail fan made of five parts. The central part of it is the final segment of the body and either side is composed of the two parts of a modified leg. Were you to investigate it more closely you'd thus discover it is not at all "fish like"

It looks very similar to the grey shrimps that can be catched on sandy beaches of Normandy (on the English Channel).

It looks very similar to freshwater shrimp from this site:


text:
Why does my corn appear to have perfect flowers?
Corn is said to be a synchronously monoecious plant with separate male and female flowers.
I am growing a cross between a Peruvian and heirloom variety which seems to be growing some perfect flowers on both main stems, and suckers. I have googled this and find nothing to suggest this happens.
Is this common? And did a corn ancestor also have perfect flowers?


text:
Does atrophy of the thymus not effect T-cell selection and tolerance?
The thymus atrophies as age progresses. Does the T cell selection (which happens in the thymus) continue to take place? This doubt came into my mind because in the cadaver we dissected, the thymus was hardly more than scanty fibrous tissue. This definitely should have some effect on immune tolerance right? Is this the reason why the elderly are more prone to autoimmune diseases?
Or is it that selection happens only in children? This line of thought would pose a problem since T-cells are short lived and they continuously need to be produced. Or is it that the site of selection is shifted to some other place?
P.S. I am asking these questions assuming that selection is necessary every time new T cells are made. Correct me if this primary assumption is wrong.

T cells have a long half life (both naive and memory cells have halflives measured in years), especially when taking into account the fact that memory cells in particular can slowly proliferate and renew themselves.  An adult human therefore has 20-50 years' worth of accumulated T cells by the time they grow old, and those include both memory cells and naive cells that are potentially able to recognize new antigens. The thymus does continue to produce some new cells at a slow rate, but the backlog of previously produced cells are also able to monitor for pathogens.

Thanks! Just thought memory cells have long half live, dint know about the naive cells also being similar. So hematopoiesis in later stages of life wouldn't include T cell synthesis? or rather a decilne. Does creation of new leukocutes majorly mean, new non-lymphocytes?

@Polisetty if you have a new question, please ask.

@mattDMo the question is related to the answer he's given. Was just clarifying. I'll post if the answer doesn't turn up here :)


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If chylomicrons can not get into the capillaries, how do they supply to tissues?
The transport of chylomicrons is into the lacteals mainly because they are too big to get into the capillaries and yet they later supply triglycerides in the extra hepatic tissue by traversing in the capillary bed. This seems utterly illogical and self contradicting. So something seems to have gone wrong in this line of thought.

chylomicrons travel via the lacteals into the lymphatic vasculature that forms the cisterna chylii and thoracic duct...chylomicrons and other large molecules that are unable to pass into the fenestrated capillaries of the intestinal tract use this route into the thoracic duct, which ultimately drains lymph directly into the left subclavian vein - completely bypassing any first pass metabolic effects of the liver

But they use the capillaries later to deliver triglycerides to the tissues. So I mean to say, they are anyway able to get there (in the capillaries) so why not absorb into capillaries initially itself?

I have asked my self that as well - though the triglycerides and the particles that carry them (VLDL, chylomicrons) are huge... see this question for some related comments: http://biology.stackexchange.com/q/30883/16299

also - note that the chylomicrons and VLDL particles do not traverse the capillaries - the lipases that hydrolyze the triglycerides are located within the capillary endothelium - so when free fatty acids are released they are able to traverse the endothelium and be taken up by the adipocyte or other cell on the other side of the capillary.

@vance hey! I get it all now. Chylomicron size ranges around 300nm but the capillary diameter is around 40um. So the diameter is very much bigger. So they can very well traverse the capillaries, though they keep getting smaller due to lipoprotein lipase. On some further thought it occurred to me that while absorption in the gut it has to travel BETWEEN CELLS and here it has to travel WITHIN the lumen. So that happens to make all the difference!correct me if I happen to be wrong :)

Its my question too,does anyone know it?

@Nemexia  check ot the comment above, there is a difference between 'within' and 'between'. I assume that's right but yeah, someone has to answer with a reference

Please explain: "but the capillary diameter is around 40um" - that should read 40 n m (nanometer)? You do not speak of  the pores? Pores of/in the capillary endothelium?

@Vance L Albaugh Would be interesting to have your comment as answer, alternatively to have some reference.


text:
Can oral bacteria be targeted by white blood cells?
Today I was told from a dentist that a leukocyte is much larger than a bad bacterium. So a leukocyte cannot remove bad bacteria when they hide in very places like the space between the gums and teeth for example, because leukocytes cannot exit the body.
So am I right that a colony of bad bacteria cannot be removed from the oral cavity by leukocytes, because they are too big to exit the gum?

A colony in the gums or teeth are protected by building a strong film around them. There are leukocytes in the mouth, but they can't really breach this strong barrier. It has nothing to do with size.


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How does valerian make you calmer?
Why do Valerian pills make us calmer? What is the mechanism behind it?
I understand how artificial tranquilizers work. Do valerian pill have similar chemical components?

Short answer
Valerian preparations contain many compounds, but it is not known which may be responsible for its sedative effects. It is likely that there is no single active compound and that valerian's effects result from multiple constituents acting independently or synergistically (source: NIH). Overall, I think it is safe to say that valerian's sedative properties are related to its GABAergic properties (Yuan, 2004).
Background
The constituents of the volatile oil obtained from the rhizomes (underground stems), and stolons (horizontal stems) of Valeriana spec are variable due to  the variability in genetic make-up and environmental factors impinging on the batch of plants used (source: NIH).
The major constituents include the monoterpene bornyl acetate and a variety of sesquiterpenes including valerenic acid.
Some of the sesquiterpenes have been shown to have a direct action on the amygdala, which is a brain structure in the limbic system. The amygdala is responsible for feelings of fear and anxiety. Valerenic acid has been shown to inhibit the breakdown of GABA in the brain, resulting in sedation. GABA is the principal inhibitory neurotransmitter in the nervous system.
The non-volatile monoterpenes known as valepotriates possess sedative activity, but their mode of action is not clearly known. The valepotriates themselves act as prodrugs, and are transformed into homobaldrinal which has sedative properties.
Extracts of valerian roots contain substantial amounts of GABA which could directly cause sedation. However, whether GABA reaches the central nervous system is debated.
Another compound present in extracts is a lignan, hydroxypinoresinol, and it binds to benzodiazepine receptors, which are GABAA receptors and the target of benzodiazepines, i.e. tranquilizers and sedatives (Houghton, 1999).
References
- Houghton, J Pharm Pharmacol (1999); 51: 505-12
- Yuan et al., Anesth Analg (2004); 98(2): 353-8

Valeriana is an extract from the flower of Valerian.

We don't know the mechanism by which it affect our physiology but we have a number of hypotheses.
Quoting the USA National Institue of Health:

Many chemical constituents of valerian have been identified, but it is not known which may be responsible for its sleep-promoting effects in animals and in in vitro studies. It is likely that there is no single active compound and that valerian's effects result from multiple constituents acting independently or synergistically [18, reviewed in 19].
Two categories of constituents have been proposed as the major source of valerian's sedative effects. The first category comprises the major constituents of its volatile oil including valerenic acid and its derivatives, which have demonstrated sedative properties in animal studies [6,20]. However, valerian extracts with very little of these components also have sedative properties, making it probable that other components are responsible for these effects or that multiple constituents contribute to them [21]. The second category comprises the iridoids, which include the valepotriates. Valepotriates and their derivatives are active as sedatives in vivo but are unstable and break down during storage or in an aqueous environment, making their activity difficult to assess [6,20,22].
A possible mechanism by which a valerian extract may cause sedation is by increasing the amount of gamma aminobutyric acid (GABA, an inhibitory neurotransmitter) available in the synaptic cleft. Results from an in vitro study using synaptosomes suggest that a valerian extract may cause GABA to be released from brain nerve endings and then block GABA from being taken back into nerve cells [23]. In addition, valerenic acid inhibits an enzyme that destroys GABA [reviewed in 24]. Valerian extracts contain GABA in quantities sufficient to cause a sedative effect, but whether GABA can cross the blood-brain barrier to contribute to valerian's sedative effects is not known. Glutamine is present in aqueous but not in alcohol extracts and may cross the blood-brain barrier and be converted to GABA [25]. Levels of these constituents vary significantly among plants depending on when the plants are harvested, resulting in marked variability in the amounts found in valerian preparations [26].

Quoting wikipedia

Because of valerian's historical use as a sedative, antiseptic, anticonvulsant, migraine treatment, and pain reliever, most basic science research has been directed at the interaction of valerian constituents with the GABA receptor.[16] Many studies remain inconclusive and all require clinical validation. The mechanism of action of valerian in general, and as a mild sedative in particular, has not been fully elucidated. However, some of the GABA-analogs, particularly valerenic acids as components of the essential oil along with other semivolatile sesquiterpenoids, generally are believed to have some affinity for the GABAA receptor, a class of receptors on which benzodiazepines are known to act.[17][18] Valeric acid, which is responsible for the typical odor of mostly older valerian roots, does not have any sedative properties. Valeric acid is related to valproic acid, a widely prescribed anticonvulsant; valproic acid is a derivative of valeric acid.[citation needed]
Valerian also contains isovaltrate, which has been shown to be an inverse agonist for adenosine A1 receptor sites. This action likely does not contribute to the herb's possible sedative effects, which would be expected from an agonist, rather than an inverse agonist, at this particular binding site. Hydrophilic extractions of the herb commonly sold over the counter, however, probably do not contain significant amounts of isovaltrate.[19] Valerenic acid in valerian stimulates serotonin receptors as a partial agonist.[20]

@christiaan wouldn't like this very much!

@Polisetty - and how do you know that :-) you just unveiled my downvote :-)

Come on, Remi. An answer consisting entirely of two long block quotes, and you didn't even maintain the wikilinks? I expect more out of you... :(

Looks like users with more reputation are more harshly noted. Sometimes, I am willing to help but don't have time to work on the format.

Remi.b - it is one big copy-paste answer, the quotes are stacked with irrelevant info, and include many references not even mentioned in your answer. As @MattDMo says, I just expect better of hi-rep users like you. That's not harsh, it's high expectations not being met. I count on users like you to be critical on my answers too.

Well that's what I meant. Hi-rep users are not judged the same way as low-rep users. But it's fine, no big attack here. I agree that your answers is much better than mine (+1 btw). I though leaving my answer as it links to webpage that offer tons of references.

@Remi.b - a new user would've either gotten a comment, or a comment and -1 when pasting wiki sections, depending on the answer. I basically systematically downvote wiki paste's. In your case I was indeed quicker with the -1 given your rep, true. And thanks for the +1, you deserve the sportsmanship badge!


text:
Would a vial of anticoagulated, warm blood attract mosquitoes?
Would mosquitoes feed on free blood as an easy source of nutrients? They home in on veins by means of infrared light (heat detection). Also, blood needs to be in liquid form. So would they feed on anticoagulant-treated blood kept at 37oC? Or is there some physiological phenomenon that mosquitoes necessarily need to pierce something to draw in blood?
I am asking this, because just keeping a vial of blood at the end of a room might save us from mosquito bites.

Here's a link to the answer - https://redd.it/4h2j0g

Feel free to answer your own question if you found an answer elsewhere. Other option is to delete the post (not advised).

According to wikipedia they locate "prey" by detecting CO2 and some other compounds, so I don't think mosquitoes will actually find the blood unless they're accidentally right on top of it.
And for your reason: if you have the equipment to regularly draw some blood, keep it at 37 C and have some anticoagulants on hand, you might be better off using some tried and true anti-mosquito tech (nets, insecticides, preventing them to breed in the local area).
Or maybe this: https://en.wikipedia.org/wiki/Mosquito_laser


text:
What is the meaning of the "d(...)2" notation when writing a DNA sequence?
When the sequence of a DNA oligo is written as d(CGCTAGCG)2 what is the meaning of the d(...)2?  Why would it not simply be written as CGCTAGCG?
I recognize this sequence is the complement of itself.  Is that what this notation indicates?

Speaking to the author of this publication, they used d(...) to denote a double-stranded sequence and d(...)2 to denote a self complimentary double-stranded sequence.
This publication instead uses the subscript number after the parenthesis to denote the number of repeats in the sequence, e.g., d(AT)10 was used to represent the dsDNA sequence ATATATATATATATATATAT.

Assuming that you were referring to this specific usage of d(CGCTAGCG)2, the image provided for the crystal structure clearly shows that the structure refers to the fact that two strands of deoxy-ribonucleotide oligos were dimerised to each other.
Had the same structure been formed by double-stranded RNA instead, the resultant dsRNA duplex helix would be referred to as r(CGCTAGCG)2

If I understand, the d refers to DNA and the 2 refers to double-stranded, correct?  If I want to refer to triple-stranded DNA would I then use d(...)3, etc?  (The sequence I posted actually came from a study of the middle 8 bp of PDB ID: 1DCV but the structure should be quite similar to PDB ID: 1G7Z and it should not affect the answer.)

@stvn66 If they were 3 independent molecules hydrogen-bonded together, sure.

Can you point to any sort of reference which verifies your description of the notation?  This would allow me to more confidently mark this as the accepted answer.

@stvn66 I assume it is because of standard chemical nomenclature for dimerised molecules, and I don't think there will exist a source that says this for DNA specifically.

Reading this paper, they reference 'd(A)10-d(T)10'.  This seems to indicate the DNA sequence 'AAAAAAAAAA' and its complement.  Therefore, I do not think the '2' refers to it being double stranded, but instead that the molecule have 2 copies of that DNA sequence, since it is the complement of itself.


text:
What is the direction of current flow in myelinated nerve cells?
Is it correct to say electric current flows through the extracellular space, or cytosol of a nerve fiber during impulse conduction?
I know that an impulse is actually a change of membrane potential which is transferred along the length of a neuron through transfer of ions (by a series of ion channels and pumps).
In myelinated axons our professor told us the following:

When a nerve impulse propagates along a myelinated axon an electric
  current (carried by ions) flows through the extracellular fluid
  surrounding  the myelin sheath and through the cytosol from one node
  to the next.

How exactly does the current flow in myelineated nerve fibers?

@Christiaan It answered my question to some extent but I have a query, I have already posted it.

During an action potential current flows across the neuronal membrane. Basically, during depolarization, Na+ goes into the cell, during repolarization K+ goes out. This process for a myelinated axon is shown in Fig. 1.
Action potentials in myelinated neurons jump from node to node, a process called saltatory nerve conduction. These nodes, called nodes of Ranvier, lack myelin and contain Na+ and K+ channels. Outside these nodes there is insulating myelin wrapped around the axon and the axonal membrane lacks Na+ and K+ channels there.
What happens during an action potential at a node is the following: Na+ rushes in at the node. Because of the insulating myelin in the next axonal segment leading up to the next node in line, Na+ can run through the axon to the next node without much signal loss. This passive spread of depolarizing current is much faster than repeatedly generate a new action potential along the length of the axon.
To answer your questions now:

Question: Is it correct to say electric current flows through the extracellular space or cytosol of a nerve during impulse conduction?

Answer: Yes... and no. No, because electric current and notably Na+ and K+ flow perpendicular to the axonal membrane during action potentials. Yes, because the Na+ ions do move through passive current spread through the axon to the next node.

Question: How exactly does the current flow in myelineated nerve fibers?

Answer: Your professor was spot on. During depolarization, ions (notably Na+ in this case) are carried from the extracellular space through Na+ channels in the node of Ranvier to the intracellular space. From there it spreads through passive diffusion to then next node.

Fig. 1. Action potential generation in myelinated axons. source: Purves et al.(2001)
Reference
- Purves et al. (ed). Neuroscience. 2nd ed. Sunderland (MA): Sinauer Associates (2001)


text:
Why does BLAST employ local alignments?
Why does BLAST use Local alignment, not Global alignment? And when would a global alignment be useful?

This sounds a little like a homework question. Otherwise, there are too many answers, so it would be good to narrow down the question.

BLAST was devised to compare one sequence (the query sequence) with all the sequences in a database (target sequences), in particular the Genbank database(s). In 2012 Genbank contained over 3x1011 nucleotides in approx 109 sequences. So it is not feasible to do a rigorous comparison of the query sequence with each of the target sequences in the database, e.g. by the dynamic programming method, either local or global. It would just take too long. Instead BLAST uses heuristics to get the most likely best matches in a reasonable time.
The key assumptions of one of the heurists used is that any good overall match between sequences will contain some high-quality short matches, called high-scoring pairs (HSPs). (HSPs would be perfect matches of short runs of nucleotides, or high-score matches of amino acids (tripeptides) when one uses an amino acid comparison scoring matrix.) The program can make an index or library of those HSPs present in the query sequence and then just compare these (i.e. make a local alignment) in turn with target database sequences — a great time saving. So that is the basic answer to the first part of your question.
Just to quickly complete the story, an attempt is then made to use these high scoring pairs as 'seeds' to extend the alignment in either direction, and high scoring target sequences are saved and ranked.
An answer to your second question is you would do a global alignment when you were working with just a couple of sequences and had some scientific reason to believe that they were related, even though there were regions that had diverged appreciably. For example, you might be aware of key rare amino acids or nucleotide sequence motifs that should align in these regions and want to display them. Or you might want to align a protein of unknown three-dimensional structure with a related one of known structure to model it. But you wouldn't use BLAST to do the alignment, you'd probably use an implementation of the Needleman and Wunsch dynamic programming algorithm.