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Possible reasons for DNA getting stuck in well
I am in the process of Library preparation for Illumina MI-Seq using mtDNA. Using NEB Hotstart LongAmp Polymerase, I was able to obtain upto 10kb amplicons of mtDNA. However, when I switched to a different DNA sample, I am not noticing bands anymore in the gel. Strange thing is that, if I fragment these samples (Diagenode Bioruptor acoustic shearer) I get fragmented smears similar to the ones I expect from fragmenting a 10kb amplicon, even though these are stuck in the well.
Therefore, I dont know if a 10kb amplicon is stuck in the wells and is not migrating (given I see similar results for fragmentation for the samples that got stuck), or I am seeing in the wells what is genomic DNA and no amplification has occurred. Does the 260/230 value affect PCR amplification in any way? (I have a very high 260/230 value ~5 for the new DNA sample I am using)

What kind of gel (agarose, acryl amide) and which percentage do you use?

I use 1% agarose gel.

I don't know enough about your gels to know what's making your bands stick, but I've seen bands stay in the well when binding DNA to certain proteins and peptides, but I do it intentionally. Could something be bound to your DNA? Could the DNA in your wells be larger than you assume, but fragments under sonication to make small enough fragments?

I have put forward some possible solutions/trouble shootings below however @user137 raises very interesting points, which should be strongly considered! I have put a potential solution to potentially address this point including the DNA size issue.

There is one simple reason for that, your agarose gel is most likely too dense. Depending in the type of agarose, I would prepare a 0.5-0.6% gel at maximum.

Synbio gives this list for "standard" agarose, which fits pretty good with my experiences. If you use low melting agarose, this table looks a bit different, as the gel matrix is not a dense. The disadvantage is that the gel is much more prone to get damaged while handling.

I was getting the band at 10kb corresponding to 10kb molecular marker before. So I am not too sure if the density of the gel is the issue here. Also, even when the sample is stuck, the molecular marker ladder runs fine.

The problem is that this really depends on the agarose (and there is a plethora of different brands available). I would say that you are in the region where it gets difficult to get a good resolution. If your fragments are getting a bit bigger, than they will get stuck and you get something when fragmenting it. I would try a lower percentage gel and see, how this looks. Ideally with the same sample that made problems for you.

@AnuragMishra be rational. you need to try a less sense gel of a different brand before making the assumption that his solution is incorrect

Chris has 9k points for a reason

@caseyr547 This doesn't mean that I am always right.

@Chris yes but I am always right and I agree with you lol jk

Given that the OP knows the behaviour of markers in this gel it seems unlikely that this is the problem. Also although 1% agarose may not be suitable for achieving good resolution in the 10 kb range, this is very different from a fragment not entering the gel. I would try cleaning up the template further.

This is hard to judge without seeing a gel image. When the library preparation didn't went well, the DNA might be bigger in size.

I think this is a case where Occam's razor can be applied. The problem appeared with a new DNA sample, so that sample must be the prime suspect.

That's correct. I would run it on a lower percentage gel to see what happens. If it is then still not working, it is probably better to prepare fresh DNA and stop riding a dead horse.

After you check your gel it would behoove you to check primers, preparation, the quality of the XNA itself, then proper electrophoresis levels and other mechanical failures. I would think improper resistance of the electrophoresis wiring would cause your problem.

First as you mentioned, which is I think the key thing, is that you need to clarify what DNA sample it is that you are observing in the gel. The best thing to do to ensure that you only have PCR generated DNA samples is that once your PCR is over, treat your DNA mixture with Dpn I enzyme, which cuts methylated DNA, which is essentially cellular DNA as they get methylated in cells and it should not effect you PCR generated DNA as it won't be methylated. Look at page 7 and page 12 of this document for further instructions on using Dpn I (http://www.chem.agilent.com/library/usermanuals/Public/210518.pdf). You can subsequently clean and isolate your PCR generated DNA using any kit such as QIAquick gel extraction kit (QAGEN) using essentially this protocol but you are not using any gels (http://sites.bio.indiana.edu/~chenlab/protocol_files/agarose_gel_extraction.pdf). You can use other kits but this always worked for me! (please note that I'm not promoting any kits here!!) Now if you have any amplicons from your PCR then you should be able to nanodrop it (using the 260/230 ratio as your guide) and get a reasonable value for your amplicon concentration.
Now if at this stage you still have your PCR DNA as indicated by nanodrop and perhaps a test digest still gives the expected bands then the problem is with the running process and highly likely your gel which was the first thing I suspected to be the case. If not then you do not have any amplicons and you are simply trying to run your original DNA.
Although I have never worked with very large cellular DNA molecules before (I work with plasmids), however I was trained to run very large DNA (in agarose gel) on very low voltage such as 10-50 V overnight in a cold room since large cellular DNA doesn't tend to run very well in gels although that mostly applies to chromosomal DNA but 10kb is still quite large. I have run plasmid DNA of 12 kb in gels before at higher voltages but low voltage is best and it avoids tearing and shearing the DNA!


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Bohr effect in respiration
Would I be correct in saying that the Bohr effect is ONLY related to the concentration of [H+] in the tissues.
Obviously the concentration of carbon-dioxide can contribute to this concentration by producing protons (through carbonic anhydrase) but it isn't directly involved in the effect?

Would I be correct in saying that the Bohr effect is ONLY related to the concentration of [H+] in the tissues.

I would say no. Because oxygen binding affinity is inversely related to both [1]:

high $[H^+]$ concentration and
$CO_2$ increase (which is can be a consequence of the first)

$CO_2$ is involved in the Bohr effect:

The biological significance of the negative influence of the carbon dioxide pressure on the oxygen binding of blood is obviously very big. [...] During the bloods movement through the body the oxygen-pressure will decrease to a relatively low value, whereas at the same time the carbon dioxide-pressure rises. This will greatly support the oxygen release from the blood, resulting in an improved efficiency in oxygen usage [2].

References:

Wikipedia contributors, "Bohr effect," Wikipedia, The Free Encyclopedia, http://en.wikipedia.org/w/index.php?title=Bohr_effect&oldid=618215597 (accessed August 4, 2014).
Chr. Bohr, K. Hasselbalch, and August Krogh. Concerning a Biologically Important Relationship - The Influence of the Carbon Dioxide Content of Blood on its Oxygen Binding. Available from http://www.udel.edu/chem/white/C342/Bohr%281904%29.html (accessed 04.08.2014)

In a strict sense, I think you are correct that [H$^+$] contributes directly to the Bohr effect. A paper by Perutz et al. (1980) identified at least two amino acid residues in hemoglobin that account for the Bohr effect by interacting directly with H$^+$. CO$_2$ is not directly involved. Further, the Bohr effect (and the Root effect) are defined in terms of pH.
You and @Cornelius are correct that CO$_2$ contributes to the Bohr effect but speaking strictly it is a contributor and not the proximal cause. CO$_2$ dissolved in water produces H$_2$CO$_3$ which dissociates to release H$^+$, decreasing pH. But, lactic acid (for example) can also contribute to the Bohr effect again through the release of H$^+$.
While CO$_2$ and lactic acid contribute to the Bohr effect through the release of H$^+$, the H$^+$ is the actual cause through interaction with amino acids in the hemoglobin.

Perutz, M.F., et al. 1980. Identification of residues contributing
to the Bohr effect of human haemoglobin. J. Molecular Biology 138:
649-668.
Root, R.W. and L. Irving. 1943. The effect of carbon dioxide and
lactic acid on the oxygen-combining power of whole and hemolyzed
blood of the marine fish Tautoga onitis (Linn.). Biological
Bulletin 84: 207-212.

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Animal altruism?
My first impression of http://www.youtube.com/watch?v=Za4uT1ob8qE is that the baboons were being altruistic and benevolent, but is this guess proven or affirmed by science? I sense there's more to this video.
User dekar6279 comments:

They didn't save the impala, they just defended their territory. Moreover, the baboons didn't eat the impala because surrely they were not hungry, animals don't kill if they don't have to eat or to defend something.

I'd love to be enlightened by more videos. Some other  examples:
http://www.youtube.com/watch?v=77pK7D7A6I4, http://www.youtube.com/watch?v=nJzYhxpKYuM,
Yet the hippo appears to capitulate here: http://www.youtube.com/watch?v=4LyVnzVVECA

another cool example: bear rescues crow! https://www.youtube.com/watch?v=gJ_3BN0m7S8

User dekar has never seen a housecat? They kill for fun.

https://www.youtube.com/watch?v=gJ_3BN0m7S8

is this guess proven or affirmed by science?

It is a debated topic.

Such altruistic behaviors (toward non-kin) are extremely rare evolutionarily, with some theorists even proposing that they are uniquely human [1].
Experimental evidence indicates that human altruism is a powerful force and is unique in the animal world. [...] Current gene-based evolutionary theories cannot explain important patterns of human altruism, pointing towards the importance of both theories of cultural evolution as well as gene-culture co-evolution [4].

Yet, similar behavior was observed in chimpanzees:

In addition, we demonstrate similar though less robust skills and motivations in three young chimpanzees [1].

Altruism has evolved under some conditions:

We show that at least one of the four following conditions needs to be fulfilled: direct benefits to the focal individual performing a cooperative act; direct or indirect information allowing a better than random guess about whether a given individual will behave cooperatively in repeated reciprocal interactions; preferential interactions between related individuals; and genetic correlation between genes coding for altruism and phenotypic traits that can be identified. When one or more of these conditions are met, altruism or cooperation can evolve if the cost-to-benefit ratio of altruistic and cooperative acts is greater than a threshold value [2].

Altruism is related to kin selection:

In 1964, Hamilton formalized the idea of kin selection to explain the evolution of altruistic behaviours. Since then, numerous examples from a diverse array of taxa have shown that seemingly altruistic actions towards close relatives are a common phenomenon. Although many species use kin recognition to direct altruistic behaviours preferentially towards relatives, this important aspect of social biology is less well understood theoretically [3].

References:

Warneken F, Tomasello M. Altruistic helping in human infants and young chimpanzees. Science. 2006 Mar 3;311(5765):1301-3. doi: 10.1126/science.1121448. PubMed PMID: 16513986.
Lehmann L, Keller L. The evolution of cooperation and altruism--a general framework and a classification of models. J. Evol. Biol. 2006 Sep;19(5):1365-76. doi: 10.1111/j.1420-9101.2006.01119.x. PubMed PMID: 16910958.
Agrawal AF. Kin recognition and the evolution of altruism. Proc. Biol. Sci. 2001 May 22;268(1471):1099-104. doi: 10.1098/rspb.2001.1611. PubMed PMID: 11375095.
Fehr E, Fischbacher U. The nature of human altruism. Nature. 2003 Oct 23;425(6960):785-91. doi: 10.1038/nature02043. PubMed PMID: 14574401.

I would argue that the behaviors you saw in these are not altruistic.
Baboons will aggressively defend their territories against predators.  For example, watch this baboon chase a female lion.
http://www.youtube.com/watch?v=4ebd36p4zkw
The baboon eventually loses but only when the lion gets help. I'd say the baboons were just chasing away the cheetah and the hyenas as a matter of self defense. The antelope just got lucky.
The same applies for the elephant. It doesn't really approach the buffalo and lion. The lion runs off soon after the elephant arrives in the area.  Elephants will also aggressively chase off predators likelions. The lions are right to be afraid.
https://www.youtube.com/watch?v=JDJV_nSqDDw
Same applies for the hippos. They can be aggressive towards crocodiles.
http://www.youtube.com/watch?v=BTcMHB1Wubc
As for the hippo "saving" the wildebeest, we always have to be careful about interpretation. Just because it looks like the hippo was trying to save the life of the wildebeest does not mean that it was the hippo was actually doing. For example, it may have simply been trying to remove the wildebeest from its territory. At times, the hippo puts its mouth around the wildebeest. Was it considering taking a bite? Was it trying to prod the wildebeest? Was it trying to play with the wildebeest?
It's very difficult to demonstrate that any of the behaviors in the videos were displays of altruism.

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Why does the pET- expression vector contain a LacI gene additionally to the one in the genome?
The pET plasmid is used for protein expression with T7 promotor in expression strains, such as E.coli BL21(DE3)
It contains a lacI gene which codes for the lac repressor protein, a protein of interest under the control of a T7 promoter for T7 RNA polymerase and a lac operator which can block transcription, directly behind the promotor. The lac operon is another control of transcription of the protein of interest.
Furthermore, T7 polymerase is located in the genome as well under the control of the lac operon.
When IPTG is added, the lac repressor is inactivated -> T7 polymerase and therefore the protein of interest will be expressed.
The Lac I gene is already present in the genome of the expression strain used, why is it also cloned into the pET vectors?

Because you can then use this system in bacterial strains which do not have LacI.

Thanks for you comment @Chris. Are there strains that have the T7 RNA polymerase but do not have lacI? Or are those then just infected with T7 phage to express the protein? Could you find a reference for your statement and post it as an answer?

I don'T know about all strains - sorry. But you could co-express it from another plasmid.

Another possibility (and probably more likely) is that the construct is less leaky that way.

According to this article, a single lacI gene copy gives rise to about 10 copies of lacI protein per cell, and we can conclude, therefore, that this is the amount required to keep a single lac operon repressed.  The article also mentions the lacIQ mutation in the promoter of lacI that results in a ten-fold increase in the level of lacI protein.
If a lac expression construct is present at more than 100 copies per cell the result will be leaky repression, and this can result in selection for mutations in the gene of interest if it has deleterious effects on the host bacteria. The easiest way around this problem is to put a lacI (or lacIQ) gene on the expression plasmid so that repressor levels are commensurate with the number of copies of the lac operator, as in the pET vectors.


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What if a Point Mutation is seen in only half the coverage for its location?
I've been looking at some sequenced exomes and found an interesting point mutation that causes a Proline-to-Leucine amino acid change in the protein. This seems like it could have a big impact on the protein's functionality but before I go any further I want to explore whether or not the variant is a sequencing artifact.
I looked at the coverage for this particular region of the genome and found that in some samples, the point mutation is seen in every single read covering the base in question while in others the point mutation is seen in approximately half of the reads. In all my samples, the base in question is covered by at least 15 separate reads but usually its more than 20.
My primary question is: how should I interpret the cases where the point mutation is seen in some but not all of the reads covering its location?
I'm also interested in any suggestions/advice on the more general topic of determining whether or not the mutation I've found is a sequencing artifact.

I don't know, whether the organism you are working with is diploid, but suspect it's an animal (or even a mammal), so the most parsimonious explanation would be that you have homozygotes and heterozygotes at this SNP-position.

Yeah, its a human. That's a really great answer; I can't believe I didn't think of such an obvious explanation.

Just to ascertain this- check the quality scores (phred), sequencing lanes, replicates etc at the SNP region: to make sure that it is not an artifact.

@WYSIWYG: the probability of this being an artifact is negligible given the systematic nature of the phenomenon: it's not about two reads having one mismatch.

I totally agree.. If it is really half the reads sort of situation. However, it is always good to confirm that there are no other hidden patterns.

Also I don't know what kind of genetic input your given but if there is variation in origin ie some saliva some cheek skin then there could be a tissue based difference in the genome.

If it's cancer good luck finding a consistent set of tissue.


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What would be the scientific name of this worm
I saw this pic while crawling online and it was a bit different for me to predict which worm is this.

Source: http://www.seafishingtackle4u.com/softbaits/ragworms-latex-lures/
It appears somewhat different form other annelids as parapodia or setae are somewhat transparent and very attractive too.
What worm is this?

That worm is plastic.

So, in summary, it is Nereis effigiei

@J.Musser i too think the same as i cant see any correct parapodia on its body

As Cornelius correctly pointed out, it's not a living worm :)
As to the question, what kind of worm they tried to imitate, I'd say, they had a nereid (errant, i.e. wandering) in mind and were likely inspired by the segmentation of Arenicola (sedentary), which together created this appearance, unrealistic for an errant polychaete: with the body segments outnumbering parapodia.
EDIT:
They also paid no attention to the head (a very important body part in polychaete systematics!), which seems to be absent. This feature could also be "inherited" from Arenicola, the head end of which is not prominent and bears no appendages.

what is the appandage like thing arising from mid part of its body

@agharehanabbas: hmm, you mean the hook?

yes can i get any details about its morphology anatomy and role in daily physiology?, i think it is special character of polycheate nerieds

The hook is actually part of the lure.

If you would have read the text from the source of that image (which by the way you didn't mention, I did a Google Image search and edited your question to include it), you would have known that what is seen in the picture is not a living thing, it is a latex fishing lure:

Product Description: Sandworm/Ragworm 8″ size, sure fire fish catching lures. Costing less than live worms, but lasting much longer, never be without worms again.

Source: http://www.seafishingtackle4u.com/softbaits/ragworms-latex-lures/

Rotf lol Awesome answer


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Is there a difference between endorphins that are released while physical activity and sex/masturbation?
I observerd myself and I can identify two different types of "happines".

First - called by me - After Pleasure :
Occurs AFTER (and last long) long activity that require from me engagement focus and effort  for example :

running 16KM
learning for an hour things that I think are worthwhile
reading book
generally any mental or physical activity

Second - called by me - During Pleasure
Occurs DURING (and last short time) activity that DON'T require any engagement, focus or effort, for example :

masturbation
eating sweets
eating tasty things in general
having hot bathing time
watching funny videos/TV

I wonder is there any scientific distinction between those two states of my body and mind. And assuming that endorphins are the hormones are responsible for the "oh-good" state, are different kind of endorphins are released while taking this 2 different activities (like studying for 1hour and masturbation) ?
Thanks for an answer in advance.

What kind of difference? Concentration, type? Can you clarify this?

@Chris I just suspect there is a difference between endorphins that are released during this 2 activities since the "oh-good" state is longer in the first one, and shorter in the second, because one is released after Activity, and second During activity.

The title is a bit overspecific and thus confusing. I guess you're asking about short-term and long-term rewarding system action. If so, then yes, there's a whole lot of things that differ between these, them are actually two different modes of rewarding, involving different mediators and subsystems. I won't give you any direct references, but you can search for yourself: look for dophamine receptor types and their action, oxytocine and other mediators. The main plot is that "during" pleasure is related to passion while "after, long-term" is related to stability, ensurance and persistance.


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How is photosynthesis observed?
How is photosynthesis observed?

Say I have plants A and B, and I want to find how fast they are able to turn carbon dioxide into oxygen. How would I experiment this?
Say I have one plant A, which has two kinds of leafs B and C. I hypothesize the B-leafs produce oxygen faster than the C-leafs. What kind of experiment could I set up to test this?

Is that a homework question?

No, I'm just interested. Anyway, if the question is too simple for this site, I would be happy with a good reference alone.

No, that's fine. I am just asking.

What do you want to measure- $CO_2$ consumption/carbon fixation, $O_2$ production or $ATP$ production ?
All rates need not be the same..

You can try isolating the leaf/bunch of leaves (in a transparent cellophane paper or something similar), and then pass the air content inside the isolated region after a while, through solutions such as $KOH$ or alkaline pyrogallol. $KOH$  dissolves $CO_2$, whereas pyrogallol dissolves $O_2$. The reduction in the total gas volume will be equal to the amount of the particular gas. You should normalize this with the total surface area of the leaves.
This is just my guess for a homework type experiment. I am sure complex equipments exist.

Not sure, this what you need, but here you can find a detailed description of how photosynthesis efficiency can be measured in the field, with a list of modern devices. In short, it's about measuring the uptake of CO2 and release of H2O of individual leaves.

Hydrogen carbonate is an indicator commonly used for testing photosynthesis. It shows changes in carbon dioxide concentration in the air. You would set up the plant in a sealed system next to a tray of hydrogen carbonate indicator solution and observe the colour change.


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Can we attack viruses by attaching proteins and such to their shells?
Haven't looked into this to very long, but an initial search didn't return anything.
HIV uses certain co-receptors to enter our cells. Could we flood the blood stream with specially designed proteins that mimic cell receptors, either locking the virus out of vulnerable cells, or even causing the virus to release its genetic material (pre-mature ejc. for viruses... :|), so it can't accidentally get away and infect a cell anyway? It seems like an obvious idea, so the fact that it may not already be happening must mean there are a host of challenges to it? Basically we design a protein that acts like a strait jacket, with tags that allow our body to recognize it as a 'friendly' body. T-cells use the same receptor though, so are there ways to identify a T-cell compared to a HIV virion?
Obviously this wouldn't prevent some viruses managing to infect actual cells, but over time, if we can attack enough, say 2/3 of the virions, for each generation, we could seriously harm the population, and maybe keep it in check?

Sorta near the mark, but this is a case of virus-on-virus crime: http://discovermagazine.com/2009/jan/033                                             It still shows a viable concept for attacking viruses though...

Maybe antibodies. If you could grow large amounts of neutralizing humanized antibodies in cell culture and inject them IV it might help reduce active virus loads. Antibodies would probably have better stability and higher affinity than receptor mimics, and the technology behind them is well developed. And as far as HIV treatment is concerned, small molecule antiretroviral drugs are already pretty good as long as you take them early on in the infection and take them regularly. These can keep viral loads so low that passing the infection to others is very difficult.

Here review  and here are reviews such approaches.  The complex peptide Trimeris/Enfurvitide and small molecule Maraviroc are FDA-approved inhibitors of HIV entry into cells.

This is the whole end goal for vaccines

Yes, that should be possible. And it is one of the ways antibodies work. It is already used as a treatment against rabies. There you get a dose of immunoglobulins directed against the rabies virus together with the vaccine. The immunoglobulins neutralize the virus.
The same is possible when you vaccinate against the surface proteins which a virus uses to dock to a cell. With the resulting antibodies this docking is at least hindered if not completely prevented. And there are interesting results from the Ebola research which used a small molecule inhibitor to identify the protein which is important for cell binding of the virus. It is called NPC1, when the receptor on the virus surface is blocked, no docking can take place. This will be one of the approaches to make a therapeutic. See here for more details.
And it is of course possible to design more of the molecules - the problem is to find substances which do not interfere with body functions or which stimulate other pathways.

Ah...so this HAS already been considered and is actively being researched. I had already run into the idea of the issue with anti-viral medications interfering with our normal bodily functions, oddly enough in an article about Ebola, as you were mentioning. I am very interested in Micro-biology, just haven't taken the time to sit down and learn in depth about it, so I wasn't aware this was how anti-bodies worked. But I was just wondering, with the developments in recomb. genetics, if anyone was researching synthetic drugs. Thanks for your answer.

This approach actually works on almost anything, given enough proteins and nanoscale "griefing".
There was an experiment a few years back where scientists wrapped normal cell membranes around polyurethane beads. The surface looks like a normal cell, allowing it to soak up toxins and trap viruses.
Then there's the offensive approach where proteins are used to block structures on a virus, preventing it from recognizing and entering host cells. Alternately you could include immune-reactive structures on those proteins, painting them for clean-up.
This approach also works on bacteria. Block membrane channels used to get rid of waste, or outright cover the bacteria in sticky garbage "griefing" gunk preventing them from eating. Build exceptionally heavy proteins that bind to bacterial flagella and stop them from moving.
Scale it up to worm parasites. Build proteins that stick to their mouths and refuse to leave. While you're at it, build another set that sticks to the opposite end of the worms' digestive tracts, preventing them from eating or removing waste. It's a major headache and a pain in the behind - at the same time.


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Mechanism of DNA gyrase inhibitor
Why DNA gyrase inhibitor, such as Nalidixic acid and Norfloxacin, do not stop gyrase from cutting DNA helix but only prevent them from decatenation replicating DNA?

Crysallographic studies do not exist for this yet. It has been predicted by computational methods that quinolones bind to DNA-gyrase complex and stall the enzyme at that step.

@WYSIWYG you should make that an answer

I didn't really answer the question.. If no better answer comes up then I'll find details and post it as answer

This might be a good article to read: http://www.ncbi.nlm.nih.gov/pubmed/24497635
Robert Kerns's lab has been doing a lot of work on fluoroquinolines, so look into his other work as an entry to the literature. And apparently X-ray crystals have been done for at least parts of this complex. There is some evidence for fluoroquinolines binding to DNA, then moving into the protein as it moves along the DNA.


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Regarding apoptosis and turning it 'back on'
Is there some chemical or chemicals or even special molecules that can be 'injected' into cancer cells that will turn any Apoptosis mechanisms 'back on'?
Or maybe chemicals and/or molecules that might cause a certain gene or set of genes to switch to a configuration favorable to apoptosis?

There are many. The two main problems are 1. regulatory network in cancer cell is different from normal cell, 2. Specific delivery of the killing molecules to cancer cells

If the regulatory network in a cancer cell is different from a normal cell could some of these differences be 'marked' by some chemical so as to identify a cancerous cell? Could such a cellular difference being marked with a biological marker be a useful target for a modified 'mild' virus?

Yes, tons of things induce apoptosis. Here is a good list that you can get for research grade
Sigma-Aldrich
Even your immune system can tell cells to "commit suicide." Now the trick is, getting drugs, proteins, pathways, and your immune system to selectively target cancer cells.

If it is tricky to selectively target cancer cells does this mean they are hard to detect by the host body? Are they almost invisible to medicine? Could cancer cells emit or give off chemical signals that make them hard to detect?

Yes to all of those questions. They are especially tricky to the immune system. Usually what chemotherapy targets is rapidly dividing cells, which coincidentally also non-specifically targeting hair root folicles.

I heard on the radio some Biologist named Michel Fossil who wrote about 'Reversing Aging' had researched about increasing Tellomeres or 'resetting' them to a state similar to how they used to be actually improved cellular functions as if they were 'younger'. Could improving the Tellomere 'length' or functioning in a cancer cell make the apoptosis mechanisms in the cell 'turn back on' or start functioning as 'they' used to before the cell became cancerous?

Do cancer cells have telomeres and would they be 'extra durable' ( as a cancer cell keeps functioning indefinitely)?


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Could the growth rates of Vibrio vulnificus be affected by an oil spill?
I live on the Gulf Coast, and Vibrio vulnificus has recently made the news due to an increase in the number of reported infections. Naturally, it has people around here worried. I live in an area that was affected by the BP Deepwater Horizon oil spill, and many people are concerned that the oil or byproducts of the clean-up could be fueling the growth of this and other bacteria.
I know that bacterial species which are capable of metabolizing the components of crude oil exist, but are rare. I also know that Vibrio vulnificus thrives in warm salt water, and since it is a "flesh-eating" bacteria that infects shellfish, it must be capable of "eating" organic material.
I can think of several possibilities that might explain an increase in reported infections:

The amount of bacteria and the number of infections is actually the same, but reports have increased due to more awareness in the public and in the medical community.
Warmer water temperatures in the Gulf in recent years have led to more bacterial growth.
The bacteria is capable of metabolizing crude oil, its degradation products, or one of the other cleanup chemicals (Corexit, for example).
The oil spill has compromised the immune systems of the organisms that are typically V. vulnificus hosts, which has led to higher infection rates and therefore, more bacteria.

There could of course be other explanations, but these are the ones I came up with off the top of my head. I imagine that if bacterial populations actually have increased, then any of these scenarios that are possible would likely contribute something.
However, in the short amount of research I have done, I haven't been able to find any concrete data that shows whether populations have increased at all, or whether they could be affected by the oil spill.
My questions are:

Are there any studies that show the population of V. vulnificus over a time period covering the BP Horizon spill (this happened in April 2010, and oil products are still washing up on beaches in small amounts)
Is it possible that it could be metabolizing oil or other chemicals related to the spill?

Wikipedia says that the strain is common in the gulf of mexico. Probably the living conditions were better in the last time so the population got much larger.

My educated guess is that it's a little of one and two, a lot of four and things like four(decrease in biodiversity, lack of predation, habitat disruption, etc), and probably not 3. 3 would be a big deal, because it could revolutionize oil spill cleanup technology. Worth checking to see if it's happening, though.

I found these article, which show exponential increase in population of Vibrio in BP oil spill region (published in 2011 supported in 2013).$^{1,2}$
There is evidence that Vibrio representatives can metabolize oil-derived compounds $^{3,4}$. There is a sizable amount, more than 31%, where found in the Deepwater Horizon Spill.$^5$. Though the reason is still to be proved $in\ vitro$, but studies shows they can persist in the presence of oil.$^6$
Source:
[1]:
High Numbers of Vibrio vulniﬁcus in Tar Balls Collected from Oiled Areas of the North-Central Gulf of Mexico Following the 2010 BP Deepwater Horizon Oil Spill
[2]:
Associations and dynamics of Vibrionaceae in the environment, from the genus to the population level
[3]: West 1984, Numerical taxonomy of phenanthrene-degrading bacteria isolated from the Chesapeake Bay.
[4]: Moxley K., Schmidt S. (2010). Preliminary characterization of an estuarine, benzoate-utilizing Vibrio sp. isolated from Durban Harbour, South Africa. Curr. Res. Technol. Educ. Top. Appl. Microbiol. Microb. Biotechnol. 1249–1254
[5]: Hamdan L. J., Fulmer P. A. (2011). Effects of COREXIT® EC9500A on bacteria from a beach oiled by the Deepwater Horizon spill. Aquat. Microb. Ecol. 63, 101 10.3354/ame01482
[6]: In situ and in vitro impacts of the Deepwater Horizon oil spill on Vibrio parahaemolyticus.

These are all good articles - thank you. I don't agree that refs 1+2 show an increase in Vibrio outside of populations within the tarballs themselves, but since I can't find anything else to support/refute that idea, I am accepting this answer. Thanks again!


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is it necessary that every theca of an angiospermic anther must contain two microsporangia
i basically don't know the procedure or sequence of steps involved in the formation of anthers but i have read it somewhere it is formed from the dedifferentiation of shoot apical meristem of the axillary bud through mitotic divisions

so is it necessary that every theca of an anther of an angiosperm must contain two microsporangia, if yes then why are they two in number., can i get an account on the development of microsporangial lobes [here i am not asking about the process of development of pollen grains in them].
i am asking how the microsporangial lobes itself are formed
a diagrammatic answer would be highly appreciated

Is the necessary that stamens have two microsporangia per theca? No. Many species in Cryptocarya group of Lauraceae have microsporangia that have fused such that they have only two microsporangia instead of the typical four (Rohwer et al. 2014). I interpret their description as saying that the microsporangia within a theca but it's not clearly stated as such.
Within the Magnoliidae, one pollen sac of a theca is lost is some taxa (Endress et al. 2008). Evolutionarily, the Hamamelidaceae have reduced the number of pollen sacs from two to one (Endress 1989). I could not find examples of plants with more than two microsporangia per theca.
Why do most plants have two pollen sacs per theca?  It's probably a result of the evolutionary history of plants in general because it is so common. Even those that have only a single pollen sac seems to start out developmentally with two.  It's probably due to the underlying genetics.
The genetics of floral development is complex but being slowly teased apart. The overall development of floral patterns is set by a group of developmental or regulatory$^1$ genes called MADS genes.  Collectively, the MADS genes (along with other regulatory genes) control the overall organization of the flower structure. For example, MADS genes determine the arrangement of floral whorls from sepals (outermost whorl) to petals to stamens to carpals (innermost whorl). Changes in use or timing of the MADS genes can contribute to different types of floral morphology, such as the loss of sepals or big, showy sepals but no petals.
Some of these same MADS genes contribute to the formation of the stamen structure. The review by Goldberg et al. (1993) gives a thorough but now dated review of the developmental genes that control anther development. The figure below (their figure 3) gives a nice overview of the stages that lead to development of the theca with two microsporangia and ultimately to the final stage of fertilization. Even more specific, Bowman et al. (1991) show that AGAMOUS is one regulatory gene that is active during the development of the theca and microsporangia.

I can't speak in detail about how regulatory genes work in flowers (I know a bit more about regulatory genes in animal development, especially from an evolutionary developmental perspective). In animals, regulatory genes often work by concentration gradients, both by the concentration of the regulatory gene itself, by the concentration of other regulatory genes, and by the concentration of the regulated genes. This process helps to determine the anterior-posterior axis in animals with bilateral symmetry, as well as the left and right sides.
I suspect that floral regulatory genes work in a similar fashion.  Changes in regulatory expression can lead to bilaterally symmetric flowers (think of mint flowers, monkey flowers, etc. See Hileman and Cubas (2009 for a good review.). I suspect it is some type of symmetric expression of regulatory genes that leads to the formation of two microsporangia per theca.  Mutations that cause changes in the expression patterns of other regulatory genes can cause the initial expression but subsequent loss of one of the microsporangia, as noted for the Lauraceae and the Hamamelidaceae.
Footnote
Broadly but simply, regulatory genes are genes such as transcription factors that regulate or control the expression of other genes.
Literature Cited
Bowman, J.L., et al. 1991. Expression of the Arabidopsis floral homeotic gene AGAMOUS is restricted to specific cell types late in flower development. The Plant Cell 3: 749-758.
Endress, P.K. 1989. Aspects of evolutionary differentiation of the Hamamelidaceae and the Lower Hamamelididae. Plant Systematics and Evolution 162: 193-211.
Endress, P.K. and L.D. Hufford. 2008. The diversity of stamen structures and dehiscence patterns among Magnoliidae. Botanical Journal fo the Linnean Society 100: 45-85.
Goldberg, R.B., et al. 1993. Anther development: Basic principles and practical applications. The Plant Cell 5: 1217-1229.
Hileman, L.C. and P. Cubas. 2009. An expanded evolutionary role for flower symmetry genes. Journal of Biology 8: 90.
Rohwer, J.G., et al. 2014. A phylogenetic analysis of the Cryptocarya group (Lauraceae), and relationships of Dahlgrenodendron, Sinopora, Triadodaphne, and Yasunia. Phytotaxa 158: 111-132.


text:
Is this ladybird larva secreting a protective fluid?
I know that adult ladybird beetles can secrete a fluid to keep predators from eating them. Can the larvae do that too? Or are these yellow droplets something else?

Welcome to Biology Beta!!!

In larvae stage Ladybird beetles secretes yellow gooey alkaloids from its abdomen.
Ladybird beetles oozes hemolymph(in other word its blood), which is toxic and very smelly, when threatened. It's a mixture of various alkaloids and repulse the predators.
Good Job, There might be no picture more clearer than you provided

source:
[1]: Ladybird defence alkaloids: Structural, chemotaxonomic and biosynthetic aspects (Col.: Coccinellidae), Désiré Daloze, Jean-Claude Braekman, Jacques M. Pasteels
[2]: 10 Fascinating Facts About Ladybugs

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text:
Waste generation by embryo
How does an embryo produce waste products even when its organ systems are not developed fully ? How does the placenta identify or differentiate waste materials from embryo ? Which organelle or specific cell acts as excretory organ ?

Embryos still metabolize the nutrients delivered by the mother. The metabolism takes place in the cells, including in the developing organs. Metabolism produces waste products that must be removed. The allantois is the structure that removes waste from the embryo.
I'm not sure what you mean by the placenta identifying or differentiating waste materials from the embryo. The waste simply diffuses passively into the mother's blood from the embryo. The mother's excretory systems then handle it.


text:
Why was the Davson-Danielli model rejected?
According to my textbook, Davson-Danielli's model of a phospholipid bilayer sandwiched between two layers of globular protein was incorrect. The nonpolar protein portions would separate the polar portions of the phospholipids from water, causing the bilayer to dissolve. Meaning, the Davson-Danielli model is not only incorrect, but it is also impossible.
I understand why the model is incorrect, but not why it is impossible. In my view, the nonpolar proteins would remain together in a micelle shape due to hydrophobic exclusion. Because of this, the phospholipid bilayer sandwiched on the inside would remain isolated from the water.
Why would a bilayer dissolve if the proteins were in contact with water and the phospholipids were isolated from the water?
I think that my confusion stems from many misunderstandings about the chemistry and structure of the cell membrane. In depth illustration of the error that my book mentioned would be most helpful.

The original figure that Danielli and Davson proposed looks like this (from the original publication):

It shows the phospholipid bilayer of the membrane (which is correct) embedded between two layers of globular proteins. The hydrophobic tails of the lipids are orientated towards each other, while the hydrophilic heads are oriented to the outside.
Although the membrane composition is correct (this was already published 1925 by Gorter and Grendel), there are some problems with the proposed model:

Membranes are not identical. The differ in thickness and the ratio of
proteins:lipids.
Membranes have distinct inside and outside layers (defined by the
membrane proteins which are present on the surface of the membrane)
Other than predicted by the model, the membrane proteins do not have
a very good solubility in water - in fact they are amphiphatic,
meaning they have hydrophilic and hydrophobic regions. The
hydrophobic side is anchored inside the membrane.
When the membrane proteins would cover the lipid bilayer, their
hydrophobic regions would be in contact with water, which
destabilizes this construct. Even if they would be oriented towards
the membrane, they would face towards the hydrophilic heads of the
phospholipids causing the same effect. Additionally the proteins
would also seperate the hydrophilic phospholipid heads from the
water. So there is no real stable solution in embedding the membrane
with proteins.

Just remember that some proteins can stick to the membrane kind of that diagram propose, although they are not true membrane proteins. For example, Bee Venom Phospholipse A2 has a membrane binding surface where it binds to the membrane and hydrolyzes phospholipids. Of course it doesn't stick on the membrane forever, it binds to the membrane, breaks down a few lipids, then floats away to repeat the cycle.

But these proteins doesn't cover the whole membrane as the model suggested. Most proteins simply "float" in the membrane.

Problems with the davson danielli model :

freeze-etched micrographs:

This is a technique of rapidly freezing the cell and then fracturing them. The fracture occurs along lines of weakness and in these micrographs there were two prominent dark lines which indicate the phospholipid bilayer and but there were transmembrane proteins even in between the phospholipid bilayer unlike what the davson danielli model suggested (that the phospholipid bilayers contained two layers of proteins on top and on bottom.)

2)structure of membrane proteins :
improvements in biochemical tech allowed people to extract proteins from the membranes. They were different sizes and globular in structure.They were unlike the type that would form continuous layers on the periphery of the membrane. Proteins were hydrophilic in nature and hence should have been attracted to the tails and not the heads.
3)Fluorescent anti-body tagging :
red and green markers were attached to the antibodies that bind to membrane proteins. these two cells were fused together and 40 minutes later it was seen that the red and green markers were mixed throughout the membrane of the fused cells. therefore the proteins were free to move within the membrane rather than being fixed in a peripheral layer.


text:
How are DNA segments selected in PCR?
I understand that in PCR we're able to amplify only selected portions of the DNA... however despite reading it from multiple sources, I cannot figure out how this selection actually takes place.
I know that by using proper primers, one each for coding and template strands, we can direct the DNA polymerases to specific sites to start with. I also understand that these primers make the replication proceed in opposite directions, towards each other. Like follows:

However, I wonder what makes the replication terminate when the polymerase reaches the primer at the other end? Because as far as I understand, replication should continue indefinitely until the physical end of the sample strand is reached... such that we may decide the starting points but never the ending points.

Termination of replication on the original template is dependent on the processivity of the enzyme or the length of the DNA, but think about what happens if a newly synthesized strand is used as the template.

Note: In your PCR program you always set extension time.
Case:

Product length = 500bp
PCR extension time = 50sec
Assuming that polymerase adds 1000 nt/min

Cycle 1:

Strand that binds FP: extends ~800nt to the right (as per the polymerization rate): 300 bp ahead of RP complementary site. This product is lets say P1
Strand that binds RP: extends ~800nt to the left: 300bp ahead of FP complementary site. This is P2

Cycle 2:
The products of cycle-1 become templates for next round.
FP binds to P2 -300nt from its 3' end. Similarly RP binds to P1 -300nt from its 3' end.
The resultant products will be 500nt which give rise to a 500bp perfect dsDNA.

Some P1 and P2 will keep forming at a linear rate; since your template is low in amount compared to the amplified cycle1 and cycle-2 products, your expected PCR product will be much higher (which gets produced at an exponential rate).

The long products are amplified linear, while the short product (with the primer sequences on the ends) are amplified exponential.

yep exactly... :)

Wow, beautifully explained.

Only now I understand why there are highly controlled timings and temperature control in PCR.

I think that the DNA produced with overhanging ends (i.e that made of P1 and P2) must grow as exponentially as the one of perfect size... only that it will lag one order of magnitude behind.

I'm not completely clear when you say "what makes the replication terminate when the polymerase reaches the primer at the other end" since when you perform a PCR you go through three phases. The denaturation, whereby the two DNA strands become single stranded, then the annealing, which is when primers attach to their appropriate matching site (but the original DNA template is still single stranded) and extension, which is when DNA polymerase use the primers to extend make the matching strand the primer is attached to (http://en.wikipedia.org/wiki/Polymerase_chain_reaction). DNA polymerase continues to make the strand until it essentially either drops off or until the cycle is over and it is time for the cycle to repeat itself. The way you make sure to terminate a specific DNA replication at an appropriate length is to use the extension time as a control since as pointed in the above answer by @WYSIWYG the extension is largely assumed to be 1000 nt/min so if your product of interest is 500 bp, then you do 30-40 sec of extension in your PCR extension cycle program and if the product of interest is 1000 bp you do 60 sec of extension and so on.
In the training I received, it is usually not recommended to PCR DNA template which is very large such as an entire plasmid such as pUAST. The main issue even with high fidelity/proff-reading DNA polymerases is that you can get errors in replication if the strand is very long. what often happens is that you amplify a section of DNA if you want to check for the presence of something or if you need to use the amplified fragment then you design restriction sites at either end of your fragment by incorporating it in the primers itself then you go ahead with you digestion and fragment purification and then you sequence your fragment to make sure you do not have any errors although PCR has much much more applications.

I see... incorporating restriction sites within primers sounds pretty smart. Thanks for the wider perspective.'

authors: ميثم يحيى عبيس الشمري


text:
Datasets of aligned nucleotide sequences
Where can I find some datasets of aligned nucleotide sequences? And what should I assume about the accuracy of the alignments there?
(I would like to use such datasets for training the alignment model I am working on. In particular, to help me get an estimate on some parameters such as the frequency of single nt INDEL at some locations.)

What do you want to do with this aligned sequences? Test algorithms? Actually your question is a bit unclear.

I would like to use such a dataset for training, i.e. to help me infer some parameters for the alignment tool I am working on. Thank you for your comment; I will edit my question to clarify.

I agree with @Chris! do you mean if the alignment itself can be trusted based on the algorithm used or the sequences themselves can be trusted. Are you worried about the semi-conserved sequences being aligned in a variable manner depending on the algorithm used? For different alignment algorithms please see this post (http://biology.stackexchange.com/questions/20075/what-is-the-state-of-the-art-algorithm-for-multiple-sequence-alignment). I could be totally wrong but multiple alignment and semi-conserved sequences is mostly an issue for AA not nucleotides since they either match or they don't

Thank you for your comment. Amino Acid alignment wouldn't work for my purpose (I think), because I am trying to infer the probability of a single nt INDEL at a given location.

So the alignment has to be trusted in the sense that the nucleotide INDELs predicted by the alignment are correct.

Well.. Indels are read by your sequencer.. There are machine errors and sample prep errors. You have to set up controls in your machine and train your set.. I haven't really understood your question, however.

I haven't really understood your comment but that is probably because I'm relatively new to this world. What I'm trying to do: A pair of aligned nt sequences can have regions that are conserved, it can also have insertions/deletions. Those insertions/deletions can be of full codons, but there can also be insertions/deletions of single nucleotides (Am I right so far?). My purpose from a dataset of aligned nt sequences is to study those insertions/deletions (and infer parameters based on them for the alignment tool I'm working on).

@AnasElghafari.. I would suggest that you use some diagram to make your question clear.

Okay, let's forget about the "goldstandard" and "absolutely correct" business. I edited the question so now I am only asking for the datasets of aligned nt sequences.

Hey guys, I edited my question into something which -I hope- is clearer. Can you please remove the hold?

what do you mean by aligned nucleotide sequences: pairwise alignment or MSA?

pairwise would be enough for my purpose.

There are some manually curated HIV alignments at LANL. HIV is quite variable in length so you will find many indels in these alignments.

You can find 46-way multiz alignment from UCSC genome browser, it is down on comparative genomics part and labelled as "cons 46-way", which is a genome alignment of 46 vertebrate species. You can use data on their genome browser on the site, or get download information here.
If you are interested in pair-wise alignments, I don't know of any pair-wise alignment database, but in fact you don't need one. You can search for nucleotide sequences from NCBI nucleotide database and align them using BLAST on their website. BLAST is maybe the most common tool for pair-wise alignments and also for database alignment searches, where a single query sequence is searched for matches throughout a database of sequences. If you want to do a large number of alignments, you can download BLAST to your computer to do them faster.


text:
Relationship between mN and mg in vessel contraction studies?
What is the relationship between mN and mg as the units involved to measure the changes in contraction?  A tool most widely used is an instrument called myograph. In these exoeriments, either units of mg or mN is used without any mention of why. Note that the first two examples use an experimental tool called a myograph - used to measure the force produced by a muscle (in this case muscular blood vessels) when under contraction. Both examples mention tension. Wether these myograph experiments are completely different i'm unsure.

This example shows force as 'mN' from this paper Fig 1A a.
Those who are interested the caption is as follows
"Effects of Li+-PSS and NMDG-PSS in PGF2α-preconstricted pulmonary arteries. Intrapulmonary arteries (IPA) were first exposed to 80 mM K+, and endothelial function was assessed by relaxation of PGF2α contractions (10 μM) to acetylcholine (10 μM). Following a period of recovery, IPA were preconstricted to 10–15% 80K using PGF2α, and then physiological saline solution (PSS) was replaced by Li+-PSS in the continuing presence of the same concentration of PGF2α in endothelium-intact IPA"

This example shows units as 'g'. note that some examples from other papers also use units of mg essentiall x1000 similar to other unit conversions from
this paper Fig 1a.
The caption is pretty much the same as 1. Particularly thromboxane A2 (TXA2) is a pharmacological agent affecting a set of ion channels:
"Requirement of thromboxane A2 (TXA2) for hypoxic pulmonary vasoconstriction (HPV) in rat pulmonary arteries (PAs). A: hypoxia alone (3% PO2) did not induce contraction of PA (left). In the presence of 10 nM U46619, hypoxia induced a strong contraction equivalent with the response to high K+ (80K, right)"

For a third example click here. It does interestingly state "The PA rings were stretched to a predetermined optimal passive tension of 750 mg". As such mg (or g) is an alternative representation of a unit of force as presumed. Figure 1 in this link again demonstrates mg as an y-axis unit of measurement under myograph experiment

1kg weight = 9.8 N but I am not sure if that is what they mean here.

Ick, unlabeled axes. Do you have a description of the figure from the text? Something like 'In figure A we describe...' would help a lot. g doesn't seem like a unit of force, but I'm not sure what else they could be measuring. Perhaps it's literally a gram weight?

@woosah: Can you post a little bit bigger (2nd) picture?

@DevashishDas
I added some more examples and made images bigger. Plus links to articles

@JeremyKemball I added some more notes and caption and also links to articles. If you think I should write more on this question let me know I'll change it

@WYSIWYG May be you're onto something. As mentioned above which i noticed in example 3: "The PA rings were stretched to a predetermined optimal passive tension of 750 mg". Clearly its a unit of force. 750mg is approximately 7350 mN? That sounds too big here though if my calculation are correct. As you said don't know what they mean, seems unusual to use that formula anyway

Something looks off. $1^{st}$ is N/m or Tension or unit force exerted on the artery walls. Whereas $2^{nd}$ one is actually change in mass of thromboxane $A_2$ ($TXA_2$) with time. Can you clarify that?

@DevashishDas I wouldn't even know fully but that force represented in the graphs are 'resultant' forces ins response to various stimulus'. The 2nd graph is also change in contraction from a myograph experiment (I included some caption). Thromboxane A2 (TXA2) is just a pharmacological agent used in some experiments to affect certain channels. TXA2 is an example of a stimulus during a typical myograph experiment along with introducing hypoxia or change in ionic concentrations (e.g. 80K+ Fig 2 in question).

@DevashishDas Maybe there are different myograph experiments hence different units due to different types of contractile force. I just found out there  are several set ups of a myograph whose sole aim is to measure contraction in pieces of muscle (in my case pertaining to blood vessels but apply to anything muscular).
Two types of experiments I just come across are wire and pressure myographs

The difference between above two units is a matter of metric systems used:
The newton (symbol: N) is the International System of Units (SI) derived unit of force. One newton is the force needed to accelerate one kilogram of mass at the rate of one metre per second squared.
Another system:  kilogram (gram, milligram)-force
The kilogram-force (kgf or kgF) is a gravitational metric unit of force. It is equal to the magnitude of the force exerted by one kilogram of mass in a 9.80665 m/s2 gravitational field (standard gravity, a conventional value approximating the average magnitude of gravity on Earth). Therefore one kilogram-force is by definition equal to 9.80665 N. Similarly, a gram-force is 9.80665 mN, and a milligram-force is 9.80665 µN.
Kilogram-force is a non-standard unit and does not comply with the SI Metric System.
See:
http://www.sengpielaudio.com/ConvForce.htm

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text:
X-inactivation in ovaries
Background
In all eutherian (mammals excluding the marsupials), the female (who is $XX$ for the pair of sexual chromosomes) inactivates one of her $X$. This is called dosage compensation. This inactivation occurs at a given time during the development when randomly one $X$ is silenced. The daughters of this cell inherit the $X$-inactivation pattern epigenetically, which results in some part of a tissue having the maternal $X$ inactivated while others having the paternal $X$ inactivated (daughters of some other cell which silenced the paternal $X$). This process yield to the famous turtoiseshell coat in female cats.
Question
In short
Assuming X-inactivation occurred in the lineage of the oogonia/oocytes, when does the X-inactivation and X-reactivation occur in the lineage of the oocytes?
A bit developed
Are the X inactivated as well in primary oocytes? If not, is the $X$ inactivated in the secondary oocytes in a primary follicle? If not, did the diploid mother cells of the secondary oocytes have one $X$-inactivated? If yes, did all diploid mother cells of oocytes have the same $X$ inactivated (inactivation occurred relatively early in the development or is there an imprinting) or did the mother cells of oocytes differ in the $X$ they have inactivated (inactivation occurred relatively late in the development)

I'll post an elaborate answer in some time. Little occupied now

See these two papers:

Early Loss of Xist RNA Expression and Inactive X Chromosome Associated Chromatin Modification in Developing Primordial Germ Cells
X Chromosome Reactivation Initiates in Nascent Primordial Germ Cells in Mice

Basically it happens just before the meiosis.


text:
Can a broken thumb/finger bone not require realignment of the bone?
Is it possible that a finger/thumb bone fracture is so superficial, that the doctor does not need to realign (re-set) the bone before applying the cast? Or does it always require for even a finger/thumb broken bone to be put back in place before applying the cast?

It is possible for bones to be broken and heal without any intervention, but it's rare. This is anecdotal, but my grandfather fell out of a barn and broke the top of his femur without knowing it. He kept walking on it, and a few years later he needed 2 canes to walk ( was in his 30s ). He saw a doctor, and X-rays showed he had broke his hip and when it healed it misaligned and caused wear to the hip socket. That also eventually healed after he was told not to put so much pressure on it. So if a hip can do it, fingers probably can too, but I don't recommend it.

Yes. You can figure that yourself if you look a bit at the types of fractures on Wikipedia, the Bone Fracture page:

Other considerations in fracture care are displacement (fracture gap) and angulation. If angulation or displacement is large, reduction (manipulation) of the bone may be required and, in adults, frequently requires surgical care.
[...]
Other types of fracture are:

Complete fracture: A fracture in which bone fragments separate completely.
Incomplete fracture: A fracture in which the bone fragments are still partially joined. In such cases, there is a crack in the osseous tissue that does not completely traverse the width of the bone.
[...]

Incomplete fractures and fractures with less or no displacement may heal correctly in some situations without needing realignment.

Most finger fractures (including the thumb) and, for that matter, hand fractures will not need to be "reset" before applying a cast, as most fractures are simple and non-displaced. More serious fractures (displaced, involving an articular surface, and many comminuted fractures) will need manipulation and possibly pinning.
But to answer your question, the fracture need not be incomplete to be casted/immobilized without manipulation. It is not rare, but common.


text:
Dataset of microscopic images before and after staining?
I am looking for a freely distributed dataset of microscopic images. I am hoping to find a dataset that would feature histological images before and after staining (e.g. H&E or some other standard one, preferably). I have been searching through various databases, but I cannot find a proper set. I hope the sample size to be at least about 100. Suggestions?

What do you mean, "before and after staining"? An image taken before staining won't show anything...

Oh, I must have understood something incorrectly. Well, I hope I can have access to the "raw" data, as well as the processed versions.

There should be very minimal processing for scientific images - otherwise you are not looking at true results.

Do you have a particular species in mind? are you looking for something like this? (http://www.virtualflybrain.org/site/stacks/index.htm)

Virtual fly brain (http://www.virtualflybrain.org/site/stacks/index.htm) is an excellent database of fly (Drosophila) brain sections, which can be electronically processed/annotated/highlighted on the fly to show different areas of the fly brain as an overlay on top of the original images.
Alternatively, you can use BrainTrap (http://fruitfly.inf.ed.ac.uk/braintrap/) for the expression of proteins in the fly (Drosophila) brain using brain sections. Another database which has silver stains of Drosophila brain sections is the flybrain (http://flybrain.neurobio.arizona.edu/Flybrain/html/atlas/) database. This database also contains 3D models of different fly brain structures and much more!
I'm sure there are many many similar databases, but these are the ones I knew of, which are widely used in the Drosophila community.


text:
What could cause no pain but sense of touch?
What could cause a mammal to have and respond to a sense of touch with only isolated numbness but not feel pain?

CIPA?

Loss of nociceptive pathways.

I think Congenital insensitivity to pain with anhidrosis might be what you are looking for, it is the closest thing I can think of right now.


text:
Are efflux pumps mutations or are they originally present in N. gonorrhoea?
I'll start by saying that I am no biologist. I am a math major trying to create a mathematical model for gonorrhea strain competition. My assignment is to create a model similar to a model that was already was already created, see page 9 of Evolution of within-host Antibiotic Resistance in Gonorrhea.
I wanted to try to incorporate the efflux pump into a mathematical model. Before I do that, I would first like to see whether efflux is gained through mutations. If it is, my model will be pointless since mutations are already covered in the original model from the research paper.
Feel free to add better tags. I thought mine was appropriate.

Efflux pumps are common in bacteria, as well as eukaryotes. The mutations included in their model would not include efflux pumps. A mutation could potentially affect the efficiency of a pump in a strain but the mutations in their model are not creating the pumps.


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Human Evolution in Modern Times
I understand that evolution occurred to form the current hominids from a common ancestor millions of years ago. As evolutionary processes take a long time, is there proof of evolution occurring with humans today?

I don't think this necessarily needs to be closed. A good answer would simply point to some recently observed evolutionary trends in humans.

@canadianer i too support you i.e. downvoting a new user at his first post itself would be very bad

Whats wrong with this question? It's short and legitimate, so why downvoting it?

With @Chris editing, there is definitely no reason to not reopen this post.

Common examples of recent human evolution include Lactase (and its associated selective sweep), sickle-cell disease and malaria resistance in zone where the prevalence of malaria changed, height, skin color, blood type and finally various diseases linked with bottleneck. That would be good to have an answer that encompass at least all these examples.

I agree with @Chris's edit. The question is improved.

Yes, there are examples. First: If you want to say, that humans and monkeys evolved, than it is better to say that they evolved from a common ancestor. This makes quite a difference.
If you are looking for examples of human evolution then one of the most obvious traits under evolutionary selection is pigmentation. There is a clear correlation with lattitude (and this UV-index):

The changes in pigmentation occured - seen from a evolutionary perspective - pretty recent when humans moved out of africa and to other regions (see here).
See these papers for more details:

The evolution of human skin coloration
Colloquium paper: human skin pigmentation as an adaptation to UV
radiation.
Epidermal pigmentation in the human lineage is an adaptation to
ultraviolet radiation.

Other examples would be the tolerance for lactose (the sugar contained in the milk) in adults which arose during the last 5-10.000 years. Normally only babies can process these sugar which is contained in large amounts in the mothers milk. When they are weaned, usually the enzyme is not expressed anymore. However with the settling of the humans and the domestication of cattle this changed, so we can still drink milk and eat milk products without producing intestinal problems. See here for more details:

Genetic signatures of strong recent positive selection at the lactase
gene.
Adult-type hypolactasia and regulation of lactase expression.

A third example would be the sickle-cell anemia, which happens due to a point mutation in the human hemoglobin protein. This causes an aggregation of the hemoglobin molecules in the red blood cells which then leads to a reduced elasticity (see here for more details). It also leads to a protection against malaria (most likely by the reduction of the life span of the erythrocytes). The areas with high prevalence of the sickel cell anemia in africa correlate pretty nicely with the distribution of malaria.

An Immune Basis for Malaria Protection by the Sickle Cell Trait
Sickle Cell Anaemia and Malaria

If you look further, you will find a number of different examples, where evolution is present after humans went through a genetic bottleneck (meaning the number of humans was drastically reduced).

Lactase persistance is evidence of recent and ongoing natural selection in humans.
Mammalian young produce lactase, an enzyme needed to break down the lactose sugar in the mother's milk. The young quit producing lactase after they are weaned because they no longer drink milk. Most humans (roughly 70%) also quit producing lactase when they are young. Without lactase, the adults can't break down the lactose sugars if they consume milk. The lactose builds up in the gut, which supports large populations of bacteria that cause gas and indigestion. This is lactose intolerance.
The remaining humans (about 30%) continue to produce lactase into adulthood. They can digest the lactose milk sugar so they do not suffer lactose intolerance. The persistence of the lactase enzyme in adults is associated with the human domestication of cattle.  A study by Todd Bersaglieri and colleagues (2004) showed that a mutation that allowed for continued lactase production spread rapidly by natural selection through populations in north European-derived people between 5000-10,000 years ago.
Interestingly, a separate study by by Sarah Tishkoff and her colleages (2007) identified a different mutation that also allowed for continued lactase production spread quickly by natural selection through populations in east central Africa during the past 7000 years.
Together these studies show how natural selection can act very quickly in humans. Two different mutations occurred in two different populations of humans. Both mutations, however, gave the same selective advantage of lactase persistance in developing agriculturally-based societies.
Literature Cited
Bersaglieri, T. et al. 2004. Genetic signatures of strong recent positive selection at the lactase gene. American Journal of HUman Genetics 74: 1111-1120.
Tishkoff et al. 2007. Convergent adaptation of human lactase persistance in Africa and Europe. Nature Genetics 39: 31-40.


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What is the purpose of DNA?
My very basic understanding is DNA gets transcribed into RNA by effectively replacing thymine with uracil, then RNA is translated to make proteins. Looking at it from an engineering perspective, it would appear that, while the RNA to protein translation is non-trivial, the DNA to RNA transcription process is rather redundant: As it's just a simple replacement, why not start with RNA in the first place? My assumption therefore is that there is something about the RNA molecule (e.g., too reactive, too unstable, etc.) that requires it to be put in "cold storage" as DNA.
I don't have a background in genetics or biology, so could someone ELI5 why DNA is needed?

Imagine you want to produce a widget. You have thousands of worker, but only one blueprint. Each worker needs the blueprint to build a widget (they're really forgetful and can't build from memory). So only one worker at a time can build your widgets.
What you would do is to create copies of your blueprint and distribute them to your workers. That way multiple workers can produce the widget at the same time.
DNA is the blueprint, and RNA is the copy. Your workers are the ribosomes that translate the RNA into proteins.
This is of course grossly simplified, and there are other reasons for the specific arrangement, but this is certainly one of the reasons why the intermediate RNA is used.

To make this analogy work, one has to substitute the "DNA is the blueprint" with "every gene is a blueprint".

@har-wradim I intentionally made it only about one widget/gene/protein to avoid making the analogy more complicated than it has to be

An analogy has to be realistic, otherwise it produces misunderstanding and new questions.

RNA was almost certainly the first genetic molecule of inheritance. However, the single-stranded nature of RNA is not particularly stable and thus would not be reliable for the long-term storage of genetic information necessary for reproduction (and ultimately evolution).  The necessary stability is provided by DNA.
The question becomes, how did DNA evolve to replace RNA? This is an area of active research but here is a nice summary.

OK, I found this on Wikipedia. I probably should have checked there first!

DNA has three primary attributes that allow it to be far better than
  RNA at encoding genetic information. First, it is normally
  double-stranded, so that there are a minimum of two copies of the
  information encoding each gene in every cell. Second, DNA has a much
  greater stability against breakdown than does RNA, an attribute
  primarily associated with the absence of the 2'-hydroxyl group within
  every nucleotide of DNA. Third, highly sophisticated DNA surveillance
  and repair systems are present which monitor damage to the DNA and
  repair the sequence when necessary. Analogous systems have not evolved
  for repairing damaged RNA molecules.

"Analogous systems have not evolved for repairing damaged RNA molecules" ..because some of these are impossibilities, e.g. the very common C to U deamination couldn't be detected in an RNA genome. This is also the most likely reason why our genomes are made of DNA instead of U-DNA..

No this doesn't explain, why the RNA step is needed.


text:
Could habitat selection pattern be deformed in environment with low variability?
It is possible that strong (clearly visible) pattern of selection towards particular parameter is detectable only in environment with high variability (difference between used (red) and non-used (grey) space will be significant) whereas in sub-optimal environment used and non-used space do not differ due to low variability.
And if this is possible, is there any relevant study which focuses on such issue?

P.S. It seems to be very basic idea, however I could not find any relevant sources on this topic.

What is an environment with high and low variability? Does "variability" mean spatial heterogeneity?

Hi @Remi.b! For example: Parameter = tree height. High variability environment will be primeval forest, whereas low variability environment will be even aged monoculture (extensively managed forest). If we hypothesize that squirrel will prefer high positioned places for roosting, we could detect such selection only in "green" area. I need an article on this topic. Animal species is irrelevant.

I am sorry if picture above is not clear. In circles are histograms of tree heights. In first, we have "normal" distribution from which the squirrels are selecting trees with higher than average height. The second histogram is probaly close to uniform distribution. In such sub-optimal conditions is selection not detectable due to absence of height difference between used and available trees.

If I understand your question correctly, I've seen this idea in many papers, sometimes stated clearly and sometimes in more implicit terms. After a quick look I found a paper which should be relevant as a starting point for you: Mayor et al. 2007. Spectrum of selection: new approaches to detecting the scale-dependent response to habitat. Ecology 88(7).
In my mind, there are two questions here. First, to what extent will low population size in sub-optimal environments (leading to a smaller sample to work with) lead to more uncertain inferences of preferred habitat/substrate; basically saying that noise might swamp signal in sub-optimal environments. Second, to detect selection for a particular habitat/substrate, you must sample a wide enough range of environments so that you capture both preferred and unpreferred habitats and transitions between them. In the paper I linked to this issue is touched upon in the discussion:

Second, evidence of habitat selection depends on the scale of analysis. To understand scale dependence, investigations must encompass a spatial scope sufficiently wide to uncover scale domains of selection and the thresholds or transitions between them. In both cases, spatial scale is the empowering principle, and scaling continua are the means of application.

I've seen similar ideas as this show up in papers on habitat choice in birds living in agricultural landscapes as well, where some species are often found in rather poor environments (because these environments are common). Looking at habitat preferences only in these environments might then give a misleading view, since individual choices are constrained. Also relevant, even if not mentioned in your question, is the concept of maladaptive habitat selection (sometimes called ecological traps), where you can have situations where species use environmental cues that used to indicate high fitness habitats, but might now result in maladaptive choices, see e.g. Pärt el al. (2007). However, in this case you will still have a clear preference/selection (as in your high variability environment), the problem being that the organism is selecting suboptimal habitats from a fitness perspective.

Perfect @fileunderwater. This finding is exactly what I need....[this study] is the first to quantify [recognize] habitat selection explicitly as a response [function] to habitat heterogeneity...


text:
Is dried grain dead or dormant?
Is dried grain considered dead or dormant botanically?
Related to a BH-SE question.

Relevant to the BH-SE quote, a seed considered biologically dead (cooked, too old, etc.) will not then produce a crop.

I would imagine this might vary by species, where the seeds of different plants could survive different degrees or duration of dryness.

Dried Whole Grain is obviously dormant, not dead, because, used as a seed it can grow into a plant.

Dried grains are very mostly viable means they are in a dormant state until and unless suitable condition are provided. More dried it will be viable for longer.
In fact there are seeds found in Siberia which are ~32,000 years and still viable.

Courtesy: National Geographic
Source:
US Emergency Supply: Introduction to Seed Viability

I got to thinking that there must be a distinction between grain and the germ. The grain must die in order for the germ to come alive. I am confident that the germ will not grow so long as the grain is alive. It is through the process of its dying and acquiring moisture from the earth, that the grain converts to sugar which supports the germ and enables it to sprout. The germ is in the grain, but separate & distinct from the grain, like a baby in the womb is in the mother, but separate and distinct from her. With grain, the mother must die for the germination to occur. With humans not so.

This response can be moved to BH-SE if it is more appropriate there.


text:
Why are high levels of epinephrine and low levels of cortisol signs of stress?
According to my psychology textbook (Psychological Science: Modeling Scientific Literacy), high levels of epinephrine and low levels of cortisol are signs of stress. However, earlier in the textbook it is shown that the autonomic response of the human body releases norepinephrine and epinephrine, while the hypothalamic pituitary adrenal (HPA) axis pathway releases cortisol. So it seems to me that signs of stress would be high levels of both of these things. Is my textbook wrong or am I just understanding what stage of stress it's describing?

So it seems to me that signs of stress would be high levels of both of these things.

Yes. Wikipedia claims [1] the same:

Stressors [...] activate the HPA axis, though via different pathways. [...] Stressors that are uncontrollable, threaten physical integrity, or involve trauma tend to have a high, flat diurnal profile of cortisol release (with lower-than-normal levels of cortisol in the morning and higher-than-normal levels in the evening) resulting in a high overall level of daily cortisol release. On the other hand, controllable stressors tend to produce higher-than-normal morning cortisol.

The same on a webpage of Society for Endocrinology [2]:

In addition, in response to stress, extra cortisol is released to help the body to respond appropriately.

Yet, there are conditions in which stress can lower cortisol levels. One of them is psoriazis [3]:

[...] patients with persistently high levels of stressors seem to have a specific psychophysiological profile of lowered cortisol levels and may be particularly vulnerable to the influence of stressors on their psoriasis.

And some psychiatric disorders [4]:

Several stress-associated neuropsychiatric disorders, notably posttraumatic stress disorder and chronic pain and fatigue syndromes, paradoxically exhibit somewhat low plasma levels of the stress hormone cortisol.

References:

Wikipedia contributors, "Hypothalamic–pituitary–adrenal axis," Wikipedia, The Free Encyclopedia, http://en.wikipedia.org/w/index.php?title=Hypothalamic%E2%80%93pituitary%E2%80%93adrenal_axis&oldid=619115237 (accessed August 7, 2014).
Society for Endocrinology. Hormones. Cortisol (2013). Available from http://www.yourhormones.info/hormones/cortisol.aspx (accessed 07.08.2014)
Evers AW, Verhoeven EW, Kraaimaat FW, de Jong EM, de Brouwer SJ, Schalkwijk J, Sweep FC, van de Kerkhof PC. How stress gets under the skin: cortisol and stress reactivity in psoriasis. Br. J. Dermatol. 2010 Nov;163(5):986-91. doi: 10.1111/j.1365-2133.2010.09984.x. PubMed PMID: 20716227.
Yehuda R, Seckl J. Minireview: Stress-related psychiatric disorders with low cortisol levels: a metabolic hypothesis. Endocrinology. 2011 Dec;152(12):4496-503. doi: 10.1210/en.2011-1218. PubMed PMID: 21971152.


text:
Microscope scale bar
In some microscopic images, there is a bar scale at one of the corners or near a specific object. How are they added to the images? Does the slide have some markers, or are they digitally added? If so, how are they computed? I am planning to buy a microscope and wondering is there something I should look for. Thanks for any help!

There are two common ways to generate a scale bar:

Measure it.  You can take a picture of an object with known spacing such as a grid target and then measure the size of each pixel.
Compute it.  If you know the magnification of your objective, and the magnification of any relay optics after the object but before your camera, you can compute the total optical magnification.  Then using the pixel size on your camera, you can get the actual pixel size.  For example, suppose you have a camera with 7.4 micron pixels, a 20x objective, and a 0.5x adapter lens before your camera, then you would have a pixel size in your image of 7.4/20/0.5 = 0.74 microns.

It depends on the type of microscope you want to buy. Most microscopes come with a slide with precise measurement bars on them and you select the objective and if it is connected to some sort of camera and comes with a software then you can calibrate the scale bar for a particular objective using the software it comes with. Otherwise if you know the pixel per micron for each objective, then once you acquired your images, you can draw a scale bar using a software like Image-J. In terms of what microscope to buy and what to look for, it depends on the application so you need to clarify the question. I have answered a question similar to this here (What to look for when buying a light microscope?).


text:
Machine learning for light microscopy -- problems to solve?
I would like solve some biological problems that would improve the state-of-the-art of biology or bioinformatics. In particular, I want to apply machine learning on light microscopic images. The equipment and experience I have are:

Bright-field, dark-field, and phase-contrast microscopy
Modern laptop
56-core super-computer with >100 GB of memory (on request)
Intricate knowledge of machine learning algorithms and signal processing
PhD-level research skills
Programming skills that would get me to work at Google
Limited knowledge about biology, bioinformatics, and microscopy (yet)

I want to do some publishable research free from all academic hassle. I will do this solely on my own time, without hurry to publish, in an attempt to do something good for the mankind. I can throw a few hundred dollars on the project every two months (or abour 1000 USD per year).
Much of the biological research published in Science, Nature, PNAS, Cell, etc. are so specialized that I find it difficult to detect important problems I could have a good chance of solving given my skill set. Thus, I am asking your help:

What kind of software you always wanted for light microscopic research, but did not know how to build?
What are some important biological problems you would like to get solved? (For machine learning, problems with a binary decision task are particular well suited -- e.g. "does this person have malaria or not"?)
What are some recent, high quality reviews on open problems in biology?
Something else?

While my question is a bit broad, I think this goes under the "good intention" (or whatever it is called) SE policy.

Neat question, but I'm, afraid there isn't one answer to accept and this one might get voted off... while it's up, though, how about pollen identification? There are ecology, paleoecology, forensics, health, and food safety implications, it's a challenging computer vision problem, and there should be plenty of imagery online to train an expert system with.

This is a great question and should not be voted closed since it is attempting to address an important issue, which (if solved) can have great implications in automation of imaging and data flow and the type of data obtained! Surely biology stack exchange is designed to help with questions such as this!! Kudos to you @days_of_good. One great place you can start is looking at fiji image-J (image analysis software) and look at its plugins. Most are open-source and it would be great if they could be incorporated in microscope imaging softwares and perform instructive commands to the microscope!

@days_of_good is there a scope for your work to cover fluorescence microscopy such as confocal or snapshot widefield and deconvolution microscopy of z-stacked images? a very very large portion of microscopy in the current scientific landscape uses fluorescence techniques to detect molecules or structures at cellular level, mainly using either fluorescing molecules GFP, RFP, YFP, etc attached to the molecule of interest or antibodies which detect a molecule and they themselves are detected by fluorescing secondary antibodies. The main problem in the field of microscopy is the noise-to-signal.

@Bez No, unfortunately I do not have access to fluorescence microscopy. Is there need for deconvolution methods applied to light microscopic images? I know some blind deconvolution methods, which could maybe used to pass the diffraction limit (kind of super-resolution).

@Oreotrephes Do you know any good recent review about pollen identification? The problem sounds like it could be solved using some supervised multi-class machine learning algorithm.

@days_of_good it should be possible (though never done it for visible light) since you are still dealing with light waves/particles except the wavelength is different to fluorescence. SoftWoRx software (Applied Precision) in my opinion produces one of the best deconvolution images using iterations, which comes with delta vision core microscope. I'm confident if you contact your nearest university and discuss what you would like to do, they will be more than happy to put their equipment at your disposal and they even provide help! I know may PIs that are desperate for such talent and enthusiasm

@days_of_good I know for example people use light microscopy to assess embryo phenotype to predict its development. Although I can't access this article but I assume they use light microscopy and look at the overall shape (phenotype of the embryo for the study) so deconvolution would be very handy for this (http://www.fertstert.org/article/S0015-0282(14)00203-9/pdf)

@days_of_good This might be a good starting point for pollen-ID http://tinyurl.com/p44loza

Unfortunately exactly that :/ This question fits several of the "what not to ask" examples in the FAQ. (http://biology.stackexchange.com/help/dont-ask) You can of course bring these sort of things to chat! (link at the bottom of the page)

Blind deconvolution is already a Bayesian algorithm of sorts. Scaled-gradient-projection deconvolution is a faster computational approach leading to similar or better increase in resolution. It's currently applied to optical microscopy and could be extended to super-resolution microscopy.

This is a great and thought provoking question. If it were in chat I would never even have seen it. Many years ago I worked with a scientist at Kodak's research division in Harrow, London. The work was to count the number of photons required for activation of silver halide grains (interpolated from silver nuclei). The bulk of the counting was done on a Cambridge Instruments Image Analyser hooked up to a microscope with a TV camera attached. Not much call for it these days but I could envisage the equipment discussed being used for counting particulates in polluted water and other such tasks.

I know this question is going to close. But, if you want to work something you can work on:
Cryo super-resolution fluorescence imaging

Highlights

CryoFM allows imaging of vitrified biological samples with fluorescence microscopy.
There are significant challenges to achieve high-resolution cryoFM imaging.
Fluorophore characteristics at low temperature offer additional advantages.
Cryo super-resolution fluorescence imaging will give dramatic resolution improvement.

Source: Fluorescence cryo-microscopy: current challenges and prospects.

RE: What kind of software you always wanted for light microscopic
  research, but did not know how to build?

I research fruit flies and in this field (and many other insect ecology model systems like beetles, moths, butterflies) we use a lot of visually scored data, e.g. body size, wing size, wing morphology, eye colours, bristle numbers, genital morphology, sex comb morphology... the list is huge! One program used is WingMachine - though the link to the software seems to be broken - which can measure morphology aspects of a fly wing.
Something I'd like to be able to do is put a vial of food under a scope and have it quickly count the number of eggs on the surface of the food. I asked a question about it a while back.. This would be very useful, many labs have to count eggs (to make the number of eggs constant in each vial, variation here can have serious effects on the adult fly so control is important in ecology studies) and it is a slow, difficult and highly inaccurate, particularly variable between people. If there was some way of putting the vial under the scope, hitting a button and getting an approximation of the number it would be great!
A colleague counts dead beetles at the moment, I'm sure he'd appreciate a similar kind of program where he could image and have the software count automatically. I think both of these problems would be easy to solve with very similar software. Making software that is easy to "teach" how to recognize individuals is the key.
A slightly more complex bit of machine learning might be getting it to count different phenotypes in one image. Fitness assays in flies often use a wild type fly with dark bodied (ebony) competitors, the body of the wild type is comparatively more yellow. The fitness of the focal wild type fly is then the number of wild type offspring among the total (the dark body phenotype is recessive, therefore when the focal wild type mates with an ebony it produces wild type flies, if two ebonies mate we get a dark body offspring). Here the machine would have to be able to tell the difference and count both.
I'll attach a proper picture from under the scope later, the picture in my previous question was taken with a digital camera, not via a scope but it gives an idea of what it looks like.

You might be interested in reading the article "Machine learning in cell biology – teaching computers to recognize phenotypes" (http://jcs.biologists.org/content/126/24/5529.long)

Please summarize the relevant aspects of the link in your answer. See the 'provide context for links' section of the Help Center.

One of my colleagues does lots of histological work, staining and identifying tissue at the microscopic level. Software that could be helpful to that discipline might be the ability to distinguish among the different types of tissues present, and perhaps calculate the "area" occupied by each tissue type as well as empty space. This would not be unlike a GIS type problem, but I don't know if it fits well with a Yes/No binary decision framework. I don't know if it could be trained to learn to identify specific types of tissue, but perhaps it could recognize each distinct area of a cross section as different from other such areas.  Here are a few cross sections to show you what I mean:
Colon:

Source
Smooth muscle:

Source
Seminiferous tubules from testes:

Source
Notice the different tissue types in each cross section, plus the white space. Each tissue type has different light transmission patterns, which may allow a computer to learn to distinguish among the different tissue types.

Look into WEKA segmentation algorithms implemented in FIJI/ImageJ.