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Purpose of dilution streaking or streak purification
In dilution streaking a drop of liquid culture is collected with an inoculating loop and then streaked across the agar plate surface. At the end of the streaking the number of organisms clinging to the loop until only single cells are deposited at a given location and you get colony-forming units.

I am wondering now what exactly the purpose of this streak purification is. If you want to grow your bacteria why would you not just put a few drops of the liquid culture on the agar plate? Why is it particularly useful to use this technique? Or, why would you choose this method over the "spread plate" technique, where a liquid culture undergoes a set of dilutions first and each dilution is then placed directly on the surface of separate agar plates.

The purpose of this technique is to dilute the bacterial cells so much that you get single cells, as can be seen on the image of the plate. You can then pick the colonies grown from these single cells, characterize them, test them for the mutations/plasmids, or whatever change you introduced, and can be sure that you have only the descendants of a single cell in your culture.
This way you ensure that you don't grow a mixture of different cells with different characteristics, of which one will eventually overgrow the other one. The streaking is a fast and reliable technique, which works especially well when you want to test a larger number of bacterial cultures. It also allows to check a stock culture very fast for contaminations with other bacteria by simply inspecting the single colonies by eye (different bacteria often look different).
Diluting the cultures would work as well, but needs to be done in more than one step and is more work when you want to do it for more than one culture. Also for dilutions you often plate more than one plate to be sure to have a plate with single colonies (when the cell number is unknown).

Maybe you were also implying this, but it's a fast method to see if your stock contains one strain or multiple (assuming you can distinguish them by eye).

And if you don't know how many cells you have you'd also use more than one plate when you plate dilutions.

@VonBeche Good points, I added them.

Great answer, I loved this technique as it is so quick to quickly get single-cells/mono-clones. One can not practically do serial dilutions when you have 10s of cultures or cell types to go through.


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How to measure surface area of plated bacteria?
For my project, I'm growing Baker's yeast and probiotics in two liquid cultures before mixing them together and plating them.
I'm trying to measure the impact of the probiotics on the yeast.
How could I measure the amount of fungi on the plate, whether by cell counting or surface area?

You can count the individual colonies on the plate, with this number being the number of "Colony Forming Units" (CFU), as theoretically, only a single cell is needed to spawn a colony.
To do this though, you will need to do a serial dilution of your liquid cultures before plating, so you would have one plate of 10$^0$ dilution, then 10$^1$, 10$^2$, and so on, generally a ten-fold dilution is performed.
Hopefully this will yield at least one plate with a countable number of colonies, that is - not too many, and not too few - usually 30-300.
cfu/ml = (no. of colonies x dilution factor) / volume of culture plated
This usually yields a very large number, so it is common to then take the log of this number, and report that as your result.
And then you will be able to compare your results between probiotics. It's a very good idea to do replicates of each dilution!

As explained by user GrumpyMammoth, you can do serial dilutions until the colonies are few enough to be counted and then calculate the CFUs using the dilution factor.
If you do not want to count the colonies yourself, you can use ImageJ's "Analyze particles" function. This will give you the number of colonies.
ImageJ's "Analyze particles" function will also give you the colony size (surface area) in pixels. This can be converted into millimeters in ImageJ by opening the Image>Properties tab and changing the pixel width parameter.

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Why do two different E. coli reference genomes have different lengths?
I've downloaded two different reference genome of E. coli (E. coli K-12 MG1655: U00096.1 and E. coli K-12 MG1655: U00096.2) and they have different lengths. I searched for the meaning of reference genome numbers in detail but I couldn't find anything that help me with my question: Why do two different E. coli reference genomes have different lengths?

U00096.2 is an updated version of U00096.1; you should preferably use the former for your analysis. In fact, even U00096.2 has been updated. The latest version is U00096.3. In general, the number after the dot (period) in NCBI accession numbers, denotes the version.
From NCBI:

VERSION is made of the accession number of the database record
  followed by a dot and a version number (and is therefore sometimes
  referred to as the "accession.version")

thanks for your answer, but what is the difference between versions? what is new in the latest version?

@user137927 With more and better sequencing experiments (also better sequence assembly algorithms), the genome sequence gets more accurate. It can be smaller or larger than the previous versions and may have different sequence in certain regions etc. I am not sure if the changes are explicitly documented.

As WYSIWYG answered, they are updated versions.
The difference in length is mainly because that later versions are sequenced / aligned with better equipement and techniques, providing results that better reflects the reality.
Some sections of the genomes can be harder to sequence and efficiently align, but with more advanced techniques it can be done.
Sequencing 100% of a genome with no error and perfect alignement is not yet possible but we are getting there slowly.

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Why is coffee a stimulant?
The effects of coffee as a stimulant are quite well-known. What are the mechanisms by which coffee helps prevent sleepiness? I have heard of the presence of caffeine, but what does it actually do inside our body?

This is a rather broad question involving adenosine receptors (mostly) but with plenty of other biochemistry in there as well. I'd suggest you Google around (or, better, hit PubMed) and target something more specific.

Did you go to, say, Wikipedia and read their bit on caffeine?

This is much more of a biology- (more specifically neurobiology) related question. I would highly suggest seeking more info from the usual wiki(s) and checking out various google results for further explanation of caffeine's effects. Maybe a search for "caffeine adenosine antagonist" will get you further than you might want the chemists here to take you. Cheers

https://www.quora.com/What-happens-when-you-water-plants-with-coffee-or-tea

Drowsiness is caused by the chemical adenosine binding to a nerve cell's adenosine receptor. A compound that binds and elicits a response, in this case a slow down of nerve activity, is called an agonist.
Caffeine is also capable of binding to the adenosine receptor. However, it does not elicit a response and no drowsiness is experienced. This type of compound, binds with no response, is called an antagonist.
When caffeine is in your system it blocks the nerve cell from "seeing" any adenosine, causing the cell to increase activity. This increase of neural activity is interpreted by the brain as an emergency resulting in the release of adrenaline, the "fight of flight" hormone.
Caffeine stops you from being drowsy, speeds up your nerve activity, and gives you an adrenaline rush. All of these interfere with sleep.

Adenosine is a naturally produced hormone. It inhibits neurons and makes you tired. The longer you stay awake, more adenosine is produced.
Caffeine is a competitive inhibitor. It will bind to the adenosine receptors and prevent adenosine from binding. The adenosine is unable to bind and thus you don't get tired.
For (much) more detail take a took at the pharmacology of caffeine.

I think, caffeine is one, main, but not the only-cause behind stimulant effect of coffee.
It seemed to me, that coffee works as stimulant within moment; is due to its aroma. And after some google search I found following facts.

Caffeine is odorless:  Wikipedia (though wikipedia tells about pure dry-sample) , PubChem, ILO-ICSC.
...  so caffeine is likely not responsible for coffee aroma.
Caffeine is not well evaporable: PubChem, PubChem
... so likely caffeine is present in very little amount in the aroma coming out from the cup.
Also; after consuming coffee, there should require certain time to onset action after consumption (Wikipedia info-box: onset of action take place at approx 1 hour, and same wiki-page another place, 45-min.). If inhalation of caffeine take place in small-amount, it should take certain time.
...but just sitting beside a cup of warm coffee ant taking smell,  stimulates me (and perhaps others too). And it is quite clear, the 'smell' is refreshing.

... so it is quite clear that the coffee aroma-components (where possibly is negligible role of caffeine) have some part in stimulation action. Maybe that includes the signaling through olfaction.
This website gives a list of aroma compounds in coffee.

The website tells, coffee aroma can show change in certain gene expression in rat's brain, associated with some stress-. They hyperlinked to a paper: NCBI link , PDF
The paper presented their data in followed table.

The similar information also mention on WebMD, and some other websites like this and this
Source: Google.


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What is the name of this brown, "flat hat", fungus?
I've seen this in October 2016 on Corsica (Island of France):

See https://commons.wikimedia.org/wiki/File:Gr-20-petra-piana-to-onda-08.jpg for more images and higher resolutions.

feels like it could be some sort of Amanita. i only see that one image in your link, are there more from other angles?

Pretty sure (but not 100% certain) that it is a Amanita porphyria bk9845, which in german is called a "Porphyrbrauner Wulstling"

Cap: 3-12 cm; convex, becoming broadly convex, often with a central bump; sticky at first or when wet; bald; appearing streaked radially; the margin not prominently lined; grayish brown to brown or purplish brown; often with scattered gray to purplish gray warts or patches.

Source:

amanita porphyria


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How is monoclonality or polyclonality determined?
I was reading up Kaposi sarcoma and Robbins Pathology says,

..many features suggest that KS is not a malignant tumor despite the ominous name ...spindle cells in many KS lesions are polyclonal or oligoclonal

This is also seen in multinodular goiter where the lesions are polyclonal, but some monoclonal nodules are found.
My question is, how are these determined? By sequencing, is it not that, in cancerous growth there are myriad mutations, how can you map whether the mutations present are due to monoclonal expansion or polyclonal expansion? In non cancerous growths, wouldn't all cells have the same genotype?
Polyclonal and monoclonal expansion in B-cells is clear to me since a polyclonal lineage would have different vdj recombs while monoclonal would have the same. Here also, is it decided by genomic sequencing or the Ig sequence?

There are a few ways to determine clonality. Sequencing-based methods are probably the cheapest, given the current costs of either sequencing, or the even cheaper PCR-based clonality assay. Other methods might include histomorphology, looking for known chromosomal aberrations and/or immunophenotyping, among others. Here's a nice review of some of the clonality testing methods.
Sequencing and PCR would be the most definitive ways to determine clonality of a tumor, since they provide information on the exact sequences of sets of cells.
Exome sequencing would be a good way to determine clonality in a large group of cells, where you don't necessarily know what to look for a priori. PCR is a lot cheaper and more focused and might make a better choice when you do have a specific target to sequence, such as highly polymorphic genes like some androgen receptors and the genes involved in VDJ recombination.


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Can fat cells get into muscle cells?
I heard a prof. saying that when people are getting older that there aren't only fat cells getting between and around muscle cells, so that humans gets weaker and weaker, but also that fat cells can get into muscle cells.
Is this true, and how is this done?

Fat in muscle cells or fat cells in muscle cells? The latter seems unlikely.

She talked about cells

I might double-check with your professor about what exactly she said. Fat accumulating in muscle cells is something that happens, but fat cells entering muscle cells seems pretty far-fetched.

I got her answer, and indeed she meant droplets of fat. So by this my question is answered


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Carrying out a BlastP on ORF and achieving hits but 2 have the exact same score, evalue and query cover?
I'm working on a project in my university and we were all given different sequences to work off of. I am meant to compare my blastN to my blastP result. However, when I carried out my blasP I got many hits but the top 2 hits had 100 percent cover, 100 percent identity and 0.0 evalue. I am meant to work off of one of the species I achieved from blastp to compare to blastN. How do I know which one to compare to see what's most significant to my blastn species? I have to continue on and use clustalw and phylogeny after so I need to be sure.

We can't help really help unless we know the sequences you are working with. Please [edit] your question and show us i) your query protein and nucleotide sequences and ideally ii) the HSPs (the matching sequences) you found. That said, you could always just compare both. Running a blastN is not very hard or time consuming.

If I understand it correctly, you have two subject protein sequences that are exactly the same as your query. You say they are different species, so I guess you made sure they are not the same species and different strains, or subspecies.
I would suggest to now query your nucleotide sequence using blastn against both results (since a priori it could be either species, or neither), and focus on the one that gets a higher score using blastn in your phylogenetic analysis. Due to codon degeneracy, it could be that your blastn results differ between the two.


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Challenges of Industrial-Scale Fermentation
I was reading the wikipedia article on industrial fermentation, and it mentions that

It is well established in the field of industrial microbiology that what works well at the laboratory scale may work poorly or not at all when first attempted at large scale.

Why is that?  What are the barriers to large-scale fermentation of bacterial culture?
Also, I know that cell cultures have distinct phases of growth and decay, but what happens after the cells die?  Would an industrial fermentation process have to "re-culture" the bacteria?


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What species of ant is this, and is it a queen?

I found her underneath a big rock along with a bunch of much smaller Lasius niger workers, so
I suspect it might be a queen. I know Lasius niger doesn't have soldiers, so what could it have been doing there if it wasn't their queen? Also, sorry for the bad picture quality, I couldn't find a better camera, and also don't have a proper magnifying glass.
Country: Belgium
Environment: forest
Location: underneath big rock
Behaviour: calm when walking in lighted up areas
Species it was found with: Lasius niger workers running around frantically (note: this specimen was much bigger than the workers)

Wikihow > How to identify a queen ant might be a good first series of step to determine if it is queen. I suggest that you address the questions of this article into your post.

In which country and which environment (forest, prairie, ...) did you find it?

I know what a queen looks like, i've had many lasius niger and flavus colonys in the past, i've only never seached in forrests before.

You given many useful information. But you didn't mention its size, even approximate size. (From the appearance of cotton it seems to be within 5 mm to 1.5 cm but no better cue is there. Btw what do you mean by "Found with other insects: yes"? did you mean it was in a herd of similar-other ants? or you mean it was found mixed with insects of other species?

I dunno what i meant, with that, i'll remove it, but it's larger than 6mm, and smaller than 1cm, she's moving around very franticly when i try to measure her legnth.

This ant looks very much like a Camponotus pennsylvanicus queen, but since it was found in a Belgian forest, I could be wrong. I am almost certain it is a Camponotus species though. I hope I could have been helpful to you!


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Measuring optical density with/without re-suspending cells
When measuring absorbance using a plate reader, is it necessary (or better) to resuspend the culture if the plate has been sitting still for 1-2 days?
While this could be a good physics question, I am more interested in the correct biological assay technique.
--
The two options are:
1) growing microbes in a plate inside a static incubator and then put the plate in a plate reader without agitating the liquid
2) growing microbes in a plate inside a static incubator and then put the plate in a plate reader after agitating the liquid
In option 2, the agitation could be achieved by gently pipeting the liquid up and down a few times...

Definitely (2). Clumps of cells will cause a lot of noise in your absorbance measurements (depending on whether the light beam hits a clump or some empty space).
I don't know what your microbe is or what growth medium you're assaying on, but typically it's very important to maintain the culture well-mixed at all times, not just during measurement. If your cells clump to the bottom, you will not get the same aeration as you will if they're well-mixed, and accessibility of other nutrients could potentially be limited as well. Generally the most controlled condition is to maintain good mixing at all times, but certainly this is organism- and medium-dependent.

+1 If a liquid culture had been standing for a few days with no shaking, there must be many dead cells. Shake or no shake, the OD will be misleading.


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flying insect the size of a bird
On my farm a few weeks ago I started to see a large insect(?) I never, in my 76 years, seen before.
It is bright yellow, about the size of a man's hand, flies not like a bird but more like a butterfly and its large long legs hang down in flight. Observations are from 75 yards away.
The encounters are too brief to get a picture or even a magnified view without stationing myself in position all day.

It could be a hornet, try to film it, maybe it's easier to recocnise it then.

Could be a bat or such?

There seems too little way to proceed with so little information. Man's hand mean entire hand from shoulder to fingers (near 3 feet or 1 meter)? or you meant palm (half feet or less)? please write in clear way. If you mean palm, then yes I saw palm-sized butterflies in many museum (such as Papilio krishna). When it comes out? Day? night? morning? dawn? Which place or locality or region it saw it?

@BunyanvanAsten Hornet of size of man's hand? you mean approx 1 meter long hornet?

The hand of a man; 6 or 7 inches. See them (4) morning and afternoon. The legs are long and hang down in flight. Wish I could get closer or maybe snap a picture. It's one of those things, like a movie, you wait for an hour, see none, then when you turn and walk away, they appear.

@AlwaysConfused: Your hands are 1m long?

@Edwin: Please edit your question.

@MartinSchröder Oh god I told in approximate way. I was trying to understand about-whom the OP using the term 'hand'. I cant imagine a hornet of full-length of my 'hand'. Ok I'll measure my hands later plz wait...

@MartinSchröder Perhaps you're meaning 'palm' with your 6 or 7 inch.

plz Visit this. http://meta.biology.stackexchange.com/questions/3452/are-there-any-guideline-about-species-identification-questions/3453#3453. It might help.

Without seeing it my guess would be a Hummingbird moth or Clearwing.. Look it up


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Introducing evolution into the Hodgkin-Huxley equation
How would the Hodgkin-Huxley equation change when the geometry of dendrites and axons are introduced?
Also can we model a situation of membrane activity during the corse of evolution, hence the equation would be subject to a periodic function ad it varies with time?
Taking the example of membrane transmission of electronic signals(in humans), can we model the change in conduction of the e-signal through the axon as its speed and geometry changes with evolution?

The two processes occur at drastically different time scale. One could clearly model that by assuming the evolutionary state (whichever way you track it) is a constant while the other process reaches its equilibrium conditions.

Although you mention evolution, I think what your question is really asking is in your last paragraph: what happens to conduction within dendrites and axons when geometry changes. There might be some evolutionary implications of this question, but you will also find vast variations in geometry among neurons in any one organism, as well.
You might want to look into expansions of Hodgkin-Huxley into compartment models that allow you to test the influences of geometry, see wikipedia for a list of different models at different scales of complexity.
There is a tool available called NEURON that is good for student or curious non-student experimentation, though you will have to read the documentation and hopefully find some examples that are close to what you want and then tweak them.


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Why do parasites involved with malaria going into red blood cells?
When someone is infected with the mosquito bug which has the parasite, this parasite will go into the liver to grow. Afterwards he goes in the red blood cells and blocking the vains of the brains. But why do they leave the liver and go into the red blood cells?


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What is the identity of this fruit/tree found near Berkeley, California, USA?
Please help identify this fruit/tree found near Berkeley, California.
The tree had no leaves. The fruit looked like a pear from far. It has no flesh. When the outer skin is peeled, the seed looks like a large avocado seed. Very little smell from the fruit/seed not a bad smell and not an appetizing smell as well.
Could this be a Yellow Buckeye?

Ask any Ohioan. Looks like a Buckeye.

Given that it's in central California, it's almost certainly California buckeye (Aesculus californica).  The tree is common in the Coast range and Sierra foothills of California.  It has adapted to the Mediterranean climate of the region by growing during the wet winter and spring and then dropping its leaves during the hot, dry summer.  The large seed is toxic if consumed.


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How many various types of Memory B cells does an average person has in his body?
Memory B cells are a B cell sub-type that are formed within germinal centers following primary infection and are important in generating an accelerated and more robust antibody-mediated immune response in the case of re-infection.
Now there is an accumulation of cells of a single clone population which expresses many of the one same type of antibody and that these memory B cells survive for long periods of time in a body.
Disregarding the number of different cells applying for one and the same antibody, how many Memory B cells are there in average humans which relate to different antibodies?


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Do alleles, by definition, code for the same trait?
A trait is defined as an inherited characteristic, like eye color and height.
A phenotype is defined as the specific physical manifestation of a trait, like blue eyes and 6 feet, respectively.
Now, genes code for traits. And because alleles are different versions of the SAME gene, they must code for the same trait. Let's say gene A codes for hair color (trait). Gene A(1) (allele) codes for brown hair (phenotype) while gene A(2) codes for blonde hair. Therefore, alleles code for the same TRAIT, but differing PHENOTYPES.
Here is the problem. When I google: "heterozygous", I get a bunch of websites defining it as "referring to a gene pair in which the two alleles do not code for the same trait"
This is not correct because a gene-pair refers to genes located at the same locus on a chromosome. In other words, they are alleles of the SAME gene and code for the SAME trait. They only code for different phenotypes associated with that trait.
So. Either my definition of traits is wrong. My definition of alleles is wrong. My understanding of alleles being different versions of the same gene is wrong. OR. The internet loves to be imprecise with their language and interchangeably use terms that mean different things.
Which is it?

Depends on what you call a trait. One gene (allele) can contribute to multiple traits and vice versa. IMHO, terms like "trait" and "phenotype" have little relevance in modern genetics.

I disagree that (1) the issue behind the question is related to the definition of trait and (2) that the concept of phenotype has no room in modern genetics. I don't think many geneticist, evolutionary biologist, medical geneticist or anyone would really agree that anything in modern genetics remove relevance of the concept of phenotypic traits.

I fear you won't get a definitive answer on this. A survey indicates both usages of trait all over the Internet. As a teacher, I generally used trait to apply to the gene. This made teaching the "central dogma" clear: DNA -> RNA -> protein -> trait. Of course this simplification gets added to later as the course progresses.
One interesting question this poses is in the case of skin color. Is that a trait? Last I read, at least four different genes interact to produce skin color.
I'd side with you on this but acknowledge the fact trait doesn't seem to have the consistent, well-defined meaning that allele does.
On the other hand, a visit to UC Berkeley's evolution site shows them applying trait to the variations due to allele combinations.
Hope that helps! :)

I appreciate your answer! I think you're probably right. NOTE: I would argue that skin color is indeed a trait. And you can have multiple genes code for one trait. In fact, that is the definition of a polygenic trait!

What is a trait?
Many people have talked about the issue of defining a trait. Of course a trait can be anything and there is no objective way of delimitating or counting the number of traits of an organism. However, the issue in this question is completely unrelated to the definition of traits, it is an issue of semantic of causality.
Semantic of causality
The whole issue boils don to what you mean by code for the same trait. In reality, this expression makes little sense. To explain the semantic behind this concept I'll use the existing semantic from probability theory (which applies not only as a vague analogy).
Semantic issue explained in probability theory
If you have some basis in probability theory, you know that you can consider a covariance between two random variables but it doe snot make any sense to consider covariance between the outcome of a random variable and another variable. For example, it makes sense to ask whether footedness is related to handedness, but it makes no sense to ask whether right handed is related to footedness.
Above semantic applied to genetics
Following the above logic, consider a locus (=position on the genome, may correspond to a gene) as being a random variable and the alleles at this locus being the possible outcomes of a random variable. Trait is another random variable which outcomes are the different trait value. It makes no sense to ask whether a given outcome (a given allele) affects a trait (random variable), but only if a locus (random variable) affect a trait (another random variable).
In other word, one can only consider whether variation at a given locus affect variation for a given trait, and not whether a given allele codes for a trait. A locus can indeed affect several traits. Typically, an allele will cause investing into building trait A, while the other allele at the same locus will cause investing into building trait B. As such this locus explains variation for both trait A and trait B but one could not say that an allele code for A, while the other codes for B.
The above case where one locus affect several traits is called pleiotropy. When several loci affect a single trait, it is called epistasis.

The way I see it, the semantics in this area of genetics are somewhat loose and you are correct about all your definitions.
I think the word 'trait' is not currently used as much as it used to e.g. in early 20th-century genetics, or earlier. The meaning of 'trait' can be compared to that of 'feature' (i.e. does it refer to 'having eyes' or 'having blue eyes'?).
In short, I would use 'phenotype' rather than trait when you refer to the  different alleles, and if necessary use 'trait' as height, eye colour, etc.

Really? Every modern introductory genetics book I've encountered definitely use the term "trait" to describe a characteristic...

in other words, it is mostly used in Mendelian genetics... so it will not be a problem you will encounter in more advanced genetics, in my opinion


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Is it a coincidence that the sensory systems for smell, vision, taste, and hearing are all near each other in the head?
I was wondering if it's an evolutionary advantage to have many sensory systems in a small place of the body, the head. This applies to mammals, reptiles, synapsid, dinosaurs... and many more.
My theories:

The distance to the brain is short and thus smaller time delay to
respond faster to the outside world,have more reflexes, hunt faster
prey and fight more accurately.
The short distance makes the "wire" (signal carrying) shorter and
thus less vulnerable to be cut from a injury, because for a organism
losing an eye reduces possibilities of survival dramatically.
In humans at least the head is the upper part, then vision organs
see more with less obstacles such as vegetation or terrain irregularities, or anything that obstacles vision, normally higher
means seeing more things. This I'm not sure applies so strongly to
smell. To taste, certainly not. To hearing, possibly a little,
thought nor much as vision.

We evolved from a common ancestor that was like that but that doesn't explain why it's not common to get out of that coincidence.

The existence of a common ancestor is part of the answer to the question of why the layout of vertebrate sensory systems are so consistent (it's included in both answers). The identity of the common ancestor is a separate question and I think it's off-topic for your main question so it would be best posed as a separate question may with a link to this one.

It's called "design"

@BenPiper Who or what designed what? Do someone designed the organs to be all in the head, that's what you are saying?

No it's not a coincidence that eyes, nose, mouth, and ears are all near each other in the head. As you note the layout is inherited from an ancestor, that's your answer.

A study of vertebrate head sensory systems shows that the

The olfactory, vestibular auditory, and lateral line sensory organs displayed a strong link with the urochordate-vertebrate ancestor.

So this paper highlights that these structures go back earlier than the animals in your list. The development of vertebrates is very complicated so major departures from this developmental program which are successful are going to be rare events. This is reflected by blind cave dwelling animals that have vestigial non-functional eyes. The lack of selection pressure means the eyes don't work but they are still there because building an eye is part of a deep developmental programme. The image below shows (in orange) the key drivers of differentiation for various cell types. It makes it obvious that the program that produces olfaction also produces vision (otic) so modifications to the developmental program will have wide-ranging effects.

The theories that you've listed are interesting and there is work going into developing new senses. Udo Wachter wore a belt that vibrated to north 24/7, "north" became part of his dreams, he always knew where home was, and he mourned the loss of the the sense. So proximity to the brain is not a critical factor for the senses.

It's not a coincidence. To understand why, you have to know what is anterior and posterior in zoology.
The first bilateral animals arose in the precambrian. Those free swimming animals had a polarity: the extremity of the body pointing to the direction of movement is the anterior region (in the anterior-posterior axis). Therefore, with the bilaterians the very concept of a head appeared.
Over time, sense organs started to develop in this anterior region (the head), because this region is the first one to explore the environment. Almost all the bilateral animals that exist today (as you and me) inherited this pattern.
But this is not mandatory. Animals have sensorial structures all around the body, and sometimes somatic exteroceptors are located in "strange" positions, as the chemoreceptors in the legs of insects.
PS: just to be precise in the definitions, you have hypothesis, not theories.

the question is about vertebrate sensory organs so the sensory systems of insects seem off-topic to me. Can you update the last paragraph with a vertebrate example? I can't think of any but I'd be interested to know if there were some.

@Michael_A Are you sure the question is about vertebrates?

The question hasn't been asked precisely but I think it is implicit as the OP lists only vertebrates ("this applies to mammals, reptiles, synapsid, dinosaurs... and many more") while also mentioning a "common ancestor". Does the question remain valuable if we include taxa that frequently diverge from the central tenet, that sensory organs are always in/near the head?

The answer of this question, even if it was (but it isn't) explicitly about Vertebrata or Craniata, lies in the origin of the Bilateria.

I disagree. This is the crux "We evolved from a common ancestor that was like that but that doesn't explain why it's not common to get out of that coincidence." So it's not about the origin of the inheritance but the difficulty of diverging from the inherited path. Anyway, I doubt we'll convince one another so thanks for kicking about these ideas.


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Is there a reference for the composition of viral genomes?
First of all forgive me for the bad written question.
I'm not a biologist. I'm neither a doctor nor a virologist. I am a physicist actually, and I have this question in mind since a long while.
What I'm trying to ask is if there is a sort of text file or a website (or a book) where I may read about viruses "composition".
"Composition" means something like
"This is the rhinovirus, and it's genetic "composition" is ACTGCT" (of course I just invented...).
I don't know how to express myself with good terms because I am not familiar with this field, so please feel free to edit the question if it may appear unclear.
Again, what I'm asking is for a sort of database of genetic sequences about viruses and so on.
Thanks in advance!

NCBI houses a collection of viral genomes at the aptly named Viral Genomes portal. They currently have 5921 viral genomes and by going to the previous link you can browse sequences from the major viral families.
If you have a nucleic acid or amino acid sequence it can be searched against NCBI's sequences here.
Uniprot also have a viral protein sequence annotation project which they describe as such;

The concept of this website is to associate specific knowledge for each virus family with viral protein and genomic sequences. All the available information is presented in a concise and accessible virus fact sheet, associated with the ordered list of reviewed entries. The site covers the whole known virosphere. The database section allows access to UniProtKB protein entries, as well as to specific virology databases.
Our efforts are currently directed towards viral ontology and reference strain annotation. A robust ontology will allow a more precise definition of the involvement of each protein in viral replication steps. The reference strain annotation will become the benchmark for each of the 334 genera.

Their work can be accessed through uniprot.org or through the project portal at; http://viralzone.expasy.org/

No worries. Uniprot or NCBI provide the sequences as flat files but the people who assemble the viralzone do a great job; their linked cartoons tie function to genes to taxonomic groupings with great clarity.


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How are limits determined for systotic and diastotic blood pressure?
I know that the upper limits for systotic/diastotic blood pressure are 120/80. What is the mathematics behind these numbers? I am curious because I did not find information regarding how the numbers are arrived at. I am not sure if the numbers are based on statistical study or is there a scientific basis for the same.

120/80 are not upper limits on blood pressure - many people have blood pressures far in excess of those numbers. Instead, these are numbers beyond which studies have shown connections to negative health outcomes - heart disease, for example.
There is nothing magical about the numbers 120 or 80 besides their divisibility by 10; a blood pressure of 121/81 is no more risky than 120/80 than 122/82 is over 121/81. Because of this, drawing a hard line isn't possible - it's just a suggestion.
Typically, systolic pressures less than 130-135 aren't given any special consideration beyond normal advice to exercise and eat well, unless there are other conditions/risks. Guidelines from the American Heart Association and the UK's NHS are to consider treatment only for diastolic pressures above 140mmHg. There has been some disagreement about these precise limits, with some recommendations for lower targets, for example here. Some of the disagreement seems to be the types of interventions - the guidelines to treat diastolic hypertension only above 140mmHg are mostly considering medications, whereas the guidelines to treat prehypertension are aiming for improved lifestyle: diet, exercise, etc.

Thanks. Can you point to a specific study that drew these numbers? I am not familiar with the literature around this. I am curious about the way the sampling is done and the statistical methods that helped that highlighted these number.

Some of the information contained in this post requires additional references. Please [edit] to add citations to reliable sources that support the assertions made here. Unsourced material may be disputed or deleted.

Added references; for some of your questions about sampling etc, @randominstanceOfLivingThing, those questions might deserve their own topic


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How can both strands of DNA code for proteins with similar functions?
It's not clear from the question but for example:
AAAAAAA
TTTTTTT
The top strand would create a different protein than the bottom, and with the huge amount of nucleotide in a gene, I think it's very unlikely that the same region on both gene could create proteins that are similar to each other, even though they're alleles of the same gene. This would also affect codominance/incomplete dominance, since I'm assuming that only one of the strand would create a functional protein.

Welcome to SE-Biology. However I'm not clear what you are asking. The use of 'can' in your question suggests that you think that this happens, in which case your assumption is wrong. The actual question suggests that you are asking a hypothetical question (in which case you should change 'can' to 'could').  However as you go on to say that in this hypothetical case you assume only one strand would create a functional protein, this seems less of a question and more thinking aloud. Please clarify.

Is this a duplicate of this?

You are confusing the the forward and reverse strands of DNA as two alleles. They are not. Remember you have a double stranded DNA from each parent. Each of those two pieces of double stranded DNA represent alleles for a given locus.
For the example you gave, you can have different genes that overlap the same region of DNA. One is on one strand and a different gene is on the other. The DNA is read 5' to 3' so we think of one strand as forward and one strand as reverse.
See embedded pic for examples from this publication about different kinds of overlap and whether they are conserved across species.

But the poster is asking about proteins, and not all those genes pictured are protein coding.

The figure shows both protein coding and non-protein coding. I addressed the misunderstanding of alleles, which seemed to be the reason for the confusion on how two "alleles" could produce a protein what was supposed to be very similar.  This stemmed from a misunderstanding of coding/template strands for a given allele vs. two separate alleles. At least that was my interpretation.

In general, protein-coding genes don't overlap, so the problem you've identified doesn't come up.
And no, complementary strands are not different alleles.  If that were so, bacteria and gametes would have two alleles of every gene, because they each contain one double stranded copy of the genome.
You have two copies of each double-stranded chromosome, that is why you have two alleles for each gene.

I think it's very unlikely that the same region on both gene could
  create proteins that are similar to each other, even though they're
  alleles of the same gene

I think your reasoning is faulty here. It's not that the two alleles are in the same chromosome and each in one strand. Each allele is in a different chromosome (one from each parent).
Overlapping or nested genes are a different topic altogether.

So brown eye allele is at the 5' end of the maternal DNA, which means the paternal's green eye allele is at the other 5' end, so that they're at opposite ends?

I made a diagram since perhaps it's the easiest way: https://s21.postimg.org/kap5b2gsn/Untitled.png

Usually not the whole gene overlaps, and it's not usually in-frame, this makes it a lot easier.
You also have some flexibility because of the redundant codons (20 AA for 64 codons), so you can more or less change every 3rd base to fit the "other" gene.
"Similar" could mean anything, possibly referring to two proteins that are not even 20% identical. At 20% identity you can still be sure that that enzyme is of the same class, catalyzing the same reaction. It might accept different substrates, but it could also still accept the same substrates.
Together, this means that on the non-coding strand of every gene you can put a gene coding for a protein that's more or less doing the same thing.


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Which organs/tissues are defined as "peripheral organs/tissues"
In the following paper [1], I encountered one term "peripheral organs". Literally, based on my understanding, it should be related to the organs/tissues, such as skin, hair and ear in the human, and wing, antenna and leg in the insect. However, in reference [1], fat body, oviduct and hemocytes are listed as peripheral organs. Is there specific definition of "peripheral organ/tissue"?
Thank you!
[1] Verlinden, H., et al. (2010). "The role of octopamine in locusts and other arthropods." J Insect Physiol 56(8): 854-867.

I have the same question.  Saw it used here, referring to humans: , "B cells in peripheral organs and the CNS cannot be reached by intravenous rituximab..."

The most common usage of "central" vs "peripheral" organs/tissues is: central nervous system (brain/spinal cord) vs all other organs/tissues:

"B cells in peripheral organs and the CNS" (from the article linked in the comment)
Nervous system includes central nervous system (brain/spinal cord) and peripheral nerves (spinal and all other nerves) (Central nervous system and peripheral nervous system).
n-3 PUFA and obesity: from peripheral tissues to the central nervous system (PubMed)
Atrial natriuretic factor receptors: distribution and regulation in central and peripheral tissues (PubMed)

However, depending on the context, different organs/tissues can be considered peripheral:

From the liver metabolism viewpoint, liver can be considered central and muscles and fat peripheral (Apoptosis and insulin resistance in liver and peripheral tissues...).
From the intestinal absorption viewpoint, gut can be central and all other organs peripheral (From the gut to the peripheral tissues...).

Peripheral organs and tissues are simply parts of the body that act as a response to a change in the environment, the body's functions, molecule levels, etc. They include the endocrine system organs as well as organs producing hormonal responses such as the pancreas producing insulin. When the skin and therefore the hypothalamus senses a drop in temperature, your body goes through natural responses such as shivering and contracting of the limbs. As for the oviduct, it is an organ that will respond with contractions and movement when an egg moves down it. As for hemocytes, it would make sense for them to be peripheral organisms for the body as they respond to oxygen deprivation in a cell. As a large multi cellular organism, it can be said that peripheral organs/tissues are parts of the body that provide intricate function or a reaction to an endangerment to the body.

references missing.


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What is an aromatic cage and what does it do?
Epigenetics, 2. ed, Chapter 3.6:

Similarly, methylated lysine residues embedded in histone tails can be
  read by “aromatic cages” present in chromodomains, or similar domains
  (e.g., MBT, Tudor) contained within complexes that facilitate
  downstream chromatin modulating events (see Ch. 7 [Patel 2014] for
  structural insights

I understand it is something like a protein motif, but I cannot find a good definition using google.

googling "chromodomain aromatic cage" leads to this paper : "Epigenetic Virtues of Chromodomains" (Crit Rev Biochem Mol Biol. 2011 Dec; 46(6): 507–526.) which references "aromatic cage" as "Structure of the HP1 chromodomain bound to a lysine 9-methylated histone H3 tail." (Science. 2002;295:2080–2083.). See figure 3c in the first paper : " The peptide sits on the DNA minor groove, with its methyllysine inserted in the four-residue aromatic cage."

Sentence from same book: ...The chromodomain forms an aromatic cage that has been well documented as a specific binding pocket to methylated histone residues.

It refers to the structures in the PHD-finger domain and chromodomains. The aromatic amino acid residues form a cage like structure which covers and interacts with the methylated ammonium of lysine via a cation-pi interaction.

The BPTF-PHD structures reveal the main characteristics of PHD fingers that can read H3K4me3. The binding occurs through an aromatic cage where a trimethyl ammonium group is stabilized by van der Waals and cation-–π interaction, which is similar to the ones observed in chromodomain, MBT, PWWP, and Tudor domains. This aromatic cage is composed of one Trp and three Tyr residues; and it has three faces and a 'lid' that is beyond the tip of H3K4me3. Subsequently determined structures of other fingers in complex with the H3K4me3 peptides show that the cage varies and can contain a combination of two to four aromatic and hydrophobic residues.

 Margueron et al., 2009

Interesting, so in the image on the left, the cage is supported in a 7-propeller fold, but it is also found in this minimal PHD-finger domain (eg 1WEN) which is much smaller. cool.


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can a protein recognized by antibodies not be immunogenic?
I have a protein that is produced with the baculovirus system that is recognized by antibodies generated by immunization of rabbits with the same protein produced in E. coli. However the baculovirus protein did not induce an antibody response when I immunized some pigs.
Could it be that the baculovirus protein is not immunogenic? Even if the same protein is recognized by antibodies? If the rabbits produced antibodies with a protein that did not have post-translational modifications, how can not be immunogenic when the modifications are added?

What kind of protein is this? A protein from pigs? Or one which is at least a highly homologous with a pig protein?

Did you add some special tags in your bacterial expression system? It is possible that the original baculovirus protein does not elicit immune reaction because it mimics a host protein. Many viruses use this strategy to evade immune response. The bacteria-expressed protein may have folded differently leading to the loss of the molecular mimicry.

it is a viral protein. I infected rabbits with the E. coli version and I got an immune response; the baculovirus version instead did not elicit a response in pigs. I used adjuvants to infects pigs

Pure proteins are often poorly immunogenic because you need to have some kind of "adjuvant" effect to induce a strong effect. Bacterially-produced proteins may well have some bacterial LPS or other immune stimulants still present after purification which would drive a much stronger response than the same protein produced from eukaryotic cells. There are many other possible explanations -- one or the other protein may have aggregated or misfolded, which could drive a different response, for example.
In other words the effect you're seeing may be annoying but is not particularly shocking, and you have no choice but to do some routine troubleshooting at this point. Is your protein more immunogenic when administered with an adjuvant? Are the two versions identically folded? Are there antibodies present to a misfolded form that you're not detecting? And so on.

Thanks, different folding was also my guess. I did not consider the LPS residual though.

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Why do these 2 dots frequently occur in dogs' eyebrows? Does it serve/served any advantage?
I have been wondering why, in spite of the variation in color-patterning in dogs, these 2 dots (1 on each eyebrow) seems to be frequently occurring.
Dog-1:

This one has a white dot. Photographed from Kolkata.
This one is from Uttarakhand, Western Himalayas. Also has white dots.  I've seen brown dots too, which I have not photographed, so I cite an example from internet (wikimedia:

Why are these 2 dots are so conserved? Is it associated with some conserved region of a chromosome? Or maybe it has/had some purpose or provided an advantage (such as recognition or non-verbal communication or to mislead their prey since if the prey think of them as eyes, then they would miss the gazing direction of actual eye) so that it was selected by nature? Some wolves have similar paired-spots, so I could guess that once upon a time an ancestor of all dogs and wolves contained these paired dots?
PS. I've not found helpful discussion about that dots. From this webpage it seems to me, it is being called false-white black and tan atat genotype. I Don't know if have I understood correctly or not.

I suspect but can't prove that these markings are not adaptive, but are accidents or epiphenomena of the general genetic system that determines coat colour.
On the one hand, an Australian Broadcasting Corporation documentary claims that canid eyebrows are adapted for social interaction: they have specialized muscles (which are not present in other carnivorous mammals such as cats), and ...

One study showed foxes who hunt alone had about half the facial expressions of wolves who work in packs. In fact, in wolves and dingoes, the eyebrows are often even a different colour, exaggerating the movement.

(they don't give any primary references).
On the other hand (supporting my guess) a lot of the evolution of these colour patterns seems to have occurred after domestication. These markings (not the eyebrow spots in particular) seem to be called tan points:

Red (tan) appears as pips above the eyes, on the sides of the muzzle extending to the cheeks, as pips on the cheeks, on the front of the neck just below the head, as two triangular patches on the front of the chest, on the lower legs and feet (and inside of the legs), and as a patch underneath the tail (and sometimes along the bottom edge of the tail too).

(I don't know whether eyebrow contrast in animals that aren't strictly brown/black is caused by the same genes ...)
A PhD thesis by Dayna Dreger (some material published in Journal of Heredity 2013:104(3):399–406 doi:10.1093/jhered/est012)

The black-and-tan phenotype, associated with the at allele, is a predominantly eumelanistic phenotype, with phaeomelanin restricted to distinct regions on the lower limbs, cheeks, eyebrows, chest, and around the anus. (p. 7)
Genome wide association study analysis, fine mapping, and sequence analysis identified a 16 bp tandem duplication in intron 5 of the hnRNP-Associated with Lethal Yellow (RALY) gene that segregates with the black-and-tan phenotype, versus saddle tan, in Basset Hounds and Pembroke Welsh Corgis. In breeds that never have the saddle tan phenotype, but frequently have the black-and-tan phenotype, the RALY duplication does not segregate with black-and-tan. This, together with further genotype analysis, suggests a gene interaction of ASIP, MC1R, DEFB103, RALY, and an additional modifier gene is required for expression of saddle tan or black-and-tan. (p. ii)
Neither the coyote nor 9 of the 10 wolves had the RALY duplication and the tenth atypical wolf was heterozygous (+/dup) (Table 5.1), suggesting that the lack of the duplication is the ancestral or wild-type allele (+). It follows then that the saddle tan phenotype is ancestral to the black-and-tan phenotype, despite the relatively limited number of breeds that currently express the saddle tan phenotype, making black-and-tan a modification of the saddle tan phenotype. The popularity of the black-and-tan phenotype across breeds and breed types is likely explained by artificial selection for the striking black-and-tan phenotype over that of saddle tan. Since the saddle tan pattern is found primarily in terriers, scent hounds, and a small number of herding breeds, this finding may also shed light on the development and relation of modern dog breeds, hinting at common ancestors between breed types.

Dogs are actually not prey animals and are pretty high up on the food chain, so the theory that the eye dots are "decoy eyes" doesn't make a whole lot of sense. Realistically speaking, dogs are pack animals, and use several parts of their body to interact and 'converse' with other dogs. One of these body parts are the eyes. Like humans, dogs can widen and narrow their eyes to show emotion. The eye dots simply accentuate these movements, aiding greatly in pack conversation while hunting. Besides that, they're just plain cute.

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


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What is the evolutionary purpose of shingles afflicting only one side of the body?
A question here asks for the name of the category of viruses that affect only one side of the body. My question is about the  evolutionary purpose of that 'affects only one side' behavior.
Chicken pox is not usually fatal, and it's not clear to me why evolution would set such a low bar for eliminating the weaklings in the herd. On the opposite end, small pox was excessively fatal; I guess that's the price of evolution biohacking its way by trial and error.
On the other hand, I can see how shingles, afflicting people only in later life, can be debilitating enough to keep one from going hunting and gathering and moaning one's way to death by starvation. But for that to happen isn't it more efficient for the virus to resurface across the entire nervous system instead of parts of just one side? If shingles happened, say, in the late teens, I could understand that 'affects-only-one-side' eliminates only the weaker part of the herd. But it's mostly older people, well past their reproductive prime, who get shingles, and get it only on one side. I see no benefit to the individual or the group of contracting an 'expire by date' virus early in life and then the virus goes about its expiration-dance in a half-hearted, tentative way. Makes no sense.

You seem to assume that the virus does not evolve or maybe you mean that it is selected for hurting its host (which is wrong). It is quite unclear what you mean by "evolutionary purpose" as well. You might take advantage of following a short intro to evolutionary biology such as Understanding Evolution for example. You might also want to have a look at Why do parasites sometimes kill their hosts?.

This is a bit like asking what the evolutionary value is of developing cancer in only one lung. There is none. Cancer is cancer; it has to start somewhere. Shingles is a physiological process involving viral reactivation in one dorsal root ganglion. Why should it be bilateral? You're looking at this from a teleological standpoint, which is very often a mistake in science.

Well since the chicken pox virus (hhv 3) that also causes shingles, practically spares no one, is it not already successful?

@Polisetty Good point and similar to one in the accepted as answer below. @ anongoodnurse Cancer is the cell division system gone haywire (even if triggered possibly by a virus such as HPV?), whereas a virus is not intrinsic to its host?

The premise of your question is wrong. Although evolution is often a good guide when looking for "purpose" in biology, sometimes there are other proximate causes.
Shingles is caused by activity in a previously dormant version of the virus that causes chickenpox. Essentially, your immune system clears out the virus from everywhere in the body except some that hides in the nerve roots.
Peripheral nerves to the skin are arranged into "dermatomes" which are essentially the group of nerves that enter the spinal cord at a particular vertebra.
Shingles happens when the virus becomes active again. Since a dermatome only covers one side of the body, shingles usually only affects that side of the body (in particular, that dermatome).
http://www.webmd.com/skin-problems-and-treatments/shingles/shingles-cause looks like a decent reference for this information.
I don't personally know of research on the evolution of varicella zoster, but if you want to think up a speculative evolutionary process, you should be thinking about the virus and spreading of the virus, which is the activity that natural selection will support. In that case, lying dormant can give the virus an opportunity to spread again at a later date, preventing it from being completely eliminated by the host's immune system. All the business about rashes on one side of the body comes about by 'accident,' as a matter of convenience since the virus hides out in peripheral nerve roots.

The virus' replication and its own spread makes sense. I was looking at a greater degree of symbiosis, if you will, between parasite and host. Unlike the common cold virus which typically has non-fatal affects on humans and hard to say surviving a makes one stronger than another. I think you can make that argument that only people with stronger immune systems survive the small pox virus. I am still puzzled by the chicken pox virus - non-fatal in kids, hibernates for 25-30 years before re-emerging - why? Why this cicada-style lagged cycle?

While symbiosis is possible between "parasite and host" it isn't necessary; many parasite/host relationships are not at all symbiotic. It isn't correct to say that a virus that kills people with weaker immune systems is symbiotic by "improving" the immune systems of the population of hosts. The hibernation is a way for the virus to avoid the host's immune system while that immune system is most prepared to hunt it down; it doesn't need to have any benefit to the host.

Understood - a consequence of a small pox epidemic be people with better immune systems but that 'gain' is not necessarily obtained via a symbiotic relationship.

Yeah, I'm not certain that treating that as a 'gain' is really appropriate - stronger immune systems might also lead to autoimmune disorders, for example. I think it is safer to think of it as an evolutionary adaptation: animals including people evolve defenses against viruses of all types because those viruses cause harm if not kept in check. But that is a result of the evolutionary process, not a "reason" or "purpose" for viruses to exist.

@Bryan Krause Symbiosis is an interaction between two organisms. May be parasitism, mutualism or commensalism. Although its just semantics, still, its a consensus. https://en.m.wikipedia.org/wiki/Symbiosis so all parasites are in a symbiotic relation with the host

@Polisetty Thank you for clarification; the wikipedia article you link actually describes the controversy on terminology a bit, where symbiosis was originally used to describe a beneficial interaction but now that has changed where mutualism has supplanted the earlier definition.


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Can the concentration of a kinase be used to identify its substrate?
I'm currently working on a dataset were I'm trying to identify substrates of an kinase in silico, I have a dataset which contains the concentrations every 0h 2h,4h,6h,8h,10h,24h for a lot of proteins found in the sample when the kinase was active. However some of these aren't targeted by the kinase but other proteins that got activated or were indirect activated by the kinase. So what I did I used R to plot the concentration of the detected proteins only if they fitted the concentration line of the kinase of interest(with a little devition allowed) this gave me the following graph:

the blue line is the kinase and the other lines are proteins found in the dataset. I know there could be postive or negative feedback which has effect on the concentation of these proteins.So my question is could the lines shown here be a possible substrate?

The concentration of a kinase is completely independent of the concentration of the substrate, and vice versa. In a typical kinase cascade (such as the Ras→Raf→MEK→Erk pathway), signal transduction is generally amplified with each successive step. A relative small population of one kinase (like Raf) phosphorylates orders of magnitude more of its substrates (like MEK1/2), which in turn phosphorylate orders of magnitude more p44/42 MAPK (Erk1/2) molecules. These then phosphorylate transcription factors like c-Myc which translocate to the nucleus and affect the expression of target genes. Over time, protein levels inside the cell are changed, including the levels of the various components of the pathway or their inhibitors (such as phosphatases, components of the protein degradation machinery like ubiquitin ligases, etc.), allowing for regulation of the signal.
Therefore, for any given kinase at any given time post-stimulation, such as with a growth factor, the concentration and phosphorylation state of its substrate(s) can vary tremendously. For example, in the classical NK-κB pathway, activated by TNFα, one of the main substrates of the IKKα/IKKβ kinase complex is the inhibitor IκBα, which upon phosphorylation is rapidly ubiquitinated and degraded by the proteasome. However, one of the first target genes of the activated NF-κB p65/p50 transcription factor dimer is Ikba itself, which negatively regulates activation of the pathway.
I don't know exactly what information your data set contains, so I can't comment too much on your results. However, just graphing substrate concentrations that correspond to kinase concentrations at various time points will only give you one piece of information - that some substrates have grossly similar concentrations to the kinase - which means nothing. All that is is confirmation bias - you've decided on your result, then picked the data that confirm it. I bet if you were to graph the concentrations of direct substrates along with your kinase, you would find no relationship whatsoever, because as I've described above, there is none biologically.

Thankyou for your explanation! I have a dataset which contains all proteins downstream of the kinase (so substrates and non substrates), but I found it quite remarkable that the pink line has almost exaclty the same concentration changes as the kinase has, maybe this could be coincidence? @MattDMo

@RickBeeloo most likely it's just a coincidence. It could also be that your protein of interest is some sort of regulator of the kinase, and expression levels may correlate with it. You'll have to dig into the biology to answer that.

The hardest part is that there is nothing to find about the proteins of interest because they aren't identified before, but thankyou anyway! @MattDMo


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What decides the nocturnal periodicity of microfilariae?
Microfilariae, which are the larvae of filarial worms show a nocturnal periodicity of entering into blood in south Asia and China. This coincides with the biting habits of its vector.
The same very species in Malaysia, the larvae are present throughout the day and night but peak at specific time points (subperiodic). The vector there hase different feeding habits.
This understandably is beneficial to the worm.
What are the cues that the worm uses to understand day and night?
Reversing the sleep wake cycle also apparently reverses the periodicity of the larvae from nocturnal to diurnal.

The circadian clock is one of the primary drivers for most day-night cycles. Additional factor entrain the clock. This would be one place to start.

@WYSIWYG the problem here is that the microfilariae, figure out the 'absolute' night and not relative to the hosts sleeping habits. Isn't the circadian rhythm relative?

Circadian clock is an endogenous clock. It can operate without stimulation by light. However, light exposure regulates circadian clock so that it can adjust to the natural light-dark i.e. day-night cycles. Host/vector sleeping habits are also affected by circadian clock. When you say that reversal of sleep wake cycles affects the worms then it is likely that they are controlled by some molecules produced by host. Cortisol would be my wild wild guess.


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How much time does HIV live outside the body?
I'm wondering HIV viability outside the body of an infected person, for example in a knife that contains blood of an infected person, with N virus cells. (N could be for example, 1000).
Some virus might live more than others, then I'm asking the half-life of it.

The general response to that question is not long, the HIV is a weak virus and that once exposed to air, it can survive for maybe a few minutes at best.
BUT Under specific conditions, HIV can survive for a far longer period of time, sometimes for hours or even days if the right temperatures, pH balance, light exposure, and humidity are achieved.  It is a very difficult set of conditions but is nevertheless possible.
Source : How Long Can HIV Live Outside of the Body ?

In certain conditions, the virus can survive outside the body for several weeks.
Survival depends on which body fluid it is in, volume of the body fluid, concentration of the virus within it, temperature, acidity, and exposure to sunlight and humidity.
HIV transmission has not been reported as a consequence of contact with spillages of blood, semen or other body fluids.

Source : HIV transmission & testing, Survival outside the body

If you've come into contact with some blood or other body fluid that you think might contain HIV, it's understandable to have some concern about the possibility of HIV transmission. But you can rest assured that there haven't been any cases of HIV transmission through casual contact with blood or semen that has left behind on a surface. There haven't even been any cases after people have come across discarded syringes or needles.
This is partly because it's extremely unusual for this situation to involve any opportunity for an infected body fluid to enter the person's bloodstream -- it does not reach a mucous membrane (such as the vagina or rectum) or an open wound.
So in practical terms, there's little reason to worry about contact with body fluids that have already been outside a person's body for some minutes.
There isn't a simple, straightforward answer to the question of how long HIV survives outside the body. In certain, specific circumstances it may survive more than a few minutes. But it generally does not remain infectious and certainly does not pose a threat to people's health.
The conditions that a body fluid is exposed to greatly affect survival. Air dries out the fluid, which contains the virus, greatly reducing viral amounts. On the other hand, in the enclosed space inside a used syringe (with limited exposure to air) the virus can survive some time -- this explains why re-using needles and syringes is risky.

This question is about virus time survival, not about my concern of contact with virions, and that's reflected in my question. You aren't providing a source of a experiment or any source with a numerical response to how much time does it take. You have used this link  ( or another source with the same text) in for example the last sentence of your answer this explains why re-using needles and syringes is risky.. without citing it, that's wrong.


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Why some tissues like small intestine epithelium are able to be replaced so often, yet they are not one of the most common cancers?
My small intestine epithelium cells are replaced thousands times more than my prostate. Yet I'm much more likely of getting a prostate cancer than cancer on my intestine epithelium. Is there a known cause for this?
Does our body have better DNA-repairing mechanisms or something like that for those tissues ?

Just a quick thought: These cells have a relative short livespan and thus less chances to develop into cancer cells. This would be different for the prostate for example.

Interesting question!  @Chris has a good point. I think the relevant factor is how often a long-lived stem cell (or similar) would divide in these two tissues. Is prostate less proliferative than small intestine in this regard? Also, some cell types maintain a more differentiated state while proliferating (hepatocytes in regenerating liver, for example) and this could be a factor I think. Just some suggestions.

@Roland There are stem cells present in the small intestine, which clearly play a role in regenerating the tissue. I can look up some references for this later.

The human prostate has two main epithelial cell types, basal and luminal, as well as a minor population of neuroendocrine cells. Primary prostate cancer nearly always has a luminal phenotype characterized by atypical glands, strong androgen receptor (AR) signaling, and an absence of basal cells .                  Intestinal epithelium. The intestinal epithelium is the single cell layer that form the luminal surface (lining) of both the small and large intestine (colon) of the gastrointestinal tract.

Hi malay and welcome to Biology.SE. Your answer has unfortunately two flaws, while it highlights the difference between the 2 tissue it does not address why one would be more likely to develop cancer (the original question). Moreover it lacks of references. References are really important to verify the source reliability.


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Are evolutionary mutations spontaneous?
My question is whether mutations which lead to evolution occur by any environmental force or it occur spontaneously? I have read in genetics that x-rays, ultraviolet rays and chemical mutagens are the causes of mutation but how are they responsible for evolutionary mutations?

Why do you distinguish between "mutation" and "evolutionary mutation"? What do you think is the difference?

I think all mutations do not lead to evolution and I wrote evolutionary mutation because I wanted to know the variations that contributes in evolution.

Your comment shows that you do not understand the definition of evolution. I would recommend that you have a quick look at a short intro course to evolutionary biology such as Understanding Evolution by UC Berkeley for example.

Mutations occur spontaneously because all molecular processes are stochastic in nature: DNA replication is an imperfect process. However, certain external factors can increase the probability of a mutation to occur or even cause specific types of mutations.
Both spontaneous mutations and this kind of externally driven mutation contribute to the genetic variability that is the basis for evolution. It is sufficient that variation exist for evolution to be possible, no matter the origin of this variation. X-rays are probably not common in nature, but there is plenty UV on the surface of earth, and there probably exist chemical mutagens that are formed without human contribution.

You should also mention that mutation is a highly biologically controlled process. Many experiments have shown that mutation rates themselves can change in response to evolutionary pressures. So at least some mutations are not just the result of "imperfections" in DNA replication but are actually an evolved feature of the replication mechanism.

This answer is very related

@Nathaniel Interesting, sources for that?

Evolution is, by definition, not spontaneous.
Be wary of conflating "mutation" with "new or changed features".
Mutation is only one of many causes for feature change between generations; inheriting traits from parents is another. Changes in nutrition and education can cause population-wide changes in height and IQ, without being based on mutation. All these things can lead to new features without mutation being involved at all.
The term mutation covers a lot of things which can cause inheritable and non-inheritable visible changes in future generations.
A genetic mutation (as opposed to an in-utero developmental mutation, etc) is a change in genes. The mutation may be in a non-functional section of the genome, so may do nothing. Or it may cause cell division to fail and kill the child. Or it may do anything in between.
But it's not evolutionary. No mutation is, since mutations are one-off incidents.
Now, over time, favorable genetic mutations may be selected for, and built upon by other mechanisms of feature change, to the point where everyone has it. Again, this is not instant, and will take many generations to spread through everyone.

In a sense all mutations "lead to evolution". The genetic make up of the population has changed. Some mutations become "fixed", are persistent in the gene pool. You are thinking of evolution as progressive, it isn't; it is statistically adaptive.
Is melanin depletion (pale skin)"evolution"? In gloomy high latitude places it enhances vitamin D production. In hot low latitude places it makes melanomas more likely.


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Why do the ancestors of birds still exist?
If I am not mistaken, scientists believe that birds are evolved from reptiles. Why do the ancestors of birds (that is, reptiles) still exist?

Does this answer clear it up? Species don't evolve into other species. They evolve from them.

Birds evolved to use different environments than reptiles.  Reptiles are still better adapted for their own environments, so birds haven't displaced them.  There are so many problems with your question's assumptions that this ultra-simplified answer is barely a start; I suggest you learn more about evolution.

You appear to have several (rather common) misunderstandings about how evolution works. I strongly suggest reading through Understanding Evolution from the University of California, Berkeley. It is a short but thorough and easily-understood introduction to the topic that should address your misconceptions.

Reptiles are not ancestors of birds. There are many answers in this site (including the one here by Remi.b) that have clarified it. I am putting this question on hold as a "homework" because you have some misconceptions regarding the concept of evolution properly and any answer would simply be a crash course on evolution. Moreover, since your assumption itself is incorrect, the question gets invalidated.

As this type of question results from a common misconception, I think we should make sure to keep this post around to be able to link to it. I am voting to reopen.

Introduction to phylogeny
Short Intro to Speciation
Let's talk about speciation. Speciation is the process by which a single lineage split into two. This happens in a number of ways (allopatric vs sympatric vs parapatric, BDM model and others). I will consider a simple case of allopatric speciation below as it is the simplest one to understand (although not necessarily the process causing most speciation events).
Following the story of a lineage through its speciation events
Think of a population at time $t=0$. Let's call this species A (for Ancestor). Imagine that an ecological change brings a barrier right in the middle of the range of this population of A. Such a barrier could be originally caused by a fire, or a river that has changed direction or a mountain range "popping up". The two now isolated populations are free to diverge randomly through time. This is what we call a speciation event. Note that under this model, there is no necessary need for selection to explain speciation. Let's call the two diverging population B and C which exist at time $t=1$.
Now, imagine C goes under another speciation event and split into the populations D and E. In the same time, population B may have changed quite a bit so that we might want to call them F. Here is a diagram of the situation
  F           D ----- E     t=2
  |               |
  B ------------- C         t=1
          |
          A                 t=0

A is an ancestor of B,C,D,E and F and does not exist today. B is an ancestor of F but does not exist today. C is an ancestor to both D and E and does not exist today. Let some more time pass by and you may eventually end up with the following tree
  G ----- H       K   I ----- J t=3
      |           |       |
      F           D ----- E     t=2
      |               |
      B ------------- C         t=1
              |
              A                 t=0

At time $t=3$, only species G, H, I, K and J exist today, the other are ancestors of current species. Let's expand this tree even further.
  L ----- M   N       O       P ----- Q      t=4
      |       |       |           |
      G ----- H       K   I ----- J          t=3
          |           |       |
          F           D ----- E              t=2
          |               |
          B ------------- C                  t=1
                  |
                  A                          t=0

You will note that lineage I went extinct at some point between $t=3$ and $t=4$.
Naming subsets of the tree
Reptilia
I am now suggesting to give a generic name for all the lineages present in the tree we drew (which we call a phylogenetic tree by the way). Let's call them Reptilia. So all the species A,B,C,D,E,F,J,I,J,K,L,M,N,O,P and Q are Reptilia.
Birds and Mammals
Now let's consider a subset of this tree. Let's consider the subset made of the species J, P and Q only. Let's call them birds. Let's also call mammals the subset composed by the species G,L and M.
Lizards (and others)
Finally let's call lizards all reptilia that are not birds, nor mammals (in reality it would be more correct to call this group lizard_crocodile_turtles_snake_amphibians_tuatura). Of course, the right tree is much bigger! By the way, you can explore the tree of life yourself on OneZoom.org.
What is a taxon
By the way, a group of species is called a taxon (plur. taxa).
Monophyletic taxa
It might be straight forward to you that there is something fundamentally different between the groups that we called mammals, birds and reptilia to the one that we called lizards. Indeed mammals, birds and reptilia are called monophyletic as they are composed of a given ancestor and all its descendants. lizard on the other way is not monophyletic. A monophyletic taxon is also called a clade. Below is a graph representing what a monophyletic taxon is. It also uses the terms polyphyletic and paraphyletic to describe different types of non-monophyletic taxa

Concept of species
You might want to learn more about the issues behind the concept of species in the post How could humans have interbred with Neanderthals if we're a different species?
Concept of taxonomic ranks
What we decide to call a class, an order or a family is also somewhat arbitrary too. For example, we generally consider the monophyletic taxon Mammalia is a class. However, there is no non-arbitrary reason for calling Mammalia a class rather than Eutheria (eutheria = placental mammal).

Online resources
I suppose the above answered a big part of your question. You will be able to read all of what I just wrote (and much more) on any good introductory course to evolutionary biology. Consider having a quick look at Understanding Evolution by UC Berkeley for example as @MattDMo suggested in the comments.
Issues in your post
There are issues in your post that cannot be addressed in a single post (another reason for you to follow a quick intro course to evolution). Below I consider your post piece by piece mainly to point to some issues

Scientists believe

Terrible statement. By belief, we often refer to a non-justified belief, that is a belief about the world that is not justified (in science, the method of justification is called "the scientific method"). The statement, therefore, suggests that non-justified beliefs have a place in science while they don't. By being a little lose on the semantic, one could say that scientists "know" or they don't know but they don't believe without good reasons to believe.

that birds are evolved from reptiles

This is misleading (and it mislead you) because by "reptile" you think of a lineage that currently exists. Also, the expression "are evolved from" sounds very wrong. The expression "has evolved from" would be more correct.

evolution occur so that the organism can survive in the environment by developing new characters

This is wrong both in terms of the semantic (issue of causality when saying so that) and in term of the definition of evolution. You seem to confound evolution with natural selection.

According to natural selection

Natural selection is a process, not an explanation. It is like saying "according to gravity". The semantic is wrong, you should say "according to the theory of gravity" or "according to the theory of evolution" (or eventually "according to the theory of natural selection").

According to natural selection, those with favourable variations will survive and those with unfavourable die

You seem to apply that statement to population-level fitness (which would be mainly wrong) rather than to fitness variance within a population.

Why do the ancestors of birds (that is, reptiles) still exist?

The ancestors of birds don't exist anymore. I hope that was made clear from the above explanations.

Why didn't they get eliminated by natural selection?

This sentence suggests that you do not really understand what natural selection is but this is a story for another time. You can learn about natural selection on Understanding Evolution by UC Berkeley.

+1 Thank you for the extremely clear answer here (as well as on my question)

Reptiles evolving from birds is an example of divergent evolution. This wiki article has more information. Essentially both birds and reptiles are still around because they both fill a niche. That is, birds and reptiles separated have a common ancestor, and at some point their evolution diverged. At that point, birdoids which better filled the "bird" niche had higher fitness, and reptiloids which better filled the "reptile" niche had higher fitness, so birds evolved to be more like birds, and reptiles evolved to stay reptiles.

This answer is not fully accurate either, and shares some misconceptions with the original question. Reptiles did not evolve from birds, nor did birds evolve from reptiles; both evolved from a common ancestor, which we may today think of as more "reptilian" but is not a modern reptile. It is possible for species to be thought of as more "ancient" if they have not changed in gross structure over long time periods (i.e., crocodilians are often described in these terms), but those species still spent just as much time "evolving" as have humans, for example.

It is surprising to see an upvote on this answer. The answer is in between misleading and wrong.

Reptiles did not evolve from birds as Bryan said.


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Does zygosity have meaning for mitochondrial variants?
I am working on a system that annotates variants in human DNA sequences. One of the pieces of information reported is the zygosity of the variant. I noticed that mitochondrial variants are also shown to be either homo- or heterozygous.
How does that make sense? Does it make sense? As far as I know, the mitochondrial DNA is just a single, circular DNA molecule. So I can understand considering all mitochondrial variants heterozygous, by definition. I could also accept that one could think of them as homozygous by definition. I just don't see how some variants can be homo- and others heterozygous. Am I missing something or is the annotation system I'm using not making sense?

Since all the mitochondria in a cell (I'm thinking mammalian, through it may apply to others) are derived from the mother, mtDNA should all be homozygous - in fact, I don't really understand how zygosity even makes sense when talking about mitochondria. I suppose it's possible that some mtDNA in a cell is damaged or mutated, likely through the action of ROS, so there theoretically could be two (or more) "alleles" in a cell if there is a mixed population of mitochondria. I don't know quite enough about mitochondrial genetics to make this an answer, though. Just my 2 cents.

@MattDMo ah, I hadn't considered mized populations, that makes sense. I guess it's theoretically possible to have ~50% of mitochondria having a given variant but I would expect that to be vanishingly unlikely. If there is a variant specific to a given mitochondrion, I don't really think there would be enough sequence data to be able to call it. I guess my main question is whether mtDNA is somehow doubled in a way that makes zygosity even remotely relevant.

as far as I know, the only doubling is mtDNA replication just before a mitochondria undergoes fission. You probably want to verify that, though.

You abosolutely can have mixed populations of mitochondria in a cell (it is in fact very common). Therefore when you sequence the mtDNA you will get a completely variable percentace of reads containing a variant from close to 0% to 100% (there is a lower limit based on the quality and read depth of the sequencing data).
You can't consider the variants to be heterozygous or homozygous as conventional zygosity doesnt apply. Heteroplasmic and homoplasmic are the terms which are used.

So how would I, or a variant caller, call one or the other? Some arbitrary threshold like ">70% reads carry the variant so it's homoplastic" and "~50% carry the variant so it's heteroplastic"? Is there some literature you could point me to? Your whole answer could really benefit from some references to back your claims (I know your claim is true, but you're not supporting  it in you answer). Still, it sounds like it would make more sense to just look at allelic balance values and forget zygosity for mt vars.

Welcome to Biology.SE! Your answer would be even better if you included supporting references (primary literature is best). ——— You might also want to go through the [tour] and then consult the help pages for additional advice on [Answer effectively] on this site. Thanks!


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Rescue cell lines function
I'm reading in a paper in which the authors have made three cell lines to study the function of a gene of interest (Mbd3):
The one is knocked out for the gene of interest [Mbd3 -/-], the other is floxed for the one allele [Mbd3 fl/-], and the third is rescued knock out cell line [Mbd3 -/- (rescued)], that means that in the cell line of knocked out cells they have stably transfected a plasmid expressing the gene of interest. I am then wondering, why they use this rescue cell line, instead of using the wild type cells with the wildtype alleles of Mdb3?

Rescue experiments are the gold-standard for confirming that an effect is due to the gene of interest.
Removing a gene may have off-target effects but if you can return function to 'normal' by supplementing the gene back into the cell-line/animal then this is strong evidence that the gene and its product are the cause of effects that are seen in the experiment.
Wild-type cells would normally be included to show what 'normal' response  is.


text:
Are neurons clustered? How do neurons make thousands of connections?
According to this source, a neuron can connect to up to 10,000 other neurons. Does this imply that neurons are clustered, that is, not evenly spaced? Argument:
Say axons are length $L$, and dendrites are length $D$. Say a neuron $N$ has 10,000 outgoing connections. Then there must be 10,000 neurons within distance $D$ of $N$'s axon terminal. Then each of those 10,000 neurons are within distance $2D$ of each other by the triangle inequality. Assuming $2D<L$, then all of those 10,000 neurons are less than an axon's distance from each other. But for this to be true, the 10,000 neurons must be closer to each other than they are to $N$. Since this argument holds for any neuron, we get the result that neurons must form clusters of around $10,000$ neurons, or their dendrites must be longer than half their axon length.
Similar to this question.

Why should spacing and number of connections be inversely proportional? Different regions of brain have different types of organisation. Perhaps you should read about it and narrow down your question. In some lower organisms there is no centralized nervous system but a "neural net". You can read about that too.

Say each neuron had exactly one connection. Then neurons could be evenly spaced. However here I argue that if neurons have many connections, then they must be clustered.

It is not really necessary. Check neural nets in hydra.

Hydras have a decentralized nerve network, true, but here I'm referring to the local neural topology. I argue that if a hydra's neurons had thousands of connections, then they would still be locally clustered, even if there is no "central authority" like a brain.

Your assumptions about the length of axons and dentrites are incorrect. They can vary tremendously from one neuron to another, and in the same neuron. There could be very short connection lengths between two adjacent neurons, and much longer ones between the same neuron and one on the other side of the brain.

@MattDMo Okay, so it's not usually true that $2D<L$?

I think for neurons to be truly evenly spaced, we'd need $D>L$ on average for thousands of connections.

It's possible the info in the link was incorrect. Another source says that neurons have up to 10,000 synapses, so maybe the actual number of unique neurons connected to is far less.

In addition to the comments pointing out other inaccuracies, I think the biggest, most obvious misconception that completely invalidates the whole premise is that axons most certainly do NOT have a single terminal; axons branch and make thousands of individual synapses along their length and at the ends of any branches. For excitatory projection neurons in the cortex, for example, the axons can stretch for many millimeters (or centimeters in larger brains), but also typically branch near their origin to contact the dendrites of neighboring cells.
The number of synapses and number of neurons contacted varies greatly across brain areas, species, cell types, etc.
You might be interested in "small world" organization, such as at link, which I suppose could be considered a form of clustering, but it has absolutely nothing to do with the mathematical distance explanation you are proposing.
The only correct equation you can write here is that the spacing S between neuron A connected to neuron B, must be S<=D+L, where L is the length of A's longest axon, and D is the length of B's longest dendrite; for many pairs, S << D+L. These equations will not lead you directly to any valid conclusions of clustering.


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Muscle contraction/extension percentage during normal ranges of motion
What is the typical percentage range/limits of extension/contraction during normal ranges of motions for muscles?  Assuming a rest length in a typical relaxed state.
I'm mostly interested in humans but I am also curious if it is typically the same range across other animals too?

can you be a little more clear - do you mean what percentage of muscle shortening occurs (i.e. with 100% defined as resting/non-stretched muscle)?

Yes so for example given a rest length at 100%, saying typically muscles extend to 110% and contract to 80%.  Specifically it's to determine a sensible default starting range for a motion simulation I am working on.


text:
Ray wu DNA sequencing methodology understanding
I'm trying to understand the method which Ray Wu, developed to sequence the DNA 5' cohesive ends of a lamda phage. I'm reading these two papers written by him, but i stuck at the point where he uses the 32P nucleotides.
Structure and base sequence in the cohesive ends of bacteriophage lambda DNA
Nucleotide sequence analysis of DNA: II. Complete nucleotide sequence of the cohesive ends of bacteriophage λ DNA
It's not clear to me, by reading the papers, the step in which he runs the polymerization of the DNA. Did he use all the 32P nucleotides at once or each one at a time. As i understood he made the DNA pol to use the tritiated nucleotides to fill in the gaps of the 5' cohesive ends and then he cleaves with a DNAase in many  oligonucleotides which later fractionize with electrophoresis. If he added all tritiated nucleotides at once how did he recognize which one is at a specific place ?
Can someone describe the process in more detail using step by step aproach?
Thank you,

Those two articles are located behind a paywall

Do you want me, to upload them somewhere else or is it illegal?

I'm not a lawyer (I'm a biochemist). Don't worry, I think I have a new account for access. So you're still seeking an explanation? How did you come across these classics?

I just wanted to see how people used to think back then with their only tool the analytical chemistry and some little knowledge of enzymes. 2 days i read it again and again and tried to put an order of the process/method he was used. His work is about 28 pages and he finally read about 20 nucleotides. Maxam's and Sanger's  papers are around 8 pages and they cloud sequence 100 - 1000 nucleotides at once. Times are changing and it seems fascinating to me knowing a little bit of history. If you want the papers, let me know.

That's very cool (IMHO). As my martial arts sensei used to say "You gots to know the basic fundamentals" (he was not a native english speaker). I think the second paper has the full story(?) because based on the abstract in the first paper he only found out which bases were present, not the order or sequence. Can you upload PDFs here to Stackexchange as attachments? I don't remember how that works.

What stage are you at in your education/training?

After reading your original post again, I am going to speculate that the combination of isotope labelling and DNAse digestion means he used a combination of something called nearest neighbour analysis, probably coupled with wandering spot thin layer chromatography (TLC)

Nope, according to this review article I was wrong "It was around this time that various researchers began to adapt their methods in order to sequence DNA, aided by the recent purification of bacteriophages with DNA genomes, providing an ideal source for testing new protocols. Making use of the observation that Enterobacteria phage λ possessed 5′ overhanging ‘cohesive' ends, Ray Wu and Dale Kaiser used DNA polymerase to fill the ends in with radioactive nucleotides, supplying each nucleotide one at a time and measuring incorporation to deduce sequence [17,18]"

Check out this site: http://www.whatisbiotechnology.org/exhibitions/sanger/dna

I couldn't create attachments in comments so here are the links for the files
http://s000.tinyupload.com/index.php?file_id=73908298645007027481
http://s000.tinyupload.com/index.php?file_id=30732501249180823829
I just started my Msc. at protein biotechnology.
I've already read that page. All i wanted was to understand the chemical perspective they used.

Also,  by reading these papers, a new question came in the air posted here. https://biology.stackexchange.com/questions/52809/doesnt-the-radioactive-labeled-molecules-of-dntps-or-dna-harm-themselves-or-the
If you have an idea for that too... let us know :-)

I am not going to post this as an answer, but I have skimmed the paper, and it is an absolute beast.  Some facts worth noting. They do not use electrophoresis, they use ionophoresis.  They also use a scintillation counter to calculate the number of molecules of radio labelled dNTP incorporated.  After ionophoresis they purify the radioactive peaks and analyse those by nuclease digestion, and nearest neighbour analysis.  Essentially they use the labels to purify the new oligos, and then fragment them to figure out the sequence of every dinucleotide. Then they build a map.