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How long does it take for a genetic trait to dissipate if its no longer selected for?
Have their been any studies or experiments done that provide insight into the persistence of genetic traits if an environmental shift suddenly causes that trait to be neutrally selected for? Does it take 100s of generations to reach equilibrium or only a few?
For example, how long can we expect the effects of birth control to take in decoupling human behavior related to sex from human behavior related to having children?

It depends on whether it is neutrally or negatively selected (and how strongly so), it depends on the population size, it depends on the mutation rate and mutational variance and - most important of all - it depends on the level of genetic variance for this trait to start with. This variance can be calculated at equilibrium (assuming no important demographic change "recently") from the above parameters though. It may take between 1 generation and a biliion generations.

Lets say its neutral, not negative. I added an example case for reference. Of course it depends on those things, but I'm looking for a more quantitative answer.

The answer still varies between almost 1 generation to many generations.

@Remi.b No it doesn't. There is literally no statistically probable way that a trait will be randomly removed in a single generation. Your comments aren't helpful at all.

If the population is 2, yes it is even quite likely. I wrote an answer to give you a hint about how variable it can be depending on the exact scenario of interest.

I would need to see some logic or evidence that even a population of 2 would dissipate a neutral genetic trait in 1 generation unless the entire population dies. Ya, your population dies you won't have the gene, and that's obviously not what my question's about.

if there is a standing genetic variance of 0.5 (one is carrying the allele A and the other one is carrying the allele B), then the guy with the allele A reproduce while the other don't (let's assume hermaphrodism) and it's done. End of the story. Of course, in such a small population it is likely that there is no standing genetic variance but this very much depend on the detailed scenario of interest. Experimental evolution of selection sometimes don't last more than 40 generations and you already see a strong response.

There is no way to answer this question as there are way too many factors influencing this time.
It depends on too many factors
It depends on:

whether it is neutrally or negatively selected (and how strongly so)
the population size
mutation rate
mutational variance
level of genetic variance for this trait to start with.

This variance can be calculated at equilibrium (assuming no important demographic change "recently") from the above parameters though.

It may take between 1 generation and a billion generations.
For example
Consider for example that your trait is neutral. Assume that the trait can only take two binary state A and B and that only a single locus affect this trait, which two states are also named A and B for simplicity. Let's say A is the ancestral state and we want to know how much time it takes to have a population of B. Imagine the haploid population size is $N=10^5$. The mutation rate for the locus of interest is $\mu=10^{-9}$.
Slow Case
If at the start there are no alleles B, then you have to wait for a mutation to occur. The time for such a mutation to occur follows an exponential distribution with parameter $\mu=10^{-9}$. Because we assumed neutrality, the probability of fixation (fixation is the state when the whole population carry the same allele) is $\frac{1}{N}=10^{-5}$. Conditioning on fixation, the expected time for fixation to occur is $-4N \left(\frac{1-p_0}{p_0}\right)\ln(1-p_0)=399998$ generations. In consequence, the expected time to fixation in this case is $10^{5}*10^{9}+399998 ≈ 10^{14}$ generations, that is about 77 times the age of the earth assuming there is one generation per day! So Obviously, the environment has time to change again. Note that variance is about $10^{28}$ generations! Of course this example is just an extreme slow case, but I have been using realistic parameter values.
Fast Case
If you have a population size of $N=50$ and the B allele is already present at frequency 0.1 and that the B allele is beneficial with a selection coefficient of 1.5, then it might take about 100 generations.

Thanks, this is much more informative. FYI, the answers I'm expecting are along the lines of equations, not a constant answer like "10-15 generations".

Happy that it helps. Note that there way too many processes in play and therefore too many equations (if you're looking for equations). I would recommend that you follow an introductory class to population genetics.


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Calibrating Motic Camera to Stage Micrometer
Whilst calibrating my Motic Microsope's camera, I am able to calibrate the 10x object lens against the stage micrometer accurately.  However when I calibrate (using the Motic 2.0 Plus software) the 40x object lens, it always sets the ratio incorrectly.
For example, in the calibration panel, I load a photo of the scale that I took and then I draw the circle so that it measures the pixels both in height and width and then I tell it that the circle is 10 µm.  But it doesn't seem to get the ratio correct.  When I did this for the 10x lens it worked perfectly.
So I took a photo of the scale with the 40x object lens and then went to calibrate that.

Here you can see how the calibration is performed: you position a circle over the photograph and tell it the size in µm (it's rather large, sorry):

Here you can see the measuring line out of whack.  It gives me 8 µm for a length that should only be 4 µm.

Am I missing something?

The way I solved this was by using the scale line method.  First, I understand that each division on the stage micrometer is equal to 10 microns.  Then, using my photograph of my stage micrometer and the Motic software on my computer,  I draw a horizontal line over oh, say, 3 divisions and tell it that this distance (measured in pixels) is equal to 30 microns.
Now, using the same method, this is also possible:
I found another Windows program called Meazure which you can use in the same fashion without any special microsoft software.  For this I use XnView to open the photograph of my stage micrometer, set the zoom to 100% and then draw a straight line over oh, say, 3 divisions.  Then I see how many pixels long that is.  Then I tell Meazure that this many pixels is equal to 30 microns.  Now I can measure, in XnView, any image taken by the microscope's camera - I just have to remember to assure the view is exactly the same.
The Meazure program is very nice and easy to use, and I actually prefer it, although the Motic software provides labels and such that are useful.

It looks like the shape is an ellipse rather than a circle. The ellipse has major and minor axes, which are described in terms of half-axes (177 and 175 pixels respectively). Is it possible the software is incorrectly using the half-axis measurements, whereas when you draw a perfect circle it will correctly use the diameter? This is consistent with the x and y scale numbers being different from each other.
So I would suggest re-calibrating with a perfect circle.
Hope this helps.

When I calibrate, should I calibrate to the edges of that black box?  It's supposed to represent 4µm.  If they were tick-marks I would think to measure to the insides...  It's kind of confusing.  Do I count the tick mark or not? Or do I measure to half of it?

With my own calibration slide that has a linear scale (like a ruler), I measure from the left side of one tick mark to the left side of another one.  I'm not familiar with your calibration slide, so I don't know what the outer lines represent. Do you have any documentation or are there other areas of the slide that are more clearly labeled?

My Mycologist says that it's supposed to be 10 microns from one tick to the next - whether left to left as you say (which is easy to see - thanks!) or from half to half of the tick.  So I tried this by capturing the scale with the 10x lens and calibrated four ticks to be 40 microns.  But when I measure from tick mark to tick mark I get 18.10 microns.  I'm still missing something.

My Stage Micrometer has five calibrators: a circle at 1.5mm, a circle at 0.6mm, a scale cross (1 DIV=0.01mm), a tiny circle at 0.15mm and a circle at 0.07mm.  Should I be using a particular one of these?

Okay, I think I've got this.  Instead of calibrating by drawing a circle over the scale cross, I used a different calibration setting where I just drew a straight line vertically and a different line horizontally.  with my Mycologist's directions that each length between tick marks = 10 µm I am now able to come up with correct dimensions.  Thanks for your time and attention!  Should I post this as it's own answer, or should you update yours to match so that I can accept a solution?

Great to hear that you solved it! I'm not a Stack Exchange expert, but I think the solution you found is different from my original idea. So for me, it makes sense for it to be its own answer.

source: Stack Exchange

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

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Wheatgrass in thalassaemia
In local newspapers there was a not so recent story about wheatgrass juice being "curative" in thalassaemia. Although I do not take the article at face value, it would be enlightening to know if there was any basis at all in the claims that wheatgrass juice or extract can help mitigate some symptoms of thalassaemia.

Wheatgrass juice or extract has shown some promise for reducing the required frequency of blood transfusions in thalassemic patients, possibly due to iron chelating activity.  However, few high-quality controlled studies have been conducted so it may be too early to form a definite conclusion.
References:

Choudhary, Dharma R.; Naithani, Rahul; Panigrahi, Inusha; Kumar, Rajat; Mahapatra, Manoranjan; Pati, Hara Prasad; Saxena, Renu; Choudhry, Ved P. (April 2009). "Effect of wheat grass therapy on transfusion requirement in β-thalassemia major". The Indian Journal of Pediatrics 76 (4). pp. 375—376. doi:10.1007/s12098-009-0004-6.
Das, Priyabrata; Mukhopadhyay, Ashis; Mandal2, Suvra; Chandra Pal, Bikas; Mishra, Raghwendra; Mukherjee, Debarati; Mukhopadhyay, Soma; Basak, Jayasri; Kar, Manoj (2012). "In vitro studies of iron chelation activity of purified active ingredients extracted from Triticum aestivum Linn. (wheat grass)". European Journal of Medicinal Plants 2 (2). pp. 113—124. doi:10.9734/EJMP/2012/1059.
Marwaha, R.K.; Bansal, Deepak; Kaur, Siftinder; Trehan, Amita (July 2004). "Wheat grass juice reduces transfusion requirement in patients with thalassemia major: A pilot study". Indian Pediatrics 41. pp. 716—720.
Mukhopadhyay, S.; Basak, J.; Kar, M.; Mandal, S.; Mukhopadhyay, A. (2009). "The role of iron chelation activity of wheat grass juice in patients with myelodysplastic syndrome". Journal of Clinical Oncology (Meeting Abstracts) 27 (15S). p. 7012.
Singh, Karnail; Pannu, M. S.; Singh, Palwinder; Singh, Jaswinder (January 2010). "Effect of wheat grass tablets on the frequency of blood transfusions in thalassemia major". The Indian Journal of Pediatrics 77 (1): 90—91. doi:10.1007/s12098-010-0002-8.
Tirgar, P. R.; Desai, T. R. (September 2011). "Investigation into iron chelating activity of Triticum aestivum (wheat grass) in iron-dextran induce iron overload model of thalassemia". Journal of Pharmacy Research 4 (9). ISSN 0974-6943.

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


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Why is one testicle larger than the other?
Why is one testicle generally larger in humans? Just due to asymmetric development, or is there a hypothesis as to some utility it serves? I read that the different heights may be attributed to attempting to keep them from hitting against one another. Is there a similar guess to the purpose for the difference in sizes?

Welcome to Biology. Could you tell us where you got this information from? It's interesting, though, given that one lung is larger than the other.

@AliceD And if I am not wrong, its true for our feet as well?

I would strongly question whether the underlying claim that testicular asymmetry is generally true. While there is no known clinical significance of testicular asymmetry, most men probably have no noticable difference in testicular size. There have been a number of studies over several decades, and findings have been inconsistent.
Braus (1956) stated that the left testis was heavier and lower; Chang et al. (1960) determined on study of cadavers that the right testis was generally larger than the left.
A 2008 study in 0 to 6-year-old boys found no difference in testicular volume measured ultrasonographically.
Age or level of sexual activity may also play a role; it is known that testes get larger during sexual activity.
The reason for testicular asymmetry is unknown. It has been reported in many different species (see Yu, 1998). The most common explanation provided in humans is that the right testis is more commonly larger than the left due to a difference in vascular anatomy: the left testicular vein empties into the renal vein while the right testicular vein empties into the inferior vena cava. However, anatomy alone would not explain testicular asymmetry in other species as well, so there is no doubt more to this than presently understood.


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Non-ribosomal peptide synthesis: why Glutathione cannot be produced by the ribosome?
Case: I am writing a summary for a class in protein structure and function, and was asked to describe some different ways that peptides are synthesized (that does not involve the ribosome). I understand that glutathione is a tri-peptide consisting of L-cystine with a "gamma" bond to L-glycine which is then bound to glutamic acid.
Problem: Why is it that the ribosome cannot produce this peptide? What is special about the peptide-gamma-bond?
My reasoning: The peptide is too short, meaning that the large ribosome complex cannot bind to mRNA of this length as it need many different binding spots in order for the large and small subunit to come together. Also, the "gamma" bond is very special, and the ribosome can only produce peptides with the "Standard" peptide bonds.

Is this correct, and is there something else I am missing?
Does the "gamma" bond relate to the fact the glutathione is not that easily degraded by peptidases in the cytosol?

It's definitely not the length. Although ribosomes can't make really really small peptides because they need something to hold onto and in any case proteins start with methionine(usually), there are workarounds. There's no reason why a tripeptide couldn't be coded for by a gene directly.
The 'traditional' method of producing very short peptides is producing a longer protein and cleaving off a chunk of it, which works great for signal peptides and a number of other systems. Very small peptides are more efficiently made by enzymes like this but in principle there's no reason to besides efficiency and complexity. (You need a special protease for each small peptide etc etc etc)
However, this gamma bond is a different beast entirely, and no ribosome could ever produce it, even in the middle of a longer protein. Amino acids 'snap' together in a very specific way. The amino group bonds to the carboxyl group of the previous amino acid, making a chain. The side groups of an amino acid aren't involved. Like Legos that snap together only one way and can be any color or have any designs on the side. The difference here is glutamate has a carboxyl group as part of its side chain. It's like a Lego with holes on two sides. The NRPS here connects the cysteine to the side chain of the glutamate instead of the 'bottom' where it would go if a ribosome-synthesized glutamate-cysteine bond.
This gamma bond also explains the increased longevity of the product. Proteases aren't designed for things that look like this. The gamma bond doesn't 'fit right' in the protease active sites and therefore activity is slower.

From I've read about glutathione, I think the answer to your question is :
"Because there is no glutathione gene ", and hence, no glutathione mRNA.
Concerning the gamma bond, this wikipedia article quotes :

This peptide coupling is unique in that it occurs between the amino
  moiety of the cysteine and the terminal carboxylic acid of the
  glutamate side chain (hence the name gamma-glutamyl cysteine)

citing this paper as a reference.
Also, it seems like the gamma bound is indeed the reason why is not degraded in the cytosol.
I don't know how you perceive wikipedia, but to me the english version is a good way to gather general informations about an unknown subject, before going more deeply in details with scientific litterature.

Yes, it makes sense that there is no mRNA and thus is has to be produced with other methods. But, is there a general reasons why the ribosome has problems with short peptides? It would be good if someone has a reference of why that is - or is it just as simple as I stated "ribosome is too large". Also, is the gamma-bond just a concertino between the "gamma" carbon and the amide group?.. what is the regular binding patters "beta" carbon to amide group?..

I am not sure that the ribosom could have a problem with short peptides, because the size of the mRNA that code for a peptide is not exactly 3*(number of amino acids of the peptide) : there is the ribosome binding site in 5' of AUG, that can be a part, or the whole, 5'-UTR. But it's an interessting question, and I wonder what's the shortest mRNA known.
The gamma bond is an unusual link between the two amino-acids. The classical bound is between the carboxyl group bound to the alpha carbon of the first amino acid and the amino group bound the the alpha carbon of the second amino acid.


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What is the difference between muscle fascicle and muscle bundle?

In the photo above (given by Bio teacher), the muscle bundle is shown to be as a bundle of fascicles, but in most web definitions I've seen, the two terms are used interchangeably. What is the correct name for the part labeled "muscle bundle" if there are in fact no distinctions between bundle and fascicle?

Short answer
Muscle fascicles are the building blocks of skeletal muscle.
Background
Skeletal muscle, or striated muscle is composed of many units called muscle fascicles. The fascicles are bound together by a type of connective tissue called fascia.
Fascicles in skeletal muscle are composed of muscle cells, called mycocytes. These cells are referred to as muscle fibers in skeletal muscle. Myocytes contain small strands called myofibrils, which are the contractile elements in the muscle cells. The myofibrils move as skeletal muscle contracts.
Putting it all back together, myofibrils are the contractile elements in muscle cells (muscle fibers); muscle fibers make-up muscle fascicles; and muscle fascicles are bound together by fascia to compose the skeletal muscle.
Hence the part labeled 'muscle bundle' is a muscle, made out of a bundle of fascicles.
Source: Penn Medicine

I'm confused. In your categorization, where is the single muscle cell (is that the fiber?) Should that be part of the explanation of the organizational structure?

@anongoodnurse - nice catch. Thanks. I added an explanation (you are right, as always :-) and I added some web links to wikipedia and other sites for background reading.


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Why do chlorotic leaves have green veins?
If chlorotic leaves are chlorophyll deficient, why should the veins be green? shouldn't all the available chlorophyll be directed to the leaf lamina?


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Why is beta actin commonly used as a control in Western blots?
It is about the western blot question. The paper:http://www.sciencedirect.com/science/article/pii/S1931312813001145.
In the western blot experiment in this paper, they use beta actin as control. And also I saw other research paper also use beta actin as control. So why is beta actin used, not other gene? is it because it expressed in all different kinds of cells?

Other genes can be and are used. Basically any gene which is expressed constitutively at high levels and is a different size than your protein of interest can be used as a loading control.

β-actin belongs to a class of genes called housekeeping genes. Their proteins typically perform functions that are required across essentially all cell types (for example, β-actin is part of the cytoskeleton's microfilaments), and are supposed * to be not affected by experimental conditions. In Western blotting, they are run as a "loading control" to show that very similar amounts of protein were loaded in each lane. This is absolutely essential in some experimental systems where it may not be possible to always collect the exact same number of cells for each sample, such as when working with primary cells, tissue samples, or systems where you may be altering protein synthesis, cell size/number, or apoptosis.
There are many different loading controls to choose from, and some may be dictated by the cell/tissue type you are examining — for example, when working with stem cells, you may want to show that your experimental conditions didn't induce differentiation in the cells, so a pluripotency marker like Oct-4A or Sox2 may be chosen. In other cases, you may be examining fractionated lysates (a membrane preparation, just the nuclei, mitochondria, only the soluble fraction, etc.) and so may choose Na/K ATPase, Histone H3, COX IV, or GAPDH, respectively.
The choice of loading control can also be influenced by the size(s) of the protein(s) you are analyzing, as investigators frequently either strip Western blots and reprobe them with the loading control, or run two different species and detect with different colored secondary antibodies when performing fluorescent Westerns. In either case, you want your loading control to be a different size than your original targets.
Finally, all of this is assuming that the researcher has already attempted to load equal amounts of total protein per lane by using any one of a variety of methods for quantitating protein concentration. These include Bradford, Lowry, and BCA type assays, which may or may not be detergent compatible, staining the membrane after transfer with dyes such as Ponceau S, SYPRO Ruby, or India ink, or staining the gel with Coomassie or other proprietary Western-compatible stains.
*In reality, some scientists are becoming more and more aware that many experiments actually do affect a number of "housekeeping" genes, but when most see variations by, for example, Western blot or qPCR, they often choose a different loading control to use.

Good answer. You might also add total protein as an option for a loading control, e.g. Comassie or Ponceau stains, or a Lowry/Bradford assay; this does not assume anything about a specific protein, but allows expressing the changes of protein X relative to total protein.

@Roland thanks for the comment. I had kind of assumed that the researcher would already have done a protein assay before loading the sample, but I can make that explicit.

I meant using total protein instead of housekeeping genes. (In my humble opinion the "housekeeping" gene concept is fundamentally flawed; typically such genes are in the end verified against total protein anyway, so why not use total protein in the first place.)

Beta-actin control provides assurance that effect you see in protein expression is not due to overall protein synthesis change.
For example, if you study some illness, it might cause change in metabolism, weight loss, loss of ability to synthesize different proteins or absorb amino acids from diet. You have to control for that, and something as universal as actin is one option.


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Question about cutting gene in Plasmid
I am designing a researching proposal for the class. Because it uses microinjection to up-regulate the gene in C. elegans, the plasmid pCFJ104 - Pmyo-3::mCherry::unc-54 sequences has been chosen. But because the plasmid already has a unc-54, I wonder if there a way that to cut the unc-54 out of the plasmid?

Can you give more information on what the unc-54 gene does? Try and be a bit more clear maybe even a picture or link of the plasmid with the unc-54 location, thanks.

unc-54 encodes the major bodywall muscle myosin. In these plasmids the only portion from unc-54 is usually the 3'-UTR and the polyA addition site (AATAAA). myo-3 is either another BWM myosin, or a pharyngeal-specific myosin. This is providing the tissue-specific promoter. The expression plasmid drives expression of the mCherry fluorescent reporter in muscle cells.

pCFJ104 - Pmyo-3::mCherry::unc-54  is the plasmid I choose, here is the link: https://www.addgene.org/19328/; because the experiment need to up regulate a gene that is also in the muscle, so before doing the microinjection, the unc-54 need to be cut out before insert the gene I use. So I am wondering how to cut the gene out. Thanks!

Following the link you provided confirms that the C. elegans expression vector will express your insert of choice in the transgenic animals' pharyngeal muscle cells (driven by the myo-3 promoter).
From examining the two images of the plasmid's restriction map on the page you linked to, I infer that a SacI x XbaI double digest should excise the mCherry insert, and be suitable for sub-cloning your fragment of choice.
However you will need to confirm this for yourself. In general, I think it extremely unlikely that you would find an individual on Biology SE who could provide such precise information as "what enzyme sites should I use for my sub cloning experiment."
A general approach would be to

Research to find out if you can obtain a fasta file containing the complete DNA sequence of the starting plasmid.
Search GenBank to see if there is a record containing annotations for the starting plasmid sequence--that will tell you the start points and end points of each functional region.
If the plasmid is not in a sequence database try using the sequence in a BLAST search of a Non-redundant sequence database. In this example you would have retrieved high scoring hits on the unc-54 gene, the myo-3 gene, the mCherry gene, the beta-lactamase gene from pMB9/pBR322/pUC, and the E. coli lacZ gene (among others).
You should also consult the original publication (if there is one) because it may contain additional useful information, including how to contact the authors--who may have sequence files, useful maps, etc.
With the sequence in hand you will be able to create your own restriction map using a suitable software program (there are many commercial ones), e.g. the EMBOSS suite of open source bioinformatics software.

In your case most of this work was done for you because the AddGene site had two annotated restriction maps that showed almost all of the information you needed.  N.B. One map had the locations of the useful restriction enzyme sites, and the other map had the annotations showing the extent and locations of the worm fragments and the reporter gene. It was only by integrating the information from both maps that I was able to suggest one possible solution to your query.


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What causes the bright flash of light when poking my eye?
Recently, I poked myself in between my eye and eye socket, right below my eyebrow, and sometimes I would get this flash of light. Others have tried this too, and they also had a flash of light. I am wondering why is this the case. Does it have to do with the nerves in the eye?

Yes. You somehow stimulated your optic nerve.

Im probly stating the obvious here but i reckon you should probly go to the doctor for this one:)

@MattDMo so really, I am really asking which optic nerve I stimulated?

I would like to point out to you that that is exactly what Isaac Newton did and set off his interest in light. I hope you become like him! ;) (you might find this interesting: http://www.psmag.com/health-and-behavior/newtons-needle-scientific-self-experimentation-86583 or even watch http://www.ensemblestudiotheatre.org/isaacs-eye-lucas-hnath)

@TanMath - there's only one "optic nerve" per eye. That's the name for the bundle of nerves, made up of (?hundreds of thousands?) of nerve cells receiving signals from various nerve endings in the eye.

Short answer
Pressure phosphenes are believed to be induced by stretch-induced activation of retinal ganglion cells.
Background
Flashes of light (phosphenes) due to pressure on the eye ball are referred to as pressure phosphenes. Based on an electrophysiological study (Grüsser et al., 1989), eyeball indentation presumably tangentially stretches the retina locally, which variably depolarizes horizontal cells. This in turn depolarizes ON-bipolar ganglion cells, while hyperpolarizing OFF-bipolars. Some ON-center neurons also seem to respond to the removal of the deformation. Bipolar cells connect to the retinal ganglion cells. These ganglion cells carry visual information from the retina via their axons in the optic nerve to the brain. Hence, to answer your question: yes, pressure phosphenes are related to activity in the optic nerve.
Reference
- Grüsser et al., Vis Res (1989); 29(2): 181–94


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Differences between synaptic connections
Consider the following synaptic connections (from here):

axodendritic - A term pertaining to an excitatory or inhibitory synaptic connection between the presynaptic axon of a transmitting neuron and the postsynaptic dendrite(s) of a receiving neuron in a nerve impulse pathway; such connections can influence whether or not a graded potential will be generated on a postsynaptic dendrite.
axosomatic - A term pertaining to an excitatory or inhibitory synaptic connection between the presynaptic axon of a transmitting neuron and the postsynaptic cell body/soma of a receiving neuron in a nerve impulse pathway; such connections can influence whether or not an action potential will be generated in the postsynaptic axon trigger zone at the axon hillock.
axoaxonic - A term pertaining to an excitatory or inhibitory synaptic connection between the presynaptic axon of a transmitting neuron and the postsynaptic axon hillock or axon of a receiving neuron in a nerve impulse pathway; such connections can influence whether or not an action potential will be generated in the postsynaptic axon trigger zone at the axon hillock.

What exactly are the differences between the connections in terms of their influence on the neuron?
To my understanding:

axodendritic: influences a dendrite $\rightarrow$ hence influences the graded potential of the neuron
axosomatic: influences the graded potential of the neuron directly
axoaxonic: influences the axon only (independently of the neuron?)

Hence, to my understanding the axodendritic and axosomatic connections yield the same result: they influence the graded potential of the neuron (e.g. whether the neuron "fires"), where the axoaxonic connection only influences whether the axon fires. Is this correct?
If so, then what is the purpose of dendrites? If axons can connect to the cell body directly, then why would they need dendrites (apart from yielding a larger connection surface to the neuron)?
Note: I have read this answer, which partially explains the use of dendrites. However, it also states that the signal decay due to the synaptic location is compensated for by the local potential change. Therefore, IMO, the answer states that the main advantage of having dendrites is that inhibitory axosomatic synapses can capitalize on the location-dependence of the axodendritic synapses. Is that the true and only purpose of axosomatic synapses? (Please, correct me if my inference is wrong!)

I wrote that linked answer. I did not mean to imply that synaptic location is always compensated by local potential change.

@yamad Thank you for clarifying. Do you happen to know the differences (in functionality) between axosomatic and axodendritic synaptic connections?

Neurons are all about specialized structures having specialized roles. You've given a good justification for dendrites---an efficient way to fit lots of connections in a small space. A pyramidal neuron in cortex, for instance, will have tens of thousands of synapses. If you only had axosomatic connections, the soma would have to be enormous to fit all of them (and this would cause lots of other issues).
Dendritic structure also allows the cell more efficient electrical properties (see cable theory) and to process inputs independently. In fact, different parts of the dendrite are now thought of as independent computational compartments. For instance, the cell might want to selectively strengthen a single synapse or all the synapses on one dendritic branch. By physically isolating those synapses in small dendritic structures, it is easier to make those targeted changes without unwanted "crosstalk" on other synapses or cell activities. What's more, incoming connections from different areas often segregate into regions of the dendrite (e.g. in CA1 hippocampal pyramidal neurons, cortical connections to the most distant part of the dendrite, internal hippocampal connections to the part of the dendrite closer to the soma).
When a cell has a large dendrite (some neurons have no dendrites), its useful to think of axodendritic synapses as the normal inputs that contribute to fine-grained computation, and axosomatic and axoaxonic synapses as more global gates. These latter types take advantage of their location to short circuit the "normal" computation in the dendrites. An inhibitory axosomatic synapse, for example, will reduce the effect of all dendritic inputs when activated.

Extremely informative. Thank you. If I may, I would like to know your opinion about the theory that the "firing" of neurons is somehow connected to the specific combination of excitatory dendrites. E.g. if we neglect differences in potential change and assume 3 dendrites to excitate with the same potential effect on the membrane potential, do you think that different combinations of these 3 dendrites have a different effect on whether the neuron fires? Or are the potential changes from the three dendrites always simply summed up? So, given equal potential change, does location matter?

@Jean-Paul Yes, location matters. In general, the spatial and temporal pattern of synaptic activation matters a lot. Two synapses activated at the same time on different dendritic branches will have a different effect from two synapses on the same branch. Two synapses on the same branch will have a different effect depending on the order of activation. Good rule of thumb for thinking about neural computation: if something can vary, it probably matters (and if it doesn't matter, there is probably a very interesting story about how the neuron ignores the variation).

Thank you very much for your time and effort! This is very helpful. I'm just curious now: does location matter in terms of signal strength or does it matter for the pattern in which the neuron fires?


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Distribution of synaptic connections
What is the roughly the distribution of the various synaptic connections in the brain.
Consider the following types:

axoaxonic synapse between the axon of one neuron and the axon of another neuron.
axodendritic synapse between the axon of one neuron and the dendrites of another.
axodendrosomatic synapse between a neuron's axon and the dendrites and body of another.
axosomatic synapse between the axon of one neuron and the body of another.
dendrodendritic synapse from a dendrite of one cell to a dendrite of another.

I know that the axodendritic synapse is the most prevalent, but what is order of the others? Are there any sources for this (couldn't find this anywhere). Specifically, rough percentages of the distribution (amount) of these synaptic connections in the nervous system would be very helpful.

The adult human brain contains ~86 billion neurons with trillions of synapses estimated at 0.15 quadrillion. I am unsure if this question can be answered.

@AliceD I understand that there are many synapses, but don't we know anything about which synaptic connections are more common than others?

I expect there may be studies that have addressed some of the various connections in particular brain structures, but to find data that provide an order of appearance of all of your mentioned connections in the whole brain, I am doubtful of. It's an intriguing question, though. It's quite of a textbook question and I doubt a literature search will be helpful.

@AliceD I understand, but I couldn't find the answer in three different textbooks. That's why I'm asking the question here. Maybe somebody knows a study about this?

It would be good to mention those textbooks - it may save people work. If I would give this question a try I would start looking in Kandel's Principles of Neural Science - did you check that? if not, I'm happy to look once I'm back in the lab. Might take me a few days.

I don't have time for a full answer, but here is a study on the hippocampal CA1 pyramidal neuron that makes an exhaustive catalog of all synapse types and locations: Megías, M., Z. Emri, T. F. Freund, and A. I. Gulyás. “Total Number and Distribution of Inhibitory and Excitatory Synapses on Hippocampal CA1 Pyramidal Cells.” Neuroscience 102, no. 3 (2001): 527–40.  I know such papers exist for a few other cell types. This paper might provide a lead for finding those too.

@yamad Perfect! I'll take a look at that one and see if I can find others.

Are you still interested in this kind of questions? Have a look at mine: https://biology.stackexchange.com/questions/53587/the-human-brain-in-numbers-i-neurons, https://biology.stackexchange.com/questions/63950/the-human-brain-in-numbers-ii-synaptic-connections


text:
Why does depolarisation by high intracellular K+ trigger calcium channels opening?
I have learnt that in pancreatic beta cells, glucose being metabolised in the cell causes a high ATP level, which triggers ATP-dependent potassium channels to close. This means that potassium can't leave the cell anymore, which depolarises the membrane and causes voltage-gated calcium channels to open and release calcium into the cell to trigger insulin release. I don't understand why this happens, because both potassium and calcium being positively charged. Wouldn't this depolarise the membrane even more? I thought this would be unfavourable.

Ca2+ is very often the trigger to release neurotransmitter or, in this case, hormones. Ca2+ entry in the cell is important to activate the fusion of secretory vesicles with the membrane in pancreatic beta cells as shown in Fig. 1 (Thurmond, 2000). The function of Ca2+ entry is not so much related to its depolarizing actions.

Fig. 1. Ca2+-mediated insulin secretion. Glucose-stimulates insulin secretion by increasing the ATP/ADP ratio, which inhibits the ATP-sensitive KATP-channels, leading to membrane depolarization and opening of voltage-dependent calcium channels (VDCC), with a resultant major increase in cytosolic calcium, which, in turn, triggers exocytosis. SNARE proteins play a critical role in insulin granule secretion. The linking of the plasma membrane proteins syntaxin and SNAP-25 to vesicle protein VAMP-2/synaptobrevin-2 cause the docking of the vesicle, bringing insulin granules in close contact with the plasma membrane and calcium channels, after opening of calcium channels, the readily releasable pool (RRP) insulin granules located nearby are exposed to high level of Ca2+, resulting in RRP granule exocytosis. Source: Ren et al. (2007)
Ca2+ entry in the cell is potentially toxic and closely regulated. For example, internal stores are actively involved in the release and re-uptake of Ca2+ (Pian-Smith et al., 1988). Although Ca2+ influx will depolarize the cell further, it will not contribute substantially to the membrane potential compared to the effects of K+ and Na+.
References
- Pian-Smith et al., Endocrinology (1988); 123(4):1984-91
- Ren et al.,  J Transl Med (2007)
- Thurmond, Landes Bioscience (2000)

First of all, this is a complex question with no easy answer. Ion channels and electrophysiology can be a very confusing topic. Part of the challenge to understanding these processes is that you need to be able to remember that ions (e.g. sodium, potassium and calcium) are not only trying to move towards chemical equilibrium, but also electrical equilibrium as well.

In the pancreatic beta-cell insulin secretion is tightly regulated. As you state in the question, glucose enters the beta-cell and is metabolized creating an INCREASE in the ATP content of the cell. This increased ATP binds to ATP-sensitive potassium channels and CLOSES them. Remember, these channels are typically OPEN and allow potassium to normally flow OUT of the cell (because that would be potassium flowing DOWN its concentration gradient... potassium concentration is higher inside the cell than outside the cell). Note: This is the opposite for calcium, which would flow INTO the cell and down its concentration gradient (calcium outside the cell is higher than calcium inside the cell).
At the same time the ATP-sensitive channels are acting, there are Na/K ATPase pumps at work to move sodium OUT of the cell and potassium INTO to the cell (against the concentration gradients of both those ions). When the ATP-sensitive potassium channels close, it causes a build up of potassium INSIDE the cell because you have made the cell less permeable to potassium (when potassium can't flow OUT of the cell through the CLOSED ATP-sensitive channels it makes the membrane less polarized - i.e. become less negative or more positive - however you want to think about it).
When the cell reaches a threshold potential (that is, when it becomes depolarized to a certain point), it will cause opening of a type of voltage sensitive calcium channels. At this point, calcium channels open and allow calcium to flow down its concentration gradient and INTO the beta-cells. This calcium entry is required for the release of insulin vesicles through a mechanism that is outside the scope of this question, but unrelated to the calcium channels opening and closing.

The interesting thing about the calcium channels is that they INACTIVATE after a short amount of time and CLOSE on their own. Inactivation and closure is an intrinsic property of that type of calcium channel, and the channels do not REACTIVATE until the cell returns to being polarized once again. This inactivation is what limits the amount of calcium flux INTO the cell, which as mentioned in the other answer can be toxic to the cell.
So, in brief... the ATP-sensitive potassium channels CLOSE, the cell depolarizes when it reaches the threshold potential for the voltage-sensitive calcium channels. Those calcium channels open, calcium flows into the cell and works with other machinery to cause insulin secretion. In the meantime, the calcium channels quickly inactivate and close. The basal ion pumps then return the membrane potential back to its resting state. This return to a polarized resting state allows the voltage-gated calcium channels to 'reset' or reactivate, and then the entire process can occur once again.
I have simplified the explanation and left out some extraneous details - for more information about the specific types of channels see the references.
References to Read More:
(1) Review discussing ATP-sensitive potassium channels and voltage gated calcium channels in insulin secretion.
(2) Comprehensive review from the Endocrine Journal on insulin secretion, which discusses specifically both fast and slow calcium channels, inactivation and insulin secretion.
(3) Review talking about voltage gated channels in insulin secretion from the journal Diabetes.
(4) Open access article with a heavily detailed figure of the beta cell. However, has the different types of calcium channels and other ion channels to help with the understanding of this complicated topic.

As far as I know K⁺ channels remain closed unless triggered. You are saying that ATP closes the channel which means it was already open. How? What is the trigger?

@WYSIWYG the potassium channels in the beta cell are inward rectifying potassium channels (KIR) that are typically open - they are sensitive to the ATP/ADP ratio within the cell... that is, when glucose (the stimulus for insulin secretion) enters the cell it is metabolized and generates more ATP... the channels "sense" this change in ATP and CLOSE in response to that.

There's a great explanation on wikipedia on these channels as well - stated more elegantly than I can... https://en.wikipedia.org/wiki/ATP-sensitive_potassium_channel

@WYSIWYG - the picture from AliceD actually shows the ATP/ADP ratio changing and then an arrow drawn to the K-channel indicating that it closes


text:
Brandywine Maple?
I'm collecting and classifying leaves for biology. Teacher took us on a 'walk' to help. She let us pick and told us one leaf was a Brandywine Maple and another later on, a different leaf, was a Red Maple. I'm googling around to classify, but everything says that a Brandywine maple IS a Red maple (different name).
What the?
Help please...

Perhaps you should talk to your teacher instead of asking strangers on the internets...

Wow. That was extremely helpful.
Not. What's the point of this site to students then? What if I want to finish this project this weekend before school starts again?
Not to be really harsh in tone. But I would appreciate an answer a lot more than that.

First, when your project is due is of no concern to us. If all of your research points to "Brandywine Maple" simply being another name for red maples, then perhaps you should speak to your teacher to find out why she was differentiating between the two. On the other hand, if the two leaves are clearly different, you should [edit] your post to include focused, well-lit, labeled images of each of them and a clearly-articulated question about them. "What the? Help please..." does not qualify, I'm afraid. You may want to take the [tour] and read the [help] to find out more about this site.

I'd also suggest reading our (rather brief, but to-the-point) homework policy. We are not a homework service, but with enough thought and work from you, we may be able to help point you towards an answer.

@MattDMo I disagree that this is a poorly researched homework question. The OP has clearly made attempts at answering the question (see the googling line), which is backed up by my own search.

@MarchHo I never said it was a poorly-researched homework problem, nor have I voted to close it as such. I was simply pointing out our homework policy.

It was kind of implied, whether you meant to imply such or not, in your comment. I don't see why you would point me to the homework policy otherwise (If you wanted me to tag it homework, which I neglected to do accidentally, you coulda just said so).
Also, I'm not telling you to be concerned about the due date (it's in fact not due tomorrow, it was just an example, that), but I was irked by the fact you left a basically useless comment.

According to the Missouri Botanical Garden and Washington State University, Acer rubrum var. Brandywine is a cultivar of the red maple, Acer rubrum.

'Brandywine' is the result of a 1982 cross (Acer rubrum 'October
  Glory' x Acer rubrum 'Autumn flame') conducted as part of a U. S.
  National Arboretum research project. It was subsequently introduced
  into commerce in 1995.

[...]

As a cross of the red maple cultivars ‘October Glory’ and ‘Autumn
  Flame’, the variant ‘Brandywine’ was released for its resistance to
  leaf hoppers. It turns a burgundy color later in the fall than the
  popular October Glory.
As with other red maple cultivars this one does well on many different
  types of sites. As such, red maple is well adapted to sites to that
  are wet.

Therefore, you are correct to say that a Brandywine maple is a red maple. However, it is not the alternative name for a red maple. All Brandywine maples are red maples, but not all red maples are Brandywine maples.


text:
Is a variable domain in immunoglobulin's heavy chain different from the one in light chain?
I guess yes, there is difference in amino acid sequences of $V_L$ and $V_H$. And so we have 6 different complementarity determining regions (CDRs) per monomeric immunoglobulin as two heavy chains are identical, and two light chains are the same. Is that correct?

I think if you read up on V (D) J recombination, that will help. Try this http://www.ncbi.nlm.nih.gov/books/NBK27140/ .

You are correct. In an IgG antibody, there are a total of four protein chains — two identical heavy chains, and two identical light chains, each heavy pairing with a light to form one of the two "arms" of the molecule. Each heavy chain has three CDR regions — H1, H2, and H3 — as do each light chain (L1, L2, and L3). When the full molecule is assembled, three "full" CDRs are formed — 1, 2, and 3 — from the "partial" CDRs in the respective heavy and light chains.

from novimmune
You can see on the left the six individual heavy and light CDR loops separately, and on the right they are combined into the full CDR1, CDR2, and CDR3.
Here is a slightly more molecular view:

Thank you very much for the explanation :). The fact I missed many times in immunology textbooks is clear for me now !


text:
How does Darwinian Evolution work?
Let me explain... A friend and I read some articles, part of a Biology book, and watched a video on evolution. We then tried to explain what Evolution is to each other.
My friend said that Natural Selection is a mechanism inside the organism that mutates the DNA to make its offspring survive in an environment; that natural selection mutates the DNA beneficially and that random mutations are not useful (like blue eyes). But I disagree and think that it is closer to Lamarkian theory.
I told him that DNA from male and female recombines and randomly mutates making a new "recipe" for the offspring (adding a new characteristic(s)). If the offspring is well suited for the environment, then it survives and passes on its characteristics to its offspring. If it does not have fitness for its environment, it dies. So, Natural Selection is were nature "selects" who survives and reproduces a lot.
So is the DNA mutation process random or is mutation directed to make an organism that is suited to survive its environment?
None of my friends are Biology students, so I can't ask then which explanation is correct (or at least more valid).
I'd prefer you don't answer: "None of these explanations are correct," but to say which one is more valid and correct misconceptions or add more that is missing (of course these are only summaries of our discussion). But of course, you can answer that neither of our explanations is correct...

Mutations and evolution are both complete random processes which are undirected.

Well evolution as i understand is not random because of natural selection but mutation is.But even if evolution is not random i think is undirected too .What do you think ?

@Chris It's not really accurate to call evolution 'random' (depending in part on how you define 'random'), but either way, the randomness in mutation and evolution are very different. Mutation is (mostly) a random process while evolution can be driven by different processes (natural selection, sexual selection, genetic drift etc). Evolution by natural selection is certainly stochastic but natural selection is also injecting alot of information into that process, and it cannot be seen as "undirected" (rather the opposite).

@chris mutation is (mostly) random but evolution is NOT random, Natural selection is a non-randomizing process. evolution is the coupling of a random and non-random process.

I accidentally wrote a lot!
I first discuss the term Darwinian evolution. I then describe the main evolutionary processes insisting on the two elements of interest in your question, that is mutations and natural selection. In the end, I directly address your two statements and bring a few more complications into the subjects.
Did you say Darwinian evolution?
Evolution is more than Darwinian evolution
The expression "Darwinian evolution" easily yield to misunderstandings. Darwin was probably the most important scientist and one of the first (if not the first) to develop the theory of evolution but evolutionary biology today is so much more than Darwin's theory of evolution.
Examples of very basic things Darwin did not know

We discovered the structure of DNA in the 1950s-1960s only with Miesher, Chargaff and most renowned Watson and Crick (history of the discovery). Darwin had no idea of the existence of DNA and had not even hypothesized about the existence of such a molecule (which came first by Erwin Schrödinger).
Darwin was not aware either that inheritance was through the transmission of "particles/atomic" and not through the inheritance of some kind of "fluid/continuum". In other words, Darwin did not know the Law of Segregation by Gregor Mendel (even if they lived in the same epoch).
Darwin had no idea about Evo-Devo, that is he had no idea about the similitudes in developmental processes among related (even distantly related) organisms.
Globally speaking, while Darwin managed to touch a little bit about many of the subjects of modern evolutionary biology (which is very impressive), he only manages to mention them and failed to provide any prediction. This is a large part because no one had no concept in genetics at that time.

Evolution is more than natural selection and mutations
Evolution is not only about natural selection. Even C. Darwin knew that evolution is way more than natural selection. It is for example very important to consider random events. One of them is mutation, another is genetic drift (I am not trying to list every process that influence evolution but only to give you a sense of why natural selection is different than evolution with a goal of explaining why a trait that is needed do not necessarily appear). Both mutations and genetic drift explain why a species will not necessarily be perfectly adapted to its environment. Evolutionary biology is a big field of knowledge and there is a lot to know about evolutionary processes.
Natural Selection and Mutations explained by the Lewontin Recipe
The Lewontin's recipe is a good way in order to understand what is natural selection and when it occurs. The Lewontin's recipe says that natural selection occurs whenever:

Individuals in a population vary in terms of a given trait
This trait has some (additive) heritability. Here is one of the several posts that explain the concept of heritability. It might be slightly a post that is a bit advanced for you though but shortly speaking it means that offspring are more similar to their parents more than they are to other non-kin individuals in the population.
The fitness varies (not necessarily linearly) as the trait varies.

Simple example:

In a population, there are blue pens and red pens
Reproduction is asexual and blue pens create other blue pens while red pens create other red pens.
blue pens make more offspring than red pens.

In such a situation, natural selection occurs yielding the frequency of the blue pens to increase in the population while the frequency of red pens will decrease.
Natural Selection
Natural Selection is the process by which variants of genes called alleles are selected and therefore increase in frequency. This selection result from a differential reproductive success.
Mutations
In the broad sense mutation is any change in the DNA sequence. Some changes are more likely to happen than other but in any case, the likeliness of these changes to happen is not dependent on the consequence they will have on the phenotype (shortly speaking, a phenotype is how an individual looks like) and on the reproductive success. So mutations occur randomly and the specific mutation that would be needed in the population may not occur. Therefore saying, if a trait is needed (in the sense of "if a trait would be beneficial"), then a mutation will occur to make this trait existing is wrong. Note that most mutations are deleterious (decrease the reproductive success) while few of them are beneficial (increase the reproductive success) and those that are beneficial are more likely to rise in frequency in the population.
Genetic drift
If the change in frequency of mutations would depend exclusively on natural selection, then I would not have said before that a beneficial mutation is more likely to raise in frequency but I would have said that a beneficial mutation will raise in frequency deterministically. An intuitive explanation of what is genetic drift can be found on this post. It will also allow you to understand why small population undergo a more random change in frequency of their genes than are big population.

Considering your opposing statements
Hopefully, the following is clear from the above discussion but I would like to directly address your statements.

My friend said that Natural Selection is a mechanism inside the organism that mutates the DNA to make its offspring survive in an environment; that natural selection mutates the DNA beneficially and that random mutations are not useful (like blue eyes). But I disagree and think that it is closer to Lamarkian theory.

You are right that your friend is wrong!
It indeed sounds more or less Lamarkian. In any case, it is very wrong, as you said. Mutations are not caused deterministically under the pressure of natural selection to do specific things.
Are mutations completely random?
See Are mutations random?.
I do not want to go into too many complications. The sentence "mutations are random" is unclear. Does it mean that the mutation rate is random? Does it mean that the effect of a new mutation is random? And also the concept of randomness only make sense if we consider a set of a priori knowledge. So it is a little hard to fully answer this question and the easy, close-enough approximation for a starter in evolutionary biology is just to say that mutations are random (whatever that means). A slightly better approximation of reality is that mutation rate is an adaptive trait and can vary depending on the environment where the individual is found (adaptively or not). However, the effect of new mutations is really not deterministic.
The mutation rate varies with the type of sequence considered. For example, a microsatellite sequence is a sequence or repeated DNA. For example AATAATAATAATAATAATAAT etc.. (note that the genetic code is written with 4 letters, A, T, C and G). Such sequences are highly mutable. So a mutation is more likely to occur in this region than in the middle of a coding region. And it is more likely for a mutation occurring in a coding region to affect fitness than for a mutation occurring in a microsatellite (it is possible that a mutation occurring in a microsatellite will affect fitness).
Depending on the level of stress some organisms (plants mostly to my knowledge) can change their mutation rate. Consider for example an individual that is maladapted to its environment. If it mutates little, then the offspring will likely be as maladapted and in the long run, the lineage will disappear. If the individual is mutating a lot then, most offspring will have a very low fitness but eventually one will receive a beneficial mutation that will make it very strong and by itself, this offspring may save the lineage. This is what is called a bet-hedging strategy. The concept of bet-hedging can be summarized with the expression "Don't put all your eggs in the same basket".
You will note that the mutation rate is an evolving feature of an organism. This yield observation such as what is now called Drake's rule (original paper). Drake's rule indicates that the genome-wide mutation rate is always at the order of 1 (there is quite a bit of variation but it is a good approximation).

I told him that DNA from male and female recombines and randomly mutates making a new "recipe" for the offspring (adding a new characteristic(s)). If the offspring is well suited for the environment, then it survives and passes on its characteristics to its offspring. If it does not have fitness for its environment, it dies. So, Natural Selection is were nature "selects" who survives and reproduces a lot.

Sounds quite right!
You pretty much nailed it. Mutation adds genetic variation and natural selection selects from the available genetic variation. Your wording is a little uncommon though :). For example, an individual, it is incorrect to say that an individual has fitness or not. Each individual has a fitness, that is some value that encompasses both its fertility and survival probability. In a simple model, fitness is simply the expected number of offspring.
Note also, that the majority of mutations that affect the fitness of the individuals are not so much dependent on the details of the environment. Many mutations are just bad wherever you are. Think about a mutation that would reduce the efficiency of energy production (ATP in mitochondria). Such a mutation will be deleterious regardless of whether the weather is hot or cold for example.

Introductory course to evolutionary biology
You probably want to have a look at an introductory course to evolutionary biology such as Understanding Evolution.

Wow :) 'Accidentally' :P

"the likeliness of these changes to happen is not dependent on the consequence they will have on the phenotype (shortly speaking, phenotype is how an individual looks like) and on the reproductive success."
The following paper seems to have shown that this claim is false.
Non-Random Directed Mutations Confirmed
http://www.i-sis.org.uk/Nonrandom_directed_mutations_confirmed.php

@MakotoKato I am not going to be able to address all the unclear questions and bad claims that you are making in comments of my various answers on this website. As I already said, if you have a (well defined and concise) question, just open a new post and ask it.

Your link is not a scientific paper and is not showing any evidence. Also, the author (Mae-Wan_Ho is criticized as doing pseudo-science and not science). You should read it before claiming what they did. However, from the text you link, Ho cite a paper (Cairns et al. 1988) that seems (from reading the abstract) that cells may have mechanism for choosing which mutations will occur (which contradict what I said indeed).

You might want to ask a question specific to Cairns et al. 1988. But before you do so, I recommend 1) following an introductory course to evolutionary biology so that you are are to ask a clear question, 2) reading this article who seem to be a direct response to the previous paper and 3) consider the generality and potential importance of the mechanism described by Cairns et al. 1988 (I haven't read the paper).

@Remi.b "As I already said, if you have a (well defined and concise) question, just open a new post and ask it."
Unfortunately I cannot do so because all the previous questions of mine were closed as being too broad while they were specific enough. It seems that questioning the tenet of the theory of evolution is kind of taboo in this site, which I think is a pretty unscientific attitude.

No, it is not taboo! If you have further questions about why your questions have been closed, ask them on meta.biology.SE.

Please just accept learning about evolutionary biology a little bit and you will be able to ask better question. I promise that I am doing my best to help (i.e. right above I have suggested a question and have described steps on how to best ask this question). I will not react to any further comments below, we already wrote too many useless comments here.

@Remi.b "No, it is not taboo!"
I asked for some evidences(e.g. papers) for the following claim of yours in my comment in another thread, but not only did you refuse to answer it, but it was deleted by a moderator.
"the likeliness of these changes to happen is not dependent on the consequence they will have on the phenotype (shortly speaking, phenotype is how an individual looks like) and on the reproductive success."

@Remi.b "Your link is not a scientific paper and is not showing any evidence."
How about this?
Predictable Evolution Trumps Randomness of Mutations
http://www.scientificamerican.com/article/predictable-evolution-trumps-randomness-of-mutations/
The following brand new paper(published on August 25, 2015) has confirmed the directed(or adaptive) mutation.
Evidence for Retromutagenesis as a Mechanism for Adaptive Mutation in Escherichia coli
http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1005477

That looks like an eventually interesting paper (the second link). I never heard of such process. I would love to hear more on this subject. I'll include your paper in my answer and might modify the answer later once I read the paper. Thank you.

@Remi.b. Don't. I read the paper. It is bad science, whether or not it was published on Plos. In their methods, they mention that their strain is AmpR, but they then make no mention of using antibiotics. That is a recipe for contamination. They also do not check to see whether or not any of their strains were LacZ diploids with an F Plasmid. Their controls are bad, their analysis is bad, and their conclusions are based on incorrect assumptions. No one ever said that you cannot have revertants within a species, gene conversion is well documented, but they aren't reverting to an ancestor.

The article was published more than 3 months ago, and does not have a single citation in a peer-reviewed paper.

@Remi.b I wasn't telling you to not read it, just that I didn't think that you should edit. The paper is troubling me, because it could be one of those papers that could be pure crap or could actually have something profound to say, but would require several read throughs and needs to be debated many times. I still am heavily leaning towards it being pure crap, but... I still maintain, however that MK is vandalizing posts, even if the paper has something interesting to say.

Your description of Evolution seems more accurate than your friends. DNA cannot mutate with a particular goal in mind, mutations are random. Most mutations have no effect on an organism's survival, but some will be detrimental, and a few will helpful. Helpful mutations will improve an organisms odds of surviving and passing on its DNA, so those traits will eventually spread through a population.
However, if we wanted to talk about "goals" for evolution, then the goal of every piece of DNA is to be copied and passed on. (of course it cannot think about achieving that goal, it's just a chemical.) DNA mutations that make an organism more suited for a particular environment will be selected for, and those that are detrimental will be selected against. This competition between different copies of DNA eventually optimizes the species for that environment.
So at the molecular level, mutation is a totally random process, but if we zoom out to the ecosystem and population levels, then evolution "designs" a species to better survive in its environment. But this design is a result of random mutations and trial and error.

Mutation is a random process that mainly happens when a cell's DNA is replicated (= copied) before the cell's division, because the enzyme responsible for this replication sometimes makes mistakes. It's a rare process, as for eukaryotic cells (the ones with a nucleus, so animals and plant cells), it happens once every $10^9$ nucleotide.
Now, let's say we consider an organism that has sexual reproduction.
To be transmitted to the descendants of the organism, the mutation must appear in a cell of the germline (spermatozoid or ovule for example).
If transmitted, this mutation can have several effects :

It can be lethal, the organism cannot survive because the mutation makes a vital protein inoperative
It can give the organism a disadvantage in his environment (e.g. living in a snowy environment, the pigmentation of the organism's skin becomes glowing red)
It can be neutral, something is modified, but it keeps working (e.g. a certain protein has a different amino acid sequence but keeps working)
It can give the organism an evolutive advantage, the protein works better, in a way that favorises the organism vs. its fellows' organisms in surviving in their environment (e.g. in the snowy environment, the pigmentation of the organism's skin becomes perfectly white, whereas one of its fellows is greyish)

In the fourth case, this organism has more chances to reproduce (because he is less likely to be killed, or more likely to access a resource), and hence, to transmit this mutation. This is where natural selection applies: the "fitness" of the organism in his environment is greater than the one of the other organisms of his species.
Now, it's important to note that the evolution (= the change in a specie) is driven by the natural selection (= the process of selection), and that those changes, in nature, are random and take a long time and aren't easily noticeable at the scale of a human life.

Great answers have been given already. But one phenomenon that is mostly not explicitly mentioned that can and should be regarded a part of the process of Evolution is symbiosis.
symbiosis
The probably most fundamental example for symbiosis is endosymbiotic theory. This theory in strongly simplified terms says that eukaryotic cells are the result of a symbiotic relationship between prokaryotes and early bacteria: both evolved separately with the prokaryotes probably being predators of some bacterial species. These species then are proposed to have evolved towards mutually beneficial, symbiotic relationship which essentially created a new form of life, eukaryotes.
From a more abstract point of view, symbiosis can be regarded a further mechanism of evolution: while mutation and recombination act on a molecular level, symbiosis acts on a similar level to selection. It is basically a macro-level recombination of not just genes, but whole or partial organisms into new life forms.
Some random examples:

eukaryotes: mitochondria from proteobacteria, chloroplasts from cyanobacteria.
bioluminescence in "fireflies" by vibrio bacteria
microbiome inside "guts" of more complex organisms
mycorrhizae (phosphor fixing) at the roots of some plants

Short Answer: As far as we know, it doesn't.
Mutations at Conception
The mutations you describe as occurring during conception which generate new information have never been observed to take place. Instead, we have observed mutations which reduce existing information. In humans, approximately 100 such mutations take place every generation.
Necessarily if information-additive mutations existed, they'd need to produce a lot more information to make up for the loss. Necessarily, descendants would have a larger and more complex genome than their ancestors. The opposite has been observed, where descendants have smaller genomes than their ancestors.
Abiogenesis
Before Darwin had written On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life, Pasteur was disproving the idea of abiogenesis, as the theory had gone around that germs could spontaneously appear. Despite this, Darwin took abiogenesis as part of the theory of evolution, which has consistently proved impossible in tests with no observable data to the contrary.
Genetic information is fragile and is quickly destroyed over time if it doesn't have enzymes to continually maintain it. There is no gradual process of accumulated information that can result in life able to reproduce, as far as we have found from study and observation. The very difficult process of creating amino acids to bond and form the nucleotides (necessary to form DNA chains) is complicated by the chirality problem, where artificial tests have resulted in both left-handed (L) and right-handed (D) optical isomers were created in a racemic mixture. In biological systems, almost all of the compounds are non-racemic, or homochiral, and biological creatures only use left-handed amino acids in the construction of DNA and RNA. All subsequent have tests run into the same problem.
Theory
As for the theory itself, you and Remi.b have described it accurately. As genetics was an unknown field at that time, it was the mistaken idea that natural selection changed a creature through the creation of information, rather than the reformation, sharing, and loss of existing information.
Sources: Genetic Entropy and the Mystery of the Genome by John Sanford. The Miller–Urey experiment.

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


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How do neurons inverse an action potential?
See the following figure (source):

The pathway on the right (SN $\rightarrow$ interneuron $\rightarrow$ F Neuron $ \rightarrow $ flexor muscle), is explained as follows:

The action potential in the sensory neuron invades the synaptic terminal of the sensory neuron causing the release of transmitter, and subsequent excitation of the postsynaptic interneuron colored black.  This neuron is called an interneuron because it is interposed between one neuron (here the SN) and another neuron (here the MN).  The excitation of the interneuron leads to the initiation of an action potential and the subsequent release of transmitter from the presynaptic terminal of the interneuron (black triangle), but for this branch of the circuit, the transmitter leads to an IPSP in the postsynaptic flexor (F) motor neuron (colored red).  The functional consequences of this feedforward inhibition it is to decrease the probability of the flexor motor neuron becoming active and producing an inappropriate flexion of the leg.

Specifically, it states that but for this branch of the circuit, the transmitter leads to an IPSP in the postsynaptic flexor (F) motor neuron. But it doesn't give an explanation of how this works.
How can a neuron generate an inhibitory postsynaptic potential when it is given an action potential? Can this specific neuron inverse the signal? How does that work?

The University of Texas site where you obtained this picture states in section 6.7:

What about the transmitter substance that is released by the inhibitory interneuron in the spinal cord? The transmitter substance is glycine, an amino acid which is used frequently in the central nervous system as a transmitter that produces inhibitory actions. It is not the most common, however. The most common transmitter with inhibitory actions is gamma amino butyric acid (GABA).

Glycine receptors activate a chloride-selective transmembrane channel, which is predominantly expressed in the spinal cord and brain stem (Rajendra et al, 1997). Chloride hyperpolarizes the neuron, thereby inhibiting the motorneuron controlling the flexor muscle, and thereby facilitating the extensor muscle to contract. If the opposing flexor muscle would not be inhibited, the extensor muscle would be counteracted and the knee jerk reflex would be less efficient, if present at all.
Typically, an inhibitory interneuron will only release inhibitory neurotransmitter. In the example here, the opposite circuit to bend the knee would activate the flexor muscle. This would be accompanied by opposite events. However, the inhibitory F neuron above in your figure would not reverse its action though, it will simply be silent, thereby allowing the acetylcholine from the E neuron do its job. In more general terms, neurons cannot reverse their action from inhibitory to excitatory. Their outputs are typically simply the release of a pre-defined vesicle pool, which is a yes/no event without further qualities. In other words, an inhibitory neuron will be inhibitory and it cannot change the nature of the neurotransmitters released (excitatory versus inhibitory) based on different inputs.
Reference
- Rajendra et al, Pharmacology & Therapeutics (1997), 73(2): 121–46

Thank you! That explains a lot. Just one more thing so I fully grasp the concept: some neurons will only release inhibitory neurotransmitters when receiving an action potential. These neurons cannot release excitatory neurotransmitters. Am I correct?

@Jean-Paul Yes, a neuron will release the same set of transmitters at all of its synapses--often it will release just one neurotransmitter, but sometimes two or more at the same time. An inhibitory interneuron will not, for instance, release an inhibitory transmitter onto one cell and an excitatory transmitter onto a different cell. This is known as Dale's principle (https://en.wikipedia.org/wiki/Dale%27s_principle).

@yamad To be very precise, the effect upon the postsynaptic neurone is determined by the type of receptor that is activated. With regard to the figure, is it true that the sensory neurons in the knee transmit neurotransmitters that generate an excitatory effect in combination with the receptors of the motor neuron that flexes the extensor muscle, and an excitatory effect within the inhibitory interneuron too? Then, does the inhibitory interneuron release neurotransmitters that in combination with the receptors of the motor neuron that flexes the flexor muscle yield an inhibitory effect?

@Jean-Paul Close, but with one major misunderstanding. In this reflex, the flexor muscle is not flexed (contracted). It is being relaxed by the reflex. How does this work? In the diagram, activating the E neuron contracts the extensor muscle, activating the F neuron contracts the flexor muscle. No activity in these neurons means the corresponding muscle is relaxed.  By inhibiting activity in the F neuron, the interneuron indirectly causes the flexor to relax. All the connections in the diagram are excitatory, except for the interneuron to F neuron connection which is inhibitory.

@yamad That is exactly what I meant: I referred to the motor neurons as "flexing the ... muscle" to indicate which motor neuron I was referring to (I should have used their names, E and F, to avoid confusion). But your comment nevertheless completely answered my final question. I fully understand the concept now. Thank you :)


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Conjugated deoxyribonucleotides
I'm currently learning about using PCR techniques to make fluorescently labelled DNA probes, and the textbook mentions "conjugated deoxyribonucleotides"
Can someone explain what these are? Nothing too in-depth and detailed. Just a decent description/explanation so I can get somewhat of an understanding.

To "conjugate" means to join or couple something together. Deoxyribonucleotides are the "letters" of DNA - A, T, C, and G. In biology/biochemistry, when you conjugate something you chemically modify it by adding something to it. Given the context of your question, the conjugated deoxyribonucleotides are fluorescently-labeled — a fluorescent dye has been covalently attached to it.


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Problem on Probabilty of a restriction enzyme cutting a random DNA sequence
I think its a silly question to ask here. When I came to this site all I could see were the questions which asked detailed explanation behind a phenomenon and reasoning was there at first place. I am bringing quite math here!!!
First, I am a beginner.
Second, I would like to mention some problems..

Genomic DNA is digested with AIU I, a resrtiction enzyme which is a four base pair cutter. What is the frequency with which it will cut a DNA assuming a random distribution of bases in genome?
Eco RI and Rsa I restriction endonucleases require 6 bp and 4 bp sequences respectively for cleavage. In a
10 kb DNA fragment how many probable cleavage sites are present for these enzymes?

These questions were solved by my teacher using some probability results or rules.
I would like to mention it here.. [you know already...!!! ;-)]
(1/4)^n *10,000 or simply (1/4)^n. By putting n = number of base pair cut by enzyme.
I get the frequency with which enzyme will cut a DNA assuming a random distribution of bases in genome by using (1/4)^n and I get probable cleavage sites are present for Eco RI and Rsa I in 10 kb DNA fragment.
But why do I do that? I mean why that formula? How to understand how it was derived? Can you explain me that?
Please suggest some good books containing concepts and numerical problems like these so that I can work on it.. [Please let me know your source]. Thank you.

EcoRI recognizes, binds to, and cleaves the hexamer 5'-GAATTC-3'. In a completely randomized DNA sequence, with 25 % A's, 25 % C's, 25 % G's, and 25 % T's we would expect to randomly discover the sequence GAATTC, once every 4,096 base pairs, on average. The actual distribution of EcoRI fragments (a fragment where each end contains a cleaved EcoRI site) in our random genome will vary and yield a normal distribution, or curve, with some fragments longer and some shorter. The mean value should be 4,096.
The expectation of 1 site per 4,096 bp is indeed (1/4)^6.
1/4 = 25 %
6 = the number of contiguous base pairs in the recognition site.
In a model like this it is important to keep in mind that the probability of one base occurring in the sequence is completely independent of the sequences before that base, and the sequences after that base. In other words, for each and every position the probability of getting a base that will contribute to an EcoRI site is 25 %, or 1 out of 4 = 1/4.
75% of the time, the next base will not contribute to an EcoRI site (and a quarter of the time it will).
Let's start with your 10 kb fragment, and go through from one end to the other, and mark every time a 'G' occurs. Theoretically those could all be the beginning of EcoRI sites, right? There will be approximately 2500 such 'G's. Now to match our pattern, we need an 'A' in the second position, so let's mark all those sites that contain the dinucleotide 'GA', there will be about 2500 x 0.25 = 625 of them. The next match we need is position 3, another 'A', so in a similar fashion, let's go through the positions of all those GA dinucleotides, and just mark the ones that have an 'A' at the next position. So that will be about 625 x 0.25, or approximately 156 'GAA's distrubuted randomly along the 10 kb fragment.
If we continue, essentially filtering out more and more of those 'G' sites in our initial list then we will find, on average, that there are
39 sites with GAAT
10 sites with GAATT
2 sites with GAATTC
If you don't believe me just pick a sequence and try it yourself.
10,000/4,096 ~ 2.5


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Organ secretions
If an animal secrets an enzyme from an organ that is entirely dedicated for the same secretion, can one or cannot one just use the gene coding for that protein to obtain the protein in vitro. How much relevance does the organ have for production of a particular enzyme. For example, hippopotamus releases the blood sweat from glands in its fat skin. Can one use just the gene coding for the blood sweat and produce it in vitro, or the organ is necessary for it's production?

That is a complicated question that ends up with the answer of, it depends. Most Eukaryotic proteins require chaperone proteins to fold correctly. Many proteins also undergo post-translational modifications, especially those produced in the ER for secretion of presentation on the cell surface. That being said, pharmaceutical human insulin and growth factors are produced by bacteria. Also it is the cell that is relevant, the organ is just the conglomeration of cells of a certain differentiation type. Those cells will express their genes based on how they differentiated.

Also, blood sweat sounds like it results from two compounds, and are small acidic molecules. If you were to isolate the enzyme(s) that produced them and added them to their substrate, then they should catalyze the reaction to produce the molecules, assuming that there are not other cofactors necessary that you have not added to the reaction.

It's not a product of two compounds.....it is called blood sweat as it is red in colour and is released as sweat from the skin

"The secretion is sometimes referred to as "blood sweat", but is neither blood nor sweat. This secretion is initially colourless and turns red-orange within minutes, eventually becoming brown. Two distinct pigments have been identified in the secretions, one red (hipposudoric acid) and one orange (norhipposudoric acid). The two pigments are highly acidic compounds." https://en.wikipedia.org/wiki/Hippopotamus#Description


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Needle-like crystals observed in wild-grape wine under microscope. Potentially harmful?
I recently crushed and strained about thirty pounds of wild grapes to ferment into wine. About a month in, I did a visual inspection of the wine under microscope to try and identify some yeast and bacteria species. However I was more taken by the sight of many sharp, needle-shaped crystals in the wine (along with microbes). Pictures are below:

My best guess is that they are raphides (crystals of calcium oxalate/carbonate), a supposed defense mechanism of some plants. These seem to be complicit in causing acridity in certain plants, and indeed the grapes (and resultant wine) were extremely tart. I've not, however, heard of any wild grape species having known toxicity.
My question is, then: are any wild grape species known to produce such crystals and, if so, are they known to be harmful in any way? Is there another explanation?

They certainly do look like calcium oxalate crystals!

You just reproduced some of Louis Pasteur's work. https://en.wikipedia.org/wiki/Louis_Pasteur#Molecular_asymmetry

Try here. https://www.awri.com.au/industry_support/winemaking_resources/wine_instabilities/hazes_and_deposits/crystalline_deposits/#calciumoxalate

If they are really oxalate crystals, the harm depends on the concentration. Some ppl are on oxalate diet, because they would develop gallstones or kidney stones otherwise. It is not considered toxic, you can drink it.

you are correct that these grapes have raphides. After doing some research, I found out that the grape raphides are twinned crystals. Raphides can cause much irritation for many herbivores (therefore, it is a protection mechanism) but less so for humans. In grapes, however, the irritation is much less than other raphide-containing species. This probably has to do eith the fact that it has a twinned structure (this is what I think, but I haven't found any research on this).
As a side note, what you have done is known as a whole mount, in which is entire organism specimen is placed on the slide, usually after crushing. It is a geeat way to examine the contents of the cell vacuole, which is where this raphides are commonly found.
References:

http://www.ncbi.nlm.nih.gov/pubmed/10648203
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0091341

You should add some references. :-)

@inf3rno I have added references


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Relative densitometry from SDS PAGE
I'd like to perform densitometry on a Coomassie stained SDS PAGE gel to compare a recombinant protein's expression levels under two conditions. I'm using BioRad's Image Lab software.
My questions are about what estimates can be made, given that Coomassie staining can be nonlinear has protein-to-protein variability. Unfortunately, I do not have a standard curve, and the lanes contain total lysate.

Can I take the percentage of band volume to lane volume as an estimate of percentage of total cell protein mass? (25% vs 20% total cell protein)
Or would it more appropriate to take the band volume normalized to an arbitrary band in the lysate, and then report the percentage difference between conditions? (6 vs 4.8 normalized band volume, or 20% decrease in expression levels).

I don't think you can get away with either. You have no way of knowing that a specific band represents a single protein. Sounds like you should be doing a western blot.

@canadianer Even western blots have nontrivial levels of background staining (especially for polyclonal antibodies), so one will still need to run a standard curve.

@MarchHo that depends on the antibody...


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Does common PCR amplify genes regardless of what cells / barriers they are in?
I have some understanding of how PCR testing works. What I have always been wondering: how can we be sure that a primer reacts with the targeted gene(s) regardless of where¹ the genes are inside a sample?
¹: Specifically with "where" I mean what cells or other barriers they are inside. In other terms my question is: how can we be sure primers reach every possible target?
In more detail: when targeting a gene that is part of the host organism's own genome things might be quite clear, we can have strong assumptions of "where" the gene is. But when targeting genes that are part of organisms that have a parasitic relationship with the host, a very complex system of  interactions (mostly called "immune system") should govern the (co)existence of host and parasite. These complex interactions might lead to situations in which the parasitic organism is present in a very special, isolated manner / place in the host. To give one example: micro organisms in the cell walls of macrophages that are about to undergo lysis. Can we be sure that common PCR would detect genes of such micro organisms? Why?
EDIT: as pointed out in the comments the perhaps most correct phrasing is, how do the DNA isolation techniques employed guarantee that primers reach every possible target?

PCR isn't conducted inside living organisms. The DNA must be isolated first.

That is correct and was clear to me when posting the question. So my question based on your comment also could be phrased: how do DNA isolation techniques guarantee that all possible targets' DNA is isolated from a sample. I shall update my question with your more precise phrasing, thanks!

You will only detect the DNA that you put specific primers in for. You could use random primers, but then you will have a hard time quantifying what you are amplifying. If you are doing Transcriptome analysis in Eukaryotes then you can us a Poly-T primer and Reverse Transcriptase to take mRNA to cDNA. From there you would need to run some form of microarray to detect what it is that you are pulling down. So, no, unless you are putting primers in for specificity for the microorganism you have, you should not get amplification, unless you use random primers.

@canadianer That is false. Colony PCR can allow amplification of bacterial DNA even when the bacteria are added into the PCR mixture while still alive and viable, and the same applies to mammalian cell culture.

@MarchHo Nowhere in that description do I see PCR conducted inside living organisms.

@MarchHo canadianer is basically correct: the KIT you have linked uses denaturation of proteins at mostly 95°C as described in the instructions. Thus any organism whose DNA is isolated is dissolved. You are right the microorganisms and mammalian cells are alive when added, but they are decomposed during the process exactly the way canadianer explained.

While your understanding is correct, I still disagree with @canadianer 's phrasing. The DNA is released from the cells, but at no point in time was the DNA ever purified or isolated prior to the PCR reaction's completion.

There are many methods of DNA isolation, so it is difficult to make broad statements about all situations. Typically, though, during the DNA isolation protocol, essentially all proteins are denatured and removed, as is RNA, cell membrane components, extracellular matrix, etc. If you are using a high-quality well-validated kit from a reputable supplier, your final product should be just DNA. In your hypothetical scenario where parasites have been engulfed by macrophages (BTW, eukaryotes don't have cell walls), as long as the parasitic DNA hasn't been degraded, it will be present at some level after the purification process. As long as it is above the minimum sensitivity of the PCR reaction, any parasitic genes that are being targeted will be amplified.
During the PCR process, the heating step to 95°C completely denatures and melts all the DNA present, allowing the primers unrestricted access to their complementary sequences, where they can then base-pair during the annealing and extension step.

Thanks for answering! Can you explain in more detail how the DNA from a microorganism engulfed in the cell membrane of a macrophage will make it through the isolation process? Why does high-speed centrifugation not discard the macrophage entirely? Can denaturation (or another process) as employed in isolation techniques decompose a macrophage's lipid membrane and the engulfed microorganism's cell wall?

@BM there are different kits for different types of samples, so if you're processing samples that have cell walls, make sure you choose the correct reagents. The lysis process is quite harsh, denaturing pretty much everything. Look through some of the information at Qiagen, one of the most highly-regarded companies in this field. The centrifugation steps are after lysis (the other answer is rather confusing in this regard), so you're not losing any cells.

@BM Here is a selection guide for what type of kit to choose for purifying genomic DNA.

Thanks for the link and your comment. I see that the whole issue is more complex than I thought and boils down to what isolation KIT you use. I still want to know much more precisely how those work however, so I will accept your answer and open a new question with more details.

@BM thanks. If you search around on Qiagen's website, and go to the product pages for the various kits, you should be able to find documentation on how they work, and what the different buffers do.

I will and I might even ask Qiagen directly. For now, my follow up question if you are interested: http://biology.stackexchange.com/questions/40198/what-evidence-is-there-that-common-pcr-dna-purification-kits-can-isolate-dna-fro

The polymerase chain reaction is done on free DNA that has been released from the cell by a variety of chemical or physical methods.
There are no cells involved in PCR as the components you don't want are separated by high-speed centrifugation.
PCR also requires the cycling of heat as to aid in the unwinding of DNA for the binding of primers which also allows for the functionality of TAQ polymerase which is a high heat DNA polymerase isolated from the bacterium Thermus aquaticus.
So unless you're talking about a different reaction PCR does not involve any living organisms including cells. They are removed.

Thanks for your post! I have perhaps not phrased my question precisely enough. My question as mentioned in the edit can also be phrased: "can we be sure that the isolation techniques will not discard possible targets, e.g. from macrophages?" Taking your post the answer seems to be: "we can be sure that isolation techniques will discard most relevant targets." Can you elaborate?

I think the right answer is "they don't". If you were doing pcr on some sample that you didn't know much about, you would certainly include a positive control, meaning a primer that should amplify something that you think is definitely present in your sample. It you get a band for the positive control, then you know you successfully were able to lyse the cells and nothing else interfered with your pcr.
Most modern techniques on typical samples are quite good, so it's rarely a problem. But generally you would prefer to design your experiment to rely on positive results from pcr rather than negative ones.


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Why do snails come out after the rain?
Many times, when there is rain after a long time, snails come out afterwards, and you can see snails and slugs everywhere! I have two questions:

Why do they come out after the rain?
Where are they usually found, not after a rain?

Note that I do emphasize when there is a rain "after a long time"

They probably need oxygen. If they are living in the dirt, then the water will force them to the surface.

A yahoo answer post suggest that they come out to flee drowning as @AMR suggested.

Snail Behavior Rain... 20,400 results; Snail Locomotion Rain 4,520 results; Snail Movement Rain... 22,500 results.

http://chat.stackexchange.com/transcript/message/25100934#25100934

In most species, slugs and snails survive droughts (which would otherwise kill them by dehydration) by creating "slime tombs" (initially-viscous bubbles of slime) around themselves. these tombs or pellets will quickly dry out, on the surface, while resisting total dehydration. When it rains, these capsules will re-hydrate or "melt," beginning on the surface, and the creatures will crawl free.
Because they've gone without food, they're ravenous, and go everywhere, "rasping" softened nutrients from the surfaces of plants and even objects where "blossoming" single-cell organisms (also recently re-hydrated) can be found.

Welcome to Biology.SE! Can you please add references? (I am not trying to be rude) I like your answer, but references would certainly complete it.


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How do furniture beetle larvae drink?
I have read that the furniture beetle (Anobium punctatum) has larva that will burrow for three to four years in wood before emerging and pupating. How do they obtain water during that time if they are just eating wood?

It is likely that the oxidation of the organic compounds in the wood provides the water, much like many desert animals get their water.