text:
Hill-Roberston effects and effective population size
From this article, first page, middle of the second column:

Even if harmful alleles do not become fixed, they can still reduce the efficacy of selection on neighbouring loci through a process called Hill–Robertson interference. This effect occurs because individuals bearing deleterious mutations are less likely to survive and reproduce, reducing the number of individuals that contribute genetically to the future population. This reduces the effective population size witnessed by a focal locus

I don't understand the link between the Hill-Robertson effects and the effective population size. Why would the effective population size be greater in absence of Hill-Robertson effects? Can you please make this link clear to me?

Here is another question on the same article.

your name changed, I preferred Remi.b because I am not sure how to cite a name with a space!

@hello_there_andy Ha ha you're a funny dude! But thanks for noticing, I didn't change my "display name" on purpose; Mac's auto-filling made it for me! I just wanted to add my "real name". I'm Remi.b again! Thanks for your answer below.

Hopefully this syllogism will answer your question.
Given the following premises:

In the absence of selection, fitness of individuals are at a theoretical maximum.
If a theoretical maximum fitness is achieved then effective population size is maximum.
If there is an allele that confers both increased and decreased fitness you have a genetic conflict (e.g. an allele that turns you green gives you good woodland camouflage but is un-attractive).
If a deleterious allele is linked to a beneficial allele this is similar to having a genetic conflict.

The conclusion follows:
Strong linkage between beneficial alleles and deleterious alleles (Hill Robertson effects, i.e. 3. and 4.) prevents a theoretically maximum fitness to be attained (1.) and thus a reduced effective population size (2.). Which can only be overcome by high levels of recombination and mating (i.e. by separating deleterious and beneficial alleles).

I don't want to repeat the same thing every time you answer my questions (this happened twice I think) but really: As soon as I start reading your answer I realize how obvious was the answer and feel stupid I didn't get it before. Thanks for your help.

No no please don't feel that way!! Funny because I felt the  same way when being taught these things by my research supervisor, Prof. Burt (who's worked closely with "R" as you call him). The only stupid thing to do is lacking bravery to ask the questions.

Who is "R" (as I call him)? Robert Trivers?

ah yes, perhaps it wasn't you who called him that oops :P


text:
Can we define biological age?
How can we define ageing from a biological standpoint without making an appeal to chronological age?
Related, but less important, are there any metrics we can use to determine someone's biological age other than their chronological age?
Telomere length is an obvious candidate, but it is imperfect.

Basically, you're looking for some indices allowing to estimate the age of an organism, is it correct? If you meant estimating the "real biological age" rather than the "chronological age" then, the problem of finding indices is just the same as defining biological age. And just like any words, you can define them the way you want if you're the first to use them. Are you only interested in humans or can we talk about stuff like dendrochronology?

I guess what I had in mind was about humans. If something is correlated with chronological age, its not necessarily a part of ageing. What definitions of ageing are there to clarify when something is part of ageing and when something is just correlated but not causally related?

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text:
GULO only for mammals?
I am not a biology student, but just want to know if GULO gene are present only in mammals or all species possess it ?
And is GULO gene active in human fetus?

On Genecards it is mentioned that the GULO pseudo gene being expressed in humans in many major tissues. In that case the gene might be active although not encoding for a functional enzyme.

GULO encodes L-gulonolactone oxidase which catalyses a step in the biosynthetic pathway to ascorbic acid (vitamin C).
I did a BLAST search at NCBI using the mouse GULO protein as probe, excluding mammals, and I saw highly significant hits in reptiles, birds, sea urchins, fungi and bacteria. I conclude that this enzyme, (or very close relatives) is ubiquitous.
Humans (and other primates; also guinea pigs and the Dalmatian coach hound) have a defective GULO gene and so require dietary ascorbate.
Since the gene is non-functional in humans it isn't expressed in the foetus.

Wrong in regard to "Since the gene is non-functional in humans it isn't expressed in the foetus." See my answer.

De Tullio writes

We know from other studies that pseudogenes are not inert, but can have a significant role in epigenetic control of gene expression (Poliseno et al. 2010). Could this also apply to the human gulonolactone oxidase pseudogene? Time (and much research) will tell.
De Tullio, M. C. (2010) The Mystery of Vitamin C. Nature Education 3(9):48
https://www.nature.com/scitable/topicpage/the-mystery-of-vitamin-c-14167861/

On Genecards it is mentioned that the GULO pseudo gene being expressed in humans in many major tissues. In those cases the gene might have an epigenetic role.

This is just another example of Stack Exchange not working. I wrote the same thing as in this answer in a deleted answer. It was not reopened.

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Shigella's O antigen (PAI synthesised) and passage through host defences
The O antigen is synthesised by Pathology islands (PAI).
O antigen may be a factor why Shigella survives the passage through host defences.
I am interested in which step of pathogenesis.
There are Bacterial ATPase (actin tail, intracellular movement), M-cell (enter) ...-> extracellular movement.
Where can the O antigen affect in Shigella?

The outer layer of the cell envelope of Gram negative bacteria is the outer membrane, and the outer leaflet of that membrane is composed largely of lipopolysaccharide (LPS). The O antigen is the name given to the outer glycan portion of the LPS - there is a nice diagram at the Wikipedia article I have linked to which makes this clear.
Because this structure is exposed at the bacterial surface it is a target for the immune response, and the serotyping of many bacterial species incorporates this O serotype information.
Table 1 of the review that you link to indicates that PAI SHI-O carries genes gtrA,B,V (originally derived from a bacteriophage - not unusual for a pathogenicity island). These genes encode enzymes which modify the O-antigen via a glucosylation reaction. Presumably this helps the bacteria adapt to an immune response via a shift in serotype. It may be, for example, that an invading population of Shigella includes variants which do or do not express these genes so that a subpopulation can arise which is not recognised by an existing immune response. This is what is meant in Table 1 of the article by "evasion of host immune response". It is a common strategy - examples in Salmonella (flagellar phase variation) and Helicobacter (induced transformation) spring to mind.

Do you mean by the induced transformaton of H.pylori the generation of lophotrichous flagella (mucinase) which permits intracellular movement?

No, I mean that under stress conditions, (such as an immune response), when cells ares dying, other cells will take up their DNA (transformation). This results in new variants arising (through recombination) some of which are able to continue the infection.


text:
Why do we exhale after we hold our breath?
I tested this out with my friends, and I find that after they hold their breath and can't hold it anymore, they exhale air, instead of inhaling air.
Interestingly, they all try to inhale in as much air as possible before starting to hold their breath. When I told them to exhale as much air as possible before starting to hold their breath, they inhaled air after they can't hold it anymore.
It's understandable that when one exhales then holds his breath, he needs air and thus he inhales afterwards. But when one inhales then holds his breath, shouldn't he inhale again after "using up all that air he inhaled before holding hi breath"?

The lungs are not consuming the air as such, they are just adding a Carbon element to the O2 in it.

@HermannIngjaldsson ??? I thought CO2 was the by-product of cellular respiration.

O2->CO2 is what the lungs do with the air you give them.

@HermannIngjaldsson um.. could you be more specific? I don't think the lungs convert O2 to CO2; it should be the cells throughout the body that uses O2 and produces CO2, which is sent out from the blood into the lungs. Or do you mean the conversion of O2 to CO2 in the cells of lungs?

you breathe in air, which contains that necessary thing, oxygen. and you breath out that same air, just then a bit of the oxygen has been combined with a carbon atom. the cells throughout the body take o2 and give back co2, its just that the lungs take care of extracting that necessary o2 out of the air for them.

@HermannIngjaldsson ah, I see.

Try maximally exhaling, and then hold your breath. ;)

@HermannIngjaldsson I think that's a very limited and confusing way to describe it, especially the first two comments.  Your statements suggest that C is added to O2 in the lungs which is not the case.  The lungs are purely a gas exchange organ in this sense.  O2 is brought in, CO2 kicked out, following concentration gradients.  The air you breath in is not the same as you breath out.

This is more about basic physics than biology. When you hold your breath, you normally take in one last long breath and keep it in as long as possible, Your lungs are therefore already full of gas (remember that the oxygen used by our lungs is only ~22% of the total volume of air you inhale). Therefore, when you release that breath and want to take in a new one you need to first empty your lungs out in order to refill them.
In addition, you need to have your lungs empty in order to be able to expand them and draw in more air. There is no biological reason for any of this, it is the same principle as trying to use a turkey baster:

If you use it once and pull up some liquid into it, you will have to let air out before you can use it again. Your lungs work in the same way. Test this by exhaling all the air from your lungs and then holding your breath without inhaling. When you want to start breathing again, you'll be able to breathe directly in without needing to exhale first.

Good question.
If you inhale on top of inhaled air this is more work. There is more dead air, air which is not as useful due to the lower concentration gradient. And we breathe more to exhale carbon dioxide than we require oxygen. Low oxygen levels only push us to breathe when oxygen levels are a good deal lower, however tiny changes in carbon dioxide causes changes in our ventilation rate almost immediately.
It is also more work as our muscles require more energy to inflate an already inflated chest. This is the case in COPD patients. Try this: take a deep breath in and now holding that air in, breathe normally on top of that air. Feel how difficult it is and how breathless you feel.

It's understandable that when one exhales then holds his breath, he needs air and thus he inhales afterwards. But when one inhales then holds his breath, shouldn't he inhale again after "using up all that air he inhaled before holding hi breath"?

Before we hold our breathe we first inhale some air inside.
So, after holding it for some times, carbondioxide (CO2) which can be toxic to our body will be released after completing metabolic processes inside our body which will be pushed to our thorax, ready to be expelled.
The partial pressure of this gas (pCO2), is the primary fast (minutes or hours) trigger for breath; where partial pressure of Oxygen (pO2) is a slow trigger (hours or days). This explains why patients with severe re-acutized cronic obstructive pulmonary disease (COPD) stop spontaneous breathing, even if their pO2 falls, because of augmented pCO2.
The pCO2 is sensed in the human body in the Central Nervous System (CNS), precisely in the ponto-bulbar centers of breathing. The pO2 is sensed at periferical strucrures as the glomi aorticus and carotideus.

Welcome to the site! While you may have the beginnings of a good answer, it is trapped inside of a gigantic run-on sentence with several misspellings and run-together words that make it very difficult to determine what exactly you're trying to say. Please [edit] your answer to improve it, highlighting your answer to the question and not just giving a review of the mechanics of breathing, which isn't really relevant.


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Does a neuron ever generate an action potential without stimuli?
Most accounts I read involving action potentials and synapses and the like tend to focus mostly on the action potential as a mere automatic reaction to another similar event happening upstream.
From a more theoretical point of view, it would be nice to know if (and under what circumstances) a neuron would be able to generate an action potential, in the absence of an upstream neuron firing first.
I suspect that the nervous system, at least in higher animals, is not simply a relay system that processes and transmits information from senses to actuators like the limbs. The relay system picture is fine for short-timescale, reactionary behavior but it is hard to imagine any longer-timescale learning processes happening this way. This is what motivates my question.

Pacemaker cells in the heart might be an example for you

You might be interested in this quetions on neurons firing 'randomly'.

There are many spontaneously active neurons. This has been known for many years [1]. There are multiple sources that could make a neuron spontaneously fire. In cortical culture of neurons where there is no external input to the system, neurons are spontaneously active, for example [2]. Of course, there are spontaneous vesicle releases from synapses (miniature EPSC) in this case, so you might say there are still some "input" to each neuron. However, even if you block synaptic transmissions, and some neurons do fire spontaneously [3]. It could be ion channels, or some internal chemical process. If you include the network level spontaneous dynamics, there are even more possible ways to have active neural system without any stimulus.

Alving BO (1968) Spontaneous activity in isolated somata of Aplysia pacemaker neurons. J Gen Physiol 51: 29-45.
Potter, S. M. and Demarse, T. B. (2001). A new approach to neural cell culture for long-term studies. Journal of Neuroscience Methods, 110:17-24.
Häusser, M., Raman, I. M., Otis, T., Smith, S. L., Nelson, A., du Lac, S., Loewenstein, Y., Mahon, S., Pennartz, C., Cohen, I., and Yarom, Y. (2004). The beat goes on: Spontaneous firing in mammalian neuronal microcircuits. The Journal of Neuroscience, 24(42):9215-9219.

Neurones fire when they're sufficiently depolarised past their threshold. In the sensory system this is in response to an external stimuli which sets of a chain reaction. Then motor neurones may relay signals back and in this case the signal or initial depolarisation is occurring in the brain. However this is still caused by a stimuli even if indirectly. If we take an action it is generally because we thought which action we should take because of some sort of stimuli e.g. we are cold so we put a coat on.
But anything which depolarises neurones can set of an action potential. However there's always something which causes it to depolarise, perhaps a drug or a stimulus or another neurone. If any of these don't count as a stimuli depending on your definition, there's your answer.
Or perhaps if you consider cardiac muscle which can intrinsically depolarise. Not a neurone but there's an action potential. They just naturally depolarise over time and action potentials are set of regularly with no stimulus required.
As for learning, where the structure of neurones can change so they connect to new neurones or not to old neurones or vary in the strength of their connection.

There are spontaneously firing neurons known as intrinsically oscillatory neurons, or simply pacemaker neurons. Under the right conditions these can fire action potentials in a rhythmic pattern without neuronal input. Examples are the thalamocortical relay neurons in the thalamus and inferior olive neurons. The basic mechanism is that a low-threshold Ca2+ current generates a small depolarization that in turn activates full-blown action potentials. In the recovery phase after the burst of action potentials, a hyperpolarization-activated cation current is activated (Ih), which in turn depolarizes the neuron. This depolarization then initiates another Ca2+ current and the oscillation continues.

Thalamocortical cell with oscillatory behavior in vivo. Source: Steriade et al. (1993).
The thalamocortical oscillations are thought to be imprtant in the generation of the slow-wave EEG seen in the early phases of sleep, as well as during absence-epileptic seizures (petite mal).
Reference
- Steriade et al., Science (1993); 162: 679-85


text:
What is the right spelling for this agar?
I could not spell the agar [gonoline-uroline] which I heard yesterday.
My spelling is so wrong that I could not find it in Google.
What is the right spelling for this agar?

Might help if you tell us what it is used for.

It's completely illogical to change the question after a comment and an answer to the original question.

@AlanBoyd I agree, now it looks I did not answer question at all. The authors suggested to open a new questions if the original one has solved and generated other questions.

I rolled back and opened a new a question: http://biology.stackexchange.com/questions/15261/what-is-the-benefit-of-using-gonoline-euroline-in-combination

The first word is ok, there is agar called Gonoline, the second one is probably Euroline and there is an agar with this word too (Liver IgG Euroline).
I've found both of them on the Italian site, probably the are not one, but two agars.

Now, I am thinking why they are using these two agars in combination. The topic was Pathogenous cocci.

I actually don't think this is right (not that it's your fault given the question), but I'm pretty sure Euroline is brand name for a synthetically printed ELISA like assay.  I really don't think there's any agar involved.

Looking at your two questions together, I think you mean gonoline media, followed by blood agar.  To be honest, I feel like this question would be off topic.  You may be referring to a specific blood agar, like Chocolate agar, but that would be wild speculation.
Gonoline media is often used for Neisseriaceae, so perhaps you are specifically looking at Gonorrhea?


text:
What are the best detection medias for cholera?
I heard this fact that you can use some [hypertriade] for vibrio cholera diagnosis which has compontents

sucrose (yellow)
mannose (yellow)
arabinose (do not ferment; stay dark pink)

I did not find this hypertriade agar on Google.
It reminds me of Egg Yolk Agar, but I think cannot be it because of the arabinose.
Otherwise, it seems to be similar.
What are the best detection medias for cholera?

I don't see how you could have a single medium that would simultaneously test for fermentation/non-fermentation of three different sugars. From the colours that you mention this is clearly based on a tetrazolium salt, but if all three sugars were present then two of them would be fermented and you would get a conversion to a yellow product, regardless of the inability to ferment arabinose.

@AlanBoyd I added an explanation what the hypertriad may refer to: there can be three selective media in one petri dish. I am not sure why they are using the word hypertriade or hypertriad. They seem to be using only sucrose, mannose and arabinose. Is there any collective name for such combination?

Is there a reason you wouldn't be using TCBS?  Why the "hypertriade" in the first place?  If you're designing a specimen screen, you might use 4 instead. I also, I've never heard the phrase hypertriade, and DDG/Google failed to teach me. Do you have a reference for that term?

@AtlLED Make that an answer and I will accept it. I do not know why the assistant was using the word hypertriade. I have no idea of the origin.

You should use Thiosulfate-citrate-bile salts-sucrose agar for the detection of all vibros, including cholera.  When cholera is presant, you should expect round, largish (not huge), yellow colonies.  This is the CDC recommended diagnoses method.
Again this question might be better phrased "what are the best detection medias for cholera," or "what plate screens should be conducted when vibros are suspected?"


text:
What is the benefit of using Gonoline-Euroline in combination?
I was heard that this combination first Gonoline and other culture another culture on Euroline is good one.
What is the benefit of using Gonoline-Euroline in combination?

What's the context, I've never heard of using them in combination/not sure you really mean to be asking about Euroline.

Please, close. This is too unclear to be discussed.

Looking at your other question, I think there's some serious editing that needs to be done to clarify this question.
Still I think there is a quick and easy answer to your question.  Gonoline media makes an excellent transfer media.  If you are out in the field some where and want to take a swab for further analysis, you could easily choose a gonoline media for transport.  Then you would want to follow that up with some selective blood agars that might show a pathogenic species that you were looking for.  Thus to use gonoline media with any other medium, is merely to preserve your sample for plating on your diagnostic media/agar later.
Again, looking at your related question, I could only guess that you meant chocolate agar, because you might be hunting Neisseriaceae (which you should put in the question if you are).

I'm also ok with closure


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Why do humans circulate monosaccharides instead of disaccharides as in plants?
Plants transport food mostly in the form of disaccharides like sucrose but humans transport them in the form of a monosaccharide -  glucose.
What is the reason behind this ?

One of the reasons could be  -

humans and many other animals have active circulatory systems,
  there is little need for targeting sugars for specific parts of the
  body. The entire body would rapidly reach equilibrium with the glucose
  level of the bloodstream, and thus there likely never evolved the need
  to target specific organs to receive sugars via disaccharides

Source : This
Other reason could be that disaccharides are harder to transfer inside the cells than monosaccharides.

plants are earlier than animals in the phylogenetic tree.  animals later evolved the circulation of monosaccharides I would assume, so there could be an advantage to monosaccharide circulation.  I would look at fungi to see what they do there.


text:
Why do doctors do chemo or transplantation for cancers that don't respond well to these treatments?
From the UpToDate article on multiple myeloma:

In most people, chemotherapy partially controls multiple myeloma;
  rarely, chemotherapy leads to complete remission.

Also:

Transplantation, when successful, prolongs survival, leads to a
  remission, and, infrequently, cures multiple myeloma. However,
  transplantation has several limitations. The high-dose chemotherapy
  given before transplantation usually fails to kill all of the plasma
  cells, allowing the condition to relapse after transplantation. Such
  treatment also puts the patient at risk for serious infections and
  bleeding, which can be fatal.

UpToDate is used by 700,000+ physicians worldwide; it's not alternative medicine. Thus, if even mainstream medicine recognizes the relative ineffectiveness of chemo and transplantation for multiple myeloma, why do they do it?

This is really a question about healthcare, not about biology and it is off-topic here.

@MadScientist Is there a healthcare StackExchange or something equivalent? thanks

To long for a comment: Its more an ethical thing I would say.
I do research which is connected to melanoma - a cancer which is notoriously treatment resistant, once it started moving. Until very recently there was only one chemotherapeuticum which has pretty low (around 20%) response rates. It was usually tried anyway because its possible that the patients belong to this 20% which respond. If not, treatment was usually not prolonged.
I think its something similiar here. The other problem for chemotherapy is that it is cytotoxic (until we got the small molecule inhibitors which are tested and used today) and the problem is to kill the cancer cells (all when possible) while you leave the rest of the body as unaffected as possible. To get this balance is hard (people tend to react differently to chemotherapy). The other problem is that cancers are not homogenous. So its possible that 99.9% of the cells present respond to chemotherapy and get killed, while a few acquired an additional mutation, which gives them an advantage. The conditions of chemotherapy are very selective.

I know that 97% of multiple myeloma patients have anemia, but do you know if chemo causes anemia?


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Multicellular organisms as DNA banks
Animal -> bacterial gene transfer seems easier than bacteria -> animal (rotifers are an interesting exception); there are bacteria live in close contact to us but our germ-line cells are protected. Given enough time, even free-living bacteria would start to pick up some of our genes (once the introns were lost).
Is this true? If so, do we see animal/plant genes gradually spreading into single cell organisms as time goes on (although "seeing" this would be difficult)? Is this effect "significant" for evolution in microbes?

This paper seems relevant. I just found it and don't have access, so I haven't read it. It does seem to suggest that there is evidence for eukaryotic genes being taken up by a prokaryote.
I would imagine this is rare, though. Eukaryotic cells don't tend to just spew their genetic material everywhere. Most death pathways involve breaking down any genetic material in the cell, I believe.

But prokaryotic cells infect Eukaryotes and then can leave and go on. During the infection DNA can be transferred.

Maybe, but this is the only example I found searching the literature. If you find more evidence, feel free to link.

This sea slug is one example of prokaryotic genes ending up in an animal. The slug ingests chloroplasts from algae and incorporates them into its own cytoplasm. It has also acquired, presumably through horizontal gene transfer, some or all of those genes necessary to maintain the chloroplast. While this is not a gene transfer from a free-living prokaryote, chloroplasts are essentially cyanobacteria.
For the paper (PDF), see here.
Also see a more general review here (free full text).

If we're allowing gene transfer from endosymbionts to their host, then human cells are an example. Almost all of the mitochondrial proteins are coded for in the nucleus.

This isn't your typical case though. Also see second review.


text:
Clarification on Hatch and slack pathway
The following is a minor clarification that I want to make, since it is rarely addressed directly in most of the texts I have gone through.
In C₄ pathway, the chloroplasts are dimorphic, that is, the bundle sheath chloroplasts contain RuBisCO, but lack grana and can hence perform only the light-independent reactions. The mesophyll chloroplasts lack RuBisCO but contain the granal apparatus to perform light reactions for synthesis of ATP and NADPH. The bundle sheath cells are impervious to gaseous transport (to prevent the entry of O₂), but recieve the required CO₂ by the intake of an organic acid produced by CO₂ fixation by the mesophyll cells.

But, to effect the Calvin cycle in the bundle sheath cells, it
  requires a high concentration of the light reaction products, i.e.,
  ATP and NADPH. Since they themselves lack grana, they must obtain the required share from elsewhere. Where do they obtain it
  from?

My guess is that NADPH enters the bundle sheath cell with the organic acid primarily produced in the mesophyll cells where light reaction occurs. ATP is met by a similar uptake plus the utilisation of the ATP produced by respiration. I need to confirm this as it is usually never addressed in texts.

I guess they go via plasmodesmata.

I am not sure about the source of ATP but I can tell you something about NADPH.
The conversion of malate to pyruvate and CO₂ by malic enzyme is carried out in the bundle sheath cell. This process produces NADPH.

See the very 1st thing is bundle sheath cell shows very less concentration of Grana, hence we say Grana is absent,  the required amount of ATP & NADPH₂ are also transported from mesophyll cell to bundle sheath cell via plasmodesmata.


text:
How many systemic reactions in inflammation?
I have this sentence in my notes

Inflammation consists of two local reactions and one systemic reactions.

which is difficult for me to accept.
Two local reactions are vascular and cellular.
I think there are two systemic reactions too:

White blood cell response
Acute-phase response

How many systemic reactions there are in the inflammation?

There are two systemic reactions in inflammation too: mediated by leucocytes and acute-phase response (proteins).


text:
Reverse tomography to create 3D scalpel
Isn't it possible to reverse tomography methods to create means to deliver heat or radiation precisely in 3D? This would be "3D scalpel" i.e. device which would be able to eradicate tumor cells precisely in otherwise unreachable areas?

This is the idea behind http://en.wikipedia.org/wiki/Radiosurgery (a.k.a., "Gamma knife")

Some people are also studying that kind of things with ultrasounds using time reversal. For example against kidney stones. But ultrasounds have problems (mainly because of their wavelength) and are not that easy to use against tumours in unreachable areas. I think there are also studies about time reversal for electromagnetic waves, but that also yields some problems.

The principle of targeting cancers with high intensity radiation is already in use. For example:
http://www.mayoclinic.org/tests-procedures/gamma-knife-radiosurgery/basics/definition/prc-20014760


text:
Microtiter Dish Biofilm Formation Assay- Pseudomonas and Crystal Violet
If Pseudomonas is a gram negative bacteria, it does not retain crystal violet but why is it that so many people are using crystal violet staining in theri Microtiter Dish Biofilm Formation Assay?

Could you provide more context? A citation to a paper that uses this assay?

heres an assay citation: http://www.ncbi.nlm.nih.gov/pubmed/21307833

I think the answer is along the lines of: gram negative bacteria still use glycans externally when they form biofilms and stain with Methyl violet as a result.

So effectively, we not not actually enumerating the number of cell but instead the extend of the biofilm matrix?

Using the Gram stain for differentiation between G- and + requires the addition of alcohol, the critical step in Gram staining. Actually the first step, simple staining, goes the same for all types of bacteria. All bacteria gain the stain, but addition of alcohol makes the lipid in bacteria like Pseudomonas to lose it.


text:
calculate the number of heterozygotes
The ability to taste PTC is due to a single dominant allele "T". You sampled 215 evolution students, and determined that 150 could detect the bitter taste of PTC and 65 could not. Assuming this trait is in Hardy-Weinberg equilibrium in this population and that there are only two alleles, calculate the number of heterozygotes for this trait there are in the population.

How do I formulate this into hardy-weinberg eqbm form need help.

This looks like homework. What have you tried so far?

Total  215  Calculations
Can taste PTC  150
Cam't taste PTC  65
For recessive  0.3023255814
Sqrt of recessive q  0.5498414148
p=1-q  0.4501585852
2pq  0.4950316667

Maybe just edit your question to add that information.

@krushna this site is not a homework answering service. I suggest you read this post about homework questions. http://meta.biology.stackexchange.com/questions/266/homework-policy-for-faq/267#267

Hardy-Weinberg law gives the frequencies of genotypes from allele frequencies: $p^2 + 2pq + q^2$
Because the allele "T" is dominant, the frequency you're directly measuring through the experiment is the addition of $p^2$ and $2pq$.
$$p^2 + 2pq = 150/215 ≈ 0.6976$$
solving for $p$ (and replacing $q$ by $1-p$) gives:
$$p = 1 - \sqrt{\frac{13}{42}} ≈ 0.45 $$
The frequency of heterozygotes is given by:
$$2p(1-p) ≈ 0.4950 $$
And the number of heterozygotes in a population of 215 individuals is given by:
$$215 \cdot 0.4950 = 106.43$$
That sounds very alike what you wrote in the comments!

yeah I calculated the heterozygotes frequency but I was clueless how to find the number...of heterozygotes...but thanks for your help..


text:
Is there any evidence of increased life expectancy for animal species?
Life expectancy for human has significantly increased during the last century or so. We all know that there are many reasons that are not linked with "evolution", but I am wondering if such change in life expectancy has been observed "naturally" (not counting animals in zoos or domestic ones). Does evolution favor long lasting individuals?

The prolonged life expectancy over the last century can be explained by better medicine, hygiene, food and better working conditions. It is not connected to evolution (which generally takes place over long time periods, not just over the course of only three generations). The same is observed for zoo animals.

There is life extension work with animals, but just as Chris says its more about changing conditions or finding mutations that change life expectancy.

@Chris thanks for your comment. I've tried to edit my question to make it more clear. I know that it is not due to evolution for humans and zoo animals, but I was wondering if it had been observed for some species as a consequence of the "survival of the fittest". A millenimum was maybe to short (though it is more than 3 generations), but I guess that it is difficult to observe, so maybe it can only be shown for species with small longevity.

@shigeta thank you for your comment. Are the mutations that change life expectancy beneficial to the population ? I mean, long life expectancy can reduce the possibility to adapt quickly, so this can make the species more vulnerable to, e.g. habitat change, but does it provide any advantage.

The answer kinda depend on what you'll accept to be an observation. It seems that you want an observation where we measured the mean life expectancy of a species over a (very) long term and find out that it is increasing. Such study very probably does not exist for obvious reasons. But you might be interested in some key mutations that changed life expectancy and on proof that this mutation rises through time (selective sweep) or you might be interested to know more generally about life history traits or to seek for correlations between life expectancy and some ecological traits.

As far evolution is concerned, there is no benefit whatsoever in having long lived individuals. Evolution only "cares" about individuals while they are capable of reproducing. Survival past the maximum age of reproduction is irrelevant from the evolutionary point of view since it does not make you any better at reproducing, and therefore your genes will not be selected for.
This is highlighted by the various species that die to give birth to or feed their young. One of my favorite examples is the giant pacific octopus (Enteroctopus dofleini) whose females lay their eggs and then die, leaving their body to feed the emerging young.
Now, a mutation that makes an individual both longer lived and capable of reproducing at a greater age could well be selected for. It just always needs to be combined with the ability to reproduce. By itself, dying older will confer no selective advantage unless it is combined with producing more offspring.

The life expectancy of an animal (or anything) is just one aspect of how 'fit' they are to survive.  having them live too long can be a detriment to the species.
There is no simple 'better/worse' relationship of fitness to life expectancy.  In simple population models predators which reproduce to much or live too long will tend to eat all the prey and starve to death for instance.
The most famous example of life extension molecular biology is the discovery of a 'Methuselah worm' by Cynthia Kenyon about 10 years ago.  With a single mutation these C. elegans worms can live about 50% longer, and seem to be pretty energetic while doing it.
It would be interesting to put some of these Methuselah worms into a wild population and see what happens to their life span as they interbreed.  C elegans is a highly programmed organism - each cell has a predetermined plan for development and lifespan, which made this worm relatively easy to find.
For human beings (the best studied animal on Earth) there is no simple genetic relationship to longevity for most of us, but there appear to be some simple combinations that are responsible for the oldest living humans:

a genetic model comprising 150 SNPs in order to compute the predisposition of an individual toward EL. Their model successfully predicted exceptional longevity in a different sample of centenarians (individuals that live to age 100) with 77 percent accuracy. This demonstrates that EL is strongly associated with complex combinations of genetic variants.

So for humans this experiment has sort of been done.  Longevity phenotypes are possible but don't overall convey a reproductive advantage and so while they hang out in the gene pool,  they aren't enough of an advantage to reproduction to be spread about widely...


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RNase and EtOH issue
I work with RNA and I have some RNase issues. For example I am using RNeasy mini kit and at one step I use 100% EtOH. It does not say it is RNase free or not. Does absolute EtOH inhibits or removes RNase or should I be worried about it?
Addition: I am using eppendorfs directly from the bag. So they supposed to be RNase-free, right?
Thanks.

If nobody else used your EtOH it should be RNAse free, the same is true for tubes. I used tubes fresh from a new bag without problems. But again: Make sure they are handled with gloves all the time and that nobody else uses them.

I have my own bag for tubes and I am taking them from the bag and putting in a box and I use that box only in "RNase free area". Would that be OK?
EtOH is an 1L bottle and everybody taking aliquots from it actually. I have also my own and just me using it.

Ethanol is not a problem, we use it without any further precautions and it seems to be RNAse free. You should take the usual precautions you should take with all chemicals when you work with RNA, never use a spatula or spoon to get anything out of the bottle (unless you want to bake your spatulas all the time), always pour them to avoid any contamination.
We autoclave the Eppis once, this might be an unnecessary precaution. I think you can also buy them certified RNAse free, but I'm not sure if they are actually treated any different or simply more expensive.

Thanks. What do you think about glass bottles? For instance, I am preparing RNase-free buffers and putting them clean and autoclaved bottles. Do you think it is ok or should I just use plastic containers?

I'd probably clean the glass bottles with DEPC first to get rid of any RNAses. Usually baking at 200-250 °C is the way to go for glass, but the bottles typically have some plastic which would not survive this. I also tend to just reuse the same bottles for identical content, then you don't have to make them RNAse-free again.


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basic programming and bioinformatics
As a molecular biology graduate student I have decided to learn some basic programming and bioinformatics since everybody says that it is crucial. For example, what would you learn if you need to work with RNA-Seq data, compare and interpret them?
Thanks!

I think that you should try to be more specific with your question. Right now it is too broad (you can do an entire degree in bioinformatics). What do you do now? What do you want to be able to do?

I know its too broad and thats why I am asking actually. Now I am a masters student in neurosciences and will continue with a PhD in the same area. A post-doc from my lab was saying to me that I need to be able to understand basic stuff about programming and bioinformatics. Lets say I am going to compare RNA-seq results and interpret them.

Then the question might be better suited for academia.SE or biostars. I think you're going to get too many discussion-type answers here.

The coursera classes are a good introduction - one is starting next week!  the focus on python a lot I think...

Thanks! Is it the one that you mentioned?: https://www.coursera.org/course/pkubioinfo

I was thinking of this one, https://www.coursera.org/course/bioinfomethods2 but that one looks good too.  If you are a PhD student you should learn computation closely related to your research - that will motivate you. either R or better yet python as tools.

Indeed the question is broad and quite hard to answer I think. I'll give a try. I very welcome editing to improve this answer.
The field of bioinformatics is a big field. Bioinformaticians need basic knowledge in

biology
molecular genetics
Population genetics
programming
statistics

You may find courses on statistics applied to bioinformatics here (R-language) and here (I haven't watched these sources).
How to start programming? - Python
You seem to be mostly interested in is programming. I think that Python is a very good start to get in touch with programming. Programming might look a bit scary when you don't really know what it is about but you can easily, in a few days, acquire basic knowledge in this field and already solve some pretty neat problems. Many people actually have lots of fun learning how to program. And you'll probably be amazed by all the power this tool will offer to you. I personally really enjoyed learning to programming in Python. I did it (I was mostly interested in object-oriented programming, you'll learn what it means) in a day or two with a very good source but unfortunately, this source is not available in English. But there are tons of introductory documents, you'll have no difficulty to find a good one. I'd counsel you to directly download Python and to look at online courses on khan academy or EdX (I haven't watched them).
Data analysis - R
While Python is very popular, I think that, as a biologist, it is very important that you know about R. R is a programming language which is slow (compare to Python, C, Java, …) but it is very useful for statistical analysis and visual display of data. Also, many people use R in bioinformatics (for phylogenetic analysis typically). I think that acquiring basic knowledge in R takes more time than in Python because we tend to use R because of its huge amount of already existing functions and therefore, we have to learn many of these functions before understanding that R can indeed be much more useful than Python for some tasks.
Command line - Shell script
Shell script (BASH for example) is a very specific and very important language too. Very useful for manipulating, transferring files, managing processes or pretty much anything that is happening on your computer.
Other
C and C++ are very fast and very much used as well. Perl is commonly used for genomic sequence analysis (although Perl is slowly losing users to the advantage of Python).
Usefulness of programming
You also ask about the usefulness of programming. Well, it is used in pretty much all areas of biology. It is used for analyzing empirical data, computer simulations in population genetics, graph theory, annotating DNA sequences, … I guess that 98% of biologists have at least some basic knowledge in programming. The main point about programming is that it performs calculation much faster than anything you could ever realize with your calculator. Typically, in bioinformatics, analysis of DNA sequences often asks for very intense calculation and asks for big computation power. Processes such as constructing phylogenetic trees, determining a goodness of fit of evolutionary models, annotating DNA, aligning DNA sequences, analyzing microarray and many other things are all sorts of tasks that require programming.

This is the answer I was looking for actually. Thanks a lot!

I'm not at all sure that R is slower than python. Both are interpreted scripting languages. C and Java are completely different.

What you need to remember is that R is more of a domain-specific language (statistics and related fields like visualization), while Python is more of a "generic" programming language like the C superfamily, Java, Ruby, etc. What sets Python apart is its comparative ease of learning and use, the "batteries included" philosophy of the standard library, and the huge number of 3rd-party modules available for everything from bioinformatics (Biopython, etc.) to visualization (matplotlib) to numerical analysis (numpy/scipy) to web frameworks to natural language analysis and more...

Python also has interfaces to other languages (R, C/C++, Fortran, Java, etc.) so you can do domain-specific work in the best language for that project, and use Python as the "glue" to piece it all together.

@terdon R is definitely slower than Python, though not dramatically.

Why are you making a trivial edit to a question that was closed almost two years ago?

I did not realize it was closed when I edited it. I often improve my past posts. Why are you asking?

...because it comes back to the view of everybody and waste your time probably....mmhh ok. Well sorry about that.


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Comparing SIFT and PolyPhen to other methods
I'm looking for a database of nsSNP (non synonymous single nucleotide polymorphisms) and their effects. As I understand, the common methods to predict this are SIFT and PolyPhen, and I want to compare them to other methods.
The database needs to list the old sequence and the new one (or that I'd be able to infer that somehow), and their effect (whether harmful or not).
What are my options?

I will strongly suggest you:
PredictSNP: It's the best tool for nsSNP detection as it compares and throw out result from all the tools available.
http://loschmidt.chemi.muni.cz/predictsnp/
Paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3894168/


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Why is succinate dehydrogenase attached to the inner mitochondrial membrane?
Succinate dehydrogenase is attached to the inner mitochondrial membrane. All the other enzymes of the Krebs cycle are located within the matrix of mitochondria, though.
In biological systems, there is often a relation between structural properties and function. For example, two enzymes that function sequentially in a metabolic pathway are sometimes held in close proximity to one another by a scaffold  (e.g., in fatty acid synthesis). Is there a similar biochemical reason why succinate dehydrogenase is attached to the inner mitochondrial membrane, as opposed to being dissolved in the mitochondrial space?

The reason behind this lies in the properties of FAD+. Unlike NAD+, FAD+ is not free to diffuse within the mitochondrion, it is an integral part of the inner mitochondrial membrane. Its reduced form FADH2 contributes electrons directly to ETC.

Succinate dehydrogenase is also known as Complex II in the electron transport chain.
Although textbooks often show Complex II as taking FADH2 as a substrate, this is a little bit misleading. Succinate is the substrate, the oxidation of which facilitates the reduction of an FAD cofactor, which is already bound to Complex II. The resulting FADH2 is then oxidized in order to reduce ubiquinone, and feed electrons to Complex III.
This is a pretty good image explaining the electron transport chain.

A note on the ETC image I just realized - succinate is oxidized to fumarate, not "funarate" as the image mistakenly says.


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Diffusion of FAD+
Why is NAD+ free to diffuse within the mitochondrion whereas FAD+ is not ? What biochemical properties cause this difference ?

As explained at the Wikipedia page for succinate dehydrogenase the FAD is covalently attached to one of the subunits of the protein. It is the first carrier in a short intramolecular redox chain involving Fe-S clusters, and possibly a haem, before the electrons derived from succinate are passed on to ubiquinone and on down the respiratory chain.
As you say, this contrasts with NAD which is a diffusible coenzyme.


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PAH gene mutation
Analysis of the DNA of the Phenylalanine hydroxylase (PAH) gene in a
patient with phenylketonuria revealed a mutation in the protein coding
region whose predicted effect would be to replace the amino acid aspartic
acid, with histidine. Nevertheless, no mutant protein could be found in the
patient’s cells.How this could be as mutation is in the protein coding region,can anyone explain?

Can the mutation be in an intron? Otherwise I assume that some kind of post-translation modification is involved.

Can you be a bit more specific about the mutation?

Please add more details.. When you mean DNA is mutated do you mean one allele or both..

In terms of the way that the question is worded, I imagine the most likely answer would be that the amino acid substitution D > H disrupts the folding of the protein so that it is recognised as being aberrant and is rapidly degraded.

There are many possible reasons for this, the two most obvious ones are:

Alternative splicing. Perhaps the mutation is indeed in the coding region but of an exon that is not constitutively expressed. As a result, the majority of transcripts created from this gene would not contain the mutation and neither would their resulting protein.
Post translational modifications. Proteins with the mutation might actually be produced but the histidine is changed to an aspartic acid by post translational modification so the mutation is not detectable in the cell's proteins.


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Benefits of CLARITY?
What are the benefits of CLARITY over this technique that was published more than a year earlier?
Of course the second technique needs a fancier microscope that is likely more expensive and requires more technical ability. But CLARITY requires an objective with a very long working distance. I'm no expert in optics, but I'm pretty sure this results in a significant decrease in numerical aperture and therefore resolution.
It seems as though the other method is simply better than CLARITY, and that a lab serious about doing whole brain imaging could afford to invest in a setup similar to the one described. Yet this technique received none of hype that was bestowed on CLARITY. Am I missing something?

To start with, CLARITY is a whole-brain imaging technique , there is no need for sectioning which destroys connections and can cause the brain slices to warp as they are being cut. The costs for setting up CLARITY are much lower because all that is needed is chemicals to get the prep ready for imaging whereas in the Nat Methods paper you have to set up an automated slicing and imaging system,not an easy task by any means. Therefore an investigator is more likely to use CLARITY due to its easy of setting up and low start up costs. Also, as with any brain slice technique , you lose patterns of connectivity among neurons that are more than the slice distance apart(i.e in the next slice) and you don't look at the "whole picture". Thus due to the complexity,high start-up costs and specialized machinery STP is a poorer method than CLARITY for whole-brain imaging.As for resolution, I agree with you on principle that CLARITY has worse resolution(I looked through the paper but couldn't find exact figures) although you have to consider this in terms of all the trade-offs.

I don't think this is fair to the serial two-photon technique. For each Z-stack the sectioning occurs after the optical slice is recorded, so I don't entirely see how the warping is a big issue. Also, even using CLARITY you eventually need to take optical slices, so you don't really get a "whole picture." You get a z-stack that then has to be computationally reconstructed. The same problems with this reconstruction that you point out (loss of connectivity patterns) is a concern in CLARITY as well.

This is not quite true. You don't need to section the brain with CLARITY because the how point is you clear away all the fats so you image cells directly in their native configuration without disturbing them. When I said slices I mean physically cutting the tissue which you do for STP but not for CLARITY. Hopefully this clarifies my response.

You don't need to physically section the brain, but you still need to take optical sections for CLARITY. Unless there is a microscopy technique for creating 3D images that doesn't involve stacking a bunch of 2D images, of which I'm not aware.

Right, but optical sectioning does not disturb the tissue like slicing, nor does it destroy connections or cause swelling.


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What are the movement mechanisms of thrombus?
I am thinking how thrombus (veins, arteries and heart) can move.
Secondary mechanisms come to my mind only:

some enzyme which lyses it, probably adhesion mechanism.
Blood circulation (flow rate) is one secondary measure, I think.

I am not sure if there exist any primary mechanisms:

In veins, there are valves which probably can help thrombus go forward by pushing.
Veins can also dilate so dilation of vessel can help.

Arteries do net dilate their diameter.
So aim would be there to maximise laminar flow, and decrease turbulence.
So probably the question is related somehow to the laminar flow which could help thrombus to move.
How can thrombus move in veins, arteries and heart?

Have you found the answer of this one? Is this the thing :http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3681659

@DevashishDas I considered your pointed paper. I added my considerations about it. I think the paper makes big simplifications about the processes in movement of thrombus.

This answer aims to list existing models and do meta-analysis about them.
This answer is a draft.
There are many models made based on the thrombus movement.
One of them is proposed by DevashishDas' answer but it seems to focus only on the first stage of hemostasis:

The model assumes thrombin is generated on the surface of activated
  platelets in the thrombus core and is transported through the fibrin
  network that surrounds the core both by advective flow of fluid
  permeating through the fibrin network and by diffusion through the
  fibrin gel.

and particularly the model keeps these values constant and simplifies

To calibrate the model, we experimentally determined fibrin clot
  permeability and thrombin diffusion rates through a fibrin network.

which I think should be dynamic (not constant) because of the three endothelium main factors listed below.
Endothelium is a dynamic structure controlling the fibrin clot.
Thrombus Hemodynamics Model

Fibrin Networks Regulate Protein Transport during Thrombus Development by  diffusion-advection equation (Stokes, continuity, Brinkman equations)

which is about the first stage of hemostasis because of its simplification about fibrin clot permeability and thrombin diffusion rates.
Hemostasis
There are three stages of hemostasis altogether which work parallel together:

primary (formation of the platelet plug)
secondary (formation of fibrin through the coagulation cascade)
tertiary hemostasis (formation of plasmin for breakdown of the clot)

Primary hemostasis is the formation of the primary platelet plug.
It involves

platelets
blood vessel wall
von Willebrand factor

Normal endothelium prevents hemostasis.
Injury of endothelium

involves vasoconstriction (local)
enhances adherence of platelets to exposed platelet subendothelial surfaces
and activation of coagulation process

The formation of primary platelet plug involves

Platelet adhesion,
Platelet activation, and
Platelet aggregation.

Main steps in blood coagulation:

Formation of prothrombin activator complex (thrombokinase)
Conversion of plasma protein prothrombin into thrombin
Conversion of dissolved plasma fibrinogen into fibrin (makes filamen- tous skeleton of fibrin clot)

Clot retraction

The platelets in the clot contain contractile proteins.
They bring the edges of the wound together, which also reduces the chance of further bleeding - not vasoconstriction here!
The contraction process also supports the wound healing process as it brings the ends of the wound together.

Clot retraction is the process of getting clot towards fibrinolysis process. Fibrinolysis is the process where a fibrin clot (product of coagulation) is broken down. Its main enzyme plasmin cuts the fibrin mesh at various places, leading to the production of circulating fragments that are cleared by other proteases or by the kidney and liver. Clot retraction and fibrinolysis are necessary to remove clot so wound healing can proceed.
Myogenic and metabolic autoregulation by endothelium
Myogenic control involves the localized response of vascular smooth muscle to passive stretch - reflex contraction when stretched to decrease flow, reflex relax- ation when stretch is reduced to vasodilate and increase flow. This maintains a relatively constant flow locally when pressure fluctuates.
Myogenic and metabolic Autoregulation is the automatic adjustment (local) of blood flow to each tissue in proportion to its needs (oxygen, nutrients, ...), and is controlled intrinsically by modifying the diameter of local arterioles. It involves localised response of vascular smooth muscle to passive stretch - reflex contraction when stretched to decrease flow, reflex relaxation when stretch is reduced to vasodilate and increase flow. This maintains a relatively constant flow locally when pressure fluctuates.
There are three types of substances secreted by the endothelium (1):

NO
Endothelium hyperpolarising factors
Endothelins.

where I think the modelling should focus on these three factors.
Sources

My discussion with a researcher in this field 7/2014
My notes in three Physiology courses during years 2011-2014
Costanzo, Physiology, book
Guyton, Physiology, book


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Why are new vessels more permeable in microvasculature?
I know for microvasculature

New microvasculature (arterioles, venules) are always more permeable
  as they lack pericytes.

and then I have this sentence about new blood vessels (not specific)

New vessels contain initially only proliferative endothelium, the basement membrane has not formed yet, and pericytes are absent.

However, I think pericytes are only around microvasculature.
I think the second statement is correct for microvasculature too.
Why are new vessels more permeable in microasculature?

Is there something I'm missing to answer your question?  Perhaps I don't understand the question then.  Otherwise, please accept to help our questions/accepted answers ratio.

In adult/pediatric humans, no they don't.  A good figure to get everyone on the same page was made by Cleaver & Melton:

It is important to note that:

In fact, endothelial diversity is reflected by vessel size-specific,
  organ-specific and even age-specific differences. (1)

Developing blood vessels in the fetus can be a bit of a different story, and highlights the fact the one should loose the "inert plumbing" mentality of the previous century.  Modern research tells us that the epithelium is a very dynamic region that participates heavily with signalling.
When large vessels are growing the fetus, mesenchymal stem cells and neural crest cells are the normal precursors to pericytes, but depending on exposure the line between pericyte and smooth-muscle cell can be blurred (2).  I'm assuming it's beyond the scope of the answer to go into the signalling differences.
A good review of endothelium generation, and the surrounding tissue, can be found here.

But think about angiogenesis. There are forming new new vessels in microvasculature which do not have pericytes. I think that should make them more permeable.

Actually they are going to have at least mesenchymal stem cells recruited before the vessel scaffolding is extended.  You might have the order backwards.  I don't know the permeability difference between full differentiated pericytes and stem cells, but it may not be drastic.  I will see if I can find some lit on the subject, but I'm worried there won't be any.


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Explanation of the terms "downstream signaling" and "upstream signaling"
In molecular biology, what's the meaning of the terms "downstream signaling" and "upstream signaling"? What's the difference between them?

You are thinking of transcription factors? Or is it more signal transduction?

@Chris well, I'm not sure. I presume that one uses the same terms in both contexts because they have something in common, right? I'm looking for an explanation of these terms in their more common uses.

It simply means after and before with respect to the flow of information in a given pathway. For example, consider this schematic representation of a pathway:
TF1 ==activates==> gene1 ==produces==> Kinase1 ==phosphorylates==> ProtA

In this schema, Kinase1 is downstream of TF1 and upstream of ProtA. Or, to take a classic example (source):

MEK1/2 is downstream of Raf and upstream of ERK1/2.

Perhaps worth pointing out that there is a flow of information in a signalling pathway so at any point in this flow you can look upstream, to where the information came from, or downstream to where it is headed. That's where the metaphor comes from.

If you think of a transcription factor, than this factor needs to be regulated. This happens either by signalling pathways and also on the gene expression level (how much of the factor is available). So everything what regulates this factor is called upstream (look at the image below).
Everything which is regulated by our factor (other genes) is located downstream of it. I think these terms come from the flow diagrams which are pretty usual in this context.
Look at the figure (from SABiosciences)

Here the signal comes from the membrane and is mediated through different factors until its passed into the nucleus.


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What is the genetic distance where linkage can be ignored?
I heard several times that two SNPs, that have at least 1'000 nucleotides between them, can be seen as 'unlinked' due to frequent recombination events. I also once saw a paper showing a graph "degree of linkage vs. genetic distance". Unfortunately I can't remember which paper it was. Does anyone know where this number (1000) comes from?
PS: I'm aware that this topic is much more complex, especially if you are interested selective sweeps.

I think you must have misremembered what you heard.
The cut-off distance for genetic linkage is 50 centimorgans which corresponds to 50% recombination. In the human genome 1 centimorgan is approximately 106 base pairs, so the 'unlinked distance' is 5 * 107 base pairs.

Do you have a citation for that?

Well, you could start at the Wikipedia page for centimorgan - that's where I got the 1,000,000 base pairs from. The table at http://www.nature.com/nature/journal/v409/n6822/fig_tab/409951a0_T1.html gives some real values, which illustrate how it varies. If "unlinked" equated to 1,000 base pairs, classic genetic mapping which relied upon measuring linkage between genes would have been impossible - everything would have been unlinked.

I totally agree with @AlanBoyd. One cannot ask whether an approximation is reasonable or not without specifying the model of interest. Depending on the model of consideration some level of recombination might be enough so that you could consider two loci to be unlinked. I have never seen this kind of approximation though!


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How to parse SCOP parseable files PDB residue identifiers?
I am trying to parse the SCOP parseable files, specifically dir.des.scop.txt ver 1.75. But, I have been facing problems with the PDB residue identifiers in the file. This is a tab limited file and the PDB residue and chain identifier is the 6th column which. An example of this identifier is A:1-28,A:77-837 for domain d1kk8a2.  Hence forward I'll represent that as domain_id (pdb_id chain&range). This particular example is straightforward, which means the domain d1kk8a2 consists of residues 1-28 and 77-837 of chain A of the corresponding PDB entry 1kk8. But some of them are unintuitive and like d3ckra1 (3ckr A:-2-385), what does the negative entry for the start mean? And this example d2p83b1 (2p83 B:61P-385), there is a P in the range (61P-385).
If you go to pdb website and search for the corresponding entries, then go to the sequence tab, you will see the alignment of the PDB chain and the corresponding SCOP domains. The ranges shown there correspond to the entries in SCOP, but it is difficult to make sense of it. Can someone please explain or provide some pointers. Thank you.

PDB residues are described by the residue number and an insertion code. Residue numbers can be any number, including negative values. In 3CKR the first residue has nr. -6, followed by -5, etc. This might indicate that there are additional residues at the beginning of the sequence, relative to other PDB entries. In 2P83, the first residue has the number 61P. Take a look at https://lists.sdsc.edu/pipermail/pdb-l/2004-March/001513.html for an explanation why PDB residue numbers have insertion codes.

Thank you very much for the helpful answer. I would like to get the residue numbers associated with each PDB protein chain. I was able to get the sequences from this location ftp://ftp.wwpdb.org/pub/pdb/derived_data/, but I could not find the corresponding residue numbering.

I think you need to get a PDB file parser and parse the information out of there ...


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Do Asian women have more difficult births than Europeans?
I recently heard a claim that Asians in general have more difficult births than Europeans. Is this true?
I have found a few studies(1,2) on the effect of ethnicity on birth outcomes but they seem to be limited to a small geographic area or focus on aspects such as risk of premature birth, neonatal and/or maternal mortality, etc. Those are of course important facts, but I am more interested in whether an otherwise normal birth is likely to be longer and/or be perceived as more difficult by this specific ethnic group, on basis of their ethnicity alone.
I found a few articles dealing with possible effects of specific genes on duration of labor. Debiec et al. (3) write that

Asian women had slower active labor than other ethnicities (P < 0.01). Asian women also reported less pain during their labor compared to all other patients (P < 0.001). Slower labor progress was associated with less rapid progression of pain, but this did not obviate the effect of Asian ethnicity on pain.

According to Reitman et al.(4,5) the genotype CC at the SNP Rs1042714(9), which is more prevalent in ethnic Asians, is associated with longer duration of first-stage labor. Polymorphisms in the oxytocin receptor (OXTR) gene have also been tied to variations in labor progress (6,8), but I haven't found data on the prevalence of these polymorphisms in Asian populations.
Greenberg et al. (7) write that "Nulliparous Asian women had a significantly longer second stage and higher rates of prolonged second stage". However, after controlling for confounding variables the actual increase in mean second-stage duration compared to white women was only  5.2 and 5.9 minutes for nulliparous Asian women with and without epidural analgesia, respectively. They also write that

When the rates of second stage of >3 hours were analyzed by epidural subgroups in the multivariate analysis, black women with epidural analgesia had lower rates than white women, and Asian women with epidural analgesia had higher rates than white women, regardless of parity, although no differences were demonstrated among women without epidural analgesia.

Considering the above sources and any other that may exist, is it reasonable to state that Asian women in general have more difficult births than white/European women?

Pure speculation: could this be related to the fact that Asian women tend to be smaller than Caucasians and would therefore have thinner hips which might make giving birth harder? Also, you might want to define "difficult labor", the first study you cite claims that Asian women had less pain, despite longer labor.

I think that was mentioned in one of the articles. How to define "difficult labor" is definitely an issue. I'd think that maybe there's some official objective or self-reported measure that's used in research?

There probably is but I have no idea. Still, less pain seems like easier labor to me. But then, I am neither an MD nor a woman, let alone a mother, so what do I know.


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Gene pool simulation
this simulation, you sampled the gene pool without replaceing beads in the beakerafter you drew each one. Thus, f(A) and f(a) in the gene pool changed slightly after each bead was drawn. For example, if you begin with 50 light and 50 dark beads, the probability of drawing a dark bead the first time is 50/100 = 0.5. THe beaker would then contain 49 dark beads and 50 light beads, so the probability of drawing a second dark bead becomes 49/99 = 0.495. Does this make your simulation slightly less realistic? In small natural populations, does one mating change the gene pool available for the next mating, or not? What biological factors must be considered in answering this question?

Homework questions should show some effort to answer them yourself.

non-replacement may work in the case of strictly monogamous/monoandrous society..

I am not sure I'm answering your question but I hope this will help.
There are two main models of genetic drift in biology: Moran model and Wright-Fisher model.
The Wright-Fisher model implies picking $N$ beads (where $N$ is the population size) with replacement in order to form the new population. Therefore, the change in allele frequency (due to genetic drift) follows a Poisson distribution.
$$\frac{2N!\cdot p^kq^{2N-k}}{k!(2N-k)!}$$
The Moran model consists of the following: At each time step you draw two beads. One disappear from the population and the other replicate in order to keep a stable population size.
The two models yield to similar results. Moran model runs twice as fast as Wright-Fisher model.
I don't fully understand your model. You say that in your model you pick one bead at a time. What do you do with this bead? How do you construct your population at the next time step? Do you allow changes in population size? Can you please try to develop how you defined your model. If it is a computer simulation you might paste the important part of your code, that might help.
Haldane and Kimura both worked a lot on these models of genetic drift. For example, they provide different ways of calculating the mean time to fixation of a given allele given their selection coefficient $s$ starting from a given initial frequency $p_0$. Also some work has been done on genetic drift in population where the population size changes over time. Some work have been performed considering more or less complex probability density function for the number of offspring per individual. This kind of literature is very interesting but sometimes ask for quite good knowledge in mathematics (especially for Kimura's articles).
I once asked this question concerning the different models of genetic drift and their assumptions but I didn't get an answer yet.


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Is there a scientific name for the field of study focusing on the hemispheres of the brain and their control of opposite sides of the body?
I'm assuming this field of study would focus on motor controls, movement, and exercise, but it could also focus on activities which strengthen the corpus callosum or stimulate a specific half of the brain.

Lateralization of brain function...


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Improving myopia
I have a friend who no longer needs glasses. He previously had myopia in both eyes but over the years it has improved until he no longer needs glasses clinically. He's had glasses for over 30 years since he was around 20.
Based on the above, I'd like to know if myopia can be improved naturally. Specifically whether not using glasses helps the underlying architecture of the visual system compensate in someway, or perhaps if nutrition can reduce myopia or finally if aging is known to decrease myopia. I'm interested in any biological mechanism at play.
I have a good understanding of Opthalmology and additionally would like any answers to be evidence based.

Apparently reduction of myopia with age is fairly common. It is thought that the improved vision comes from relaxation of the ciliary muscle as the person ages. Since the lens changes shape the aberrant myopic focusing of light can be corrected to the correct location. While age was found to be the strongest factor influencing myopia progression, other factors like ethnicity and sex also play a role.
http://archopht.jamanetwork.com/article.aspx?articleid=417134#
For additional info see:
http://www.iovs.org/content/41/8/2103.long
http://www.improveeyesight.org/can-myopia-near-sightedness-improve-with-age

Thank you! I read your reference which said improving beyond 1 diopter is rare. Perhaps there are more factors at play or certain factors tilt the balance such as genetics, nutrition etc. Could you explore these also?

I'll give you an answer based on my personal experience. I know that presbyopia usually increases with aging, so presbyopia and myopia can compensate each other with time. That's maybe what happened to your friend. But I don't know if myopia is related to nutrition or the use of glasses..


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What are the effect of microtubule or microfilament inhibition on yeast expression profile?
I was wondering whether anyone has looked at what are the expression changes in yeast when the microtubule or the microfilament polymerization is inhibited? Have there been whole-genome studies?

Browsing around GEO, I see 13 experiments focusing on microtubule disruption in yeast.
This CHIP-CHP experiment actually uses nocodazole.
This is a microarray experiment with benomyl treatment.
The rest focus on specific mutants that try to perturb the microtubules in specific ways.
What's more if you broaden the search there is an extensive body of work including human cell lines work as well...

Thanks for the answer. Could you summarize what was discovered? Which genes were downregulated/upregulated/unchanged? Thanks.

GEO doesn't store results.  I'd have to go and redo the analyses myself....


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How do scientists create specific mutations?
Suppose I want to create a mutant like Antennapaedia how will I go about accomplishing it ?
I know that radiation and certain chemicals are mutagenic. So do scientists subject animals to such mutagenic chemicals and then wait for their progeny to see what mutation it has got ? Are there any specific protocols to create a specific type(for eg.homeotic) of mutant or is it pure luck ?
Sorry if I am being too naive!

Thats basically the oldest method to induce such mutations. For this purpose either radiation (x-rays) or mutagenic chemicals (like Ethylnitrosourea) have been used for this purpose. This method is undirected, so you never know what the outcome will be untill you see the off-springs. Using this method to get specific mutations is relative difficult. Its used for the detection of genes which deliver visible phenotypes (for example it has widely been used for the analysis of pigmentation in mice, since you can easily spot mutations).
Newer methods can target genes directly and either introduce or remove sequence areas. These techniques make use of homologous recombinases. In short you bring in you gene of interest in the modified version on a plasmid into the cell which you want to change. The plasmid also expresses the recombinase (this can be under a cell specific promoter to target specific cells) which then recombines the DNA between the plasmid and the genomic DNA.
An example for that is the FLP-recombinase system (image from the Wikipedia article on it):

Other examples for site specific altertions are the Cre-LoxP-System or the Crispr/CAS-System.


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Ribosomal RNA amount in a Drosophila cell
I am isolation RNA from Drosophila larvae brain with TRIzol method. What percentage of extracted RNA will be ribosomal RNA? I am only interested in mRNA, so I am trying to figure out whether I need to get rid of rRNA. Thanks

Percentage of what? Total cell mass/volume? Of total RNA moieties? Of total nucleic acids?

Ratio of ribosomal RNA in total RNA if I rephrase it.

OK, please [edit] your question to something like "I am extracting RNA using methodX, what percentage of extracted RNA will be ribosomal?" The percentages will also depend on the method used to extract the RNA.

The protocol you are using will not only leave the sample with rRNA but also non coding RNA.
Many RNA protocols will separate mRNA by affinity of a carrier to the polyA tail.  This protocol references an older paper that estimates that only 5% of RNA is mRNA.  I'd be surprised if this ratio changed by more than 2-3 fold in drosophila.
I assume that %age is by weight but it could be a densitometry measurement which is similarly interpreted.

Thanks! As a subsequent question: Do you think that huge amount of rRNA will affect my downstream experiments such as RT-qPCR? I am only interested in mRNAs.

I've not done qPCR.  I would not hesitate to compare multiple standard protocols to get a better sample. Looking at a couple of qPCR protocols you're right I only see Triazol preparations used.  PCR is pretty efficient as long as the primers are specific.  Some more homework before doing the experiment won't hurt you :)


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What is immunosuppression? Why would one use it?
What is immunosuppression? I know it is used in cancer patients, but why would one want to suppress the immune system?
Do homeopathic physicians ever use immunosuppression, or do only allopathic doctors practice this?

Have you read the Widipedia article or done a simple Google search? Please read up on the vast array of publicly available data, then either [edit] your question to make it more specific, or ask a new question.

You should edit your question and delete the reference to homoepath as this is not medicine but pseudomedicine (or add a real reference for that). Than remove "allopathic" as this is also homeopathic terminology. There is simply medicine (which is all that works) and pseudomedicine (all that claims to work but fails to proof it).

Please look up on immunosuppressants.. you'll find all the reasons on why they are used

This question appears to be off-topic because the answer is readily available by simple web search.

Immunosuppression is not used in cancer, in fact it is typically harmful unless of course the cancer is a immune or white blood cell cancer where suppressing their growth may be helpful. What you are perhaps alluding to is that an adverse effect of cytotoxic chemotherapy used in the medical treatment of cancer can cause immunosuppression.
Immunosuppression is helpful when it is causing more harm than good. The immune system is powerful and sometimes when its fighting an infection it can go a little overboard and cause enough damage to harm someone in the long term. In this case immunosuppression is helpful in preventing too high a response. For example in an organ transplant the recipient's immune system may destroy the new organ, but immunosuppression can prevent rejection.
Another case is when there is an autoimmune or inflammatory condition occurring. Rheumatoid arthritis being an example of the former and asthma being an example of the latter. In these diseases inflammation due to the immune system perhaps targeting our own body cells causes damage to our organs or cells and causes the disease. Immunosuppression here can limit or prevent further degradation or sometimes even reverse damage due to inappropriate immune responses.
Interestingly the human body must keep a good balance between being under and overactive. Certain individuals with better ability to control HIV infections or other infections are genetically more likely to also get autoimmune conditions.

Referring to immunosuppression in cancer, I would expect him to be thinking of leukaemias or lymphomas. Immunosuppression is actually quite common there firstly because the cancerous cells are most often (in lymphomas always) themselves immune cells and directly affected by immunosuppressive treatment - on the other hand it is a typical part of bone marrow transplantation procedures, which are sometimes the best or only treatment for these conditions.

Excellent point Armatus. That's what I was referring to in my first sentence but thank you for elaborating it.


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Ferredoxin synthesis pathways
I have been thinking about some alternative CO₂ fixation pathways. As almost all of them include ferredoxin reduction I started to wonder where does the ferredoxin comes from. I could not find any of the pathway in databases (ecocyc,kegg). Does any of you know if the biochemical pathway and the genes involved in synthesis are known?
Thanks,Martin

Wikipedia:"ferredoxin". Ferredoxins are proteins containing FeS centres.

Yes, that is the definition of them. But in which biochemical pathway are they produced...

They are proteins: encoded by genes, synthesised by ribosomes.

I do understand that! But I am interested with which genes are they encoded!

http://www.plantphysiol.org/content/134/1/255.full is a link to the full text of a paper about the ferredoxins of Arabidopsis. That should get you started: if you are interested in ferredoxins from some other species you could obtain the sequences of the A. thaliana proteins and use those to search in other genomes.

http://www.ncbi.nlm.nih.gov/gene/?term=ferredoxin

Ferredoxins and variants such as fladidoxins and rubredoxins are simply electron carrying protein that need to be regenerated, like the more energetic NADPH.
The key thing to remember is that redox balance is key. You cannot have electron pair accumulate so there has to be a terminal acceptor. In the case of aerobic resipration it is oxygen, in the case of iron or sulfur dissimilation it is iron(III) or sulfate, in the case of fermentation it is a small highly oxidised carbon (e.g. methanol, ethanol, butanediol, formate, acetate, propionate, lactate, succinate, fumarate). Carbon fixation requires electron pairs, which come from somewhere. The mechanism of how the carbon dioxide is assimilated can be via the Calvin cycle (plants and cyanobacteria), the Wood-Ljungdahl pathway or from the 3-hydroxypropionic cycle Prof. Fuchs described in Chloroflexi and Sulfolobus. In all three electrons come from somewhere (generally water, carbon monoxide and sulfur respectively).
The reason why there are both ferredoxins and NADPH is a tad harder to explain, but has to do with redox control and the fact that not always ferredoxin is regenerated by a NADPH reductase (also: NADH = catabolic, NADPH anabolic), but could be a fumarate reductase or similar.

Thanks for your answer - Could you add resources and references?


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Are the 8 principal sugars in glycoproteins "essential sugars"?
Are there "essential sugars"? Some have suggested that the 8 principal sugars found in glycoproteins are "essential sugars":

Galactose
Glucose
Mannose
N-Acetylneuraminic acid
Fucose
N-Acetylgalactosamine
N-Acetylglucosamine
Xylose

I realize the liver can convert glucose to many different sugars, so by "essential sugar" I mean a sugar that is difficult to obtain from diet or that the liver requires much energy to convert from glucose.
How difficult is it for the liver to convert glucose to the other sugars listed above?

Your main question can be answered by simply copy/pasting it into google. Did you try to research this before posting? I assume you did, so what is it that was unclear to you?

that wasn't so classy changing the question when we tried to answer your original one. oh well.

@shigeta: Well, the question was about to be deleted anyways…

There are no essential sugars.
In the context of nutrition "essential" usually means "must be obtained from the diet". So for example the amino acid methionine is an essential amino acid (for humans).
Within this definition there are zero essential sugars. A Google search for essential sugars reveals lots of sites like this one. The site lists glucose as the first "essential sugar". In fact we can make glucose from a range of other nutrients including amino acids, lactic acid and glycerol. The second sugar on the list is galactose - we can make that from glucose. And so on...

To put it in hard words: Its pseudoscientific bullsh*t.

By "essential" I mean "difficult to synthesize of not obtained from the diet."

I think you will have to define "difficult". But really, now that you have edited your question, you are asking for an entire chapter from a biochemistry textbook.

@AlanBoyd is right that the term 'essential sugar' is not a scientific or biologically defined term and is not true given the meaning of the word essential that is in use in biology.
In alternative health and diet circles, the term 'essential sugars' refers to a set of simple carbohydrates which are hypothesized to be important for good health and nutrition in people.
Even if this were a valid approach in humans its very unlikely to be the same specific sugars and proportions for other animals and living things.
So given all these caveats the reference I found for 'essential sugars' lists these 8: glucose, galactose, fucose, mannose, glucosamine, galactosamine, neuraminic acid, and xylose.
As far as whether this really helps us, I personally don't think this is the key to good health in and of itself.  It really oversimplifies all of the biomachinery we have to break down and utilize carbohydrates.
As the diet recommends the eating of vegetables which aren't too green, avoiding fructose, it doesn't seem to hurt.  Carbohydrates from food are often the product of breaking down complex carbohydrates.  I feel as if watching the glycemic index of your food and avoiding soft drinks and too much fruit juice will get you further in terms of health.  Avoiding simple carbohydrates entirely in your diet also has advocates and there is some medical research that backs it up.

I don't even see reason to avoid frucose, since the body can make frucose-6-phosphate from glucose-6-phosphate. Frucose, which the cells take up also get phosphorylated, so this doesn't make any difference.

thanks for mentioning.  I take it you mean fructose?  That part about not taking in high fructose has some pretty good science behind it.  In humans (and rats etc) fructose is only metabolized in the liver so when you have a large ingestion  of fructose the local concentration in the liver becomes very high and it manufactures fat as opposed to breaking down to other carbohydrates.  http://www.sciencedirect.com/science/article/pii/S0168827808001645

Yeah, I mean fructose, damn typos. But it doesn't make too much sense to worry only about one carbohydrate. Nutrition has to be balanced, so if we avoid fructose, but live otherwise unhealthy (meaning too much fat and so on) this will change nothing.

hey @Chris - that's biochemistry for ya  - the devil's in the details :)   in general engineered foods are suspect as far as i'm concerned and probably aren't healthy as they are not a product of the environment we evolved from - my soapbox...

I am a biochemist :-) And I don't worry too much about food - but I try to avoid a few things.


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Why are cats attracted to catnip?
According to wikipedia, the active substance is nepetalactone ($\ce{C_{10}H_{14}O_{2}}$) which has weak sedative, antispasmodic, febrifuge, and antibacterial effects in humans. Why are cats so fond of it? Why do they seem to get high on it?
According to the same wikipedia page, the effect is gene-linked but it does not mention which genes, what they code for or any details whatsoever. Are all felines affected in this way or only Felis catus? What is the biochemical mechanism by which cats are attracted to catnip?

This is essentially answered on Wikipedia:  "catnip", although there is no reference to addiction.

if something is on wikipedia a question you can't ask for the same information on stackexchange? I doubt that this is in the guidelines. We would also need to clear out maybe 20% of our content here.

@shigeta I believe that the policy on StackOverflow is the exact opposite. i.e., answers should ideally be canonical and stand on their own and duplicating information found elsewhere is alright. I can't be bothered to find the meta link at the moment, but it's there somewhere.

what I can see here is that catnip is not addictive and i think cats might not be attracted to it until they actually take it in.. http://chemistry.about.com/od/medicalhealth/a/Nepetalactone-Chemistry.htm

Nepeta cataria(Catnip, Catmint, Catnep) is a plant belongs to the family Lamiaceae.It is a  herb that has been recognized for its medicinal properties for many centuries. Over time it has been used in remedies to cure internal cancer, smallpox and scarlet fever.Also it was believed that a dense growth bordering fields helped to protect crops because of its ability to repel rats.
Major Active Constituents of catnip includes a and ß nepetalactone  citronella , a and ß citral , limonene , geraniol , thymol , and carvacrol  epideoxyloganic acid and 7-deoxyloganic acid

Nepeta cataria has a carminative, anti-spasmodic, astringent and anti-flatulent effect on the gastrointestinal system, particularly on the stomach . It is also a diaphoretic and antipyretic in times of fever . Nepeta cataria is similarly recognized as a tonic, mild nervine, and sedative, with a slightly emmenagogue action . With respects to cats, Nepeta cataria produces an aphrodisiac effect.

http://scu.edu.au/scps/index.php/125/
A research paper published in 1994 states that,

Catnip was  the most promising candidate lures tested. The 'catnip-response' is
  inherited as an autosomal dominant (Todd 1962). In trials, behavioural observations showed
  that 50% of the subjects (including all four domestic cats and 8 of 20 feral cats) showed the full catnip response (B. K. Clapperton, unpublished data). This includes sniffing, licking, rubbing and head-over rolling (Tucker and Tucker 1988). Nine of the remaining 12 feral cats approached and sniffed at the catnip samples. This suggests that, although not all cats are genetically determined to respond to catnip , these odours may act as more general attractants.

http://www.southwestnrm.org.au/sites/default/files/uploads/ihub/clapperton-bk-et-al-1994-development-and-testing-attractants-feral-cats-felis-catus.pdf

When cats inhales nepetalactone it stimulates the olfactory bulb, the part of the brain that processes odors. The olfactory bulb then interacts with the amygdala, the brain region associated with emotion and decision-making, and hypothalamus, which controls a variety of bodily functions. From the hypothalamus, nepetalactone stimulates a sexual response in cats that are genetically predisposed to sensitivity to catnip. (About 20 to 30 percent of cats don't seem to react to the plant.)this is why mostly adult cats shows significant addiction to catnip.

http://www.compoundchem.com/2014/06/08/catnip/

The catnip stimulates an Innate Releasing Mechanism(IRM) in domestic cats that elicits a predictably playful behaviour pattern apparently independent of experience and learning(Ewer,1973 and Leyhausen,1975) ,trans-nepetalactone is reported to produce behavioral respondse in cats.It has been verified by Todd in 1963 that capnip is mediated by Olfactory and not gustatory stimuli.Catnip sensitivity has been related to a dominant autosomal geneand to the estrous cycle by Todd.The reports shows catnip elicits behavioral respondses in domestic and wild cats, but these responses are not shown by female sex.In addition, it has been suggested that catnip mimics a pheromone found in cat urine, however evidence supporting this theory is scant.(Todd 1962)

http://link.springer.com/article/10.1007%2FBF00987747#page-1

Seems to be lots of good information here. However, you need to be more careful about including references and to clearly show when you are quoting from other texts. At the moment this is borderline plagiarism. I'm saying borderline since some of the sources are linked in your answer, but it is not clear that the actual text in your answer has been lifted, see e.g. http://scu.edu.au/scps/index.php/125/ and http://www.popsci.com/science/article/2013-04/catnip-effects-humans

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


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What evidence do we have to derive a rate of evolution?
When analyzing how the human species evolved and will continue to evolve over time, what evidence and tools (theory/models) do we have available to derive the rate at which this happens? Is it even possible to set reasonable bounds on such a rate?
Also, how large is the available dataset? And how does the dataset match with theory? I would especially like to get an idea of how well statistical (Bayesian/likelihood) analysis matches with empirical data and more conceptual models.

there are several such clocks, but a main methodology is to watch the number of mutations that appear in genomic dna over time. Their sequence divergence varies over time at varying rates, but overall that's the clock.

And is there a good database containing such data, or is it mostly to be found separately in published papers?

This question is very broad. And because of its broadness, I am afraid you won't find a database that will give you what you're looking for.

Are you interested in some specific phenotypic traits?
Or in some specific genes?
What time scale are you interested in?
Do you want to know about the time that a given allele needed to reach fixation?
Do you want to compare the number of mutations that accumulated in a given DNA sequence between human and close relatives (apes, primates, mammals, ..)?
Do you want to compare the evolution of the mitochondrial DNA between human populations that have different mating systems?
Evolution in response to HIV?

If there is one specific gene or trait (including traits such as the mutation rate) that interest you, you might want to ask a more specific question on another post.
Concerning the methodology, I agree with shigeta that probably the main methodology you'd be interested in is molecular clock. The ratio of synonymous over non-synonymous mutations are also of interest to compare rates of evolution. Comparisons of mutations accumulation between different sequences. But you might also be interested in fossil records (depending on the trait and the time scale you're interested in). Or more interestingly in selective sweeps. Selective sweep is the reduction in polymorphism and heterozygosity of linked loci to the locus under selection. In humans examples exist in the microcephalin gene or in the lactase gene for example. You might also be interested into allele frequency cline over spatial distribution and things like that. Comparison of evolutionary rates between populations of different size might also give you some insights in how quick does evolution occurs in humans. There are probably tons of other methodologies one could use.
You talk about comparisons between empirical data and theoretical model. But again the question is too broad I think. There a tons of different models to be considered depending on what you are interested in.

Let me expand on my comment...
There are several such clocks, there are a couple of methods in use.
The oldest and primary methodology is to look at the bodies of the plants and animals and assemble the evolutionary tree by how closely these animals resemble each other (taxonomy).  There are several authoritative databases on this data.  The encyclopedia of life is a major aggregator for taxonomic analysis.  They are tied into the Integrated Taxonomic Information system (ITIS).  The millions of species known have not been sequenced and this is probably the most comprehensive overview of life as we know it on earth.  The ITIS data is downloadable.
On the other hand the taxonomic record has many known problems.  For example Rodentia (rodents) are known to be a bit of a dumping ground where hard to classify mammals are put because we just don't really know where they go.
In cases where there is money and energy to resolve an issue like this, a main methodology to gauge the evolutionary distance is to observe the number of mutations that appear in genomic dna over time. Their sequence divergence varies over time at varying rates, but overall that's the clock.  This is pretty indisputable, but the coverage over the phylogenetic tree is low.  There are a few databases focused on bacteria for instance and fungi, but you have to know what you are looking for.  Often such evidence is entered into databases such as ITIS over time.

There are currently 7 billion human organisms on the planet.  We each have genome of about 3 billion letters, and we all  have millions of differences in our DNA from each other.  Some of these differences are private, only found in one individual, some are found in only one family, some only found in some larger kin groups.  Over time, more novel polymorphisms will arise, and those and the existing ones will change proportion in sub populations, and in the human species as a whole.  Some will have phenotype effects that we can measure.
You think the changing of those millions of DNA sequences in a population of 7 billion can be meaningfully summed up in some single measurement?

I'd argue against using models of any sort, because the answer will be way off even if you use it on existing hard facts. Common sense is required here, I personally think it's silly to be trying to find a model for evolution when it is known evolution isn't a constant process and has no intent. Also, evolution can lead to a dead end.
The main reason why common sense is needed is that only then you can know when a species stopped evolving because there's no selective pressure. There are very few human groups today which are still evolving, but the species as a whole isn't evolving anymore and it won't in the future. There - just saved you the trouble of modeling future evolution because there won't be any.