Do fat people have more chances of developing nitrogen bends? I was reading some text on deep sea physiology. I got to know that solubility of nitrogen in fat is five times that in water. The exact text from the book animal physiology adaptation and environment by Knut Schmidt-Nielsen, was:-

  The body fat, which in a normal lean male constitutes about 15% of body weight, dissolves about five times as much nitrogen per unit weight as does water

I think that having more body fat increases your body's nitrogen saturation capacity, thereby increasing the probability of nitrogen bends.
(Nitrogen bends or aeroembolism is the phenomenon in which nitrogen gas forms bubbles in the blood stream near joints and cause pain)

So can I conclude that fat people (those who have more body fat), are more likely to develop nitrogen bends in their blood stream?

I'd be grateful if anyone out there can help.

Well, you're right! First of all,

  Nitrogen Bends or Decompression sickness (DCS) is a disease that arises as a consequence
  of bubbles forming within tissues. Inert gases, such as nitrogen
  and helium, enter the body through the lungs during inspiration.

  Increased BMI (Body Mass Index) implies an increased fat content of the body. This
  increased body fat leads to increased nitrogen storage and hence
  possible excessive nitrogen bubble formation and thus increased the
  risk of development of DCS.

Learn more about the relation between Fat and Nitrogen Bends by reading Diving and Hyperbaric Medicine  Volume 36 No. 3 September 2006


What volume of elution buffer for plasmid-containing filter paper? I am attempting to elute a 9kb plasmid from a square of filter paper sent to me to be transformed into DH5a E. coli (photo below). Each filter paper square has been spotted with 1ug of plasmid DNA.

I have two questions:

AddGene's protocol states to elute the DNA using 30ul of TE (I'm using H20 as that's all I have atm). Using a similarly sized piece of filter paper to test, I added it + 30ul of h20 to a 1.5ml tube with a quick 4k spin down and have observed that the 30ul is completely absorbed by the paper as shown in the photo. How should I resolve this? Add an additional 30ul? I also tried to use a pipette tip to shove the paper down and squeeze out the water but you can see it didn't work.

What volume should I use for transformation knowing that the filter paper contains 1ug and I need to use additional elution volume? Most protocols I've read call for 1-5ul of DNA and AddGene calls for 2ul assuming 30ul elution volume.

Thank you.

The answer to this is... some.
You only need a tiny amount of plasmid DNA to transform bacteria like DH5$\alpha$, typically in the 1-10 ng range, but much less, as low as about 10 pg (10 picograms) may still work. If you can get even 0.2 ul of the liquid out of that tube, try using that in the transformation.
Things you can try;

remove the paper, spin the tube down and see if you can recover even a tiny amount of liquid.
Add a bit more liquid - another 30 ul will be fine
Snap the tube lid closed on the paper to hold it in place, then spin the liquid out of the paper - this is quite difficult to do.

Note - even with 10% DNA recovery (very low for this method), with 30 ul you will still have 100 ng of DNA, or about 3.3 ng/ul.


How does Organ Transplant work well despite having Foreign DNA My question is little bit related to this one Why does organ transplant work although it seems organ's motor neuron isn't connected to recipient's CNS but only little bit.
Problem
Suppose the case in which person A got his kidney transplanted (and person B is donor). Now both A and B have different DNAs and how come lung (organ) transplant works well for person A and how does person A's DNA going to "accept" the lung's DNAs and how is replication going to work across the foreign lung?
Question
Will person A's lung contain:

Person A's DNA
Person B's DNA
DNA of both Person A and B (will convert to person A's after some-time having a certain half-life for it)
or
Forever contain both DNAs

Thanks in advance and kindly provide reference for your answer. Thanks

4. Forever contain both DNAs
Yes, the donor kidney still has (and will remain to have) the donor's DNA. That is irrelevant to the acceptance and continued functioning of the organ, though.
The thing that could make an organ transplant fail is the recipient's immune system. If it detects the organ as "alien", it will attack it like any other foreign particle, and the body will reject the transplant.
To avoid this, two things are being done:

A donor is sought whose organs have similar protein markers to those of the recipient. (Those markers, and not the DNA, are what the immune system looks for when trying to tell friend and foe apart. DNA is inside the cell, the protein markers are on the outside.)
Similar protein markers are usually found in people with similar DNA, which is why close relatives are tested for this kind of compatibility first.

The recipient recieves special drugs that partially suppress the immune system.

If the recipient's body does not reject the organ, it can continue to function normally despite its different DNA. If, for example, there is a genetic defect in there that will lead to some kidney-related issues at a later time, it will be the donor's defect. If there has been a defect in the recipients kidneys that would have led to issues later in his life, that defect would be gone with his kidney. Other cells in his body would still carry the same defect, but those cells are not kidney cells, and thus that particular issue will not manifest itself.
Replication of cells will follow the same pattern: Cells from the recipient will replicate the recipient's DNA, cells from the donor's organ will replicate the donor's DNA.


Regarding cellular self-destruction I heard and read telomere 'health' or 'length' ( if that's right ) has alot to do with cell 'health'. If telomere 'abilities' are 'restored' to a 'healthier' status then the cell it is in functions as though it were 'younger'.  I was wondering since cancer cells grow without limit and 'older' cells or unstable cells grow with less ferver do cancer cells have functioning telomeres within them and would they somehow be alot more 'robust' then telomeres in normal cells? If this is true could telomeres from cancer cells somehow revitalize the telomeres in normal cells?

Telomeres are at the end of the chromosomes and get shorter with every cell division, since the lagging strand is missing a start point for the DNA polymerase. This limits the number of cell divisions to 40 to 60 before the cells go into senescence and stop dividing (they are not dying at this point). This phenomenon is called the "Hayflick limit".

Cell populations which need to divide more often or cells which need to maintain a long telomer status (stem cells) because they give rise to other cell populations, have an enzyme called telomerase which has it's own (RNA) template and can enlarge the length of the telomere. See the figure how this works (from the Wikipedia article on Telomerase):

To answer your question: Younger cells have longer telomeres (compared to older cells). Usually cells stop dividing, when their telomeres get too short to avoid chromosomal damage, due to the progressive shortening of the chromosomes. In cancer cells the pathways controlling this (for example p53 and the retinoblastoma pathway) are often mutated, so that the cells divide forever. This leads to chromosomal instability, further mutations and chromosomal disarrangements, which can cause real havoc.

It also happens for some cancers that they manage to reactivate their telomerase, thus keeping their telomers at a healthy length and preventing chromosomal damage. By this activation they get around reaching the Hayflick limit for the maximum number of cell divisions and are truly capable of living forever. The famous HeLA cell line for example is telomerase positive.

The activity of the telomerase in one cell has no effect on the neighboring cells.


What kind of caterpillar type bug is this? I've made a photo using the reversed 58 mm lens and my cropped DSLR:

Could you please help? I really don't know where this came from.

I found it in Russia.

Likely to be a black carpet beetle larvae

http://www.ipm.ucdavis.edu/PMG/PESTNOTES/pn7436.html

For more facts try: http://www.ipm.ucdavis.edu/PMG/PESTNOTES/pn7436.html
Don't worry though, they live everywhere!

Wikipedia has some info on the family of beetles that they belong to (http://en.wikipedia.org/wiki/Dermestidae). I don't think they really cause any harm, except in natural history museums where they tend to munch the collections of animals...although this can also be a good thing:

'They are used in taxidermy and by natural history museums to clean animal skeletons' 1

1 VanClay, Mary. "Bitten By the Bug". www.johnsonstring.com. Retrieved November 10, 2012.


Can genetics be an answer to our human flaws? Ok I have been thinking genetics is that part of biology wich has the ability to change the genes of an organism as such it changes their abilities as well if so why cant we use this technique to change the problems that we face for example:
The cells of plants contain chlorophylle as such they can create their own food thanks to sunlight+water+CO2 what if we take the gene responsible for this and transfer it to a human being like this he will not have any need to eat(but he still can if he wants for more energy like meat-eater plants) however a downside would be green skin but I think is worth another one would be the lizards wich have the ability to regenerate limbs and other body parts that were lost this can help those who suffer from absence of body parts. Wouldn't this be amazing like a human with different abilities to adapt and survive these that I mentioned are simply core of our problems these days there can still be more to it.  SO why isn't this technique used for a solution to our problems?

Here are three elements you want to consider

we are not able to make genetic manipulation of all the cells in a grown-up individual. There exist a whole bunch of treatment making use of genetic engineering in adult humans but they are typically quite costly.
The phenotypic traits that you mention are extremely complex. There is no simple gene that will allow a lizard to regenerate a lost limb. You will have to learn more about cell specialization in order to understand why lizards have a power of regeneration that we don't. Similarly, you can't just transfer a few genes and expect a human to be able to photosynthetize. Photosynthesis is a very complex process which require the ability to perform a whole bunch of reaction, which require organelles we don't have for the reactions to take place, which requires the ability to gather and concentrate lots of $CO_2$, etc... It is really really not that easy. You should learn more about the specific traits you are mentioning to get a notion for why it is not that easy.
Genetic manipulation on human is vastly illegal for ethical reasons. But these ethical reasons are to be discussed on philosophy.SE.


Why is there a compound highlighted in red in a KEGG Module search? Considering the following module:
http://www.kegg.jp/kegg-bin/show_module?M00115+C00003
why is the compound C00003 marked in red?

It is just a way of highlighting your search term. If you search M00115+C03722, you will see C03722 in red.


Differences between neurotransmitters and neuromodulators According to the Wikipedia article on neuromodulation

  a neuromodulator can be conceptualized as a neurotransmitter that is
  not reabsorbed by the pre-synaptic neuron or broken down into a
  metabolite.

In another Biology SE answer I read that

  neurotransmitters can be considered neuromodulators when their action
  is on channels outside of the synaptic cleft.

Trying to bring these two conceptualizations together I come up with the following more specific differences between neurotransmitters and neuromodulators:

Neurotransmitters have typical short delay times (until they reach a receptor). Neurohormones may have arbitrary long delay times (the time they need to diffuse through the extracellular fluid). As a slogan: "Neurotransmitters work at once, neurohormones with a distance-dependent delay."
Neurotransmitters have specific target neurons (via the receptors of the synapse where they are released). The number of target neurons of a neuron (affected by the neurotransmitters it releases at its synapses) is rather well-defined (and goes into the thousands). The number of target neurons affected by the neurohormones a neuron releases is not so well-defined (and I'm missing an idea of the order of magnitude).
Neurotransmitters are effective only once and for a short time (due to fast reabsorption or break down into metabolites). Neurohormones can be effective for a long period of time.
This is due to different biochemical mechanisms by which specific neurotransmitters and neuromodulators affect specific receptors.

I wonder if this list is somehow correct and complete. (This is my question.)

Next to this list a list of commonalities would be interesting:

The same molecules can be neurotransmitters and neuromodulators.
Both are stored in and released from vesicles by similar mechanisms.
Both get effective by interacting with receptors and affect if a ligand-gated ion channel opens or not.

Key points:

Neurotransmitters directly stimulate or inhibit ionotropic receptors (the receptors of ion channels) in the postsynaptic membrane within a single synapse.
Neuromodulators act on metabotropic receptors within or outside the synapses of many neurons at the same time; they modulate the release of neurotransmitters and excitability of ionotropic receptors; the signaling between metaboreceptors and ionoreceptors usually involves a cascade of secondary messengers.

Neurotransmitters

"Classical neurotransmitters" stimulate or inhibit the fast-acting ionotropic receptors of ion channels. Their actions last few milliseconds and are limited to a single synapse, which means they are released from a presynaptic membrane of one neuron and they target the postsynaptic membrane of one (or, sometimes two or maybe more) postsynaptic membranes of the neurons involved in the same synapse, or a single muscle cell or other target cell (Oxford Scholarship, The Revisionist).

Examples of neurotransmitters: noradrenaline, acetylcholine, dopamine.

Neuromodulators

Neuromodulators act on the slow-acting metabotropic receptors inside or outside the synapse of "thousands" of neurons at the same time. In long-term (minutes), they modulate the release of neurotransmitters and excitability of ionotropic receptors. They are usually (but not necessary) released from presynaptic membranes into the synapse by the same mechanisms as classical neurotransmitters but can then leave the synapse through "spillover" and act on the neurons other than those involved in the synapse. So, their action is diffuse, but usually still limited to to certain neural pathways. (International Encyclopedia of the Social & Behavioral Sciences, 2001, Encyclopaedia Britannica, Wikipedia, Current Opinion in Neurobiology)

Examples of neuromodulators: dopamine (D receptors), serotonin (5HT receptors), acetylcholine (M and nicotinic receptors), noradrenaline (alpha and beta receptors), histamine (H receptors), endorphins and neuropeptides (Wikipedia, Journal of Chemical Neuroanatomy, 2011.)

Neurohormones are released from neurons into the bloodstream and have a systemic effect, for example:

Oxytocin and vasopressin, which are produced in the hypothalamus travel to neurohypophysis from where they are secreted into the blood and act on the mammary glands and uterus.
Adrenaline, which is secreted from adrenal medulla acts, via sympathetic nervous system on various tissues, usually on the smooth muscles of the blood vessels, heart, gut, etc.

Can a certain molecule can be a neurotransmitter, neuoromodulator and neurohormone at the same time?

Yes, for example:

Noradrenaline acts as a classical neurotransmitter and neuromodulator in the postganglionic neurons of the sympathetic nervous system and as a neurohormone secreted from the adrenal medulla (International Encyclopedia of the Social & Behavioral Sciences, 2015)

Dopamine acts as a classical neurotransmitter and neuromodulator in the dopaminergic pathways in the deep areas of the brain, such as thalamus and pituitary gland (picture); as a hormone, it inhibits the secretion of prolactin from the pituitary gland.

Are both neurotransmitters and neuromodulators stored in and released from vesicles by similar mechanisms?

Yes or no. Neurotransmitters are always released into the synapse, while neuromodulators may or may not be released into the synapse (Oxford Scholarship).

Do both neurotransmitters and neuromodulators get effective by interacting with receptors and affect if a ligand-gated ion channel opens or not?

Neurotransmitters can be effective if the ligand-gated ion channel are open and neuromodulators can open or close the ion channels.

Since the same molecule can be both a neurotransmitter and neuromodulator, it may not be that important to define the differences between the both in detail:

  It could, therefore, be concluded that the aspect of defining
  neurotransmitters has taken a back seat to the investigation of the
  actions of individual signaling molecules. (International Encyclopedia of the Social & Behavioral Sciences, 2015)


Identifying internal structure of dissected prawn Note: Some of the images might be disturbing.

I have dissected prawn for the first time. Would like your help in identifying some structures
.

This is the dissection of the posterior part of the prawn. What is this blackish structure in the middle ? This structure becomes whitish farther down. Then, it forms a small sac like structure and then becomes thin again. This whole structure appeared just after I cut the exoskeleton. It is directly above the muscles.

I think that this is it's alimentary canal and the black area has digested food in it. The sac like structure might be the rectum.

It is, indeed, the alimentary canal. It is actually this canal that it's important for one to remove when "de-veining" shrimp, rather than the vein itself, which lies immediately dorsal to the digestive tract.

In the future, I might suggest doing a little more research prior to asking the stack exchange, as frequent users of the site do like to see evidence of effort on the part of the user to find their own answers. A quick search for "alimentary canal prawn" or "arthropod anatomy" would likely have turned up your answer.


Why is there no symmetry in pigmentation when comparing people north and south of the equator? If you are at the equator and start moving north, the further you travel, the lighter the skin of the indigenous peoples. Considering that we live on a ball, why do we not find the same traveling south from the equator? This relationship does not hold for individuals as you move south from the equator.  At the very least, one could say there are no blond hair blue eyed peoples south of the equator.

I rather would say that the lack of North/South Symmetry in pigmentation is that we forget how quickly human beings have spread. In prehistory, people have come to populate every continent over perhaps the last 60,000 years.

While in that time its clear that several mutations have popped up to influence skin color, they are pretty rare compared to the speed with which we migrated over the globe.  The dark color of our earliest ancestors has been lost and regained more than once, but not so often that the selection pressure of latitude have made indigenous in the tropics of south america or south east asia uniformly as dark as africans. Or for that matter have lightened the skin of pre-colonial South Africans.

One might guess that clothing and shelter have reduced the selection pressure on pigmentation further over the past few thousand years.

Individual cases should be studied - this is just a sketch - but the general thought here is that the pigmentation of human beings have more to do with where they have been and how quickly they have recently come from in their migrations.

Summarizing the comments below: There is a correlation between pigmentation and latitude.  The answer is really a combination of latitude, how long a people has been there, and the speed at which pigmentation mutants show up. It doesn't change so quickly that all people are equally dark at the same latitude or so slowly that you find completely pale people at the equator.


What causes cells to inactivate one X-chromosome? Normally, when a cell has two X-chromosomes (female genome), one is randomly inactivated. How does the cell detect that there are two X-chromosomes in the first place?

Is there some kind of protein that's coded in the X-chromosome, such that having two X's increases the protein concentration and a dosage effect causes one to become inactivated? I can't find any information about it in my textbook, nor on Google. A citation would be appreciated - especially for peer-reviewed research.

Even a male cell can count the number of X chromosomes. (Lee et al. 1996; Cell 86: 83-84)

When X inactivation is getting started the two chromosomes "kiss" - a process that lasts for a couple of hours (first shown by Jeannie Lee in 1996). The physical contact between two X chromosomes is over a small fraction of the chromosome but it's essential for triggering inactivation. (Xu et al. 2006: Science 311: 1149-52)

If it doesn't happen then the X chromosome assumes it's alone which would mean that Xist never gets switched on and inactivation never happens (a key stage in chromosome counting).

  Chromosome counting is a process in which cells determine somehow
  their intrinsic chromosome number(s). The best-studied cellular
  mechanism that involves chromosome counting is 'chromosome-kissing'
  and X-chromosome inactivation (XCI) mechanism. It is necessary for the
  well-known dosage compensation between the genders in mammals to
  balance the number of active X-chromosomes (Xa) with regard to diploid
  set of autosomes. At the onset of XCI, two X-chromosomes are coming in
  close proximity and pair physically by a specific segment denominated
  X-pairing region (Xpr) that involves the SLC16A2 gene.

Take a look at Xist and Tsix. Some more papers worth taking a look at:
Xist regulation and function eXplored
Mechanism of regulation of ‘chromosome kissing’ induced by Fob1 and its physiological significance


Additive genetic variance with $n$ loci The genetic variance of a quantitative trait (the quantitative trait in question is fitness) can be express as the sum of two components, the dominance and additive variance:

$$\sigma_D^2 + \sigma_A^2  = \sigma^2$$

, where $\sigma$ is the genetic variance, $\sigma_D^2$ is the dominance variance and $\sigma_A^2$ is the additive variance. $\sigma_D^2$  and $\sigma_A^2$ are given by

$$\sigma_D^2 = x^2(1-x)^2(2 \cdot W_{12} - W_{11} - W_{22})^2$$

$$\sigma_A^2 = 2x(1-x)(xW_{11}+(1-2x)W_{12} - (1-x)W_{22})^2$$

, where $W_{11}$, $W_{12}$ and $W_{22}$ are the fitness of the three possible genotypes and $x$ and $1-x$ give the allele frequencies.

Question

The above definition makes sense for one bi-allelic locus only.

How are $\sigma_D^2$, $\sigma_A^2$ and $\sigma^2$ defined for $n$ bi-allelic loci? Is it:

$$\sigma^2 = \sum_{i=1}^n \sigma_i^2$$ $$\sigma_A^2= \sum_{i=1}^n \sigma_{Ai}^2$$ $$\sigma_D^2  = \sum_{i=1}^n \sigma_{Di}^2$$

Here is a related question

Not in general -- there can be linkage disequilibrium among the loci. For instance, say that there are two di-allelic loci, $A/a$ and $B/b$, and that the frequencies of the $A$ and $B$ alleles are both $1/2$ and that they have the same effect on the trait, with no dominance. If all haplotypes in the population are either $Ab$ or $aB$ (with no $AB$ or $ab$ haplotypes), then the genetic variance at each locus is high, but the total genetic variance for the trait is 0!


What is neutral genetic differentiation? What is neutral genetic differentiation? Presumably it's a measure of the distance between organisms in terms of their genetics, but what does 'neutral' refer to?

Neutral genetic variation is variation that has no effect on fitness. I suggest reading more about neutral theory on wikipedia.

Neutral genetic differentiation is a way of talking about neutral genetic variation that follows some historical pattern, for example two populations isolated from each other for a long time will show neutral genetic differentiation even if they are individually in Hardy-Weinberg equilibrium. In other words, the two populations will have somewhat different allele frequencies from each other for no reason related to natural selection but rather because of random sampling and genetic drift over time.

It is generally thought that most genetic variation is neutral or nearly neutral. For example, most of the human genome is useless DNA or genomic parasites such as transposons. Almost all of the genetic variation that happens in those regions is not important to human fitness, in other words it is "neutral".


PCR Mastermix Preparation I am currently preparing a PCR mastermix for the first time, and have a few questions regarding the distribution. I am trying to amplify a specific gene cluster in a sample of DNA so I can use it in a cloning vector; however, I am not sure how many separate PCR reaction mixtures I should prepare in my mastermix for this purpose? Also, what is the purpose of a negative PCR reaction mixture (withouth the template DNA), as I saw a procedure recomend making one. Should I prepare the same number of negative reactions as positive, or should I prepare only 1?

A PCR Master Mix is just a way to speed up your pipetting. Instead of preparing 10 different reactions of 20ul each (for example) you prepare one reaction of 200ul and then you split it into 10 tubes. This also reduces distraction errors (it is less likely to forget to pipet once 100ul that 20 times 5ul). Also, less plastic (pipet tips) is used.

Some tips:

Given the error of some pipettes, it's generally good to count for an extra reaction every 10. For example, if you need to run 10 PCR, make a Master Mix for 11.

If you are planning to run the same PCR on different templates (which is often the case) then you don't need to add the template in your Mix.

Negative and positive controls should always be included.

The negative control of a PCR reaction is often done by substituting the template DNA with water. The negative control should not show any amplification band. This guarantees that you don't have DNA contaminants in your mix and that you primers do not amplify each other.

A positive control is a reaction that is expected to work. In this case, if your positive control shows amplification but your sample don't, you know it is not because of some component in the reaction behaving unexpectedly (Polymerase, buffer, etc..).

Let's make a practical example.

Let's say I want to amplify the same target sequence from 10 different DNA samples.

The 1X reaction looks like something like:

**PCR 1X**

Template     1ul
Primer F     1ul
Primer R     1ul
H2O         10ul
MgCl2        2ul
dNTPs        2ul
Buffer 10X   2ul
Polymerase   1ul

Now, considering the positive and negative controls, and 10% extra volume, I would prepare a Master Mix for 13 reactions. Of course, the template must be excluded.

**Master Mix 13X:**

Primer F     13ul
Primer R     13ul
H2O         130ul
MgCl2        26ul
dNTPs        26ul
Buffer 10X   26ul
Polymerase   13ul

Now aliquot 19ul in the 12 tubes, add 1ul of the right template to each of them (in the C- just add 1ul H2O) and run it!

There are cases in which you may want amplify different targets sequences from the same DNA. In this scenario, you want to include the template in the Master Mix, since it is the same for all the reactions, but you want to add the primers separately since each reaction will contain a specific set of primer to amplify a specific sequence.


Biological EM emissions What sorts of EM frequencies are emitted by the human body?
Are there any processes in the human body that produce Radio/Microwaves or uv/x-rays/gamma rays?

According to this author (1) the human body emits radiation, mostly in the infared region. Human body temperature generally exceeds that of its surroundings and so there is a net flow of heat from the body into the environment, some due to convection and some due to thermal radiation.

This Czech paper suggests (2) human EM emission in a particular low-frequency band (0.5 - 30 Hz), but the writing is awkward and I do not think this is peer-reviewed.

A more comprehensive Russian paper (3) discusses, among other things, emission of photons (light!) from human skin. The energy of this light is not very high (1-3eV, which is 1-3 times $1.602~ \text{x}~ 10^{-19}$ Joules), but it's not nil.

This interesting topic has been studied extensively and this is a quick glance. Am adding the link furnished in a comment by OP above which does suggest that the body can emit energy via radioactive decay.

Also, this link (4) based on the paper by Toohey below discusses radioactive emission by humans in some detail, including radioactive decay of potassium-40. There is apparently a mechanism by which ambient gamma radiation can interact with atoms in cells (photoelectric effect) to produce x-rays, which are emitted from the body.

(1) Olivia Lee, Hong Kong Observatory, Sept. 2010

(2) Lipkove, Cechak, Human Electromagnetic Emission in the ELF Band,Measurement Science Rev. vol. 5 sec. 2, 2005

(3) Ignativ et al., Fields in the Electromagnetic Spectrum Emitted From the Human Body..., J. Health, Medicine and Nursing, vol. 7, 2014

(4) Toohey RE, Keane AT, Rundo J. Measurement techniques for radium and the actinides in man at the Center for Human Radiobiology. Health Phys. 44(1):323–341; 1983.


Is a minimum size/complexity necessary for an organism to exhibit territoriality? A follow-up to Is territoriality only the domain of the male of a species?

I've seen a large butterfly chase a different kind of butterfly around - it may, or may not have been territoriality. Is there a minimum scale of size, sentience(?) an organism must attain to exhibit territoriality?

With some bacteria (e.g.. Bacillus subtilis) when food gets scarce they will start trying to kill their neighbors. (See this arstechnica article) This appears to be a fight to the death between children and parents. That's a kind of territorial behavior, selectively applied only when there are not enough resources to go around. As there is no "recognition" of a specific territory being defended, just wherever the bacteria is currently, this might not meet a strict definition of territorial behavior. But the only thing simpler than bacteria are viruses.

Come to think of it, I bet there are viruses that, once they infect a host cell, will change the cell's membrane or metabolism in a way that reduces its chance of being infected again by a similar virus. Such 'behavior' could be compared to defending a breeding ground. Can't find any examples though.


What is the composition of human feces? Are there any studies or general information on the composition of human feces?

I'd specifically like to know the percentage of carbohydrates and amino acids relative to the amount that was ingested in diets of various types and amounts.

Any additional facts are also welcome.

This is a bit hard because the usual composition statements are a combination of different types of molecules.

Most of faeces are, by dry weight, bacteria (30%), undigested food and fiber (30%), fat (10%-20%), inorganic matter( 10-20%), other protein(2-3%). (reference)

As you can see the bacterial portion contains proteins (amino acids) and other types of molecules.  the inorganic matter includes bilins which are part of the used up hemoglobin from red blood cells which have been retired.

There's also a lot of variation from one sample to the next - 10% seems pretty common here as you can imagine).  What makes faeces so dangerous is the bacterial portion, which can pose quite a health risk.


Do dead bivalves always float in water? This 2014 Oct 14 article by Jolene Bouchon avouches:

How do you know if your bivalves are alive? Immediately get rid of anything with broken or damaged shells. Clams and mussels shells should be slightly open, and should shut quickly when you tap on them. If they're closed, don't shut, or float in water, they're dead. Introduce them to the trash. Oyster shells, on the other hand, should be closed tightly. And, as with all fish and shellfish, your bivalves should have a fresh, oceany smell with no hint of fishiness or ammonia.

Screenshot below hails from 0:15.
Jasper White avouched the opposite on Epicurious.com

When submerging the steamers in the water, watch for any that float—this means that they're already dead and should be discarded. (Note that when preparing mussels, the opposite is true: They clamp shut tightly, trapping air in the shell, and therefore should float when alive. Discard any that sink.)

So who's correct, and why?

Do they close is a better predictor.

before cooking tap the bivalve if they remain open do not cook or eat them.  Unresponsive bivalves of any kind not safe to eat are dead and there is no way to tell for how long. Whether they open during cooking is meaningless for mussels they can stay locked tight even if healthy and freshly killed.  Smell is also a good predictor never eat shellfish that smell off.

The differences between wild and farmed mussels makes this even less useful, wild mussels may be filled with sand making them heavy even if dead. Of course if a mussel is comes pre-cooked only smell is useful.

float vs sink is not really useful since it relies on how tightly sealed a bivalve is and whether it trapped air when it closed. A air seal is not a guarantee with many bivalves, mussels included, nor is trapped air. It is just not a useful metric.


Does ingestion of alcohol with methylphenidate make it act more like dexmethylphenidate? Methylphenidate (MPH) is a dopamine and norepinephrine reuptake inhibitor. It is the racemic mixture of d-MPH and l-MPH. According to the binding profile info on Wikipedia, based on studies, it is at least 6 times more potent at inhibiting the dopamine transporter (DAT) than the norepinephrine transporter (NET).

The dextrorotatory enantiomer, d-MPH, is said to be the main responsible for the therapeutic response of methylphenidate, and to be "much more bioavailable than levomethylphenidate when administered orally" (this paper from 1999 is given as reference). I read it "can be anticipated to be twice the strenght of the racemic product". One distinct property of d-MPH is that it is much less selective for DAT inhibition as opposed to dl-MPH - in fact, it is a bit more potent at inhibiting the NET (at a ratio of about 1.2 - 1.3) compared to the DAT).
The way I see it, this may have clinical significance since dopamine reuptake in the prefrontal cortex is mainly carried by the NET, since DAT expression is significantly lower in this region of the brain [1] [2].

The Wikipedia article also states that "Coingestion of alcohol (ethanol) also increases the blood plasma levels of d-methylphenidate by up to 40%". It references this study from 2011.

What I want to know is: Does that all mean that the ingestion of alcohol, when taking (racemic) methylphenidate can actually make it more potent, at least at lower doses?
Of course, alcohol has an increased activity effect on GABA receptors, which complicates things.

Thanks

Does the ingestion of alcohol, when taking (racemic) methylphenidate can actually make it more potent?

It is the 2011 study you've mentioned that answers most of the question.

In the study, ethanol co-ingestion with racemic MPH elevated maximal plasma levels of d-MPH by up to 40%. The participants reported greater stimulant effect after alcohol + MPH than after MPH alone (Table 2).

Now, the completely different question is if such combination of alco + MPH is also beneficial and safe.

Also:

  MPH–ethanol coabuse has been widely reported in both annual Drug Abuse
  Warning Network data and the clinical literature.


Why should I degas my gel solution for polyacrylamide gels? In protocols for polyacrylamide gel electrophoresis (PAGE) I often see instructions to degas the gel solution by putting it under vacuum for 10-15 minutes before polymerizing the gel.

I usually don't do this, and when I tried it once I couldn't see any difference. So I'm wondering what exactly the degassing is meant to achieve and how big the effect should be.

What effect is degassing the gel solution supposed to have?
How important is degassing to achieve good gels?

Any literature that examines the effect of degassing would be appreciated.

The reason for degassing your gels is to remove oxygen. Oxygen in the gel interferes with polymerisation, slowing it down and making it less consistent, so degassing makes it faster and more uniform.

From the EncorBio SDS-PAGE protocol:

  Polymerization is quicker and more uniform if you degas the first three solutions for a few minutes in an Ehrlenmeyer flask on a house vacuum prior to addition of the last three reagents. Molecular oxygen inhibits polymerisation by reacting with the free radical SO4- ions, which is actually the reason why PAGE gels are poured in tubes or between plates and not in open top horizontal apparatuses, as can be done with agarose. Also it's a good idea to layer some isopropanol on top of the gel as this prevents oxygen getting in and inhibiting polymerisation.

Oxygen can also lead to oxidation of protein products, which might be crucial if you then want to extract the products and use them for something else (e.g. Sun & Anderson, 2004).

Finally, having bubbles in your gel can distort the results and make them less reproducible, as the bubbles will not form consistently with each repetition and they disrupt the physical medium of the polyacrylamide. So another purpose of degassing is to ensure repeatability.

The Bio-Rad acrylamide polymerisation info sheet has the best info I could find:

  The formation of polyacrylamide gels proceeds via free radical
  polymerization. The reaction is therefore inhibited by any
  element or compound that serves as a free radical trap
  (Chrambach 1985). Oxygen is such an inhibitor. Oxygen,
  present in the air, dissolved in gel solutions, or adsorbed to
  the surfaces of plastic, rubber, etc., will inhibit, and in extreme
  cases prevent, acrylamide polymerization. Proper degassing
  is critical for reproducibility. Therefore, one of the most
  important steps in the preparation of polyacrylamide gels is
  the evacuation, or “degassing” of gel solutions immediately
  prior to pouring the gel. This is done by placing the flask of
  gel solution in a vacuum chamber or under a strong aspirator.
  In some cases, a vacuum pump may be required.

  Buffer stock solutions and monomer stock solutions are usually
  stored at 4°C. Cold solutions have a greater capacity for
  dissolved oxygen. The process of degassing is faster and
  more complete if the gel solution is brought to room
  temperature (23–25°C)‚ before degassing begins.
  Furthermore, if a cold gel solution is placed under vacuum,
  the process of evacuation tends to keep the solution cold.
  Pouring a gel with a cold solution will have a substantial
  negative effect on the rate of polymerization and on the
  quality of the resulting gel.

  Polymerization in which riboflavin is used as one of the
  initiators calls for degassing. The conversion of riboflavin from
  the flavo to the leuco form (the species active in initiation)
  actually requires a small amount of oxygen (Gordon 1973).

  This explains why polymerization initiated primarily by riboflavin
  can be completely blocked by exhaustive degassing. However,
  oxygen in excess of that needed to convert riboflavin to the
  active form will inhibit polymer chain elongation, as it does in
  reactions initiated only by ammonium persulfate and TEMED.
  Thus, while degassing is still important for limiting inhibition,
  it must not be so extensive that it prevents conversion of
  riboflavin to the active form. For polymerization initiated by
  riboflavin/TEMED, or riboflavin/TEMED/ammonium persulfate
  systems, degassing should not exceed 5 min.

  A consequence of the interaction of riboflavin with oxygen is
  that riboflavin seems to act as an oxygen scavenger. This is
  supported by the observation that the addition of riboflavin
  (5 µg/ml) to stacking gel solutions containing ammonium
  persulfate/TEMED initiators results in cleaner, more uniform
  polymerization at gel surfaces exposed to oxygen (such as
  combs). The same effect could likely be achieved by more
  thorough degassing of solutions without riboflavin.

  Whether using chemical polymerization (ammonium
  persulfate/TEMED) or photochemical polymerization
  (riboflavin/TEMED or riboflavin/TEMED/ammonium persulfate
  initiators), reproducible gel quality and separation
  characteristics require careful attention to gel solution
  temperature before degassing, and to degassing time,
  temperature, and vacuum. These parameters should be
  kept constant every time gels are prepared.

Sorry for the long quotes, but they are pasted here in case the original sources disappear.

References:

Sun, G. & Anderson, V.E. (2004) Prevention of artifactual protein oxidation generated during sodium dodecyl sulfate‐gel electrophoresis. ELECTROPHORESIS. [Online] 25 (7‐8), 959–965.


How did bullying arise evolutionarily? By bullying, I mean individuals harassing others with name-calling or violence but not for the purpose of gaining resources such as with extortion or theft. The only explanation I've thought of is that bullying offers practice for types of extortion that do result in increased resources.

I think bullying is really more of an emergent behavior that manifests itself because of natural aggression built in for survival, as well as our complex social-based psychology leading to insecurity when dealing with other:

People who are highly aggressive, and or apathetic to the suffering of others are more likely to control a majority of resources if they don't face significant opposition. This leads to their favored propagation obviously. Then, in their free-time, with all resources under control, they simply continue to do what comes naturally to them: dominating others. It can also work even in those without the ability to actually control resources, due to lack of intelligence for instance. I have met far more non-intelligent bullies than the reverse. The reason for their behavior is still explained by an attempt to control their territory and social status, however ineffective.
Again, due to our complex psychology centered around social interaction, we can develop insecurities about our self-perceived 'fitness', and therefore acceptance by mates and peers. This low self-esteem can lead to bullying others to boost one's ego. Chemically, this can result in a release of endorphins because they feel they have achieved something, which supports bullying behavior as an emergent behavior. Also, those with lower intelligence are likely to have trouble with reasoning skills, and therefore find it difficult to self-analyze and realize their behavior is negative. This leads to bad interactions with others, which can make those individuals feel even more insecure, which in turn fuels their drive to assert themselves through bullying.

Many studies have been conducted on sociopaths/psychopaths. Just like any other evolved trait, whether or not their "personality disorder" is beneficial to the propagation of their genes depends on environmental factors. If they face only opposition from entities that are relatively weak, physically and mentally, then they have an advantage over those peers. But if their peers are sufficiently strong and organized, then the personality disorder becomes a disadvantage if they can't adapt, because they will be attacked by those seeking cooperation from others when they misbehave. Obviously, when our species' numbers were few, high-aggression and a willingness to kill for resources needed for survival aided in survival. In these modern times, its less acceptable for socio/psychopaths to display their innate behavior, due to modern laws, but obviously society can take turns that allow them to express themselves without worry...see the holocaust or any other genocide for an example.

https://link.springer.com/article/10.1007/s40806-017-0097-5

https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=2&cad=rja&uact=8&ved=2ahUKEwj5vKjk88bjAhUfJTQIHaFDA9wQFjABegQIARAC&url=https%3A%2F%2Fwww.apa.org%2Fpubs%2Fjournals%2Freleases%2Famp-a0038929.pdf&usg=AOvVaw1fUJiPHl8rSKMm6Gc9VEeA


Gemini usage of --sample-filter I am using gemini to query databases made from vcf files, which contain data from multiple samples. However, I need to query data only from one sample, (for which I currently use grep to filter the results and > it into a txt file).
I tried experimenting with the --sample-filter option in gemini, the documentation I found however says only:

  gemini query --sample-filter "phenotype=2" -q "YOUR_QUERY"

db_info says the table samples contains name, but when I try doing

  gemini query --sample-filter "name='S2'" -q "YOUR_QUERY"

I'll get error, that I have an syntax error in my query. I tried putting there "sample_name=='S2'" even tried other criteria, like sample_id, but couldn't get this work.

So please, do you know how should I get this work, or have any other advice?

Thank you very much.

I've found a possible workaround to my problem, I filter the vcf input file before loading it into the db by vcfkeepsamples from vcflib.

But I still don't know if the --sample-filter in gemini works, so if you have any ideas, it would be helpful.


Are there any half-evolved animals alive today? I know that there are animals that are "simpler" than other animals but are there any that are half-evolved? Are there any animals with half-evolved functions, like arms, legs, etc?

This was part of the original question, but it was incorrect.

Saying that every species on the planet is "transitional" is an unacceptable answer because it only works on the assumption that macro-evolution is true.

Saying that all the transitional animals just died off also doesn't seem quite right. If all the previous transitional  animals just went extinct, then wouldn't we just have a few specialized species alive today? This wouldn't allow for the diversity we see today.

I know that there are animals that are "simpler" than other animals but are there any that are half-evolved? Why aren't there living half ape and half humans?

Oh come on. You know if Australopithecines or Homo habilis still existed you would be asking "Why aren't there living half Homo habilis and half humans"? And when the other Great Apes go extinct you'll be wondering why there are no transitional forms between humans and monkeys. The answer to that question is, humans are apes; chimpanzees and we are pretty much as close as two species can be; we could have closer forms that survived but we could also have a much bigger gap between us and our closest relatives than we currently do. In other words, any ape is a valid example of something "half-human half-ape". It's like asking for a vehicle that's half-car, half-volvo.

  Are there animals that are just starting to evolve arms and legs?

You mean, modifying fins into limbs in a general movement from water-living to land-living, like the first tetrapods are thought to have done? I like mudskippers.

  Saying that every species on the planet is "transitional" because there are no ultimate or final species is an unacceptable answer because it only works on the assumption that macro-evolution is true.

Not quite, it is an explanation of what "macro-evolution" is and what things it predicts.

There are two aspects to the theory of evolution that are often confused; one is how it works to generate diversity and change in living organisms, and the other is how it works to adapt living organisms to their environment and create what we humans see as "design", "function". Both things are results of evolution, but the latter is much less important than we'd think, which leads people who explain evolution to de-emphasize it, which then leads people to be confused as to how it can happen at all.

The thing is, both "design" and "goals/purposes" are concepts that are meaningful in considering evolution, it's just that the words are dangerous because they imply an conscious intention that isn't there. You could replace "design" with "optimization"; random mutation combined with natural selection can form an optimizing process, i.e. a process that will over time generate forms that have specific properties. In the case of life, whatever properties promote the spread of the organism we're looking at.

As for "goal", that's just the physical fact of the world that some arrangements of matter have different effects from other arrangements of matter; meaning that if some arrangements of matter will lead organisms to reproduce better, the optimizing process of evolution will predictably lead to organisms having that arrangement of matter. So we can talk about, say, eyes being "designed" by evolution "for seeing"; the difference between that and a rock "being designed" "for having its shape" is that "seeing" (i.e. that organisms ancestors surviving and reproducing based on how well they interpreted light signals) had a causal influence on the organism's eye's structure.

So in that sense we can think there are "goals" in evolution; seeing, flying, swimming, breathing... and many lineages can be retrospectively seen as evolving "in the direction" of those goals. But the important thing is that those "goals" are completely dependent on the environment; as long as there's selective pressure for improved sight a lineage will evolve to have better eyes, but the second the selective pressure disappears or reverses, the lineage will evolve to maintain its current eyes or to lose them. And of course different lineages may have different selective pressures on them and "evolve in different directions". That's why there isn't a single overriding goal in evolution, just millions of lineages under different selective pressures that might change tomorrow.

That's why we can say every species is "transitional" (because they'll all be something different tomorrow, or not) and at the same time not be able to say transitional towards what (because the environment is complicated and we usually can't tell under what sustained selective pressure a given organism is under, and even if we could we couldn't be sure it remained the same over the next thousand or million years).

Having said that, when our human brains say "half-evolved" we often have specific goals and images in mind - like "halfway towards flight", "halfway towards eyes", "halfway towards limbs", "halfway towards dolphinhood". And there are plenty of "transitionals" by that definition - I brought up the mudskipper; there are also plenty of gliding animals, a plethora of eyes (or "eyes") at every point on the "good at seeing" continuum (more of a state space than a continuum really), aquatic mammals that may remind one of what the ancestors of cetaceans were like and might evolve to be more aquatic in the future...

  Saying that all the transitional animals just died off also doesn't seem quite right. If all the previous transitional animals just went extinct, then wouldn't we just have a few specialized species alive today? This wouldn't allow for the diversity we see today.

Ah, but what diversity do we see today? What we observe in the fossil record is the constant extinction of some forms and diversification of others, that nevertheless remain more like each other in important ways than they were to their earlier aunts and uncles - meaning while at some point you might have forms A, B, and C, a million years later you have A1, A2, A3 and A4. To illustrate, the earliest tetrapods had a wide variety of number of digits on their limbs. Of course they all basically looked like fish. Most of those early tetrapods went extinct; the only line that survived had five digits. And millions of years later we have a stunning variety of organisms descended from that lineage, most of which look nothing like fish or each other, yet they all follow the same basic skeletal plan, down to the five digits. So which is more diverse?

Basically your question accurately describes the biosphere as the fossil record shows it, you just missed one thing: diversification. Meaning the "few specialized species" are actually a "few specialized families/orders/classes/phyla that themselves contain many species".

When thinking of evolutionary change it's better not to think of a line from A to B, but something like self-spawning fireworks. One group expands, a lot of its elements fizzling out but some of them spawning their own subgroups that expand in turn while still being recognizably part of the original group, and so on so forth with the fizzling of the most and spawning of the few, at some point the older groups might be so large and full of different subgroups that they start losing their definition, and basically at some point you realize the whole big mass of elements that now cover the sky includes both A and B, meaning if you roll back the tape you can certainly track how something that looked like A changed over time into something that looked like B, but it's really a very small part of the whole show.


Is 100% accuracy in DNA sequencing possible? I would like to obtain a complete genome of a canine (with mitochondrial DNA too) at 100% accuracy. Is it even possible with the current technology? The source I have is potential degraded, i.e. dried saliva, dried blood, whisker root, fur roots, etc...

Current DNA sequencing techniques are based on shotgun sequencing, randomly breaking the chromosomes into small pieces, sequencing the pieces (by various techniques), and then computationally reassembling the pieces by looking for overlapping patterns. This depends on sequencing each piece of DNA multiple times; the more coverage or depth, the more reliable the results. However, especially with long repeating base sequences, 100% coverage is uncommon with small genomes, and almost impossible with large genomes.


How HIV Affects and Its Treatment using Combination Therapy Can someone please help me with the following questions. I've written my specific questions right after the text question.

Human immunodeficiency virus (HIV) is a retrovirus. Its genome is a single (+) stranded RNA that is packaged with the reverse transcriptase enzyme within a protein capsid. This is further packaged into an envelope that is derived from the plasma membrane of the host cell in which the virus had replicated. The surface of the envelope is covered with the envelope glycoprotein, called gp120 & gp41.

a) HIV specifically infects the T-helper (TH) cells of the human immune system. If the HIV enters the host cell by means of host receptor recognizing a viral protein, what would be the most likely ligand and its corresponding receptor during HIV infection?

b) Some individuals are resistant to HIV infection even after repeated exposure. Assuming that these individuals express a normal level of the functional receptor that you have recognized above, how can you explain their resistance to HIV?

c) In recent years, therapies have been developed to fight AIDS using nucleotide analogs. The drug used to combat AIDS is Azidothymine (AZT). The structure of AZT is very similar to thymidine except that in AZT, the 3’-OH group on the deoxyribose sugar is replaced by an azido (N3) group. Which process of the life cycle of HIV do you think is inhibited by AZT?

d) Combination therapy is the new treatment strategy for treating HIV patients.

i. Why is combination therapy more successful in preventing the emergence of the disease resistant clones?

ii. If the combination therapy involves a drug that prevents…

1) HIV binding to the target cell, what protein does this target?

2) Integration of HIV genome into host cell genome, what protein does this target?

3) The cleaving of viral polypeptide into individual proteins, what protein does this target?

e) If the AIDS patient were given combination therapy, would the patient still be able to transmit the HIV virus to his/ her partner (Yes/ No)? Explain your choice.

**

a) No idea.

b) Maybe their T-helper cells have some sort of mutation that makes it impossible for HIV to bind to them?

c) I'm thinking "formation of HIV RNA" because in the absence of 3' -OH bonds, phosphodiester bonds cannot form.

d)
    i. It kind of makes sense because a virus being resistant to multiple drugs would be very unlikely but maybe there's some definite reason why?

ii. No clue. Is this talking about proteins of the virus or of the host? Also, enzymes are also proteins, right?

a) HIV uses a certain receptor that's expressed widely on T helper cells. As this is homework I suggest looking at the wikipedia article to look this up for yourself. It is under tropism.

b) You mentioned mutation. That's very true but this question is excluding people with that mutation called the delta 32 mutation. Thus HIV can infect these people, but what happens to any virus in the context of infection? How does the human body deal with viral infections. Is there any variation that would account for why some people can be resistant to HIV and others not be?

c) Yes! Well done :) You're thinking along the right lines. Look up the drug on wikipedia and look up it's mechanism.

d) i) Yeah exactly that. But more than that. There's optimal HIV which in the absence of drugs does the best job at infecting. If we give a drug then HIV has to mutate away from optimal HIV to stay alive, but it's weaker. Give multiple drugs and it can't mutate away from all of them because if it did it would be so far from optimal it would be a rubbish virus.

ii) 1) It could affect the HIV binding receptor protein or the protein with which it binds on the host cell. So both! Logic would dictate we would use self receptor blockade because at least they're more conserved but I'm sure both are probably used. Enzymes and receptors are both proteins.

2 + 3) Look up the lifecycle of HIV

e) Theoretically possible. He might not take the drugs. If he takes the drugs unlikely because the virus basically becomes undetectable. Look this up, it should be on wikipedia again.


What happens in a nerve cell when a thought is generated? I know basic nerve physiology of impulse conduction and transmission, but I don't know what actually happens in a nerve cell when a thought is generated. When a external stimulus (like tactile stimulation, injury causing tissue damage) leads to stimulation of respective Na+Channels and action potential is generated. But what is the stimulus in the neurons of the Central Nervous System when we think about something? What exactly is the stimulus that cause the neuron to generate action potential and then following it, it is transmitted to different circuits and then we react accordingly?

This is a recurring question that many people are bothered with. I read an interesting answer on Quora. Basically, the author says that there is always on-going activity in the brain. Each thought is triggered by something, let it be conscious or unconscious. The brain is never silent, even in your deepest sleep with only slow-wave synchronized activity, there is still activity. Even when it seems that a certain thought pops up totally randomly, it is still triggered by certain inputs, let they be sensory or internal. Note that action potentials can be triggered either by signals from the outside world (sensory receptor neurons), or by signals from other cells in the brain and body.

Also note that most, if not all neurons show background activity ('neuronal noise'); they never stop firing even without inputs. When one or more of those background potentials impinge on a postsynaptic neuron, that neuron may be activated an fire an action potential. This may also explain some random events in the nervous system.


Alternatives to trypsin for cell detachment? I have ran out of trypsin and need to passage my cells (immortalized chondrocytes, C28/I2) today or tomorrow. I have been out of town and forgot to order more trypsin.

I was wondering if there are any alternative, "homemade" ways to detach cells. Googling this results in a lot of commercially available detachment solutions. I may or may not have a cell scraper available, but I have never tried it. I have hyaluronidase and I was thinking that might work.

Lets make this a proper answer: There are a few possibilities to detach adherent cells without Trypsin.

PBS/EDTA: Integrins and Cadherins play an important role in the adhesion and also in maintaining cell-cell contacts. These function of these proteins depends on Calcium2+ ions, so EDTA will chelate them and make them unavailable. First remove the culture media, rinse the cells with warm PBS to get rid of most ions and then incubate them for 5 min (the time needs to be optimized for each cells line) in PBS with 10mM EDTA in it. The cells either detach themself, can be washed of the surface with a pipette or can be gently knocked off the surface (this works only in tightly closing flasks). Centrifuge the cells shortly to pellet them and get rid of the PBS/EDTA and take them up in fresh medium.

Wash cells of the surface: Some cell lines are so loosely attached (which makes working with them pretty hard), that they can simply be washed off the surface. To do so, use the pipetboy to get some medium and then pump it out again against the cell layer. You can see the cells disappearing from the surface and the medium (or the PBS) get more cloudy.

Knock off cells: To do so, you take the flask with medium in one hand and knock it gently 4 or 5 times against the palm of the other hand. The cells should come off then and can be centrifuged down to separate from the medium. Alternatively you could replace the medium first and then knock them off. This method is not recommended for very sensitive cell lines.

Besides these methods, there are a number of commercial products available which claim to be better than the classical Trypsin/EDTA method and to be less harmful for the cells. Since I haven't tested them, I cannot say anything about them. In my experience Trypsin and the methods described above work perfectly.


Antibody-antigen database Is there a database where I can find an affinity estimate if I provide a given antibody and a given antigen sequence ?

Input : antibody + antigen sequence
Output : quantitative binding/affinity estimate

Many thanks.

The binding constant of an antibody-antigen complex remains an empirical measurement.

There have been many efforts to solve this problem quantitatively and qualitatively over the years since the original crystal structures of an lysozyme-Fab complex there are over 400 structures at the www.rcsb.org in a search for antibody antigen complexes.

At this point the general methodology is to model the structure of the antibody-antigen complex.  Then from the complex a free energy of binding is estimated, or more reliably, variants which might bind more tightly can be modelled.

There are tools available to do this work, but they are still far from perfect.  This 2012 paper compares a new antibody-antigen crystal structure against the results of several modeling suites.  In Table 4 the authors show that the invariant parts of the structure as well as some of the hypervariable loops are really precisely modelled, but hypervariable region 3 was way off in this case (rms error of about 2 Angstroms).  Which is not precise enough to calculate actual free energy of binding.

Currently while free energies of binding and therefore estimates of binding constants are not reliably calculated from protein complex structures.  Such software is in practice used to rather compute the relative binding strength of two models (see this 2012 example).

This 2010 paper which describes SnugDock, a newer suite of software, outlines a state of the art antibody-antigen design process (emphasis added).

  One could envision a complete computational antibody engineering pipeline starting from the antibody sequence and ending with accurate predictions for optimized antibody-antigen interactions. In this paper we have been successful in reaching the second step by computational docking using computational models of the monomer antibody. The next stages may be additionally challenging. High-resolution complex structures might next be used for computational alanine scanning, computational affinity maturation or alteration of binding specificity. For antibody therapeutics, structures will help define drug mechanisms for regulatory approval, enable epitope mapping and humanize constructs. These applications require varying amounts of resolution and further testing will reveal the full utility of the SnugDock predictions.

As you can see, the method recommended is to create a series of models to try to create tighter relative binding.


Can the absorption of vitamins be enhanced? Are food additives like vitamins better absorbed when you mix them among fruits?

I heard that secondary substances in fruit promote the absorption.

There are two types of vitamins:

Fat soluble vitamins - Vitamins A, D, E, K
Water soluble vitamins - B complex Vitamins and Vitamin C

Fat soluble vitamins get better abosorbed when fat content of food is good. The bile secretion is also very important. These vitamins form miscelles with the fat molecules and get absorbed as such. The absorption of these vitamins can be enhanced by taking fatty diet.

The water soluble vitamins are absorbed freely and they are also excreted freely - Excess are expelled through urine.

There are inter-vitamin competition and some food biomolecules can inhibit vitamin absorption. For example avidin in the egg would bind to biotin and prevent its absorption. The articles below deal a little with such inhibitions.

For more see:

http://healthyeating.sfgate.com/improve-bodys-absorption-vitamins-2898.html
http://www.ncbi.nlm.nih.gov/pubmed/17023940
http://health.howstuffworks.com/wellness/food-nutrition/vitamin-supplements/body-absorb-vitamins.htm


What is the difference between Integrin to Cadherin? My question is probably very basic but i couldnt get it in lecture and not from looking in the net.

  What is the difference between Integrin to Cadherin.

  By difference I am looking for say:

  structural difference
  functional difference

If i understand correctly both of them helps in cell adhesion.
But, probably in different way? or shortly, what is the difference?

Thank you!

Cadherins look like chains, that are stretched out only when bound to Ca++. They contribute to cell adhesion through adherens-junctions and desmosomes (cell-cell adhesion). They bind weakly by themselves, but function sort of like velcro, in that they make a strong junction when they are many.

Integrins can be of alpha and one beta type. Both types are used in a junction, and they sort of "claw" around the ECM. They also depent on Ca++ (and also Mg++) for correct binding. They join the cell to the extracellular matrix through aktin-linked cell-matrix juntions and hemidesmosomes. There's one alpha and one beta integrin per junction (i think) and they sort of "grip" the ECM by one of them going in the front and the other in the back of the ECM unit.

Both integrins and cadherins are transmembrane proteins, that also need adaptor proteins on the intracellular side.

For clarification:
Adherens junctions transfer the force of aktin filaments from one cell to another, using classical cadherins between the cells.
Desmosomes connect intermediate filaments between neighbouring cells.
Aktin-linked cell-matrix junctions link aktin filaments to the ECM.
Hemidesmosomes link intermediate filaments to the ECM.

Source: lectures at the university of Tromsø, Norway. Also my textbook.


Does photosynthesis occur on cloudy days or does it require direct sunlight? In my basic science classes in high school, I have learned that during photosynthesis, plants absorb sunlight and produce food by converting carbon dioxide and water into sugar and starch.

To me, this seems similar to the analogy of solar cells that convert sunlight into electricity. When sunlight falls directly on the solar cell, it produces electricity, but even when it is cloudy with no direct sunlight available, electricity is produced, but with less efficiency.

So can photosynthesis occur in plants only when they are in direct sunlight or does photosynthesis also occur during cloudy weather when the light is diffuse or indirect?

Yes, photosynthesis does occur on cloudy days where the light exposure is diffuse - but the overall picture is not as simple as your solar cell analogy.

Consider one of the findings of the following article: "Impact of clear and cloudy sky conditions on the vertical distribution of photosynthetic CO₂ uptake within a spruce canopy" (Urban et al. 2011), where one of the findings is that

  that shoots from deep within the canopy contribute substantially to the overall carbon balance during cloudy days. But, although shade-adapted shoots had a markedly positive carbon balance over a 24-h period on cloudy days, their performance was impaired on sunny days contributing only a marginal or even negative carbon balance from the middle and shaded parts of the canopy.

So, while leaves at the top of the canopy have a reduced rate of photosynthesis on cloudy days, leaves within the canopy and those that are shade-adapted, still photosynthesised.

I hope this helps a bit.


What is the name of the appendage that mantis shrimp use to rub their eyes? In this short clip, you can see the mantis shrimp using some sort of feathery arm/claw to rub its eyes. Looking at a diagram here, it appears possibly that it's using maxillipeds. Someone with knowledge of crustaceans (the behavior is probably not unique to mantis shrimp) would be appreciated.

Mantis shrimp use their first maxillipeds for grooming (maxilliped=modified appendage), which is specialized for this purpose. Details and a picture of the organ can be found in the link. The second maxilliped is their famous specialized organ for striking or spearing prey with enormous force. More about their raptoral appendage, with links to further references. Mantis shrimp also have very complex eyes, described as "...the most complicated visual system of any animal on Earth". Their eyes can see a range from ultraviolet to infra-red and has specialized regions for observing motion, form, depth, and color. More on Mantis shrimp eyes can be found in Marshall & Oberwinkler (1999).


Origin of the double membrane of mitochondria and chloroplasts Most websites and textbooks say that the double membrane of mitochondria and chloroplasts are a result of the endocytosis of ancient prokaryotes (the outer membrane is from the vesicle containing the prokaryote, the inner membrane is from the prokaryote itself).
However, some sources say that this is not the case. The precursor to the mitochondrion (alphaproteobacteria) was a gram-negative bacteria, which has a double membrane. This site says that the reasoning for the double membrane that is often taught is a lie, and that the mitochondrial precursor had a double membrane already to generate ATP through the ETC.

So, if this is the case, why do mitochondria now have two membranes, and not three (two from the prokaryote and one from the vesicle)?

The answer lies in the protein composition of mitochondrial membranes, which undoubtedly prove that the outer membrane (OM) is of alphaproteobacterial origin, and the phagosomal membrane (if there was any) is lost. Though the endosymbiotic origin is without question, bear in mind that the phagocytotic origin is still debated (cf. López-García & Moreira 2015). And if the symbiont has entered the host some other ways than phagocytosis (cf. papers of Tom Cavalier-Smith) or syntrophic engulfment (cf. papers by Bill Martin; Searcy; López-García & Moreira) (e.g. puncturing the plasma membrane as a pathogen), then there never was a third membrane.

From Symbiogenesis Wikipedia:

  Porins (transport proteins) are found in the OM of mitochondria and
  chloroplasts, are also found in bacterial cell membrane (Fischer et
  al. 1994Zeth & Thein 2010Fairman et al. 2011). The
  membrane lipid cardiolipin is exclusively found in the inner membrane
  of mitochondria and bacterial cell membrane Mleykovskaya & Dowhan
  2009.

According to many (Cavalier-Smith 2002, Cavalier-Smith 2006, Zeth 2010), the presence of β-barrel transport proteins proves that the OM evolved from the bacterial OM, not from the host food vacuole membrane. Both mitochondria and plastids contain in their OM β-barrel proteins (e.g. Tom40, Sam50 and porins in mitochondria, Toc75 homologue of Sam50 and their joint negibacterial ancestor Omp85 in chloroplasts) and these are only present in the OMs of gram-negative bacteria (cf. Schleiff & Soll 2005). All Alphaproteobacteria are gram-negative, hence the ancestor of mitochondria originating from the Rickettsiales or very close was also.

Note, that many secondary and tertiary plastids still retain their third, outermoest phagosomal membrane originating from the host's plasma membrane (cf. Keeling 2010).


If hermaphrodite C. elegans can reproduce with females? C. elegans can self fertilize, or they can mate with males. But are they able to mate with females? Or is there some kind of morphological barrier that prevents that?

Since only the male tail is equipped with various specialized sensory and copulatory structures that enable him to locate the vulva and successfully inseminate the hermaphrodite.  Hermaphrodites can self-fertilize, but only males can cross-fertilize a hermaphrodite.

sources: Wormbook: Male development
C. elegans II (2nd edition): Sexual Dimorphism


Is there a definition of species where Lions and Tigers are the same species? According to Species concepts

  There are at least 26 recognized species concepts

And according to Why are lions and tigers considered different species (not sure how reliable this source is though, but I've seen exactly the same answer in another website)

  The reason tigers and lions are different species is because of different behaviours, different habitats, different social hierarchies, and they each have their own subset of genes that they share within their species (like the genes for stripped fur or for manes).

Now, I'm not sure about "social hierarchies" (which I'm sure it's a fuzzy concept) , but there are different breeds of dogs with different behaviors, living in different habitats, and there has to be differences in genes in different breeds, since even in humans populations there are 1% of differences in genes and according to other sources more.  Then my question is, since Tigers and Lions are closed to each other to the point they can produce offsprings, is there any of those 26 definitions of species where lions and tigers are the same species?

The concept this would fit under would be the "Biological Species Concept."

Concerning this concept, the Evolution site for Berkeley says "members of populations that actually or potentially interbreed in nature..." constitute a species. By this definition, since lions and tigers can (and do) interbreed, they would be considered the same species under this concept.

EDIT: As Bryan pointed out, though, lions and tigers do not breed outside of captivity. NatGeo and Britannica both second this. With this, then, the Biological Species Concept would not be viable.

EDIT2: With the above in mind, there don’t seem to be many options.

Mate-Recognition: This idea posits that organisms who “recognize one another as potential mates” (Wikipedia, “Species”) make up a species. By this, it could be argued lions and tigers are the same species, but I would be hesitant for this to be the concept, for the same reasons against the Biological Species Concept (not occurring in nature).

Ecological: Using this definition, a species is made up “of organisms adapted to a particular... niche, in the environment” (Wikipedia). Again, this is very fuzzy, as I wouldn’t define them in the same niche (though this might depend on how specific you get).

Conclusion: These seem to be the most likely, though that’s a very loose term. I couldn’t find any others that would fit nearly as well. I would say the answer is “no”, but I don’t think I found all of the concepts.


What causes morning wood? Sometimes men wake up with an erection in the morning. Why does this happen?

Sometimes men wake up with an erection in the morning. Why does this happen?

Shortly speaking: REM (Rapid Eye Movement) is one phase of sleep. During this phase, we dream and some of our neurotransmitters are shut off. This include norepinephrine, which is involved in controlling erections. Norepinephrine prevents blood from entering the penis (preventing the erection). In absence of norepinephrine—during REM phase norepinephrine is absent—blood enters the penis, leading to an erection. This phenomenon is called nocturnal penile tumescence. Such erections typically occur 3 to 5 times a night. A related question concerning similar erections in women can be found here.

High pressure in the bladder may also lead to a "reflex erection". This erection allows for preventing uncontrolled urination. The drawback is that when in the morning one has an erection and can't wait to pee it might get hard to accurately target the toilets!

This video is also a nice and easy source of information on the subject.

Is it bad?

(Reading my "note" below, you have edited your post to get rid of this question, thank you)

It is perfectly healthy you don't have to worry about that. These erections are even thought of as contributing to penile health. At the opposite end of the spectrum, the absence of erections during the nights are an index of Erectile Dysfunction (E.D.).

Note

Be aware that medical questions are often considered off-topic on this site. Asking "is it bad?" turns your question into a medical one. Health-related questions (but not personal health) should be asked on health.SE


Gender of BEAS-2B cell culture I recognize some interesting patterns when analysing DNA methylation of BEAS-2B cells. Does anybody know, if the cell culture is female or male? I already asked the customer support of Sigma Aldrich without success.

Information on the official website just mention "non-cancerous individuals" as source organisms.

http://www.sigmaaldrich.com/catalog/product/sigma/95102433?lang=de&region=DE

The cell line is most likely genetically male. On the English (US) site, the Description box has several sections, of which one is DNA Profile. In there, it lists amelogenin as X, Y. This gene is located on both the X and Y chromosomes (AMELX and AMELY, respectively), which have distinct PCR-detectable sequence differences. It is often used in helping to determine the gender of unknown samples in the realm of forensics - it is not 100% accurate, so other genetic tests (such as for SRY) are also performed.


Why do seeds grow upwards? Why do seeds grow upwards?  Surely gravity would pull them towards the earth's core?  Can anyone shine any light on this? Do seeds that are planted deeper grow more quickly.

It is a reaction to gravity, it is called geotropism or gravitropism. The roots tend to grow in the direction of the gravity (positive geotropism) and the stem is going against gravity (negative geotropism).

The mechanism works with auxins, or plant growth hormones. They are pulled by gravity toward a side of the plant and will either stimulate or inhibited growth in that area.


The difference between the two ways of glycine represntation I'm confused because I see now two different way to represent the glycine amino acid. while I understand the first way of the representation the second one I don't understand at all. I believe that both represent the same amino acid but I see that some of the componenets are absent in the second way (no COOH and no carbon). I would like to know the explanation.

This is the first (and the simplest way):

and this is the form that I don't understand:

The first method of representation is the regular way, where all groups, including carbon and hydrogen are shown.

The second method is the "skeletal form", where every bend in the line means a carbon group, and the hydrogen atoms attached to the carbons are implied. It does seem a little tricky to visualise, but it is easier and faster when you come to larger groups.

Check this out.


I need help identifying a completely unknown plant for my biology class I know two things about this plant
1 is that it does not need to be watered for a long time because it has been able to survive in my schools greenhouse for quite some time without water and 2 my teacher says she "thinks" it blooms purple or pink flowers.
Thank you in advance for any help given!

I'm no expert on plants but it could be a kalanchoe. That's based mainly on the leaf characteristics and size.

There's some 120 or so species mainly originating from the old world. These are quite drought tolerant as yours seems to be. They are a common houseplant and there are ways to stimulate reflowering so that also makes it a good candidate.

Image source.


Are the processes on afferent neurons that go from the sensory receptor to the cell body considered axons or dendrites? References on pain fibers say impulses move along axons to the CNS, but I thought that by definition axons carry impulses away from the cell body.

They are considered axons. Pseudounipolar cells have a bit of an odd morphology.

The reason you consider the entire length an axon is because it all grows from a single process from the soma which then branches. Terminology is just terminology, so "rules" are often made to be broken in biology: yes, an axon typically carries information away from the soma, but that's not the case here for neurons where the information sort of bypasses the soma.

Besides the developmental origin from a single process, the initiation site for an action potential is out in the distal end of the axon, rather than at an axon hillock connected to the soma, and if you had a section of axon on either side of the soma it wouldn't be apparent which end you were looking at.

Tandrup, T. (1995). Are the neurons in the dorsal root ganglion pseudounipolar? A comparison of the number of neurons and number of myelinated and unmyelinated fibres in the dorsal root. Journal of Comparative Neurology, 357(3), 341-347.


How much generation of hamster's family it takes to get first bad mutations So if I have two humsters and they start to reproduce themselfs then how much generations of hamster's family it takes to get first bad mutations?

The info here does not help to find answer https://www.reddit.com/r/askscience/comments/32x33j/how_do_animals_like_hamsters_and_snakes_avoid_the/

Thank you!

Everybody carry deleterious mutations anyway

Your two hamsters most definitely already carry a number of deleterious alleles at segregating sites (segregating sites = polymorphic sites). Also, I will not talk about inbreeding depression in your population coming from only two individuals which will be very important but I will only answer your specific question. In short, I will assume your are not interested in segregating sites...

Probability of an offspring to carry a new deleterious mutation

The vast majority of new mutations are deleterious (Shaw et al. 2003). I don't know of estimates of mutation rate in hamsters but in mammals (and in all eukaryote species anyway generally speaking; e.g. see this post and this post or directly bionumbers#mutationrate), the genome-wide mutation rate is of the order of 1 to 100 mutations per offsprings.

If the couple of hamsters have $x$ offsprings, then the probability to have at least one new mutation in at least one offspring is given by the cumulative exponential distribution

$$P = 1-e^{-U x}$$

, where $U$ is the genome-wide mutation rate. With $U=50$ and $x=1$ (one offspring), this probability is $P = 1-e^{-50} = 1 - 1.9 \cdot 10^{-22} ≈ 1$.

In short

In short, to a fair level of approximation, every new offspring carry at least one deleterious mutation that was not present in either parent.


Almost philosophical question about controlling a pest/plague Once in a math congress someone presented a paper on a mathematical model used to predict the impact of certain measures that could be taken in order to control some pest/plague. A guy in the audience interrupted the speaker and asked why not to "kill them all"(referring to the specimens of the pest/plague) and put a stop to the problem. The speaker observed that we were thinking that kind of things because almost all of us were mathematicians and so we were not aware that it would be a big problem to do that.

From my point of view, he was suggesting that "the right way to control a plague is not to kill them all" is a standard, uncontroversial fact that all biologists would agree. My question is about this last point.

Is that a scientific thesis or an ideological one? I mean, do biologists have theories that allow them to know that the "right" way to control a plague is not to kill every specimen of the species?

Why is it the case that we can assure that exterminating a species is necessarily going to affect, directly or not, humankind?

Is it a matter of chance and, as we are not completely certain of what may happen after exterminating the species, then we don't want to take a risk?

Thanks! And feel free to edit tags :)

Biologists are certainly not afraid to exterminate pests and plagues in the wild. See: smallpox and polio. However, such exterminations are nearly impossible and very expensive. See: smallpox and polio. In both cases extinction is through  extensive vaccination, preventing the disease from having any hosts to live in. To achieve this you need to vaccinate a huge fraction of the human population for quite some time.

Practically, how would you go about exterminating an agricultural pest? A beetle, for example? Perhaps an army of men, forming a cordon the width of the united states, turning over every rock and every tree from the west coast to the east coast. With a high net or something to prevent beetles from flying over the cordon. And some method for dealing with cities and roads and tunnels and things, because if you miss only five or six they'll be back soon, depending on life cycle and offspring numbers. Or if you forget Canada.

And to use a biological solution to a biological problem, consider myxomatosis and the Australian rabbit problem. Rabbits were(and are) a pest, myxomatosis is a rabbit plague that has a 99.99% fatality rate and is fiercely infectious. Sure enough, myxomatosis wiped out the rabbit population. A few years later the rabbits were back but now the survivors were resistant to myxomatosis.

I would argue that it's a scientific thesis based on hard lessons biologists have learned about doing 100% of anything. There are many biologists with moral precepts against the extinction of pest species. It's a bit of a moot point, however. The only reliable method of extinction is habitat destruction. Whether that's immunizing all the humans or cutting down the rainforests, it does work. It's just usually impractical.


Is there evidence that some non-human species perform sexual selection based primarily on intelligence? How do they do this? I'm a biology amateur, but it seems like sexual selection is almost always performed based on physical characteristics, the outcome of physical contests, or some sort elaborate courtship. But do any non Homo-Sapiens perform sexual selection based on intelligence factors, like problem solving abilities? If so, how does the species accomplish this? I know natural selection as a whole would definitely favor intelligent individuals, but I'm curious if any species actually takes this into account when choosing mates.

Very intresting question. The problem is that animal intelligence is hard to measure not only for scientists, but probably also for the potential mate. Paradoxically, that is why selection for intelligence, if it occurred, may be very strong. One has to be smart in order to recognise smart behaviour, so preference and preferred feature are strongly connected. But that's only my opinion.

Boogert et al., 2011 1 reviews the current knowledge about animal preferences for cognition skills. They conclude that there is very little data on this subject. The given examples are:

1) Preference for elaborating birds songs (as songs are not inborn and have to be learned)

2) Spatial abilities:

  In meadow voles (Microtus pennsylvanicus), males with better spatial learning and memory abilities were not only found to have larger home ranges and to locate more females in the field (Spritzer, Solomon, et al. 2005 2) but were also preferred by females in mate-choice tests, even though the females did not observe males’ performance on spatial tests (Spritzer, Meikle, et al. 2005 3).

  In guppies (Poecilia reticulata), males that learned faster to swim through mazes to gain a food reward were found to be more attractive to females (Shohet and Watt 2009 4). However, females were not able to see the males’ performance in the mazes. Although male learning ability was weakly correlated with saturation of the orange patches on his body (a sexually selected trait (...)), orange saturation surprisingly did not correlate with female preferences. Thus, the cues leading female guppies to prefer faster learners are unknown.

It is possible, that females base their choose on some factors that correlates with cognitive skills or on total wellness, what may depend on intelligence.

3) bowerbird's abilities to build bowers (courtship constructions):

  Comparative studies across bowerbird species have shown that relative brain size is larger in species that build bowers than in closely related nonbuilding species (Madden 2001 5). In addition, relative brain size increases with the species-typical complexity of the bower (Madden 2001 5), and a comparative study on the relative size of specific brain regions showed that species with more complex bowers have a relatively larger cerebellum (Day et al. 2005 6).

4) foraging performance

  A recent experiment by Snowberg and Benkman (2009) 7 using red crossbills (Loxia curvirostra) showed that, after observing 2 males extracting seeds from conifer cones, females associated preferentially with the more efficient forager of the 2. The authors were able to exclude female choice for correlated traits by experimentally manipulating foraging efficiency, such that fewer seeds were available in the cones of one of the males. The males were also swapped between treatments (i.e., slow vs. fast forager) so that male identity could not explain the females’ preferences for the most efficient forager.

Another way that intelligence may be favored by sexual selection is "cheating" during courtship. For example most frog species call to attract females. But this signal may also attract aggresive rivals or predators. Some males, especially the weaker ones, do not call  but stay near calling individual.  This allows them to avoid confrontation and wait for approaching females [8]. The successfulness of this strategy may depend on how "smart" the individual is (only my opinion).

[1] Boogert, N. J., Fawcett, T. W., & Lefebvre, L. (2011). Mate choice for cognitive traits: a review of the evidence in nonhuman vertebrates. Behavioral Ecology, 22(3), 447-459.

[2] Spritzer MD, Solomon NG, Meikle DB. 2005. Influence of scramble competition for mates upon the spatial ability of male meadow voles. Anim Behav. 69:375–386.

[3] Spritzer MD, Meikle DB, Solomon NG. 2005. Female choice based on male spatial ability and aggressiveness among meadow voles. Anim Behav. 69:1121–1130.

[4] Shohet AJ, Watt PJ. 2009. Female guppies Poecilia reticulata prefer males that can learn fast. J Fish Biol. 75:1323–1330.

[5] Madden J. 2001. Sex, bowers and brains. Proc R Soc Lond B Biol Sci. 268:833–838.

[6] Day LB, Westcott DA, Olster DH. 2005. Evolution of bower complexity and cerebellum size in bowerbirds. Brain Behav Evol. 66:62–72

[7] Snowberg LK, Benkman CW. 2009. Mate choice based on a key ecological performance trait. J Evol Biol. 22:762–769.

[8] Bateson P. 1985. Mate choice. Cambridge University Press. 181-210


What organisms are Chloroperoxidase enzymes found in? Are they found in humans? I'm wondering because they display a structural similarity to glucose-6-phosphatase, which is an important enzyme in gluconeogenesis.

It is only found in an ascomycetes which is named Leptoxyphium fumago, also known as Caldariomyces fumago.

It isn't found in any other specie that we know of yet as searched on the RCSB PDB and Uni-Prot.

In researches that uses it they extract it from the organism, it is also available to buy from companies like Sigma Aldrich who extract it from the ascomycete too.

Sources:

Improvement of activity and stability of chloroperoxidase by chemical modification

Over-expression of chloroperoxidase in Caldariomyces fumago.

RCSB Protein Data Bank

Uni-Prot


Trigger allergic reaction in non-allergic people? Is there a proven way to trigger an allergic or allergic-like reaction in non-allergic people? I have wondered if this is possible, since allergies are basically just a form hypersensitivity - so could this be triggered somehow?

Is there a proven way to trigger an allergic or allergic-like reaction in non-allergic people?

No.

At least, not that I've ever heard of. Allergic reactions, as you point out, are an overactive immune system response to an allergen (anything that causes the reaction). What determines who is allergic to what is a mix of genetic and environmental factors, and because an allergic reaction is categorized as an error on the immune system's behalf, inducing an allergic reaction is essentially finding a way to force the immune system to make a very, very specific error.

What can (and does) happen is the development of new allergies. Almost all allergies are acquired after birth, and repeated exposure to substances can lead to the appearance of new allergies - one case that stuck out in my head was a woman developing an allergy to a copper IUD that she tolerated well when it was first put in place.

I am not aware of any ability to predict what substances will cause the development of a new allergy. Both the unpredictability and inability to induce allergies comes down to how the immune system reacts to antigens (foreign substances). The machinations of the immune system's response to an allergen or antigen is fairly complicated, and at any point in the chain of events the potential for an overreaction is there. That's probably another question, though, and a much longer answer.


Filter proteins by domain with InterProScan I have a bunch of proteins (over 300000) in fasta format, and I want to find the ones that contain a specific domain (using a specific InterPro accession).

I can run InterPro on the proteins and get every domain they have, but with so many proteins, it will take a large amount of time, which I'm short on. I'd like to limit my search to the specific domain I'm looking for, as I assume it will be considerably faster.

Is there a way to do this with InterPro? Browsing the docs doesn't give me any hope. If InterPro isn't capable of that, would it be doable with a single database like Pfam or CDD?

1. Limit the InterPro scan to a specific database:
As you said you know the domain you are interested in so you know which database this is in then you can limit you InterPro scan to that database, which whill save a lot of time:

Then only select the database in which the domain is stored (e.g. ProSite)

2. If your domain is in the ProSite database (which it probably is) you can use
ScanProsite and limit you search to a specific domain.
You do this by going to the above link and select the last option:

Then, if you scroll a little bit down you can enter a ProSite accesion code of the domain/profile you are interested in:

3. Use PFAM scan

I have never used this before, so I don't know whether this would be faster than limiting the InterPro scan to the PFAMa database. You can of course check this out.

4. Clustering your sequences first

This will only work if your sequences look like each other. Depending on the size of the domain and the location in the sequences you can cluster all your sequences first (using for example CD-HIT). And then choose a representative sequences for each cluster and use these to subject to your analysis. For example when you know your domain is always at the end of the sequence then you trim the first part of each sequence and cluster the proteins over the whole length at 100% identity. If you then determine whether each cluster contains the domain or not (based on the representative sequence, which CD-HIT will provide you with) then you can assign these results to the sequences making up each cluster. But of course this will only reduce the search space whenever your sequences look like each other (or if parts do)

5. MOTIF search using downloaded profile or HMM

MOTIF search allows you to query against serveral database, such as PFAM, CDD, PROSITE etc. More interesting, it also allows you to specifiy your own profile or HMM.

So you can download the HMM of your desired domain from e.g. PFAM  or the domain profile from Prosite.

6. Downloading HMM and use HMMscan (or HMMER)
This was suggested by @seven11, you can search your HMM domain in the PFAM database and then use HMMscan.

Conclusion

If you are really interested in one domain. I think downloading the ProSite scan tool would be your best option. Notably, all webtools I mentioned above are available as command line tool, and that is what you need when having that amount of sequences. Back to ProSite scan, you can download this here and don't forget the README. As mentioned in the readme:

Input/Output:
  -e : specify the ID or AC of an entry in sequence-file
  -o : specify an output format : $formats_string
  -d : specify a prosite.dat file
  -p : specify a pattern or the AC of a prosite motif
  -f : specify a motif AC to scan against together with all its
       releated post-processing motifs (but show only specified
       motif hits)

You can use the -p to specify the acc of the pattern you want.

I'm quite busy so I typed this one really fast, please let me know when something is not clear.