text:
Can the value of heritability be greater than 1?
Heritability defined as genetic variance divided by total variance seems to be bounded between 0 and 1.  However, I see a way of calculating heritability on this page (http://www.radford.edu/~rsheehy/Gen_flash/Tutorials/Linear_Regression/reg-tut.htm) with:  2*Covxy / Varx.  However, a result calculated in this way could be greater than 1.  What am I missing?

I am missing where on that site it is stated the formula you are giving is calculating heritability.

Where it says "Calculating the slope," but I multiply by 2 for a sexual population, according to the last paragraph on the page.

@skymningen It's at the bottom: "Regression of offspring on only one parent underestimates narrow-sense heritability by about 50%. Therefore, Christine's analysis suggested a narrow-sense heritability of 2 x 0.414 = 0.828." The problem is that if you had both parents, the slope would be closer to 0.828, and it wouldn't be doubled.


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What is the mechanism behind the association of a sensation with a stimulus?
I'll explain the question with an example.
Consider Gustation: glucose tastes sweet, bitter gourd tastes bitter and salt tastes salty. Now, sweet obviously feels good but suppose there is an alien species whose biochemistry is different from us,  they don't use glucose as a fuel. Now glucose maybe toxic to them so they experience a bad taste whenever they ingest glucose. In this case, the sensation is different!
Another Example would be Photoreception. How is it decided that light having wavelength of 700–635 nm would be considered red and not blue? I know that your answer would be "This is because light of this wavelength stimulates the red cone and not the blue one." Then my question would be why stimulating the red cone gives us the sensation of red colour and not of blue colour?
Similarly, Why does air of temperature higher than our body gives us a sensation of "Hot" and not of "Cold"?
I know that having different sensations for different stimuli affects our reproductive fitness. Those which can detect changes in the environment are more likely to survive than those which don't. Those which developed "sweet sensation" for glucose can gain more energy than those who don't. But it doesn't explain the relationship between the experience of a stimulus and the stimulus.
It seems like our own body has invented experience and sensation and these phenomena don't have any physical significance.

We call this a problem of qualia. Maybe this answer interests you: https://biology.stackexchange.com/questions/47828/what-really-is-color-and-how-do-we-perceive-it

Also, have in mind your last parahraph: "It seems like our own body has invented experience and sensation and these phenomena don't have any physical significance." They don't! Sensations are idiosyncratic. A blue light with a given wavelength is captured by the same cones in you and me, and we both call it "blue", and we agree in every aspect of the experience... however, how do you know that the colour I feel is the same colour that you feel?

"...these phenomena don't have any physical significance." That's a bit confusing, if you consider survival a "physical significance".

@anongoodnurse What I mean by "Physical significance" is that they are just illusion and don't actually exist. How anything "looks like", "smells like" or "tastes like" are just things completely made up concepts by the brain.

@ShivanshuSiyanwal Don't get me wrong: your sensations do exist. However, they do not correspond to any physical property: The feeling that you have when you see a blue object is very real. However, the blueness  of the object has no relationship (regarding your sensation) with the wavelength of the blue light it emits.

source: Stack Exchange

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

sort: votes


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Does the Spinoreticular Tract end in Brainstem?
According to this book on Springer spinoreticular tract is :

As the name implies, the tract originates in the spinal cord and terminates in the reticular formation (RF) in the brainstem. While most of the fibers appear to terminate in the RF of the medulla and lower pons, some may ascend as far as the midbrain.

But according to Wikipedia :

The spinoreticular tract is an ascending pathway in the white matter of the spinal cord, positioned closely to the lateral spinothalamic tract. The tract is from spinal cord—to reticular formation— to thalamus.

What I am unable to understand is if Wikipedia is true then why do we consider this tract as ending in the brainstem rather than ending in the thalamus?
Also I am getting different information about the location of the origin of spinoreticular fibres,
My Textbook says:

The spinoreticular fibres begin from the spinal neurons mainly in lamina VII (also V and VIII).

But this site says:

The term spinoreticular tract refers to a fiber bundle that arises largely from lamina I, lamina IV and lamina V of the spinal cord.

Which source is correct?

I'm curious... the Wiki article is identified as needing more citations, so I'm wondering why you are weighing an admittedly incomplete Wiki article against your textbook.

Sometimes my textbook too gets wrong. Also who is correct in the second part?

Depends on who you read. One reputable source stated the spinoreticular tract originates from neurons located mainly in contralateral laminae 7–8, the lateral reticulated part of lamina 5. They are also located more sparsely in lamina 1, area 10, and the lateral spinal nucleus. Its axons are myelinated, and the majority cross the midline to ascend in the ventrolateral funiculus, intermingled with spinothalamic fibers. Some spinoreticular tract axons are collateral branches of the spinothalamic tract neurons. Another stated something slightly - very slightly - different.

Could you please cite the source for further reading?

In the top 5 f hits on google.

When will you answer the question about chassignac's tubercle?

From my previous answer/comment, it should seen obvious when I will answer it. The answer is nowhere written in stone.

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


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What is the name of this red plant?
I came across this plant yesterday (14th May) and was wondering what it might be? Would anybody know the scientific name and if it's indigenous to the UK (personally I doubt it is)? The plant grows in an Asian style garden near Cumnock, Scotland.

Close up of leaves:

I keep seeing this in the Hot Network Questions, misreading it as "What is the name of this red planet?" and thinking, "It's Mars, duh."

I'm pretty sure the sun is the only red planet /s

Yes this is Acer Palmatum . We have one in a container in our garden which is twenty years old and does look amazing when in full leaf. It is completely hardy though hard late spring frosts might affect leaves already out.

Red? Something wrong with your photo or your colour vision.

This is the "Acer palmatum" or Japanese maple, which shows a wide variety of different leaf forms (from here):

Specically you found "Acer palmatum dissectum 'Red Dragon'", for more information look here (picture also from this site):

Wow. Thanks for the quick answer. I am well impressed.

Looks like a cultivar of the Japanse maple (Acer palmatum). I assume that is why you have found it in an Asian stlye garden. There are various cultivars that differ by color and shape of the leaves, as you can see in this picture form Wikipedia:
Image source:
https://en.wikipedia.org/wiki/Acer_palmatum#/media/File:Acer-palmatum-ssp.jpg

It's an acer dissectum ( spelling may not be quite right!). It is Japanese and one of a number of similar plants from there. Becoming popular in UK.  Needs slightly acid soil, PH of about 6. semi shade and shelter from winds

Welcome to Biology.SE. Why do you answer a question that has already been answered and provide the same answer (without references, and actually borderline wrong as this is not A. dissectum - which does not exist - but A. palmatum in the dissectum variant) as the accepted answer? Your answer as is might be down-voted or deleted. Please take a look at the tour and the guidelines for good answers. Thanks!


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Can you identify this tree?

This was photographed near Budapest, Hungary, though my friend said she'd only ever seen these in the USA before.

A question about the same plant: Viburnum.

Yes this is definitely another example of a Viburnum like the one in this post. Without additional pictures, I'm not sure we'll be able to identify it accurately to species/cultivar. As such, -- even though it appears to be a different species/cultivar -- I'm going to vote to close this as a duplicate of the linked post.


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What's the difference between Phage DNA and Recombinant DNA
Genetic engineering:
In my textbook the following sentences describe the two, but to me they seem the same:

The new combination of bases in the DNA (vector DNA + DNA fragment)
is called recombinant DNA.
With bacteriophage vector, the bacteriophage will infect the bacteria by injecting its DNA into it. The Phage DNA (with the
desired gene in it) then integrate into the bacterial DNA.

Without going too much into it. What is the difference between Phage DNA and recombinant DNA?

Phage DNA is the DNA in a bacteriophage.
Recombinant DNA is synthetically combined DNA used in genetic engineering.
In your case, since the phage's DNA is used as a vector, the phage DNA is the recombinant DNA, but that does not mean every phage's DNA is recombinant, since phages occur naturally. The point is, the phage DNA was altered to become recombinant DNA.


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How can a pathogenic bacterium be avirulent?
Streptococcus pneumoniae R6 is a pathogenic bacterial strain but it is avirulent. How can a pathogen be avirulent. What does it mean if a pathogenic bacterium is avirulent?

Streptococcus pneumoniae is a pathogenic species. Streptococcus pneumoniae R6 is an avirulent strain of this species. Presumably this means that specific virulence genes that are present in virulent strains of Streptococcus pneumoniae are missing or mutated in the R6 strain. In fact the most likely difference would be that virulence factors are encoded by a plasmid that has been lost in the avirulent strain.
The use of avirulent strains is a common strategy for studying pathogenic bacteria, although obviously it precludes studying mechanisms of pathogenicity directly.

Details as to what render the strain avirulent detailed here. Namely, the lack of a capsule.


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Single wire pacemakers
There are single wire pacemakers used for regulating heart beat. The wire will conduct pulse to the heart. How can one wire be enough? Where is the reference wire for the stimulation of heart?

Hi, welcome to BIO.SE! What research have you already done on the topic? We ask that all questions here provide some evidence of previous research. Thanks


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What are the effects of buffer on genomic DNA shearing by sonication?
Expt: I have isolated genomic DNA from LNCaP cells and would like to crosslink a small molecule (Chem-seq) to the DNA.  The small molecule is an alkylator so it will crosslink DNA on its own.  The buffer I am using for the crosslinking is TKMC (10 mM Tris-HCl [pH 7], 10 mM KCl, 10 mM MgCl2, 5 mM CaCl2).  After crosslinking I want to fragment the genome to 100 - 600 bp (300-400 bp average).  I am using a Bioruptor 300.
Question:  Should the TKMC buffer be sufficient for sonication?  Most references I have found use TE buffer (pH 7.5 - 8), and I can't find a reference using TKMC.
More info:  I tried a direct comparison between the two buffers (TKMC v TE pH8) and the TE buffer seems to fragment to smaller sizes compared to the TKMC buffer.
For example: Biorupter 300, Low setting, 1 cycle = 30/30 ON/OFF @ 3 C, 5 ng/uL DNA in 300 uL
average frag size @ 30 cycles: TE = 350bp, TKMC = 500bp
Any suggestions?  Using TE buffer for my alkylation crosslinking would not work due to presence of EDTA.  Should I play around with the cycle ON/OFF times?
Any help would be awesome!  Thanks.
UPDATE:
After running a comparison between TKMC, TKMC + 1mM EDTA, TKMC + 10 mM EDTA there was a slight tightening up of the fragment range as I added EDTA.  In addition, the fragment range (sizes) was smaller when EDTA was added (compared to TKMC w/o EDTA, after the same number of cycles).  The results were not drastic but there was indeed a noticeable effect on fragment size and range.  I will proceed with adding EDTA before sonication.  Thank you for your suggestions!

As long as kept cold I would increase the on/off until you achieved the average size you are looking for.  I'd start the next one with 40 cycles and examine.  This manual page 17 seems to indicate this would be very appropriate https://www.diagenode.com/files/products/shearing_technology/bioruptor/Bioruptor_manual.pdf

I know nothing about this, but if divalent cations somehow affect fragmentation, you could try adding EDTA in excess after cross-linking.

@canadianer Yes, of course, better than my suggestion of buffer exchange!

@AlanBoyd I'm kind of curious if it works. It's surprising to me that Mg would have such a drastic effect, but I'll have to read the paper you found.

Note that there is 10 mM Mg and 5 mM Ca, so you may need to add in excess of 15 mM EDTA.

I diluted the TKMC/DNA 1:1 when adding the 10 mM EDTA (keeping the Tris-HCl @ 10 mM) this dilutes the Mg2+ (5 mM) and Ca2+ (2.5 mM).

Could you use a spun column to exchange the buffer? Some sort of gel filtration column; equilibrate column in TE; add your DNA sample, spin through excluded DNA. TKMC components will be included in the column and thus retained.
Update
Have a look at this paper, and references therein. Apparently magnesium ions influence the flexibility of DNA. Clearly if the shape of your DNA in the two buffers is different this would impact upon the effects of shearing forces.


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Can anyone identify this queen ant?
I caught my first queen but I'm having trouble identifying her. Could anyone help me out? She has a reddish brown body and black legs.

It's important to get a clear picture and to have some sort of scale for species identification.

Probably not very accurately...

It's hard. I'll try to get a better picture tomorrow


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Cytoscape export network
I'm using Cytoscape to visualise a ppi network having 2000 proteins ... I m trying to export it but the supported format are only cytoscype formats not a usable ones
and for the table format the network is separatted , I don't find it explorable .
How to I export that network in format convertable to csv . or csv so that I can use it in a tool supporting only csv  file format format

The SIF network format produces an edgelist. If you have attributes attached to nodes or edges then you'll need to export in xgmml, graphml or xml and then parse from there.


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Why do stomata close in low intensity light?
Stomata close during high intensity light to prevent excessive transpiration but why did they close during low intensity of light? Please explain in easy- understand language because i'm  in just 10th standard.

Think closed state as default state, it is the light which opens the stomata, So in the absence of light stomata go backs default(closed or resting or inactive) state.

Do you have a source in support of your assertion that high light intensity causes stomata to close?

The primary function of open stomata is to promote gas exchange in leaf tissue: atmospheric carbon dioxide is a substrate for photosynthesis. A side effect of opening the stomata is an increase of water loss through transpiration. If light intensity is low then photosynthesis will be depressed: under these conditions it makes sense to close the stomata to conserve water.


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Familial Hypercholesterolemia
Why does Familial Hypercholesterolemia shows autosomal dominant pattern?
Let us take that there is mutation in LDL receptor gene, it is said that:

The LDL receptor gene is located on the short arm of chromosome 19 (19p13.1-13.3).[6] It comprises 18 exons and spans 45 kb, and the protein gene product contains 839 amino acids in mature form. A single abnormal copy (heterozygote) of FH causes cardiovascular disease by the age of 50 in about 40% of cases.

Shouldn't the expression of the other normal allele mask the effect of abnormal allele by producing the receptor protein?
So, why does this disease show dominant pattern?
Is there anything extra?

Source: https://en.wikipedia.org/wiki/Familial_hypercholesterolemia

Think this way: two wild types --> normal amount of receptor: normal individual. One wild type and one mutant --> half the amount of the receptor: hypercholesterolemia. Two mutants --> no receptor: child with atherosclerosis.

Why does the cell not up regulate the expression of normal allele?

I believe you have some misunderstanding about how cells regulate gene (not allelic) expression.

According to Wikipedia : Up-regulation occurs, for example, when a cell is deficient in some kind of receptor. In this case, more receptor protein is synthesized and transported to the membrane of the cell and, thus, the sensitivity of the cell is brought back to normal, reestablishing homeostasis.

So, why does cell not produce LDL receptors by up regulation?

You're talking about homeostasis in an homozygote. In an heterozygote, how can the cell know which allele to use?

Let us continue this discussion in chat.


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How do transport/carrier proteins rotate during facilitated diffusion?
In my book, it is written that when a molecule binds to the carrier protein then the protein rotates and releases the molecule inside the cell. I want to know how is this possible. Wouldn't the surrounding phospholipid molecules or other proteins hinder its rotation?
EDIT
The rotation axis is in the plane of membrane
Source : http://ncert.nic.in/ncerts/l/kebo111.pdf (page 177, Third paragraph)

Rotation of carrier protein in which axis? is the axis in the plane of membrane or perpendicular to it? If latter is the case then  there shouldn't be any noticeable  hindrance as the membrane is quasi fluid in nature.

@JM97 The rotation axis is in the plane of the membrane.

Please cite the source, or upload a photograph showing rotational axis.

@JM97 I've added the source in the question.

Where does it says that axis is in the plane?

@JM97 Look at figure 11.1 on page 177 and read the third paragraph. Though they've not said that the axis is in the plane of the membrane but you can figure it out yourself. Perpendicular axis don't make sense because then the molecules won't be transported inside the cell

Let us continue this discussion in chat.

The text referring to Fig 11.1 says that the carrier rotates, but this is clearly wrong even in terms of the way the Figure has been drawn: there are arrows to represent a pathway through the carrier, and there is no indication at all that the carrier rotates.

@Alan Boyd Yes. This is confusing.

"How do transport/carrier proteins rotate during facilitated diffusion?"
They don't. The explanation in the PDF you linked...

Figure 11.1 shows an extracellular molecule bound to the transport protein; the transport protein then rotates and releases the molecule inside the cell.

... is an oversimplification, to say the least (you could simply say that this is plain wrong). What really happens is way more complex.
We call it conformational change.
According to Alberts, Molecular Biology of the Cell (2002):

Each type of carrier protein has one or more specific binding sites for its solute (substrate). It transfers the solute across the lipid bilayer by undergoing reversible conformational changes that alternately expose the solute-binding site first on one side of the membrane and then on the other. (emphasis mine)

This is an image that explains way better the process, from the same chapter in Alberts (the legend provides a detailed explanation):

Figure 11-11A model for the molecular mechanism of action of the bacterial lactose permease (A) A view from the cytosol of the proposed arrangement of the 12 predicted transmembrane helices in the membrane. The loops that connect the helices on either side of the membrane are omitted for clarity. A glutamic acid on helix X binds H+, and amino acids contributed by helices IV and V bind lactose. (B) During a transport cycle, the carrier flips between two conformational states: in one, the H+ -and lactose-binding sites are accessible to the extracellular space (1 and 2); in the other, they are exposed to the cytosol (3 and 4). Unloading of the solutes on the cytosolic face (3 → 4) is favored because the lactose-binding site is partly disrupted and a positive charge contributed by an arginine on helix IX displaces the H+ from the glutamic acid on helix X. (A, adapted from H.R. Kaback and J. Wu, Accts. Chem. Res. 32:805-813, 1999.)
Thus, as you can see, we have conformational states: one of them exposes the binding site to the extracellular space, while the other one exposes the binding site to the cytosol. Just like what happens when an enzyme changes conformation, the 3D changes in the protein structure are quite small, and it's hydrophobic regions keep in the same place in both states.
Source: Alberts, B., Johnson, A. and Lewis, J. (2002). Molecular biology of the cell. 1st ed. New York: Garland Science..

+1 but why beat about the bush? Just say it's wrong.

@alanboyd welcome back! (I suppose you've come back today...?) As you see, there are some new faces here (although mine is a bit ancient :P). So, when are we seeing your next answer? Oh, and +1 for Gerardo ;-)

@AlanBoyd I'm trying to be nice and polite :-)

@another'Homosapien' Yes, I've been back for about a week - a sprinkling of answers. I'm trying to be more selective than I used to be.

@alanboyd a week?! (How ignorant of me) anyways, eagerly waiting for some masterpieces :)

@Gerardo Furtado  This makes much more sense than rotation.


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Bird identification: song two low, two high, five short
This morning I heard a bird that had a song which was two low notes, two high notes, and five quick notes in succession. Location is New England.
Is there any way, short of asking an expert, that I can find out what a bird is from a description of its song or call?
Update - Bird Song Uploaded
I have been able to host a sound clip on Vocaroo:
Unknown bird, Massachusetts, forested suburban environment

It's hard to say by your description. But you could try a song database: http://www.xeno-canto.org/ Click "explore by region", drag a box over New England. I got 125 species. It will take a while, but perhaps you find yours (125 is not that much).

@GerardoFurtado Nice website! Haven't heard of it before. I will add it to my repertoire of ID tools. Thanks! :D

Best guess is that the bird is a Song Sparrow, Melospiza melodia. Cornell Lab of Ornithology has a good website for basic facts about birds. Here is the account for Song Sparrow. There is a sample of typical song, but there can occasionally be some variety.
The song is kind of complex and the recording you linked to seems to garble or not capture some of the song, but the changes in phrases throughout the duration seem to match as does the pitch of most of the phrases.

+1 The first audio here is very close to OP's bird's song.


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BLAST 16s rDNA: Everything alligns to Bacillus sp
I'm trying to identify and isolate Pseudomonas and Bradyrhizobium strains from rhizosphere and endophytic compartments of a tree. I plated the strains on selective media (King's B. for Pseudomonas and YEM for Bradyrhizobium) and purified the colonies grown by picking them and let them grow on separate plates. There is a lot of variety in morphologies.
When I had grown colonies of bacteria and was able to pick up single colonies I did a 16s rDNA pcr reaction on the colonies. After sequencing the 16s rDNA sequence I did a quick BLAST search to annotate the sequences and thus the bacteria to a species. But from all colonies till now (already 25 reactions sequenced) I only found that they allign best to Bacillus. I think this is strange because there should be a lot of variety according to their morphology.
Does anyone has a solution for this? Is it, for example possible to exclude the Bacillus group from the BLAST search? Or does this mean my colonies are still contaminated?
This is probably not enough information to answer my question but maybe you have experience with doing this and have some ideas.
Thanks!

As you guessed in the last sentence, it's hard to answer your question without some more information.
For example, how much of the 16S rRNA gene did you sequence? Most people just sequence the v3-v4 regions which are the most variable, but they only comprise a few hundred bases. Sequencing the entire 1500 bp gene gives more specificity when doing searches, but is also more expensive.
With regards to selection of colonies, do you know from the literature how selective your two different types of media are? We did similar studies with environmental E. coli including several rounds of screening and selection, and you would be surprised how much "junk" we got. If you're isolating from soil, Pseudomonas and Bacillus spp. are going to both be highly prevalent.
With that in mind, it is not enough to grow on selective media, do one transfer, and call it good. Really, you should have a screening method in addition to your selective media. Maybe some compound that yields fluorescence or a visible change to the surrounding media that you can use to differentiate your target bacteria from contaminants. Once you have your candidates, you need to isolation streak them onto fresh selective media. Then screen again and isolation streak again. Repeat this process 2-3 times, or until you have monomorphic, pure cultures. Only then should you start doing genetic/genomic testing on your isolates.
Hope this helps.

Sorry, just realized this was asked 7 months ago. My two cents though, for what it's worth.


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How long ago did the mutation arise that gives rise to sickle-cell disease?
Is it known how long ago the mutation arose in Africa that gives rise to sickle-cell disease and protects from Malaria in heterozygote carriers?

Is it safe to assume that the mutation arose after the out-of-Africa migrations, since sickle-cell disease is almost exclusively prevalent in people with more recent African ancestry (i.e., black people)?

In a fairly recent review P W Hedrick surveys a number of gene variants associated with resistance to malaria.
He explains that:

The impact of malaria is thought to have increased between 10,000 and 5,000 years ago when there were the beginnings of agriculture and consequently more human settlements. During this period, the numbers of both the human population and the mosquito vector increased, resulting in higher spread of malaria.
  Recent molecular studies suggest that malaria in humans from Plasmodium falciparum may have originated from gorillas. Using these data, an initial timeline for the origin of P. falciparum as a human pathogen suggests that it may be more recent than previously thought.

As you can see from his Table 1 (reproduced below), the S variant of β-globin is suggested to have arisen 1440 years ago.

The study of the origin of sickle cell anaemia is complicated by the fact that the allele responsible is found associated with five different β-globin haplotypes (four from Africa, one from Saudi Arabia/India). This has sometimes been interpreted as indicating that the allele arose on several independent occasions. However, the picture is complicated by patterns of human migration, and recent papers suggest that the observed distribution of the S variant is not inconsistent with a single origin, e.g. this paper.


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Down syndrome in subsaharan populations
What is the rate of occurrences of Down syndrome in subsaharan African populations? Is it the same as in white European populations?
An interesting hypothesis came to my mind:
Could it be that Down syndrome is the result of interaction of different dominant or recessive Neanderthal or Denisovan genes that European and Asian populations cary in small percentages?

See UN > stats Down Syndrome per country.
What the data says
I have not made a proper statistical test (as I am too lazy to reformat the data in anything convenient to perform a statistical test) but the prevalence seems to be consistently around 0.12499% all around the world with very very little variance. I doubt there is any significant difference in the frequency of birth that have down syndrome.
As @Markonionini rightly noticed, these estimates of prevalance are slightly far fetch extrapolation and the UN specifically advice to consider them with caution. It is probably the best data we have though.
The hypothesis seems improbable to me
Do you have any good rational behind your hypothesis? Down Syndrom is typically caused by de novo mutations and not due to standing genetic variation (Veltman and Brunner 2012) so your hypothesis seems rather implausible to me.

Well, seeing only white people having Down syndrome, made me think in this direction. Other than that, I have no other arguments for this hypothesis.

Good answer. +1 Would also be weird to have this kind of ploidy polymorphism floating around in the population ... but this gives me an idea.

@AlexDeLarge Thanks.... but now we all want to know your idea!

@Remi.b totaly!

I invite whoever down voted to comment on the reasons. A down vote without comment does not help to improve a post.

@Markonionini and Remi.b, I posted this following that idea. I hope it is not too unclear.


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Predicting DNA nucleotide bases sequence from fully formed protein
I know there are many algorithms (and a lot of different implementations) that allow predicting the outcome of protein synthesis given a set of nucleotide bases present in the DNA. In other words, given a sequence of such bases, produce a final protein (going through a simulation of the various processes that end up in a protein). However, are there any algorithms that allow to predict the opposite, i.e. the sequence of nucleotide bases that were the basis for the synthesis into a given protein?

It's trivial in principle, but remember that there are multiple codons that can produce a single amino acid, so reverse-translating a protein will either give you the most commonly-used codons for the protein, or will give you a large number of possible sequences.
Here and here are online programs that will give a single consensus, and here is one that considers ambiguities.

This is a standard method used in bioinformatics.
First step is to convert the amino acid sequence to a degenerate nucleotide sequence using the relevant codon table.
Once you have the degenerate nucleotide sequence, you can blast it against all known nucleotide sequences, including whole genomes.
Since the degenerate nucleotide sequence essentially is a degenerate cDNA sequence, you can then simply identify any genes with exons capable of producing the necesary cDNA through splicing events.
This method is called tblastn and is available here: https://blast.ncbi.nlm.nih.gov/Blast.cgi


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Polymorphism in number of chromosomes?
The answer to this question, saying that Down Syndrome - a trisomy of human chromosome 21 - is caused by de novo mutation (rather than resulting from standing variation) made me think about polymorphisms in the number of autosomes (not so much for sex chromosomes because of dosage compensation). The reason for this question is that I would never have thought that an aneuploidy, in theory, could be a segregating trait because of meiotic barriers.
I found evidence of ploidy polymorphisms in plants (especially their hybrids) that occurs when plants with different karyotypes hybridise [see, for example, Vandenhout et al. (1995) and Husband (2014)]. Additionally, I also found that this also applies to some aquatic vertebrates, however, 'fish' are also known for karyotype diversity (see Zhou et al. (2007) and Zhao et al. (2016)).
In rather sharp contrast to that, mammals are (almost) strictly diploid and most mammal species are characterised by fixed chromosome numbers, even though exceptions exist, i.e in mice and other rodents that exhibit intraspecific variation in diploid numbers - these are created by Robertsonian translovations [Graphodatsky et al. (2011)].
However, all of these are diploid and variation always needs to be expressed as a chromosome number of the form $2n$ because of meiosis. The karyotype of a human with trisomie 21 cannot be expressed in that form as this person has $2n +1$ chromosomes. All cases of aneuploidiy in autosomes I am aware of cause disease. My (related) questions now are:
(1) Are there described cases of non-deleterious aneuploidies in autosomes?
Those cannot be segregating in the populations as aneuploidies are not inherited to children, so more importantly:
(2) Are there indirectly segregating aneuploidies in autosomes (i.e. some sort of heritable trisomy that e.g. result from a trisomy followed by chromosomal rearrangement)?
If so, do any of these also exist in mammals, particularly in humans?

There is definitely long lasting variation in copy number (CNV) where the number of copies is not a multiple of 2. I don't know about whole chromosome number variation. I guess sexual chromosome would not count as long as there is a pseudo autosomal region (PAR) unless for XXX individuals.

According to Wikipedia, XXX and XYY snydrome cause no or little symptoms. https://en.wikipedia.org/wiki/XYY_syndrome https://en.wikipedia.org/wiki/Triple_X_syndrome

@adjan, sorry, I should have clarified that I was not asking about sex chromosomes because of dosage compensation.

I suppose XXX individuals would still qualify as an answer, wouldn't it? It is a "unusual" (unlike the standard XY) case of a chromosome number that is equal to 2n + 1.

Good questions, but you make a claim that isn't necessarily true:

However, all of these are diploid and variation always needs to be expressed
  as a chromosome number of the form $2n$ because of meiosis. The karyotype of a
  human with trisomy 21 cannot be expressed in that form as this person has
  $2n+1$ chromosomes.

The emphasized text isn't necessarily true - there are certainly more involved ways to describe the karyotype of a given individual or cell line. For instance, take the GM12878 cell line, likely the most well-defined cell line in terms of genetics, epigenetics, and chromatin biology today. It's karyotype is listed as:

46,XX[23].arr[hg19] 9p13.1(38,787,480-40,911,212)x3

This is a fairly common way of representing changes known as copy number variation, wherein only a small region of a given chromosome is duplicated or deleted. For this cell line, which relatively closely mimics lymphoblastic B cells, the genome is nearly normal (46 chromosomes, XX) with only a small amplification on chromosome 9 (9p13.1(38,787,480-40,911,212)x3). This is a mild example, but smaller copy number variations like this are quite common and can amplify or delete both large chunks or very focal regions of genomes.
But to answer your first question, no, there are no known non-deleterious trisomies in autosomes. Trisomy 13 (Patau's syndrome) and trisomy 18 (Edward's syndrome) children can live to birth, but die within the first few months of life. Unsurprisingly, these chromosomes are also the smallest chromosomes with respect to the number of transcripts that they encode 1. This suggests that the additional amount of genetic material determines the severity of the defects, and this trend also holds true in mice. From a figure caption of the cited paper (which is likely behind a paywall for those without institutional access):

A correlation between degree of aneuploidy and organismal fitness in humans and >mice. (A) The number of known human transcripts/chromosome in humans. Trisomies >below the line develop to birth. Trisomies above the line are embryonic lethal. Only those chromosomes containing the least amount of transcripts survive birth. (B) In mice, survival of the embryo is inversely correlated with the size of the chromosome that is present in three copies. Linear regression analysis fits the data with an R2 of 0.71.

I was unable to find any examples for your second question. Cancer cells can get very messed up in terms of copy number, but I've never seen anything about heritable aneuploidy.

Fascinating, thank you very much for your answer! This is a very interesting way to think about CNV - actually these large CNV chunks are already examples for my second question. I will have a deeper look into that.


text:
Are penguins plantigrade or digigrade?
I'm trying to rig a 3D model of a penguin, but I don't know where to put the bones near the ankle because I can't tell if they're digigrade or plantigrade. Nearly all birds are digigrade, but penguins spend a lot of time walking and don't generally grasp or run with their talons.

Plantigrade.

The penguins are highly specialized for their flightless aquatic
  existence. The feet are located much farther back than those of other
  birds, with the result that the bird carries itself mostly upright;
  its walk can thus be described as plantigrade (i.e., on the soles).
  The sole comprises the whole foot instead of just the toes, as in
  other birds. The most notable characteristic of the group is the
  transformation of the forelimb into a paddle. This is accompanied by a
  body morphology particularly adapted to movement in a liquid medium.
  The thoracic (rib) cage is well developed, and the sternum bears a
  pronounced keel for the attachment of the pectoral muscles, which move
  the flippers. The flipper has the same skeletal base as the wing of
  flying birds but with its elements shortened and flattened, producing
  a relatively rigid limb covered with very short feathers—an ideal
  organ for rapid propulsion. The body plumage likewise consists of very
  short feathers, which minimize friction and turbulence. The density of
  the plumage and the layer of air that it retains provide almost
  complete insulation of the body.

https://www.britannica.com/animal/penguin#ref3467


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If I workout, will this inherited trait (of being stronger) not be passed down to my offspring (Lamarck's theory on evolution)?
I'm a student in biology and just recently learned about Lamarck's theory on evolution and how it has been disproved. While I understand that you cannot alter your genes, I'm still having a hard time understanding some parts of it, mainly how inheriting strength (such as working out) will not be passed down to my offspring. If someone was obese, exercised to the point of no longer being obese, will this person's offspring still start off as obese?

You inherit genes for muscle from your parents. What you do with that muscle is not passed on. Your physical attractiveness if you work out may benefit you passing on your gene pool, but that's about all you can do genetically. Obesity may have something to do with gut flora, which can be traded between two individuals, e.g. from mother to offspring. But there is much to obesity which is not understood yet.

Indeed, whether you work out or not will not change how strong your offspring will be. This is exactly why Lamarck's was wrong.

I would note however that Behaviour can be heritable and Your behaviour can affect your kids environment
Behaviour can be heritable
The probability of you working out is affected by your genes and so if you have a genetic predisposition for willing to work out, this will be passed on.
Assuming there are genetic predisposition for liking to work out, the fact that you worked out would not increase the probability of your kid to work out via genetic inheritance but the fact that you have a genetic predisposition for liking to work out will increase the probability that your kid will have the same preference and will work out
By the way, if you want to learn more about the concept f heritability you should have a look at Why is a heritability coefficient not an index of how “genetic” something is?
Your behaviour can affect your kids environment
Working out won't affect your genes but it will likely affect the environment in which the kid will grow. Here are three examples

Teaching

If you eat healthy, you will probably teach your kids to eat healthy too.

Womb environment

Also, if you eat healthy and are a woman, you will likely give the right nutrients to your offspring while still in the womb (assuming you are a lady).

Epigenetics

Your environment will cause epigenetic changes (changes not in DNA but in the very close environment of the DNA such as typically histone tail methylation). These epigenetics modifications will be directly passed to the foetus.
More information
A post your question is almost a duplicate of...

Is it the case that all changes in phenotype during life are not inheritable?

A post on heritability

Why is a heritability coefficient not an index of how “genetic” something is?

And finally an answer that talks about non-genetic inheritance

Why does evolution only involve heritable traits?

"...the fact that you have a genetic predisposition for liking to work out will increase the probability that your kid will have the same preference and will work out..." Can you please support this with a reference? I.e., is there any evidence that points to a genetic predisposition to work out?

I added Assuming there are genetic predisposition for liking to work out [..]. My goal was to explain the basics of inheritance, not to review the heritability of specific trait. Thanks for noticing this potential confusion. I would notice however that given there is very likely heritability for such life style given that many of hormones concentration are heritable (incl. testosterone typically).

There's no evidence that I'm aware of that testosterone levels contribute to a propensity to work out. A propensity towards some things (like hostility, aggression, etc.) but exercise, again, not that I'm aware of.

It is pretty tough to investigate liking independently of an environmental context and of abilities (as many physical properties relating to sport abilities being heritable) but anyway.... it really is not the point of the question nor of the answer. But thanks for clearing the possible confusion.

Also not that it has recently be shown that learned behaviour can be inherited through epigenetic mechanisms. Mice born to parents that were conditioned to fear a certain smell, still reacted to that smell despite never being conditioned (see news article or original paper)

@Nicolai Yes, I did mention that in the answer. Thanks for the references.

@Remi.b Your answer states that behaviour can alter the environment of offspring and thereby affect epigenetic markers on their DNA (which they indirectly inherit this way). What the paper I linked proposes (or shows) is that learned behaviour of the parent is directly passed to the offspring via epigenetic changes in the germline. (The offspring reacts to smell it has never encountered before).

We are saying exactly the same thing IMO. I edited the post to add a single word hoping to make it more clear.


text:
What species is this black, blue and white bird?
I think this species is native to Edmonton, Alberta, Canada, as I see it regularly, especially around the urban locality (Downtown Edmonton).
Season: Early Spring
Date: May 18, 2017
Basic Description: Medium sized bird, and I was not able to observe a characteristic chirp from the bird while I was taking a photograph. Most distinctive feature is the bright royal bluish gradient on the tail and tips of the wings.

If you were in the UK, you'd now have to say "Good morning Mr Magpie. How is your lady wife today?". It's practically a law.

I once took some pictures of this bird while in Africa (in Zaire, as it  was called then.) The onlookers laughed at me (quietly and affebly). It was so common in Zaire it would be like someone marveling at a pigeon in NYC. Good memory, thanks.

That bird is commonly called a magpie. The only species found in Alberta is Pica hudsonia. You can see a reference image on the left and their distribution throughout Canada on the right:

[source]
Interestingly, it is one of the only non-mammals studied that is able to recognize itself in a mirror. In fact, these and other corvids are thought to be some of the most intelligent species on Earth.
You mentioned that you didn't hear them chirp. These birds are actually quite loud and about fifty of them used to wake me up every morning. Have a listen (not my video).

Your attached video makes me realize how lucky I am to not have heard the bird chirp.

@ImtiazRaqib Ha! Just imagine 50 of them on your roof at 6 am ;)

A species-id question with no research effort again. :)

It's clearly a magpie, a member of the crow family (Corvidae). There are many magpie species throughout the world, but since you say it's native to Canada, it must be the black-billed magpie (Pica hudsonia). There are only two magpie species native to Northern America, the other being the yellow-billed magpie (Pica nuttalli), occuring in California.

Image source:
http://www.audubon.org/field-guide/bird/black-billed-magpie

Finally one of these silly questions I could answer and you beat me to it!


text:
CRISPR guide RNA design and primer synthesis
I am trying to knockout huntingtin gene from HeLa cells (human epithelial cells). I used CRISPR explorer and benchling.com to determine the best guide RNA sequence that would bind to the target DNA sequence and cas9 could then make the cut. The gRNA I have is as follows:
GGAGGCCTCGGGCCGACTCG
Strand (-)
The next step for me is to design the primers with the following sticky ends
Forward primer: 5'-TTGTTGN(19)-3'
Backward primer: 3'-ACN(19)AAA-5'
The problem I'm having is writing the oligonucleotide sequence of the primers. Since the gRNA strand is negative, I'm assuming it's a 3'-5' sequence, hence the reverse of it will be the 5'-3' sequence, which I can then just use as the forward primer. Sequentially, I can take the reverse and complement of this forward primer sequence to then determine the backward primer. Is that correct? I appreciate all your help.
Thank you!

Is GGAGGCCTCGGGCCGACTCG the output of the gRNA finding software? If so this sequence is most likely 5'→3'. Can you share the output file of the software. If it is an online tool then can you provide the link?

As CRISPR is quite a popular topic, it would be nice to have some basic explanatories for newbies, like:  Backward primer is the term equivalent to reverse primer   in pcr? More blunty: why do you need a backward primer in CRISPR, at all?

A quick check with BLAST returned the following result:
Homo sapiens huntingtin (HTT), mRNA
Sequence ID: NM_002111.7Length: 13669Number of Matches: 1
Related Information
Gene-associated gene details
GEO Profiles-microarray expression data
PubChem BioAssay-bioactivity screening
Range 1: 267 to 286GenBankGraphicsNext MatchPrevious Match
Alignment statistics for match #1

Score           Expect  Identities  Gaps        Strand
40.1 bits(20)   0.017   20/20(100%) 0/20(0%)    Plus/Minus
Query  1    GGAGGCCTCGGGCCGACTCG  20
            ||||||||||||||||||||
Sbjct  286  GGAGGCCTCGGGCCGACTCG  267

The sequence you have is 5'-3' and it matches the Minus strand on the human genome. You don't need to reverse the sequence!
Here is a screenshot from IGV showing the gRNA sequence matching the minus strand of the HTT gene.

For those unknowing it would be nice to have some more information. The question is right in assuming the sequence is negative according to your answer (how can you tell by that sheet?).  The question then says "hence the reverse of it will be the 5'-3' sequence, which I can then just use as the forward primer." That conclusion, implication is not correct. That's what you mean? For the forward primer, what you need is the 5'-3' sequence? "You must not" reverse?

@PeterBernhard the gRNA sequence is written in 5'->3'. There is no need to reverse it. If you see the BLAST output, the Query sequence matches perfectly a minus-strand. Note that the minus strand coordinates are from 286 to 267, indicating that the Sbjct sequence is already reversed in the output. The gRNA sequence is already in the 5'-3' order, so there is no need to reverse it. I have added an IGV screenshot showing the gRNA sequence matching on the genome, I hope that will help clarify.

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


text:
Why don't restriction endonucleases digest transformed plasmids?
In the textbook that I'm using, it explains that bacteria does not digest its own chromosomal DNA because the sites that would be cut by its own endonuclease are methylated. Is there a similar mechanism involved for protecting its own plasmids? If so, how are plasmids cut while serving as vectors?

You're asking about engineered plasmids, as opposed to natural ones?

Sure, but I guess it can apply to both; for example, if an engineered plasmid is inserted into E. Coli, what prevents E. Coli's own endonuclease from digesting the new plasmid?

Welcome to SE Biology. Your question seems to imply that you think that restriction enzymes are involved in recombination, which is not so. Perhaps I misunderstand, but I do not see what relevance recombination could have. You will need to clarify if your question is not to be closed as unclear.

I'm sorry; I have no idea why I said recombination there at the end. I think I was thinking of ligation during DNA cloning and got confused because of "recombinant DNA."

Laboratory strains used for the purposes of cloning have been genetically engineered to address this issue, typically by deleting genes of the various restriction-modification systems. There are four broad classes of restriction modification systems, which I will discuss individually. Unless individually referenced, most information below is based on the following supplier technical notes:
Promega: What are the effects of the bacterial DNA restriction-modification systems on cloning?
New England Biolabs: Restriction of Foreign DNA by E. coli K-12

Type I
In Escherichia coli, this system consists of the hsdR, hsdM and hsdS genes and is capable of both restricting (digesting) unmethylated DNA and methylating hemimethylated DNA. Knockout of hsdR and/or hsdM prevents restriction and methylation, respectively. This allows engineering of strains for specific purposes. For example, a common E. coli strain used for cloning, DH5α, has the genotype hsdR17 (rK–, mK+) which abrogates restriction activity but maintains methylation activity. This means that exogenous DNA will not be restricted, but will be methylated and therefore able to be subsequently transformed to r+ strains without worry of degradation, if the need may arise.

Type II
This is the class of restriction enzyme commonly used in the lab to cut DNA because they generally recognize short, palindromic sequences and cut within or near the recognition site. The E. coli background strains K and B, from which most lab strains are derived, do not contain Type II enzymes. The Type II enzyme EcoRI, for example, was isolated from the E. coli RY13 strain (Yoshimori, 1971; PhD thesis).

Type III
Similarly to Type II, the K and B strains do not possess this restriction-modification system, which was first characterized in E. coli 15T-.

Type IV
This system differs from the others in that it cleaves methylated and hemimethylated DNA, though it does not recognize methylation by Type I or Type II modification systems, nor Dam or Dcm methylation. In E. coli, this system consists of the mcrA, mcrBC and mrr genes and is most problematic when attempting transformation of DNA from organisms with ubiquitous cytosine or adenine methylation (eg plants and mammals). For example, the lab strain T7 Express, which is derived from the common strain BL21, has the genotype Δ(mcrC-mrr)114::IS10 which deletes mcrBC, hsdRMS and mrr.

Note on Dam and Dcm Methylases
These bacterial enzymes methylate adenine and cytosine residues, respectively, but are not directly involved in the restriction-modification systems discussed above. However, some Type II enzymes used for cloning are sensitive to this methylation and so lab strains are available with these enzymes deleted.

Thank you for coming back and making the detailed edit; I appreciate the explanation!

@JohnSmith You're welcome. If this answered your question, you can click the checkmark next to the answer to mark it as accepted (as well as upvote).

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


text:
How to incorporate size data with shape in stereographic morphometrics?
This may be an extremely simple point that I am missing, but how are you supposed to know the exact size of a structure being analyzed in three dimensions? When doing two dimensional morphometrics, you simply have a scale bar with your image. I know that microCT and some other methods may do this automatically, but some are now using free software like 123D Catch from Autodesk to create mesh models. In this case, are you strictly restricted to shape independent of size? If not, how do you add in a 3D scale bar, so to speak?

A cube of known dimensions in your field of view would suffice.

But can I then set the scale in these programs just as I would using a 2D ruler? How does the actual calibration occur with the object in view? None of the programs I've looked at using (tps, landmark, R, etc...) seem to have a way to do this.


text:
Can someone identify this tree from the Pacific Northwest?
A tree at my house in Seattle, Washington, USA has these leaves. Can someone tell me what it is?

Do you have a photo of the flowers?

It looks similar to a Cotinus coggygria, which is a shrub that we call a Smokebush in the UK. But given your location, it could be Cotinus obovatus, known as American smoketree.
See http://dendro.cnre.vt.edu/dendrology/syllabus/factsheet.cfm?ID=415
The leaves will start green and progressively change colour to deep reds in the autumn with sprays of pink-purple flowers in the summer that from a distance look like smoke, hence the name.
Here are some images I have found on the web.

http://www.cirrusimage.com/tree_American_smoke.htm

http://allthedirtongardening.blogspot.co.uk/2012/08/smoke-tree-smoke-bush-coninus.html

Hello Martin, could you explain why you think it is Cotinus  sp, ideally with links to references and images. You may also like to read this and find many sample responses to some highly received species-id questions here.

I think this may be a Chokecherry. Prunus virginiana 'Canada Red'
Found this on a Washington nursery website so it would make sense that it would be planted in your region. I am inclined to think it is closer to this species than a smoke bush based off what I can see from the flower in the photograph.

Possibly, although the leaves appear to be smooth-edged, rather than serrated

That's a good point. I would have rather left a comment because not 100% sure, but didn't have enough reputation.


text:
What is this ornamental, yellow flower that looks like a smooth pineapple skin?
My mom got this in her Mother's Day arrangement and we have no idea what it is.

Welcome to Biology.SE. As it is ornemental, the question might be a better fit on Garderning.SE.

I don't understand why there are already 2 close votes in this question. Asking for species identification is perfectly valid here at biology SE. Is the issue just the fact that the plant in question is an ornamental one? It makes no sense to me.

The problem here is different, @Tytoalba. The discussion on Meta talks about a good answer making it worth to keep a question, be it a good or a bad question. What I'm asking here is: why the close votes in the first place? species-identification tag doesn't explicitly says "just for non-ornamental species" or anything like that. OP just wants to know the species of that plant, that's it. It makes no difference if the plant is in a park, in a forest or in his/her mom's table.

@GerardoFurtado See the last paragraph of Madscientist's answer. I didn't remember the question, and wrongly said valid 'discussion', I'll remove it now.

I've read it, thanks, but I'm still think the issue here is unrelated to that discussion.

The issue is not the fact that the plant is ornamental, but the fact that identifying cut flowers makes it impossible to define the "localization" of the species. For anything grown in the garden, we would at least know that it can grow in that specific location. Here we have very little to go with (even if it could be identified successfully this time).

This is a beehive ginger, Zingiber spectabile.
Its inflorescence will become a bit different sometime soon:

I believe the one in your image is not yet fully developed, like this one here:

Source of the images:

http://www.geneticjungle.com/2008/08/deceptive-petals-7-orchid-mimics.html
http://specialflowersintheworld.blogspot.com.au/2015/04/zingiber-spectabile-flower.html


text:
On parents' similarity
I don't know if this is a real claim, I live in Mexico City and most of the people I know are more similar to their father than to their mother? Why is that? Are the x and y cromosomes somehow related to the strength of a particular gen?

It doesn't look like a proper claim. Unless you can support it with verifiable data it's just your opinion.

Good observation:  http://www.dailymail.co.uk/health/article-2977710/People-genetically-like-fathers-mothers-Scientists-discover-use-paternal-DNA.html

Well then, now we have a source, so which characteristics make the father's genes stronger?


text:
Is this plant "Hedera canariensis"?
Location: South India
I found this plant beside bus stop.

Side view of the Plant.

Actually, Wikipedia says Hedera canariensis is "native to the Atlantic coast in Canary islands and northern Africa", but it is growing in India, so is it really Hedera canariensis?

What makes you think that could be Hedera canariensis? It does not look anything like it ...

Looking at your profile, you are using this community to provide the species identification for everything you find, until you find something nobody knows and you can finally declare you found an unknown species. For one, it is highly unlikely you will find an unknown species near a bus stop. Or anywhere near where humans are. Otherwise, please start to read up on how to identify plants and do some preliminary work. We are not some kind of "free expert service".

Apparently looks like Xanthium strumarium (asteraceae) and Chrozophora rottleri (Euphorbiaceae) .

@AlwaysConfused Well! your plants exactly match with my plant, but I added side view of my plant. does it ring any bells?

@ManoharRantam Sorry I couldn't tell without its sexual-reproductive structure. Could also be something else than the 2 i mentioned in the previous comment. However never like Hedera canariensis. The title could be potentially misleading.


text:
Where can I find large datasets of protein-interaction networks?
Where do I find large datasets of protein interaction networks for cancer or alzheimer diseases?  So far, I found String but it is does not have enough proteins for my purposes. Are there such databases with more entries?
I'm still open to any proposition of the disease to choose from .
the most important part is the volume of data .
And how can I get the annotation of each protein  of the extracted network from Uniprot ?

Welcome to Biology.SE. I edited your question to make it more clear. Please feel free to further edit. Thanks!

The String database is one of the best available, how many proteins do you need? (consider that the human genome is predicted to have around 25k protein-coding genes)

@alec_djinn I need for about 5k or 6k proteins for alzheimer or cancer  but i don't know how to retreive that quantity at once

@AM I can't find the exact number of entries for the human proteins, maybe you should contact them, 5k sounds reasonable, I would expect them to have it. If not, maybe you can integrate with other mammalian proteins. As far I know, STRING is the most complete you can find now.

@alec_djinn Okay. Thank you, I will contact them

@AM What makes you think you can find 5k proteins for Alzheimer? Do you hypothesise that 1/5 of the human genome is involved in Alzheimer?
Nevertheless, you could take the genes in the KEGG pathway for Alzheimer disease, or take the genes known to be genetically causative for or associated with AD and include all their interactors. I think the network will get quite big as such.

@alec_djinn ehm, the STRING database is one of the largest available but absolutely not one of the best. Probably the worst, actually, in that it has a lot of crappy data in there. Unless you are knowledgeable enough to parse out the bad stuff, do not recommend it.

@AM please [edit] your question and clarify your needs. Do you want to limit the results to binary interactions only? Are you also interested in non-direct interactions like forming part of the same complex? Do you want only experimentally verified interactions or also those inferred by electronic annotations? Do you have a list of proteins of interest? Please add more details.

@WouterDeCoster would you suggest me an application where i can get such huge dataset ?  I'm not really limited to Azheimer it was just a proposition . I'm open to any disease which will get me this proportion of data

@terdon if it is not then what database would you recommend ? I do not have a protein of interest, I only want a huge dataset of protein protein interaction  for a disease , that's all I'm open to any suggestions .

@AM yes, but what do you mean by "protein-protein interactions for a disease"? How would you define the list of proteins you care about? You normally start with a small list of "bait" proteins and then collect their interactors, moving as many steps down the network as you need.

@terdon  I do not care about the list pf proteins I need , more than the idea of a specific network for a disease , having 4k to 5k of proteins that's all

I don't know how you could even define that. Whether you include a protein in the list of proteins involved in a disease depends very much on how you define disease association. Is it only proteins with a function affecting this disease? Is it also the proteins that interact with them? How many steps removed? How about proteins controlling the expression of related genes? Or proteins that interact with those? Or should it only be protein interactions whose disruptions affect the disease? And should that include ubiquitous proteins that are involved in almost everything?

There is a bunch of decent protein-protein interaction databases: Biocarta, BioGrid, DIP, InnateDB, IntAct, MINT, PPID.
Some of them aren't available now, but you can download datasets from the Expression2Kinases download page because they are integrated into X2K pipeline as part of Genes2Networks analysis. If you need more proteins, you can submit your list of proteins to X2K and use G2N analysis to connect enriched transcription factors through known protein-protein interactions.
Also, the new dataset called hu.MAP was published recently. It is a dataset of human protein-protein interactions determined by over 9,000 mass spectrometry experiments performed by the Marcotte Lab from UT Austin. A paper that describes the hu.MAP project is available on Biorxiv.
BioPlex (biophysical interactions of ORFeome-based complexes) is another database with experimental verification. Authors describe it as a network that is

the result of creating thousands of cell lines with each expressing a
  tagged version of a protein from the ORFeome collection.
  Immunopurification of the tagged protein and detection of associated
  proteins by mass spectrometry are the building blocks of the network.
  The overarching project goal is to determine protein interactions for
  every member of the collection.

I have checked IntAct, and it kind of offers what I've been looking for , I'm wondering If there is a way to  extract all the associated proteins' annotations from uniprot  . because I need to get all the annotations of every protein contained in the dataset


text:
Earth's history: The Great Oxidation Event and the 'Boring Billion'
From what I understand the 'Great Oxidation Event' occurred around 2.4 billion - 2.3 billion years ago, when cyanobacteria flooded Earth’s atmosphere with oxygen.
The 'boring billion' period was around 1.8 billion years ago, during which it is thought not a lot changed on planet Earth. Low oxygen levels were thought to be 1-40% of modern oxygen levels during this time.
Why did the atmosphere go from 'flooded with oxygen' to 1-40% of modern oxygen levels. Was it because during the Mesoproterozoic era, the rate
of burial of decaying organic carbon matter under marine sediments
flatlined?

Doesn't the question contains an answer inside? ("when cyanobacteria flooded Earth’s atmosphere with oxygen").  Cyanobacteria can do oxygenic-photosynthetic (and seemingly the first oxygenic-photosynthetic organisms were cyanobacteria aka blue-green-algae). Are you telling about some other different event?

@AlwaysConfused there was a big drop in oxygen levels after the GOE, which led to the "boring billion". OP is asking why that drop happened.

Your question probably arises from a misunderstanding regarding the 'flooding' metaphor. I would not assume that 'flooded Earth's atmosphere with oxygen' means a lot of oxygen in the first place ... the metaphor means that oxygen levels rose from basically absent to noticeable.
If you look at the history of oxygen in Earth's atmosphere you see a general trend of gradual increase with a 1GY lasting stationary phase (Holland (2006), picture taken from above linked Wikipedia article - red and green lines are upper and lower estimates, respectively):

After initial atmospheric oxygenation about 2.5 GYa, Earth's oxygen sinks (mainly the oceans, after that landmasses and the ozone layer) were filled and buffered atmospheric oxygen levels, keeping them low. Once those sinks were saturated (approx. 850 MYa), the atmosphere started to oxygenise rapidly.
The constant (or as discussed below: drop in) oxygen concentration is caused by these sinks. The oxygen that is produced by photosynthesis was just not available to Earth's organisms as it was not atmospheric.
As @GerardoFurtado points out in the comment, modalities of the stationary phase are still debated. A review by Lyons et al. (2014) presents evidence that after the initial increase in oxygen levels, a drop in atmospheric oxygen preceded the stationary phase (see their Fig. 1, blue boxes). This does not change much as the newly inferred stationary phase, though probably a more fluctuating stationary phase than suggested by Holland (2006), is still higher than before the great oxidation event and lower than at present.
The major conclusions remains the same: There is evidence that the seemingly slow evolution 2-1 GYa was probably caused by oxygen limitation and oxygen levels were buffered by oxygen sinks. The change of oxygen concentration was determined by both the rate of oxygen production and the rate with which oxygen is stored in those sinks; the interplay of those rates caused the oxygen concentration to remain constant, drop or occasionally even rise, i.e. fluctuated.

I believe OP's premise is correct, and your answer is based on the wrong assumption that there was a "gradual increase with a stationary phase". There was a reduction in oxygen levels after the GOE, during the "boring billion". From Nature: "Earth’s early atmosphere has seen two major spikes in oxygen concentration [...] Rather than accumulating steadily, new findings suggest oxygen levels dropped precipitously soon after the first peak" (emphasis mine). Source: http://www.nature.com/news/oxygen-fluctuations-stalled-life-on-earth-1.15529

@GerardoFurtado: Thanks for pointing that out. I do not think this changes much but incorporated a recent review that supports the claim of dropped oxygen levels and discussed this a bit.

Good to see that, cheers.

Maybe the introduction of any amount of oxygen altered the availability of nutrients.  The oxygen producers had evolved in low / no oxygen conditions and it was only when they reached critical mass that the great oxygenation event could occur.
Once it did occur, nutrients that had once been soluble and available were in short supply: specifically iron and reduced nitrogen.
Fe2+ is soluble and so before the oxygenation event there was probably a fair bit sloshing around.  Once oxygen came the iron turned to Fe3+ and was much harder to come by.  https://www.princeton.edu/~cebic/ironIIvsIII.html
Iron is still growth limiting in large areas of open ocean, as evidenced by this experiment supplementing the open ocean with iron.
http://www.nytimes.com/2012/10/19/science/earth/iron-dumping-experiment-in-pacific-alarms-marine-experts.html
Nitrogen is the other nutrient whose availability would have changed.
The ancient enzyme used by nitrogen fixers is poisoned by oxygen and once oxygen was around, the activity of these organisms no doubt plummetted and with it, availability of reduced nitrogen.  Lack of iron would be a double whammy for the nitrogen fixers in which the enzyme requires iron.
So: maybe the boring billion occurred because oxygen-induced nutrient starvation handicapped proliferation of organisms, and with low proliferation you have fewer chances to evolve something new.


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Share of water usage by plants
From the total water absorbed by the root system, how much water does the plant use for transpiration and how much water does the plant use for photosynthesis?

This seems like a homework question. Can you provide more information regarding your thoughts on this or any efforts towards finding this particular statistic?

Your question does not have a single answer, and depends on several factors: the type of photosynthesis (C3, C4 or CAM), the species of the plant, temperature, amount of ground water, relative humidity, luminosity etc.
However, as a good guess, I used to say to my students that around 1% of the absorbed water is used in photosynthesis, the remainder (99%) being either lost by transpiration or used for cell growth. Once more, have in mind that this is a rough estimate, the real number varies.
Now let's have a look at more precise figures, from Bieleski et al. (1999):

As you can see, we have here three kinds of plants (C3, C4 and CAM) here. The column you want is TR ratio (which stands for Transpiration/Photosynthesis ratio). If we consider a C3 plant, the number goes from 450 to 600.
Let's take 600 as an extreme example. A TR ratio of 600 means that the plant loses 600g of H2O to fix 1g of CO2, using approx. 0.4g of water (You'll have to do some math here, using photosynthesis equation), but that tell us that the amount of water used for photosynthesis is less than 0.1% of the transpired water.
Source: Bieleski, R., Farquhar, G., Eamus, D., Atwell, B., Turnbull, C. and Kriedemann, P. (1999). Plants in action. 1st ed. South Yarra: Macmillan Education Australia.

PS: sorry for that pale green colour the typographer chose for the table. Blame the book editor, not me!


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Which is a good methodology to find out a domestication process?
I just started with my course in genomics and I'm working with domesticated animals (cows, chickens, pigs, etc) and I would like to know which methodology is better to trace the process of domestication since the origin of these species. I'm thinking of using SNPs of a particular gene to identify punctual traits that were selected, but also I was suggested to do a complete screen analysis and identify all the polymorphisms present in each variant and compare them with the species that gave them origin.

Yes, everyone use SNPs today for such analysis. Some RADseq is probably the way to go.
Detecting selection is not an easy task as many technics exist which differ by their assumptions and by the applicability. You should probably try to find papers having done the same type of analysis with the same types of data and eventually talk with authors. Your lab might already be experienced in such analysis.
What test to detect genomic signatures of selection? might help but the suggested algorithms are mainly for the analysis of within species variation. Procedure like mcdonald-kreitman test and other more advanced methodology to detect selection over a phylogeny (such as OUWIE if you have phenotypic traits) might be of interest. You could also simply use some rank tests when having many independent domestication events. The exact methodology you end up using very much depend on your data (how many independent domestication events do you have for example, do you have phenotypic traits, ...).

compare them with the species that gave them origin

Do you really have sample of the ancestor? Most of the time people simply consider a non-domesticated descendant of the non-domesticated common ancestor. Don't make the mistake of considering an extant lineage as if it was a descendant. This extant lineage evolved too!


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What in fast food fries have that regular fries don't?
Why is it that a french fry from a fast food restaurant doesn't seem to spoil the same way as one that one would cook at home?
PS: If given enough time will fast food french fries eventually decompose; if so, how long?

Why did you tag this "neuroscience"? Your question seems to be about preservatives in food. You might be able to get answers if you edit your title and body to make that more clear.

I suspect you are asking why a fast food fry doesn't spoil?  Water availability...  Read my answer to this post:  https://biology.stackexchange.com/a/57877/19432

Could trans-fat be a reason?

I went through a longer winded explanation here:  https://biology.stackexchange.com/a/57877/19432.
In brief, food spoils if water is bio-available to micro-organisms.  In the case of a french fry from say, McDonalds. This fry has a very small volume to surface area ratio, and hence is able to dry out what little water is left after the frying process before micro-organisms can proliferate enough to visibly "spoil" the fry.
If, in your own kitchen, you were take a fresh potato, cut it into fries, and cook them in oil long enough to nearly dehydrate the fry, it would not spoil either in a dry environment.
Take either of those items that had been allowed to cool down and pick up micro-organisms (yeast and bacteria) from the air and place into a sealed ziplock bag with a little water and they would both spoil.
For your last question, in a dry environment, once something has become desiccated, decomposition stops and your fry would only decompose if the environment became more humid.  Think about naturally preserved mummies in an arid environment.
Edit: Light also can break bonds...and lend to further decomposition in the absence of micro-organisms. As can physical abrasion from wind, sand etc... So naturally mummified remains of great age would also have been protected from light and abrasion as well.


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Trypsin and Cell Surface Receptors
Can adding Trypsin to mammalian cells affect the expression of or hydrolyze cell surface receptors?

Yes. Trypsin cleaves proteins and can do so quite indiscriminately if left on for very long. Trypsin is primarily used to cleave the proteins that cells use to adhere to each other and the plate in culture. It can cleave other membrane bound proteins as well, including receptors.
https://jbiomedsci.biomedcentral.com/articles/10.1186/1423-0127-17-36


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How to turn teosinte into corn?
If I want to turn teosinte into corn, using ancient methods like the Native Americans did, then how much time it takes, and what do I have to do?
For the sake of the question, let's assume that time is not a problem for me. Say I live 10,000 years. But of course, I prefer to have maximum efficiency. If I can get the result in 3,000 years, that's better than 5,000 years.

Breed together the plants that have any properties that seem more like modern corn, like bigger or more accessible kernels, stir gently, find a cure for aging, repeat over a few thousand generations.

@BryanKrause "repeat over a few thousand generations"... one needs way less than that.

@GerardoFurtado Even modern corn (not counting GMO) is quite a bit different from corn 200 years ago. I guess I agree that it doesn't take as many generations before you would classify the plant 'corn' rather than 'teosinte' but it seems like it took at least 1000 years to get to that point, with thousands of years further selection since then to get closer to what we are familiar with today.

Agrred. My point is that people in general, specially laymen, tend to think about domestication as something that requires thousands and thousands of generations to happen. However, domestication of plants (wheat, hemp, corn...) or animals (wolf, sheep, cattle) took fewer generations than what people suppose, sometimes a very small number.

@GerardoFurtado FYI someone at my institution is trying to do this see here but expects only fairly minor changes over 30 generations. But your broader point is well-taken. I believe some Russian scientists domesticated a fox within just a few generations, for example. I would say there is a difference between initial domestication and the extreme changes we have built into plants over thousands of years of agriculture.

Nice! It brings up the question: is this teosinte she/he is using the same (kind of) teosinte from before first human migration to Americas? By the way, when I wrote my comment I was think about the Russian foxes, on which I wrote an study (unfortunately I can't share, because it is on other language).

From the link I gave: "Teosinte from this area is the least maize-like of the Mexican annual teosintes and it only rarely hybridizes with maize (Wilkes 1967, 1977). Being free of maize "contamination" is important for my selection experiment because I don't want to merely filter out maize genes that were introgressed into teosinte, but to select natural teosinte variants and thereby move the phenotype in the direction of maize." I don't know if its possible to know how similar this strain is to the original, just that it isn't contaminated with modern corn.

It's of course possible that, being a strain that doesn't hybridize well with maize, it might actually more teosinte-like than the original strains that were eventually bred to corn. Not my area of expertise I'm afraid.

Yes, I read that, and actually "the least maize-like" was the part that made me asking you about the similarity.

Initially I didn't like this question very much, but I changed my mind when I realized that there is actually ongoing research to do exactly what you propose in order to study just how long it takes to get maize from teosinte.
John Doebley at the University of Wisconsin-Madison has a project ongoing to breed 30 generations of teosinte to be more "corn-like" on a single parameter, the length of the lateral branches.
The first challenge is to find a strain that isn't already contaminated by modern maize - that isn't completely possible, but he selected a strain that has minimal hybridization. You would have to do the same.
Second, you have to plant someplace isolated to further prevent hybridization. Dr. Doebley has a plot in Hawaii for this purpose.
Note that even though this scientist is only selecting over 30 generations, he doesn't anticipate that much of a change (i.e., he doesn't expect to have anything like corn when he is finished), and he is only selecting on a single parameter and furthermore, this parameter was chosen specifically for being easy to score, showing a lot of variation in the existing population, and influenced by a known single gene. Many more generations would be expected to get a product like modern corn. And even domesticated corn has changed significantly over thousands of years of agriculture.
For this answer, I simply reference the project site that I linked above, but in case that link goes dead, here is some literature that the project cited directly:

Beadle, G. W., 1977  The origin of Zea mays, pp. 615-635 in Origins of Agriculture, edited by C. E. Reed. Mouton, The Hague.
Beadle, G. W., 1978  Teosinte and the origin of maize, pp. 113-128 in Maize Breeding and Genetics, edited by D. B. Walden. John Wiley & Sons, New York, NY.
Doebley, J., A. Stec and C. Gustus, 1995  teosinte branched1 and the origin of maize: evidence for epistasis and the evolution of dominance. Genetics 141: 333-346.
Doebley, J., A. Stec and L. Hubbard, 1997  The evolution of apical dominance in maize. Nature 386: 485-488.
Doebley, J. F., A. Stec, J. Wendel and M. Edwards, 1990  Genetic and morphological analysis of a maize-teosinte F2 population: implications for the origin of maize. Proc. Natl. Acad. Sci. 87: 9888-9892.
Iltis, H., 1987  Maize evolution and agricultural origins, pp. 195-213 in Grass systematics and evolution, edited by T. Soderstrom, K. Hilu, C. Campbell, and M. Barkworth. Smithsonian Inst. Press, Washington, D. C.
Wang, R.-L., A. Stec, J. Hey, L. Lukens and J. Doebley, 1999  The limits of selection during maize domestication. Nature 398: 236-239.
Wilkes, H. G., 1967  Teosinte: the closest relative of maize. The Bussey Institute, Harvard University, Cambridge.
Wilkes, H. G., 1977  Hybridization of maize and teosinte in Mexico and Guatemala and the improvement of maize. Econ. Bot. 31: 254-293.

Thanks a lot. While your answer is very informative and useful, I'm still confused about how much time it takes to convert teosinte into corn. What I need is an order of magnitude: 500 years, 1000 years, 3000 years..

@BearBear Well, all of those time frames you give are roughly the same order of magnitude :) I think it's partly a semantic issue of when you declare the crop to be "corn": the archaeological evidence suggests that corn has changed a lot over the last 3000 years, but even before that was already distinct from teosinte.


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How do I interpret this depiction of dopamine neuron signaling?
I am studying the work of Wolfram Schultz on reward signals. He depicts dopamine reward signals as shown below, which I do not know how to interpret. Each dot represents an action potential in a dopamine neuron, but is each row a different trial of the same neuron, or is each row the activation pattern of a different neuron? And are the bars at the top showing a sum of the count of the action potentials at each time step?
Schultz, W. (1999). The reward signal of midbrain dopamine neurons. Physiology, 14(6), 249-255.

Can you provide a reference? The bars at top are definitely a summed histogram. I suspect with ~90% certainty that the depictions are of one cell on multiple trials, though it is also possible to present simultaneous recordings from multiple cells this way.

From the figure caption for that figure:

Each line of dots shows one trial, the original sequence in each panel being from top to bottom.

The bars at top are a summed histogram. Dots mark the time of spikes (this is called a "raster"). Each line is a different single trial from the same neuron.
(also note: this type of paper is called a 'review' paper, i.e., it isn't original research, although the original research might have been done by the same author. That doesn't mean anything bad, reviews are an excellent place to start understanding a topic, but you should be aware that the figures here are just representative examples or in some cases schematic diagrams. There is a lot of other data behind the conclusions drawn besides these single examples)

Thanks! I was ~90% sure that's what it meant, but I needed confirmation.


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Why is sexual reproduction so much more common than asexual (in macroscopic organisms)? Fundamentally, what makes it better?
I'm experimenting with an evolutionary method of creating a neural network. I use an asexual approach, but I've seen others use sexual approaches.
So I'm interesting in learning what's better about sexual reproduction as apposed to asexual, and biology is probably the best way to approach that question. So, why is sexual reproduction so much more common than asexual (in macroscopic organisms)? Fundamentally, what makes it better?
I'm struggling to understand what the combination of two gene sets does that couldn't be achieved by mutations to a child of asexual reproduction.

I'm not so sure "more common" is true unless you are talking about particular types of life. There are many very successful organisms that reproduce primarily via asexual reproduction.

I edited to specify macroscopic

Genetic diversity is needed to prevent everyone from dying of the same disease. This is the problem with monocultures. Higher organisms are more susceptible to disease and thus reproduce sexually.
Furthermore, basically all organisms exchange DNA so they are effectively sexual.


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What does it mean to combine in-solution capture of chosen RAD tags to target sequencing reads to desired loci?
The article about "rapture sequencing" found
here says:

"This protocol also recovers more unique (nonclonal) RAD fragments, which improves both standard RAD and Rapture analysis. Rapture then uses an in-solution capture of chosen RAD tags to target sequencing reads to desired loci. Rapture combines the benefits of both RAD and sequence capture, i.e., very inexpensive and rapid library preparation for many individuals as well as high specificity in the number and location of genomic loci analyzed."

My question is regarding the second sentence. What does it mean to combine in-solution capture of chosen RAD tags to target sequencing reads to desired loci? How do the RAD tags target sequencing reads, if that is what is being said here? How does this relate to combining the benefits of both reduced representation sequencing techniques, or am I missing the crux of the paper?

This method is essentially combining the techniques of RAD sequencing with targeted sequence capture. Both are reduced-representation DNA sequencing techniques, meaning that instead of sequencing all the DNA from a sample, only a portion of the DNA is sequenced. The main advantage is for studies that don't require a completely sequenced genome for every sample, allowing reduced sequencing for many samples and more effectively using limited sequencing capacity.
RAD sequencing reduces the sample genome essentially randomly, though the selection should be similar for closely-related individuals (it's based on the locations of restriction enzyme sites). Targeted sequence capture allows for specific genes or genomic locations to be sequenced, discarding the rest, but this requires some prior knowledge of the locations of interest (it anneals complimentary nucleotides to the region, similar to how PCR primers work).
This method first performs the "random" reduction of RAD, and then from those fragments captures the loci of interest (500 in the referenced article).
The authors claim this makes for easier library prep and cleaner results.


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Why some cells don't produce purines?
It is said that erythrocytes, polymorphonuclear leukocytes and brain cannot produce purines. And the reason given as per this site is:

Human brain tissue has a low level of PRPP glutamyl amidotransferase (reaction Image, Figure 33–2) and hence depends in part on exogenous purines. Erythrocytes and polymorphonuclear leukocytes cannot synthesize 5-phosphoribosylamine (structure III, Figure 33–2) and therefore utilize exogenous purines to form nucleotides.

My question is why do these cells don't produce the required enzymes for the synthesis of purines? What could be the functional significance for such absence?
My attempt : At first I thought that Erythrocytes as such don't have nucleus so they don't need purine synthesis for cell division , but I don't understand why then they need purines from external source( as said in the above site). Also brain cells are neurons and neuroglia, of which former doesn't divide( except in some areas of brain) but they too need purines.
 The later divide but they don't produce required enzyme. Why?
So my questions are:

Why do cells which don't replicate need purines?( May be for formation of Coenzymes , correct me if Iam wrong)
Why do the cells which divide too don't produce required proteins(enzymes)?

Should I make it in two parts?

I can't answer it, but it seems a reasonable question to me. It has received a close vote as too broad. But perhaps you should remove questions 3 and 4 as understanding why the nucleated cells here differ from other cells in purine metabolism will probably suggest answers to those questions.

@David I have edited the question, have a look at it.

Question seems valid enough to me. And interesting.

I agree.  A stellar question.  Erythrocytes start with nuclei and jettison them before leaving the marrow so that is not it.  There are active synthetic systems making the stuff nearby and so it would be no big deal for these cells to do it too.  The synthetic path must be off for a reason.

I am going to throw this idea out there. I was unable to find it stated anywhere so far.
There are several very ancient parasites that make their homes inside erythrocytes and neutrophils. Plasmodium is one, the causative agent of malaria. Trypanosoma is another. These things are ancient degenerate eukaryotes and their lifestyle as intracellular parasites is probably ancient too.
These things cannot make purines either but they need them and they need a lot of them, because they are reproducing fast. If the host cell does not have the machinery to make purines, that machinery cannot be hijacked by the parasite to really crank out the purines.  The best they can do is hijack the salvage pathways these cells have.
From https://www.ncbi.nlm.nih.gov/pmc/articles/PMC259377/

The apparent competition between parasites and host cells for available purines suggests that depletion of extracellular purines should be considered as an approach to treating extracellular trypanosome infections.

From https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4405406/

Plasmodium species parasites, like many other protozoan parasites, are purine auxotrophs, unable to perform de novo purine biosynthesis. They rely on the host to provide purines

That does not explain brain cells  - unless lack of purine synthesis is a defense of brain cells against Toxoplasma, yet another eukaryotic parasite.
Nothing would please me more than for someone to poke holes in this theory. A prediction from this theory: erythryocytes in all animals should lack purine synthesis - including birds, who suffer from a form of malaria and whose erythrocytes do have nuclei.

Quite interesting theory.

What about hepatocytes? They too get infected by plasmodium, but are the major sites of purine synthesis.

@JM97: I suspect the circulating cells & esp erythrocytes are more dispensible (like pawns in chess) so adaptations there are less detrimental to the organism.  Hemoglobinopathies (sickle cell, thalassemia) are thought to have evolved as defenses against plasmodium infection and their actions are also specific to the erythrocyte.

Then why Polymorphonuclear leucocytes too don't produce purines?

@JM97 Same argument as RBC.  PMNs are shortest-lived wbc and dispensable: shock troops.  They engulf parasites and then die, taking parasite with them.  Some parasites (Leishmania, trypanosomes) can survive and reproduce in  PMNs.  Lack of endogenous purine synthesis machinery makes life harder for these parasites.  Be aware: I am making this up as I go.


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Behaviour of neuron when membrane potential is maintained at threshold potential or more
Via an external electrode the membrane potential of a neuron or group of neurons can be increased from resting potential of -70 mV to -50 mV or more. This will cause them to fire an action potential. What happens if the electrode maintains the membrane potential at -50 mV or more for say 1 minute? Initially it should fire once, but then it will not reach the resting potential, will it stop firing or keep on firing continuously since it is above threshold potential? Will this kill the neuron or make it malfunction permanently?

Before I start, I should point out that in order to change the membrane potential (known as the Vm) of a neuron you really need an internal electrode - so that you can pump current in to it, so increasing the potential above the resting membrane potential (RMP). The RMP is simply the Vm of a neuron at rest, without any external meddling by pesky scientists (or synaptic inputs).
When you depolarise a neuron - in other words, make it less negatively charged, it will fire an action potential once it crosses the spike threshold. This value is different for different neurons, but -50mV is usually not enough to trigger an action potential - normally it's more in the range between -30 and -40. But let's say it does, as it doesn't change the thrust of the question.
The major part of what happens during an action potential is that sodium channels open, allowing the spike to fire. Once closed, these channels have a 'refractory period' - essentially a time out, during which they are less likely to open again. So even though your neuron is still above spike threshold, it can't fire because the channels can't open. (For the aficionados, you can actually think of this as the spike threshold becoming temporarily more positive - going up to, say, -20mV).
So your neuron doesn't fire again for, say, 10ms, until the sodium channels reactivate. Then it does. So you get a train of regularly spaced action potentials at a certain frequency. The more you depolarise the neuron, the faster this frequency becomes until a point where the channels just become totally inactivated and the neuron stops firing. If you hold the cell at this voltage for more than a few seconds, in general it will die.

Edit 2: On second thoughts, maybe secondlevel isn't quite correct. Assuming a the membrane potential is held at -50 mV, using a patch pipette, in whole-cell voltage clamp, then the neuron generally won't fire action potentials. Not as we know them anyway as the cell membrane potential is "clamped". This controls the open probability of ion channels and allows ions to flow in and out of the cell, which can be measured as currents.

Unless the membrane potential is controlled by injection of current, in "current-clamp" mode. This could be controlled in patch-clamp, or done via an external electrode, which would provide local current, but wouldn't be so well controlled.
Secondlevel is pretty much spot on, here's an image of a neuron stepped to approx -60 mV from -78 mV.
The below cell's voltage is not being controlled directly; it is a recording in current-clamp mode, being depolarized by injecting positive current. Action potentials do not occur in a proper voltage-clamp.

Note that the action potentials aren't entirely predictable, there's a bit of variability in the frequency, but they're roughly every 20 ms. Also, this is just one example, from one cell type. Other neurons will behave differently.

Your current clamp example is fine. The OP's question doesn't make any sense if interpreted in voltage clamp terms, because you wouldn't get action potentials in voltage clamp.

Thanks, I was just in the process of trying to clarify. Not sure it makes sense without a thorough understanding of electrophys though.

Since the OP directly said an action potential is fired, and was also initially referring to external stimulus (though like the other answer mentions, it would be nearly impossible to maintain a steady depolarization that way), I think it is safe to assume two things: 1) the voltage is not clamped, and 2) the cell has a threshold no more depolarized than -50mV. I think your answer was more clear without the added explanation of current/voltage clamp.

Also, real life voltage clamp is simply not quick enough to prevent action potentials (usually referred to as action currents) occurring. They do happen in all but the lowest access resistance cases.