text:
Are all Y-chromosomes the same?
Since the Y-chromosome can only pass from male to male child, it would seem to pass intact. Thus, a boy's Y-chromosomes would, I guess, be the same as his father's. Going backwards, would not all men have identical Y-chromosomes for this reason, being somewhat like mitochondrial DNA?

Because the Y stops recombining and has a small population size it is expected that variation will be rapidly depleted.  Mutations still occur on the Y which can maintain some within population variance. http://www.ncbi.nlm.nih.gov/pubmed/26230387

There is a difference between an evolutionary process and a genetic process so to speak: you don't need recombination for evolution. A lot of organisms use cloning to generate "offspring", but these evolve as well because of mutation.

Actually, no. There are also recombination prone regions of the Y chromosome that recombine and exchange material with X chromosomes, and these are called pseudoautosomal regions (PARs).
Y chromosomes can be used similarly to mitochondrial DNA to build up profiles of ancestry, but the sequences used for this purpose lie outside PARs, in the non-recombining region.
What about seqeuences outside PARs, do they show genetic variation?
As pointed out in the comments, PARs comprise only 5% of the Y chromosome, but even in the non-recombining regions of the Y chromosome studies in well-characterised populations have found that the mutation rate can approximate autosomal mutation rates in some regions of the chromosome, and exceed them in others.
What processes, other than recombination, drive mutations?
There are loads of different mechanisms by which mutations in general can be generated, including exposure to UV, free radicals, tobacco smoke, aristolochic acid, and perhaps most importantly spontaenous deamination of methylcytosines, which is an age related mutational process, proofreading errors inherent to DNA polymerases. Also, it is well known that in sperm, with age the mutation rate goes up throughout the genome. While UV is unlikely to be a prominent mutagen as was pointed out to me in the comments insofar sperm are concerned, factors like smoking still play a role.
An illuminating read about mutational processes and the mutational footprints they leave in genomes, as understood from studying cancer genomes, is here.

Ok, but those regions are only 5% of the chromosome. Is the other 95% the same in all men?

Nope - those regions too are subjected to mutations at various rates, that in some well characterised populations approximate the autosomal mutation rate in some regions of the Y chromosome, with other regions showing elevated mutation rates.
http://www.nature.com/ng/journal/v47/n5/full/ng.3171.html

Without recombination, how is the chromosome mutating? I know that it might get struck by a cosmic ray or something, but barring that, how?

There are loads of different mechanisms by which mutations can be generated, including exposure to UV, free radicals, tobacco smoke, aristolochic acid, and perhaps most importantly spontaenous deamination of methylcytosines, which is an age related mutational process, proofreading errors inherent to DNA polymerases.
Also, it is well known that in sperm, with age the mutation rate goes up throughout the genome. http://www.nature.com/news/fathers-bequeath-more-mutations-as-they-age-1.11247

One of the places where mutational processes and signatures have been best studied is in cancers; and this paper should make for illuminating reading. http://www.nature.com/nature/journal/v500/n7463/full/nature12477.html

I am not sure if you can have UV exposure on your list, as I do not think it is likely that UV has the energy to penetrated deep enough into the tissue to cause damage to germline cells, which is the only way to pass on mutations. More energetic EM waves such as X-rays obviously could do the damage, but there you start to have to think about how much damage can be done before the sperm is ineffective. I am also not sure if there are mutagenic effects to germline cells from tobacco smoke. I could see where you might get decreased fertility due to vascular changes. I agree with the others.

@AnkurChakravarthy please can you edit all of your comments into the body of your answer: they make it a much stronger answer, and it means they will be preserved long after the comments are deleted (comments are ephemeral, questions and answers are to keep)

@ImprisonedRhesus That's what mutation is. Crossovers and similar "operations" are not mutation - only DNA damage is. Apart from what Ankur already mentioned, there's a few more interesting ways - for example, errors when repairing damaged DNA. By far most of those happen in your somatic cells, of course, so they are not long-living, and they do not propagate to your offspring, but there's still plenty that affect your germ cells (not to mention possibly affecting the development of an embryo, where there's a chance to affect the whole organism rather than just a cell or two).

@AMR It's not about having too little energy, really - visible light penetrates far deeper than UV. But other than that, I think you're right - the deepest penetrating UVA only penetrates about 4mm. It might be possible a small amount penetrates deep enough to affect germ cells, but probably not significant enough to matter.

@AMR I don't think you read my comment right - visible light (lower energy than UV) penetrates deeper. It's not a matter of bigger energy penetrating deeper - rather, it's about the energy levels available for absorption (after all, how else would different materials be transparent to different spectra of light?). If you want to know how X-ray imaging actually works, it's a very interesting subject (bones are indeed absorbing a lot of X-rays, but we get a lot more information from scattering, which also happens in soft tissue).

@Luaan you are correct about absorption, I was mixing my arguments. This figure illustrates your point well. http://ec.europa.eu/health/scientific_committees/opinions_layman/artificial-light/en/figtableboxes/8.htm

AMR - I agree UV is likely to be a weak contributor to germline mutations. Smoking on the other hand has been shown to be a germline mutagen (see http://humupd.oxfordjournals.org/content/6/2/122.full.pdf)
EnergyNumbers I will make that edit.


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What would be the estimated cost sequencing?
I'm a newbie to the world of NGS, but I thought it might be a suitable and cheaper alternative to doing traditional Sanger sequencing for this particular application. However, I'm not so sure on how to approach calculating this cost, so I was hoping to reach out and see if someone could help here. This is for my grad school research project.
Problem Statement
I am about to make a rational library of ~1000 protein complexes belonging to the same family of proteins. There are 4 protein's plasmids to make per complex, and they are to be made by a combination of synthetic genomic cloning methods using cDNA, and multi-site directed mutagenesis on existing plasmids. Before testing their function as a complex, I need to verify that the cloning steps succeeded by sequence verifying each plasmid.
I could do traditional Sanger sequencing on each of the protein sequences, but given that each protein is ~2kb long, I would need 4 single direction sequencing reactions per plasmid to cover the CDS. In total, per protein complex, that's 16 sequencing reactions. At USD5 per sequencing reaction, each protein complex would cost USD80 to sequence. At 1000 sequences, that would be USD80,000 in Sanger sequencing.
I was thinking of doing something else - after creating the library, say in chunks of 384, send them for NGS on an Illumina MiSeq.
Request for Help
Given that:

I am not wedded to any particular NGS protocol,
Our only goal here is to, by one way or another, sequence verify the cloned plasmids.
1000 proteins is the right ballpark for the number of proteins that need to be sequence verified. 4 plasmids per protein complex.

What would be the appropriate sequencing strategy that could help us get way below 80K for sequencing costs?

How would NGS help you? Are you planning on mixing all 1000 plasmids together and trying to get complete coverage on all of them?

@MattDMo: Yes, that's the plan. It's 4 plasmids per sample, 1000 samples in total, each needs to have (at minimum) its 2 kb insert sequenced. But if we could get full coverage of the plasmid that's cool too.

Most NGS approaches should enable you to sequence all those plasmids at very low cost-per-base values (Please see here for more on prices). The challenge in sequencing them all, if there are sequences common to all your plasmids, will be to get adapters for each sample/plasmid so that reads can be mapped back to the correct plasmids.

Thanks Ankur - yes. These are a family of polymerases with 4 proteins. We are planning to make a rationally designed library of 1000 polymerase variants. 4 plasmids per sample, each of a different sequence, 1000 samples in total.

OK - as long as there are no sequences that overlap between those plasmids you should be able to get good depth of sequence for a grand or two I would imagine and then map back to the reference sequences to see if assembly has worked. NGS is defo the way to go.

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how to find full mitochondrial genome of plants in GenBank?
I am searching for full mitochondrial genome of a species of Malvaceae family.
To be more specific, I need the genus Corchorus. But I could not find the location where it is in gene bank. After searching in google, I found this, but here I did not found anything for plant.
Can you help me to locate its actual location?
Scientific classification from Wikipedia:
Kingdom:    Plantae
(unranked): Angiosperms
(unranked): Eudicots
(unranked): Rosids
Order:  Malvales
Family: Malvaceae
Subfamily:  Grewioideae
Genus:  Corchorus
L.

Related post: http://biology.stackexchange.com/a/16168/3340

I think, manetsus wants sequence , not definitions. Plus link given in that post is for Human Mitochondria database not plant. The species he/she looking for is not available on NCBI (at least I couldn't find it).

When you search a genome for Corchorus on Genbank you will only find genomes of a virus related to it. There is not a lot of plant genomes available and for the ones you can find it is quite often the case that there is only the chloroplast assembled.
So unfortunately the most plausible answer to your question is: It is not yet available for this plant. There are only very few hits for Malvales at all, and none of them seems to have the mitochondrium assembled.
There might be chances that there is a specific project/database for Malvales or mitochondria, where you could search, but I am not aware of one.

Is this one? http://www.ncbi.nlm.nih.gov/genome/38606?genome_assembly_id=233326
What I did was Google: "search mitochondria genome BLAST"
and clicked the first page for me "Organelle Genome Resources". I then selected
"Browse by Organism" on the lefthand side, which took me to a new page.
I then entered in the top left text box the phrase "Malvaceae" and up came a scroll down list from the text box of choices for the text field.
I chose the first "Malvaceae (taxid:3629)" and upon clicking that, 26 entries came up for organelles. Two of which were from Mitochondria under the "Type" column.
The other entry being: http://www.ncbi.nlm.nih.gov/genome/10704?genome_assembly_id=233221
Sorry if I  was totally off base, I am just a undergrad.

No. This is wrong species.

To be more specific, I need the genus Corchorus, you can see the scientific classification there.

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How does NHEJ cause indels?
I was reading up on CRISPR-cas9 and how it works and I am having trouble wrapping my head around how NHEJ to repair the DSB can cause indels to occur. Shouldn't the NHEJ just stick the two strands of DNA back together?
I believe I read somewhere that if other agents cause a DSB, such as certain chemicals, they can also damage / cleave nucleotides ; the damaged nucleotides would have to be removed and overhangs filled in by polymerase before the ligation, which could result in the errors that NHEJ is famous for.
Since cas9 does not cause such damage, how can it result in an indel?
Thanks.

This is a very interesting question and I had not thought about it before. I am reiterating the background of your question.
Background
Cas9 cuts the both the strands of the target DNA at the same location thereby making a blunt end cut. Usually sticky ends and microhomologous ends lead to indels because of exonucleolytic clipping and addition of extra bases by pol-µ. The question is how do indels arise during NHEJ mediated re-ligation of blunt ends.

NHEJ may not always lead to indels. Most blunt end cuts can be repaired without error. Some non blunt cuts are also perfectly re-ligated; the best example for this is VDJ recombination. The binding of Ku proteins is essential for a perfect re-ligation (canonical NHEJ/C-NHEJ).
However, there are some variant non-canonical pathways which include alternative-NHEJ, backup-NHEJ and microhomology mediated end joining (MMEJ) (Bétermier et al. 2014). Some studies also refer to all of these pathways as alternative-NHEJ or altNHEJ. These alternative pathways involve resection of nucleotides by exonucleases such as Mre11 to produce overhangs. Imperfect alignment of these overhangs prior to ligation leads to indels. Sometimes non-templated addition of nucleotide happens by the action of terminal deoxyribonuclotide transferase (TdT). Pol-µ can also add random nucleotides at the 3' end (Lieber 2010).
In general, the propensity of DSBR via alternative NHEJ pathways would be higher when Ku activity is lower. Even with a moderate Ku activity, there is always some likelihood of alternative pathways in action. Moreover, it is to be noted that sticky end ligations are more efficient than blunt end ligations.

 Reproduced from Bétermier et al. 2014


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Solubility of Amylopectin and Glycogen in water
The only difference between the structures of Amylopectin and Glycogen is that Glycogen is more highly branched than Amylopectin. How this difference between their structures makes difference between their solubilities in water?

The answer is relatively simple: Amylopectin is watersoluble, and this seems to be a classical textbook error, which has been propagated now for decades. As you say yourself, the only difference is the number of 1,6-glycosidic branches, which occur every 8-12 glucose monomers in glycogen and every 15-30 monomers in amylopectin.
There are even scientific articles which show that amylopectin is watersoluble, see the references below:

Green et al., Journal of Chemical Education vol 52, p.729 (1975) Which  Starch Fraction  is  Water-soluble,  Amylose  or
Amylopectin?
J. Robyt, Encyclopedia of Life Sciences (2001) “Polysaccharides: Energy Storage”

The question is incorrect in asserting that the only difference between amylopectin and glycogen is their extent of branching. This is only an incidental difference.
As I explain in more detail in the answer to another post, the key difference is in the topography of their branching.

This leads to spherical size-limited globules, in the case of glycogen, and large semi-crystalline extended structures, in the case of amylopectin.
This is the basis for their different chemical and physical properties within the cell (glycogen is soluble, starch is in a semi-insoluble form), which is all that is of biological interest to me. I cannot adjudicate on, nor am I concerned with, the properties chemists observe when extracts are manipulated in vitro.


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How can I find some pieces of the genome of a microorganism?
I have figured out how to download the fasta of the genomes of microorganisms, for example the botulism bacteria and the spirulina algae. However, I want to find a fasta file for some significant extraction of those genomes - say, some important gene, some mutation, some protein that occurs in a microorganisms genome. What should I look for, and how can I find it in genbank?

You can use already available tools to extract information from available database. For finding specific genes, use this. For protein, use this. There are lot more tools. Just explore NCBI, EMBL or DDBJ sites. All information is self explanatory.
If you want specialized information for specific organism, you can use specialized database ( like Flybase for flies, SGD for common yeast, EnsemblBacteria for bacteria and archaea or HGMD for human mutations. Best way is to search in Google. You will get everything you want :D

I found these websites a bit daunting. I don't know what genes to look for - I don't know the names of any genes in, say, arthrospira. I have clicked on some genes but I get very complicated diagrams, not fasta files.

You should have little idea about what you want, else you will be lost in sequences and genes. You can look at Gene Ontology database. Here you can search genes and proteins with annotated functions. I guess that is what you want. However this will give you only reported (or annotated) genes/proteins. You can't find novel genes there. You need proper bioinformatics study to find such genes (like searching through various domains and validating them from literature)

I used GO to find the name of a mycoplasma protein, and I found mycoplasma page on NCBI: http://www.ncbi.nlm.nih.gov/genome/1028. I can't figure out how to get the FASTA from that page - do you know?

There was direct link on that page. Click on whatever sequence you want (click on replicons column )

I guess you have found the Genome entry of your favourite genomes in Genbank and got the FastA.
Dexter is completely right, you can just search your genes in the databases and filter them for your genomes of interest.
Another possibility is to get the GenBank-formated file "GenBank (full)", instead of the FastA, then use a Genome Browser (for example Artemis) which allows you to search for genes/proteins in a genome and save them as separate FastA files.
Generally it is a good thing to get the GenBank format file for an organism you are interested in, as you can extract the complete genome sequence as FastA easily, but also keep all the other information you might need later.


text:
use of adjuvants and peptides in modern vaccines?
when preparation of modern vaccines we generally use a part of the microbe or the antigen such as polysaccharides to create an effective vaccine against the vaccine. so when the preparation of sub unit and conjugate vaccine we use adjuvant? so what is the use of using an peptide in case of babies having week immune system?
Basically my question is What is the use of peptides when we are using adjuvants to enhance the immunogenic response?

I really don't understand your question, can you please clarify it? What do you mean by "effective vaccine against the vaccine" or " so when the preparation of sub unit and conjugate vaccine we use adjuvant"?

What is the use of peptides when we are using adjuvants to enhance the immunogenic response?

Ah, ok, now I understand. You should probably still rephrase your question to avoid closure because of non understanding.

In many vaccines, there are two components: One immunogenic substance, these can be parts or complete (inactivated) pathogens (for example the small pox vaccination), peptides or proteins (like the tetanus vaccination) or polysacceride components from the capsule of bacteria (for example against MenC). Against these components the actual immune response is directed. See references 1 to 3 for some more details.
Then they can (depending on the vaccine) contain adjuvants, which enhance the immunologic reaction of the body. This is done either to enhance the reaction and to get a proper immune reaction but also to be able to reduce the amount of injected antigen. So the adjuvant simply causes a general inflammatory reaction. Classically Alum (aluminium hydroxide is used here), newer adjuvants are squalen based oil-in water preparations or CpG olinucleotides (see references 4 and 5 for numerous examples on adjuvants and literature).
So what you basically do is to identify (more or less) a part of the pathogen which can serve as a vaccine and use this part for the vaccine.

Making Vaccines: How Are Vaccines Made
Designing Tomorrow's Vaccines
Strategies for designing and optimizing new generation vaccines
Dose Optimization Strategies for Vaccines: The Role of Adjuvants and
New Technologies
Vaccine Adjuvants Review


text:
why monocot roots have a wide pith while dicot roots have a narrow pith?
Normally dicot roots have a nartow pith at the center but monocot roots have a wide pith. Is there any specific reason to this?

Welcome to Biology. Could you add a source or reference?


text:
Which organism is this?
Place: Bangalore, India
Month: September, 2015
Current weather: Cloudy and rainy
Google images search was just giving me dragonfly photos. That organism is on grass blade.

Image is captured by me.

Certainly not a dragonfly. This looks like a grasshopper but I can't tell the species.

I doubt it is grasshopper. Few of my friends suggested it is some kind of grass insect which uses it's wing to camouflage.

This is an insect in the order Neuroptera, definitely neither a dragonfly (order Odonata) nor a grasshopper (Order Orthoptera).  The name of that order means "nerve-wing", which referes to the intricate network of veins throughout the wings, which have a very different appearance and pattern than the wings of either dragonflies or grasshoppers.  I'm not familiar with Indian fauna per se, but the long antennae with slightly curved/hooked tips make it look more like an antlion (family Myrmeleontidae within the Neuroptera) than an owlfly (family Ascalaphidae within the Neuroptera; their antennae have small clubs at the ends), though it's a bit hard to tell from the photo.

I also think that an antlion is likely. Either way, the front legs and antenna seems to be directed forward along the leaf/overlaid, which makes the antenna look a bit weird.


text:
TSS of a gene vs TSS of a transcript
I have an annotation from gencode.vM1.annotation of a mouse. Exons, genes, transcripts and UTR are listed there. For each feature a start and end positions are present.
I need to find a TSS for each gene. Will it be wrong to define one TSS for all transcripts belonging to one gene? So, I want to define a TSS for each gene as a minimum start UTR from all transcripts.
Example:
gene id, transcript id, feature, start, end

gene A, transcript A1, UTR, 102, 205
gene A, transcript A1, UTR, 506, 520
gene A, transcript A2, UTR, 78, 205
gene A, transcript A2, UTR, 502, 512

So, for gene A I would define a TSS on position 78 (minimum start UTR). And the gene body end on the position 520 (maximum end UTR).

There is no TSS of a gene. Geneic region will be a union of all the transcripts arising from that locus (including introns).
Sometimes two variants of a gene can have different TSS. You can define a 5' boundary of the geneic region which would be the most 5' TSS amongst all variants. You can also give scores to the TSS based on the expression of the different transcripts.
Nevertheless, I am not sure why you want this.


text:
What is the essence of difference of how different chemicals affect the same receptor?
It is known that various chemicals can bind to the same receptor type, producing different effects. Be these chemicals agonists or antagonists, there are more variations in how they influence the receptor than just sending an activation or inhibition signal. There seem to be various flavours of activation (not sure about inhibition), where, for example, a psychedelic drug binding to a serotonin receptor produces a different result than serotonin itself.
For a more clear representation, I have split the question into logical parts:

What is the essense of this difference? Does it come from the chemicals molecule properties like shape and electron configurations of the atoms?
If we were to draw two comparative pictures of how two such different chemicals affect a receptor, how would we picture that? What would we chose to be the characteristic figure(s) on our pictures? What qualities of the connection (probably changing over time) would we consider to display on the picture?

Does this question make sense or are there any false assumptions?
UPDATE:
Response to the comment by WYSIWYG: I cannot cite any source saying so. It is that I got this question at some point: is ligand-receptor activation a binary function, which can only give either 0 (no interaction or inhibition) or 1 (activation) values, or it is something more varied?
Taking into account that ligand-receptor interaction is molecule-molecule, it is logical to assume that the resulting complex can put the receptor molecule in a variety of states, depending on the ligand molecule structure. Here the Ionic Bonds and Hydrogen Bonds sections shed some light on this - the described interaction patterns seem like they can produce quite different results. Like, for example, they put receptors molecules electron cloud configurations in different states. But does in reality such interaction always result in either 0 or 1 state of the receptor?
The pdf paper refered from this question leaves the reader to guess: are the varying effects of the chemicals produced solely by their profile of different affinity to different groups of receptors, or do they also interact with each receptor type differently. In other words, is the drug effect produced by a certain amount of 1s being fired by the receptors, or is it changing the quality of their firing signal itself, i.e. making the receptor to initiate different, non-typical processes inside the cells?
Or, in the cited Wikipedia article, under section The specificity of drugs it is said that muscarine and nicotine can selectively activate specific subtypes of acetylcholine receptors. Is the result of these chemicals activating these receptors exactly the same as of acetylcholine? If we deliver both muscarine and nicotine to their sites, will they produce the same effect as if we deliver acetylcholine to both of them?
Also, I cannot really find much information on what lies beyond the receptor, namely - how does it send the signal somewhere else.. but I guess that's molecule-molecule again, so here we get the chance of varying result too. Or don't we?

Agonists primarily act by mimicking the actual ligand (molecular homology). They basically elicit the same effect as the actual molecule. Can you cite an example where two ligands binding to the same receptor elicit different responses. This seems theoretically possible depending on the signalling network downstream of the receptor.

@WYSIWYG: I have replied to your question in the update to the original question.

Search term you are looking for is "promiscuous". GPCR are very promiscuous. Look at these articles 1, 2, 3, 4. Similary you will find many explaining this common phenomenon.


text:
What are constrained genetic elements?
I am somewhat of a newbie in evolutionary biology currently taking my first steps in bioinformatics. I was reading a paper when I came across the term  "constrained genetic elements", referring to sequences in the genome.
From what little I found googling the term, a constrained genetic element is a sequence/region in the genome that can be found preserved in many generations of a species. Is my understanding correct? What are the criteria by which those regions are identified?
The paper is Analysis and Classification of Constrained DNA Elements with N-gram Graphs and Genomic Signatures.

In what paper did you find the term? And in what context in the paper?

@kmm I added the paper title. The term is mentioned when explaining that classification is applied to "conserved sequences" in the genome, but no further explanation is given.


text:
Why are many fruits sour?
Many fruits (like apples, berries, citrus fruits etc.) contain high levels of organic acids, especially malic acid and citric acid. Are there any evolutionary functions of those acids in ripe fruits? In unripe fruits the sour taste may protect fruits from being eaten prematurely by herbivores, but why are those acids still present in ripe fruits? Are they there for increasing osmotic pressure so plants can make bigger fruits in a cheap way by just inserting more water in them? Or do organic acids perhaps play a role in pathogen protection? Or are they just a by-product of some other biochemical mechanism in fruit development?

Most apples are not very sour, same with berries. Citrus fruits (especially lemons) are an interesting case. Moreover, these fruits also contain peels which have aromatic oils. I am not sure if animals find the peels tasty. One direction to look at is how the citrus seeds are dispersed. I am trying to look for articles on this.

One possibility is that the organisms responsible for dispersing citrus fruit do not taste the extreme sourness, like how birds can't taste capsacin produced by peppers. That's just a guess, though

Fruits are sour for the same reason our skin has an acidic pH. To defend bacteria and other microbes that cannot grow on a fairly acidic environment. That's why even coca-cola and other drinks are highly acidic to inhibit bacterial growth. All the same strategy.

Here's a modelling paper for malic acid accumulation in fruits, just for extra reading! (malic acid is what they put into sour candies to make them sour along w/ citric acid, generally) http://jxb.oxfordjournals.org/content/57/6/1471.full

You mean malic acid, not maleic acid?

Short answer
Great question! I have done some research on the topic and found so much interesting information. It still seems like a topic that i being researched on, but so far, the research shows that malate is created by a CAM and C4 like pathway while citrate is created from TCA cycle.  Their functions are that they are important biomolecules in metabolism, in particular respiration.
Background
Malic acid and citric acid are the two main organic acids that are accumulated in the fruits and cause the sour taste. Citrus fruits contain more citric acid and other fruits like apples and pears contain malic acid. I will provide a detailed analysis for both cases.
In an article by Deshpande & Ramakrishnan they mention two hypotheses about the accumulation of the citric acid in fruits. One was that the organic acids are not formed in the fruit, but transported to the fruit, in which the fruit acts like a storage organ. The other hypothesis is that the carbohydrates in the fruit is converted to the organic acid. In their research. they tried to isolate some enzymes from the Garcinia fruit to support the second hypothesis. They say:
This [reciprocal relation between acid and sugar content] would indicate the transformation of sugar to citric acid in the fruit tissue itself due to the presence of the requisite enzyme systems.
They suggest that the TCA cycle is how the citric acid is being accumulated and stored.
The article in the comments by Lobit et al. also supports a similar hypothesis of the accumulation of malic acid. The authors tell us that the malic acid is most likely produced in the fruit itself because the pH of the xylem and phloem (the transporting organs of plants) have a pH of close to 7 or higher. It seems that the malic acid is stored in the vacuoles of the mesocarp cells and that the amount of malic acid in the fruit depends on the transport of the malic acid to the vacuoles in the mesocarp cells.
Pathways
The actual pathways for the creation of citric acid and malic acid are very complex. Here is a picture of the different pathways in the cytosol of the mesocarp cells thst create these organic acids (picture taken from Etienne et al.)
The first pathway described is the PEP pathway, which is really a modified CAM or C4 pathway (which are teo ways to deal with photorespiratin, and are adaptations to hot, dry environments). The PEP is converted to oxaloacetate by PEPC, which also takes in CO2, then that oxaloacetate is converted to malate by NAD-MDH. PEPC is regulated by malate concentration and cystolic pH, showing that the activity of PEPC is to indirectly increase the malate concentrations, not just to create more oxaloacetate.Let me note that I still don't fully understand why C4 and CAM-like pathways are present in Fruits from C3 plants.
The major pathway for citrate synthesis is the TCA cycle. Both are also involved in metabolism. TCA cycle (the citric acid cycle) is an important cycle and the second pathway in aerobic respiration. This pathway occurs in the mitochondria. Malate reacts with acetyl-CoA to make citrate and the CoA is released. The citrate then goes on to be repeatedly oxidized and ends up back to oxaloacetate. Now, for metabolic reasons, for example, if the amount of ATP created is top much at the end of aerobic respiration, the citrate could be transported out of the mitochondria, leading to citrate accumulation.
Control of acid accumulation
The control of the organic acid accumulation is different for both malic acid and citric acid. Malic acid accumulation in the vacuoles is controlled by vacuolar storage and vacuolar transport (Etienne et al). This hypothesis was really the subject of the article in the comments. Their article was about modeling the malic acid based on this hypothesis and compare it to actual biochemical analysis of fruits. Their results supported the hypothesis.
The accumulation of citric acid is more dependent on metabolism, therefore respiration. This is since the vacuolar transport is slower for citrate than malate, and so whatever limits thr speed of malate vauolar transport affects citrate. But citrate concentration in thr cytosol would be the only other main factor affecting the vacuolar transport. A model by Wu et al. was created based on this hypothesis and compared to the actual citrate concentrations, and once again, this hypothesis also supported.
Functions of these organic acids
Suprisingly, the only functions of malate and citric acid cycle is mainly for respiration(mainly TCA cycle), and other metabolic processes. Malate does affect the texture, ripening, and starch metabolism and more of fruits, as described in this article. But, malate and citrate are important for all respiring organisms, including us.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4536381/ Some of the acids are for controlling plant pathogens. But probably not all of them.

@inf3rno true, but those talk about benzoic acid and quinoic acid, which aren't the main organic acids causing the sour taste...It is mainly malic and citric acid

It's not true that the only function of citrate, malate and the TCA cycle is respiration. (Strictly speaking, the TCA cycle does not do respiration at all; that would be the respiratory chain.) The TCA cycle is involved in a number of metabolic conversions, including amino acid and fatty acid synthesis. Citrate is the precursor of fatty acids, and malate is important in the malate-aspartate shuttle that helps control cellular redox state.

Also, it would be good to clarify that sour taste is not caused by citrate or malate, but by free protons (pH). The taste receptor detecting H+ was discovered 2006, see http://www.nature.com/news/2006/060823/full/news060821-9.html

This does not really answer the question. You are just saying how acid accumulates and not why acid accumulates, which is what the question is about. Please revise your answer to add more information on this aspect or the answer may be removed.

I like that the left hand image (labeled "mitochondrion") actually looks like a piece of fruit :)


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Why do cells not spread on soft substrates?
I recently read a paper discussing how cells (primary mouse embryo fibroblasts) fail to spread and proliferate properly when plated on a soft substrate (i.e. soft PDMS pillars with stiffness k = 2.3 nN$\mu$m$^{-1}$), but spreading and proliferation can be restored with cyclic stretching of cells.
http://www.nature.com/ncomms/2015/150223/ncomms7333/full/ncomms7333.html
My question is if we understand why cells need to be on a hard surface to do normal operations (proliferate and spread)? It doesn't seem to me that a soft surface would be any more difficult for a cell to attach to. I would think that a "slippery" (I'm not sure of a correct biological term for this) surface may have this effect, but I wouldn't expect this from a soft surface.

Some cells need a matrix to adhere. Adherence relays proliferative signals in these cells. If you coat the PDMS pillars with polt-D-lysine or collagen then the cells may grow well.

Please keep in mind that this is about a single cell type (MEFs), and not extensible to all cell types and environments.

@WYSIWYG so are you saying that it's harder for cells to adhere to a softer substrate (or matrix)? for some reason, it's just not intuitive to me that that is true.

@MattDMo is this not a general trend observed for most cell types? Am I way generalizing a result from one paper by thinking it would extend to most cells? I suppose fibroblasts don't typically need to move that much, but would you expect this result to hold for macrophages or any other cell that needs to move a lot?
My apologies if these questions are too general -- my background is not in biology!!

@NaiveHalmos it is not about being soft. Cells need some kind of interaction with the substrate. Some proteins allow this interaction because of their functional groups. This article says that hydroxyl groups in the substrate facilitates cell adhesion.

@WYSIWYG Oh, so the paper I presented above didn't need to include that they used a soft substrate? They could have just mentioned that before cyclic stretching, the cells weren't adhering to the PDMS pillars? Thanks!

@NaiveHalmos Please note that texture and other surface properties of the material can play a role in adherence but not the bulk properties such as tensile strength etc. I am not really sure if by soft they mean smooth or not-rigid. I haven't read the paper yet. Will read it and let you know. As far as I can understand from the title and abstract they say that when the cells are attached to PDMS then mechanical stimuli like stretching promote growth.

@NaiveHalmos no, this is not a general trend. Some cell types, including the many kinds of white blood cells like T and B cells, grow and proliferate just fine while growing in suspension, with no substrate needed at all. Others form colonies in soft agar. Just like any research paper, you need to look carefully at what the investigators analyzed, and how they drew their conclusions. If they did all their work with a single cell line or cell type, and didn't look at any others, then the results are not necessarily generalizable at all.

As both @MattDMo and @WYSIWYG have already so succinctly answered this question in their comments I'm just going to attempt to expand a bit on their answers.
@MattDMo and @WYSIWYG have explained that the aforementioned paper from the question has results that are "not extensible to all cell types and environments" and "Some cells need a matrix to adhere. Adherence relays proliferative signals in these cells."
I'm just going to expand a little bit on these points... I know this addressing an erroneous assumption in the question rather than the question itself but bear with me.
Ok, so as has already been mentioned, different cell types in a multicellular eukaryote (like a mouse, or a human) only grow in certain environments and this is really important . Think about it like this, a mouse's body is made up of many different cell types all working together to create functional organs and systems and to ultimately make up the mouse. The individual cells don't know they are all coming together to make an entire animal and a cell is designed to grow and proliferate in order to make more copies of itself and spread. So why don't all cells just grow all over the place, on top of each other and spread to all parts of the body.
The reason you and the mouse aren't a formless mass of undifferentiated cells - like a big soft tumour - is because different cell types develop in such a manner that they can only grow in a restricted, structured way in a certain environment in your body. There are mechanical and chemical signals along with unique sets of growth factors that are found in different environments in the body that make it possible for certain cell types to grow in one area while not in another. It's why only blood cells can survive suspended in the blood not adhered to anything and your fibroblast cells (they make up your structured connective tissue can't, they need to adhere to a surface to grow. The different cell types only get their signal to keep growing when they are in their proper environment.
This is why when scientists are growing various mammalian cell cultures they have to be aware of what environment and growth factors the specific cell type they are working with requires in order to grow. Some mammalian (e.g. mouse) cells need a structured scaffold to grow them in culture and some can grow in soft or liquid culture.
Source: Hallmarks of Cancer: The Next Generation http://www.cell.com/cell/abstract/S0092-8674(11)00127-9?_returnURL=http%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0092867411001279%3Fshowall%3Dtrue [This is a classic paper that explains this far better than I can hope to - look for the section 'Sustaining Proliferative Signaling'.]


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Effects of Fixation on Cell Membrane
Why does fixing of cells with something like formaldehyde disrupt the membrane enough for probes, antibodies, and dyes to get into the cell?

It doesn't. You generally also need to permeabilize with a detergent in order to do antibody staining. Fluorescent dyes are very small when compared to antibodies or large nucleic acids, and so can diffuse across the membrane or fit through very small pores created by (para)formaldehyde fixation.

In my experience, somehow antibodies are accessible to the inside of cells without permiabilization. But I do not know the explanation.

243 is right, however fixing tissues with formaldehyde or PAF usually leads to the formation of methylen bridges cross linking proteins and potentially masking epitopes. Therefore in most of the cases you'll need an antigen retrieval step based on heat induced or proteolytic protocols to properly access to the antigens. While working with cell some chemical will at the same time fix and permeabilize your cells (like aceton)


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How do mosquitoes react to blood feeding on a highly ethanol intoxicated host?
Considering that a mosquito can consume up to five times its body weight in blood during a single meal (Encyclopedia of the Arctic, M.Nuttal), and considering a very strong alcoholic intoxication of about 3g of ethanol /l of blood, what could be the effect on the mosquito of such a "binge blood feeding" ?
Blood with a 3g/l ethanol concentration corresponds to a a beverage with 3/789 (ethanol density) = 0.38 % of alcohol.
Brought to a human level, it is as if a 80 kg man would drink 400 kg of blood, which would have a volume of 400/1.06 (human blood density) so 377 L. Within these 377 L, 1.43 L is pure alcohol. Weight of that alcohol would be 1.13 Kg.
In mammals, blood weight represents about 1/13 of the total body weight, therefore in our example for a 80 kg man about 6.15 kg, hence 5.8 L.
So since alcohol is readily absorbed through the gastrointestinal wall, this would quite quickly lead, based on the "unfed" weight, to about 195 g of ethanol / L of blood. Ethanol lethal dose in human is commonly reported to range between 8 and 14 g / L. So with that dose you're dead about 15 times.
So I am perfectly aware that I am asking about mosquito and not humans, and that i am not taking into account several other parameters, but the demonstration was just displayed to prevent answers like "naaaaah no way dilution is way too high", so please elaborate your answers and comments and don't hesitate to provide references.
On another level those comments would be useful to clarify many animal models used on studying vector borne diseases involving the blood feeding of the vector on anesthetized animals.

The body weight of the mosquito is 10 gr, so it wont drink too much "alcohol" for the 50 gr of blood that it drinks.


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Disease causing variants and Hardy-Weinberg Equilibrium
Is it true that many disease causing variants/mutations do not follow Hardy Weinberg Equilibrium?  If so, then please elaborate on why this may be true (or not) and provide examples.
I am interested in single-gene disorders or those linked with single nucleotide variants.  I was told that many disease causing variants/mutations do not follow Hardy Weinberg Equilibrium, but I cannot find any documentation showing this (so I am looking for a reference on this matter).  In particular, I have considered Huntington's disease, Sickle cell anaemia and Hemophilia, but have not found any special relationships with these diseases and HWE.
Thank you.

Welcome to Biology.SE. Homework questions are considered off-topic unless the OP shows attempts of answering its own question.

This is not a homework question. I am a research data analyst proposing a bioinformatics model and I imagine the answer to this question will be helpful to my work.  I have done much searching, even considering HWE along with single-gene disorders such as Huntington's disease, Sickle cell anaemia and Hemophilia. I turned to StackExchange because my searches have proved unfruitful thus far. Thank you.

Ok, I retracted my close vote!

@user918804 in that case, please [edit] your question and add more details as to what you've already looked at, what you've learned, and what exactly you're still having problems with. Citations would also be helpful. The more detailed a question, the better the chances of getting a good detailed answer.

Hardy-Weinberg law makes a series of assumptions. One of them is the absence of selective effects. As you talk about disease, this assumption of neutrality is obviously not met.
At the moment of fecundation
Imagine for example that at the moment of the fecundation, the genotypes AA, Aa and aa are at Hardy-Weinberg equilibrium. Let x be the frequency of the allele A at the moment of fecundation, the frequencies of the genotypes AA, Aa and aa are $x^2$, $2x(1-x)$ and $(1-x)^2$, respectively.
After selection
As all genotypes aa die off, you're left with the A allele being at frequency $y=2x^2 + x(1-x)=x(1+x)$ and the frequencies of the genotypes AA, Aa and aa are $\frac{x^2}{x^2 + 2x(1-x)}=\frac{2x-2}{x-2}$, $\frac{2x(1-x)}{x^2 + 2x(1-x)}=\frac{x}{2-x}$, and $0$, respectively.
Expressing the genotype frequencies in terms of the new allele frequency
You can as well plug $y$ into those genotype frequencies to get the expression in terms of the genotype frequencies at birth ($y$; after selection). It gives you $\frac{1-\sqrt{4 y+1}}{\sqrt{4 y+1}-5}$, $\frac{2 \left(\sqrt{4 y+1}-3\right)}{\sqrt{4 y+1}-5}$ and $0$ for the genotypes AA, Aa and aa respectively. So, obviously, it is not at Hardy-Weinberg equilibrium.
Assumptions
You can make some more interesting calculations by leaving out the assumptions that all aa genotypes die at birth and you could use a Leslie matrix to describe the probability for an individual of each genotype to make to the next age. I also assumed that the a is completely recessive. You might want to release this assumption as well by computing the death of a fraction of the Aa genotypes.

I welcome the readers to double check my calculations.

I think the real surprising effect is the rather high frequency of the sickness causing alleles. For sickle cell anemia there is a well-known explanation, but I am wondering about Huntington Chorea.

In the case of sickle cell anemia, there is a positive selection effect of the illness causing gene variant: Heterozygous gene carriers have some immunity against malaria. Therefore, sickle cell anemia is quite frequent in malaria affected regions of the world.


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What is a selective constraint?
I encountered the term selective constraint in Huber et al. 2015, page 4 (last paragraph) in:

If invariable  sites are included in the   analysis, then both the methods of
  Kim   and Stephan (2002)  and Nielsen et  al. (2005)  may be  sensitive
  to    assumptions regarding selective constraint  and mutation rates.

but the context does not quite help.
What it the definition of selective constraint?
Does it has to do with lethal mutations in non-coding regions? Does it has to do with selection interference?...

Please use the quote environment instead of the code environment (as far as I know most screen readers will start reading this character-by-character).

It is selective pressure that determines and limits the number of neutral/beneficial mutations that can take place. The more constrained a locus is under selection, the easier it is to generate deleterious mutations and the harder it is to generate beneficial ones; this can be reflected in low substitution rates at such loci in populations with time.
One widely used method to measure this is to compute the Ka/Ks ratio to infer if a locus is selectively constrained or not.

+1 Thank you. Can we associate a value to this concept? For example the  selective constrained could be $S = K_a/K_a$ or $S = mu_b/mu_d$, where $mu_b$ and $mu_d$ are the beneficial and deleterious mutation rates, respectively.

It is easier to measure Ka and Ks , so if something is under no selection (neutral) you'll see a ratio of 1 , less than 1 indicates purifying selection, more than 1 indicates positive selection. More here http://www.cs.mun.ca/~banzhaf/papers/ppsn08_evorate.pdf


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What DNA has the most info for getting a person's likeness?
I understand that DNA can come from hair but also from other places.
Let's suppose a person gets their DNA mapped by a company (there are some companies claiming to offer analysis of DNA.. e.g. maybe $200 and maybe some may send the DNA on a DVD)
I understand from this link that human DNA should fit on a DVD
https://stackoverflow.com/questions/8954571/how-much-memory-would-be-required-to-store-human-dna
Would it be possible to get a person's likeness..  if not now, then in future, based on the DNA I might be able to get sent to me digitally.
And presumably the DNA of a 28 year old would be the most ideal for getting (in a computer program) the likeness/image of that person at 28 - the age the DNA was taken?
I hear of the cost of sequencing the human genome to be millions or billions.. Is that more about scientists figuring out what the DNA does, rather than capturing it all?
For example, if I got my DNA captured by a company for $200, then in 50 years time or the future when technology develops, could I use it to produce a likeness of myself?    Or would what a company would send me, not really be all my DNA or be vastly insufficient to create a likeness?
I'm interested in if the kind of test that copmanies off for $200 provides all the information to create an exact replica.
Is a complete replica of a person possible in theory? (e.g. if in future they have a machine to build somebody from DNA) (with the information gathered and that could be sent to the customer by a DNA test for $200, or is it impossible even in theory because the DNA collected and sent is insufficient?)
I'm more interested in the possibility of (in theory) getting a really good likeness, than the personality of a person.
If a company only collects Saliva, is that just a fail.. would they need hair too and DNA from all sorts of human parts, in order to get a good likeness? or better likeness?  Or would it not matter whether it's the hair or the saliva?

Basically you mean cloning a person? Yes, theoretically possible. The DNA is (more or less) the same in all of a person's cells whether from saliva, hair or other tissue. Also, please clarify exactly what this $200 test is.

@vervet somewhere like https://www.23andme.com/   turns out they charge $100  though it doesn't say they send the DNA.  I will have to research further,  I guess since as you say, all DNA of a person whichever part it's from is much the same it shouldn't cost the earth to get all my DNA on DVD so if they can't do it then some company can at reasonable/similar cost.

23andme do not do full genome sequencing. They test a relatively small number of markers (single nucleotide polymorphisms or SNPs) in your DNA, to determine relationships between individuals and deep ancestry.

In addition to vervets' point, you seem very confused about DNA.
Your DNA essentially is the same in almost every cell, throughout your life.   You will get the same sequence from cheek cells at age 28 that you could from a blood sample as an infant.

@vervet ah thanks, got it.. so whati 'm looking for is full genome sequencing which is mentioned here https://en.wikipedia.org/wiki/$1,000_genome   and is $1000 as of Jan 2014

@swbarnes2  You write "You will get the same sequence from cheek cells at age 28 that you could from a blood sample as an infant" <-- Though what about epigenetics.. where genes change over time due to environment.  Or genes getting damaged with age, or how smoking changes your genes.

The raw DNA sequence, the sequence of ACGT will not change.  Your standard DNA sequencing won't chart epigenetic modifications.

I just voted to close because the question is getting too broad including epigenetics. It should be focused and perhaps trimmed down to remove the fluff leaving the essence. Happy to remove the downvote once clarified.

Except for Red Blood Cells, every somatic cell contains two copies of the autosomal chromosomes and a pair of sex chromosomes, either XX or XY (Assuming an average human being) One set is maternal and one is paternal
Some lymphocytes actually recombine their chromosomes, so their DNA will be functionally different to all of the other somatic cells in the body.
Gametes undergo Meiosis and will be haploid, only containing one copy of each autosomal chromosome and one of the sex chromosomes
Cells accumulate mutations over time. The closest you could probably come to an exact clone of a person is if you harvested one of the cells from the eight-cell stage of development. The other seven are able to go on and produce a viable and healthy person. The harvested cells DNA would be the closest to the DNA that combined in the fertilization of the egg. The next closest would likely be stem cells from cord blood. Then probably neurons, as they tend to divide the least.
As the link you posted said, ATCG can be represented in a two bit code, so for about 6 billion bases, you would need about 1.5GB of storage (You need to capture both sets of chromosomes in order to produce a person).

There are places where you could compress the data. Telomeres could be removed and just added back after the fact, as there is likely a standard length for each chromosome of the six nucleotide repeats.
Though you could have a minimum of a two bit code, you would really need a larger data set. You would need metadata, so things like polarity of DNA and chromosome number.
You might also want data about the alleles of each and every gene, that way any errors could be fixed. If you are making the DNA from a data set, there is no sense keeping any genetic defects or diseases in the sequence when you remake it.

Craig Venter, one of the protagonists of the Human Genome Project has a company that is able to produce synthetic DNA for a whole organism. They have reportedly produced a synthetic bacterium, so in theory, they could print DNA from a database and recreate an entire genome, though at what cost and how long I am not sure.
The Original sequencing of the Human Genome did cost Billions of Dollars, however today's sequencing machines can produce an entire genomic sequence more in the range of thousands of dollars. I am not sure if they have broken the $1,000 threshold yet.
Most of the commercial companies do not produce full genomes. They likely do not even sequence a full exome (The areas of all genes that make up the coding sequences of mature mRNAs). They likely do some form of polymorphism analysis to determine if for any given gene you have certain allele other than the Wild Type allele. In this kind of analysis, you do not really need a full sequencing to determine what gene a person has, you only need to identify areas of key differences to determine what is what. That being said, the data collected by a commercial genetics company would likely not be sufficient to recreate an entire genome.
Another important factor is Epigenetics. Just because you have the entire base sequence of the person, doesn't necessarily mean that synthetically creating all 46 of that person's chromosomes would give you the necessary material to transfer into an enucleated oocyte to then produce a new person. You would likely also want to capture the epigenetic encoding as well as the full genome. The epigenetic code that you would likely want would be from one of the cells from the 8-cell stage of development I mentioned earlier. While we have been able to clone adult mammals by nuclear transfer, those animals have had issues with cancer and premature aging. This may have something to do with telomeres, but it also may have something to do with the epigenetic code in early development.
There are other considerations in development as well. There is exchange of nutrients between mother and fetus during development. There is also a sharing of immunity and probably hormonal signals from the mother that can effect development.
Also women are mosaics. A woman would also have the added challenge that every single one of her cells has one of her two X chromosomes inactivated, so depending on which one is inactivated, at random, will determine which of the two X alleles she will be expressing in that cell. It is very possible that her clone would be different from her in appearance.

That is a pretty extensive list. I probably have missed some things. One thing I have definitely left out are all of the structural proteins of chromatin and how to package the DNA into a nucleus. We do not yet understand all of the mechanisms to compact DNA down into a nucleus, so we would have to answer all of those questions before we could figure out how to print and package the DNA to make a clone of a person from a database of their genome.
As we have not currently cloned a human, then it is difficult to say if it is possible. Things that we can do, even in other mammals do not always translate to humans and human cells. There would also be significant ethical hurdles to overcome and based on the current sentiments, it is unlikely, even if we have the technology, that society would allow human clones to be produced.

Neurons undergo a lot of somatic mutations mostly due to L1 retrotransposons. It creates somatic heterogeneity in them. Cells with least number of somatic mutations would be the germ cells.

@WYSIWYG can you post sources. I would be interested in reading more about that. Also which germ cells are you referring to?

You can have a look at this post. I posted a reference there. Germ cells mean spermatids or oocyte progenitor (but most oocytes undergo meiosis at a very early stage and are arrested at metaphase). But you are right that the cells from ICM would be the best but I guess it would be difficult to collect them.


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What is the sedimentation coefficient of Mycoplasma?
I have attempted to find the sedimentation coefficient of a number of bacterial species, namely E. coli and a number of Mycoplasma species, but they seemed to be rather elusive in the literature.
If such values cannot be easily found, is there a reason sedimentation coefficients of whole cells are not widely reported, but sedimentation coefficients of proteins are? Mentions of "70S ribosome" and "26S proteasome" are common, but I have never seen any mention of "kilosvedberg" or "megasvedberg" appearing in the literature, and I presume the sedimentation rate of whole cells would fall somewhere in this region.

Alternatively, use regular centrifugation speed to pellete down bacteria for calculation of sedmentation coefficient. Generally its 5000 RPM for 6 min at 4 degree (convert this into terminal velocity). Just find out radius of rotor and angular velocity of your centrifuge then calculate $s = \frac{V}{r*w^2}$


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In the future, it is plausible that we can change the physical appearance of a living animal by editing DNA?
http://www.independent.co.uk/news/science/revealed-scientists-edit-dna-to-correct-adult-genes-and-cure-diseases-9273555.html
This article explains that scientists managed to change the DNA of adult laboratory mice with an inherited liver disease, thereby curing them of the disease.
The change in the liver is not be a change in physical size and shape, instead it was a change in the liver metabolism.
If we used this same method to edit our hair follicles, could we alter our hair color? The new hairs would have altered DNA, and come out a different color depending on what the cells have been altered to.
And then, is it possible to change the physical size and shape of a living animal by editing DNA? For example, if an animal has porous and small bones, is it plausible that we could edit its DNA so that its bones start to become more dense and thick? The physical appearance of the living animal would be changed, since the bones are larger than before.
Along these lines, could we then edit DNA of an adult human to change bone structure so that we have sharper noses? Larger eyes?

Yes it is perhaps possible. I do not really understand what the fundamental point of your question is. Anything can happen in future. Please ask a precise question as this tends to be opinion-based.

@WYSIWYG I am asking if it is a scientific possibility to change how a living animal looks. This is not an opinion based question.

This article explains that scientists managed to change the DNA of adult laboratory mice with an inherited liver disease, thereby curing them of the disease.

Yes, Read about CRISPR-CAS9 method of gene editing. This is not the only method which can achieve this. There are many others like TALEN or Zinc Finger.

If we used this same method to edit our hair follicles, could we alter our hair color?

Yes, similar studies like this has already shown this potential but using different method as mentioned in article you linked.

The new hairs would have altered DNA, and come out a different color depending on what the cells have been altered to.

For this you need to express such constructs in cell specific manner. Drosophila geneticists are doing such things for long long time.

And then, is it possible to change the physical size and shape of a living animal by editing DNA? For example, if an animal has porous and small bones, is it plausible that we could edit its DNA so that its bones start to become more dense and thick? The physical appearance of the living animal would be changed, since the bones are larger than before.

Plausible but remember such characteristics are controlled by many factors which will be hard to control. Plus there will be age/environmental/epigenetic factors which you can't control with such techniques.

Along these lines, could we then edit DNA of an adult human to change bone structure so that we have sharper noses? Larger eyes?

Most of these techniques required change in germ cells. Hence it will be difficult to implement such techniques in adults. However 'ideally' you can use techniques like RNAi which can be triggered by specific inducers at any stage of life (like temperature sensitive UAS-Gal4 system used in fly genetics).


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What are these white spots on a dracena
I have a Dracaena Marginata which started to have some white spots. They turn out to be some kind of "mold"

which can be removed when swapping the leaf and then leaves some discolored spots

They usually appear when the leafs get yellow (because of it, or because I have forgotten to water for too long) and seem to be more present at the base of the leaf.
What is this?
And more importantly: is it a problem for the plant? (minor issue, though it is a gift from my children) or for me? (major issue, and death sentence for the plant)

I think  they are bugs for further info, I dont know much about plants.

I do not think so, they are completely immobile and look like some sort of mold when scrubbed

It is, as har-wradim suggested, scale. We had them on our Dracaena, I suggest you get a pesticide on them quickly, make sure to get all of the plant, they like to be around the base of the leaves near the trunk of the plant, and contemplate removing the worst affected leaves, we lost our plant because of it!

Looks like some kind of scale insect

These are plant pathogens commonly known as scale insect (Coccoidea). Among the genera mentioned to infect Dracaena marginata here and here the most likely candidate is Pinnaspis.
They are close relatives of aphids and psyllids (and more distantly -- also to true bugs). Cochineal is probably the most famous representative of the superfamily. Scale insects suck host's sap and can be quite dangerous to the plant. Adult females are immobile and the spreading is performed by nymphs and (when present) males.
As far as I know they are harmless to humans. When digested (products of) at least cochineal can cause allergic reaction in some persons.

Thank you - I will use some of the methods I found on the net to hopefully get rid it.


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Black/dark-red smooth West African worm, full of red blood
This chap was strolling across my bathtub in Freetown, Sierra Leone, one day after very heavy rains and flash flooding. From its course, it appeared to have come up the bath plug from the drains.

It's about 2mm-3mm wide at the fattest points and 1mm wide at the thinnest points (which vary as it moves). It's maybe around 10cm in length. The picture's not the clearest but (to the naked eye) it looked almost completely featureless - smooth (no visible rings), and no obvious hooks or features at either end.
It was moving to the right from the point of view of the photo, and moved by narrowing and elongating unmarked segments about 2-4cm long each rather than the whole body. I say segments, since it seemed to be the same sections each time, but when it wasn't moving there was nothing to distinguish these segments. Its movements began by elongating the very front 2-3cm, then it'd feel around, come down, and other (unmarked) segments in the body would expand and contract to bring the rest of the body after it.
While I'm pretty sure it's not either of the two most notoriously nasty West African parasitic worms (Loa Loa or Guinea Worm), I didn't want to to take any chances, and we had nothing to isolate or store it in, so we carefully squashed this one after taking photos then cleaned the plug hole with boiling water and cleaner.
On squashing it, it burst in a very similar way to a recently-fed mosquito or bed bug with a splatter of what looked exactly like regular human/mammal blood. I've not seen this before from a worm. Each 5mm or so of worm body contained about as much blood as a well-fed mosquito.
I've done a little browsing of species of bloodworm but didn't find any obvious matches.

This might be unrelated, but the bathroom in which this worm surfaced has for several weeks had a small but constantly replenishing population of tiny flies like this, which I never questioned because they look almost exactly like regular drain flies. There's usually 1-3 of these flies on any given day, even after wiping out all of yesterday's flies, and I've not seen them anywhere else in the country. In this image it's about 3mm from wingtip to wingtip - much smaller than the worm.

There are not so many potential candidate worm groups with similar appearance, namely: (free-living) flatworms, Nemertea and annelids.
While there are several terrestrial and freshwater flatworms, some of which are quite long, they do not approach such an elongated vermiform body shape and their mode of locomotion is different. There are around two freshwater nemerteans in Africa, neither of which looks like your worm, and in any case most nemerteans move by gliding using their cilia.
So the remaining group is Annelida. There are three groups of annelids relevant in this context: polychaetes, oligochaetes and leeches. Polychaeta are predominantly marine and normally have more or less pronounced parapodia ("limbs"). Some of the do behave according to your description, but they are very characteristic in their appearance and you would not expect to find them in a bathtub.
What remains are oligochaetes and leeches. Leeches are more or less dorso-ventrally flattened and have very prominent suckers. Moreover a fed leech (from which you would expect large quantities of blood) would look swelled (the gut in leeches has diverticula).
So, the only worm group I can reasonably suggest is oligochetes. In fact your worm looks and behaves very much like a common earthworm. It is very typical of them to be highly mobile during and after rains and their blood pigment is hemoglobin (i.e. red). The only contradiction is that your worm had no clear true segmentation, but I believe, in some forms it is easy to overlook it.
The fly is indeed some species of Psychodidae.

Great, so nothing to worry about then! Thanks for the thorough answer


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Fibronectin glass surface adsorption
Short summary
I'm having a glass surfaces and I want to adsorb proteins onto them. I have no problem, when I first adsorb fibronectin (human) onto some areas and afterwards any other protein. The second protein will only adsorb onto the remaining "free" areas.
But as soon as I apply fibronectin in the second place, it just adsorbs everywhere. And I want to avoid this.
More detailed Protocol
(direct microcontact printing):

Incubate a pdms-stamp with Protein-Solution #1 for some time and concentration
Dry pdms stamp and press onto coverslip for some time
Remove stamp and put a drop of Protein-Solution #2 for some time and concentration onto the coverslip

I varried already concentrations and times without noticeable success. I also tried adding some BSA to Fibronectin - also without success. All solutions are within PBS.
Further steps I anticipate:

Varying pH around the protein's isolectric point (Fibronectin: around 5.2)
Adding some detergens to fn-solution (e.g. Tween)
Variation of salt-content in fn-protein-buffer

My question
I'm wondering what the exact reason for the stickiness of Fibronectin is and which parameter is the best to vary? Did I miss something? Does Fibronectin stick to the other proteins or rather to "free areas" of the surface?
Please note: surface modification techniques (e.g. using epoxys) are no option.
I'm not sure, whether this topic perhaps suits the chemistry-community better. Feel free to move.

What exactly do you mean by "But as soon as I apply fibronectin in the second place, it just adsorbs everywhere."? Are you applying another protein (which one?) in spots, then flooding the coverslip with fibronectin? Fibronectin, like the related collagen proteins, is extremely "sticky" and will bind to many surfaces, as well as many different types of proteins.

Exactly, that's what I'm doing. I tried various other proteins (e.g. Laminins and Vitronectin). My idea is to modify the conditions when applying Fibronectin (e.g. pH), to make FN less sticky.

What is the exact reason for the stickiness of Fibronectin?

Fibronectin interacts with diverse substrates which reflects its non-specificiy and its interaction with hydrophobic substrates is better suggesting that the adsorption is dependent on hydrophobic interactions.

Does Fibronectin stick to the other proteins or rather to "free areas"
  of the surface?

It can stick to both as you can see from the table. However, its binding to hydrophobic materials like polystyrene and PVC is the most efficient.

which parameter is the best to vary?

Note that there will be a lot of free regions in the substrate. You cannot block all the sites unless you use a high concentration of fibronectin. So the best parameter to vary would be the concentration of fibronectin. You may also use fibronectin-BSA mixtures as their mutual binding is not that great (A stepwise method would be nonetheless better). You can also vary the adsorption time (see the figure below) but that is not as easily controllable as concentration. Since fibronectin does not bind to agar, you can also block some sites on your coverslip using molten agar (or agarose).

Reference:
Klebe, Robert J., Kevin L. Bentley, and Robert C. Schoen. "Adhesive substrates for fibronectin." Journal of cellular physiology 109.3 (1981): 481-488.

Thanks, really nice answer! Thanks also for the reference. So in my experiments (which is actually not exactly micro-contact printing) I varied Protein concentration/Incubation time already a lot. However, this does not yield the wanted result - Fibronectin will just adhere onto the first Protein (Laminins/Vitronectin etc), even tried BSA-blocking. Just out of curiosity: what is telling you, that there are lots of free areas on my substratum after adsorption?

@Vincent Well just an intuitive calculation. If surface area of the substrate is  in the order of mm² and lets say the area occupied by each FN molecule is in the order of nm² (taking the length of FN as diameter of a circle). You can adsorb at least ~10⁶ molecules. So you are coating with a layer of lamins and then FN? Reducing the concentration should work.

Well I reduced the concentration, still FN seems to stick to "laminin"-areas. Sure, I will accept your answer. I'm just waiting one or two more days - perhaps someone had already a similar problem and another hint.


text:
Why do I often see male robins with female robins?
Even when it is not breeding season for robins I still often see male robins with female robins. But why?
I know that the male robin often chirps to find female robins within his territory. I also know that the male robin puffs his chest to try to impress a female robin.
But I have seen out in the country that even during the fall and late summer the male robins are still with female robins. I don't know whether it is to raise their fledgling chicks or what because only in videos and pictures have I seen robin chicks and robin eggs.

Male and female robins have the same habitat, so it is not surprising you see them both in the same area. Robins do not mate for life, but do stay together during the full breeding season, which may include 2-3 nestings. Sometimes in the spring a particular male and female will return to the same territory, and may end up staying together for another year, especially if they successfully raised chicks together the previous year.

@MattDMo You can probably expand your comment into an answer if you want.

This has since been asked and answered at http://outdoors.stackexchange.com/q/10290/66 - dunno if you want to close it here?


text:
How do I offer a generous gift to sweet-seeking wasps, bees, hornets, bumble-bees?
I was having ice coffee and melon ice and after visiting the lavatory I saw that a wasp was having a good time with my already finished ice coffee.
Trying to begin the melon ice the wasp kindly insisted to take a first bite despite my insistence to not do that.
Feeling generous, I offered the wasp the already accepted ice coffee, but despite my best efforts (Waving it in the correct direction so that it get the smell directly before its nose) it only flew uselessly in circles.
Is there any method to give those sweet-seekers a meal which they gratiously accept (and in effect save us the nuisance to shoo them away) ?

So... you're looking for something you can have on-hand that will entice wasps and bees to follow it so you don't have to swat at them?

Or present the already available stuff (sugar, ice, honey, sweets etc.) in a rather compelling fashion, yes.

There are many scientific methods for that which are widely used in animal behavior studies, specifically in honey bees. Read this this. If you search you can find similar for mice and rats also :P

Dead link, already. Care to summarize?


text:
Does this recording sound like the pulses emitted by bats?
Out of curiosity, I recorded sounds in an area with lots of bats, hoping to be able to "hear" the bats communicating by lowering the ultrasound to a level down to the frequency which can be heard by a human.
After a bit of post-processing, I actually hear interesting sounds, but I'm not sure about the origin. It seems that the frequency of the pulses is too low compared to bats.
The final audio is available on YouTube.
Are those actual sounds emitted by bats? If not, what other animal could be the source of those sounds?
About the audio
The sound was recorded at 10 p.m. at 46°34'32.0"N, 0°20'45.4"E near a river, with more of a dozen bats flying in this zone. There is a bridge nearby, and the sides of the river are flat concrete, which means that there are a lot of opportunity for sound reflection (although high frequency sounds don't reflect well).
Zoom H5 with the default XY directional microphone was used. The bitrate was set to 24-bit. Unfortunately, I used the sampling frequency of 48 kHz instead of the maximum 96 kHz.
The following transformations were made to the original audio:

The pitch was shifted by -12 semi-tones, which means that the 20 kHz sound becomes 10 kHz, and 15 kHz becomes 7.5 kHz.

All sounds below 6 kHz were removed.

The sound was amplified.

Severe noise reduction was applied to eliminate everything but the actual sounds emitted by the bats.

The empty parts of the audio were removed.

The sound was amplified once again.

Frequency
The frequency analysis of the transformed audio a peak around 9 kHz (18 kHz in the original audio), slowly fading to suddenly drop at 16 kHz (32 kHz in the original audio).

hypertextbook contains many sources with different indications about the frequency range of the sounds emitted by bats, only a few referencing the frequencies low enough to be heard by a human:

Frequency Produced 10kHz-120kHz
Ramsey, Gabriel, McGuirk, Phillips, Watenpaugh. Holt Physical Science. New York: Holt, Rinehart and Winston Publishers, 1986.

while most agreeing on the fact that bats use frequencies higher than 20 kHz.

Most bats use frequencies in the range 20-80 kHz, only a few bats use frequencies less than 20 kHz.
Long, M.R. & Savage, J.G. Mammal Evolution. New York: Harper, 1976: 108.

The observed range of 18..32 kHz seems too low compared to the sources, but I have an impression that the frequencies vary a lot between different species of bats.
Pattern
When viewing the audio track (see below), each cry consists of several pulses in two to three sub-groups which are in turn in two groups. Each peak is a bit less than 1 ms. The second group occurs from 40 to 200 ms. after the end of the first one. Each sub-group is separated by 5 to 10 ms.
The frequency of every pulse doesn't vary, except the very first pulse. The first cry starts by a more quiet pulse at 6 kHz (12 kHz in the original audio). The second and third cries don't follow this pattern.
Hyperphysics indicates that there are three categories of sounds emitted by the bats:

Short clicks,

Frequency-swept pulses,

Constant frequency pulses.

It looks like it's still the third category which we are observing here, and the overall pattern looks similar to the one described for the bats.
The gap between the left and the right track is mostly irrelevant: at higher frequencies, microphones become more and more directional, and the sound is reflected less, which leads to such difference.

Note: this question was considered to be on-topic at Biology.SE on Meta.

See Bat Detector. There are few examples of Bat calls.

Looks like the examples are not there anymore?

This is a good question (+1), but I think you should re-record the sounds with the appropriate sampling frequency. With a sampling frequency of 48 kHz, you are likely to get lots of aliased high-frequency noises (in the absence of lowpass filtering) which could hamper data analysis.

Should I add a bounty for this??

@DevashishDas; probably not now. I'll do very soon another records at 96 kHz, as suggested by March Ho above, and I'll also search for additional sources (especially books) which may be helpful.

ah, this is good mate

Just to add to your references: some bats can reach frequencies as low as 12 kHz and as high as 160+ kHz (Yalden & Morris, 1975).

Though I cannot be 100% sure from the sound quality, it certainly does sound/seem like bats are making the calls you are hearing/seeing. I spent a number of years as a bat bioacoustics researcher and I came across similar sounds frequently and was able to confirm they came from foraging bats.
I'll have to see if I can find any old spectrograms or recordings on an old data hard drive. If I can find clear examples similar to yours I will add them to my answer. (Though I haven't seen that hard drive in years, so don't get your hopes up!).
These sounds can likely be explained by one of the following:

Some bat species have been known to echolocate using calls that sweep into human hearing range (i.e., below 20kHz; Fenton, 2015; other sources already mentioned).

Many bats actually emit calls during flight that differ in structure from echolocation calls; these calls, often referred to as “social calls,” may occur between echolocation calls and often consist of broadband calls with low-frequency components and multiple syllables (Altringham and Fenton, 2003; Wright et al., 2013).

Some bats use special sounds to avoid collisions with each other while in flight (Fenton, 1983).

You can see and hear examples of some social calls (used broadly in this case) for a pipistrelle bat in Britain here.
I copy a spectrogram of one of these social calls from the above link (see the middle call signature):
Wright et al., 2013 also provide a spectrograph demonstrating all the various call signatures they recorded from various Eptesicus fuscus (big brown bats) in the United States:

Purchasing some bat bioacoustic analysis software should assist with your recordings and call interpretation. I recommend Sonobat (best, but expensive) or SCANR (from Binary Acoustic Technology). There are other less used options as well (e.g.,the Echo Meter Touch Bat Detector for Apple, for which I picture an example screen shot below):

I also want to provide some information and citations about bat echolocation to help inform those interested in this question:
Bat Acoustics 101

Shorter wavelengths (higher frequencies) provide a better resolution of target detail allowing the bat to receive a more detailed picture of its target (Fenton, 1983).

Acoustic energy reflected from a target is theoretically greatest when incident wavelengths of calls are near the same size or smaller than the target (Jones and Rydell, 2003); otherwise, if the object is smaller than the wavelength, the sound will be scattered instead of reflected (Yalden & Morris, 1975).

Bats need to be close to objects to "see" them: range is typically 1-5 m for frequencies around 20 kHz and increasingly closer for higher frequencies (Jones and Rydell, 2003).

In addition to target range, bats perceive target shape and texture from the delay of multiple reflections (echoes).

Calls contain base frequencies, but they can also add harmonics & overtones to the bandwidth of the calls, which can enhance target ranging and localization (Jones and Rydell, 2003) and thus increase acuity (Fenton, 1983). They can also suppress certain harmonics and use variations of combinations of tones.

Bats can also vary the amplitude, or loudness, of their calls (Yalden & Morris, 1975).

Bat calls can be composed of frequency modulated (FM) or constant frequency (CF) components or a combination of both types of calls (Jones and Rydell, 2003).

FM = each signal, consisting of discrete pulses of sound (Fenton, 1983), starts at one frequency and sweeps down to another. Sweeping through a range of frequencies allows bats to achieve some protection from errors associated with Doppler shifts; in addition, the modulation of frequencies helps to tell the bat about the texture of the target (Fenton, 1983).

While foraging, FM bats create a series of repeating ultrasonic pulses in various phases.  There are three major phases, each with an increase in repetition rate.   The change in rate across the phases can go from 4-5 pulses per second to 200 pulses per second.

The signals bats produce may serve multiple functions; they can be used for echolocation as well as for communication, whether intentionally or unintentionally.

Use echolocation calls of others to locate roosts, and eavesdropping also allows a territorial bat to distinguish between another bat trying to steal its food or just one passing through its territory (Fenton, 1983).

“Social calls" (Altringham and Fenton, 2003; Wright et al., 2013).

Collision avoidance sounds (Fenton, 1983).

Alarm calls and distress calls when in stressful situations.

Mother-young communication.

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


text:
Do snRNAs exit the nucleus or not?
In Molecular Biology of The Cell (Alberts, et al., 2015), it lists the various RNAs that are trafficked through the Nuclear Pore Complex (NPC) into the cytoplasm.
The list includes snRNAs, but I have seen it stated elsewhere that snRNAs don't leave the nucleus, that they are made there and perform their function there.
Is MBOC's version correct and snRNAs leave the nucleus, or are the other sources correct and the snRNAs are made, remain, and function in the nucleus?

After transcription of some UsnRNAs, the RNAs leave nuclei first. After assembly of various proteins and modification on the RNAs in cytosol, the RNAs come back to nuclei. In addition, it has been shown that mature U6snRNP shuttles between nuclear and cytosolic fractions in yeasts, if I remember correctly.
http://openi.nlm.nih.gov/detailedresult.php?img=2582628_gkn658f1&req=4


text:
Specificity of the adaptive lymphocytes
T cells are known for their ability to bind multiple antigens, owing to the degeneracy of the recognition sites on their receptors. [I] When examining the structure of the T cell receptor, we can observe the ɑ and β chains which have a highly variable region, in their extracellular domain:

From what I understand, TCR degeneracy means that one receptor can bind to different antigens.
In comparison, the B cell receptor consists of a recognition site that contains a membrane-bound isotope of immunoglobulin. Again, from what I gather, variation in both the Ig on B cells and the TCR occur as a result of genetic recombination. [II]

Question:
Does the membrane-bound Ig in the BCR exhibit the same degeneracy as TCRs? Does variation caused by V(D)J recombination work the same way for both these receptors?
References:
[I] https://en.wikipedia.org/wiki/T_cell_receptor
[II] https://en.wikipedia.org/wiki/V(D)J_recombination
[Images] http://what-when-how.com/acp-medicine/adaptive-immunity-antigens-antibodies-and-t-cell-and-b-cell-receptors-part-2/

What do you mean by "degeneracy".

"From what I understand, TCR degeneracy means that one receptor can bind to different antigens."

Quick answer: No, individual T cells can only bind one antigen with their TCRs, just like B cells.

From the wiki TCR article: "TCRs have very high degree of antigen specificity, despite of fact that the affinity to the peptide/MHC ligand is in the micromolar range."

From the same article: "The binding between TCR and antigen is of relatively low affinity and is degenerate: that is, many TCRs recognize the same antigen and many antigens are recognized by the same TCR."

In addition to that, low affinity with an MHC-antigen complex would simply mean specificity is narrowed down - not necessarily to one antigen per receptor.

This is incredibly oversimplified, but the short answer is that both T and B cells can have degenerate recognition, though the molecular mechanisms are somewhat different.
T cells recognize linear sequences of amino acids that have been excised from their parent proteins, from 8 to 16 or so amino acids long, and that are associated with MHC proteins.  The association with MHC proteins depends on the specific sequence of amino acids, and you can think of this association as depending on a number of amino acids (let's say 4 or 5) that point "down" into the MHC.  That leaves maybe 4-10 amino acids pointing "up" that can interact with the T cell receptor.  If you search for a random set of 4 amino acids with a given spacing, it's quite likely that it will turn up several times in a large protein database; even more often if you allow some degeneracy (similar amino acids can substitute sometimes).  Therefore, yes, T cells tend to have a moderate amount of degeneracy in their epitope recognition.  However, while search a whole database may find duplicates, the degeneracy is not terrible, and the MHC binding requirement also reduces it quite a bit. Also, of course, during T cell development, TcRs that have broad and degenerate recognition of many structures are selected against.  So T cells are definitely cross-reactive, and sometimes extensively so, but in single individuals it's probably not a common thing.  (Ray Welsh and Liisa Selin have looked at cross-recognition between viruses and find quite a bit of cross-reactivity, though, so this may be understated.)
Antibodies, unlike T cells, recognize conformational epitopes rather than linear sequences.  However, just as with linear epitopes, it's not impossible for two unrelated proteins to end up with similar conformations, even with rather different amino acids.  As well, antibodies can be more or less "forgiving" in their recognition; some are extremely specific, but others can interact with a wider range of shapes.  You can imagine a "flat" antibody binding surface that is rather generic, that could interact with many different shapes. Again, B cells with broad cross-recognition are selected against during development, though not as rigorously as are T cells.

There's a lot more data on TCR degeneracy than for the BCR, but they do have a quantitative study here on CD8+ T cell cross-reactivity and they found that a single TCR was capable of responding to over 10^6 decamer peptides.

Yeah, but that's not every TcR -- that's one specific one that, because it's autoimmune, must have avoided much of the usual developmental checks already.  Probably most TcR that have gone through the negative selection process would have less degeneracy than that one.  But there's certainly still room for recognition of a large number of peptide variants.


text:
How to use DRAQ5 and MitoTracker CMXros dyes to stain turtle erythrocytes?
I am working on turtle species and want to use DRAQ5 and MitoTracker CMXRos to stain turtle nucleated erythrocytes. Can anyone suggest me a protocol to carry this stain out? Would the two stains complement each other?

Welcome to Biology. Why use two stains and not one? Could you provide additional info and a link to these staining methods?

Have you tried just using the manufacturer's recommended protocols? The structures bound by DRAQ5 and MitoTracker are pretty conserved across eukaryotes, so these reagents should work in just about any cell type.

I havent tried this yet, I got to know that DRAQ5, a far red fluorescent  stain is most used for flow cytometry analysis. Can any tell me whether it can be used for fluorescent microscopy observation along with Mitotracker red?

If yes suggest me the protocol to start.


text:
Is organ transplantation race dependent?
I watched (IMHO canibalistic) movie "Seven Pounds" where protagonist donated many of his organs to other people and I noticed, that most recipients were black also as protagonist was.
Is race really taken into account when organ transplanting?
UPDATE
The question is not just about if interracial transplantation really good or bad. I can imagine, that transplantation is done same-race just in case, in favor of "do not harm" principle.

Interesting that pillay et al. (1990) contradict organedono.gov. Organdonor.gov don't have any reference but the article is quite old (1990) while oraganedonor.gov is probably frequently updated. We'll need some more recent research in order to answer this question.

No, race is not a factor taken into account. However, due to higher genetic similarities between people of the same race, it is usually easier to find a match within a race.
Source 1
Source 2

The two statements seem somewhat contradictory. Can you add some explanation?

Race is not taken into account in the sense that they do not use it as a factor in finding a match. E.g., if you are black and need an organ, they do not look only to black donors. However, it is more likely that someone from your own race is a match simply because of genetic similarity. Therefore, it is going to be more common to see people have a donor of the same race only because the probability of a match being the same race of a recipient is higher than the probability of a match being a different race.

It makes sense. You might want to rephrase the question just to avoid the confusion. I also first thought that you were contradicting yourself.

Also keep in mind the most likely match is  direct family which of course will tend to be the same race.

Here is a really interesting article discussing this topic and finding no statistically significant difference in survival rates between donations across race and those within a race.

Everyone is correct, it depends on which organs are being offered.With kidneys and pancreas the HLA (the tissue matching) is used and important for graft survival. Since our HLA will more likely match another of a similar race then you could say race may matter with those organs. There are some interesting studies that are emphasizing that race does play a factor in the success of the kidney transplant, as well as the HLA. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2826243/#__ffn_sectitle   In liver transplant, race still does not matter for the success of the organ transplant.https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2954674/

Welcome. Can you add sources or references to your answer? Without those, people can't background read on your post.