text:
To what extent do gonads affect differences in gendered behaviour?
I'm not sure whether this question makes sense, but someone said that they result in gender differentiation on an organisational level in the brain. I'm wondering how important these changes are, in terms of magnitude of average differences in neural structure between males and females?

Can you specify whether you refer to humans? Because in different species (e.g. lizards vs mosquitoes) the importance of the gonads on behaviour changes  quite dramatically.

@havefun I was referring to humans, but would you be able to explain the other factors involved for lizards - and how the gonadal hormones play a role?

Yes
During embryonic life,there is formation of new synapses by a process termed as exuberant synaptogenesis.
Their differential formation in the males and females could be due to the effect produced by the gene PCDH11X/Y located in the allosomes.

PCDH11Y is a gene unique to human males that encodes Protocadherin 11Y, aprotein that guides the development of nerve cells. PCDH11X, located on the X chromosome, is common, in both sexes, to humans and our nearest relative, thechimpanzee; however, PCDH11Y, located on the Y chromosome, is unique to males.[3]
  ...PCDH11X/Y are cadherin family genes. They make proteins, involved in signalling, that attach to the surface of nerve cells.[4] PCDH11X and PCDH11Y, respond in different ways to Retinoic acid, a chemical involved in the development of embryos. The acid stimulates the activity of PCDH11Y but suppresses PCDH11X. This is likely one of the explanations for the differences between the brains of men and women.[3]
  [source]

About the parts of the brain which are deemed"sexually dimorphised" a few of them are:
1.hemispherical differences due to which inter hemispherical functioning is better is females
 whereas intra hemispherical functioning in males
2.hippocampal and amygdaloid laterisation

on average males had larger grey matter volume in bilateral amygdalae,hippocampi, anterior parahippocampal gyri, posterior cingulate gyri, precuneus,putamen and temporal poles, areas in the left posterior and anterior cingulate gyri
  ...females on average had larger grey matter volume at the rightfrontal pole, inferior and middle frontal gyri, pars triangularis, planum temporale/parietal operculum, anterior cingulate gyrus, insular cortex, and Heschl's gyrus; bilateral thalami andprecuneus; the left parahippocampal gyrus and lateral occipital cortex
  Source:Neuroscience of sex differences

Furthur,since synaptogenesis may occur throughout one's lifespan perhaps not as greatly as during embryonic life and as receptors for gonadal hormones are present in the brain it can be said that the gonads may affect the phenomenon,though mainly after puberty when their concentrations are higher than during childhood.

Regarding the third Wikipedia link, it would be best if you could include some significant passages. Links die, or the content might be removed, and it really is best to have relevant content available in the answer itself. You don't have to go overboard, but making the answer a bit lengthy isn't a problem if it's a good answer.

@Harris Weinstein thank u for ur suggestion..i will brief them.hope it helps.


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Alternatives to NCBI BLAST during US government shutdowns?
Many molecular biologists are used to going to NCBI BLAST for quick, hassle-free BLAST searches of their genetic or protein sequences.
However, during the last American government shutdown in 2013, BLAST was rendered unusable due to lack of funding.
The incumbent president is also threatening to shutdown the government if funding for the Mexican border wall is not approved by the Democrats.
What are some alternatives for NCBI BLAST that are reasonably fast, easy to use, and would not be rendered unusable in the event of American government shutdowns? Ideally, the tools should encompass all of the standard BLAST sub-functions (pblast, PSI-blast, etc).

b.nota is correct - Just further adding to his answer. The International Nucleotide Sequence Database Collaboration (INSDC) is a consortium between DNA Data-bank of Japan (DDBJ), EMBL-EBI and NCBI. Contributions to each of the 3 databases are shared on daily basis.
(Thanks to @KonradRudolph) Since EMBL-EBI is not directly accountable to any single government either financially or in terms of research directions so a (temporary) shutdown equivalent to that of the NCBI is vastly less likely. Rather, like CERN, it’s an international treaty organization and thus probably a lot more robust.
BLAST
Answering part 2 of your question: YES! BLAST is available in both DDBJ and EMBL-EBI on following links:

BLAST - DDBJ
NCBI BLAST+

Scope
Here is what INSDC's website says about its scope:

INSDC covers the spectrum of data raw reads, though alignments and
  assemblies to functional annotation, enriched with contextual
  information relating to samples and experimental configurations.

Following table (taken from INSDC website) may help you have better understanding about respective data types comparison for 3 contributors:

It’s worth noting that EMBL-EBI isn’t directly accountable to any one government either financially or in terms of research directions so a (temporary) shutdown equivalent to that of the NCBI is vastly less likely. Rather, like CERN, it’s an international treaty organisation and thus probably a lot more robust.

BLAST can be localized to your machine. There are tutorials, such as  Run-Blast-Local provided by NCBI. Note: you will need to download any/all databases you want to BLAST against locally. Other options for identifying ORFs and trying to identify potential genes include:  USEARCH, VSEARCH (both claim to be as fast, or faster).
If you download entire databases, for example the nr db, running BLAST locally will be far slower than through a browser. I imagine creating customized, more specific databases would speed this up greatly (though I cannot confirm as I didn't get this far in my research).

While this is certainly a legitimate alternative, I don't imagine that a majority of molecular biologists (as opposed to bioinformaticians) have the requisite skill to install all of the packages on their own.

@MarchHo Thank you for the helpful criticism. The link provides an brief how-to instruction to localize BLAST and includes a support email for any who require additional assistance. I should have included this information in the answer. I don't mean to claim this is by any means easy, you are indeed correct in putting forth that this method isn't without its challenges. Just providing additional solutions that I know of :)

The SequenceServer software (which I help make) can also  help set up personalised point-and-click BLAST databases (it is free an open source). It can be helpful for a bioinformatician running it locally on their computer. But it can also be installed on a shared server for access through the web browser. (OR, there is also a cloud BLAST hosting service for those who want to set it up by pointing and clicking. )

I think via Europe (EBI) will be an option, but I am not sure if it uses the American server or if its run on European servers.

Data is exchanged between both organisations which run their own servers. So the results should be the same.

If the university also has the informatics department, they can setup BLAST server for the university no problem.
The server only needs to capture the input from the form and render the output as plain text, an easy task that can be implemented with the wide range of programming languages, server frameworks and operating systems, from Java to .NET, from Apache to node.js. Just restrict IPs for campus only to avoid abuse from the side.
Asking informaticians would eliminate the problem that may be difficult to run BLAST locally for each biologist separately. This can even be made an assignment for students, later putting the winner on the web.

source: Stack Exchange

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

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Is protein production doubled if you have homozygous dominant genes as opposed to heterozygous genes?
At school we were taught in quite simplistic terms. We were told that there is a dominant and recessive type of every gene and that if the dominant gene was present, the protein is produced and if it isn't, then a protein is not produced. We were just told that dominance was just an intrinsic property of some genes.
However, upon researching a little, I see that some genes are dominant because their corresponding allele simply doesn't make the protein but the dominant one does (please correct me if I'm wrong).
Does this mean that if someone is homozygous dominant for a particular gene, they produce double the amount of that certain protein as someone who has heterozgous genes or is there a mechanism that suppresses the expression of one of the dominant genes?

Dominance is defined based on the phenotype
Dominance is defined based on a phenotype of interest. Pick a phenotype, say coat color for example. If genotypes AA and Aa have the same coat color while aa has another coat color, then A is domiant over a.
The concept hold even for sequence that do not produce proteins
The concept of dominance can be applied to any locus which variance explains phenotypic variance, whether this locus codes for a protein or not.
Most sequences that affect the phenotype are regulatory sequences that do no produce any protein. In such case, your intuition that dominance is the allele that produce more proteins really does not make much sense.
Mechanism
A whole lot of mechanism can yield to such dominance relationship. It is not uncommon that the recessive allele comes from a loss-of-function mutation. In such case, yes it is likely that the AA genotype produce twice as many proteins as the Aa genotypes. But this is definitely not the only possible mechanism. Note that whether the number of proteins produced of the AA genotype is twice the number of protein produced of the Aa genotype, won't change anything to the phenotype of interest by definition of what dominant mean.
Dominance is actually pretty unusual
Most phenotypic traits actually result from the influence of several loci and allelic relationship at these loci are rarely perfectly dominant. Perfect dominance exist in reality but is definitely over represented in intro classes as they are simple to understand study cases.
Fitness
Note that there is a positive correlation between how recessive an allele is and how deleterious it is. It does not mean that the recessive allele is necessarily deleterious but there is a tendency.

Suppose that the allele for a curled tail is dominant (A). So if you had Aa for particular phenotype, does that mean that the loci and protein coding genes associated with the "a" allele are expressed as well as the ones associated with "A" but only the effects of the "A" gene is seen on the outside? Or does it mean that the expression of the genes to do with "a" is suppressed, possibly epigenetically?

There are many possible mechanisms of dominance. It is not because a is recessive that it necessarily does not express anything (but it is possible). It can be, but not necessarily. The notion "seen on the outside" is a bit misleading. It could be possible that A is dominant but Ao individuals (individuals that have lost one copy of the gene on one haplotype) differ from the Aa individuals. So really, the mechanisms are multiple, the only that matters to the definition is that AA and Aa have the phenotype while aa has a different phenotype.

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How do polygyne Carebara affinis or C. diversus (a.k.a. Pheidologeton affinis and P. diversus) colonies work?
I live in Hong Kong. Typhoon Hato hit yesterday and a whole bunch of Carebara queens decided to take their nuptial flight. I caught close to 20 of them within 15 minutes.
I'm pretty sure they are Carebara affinis, though they can also be Carebara diversa. They are also known by their old names Pheidologeton affinis and P. diversus, respectively.
In any case, I have read from multiple places that both Carebara affinis and Carebara diversa are polygyne, which means they can found a large colony with multiple egg-laying queens.
So I decided to temporarily put them into the same lunch-box-sized plastic container.
However, soon after I put them into the same container, I discover that some of them would get their legs and even their antennae bitten off. I thought maybe it's because they found the container too crowded and wanted to eliminate some competitors, so I added two layers of toilet paper to give them more surface to crawl around. That didn't really help. Tonight, after coming home from work, I found most of them have been completely amputated. They aren't dead yet though; they are just left there wiggling around without legs. A few of the queens come out intact so I suppose they are somehow dominant. The ones who get amputated tend to end up in a pile. I'm not sure if the "dominant" queens decided to drag them and pile them together.
Is that at all normal? Is that how Carebara ants start a polygyne colony? Basically one or a few dominant queens amputating their sisters to turn them into egg-laying slaves of some sort? If the dominant queens wanted to kill the weaker ones, why not bite their heads off? I'm pretty sure they had the jaw strength if they wanted to. So, supposing that the amputated queens do survive, I'm not sure I see how that helps in the evolutionary sense. Unless that's actually how it works: one or a few dominant ones amputating weaker ones to force them to lay eggs together?
Does anybody know how to properly start a polygyne Carebara diversa or affinis colony from scratch?

I don't know about their polygyne nature, but carebara diversa queens are between 20-25mm and carebara affinis queens are between 14-16mm and are slightly lighter in colour. Hopefully that should help you identify them.

They are not polygynous, they just participate in pleometrosis. This means a colony is founded by multiple queens. The workers select a "dominant" queen and execute the others, so after a short time the colony has only one queen.

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How some virus are able to reach the CNS?
I know that the lymphocytic choriomeningitis virus (LCMV) could provoke meningitis and encephalitis when this virus reaches the brain. However, there are other viruses like Varicella (VSV), Cytomegalovirus (CMV) or Herpes (HSV) that are able to reach the brain, hence, to pass trough the blood-brain barrier (BBB) and damage the central nervous system (CNS).
1) Since the blood-brain barrier allows only the free diffusion of some molecules such as water, some gasses and lipid soluble molecule, I was wondering by which mechanism a virus is able to pass trough the BBB.
2) Since the CNS is an immuno-privileged space (where basically the immune system is down-regulated), how does the body eliminate a virus that had reached the brain?

What on god's green earth is the "SNC"?

@4DNeuron sorry is CNS, I've already edit the question

you should do some homework before posting, maybe start with https://en.wikipedia.org/wiki/Central_nervous_system_viral_disease and https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3367119/

some viruses like rabies get into the peripheral nerves, and travel through those to the spine , unimpeded by any obstacle.


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What Kind of Bug is This?
I took a picture of this bug when I was camping with my boyfriend in Ontario, Canada. The little guy (or gal) kept wanting to climb onto my hand which kind of freaked me out. I'd love to know what kind of bug this is!

It looks like an assassin bug. Spined assassin bug perhaps?

Ogre71, I looked at the picture to which you refer,and I think you are correct. It has a smaller abdomen,but it might mean that it is male.


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The title et al
I have found the extension "et al" with biologists from different nationalities like : Avery et al ; Taylor et al etc.
My question :
1. What does it mean?
2. Why only biologists?

It is just to abbreviate the names of the authors that is used in all fields of knowledge. For example, if I have to refer to this paper that has 9 authors, I will not write every name, I will just write Gilbert et al. 2017. I am not sure why you would care more about nationalities than whether they prefer chocolate over caramel. They are just authors.

I am voting to close because your question is off-topic here but would be on-topic on Academia.SE (although they will likely say "Just google it!").

I'm voting to close this question as off-topic because it is not about biology.

The Latin phrase et alia (abbreviated et al.) means and others.
It is not limited to biologists, nor those of different nationalities. If I refer to this computer graphics article, I can refer to it as "the paper written by Henrik Jensen, et al., regarding physically based modeling of fire..."
Note that the expansion of et al. can also be et alii and et aliae, which are the masculine and feminine forms, respectively; et alia is the neuter form.

Actually, in Latin "al." can be the abbreviation of 3 things: alii, aliae and alia. The first is masculine, the second is feminine and the third is neuter (all of them are nominative plural).

@GerardoFurtado - So how do we know to which "et al." is referring? And if the genders of the authors are mixed, why isn't it, et. al. et. al.?

@anongoodnurse you don't. Since "al." is the abbreviation for alii and aliae, it covers any combination of researchers: all male, all female or mixed. Also (and this answers your second question), Latin is a very "sexist" language: a group of one thousand women is aliae, but a group of one thousand women with a single man among them is now alii. So, a mixed team is just et alii.

Actually, Latin is so "sexist" that, even possessing neuter pronouns, if you're taking about a person of unknown gender you use the masculine pronoun.

@GerardoFurtado - I was pilling your leg. :) I love Latin; I taught it for about six years. But there is no one - and I mean no one - I know that shares that love of Latin, so you were the victim. Please forgive me. :)


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How can I perform virus neutralization assay for influenza?
How can I perform a Virus Microneutralization assay for influenza virus using serum from mice vaccinated with this virus?

There are a number of different protocols, but the canonical one is published at the WHO Influenza site:
SEROLOGICAL DIAGNOSIS OF INFLUENZA BY MICRONEUTRALIZATION ASSAY
It gives a detailed, step by step protocol.


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Do creatures exist which can stop their hearing at will?
Many people would love to have the ability to shut out noise while sleeping, in the same way that we have eyelids to shut out light. If this capability exists in nature, it could offer clues to researchers in the field of sound proofing.
Are there creatures which are capable of 'switching on or off' their hearing capabilities at will? At least partially?
I don't see why this cannot be evolutionarily possible. If perception of sound was necessary to know a predator was approaching while the creature slept, then according to evolution, creatures would not have had the ability to shut out vision either.

In what sense do you mean "not hearing"?  Physically shutting off the hearing mechanism (as with ecolocation), or not allowing the stimulus to propagate to higher brain areas?   That is, whether it's "not hearing" or "not paying attention".   My friend's dog seems to be able to do the latter, as can many children :-)

I think the "not paying attention" part is something that is a very pertinent concept that should be taken into account for any AI that processes sound and/or images.

A related subject is how we can give selective attention to some sounds while tuning out others, like picking out one conversation in a crowd, or tuning out background music.  Or pick out one instrument or line from a symphony...

Yes
Many echolocating bats use the stapedius muscle to separate the inner ear bones
when they emit their call so they are not deafened by their own call. Their ears are highly sensitive to the very frequency they are making so they need a way to protect against it. They are only deafened for 2-8ms but that is enough to protect their hearing while still being able to hear any echo.
Source

You can philosophically start arguing that bats see with their ears when echo-locating, and hence that they do not shut down hearing. +1 nonetheless, nice answer ;-)

Hmm...separating inner bones would reduce the sound. I was also considering that perhaps the true way of shutting out sound would be to block the signals that convey the message to the brain.


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Species ID: What's this mushroom?
So this one is found in white mountain forest in New Hampshire, and I have strong suspicion it is actually just a boletus.

My question would be what's is the name of this fungus?

It actually looks very much like a boletus. It should have pores, which I just can't see on your picture. Is that your kitchen? Mind though that not all Boletus are edible...

There are different types of boletes. For a better answer we would need a picture of the underside and a spore print. Also, specific information about the environment of growth would help.


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Role of non-inflammation in H.Pylori positive people
Quoted from Saudi J Gastroenterol. 2009 Jul; 15(3): 201–207 publication :

Approximately 50% (over 3 billion) of the world populations are known
  to be infected with Helicobacter pylori, mainly in the developing
  countries. Among those, hundreds of millions of people develop peptic
  ulceration during their lifetime ....

I know that many people have H. pylori in their stomach, however, just a small percentage of them develop peptic ulceration. Does anyone know the role of this? Why don't more people develop any symptoms?

The answer is no, we don't know why some people are assymptomatic. Why? Because it's easier to prove causation than non-causation. But there is much more to H.pylori than ulcers. Chronic gastritis, lymphoma, gastric cancer, GERD, and other conditions (even bad breath) are associated with it. Given that H. pylori was only discovered 35 years ago (and taken seriously for far less than that), I'd say it's still early.

@anongoodnurse thank you for your reply. May be we should make a full genome sequencing of those H.Pylori on people with and without symptoms to see if there was a different type of H.Pylori that harmful and unharmful.

@anongoodnurse i known it's weird but I was healthy before - until I make an eradication H.P on my stomach, I started develop inflammation and GERD when the H.P become negative. I was though there must be a relevant between the eradication of H.P and my symptoms. I'm trying to find an evidence that some type of H.P may protect the lining of duodenum and stomach  from acid and bile. As it can produces urease to neutralize gastric acid and other mechanism to resist bile.

No, to my knowledge, H. pylori is not protective at all. BUT  our knowledge of all its effects is in its infancy. The present stance is if it's detected, it's treated (100% of the time), even though risks of treatment exist, and even if the patient is assymptomatic. I have some doubts about this approach, but as my mother died of gastric cancer and was discovered to have had H. pylori, I should be more open to this. I don't know. If I have time later today, I'll scrape up an answer.


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Do organisms have a mechanism to control how fast mutations occur?
Sometimes the environment and other species can change rapidly (climate changes, changes in terrains from erosion, new river paths, etc), and it seems like a regular slow mutation rate would be bad, and faster-mutating species would thrive. On the other hand, this fast mutation rate seems wasteful and inefficient when the environment is changing slowly, thus slower mutating species thrive with less waste in this situation.
Organisms capable of responding to the pace of environmental change would seemingly do well in both situations. Does such ability to modulate the rate of mutation/evolution exist in nature?

The ability of a population to respond to environmental change through evolution occurs over generations, and so the generation time of an organism has to be less than the time scale of the environmental change for such an increase in mutation rate to be beneficial.
For bacteria at least, the answer to your question is yes. Bacterial stress responses involve upregulation of error prone polymerases and thus lead to an increased mutation rate. Check out this paper (links and emphasis added):
Foster PL. 2005. Stress responses and genetic variation in bacteria. Mutat Res 569(1-2):3-11.

Under stressful conditions mechanisms that increase genetic variation can bestow a selective advantage. Bacteria have several stress responses that provide ways in which mutation rates can be increased. These include the SOS response, the general stress response, the heat-shock response, and the stringent response, all of which impact the regulation of error-prone polymerases. Adaptive mutation appears to be [a] process by which cells can respond to selective pressure specifically by producing mutations. In Escherichia coli strain FC40 adaptive mutation involves the following inducible components: (i) a recombination pathway that generates mutations; (ii) a DNA polymerase that synthesizes error-containing DNA; and (iii) stress responses that regulate cellular processes. In addition, a subpopulation of cells enters into a state of hypermutation, giving rise to about 10% of the single mutants and virtually all of the mutants with multiple mutations. These bacterial responses have implications for the development of cancer and other genetic disorders in higher organisms.

This mechanism may be involved in the evolution of antibiotic resistance, for example (emphasis added):
Cirz RT, Chin JK, Andes DR, de Crecy-Lagard V, Craig WA, Romesberg FE. 2005. Inhibition of Mutation and Combating the Evolution of Antibiotic Resistance. PLoS Biol 3(6):e176.

The emergence of drug-resistant bacteria poses a serious threat to human health. In the case of several antibiotics, including those of the quinolone and rifamycin classes, bacteria rapidly acquire resistance through mutation of chromosomal genes during therapy. In this work, we show that preventing induction of the SOS response by interfering with the activity of the protease LexA renders pathogenic Escherichia coli unable to evolve resistance in vivo to ciprofloxacin or rifampicin, important quinolone and rifamycin antibiotics. We show in vitro that LexA cleavage is induced during RecBC-mediated repair of ciprofloxacin-mediated DNA damage and that this results in the derepression of the SOS-regulated polymerases Pol II, Pol IV and Pol V, which collaborate to induce resistance-conferring mutations. Our findings indicate that the inhibition of mutation could serve as a novel therapeutic strategy to combat the evolution of antibiotic resistance.

To expand on the first point in this answer, that's a big reason why "diversity" both in an ecosystem and within a species is important to conservationists in the face of changing climates, etc. Low populations or genetically isolated groups are less likely to have the diversity necessary to survive changes in the environment, because for many animals there just isn't enough time to respond with new mutations when the environment changes, the diversity has to already be there.


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What are some examples of coupled reactions in the cell?
Except DNA Synthesis that requires ATP hydrolysis, which other reactions require activated carriers?

All the anabolic reaction inside our body require energy. The majority of those reactions use the hydrolysis of ATP as source of energy.
To cite a few reaction that require ATP:

Gluconeogenesis where 4 ATP, 2 GTP and 2 NADH2 are consume to produce glucose from pyruvate.
Formation of peptide bond between two amino acids.  Here the amino acid have to be first activate by binding to the tRNAc consuming ATP, as explain here (from wikipedia)

Polymerization of amino acids is what creates proteins. This condensation reaction yields the newly formed peptide bond and a molecule of water. In cells, this reaction does not occur directly; instead, the amino acid is first activated by attachment to a transfer RNA molecule through an ester bond. This aminoacyl-tRNA is produced in an ATP-dependent reaction carried out by an aminoacyl tRNA synthetase

Ubiquitin ligase, that require ATP to activate ubiquitin for conjugaison and it transfer to an E2 enzyme. This pathway is mediate by the E1 enzyme, as suggested here

There is one major E1 enzyme, shared by all ubiquitin ligases, that uses ATP to activate ubiquitin for conjugation and transfers it to an E2 enzyme. The E2 enzyme interacts with a specific E3 partner and transfers the ubiquitin to the target protein.

Hope that it helps.


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Is it inevitable that antibiotics will become useless in the future due to bacteria immunities?
Antibiotics are developed in an ever smaller amount due to the difficulties of discovering new ones. Bacteria, on the other hand, keep "finding" more ways to render antibiotics ineffective, and they are doing it faster than new antibiotics come to market. It seems that by a simple qualitative assessment at some point in the future all antibiotics will be ineffective.
However, there are 2 things I could think of that can suggest otherwise:

Antibiotics which were rendered ineffective long ago can be reintroduced since it's possible that the bacteria mutated away from their defense mechanism. This would allow for cyclic reintroduction provided we have enough types of antibiotics to sustain the cycle.
Antibiotics which bacteria can't defend against.

Are any of the above 2 possible futures? Can it be (at least theoretically) proven that antibiotics in point 2 can exist? Are there any other methods to "win the antibiotics war against bacteria" (assuming we are losing it as I assessed)?

http://mobile.the-scientist.com/article/37629/giving-antibiotic-cycling-another-shot

@canadianer Thanks. The sentence "as soon as the drug that is stopped cycles back on, the resistance comes right back" confuses me as it implies some long term memory of the system. If we cycle A-B-A then it's understandable, but I assume we would cycle A-B-C-D-E-A, and by the time we reach E do the bacteria still "remember" how they adapted to A in first place and can use that to adapt faster than they did in the first place?


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Why are excess amino acids toxic?
While learning about deamination, I learnt that excess amino acids must be converted to urea and excreted, since the nitrogenous group can alter the pH and affect proteins. But shouldn't the pH stay the same since they have NH2 that becomes ammonia as well as a carboxyl group (weak base and acid). So why are amino acids deaminated?

"they have NH2 that becomes ammonia as well as a carboxyl group" you mean, like -$\ce{NH_2}$ converts to -$\ce{COOH}$ or that the latter cancels the pH change caused by the former?

Firstly excess amino acids are deaminated to form keto acids and not urea.
Urea is formed utilising the ammonium released as a consequence of deamination via Ornithine-Arginine cycle
Secondly the released ammonium is toxic because of two reasons:
1)pH changes in the tissues (as mentioned in the question)
2)disturbs the balance of K+-Na+ gradient between the intra and extracellular fluids.

ammonium ions compete with potassium ions for inward transport, over the cytoplasmic membrane, via potassium transport proteins like the Na+/K(+)-ATPase and the Na+K+2Cl(-)-cotransporter.

This causes increased demand for maintenance energy, caused by the need to maintain ion gradients over the cytoplasmic membrane.That is why converting the ammonium to urea is neccessary.
why amino acids are deaminated:
to form glucose via gluconeogenesis or to form anaplerotic compounds
why acidic group of keto acids fail to neutralise the basicity of ammonia:
because they keep getting utilised for the energy expenditure that increases in the tissues as mentioned above.

In addition to what @CATHARANTHUS has said I would like to mention that ammonia has its direct effects on brain metabolism.
Ammonia is an important substrate as well as a product for at least 16 different enzymatic reactions in the brain (Cooper and Plum 1987).
For instance its effect on Tricarboxylic acid cycle(TCA) is as follows:

So accumulation of ammonia will shift the equilibrium towards right hand side resulting in depletion of alpha ketoglutarate ,a key intermediate in TCA cycle which ultimately, results in decreased production of ATP, so one can say that ammonia exerts its toxic effects on brain by impairing ATP formation.

Sources:
1-Biochemistry by Satyanrayna
2-Source of last image


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What makes a cancer contagious?
Most human cancers are not (very?) contagious (perhaps besides a couple of incidents). But the Tasmanian devil seems to have a form of cancer which is contagious. Now what makes the difference between a contagious cancer and a non contagious cancer in the DNA mutations of a cell?

There are two relatively common contagious cancers: Tasmanian Devil Facial Tumor, and Canine Transmissible Venereal Tumor.  Both are truly contagious cancers, in that the cancer cells themselves are transmitted from one host to the next, and expand and cause disease in each successive host.  (There was also a contagious cancer of hamsters, which has long since gone extinct, and there are some transmissible tumors in clams and oysters; the latter don't have immune systems that are remotely similar to dogs, Devils, or humans.)
It's believed that one key aspect of the Devil Facial Tumor is that Tasmanian Devils are immunologically closely related.  Normally, cancer cells from one host would be a tissue graft in a different individual and would be rapidly rejected as with any allograft.  However, immunologically closely related individuals can tolerate each others' grafts, and it's believed that this is part of what allows the Devil tumor to spread -- a lack of genetic diversity among Tasmanian Devils.

Major histocompatibility complex class I and class II genes have extremely low levels of sequence divergence in the devil population from the Tasmanian east coast (Siddle et al., 2007a, 2007b). ... The lack of diversity at MHC loci, coupled with weak responses of east coast devils to allogeneic mixed lymphocyte culture, has led to the suggestion that this population may be functionally identical at MHC loci, thus permitting the spread of DFTD as an allograft.

--Clonally transmissible cancers in dogs and Tasmanian devils
The genetic diversity explanation is widely accepted, but it hasn't been formally proven and there are a number of points that suggest that it isn't the whole story.  There are several other molecular features of the tumor that probably make it less immunogenic (see the review The role of MHC genes in contagious cancer: the story of Tasmanian devils) and the full story probably involves a combination of these things.
CTVT is different.  It's astonishingly ancient (it apparently arose in a dog, or a wolf, 11,000 years ago and has been passed from dog to dog continuously since), so it's obviously very successful at what it does, but it's not at all understood how it does it. Dogs are genetically pretty diverse and definitely don't tolerate arbitrary grafts from each other, so that's not the explanation. Lots of other possible explanations have been put forward, most of which point to various immunological features of the tumor; however, while that's clearly an important point, none of the things people have implicated are unique to CTVT -- tumors invariably have immune suppressive abilities and don't have the same ability to spread. (Going back to the Devil tumors, the low expression of MHC molecules on the cancer cells is probably a factor there too, but it's important to understand that low MHC expression is almost universal among tumors, including the vast, vast majority that can't transmit.)
Summary:

There do exist a very small number of truly contagious cancers.
The reasons for their transmissibility are not fully understood.
Genetic diversity and immune evasion are probably two of the causes.

Thanks a lot. The reading is quite diverse and very informative (read abstracts, will read the rest slowly.)

Very nice answer.

Joined just to upvote, very elaborate and interesting answer.

Different mechanisms can explain why some cancers are contagious. They don't necessarily belong to the same category.
For instance, certain cancers, like the cervical cancer, can be caused by viruses (in that case, HPV). The cancer itself is not contagious, but the virus is. Other famous viruses that can cause cancer are HTLV-1, MCV, Herpes Virus 8 (or KSHV), HCV, HBV and EBV.
The case of the Tasmanian Devils is more complex. It was thought for some time that the same viral mechanism could explain the Devil Facial Tumour Disease, or DFTD, specially the fact that DFTD is contagious. However, there is no evidence (to date) of such a virus.
Thus, some alternative hypothesis have been proposed, such as environmental toxins.
However, the most accepted hypothesis nowadays is the Allograph hypothesis. According to the Save the Tasmanian Devil Program:

Trials are being held to examine the transmission of Devil Facial Tumour Disease. Preliminary results support the increasingly accepted hypothesis that we are dealing with a transmissible cancer and that cancerous cells are passed directly between devils as an allograft. Put more simply, we are getting more and more evidence to support the theory that DFTD is spread by the cancer cells themselves being passed from one animal to another. (emphasis mine)

There are two relatively common contagious cancers: Tasmanian Devil Facial Tumor, and Transmissible Canine Venereal Tumor.  Both are truly contagious cancers, in that the cancer cells themselves are transmitted from one host to the next, and expand and cause disease in each successive host.  (There was also a contagious cancer of hamsters which has long since gone extinct.)

Yes, the Transmissible Canine Tumor is in the page I linked about the allographs. However, it's important to mention that the case is not closed for the TDFT: it's still a hypothesis.

What about immune system killing non-self cells?

it's still a hypothesis -- that's fair. My response was too long for a comment so I wrote another answer, basically to say I agree with you.  @roni-saiba the immune system killing non-self cells is that issue we raised in the comments

@iayork a good answer indeed.


text:
What does a female mosquito need from blood?
I have come across many articles stating that female mosquitoes suck blood from vertebrate hosts to develop their eggs. Some also state that they need proteins, carbohydrates, iron etc., from human blood. But none of them (as far as I know) have stated what components exactly are needed from blood for their egg development. If proteins, what kind of proteins?

According to the Introduction to this paper:

Attractiveness to biting insects is important in medical contexts, mostly in the dynamics of transmission of pathogens by mosquitoes that cause diseases such as dengue and malaria. Blood feeding is an essential part of the lifecycle for most mosquito species as it provides females with the proteins necessary for egg production.

I imagine that the blood protein is simply a rich source of amino acids. This is supported by the finding that an artificial meal consisting of bovine serum albumin can support egg production in Aedes albopictus.
Update following answer from Greg Thatcher
Clearly there is evidence that iron from a blood meal reaches ovaries and eggs, although the paper doesn't provide direct evidence that this iron is essential. However this made me think more deeply about the paper that I cite above about feeding bovine serum albumin as an blood substitute. Could this have also supplied a significant amount of iron? The artificial meal was BSA dissolved in a phosphate-buffered saline. The authors don't specifically address the problem of iron contamination. The main component of PBS is NaCl. If they used AR-grade NaCl then the iron content will have been very low (0.0002% in one example that I found online). However BSA itself can bind metal cations (see here for example) so the protein may have contributed some iron. The authors do quote the source of the BSA that they used but I haven't been able to access a data sheet that might shed light on the level of iron contamination.
Of course it is entirely possible that blood is an essential source of both protein and iron.

What does a female mosquito need from blood?

This paper seems to indicate that iron is the most important ingredient.
To quote from the paper,

Among many nutrients in the blood meal, iron is required for optimal
  egg development and viable offspring

I would imagine that mosquitoes could get plenty of of proteins by feeding on other parts of the body or plants, but the blood of their chosen victims contains much iron, as hemoglobin requires iron to carry oxygen safely throughout the body.

+1 good find, but I'm not convinced by your suggestion for other sources of protein – aren't mosquitoes nectar feeders?

Certainly, mosquitoes get most of their protein from other sources, but the females need iron to produce eggs, and blood is a rich source of iron.  According to the virologists and  parasitologist I listen to on TWIV (http://www.microbe.tv/twiv/tag/mosquito/), it is the occasional female that bites two victims for her iron meal who then can spread various diseases.

Mosquitoes generally feed on plant nectar and fruit juice. Male mosquitoes do not take blood, so when you feel a mosquito plunge into your skin and start siphoning your blood, you can bet it is a female, every time.
female mosquitoes need nectar for nourishment, they also need protein to develop their eggs. That protein comes from your blood. Once they've gotten blood, the mosquitoes fly away to a warm, damp place to rest and wait for their eggs to develop. That takes up to five days. The females lay their eggs, and then move on to the next blood meal to feed the next batch of eggs.
Female mosquitoes can lay a set of up to 100 eggs about every third night after mating only once. They typically lay as many as three sets before dying.
Those eggs eventually hatch, and the whole mosquito life cycle starts over again.
This is what I got from :
tap here

Thanks for the reply. I agree that female mosquitoes suck blood for their  egg development. And, they need some proteins from blood. I'm just curious to know what kind of proteins are needed for egg development.


text:
Why is the prefrontal cortex called such?
Pre means before. Frontal means front.
What does cortex means? Brain?
Is it the front most part of the brain? Is it located at the most frontal part of the brain and that's why it's called prefrontal cortex?
Is morality processed at ventro medial pre frontal cortex or at anterior singular cortex?
My background: I am a programmer. I just want to understand humans brain the way a programmer understand computer. It seems that we don't have CPU. We have huge analog based memory. And we got registers instead of tons of abstract variables. Understanding why certain part of the brain is named under certain things will help me a lot in remembering where exactly that thing is and why. It's something very useful in my ways of learning math and programming.
Basically there are 2 theories.

Prefrontal cortex is named as such because it's before (or in front
of) prefrontal lobe.
It's because it's behind prefrontal bone (the
way other brain lobes are named)

Some people told me to just look that up on wikipedia. If you can show me something in wikipedia explaining the exact answer I am looking for I will be very happy.

It seems your question can largely be answered by reading the wikipedia article

I have read wikipedia article. Most contain info such as occipital lobe is named such because it's behind occipital bone. I got to dig a lot before I found what ob caput mean.

From the Wikipedia article: The term "prefrontal" as describing a part of the brain appears to have been introduced by Richard Owen in 1868.[6] For him, the prefrontal area was restricted to the anterior-most part of the frontal lobe (approximately corresponding to the frontal pole). It has been hypothesized that his choice of the term was based on the prefrontal bone present in most amphibians and reptiles.[6]

I think in general "cortex" means "outer layer", and it's used for many things besides the brain: https://en.wikipedia.org/wiki/Cortex_(anatomy)

Okay I didn't found it when I look for it. People got to read the whole article. Do you think this kind of question is appropriate? I am not a doctor. I just want to learn a lot because it fascinate me. I am a programmer.

You don't have to read the whole article. The contents directs you to a section called Etymology.

The prefrontal cortex (PFC) is a part of the frontal lobe (Fig. 1).
Lobe means

[A part] demarcated from the rest of the organ by a fissure (crack), sulcus (groove), connective tissue or simply by its shape. For example, there are the frontal, parietal, temporal, and occipital lobes of the brain.

Cortex means

The outer or superficial part of an organ or bodily structure (such as the kidney, adrenal gland, or cerebellum or a bone); especially: cerebral cortex

The frontal lobe is called as such, because... it's in the front of the brain.
The prefrontal cortex is called that way because it forms the frontmost part of the frontal cortex. Prefrontal means

anterior to or involving the anterior part of a frontal structure

Anterior meaning

situated before or toward the front

Indeed Siddiqui et al (2008) mention:

The anterior part of the frontal lobe referred in the literature as ‘pre’-frontal lobe has been simultaneously referred to as ‘frontal granular cortex’ and ‘frontal association cortex.’ The anterior most portion of the frontal lobe is occupied by the PFC...

Reference
- Siddiqui et al., Indian J Psychiatry (2008); 50(3): 202–8

Fig. 1. The frontal lobe includes the prefrontal cortex (PFC). source: Socratic

I think the term pre-frontal does not mean anatomically in the front of the frontal lobe of the brain. This is regarded to the history of discovered area , that the choice of the term was based on the prefrontal bone present in most amphibians and reptiles.you can find this in etymology part ▶enter link description here

Interesting. There is no prefrontal bone in humans.

Are you sure? got sources?

@J.Chang not in the human ,the prefrontal bone which is present in most amphibians and reptiles and this has been hypothesized for the choice of the term .

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


text:
Is my terminology for proteins correct?
Statement: Protein X consists of 20 amino acids.
Question 1: Is it necessary to write "Functional" Protein X or is it already implied, that it is functional?
Question 2: Referring to question #1 - Does "Active," "Functional", "Native", "Mature," and "Stable" all serve as the same as synonym?
Question 3: How would I refer to the 16th, 17th, 18th, 19th amino acids?
Option 1: AA-16 through AA 19
Option 2: (Subscript) A16A17A18A19
Option 3: The 16th through 19th amino acids ...

1) I don't think so. I would not assume functionality.
2) People may diverge a bit on the semantics, but here's what I would say (my background is more cell bio and structural bio than biochem or genetics).

Active - Has enzymatic or signalling activity (or some other functional capability). Often proteins have multiple activities, or different active sites, so activity should be with respect to a specific function.
Functional - I interpret this to mean has all of its native activities intact. (I don't take this to mean anything structurally). One could also use this as a synonym for active, especially for a specific functionality.
Native - I take this to mean the protein has not been altered from its form found in nature. This implies it is functional.
Mature - My natural feeling for this is that it means the protein is structurally mature, i.e. it has been folded properly, transported to the correct cellular compartment, post-translational modifications completed, etc... For a non-functional mutant protein, I would hesitate to call it mature though, even if it were not semantically incorrect.
Stable - I interpret this entirely structurally. i.e whether the protein has folded to an energetic minimum or their natural structural state (incl. proteins with disordered domains). People might say, though, that stable means it has a natural lifetime, i.e. the cellular environment or the enzymes present are not destroying it at an abnormal rate.

I'm not quite sure what (3) is asking; if you edit, maybe I can comment.


text:
Will a polyclonal antibody attach to proteins of different kDA?
If I have a GST 26kDa polyclonal antibody, will it bind to the GST 28kDa protein as well?

If the sequence of the 26 kDa form is included within the sequence of the 28 kDa form then the answer is 'probably yes'.
However if the N- or C-terminus of the short form is an important/dominant epitope and it is masked in the long form (by being extended) then the activity of the serum against the long form could be significantly reduced.

As Alan said, it depends but I'd guess that, yes, it probably does.
Given that you are using polyclonal antibodies against a not so dramatic extension, I'd say it's even more likely that you'll see signal. The various antibodies within the polyclonal mixture will bind different parts of the smaller protein, so unless the additional segment causes a dramatic change in shape or somehow blocks most of the binding sites, you should see binding.
I don't think you can directly compare binding signals between the different protein forms, but it should work for simple detection or purification


text:
Why do some trees flower year round, others only once
Depending on latitude, rains, and pollinator behavior, etc. some trees flower only once a year such as oak trees, others twice (such as pipe organ cati as a response to pollinating bats) and yet others continously such as figs (I believe, not sure).
However I noticed that arbutus unedo (straberry tree) has both immature flowers, mature flowers young fruit and ripe fruit on the tree at the same time. To mky knowlesge, fig tress in amazonia behave differently: the whole tree is roughly in the same state at once, either "flowering" developing fruit, bearing ripe fruit.
My question is what ecological role does Arbutus U. fill that it has this feature?


text:
Difference between autonomic and paratonic movements in plants
I can't understand the difference be because both involvery the main cause that is an external stimuli, so how do they differ(

its about the gene that is involved in autonomic movements. while, there is no gene involved in plants for paratonic movements.furthermore, autonomic movements are presents in plants by birth, and paratonic movements are induced in plants by an external stimuli only and not present in plants by birth.

There is no need to post a second answer to supplement a previous answer you gave. Instead, you can use the edit button of your previous answer.

In other words for autonomic movements the plants use an internal cause( simply indicating to gene) and external stimuli both. while, paratonic movemens use external cause only( light, temperature,gravity etc.Hope you understand


text:
Re-establishment of Hardy Weinberg Equilibrium After Selection
I have been given this question:

In a population of 2500 mice, light-colored fur is dominant to dark-colored fur. 2400 mice originally have light-colored fur. However, an owl species moves into their environment, preying mainly upon the light-colored mice as they are easier to spot when hunting at night. When the owls finally leave, 80% of the dark-colored mice are left, and only 10% of the light-colored mice. After many generations, Hardy-Weinberg equilibrium is re-established. Approximately what percentage of mice now have dark-colored fur?

Answer choices are:

A) 10%
B) 15%
C) 20%
D) 25%
E) 30%
F) 35%

My thought process goes as such:
When the owls leave, the groups are 240 light mice and 80 dark mice.
$q^2 + 2pq + p^2 = 1$
q is recessive allele, p is dominant allele.
$0.5^2 + 2*0.5*0.5 + 0.5^2 = 1$
Apply fitness:
$0.8*(0.5^2) + 0.1*(2*0.5*0.5) + 0.1*(0.5^2) = 0.275$
(0.8 and 0.1 correlate to the fitness of dark and light mice, respectively)
Now divide everything by 0.275 to figure out new allele frequencies:
$0.727 + 0.182 + 0.091 = 1$
This means that 0.727 = 73% is the new frequency for homozygous recessive (dark) mice.
However, the correct answer is B) 15%
Any idea what I did wrong/how the correct answer is achieved?

After many generations, Hardy-Weinberg equilibrium is re-established. This is a pretty awful sentence (not your fault). HW equilibrium is reached after in a single generation.

I agree it's not written well. But as long as it doesn't alter the meaning of the question... :)

Revised to add complete solution
Before the owls arrive, 100 out of the 2500 mice are dark-colored. This ratio provides the frequency of the recessive allele
$$q^2 = \frac{100}{2500}$$
So $q$ is 10/50 or 0.2. This means that the frequency of the dominant allele $p$ is 1 - 0.2 or 0.8.
Knowing these frequencies, it is possible to calculate the number of each allele
$$AA = (0.8)^2 \times 2500 = 1600$$
$$Aa = 2 (0.8) (0.2) \times 2500 = 800$$
$$aa = (0.2)^2 \times 2500 = 100$$
Of the light-colored mice, 2/3 are AA and 1/3 are Aa. The same proportions hold after the owls leave, but the total humber has been reduced. The dark-colored mice are all aa.
$$AA = \frac{2}{3} \times 240 = 160$$
$$Aa = \frac{1}{3} \times 240 = 80$$
$$aa = 80$$
From these values, the total number of each allele may be calculated
$$A = 2 \times 160 + 80 = 400$$
$$a = 80 + 2 \times 80 = 240$$
These numbers provide the frequency of each allele post-selection
$$p = \frac{400}{640} \approx 0.63$$
$$q = \frac{240}{640} \approx 0.37$$
Applying Hardy Weinberg for the new equilibrium
$$aa \approx (0.37)^2 \approx 0.14 $$
which is, "approximately" 15%.

0.8*(0.2^2) + 0.1*(20.20.8) + 0.1*(0.8^2) = 0.128. Dividing homozygous recessive (0.8*0.2^2 = 0.32) by 0.128 leads to a frequency after selection of 0.25 = 25%. That's still not the correct answer... unless the answer key is incorrect.

I'm sorry, but I don't understand what that calculation is supposed to be saying. I updated my answer with the complete solution.


text:
Why are there no WINGED flying arachnids?
There seem to have been no arachnids flying WITH WINGS of any sort at any location or any time in the present or in the fossil record.  Why is this?
Rationale for question :
If the process of evolution can be expected to explore all (or large numbers of) possibilities open for adaptation of any form, why has this never happened for arachnids which have been present on land in large numbers of species and individuals for about as long a time as insects?
Arachnids were among the first air-breathing terrestrial creatures so have had this option available for all this time, with apparently no sign of wings at all.
Winged flight offers major advantages to creatures that have evolved it, and has been evolved independently by many branches of the animal kingdom and apparently over relatively short timescales among those that have done this (e.g. bats have presumably evolved flight since the kT extinction of about 65 MY bp).
Flight is easier for smaller animals such as arachnids, as insects have shown, and insects have also shown that flight for small creatures is possible in oxygen levels at present, and levels have been much higher at times in the past.
N.B. !! We all know about spiders ballooning on silk ! This question is about WINGED flight. Please do not waste any of your time or ours on comments about ballooning ! That does not allow directed purposeful flight as wings do and is not a substitute adequate to account for this absence.

This isn't true on small scales: "evolution can be expected to explore all (or large numbers of) possibilities open for adaptation of any form".  If you take the entirety of natural history into account then you see incredible diversity and different ways of solving problems, but that doesn't mean every lineage gets to try out every solution. Because evolution is incremental and most mutations are bad, major changes to lineages happen rarely, for example flight's only evolved 4 times. Bats may have evolved it quickly, but they would have done so under specific circumstances.


text:
Can fish live in the dark completely?
I have got 6 pet fishes in an algae ridden  tank.  My plan is to place the tank completely away from sunlight so the algae dies.  How would this affect my fish?
Edit: Just checked all my fishes died today.  Either its the lack of light or just that i forgot to add the chlorine removal or water pump.

@Remi.b why would it be?  I just want to kill the algea not the fish

@Remi.b I don't disagree that this sounds ill-advised, but I am also curious what would make it actually illegal.

Probably depends on the kind of fish: there are some fish that live in the ocean depths, or in caves.  You might also ask whether the darkness would actually kill the algae, or just make it go dormant until the tank is placed in the light again.

Why not just get some snails to eat the algae?

Or clean the tank once in a while?

What kind of fish were they? Was there algal bloom?

Excessive algal bloom is normally because of sunlight and lots of iron/phosphate/chalk/ micronutrients in the water: tapwater that causes limescale... I lived in a house where the water caused massive algal blooms out of control. if you switch to rainwater on the contrary it keeps the water transparent for a long time. Try goldfish first. they are very tough. I had dead fish when i was young and later i kept puffer fish and exotic fish very easily by not keeping the aquarium like a child.

all you have to do to keep the water good in difficult times, is change half of the water and clean the water pump. dont use tap water unless it is very soft water (no limescale). the solution is to use good water, not to put your fish in the dark until the algea dies. and don't use anti-chlorine, use natural water which didn't have industrial treatments.

As noted fish live in the dark , to the extent that they no longer have eyes.As noted the algae will just go dormant until there is light. I use plants to compete with the algae for nutrients , works well. Algaecide is not a long term solution. I expect you could find some lights which have very little output in the frequencies/ spectrum needed by chlorophyll ( and block any sunlight) but you still have light to see the fish.

Fish can live in the dark completely however they will potentially have no source of food at most Algae cannot reproduce without sunlight.
Some new research has been conducted where algae can gain energy from other means apart from the sunlight including dim light from hydrothermal vents deep in the ocean. https://indianapublicmedia.org/amomentofscience/photosynthesis-without-sunlight/

There are lots of fish that live in environments without any light (below 1000m in the ocean there is no useful light for vision), however most aquarium fish have not evolved to live in those sorts of conditions. In the future, I think your best bet would be to remove the fish, clean the tank, and then try to manage your nutrient inputs so that the algae doesn't grow out of control.


text:
How Excessive masturbation can make a person unfit for army?
Recently I saw this news trending, I never heard single
disadvantage regarding masturbation.
But China Army considering it has danger for army.
So How Excessive masturbation can make a person unfit for army?

Maybe don't get your medical advice from the Chinese army.

Maybe step back a bit, and ask just what's an enlarged testicular vein, how it's detected, and (if such a thing actually exists) whether it is indeed caused by "excessive" masturbation?  Or maybe consider that it's just ignorant prejudice, like the Western ban on homosexuals that existed until fairly recently.

Well, using some common sense I'm pretty sure the reason is that a soldier who is busy masturbating won't be a good soldier. It's the same with any kind of addiction, causing the person to not perform the tasks they're supposed to do.


text:
Free online image libraries of trachoma
I'm looking for an online source with images of the eye disease trachoma. I'm looking preferably for resources from a credible source that have images from each stage of the disease.

According to wikipedia there are two different way to distinguish stage of the disease. One is from McCallan and one from the World health organisation (WHO). For the second one, on WHO website, you can find their grading card with eyes images. You can download it with also a little description.
Hope it helps.


text:
Why do earthworms surface after a rain?
Googling, I find two different explanations for why earthworms tend to surface after a rain.
This page from UCSB, for example, gives both answers, contradicting itself:
The first explanation is that worms can breathe fine when it's wet underground, but surface after rain because it's their only chance to surface without drying out:

Worms, like all other animals need to breathe, but since worms do not have mouths, they have a different way they breathe. Worms breathe directly through their skin, but they can only do so if their skin remains moist. Deep down in the soil, where worms typically live, it is normally moister than the surface. For this reason, worms prefer to live underground. After it rains, the surface becomes wet enough to support worm life, so they can come above ground to explore new areas more quickly. Fun fact: worms actually don’t come above ground after it rains to avoid drowning. Earthworms can live underwater for approximately two weeks. Thank you very much for your question!

The second answer is that worms drown if they stay under ground after a rain

Worms are animals and, like you and me, they require oxygen to live. Instead of breathing air though their mouth into lungs, worms absorb oxygen from the air across their skin. Worms eat dirt. They burrow into the soil and normally live underground, where they are protected from the sun and so won't dry out. If you've ever played in the dirt by digging holes, you probably noticed that there are small holes or tiny pockets of air. The worms use that air, and the air that enters through their burrow holes, to breathe. When it rains and the dirt absorbs a lot of water, those air holes disappear, and the worms' burrows fill with water. If the worms do not come to the surface during a heavy rain, they will suffocate. Likewise, if they do not return to the soil after the sun comes out, they will dry out and die.

Which of these two is correct?

It looks like certain species of earthworms need to surface because they have higher oxygen consumption, while other species do not need to surface because of their lower consumption.
In particular, specimens of Amynthas gracilis were found to have low water tolerance, hence they

crawl out of the waterlogged soil, especially at night when their oxygen consumption increases

while Pontoscolex corethrurus

survived longer under water and was never observed to crawl out of the
  soil after heavy rain

Role of diurnal rhythm of oxygen consumption in emergence from soil at night after heavy rain by earthworms

Indeed annelids breathe through their skin, which needs to remain moist, but not immersed underwater. A thin layer of moisture is required for oxygen, CO2 to exchange. If totally immersed there is typically not enough oxygen in the water to support the rate of respiration required and they will literally drown.
The reason they surface after a rain is because the soil becomes saturated with water, again they will drown.

This answer needs authoritative references.


text:
Is there a difference between sleeping late and waking up late vs sleeping early and waking up early?
For example, if I sleep at 1 AM and wake up at 10 AM, will it negatively affect my health opposed to sleeping at 10 PM and waking up at 7 AM?

To add onto Louis' answer briefly, there are a lot of factors at play in this question. The way your own circadian rhythm has been set will play a role - any change away from your normal routine will be met with stress. Also, other factors like eating times and light cues that normally affect waking time will play a role in determining whether either of those schedules will impact your health. Hopefully someone more knowledgeable than me can provide a more complete answer.

In short: yes, absolutely there's a difference. Currently I'm at work, but when I get home I'll hopefully be free to provide a sufficient response to this. What @Shafter eludes to though, is accurate, and is similar to the basis that I'll be utilizing in my answer.

There is a popular theory that each person has a certain "chronotype" [Ref 1]. Based on your genetics, you could be naturally an early person ("Lark") or a late person ("Owl") [Ref. 2].  What will negatively affect your health is actually fighting what you naturally are.  You probably know which chronotype you are, and if not you can go by what time you naturally sleep/wake when you don't have school/job scheduling such as at the weekend.
[Ref. 1]:Chronotype Review
[Ref. 2]:Social jetlag paper

Welcome to Biology SE! Could you please add references to your claims? Answers without references maybe challenged or deleted. For more information please have a look at our how to answer guide.

Note there is also evidence chronotype can change with age. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5479630/


text:
Can yeast ferment maltose directly?
I have been taught that yeast can act only on simple sugars (monosaccharides) and breaks them down into ethanol and CO2
I also know that yeast can break down maltose (disaccharide) and maltotriose (trisaccharide) using maltase from its enzyme complex (zymase) into monosaccharides of glucose and then ferments the same.
My question is whether yeast can directly ferment maltose and maltriose WITHOUT first breaking them down into glucose?  If so how is it done - enzymatically and what is the chemical equation

The statement in your first paragraph is correct: for yeast to ferment a carbohydrate it must be fed into the glycolytic pathway which, in the case of oligomers of glucose (e.g. mannose) simply means breaking the oligomer into its constituent glucose monomers using a single enzyme. This is similar to how yeast processes sucrose: the disaccharide is hydrolysed by invertase to release glucose (fed directly into glycolysis) and fructose (fed into glycolysis via fructokinase).
A separate mannose pathway would require a completely new set of enzymes that somehow processed mannose in a stepwise fashion without breaking the glycosidic bond linking the two monomers - I'm sure that you can see that this is a much less likely option in terms of the evolution of yeast metabolism.


text:
Why does asbestos cause cancer?
We are probably all familiar with the dangers of asbestos in your rooftop or in various pieces of old equipment as it has been shown that the microscopic asbestos particles reach our lungs and can then potentially cause lung cancer.
Now smoking (for example) can cause cancer because of various carcinogens chemically interacting with DNA, but how can these asbestos particles, specifically prized for being quite unreactive, damage DNA to the point of triggering cancer?

I don't have time to look this up right now, but I think the particles stay in the lung for quite some time and physically damage the cells there - the resulting necessary increased regeneration increases the likelihood of mutations and therefore cancer occurring.

More basic answer; the asbestos crystals have hooks. So the cilia in the lungs have difficulty moving them out with the other dust. This irritates the tissue causing the effects of the first answer. So it is a matter of time and number of asbestos particles that increases the probability of a cancer. Decades ago , the asbestos miners in Africa typically worked for years ( eg 20 years) before getting cancer.

There are basically three hypotheses regarding the pathogenesis of asbestos-induced cancer , which may be summarized as follows:
(1) the "oxidative stress theory" is based on the fact that phagocytic cells that engulf asbestos fibers produce large amounts of free radicals due to their inability to digest the fibers, and epidemiological studies indicating that iron-containing asbestos fibers appear more carcinogenic;
(2) the "chromosome tangling theory" postulates that asbestos fibers damage chromosomes when cells divide; and
(3) the "theory of adsorption of many specific proteins as well as carcinogenic molecules" states that asbestos fibers in vivo concentrate proteins or chemicals including the components of cigarette smoke.
Source

Please add some references to your answer.

@AkramQaasim Feel free to check the edit. Please don't copy paste from the source.

@JM97 sorry for that .but i copied the only question related answer just for shortcut the source . Thanks


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Need help identifying this wasp/hornet
I am currently on holiday in southern France and have noticed that the house we are staying in has somewhat of a hornet/wasp problem.
Is there anybody that can help in identifying it? My best guess is a European Hornet but I'm no expert so may be wrong.
Below are some pictures. Sorry they couldn't have been of any clearer quality, they were taken through a window, and I didn't particularly feel like going out to get any closer because I've heard that some hornets can be quite aggressive even if unprovoked.
From what I saw, it has visible fur, and is around 2cm in length. The feature that led me to it being a Hornet is that the waist gets smaller before the abdomen.

This looks like a European hornet Vespa crabro to me. Wasp-like appearance, red on head and thorax and base of the abdomen. And the legs are red/dark, not yellow.

Picture from wikipedia
Hornets can be aggressive, especially if you come near the nest. Usually, European hornets are actually not really interested in people (unlike other wasps). But if there are many around your house, it is likely the nest is near, so be careful and perhaps contact the owner of the house.

Ahh thank you! We just found their nest in the roof of the house we're staying in for the week. I've just been reading about the social behaviour of wasps/hornets. Fascinating! We'll leave them be, no need to antagonise. Thanks again

It is quite possible that what you are dealing with are Asian Hornets.
This is a link to an article that helped me answer your question.
http://www.telegraph.co.uk/news/worldnews/europe/france/6049302/Tourists-warned-as-Asian-hornets-terrorise-French.html

Welcome to Bio. Link-only answers are considered to be comments rather than answers. Look here to a good answer on a similar question. It includes a description of the species, a photograph taken from your source and perhaps additional information.

The link you shared explicitely says it is recognizable by its yellow legs and the picture shows a wasp with red on the abdomen. So Asian hornet? I don't think so.


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Pyruvate as a final electron acceptor in the electron transport chain
During anaerobic respiration, why are electrons carried by NADH not transferred to the electron transport chain (ETC)? What happens is that lactate dehydrogenase reduces pyruvate to lactate, while removing H+ from NADH to form NAD+.

Why doesn’t pyruvate simply take the place of O2 as the final electron acceptor in the ETC during oxidative phosphorylation? Electrons would still be able to flow through the ETC and allow for the regeneration of NAD+, wouldn't they?

Someone else may come along later with a definitive answer but I found this question intriguing so here are my thoughts:
The standard redox potentials of the mitochondrial ETC carriers are:
NAD⁺/NADH              -0.32 V
complex I (Fe-S)       -0.27 V
complex II (cyt b₅₆₀)  -0.08 V
complex III ((cyt c₁)  +0.23 V
complex IV (cyt a₃)    +0.38 V
O₂/H₂O                 +0.82 V

Note that electron transport is carried out from negative to positive.
Now, for pyruvate/lactate the standard redox potential is -0.19 V so on the basis of this pyruvate could in theory accept electrons from complex I, but not any further down the chain. However, complex I normally transfers electrons to coenzyme Q within the membrane. The standard redox potential of CoQ is +0.04 V which is already too positive to be able to then reduce pyruvate at the membrane surface. Thus there would have to be a novel way of transferring electrons from the final FeS centre of complex I, which is within the membrane, to pyruvate. Pyruvate is, of course, soluble and is generated by cytoplasmic glycolysis, so this transfer would have be at the membrane surface that faces the intermembrane space of the mitochondria.
If such a scheme had evolved then it might be possible to achieve some proton pumping through the novel version of complex I, which would be  energetically advantageous.
Another complication is – assuming that a complex I with pyruvate as electron acceptor had evolved – how would the cell/ mitochondrion regulate electron flow during aerobic respiration? Presumably the pyruvate-accepting version of complex I would have to be kept inactive somehow until needed.
Clearly it is much simpler to have a soluble lactate dehydrogenase to deal with the pyruvate and regenerate NAD⁺.

Summary Answer
In anaerobic respiration the free energy change of the reoxidation of NADH by pyruvate is less than would be required to phosphorylate a molecule of ADP to ATP. The purpose of  the electron transport chain is to harness the much greater free energy change in the oxidation of NADH by molecular oxygen. So pyruvate can neither “take the place of O2 as the final electron acceptor”, nor would there be any point in modifying this complex machinery just so that it could be used by pyruvate to regenerate NAD+ when a single cytoplasmic enzyme (lactate dehydrogenase) will do the job.
More detailed numerical answer
This answer is taken from section 18.2 of Berg et al. and involves calculations of free energy changes from the redox potentials of the different half reactions and their relationship to the free energy of hydrolysis of ATP. It is worth careful reading, but I will summarize the key points.

Both pyruvate and oxygen can oxidize NADH, but the concomitant Standard Gibbs Free Energy change is very different in the two cases. This is the crux of the matter.
The standard redox potential for NADH → NAD+ is +0.32 V
The standard redox potential for Pyruvate → Lactate is –0.19 V
The standard redox potential for O2 →  H2O is +0.82

Combining these half-reaction redox potentials in the two oxidation reactions and then converting to standard free energy change (ΔG˚ʹ):

Oxidation of NADH by Pyruvate: ΔG˚ʹ = –6.0 kcal/mol
Oxidation of NADH by Oxygen: ΔG˚ʹ = –52.6 kcal/mol

But ΔG˚ʹ for ADP → ATP = –7.5 kcal/mol
So it can be seen that the energetics of the oxidation of NADH by pyruvate do not yield enough energy to synthesize even a molecule of ATP, never mind the approx. 3 that are obtained from oxygen. The electron transport chain is a device for breaking up this latter oxidation reaction into stages so that the free energy change can be used for generating the proton gradient that is used to generate ATP. It can only work with a powerful enough oxidizing agent.
The oxidation of NADH by pyruvate is useful, but only to regenerate NAD+ to allow glycolysis to continue and generate a smaller amount of ATP by substrate-level phosphorylation made possible by the glyceraldehyde 3-phosphate dehydrogenase reaction. For this oxidation only a simple enzyme, lactate dehydrogenase is required. There is certainly no reason to transport the pyruvate into the mitochondria (assuming they exist — think erythrocytes), which process, though incompletely understood, may well have an energetic cost.

It would be nice if the person who voted my answer down explained why, especially as it is correct. Can't handle numbers or thermodynamics, perhaps?


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Is most of the human genome functionless “junk DNA”?
In January 2012, David Icke published a book (ISBN: 9780955997334) entitled “Remember where you are and where you come from” in which he challenged what he claimed to be the view of mainstream science that 90–97% of the human genome was “junk DNA”, serving no function. He implied, instead, that it must have a function, but that this was unknown.
Is it still true that we do not know what all this DNA does? I see that we consider this DNA to be non-coding, but does that mean it is “junk”? I find it hard to believe that it can serve no function, otherwise why would the DNA be there? Is it possible that it is used for things we don't yet understand?

This question contains more info on what non-coding DNA is, but I think Remi has answered whether or not Icke's claim is right.

@David that's reasonable, but i voted to leave this open and downvoted. I think the reference to Icke's book as the thing that sparked the question, and the actual question (what is junk DNA and do we know what it does) is on topic (general questions about biological concepts). The question could be improved by removing the reference to the book by a professional conspiracy theorist, since it distracts from the actual question about biology.

I’d check whether there are any other questions on junk DNA. Otherwise edit the question drastically so that it deserves an answer.

"Junk DNA" is no longer used. This term originated a long time back when the function of the non-genic/intergenic DNA was not known. I'm not sure which "mainstream science" is he talking about!

I couldn't find a suitable previous question on junk DNA so I have rewritten the question. I would suggest answers address what has been discovered in the last seven years since the book was written.

I'm going to urge people not to respond to this unless they are actually working in the field. I don't know of any field in science to which the Dunning-Kruger effect applies more. If you are confident you understand this field, you almost certainly do not. There is a large and highly focused literature on this, and almost no one outside the field even knows the field exists, let alone has read any of the papers in it. If you have not read at least 100 papers specifically on the topic, your answer will be wrong and misleading.

@David I think your edit to the title implies that it was once thought that "junk DNA" is functionless; it's possible that's the case, but not to my knowledge. Unless you have a reference that in fact junk DNA was thought to be functionless at some point, I think the previous edited title "Does "junk DNA" serve no function?" is much better.

@BryanKrause — I think it better not to use a form of words that implies acceptance of the term. How about "Has most of human DNA no function?" and reference the following: http://www.junkdna.com/ohno.html?

@David What do you think of my compromise edit to the title? I think it's roughly between what each of us are suggesting.

@BryanKrause Fine. I'll add a link to the Ohno paper etc. in the question to give it a little context.

What is junk DNA?
The term junk DNA is not used that often in the scientific literature and when it is it is often used very generally, often early in the introduction. It generally refers to any non-coding DNA.
In humans, about 25% of the non-coding DNA is introns and regulatory sequences. These sequences are highly essential for the working of the organism. There are many cases of adaptation from these regulatory sequences (see this answer).
The term junk DNA is very loaded and may make it feel to people that this DNA is not important for the organism survival but this is not quite what was first meant by the term junk DNA. It is true though that repeated DNA such as those in  transposable elements are thought to have little impact on the organism phenotype. Transposable elements can however have important role on the evolution of a lineage.
IMO, the claim is false and insulting
By saying things like They do this because they gave no idea what it does and, from their version of reality, it appears to serve no function., it feels to me that David Icke is using the loaded side of the term junk DNA to insult all geneticist in general.
D. Icke is 1) doing a strawman by suggesting that geneticists think that regulatory sequences are of no use and 2) he is suggesting that geneticists are biased and will invent whatever theory in order to match with a pre-conceived opinion of the reality.
About David Icke
I don't mean to make an intentional fallacy but I would like to note that David Icke is a famous conspiracy theorist who has been illogical and obviously opinion based many times. For example David Icke claims that the moon is actually a spaceship and not a natural satellite (see here). He has made many other fantastic claims of the kind. Scroll down the wikipedia article to enjoy some non-sense!

I know a lot about Icke's material. Some is spot on and some is sketchy, but I don't think ad hominem ever discredits an argument so it's probably best to removed the last paragraph.

You say it's 5-10% that's regulatory in the other answer, which I think is more accurate

Remi.b’s last paragraph is neither an ad hominem towards Icke nor should be deleted. Icke’s scientific illiteracy is relevant to conclude that he’s in no position to criticize scientific consensus (but in this case, the consensus of "junk DNA" has been invented). Many of his claims are extraordinary and the evidence provided leaves much to be desired, so what he says has to be taken with a grain of salt. For example, he believes in “monoatomic gold”, a very problematic concept on its own (https://rationalwiki.org/wiki/ORMUS).

The term "junk DNA" is not commonly used any more by scientists. It became popular when people realized, that only 1-2% of the human genome encode proteins, and wondered about why there is so much more DNA if it's not needed. But we know today, that it does in fact serve many functions and therefore is now referred to as "non-coding DNA".
Some non-coding DNA functions:

regulatory elements: promoters, enhancers or silencers are DNA regions, where transcription or other binding factors bind to DNA to regulate the accessibility of genes to the transcription machinery and therefore control which genes are expressed
introns: DNA regions that are inserted into the actual coding region and removed during splicing. They serve a role in RNA processing and alternative splicing.
functional RNA: Not being translated into a protein doesn't mean that the RNA produced by a locus doesn't serve a function in the cell (e.g. ribosomal RNAs, microRNAs)
structural elements: telomeres and centromeres are important for chromosome stability, sister chromatid linkage, heterochromatin formation and anchoring to the nuclear envelope

We keep learning more and more about different functions of DNA regions. Even open reading frames (ORFs), which encode for functional RNAs or even small proteins keep being identified. It's therefore not true that it does not serve any function, because we have identified many functions. And while we still don't know everything about it, our knowledge is increasing.
Further reading:
Shanmugam et al. 2017 - Non-coding DNA – a brief review
NIH Genetic Home Reference - What is non-coding DNA?
Wikipedia - Non-coding DNA

How much of the 90-97% do you think the points you mention cover? The only point that is really new this century is "functional RNA". It may be true that "we keep learning more", but that hardly answers the question.

On the other hand large segments of non-coding DNA have been removed from mice with no apparent affect on their phenotype. It's a complex topic that is far from settled.

@David: The question was if if non-coding DNA is junk and has no function as put forward by the quote from David Icke that you edited out of the question, which also implied that scientists don't seem to be interested in it, just calling it junk. That's not true, since we have discovered functions for a number of non-coding elements. There might be even more that we haven't figured out yet. Effects might be less direct (e.g. evolutionary, as mentioned in the answer by Remi.b), but scientist keep working on it.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5570035/


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Is genetic purging based on random shuffling of the genes of an individual or is it more intentional way of removing deleterious recessive alleles?
Inbreeding depression may be reduced by selection against deleterious alleles, which eliminates, or purges, them from the population. I have two questions:

Is genetic purging based on random shuffling of the genes of an individual or is it more intentional way of removing deleterious recessive alleles?
Do the individuals/couple with deleterious alleles that breed together, pass down the purged genes EACH AND EVERY TIME they produce offspring? Does it happen every time they mate or just some times?

Your terminology is a bit off: especially 'genetic purging' can easily be understood in a very negative way, and I'm not sure you are using inbreeding in the correct way. Otherwise reading up on how genetic inheritance works should help you to answer your question (which is very broad and doesn't really have one general answer).

Check out the Chillingham cattle. They were sectioned off in the 1200s and no new outsiders have been introduced in 300 years.

Is genetic purging based on random shuffling of the genes of an individual or is it more intentional way of removing deleterious recessive alleles?

There is no intention in evolution. Purging refer to the action of selection at removing deleterious alleles. This term is specifically used when a population goes through a demographic change under which purifying selection becomes more efficient (such as an increase in inbreeding coefficient).

Do the individuals/couple with deleterious alleles that breed together, pass down the purged genes EACH AND EVERY TIME they produce offspring? Does it happen every time they mate or just some times?

Purging is a population-level process so your second question does not make much sense
Rephrasing the above a bit differently, purging refers to the reduction in frequency of deleterious alleles in the populations. Individuals will transmit whatever allele they can transmit.


text:
Plant identification - variegated ivy-like
What plant is this? It's in the UK, grown in a pot, and looks like a variegated ivy.
Leaves are about 2 cm in diameter, and the full plant about 50 cm.

Found an answer myself, so here it is.
This is Ceropegia linearis ssp. woodii, also known as hearts on a string or hearts entangled.
More information about the plant can be found at https://www.rhs.org.uk/plants/details?plantid=5862


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How fast can the human body temperature change?
I'm really curious about how fast can a human body temperature change?
E.g. how fast can the human body temperature change when the human has fever?
I'm not interested in how fast fever changes the temperature, more likely how fast the human body is possible to change it?
I found allot information about how much the temperature changes over the day and so on, but now how fast the human body is "capable" to change it in a certain time span.

This depends on a lot of things. It's pretty slow if you are limiting the change to be entirely internal. If we get help from environmental extremes though, the change can be quite rapid.


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Why does the posterior region and the right ventricle of the heart are not well represented in standard 12 leads?
When assessing an ECG we divide our 12-lead into four main contiguous lead groups: inferior, lateral, septal, and anterior. Regions not well represented on a standard 12-lead are the posterior region and the right ventricle, So if there is an infarction in these regions how we can determine it ?

The answer should have source or reference and not the question and this is known in ECG that lead l , aVL,V5 & V6 looking for lateral region of heart ...ect as shown in photo above.


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How likely will 2 normal bacteria "attack" each other if they infect the same parts of your body?
I read this interesting article online about how deadly bacteria are known to attack other deadly strains of bacteria.
https://www.google.com.sg/amp/s/phys.org/news/2013-02-deadly-bacteria-remarkable-precision.amp
I am wondering how normal bacteria that infect us like those that cause strep  throat and so on also have the capabilities to attack other bacteria and how feasible it is to use this as a treatment for bacteria infections by introducing harmless strains od bacteria to fight pathogenic versions (maybe like probiotics?)

Mixed bacterial populations, where not engaged in some kind of mutual or commensalistic relationship, are constantly at each others throats over resources. Even then, sometimes it's just rate of growth isn't terribly bad for each commensal. Not just nutrients, for example, but also precious space to colonize or attach to. There's a good review here, and among some of the tactics direct killing by antimicrobial production is an option. You also have other factors, however, such as secretion of molecules that impair attachment or quorum sensing. Also, virulence factors that give a competitive edge such as evading immunosurveillance (encapsulated B. anthracis strains vs unencapsulated, for example).
So here's the hard part: you want to engineer an attenuated bacterium that goes in and attacks a pathogenic strain. While I'm sure possible, you would certainly need to ensure that what you take away to attenuate your strain doesn't gimp it in vivo. You also need to realize that your target pathogen is very capable of simply "changing" itself to avoid dying to the engineered strain. Once your mechanism of action has been defeated, your product has been defeated. I think that it's fundamentally different from commercial virus-based products like T-VEC, as well, due to the level of variability.
One of my thoughts is your strain needs to be able to compete with the pathogen in the first place to stand a chance, which may be difficult if you cut out too many virulence factors trying to make it "safe."


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Is oxygen a respiratory substrate
I know that carbohydrates such as glucose are respiratory substrates for cellular respiration, but in this process, oxygen is also used to produce ATP so is it also a respiratory substrate?

I don't know if I've ever heard the term "respiratory substrate" before. But, I've said it many times on stackexchange, so I guess I'll say it once more.. I hate semantics. And, I really do not see the importance in being able to define something by some arbitrary human idea. So, what is important?.. What is important is that you know what everything, as a single entity, does on its own. Can you tell me what the function of oxygen is in the body? What happens to it? Where does it go?

By the way.. Welcome to stack exchange! Here's a link to a nice overview of what we're all about

You must explain what you understand the term "respiratory substrate" to mean if you know glucose is one. Also respiratory, in a biochemical sense. Then we can answer your question, but by that time you should be able to answer it yourself.


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What is the function of cystine, cysteine, and cysteine protease?
I am not a biologist, and I have a probably dumb biological question. For some purpose, I need to understand the function of the CTNS gene, and here is the definition of it:
"This gene encodes a seven-transmembrane domain protein that functions to transport cystine out of lysosomes.
I did not know what cystine is, and when I checked Wikipedia, I see that "Cystine is the oxidized dimer form of the amino acid cysteine."
What I understand is lysosomes digest a bigger peptide, and cystine is created as a result, and it is taken out of lysosomes by the enzyme produced thanks to the gene CTNS. My question is, where does cystine go and what is it used for after leaving lysosomes? And is it ever broken further into monomers of cysteine?
I also read about a term "cysteine protease". What is its relation to cystine?

I'm not sure as to what level of detail I should answer this question, but I will try to give you as much information as I can that I think will be relevant to.. whatever it is you are doing.
Cysteine proteases
Are a class of enzymes that degrade proteins, and utilise cysteine-residues as part of their catalytic mechanism.
Cystine
Is, as you said, a cysteine-dimer.. Which basically means two cysteines stuck together.
These are often formed in the intermediate steps of a cysteine protease's catalytic mechanism.
But also, during protein degradation within the lysosome, cystine can be released as a free molecule. When this happens, it will be transported in to the cytoplasm, to be processed via anabolic pathways into various products, such as glutathione (an antioxidant).

So, basically, the function of your seven-transmembrane (7TM) transporter protein is:
To make accessible to the cell, the digested products of proteins (or, amino acids).

Cystine is an amino acid. Cysteine is also an amino acid. These can all be used by a cell to create new molecules, such as proteins, or antioxidants, or vitamins or cofactors, etc., so many things. And can indeed be broken down in to cysteine.
The function of the CTNS gene, is to provide the cell with the genetic information used to synthesise the 7TM-transporter protein.

Thank you very much for the reply. Two followup questions: 1) When you say "To make accessible to the cell, the digested products of proteins (or, amino acids)", you mean specifically cysteine (or cystine), right? Other aminoacids are made accessible to the cell by other transporters? 2) When you say "Cysteine proteases are a class of enzymes that degrade proteins", do you mean "degrade any protein", or are specific type of proteins degraded by specific enzymes?

Based on the structure of cystine, I would guess that this particular transporter is quite specific to cystine.. But I honestly am not sure. Sorry, I usually try to do some research before answering questions on here since I do not actually know a whole lot about all of the questions that I answer.. but since it didn't appear that this would be needed of me, I did not do this before answering this time.

Cystein proteases are enzymes that degrade proteins. A good example of this would be papain - which comes from papaya. Often used as a meat tenderiser. And, also found in pineapple juice - if you were to take a steak and put a few drops of pineapple juice on it, and then leave it for a while, you would come back to find the steak a gooey mess of "mush".. for lack of a better term.

Thanks! One more dumb question: If cystein proteases degrade any protein, why is there a specific "cysteine" in the name, given cysteine is a specific aminoacid? Sorry that those may look like random questions, but they are in fact not. There is a paper titled "Cysteine protease inhibitors effectively reduce in vivo levels of brain beta-amyloid related to Alzheimer's disease", and I am trying to make clear the potential relation of cysteine and amyloid beta in my mind.

Well, as I said, "Cysteine proteases ... utilise cysteine-residues as part of their catalytic mechanism." Proteases are proteins! =D And proteins are made up of amino-acid-residues.. So basically, the cysteine residues are the amino acids within the protease that are responsible for catalysis. Another way to say this is: "Cysteine proteases utilize cysteine as their catalytic residues".....Does this make more sense?

And.. ohhh! I wish you had posted the paper title before I went off rambling. I think I've read this paper before, I would have related my answer to better suit this. (Do this next time). I assumed the reason you had said "For some purpose" was due to confidentiality-agreement reasons.

OMG, this is too complicated for a computer scientist! :) But yes, it makes more sense now. I was thinking that when cysteine proteases are used to break down the protein, then the product is cystine, but now I understand that this is not the case at all. The product of breakdown can be any aminoacid which would be used further for cell's purposes.

Let us continue this discussion in chat.

The cytosol is maintained as a reducing environment and so disulfides are readily broken. The resulting cysteine can then be metabolised in a number of pathways: