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How to increase pheomelanin production?
How can you increase the pheomelanin production in your body, while decreasing the eumelanin production? In other words, shifting the balance towards pheomelanin.
From what I see, sulfur and cysteine can help with this. MSM and glutathione caps can be a good way to do this, since these are used for skin lightening.
But is there another way? Something more scientific? Like deactivating the MC1R? Is that even possible?
Thank you!

Since Eumelanin is the protective form of melanin and there is some research available that Pheomelanin contributes to the generation of reactive oxygen species which are harmful to the cell (see reference 1, which contains a lot of further references on this topic), I don't see any reason to do so, but ok. Additionally removing Eumelanin from your skin will lead to a higher risk for skin cancers as Melanoma. Let's think through this:
If we look at the biosynthesis pathway of the Melanins, they both start with the same two reactions (see the figure from here):

The routs parts at the DOPAquinone, which in the presence of Gluthathione or Cysteine goes into the pheomelanin direction. The concentration of Cysteine available to the cell needs to be higher than 0,76 µM (see references 2 and 3 for details), otherwise the reaction goes exclusively into the Eumelanin direction.
There are some skin whitening (or better lightening) products available which contain L-Cysteine or GSH. This will work to some extend, but once the level drops enough, the ratio will shift back to the more natural ratio between Eumelanin and Pheomelanin. There is also no data available on the risks of doing this, so I would strongly advocate against it. See the review in reference 4 for details and additional references on this topic.
If you now think, ok, taking some pills is enough, I would call this a false hope, since this process is highly regulated. This happens on one part through external signaling through the MC1R receptor (which as you already mentioned is of importance here) and also through the availability of key enzymes in the process as well as stability of them and their regulation.
Signaling through the MC1R receptor is highly important for pigmentation and also the amount of enzymes available (the transcription factor MITF is regulated by it). If the signaling is strong, the cysteine storage is soon depleted bringing on the production of Eumelanin. If this signaling is weak
this will not happen and the production of pheomelanin is favoured. Mutations in MC1R are the reason for people having red hair and and fair skin. See reference 5 and 6.
Interfering with the signaling cascade which is activated by MC1R is certainly not a good idea either, since this will interfere with other processes in the cell as well. These pathways are also disregulated in cancers, so I would not touch these.
Summarizing I think there will only be a way of influencing this by taking some supplements, but how safe this is, is unknown. All the other possible ways are certainly more dangerous.
References:

How does pheomelanin synthesis contribute to melanomagenesis?: Two
distinct mechanisms could explain the carcinogenicity of pheomelanin
synthesis.
Rate constants for the first two chemical steps of eumelanogenesis.
Chemistry of mixed melanogenesis--pivotal roles of dopaquinone.
Systemic skin whitening/lightening agents: What is the evidence?
UV signaling pathways within the skin
The melanocortin-1 receptor: red hair and beyond.

Thanks for clearing that up!That figure surely makes things more simple.So basically the only effective solution would be interfering with the MC1R signalling.I am not talking about completely screwing it up,but making it slightly/moderately less effective.IN THEORY,how can this be done? About supplements:what would you consider effective?Vitamin C,glutathione and MSM?Or basically any form of cysteine and sulfur? My main goal is to reduce brown/black (eu)melanin and the best way to accomplish this seems by increasing/shifting towards pheomelanin production.

But I have found other approaches as well.One main approach which stood out to me is inhibiting the tyrosinase activity.For this there is a list of tyrosinase inhibitors,but two stood out to me especially: ZINC SULPHATE and CAPTOPRIL.I will attach links to the studies.What do you think about this approach of reducing (eu)melanin? And the third approach I came across was directly inhibiting melanogenesis.Messing with MSH by using MSH inhibiting drugs/supplements,like melanostatin or resveratrol. What do you think,which one of these is the most effective,and respectively the safest?

The links:Zinc sulphate: http://www.ncbi.nlm.nih.gov/pubmed/16792750 Captopril  & other tyrosinase inhibitors: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2705500/ MSH inhibitor: https://en.wikipedia.org/wiki/Melanocyte-inhibiting_factor alpha-MSH inhibitor: http://www.hindawi.com/journals/ecam/2013/632121/    As you can see,I have done a little bit of research on this,but there is quite a mess in my head since I don't know which route would be more effective.I am looking for OVERALL reduction of black/brown (eu)melanin,and I don't care if this is achieved by pheomelanin increase or other ways

It sounds like you're planning to experiment on yourself. This community is not for medical advice, although I'd strongly advise against self-experimentation.

Also, the second two papers from your comment are from publishers accused/suspected of predatory or unscrupulous publishing (MDPI, Hindawi). Frankly I don't know anything about the science in these two papers but that was an immediate red flag for me when I opened them.

@Luigi Scientifically these are ok - also I have no personal problem with Hindawi. I think Frontier Science is worse...


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Purifying large amounts of PCR product
I have had trouble purifying very large quantities of pure PCR product. We are using these as templates for the reconstitution of nucleosomes and I require hundreds of micrograms to milligrams of template.
Here are some methods I have tried:
1) QiaexII slurry--typically I use the entire slurry for one purification then regenerate the resin by washing in 1M HCl then re-equilibrating with water. This way has worked best for me so far but the yield tends to be fairly low (~100 ug from 100 PCR reactions).
2) Phenol-chloroform extraction. This method seemed to work great, however I believe I have phenol contamination at the end--the yields are often much higher than they should be even if I chloroform back extract before the ethanol precipitation. When I run it out on a gel it looks like the apparent concentration I get is off. I have not tried this too many times so perhaps it could be optimized.
3) Spin column purification. I've used the DNA Clean and Concentrator from Zymo and the yields seemed quite low, even for the columns with an apparent 100 ug capacity.
Another option I have explored is large scale purification of the parent plasmid followed by digestion to liberate the small insert. However I still run into the issue of purifying away the parent plasmid. I've seen a few protocols using FPLC and/or size exclusion but I'm not sure how effective this would be.
Anyone have any ideas?

We had to do this frequently. What I would first recognize is that all of your current methods only work for at the small scale and that for you to purify mg quantities of DNA, you need to work with mg scale equipment.
First of all, you should examine your "upstream" process. Are you doing your PCR at scale? Typically, we have scaled out by going with multiple PCR reactions rather than one large PCR reaction. Generally the reactions max out at 50uL depending on your thermocycler. If you're getting around 1ug/10uL, scale up to a 96 well plate with 50 uL reactions and get ~500 ug of material. Make sure that you mix your dNTPs! Scale-up accordingly.
To start, the DNA Clean and Concentration is designed for really small reactions. It's much better to use the next level of purification by maxiprepping everything. The  The binding capacity of those columns go up to 1 mg. Using the QIAEX II slurry works but you should make sure that you scale up correctly. Make sure that you complete your regeneration. This protocol works well.
Alternatively you can ignore the column and just ethanol precipitate everything to remove your nucleotides. I suggest following Ethanol precipitation of nucleic acids from OWW. We had to make a lot of linear template and for most applications this works great.
As with all things related to molecular biology, there is a lot of voodoo. Some things that supposively work is to chill your ethanol mixture at -20C for at least an hour (or overnight), generally, you'll see your DNA fall out of solution and that's your sign that things are working. At this scale you should be seeing your DNA pellet; that's a good sign if things are working. While eluting anything from the columns, we would warm up our elution buffers. Thermodynamically this would make sense since it would reduce the barrier for unbinding. You would also get away with a lower residence time.
I would frankly avoid using FPLC unless you're working with gram quantities of DNA. You're not Moderna.

Thanks for the advice. I am doing 50 uL PCR reactions in a standard thermocycler and usually do 96 at a time--I'm honestly not sure what my yield is per reaction since I've never purified from a single reaction. For the ethanol precipitation--are we sure this is going to remove the polymerase entirely? Also--do you have a specific protocol for maxiprep-ing from PCR reactions? Zymo has a DNA clean and concentrator with 500 ug capacity, so I am considering using that; however I've found the yields to be much lower than anticipated with other "large-scale" type column kits.

Cooling the reagents (or the complete reaction) is not necessary. See this answer which fits perfecty with my experiences.

What do you guys think about just doing a large phenol-chloroform extraction/EtOH precipitation then simply dialyzing or buffer exchanging to dilute any contaminants?

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How to detect Zika in mosquitos
I'll keep this as brief as I can. I am an engineer and I have an idea for an early detection system for the Zika virus. I want to build it. However, first I need to do research on how one detects Zika in mosquitos.
I am under the impression that to detect it in a human you would wait for the appropriate antibodies to appear in the blood. I am assuming that I would need to culture anything I get from a mosquito.
Can someone point me at any research material they can find? All of the search terms are to ambiguous for mere non medical mortals like myself.

This might get a better answer on Biology.SE.

It would not be possible to identify the virus carried by the mosquito by simple visual examination of the mosquito. You can visually identify the species of mosquito (like Aedes, Anopheles or Culex) and select the species that are known hosts. You don't need to culture, you can dissect the salivary gland and use PCR primers specific to viral DNA to test the presence of virus. This is a cheap method but still you cannot make some kind of screen to filter out carrier mosquitoes from the rest.

The gold standard would be the isolation of infectious virus from mosquito saliva. Extraction of saliva from mosquitoes is fiddly if you have to do it in containment and the survival of mosquitoes collected from the field may be low. Alternatives, in roughly declining order of strength-of-evidence, would be

identification of virus from dissected salivary glands,
identification of RNA from saliva/salivary glands,
identification of virus or RNA from heads,
virus or RNA from whole bodies of insects that are not visibly
engorged with blood (and we're getting
into not-very-reliable-at-all territory at this point).
detection of viral RNA from pooled field-collected (unsorted) insects, possibly including those which have recently blood-fed.

There are also other technologies that are beginning to be used for field surveillance of arboviruses in vector populations, such as sugar-coated or honey-coated Whatman FTA cards (mosquitoes sugar-feed on the cards which preserve RNA).
Two other things are worth emphasising here. One is that not all mosquitoes which ingest infectious virus will develop a transmissible infection even if they survive to complete the necessary incubation period. Some will clear infection completely, others may develop a disseminated but non-transmissible infection due to the existence of barriers to replication within the vector's tissues (see this paper for a nice review).
The second is that the importance of a vector is not determined solely by its competence (the probability that a mosquito ingesting an infectious dose and surviving the extrinsic incubation period develops a transmissible infection) but also things like vector:host ratio, biting preferences, and typical lifespan. Vectorial capacity is more important (this is a recent paper pointing out the differences).

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Bacteria surviving a β-lactam antibiotic
What changes can occur in the cell wall of a bacteria for it to survive a β-lactam antibiotic?
I think that because a bacteria possesses peptidoglycan in its cell wall, they are β-lactam sensitive, hence the only way it could survive a β-lactam treatment would be the presence of a resistance gene caused by a mutation.
I can't think of another way.
Any ideas?

There can be infinite possibilities actually. One can even say that the bacteria can evolve to make the cell wall made of a different material. This question is broad. Please add details to narrow down the question or else it will be closed.

There's no need to add more details, this question is the basis of a question I got from a General Microbiology exam a few years ago, now I'm studying for my exam. Moreover, the only detail was given in the exame was that the bacteria had peptidoglycan in its cell wall, and it survived a β-lactam treatment, then what changes may have occur in its cell wall?

This question formulated as it is, shows that I've thinked of it, I've developed my own theory. Moreover, I've read a lot the Brock's book and still I don't know the full answer to this question. I've seen lots of questions don't showing even a little bit of own work, and still with positive reviews. I see absolutely no reason for this question to be closed.

Just because it was asked in an exam doesn't make it a precise question. The possibility of a resistance gene, as you mentioned in your answer is one of the obvious reasons and I am pretty sure the examiner wants this only. However, as I said, there can be several reasons. Penicillin-binding proteins can lose their affinity to penicillin or cell wall composition itself might change such that penicillin has no effect. Bacteria can also express efflux pumps to remove ampicillin or simply the bacteria may remain as protoplast and survive the treatment.

I am not saying that this is a bad question. Just saying that there can be a lot of possibilities and hence the examiner who asked this question should have asked a better question. One way to make the question precise is to ask what are the documented mechanisms which let the bacteria survive the antibiotic treatment. Then we can at least not think of the myriad of theoretical possibilities.

@WYSIWYG, thanks. Your second comment it more like an answer. Then one answer could be saying some possibilities, and say that these are not all. That is all I wanted. New ideas.

Although changes in the bacterial cell wall are theoretically possible, I don't think this is really feasible since you need to change a lot of biosynthesis pathways and their enzymes in very short time.

What kind of Beta-lactam treatment? When using ampicillin resistant plasmids, I often skip the SOC media incubation and just plate the cells. They usually stay alive long enough to make the lactamase and then begin to grow on the media. It's also feasible that if the dose were insufficient the bacteria in question could "coast" until the antibiotic concentration was low enough to no longer matter, beta-lactams aren't exactly the most stable molecules around.


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When and why did humans start disliking the way we naturally smell?
Like many animals, humans produce a myriad of scents from sweating, bacteria, possibly pheromones, etc. Many of these scents are used throughout the animal kingdom for mate choice, recognition of individuals, or signifying presence or territory.
I know that humans subconsciously react to some scent cues (see here, here, or here for examples), but it seems many humans find natural human scent to, well, smell. Interestingly, this article suggests that humans' smell is worse than that of other animals.
My question is: if these scents hold so much information, how/why did humans develop an aversion to the natural scent of other humans?
Further, when did this occur? -- recently or long ago in human culture? I know Egyptians made perfumes thousands of years ago, so this is not a fully recent trend. Perhaps someone could comment on the ubiquitousness of this aversion across modern cultures as well.

I don't believe this question is opinion based. It is fairly well known and demonstrated in my links (and countless other sources) that people find the body odor of others repugnant at times. The question asks for a historical /evolutionary explanation of why that is. That falls well in the range of accepted questions on this SE site. I feel those that voted to close nitpicked details in my text instead of focusing on the actual question, which is valid here.

I think that the "humans produce pheromones" part is problematic, you might want to remove that. To my knowledge no human pheromone (a specific molecule) has ever been identified, although some behavioral studies have suggested that there is information in smell. But this is really not so relevant to the question in the title anyway, so you could take out this part. Just the question of why our "natural" odor is repugnant to us is interesting in itself, regardless of what "information" it might carry,

@Roland I've modified this portion. I've now included the phrase "possibly pheromones" and included a link to a TED talk by one of the world's experts on the subject, Tristram Wyatt, who gives a good summary of the pheromone subject (which I believe is pertinent to this question). Please vote to reopen if you see no additional issues with this question.

I don't think there is a general aversion against other people smells. In fact, smells seem to me to be a very important part of a romantic relationship.

@Remi.b but there is a general aversion: that's ultimately why the deodorant industry exists (and arguably why perfumes and soaps exist as well...).  For further discussion, for example, see here

I think it's not human smell per se, just sweat. Probably because of association with bad hygiene and therefore risk of infection as you mention yourself - disgust as part of the behavioural immune system. I'd guess we gave up on smell in favour of social cognition and language, which we use for some social functions for which other animals use smells. So it wouldn't surprise that we find a different use for smell.

Hunting... if you smell bad, animals smell you better.  Go take bath.  Also, clean people get less diseases, go take bath.  Etc.  Therefore, smelly people are gross, weak hunters who get people sick.  Also, if you like smelling bad, you die more.

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What is the term for toes that pull together with an upstep?
I fairly recently learned the term digitigrade, to describe the anatomy of a creature that stands on its toes rather than on the flat of its foot, like cats and birds.
I'm trying to narrow that down a little more now. Some animals like a cat or dog (or us), the toes are fairly static as they walk. Contrast that to the toes of a bird where on the upstep the toes... pull together, for lack of a better description, and spread apart as they step down on the foot, as shown in this video.
What is the proper term used to describe that motion and style of walking, or that type of functional foot, where the toes pull together and then spread apart as the foot goes up and down?

I think the digits of cats and dogs also spread a bit but since the digits are close together you cannot discern the spread as you can do in the case of birds.

@WYSIWYG - yeah, being digitigrade also, I'm sure they do. Like you said, being much shorter toes, it's just not that noticeable. Hence the addition of fairly static. ;)

Another difference is that in cats and dogs, the dew claw doesn't play any part in walking at all, while in most birds, that back toe/claw is heavily involved in their walking and standing.

Thinking about it more, cat toes I think are also more in a row like ours, so might not do it as much, where are most bird toes are arranged more radially.


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What came first? The DNA or the DNA polymerases?
I know this sounds a lot like chicken and egg question and while the latter has an answer, I am intrigued about the former.
A modified form of the question would be, in the course of abiogenesis, what formed first? The DNA or the proteins (hence enzymes and DNA polymerases)?
The principle behind it is that the DNA needs an enzyme to replicate.(DNA pol)
But DNA pol itself, being a protein, needs a DNA pol A/B/C gene on the DNA! (Transcription and translation) Not to mention all the other proteins required for transcription and translation.
Same is the case for RNA and RNA pol.
If the DNA/RNA formed first, how did it replicate without a protein?
If Protein formed first, then how did it came to existence without DNA/RNA?
Let's make a big assumption and say that nucleic acid formed for the first time and replicated without proteins. Is it possible for nucleic acids replicate without proteins? For example, a abiogenetically formed DNA sequence just randomly attracted its complementary strand and whatever could fit, fitted and somehow the phosphodiester bonds were sealed sans proteins. That sounds too implausible.
Would love if somebody provides sources with evidences of DNA/protein abiotically forming de novo sans enzymes, genes.

The straight forward answer is: we don't know. We don't have any direct evidence for what happened at that time nor any completely developed and coherent theories for how it worked.
The widely believed hypothesis is the "RNA World" hypothesis. RNA, unlike DNA, is capable of spontaneously folding to form catalytic molecules and thus avoids the needs for translation and transcription by proteins since it can bootstrap it's own synthesis. The idea is that, over time, the RNA developed the means to synthesize proteins and then started using DNA as a more stable storage molecule. The earlier RNA-based RNA polymerases were supplanted by higher fidelity protein polymerases over evolutionary time so we no longer see them in modern cells.

You can also add a note on the self replicating ribozymes


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In the life-cycle of the HIV virus, how does the created DNA enter the nuclear membrane?
I am in a high school biology class, so I cannot truly attest to how accurate the information I am given is, but as far as I know only RNA and very small molecules can enter the nuclear membrane through the pores on it (thus excluding DNA). Furthermore, I am fairly sure that the reverse-transcriptase used in the process of reverse transcription of the viral RNA must be used outside of the nuclear membrane, in the cytosol. My question is: How does the viral RNA, after it is reverse transcripted, enter the nuclear membrane?
My teacher and I have come to the conclusion that it probably creates the provirus sometime during mitosis, as the nuclear membrane dissolves, but this is more of an educated guess.
Thanks in advance!

The nuclear import mechanism is independent of the cell cycle. Here's a recent model for nuclear import, but there's still a lot of research into this: http://www.sciencedirect.com/science/article/pii/S1879625713002022

@Kendall I think the integrase also facilitates nuclear import but I am not sure.

Some proteins are transported from cytoplasm to nucleus by the importin family through nuclear pore. These proteins have a specific sequence called Nuclear Localization Sequence (NLS) and the importin family recognizes NLS to import them. Recently it has been clear that the accessory protein vps which is translated from viral RNA and composes pre-integration complex (PIC) with viral DNA has atypical sequence like NLS.
So. it has been thought that DNA from HIV is imported into host nucleus by importin family with PIC.

You should also add some references in your answer to support your claim.

I'm sorry for having not added the reference.

I'm sorry for having not added the reference. This is Yuko N.,et al, J. Virol .,2007,81,5284-5293 http://jvi.asm.org/content/81/10/5284.full


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Find how much times blood is filtered in the kidney?
The blood that circulates in our body is about 1/12 of our mass. If the kidneys filter 7.5 liter of blood a hour, then how many times does it filter in the kidney the whole blood of a person will mass 60kg?
Here's what my teacher did:
1/12*60=5 liter blood
0.55*5=2.75 liter plasma of blood.
The plasma is filtered 60 times is 24 hours. (how did she find that?)
24 hours ->60 times the plasma filters
1 hour -> x
x=2.5 times
Do you understand her explanation? What should I do next?

Could you please explain a bit better what the question of the exercise is?

This is what is written in my book. I don't understand either if it says find how many times the blood filters in a day or hour.

@prishila, If you feel that my answer was correct or helpful, please vote up or accept it (click on the hollow check mark you see below the voting buttons). Thanks :)

I'll try to dissect your teachers answer for you:

1/12*60=5 liter blood

no explanation required here

0.55*5=2.75 liter plasma of blood.

only the plasma is filtered in the kidney (the 45% cell content remains in the blood stream), so out of the 5 l blood, only 2.75 l need to be filtered.

The plasma is filtered 60 times is 24 hours. (how did she find that?)

the kidney filteres 7.5 l per hour so if the whole blood plasma has 2.75 l, then in one hour the whole blood is filtered 7.5/2.75=2.73 times. In one day the whole blood is filtered 2.73*24=65.5 times (the numbers are slightly rounded).


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Why do crows sit on treetops even when it is cold?
It is cold outside: -1 degrees Celsius, wind 14 km/h and snow from time to time. I was wondering why crows (maybe birds in general in Northern Europe) are calmly sitting in relatively windy places even though there are plenty of potentially warmer places to go to. (see picture at the bottom).
My first guess was that it isn't cold enough for them However, I couldn't find support for this online, so it's not possible to know for certain.
NB1: This is my first post - let me know if something is inappropriate.
NB2: I am not a biologist, so please be patient.
I'd appreciate links/references where I could get information that gets closer to finding an answer to the given question.

I'd assume that they're staking out their territory most likely, or trying to attract a mate. Furthermore they might do this in order to experience the "bird-perspective", which could origin from either the fear of other predators, or the enhanced overview of the surroundings –– which could be vital for foraging

Birds (crows inclusive) have better heat conservation adaptations as compared to humans. Some of these are (but not limited to):
-Hollow tubes in feathers which provide insulation reducing heat loss.
-Reduction of appendage length especially in species that dwell in cold regions.
So conditions we perceive as cold are relatively warm for birds.

My first guess was that it isn't cold enough.

From this question on biology.se I can say it could be warm for them as it addresses birds surviving at -40C. Plus some of the answers and comments on the same question cover a couple of adaptations that birds exhibit to strive in such conditions.
edit: links that provide additional information on the same
-http://toughlittlebirds.com/2012/12/26/how-do-birds-keep-warm/
-https://beyondpenguins.ehe.osu.edu/issue/arctic-and-anarctic-birds/how-do-birds-stay-warm
-http://birding.about.com/od/birdingbasics/a/howbirdskeepwarm.htm
-http://gardenwalkgardentalk.com/2013/02/19/how-do-birds-keep-warm-in-winter/

Also WRT to wind, birds have (obviously?) evolved aerodynamic streamlining, so would not experience as much heat loss from wind.


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Why does immunity from the flu vaccine appear only after two weeks?
It is said that immunity from a flu vaccine appears after about two weeks. However, from experience, the flu usually lasts only a few days.
If sufficient antibodies appear only after two weeks shouldn't the flu also last that long? Or is there a difference between how the body reacts to the actual flu virus as opposed to the dead one in the flu vaccine (like maybe there being more viral particles in an actual infection or something)?

Most information here can be found broadly in Cellular and Molecular Immunology, 8th Ed.
Here's how the flu vaccine works: Scientists forecast months in advance which strains they think stand to cause the most problems. The vaccine is often trivalent, protecting against three different strains on flu: Two influenza A and one influenza B. You can read about the process directly from the CDC.
The two major viral receptors are neuraminidase and hemeagglutinin. They determine the serotype of the virus, such as H1N1. They serve as peptide antigens for immune recognition. Where influenza infects a cell, it starts to produce proteins essential to it's replication in the host cytoplasm.
The innate immunue system, upon realizing there's an infection, does quite a bit to try and mitigate things but it's a messy job. Looking at the link, lots of inflammation, damage and dead tissue. At that, there will be no memory of the same infection, and the same process happens over and over unless there's a better way to take care of things.
This is really where your adaptive immune system comes in, T/B cell, antibodies, etc. A wild type influenza virus stimulates the same adaptive response as the strains in a flu vaccine: Proteins such as the neuraminidase are picked up by macrophages or dendritic cells, and they enter transport to the closest lymph node. On the way, they chop up the viral protein into peptide antigens and load them onto MHC-II molecules, and export the complex to the cell surface, becoming antigen-presenting cells or APCs. T cells expressing CD4 coreceptor can interact with the MHC-II on APCs in a cascade of events that lead to effector T-helper (Th) cells. Th cells, in concert with follicular dendritic cells and recognition of cognate antigen by naive B cell can result in proliferation and differentiation of B cells to plasma cells that secrete antibodies specific to the viral antigen that was initially recognized.
The problem, is that this process takes time to ramp up plasma cells numbers and antibody production. The average time often denoted by literature is about 2 weeks.

Furthermore, with adaptive immunity you get memory cells that will remember a given infection and quickly resolve it with antibodies should you ever catch the same bug.
The difference between our wild type influenza and the ones in the vaccine is attenuation. The point of the wild type influenza people often catch is it's really good at infecting humans, and upon infection it causes a lot of damage. We can attenuate influenza's pathogenicity by growing the flu strains in tissue that is not human. Over a few generations, the virus adapts: it becomes more pathogenic/virulent in non-human tissue, but harmless to humans. You then remove the harmful parts of the hemeagglutinin and neuraminidase genes from a wild type strain to get inert HA and NA (so that you get the wild type immunogenicity), combine them with structural proteins from the attenuated strain, and combine them to form a new, live-attenuated vaccine strain that can be grown in the non-human tissue (see image below).
So also keep in mind that just because your infection resolved in under 2 weeks that the antibodies you produced wont help you from getting the same bug again. During flu season it tends to come at your from all sides and the antibodies that evetually get produced help a lot.

Thank you for such a detailed response. I'm afraid it's a bit difficult for me to follow all of the acronyms and biochemistry. In layman's terms, are you saying that basically there is no difference between a vaccine and an actual infection in terms of how fast an immunity forms? In other words, if you recover from infection in, say, three days you probably still don't have immunity which will only appear after about two weeks on average and so you can still get reinfected during that period?

Right the way they develop the vaccine you should get just about as strong a reaction as the natural infection. The chart in there is basically saying you start developing antibodies after a few days. You can always get reinfected but your immunity will determine whether the pathogen is cleared before a symptomatic stage or not.

Take a look at this figure. You can see that for a given infection there in an incubation/prodromal stage before you experience symptoms in full. Once your adaptive immunity is up to speed, it takes care of the infection at these stages.

So basically most of the fight against the infection, at least in terms of making you feel better, is waged by the shoot-now-ask-questions-later kind of cells and the smart guys appear pretty much after the symptoms subside? That is helpful, thank you.

For an average case sure, we can boil it down to that, but we want those antibodies because first-line defenses beat you up quite a bit, and they don't always succeed.

Did I read that right that you are saying that the vaccine does not allow you to build adaptive immunity e.g. memory cells that will remember the infection?

I was going to point out that it's actually "1-2 weeks", not "roughly two weeks" as you can clearly see in that chart on proliferation up there. The reason flu seems a few days long, frequently: a body usually already has at least related defenses, and flu has to ramp up, itself. Immunity response time and virus growth overlap. Sure, flu gets first move in the chess match, but it's not like your body idles as flu goes nuts. Game clock starts before you feel terrible.

And yes, vaccines provide for memory. Not as good for that as a full raging infection, (which would lead to more memory t cells) but it's pretty obvious which scenario is preferable.

Here's a short and simplified explanation.

The antibodies that arise in a flu infection are more "intended" to prevent future infections than to clear the present infection.
Infections drive T cell responses as well as antibody responses, and the T cells appear a little earlier (peaking at maybe a week) and are probably very useful for clearing the present infection.
Remember that just because we can't measure the antibodies (or T cells) doesn't mean that they're not functional.  We measure responses in blood, not local tissues, whereas a very low general response can be very useful in the local site.  T cells are probably doing something locally within 3 days; antibodies, perhaps within a week.


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differentially expressed genes of the treated with estradiol samples
I did differential analysis on samples treated (G1E-ER4) with estradiol (differentiation induced by estradiol) and control (G1E).
The genes that I gor as differentially expressed in G1E-ER4 showed following pathways.
I can explain the first five: estradiol causes stress and more hemoglobin is synthesized during cell differentiation, also tetrypyrrole is involved in hemoglobin synthesis. Cell death might also be caused by stress induced by estradiol.
However, I am not sure why I have cell division or starvation etc pathways.What is considered to be a starvation actually?
response to stress (GO:0006950)
heme metabolic process (GO:0042168)
tetrapyrrole metabolic process (GO:0033013)
regulation of apoptotic process (GO:0042981)
cell death (GO:0008219), death (GO:0016265),programmed cell death (GO:0012501)

mitotic cell cycle (GO:0000278), cell cycle (GO:0007049)
cell division (GO:0051301),nuclear division (GO:0000280)
cellular response to starvation (GO:0009267)
positive regulation of GTPase activity (GO:0043547)
regulation of localization (GO:0032879)

Maybe some mTOR crosstalk with your estradiol? As for your starvation and look here, it's hard to tell unless we know what kind of starvation it was, but I suspect it has something to do with the cell division.

Pathway analysis can be a little tricky. Because pathway enrichment is estimated from the enrichment of genes (or miRNA or what have you) that participate in overlapping pathways, certain pathways often show up for reasons that may have little to do with your experiment. Cell cycle related pathways, in particular, come up a lot, since so many genes are "cell cycle-related". These papers both go over this phenomenon in more detail. The second one is behind a paywall...sorry for that. If you can't access it, but want to read it, I'm sure we can figure out a way to send a pdf.
I deal with this a lot in my own research. My usual strategy is to make pathway analysis only one part of the overall analysis. How that works exactly depends a lot on the nature of your project. For instance, pathway enrichment could just serve as a sanity check, to see that other results aren't widely off mark. Alternatively, you might want to put other results in the context of some pathway or the other & having pathway enrichment data would naturally be a part of this.
Regarding the question of what exactly starvation means in the context of your results, it's possible that, if this pathway doesn't make sense in the context of your experiment, then it shows up as enriched because more starvation-related genes came up as differentially expressed. The degree to which that means that your cells were undergoing starvation could be debatable. I would bet money that there's significant overlap between starvation-related gene sets and those related to "cellular stress" & "cell death". Cell death is one common response to serum starvation, for instance.
Hope that helps!


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Does food continue to stay sequential once it is inside my body?
I may be very off on many scientific details here, but I'm always all ears.
As far as I understand, any food that is eaten goes to the stomach, gets broken down even further into smaller food molecules, and after a period goes through the intestines where nutrients are absorbed out of this chyme.
Let's say I eat food A sometime, and it's gone down and is now sitting in my stomach, waiting for the stomach to start breaking it down. After a while, I eat food B.
When digestion occurs, is it possible that the stomach only starts breaking down food A's material first before it gets to food B?
Is it possible that food B's output goes into the duodenum before food A's output?
Please help break any of this down if it's obvious I've been living in a cave. Thanks!

I'm curious, do you have a reason to believe the stomach would act in such a selective manner, when it is using muscles to churn the material around?  (also, did you get your question backwards?  Did you intend to ask " Is it possible that food B's output goes into the duodenum before food A's output?")

@CortAmmon I have had no strong reason to chase down this answer, but I was really curious because this could, if answered positively, in a way, help me figure out potentially which meal was causing any current discomfort inside.

Ahh, so you are specifically referring to the case where the meals are several hours apart?  Since the stomach usually digests food in anywhere from 40 minutes to a few hours, the amount of time between A and B would matter.

You would have to eat each meal independently and wait a ridiculous number of hours to figure out where your discomfort is coming from. Mean time from mouth to excretion is along the order of 40 hours, and so the time trial would determine something like is the discomfort originating in the stomach, the colon? An important fact to note is that food in the stomach is pulverized to chyme so if you eat meals close to one another, it can confound things.

@Kendall Thanks for the response, it is informative. I'm mostly interested in the pre-duodenum phase of digestion. What happens if you ingest food right during the process of the stomach converting the food in the stomach to chyme? Does it allow the new food into this process, to create... "uniform" chyme? Or is the new food kept separate in some manner?

@CortAmmon I'm not referring to any food-interval particularly, but am more interested in learning if food is kept sequential internally in any case/interval-between-foods. (I think) the scope of my curiosity is between the throat and the pyloric valve.

It all depends on the delay between the consumption of food-A and food-B. It is all a continuous process (without any thresholding) and there is certainly a likelihood that there would be some minimum delay below which you get a well mixed chyme of both foods. Also, depending on the nature and composition of food these kinetics may vary.

@WYSIWYG Thanks for your response, that is informative.

Eat Oreos and you may find your answer.

In general, food is not kept in any particular sequential order.  The stomach has a lot of smooth muscle which churns the food, very rapidly erasing any "order" to the food.  Beyond that, the stomach digests "the food in the stomach," in parallel.  Whatever is in it, it digests.
Now, in general, food eaten earlier will digest into chyme (the digested slurry which enters the intestines) sooner, but that's a very general pattern and doesn't account for any differences in how long it takes to digest various types of foods.
I don't have any sources to back this next claim up, but I do believe that if you were to chew some steak poorly, and then follow it up by more steak chewed properly, the later steak would actually digest first because it would take less mechanical processing in the stomach to get the digestive enzymes to where they need to be to work.

Thanks for the response.
When the chyme rests in your stomach, before it moves towards the intestines, how does the stomach treat new food that has just reached it?

think of it as a large ziplock bag.  Food goes in, joins whatever mix of chyme and bollus (chewed food) happened to be in the bag at the time.  Give the bag a few squeezes to mix things up.  It's really more of a continuous process than a batch process.  Most of the exciting stuff is happening at the molecular level, so it doesn't really care about what the mix looks like at the macroscopic level.  It doesn't care if its breaking down the last few protiens of the last meal, or fresh protiens from a newly chewed steak.

Any description of digestion I've read mentions it, so if you feel bad sans source, that's place to start looking. That said, you really, truly ought not need to cite every blasted well-known and fundamental fact. If someone really needs to get more input on the point, they can always post that specific question on Stack Exchange, too.

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


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Why is it advised to avoid bubble formation during mixing?
I have been told not to vortex solution containing protein. The reason I was given is bubble formation. Here I am interested in the effect of bubble formation in general.

A "bubble" per se would do no harm unless you have cells (without walls like mammalian cells) in the suspension. If you agitate the protein mixture vigourously then it may lead to denaturation of proteins by extensive intermolecular collisions. The "froth" formation is an indication of denaturation as denatured proteins stabilize these foams [1, 2].

References:

Zayas, Joseph F. "Foaming properties of proteins." Functionality of proteins in food. Springer Berlin Heidelberg, 1997. 260-309.
Schmidt, Isabelle, et al. "Foaming properties of protein/pectin electrostatic complexes and foam structure at nanoscale." Journal of colloid and interface science 345.2 (2010): 316-324.

would you not agree that denaturation because of "extensive intermolecular collisions" depends on whether there is a low or high concentration? Because low concentration = few collisions and high concentrations = more collisions. So is the rate/process of denaturation (therefore creation of bubbles)  depended on the solution which is agitated?

@JordiZambrino Yes concentration of the solute and other fluid properties of the solution such as viscosity etc also have a role. You do see more froth with higher concentrations. It also depends on the molecular nature of the protein. But my point is that froth is an effect of denatured proteins and not the cause.

I want to point out about undergrad labs: People vortex SDS mixtures and small volumes, and advertently the pipettes can't get everything out of the tube reasonably sometimes due to bubbles. You could try to centrifuge it, but if there are still bubbles, trying to pipette 50µL of bubbles is annoying. I can remember one lab where we had to pellet E. coli in 4 tubes and consolidate the pellets. The resulting solution was very viscous, and if you formed bubbles while pipetting it made things a lot harder to work with.


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new DNA sequencing technologies?
Last year I did my thesis in the field of a new method for DNA analysis.
Which I think is very interesting although I cannot seem to find any new methods in this field especially the SMRT sequencing method.
Do you maybe know a new method(s) which are introduced for DNA research in the area of SMRT sequencing ?

You mean new sequencing technologies introduced since last year?

I think you expect the development of new technologies by far to fast. I am not even sure if new experimental ideas have been developed in this time, let alone made commercial.

This question is broad. Nobody knows what you have done in your thesis. Please explicitly mention what kind of analysis you are interested in. Research is always happening and there is always some development. Unless you provide specifics, your question may be put on hold.

@WYSIWYG I already have my answer :)

Yes, there's a new technique called Sanger sequencing. Have you heard of that? In other words, if you don't tell us what you know, how can we tell what you don't know?

Community edits to clarify, and votes to reopen, I'm too new on this particular site to help rep wise, but I think from the comments that the accepted answer is conformed by the O'P'er to be excellent, the O'P'ers meaning seems therefore to be now understood sufficiently.

I don't know, which technique you worked on, but there are the so-called 'Next Generation Sequencing' methods. I think the oldest of that is a pyrosequencing technique called 454 sequencing (I think it is provided by Roche). However, this method is too expensive compared to even newer methods and the support will be stopped within the next months, as far as I know.
Furthermore, there are the Illumina and the ion torrent technique. Finally, there is SMRT sequencing of which some people say that this is even third generation sequencing. I think, this paper provides a nice overview. And if you're interested in further reading, yet you know what to search for.

thanks for you comment, so there aren't any new techniques at the moment. I didn't work with them but i know every one of them and how they work. I worked on a new nanohole based single molecule sequencing technique

I'd recommend working on your question @pwghost even though it may well not get reopened.

@alan2here edited it :)

Sorry for being vague with my comment, I've found this frustrating enough myself so I do apologise for doing it as well. I think it's the word "new", could you narrow that down, perhaps to this and last for example?


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Why do we blink instead of winking each eye independently?
Question
Why do we blink both eyes at the same time rather than winking each eye as needed?
Why would winking independently be better?
The benefit would be a minor improvement whereby a person would receive continuous sight of the area of vision shared by both eyes.  I'd also assume that it would be more likely for the wink-as-needed mechanism to evolve than the blink-as-needed mechanism were there no benefit to blinking over winking.
Why then has evolution favoured blinking?
My guess at why is that the overhead on our brain of switching between binocular vision to monocular vision is more significant than the overhead of momentarily pausing our visual processing.
I also believe that some animals don't blink, but wink; e.g. chameleons.  This supports my theory as their eyes operate independently, so their brains would have to cope with the variance in each eye's information anyway.  That said, their wink is different; i.e. they roll their eye inside their head, rather than having an eyelid.
Research so far
I found a couple of Reddit posts:

https://www.reddit.com/r/explainlikeimfive/comments/2kzx4s/eli5_why_does_blinking_take_me_almost_no_effort/ - explains why blinking is easier than winking; but only based on how we are rather than how we got there (i.e. why evolution would have resulted in different muscles for winking vs blinking).
https://www.reddit.com/r/explainlikeimfive/comments/3mijgw/eli5_why_do_we_blink_with_both_eyes_at_same_time/ - doesn't have any hard fact answers; just discussion of opinion.

Looking at it completely in terms of evolutionary pressure:
1.1 The whole idea of binocular vision for humans, (and some other species) is depth perception. If you suggest continuous, alternate winking, the cognition of the individual would be seriously affected.
The 'wink as needed' mechanism (assuming all other visual processes are as they have evolved today) would be like continuously alternating between a pair of binoculars and a telescope while still trying to move forward.
1.2 If you are suggesting that there would still be an evolutionary pressure for winking, then its very likely that the evolutionary pressure for coordinated motion/ efficient cognition acting together with the evolutionary pressure for depth perception would be much higher as compared to it. (This would especially be true if eye-brain coordination evolved before the blinking mechanism, as is seen to be the case, which explains your point on 'how we are rather than how we got here'. Obviously fish have evolved some eye-brain coordination, but don't blink)
This link explains evolutionary pressure for depth perception/stereopsis to an extent
https://en.wikipedia.org/wiki/Depth_perception#Survival
2.1 As for the chameleon, the winking/ eye rolling mechanism might be very closely linked to the evolution of chameleon vision. It is seen as the link for studying evolution of binocular vision and stereopsis(depth perception) from monocular vision.
https://en.wikipedia.org/wiki/Chameleon_vision


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What does characterization mean in a genomics context?

"The resulting libraries of gene sequences allow CDC and other
  laboratories to compare the genes of currently circulating influenza
  viruses with the genes of older influenza viruses and viruses used in
  vaccines. Through this process of comparing genetic sequences, called
  genetic characterization, CDC can make informed assumptions regarding.."

I'm unsure what genetic characterization means. What do the researchers actually here?

I've made some edits to clarify your question a bit - are these suitable edits?

I think what I'm trying to ask is what genetic characterization really means.  Is it simply a comparison of genetic sequences to detect when they are different?  The CDC use of the term doesn't seem to apply in the context of genomics papers that I read but I could simply be mistaken (I am not a biologist, rather a software engineer trying to understand how the phrase is being used).

There's no technical definition for "genetic characterization". It is simply a phrase used by authors based on the normal meaning of the words: (1) having to do with genes and heredity, and (2) describing the essential character.  Of course the bounds of the genetics and the essence of their nature are entirely in the eye of the author and reader, so no particular definition applies across all papers in genomics (or in other fields).

True. The word characterization doesn't really have a defined meaning, the implication is that you've observed something and described the significance and meaning of what you've observed - so the 'essential character' here presumably refers to the likely consequences of change in the virus' genotype to it's phenotype.


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Conjoined twins formation theory
is it theoretically possible to take two fertilized mammalian eggs and push them together to make conjoined twins? How about forming non-identical conjoined twins?

The more generally accepted theory for conjoined twins is fission, in which the fertilized egg splits partially. So I don't think that what you said is possible. Not seen this happening before... even the conjoined twins share same placenta indicating they originate from same fertilized egg.


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Does the bending of a tree's trunk in the wind stimulate and strengthen root growth?
Recently Southern California experienced extreme wind velocities and afterwards the news reported over 300 trees had fallen in San Diego County. I had either heard or read somewhere that the action of the wind and bending of a tree assists to strengthen the roots ( I suppose as long as the wind is not strong enough to pull the tree out of the ground). And so that brings me to the point of my question.
Does some kind of mechanism exist within the tree that connects mechanical bending of the trunk with increased rate of root growth? I can imagine that bending might stimulate fluid movement through the phloem & xylem, and perhaps this might be the mechanism. Or does the bending cause a release of some type of growth hormone? Or perhaps the mechanism is epigenetic?
I suppose that if such a mechanism were to exist it would provide one means of evolutionary weeding; removing the weaker part of the gene pool. Perhaps that's what happened in San Diego this last week.

The response of trees to strong winds is an interesting question, but I'm not sure what you mean in your last paragraph. It seems pretty unrelated to the rest of the question.

In tree growth there is principle called The axiom of universal stress whereby the growth is in such a way as to equalise the stress across the whole of its structure. The roots, the stem and the branches are one continuous system and can not be thought of as separate.
On a simplistic level for a branch to grow, there must be a corresponding equal and opposite growth in the stem and roots. Of course it is not quite like this as the growth happens across the whole structure at the same time.
The trees on the edge of an even-age stand of trees will have grown to be more stable against wind. They are referred to as being a wind-firm edge to the stand. The trees that have grown up within a stand, with the shelter of their neighbours will not have the same stability in the face of wind, so that if the stand is opened up too quickly it can lead to wind-blow. In uneven-age woodlands, the same principle is true but the dynamics make it less pronounced.
The reason for mentioning this is just to illustrate that, absolutely the wind, and other external factors, gravity being the obvious one, will have an effect on the growth of the roots, as well as the rest of the tree. As the wind exerts a force on a tree that  force will travel through the structure and into the roots and into the ground.
To come back to the specific question then.

Does some kind of mechanism exist within the tree that connects mechanical bending of the trunk with increased rate of root growth?

Yes, and no. Because the increased rate of growth will be across the whole structure, but not equally. It will put on growth at the points where the stresses are, in order to self-optimise the loading including within the root system.
The next time you cut either the stem of a leaning tree, or a branch of a tree, take a look at the orientation, and thickness of the rings. You will see that in broadleaf trees (or more correctly angiosperms) the rings on the side under tension will be thicker. In conifers (or gymnosperms) it is the opposite. The thicker growth is found on the compression side.
Here is a great photo of compression wood in a conifer from http://www.copperman.co.uk/didgeridoo/how_to_make_a_wooden_didgeridoo/what_is_wood_2.php

The same principle will be happening in the roots also.
As to the actual physiological mechanism that causes this response I have not yet come across a definitive answer. The consenus, at least as far as I know, is that it is not fully understood.
The closest I have come across so far is from this phd in 1994. http://etheses.whiterose.ac.uk/2438/1/DX184141.pdf
I dare say there has been more work done on this in the last couple of decades.

Well organized and complete answer, after all this time. Thanks

I suspect that many of those trees were Eucalyptus. Eucalyptus trees have shallow roots. They are tall and rigid.
About 150 years ago, Eucalyptus trees were planted in San Diego with the hope of growing wood for railroad ties. The idea was that if they grow in the Australian desert, they can grow in San Diego. They do, and are now everywhere. Unfortunately, the wood isn't very strong. It isn't useful.
Usually San Diego is pretty dry. The soil is sandstone and clay. It is very hard when dry. A storm can soak the soil, making it loose and muddy.
Here is a picture of some Eucalyptus trees over 100 feet tall that blew down in San Diego (my parent's yard) in a storm about a year after your question was posted. One tree fell onto the next, knocking them over like dominoes. For reference, the pot is about 2 feet tall. As you can see, very little root was pulled up when they fell over.
Another common tree in San Diego is Oak. They have very deep roots, and are much less prone to blowing over.


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Transgenic Plant-Gene source for introduction into host organism
Let's say the plant-gene itself is known, i.e. the exact neucleotide sequence is available in a gene bank (originally sequenced from a tree sample extracted RNA). Previous work has already successfuly inserted & expressed the gene in a host bacterium, say, E Coli.
My question is: Does subsequent work on inserting the gene into other host organisms also have to start from tree samples as source of the RNA & hence DNA?
Or is there a more direct route to convert a Neucleotide sequence from a gene database into actual DNA that can be inserted into hosts?
e.g. Are there machines that can take a sequence & synthesize the correct DNA molecules? Or not yet?

If you've access or someone else does and wants to answer, there's a good article through nature current to Dec. 2013 here.
The process is known as de novo synthesis.

@Kendall Thanks for the pointer. Googling up the term is getting me lots of info.

@Kendall Would it be fair to say that in cases like the one I described e.g. a tree gene as of today extracting the RNA & then purifying it & converting it into cDNA & cutting out the gene needed is a lot simpler / cheaper than de novo synthesis?

I guess what I am asking is when does one typically choose de novo synthesis over extraction from natural source material?


text:
Could a prolonged amount of Antibiotics severely affect the digestion Gut Microbiota?
Could taking antibiotics for a prolonged amount of time severely harm or even worse kill off a large proportion of Gut Microbiota responsible entirely for  digestion, Resulting in lifelong digestion problems similar to Crohn's Disease?

I’m voting to close this question because it is more suitable for SE Medical Sciences, which did not exist when it was originally posted.


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Can tardigrades survive being eaten?
Compared to a tardigrade, the cockroach seems fragile.
But can tardigrades survive the acidic environment of being eaten by most animals?

In there natural state no, tartigrade have absolutely no way to survive the acidic content of stomachs and are fragile.
In their cryptobiosed form (extremely resilient form) there has been no research to determine if they could survive extremely acid environnements. The things that we know they can survive is:

Temperature
Pressure
Dehydration
Radiation
The outer space environnement
Toxins

However, very few organisms possess mechanisms to tolerate highly acid environnement since acid affect cell membranes by "attacking" mainly the proteins and lipids. These organisms have evolved these traits because they live in acidic environnements, tartigrades on the other side don't.
Another point to add is, entering cryptobiosed form takes time, if the tartigrade would be eaten in it's natural form, it wouldn't have the time to cryptobiose and thus it would die.
Tartigrades
I hope this gives you some useful information

That depends on how long it takes for the tardigrade to get from point A, your mouth, to point B, your rectum. Provided you aren't extremely allergic to tardigrades or eat something poisonous or die while digesting the tardigrade. Also provided you had unlimited time with the tardigrade in an area of your digestive system that does digest things, not point A or B, eventually the tardigrade will succumb to your body's attempts to kill/digest it.

Hi welcome to BIO.SE. Please provide support for your answer. We want to ensure that people are answering with reputable, supported facts, and answers that fail to provide reputable support will be downvoted or deleted. Thanks.


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How many Watson-Crick + Hoogsteen triple base pair combinations are there?
Are these triple base pairs the only Watson-Crick + Hoogsteen triple base pairs possible? Furthermore, are TAA and TAT mixed up? This image is from Wikipedia, so it's possible that it's erroneous.

You are correct in assuming that the image labeled TAA should be labeled TAT and the second one labeled TAT should be labeled AAT. The image should be removed from the Wiki page until it has been corrected (even so I find it unclear).
Only some of these images show Watson-Crick/Hoogsteen combinations. To answer your question of how many such combinations there are, let us first recall what a Hoogsteen base-pair is. As stated in the first diagram on the Wiki page, this is a non-standard AT or GC base-pair formed by purine rotation about the glycosidic bond and base-flipping. In the diagram I have produced by canabilizing the above I show W-C and Hoogsteen base-pairs with the difference in the glycosidic link shown in yellow overlay. Because the pyrimidines A and C in a W-C base-pair have no groups left to hydrogen-bond, the only way you can theoretically make a W-C/H combination is by ATA and CGC as shown in my diagram. Therefore there are only two such possibilities.

I am not quite sure why you want to know about WC/H combinations, other than to understand the diagram in the article, because they are not particularly important. The author of the diagram shows such combinations because they apparently occur in triple-helices of artificial copolymers, however his diagram also shows some non-Watson-Crick base-pairs, e.g. CGG and CGA (which are not examples of WC/H combinations). The molecule where most Hoogsteen base-pairs are found naturally is RNA, not DNA: e.g. tRNA and ribozymes, in regions which do not have a standard double-helical structure. In these case they can occur in combination with both WC base-pairs and non-WC base-pairs (e.g. the GG illustrated above), so there is nothing special about Hoogsteen base-pairs being combined with WC base-pairs.

What I would consider important to realize is that in the context of the DNA double-helix WC base-pairs give the most thermodynamically stable structure, but outside this context, especially in RNAs that have protein-like structures, a variety of alternative base-pairs and base-triples are structurally and thermodynamically possible, including but not restricted to Hoogsten base-pairs.


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Does a specific blood group enhance the Plasmodium growth?
I am maintaining Plasmodium falciparum cultures for past 6 months. For the blood culture, usually we lab members take turns  and donate blood for the culture. I observed that the parasite's normal growth cycle were fast and more healthy in B+ blood, little slow in AB+ blood. But on the whole the culture was maintained good but I really observed fast stage transitions in B+.
Is this really possible? Does a specific blood group have an impact on Plasmodium growth? Did anyone notice the same issue?
Thanks.

It is a well documented observation that Plasmodium (vivax and knowlesi) infection is dependent on the Duffy blood groups [1].
Individuals lacking the Duffy antigens (Fya and Fyb) have lower susceptibility to malaria. Plasmodium expressed Duffy Binding Proteins facilitate in establishing the initial contact between the merozoite and the RBCs.
However, Plasmodium has evolved to break this dependence on Duffy antigens [2, 3].
For, the ABO blood group system, it has been observed that the blood group-O is associated with lower severity of P.falciparum malaria in adults  [4, 5], which possibly happens because of reduced rosetting (binding of infected RBCs with uninfected RBCs) [5].

References:

Dean L. Blood Groups and Red Cell Antigens [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 2005. Chapter 9, The Duffy blood group. Available from: http://www.ncbi.nlm.nih.gov/books/NBK2271/
Ménard, Didier, et al. "Plasmodium vivax clinical malaria is commonly observed in Duffy-negative Malagasy people." Proc Nat Acad Sci, USA 107.13 (2010): 5967-5971.
Mendes, Cristina, et al. "Duffy negative antigen is no longer a barrier to Plasmodium vivax–molecular evidences from the African West Coast (Angola and Equatorial Guinea)." PLoS Negl Trop Dis 5.6 (2011): e1192.
Cserti, Christine M., and Walter H. Dzik. "The ABO blood group system and Plasmodium falciparum malaria." Blood 110.7 (2007): 2250-2258.
Rowe, J. Alexandra, et al. "Blood group O protects against severe Plasmodium falciparum malaria through the mechanism of reduced rosetting." Proc Nat Acad Sci, USA 104.44 (2007): 17471-17476.


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What would happen if a cell is poked by a fine needle?
I had seen this question in an exam:
A living cell has a protoplasm which is water based and demarcated by a lipid bilayer membrane. If a cell is pierced to 1/5th of its diameter with a very sharp needle, after taking the needle out
(a) no effect will be observed.
(b) protoplasm will leak out from the hole made by the needle for a few minutes until the cell heals the wound.
(c) protoplasm will keep on leaking out till the cell is dead
(d) the cell will burst like a balloon.
I understand that the answer is option (a) as the cell membrane will reseal itself after getting pierced.
But my doubt is that if in the question 1/5th was replaced by 1/2 or by any number greater than 1/2, will the answer be different.
Or in other words, I want to know whether the number 1/5 significant in this question.

This is a homework question. Unless you show that you made an effort to solve the question yourself it is likely to be closed. Please look here on how to properly ask homework questions.

Depends on the diameter and the shape of the needle, and the hydrostatic pressure inside the cell.

I don't believe the edits satisfy the need for an attempt at an answer, there's no effort or justification, therefore I don't think it should be reopened

@rg255 Why not? The OP is asking what (to me) appears to be a valid question about the fraction of lost cell membrane that results in cell death.

Because there is no attempt to work out an answer and is homework

Generally speaking, there is no effect in microinjections.
This is relevant in the real world example of micro-injections. A video of a pronucleus injection can be seen here, or here is a more thoroughly explained procedure involving cloning. As you can see in the video the membrane, almost no effect will be observed - molecular dynamic simulations show that the membrane can spontaneously reform from fragments in the tens-of-nanoseconds timescale.
1/5 refers to  the question "is the needle small enough?"
The question does include the term "1/5", which is a bit unusual. I guess they want you to recall a specific piece of information about the correct ratio size of needle should be. Here is a video of a microinjection at approximately that ratio. However the exit hole is unintentionally filled with the inserted material and cannot close immediately. The cell disappears out of frame before we can confirm the hole is closed.
Cell diameters are very variable
Cell sizes vary greatly.

From using these values, assuming a cell is a sphere an oocyte has a diameter of approximately 196µm, whereas a neutrophil has a diameter of 8µm. It's a bizarre question given this range because usually micro-needles are between 0.5 and 5 µm diameter in length, except in the case of oocytes where larger needles are used (according to wikipedia). I don't think this is relevant, and it is just arbitrarily picking a needle size that wouldn't completely maul the cell!


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A limit to birds affinity for high vantage points
Birds seem to have a natural affinity for high vantage points, including power wires, the tops of trees, and the sides and tops of buildings.
However I presume the top of the Burj Khalifa is not packed with birds, flyover video of cities full of skyscrapers suggest this would not be the case.

Q: Therefore, is there a cap, if so at what height, where higher is no longer better? Perhaps the birds vantage point is reduced by going higher.

Related, but I feel different: Why do crows sit on treetops even when it is cold?

Not all birds do this.  For instance, the quail I can see outside my window right now like to stay on the ground, and hide in tall grass.  Ducks and geese seldom land anywhere but water or flat ground.  Hawks & eagles may perch/nest on the sides of cliffs or steep slopes (and I've encountered them flying several thousand feet AGL).  As mesam22 says, it's all about evolutionary niches.

Birds find their niches based on many reasons. Their choice is based on primarily resource availability, predation risk, and competition. Keep in mind there are variations among species, most birds like to forage for food at a hight safe enough to avoid ground predation, at the same time to be able to see and find food without much competition. Therefore very high altitudes do not seem beneficial for food resources and its a cost in energy, thus reasonable altitudes are preferred. But again many variations depending on species and location.

Could the majority of birds fly to the top of Burj Khalifa?

wow, Excelent point as well. ("Most birds fly below 500 feet except during migration." - https://web.stanford.edu/group/stanfordbirds/text/essays/How_Fast.html) Thats 1/5th as far.


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Solving a Pedigree Between Heterozygous Half-Cousins

A man who is a known heterozygous carrier of oculocutaneous albinism marries his half-cousin (they share one common grandparent) as shown in the pedigree below. This trait is transmitted as a fully penetrant autosomal recessive. What is the probability that this couple will produce a child with this disorder?

A. 1/2
B. 1/4
C. 1/8
D. 1/16
E. 1/64

My calculation was 1/2 (for II-2 as he must be carrier) * 1/2 (for II-3) * 1/2 (for III-2) * 1/4 = 1/32. Please help me out by proper explanation to your steps and point out my mistakes. The correct answer given is 1/64. Pedigree shown in the image below.

Also a proper attempt at answering for yourself should include your working, for example, why did you do 1/2 * 1/2 * 1/2 * 1/4  rather than 1/2 * 1/2 * 1/4 * 1/4? Therefore I think it should be closed as homework.

From what I can tell, you are not including the probability of the grandfather being a carrier (it could be the grandmother who is the carrier). Calculation should go like:
P(Child is born with disorder) = P(II-2 is carrier) * P(I-2 is carrier) * P(II-3 is carrier) * P(III-2 is carrier) * P(Child is homozygous recessive)
P(Child is born with disorder) = (1/2) * (1/2) * (1/2) * (1/2) * (1/4)
P(Child is born with disorder) = 1/64

I was just about to comment, you can Google "A man who is a known heterozygous carrier of oculocutaneous albinism" and the question has been answered on other forums. For book questions I find this is often the fastest way to get an answer.

thanks a lot everyone. but how do we get the probability of grandfather as he is the first one in the pedigree so how did u get his probability to be 1/2. please explain. @ CactusWoman

@MaryamKhan The probably of the grandfather being the carrier is the same as the probability of the father being the carrier (given that the son is heterozygous). If we assume that the father is the carrier, we know that one of his parents must be the carrier. It must either be the father's mother or the father's father, giving us a 1/2 chance of the father's father being the carrier. The fact that the grandfather is the first in the pedigree does not really matter, as we calculate these probabilities up the lineage starting with the heterozygous man.

Thanks a lot CactusWoman :-) now i understand it.
Thanks a lot for your suggestion. that really helped when i searched the question on google @ Kendall


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How to solve the problem of 2 melt peaks in real time PCR?
I am facing a problem in my real time experiment. After standardizing the annealing temperature by semi-quantitative PCR, I did real time for my gene of interest. In one of my samples, I got 2 peaks in the melt curve. Thinking it would be non-specificity, I tried by increasing the temperature further by 3 degrees. But still found 2 peaks in the same sample. I ran the product in a gel and found one blazing band and below it another distinct band. Is it still non-specificity or I am starting to think it could be an isoform? Also, in the same sample, with respect to control, protein expression is increasing whereas when I analyzed my real time, the RNA levels are coming low. Please provide your inputs.
See an image of the melting curve below. The red ones are melt peaks of my gene of interest. Green is of housekeeping gene. There are only 2 samples that show two peaks.

What is the size of the band corresponding to the first peak (I suspect that it should be around 100bp. What is the GC% of your primer?). You may try reducing primer concentration and run the PCR again (for all samples). I cannot be sure if it is an isoform. Try extracting it from the gel and doing a Sanger sequencing. Did you run the RNAs on gel to check integrity? You may try doing that too. The other band can also be because of a degradation product.

Regarding protein expression not correlating with RNA expression- that can be quite complex. You may compare this case with other samples which are supposed to show the same biological effect.


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How long do viruses, such as Zika, stay in the body?
Can a virus stay in your body (after recovery) in a concentration that is sufficient to infect someone?
Is it known how long the Zika virus persists in the body?

According to the CDC the zika virus persists in the blood for around a week.

Zika virus usually remains in the blood of an infected person for about a week but it can be found longer in some people. - CDC

I can't find much information on how long the Zika virus specifically can persist after recovery, it seems unknown just now. However, it is advised to be careful about sexual contact after infection, which suggests longer persistence is suspected in other fluids/tissues.

British health authorities have suggested using condoms for at least 28 days. - NYTimes

Some viruses do persist for a while after recovery, including Ebola Virus Disease, which can be sexually transmitted for around three months after recovery:

Some viruses, including Ebola, can linger for some time after recovery in parts of the body (for example, testes, eyes, spinal column fluid) not easily reached by the immune system. - CDC

These parts of the body have immune privilege. This means they can be infected by antigens without producing strong immune responses. This is thought to occur to protect vital tissues/areas which could be damaged by inflamation and the immune response, such as the brain, eyes, spinal column, testes, and fetuses.

Since I wrote this answer there have been several reported cases of sexually transmitted zika, highlighting the problems that can arise from immune privilege.

And the rest of the body?

By coincidence I was making edits at the time of your comment - does that help @Christiaan

Some viruses can stay in your body for your entire life, for example Herpes Simplex Virus.


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Capture recapture for only two visit assuming a open population model
I have a study system where I’m doing a capture recapture analysis. I mark fish in one year and I’m recapturing a subset of them the next year.
I only have 2 capture events. Since a lot of time has passed, relative to the fish, between the two episode of recapture, I cannot assume a closed population model. Is there an alternative?
What mark-recapture model would be best for this situation given that I want to compute a recapture probability?

I would assume your goal is to estimate the population size, is that right? Do you have any idea of the migration rate in and out of your population?

Oh! Sorry, I forgot to mention that it's the recapture probabilities that I want. No I don't have the migration rate.

If the migration is 0, then it is the standard model. If the migration rate is 1, then the probability of recapture is 0. There is no way to estimate the recapture probability without having any information on the migration rate.

What do you mean then by the standard model?

I randomly referred to one of the multiple existing models. But it was misleading. Sorry about that. If you only want to estimate the probability of recapture knowing the population size, then this probability is just the fraction of those marked and the probability to recapture a given number of them follows a binomial or hypergeometric distribution depending on whether there is replacement. I am not sure I understand your question...

What fish are we talking about and in what ecosystem? Is it a migratory species in a river system (eg salmon) or not (eg pike)?

It's Three-spined stickleback in Canada, freshwater

In a classic closed population model, you can estimate population size with k=2 (where k is the number of events) but it's impossible to separate survival from recapture probability.

Seeing this formula you could expect to be able to estimate recapture probability dividing R by S but it would be an error since S = M*survival (ø) *probability of recapture (p) . Therefore it's imposible to separate p from ø when k<2.
Hope it helps !
Cheers

If you have unique ID's on each of the fish (instead of just marked and not marked) then you could use the Cormack-Jolly-Seber open population model.

Welcome to Biology.SE. Please provide some background to your answer, for example by providing an explanatory reference (and please also briefly describe what you reference which would be the CJS open population model in this case). I suggest you take the [tour] and have a look at how to provide what we consider good answers or your answer might be downvoted. Thank you.


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What is the difference between chloride shift and Bohr shift?
Does anyone know the difference between chloride shift and Bohr shift?
Is it that Bohr shift happens in respiring tissues when CO2 concentration is low, and that Chloride shift happens in the blood as a buffer?
Sorry for asking such a trivial question and thank you in advance. And sorry for any wrong tags or title (new to the community and is seeking to improve)


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How can I estimate the CO₂ uptake of a plant?
I would like to make an estimation of the CO2 uptake of plants I cultivate, including, lettuce and aromatic herbs, such as thyme, basil, rosemary. What I want is to end up with a rough indicator for business purpose, not some super-accurate measurement.

Is there already average CO2 uptake data per plant type available?
Will this uptake vary drastically per plant type?
Can I calculate the estimate through a simple measurement (e.g. of plant weight) or does it require tight lab experiments? In the former case, how is that measurement made?

Please bear in mind I'm not a scientist, but and end-user of science. Thank you for helping me this question if needed.

Can I calculate the estimate through a simple measurement (e.g. of plant weight) or does it require tight lab experiments? In the former case, how is that measurement made?

In the textbook Plant Physiological Ecology*, they state that about 40% of the dry weight of plants is carbon, and I believe the vast majority of that is from CO2 from the atmosphere. You can take a fresh weight of an entire plant, and then dry it at the lowest temperature in your kitchen oven for a couple of days to get a reasonably accurate dry weight. That dry weight times 0.4 will give you an estimated total carbon, though I have seen other factors used. Plants can also be analyzed for Total Organic Carbon in some agricultural laboratories. Fast growing plants are going to absorb more carbon than slow growing ones.

* Lambers, H, Thijs L. Pons, and F S. Chapin. Plant physiological ecology. New York: Springer Verlag, 2008. Print. ISBN:978-0-387-78341-3


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Where does the lactate produced by tumors go?
Tumors are known to burn glucose and secrete lactate (this is known as the Warburg effect).  Where does this lactate go?
Does it steadily accumulate in the neighborhood of the tumor? This doesn't seem likely. I mean, eventually an equilibrium concentration of lactate in the neighborhood of the tumor must be reached that is balanced by some process taking lactate away from the tumor. The nature of this lactate drain is what I am asking about.
Does it enter the circulation system and is degraded somewhere else in the body (as a part of the Cori cycle)?
Is it consumed by neighboring non-malignant cells?
A combination of all of the above?
Something else?

Most of the lactate produced by tumors probably enters the circulation and is taken up by other tissues (like the Cori cycle, correct). There are several studies like this one measuring glucose uptake and lactate release by tumors in vivo, and it is clear that a substantial amount of lactate is released into the veins draining the tumor site.
Oxidation of lactate by neighboring cells within tumors has been reported as well, but I don't know of any quantitative data on exactly how much lactate this process can consume. But it seems unlikely that this can remove a major fraction of lactate produced by glycolytic tumors, since glycolysis produces lactate at a much higher rate than respiration consumes it (per ATP generated).
It's also true that tumors can accumulate lactate. Some tumors are poorly perfused, with "disorganized" blood vessels and blood flow, and then waste products may not be cleared away efficiently.
So yes, all of the above :)  There are large differences between individual tumors in all these parameters, so there is no generally valid answer I think.

I guess I'm not expecting to find a general answer. But at least some references in the literature would be nice. The papers you point out are already useful.

"But it seems unlikely that this can remove a major fraction of lactate produced by glycolytic tumors, since glycolysis produces lactate at a much higher rate than respiration consumes it" Has this been measured/estimated?

@becko  I'm not aware of any quantitative data on how much lactate is re-oxidized in tumors.  But given that respiration yields 10--15 times more ATP than glycolysis for the same amount of carbon, it seems that a large population of purely oxidative cells would be needed re-oxidize all surplus lactate from glycolytic cancer cells.  And again, there is plenty of data showing that tumors generally produce lactate. (In some cases even causing life-threatening acidosis: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4497494/  )


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Is the DNA different in each type of cell? What DNA is passed to offspring?
Our body contains many different types of cells and each of those cells have their own DNA (correct me if wrong) like skin cells their own DNA that makes them skin cells instead of muscle cells.
So my question is what DNA does a human pass down in a sperm or egg cell? Is it a specialised DNA imprint from which our whole body can be created?

Nope, you are incorrect here. Everey cell carries a complete set of genomic information, it is "only" differently expressed (read out). The only exception are egg and sperm cells, which carry only half a set of chromosomes (23 instead of 46) to be able to combine with their counterpart.

In giving birth, the sex cells join to form a zygote of 23+23 = 46 chromosomes. This zygote contains both the chromosomes. These chromosomes affect a variety of things like gender etc

Only cells in the germ line are used to produce sperm and eggs, which are passed to offspring. DNA in all other cells (somatic cells) are not passed to offspring.

Most cells in a human body contain a complete set of the genome, which is two sets of 23 chromosomes. Having two of each chromosome is called diploidy.
Within an individual human the DNA is approximately identical in every cell. Different cells are produced by differential use of that DNA: certain genes are more (or less) highly expressed etc. You can read more about that here.

You inherit one copy of each chromosome from each parent. Gametes (eggs and sperm) are a bit different from regular cells because they contain one copy of each chromosome; they are haploid. These gametes fuse to make the complete set of 23 pairs in the offspring. There are some exceptions such as cytoplasmic DNA and sex chromosomes.

Good answer +1. You might want to indicate the following posts that will answer these questions: Why is there protein variation between cells without much genetic variation?, Do both parents really contribute equally? and Do our gene change as we age?.

For clarity (and due to misconceptions in the question), I think you should specifically mention germline cells (in contrast to somatic cells), and how only cells in the germline are used for reproduction.

I think you should also clarify that it's not actually the parent's chromosomes that are being passed on (looks like that in the figure), but rather a mosaic of their chromosomes, due to meiosis / crossing over.

so in a nutshell you can create a full body clone of a person from just about any type of cell's DNA ?

@user1062760  Well, you can't make a clone of a person from any type of cell -- that's not been done, it's not known how, and it isn't allowed, at least in Western countries.  But the concept is correct; mice can be cloned from skin cells, for example (http://www.pnas.org/content/104/8/2738.full).

Genetics is an evolving field : ) Concepts such as Horizontal Gene Transfer are important, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5379729/
Also the boundaries of the “body” may be considered, e.g. Obviously the DNA sequences of gut flora are distinct from the statistically major portion of DNA of human somatic cells, but are gut flora not an integral part of the body?  Sorry to answer a question with a question but such is the nature of philosophy. Another concept worth noting is microchimerism, a striking example of which is seen in the maintenance in females of a small sub population of cells in the brain and other organs that contain the DNA of former sexual partners; pregnancy specifically, often results in horizontal gene transfer with clear effects https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3458919/

Ideally, DNA itself is the same in DNA-containing cell types. Cell type depends on expression, which depends on epigenetics. I.e. histone modification, DNA methylation, and few other mechanisms.
Also, epigenetics is the mechanism for gene expression regulation. For example, it can silence (usually, methylate promoter regions) an expression of genes on one of the chromosomes in female cells. It's called genomic imprinting. In mammals epigenetics tags from gametes are not stripped after zygote formation.

Epigenetics is not only the mechanism to silence one chromosome in cats. It is the mechanism by which genes (and chromosomes) can be regulated by special enzymes. The regulation includes activation and silencing.

And DNA is not the same in each cell type; think gametes vs somatic cells, random mutations and cells without DNA (RBCs). This answer needs to be toned down.

So the removal of half the chromosomes from both parent cells happens as the zygote is formed and not before zygote formation right? otherwise you'd have a fixed set of chromosomes that are removed from each parent cell for entire species

@user1062760 a sperm and ovum are haploid cells so they have a single set of chromosomes. However an ovum becomes haploid in an oogenesis process so in the very beginning it was a diploid oogonum.

I agree with Chris. There are examples in which the gene network is capable of showing multiple types of stable responses (for two kinds this is known as bistability). Positive feedbacks, for instance, can show bistability without the involvement of additional epigenetic regulation. However, as you said epigenetic modification are essential for maintaining the differentiated lineage (a sort of memory which can be inherited). So, it would be great if you can improve your answer and also add some references.

Mitochondrial DNA is inherited mostly from the female line and is derived mostly from the ova. Mitochondria are present in all cells but retain genomes that are distinct from the host organism’s DNA, almost as if they are a separate single called organism. Here is an interesting look at mitochondrial DNA https://www.ncbi.nlm.nih.gov/pmc/articles/PMC19448/#!po=0.943396


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What happens if a non-diabetic receives an injection of insulin?
If a person without diabetes or any diabetes-related issues receives an injection of insulin, what happens? Would the blood glucose level drop or does the body naturally compensate for the added insulin? What biological process occurs?

I tried to clarify your question text a bit - FYI

Blood sugar drops (Hypoglycaemia)
There are several other uses of insulin (other than diabetic treatment)

Some of those could be:

Diagnostics
Psychology (Narcoanalysis)
Parenteral nutrition
Cardiology (Glucose–insulin–potassium solution (GIP or GIK solution) is given   after a myocardial infarction)
Malignancy (Insulin potentiation therapy (IPT))
Psychiatry (Deep insulin coma therapy (DICT))

Sources:

Niazi, Asfandyar Khan, and Shaharyar Khan Niazi. "A Grand Dame
with Hidden Aces: The Non-diabetic Uses of Insulin." Indian Journal
of Endocrinology and Metabolism. Medknow Publications & Media Pvt
Ltd. Web. 06 Feb. 2016.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3354952/.
"Hypoglycemia." Hypoglycemia. Web. 06 Feb. 2016.
http://www.niddk.nih.gov/health-information/health-topics/Diabetes/hypoglycemia/Pages/index.aspx.

Insulin coma therapy is, as far as I know, one of the things like lobotomy. Sure, patients got more "manageable", but to call it psychiatry nowadays is a mistake.

@Mołot according to "Indian J Endocrinol Metab. 2012 Mar; 16(Suppl1): S57–S59."
"schizophrenia patients were injected with insulin to induce severe hypoglycaemia for 10–15 minutes. Thereafter, the hypoglycaemia was reversed by infusing glucose". however, you are correct it cant be referred to as psychiatry nowadays, simply due to the reason of it being discredited in the late 1950s.

It is possible to overdose and die of an insulin injection. Obviously, if enough is injected fast enough, the body can't recompense appropriately and and the person would die of hypoglycaemia. Below around 20mg/dL of blood sugar levels in the blood you are likely to suffer brain damage and eventually death.

depends on how much injected, you could just feel lightheaded or you might get yourself into an insulin induced coma, serious cases, yeah, one could die. There's a certain blood insulin level that the body can naturally compensate to maintain homeostasis, like I said before, depends on the injected amount. sidenote - Watch 'A Beautiful Mind', it shows the usage of insulin shock therapy (insulin coma therapy (ICT)) to "reduce" schizophrenia.

Any sources to add?


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Why doesn't one develop immunity to bacterial STIs?
Why doesn't one develop immunity to STIs such as Chlamydia/Gonorrhea and Syphilis even after the first exposure and treatment with antibiotics?


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How does hypocalcaemia have an effect on the excitability of cell
Hypocalcemia increases sodium influx by leak channels. Why does this elevate the resting membrane potential and increase excitability?

Which cells are you talking about? Where did you obtain the information from?

Assuming the question is in respect to neurons..in a nutshell...resting membrane potential & excitability both depend upon sodium permeability which in turn depends on potential difference of the excitable cell....now as the sodium influx is increased the minimum voltage required to increase the conductance of sodium decreases far below its normal value...so for a small increase in membrane potential from the normal very negative level the sodium channel becomes activated elevating the resting membrane potential...
In fact, the calcium ion concentration needs to fall only 50% below normal level before spontaneous discharge of peripheral nerves occur giving rise to "tetany"...
Reference- Adapted from Guyton & Hall- Textbook of medical physiology (12E)
You can also refer to Berne & Levy's & Ganong's physiology book for further details


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Difference between the spinal cord and vertebrae column
What is the difference between the spinal cord and the vertebrae column, they both run through from the head to the abdomen. Does any one have any idea.

The vertebral column is a bony, segmented structure that supports the torso/head and thorax. The spinal cord is a bundle of nerves that runs inside the structure of the vertebral column. So - they run together, but are completely separate.


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Could a single cell be brought to life?
If a scientist is observing a single cell under a microscope, and then realizes that the cell has died, is it possible to bring that dead cell back to life?
For my inquiry, let's assume that the death of the cell has occurred without disease or external circumstances.
Has such process ever taken place in a lab before? Thx.

this is very speculative and vague - I tried making some changes to improve it....but still vague.

@Vance L Albaugh, thanks for your help, the question is simply about whether a dead cell could be brought back to life or not. Not sure what is vague about this. Please explain the vague point(s) so that I could attempt to clarify. Thx.

How is cell death defined?

@Remi.b, Excellent question. I am not a Biologist by any measure, so I really not sure of the accurate scientific term. However, I would assume that one aspect of cell death would include recognizing that the cell has stopped performing the chemical reactions that a living cell normally performs. However, I am trying to understand, so I may be wrong.

Well once we know the reason due to the death, then I fell we can provide a better answer. Because i dont know how a cell can just die like that. There must be a reason

There are species where cells and even whole organisms can go into a state called cryptobiosis where their metabolism is suspended but can be revived later. This usually happens when the conditions become too bad for survival (dry/cold etc.) and is reversed once the conditions improve again (rehydration warming up). One prominent and fascinating example are tardigrades.
Also, it is possible to freeze cells in liquid nitrogen where all metabolic processes are extremely slow. With modern freezing/thawing processes cell survival rates >90% are possible. However, before you ask this will not work on whole tissues let alone people!
Cryptobiosis only works for specialized species and only under certain conditions. Normally, once a cell starts to die, it either does so because it is too damaged to keep living, a process called necrosis or because apoptosis (programmed cell death) was triggered upon which its DNA is fragmented and the proteins are degraded by proteases. Neither process is reversible once started.
Note: I find your restriction "the death of the cell has occurred without disease or external circumstances" a bit puzzling and too vague. Unless something happens to them cells don't just die. Therefore I explicitly ignored this restriction until you formulate it more specifically so that it makes sense.

Thx. for the detailed answer. I assumed that sudden cell death is frequent and normal, yet In this question, I got about 3 people questioning this point which hints to me that sudden death is 'not normal'! I need to do some reading to understand the 'basics of cell death reasons'!

@NoChance If you feel that my answer was correct, please accept it (click on the hollow check mark you see below the voting buttons). Thanks :)

I expected more answers to come for such an interesting question, but you were the only one! Thx.

@NoChance Thx :)