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Can you make sperm and eggs from the same person using in vitro gametogenesis?
In a recent popular science article there is a discussion of the potential disruptive technologies that could become available with in vitro gametogenesis (IVG). Using skin cells you will be able to create either sperm or eggs. Thus, using stolen cells from Brad Pitt (simpler than getting his sperm) will allow a woman to have a nonconsensual child of him. What is not mentioned in the article and thus my question: Does this technique currently allow, (at least in mice), to make sperm from a female and eggs from a male? If that is the case, what will be the result of fertilizing sperm and egg from the same individual: a clone, a genetic "sibling" (not an identical twin), or neither of them?

Related post http://biology.stackexchange.com/q/27736/3340 (it is older than the IVG paper but some points are still valid).

Thanks guys from your comments. Also, feel free to edit the title if the edit I just made is still misleading.

Possible duplicate of Does a man contain all the genes needed to make a woman?

At present (early 2017) the answer is No.
The trick to make spermatid like cells (ie they are not real sperm cells and need to be injected into an oocyte to accomplish fertilization) from ES and iPS in a dish was just achieved last year http://www.sciencemag.org/news/2016/02/new-method-grows-sperm-dish
The trick to make oocyctes from stem cells is not as complete and still requires an lab grown ovary to complete the process. http://www.sciencemag.org/news/2016/10/mouse-egg-cells-made-entirely-lab-give-rise-healthy-offspring.
The methods above still use ES cell of the appropriate gender. Female ES cells to make oocytes. Male ES cells to make sperm.  No info on female ES cells being driven to make sperm or even spermatid like cells.
That said... we have this paper http://news.nationalgeographic.com/news/2004/04/0421_040421_whoneedsmales_2.html, where a mouse is genetically engineered to produce oocytes that have imprinting patterns similar to a sperm. This genetically modified oocyte is then forced to fuse with a normal oocyte. Success rate was very low. 371 fused oocytes, 10 live births, 1 surviving to adulthood.


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Need clarification on HKA test
I understand that HKA test tests for neutrality. And under neutrality we say that "ratio of segregating sites with species (S1) and fixed differences between locus (F1)" (S1/F2) at one locus is equal to S2/F2 of another locus.
But what will S1/F1 > S2/F2 signify? And what will S1/F1 < S2/F2 mean?

source: Stack Exchange

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How much does hearing deteriorate with age?

For the average person, what is the lowest volume of a pure tone at each frequency they can hear as a function of age?
I know some people lose hearing faster than other people, because they are exposed to loud sounds. So I am also interested in hearing loss induced by loud sounds as a function of frequency.
The brain can adapt to the hearing loss, thereby creating the illusion that a sound is just as loud as if nothing happened to their hearing. For that reason, I also wish to know what volume the ear transmits to the brain as a function of frequency and age.

Hearing sensitivity deteriorates with age, which is called age-related hearing loss, or presbyacusis. Presbyacusis is characterized by elevated hearing thresholds. Especially the high frequencies are affected by age, but eventually even the low frequencies may deteriorate substantially. Hearing sensitivity is typically expressed in an audiogram, which depicts the hearing threshold as a function of acoustic frequency. To express hearing loss as a function of age, however, it is more convenient to plot the threshold at various frequencies as a function of age (Fig. 1).

Fig. 1. Hearing thresholds at various frequencies plotted as a function of age. source: Handbook For Acoustic Ecology.

Exposure to loud sounds may be detrimental to hearing, referred to as noise-induced hearing loss. Typically this results in a loss of sensitivity at the moderate frequencies (3k to 4k); a mid-frequency dip (Fig. 2). Old age will add a high-frequency hearing loss on top of that.

Fig. 2. Typical audiogram associated with noise-induced hearing loss. source: American Hearing Research Foundation

The brain will not adapt to elevated thresholds. A threshold represents the minimal intensity level a sensory system can detect. Elevated hearing thresholds due to old age and noise-induced hearing loss are caused by sensori-neural hearing loss, meaning the hair cells in the inner ear (the cochlea) are dying. The brain can never detect a signal that is not transmitted via the auditory nerve and can hence never compensate for elevated thresholds. In turn, when thresholds are elevated substantially, a person suffering from such a hearing impairment may ask you several times kindly to repeat what you were saying, but a little louder. Then, when you start screaming after the third time, the hearing-impaired person returns the dreaded "You don't have to scream at me!". That is because the brain does not adapt to the elevated thresholds; once the sound is transmitted by the degenerated cochlea, it is transmitted at that loudness and perceived at that loudness by the brain. Moreover, a process of recruitment can occur in the hearing impaired, where the perceived loudness is exaggerated. Recruitment may occur at the hair cell level, but it is a not well characterized phenomenon.

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Maximum loading volume for agarose gel with 10 well comb
I want to load my agarose gel with my PCR products, which are 50 µL reactions.
I am wondering how much of those reaction I can load into one well if I use a standard agarose mini gel (10 well comb, ~8 mm thickness, 1.2%).
Should I try loading the entire 50 µL into one well or should I split it into two?
Thanks in advance
Phil

Why do you want to load so much sample?

Low concentration or for gel extraction I would assume...

Yeah, it is for gel extraction. I want to load maximum sample while using the minimal amount of gels

If this is for gel extraction, load two lanes. Or connect two on the comb with tape to make a bigger well.

How many samples have you got? You can tape neighbouring teeth of the comb together to create double- or triple-wide wells to load more sample.
I don't normally load more that about 20 µL.
You could also make the gel thicker potentially.

Thanks for the tip! Unfortunately, I only have one standard agarose apparatus, and it doesn't allow me to use wider gels. I tested with loading buffer in one well, whether or not it would fit 50 µL. It did, but I didn't take the risk of losing sample due to leakage, so I will just run more gels. Thanks a lot, though!

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Klenow fragment does not seem to have 5->3 exonuclease activity, but it can still displace nucleotides in front of him - How?
Klenow fragment does not seem to have 5->3 exonuclease activity, but it can still displace nucleotides in front of him - How? How would this displacement mechanism differ. My first guess is that exonuclease activity actually digests upcomming strand into single nucleotides, but how come the displacement activity not get in the way for lab work? :
"The 5' -> 3' exonuclease activity of E. coli's DNA polymerase I makes it unsuitable for many applications. "

Why doesn't the 5->3' displacement activity make the applications troublesome then? What would those applications be.
I've spend a long time looking for these answers, but unfortunately I've found nothing.
Maybe someone has any idea:)
Cheers!
References:
Image - http://www.vivo.colostate.edu/hbooks/genetics/biotech/enzymes/klenow.html

Welcome to Biology.SE. Please provide references to images you add to your posts.

Generally, the New England Biolabs website is a great resource for this sort of information.  Maybe you already know this: Klenow fragment is widely used in molecular biology today. The broad use of Klenow fragment is because it will remove 3' overhangs, thereby 'polishing' or 'blunting' the DNA.  See the famous cloning techniques manual for additional information.
It is a polymerase, though, and it does perform 5-->3' elongation in the presence of dNTPs.  (sidenote: Klenow was initially used in polymerase chain reaction (PCR) development, and later replaced with heat-stable Taq pol.)
The so-called 'strand displacement' activity of the enzyme allows the 5-->3 elongation of the new strand to occur even in the presence of an existing, annealed strand ahead of the advancing polymerase, as you say.  This may seem problematic at first glance, but the job of polymerase is to make a complete, templated copy of DNA -- that is why reseachers use it, and that is its job in nature too!  Stand displacement is really convenient for scientists when using random primers, for instance.  The DNA polymerization can continue unimpeded despite the presence of a 'downstream' barrier.  This is also why not having 5'-->3' exonuclease activity is helpful in this context.  (sidenote: pol I is not the main replicative polymerase in E. coli. and its discovery is one of the great stories of post-war biology).
I hope this addresses your question(s).

Thank you for your answer. I am still unclear on one point - how is strand displacement activity different from 5->3 exonuclease activity. They both remove nucleotides in 5->3 direction, don't they?

a nuclease digests DNA; strand displacement is not strand digestion


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When is strict sterile technique necessary? Cloning vs. protein expression
Background: I have previously worked with RNA, and then we use laminar flow hoods for any work where we do plating or inoculation of cultures while applying sterile technique. I am now working in a biochemistry lab. I'm told that I can work on a lab bench, while doing basic cloning for production of plasmids in E.coli, and don't need to use a Bunsen burner as long as I apply sterile technique (and in most cases I don't see people sterilizing the bench with enthrall prior to work). However, if I do any work which relates to expression of proteins - then I should use the Bunsen-burner while applying sterile technique.
Question: Is it really so that you don't even have to use a Bunsen-burner while plating (normal E.coli: XL1-blue cells)? in this case, why? Are there not always something in the lab which can grow on kanamycin plates? We don't use white/blue screening, we simply spread XL1-blue cells onto LB plates with kanamycin - then pick a averaged sized colony to make a LB-culture. It seems to me that we are just lucky that we usually pick the right colony (which we do confirm by sequencing after mini-prep).

As answered you can do without the flame just fine for stuff that you do not want to store for an extended period of time. In my experience if you open a kanamycin plate for a couple of minutes, only 1 in 10 plates will have some kind of contamination, almost always some sort of fungus. Yes, there's stuff that will contaminate your plate, but there's just not that much.

Short answer is it never hurts to practise thorough aseptic technique.
My general rule of thumb is, if I'm opening a culture of bacteria (plates, eppendorfs, tubes etc.) I do it under a bunsen - the exception being if I plan to lyse the cells anyway.
For protein purification, sterile technique is important if you plan to store the sample for a while. Proteases in the environment and on your sample/self can make short work of destroying all your hard work.

Never trust your antibiotics fully. For one thing, they often won't stop fungi, which will ruin your samples even in the presence of some pretty nasty chemicals. If you're using some of the crappier antibiotics (Ampicillin is a prime example), the antibiotic degrades over time. B-Lactams in particular are an issue, as the B-lactamase is secreted in to the media. By day 2 of a culture, there will basically be no ampicillin left!

The ampicillin is a very important point. I once had to train some people who always had their maxiprep fail. After going through every step many times, I saw that they had made many frozen solutions of ampicillin and kept them at -20 for 6 months or more. I never use frozen ampicillin older than 1 month, keep it as dry powder until you need it.

For most plasmid preparation, strict sterile technique is not necessary. The antibiotics in the media will select for bacteria which carry a resistant plasmid, so you don't usually have to worry about other organisms getting in.
However, when you're using several types of plasmid, you do need to be careful to avoid cross-contamination, because each plasmid is resistant, so bacteria transformed with plasmid A will live just fine on plasmid B's plate. When plating your cells, be sure to pass your cell spreader through a flame. It doesn't have to be an official Bunsen burner, I used an alcohol burner just fine.
If you make a big bottle of media and use small aliquots at a time, then the bottle should only be opened inside the hood.

that sounds rational, however, how about protein expression? because you also use antibiotics there, but I have heard that e.g. bacillus is a very common lab bacteria that a gets everywhere and grows quite fast even with antibiotics? I mean, there is a good reason why media is autoclaved before use even though you use antibiotics. Why should I not take the same consideration with protein expression using e.g. rosetta as with basic cloning using XL1-blue ?

@CuriousTree I've never done much protein expression, but I think part of why we can get away with less than ideal aseptic conditions with plasmid prep is the time. We never let the bacteria grow longer than 24 hours, then we lyse and purify the DNA. Longer than that and the antibiotics aren't reliable. How long are your protein cultures grown for? Do you keep the cells frozen? Do you plan on thawing them out and starting new cultures with them?

degradation og antibiotics is a good point, we normally grow the cell from the morning then express our protein overnight before harvesting, and don't re-culture them. All in all they grow about 24 hours, in presence of kanamycin and chloramphenicol.

That's only true if Plasmid A and B are different but contain the same basis of resistance. A kanamycin plasmid won't survive on chloramphenicol and vice versa.

@JoeHealey There aren't that many antibiotic resistance genes, so it's common to have two different plasmids with the same gene. The labs I have been in also tend to use the same vector for all our genes, so they all have the same resistance.

Yes I agree, it's important to be mindful of your samples genotypes. There are additional confounding variables as well, for example, kanamycin and neomycin have the same basis of resistance, so cannot be used to kill off one another ;)


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Explanation of ecological parameters with some model examples
I think an ecological parameter is:

A variable, measurable property whose value is a determinant of the characteristics of an ecosystem.

From eea.europa.eu
But what could these parameters be? In other words, what are some examples of 'parameters'?
I assume they possibly vary with ecosystem.

I am not sure I understand your question. Do you not understand the definition you gave? Are you looking for examples?

@Remi.b Yeah, examples for a particular ecosystem.

For a particular ecosystem, a variable will take a value. Are you looking for a description of a random ecosystem?

Any ecosystem. I just want to know how it works. There's no information on internet. At least I found none.

So you are basically asking "What is the average temperature, soil acidity, rain intensity, average daytime, .... in the toundra (or in the savannah or in other ecosystem)?". You can find many of these descriptions on wikipedia.

No, I'm not. I wanted to know what these parameters could be (like the ones you have named) ? My previous comment is kind of misleading. I just want some of their names from an authentic reference or an expert user and I'll do the rest, find out how they work.i.e how they help determine the condition of an ecosystem.

Part of the confusion lies in the fact that parameter can be used both in a technical sense (parameter in an explicit theoretical model) and in a looser, general sense ("...there are many parameters to consider when buying a car..."). Note also that you shouldn't mix up parameter and variable (which is also done here in the comments), especially in statistical models. Technically, a parameter is a fixed value, used to define a model (model parameter), while variables are things that are measured (and allowed to vary) - short summary: http://www.bmj.com/content/318/7199/1667

@fileunderwater I'll read it.

Here are some examples of ecological parameters:

temperature
yearly maximal temperature
rain intensity
Longest period without precipitation
soil acidity
salinity
nitrogen pollutants
average daytime
maximal wind speed
solar irradiance

You can just have a look at the description of any biome of interest on wikipedia to get an idea of what are the most common parameters used to describe biome. Precipitation, temperature and how their seasonality are very typical descriptors of an ecosystem.

Is it always related to the non-living components? Can there be something related to biotic components as well, like species diversity?

In the description of biome you typically assume some kind of equilibrium in the sense that the non-biotic environment is fixed and most fit species will assemble into the right communities. When making description of of te environment a specific individual experiences, then yes, biotic parameters are of great importance.

Nearly all ecological parameters (at least the ones I can think of) qualify for ecological factors.


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Can two arms-racing species be stabilized?
I am trying to build an evolution simulator in which there is group A and group B, each group has 9 members each generation. Each generation, each member of group A will enter a competition (in the form of combat) with a random member of group B, and fitness will be calculated based on how quickly and with how little losses will one member's army destroy the other. The best few members of each group then becomes the parents of the next generation.
(Note that an "individual" of each group is in fact a genetically determine neural network that controls a swarm of robots, think of it as a swarm of ants sharing the same DNA and thus can be effective consider one individual)
Will this end up with both group A and B having phenotype/strategy that do not change very much over many generations, or will it result in strategies that gradually changes throughout generation, with each successful, significant change out-smarting the opponent's old strategy until the opponent develop a counter strategy?

"Each generation, each member of group A will enter a competition (in the form of combat) with a random member of group B, and fitness will be calculated based on how quickly and with how little losses will one member's army destroy the other."  It is not clear what you mean here.  You mentioned 9 individuals per group; then what comprises each individual's army?

Question updated, to explain in short, an army is made of a swarm of identical robots controlled by said individual.

Consider adjusting your scenario: you are locking time-to-reproduce and you are only considering violence as a winning strategy. Small furry mammals are the best fit for their environments generally by being precocious breeders with massive litters. If you add these two axes, you may avoid the arms race. Consider also that eventually you will have more than two groups, but this will complicate the processing.

To rephrase Cort Ammon. It depends on how you setup the system.
Imagine each combat strategy as a point on a landscape. Good strategies are on higher ground, poorer strategies are on lower ground.
A and B each have their own combat strategy and thus start at different points on this landscape. Mutations allow a species (say A) to explore the strategies around its starting point. Selection will cause the curtail that exploration.
If A find itself on a slop of a hill, selection (ie your combat and mating system) will cause the A population to drift upwards on this slop. However if A find itself on the peak of a small hill, it has no where else to go.
So how the scenario will play out will depend on the initial start conditions of population A and B. The mutation rate/genetic variability of the population (ie how many strategies population can explore around its initial strategy).
Additional factors is the genetic system that you have. If individuals of your species can only have one strategy (haploid), the species will be bound to its local hill. However if an individual can have more than one combat strategy at a time, (ie a diploid or gene duplication in RL), then the individual can have a combat strategy that work (local peak) and have a second strategy that is free to evolve... free to explore the landscape... going down valleys of bad strategies... and may eventually find the foot of a mountain... which a peak fitness higher than even the local peak it started.

Unfortunately, the answer to this varies greatly based on your individual implementations of the simulation.
Let's assume As are dominant at a given iteration.  We can enumerate the genomes of B which can defeat A.  With that, we can see how "close" B is to one of those genomes.  If B is far enough from those "winning" genomes, it can be difficult for B to eventually overcome A.
Note I say difficult, rather than impossible.  Eventually due to random chance B will eventually find the counter to what A is doing if we assume B gets to do this in a vacuum.
Remember that, while your individuals are "competing," its actually the populations that evolve.  If your rules permit enough introspection of how B's operating, A may groom B into weakness.  A may intentionally let a few of B's least fit individuals win a fight, for the expressed purpose of abusing your rules for the next-generation to make sure B remains unfit.  Any B's which start looking interesting will get obliterated as fast as possible.
We actually do this with pest control.  One known method of pest control is to leave one small corner of a field unprotected and spray the rest.  Any insects which develop a resistance are likely to mate with the many insects that grew up on the sprayed corner, increasing the likelihood of those resistant genes getting diluted or even lost.  This increases how long a farmer can use a given pesticide before having to increase its usage or switch to a new pesticide.
On the other hand, there are games where arms-racing species never stabilize.  If you build a system based on the Chinese 5 Elements, the system is designed to encourage two entities to spin eternally on the cycle, never fully stabilizing unless you reach an overacting state (which is considered highly undesirable for both parties).
So it really depends what your particular rules do.  Your rules could permit stability, or they could not.


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Do leaves only appear on new growth?
In some willows, there is a clear distinction between floriferous buds (out of which the catkins grow) and vegetative buds. I have observed this phenomenon myself on numerous occasions (in fact, I can ID several species and hybrids on floriferous buds alone). However, I never took it further and there are things I still don't understand. What about those vegetative buds. What grows out of them: twigs with leaves on them out of some and single leaves out of others? And would there be any noticeable difference between these two types of vegetative buds (if they both existed)?

To answer the question in you title, the leaves appear both on new and old growth. In addition to vegetative and floral buds, there are also dormant buds that activate themselves on old growth after leaves or branches are cut. You can read here a list of buds.
For the following questions in the text I think the answer is different for every species.


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Evidence for annual rabies vaccine?
US companies that sell rabies vaccines routinely recommend that they be given annually. Obviously, these companies have a financial incentive to recommend that their vaccines be given as frequently as possible.
No human vaccine that I know of requires annual booster shots. The standard recommendation to veterinarians that they receive a single primary course of vaccinations and no boosters at all. It seems inconsistent that the CDC recommends that vets that work with sick animals on a daily basis get a one-time vaccination, but the USDA "recommends" house pets get vaccinations every year. My understanding is that this USDA "recommendation" is based on no scientific evidence whatsoever.
Is there any scientific evidence indicating the effectiveness of vaccines as a function of the frequency of their application?

Not going to research an answer, but canine rabies - and dogs as vectors in human rabies cases - has been eliminated in the US in my lifetime. Coincidence? Conspiracy? I can guess...

UK veterinarians get a boaster every 3-5 years.

Where I live, it's every 3 years for dogs.

@jamesqf That is only because your vet is not using Pfizer vaccines.

@Imprisoned Rhesus: But the fact that there are 3 year rabies vaccines, and that 3 years is the interval recommended by vet schools (e.g. http://www.vetmed.ucdavis.edu/vmth/small_animal/internal_medicine/newsletters/vaccination_protocols.cfm )  disproves the (implied by wording) claim that ALL US companies try to push 1 year rabies vaccines.


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Which analytical techniques could you use to research relationships between 2 proteins?
Two of the proteins I am researching are known to interact. However, I would like to know if they interact with other proteins as well, and possibly form a pathway. Which analytical technique(s) I should use to determine this if I did all in silico analysis already? Any suggestion is welcome.
I am using a nematode C. elegans in my research, and RNAi is not an option, as I have already performed it.

This question is far too broad. From the [help/dont-ask]: Your questions should be reasonably scoped. If you can imagine an entire book that answers your question, you’re asking too much. The field of protein-protein interactions is quite wide, and there are numerous techniques to consider. This is not the place to list all of them.

There are plenty of methods to use. Here is a overview and background of some common methods as written by ThermoFisher:
https://www.thermofisher.com/se/en/home/life-science/protein-biology/protein-biology-learning-center/protein-biology-resource-library/pierce-protein-methods/overview-protein-protein-interaction-analysis.html
There is also phage display if you want to find binding partners, which is a very interesting method to narrow down binding partners from an entire interactome. It simple to set up in a lab and you can perform it all in a 96-well plate using ELISA and several rounds of phage selection. And of course there are also e.g. yeast-2-hybrid (Y2H) or co-immunoprecipitation (Co-IP).


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What is the estimated number of variant surface glycoproteins that trypansomes can express?
In "Vaccination against trypanosomiasis" by Greca and Magez they assert that there are "innumerable" variant surface glycoproteins that the parasite can express. What does innumerable mean here? These proteins presumably have to conform to some sort of structural conditions, so I don't believe it is truly infinite. Is there an estimate of the order of magnitude of the number of these proteins?


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Are there endoscopic technologies for blood vessels?
Endoscopic procedures are used to look inside cavities like intestine, esophagus etc. Is it being used to look inside blood vessels?

there are endovascular procedures that we use for looking at vascular anatomy and clots/blockages within blood vessels - these are surgical procedures that are typically performed by Vascular Surgeons, but Cardiologists also do similar procedures for defining the coronary vasculature, and interventional radiologists also perform vasculature procedures as well. https://en.wikipedia.org/wiki/Interventional_radiology#Vascular

Blood is hard to see through, so visualization with a camera isn't used (to my knowledge). However, Intravascular ultrasound can be used, though it is expensive and not all that common. Instead, angiography is usually used, by filling the vessels with a radio-opaque dye
There are also many techniques used to treat vascular conditions, like balloons/stents to open and keep open blocked or partially blocked vessels, or to repair valves. You can read more about Interventional cardiology or minimally invasive procedures.

Another work [1] that might be interesting to look at is the one titled as "Interactive Volume Segmentation with Threshold Field Painting". The work addresses the problem of volume segmentation mainly for blood vessels inside the brain. It is a Human-Computer Interaction (HCI) research, however, the authors used several procedures and devices to work with. Might be interesting to answer your question.
Finally, and most importantly, it might be important to you look [2] at a paper called "3D Reconstruction with Low Resolution, Small Baseline and High Radial Distortion Stereo Images". In this paper, the authors analyze and compare approaches for 3D reconstruction from low-resolution (250 x 250), high radial distortion stereo images, which are acquired with a small baseline.
[1] Takeo Igarashi, Naoyuki Shono, Taichi Kin, and Toki Saito. 2016. Interactive Volume Segmentation with Threshold Field Painting. In Proceedings of the 29th Annual Symposium on User Interface Software and Technology (UIST '16). ACM, New York, NY, USA, 403-413. DOI: https://doi.org/10.1145/2984511.2984537
[2] Tiago Dias, Helder Araujo, and Pedro Miraldo. 2016. 3D Reconstruction with Low Resolution, Small Baseline and High Radial Distortion Stereo Images. In Proceedings of the 10th International Conference on Distributed Smart Camera (ICDSC '16). ACM, New York, NY, USA, 98-103. DOI: https://doi.org/10.1145/2967413.2967435

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Exsanguination Time from Damage to Major Arteries
For a game project, I need to study how much blood loss is suffered when the major arteries of the human body are severed. I believe there are medical textbooks that have collected data on blood volume loss from the various arteries, but I'm not sure where to look to find this data.
If there were some table with a list of arteries, and the volume of blood lost every second, with estimates for how long a surgeon has before the patient bleeds out; that would be extremely convenient. I suspect that isn't the case.

EDIT: I searched further for data on the subject, and found something dramatically unusual. I would like to ask how credible this data seems: http://realfighting.com/unconsciousness_and_death.php
The data is said to come from a Dr Lorne David Porayko and a Dr Christine Hall.
The web page has a list of times for bleeding to death from if various arteries were severed under the conditions:

There is no compression of a lacerated artery underway. This was irrelevant for a lacerated vein due to the fact that a vein can’t be compressed
The subject is previously healthy with a normal haemoglobin concentration and has a normal VO2 max prior to being wounded.
If an artery is the target, the artery is incompletely transacted.  Completely transacted arteries go into vasospasm and retract into their perivascular sheaths which markedly reduces bleeding and even stopping bleeding all together in the case of smaller vessels. On this point Dr Porayko stated that this is the reason the Ghurkhas were trained to twist their knives in the femoral artery after puncturing it- to avoid a clean surgical transaction, thus preventing the vasospasm and retraction into the perivascular sheath, and instead to intentionally cause a hole in the vessel sidewall which is much more lethal.

The adventitia (a saran wrap like layer around the blood vessel) does not seal the wound ( The doctors stated that this usually does happen in survivors) and/or a clot does no form after blood pressure drops."

They then suggested the following data:
Carotid Artery:
Approx 2-20 minutes
Jugular Vein:
Approx 15-60 minutes
Subclavian Artery:
Approx 2-20 minutes.  The doctors also noted: “this is a special circumstance anatomically because this vessel is protected by the clavicle and the first rib (sandwiched between them) if the Subclavian artery bleeds, the only way to compress it and repair it is to open the chest by thoracotomy.  You cannot compress it. Patients usually die on the scene or en-route to hospital.
Subclavian Vein:
Approx 15-60 minutes
Brachial Artery:
5-60 minutes.  The doctors also noted: “pretty unusual to see these without compression by EMS)
Femoral Artery:
5-60 minutes. The doctors also noted: “Pretty unusual to see these without compression by EMS)
Aorta or any part of the heart:
Approx 1-2 minutes.  The doctors stated that the heart conducts 100% of cardiac output.  Assuming transaction and that the hole does not seal. Ventricular holes do usually seal while the arterial ones do not due to the orientation of the muscle fibres.
Two other areas of note made by the doctors also included:
Popliteal Artery:
Located behind the knee, would be similar (but slightly less) to cutting the femoral artery
Inferior Vena Cava:
Can be attacked via a deep abdominal stab, similar to cutting the Jugular vein

Additionally, the Doctors shared anecdotes of patients who survived extreme blood loss, defying expectation:

One of the doctors has seen several patients with traumatic cardiotomies (a big hole in the
heart) survive for 20 minutes before being treated
One of the doctors treated a patient who had been stabbed in the abdomen, where the knife hit the inferior vena cava, his belly was full of blood, he was conscious, although in shock, an hour after the injury when he arrived in the ER. He survived.

The doctors stated that they have seen patients who have bled out nearly their entire blood volume, but yet are still awake and talking (although looking bad) for many minutes following an injury and  survive to tell their story.  Dr Porayko stated, “So it is a mistake to underestimate a person’s capacity to compensate for acute hypovolemia and anemia (hemorrhagic shock), even when very severe. This is especially true in the younger population.


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Protein purification: Linear elutions or stepwise elution, using imidazole or pH gradient?
I now work in a lab with a protein and a pre-made purification protocol, were they purify a His-tagged protein using linear elution which then gives a steady increase in the imidazole concentration. However, I am curious to as if you plainly have to test which elution scheme you want to use, or if there are some "rule-of thumb" on what is a more standard way to elute protein, and what in general is more common?
Also, say for instance (just as an example) that I use a protocol which in the end loses about 80% of the protein before it's pure, is one of the first things you could do is to change the elution schemes to increase the yield? Are there other very basic things one can do to optimize a purification protocol which has not been so thoroughly optimized?
So basically:

Is linear "usually" better/more common than stepwise?
Is imidazole gradient "usually" better/more common than pH gradient?

Linear is better typically. The flow rate combined with fraction size and length of time gives you better resolution for which proteins are coming off the column at what point.
Once you've narrowed down the imidazole concentration at which your protein comes off the column, you can in future just stick to concentrations around that area, though it's still advisable to use gradients either side of that concentration as your preps are never likely to be completely consistent.

How do you know you're losing 80% of your protein before achieving purity? If your protein isn't separating from other contaminants during IMAC, you can try switching to an IMAC optimised strain (I use NEB BL21(DE3) NiCo21's).
Usually you'll have to do some downstream purification in any event. Gel filtration is common. You could also consider a different column chemistry such as anion exchange.
EDIT
Typically I wouldn't expect that you would need to mess with pH very much when performing IMAC. I certainly have never had to. You are likely to need physiological pH to ensure native folding of your protein.
You can however use other additives if your protein is recalcitrant. For example, I often add 1mM DTT and 2M urea to my samples and then heat them slightly as my protein binds things easily and is extremely stable. GE Provide a whole booklet of supported additives for their columns, you may have the same thing for yours too.

thanks for the input, the optimization is just because I'm curios in general what steps could easily be altered a bit and most likely give you metter protein yield. I just stated 80% as an example, but that might be a bit extreme. Although I am working on a protocol that i know they really just went with without really trying to optimize it.

You can't say categorically that linear is better. There are cases where increasing the imidazole concentration step-wise results in cleaner, more concentrated fractions, and other cases where steadily increasing its concentration via a gradient over a period of time works better. It all depends on the protein and the starting material.

For the purposes of calibration and optimisation linear is typically better so I stand by my point. Stepwise doesn't give you the same resolution. Once you've established your ballpark elution concentration then sure.

This does answer what I'm wondering about (thanks), however what about pH vs. imidazole concentration?

Edited my answer


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Experiments on abiogenesis in laboratories
Has any scientist created an organism in a laboratory using the primitive kind of Earth's environment, like the one used by Miller, etc.?
I read that protobionts (coacervates and microspheres) have been created in the lab by Alexander Oparin and Sidney Fox respectively. I also read that these were not 100 percent living.

Abiogenesis is unrelated to evolution. It is not an evolution experiment (as we typically do with E. coli, S. cervisiae or D. melanogaster for example) of trying to recreate the environmental conditions of 3.5 billions years ago. You might want to remove the term evolution from your post.

As a start, you should read about the famous Miller-Urey experiment and the wikipedia page on abiogenesis esp. the section called current models.

@Remi.b I corrected the question's tags and title

Now the question you have is really very interesting and deep but the short answer is we still don't know enough to be able to decide
1.Precisely when an assembly of molecules and their interactions becomes a living organism and
2.We have no idea what the "alternatives" of what we know today as life are, so we can't be really sure what kinds of "other possible life forms" can be generated both in the laboratory and in the outer space on some distant planets.
In order to tackle the first question in the last decade or 2 new science has emerged-the field of synthetic biology whose goal is to "recreate" life in the laboratory from materials generally not considered to be alive-like cell membranes and DNA alone out of the cell but they are also trying to upgrade our current technology for manipulating the DNA of living organisms to the point where we can literally create new species in the laboratory. Here are some very good publications by the most renowned expert in the field of synthetic biology Craig Venter-here and here . These are seminal works for synthetic biology but if you want to know more you can search entire journals dedicated only to synthetic biology-here,here and here. There are actually hundreds of articles pertaining exactly to the answer of the question you are posing-what are the experiments we have done in the laboratory to recreate life in controlled conditions and how much we can "model" it to our own desires. Even if you only skim the abstracts of the articles in these journals you will be able to see how far we are in the de novo genesis of life and what we can do with our newest technologies to mimic the process by which the first cells arose. You would also find good work showing the prospects for manipulating current living cells to "synthesize" what scientists would consider new "man-made" species of bacteria. Although we aren't quite there yet the prospects are exciting at the least and really mind blowing at best. The discipline (I call it discipline because it isn't "just" a science but a combination of recombinant DNA technology, advances in the chemistry of large biomolecules, cutting edge genomics and proteomics, novel methods for computational modeling of metabolism and genomics and many more disciplines combined into one direction) is just in its "infancy" but even only what we can do now is enough to open the door for an entire new array of biotechnologies to come. However, I personally advise you to begin with the 2 papers of Craig Venter I already showed you and also this one and then go to these journals.
I would also recommend you seeing the reviews of Pier Luigi Luisi on the attempts of constructing self-replicating vesicles in the laboratory-here,here and here. He in my opinion is the man who has got the closest to actually achieving in the laboratory the synthesis of systems close enough to the living cell-self-replicating lipid vesicles. I think if we are ever to recreate life in the laboratory this is the closest shot we have. You might also be interested in this paper here and this here who pertain to the same field-the use of lipid vesicles as a simple way to recreate the origins of life and to build living cells in the laboratory.
Lately, there is also one brand new interesting paper from this year on the issue of creating molecules and systems of molecules capable of evolving themselves into more complex ones here.
Now on the second question-how to recognize what kinds of forms of life can exists in the universe, there is also a fast growing new science-the science of astrobiology whose goal is to devise a broader perspective on what life is. can be and how it can arise in the wide context of the cosmos. not only in the particular context it occurred here on Earth. There are 2 good journals pertaining to this field here and here which can give you very good perspective as to what the field is about and how it can shed more light both on what life generally is in the universe and how can we recreate it on Earth. I would also recommend you to read the articles Life as we don't know it, Defining life,How rare is complex life in the Milky way? and The potential of detecting "Life as we don't know it" by fractal complexity analysis. Those papers should be nice "introduction" to the world of astrobiology and if you follow through browsing the journals I just showed you can get a pretty good idea where we are today in the quest to answer your question.
You might also want to consider learning more about the origins of life. It also is a field directly related to the question you posted. Nice review on the topic is here and you can also check out this article and this article here. Then, you may want to check out the journal dedicated specially to investigation on the origins of life-Origins of life and evolution of biospheres and watch this online lecture on the subject.
Another issue pertaining to the question is the definition of life and how difficult it is to be formulated. If you become familiar with the issue you will understand why it's so difficult to tackle the problem of how to synthesize life, where it is throughout the universe and how it originated here on Earth. I recommend you these 2 seminal works on the definition of life here and here. But I would also recommend you to read this,this and this article to get a deeper look at the problems we face even defining life today. If we can't even agree on what life is how do you expect to be able to understand how it originated or how to create it?
Another direction you could also look at is our attempt to model and describe what we can call life at all levels it can appear-the field of artificial life. You can learn more about it in the journal Artificial life which deals with our attempts at modelling complexity in abstract systems close to the dynamics of the living ones. Yet another attempt at understanding the dynamics of the living is the interesting field of biosemiotics about which you can read short overview or get more accustomed into in its journal here. I think this list is more than enough to cover all the major directions your interests can take you on.
But to get "the bigger picture" of the question here you need to do much more than that and to follow virtually every publication pertaining to the definition, origin, synthesis and location of life throughout space and time and this can be daunting task, believe me, I do it every day since years! But despite the enormous quantity of papers and articles I go through there are always newer and newer things to discover and no matter how many hours I dedicate to this task and how much it fulfils me there are still gaps in my knowledge and am learning new things about different perspectives on the BIG question-What is life? all the time!
So, to give you an advice derived from personal experience-the question you tackle is really very interesting and fundamental one but even if it consumes all your time and efforts you would still not be able to follow everything which can be pertained to it, so my advice is to take only 1 or 2 approaches used in either of the fields I just described you and concentrate only on their keywords to follow the advances of the people behind them. Take something from synthetic biology, something from the origin of life field or something from astrobiology and visit the journals I just showed you from time to time to search with these keywords and see what is new. Then you would have good enough idea how close we are to synthesizing life in the laboratory and knowing more about its nature and origins. This is my long answer and the best advice I can give you.
Hope it helps :)

Wow, this answer got the size of a small paper itself! At least, I hope here are enough references and advices for everyone who wants to explore the field. The least, it took me a hell of an effort to write it.

Synthetic biology and abiogenesis are not synonymous and treat very different issues in biology.

@BryanKrause , I agree they aren't synonymous but I disagree they treat very different issues in biology. If you browse the 3 journals I just give you above with the journal Origins of Life and the Evolution of the Biospheres (done it in the past) you would see keywords like synthesis of living organisms, minimal genome, minimal set of proteins, of metabolic reactions and other "minimals" coming from both of them. The same is true if you browse The Journal of Theoretical Biology and Biosystems with the same words. For me it means different fields. the same problem. How's that for an answer?

How my God, there is lot's of things to learn and to know, and it really helped me, it's very crazy to think about creating life and your answer gave a picture of it.

@YordanYordanov Synthetic biology is mostly about figuring out what are the minimum necessary requirements for life, taken from modern (in terms of evolution) organisms, and assembling them together with modern (in terms of human technology) means. There is a practical side to this approach, but on the scientific side it is really about understanding how extant life works. Abiogenesis is about the creation of life from an unorganized soup mimicking possible early stages of life on earth and might produce life that is nothing like what it has evolved to.

@BryanKrause , how do you suppose we will know when what we have produced is alive if we don't first develop clear picture of when something becomes alive. And here is where synthetic biology comes it. I will argue that precisely the definition of Life is where the fields of origins of Life and synthetic biology meet so there is a good reason to follow them both if we want to create Life. First is the bottom-up, the second the top-down approach to the same question. Here is where they meet and they can "work out" the problem together.

@sreekara , actually I don't think creating Life is so crazy as it seems and may be one we will be able to it on regular basis, but for now as you can see there are too many gaps in our knowledge to be anywhere near it. So my advice is, if you are really interested in the field, to take the list of the journals I provided you and browse them every once or twice in the month to see what is new. Then you will have good and updated enough idea what is going on in the field and how close we are to this task.

I personally am much more passionate about this question, this is why I follow everything almost every day but unless you want to specialize in the "big questions of Life", e.g. what it is, when it arises, what is its minimal organization and how it evolves you don't need to do it. It is something that can really take up all your time and even there you won't be happy with the results. I know the field pertaining to this question well because it is essential part of my specialty but if you don't want to go deep into the theory of biology there is no need to spend so much time and effort.

Coacervates are electrostatically separated colloidal droplets. Colloids are a suspension of insoluble particles in a liquid medium. Oparin proposed that ionized organic colloids in an could interact in such a way as to form a 'metabolism' thus acting as a precursor to life. Oparin was never able to test his thesis in any way, but the Urey-Miller experiment was a partial vindication, showing that the complex organic molecules necessary for his thesis could be formed inorganically.
As opposed to Oparin, Sidney Fox based his work off the results of the Urey-Miller experiment. He addressed the next problem, that of how the molecules synthesized in the Miller-Urey experiment could develop into cells. His research into microspheres, showing that they could form 'protocells' in inorganic processes, and that they could undergo binary fission, lead him to believe that microspheres of organic materials were the precursor to cells.
If you combine microcells with coacervates, you can explain how a cell developed its form and metabolism, thus generating life.
I am not really in a position to judge the accuracy of their claims, but as far as I can tell, while there are other theories of how life formed, neither Oparin or Fox have been categorically disproven. That is the say, while there are many theories on the specific set of conditions that caused the initial formation of life, the theories of coacervates and  microspheres are critical components of many theories.
That is the background on abiogenesis research with respect to Oparin and Fox (and Miller-Urey). Regarding the specific question, 'Did any scientist creat a organism?' the answer is most certainly, no. There have been amino acids created, but no metabolism or anything that could be construed as 'life.'

@,kingledion thanks for your answer, I got to know more...

Actually, I think it is quite a haphazard answer. Just posting Wikipedia link and mumbling few words how little we know is NOT in any way near what the current situation is. If you are truly interested in the emerging science of "creating life" you should google for the term synthetic biology. There are entire journals dedicated to it! This is a good place to start. Also see the work of Craig Venter-he is the first man to claim trying to build living cells "out of scratch" in the laboratory. Here is a list of his work-http://jcvi.org/cms/about/bios/jcventer/ I suggest you pay special

@YordanYordanov It was helpful to the asker. If you know more, why don't you write a more helpful answer?

attention to this article-https://www.ncbi.nlm.nih.gov/pubmed/20488990?dopt=Citation You can also check the works of Pier Luigi-Luisi and a very good publication by Lauterbur-https://www.ncbi.nlm.nih.gov/pubmed/18290757 which is precisely linked to the subject you asked-when chemistry becomes biology. There is also a whole YouTube lecture course on the origins of life you can see here-https://www.youtube.com/playlist?list=PLguiSpvMdqIX_BP-dsPzpjrfia60NLwae&spfreload=5 . I think these links will be very helpful for you

I'm a kind of a "great fan" of the field but I will need some time to organize all the links I have here, it will take some time to find everything I have here on my computer to its proper source on the net But I'm onto it, don't worry. Can you wait for about 30 minutes?


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About sandwich ELISA
In sandwich ELISA the Fc region of primary antibody bind to the polystyrene coated well. But what are the specific interactions (like 'hydrophobic interaction' or 'van der waals force') happen between well and Fc region?

@xusr seen both use, don't know which corect. In few notebooks, "direct ELISA" used to mean direct binding of antigens into the well. but most sources treat "Direct ELISA" is where the primary antibody is itself tagged, so it "directly" gives signal of detection of antigen. Whereas in indirect ELISA the labelled secondary antibody (capable to direct bind only to primary antibody) indirectly indicates antigen. This question and Wilson-Walker seems to use second usage.

This page from Cole-Parmer includes everything you could possibly want to know about the adsorption of biomolecules to polystyrene. To summarize:

binding is neither covalent nor ionic, but
it is generally mediated by non-specific intermolecular van der Waals interactions, which generally are about 100X weaker than ionic or covalent bonds
the exception is some hydrogen bonds, which can be 10X stronger than the other types

Intermolecular attraction forces are based on intramolecular electric polarities of which two types can be distinguished: alternating polarities (AP) and stationary polarities (SP), i.e. dipoles.

these interactions can be both hydrophobic and hydrophilic, depending on the surface chemistry of the polystyrene

If you're interested in the specific chemistry of everything, feel free to read the entire thing, it's quite detailed.
I would to note one thing from your question. In the absence of a specific binding partner like Protein A, antibodies bind to polystyrene completely non-specifically, meaning that not only does the Fc region bind, but Fab as well, including the CDRs (antigen binding domains). An ELISA depends on the fact that not all antibody molecules bind this way, so many or a majority of them have their antigen binding sites available to capture their target.


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Pneumonia in children after abdominal operations
This textbook says:

Consequently,  young  children are prone to  suffer from pneumonia after abdominal operations, because they resist breathing (being abdominal) due to  pain.  As a result the secretions in the lungs tend to  accumulate,  which may become infected and cause  pneumonia.

Iam unable to find which secretions are they and how breathing removes them from lungs?
I thought it could be pleural effusion but unable to figure out the mechanism involved and how it gets infected if it remains there for long.

As an aside, it's not just young children that are susceptible to pneumonia after abdominal surgery, and the subsequent infections are almost always nosocomial. I had a very personal experience with that many years ago, in my late teens.

Mucus is always being secreted and removed by ciliated cells.

@GrahamChiu So do you think resisting breathing will lead to clog up of mucus?

Inadequate chest wall and diaphragm movement will lead to atelectasis, and an inability to clear secretions.

Abdominal surgery results in a painful wound that affects the abdominal muscles, which are important for coughing. The Lungs and respiratory tracts constantly secrete mucus that flows upwards to the Trachea then down the Oesophagus. The trachea is lined with a moist mucous-membrane layer composed of cells containing small hairlike projections called Cilia. The Cilia project into the channel (lumen) of the trachea to trap particles. The Cilia constantly move in a manner that pushes the mucus up to help clear the respiratory tract of pollutants, debris and bacteria. Here is a link to show the Cilia Movement:
https://www.britannica.com/science/cilium/media/117814/16442
Abdominal Surgery reduces the efficiency of the cough reflex due to abdominal wound pain, while the Anaesthetic results in an increase in mucus due to the upper respiratory tract trauma, with some anaesthetic drugs also increasing these secretions and suppressing Cilia movement. All that eventually results in secretions being produced at a higher rate than being evacuated leading them to accumulate and resulting in an increased risk of lung infection.

This is largely correct, though it could do with some references.

Pneumonia after abdominal surgery can develop due to:

Decreased breathing movements when lying in the bed
Anesthetics/sedation use that decrease the sensation of irritation in the lungs and hence coughing out mucus
Pain preventing coughing
Eventual mechanical ventilation, especially when the organism is not immune to hospital-acquired (nosocomial) organisms, especially staphylococci
Spread of bacteria from the gut to the lungs via the blood)
Eventual underlying lung disease

Source: Post-operative pneumonia (TeachMeSurgery)


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What forms the base of the coral reef ecosystem?
Corals are small animals that form a symbiotic relationship with algae. The algae produce sugars for the corals and are in turn provided with needed nutrients and protection from predators.
That's all great, but it doesn't explain where the amazing diversity of fish, mollusks, crustaceans, everything else comes from. As far as I can tell, the whole point of the coral's success is that their hard skeleton protects them from all but the most specialized predators.
So if the corals don't directly add (much) energy input to the coral reef ecosystem, what is it that makes the reefs so productive and diverse? Or, put another way, what makes a coral reef environment more productive than simple phytoplankton floating in the open ocean?

One role of corals is to provide structure that offers protection from predation to many prey species as well as larvae and hatchlings. Reefs also provide relief from strong currents which, again, afford protection. Many other critters such as sponges, tunicates and other sessile animals use the reef as a substrate for attachment.
Don't be fooled by the apparent inedibility of coral, many fish eat it, notably Parrotfish. To give an idea of the extent of this activity, the bleached white beaches in Palau are carbonate "sand", not silica. They are the product of millenia of Parrotfish activity on the coral. (I don't have a link, this knowledge is courtesy of the Oceanic Society guide on our snorkeling trip.) In addition to Palau, I've snorkeled Indonesia, Honduras, Hawaii and elsewhere. In every venue, multitudes of many species of Parrotfish were to be seen aggressively chomping away at coral.
Also, the reef is also a substrate for many algae which serve as a food for other varietiesw of fish. Many of the coral inhabiting algae wouldn't be recognized as such looking like bubbles, fans and other oddities unlike common kelp.
Other species also feed on coral including welks, fireworms, nudibranchs and some starfish. Here's a link:http://infolific.com/pets/coral-reef-life/eating-the-coral-reef/

So I was aware of the parrotfish, and I get that the shelter is a plus. But do you have other examples of fish that eat the coral? How do you get from coral to the incredible diversity of sea lillies, nudibranchs, and all the other various non-coral eating organisms? What is the food source?

@kingledion. I've added to my post. Sorry, I was a tad rushed before having forgotten about coral as an algae substrate.


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Why do oviparous animals not have ears?
I was chatting with my friend, and we both found that there's a relation between putting eggs and ears; we count animals and we found that if an animal is oviparous (birds, snakes, etc.), then it does not have ears. We really did our best but we did not find anyone!!
So, Is there any scientific reason laying behind this difference, I'm a little bit curious? Thanks!

Not all snakes are oviparous. For example green anaconda, boa constrictor are viviparous.

Interesting hypothesis! - all of those animals you mentioned in fact do have ears, they just don't have external pinnae. You are probably thinking of these external structures when you are thinking of ears.
Importantly, pinnae are unique to the mammals, and not even all mammals have them. Since most mammals do not lay eggs, that is probably the joint relationship you are recognizing. Monotremes (egg laying mammals) also don't have external pinnae (for example see this book). So, the scientific reason is that both non-egg laying and external pinnae evolved in the mammalian lineage around the same time.
I don't know of any shared benefit for these traits to go hand-in-hand, but you could probably come up with more traits that also largely follow these ones, again because of shared lineage rather than a particular synergy.


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Does drinking water affect oral thermometer accuracy?
According to various sources (including Mayo and Cleveland Clinics), one must wait a certain number of minutes before an accurate oral temperature reading may be taken. However, these two sources (and others) seem to disagree on the duration of this wait. In this case, the different is three fold.
When attempting to get an accurate reading of an oral temperature, what external forces play a part in the actual temperature of the tissue in the mouth, how long would it actually take for any small amount of residual tap water to assimilate its temperature to that of the mouth and body temperature, and how long does it actually take for the tissue in the mouth to fully return to normal after drinking room temperature water?


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what if there is a door for which our immune system has no key?

And as a B cell matures, it develops the ability to determine friend from foe, developing both
  immunocompetence -- or how to recognize and bind to a particular antigen -- as well as
  self-tolerance, or knowing how to NOT attack your body’s own cells.
  Once it’s fully mature, a B lymphocyte displays at least 10,000 special protein receptors
  on its surface -- these are its membrane-bound antibodies.
  All B lymphocytes have them, but the cool thing is, every individual lymphocyte has
  its own unique antibodies, each of which is ready to identify and bind to a particular kind of antigen.
  That means that, with all of your B lymphocytes together, it’s like having 2 billion keys
  on your immune system’s keychain, each of which can only open one door.

This is what Hank said in Crash course. So the b cells, each are having several unique antibodies and I also saw that this is true for T cells too and the dendritic cells  look for a helper T cell that can bind the parts of the intruders which the dendritic cell has presented on its membrane.
my question is
What if there is no antibody in any cell against an antigen?
Does the immune system has antibodies against all antigens in the world?
What happens if an antigen came into our body which has no antibody matching for it?

A clarification: each individual B cell has only one type of antibody. They can have many thousands of copies of it, but the copies are all identical.

@Matt this information is very useful for me.  thank you for the clarification

No problem. Incidentally, T cells are the same way - they have tons of T cell receptor (TCR) complexes on their cell surface, but all have exactly the same sequence, and are specific for exactly the same antigen. Now, as Joe Healey points out below, there can be cross-reactivity between antigens (sometimes substantial cross-reactivity, something he doesn't mention), which is the basis of a polyclonal immune response.

@Matt All the comments and answers are really a learning curve for me.I learned a lot like v(d)j gene, cross reactivity, polyclonal response. So thank you very much.

Most likely, another antibiody matching another antigen from the same infectious source takes care of it.

The same thing that happens to the native american when they were first exposed to smallpox. Extermination of 90%-95% of the population. https://en.wikipedia.org/wiki/History_of_smallpox
The immune system is unable to attack bacteria or virus which makes unrecognizable antigen. As a result the bacteria/virus continue to grow and grow unopposed, until the person dies.
The disease goes wild, spreads like wild fire, killing every single individual it infects. In the worst case scenario, the species may go extinct.
EDIT
Why do vaccines work.
Firstly the adaptive immune system is adaptive. The immune system generates new antibodies (ie new keys) by splicing together different version of the V(D)J genes in a big round of mixing and matching. Then it uses an enzyme called AID to induce hypermutation to that combination. The end result is a nearly limitless number of antibodies (keys).
https://en.wikipedia.org/wiki/Somatic_hypermutation
https://en.wikipedia.org/wiki/Antibody
However this process takes time. And during that time the bacteria/virus is growing and growing. Weakening the body. So it becomes a race. Can the body generate an antibody that recognizes the bacteria/virus, before the body dies.
A vaccine helps in this respect, because the vaccine is can expose the immune system to the antigen of the deadly virus/bacteria without actually using the active/live virus.
ie Some vaccines only uses pieces and parts of the bacteria/virus. The antigen is there. But the virus is dead.
In other older vaccines, the virus used in the vaccine has been weaken/mutated so much that it has a low probability of beating the body before the immune system. https://en.wikipedia.org/wiki/Edward_Jenner
In the Edward Jenner cowpox vaccine... the cowpox virus so happened to have antigens similar enough to smallpox, that antibodies against cowpox works on smallpox. And cowpox is not deadly to humans.
Now..  here is the interesting part. The arms race between host and disease has gone on for a very long time. So many viruses develop what is equivalent to chaff. These are proteins that stick out on the membrane surface and thus easily recognized by the immune system, but are rapidly changed. So by the time the immune system launches an aggressive response, the protein changes again. Kind like a disguise that a thief changed every time he robs a bank, so the police are always one step behind. The bacteria grows and grow. Constantly switching its antigen coat and eventually the person dies.
https://www.ncbi.nlm.nih.gov/books/NBK27176/
https://en.wikipedia.org/wiki/Relapsing_fever
A vaccine in this case, presents the immune system with the one part of the bacteria antigen coat that does not change. So an effective immune response can be made. However as experience with HIV antibodies has found, those constant parts tend to be protected by the parts that do rapidly change. So antibodies have trouble reaching it. And this is why we do not have vaccines for HIV. The constant regions are too well protected.
One response to this can be seen in flu vaccine. Here the virus changes it antigen coat not every few days, but on average once a year. So we try to predict what is the flu strain of the year.. and raise a vaccine to the antigens of the year. Sometimes the predictions are spot on, so the vaccine works perfectly. Sometimes the antigen predictions are a little off... so the vaccines don't work so well. And on a rare bad year, the predictions are completely off. And the flu vaccine do not work.

That's a great answer. I never read anywhere about production of new antibodies for new antigens. So I doubted how then we survived several diseases which are always evolving. you cleared it greatly.thank you for adding additional informations. thank you very much.

All the comments and answers are really a learning curve for me.I learned a lot like v(d)j gene, cross reactivity, polyclonal response. So thank you very much.

The Native Americans and smallpox
First I want to note that some of the posted answers are not quite accurate. For example, smallpox ravaged the Native American population because they did not have high-affinity MHC molecules for it, which is an evolved trait. MHC molecules must be capable of binding to a large class of peptides, at least weakly, to allow their presentation. There are only a finite number of MHC alleles in a given individual, and they tend to represent the most commonly found classes of foreign organisms.
The Native Americans were equally capable of creating anti-smallpox antibodies as any European, but that process was significantly slowed down due to not having MHC alleles which promote the presentation of smallpox, allowing the virus to accumulate to lethal levels before a sufficiently mature immune response could be mounted. You can bet that the survivors were the ones with MHC alleles that promoted rapid recognition of the virus!
Somatic hypermutation and affinity maturation
The way antibodies work is, B cells undergo both genetic recombination and an intentionally increased mutation rate called somatic hypermutation. This results in a virtually uniform distribution of new antibodies. These new antibodies are actually pretty bad at binding antigens, and at best, only roughly approximate them. This is one reason the first exposure takes so long to eradicate. When an antibody that weakly matches is found and the number of B cells rise, some of them begin to induce additional mutations to their antibody, a process called affinity maturation. The mutations that result in breaking the antibody end up discarded (those B cells die), whereas those that have an even stronger affinity result in the clone of B cells being positively selected for. This goes on and on until the resulting clone of B cells produce extremely high-affinity antigens.
The result of this is that virtually any possible "door" will have a "key", even if it is poorly fitting. Over time (and subsequent exposures), the key is fine-tuned. The only way a persistent antigen could evade an immune response, short of interfering with the immune system is if the antigen is extremely similar or identical to a self-antigen.
Some pathogens can avoid an immune response in indirect ways, such as frequently changing exposed antigens either by switching genes or through rapid mutation, covering the cell surface with self-antigens or innate, non-protein material, tucking conserved regions that act as epitopes deeply inside a protein, releasing molecules that inhibit the immune response, etc.
Foreign antigens resulting in production of anti-self antigens
An interesting thing to note is that, even if the antigen is similar to self, it will still often be detected. This can be highly problematic because selection against anti-self antibodies occurs when the B cell is first developing, during somatic hypermutation, but not during affinity maturation. A weakly binding antigen that is similar to a self-antigen may then stimulate the production of anti-self antibodies since the antigen is different enough from self that B cells specific to it are not negatively selected, but similar enough to self that the changes in affinity maturation are sufficient to convert it into an anti-self antigen (in other words, an antibody x steps away from targeting self-antigens results in negative selection, but affinity maturation results in y changes to the antibody, where y > x). This is one reason why some viruses can trigger auto-immune diseases.
Answering your questions directly

What if there is no antibody in any cell against an antigen?

If for some reason no antibody were even had the slightest affinity for an antigen, then there would be no problem, and a pathogen would trigger an immune response because of another antigen. If for some insane reason every single antigen on a pathogen (there are many) was not even slightly matched, then no humoral immune will be invoked. There still may be a cellular immune response (e.g. for viruses), and the innate immune system would still be active.

Does the immune system has antibodies against all antigens in the world?

The immune system has antibodies that bind a wide range of antigens, albeit weakly, and with high overlap. As a result, you could say that all possible antigens that are not too similar to self are countered by antibodies with at least some level of affinity. There is only a finite number of possible antigenic peptides, and of those, all that's needed is a weak interaction to trigger a full-blown adaptive immune response.
It's like going to an ophthalmologist. They don't have lenses for all possible refractive indexes, but they do have enough samples that, by trying them out, you can see which ones improve your vision. Going through this process allows gradual improvement, and eventually they are able to proscribe a perfect match.

What happens if an antigen came into our body which has no antibody matching for it?

A single antigen, as opposed to a pathogen with many antigens? Ignoring the cellular immune system, nothing would happen. It would be treated virtually identical to self-antigens (i.e. it would be ignored). Depending on how the pathogen behaves, it could be wiped out by the rest of our immune system, contained in a local cyst, or even result in a lethal infection.

If you have no antibody to a particular antigen, you have no immunity to that molecular pattern (and the organism it belongs to).
That's the basis of immunity.
This is why you have vaccinations. You are artificially exposed to an antigen your immune system hasn't seen before, so you sero-convert and then have immunity.
That passage is a little misleading though, its not quite one key-one lock, as it's possible for antigens to have slight crossreactivity (which is why you can be vaccinated against one thing, with a related thing (e.g. the old Jenner cowpox vs smallpox example).

Thank you for adding information like cross reactivity. I thought the same as in your answer i.e. we will die if we dont have any antibody against an antigen. But I cant understand sero conversion. I saw in  Wikipedia and they said it  is the time period during which a specific antibody develops and becomes detectable in the blood. I read it fully and understood what sero conversion is. But how is this is related to your answer. And if our immune system produce antibodies for vaccines why can't it directly produce antibodies for new antigens that enters our body? Thank you for the timely help.

You mix up two things: If there is no antibody, there is no immunity. And there will be none. If you vaccinate, you have at least low affinity antibodies, which are then adapted to fit better. This happens during infection, but this takes some time (around two weeks until full production of new antibodies, which might be too long for some diseases). Immunisations short-cut these time, as they mimic the infection and give the body the time to produce the necessary high affinity antibodies without being terrible sick.

@Chris The comment that you wrote, Is it  for cumulonimbus(me) or for Joe Healey?

@cumulonimbus It is to Joe's answer.

@Chris You're saying I'm mixing up 2 things? I don't see how? Your comment says exactly the same thing my answer did.

You say on one hand that if there is no fitting antibody, there will be no reaction, which is correct. Then you say that this is the reason why we vaccinate. Which is wrong, because if there is no antibody, which fits at least a little bit (low affinity antibodies), there will be no reaction to the vaccination. We vaccinate to train the body and have memory cells present in the case of an infection. This allows an immediate reaction, which otherwise takes some time.

@JoeHealey one thing I would mention is that cross-reactivity between antigens can be substantial, not just "slight" as you put it. I used to work making antibodies for research (Western blotting, IHC, flow cytometry, etc.) and I've made antibodies that cross-react with practically everything - sometimes intentionally, usually not. For example, my company has some monoclonal anti-phospho-tyrosine antibodies that just recognize a phosphorylated tyrosine residue, mostly independent of the surrounding sequence. There are many other examples - just search for motif antibodies.

@joe  All the comments and answers are really a learning curve for me.I learned a lot like v(d)j gene, cross reactivity,sero conversion, polyclonal response. So thank you very much.

@chris  All the comments are really a learning curve for me.I learned a lot like affinity, cross reactivity, polyclonal response. So thank you very much.

@MattDMo that's interesting. I was underselling it for simplicity, granted. I didn't realise it could be that extensive though, good to know!


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Identification of an insect found near Shirdi, Maharashtra

I found the insect nside house near Shirdi, Maharashtra. I have captured the image

Please add some description about it, like its size.

It's a household centipede whose scientific name is Scutigera coleoptrata.
It's venom doesn't do much harm to humans.
Sources:
Picture 1 and   Picture 2

I agree completely with the genus, but I don't know enough to be able to say if the species ID is correct. How do you know it's coleoptrata rather than another Scutigera species?


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Sensing weather conditions through bodily reactions (e.g. dry hands, arthritic pains)
Two fairly known examples of the effect of certain weather conditions on the body are dry hands due to decreased air humidity around us (more commonly in the winter, as described here), and flaring of arthritis immediately before or after it rains (as described here and here).
I was wondering if there are more examples of this kind, when what I am specifically looking for are bodily reactions through which one might be able to forecast or know something about the weather (i.e. if you have arthritis, you might be able to know it is going to rain sometime soon according to what you feel in your legs; if your hands are dry and chapped, you know that the air is drier than usual).

There is no scientific evidence for weather pains.

@JM97 Actually there is some scientific evidence, and in fact the OP linked to some studies showing that evidence. However, it is certainly true that there is not scientific consensus and studies I am familiar with show peoples' perceptions to be very exaggerated vs the actual evidence.

It's sad to see these close votes. Arguably this could be a Skeptics. SE question, but it is very interesting as weather related pains are a widely known phenomenon in rheumatic patients.

Thank you all for your interest. I saw people voted to close the question because it is "too broad". Since I didn't emphasize it, some people may have overlooked the fact that I was asking for more examples, i.e. if anyone knows of such examples they could post them as an answer or a comment. Is it really "too broad"? Perhaps this question doesn't have a single definite answer (or an answer at all), but I don't think it is too broad as phrased. As for skepticism, it COULD be an interesting subject for discussion, but that wasn't my original intention.


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Why do I hear beatings with stereo headphones?
When I play a sine wave together with another pitch shifted sine wave I hear the beating very clearly. This is the expected physical phenomenon.
When I use headphones to play the lower frequency sine wave in my left ear and the slightly higher frequency sine wave in my right (or vice versa), there should be no way for them to physically interfere with each other? But I still hear the beatings, just less strongly.
I tested it with a few different people and how strongly one perceives the beatings varies between people, but many do still hear it. Why?

Short answer
Dependent on the auditory stimuli used, it sounds like binaural beats to me.
Background
Binaural beats are the resultant perception evoked by the interaction of two auditory tones with different frequencies when presented to both ears (Lane et al., 1998). The presented tones should be below 1000 to 1500 Hz and differ in frequency between 1 and 30 Hz. For example, if a pure tone of 400 Hz is presented to one ear and a 410 Hz tone in the other, an amplitude modulated standing wave with a frequency equal to the frequency difference (10 Hz in this case) is perceived. Note that these 1-30 Hz beat frequencies are below the dynamic range of acoustic hearing. Hence, the beatings are the result of neurophysiological interactions in the brain, and not the result of physical interactions of the auditory stimuli impinging on the inner ear. From an experimental point of view, limiting the sound levels to 60 to 70 dB should prevent gross cross-over stimulation to the other ear.
Binaural beats are thought to be elicited in the auditory brainstem, and specifically in the the superior olivary nuclei, when the two wave forms mesh in and out of phase within the brainstem.
Reference
- Lane et al., Physiol Behav (1998); 63(2): 249–52
Source
- Web US
Related post
- How can binaural beats change mental state?

Thanks for your answer. However when playing a pure tone of 400Hz and a pure tone of 410Hz I hear the beating (meaning periodic varation in volume). I do not hear the frequency that is equal to the frequency difference.

No. I perceive periodic varations in volume (aka beating) as you would perceive if you play the two pure tones on one channel, due to physical interference of the waves.

Interesting. Although I would not rule out bone conduction, because bone conduction sounds very reasonable too. I will have to test with studio headphones and the little earplug headphones (since the little ones would have far less bone conduction hopefully?). I will also test with frequencies above 1000 Hz. (For example with 2000Hz and 2010Hz, since that would rule out binaural beats) From the papers presented it seems you can only perceive binaural beats with auditory stimuluses below 1000 Hz.

The ear phones versus ear buds shouldn't make any difference. Make sure to limit the sound level to say 60 to 70 dB to prevent cross over between the ears. Let me know how you go. Try 8000 - 8020 Hz too, as an extreme example (exceeding the carrier frequency by a few octaves). And try 1000 and 1100 too (to exceed the difference limit). I'd love to hear more on your experiments.

I used studio headphones at pretty low volume. I didn't find any absolute threshold frequency where I don't hear the beating anymore. It was progressively (though not totally uniform) harder to hear at higher frequencies. At about 150-1500Hz it was pretty easy to hear. Then at 2500Hz I could hear it too though weaker, and very very weakly (very hard to tell) at 5000Hz and above that I can't hear it. When you increase the difference between the frequencies you hear a faster beating (as expected) until you hear two separate tones, as you would if you played it on only one channel.

It could as well be both bone conduction (since low frequencies travel further) and binaural beats. I didn't find much research on this topic online. I don't see any argument to rule out bone conduction completely, since the beatings I hear are very weak (But they are still there!) compared to the beatings when I play the two frequencies on the same channel.

@macco -   What was the sound level?

Sound level on headphones is hard to measure exactly. I listened less loud than the human voice while speaking normally, so around ~60dB. I didn't test with other people except myself this time.

Given the observations I'd say binaural beats, otherwise you should keep on hearing it when the difference is higher than 100 Hz or so and base frequency shouldn't matter too much

Actually there is a way for waves to interact with each other. Our bones conduct vibrations very well: bone conduction. Some of hearing aids are based on this effect.
I can think about another example: the Weber test. It is a quick test for hearing.

In the Weber test a vibrating tuning fork (Typically 256 Hz ...) is placed in the middle of the forehead, above the upper lip under the nose over the teeth, or on top of the head equi-distant from the patient's ears on top of thin skin in contact with the bone. The patient is asked to report in which ear the sound is heard louder. A normal weber test has a patient reporting the sound heard equally in both sides.

So the explanation could be the bone conduction of vibrations.

Yes, I think that is what must happen. If someone knows could you please specify where exactly it cancels out physically (I think it is somewhere in the ear before it reaches the brain) and how exactly the signals get there. Maybe I will have to ask in Physics stackexchange...

What do you mean by "cancels out physically"?

Sorry, cancels out is an inaccurate word. The two soud waves have to interfere with each other which causes the beating. (See wiki page I linked in question if you dont understand)

Bones vibrations affect middle ear (mostly). In normal situation sound waves (in air) conduct into osculation of middle ear bones (incus, malleus, stapes) through the ear drum. In case of bones conduction waves conduct to middle ear directly (without ear drum vibrations). Therefore, i think, waves interference occurs in middle ear.

Bone conduction might well be the answer, but I'm quite interested in whether something neurological might also play a role. Perhaps there is interference within the neural pathway combining left and right sound input?

If it transmits to the middle ear directly through bone conduction it will physically interfere in the middle ear. I would still like if the answer were updated with these details (and maybe some more?). Right now the answer only says: bone conduction. If there is already physical interference it will make it impossible to find out if something weird is going on in the neural pathways or not. That would probably need a seperate question.

Bone conduction has nothing to do with the question. Using normal head phones the contribution of bone conduction is negligible. That is in fact the very basis of discerning middle ear problems from inner ear problems; a difference in hearing sensitivity measured with bone conduction and head phones is a strong indicator of conductive hearing loss. In these tests head phones and a bone conductor are used, respectively. The contribution of bone conduction at moderate loudness can be disregarded using head phones.

I used studio headphones, so there is a considerable area of your head that is exposed to the sound. One could test with earplug headphones to see if one still perceives the same effect.

@macco - to prevent cross-over from the contralateral ear prevent high loudness levels. That should minimize any bone conduction involved.


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In what situations, when reacting to impressions, are the signals sent directly from the thalamus to the hypothalamus?
Normally when humans react to impressions, signals are being sent through different centers in the brain through the chain of:
Impression ${\rightarrow}$ Thalamus ${\rightarrow}$ Cerebral Cortex ${\rightarrow}$ Hippocampus ${\rightarrow}$ Amygdala ${\rightarrow}$ Hypothalamus ${\rightarrow}$ Reaction
In some situations, the middle parts are skipped, handling feelings, long-term memory and understanding. The chain in the case consists of:
Impression ${\rightarrow}$ Thalamus ${\rightarrow}$ Hypothalamus ${\rightarrow}$ Reaction
Under what circumstances does this alternate path of reacting happen, and what effect does it have on the outcome of the reaction?

can you add some more detail and background to what you mean by "the signals"? - i.e. some neuroscience language that helps define what you're talking about. Are you speaking specifically about vision in the absence of the other senses. It's unclear what "the middle parts" refers to in your question - can you expand this and be more descriptive? Also, have you been able to look elsewhere for an answer to this question?

The middle parts in this case would be the diff between the first and second scenario which is the cerebral cortex, hippocampus and the amygdala. By "signals" I am referring to just general information, signals or impulses being sent through the brain. The question would be why some impressions are never processed by these three centrum, the cerebral cortex, hippocampus and amygdala. And lastly YES! I really have looked elsewhere :)

Add that information to your question – it will make it a lot better

I think this question is unclear or too broad - there are lots of neural processes that don't follow either of the chains the OP mentions, and the hypothalamus is certainly not the primary output structure that mediates "reactions." I suggest that this question be closed unless the OP is able to modify the question to be more suitable, in its current form the question is unlikely to produce good answers. I don't think this site is meant for playing Jeopardy and guessing "What is fear?" before trying to answer.

As @Pyssling states, it has to do with fear, and how we process situations that are potentially dangerous. There is a distinction between the two concurrent processes that you describe, that go under the title "short route vs long route" or "low road vs high road" (possibly more titles).
The short route (or low road) is the immediate process/reaction/response, which would enable os to avoid death in certain situations - This works on an instinctive level. The long route (or high road) is the process/reaction/response that could be defined as a thorough evaluation of the input/signal that we receive.
This site has descriptions and images that can be read on three "levels of explanation", and I find them highly informative.
http://thebrain.mcgill.ca/flash/a/a_04/a_04_cr/a_04_cr_peu/a_04_cr_peu.html
Here is a youtube video on the subject "How fear is wired in the brain" that deals with the same topic. https://www.youtube.com/watch?v=vl_B6nz3UOQ
I am in no way an expert and have stumbled upon these sites based on personal interests, so I do not know if someone may be able to criticize their validity / quality, but I found them excellent.


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What are Intersensory Associations?
While I was reading about "Neural Control and Coordination" I came across this
"Association areas in the forebrain are responsible for complex functions like intersensory associations, ....."
What are "intersensory associations"? I have searched the net but could not find anything useful.

They mean integration of information from more than one sense. For a human example, think of when you are having a conversation: you are not only listening to what someone is saying but also watching their lips move. Both give you information about what they are saying. Or you see a cat and hear a meow: you have an association between the two that allows you to identify the meow as emanating from the cat you see.

A more common terminology regarding 'intersensory associations' is multisensory or crossmodal integration. Crossmodal integration takes place in the association cortices in the brain (Fig. 1). An example is the coupling of auditory and visual input during lip reading, as mentioned in the comments. Lip reading can aid in acoustic speech understanding, especially so in the hearing impaired.
The association cortices include most of the cerebral surface of the human brain and are responsible for integrating the sensory input that arrives in the primary sensory cortices. The diverse functions of the association cortices are loosely referred to as “cognition,” which literally means the process by which we come to know the world. Cognition enables us to attend to external stimuli, to identify the significance of stimuli and to plan meaningful responses to them. The association cortices receive and integrate information from a variety of sources and in turn influence a range of cortical and subcortical targets (Purves et al., 2001).

Fig. 1. Association cortices. source: Brown, Physiology & Neuroscience websites
Reference
- Purves et al., Neuroscience, 2nd ed. Sunderland (MA): Sinauer Associates; 2001


text:
DNA centrifugation in water
If I have bacteria diluted in water and I centrifuge at max speed for 15-30 min, it is possible that I break the walls so the DNA can scape and I do not get any DNA pellet? or should I get it as a pellet everything togheter (lipids, proteins..) even if the mixure is just bacteria diluted in water?

At which relative centrifugation force (the "g number") do you work? And: Do you use plain water or do you add anything else? Where do these bacteria come from?

I recommend using a proper extraction kit. It may be possible (I mean anything can damage a cell wall) but you may not obtain a high yield.

Not with bench centrifuges.
Bacteria have cell wall and are rather small. This gives the cell wall alot of strength. I am not even sure that ultra centrifuges would work.
What you will likely get is a cell pellet. If you want DNA, pellet the cell and either go for direct PCR or sequencing. Or use a DNA extraction kit to obtain the DNA you want.

yes I use an ultra centrifuge. I am try to up-concentrate the sample but I cannot see any pellet and even when I remove volume and I resuspend the nonvisible pellet, I do real time pcr and it shows the sample was not up-concentrate, any idea why could that happen?

Why aren't you just lysing the cells first? Centrifugation isn't sufficient to lyse bacterial culture to a great degree.

Because I use bacteria direclty to do real time PCR.

Why? You will get more accurate qPCR results with pure DNA anyway. People only normally do colony PCR from whole cells directly as it's a quick and dirty method for checking for transformants and so on. I've never heard of anyone doing qPCR from culture, and I can't really think why you would want to?

because we use samples directly from a collector but maybe we could try to extract as you say. Thanks!


text:
How many cells are in prophase on this onion root tip slide?
In the following image, I have to identify the cells in the different phases (not counting the cells that are too faded to see), and it's fairly easy to identify metaphase, anaphase, and telophase, but I'm not sure I'm doing it right for prophase vs. interphase.
I try to see if there's a nucleolus or not, but sometimes it's difficult. When I counted, I got 7 cells in prophase. Is this close to what you guys see or am I way off?
Thanks!

Hard call on early prophase versus interphase, especially since these are not natural distinctions with discrete boundaries but are used to articulate a continous process.
I'd say you're pretty close, I count six for sure. That includes the one in the top row on the far left that is partially clipped in the photo. One iffy possibility is in the third row just left of the obvious anaphase on the left.
Unless your teacher is far more particular than I was with students, I think you're good to go.