text:
Plants without bacteria? is it theoretically possible?
I know from school, that all live on the Earth need bacteria as low-level "machines" that break down/extract/convert/produce chemical elements and combinations, other high-level organisms needed. But it is a natural way.
But is it possible to have a world with plants (without mammals or microorganisms and without bacteria) that could exist in the long term. Saying the atmosphere of these world has already enough nitrogen, oxygen and CO2, and of course there is water.
What could break this artificially created world with such conditions (say the world created not from low-level living structures)?
Could bacteria emerge in the world?

This is the sort of question that should be considered from more than one perspective.  Since this is speculation, take it as a given that there is a lot of 'what if' here.
I doubt most animals and plants can do entirely without bacteria - as you say most of the essential nutrients come from bacteria, who fix nitrogen.  If only plants were left on earth, eventually the plants would use up all the nitrogen and they would have to find a way to fix more.
Can bacteria emerge from just a world of plants?  I don't think viruses arise spontaneously, but since genomes often have viruses embedded in them, over the course of a billion years or so, its possible since bacteria and viruses continue to be impressed upon our genomes.  Would it happen in time?  Most would be skeptical whether that timing could work out.
In practice it would be hard to create a world like this.  I would be interested to see whether you could sterilize the microorganisms off of seeds without killing the plant for instance.  If you're asking about a small sterile environment with only plants, you could do it by adding the nutrients the plants need and giving them sunlight.  Such self sustaining systems have been made with cyanobacteria and i'd be surprised if plants could not be included.  But these are closed systems and judged by limited amounts of time, so whether this is an answer to your question is not clear.  Here it looks like some water plants and fish have been done.  If there was a plant that created CO₂ at an adequate rate its possible.
At one time there were no animals at all.  Its thought that for a while there might have only been photosynthetic structures that lay in the water and soaked up the rays.  Its not clear whether as some say there were colony formations of cyanobacteria as we see today, or whether there may have been larger pre-cellular or proto-cellular structures.  But recovering the pre-cambrian configurations of genes from just plant genomes seems like a gambler's bet to me.

thank you for your arguments and broaden answer! the link about the closed ecosystems is interesting. I think the nitrogen will be the most problem. But also it could be possible that some cells will mutate/break and create free components which can transform further. May be then will the microorganisms appear? Hm...what will be the evolution if one take cyanobacteria to another planet with water?...

Thanks.. its hard to tell with things like this - its possible that plants might evolve to fix nitrogen, if there is enough of it around the world for them to survive long enough.  If all the bacteria and animals were digested into the ecosystem its hard to say how long plants could go on - quite a long time I imagine.

See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6164190/
Turns out bacteria-free seeds are unable to propagate because root hairs require ethylene to be produced to grow. Secretions that the plant is unable to generate during the seedling phase (it is shown sterile seeds are unable to generate root hairs in the paper). When bacteria living within the plant's roots (endophytes) are fed sugars (by the plant itself), they release ethylene as a byproduct, resulting in root hair elongation, thus allowing plants to grow.
This is fascinating stuff since i too didn't know of this until and always asked "If soil microbes are important for plant growth, why can plants grow even when hydroponic systems would flush away bacteria from the plants roots?"
So no, your hemp plant would literally, physically, biologically, be unable to grow without the presence of bacteria.
You can completely replace the nutrient fixing bacteria, but until you find a way to inoculate plants with a tiny amount of ethylene (nanobubble tech?) without oxidising off the entire plant root system, bacteria are still required.

Think of it this way: Life always goes uphill, from less developed to more adapted, better at surviving and reproducing.
Early life would be a basic mechanism, trivial in nature, that under the right conditions would kind of replicate itself (kind of, since the replica would be less similar to the original, than when comparing current parent-child similarity). This would basically be a cell. And a cell would remain a cell unless combining with other cells and specializing in functionality would have a certain benefit. Check out this educational video on abiogenesis by cdk007, based on Jack Szostak's work.
But, you know that evolution isn't the process of change of all individuals of a species in a single direction, towards another species. It's a process of forking. So, basic cells of species A could evolve into single cells of species B, but that would only mean the extinction of A if the new environment with the new organisms becomes hostile, if resources are scarce, if species A is less adapted than everyone else, so everyone else occupies A's niche.
Thus, when multicellular organisms evolve, there are A LOT of monocellular organisms already present and occupying important niches. All available sources of energy are being used. If something isn't used - it's a new niche for any accidental mutation that enables the organism to use that niche and prosper as a new species. So anyway you look at it, multicellular organisms won't start existing without single cell organisms surrounding them. So all multicellular organisms will have an environment that includes these "bacteria", so they will adapt to this environment. It's easier to learn to live with something rather than learning to fight with them and then occupy their niche, because the killing and changing to occupy the niche requires much more changes in the organism.
Life on earth is balanced, such as each species occupies its important place in the circulation of substances. This happened not just by chance, but it's the only probable outcome from the process of evolution by natural selection. Having a world that's totally rid of any trace of primitive life forms is next to impossible. On earth we still have species of archaea that are similar to species present on earth billions of years ago. Read this article on Wikipedia about Nanoarchaeum equitans to get a grasp on the diversity of life.

interesting thoghts, and thank you for the links. but this point argues, why such a world could not start existing in a natural way, why it could not appear "by itself", something like our world (as I understood). but what if you have, say, isolated (physically: with all the known forces) giant spehre, where only simple plants exist: would this world survive as is, would it be destroyed by itself, or would it evolution and some day there would appear other types of organisms, due to the spontaneous mutations of plants DNAs and natural selection?

"Life always goes uphill, from less developed to more adapted, better at surviving and reproducing.". That just simply isn't true.

Amory, these are not my words. It was specifically explained, as a solid rule, by Richard Dawkins. And to explain why this happens - any mutation that reduces the likelihood of that individual to reproduce, will not propagate through many generations. That's why all changes go towards better adaptation to the environment.

static, answering your question - I don't think they would. The food chain will have missing links, so it will not be a complete biosphere. The plants might not survive long enough to reproduce, let alone become subjects to evolution.

One of the most important roles played by bacteria is the fixation of nitrogen. Biological nitrogen fixation is carried out primarily by bacteria. There are no known plants that express nitrogenase type enzyme. So plants cannot fix nitrogen.
Without bacteria in the ecology... the ecosystem is in trouble from nitrogen starvation.
That said, denitrification, the removal of fixed nitrogen and conversion back to nitrogen gas is also catalyzed by bacteria. So no bacteria, no lost of nitrogen by biological means.
Nitrogen can be fixed by lightning discharge. About 5%-8% of all nitrogen is fixed this way http://www.biology-pages.info/N/NitrogenCycle.html. However lightning does tend to cause forest fires... which results in the lost of nitrogen.
So where does that leave us? We will have to guess how much nitrogen is lost from forest fires (and burial by sedimentation) vs gain from lightning discharge.
That is is not at all easy to guess. In a world of high rainfall (lots of rain forest)... you can have plenty of lightning and no fires. But a world of swamps would have also plenty of organic matter (and nitrogen) being lost through sedimentation. A drier world would have more fires.
If anything... I would guess that such a world is unstable in the long term, certainly on a geological time scale. Eventually the environment will change to one where nitrogen is lost, and fixation by lightning is reduced... and the ecology will collapse from nitrogen starvation.

Could bacteria emerge in the world?

My guess is no. A second abiogenesis event is unlikely to occur when life is already present. The plant alive on your world would prevent any new form of life re-emerging. Plants are not quiet neighbors minding their own business. Plants secrete toxin to poison other plant. Limit growth. (Walnuts are a great example) Plant root do absorb simple sugars and amino acids. Example. http://link.springer.com/article/10.1007/BF02202082 So the raw material for new life will not accumulate.
That said... there is no reason why plant life cannot simplify itself to a single cell... such extremes have happened to parasitic barnacles of the Sacculina genus.. which look less like a crustacean (ie crab) than barnacles normally do and more like fungus. https://en.wikipedia.org/wiki/Sacculina
So we could have single cell plants.. descended from higher plants.
What is uncertain is if plants could re-evolve an enzyme to fix nitrogen. Nitrogenase (nif) appears to have evolved once in methanogens and by lateral gene transfer was moved to many other bacteria. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3733012/#B7


text:
Sodium-Potassium Pump
From my understanding, in the sodium-potassium pump we have Na+ inside the cell and K+ outside the cell, thus forming a so called "salted banana." After reading my textbook I found many statements saying that "potassium ions tend to diffuse out of the cell...sodium ions tend to flow into the cell." I initially thought that when the action potential hits Na+ leaves the cell and K+ enters the cell, which to me contradicts the previous statement.
Can someone please clarify this and differentiate between the two?
I am trying to understand the action potential process as a whole.
Thank you !

Your confusion is caused by the assumption that Na+ always leaves the cell and K+ always enters. The Na+/K+ pump is there to maintain membrane potential and relative Na+ and K+ ion concentrations stable inside. When an action potential (AP) is generated, sodium channels open and sodium rushes inside to depolarize the cell( 1st phase of AP). Next, the sodium channels close and K+ begins to leave the cell (since the inside of the cell contains too many positive charges and the cell would remain depolarized if nothing was changed). Potassium leaves through leak channels. So in summary, Na+/K+ pump and the channels that are part of AP generation result in different movement of Na+ and K+ across the cell membrane.
Here is a nice review of Na+/K+ pump and action potential generation.
https://www.khanacademy.org/science/biology/human-biology/neuron-nervous-system/v/sodium-potassium-pump

source: Stack Exchange

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

sort: votes


text:
Can two denatured DNA strands reassociate?
What matter if I increase the temperature to 95°C. So double-strand DNA denatured into two ssDNA, and then I decrease the temperature to room temperature. Are they able to reassociate after denaturation?

I've edited this to remove the use of the word recombine which has a special meaning when talking about DNA. I assume that you meant reassociate.

In PCR there is always some strand reassociation. This is why the primers are added in excess, to make it much more likely that a DNA strand anneals to a primer than back to its anti-sense strand.

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


text:
Hand motor control of the brain
I was watching a documentary (don't remember the name or the URL to the documentary) but they stated that the brain is layered and that each new layer is placed on top of the last. So the most primitive part of the brain that sends a signal to move the fingers actually has no way of moving just one, but in fact sends a message to just open and close the hand. That message is then passed on to a newer part of the brain that then filters it into individual finger movements.
I would like to know if this is true and how is the newer layer of the brain able to take an open-close message and identify what finger to move.
This sounds like a strange way for the brain to work; as I'm typing this message out at 86wpm, how is my brain doing such a complex task of moving all my fingers from an open-close message?

What do you mean with layer? The layers I-VI of the somatosensory cortex?

That is how they described it. during documentary; they stated the brain is comprised of different layers that each evolved at different times. Good chance they were dumbing it down for the show.

If you want detailed scientific understanding, I recommend reading some basic neuroscience textbooks (and take a couple of online lectures) and then the book "The Sensory Hand Neural Mechanisms of Somatic Sensation" by V. B. Mountcastle.

Thanks for the feedback. However, without the link I think this question can only be answered by guessing what was being said. Interpretation of complex matters like the evolution of the brain depend heavily on the context of the statements made. I'm voting to close therefore. If you find that link, I'm more than happy to vote for re-opening.

I'll try to find the link and include it in the question. Thank you for the feedback.


text:
Cancer in myogenic heart cells?
Why cancer does not occur in myogenic heart cells? Is there any special ability in heart cells to resist cancer ?

Could you provide a reference to the article that you read that in? I want to look at what was said before answering.

I was just reading about cancers in my book trueman..and also searched how many types of cancer were there but no heart cancer was found so I asked

@Pi5 just to let you know, the answer you marked as correct is, in fact, not. You can see my comment below it for more info.

What do you mean by "myogenic heart cells" precisely? As I understand it, "myogenic" refers to a precursor cell (myoblast, myotube etc), as opposed to a fully developed cardiomyocyte. Such myogenic cells are mainly present during early development --- are you thinking of a childhood cancer of the heart?

Related question: http://biology.stackexchange.com/questions/10809/extremely-rare-occurence-of-heart-cancer

@roland If something is Myogenic, it performs independently. I believe that the OP is referring to the Myoctyte cells in the heart. I.e. a Myogenic contraction is initiated from within the myocyte cell itself not, by the innervation of the nerves (stimulus), for example. This can be shown if you carefully remove a heart from the body - it will continue beat until it runs out of essential ATP stores. That type of Myogenic ;)

@user19679, I don't think myogenic contraction is relevant in this case. Here we're talking about myogenic cells, that normally means a precursor cell -- question is which one. This is relevant since heart cancers, when they occur, do not arise from mature (contracting) myocytes but from precursors or supporting cell types (fibroblasts etc).

@Roland I'm not sure if OP knows either ;) From the looks of it, I thought he/she was asking about "the myocardial cells that function by themself" (myogenic cells) so, I was just giving an example of one (I wasn't trying to undermine/insult you at all, either) :( You could suggest a slight edit?

@user19679 Absolutely no problem. Anyway I'll write a short answer even if I think the question is unclear.

As a preface, this isn't a comprehensive answer for everything. As MattDMo points out, some of the original answer was poor in it's presentation. In my update there's some supporting information to some expert testimonial, but this is mainly targeted at adult cases rather than pediatric cases, i.e. why would cardiac cancer be rare in an adult with no prior history of cancer. There's a reference #5 at the bottom which goes into some of the genetic conditions that result in rhabdomyocarcoma.
Cardiac muscle cells do not divide particularly often (though they may divide: Evidence for cardiomyocyte renewal in humans). This would be a good mechanism of resistance of heart tissue to a more typical or rapid cancer development, compared to say, the endothelium of a vessel or an interstitial/connective tissue cell. Not to say heart tumors are impossible, either, as rhabdomyocarcoma is a good example of a cardiac tumor. Moreover, here's an excerpt from this article on heart cancer:

“There’s not a lot of fatty tissue [in the heart],” Gaynor said. Even more, “the heart’s enclosed in a membrane,” he explained. Known as the pericardium, this fluid-filled sac may itself become engulfed by cancer, with tumors metastasizing to the outside of it, but still it does its job of protecting our precious hearts.
So, even though cancer can happen anywhere there are cells, your heart remains virtually immune due to its muscular nature and the assistance of the pericardium. Smart heart.

And then from Cancer Prognosis: Role of BMI and Fat Tissue,

Many prospective clinical trials have linked excess body weight—typically represented as a BMI of 25kg/m2 of body surface area or greater—with a higher risk of development of cancers, including postmenopausal breast cancer in women and esophageal, colon, pancreatic, endometrial, and kidney cancers in both sexes. The number of obese Americans will increase by an estimated 65 million by 2030, increasing cancer diagnoses by 500,000 (Lancet 2011;378:815–25).

So fat content has it's role in progressing cancers, determinately. Let's explore this part. The adipocyte isn't simply a storage for fat, it has it's own host of proteins it produces and secretes. In obesity, the adipose tissue becomes dysregulated in it's secretion of adipokines [1]. The book Adipose Tissue and Cancer by M. Kolonin, the author notes that two major adipokines, leptin and adiponectin, play a major role in tumorigenesis by induction of cell survival and proliferation pathways [2]. Also duly noted, increased circulating insulin and insulin-like growth factors due to insulin resistance results in mitogenic effects on tumor cells.
White adipose tissue has been shown by Pedro et al. to increase bioavailability of sex hormones such as estradiol, through increased aromatase activity and  "increased insulin and bioactive IGF-1 levels which downregulate the concentration of the circulating sex hormone-binding globulin, resulting in an increased fraction of bioavailable estradiol, but decreased testosterone production." The same study has a section on inflammation induced by adipose tissue in section 3.2, the entire article is rather long but they sum up some of the information into a figure,

Source: Pedro et al.
Generally speaking, and in reference to the expert testimonial above from Dr. Gaynor, the heart isn't a very fatty organ, and it's protected from the surrounding adipose tissue by the pericardium. You could also argue that the fast flow of blood through the heart would leave a smaller fraction of circulating tumorigenic molecules for ready uptake by cardiac cells.
Being said, and while I haven't any data for the molecular pathogenesis for cardiac tumors, nondividing epidermal cells have been shown to enter a proliferative state in response to inflammation [3]. We also see that adipokines have been implicated in heart disease due to pro-inflammatory effects [4]. My concession here is that the rarity of cancers in adult cardiac muscle cells is because this process is very slow, and it's aided in part by the sort of environment the heart finds itself in. We often see cases of cardiac tumors in children due to errors in development [5].

Yeah the first part is a good point, cardiac cancers are rare but they do occur. And lack of replication may play a big role in this. I would point out though that there are plenty of nervous system cancers that affect cells that do not divide much if at all either (so we do have to be careful about assigning causation with division rate)

That was my exact thought as well. I did want to make the distinction, though, that for the cardiac muscle cells themselves primary tumors are quite rare; More so than those of endothelial cells or interstitial cells that are part of the heart, and progress into cancer of the heart, like an angiosarcoma.

This doesn't really answer the question. Your second sentence is incorrect - cells do not have to be dividing to accumulate mutations. You then go on to say that this is your "opinion", which does not by any means constitute proof. The BMI part is irrelevant to the question - it's been well-established that excess weight can lead to all sorts of health risks, including cardiovascular disease and cancer of various body parts, but it has nothing to do with heart cancer. Please answer the question factually and support your reasoning with relevant citations from the scientific literature.

It looked good at the time, but I've tried to make something more acceptable in the little time I had.


text:
Why we do not get hurt from HCl secreted in the stomach?
I read in my book that during digestion our stomach secretes hydrochloric acid ($HCl$). Why we do not get hurt from it? It was also said that mucous provides protection, but from where is it coming?

Great answers, but it also is important to note that our HCl in the stomach acid has a low concentration as well, but high enough to kill many pathogens, in particular, bacteria. Also, some of our epithelial cells are destroyed, but the epithelial cells have the highest cell turnover rate in our body, only about one day...

Goblet cells.
These are specialized epithelial cells whose job it is to produce mucins. Mucous role is not only important in protecting the epithelium of the digestive tract from HCl, it is also a very important substance in the innate immune system, acting as a barrier defense to trap pathogens and/or prevent them from breaching the epithelium and gaining access to sterile parts of the body.

Our stomachs are lined with a special mucal layer which protects the organ from its own secretions. People with stomach ulcers have a hole in this layer, allowing the acid to get to the skin underneath.
HCl is present in our stomach to aid digestion - especially with dismantaling the bolus (food) coming from the oesophagus. The HCl separates the larger bolus to more smaller pieces. The stomach has a mucus which protects the tissues from being damaged. People with gastric problems may not have a sufficient layer of mucus to protect their tissue and the pain is from the acid eating through the tissue. Thus, a common solution for people who have Gastric problems is to use tablets which neutralizes the acid so that it is weaker.

The idea of acid causing ulcers was disproven by Dr. Barry Marshall, for which he won a Nobel Price in Medicine and Physiology, and is now known to be cause by inflammation due to an H.pylori infection.

@AMR, afaik Marshall disproved the idea that ulcers are caused by stress, spicy food, smoking, etc. Actually, H.pilory disrupts the mucus at some regions of stomach, thereby enabling the acid to get through and damage the inner layer of stomach.

@Ivan if you read my comment, I say "causing ulcers." The causative agent for an ulcer in 90% of the cases is an H.pylori infection and the damage done to the endothelial cells by the enzymes produced by these pathogens. Acids will aggravate the ulcer, but does not cause it. When you read the list of substances that Marshall disproved, acid is one of those substances. In fact much of the gastritis that occurred when he infected himself with H.pylori was in the absence of acid.

actually the ulcers are caused.. when say.. we didn't have food for long time, then the acid present in the stomach needs to dissolve some materials as, food is not there it starts to effect the layering of the stomach and thus, some kind of blisters and boils.. appears on the layering of stomach causes ulcer.

@Ashwin.N no, that is incorrect. If you read the previous comments, you'd have seen that this has been disproved. Acid on its own does not cause ulcers - H. pylori does.

We have skin under our stomach?

Simply, it's because of the mucous layer around the stomach, that prevents the strong acid, HCl to hurt our stomach.  Not only this, if there were no mucous, the HCl would digest the protein present in the epithelial cells, so the stomach itself would get digested. So the main protagonist here is the mucous layer.

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


text:
Why Egg shell is not called a cell wall?
Egg is a single cell and has a outer hard covering outside inside which there is a cell membrane. Then why isn't the egg shell a cell wall?
Is it because no exchange of materials take place through it?

Note that the cell wall in most species does allow exchange of materials. It is quite porous and unlike the cell membrane.

related: http://biology.stackexchange.com/questions/21675/why-are-hard-boiled-eggs-so-homogeneous

Egg shells are actually porous so that the organism inside can aquire oxygen and get rid of carbon dioxide as it develops (http://www.scientificamerican.com/article/bring-science-home-chick-breathe-inside-shell/).
Although gametes (eggs and sperm) are single cells, an egg shell (or "wall" if you like) is created by the mother (therefore external to the egg cell) and contains many compartments separated by protein membranes:

https://www.exploratorium.edu/cooking/eggs/eggcomposition.html
The initial egg cell is a tiny fraction of a size of the egg visualised here, so it would therefore be incorrect to call the egg shell a "cell wall" as it is a structure independent of the egg cell itself.

Also worth mentioning is that usually a cell produces its own cell wall but the fertilized egg doesn't produce the shell. It is produced by mineral deposition from the outside.

Referring to oviparous animals (given that you mention a hard shell), an egg isn't a single cell. It contains a single cell (called the zygote) for a little while, which has its own cell membrane, but that quickly develops into a multicellular organism.

Since when does a zygote contain a cell wall? Animals lack cell walls entirely.

Isn't the egg then more of an analog to an external Uterus and placenta?


text:
What is the energetic costs in KJ/g NH3 for nitrogenase fixation
What is the energetic costs in KJ/g NH3 for nitrogenase fixation.
I want to compare Haber-Bosch vs nitrogenase.
How would I force the biological stochiometry of 8e- electrons into an energy quantity.
$N_2 + 8e^- + 8H^+ + 16ATP + 16H_2O → 2NH_3 + H_2 + 16ADP + 16P_i$

Well if your equation is correct and complete (I haven’t checked) I would start  with 8 x the standard free energy  of hydrolysis of ATP to ADP to get part of the answer in molar terms. But the equation is incomplete in so far as the donor of the reducing electrons is not specified so the redox change should be found for the half reaction, and then converted to a free energy change. This is all in a chapter in Berg, which you can find on NCBI Bookshelf. Let us know what you find.

Will check thank you for the resource

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


text:
Is there any way to make protein pass through cell membrane?
Protein cannot pass cell membrane because it's a large molecule. Until now, is there any technique that can make protein pass through the cell membrane in vivo? I want to create a protein-drug that must be accessible DNA to reach it's site of reaction. How possible can i do it?

Various protein transfection methods are available.
The simplest one is electroporation. By using electric pulses, transient pores can be formed, so that proteins outside can go the inside of membrane.
Several protein transfection reagents are commercially available. I think the mechanism is similar to lipofection of DNA.
http://www.clontech.com/US/Products/Transfection_and_Cell_Culture/Protein_Transfection/Protein_Transfection_Reagent
https://www.neb.com/products/m2563-transpass-p-protein-transfection-reagent
https://www.thermofisher.com/order/catalog/product/89850
Fusion with the transactivating transcription factor (TAT) protein transduction domain from the HIV TAT protein. This 11-amino acid sequence help proteins cross plasma membrane.
http://www.nature.com/mt/journal/v8/n1/full/mt2003155a.html

I am adding a couple of methods here.
Liposomes
Liposomes were designed to deliver drugs to places where the effects are wanted. Drugs are enclosed in liposome vesicles, but when reaching plasma membrane, liposomes could fusion with plasma membrane and release drugs inside of liposomes, although all liposomes are not designed to fuse cellular membrane.  Lipo-fection of DNA is a bit different from this kind of liposomes because DNA is not necessarily enclosed in vesicles.
nanoparticles
This is relatively new. I do not have much knowledge about nanoparticles, but I know they are used to transfect DNA or RNA in vitro and in vivo. I do not know how popular nanoparticles for protein transfection are, but there are publications.
http://www.ncbi.nlm.nih.gov/pubmed/24859743

I don't think they let you electrocute patients these days, even just a little.

electroporation can perform in vivo , however it will make other free protein and free gene fragment outside pass through the cell membrane, what will happen?

@AMR There are clinical studies using electroporation. For example: http://pancreatica.org/electroporation-for-the-treatment-of-locally-advanced-cancer-of-the-pancreas/ , https://clinicaltrials.gov/ct2/show/NCT02079623

@AMR electroporation is unlike electrocution. People have used in-vivo electroporation extensively in animal studies without any significant tissue damage and moreover as 243 said, clinical trials have been conducted using this technique.

@WYSIWYG The examples of electroporation use invasive measures to deliver the electrical charge to the tissue. It would not be practical if the OP is looking at systemic treatments or longer term, maintenance protocols, though the OP doesn't say, and you already are aware of my thoughts on this question.

Another example here. http://www.nature.com/mt/journal/v21/n9/full/mt2013119a.html

https://en.wikipedia.org/wiki/Electroporation . "Scientists from Karolinska Institute and the University of Oxford use electroporation of exosomes to deliver siRNAs, antisense oligonucleotides, chemotherapeutic agents and proteins specifically to neurons after inject them systemically (in blood)."

@DucFabulous Read the prior section. It requires an invasive procedure to target the neurons. The siRNAs are packaged and delivered in the blood, but to get them into the target tissue electrodes need to be inserted into the site. How much do you think it will cost to have all of those brain surgeons operating to get the drug delivered, and do you think that countries with national health care systems would agree to pay for the expense? Just because things are researched, and even proceed to and through clinical trial doesn't necessarily mean that it is good science or even practical.


text:
Ways to identify that proteins are regulating different genes experimentally
As part of my study I have been given this hypothesis:

HIF 1a and HIF 2a regulate different genes in multiple myeloma

What ways do we have to identify that these proteins are regulating different genes in multiple myeloma? I recall in lectures something being mentioned about using antibodies to isolate the regulatory elements, but can't find any specifics.
Any help is seriously appreciated!

Chromatin immunoprecipitation (ChIP) or ChIP-Seq are the first methods that pop into my mind. Essentially, DNA is cross-linked to bound proteins (transcription factors, histones, etc.) by various methods, then broken into pieces by either sonication or digestion with micrococcal nuclease. An immunoprecipitation is then performed by adding antibodies targeting your protein of interest (HIF-1α and HIF-2α in this case), allowing them to bind to their targets, enriching them using bead-conjugated Protein G (or Protein A), then reversing the cross-linking. The enriched DNA can then either be subjected to PCR for known genes (ChIP), or it can be sequenced and aligned with a reference genome to determine all bound sequences (ChIP-Seq).


text:
Resources for understanding the basics of cell signaling, gene expression and cell fate determination, for a physics student?
I'm a physics student who will join a theoretical biology/applied mathematics research group this September. I'll link some papers at the end for further context.
The main problem I have is that my last biology class was in 10th grade. While the mathematical part isn't that harsh, the biological side of things really does get me. I don't understand half the terms thrown around, or the general context of what is being studied. So what resources would you recommend?
Chemical Reaction Network Theory elucidates
sources of multistability in interferon signaling
Transient hysteresis and inherent stochasticity
in gene regulatory networks

Welcome to the Biology.SE. Please take the [tour] and carefully read through the [help] to learn more about the site, including what is on-topic and what is not, and [ask] a good question. In particular, this seems far too open-ended and is also likely to generate opinions rather than factual answers, both of which make this off-topic on this site. This makes it likely your question will be closed (I see one vote to do so and will reluctantly be adding one of my own). ...

... I have personally found when learning about a new area that starting with a relatively accessible and reliable source like Khan Academy is very helpful. Online platforms called MOOCs offer free (or very low cost) courses on a wide variety of subjects — two I am familiar with are Coursera and edX. Finally, textbooks with a good level of detail are also freely available online e.g. from NCBI. ——— Wikipedia can also be a good starting point if you check the references.

I would recommend talking to the principal investigator of the lab and asking him/her for some good introductory reviews. You can then chase down references from there, and do searches for terms/ideas you don't understand. Also, just talk to people in the lab! Many scientists are more than willing to explain their work in excruciating detail.

@MattDMo — This is good advice, but depending on their background (and wisdom) the PI may have little or idea how to effectively advise someone with the poster's lack of background knowledge. It also sounds like the OP has talked to people, but they are using a lot of unfamiliar terminology. While many of us are willing to explain, not as many can explain cutting edge research at a 10th grade level (and even fewer will be willing to do so) ...

@tyersome true, but you'd be surprised at the number of people who haven't even pursued those simple steps. I used to work in tech support for an antibody company, and my colleagues and I would get calls/emails all the time asking for us to interpret the results of Westerns, ELISAs, etc., b/c the person for whatever reason hadn't approached other people in the lab first. I see this a lot on Stack Overflow as well. People seem to be much more willing to ask strangers on the internet for help than the person at the desk right next to them.

Time to hit the library,  caveat: my suggestions may be ~20 years out of date - pick up a general biology textbook, perhaps something like Campbell's "Biology"  if you need real basics. For genetics - try Lewin "Genes". Immunology - try "Janeway's Immunbiology".

@MattDMo — You might be surprised at how unsurprised I am ;-) ——— I am painfully aware of the large number of people afflicted with significant social anxiety (with some "positive" feedback due to a non-trivial amount of arrogant assholes) ...

@tyersome I didn't even think of the social anxiety part. Thanks for reminding me.

I could tell you to buy "Stryer: Biochemistry". It has many chapters that you need, which are:

Gene regulation (Regulation on DNA, RNA, Protein level, etc.)
Signaltransduction (JAK/STAT pathway & general concepts)
Regulatory strategies (Product inhibition etc.)
Stem cell differentiation (French Flag model, specification vs determination)

Stryer also explains the biochemical machinery behind that, which is interesting. Your other paper mentions interferon signalling, which is part of the immune system. So you could buy "Janeway: Immunology" for that. You also mentioned cell fate determination, for that the best book imo is "Scott F Gilbert: Developmental Biology".
They are awesome books, with tons of awesome pictures and are simply very very fun to read!
HOWEVER, these books are huge and contain many chapters that you will never need. So I might also tell you to just google stuff. For biology purposes my goto strategy is hammering this query into the search bar:
"pubmed review <biologic term I don't understand>"
For example when I google "genetic regulation network pubmed review" I get this pubmed link. Then you press "full text links". Then you realize there's a paywall. I would never recommend visiting a certain page (starts with sci and ends with hub) to circumvent that paywall.
So I keep searching and find another review from 2012. However it lacks those biological terms that you need. I tried finding some comprehensive reviews online about biological topics, however this kind of literature often focuses on flashy state-of-the-art topics that go into too much detail. So you might want to consider buying "Stryer Biochemistry", after all!
Or just ask your supervisor to buy those books and keep them in your research group. They are definitely worth it. And these books definitely know a lot more than anyone in a physical research group (including your PI). Yes, it will take you some time to look up those topics and read them, but I promise, they're written in the best and most understandable way possible (no background knowledge is necessary, unlike published papers!) and might save you and your whole research group a trip to the library or a lot of time and frustration trying to google terms that no one taught them.
It doesn't have to be the Stryer, maybe there are books that specialize on regulatory strategies in living beings. But it's a good start.


text:
Voltage sensitive dyes technique: What is the underlying measure?
I just discovered voltage sensitive dyes technique: first of all what imaging techniques do we use? And I have seen that figures are labeled with ΔF/F0, what does it stands for?

As for imaging method, many kinds of fluorescence microscopes can been used (two-photon, confocal, widefield, etc.). Depends what spatial scale you're interested in (e.g. subcellular compartments vs. large patches of cortex) and the context of the measurements (e.g. cell culture vs. behaving animals).

Since these are fluorescent dyes, the most likely method of use is with some sort of fluorescent (likely confocal) microscope. The various types of dyes have different hydrophobic tails, so they target different types of membranes (plasma membrane, mitochondrial membranes, etc.). An excitatory light source (typically a laser, with a single wavelength) is applied to the sample, and the $F_0$ or baseline fluorescence intensity at time zero is measured. When an event happens, such as the contraction of a muscle, the $\Delta F$ or change in fluorescence intensity is measured. This difference is then divided by the baseline, and called the fractional fluorescence (${\Delta F}/{F_0}$). It is plotted like so:

Bu G et al. Biophys J. 2009 Mar 18;96(6):2532-46.


text:
exercise of gene linkage in genetics
Could you help me solve this problem:
AAbbCC is crossed with aaBBcc and the offspring re-crossed with aabbcc. Considering that A and B are linked and their distance is 12 mapping units, while the gene C is not linked to them, find the percentage of the offspring that will have phenotype aabbcc.
I used this method to solve it (I know it's not correct but I don't know where I am mistaken):
P: AAbbCC x aaBBcc
F1: AaBbCc
AbBbCc x aabbcc
Since the distance between A and B is 12, their recombinant frequency is 12%
88% then is the recombinant frequency of the parental
Dividing by 2, 44% is the RF of parental AB/ab and 44% of parental aa/bb
In conclusion, since gene C is not linked, I calculated the probability to obtain cc from CC x cc, and that's 1/2
So my final result is: 0,44 x 0,5 = 0,22 = 22%

You did right for most of the exercise, but you got confused on one of the (apparently) easiest things.
Try to reason in terms of chromosomes, and not merely of genotypes:
F1 inherit their chromosomes from two homozygous parents, so you know that they are AbC and aBc.
You can visualize the cross with the recessive homozygote as follows:
Ab C     ab c

-- -  X  -- -

aB c     ab c

The second parent will always pass abc, so in order to have an offspring with genotype aabbcc you only need that parent 1 passes abc.
Given that the parentals are Ab and aB and that RF is 12% (0.12), regarding the first two loci, the frequencies of the gametes are
Ab = 0.44
aB = 0.44
AB = 0.06
ab = 0.06

Including locus C, the frequency of the gamete abc is then simply 0.06 * 0.5 (because c is unlinked), and that corresponds to 3%.


text:
How do stem cells produce 200 billion new blood cells every day? Does 1 stem cell division result in production of just 1 blood cell or many?
It is given on wikipedia that everyday 200 billion new blood cells are produced in the bone marrow. I want to understand how this is achieved. Does one hematopoietic stem cell's single division result in just one blood cell produced, or many so as to meet the demands of trillions of cells? For example, does single myeloid progenitor (refer to the image) produced from one stem cell further divides into several other identical progenitors before further differentiating into specialized cell, so multiple blood cells are created with the involvement of just one stem cell so that work load is shifted from stem cells towards the progenitors? Also, does the fact that RBC lacks nucleus help in producing trillions of them, making the entire process cost effective.

The hematopoietic stem cells are quite rare, and each progenitor cell produced by a stem cell gives rise to a large number of red blood cells (and other blood cell types).
I'm not sure if the precise number of offspring for the earliest progenitor cells is known in vivo, but recent cell culture models indicate that early progenitors can give rise to as many as 70,000 mature red cells. We also know that the erythrocyte burst-forming cell, a later stage cell in the erythroid lineage, gives rise to around 5,000 mature erythrocytes.
Red blood cells eject their nucleus in the final stages of maturation, and cannot divide thereafter. The ejected nucleus is consumed by a bone marrow macrophage, so it cannot be "reused" in any way. Hence, loss of the nucleus is probably not an advantage in terms of "production economy" --- a nucleus must be generated for each single red cell anyway.


text:
Is there a preferred sleeping position for humans?
I remember hearing various sleep related advice as a child, like "sleep on your right side", or " have your head pointed in X direction".
Is there any biological reason why sleeping on one side versus another, or with a head pointed in some direction is beneficial for humans?

The enWikipedia article summarizes the best/only real research on positions that I am aware of.  I read a book in high school (that is to say it was old and I have no idea what the title was) that claimed that the semi-fetal position was the best, as it supposedly maximized protection without compromising breathing too much.  I can't say I've seen anything that would indicate your head's direction actually matters, except as it depends on the position of the rest of your body.  Do you mean facing North or the door?  That's some Feng Shui stuff or something similar, which is meaningless.
In terms of which side to sleep on, there is actually an answer!  Well, maybe.  Sleeping on your left side aggravates heartburn more than sleeping on the right side1, but sleeping on your left may be somewhat associated with heart problems.2  From what I can read from the studies, the heartburn one sounds more causative, but then again dying is worse than a little heartburn...  In the end, though, about the only thing that matters is that sleeping on yours side can lower the amount of snoring (annoying) and sleep apnea (unhealthy).

By head direction I meant compass orientation like north or east

Disclaimer: Not in any way my area of expertise. Maybe someone else can expand

In relation to pregnancy, there exist one australian study (Stacey et al. 2011) that reports an increased risk of still-birth for women that sleep on their back at the later stages of pregnancy. The purported mechanism is pressure from the uterus on the inferior vena cava and aorta, restricting blood flow. Lowest risk was found for women that sleep on their left side (less pressure on the liver). Another recent study from Ghana (Owusu et al. 2013) has found similar results, with associations between sleep position (supine position) and birth weight or risk of still birth. However, the studies are relatively small and the results must be further corroborated.


text:
What non invasive methods of estimating Body Time are there?
I found this article on estimating body time using molecular timetable of 168 genes. researchers looked at gene expressions and plotted them to 24 hour cosines curve with some pretty spectacular results.
Unfortunately the techniques discussed required sampling of liver cells, which may be invasive. Are there non- invasive methods of estimating body time/ biological clock/ circadian rhythm time?
An example of body time: at 8:00 real time, a mouse may exhibit gene expressions more appropriate for 9:30, so the body time of the mouse is 9:30.

metabolism is controlled by circadian cycle. I think certain metabolites/hormones can be measured from a blood sample.

For circadian rhythm, the gold standard is melatonin secretion (blood or saliva). Also, core body temperature.
see: Circadian temperature and melatonin rhythms, sleep, and neurobehavioral function in humans living on a 20-h day
James K. Wyatt , Angela Ritz-De Cecco , Charles A. Czeisler , Derk-Jan Dijk
American Journal of Physiology - Regulatory, Integrative and Comparative PhysiologyPublished 1 October 1999Vol. 277no. R1152-R1163

Don't forget cortisol/corticosterone!


text:
Why isn't the p16-INK4a gene involved in apoptosis expressed in heart or liver tissues?
New York Times article explains how killing p16-INK4a positive senescent cells can help keep the surrounding cells vigorous.
So here's my question: why is p16-INK4a expressed in most cells other than heart and liver cells? What would happen if we knocked it out everywhere?

do you have a reference for CDKN2A (p16-INK4a) not being expressed in heart/liver tissues? On GeneCards it looks to me like it has been found to be expressed there.

That's a good question. The Nature paper referenced in the NYT article says it, but with no citation, and their tissue work backs it up. The GeneCard data does run counter to that, though. I'd add the caveat that the Nature paper is talking about mice, and mice handle senescence differently than humans do. For one thing, they don't turn off their telomerase.

p16-INK4a is a part of a very important checkpoint mechanism. It's the "bad guy" in the context of aging because it induces senescence, and too much senescence leads to aging-related  tissue degradation.
But senescence is important. It's one of the responses cells take when something goes wrong-- DNA damage, viral infection, telomere depletion, that sort of thing. Senescent cells have stopped proliferating. We have a word for cells that don't stop proliferating, and that word is "cancer". So, p16-INK4a is a major tumor suppressor. A universal p16-INK4a knockout would have a much harder time shutting down the proliferation of cells that had undergone DNA damage, and would therefore be much more prone to cancer. You'd have very young-looking tissues filled with tumors.
So, the headline question is why INK4a is not expressed in the heart or liver if it's so important. This is speculation on my part, but I think it's because those tissues are especially prone to being damaged by fibrosis, and a build-up of senescent cells would lead to increased fibrosis. Senescence is just one possible response to DNA damage, though. Another is apoptosis. If the senescence-induction pathways aren't active in heart and lung tissue, I'd expect the apoptosis-induction pathways to be pretty active.

nice answer; care to elaborate/speculate further on why senescence in favourable over apoptosis in other tissues? Or could the removal of senescent cells simply be an un-selected-for trait (by this I mean that reproduction has generally happened prior to the buildup of senescent cells)

Yeah, that's an interesting question. I'd say main advantage of senescence in most tissues is that the cell gets to hang around and do its job. If it goes through apoptosis, it's going to need to be replaced. Senescence as a strategy, then, would keep overall proliferation rates lower in the tissue as a whole, which could have upsides, like limiting the potential for errors to creep in. Which one gets selected for in which tissue could definitely be influenced by the balance of those factors compared to reproduction time.


text:
How do caspase proteins kill a cell?
Wikipedia just says...

The active effector caspases then proteolytically degrade a host of
  intracellular proteins to carry out the cell death program.

Okay, but what parts of the cell do they cleave up? And what happens to the rest of the cells' internal components, especially the parts that don't get cleaved up?

Caspase do not directly kill the cell, but rather activate a process known as apoptosis, or programmed cell death. The programmed part is there to distinguish it from other types of cell death, such as necrosis, which are more aspecific death processes.
Coming back to caspases, they are a series of proteasis, that can activate in cascade in response to a pro-apoptotic signal.
To simplify matters a lot, the pro-apoptotic signal first activates initiator caspases, such as caspase 8, 9, 10 (plus a series of other proteins).
These, in turn, cleave other effector caspases, which are the ones who effectively do the dirty job: caspase 3, 6, and 7.
Now there are many things happening at the same time (see this PDF from AbCam to get an idea of the complexity of the system).
At the nuclear level you have, for instance:

activation of DNA cleaving enzymes, such as CAD (caspase-activable DNAse), which is normally inactive, due to binding to its inhibitor I-CAD. The latter is a target of effector caspases and its degradation causes CAD to go in the nucleus and starting fragmenting DNA.
cleavage of PARP (Poly(ADP-ribose) polymerase), a nuclear enzyme involved in finding and repairing single-strand breaks on DNA.
cleavage of lamins (by effector caspases + other proteases), proteins that are important for the formation of nuclear lamina, and stability of the cell nucleus
cleavage of U1, a nuclear protein necessary for processing of mRNA.

Very complex events also happen at the mitochondria level: here you have a series of protein, which belong to the Bcl-2 family that control apoptosis mostly by regulating the levels of Ca2+ in the cell. There are 25 members of this family, that can be divided into two "sides": pro-apoptotic proteins such as Bax, Bak, and BAD and anti-apoptotic proteins such as Bcl-2, Bcl-xL, and Bcl-w.
The functioning of the Blc-2 proteins is very complex and I am not up-to-date with the last literature but to simplify, essentially what happens is that when the balance between anti-apoptotic and pro-apoptotic proteins is shifted towards the pro-, there is:

liberation of cytochrome c from the mytochondria into the cytoplasm, which can activate effector caspases.
induction of MPTPs (Mitochondrial Permeability Transition Pores), proteins which increases mitochondrial permeability which causes all sorts of trouble, eventually leading to swelling of mitochondria and loss of their function

Different events also bring to an increase in cytoplasmic calcium concentration, which can, for instance, induce the activity of calcium-activated endonuclease or other pro-apoptotic calcium-dependent proteins.
This is far from being an exaustive list of what happens, but it gives you the idea of the complexity of the system.


text:
What happens if someone with mutations to alcohol dehydrogenase (ADH) drinks alcohol?
ethanol then doesn't get converted to acetaldehyde.
in fact, could someone KO'ed for ADH be resistant to methanol poisoning?

In theory I believe that's true, but they'd also be much more susceptible to the normal intoxicating properties of ethanol / methanol, which might be just as harmful.

People, which have no ADH wouldn't be able to process methanol. Since the specificity of the ADH is higher for ethanol you get quite large amounts of ethanol for days (until the methanol level is under a specific level). Another possibility is to treat patient with the ADH inhibitor Fomepizole.
This also makes problems for the ethanol metabolization, but according to this paper ("The biochemistry of alcohol metabolism - a brief review") there are two other pathways of breakdown. One takes place in the peroxisomes and utilizes catalase and hydrogen peroxide (but is limited by the availability of peroxide), the other take place in the smooth endoplasmatic reticulum and uses the Cytochrome P450 enzyme.
I am not sure, if complete losses of ADH really happen (haven't found any reference) but mutations in this enzyme are quite common leading to a lower enzyme activity.

The flush reaction is caused by reduced activity of ALDEHYDE dehyrdogenase. The question is about alcohol dehydrogenase, which is necessary for alcohol to be converted into acetaldehyde in the first place.

You are absolutely right. I changed my answer and will look up some other reference.


text:
Why does Diphenylamine only react with the deoxyribose of purines?
The deoxyribose in DNA in the presence of acid forms β-hydroxylevulinaldehyde which reacts with diphenylamine to give a blue color with a sharp absorption maximum at 595nm.
In DNA, only the deoxyribose of the purine nucleotides react with Diphenylamine, so that the value obtained represents half of the total deoxyribose present.
Why is this the case?

Why not start with researching what happens when DNA (not just the deoxyribose part) is placed in acidic solution?

As you have correctly stated, the DNA cannot directly react with diphenylamine. First, it has to be cleaved so that the deoxyribose is exposed. In acidic solution and at high temperature, a depurination occurs several orders of magnitude faster than depyrimidination, because N-7 of the purine can be protonated and assist the cleavage.
See this mechanism of the acid-catalyzed depurination:


text:
Why can mRNA come out of the nucleus but not enter it?
I am a mechatronics engineer who stopped learning biology after high school - but this is bothering me.
mRNA is, if I recall correctly, created in the nucleus of the cells and migrates out of the nucleus inside the cytoplasm where it will be translated by ribosomes.
mRNA vaccines inject mRNA molecules inside the body, which are apparently transported by their nanolipidic particle coating across the cell membrane, correct?
I understand that the DNA→mRNA transcription is probably not reversible, but I do not understand how the mRNA is only able to cross the nucleus-cytoplasm membrane in one direction.
Care to explain? Bonus kudos for clarifications on the rest of my doubts.

mRNA vaccines are not "transported" by their lipid coating (no active transport involved). It's just that lipids are attracted to the nonpolar plasma membrane and expelled from polar water.

Nuclear pores control what gets in and out of the nucleus.  In general, mRNAs are only allowed out, they don't go back in.  Reverse transcriptases, of course, will put mRNA back into DNA, but only some viruses, like HIV, have those enzymes.
https://portlandpress.com/biochemj/article-abstract/477/1/23/221793/Into-the-basket-and-beyond-the-journey-of-mRNA?redirectedFrom=fulltext

Interesting, thanks! Do you mean that, unless a person is infected by rare specific viruses, no reverse transcriptase is present in the body and therefore the mRNA cannot reenter the nucleus?

It is very hard to categorically say something is impossible in biology; there are always exceptions.  But your cells are full of your mRNA all the time.  When you get infected with most viruses, like COVID, there is foreign mRNA in your cells.  In general, this does not cause permanent change to your DNA, let alone clinically pathogenic change.

Just note that reverse transcriptase works in the cytoplasm to create a DNA copy of an RNA, so it does not allow mRNA transport to the nucleus, it just creates DNA which could then be transported to the nucleus.

I think this is the beginning of a good answer, but it doesn't directly address OP's question: "but I do not understand how the mRNA is only able to cross the nucleus-cytoplasm membrane in one direction". Yes, nuclear pores control the flow of mRNA out of the nucleus, but they also allow things into the nucleus (like proteins). What is the mechanism by which mRNAs are exported but not imported?

@acvill: this would indeed be particularly interesting to know!

How many colds have you gotten in your lifetime?  Do you think they've all changed your DNA?

Transcription Regulatory proteins are able to enter into nucleus because they posses a specific strings of amino acid sequence called Nuclear Localization Sequence. Nuclear Pore Complex don’t let anything without that sequence pass. Nucleus membranes are temporarily dissolved during cell division and reconstituted once the process is complete so technically it’s a possibility that some enzymes could happen to be there. However during cell division, DNA is all wrapped up (DNA-nucleosome-chromatin-chromosome) so not much regulation (much less damaging alterations) can be done during this time.
And let’s just say things do go wrong and this particular cell starts to act wonky, your immune cells will recognize the “defective” cell and either engulf it to destroy it or trigger its self destruction through Apoptosis. Pretty neat huh? Inspite of all the failsafe mechanisms, some viruses do manage to disrupt DNA by inserting transposons which in some incidences could trigger/suppress oncogenes, protooncogenes, tumour suppressor genes etc with dire consequences.
Sorry David! Pardon my zeal for proteins. My comment was more for the previous posters and not the OP.
Post transcription, mRNA is modified (introns removed, spliced), 5’capped, Poly A tailed added on. 7-MethylGuanosine m7G cap plays an important role in mRNA transport and metabolism. m7G Cap attracts and binds proteins such as eukaryotic translation initiation factors and Cap Binding Proteins. They not only guide mRNA where to go (ribosomes on ER) but also protect them from being degraded by exonucleases (very efficient enzymes that break down RNA and DNA)
mRNA has a lifespan of mere 1-3minutes.
So to answer your question, cytoplasmic mRNA (foreign or m7G capped cellular RNA) tend not to make it back because

The proteins it’s bound to lack the Nuclear Localization Sequence to get past the Nuclear Pore Complex or 2. Gets degraded very quickly by exonucleases.

Reverse Transcriptase (RNA dependent DNA Polymerase) is not just found in viruses. Telomerase (that lengthen telomer caps on chromosomes) also is a reverse transcriptase. Look up human TERT. Like all polymerases it needs specific binding sites and requirements. RT just doesn’t transcribe any ol RNA into cDNA hybrid FYI. The viruses that insert viral genome into cellular DNA have evolved to bypass all the cellular fail safes.

Welcome to SE Biology. Please finish the [Tour]. Please also read the question and note that it is about the transport of mRNA. Your answer is about proteins and makes no mention whatsoever of mRNA.

Sorry I can’t spend any more time specifically to look up citation to back up my post.  randomly came across it and sensed an underlying concern regarding mRNA vaccine becoming  incorporated into your DNA.  For reasons outlined above the chances are extremely slim to zilch. Don’t get me started on the amount of noncoding and  considered junk DNA already on our chromosomes. As for citations, you can easily look it up based on the names I provided or  I’m sure other cell biologists  can back me up.  Should be working  or spending time with my kids anyway. Adios and hope I helped OP

@NunyaBeezenez Welcome to Stack Exchange! This site works different than most others. Answer posts are absolutely expected to support their assertions by citing references and including links.


text:
Why doesnt the SARS-Cov-2 affect other animals?
Why doesn't the coronavirus affect animals like dogs and cows? I know that the SARS-CoV-2 is a zoonotic virus i.e. it can affect both humans and other animals.  I also know that the DNA composition and cell structure of almost every animal on earth  is the same.

"I also know that the DNA composition and cell structure of almost every animal on earth is the same." -- that's quite the generalization. Do you not think that the differences that cause the great variety in physical appearances across animals could also cause differences in susceptibility to disease?

Even though the DNA sequence may be 90+% similar between two species, individual amino acids can make a huge difference in the interaction between two proteins. In this case, the most relevant proteins are the coronavirus spike protein and the ACE2 enzyme expressed on the surface of target cells. Even in the limited amount of time SARS-CoV-2 has existed and been studied, researchers have found single amino acid mutations in its spike protein that meaningfully affect how well it binds to ACE2. When constructing animal models for COVID-19, and for the original SARS, in some cases it has been necessary to introduce a human ACE2 gene to allow infection. It is worth noting, however, that this is not always the case--for instance ferrets and hamsters can be infected by SARS-CoV-2 without any genetic modification at all.
This paper gives a summary of the work so far: Muñoz-Fontela, C., Dowling, W.E., Funnell, S.G.P. et al. Animal models for COVID-19. Nature 586, 509–515 (2020).

Also cats and tigers: https://www.cdc.gov/coronavirus/2019-ncov/daily-life-coping/animals.html  And there have been fairly recent news reports about large numbers of mink (a fairly close relative of ferrets) dying from the virus.

This looks like a reasonable answer and it is great that you provided a supporting reference. However, please include the complete reference information since links can (and do) break — e.g. when a journal reorganizes its website. One easy way to get that information is to search for the paper on Google Scholar and click on the ‟ symbol to get reference information. This is a good example of how to format references. Thanks!


text:
Rh factor and dominance of gene

"Formation of Rh  antigen is controlled by dominant gene(R) and its
  absence by recipient gene(r).People having this antigen with genotype
  (RR or Rr) are called Rh positive and those whose blood is devoid of
  it with genotype (rr) are called Rh negative. About 85% in world are
  Europe and 97% human being in India are Rh positive."

My questions are:-
Which factors result into dominance of gene(R) and  absence of recipient gene(r)?
With difference seen in %ratio in India and Europe, can it be concluded that environmental factors affects it.?

You are using the word "dominant" in two very different ways.  I suggest you rewrite your question to avoid that.  I'd say the short answer is that you can't necessarily conclude anything from the relative frequency of genes like that.  It could very well just be luck that the r allele is a little more common in Europe than India.

There are various factors which decide the dominance of one gene over the other. Owing to the complex biochemical pathways it is difficult to predict which gene is dominant unless we know exactly how the gene is translated to protein and how the protein interacts with the body.
These are the few answers that could help:-

What makes a gene dominant or recessive
What determines if an allele is dominant or recessive?

As for your question;
There are two genes:

D- The allele which is dominant
d-The allele which is recessive.

A recessive gene is a gene that is nonfunctional or expresses its characteristic phenotype in presence of an identical allele.
For a person to have Rh negative blood group he must inherit 'd' allele from both the parents as it is a recessive trait.And as @swbarnes2 mentioned in the comments 'd' allele is more common in European countries leading to a wide range of population possessing Rh negative blood groups.

Shouldn't you replace "gene" with "allele"?
For example: "D- The gene which is dominant" into "D- The allele which is dominant"

In this specific case the dominant allele is the presence of a gene (RHD), and the recessive allele is (usually) the absence of that gene. This is why you will see the statement "there is no d gene". There does indeed appear to be an environmental factor which governs the frequency of the various genotypes - Toxoplasma gondii.
I find this topic quite a challenge. Here is a distillation of my research.
It is thought that the RHD gene may have arisen through a duplication of the adjacent RHCE gene. It seems that the possession of this gene (a D allele) confers a selective advantage in individuals suffering from toxoplasmosis (infection by the protozoan Toxoplasma gondii. Toxoplasmosis has an effect upon what is termed psychomotor performance, which is usually measured as reaction time. So, for example, it has been reported that there is an increased incidence of road traffic accidents amongst those suffering from (asymptomatic) toxoplasmosis.
Heterozygosity at RHD seems to reduce this effect of toxoplasmosis. So, the current theory is that the D allele appeared in humans because of the prevalence of toxoplasmosis, with the selective disadvantage of haemolytic disease of the newborn being balanced by the heterozygote advantage (similar to the malaria/sickle cell anaemia interaction). There is currently no biochemical explanation of why the RHD gene product has this effect.
In a region with a very low risk of toxoplasmosis there would be a strong selection for the (ancestral?) dd genotype since these individuals have the best reaction time of all (when not infected). The definitive hosts (i.e. where the parasite reproduces) of Toxoplasma gondii are cats, and these were rare in Europe before the domestication of cats. This could explain why the dd genotype is more frequent in this area.


text:
M-type potassium channels by muscarinic receptors
How does the closure of M-type potassium channels by muscarinic receptors result in increased excitation of the target neuron?

Closing of the channel through muscarinic receptors involves activation of phospoholipase C and depletion of membrane phosphatidyilinositol-4,5-bisphospate which is needed for the channel to stay open. Once the channel is closed,  potassium, which is a positive ion accumulates inside the cell eventually depolarizing it or lowering its threshold for activation. Thus, blocking the extrusion of K ions results in excitation of the target neuron.
See this for more:
Brown, D. A., and Constanti, A. (1980). Intracellular observations on the effects of muscarinic agonists on rat sympathetic neurones. Br. J. Pharmacol. 70, 593–608.


text:
Would expression of GroEL and GroES in erythrocytes be a potentially effective therapy for sickle cell disease?
Would expression of GroEL and GroES in erythrocytes be a potentially effective therapeutic strategy for sickle cell disease? Why or why not?

Apart from the answers from WYSIWYG I would add that the formation of filaments of Hb in sickle cells isn't really misfolding or misassembly, rather it is due to a new assembly pathway which results from the Glu>Val mutation. GroEL helps a protein to avoid kinetic traps en route to folding, filament formation is an extra process tacked on at the end of normal folding.

GroEL and GroES are multiprotein chaperonin complexes: Not so easy to ectopically express
Erythrocytes do not have nucleus: you cannot stably express anything in mature erythrocytes.
If your aim is to do a stable gene expression (which would require genomic integration), the better way is to do a gene therapy: culture haematopoetic stem cells, Correct the mutation by homologous recombination. Put the cells back into the bone marrow.


text:
How do Type I restriction enzymes work?
According to NCBI, type I REases have a specific target sequence but randomly make cuts at sites far from the target sequence.
How does the restriction enzyme travel from the target sequence to the distant site of restriction, and what is the point of having a target sequence if the cuts are random and far away from the target sequence?

The enzymes don't need to travel down the DNA to get from their binding site to their cut site, if the sites are far enough apart the DNA can bend back around and the protein could touch both sites at once. I'm not familiar enough with this class of enzymes to be sure.

To answer your last question first: as long as a restriction enzyme recognises a specific sequence then goes on to cut the DNA it really doesn't matter where the cut takes place, as long as the invading DNA is destroyed.
The WP page on restriction enzymes provides a useful summary of the various classes of restriction enzyme, and led me to a review about Type I enzymes here.
Unlike the familiar Type II enzymes, Type I enzymes require ATP, which they use to power their movement along the DNA, once they have been activated by binding their recognition sequence. The HsdR subunit of the enzyme (R, M and S subunits) contains sequence motifs which mark it out as being related to DNA helicases, which, of course, are able to translocate along a duplex and unwind the duplex.
One particularly striking demonstration of the DNA translocation ability of EcoK1 (a Type I enzyme) is described in

Davies et al. (1999) The DNA translocation and ATPase activities of restriction-deficient mutants of EcoKI. J. Molec. Biol. 292: 787-796 doi:10.1006/jmbi.1999.3081

The experiments are based upon the mechanism by which phage T7 injects DNA into E. coli cells.  The phage ejects about 850 bp of the 40 kb genome into the host; the entry of the bulk of the DNA is coupled to transcription, first by host  RNA polymerase, and subsequently by the phage-specific RNA polymerase, once the corresponding gene has entered the cell. If the drug rifampin is used to block transcription then the whole process stalls. This block is overcome if the initial leader of 850 bp is engineered to contain a recognition sequence for EcoK1 whereupon the restriction enzyme is able to translocate the entire genome into the cell at 100 - 200 bp per second. Mutations in the helicase motifs of the HsdR subunit abolish this activity.


text:
Can sugar alcohols, and glycerol in particular, cause intoxication?
I'm mostly curious about glycerol, which I use as a sweetener. I've been told that it can cause intoxication, because it is an alcohol. Is this true?
If so, are there any good sugar alcohols which can be used safely without intoxication (or nasty side effects)?

Well, I was intrigued by this, and my intuitive response was that it would never be toxic at reasonable doses, but I was wrong.
A quick Google search led me to this paper:

Andresen, H. et al. (2009) Severe glycerol intoxication after Menière's disease diagnostic--case report and overview of kinetic data. Clin. Toxicol. 47: 312 - 6

Apparently in the Klockhoff test for Menière's disease the patient is given an oral glycerol dose of 1.2 - 1.5 g/kg (50% in water) then observed over a period of 4-5 h. The other details of the test don't concern us here. In this case report a patient suffering neurological symptoms was found to have previously undergone a Klockhoff test at another hospital, and it was estimated that he must have received a dose of 3.88 –3.95 g/kg.
Here are two sections from the paper's introduction (references removed).

Glycerol is well known as a nontoxic substance (LD50 > 25 g/kg in the rat). Possible side effects of the Klockhoff test include headache and nausea. During treatment of brain edema, additional adverse effects such as diarrhea and vomiting were reported, symptoms comparable to those reported for intensive osmolar diuretics. The GESTIS database ranks glycerol in general as a substance with very low toxicity. However, severe symptoms after oral ingestion of glycerol have been reported to occur. Doses exceeding 0.7 g/kg BW have been regarded as potentially toxic for adults. After doses of up to 1.4 g/kg BW, only mild symptoms such as headache, nausea, and diuresis appear. Reportedly, these symptoms are also associated with glycerol treatment of brain edema. In individual cases, an oral dose of 100 g of glycerol has been reported to cause drowsiness, cyanosis, renal pain, and bloody diarrhea.
Martindale Reference Desk reports headache, thirst, nausea, and hyperglycemia as adverse effects. Glycerol may also produce cardiac arrhythmia and hyperosmolar nonketonic coma. These effects are mainly based on its dehydrating properties. Hemolysis has been reported to exclusively occur after intravenous infusion. In fact, most of the major toxic effects of glycerol, such as hemolysis, hemoglobinuria, and renal failure, seem to strictly correlate with serum concentration of glycerol and the route of administration.

It appears then that any toxic effects of glycerol are not due to its alcohol nature per se but rather because it can become elevated in the blood leading to osmotic effects. The authors estimated that 10 h after administraion of the glycerol the concentration in the patient's serum was approximately 39 mM, compared to a physiological basal level in the range 0.05–0.3 mmol/L. The patient's serum level fell to the basal level over a period of 30 hours.
Just to put this in some perspective, in the UK the legal alcohol limit for drivers is 80 mg/100 mL which corresponds to 17.4 mmol/L.
I think that recommending sugar alcohols would fall under the heading of medical advice (not that I have any such recommendations).


text:
alpha tubulin molecular weight problem
Is there any academic reference that shows α-tubulin is around 50-55 kDa? The only thing I found is some data sheets from companies. I need the real reference.

The data sheet is a good enough reference. They must have showed a gel picture also. If not then find details of the protein in Uniprot.

The paper titled Identification of α-tubulin as a granzyme B substrate during CTL-mediated apoptosis mentions it as 51KDa and the paper titled Carboxy-terminal amino acid sequence of α-tubulin from porcine brain mentions it as 55,000 Da. Hope that suffices.

This is not so easy to answer, since alpha-tubulin has at 10 known genes in this family (data from Ensembl):

TUBA1A   tubulin, alpha 1a
TUBA1B   tubulin, alpha 1b
TUBA3E   tubulin, alpha 3e
TUBA3D   tubulin, alpha 3d
TUBA4A   tubulin, alpha 4a
TUBAL3   tubulin, alpha-like 3
TUBA1C   tubulin, alpha 1c
TUBA3C   tubulin, alpha 3c
TUBA8    tubulin, alpha 8
TUBAL3   tubulin, alpha-like 3

You can go on the site linked above and choose any of the proteins. I checked TUBA1A, and get a length of 451 amino acids and a weight of approximately 50,1 kDa.

authors: Бану Балапанова


text:
Why does the protection afforded by some vaccines last longer than for others?
After reading an answer to the question of How Do White Blood Cells Learn? Or Do They?, I came to wonder something. Specifically,

The effect of this is that every new B and T cell that your bone marrow makes will recognize a unique, random protein sequence, and you will have billions of these cells floating around in your blood circulation at any given time. These cells however will only float around in circulation for a short period of time before dying and being replaced by other cells with new random sequence receptors.

Assumption: What I gather from this (and the remainder of the answer) is that basically, a vaccine "teaches" the existing white blood cells in your body; eventually, these cells will  be purged, so you will no longer be immune.
However, many vaccines seem to only be once-in-a-lifetime, or at least require a vaccine only once per decade (or less).
Some examples would be the Varicella vaccine, which can last up to 20 years, the Tetanus vaccine, which recommends a booster every 10 years, and the HPV vaccine, which lasts 5-6 years. Durations also vary with Hepatitis, Influenza, Polio, and numerous other common vaccines.
I would assume that, regardless of what a cell has "learned," it is purged with the same likelihood as any other cell; yet, it seems that some "learned" defenses can be retained longer than others. In essence, my question is: Why do some vaccines take longer to "wear off" than others?
(Note: This question is not a duplicate of Why do I need a flu shot every year, while many other vaccinations last years or even a lifetime?; I understand that some pathogens can mutate, so immune cells are of no use against mutated strains since they were not vaccinated against the mutation.)

http://m.historyofvaccines.org/content/articles/top-20-questions-about-vaccination#5

"It’s not completely understood why the length of acquired immunity varies with different vaccines... Recent research has suggested that the persistence of immunity against a particular disease may depend on the speed with which that disease typically progresses through the body. If a disease progresses very rapidly, the immune system’s memory response may not be able to respond quickly enough to prevent infection—unless they’ve been “reminded” about the disease fairly recently and are already watching for it. Boosters serve as a “reminder” to your immune system." (taken from ref. above)

The first thing I want to make clear is that, the B and T that "will only float around in circulation for a short period of time before dying and being replaced", are not the ones that have already learned to recognise a certain diseases (or vaccine) but rather the naive cells that haven't yet done so. This is also made clear later in the same answer you cited:

As these injected protein sequences circulate through your blood they
  will eventually bump into a B or T cell that has a receptor that
  recognizes them. When this happens, the B or T cell will now start to
  divide and give rise to long lasting memory cells that express the
  exact same receptor and will therefore recognize the exact same
  protein sequence again in the future. These cells will float around in
  your blood for most of your life and make you 'immune' to the
  recognized pathogen.

In order to understand why some vaccines hold for your whole life, while some need a booster every few years we need to look at the life time or recycling of those memory cells, which stay in your body for much longer than the naive immune cells.
Now we come to the actual answer(s) to your question and there multiple  factors that (can) have an influence on this:

Initial strength of the immune response: Every vaccine (and/or disease) evokes an immune response with a different strength. Generally the stronger the first response is, the more memory cells will be created initially (those actually don't have correspond to the same molecular memory either, they might recognise different aspects of the vaccine/disease) and with more cells available it will take longer until none are left
Natural exposure: memory cells start proliferating when they encounter the molecule (protein/virus/bacteria) which they have 'memorised', if there is an acute infection they will do so a lot in order to produce a lot of antibodies against it. However, even a very small amount of virus/bacteria, that wouldn't actually make you sick, will allow induce them to proliferate and preserve their numbers. Therefore memory cells against a more common or prevalent disease should be more stable in your body, than ones against a very rare one.
There very likely more factors that either I or the whole scientific community don't really know about. Cellular systems and the immune system in generally are rather complicated ...

This issue is deep but one answer is bacteria/virus genetic variability. Some organisms have the ability to change their DNA in just a few generations (for example the influenza virus which requires a new vaccine every year). When you take a vaccine for influenza virus you expect that will protect you in a short period of time (winter season) because this virus is a nasty one, i.e it has the ability to present antigen variability due to mutation/constitution of its DNA and antigen is the source of power of vaccine (a vaccine assumes the organism has a antigen that could be a protein or other biomolecule that is relatively fixed between generations and is specific to that organism) so the vaccine loses its effect because the organisms are no longer susceptible which causes immune response to be weak (no longer recognizes the organism as it recognized) and you get sick. If the organism has slow mutation/variability the vaccine will last longer because the antigens are present for a longer period of time but eventually you will need to get another vaccine years later (for example tetanus).

References are appreciated here at Biology.SE. Nice answer, though +1

So the vaccine for tetanus changes over time?

Please see the note below the question.


text:
Dilution question about RNA
I have a basic and probably silly question. I am isolating RNA with TRIzol. I have performed the basic steps and dissolved the pellet in 50 uL water. I ve measured the concentration and it was 3313 ng/uL (Around 165 ug total yield.). Now my next step is DNase treatment. It says 1 unit of enzyme for 1 ug of RNA in 10 ul reaction mix. I would like to dilute my RNA to 100 ug and use 100 units of enzyme in a 1000 uL reaction mix.
Is this logic true, and if it is how I am going to do the dilution?
Thanks!

Short answer: Yes. :-)

If I understand correctly what you mean by "I would like to dilute my RNA to 100 ug":
Your RNA preparation is at 3.3 μg μl-1.
To add 100 μg to a reaction you need to add 100/3.3 = 30 μl
Then make the total volume up to 1000 μl with enzyme and buffer as appropriate.

Thank you. That was exactly what I did but then I thought that while I am voluming up with buffer, enzyme and RNase-free water, concentration would change again? I mean I add 30 uL water more to my 50 uL stock, but then for the DNase reaction, I ve added more. So would that be a problem?

The final RNA concentration will be 100ng/ul. So add up all the single components (30ul of RNA, the buffer you need for 1000ul, the enzyme) and fill up with clean water to 1000ul.

As long as you add 50 micrograms of RNA to the reaction tube and then add other components to a final total volume of 1000 micro litres then everything will be as you wish. Dnase isn't particularly choosy about conditions anyway -  as long as there is some Mg2+ about.

I might have added much RNA though. :) My friend was using just 1 units of enzyme for 100 ug RNA and it was also working. I just followed the manufacturers instructions. I hope it will be fine! Thank you for the answers @AlanBoyd and Chris.


text:
What is the biological basis for the perception of time?
How is the "time axis" of memories encoded in the brain? I guess the time of the event could be "stored" with each event, but how is this translated into neurons etc.?

I'm no expert on the topic, but was about to find the following;
In mammals, the hippocampus region of the brain is one of only 2 regions with the capacity for lifelong neurogenesis (the creation of new neurons). This happens continuously with the creation of new memories and experiences (neurons are even created just to mark time passing - even if no memories are stored alongside - so that a perception of 10mins and 10secs is possible, even if nothing memorable happens). As new clusters of neurons are generated, they gradually differentiate and mature to become fully functional, and in this way time and memory are interlinked, and experiences are clustered together [1].
In a human study where individuals were asked to recall whether news events occurred within 1 week of each other (some related, some not), same-week and separation judgements were more far more accurate for related events. Unrelated events were essentially guesses, whereas deductions could be made about related events. [2]. This lends weight to the above argument that memories are clustered in the brain with temporal information embedded within.
The hippocampus is also involved in imaging the future. (Inconsistent) findings suggest that activation of the hippocampus allows mammals to conceive a scenario constructed from previous memories and experiences, and to store these for later use [3].
Refs

Aimone, J. B., Wiles, J., & Gage, F. H. (2006). Potential role for adult neurogenesis in the encoding of time in new memories. Nature neuroscience, 9(6), 723-7. doi:10.1038/nn1707
Friedman, W. J., & Janssen, S. M. J. (2010). Do people remember the temporal proximity of unrelated events? Memory & cognition, 38(8), 1122-36. doi:10.3758/MC.38.8.1122
Addis, D. R., & Schacter, D. L. (2011). The hippocampus and imagining the future: where do we stand? Frontiers in human neuroscience, 5, 173. doi:10.3389/fnhum.2011.00173


text:
How does Yeast-two-hybrid detect interactions between several proteins in one experiment?
I am trying to understand the Y2H screening method. I can understand how we can check if two specific proteins interact with each other. For example, if we want to check whether protein A and protein B interact, we fuse A with the Activation Domain (AD) of a transcription factor and B with the Binding Domain (BD) of another transcription factor. When the two fusion proteins are transfected into a yeast cell, the reporter gene is expressed only if the AD and the BD get together and form a complete transcription factor and that happens only if proteins A and B interact with each other.
However, I have seen claims that Y2H is a high throughput system, i.e., it can be used to detect several interactions at once. But most articles online that attempt to describe it, seem vague to me.
For example, suppose I fuse the "bait" protein to the BD and several different cDNA's to the AD and let the yeast grow. Next, I observe that the reporter gene is expressed. Doesn't this observation only imply that there exists some protein from the cDNA library that interacts with our bait protein? How do we know exactly which of the target proteins have interacted with the bait and resulted in the expression of the reporter gene?

You use a library of many yeast in which each expresses only one target, or 'prey' protein. Then you grow each yeast colony separately, for example in different wells.
It's definitely not a high-throughput method if you do it the old-fashioned way, i.e. making your own yeast library, or if you do it with only a few targets.  But these days you can buy pre-made yeast libraries with thousands of target proteins, each separated into a well on a plate, then you run the experiment for all the targets simultaneously. With a visible marker you can then easily see which wells have produced successful interactions, and thus which targets interacted with your bait.

Thanks for the answer. Is there a picture available somewhere that shows what the wells on a plate look like?

Here's an example taken from this Busch et al (2007) paper.


text:
Does an "empty stomach" have acid in it?
I know that the pH of the acid in an empty stomach is higher than a stomach with food.
I was trying to understand how water passes through stomach to intestines with the absence of food.
But this webpage : Acid reflux mythbusters has this bizarre claim :

Drinking water on an empty stomach does not dilute stomach acid because it was never released in the first place.

How is this possible? Ok sure, not "more" acid is released because it's just water. But there is still acid already present in the stomach, right?
Note : I'm not concerned about diluting the acid or not. I just want to know if there is acid in the empty stomach or not. Or if there is any possible scenario where the stomach is actually completely empty.

When an individual is fasting, acid secretion is inhibited by somatostatin from gastric D cells (some helpful stomach acid secretion scientific papers, and an article on stomach acid regulation). This causes there to be a minimal amount of stomach fluid (aka stomach acid) around, but due to the nature of the stomach a pH of 1.5-3.5 must be maintained and so there is always going to be some amount of stomach acid even if it is not the 1L pool of acid some people imagine there to be. In order for more stomach fluid/acid to be produced, neurological stimulus must occur that somehow relates to food or drinks (such as smelling food or thinking of food or obviously, consuming food/drinks).
Hope that helped!


text:
Where can I find the standard curves for Bovine Serum Albumin (BSA) and ovalbumin as determined through the Bradford Assay?
I was wondering if anyone would please be able to point me in the direction of a database or something similar which contains standard curves/absorbance levels for BSA and ovalbumin, as measured using a spectrophotometer at 595nm, with the Bradford Assay?
Thank you in advance!

Really, you should make your own standard curve, as the concentration of your Bradford reagent may be slightly different than mine, or the one used in a paper, and spectrophotometers can vary significantly. Typically an ampule of BSA or OVA at a defined concentration in PBS is included with Bradford assay kits. This can be serially diluted, then duplicate or triplicate samples added to the same plate as your samples. You can also (very carefully) make standards yourself - just be sure to agitate them long enough so that the protein is completely dissolved.

Figure 1. Absorbance of Bovine Serum Albumin (BSA) at concentrations of 0, 40, 80, 120, 160, and 200 μg/μl at 595nm.
or
Figure 2. BSA Standard Curve with absorbance measured at 595 nm, a linear regression was deduced with equation of y = 0.0127x.
or
Steps 7, 15 and 16 here
or ideally
Please just use a search engine and type in "bradford protein assay 595nm bsa" or substitute "bsa" for "ovalbumin" and see what the world has made available for you in the realms of protein spectrophotometry at 595 nm.

That’s amazing! Thank you so much!


text:
Hundreds of Red Spiders in Individual Webs
I live in the USA in south Louisiana. I woke up this morning to find my yard covered in hundreds of spider webs.

Each of those little white puffs is a spider web. Inside of each web is one little red spider.

The spiders are pretty small. Less than half an inch long.
Anyone know what they are?

http://xkcd.com/8/

@CDspace Seriously, there's an XKCD for absolutely everything...

It is a black-tailed red sheetweaver, Florinda coccinea.
Identified by its red body colour , location (USA) and black caudal
tubercle.

More images to be found on bugguide.net

It is a species of web-building spider belonging to the family Linyphiidae. It is the only species in the genus Florinda. It is sometimes known as the red grass spider. This species is common in the southeastern United States, inhabiting grasslands, lawns, and agricultural fields.

Reference: Wikipedia

You say "It's a rare species.", but the quoted text says "This species is common in the southeastern United States" could you please clarify?

Rare worldwide and common in a location.

I have seen these suckers before. Usually their web is most visible in the early morning when the grass is dew covered.  They seem to need a lot of space. I have seen them in large yards and fields but never small yards. There a little neat, but mostly harmless. Birds should come soon and eat most of them. You should try to avoid mowing them. I'd be surprised if they were there for more then a couple of days, assuming your don't have a mosquito problem.

@anothersackofchemicals Thanks for pointing out. It was my mistake to put it in that way. I actually meant they are rare worldwide as coteyr said. I've removed it.

Hey, I saw a couple of these in my yard just this morning. This one missed a meal

@WayneWerner I loved the plot twist at the end of your video. It was like deus ex machina, or dog ex machina :-)

Cat ex-machina, actually. She decided that I should be petting her instead of taking videos of boring grey patches on the ground.

@coteyr Yeah, they were gone when I got back from work that evening.


text:
What's the advantage of autocrine signalling?
In the antibody-mediated immune response, when the helper T cell gets activated by the costimulus (IL-2 and TNF-α secreted by the APC) which in turn produces IL-2, IL-2 acts in an autocrine manner. I'm just wondering why does IL-2 have to be secreted? Why doesn't it just exert an affect while it's already inside the helper T cell? What's the point of autocrine signalling?
I hope the answer isn't going to be, "Well, that's just the way it is..." because paracrine and endocrine make sense and have advantages, but autocrine just seems a bit extra.

Why doesn't it just exert an affect while it's already inside the helper T cell?

Because it interacts with membrane-bound receptors. Those are outside so there is no way IL-2 (or any autocrine factor) could signal while inside the cell. It has to exit.
Now, the next question is why the receptor is membrane-bound and outside. As far as I understand there are two parts to this answer:

Receptors are evolutionarily related so they follow similar synthesis pathways.
Membrane-bound receptors are (all?) transcribed while being secreted into the endoplasmic reticulum. This causes their agent-binding portion to reside inside the ER. From there, vesicles bud off, are transported towards the cell membrane, merge with it, and hence the formerly inside portion of the protein ends up on the outside.

paracrine and endocrine make sense and have advantages, but autocrine
  just seems a bit extra.

Autocrine also have advantages compared to internal signaling. Even if when you study mechanisms you think at single cells, cells are never alone in the body. If the message (IL-2) would be internal, each cell will individually respond according to its internal signaling levels. With the 'extra' to secrete the message, and having it sensed at the exterior (the receptor is membrane-bound), all the cells in the nearby are going to contribute to the average signal and will respond with average magnitude. It's a form of communication between a single cell population that does not affect other cells populations (the ones that does not express the IL-2 receptor).

That's a very interesting answer !! It means that fluctuations in the signalization are balanced by this phenomenon. Would there be articles about that kind of phenomenon ?


text:
What is the mechanism by which Melatonin increases dream vividness and intensity in humans?
I'm looking at the wikipedia article on Melatonin and noticed that it mentions vivid dreaming caused by melatonin. I have the "Melatonin and the Biological clock" pamphlet referenced in the article, and it does not go into too much detail of how vivid dreaming is happening.
I've personally experienced vivid dreaming side effects of melatonin today - dream after dream of profound intensity, but completely unrelated content. This makes me interested - how does melatonin influence the intensity of dreaming in humans? Is it by interaction with Serotonin? Or does it get metabolized into something psychoactive?

Check this out. Not accessible to me at this moment.


text:
What parts of the brain are involved in regulating blood pressure in mammals?
I'm reading this Wikipedia  article on blood pressure and its regulation, and it mentions that medulla is involved. however, I vaguely remember reading another article on Wikipedia and it mentioned that hypothalamus or hippocampus could be involved. So my question is - what other parts of the brain or neurotransmitters have significant effect on blood pressure regulation?

You may want to look at vasopressin

Thanks, vasopressin does appear to affect blood pressure a bit in healthy individuals. There is a duplicate mention of blood pressure in the part of the article that deals with nervous system, but I'm not sure if this is the same or different effect