text:
Are IgE antibodies capable of binding water molecules?
I learned in med school, that they are too small to trigger the IgE reaction that causes the release of histamine. However, I came across reports of this condition;
https://en.wikipedia.org/wiki/Aquagenic_urticaria
Some people with this cannot drink plain water without experiencing symptoms in their mouths and throats. In some cases, they report anaphylaxis if they drink a sip of water. The drug 'Xolair' blocks IgE and is effective in people with this condition.
But, I thought the water molecule is too small to bind to IgE antibodies? At least, that was what I learned in med school. Now I'm kind of confused. Aren't IgE antibodies literally dissolved in/surrounded by water on a constant basis? Wouldn't the water in the liquid these cells are always in be triggering a 24/7 reaction in their skin and their throats? Not just when they drink some water or take a shower. The epidermis is just dead cells, the mast cells in the skin have to be submerged in a mostly water medium to survive.
These people rely on milk and orange juice to drink, as it does not elicit the internal allergy reactions.
https://rarediseases.info.nih.gov/diseases/10901/aquagenic-urticaria
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3276800/
https://pubmed.ncbi.nlm.nih.gov/32940373/
https://www.businessinsider.com/toddler-allergic-to-water-aquagenic-urticaria-2018-2?op=1

Welcome to Biology.SE. For the reasons you mention it seems clear that this can not be a reaction to water molecules. (However, note that anything in aqueous solution will have many interactions with water molecules.) Please [edit] your post to include more reliable background information — I suggest you look at other sources in addition to Wikipedia (it's a fine place to start, but the quality of the information can be highly variable). Please see the [tour] and  [help] pages starting with [Ask] questions effectively for details of what is expected in posts on this site. Thanks!

It is as you suggest: IgE antibodies are incapable of binding to water.
The immunogenicity of water is not explainable that simply. It is also important to know that it is a variant of physical urticaria, which presents the same symptoms but via different provocation, such as pressure, cold, heat, or exercise and sweating (cholinergic urticaria). There is some discussion on the topic here.
Some competing explanations in the links you provide are:

water reacts with something on the body, and the product of the reaction is immunogenic, or water solubilizes a surface antigen that penetrates the skin, and
contaminants or impurities in the water elicit the immune response.

First, I will offer my amateur thoughts on the matter, and then provide you with transcripts of what doctors who have had experience with treating this have come to understand. Do note that this is still an incompletely understood (rare) disease and that there exists no definitive mechanistic understanding, though histopathological examination has been performed, and it does indeed seem like the presence of water induces an immune reaction. It also seems immunologic due to the fact that patients respond well to antihistamines and related treatments that suppress the immune system.
As you can guess, this is a very rare disorder and it is difficult to rule out things such as an uncommon reaction to (perhaps) improperly cleaned or cleared water. However, some studies have been done to rule out impurities in water by the use of a water provocation test, or "water challenge test", where source of the water has been shown to not matter, thereby likely ruling out the impurities hypothesis. Patients also have similar responses to rain, tap water and swimming pool water. It too may be that the preparation, processing or chemistry of milk or orange juice renders an aqueous medium as incapable of eliciting a reaction on the skin, perhaps due to the presence of molecules or simply by virtue of things like pH being different than that of water. Reportedly, pH and temperature do need seem to play a role. It is also possible, though unlikely, that the immune response to water is psychogenic, and seems to occur more predominantly in females around puberty, and has been anecdotally reported to co-occur with some diseases like Bernard-Soulier syndrome, polymorphic light eruption, familial lactose intolerance and papillary carcinoma of the thyroid.
Anyway, I doubt anyone here at this SE can do a better job than the summaries I have here below.
A discussion of the cases and literature from 2011 can be found here:

The pathogenesis of AU is not fully known; however, several mechanisms have been proposed. Interaction with water with a component in or on the stratum corneum or sebum, generating a toxic compound, has been suggested. Absorption of this substance would exert an effect of perifollicular mast cell degranulation with release of histamine. A study by Sibbald et al. demonstrated that complete removal of the stratum corneum appeared to worsen the reaction, rather than prevent urticaria. These authors also demonstrated that pretreatment with organic solvents enhances wheal formation in contact with water. They suggested that enhancement of the ability of water to penetrate the stratum corneum increases wheal formation. Czarnetzki et al. hypothesized the existence of a water-soluble antigen at the epidermal layer. The antigen diffuses into the dermis by water and then causes release of histamine from mast cells. Tkach hypothesized that hypotonic water sources could lead to osmotic pressure changes, resulting in indirect provocation of urticaria. Others have recently stated that 5% saline was more effective than distilled water for eliciting the wheal-and-flare reaction. They hypothesized that the salt concentration and/or water osmolarity may influence the pathogenic process of AU, possibly by enhancing solubilization and penetration of a hypothetical epidermal antigen, in the same way as has been postulated for enhancement of organic solvents. Another proposed chemical mediator in AU is acetylcholine because of the ability of the acetylcholine antagonist scopolamine to suppress wheal formation when applied to the skin before water contact. However, another study failed to reproduce this finding when pretreatment with atropine did not result in suppression of subsequent wheal formation. Methacholine injection testing is negative in patients with AU; however, it is often positive in cholinergic urticaria. Serum histamine levels are variable from patient to patient. Antihistamines have been used to treat AU; however, the therapeutic effect and prognosis vary. In some cases, complete control of symptoms with antihistamine has been reported, whereas in other cases, there is a failure to adequately control symptoms. Refractory cases have been treated with ultraviolet (UV) radiation (both psoralen plus UVA therapy and UVB), either alone or in combination with antihistamines. It is hypothesized that the effect of ultraviolet therapy is mediated by thickening of the epidermis, which may prevent water penetration, interaction with dendritic cells, and immunosuppression or a decreased mast cell response. Barrier methods involving application of oil-in-water emulsion creams on the skin for water protection are effective. AU responds to stanazolol treatment in human immunodeficiency virus-positive patients.

Another discussion, from a paper from 2017:

Many of these histopathologic findings are the same as those of acute
urticaria, in which interstitial dermal edema, dilated venules,
endothelial swelling, and sparse infiltration of inflammatory cells
have been described. Mast cells are concentrated around the blood
vessels of normal dermis, with one to three cells per cross-sectional
vessel profile, but in this patient there were slightly increased
numbers of mast cells around blood vessels.
Antihistamines are the first line treatment for aquagenic urticaria.
In recalcitrant cases, the dose can be increased by as much as
four-fold the conventional dose. Phototherapy and barrier cream are
alternative or additional treatments if antihistamines fail to prevent
recurrence. The efficacy of phototherapy is related to its induction
of both immunosuppression, including a decreased mast cell response,
and epidermal thickening, which disturbs the penetration of water and
thus also inhibits mast cell stimulation. Barrier cream prevents
the penetration of water into the dermis. However, the various
emollients and water-resistant creams investigated have not yielded
conspicuous success, except in a few cases in which a
petrolatum-containing ointment was applied before water exposure.
Anticholinergics such as scopolamine may also offer relief. Most of
the patients were successfully controlled with antihistamines,
although some of them changed treatment modalities because of
drowsiness.


text:
Why is FAD, rather than NAD+, reduced in the succinate dehydrogenase reaction of the Tricarboxylic Acid Cycle?
FADH2 is produced in the conversion of Succinate to Fumarate in the tricarboxylic acid cycle. Why is this so? Why not NADH?

Just a guess: FAD reduction potential is higher than that of NAD; so it should be a better oxidizing agent than NAD. NAD however would be a better reducing agent.
Source

@TalhaIrfan — I have reverted your edit. There is absolutely no reason to place the abbreviations in italics and a different typeface — and every reason not to — which is what your markup did. The poster or who ever edited it previously was quite right in formating with HTML 'sub'. If she hadn't rendered the subscript — OK, but she had. Leave well alone.

@David Latex has been the preferred mode for both Mathematical as well as Chemical equations/formulae on SE; and its italic by default. Just the answer below is an example of its use!

@TalhaIrfan — preferred by whom? This is not a mathematical construct it is a biochemical construct that would be set in a biochemistry text book (e.g. Berg et al.) in the same weight and typeface as other words in the text. Your Latex rendering is further ugly and makes reading difficult. And as I said, is in italic for no good reason. I have not changed the answer below, just as I would regard it rude to change US spelling to UK spelling. Please do not change answers just because you personally prefer a particular style.

@TalhaIrfan — I think that this question should be discussed further on Meta. I'll post a question when I have a moment. That way we can get clarification.

In general, $\ce{NADH}$ and $\ce{FADH2}$ are coenzymes. The structure of the main part of an enzyme determines which coenzyme or which prosthetic group will work with the concerned enzyme. Unlike most other TCA cycle enzymes, Succinic Dehydrogenase involves the participation of $\ce{FAD}$ rather than $\ce{NAD}$ and that is a consequence of its specific structure.
Another possible reason might have to do with the energy gap available. The conversion of succinate to fumarate liberates less free energy as compared to other oxidation reactions. Ususally, the steps which are coupled with NADH reduction have a free energy change of about $\Delta G=-100$ to $-150~ \pu{kcal/mol}$ but the conversion catalysed by succinic dehydrogenase has a free energy change of $ -80~ \pu{kcal/mol}$ (rough figures) and hence releases less energy. It therefore might not be feasible to couple with $\ce{NADH}$ reduction but it would be favourable (thermodynamically) to couple with an easy-to-reduce (since the reduction potential is higher and hence reduction is more favourable) and hence less energetic molecule $\ce{FADH2}$.
Apart from structural and thermodynamic requirement, one last possible reason might be that succinic dehydrogenase is a part of the mitochondrial membrane and involved in the Electron Transport Chain. Here, flavin molecules are excellent electron transporters (in comparison to nicotinamide based reductants) and therefore it might be more profitable to use a flavin based reductant to later facilitate easy electron transport and proton transfer.
Again all these are probable reasons and I dont know for sure.

There is a simple straightforward answer to this question, which I present here because the poster of the accepted answer seems unsure which of his three suggestions is correct, and therefore there is a danger of the reader thinking that an explanation in terms of flexibility or membrane location is correct. It is not.
It’s all to do with thermodynamics — the free energy changes in the different redox reactions. Thus, in their chapter on the tricarboxylic acid cycle Berg et al. write:

Succinate is oxidized to fumarate by succinate dehydrogenase. The hydrogen acceptor is FAD rather than NAD+, which is used in the other three oxidation reactions in the cycle. In succinate dehydrogenase, the isoalloxazine ring of FAD is covalently attached to a histidine side chain of the enzyme (denoted E-FAD).
E-FAD + succinate ⇋ E-FADH2 + fumarate
FAD is the hydrogen acceptor in this reaction because the free-energy change is insufficient to reduce NAD+.
  FAD is nearly always the electron acceptor in oxidations that remove two hydrogen atoms from a substrate.

An internet search brings up any many sets of university lecture notes that provide numbers to back this up. For example notes from Bryant Miles at Texas A & M (slightly reformatted by me):

Why is FAD the electron acceptor rather than NAD+?
The oxidation of an alkane is not sufficiently exergonic to reduce NAD+ — E˚' = –0.315 V
The oxidation of an alkane is sufficiently exergonic to reduce FAD. — E˚' = –0.031 V
Fumarate + 2e- → 2H+ Succinate — E˚' = 0.031 V
∆E˚' = –0.0002 V ∴ ∆G˚' = +0.04 kJ/mol
The change in free energy based on the steady state concentrations of all the reactants and products in mitochondria isolated from pig hearts is approximately zero, a near equilibrium reaction.

I think that flavoproteins are more flexible than NAD. NAD carries exactly 2 electrons, while FAD can carry either 1 or 2 electrons. This is important, as succinate dehydrogenase is at the crossroad between the Krebs cycle and the electron transport chain. Best I can tell, the Krebs cycles is knocking out 2 electrons per enzyme, while the electron transport chains is knocking out 1 electron per complex. So maybe FAD makes the translation between the two systems work?

Please add some references to your answer.

But in the succinate dehydrogenase reaction FAD accepts two electrons to give FADH2, so the fact that FAD is chemically capable of accepting one electron in a different reaction is quite irrelevant. The answer can be found in most biochemical texts, and comes down to the energetics of the reactions involved.

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text:
Chloride Clamp and Nernst potential
The Nernst potential for chloride is -70 mV. The neuronal Resting Membrane Potential (RMP) is -70 mV. Under this condition, if the chloride channels are open (as it happens in Inhibitory Post Synaptic Potential - where chloride channels act as postsynaptic ionotropic channels), Chambers† writes that there is a movement of chloride ions along the concentration gradient i.e from outside to inside. However as the RMP and Nernst potential are the same, there is no hyperpolarization, as would happen were the voltage-gated potassium channels to open. However, the result is that there would be a need for much greater excitatory stimuli (influx of sodium) to cause an action potential in this cell. This is called a "Chloride clamp".
I am confused about two things:

Why is there a net movement of chloride ions when the RMP is equal to the Nernst potential of chloride?
As there are more chloride ions inside the cell, why is the cell not hyperpolarized?

Cl‾- mediated IPSP: binding of
neurotransmitter opens Cl‾ channels. The
resulting intracellular movement of Cl‾ ions
usually makes little difference to the
postsynaptic membrane potential, as the
Nernst potential of Cl‾ (–70 mV) is
approximately the same voltage as the RMP.
However, to reach threshold, an excitatory
signal must trigger sufficient Na+ influx to
exceed the combined effects of Cl‾ influx and
K+ efflux, making it much more difficult to
depolarise the cell membrane; this is known as
the ‘chloride clamp’.

† David Chambers Basic Physiology for Anesthetists Second Edition, chapter 53 - Synapses and NMJ Page 233

Can you quote from your book where it says when the membrane potential is equal to the Nernst potential for chloride there is a net nonzero movement of chloride ions in a particular direction?

For question (2), make sure you understand what causes the membrane potential. This answer I wrote yesterday addresses the same issue: https://biology.stackexchange.com/questions/113638/why-dont-membrane-potentials-violate-the-principle-of-electroneutrality

Also https://biology.stackexchange.com/questions/57064/why-is-it-possible-to-calculate-the-equilibrium-potential-of-an-ion-using-the-ne/57066#57066  https://biology.stackexchange.com/a/79623/27148 https://biology.stackexchange.com/a/60547/27148

@BryanKrause I have added the verbatim quote from the book.

I don't think your book is saying that there is net movement of chloride ions at the reversal potential for chloride (Nernst potential): you are correct, that is specifically the voltage where the net flow of an ion is exactly zero; if there is net flow of an ion you are not at the Nernst potential and vice versa. See also https://en.m.wikipedia.org/wiki/Nernst_equation
What your book says is "little difference" and "approximately" rather than "no difference" and "exactly": they're assuming that the resting potential is slightly less negative than the reversal for chloride, so there will be some small but negligible flow of ions and small but negligible change in membrane potential.
The chloride "clamp" or "shunt" will work by opposing any voltage change away from the reversal potential of chloride. The same is really true for any conductance that is open: membrane potential is a weighted sum of the contributions of all permeable ions, so when you open a conductance with a reversal of -70 mV the resulting potential with any other conductances open will be closer to -70 mV than it would be otherwise. See also https://en.m.wikipedia.org/wiki/Goldman_equation

Thank you. I understand what you are telling. So in other words, if an excitatory end synaptic potential were to arrive at this point, any movement of sodium ions inside will be accompanied by movement of chloride ions inside - in other words, as the membrane potential goes toward nernst potential for sodium, chloride starts moving in and tries to keep the membrane potential close to RMP (Nernst potential for chloride). This makes it difficult to excite the cell. Thank you.

@OneFace Yes, exactly.

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text:
Why are there two mature sequences of microRNAs in miRBase entries?
In the miRBase database entries generally show a stem loop sequence and two mature sequences. For example the entry for hsa-mir-15a gives three sequences: (1) the Stem-loop sequence hsa-mir-15a, (2) Mature sequence hsa-miR-15a-5p, and (3) Mature sequence hsa-miR-15a-3p.
What is the difference between the two mature sequences? Does the stem loop structure divide into two different miRNA species?

I am not sure whether it is made clear in the Wikipedia article on microRNAs, but, yes, there are two possible mature mir species that can be generated from the stem-loop precursor — one from each side of the stem — although most often one greatly predominates.
The diagram in Wikipedia shows the generation of a single miRNA:

However, the entry mentioned in the question (hsa-mir-15a) shows that although the 5′-stem component (UAGCA…) is most abundant in this case, there is a small amount of the 3′-stem component (CAGGC…).

In Drosophila melanogaster a single stem component (more often from the 3′-stem, but also from the 3′-stem) most frequently predominates, but I have personally found microRNAs in which both components occur in similar amounts (unpublished).

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text:
Percentage of mutations caused by radiation?
Consider a gamete in a typical human being. In the interest of being specific, let us say that we're talking about a typical ovum in a typical middle class woman living in a developed nation. What percentage, on the average, of the mutations in the genome of that ovum will have been caused by electromagnetic radiation?

May we also assume the person lives at sea level?  The sun will, by far, be the greatest source of radiation in an average person's life (in practically any location).  Elevation is likely to be a key variable in how much radiation she receives (doubles every 6k ft). Radon-222 probably deservers an honorable mention, but no matter what the radiation source, the answer is going to be a very, very low percentage.

@AtlLED, yes absolutely, and that is a very good point.

You might use the frequency of thymine-thymine dimers to extrapolate the rate of UV induced damage. This has been studied but I couldn't find a paper in human cell lines. It appears different cell lines have different susceptibilities to thymine-thymine dimers. The majority of DNA mutation in healthy people comes from endogenous sources, not radiation. Recombination during fertilization may also contribute significantly to changes in DNA sequence. Wikipedia nicely breaks down some of the different sources of mutation.
Manifestations of mutations from endogenous sources is measurable as our bodies become genetically more chimeric with time. Regions of our bodies become deferentially susceptible to disease due in largest part to errors in DNA repair and replication, unrelated to electromagnetic insult.
Damage due to UV radiation, like the creation of a thymine-thymine dimer, can be repaired readily by base excision and replacement. While DNA is dividing, it is cut many times to allow the molecule to unwind. Single strand breaks resulting from DNA damage have robust mechanisms for repair. For example, when a thymine-thymine dimer is excised or single strand break is otherwise introduced, enzymatic recognition makes identification of a template for repair possible. It is also very unlikely in a single strand break that another break will occur in the same location, decreasing the mutation effect of UV.
Double strand breaks and errors in DNA replication are intrinsically more permanent as a substituted base is chemically indistinguishable from any other of the same type. Much of the new genetic information introduced into any mammalian genome comes from endogenous sources, not the environment.

Error rate of human DNA polymerase
Deamination is a major contributor to mutation rate

The only problem with this, is that the germline should absolutely not be exposed to UV radiation.  One of the big things mammals got right was the whole "mama" thing.  In fact, the mother not getting enough UV exposure for vitamin production is more likely to be a problem.

Good point. Now I want to know the correlation between different products of DNA damage and energy of insulting light. Maybe the success of internal fertilization for animals with small litter sizes is related to protection from UV.


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Why do ribosomes associate with rough endoplasmic reticulum but not other membranes?
As far as I am aware, all eukaryotic membranes consist of a lipid bilayer. Smooth endoplasmic reticulum (ER) and rough ER are distinguished by the presence of ribosome on the rough ER surface, but are apparently otherwise similar. So what causes ribosomes to associate with the membrane of rough ER but not that of smooth ER. Or do ribosomes convert smooth ER to rough ER by binding to their membranes?

probably because there aren't ribosome translocation complexes on other membranes

there is a specific binding protein that attaches the ribosome to the rough ER. There are other such binding proteins for say the cell membrane. There are free floating ribosomes as well. But the RER is a specialized structure that produces the proteins in an controlled environment separate from the rest of the cell, reducing the potential damage by improper folding of the proteins and allowing for easier modification and transport of those proteins. the binding proteins also create an additional layer of control/regulation on protein synthesis.

@John — Please read the message that comes up when you click in the comment box and do what it says: "Use comments to ask for more information or suggest improvements. Avoid answering questions in commnets." This site has a particular modus operandum underpinned by a clear rationale that is explained when you join.

I think your question is good, but I made it more precise and compact because English is obviously not your mother tongue. If I have altered the meaning, do say so.

Thank you for refining my question. I have problem expressing ideas even in my mother tongue haha

Peptides that are destined to be either secreted or included in the cell membrane have a signal sequence that binds a protein called Signal Recognition Particle (SRP). The SRP will in turn bind to translocons--basically peptide tunnels in the RER membrane. You need to have this interaction between the translocon and the SRP in order to have stable ribosome attachment. That's why you won't have ribosomes attaching to other membranes. After attachment the ribosome will continue translating mRNA through the translocon into the RER lumen.
Now here's where things get a bit dicey. If the resulting structure in the RER lumen is largely hydrophilic then it will stay in the RER lumen where it will later be targeted to wherever it needs to go based on other signal sequences.
However, if there are large stretches of hydrophobic residues, then those don't like to be in the aqueous environment of the ER lumen. Ergo they will incorporate into the RER membrane. Thus they become transmembrane proteins. A good rule of thumb is that if you have 10 hydrophobic residues in a row, then there's a good chance that is going to get incorporated into a membrane.
Once protein transcription is complete the ribosome will no longer be associated with the RER and will re-enter the pool of free ribsomes (ready to pick up a new mRNA).
EDIT: In response to question in comments about why translocons are found in RER and not in other membranes
You can certainly ask the question, but you're getting close to falling into that beautiful genesis of basic science research: something I call the 'why-hole'. I searched around, and I don't think we have a full understanding of membrane organization throughout the cell, though I would defer to any cell biologists who have a better understanding. We do have some idea of the mechanisms. What follows is a stitching together of hypothesis and some facts I was able to find.
It stands to reason that since the translocon is a complex of transmembrane proteins, its parts were at some point synthesized by a ribosome through a previous translocon. That would get it into the RER membrane. Now in order for a piece of membrane (or anything within the ER lumen, for that matter) to get to its final destination it has to have another signal sequence. This signal sequence will be recognized by unique signal recognition protein. This will localize the protein to a part of the RER that has several proteins that will form a vesicle (one of which being clathrin) and a protein attached to it called a v(esicle)-SNARE. Once the vesicle buds off it will go through the cell until its v-SNARE runs into a t(arget)-SNARE. This interaction will ultimately lead to fusion of the vesicle into the target membrane (e.g. lysosome, plasma membrane, etc). I double checked all of my facts here, where you can read more about it.
All of this is to say that if a transmembrane protein doesn't have a signal sequence it won't get targeted for transport through this system and should stay in the endoplasmic reticulum.
At this point it would be good to remind everyone that the ER--both rough and smooth--is a continuous structure with the RER located closer to the nucleus and the SER closer to the cell membrane. So it would be reasonable to ask why translocons stay in the RER and doesn't diffuse into the SER. That's where we get into more emerging science. From what I gather there are many proteins that are involved in the strutrue and organization of the ER. You can look into "the ability of NDPK-B to form microdomains at the membrane level" or reticulon2, but I think there's still a fair amount of work to do in this field. I encourage you to look into these resources, and if this is something that you're interested in consider doing some research. There is some evidence that membrane dysfunction is associated with neuronal disease, so any advances would be well received.
As always, keep asking questions!

This seems quite a good answer, but it needs a supporting reference to the translocons, so people can check it independently. If you do that and it seeems correct, I'll upvote it. The other problem with your answer is that it goes off topic. The lipid raft thing is surely not relevant and therefore detracts from your answer. You would have done better to integrate your PS into the answer. Also, How about a spelling check?

Thanks for your feedback! I've adjusted the answer accordingly.

May I ask why the translocons are on the RER but not other membrane?

Of course, always! I've expanded my answer in response to your query. It seems that you're starting to get close to the limits of my (perhaps even science's) knowledge. But that just means that the area is ripe for further research in my opinion.

Ok, as I am aware that we're on the boundary of knowledge, your expanded answer has fulfilled my curiosity. Thank you very much for your effort. Accepted and upvoted.


text:
What are the most common proteins inside cells, by mass?
I'm interested in the most abundant proteins inside cells by total mass of the protein (for example average for a whole human or for specific organs/tissues/cell lines).
It is quite easy to find that the largest % by mass in the human body is collagen (25 to 35% of total body protein).  Collagen is an extracellular protein; finding the same info for intracellular proteins has been surprisingly difficult.  Finding what is the second largest %, or a top 10 list, has also been difficult.
In the process of searching, I found PaxDb which lists protein abundance by "ppm", or counts divided by the total counts.  It is quite hard to convert that to % by mass - it would be necessary to know the molecular mass of every protein (for example by matching them with entries in UniProt), and then multiply count by molecular mass.  Another resource which seems to have a lot of data is PeptideAtlas, but I can't tell how to extract either counts or masses from that.
Is there a canonical list of (eg) top 10 or top 100 intracellular proteins by mass in a whole human?  How about the same by organ/tissue?

I can’t see why a scientist would prefer a mass-based, rather than a molar value, except, perhaps for which proteins are likely to correspond to spots on a 2D gel. I seem to remember that EF-Tu/EF-T1 was one of the stars (but that was in my field of interest). You could try searching the 2D gel literature for that sort of thing, however it will probably miss the very basic ribosomal proteins, which are analysed on a different gel system. But, really, the values for the “average human cell” would seem of interest only to stamp collectors. Have you no context?

Similar to David's comment, you want to make sure you're avoiding the XY problem: what is the underlying problem you're trying to solve? It's possible there is a better solution to the underlying problem than the one you've come up with.

@David I'm interested in physical properties which would be determined, in a mixture, by the predominant components by mass not count (think stuff like Trp fluorescence spectroscopy or XANES).  I'd like to pick a couple of single proteins as models for simplicity, but it makes sense to pick ones which would mostly determine the results when measuring an intact whole cell as well.

@AlexI I'm not familiar with that field, what percent by mass would the predominant component need to be for it to be considered "predominant enough"? And why would the mass of the rest of the protein matter for Trp fluorescence spectroscopy?

@BryanKrause Just using that as an example, my actual motivation is a different spectroscopic technique.  It would be "% of all Trp" of course, but as long as the fraction of that in aa sequence of different proteins is similar, "% of protein mass" is a pretty good substitute

"what percent by mass would the predominant component need to be for it to be considered "predominant enough"?" - This is mainly about selecting a good simplified model to study.  If actin filaments were >20% of the protein mass of a typical epithelial cell, those would probably make a good model.  I am guessing there are just a handful of things which together make >50% in most cell types, and those are probably either mostly structural (actin, intermediate filaments, microtubules); or related to the major cell function (myosin, hemoglobin).  It's been hard to get numbers to quantify that


text:
How exactly can a drug affecting squalene epoxidase affect the methylation cycle, necessitating the use of 5-MTHF?
I found a case report in which the authors say that Terbinafine might have possibly affected the methylation cycle in a patient, necessitating the prescription of 5-methylfolate to correct the imbalance. I tried googling to find some description that would include the interaction of ergosterol synthesis and methylation cycle, and found nothing.
Maybe I was not googling the right words.
I can't seem to find how exactly we can affect the methylation cycle by affecting squalene epoxidase (the target of terbinafine, the drug used by the patient in the case report).
The article quoted is titled Antifolates and MTHFR (Trachtman and Pagano, 2015)

This might be a better fit in Biology.

@CareyGregory - feel free to move the question to Biology, I wouldn't mind ))

Preamble
I have tried to follow the logic of the rationalization of the clinical case described in the report of Trachtman and Pagano, but have failed. I suspect from the quality of their biochemical illustration (arrows leading from compounds to enzymes, and talk about ends of cycles) that they do not have a clear idea themselves. However, having done the literature search, let me set out the picture as I see it, in the hope that this may enable someone else to see a connection I may have missed.
Anti-fungals inhibit the erosterol biosynthesis pathway in fungi
As the poster states, anti-fungals such as terbinafine do act by inhibiting the synthesis of ergosterol, which is a cell-membrane steroid, unique to yeast. Of relevance to this analysis, there is a methylation reaction in this pathway, that lies after the target of terbinafine, squalene epoxidase:

Methylation step in ergosterol synthesis (from Uniprot)
Inhibition of ergosterol synthesis can affect S-adenosyl methionine in yeast
The only experiments that I can find linking ergosterol synthesis with the methylation cycle in yeast do not involve anti-fungals. Rather, they involve yeast with mutations in the genes encoding enzymes of ergosterol synthesis. In a study performed by Shobayashi et al. (2006), mutants of the gene, Erg6, encoding the methyltransferase, resulted in the accumulation of S-adenosyl methionione (SAM). Clearly there are other methylation reactions in the cell which utilize SAM, but this suggests that the ergosterol synthesis pathway is so active in yeast that its disruption affects the concentrations of intermediates of the methylation cycle.
What is the relevance of this to methylation in humans?
Although the situation described above confirms a connection between the methylation cycle and ergosterol intermediates in yeast, as mentioned in the original clinical report, it is difficult to see how it relates to human metabolism. This is because, although squalene epoxidase does exist in man, the ergosterol synthesis pathway and the methylation step catalysed by the methyltransferase (the erg6 gene product) do not. In any case, inhibition of a methylation step would result in an increase in SAM, whereas just the opposite appears to be the case in the patient.
Final observations
The clinical report is of one patient with a mutation (MTHFR) in the methylene tetrahydrofolate reductase gene, which would reduce his ability to regenerate the methionine and S-adenosyl methionine needed for methylation. L-methylfolate greatly reduced his symptoms. Nevertheless, this report is for a single patient, whereas “The gene mutation known as the MTHFR affects approximately 45% of the US population”. If MTHFR were the only factor involved in this case one would expect other reports of adverse reaction to terbinafine. In the apparent absence of such reports one suspects that in this patient the affect of terbinafine — whatever it may be — involves some other, yet undiscovered metabolic interaction.


text:
Correct description of ALDH7A1 and other genes
A quote from a review paper:

ALDH7A1 gene (discovered in 2006), which is located at chromosome 5q32.2, contains a transcript of 4964 base pairs and 539 amino acids divided among 18 exons [1,10,16,17].

As I understand, a gene cannot contain a transcript, it can only encode an RNA transcript. I wonder whether the authors meant that the transcript-encoding sequence of DNA constists of 4964 base pairs, or that the RNA transcript itself consists of 4964 base pairs.
I think it's the first, because I more often read about DNA as consisting of "base pairs", but I've just read Wikipedia and started having doubts, because RNA also seem to contain base pairs. I haven't been reading about this a long time, so I'm confused.

I suspect that you're getting wrapped up in the terminology. Think about amino acid coding- the 539 amino acids * 3 = 1617 coding bases only. The transcribed portion of the gene might have 4964 base pairs. People get a bit loose with terminology, which can be annoying, but you can always go back to the iron(ish) laws of molecular biology.

@MaximilianPress — Genes encode RNA. mRNA encodes protein. The poster is correct in my opinion in saying that a gene encodes one of more transcripts. The code is dA=rA, dG=rG, dC=rC, dT=rU. Additional coding determines splice sites.

@David ... I guess. I suppose that I am responding more to genes "encoding" transcripts to the exclusion of other forms of relationship ("contain" is obviously chemically wrong, but from a genome annotation point of view is fine). Regardless, I'll delete my second comment as at best distracting from the real point, and at worst incorrect.

I think it better to say "a gene…specifies" and avoid "encodes". "Contains" is sloppy for a professional scientist, but it happens to the best of us.

It's the second: The RNA transcript of the gene (before editing) has a length of 4964 bases. The use of "base pairs" is wrong in this context since the transcribed RNA has no paired bases. This is a feature of the DNA.
This transcript (or better: the processed exon parts of it) code for the amino acid sequence of the protein which is translated from the mRNA.

Image from here.

I think the diagram is misleading. It suggests, wrongly, that the whole of the transcript exons encode amino acids, and compounds this by having the transcript start with AUG. (And there is a typo: "transcript are code for")

@David eh, the image is clearly not trying to be rigorously accurate. It's a doodle. I actually like it since it gets the main point across, let's not get hung up on the lack of UTRs and introns or the fact that no protein will ever be just three amino acids etc.

@terdon — The diagram may be appropriate in an answer to a question with a low degree of sophistication, but hardly to one that includes an explicit mention of exons.

Caveat Emptor
Scientific writing should be as precise and unambiguous as possible, and the poster is correct in implying that the language in the cited review is incorrect. A gene certainly does not contain a transcript. The sloppiness is further borne out by the incorrect reference to the length of the transcript in base pairs, as pointed out by @Chris. Finally, 4694nt is incorrect for the length of the transcript: it is 4765nt.
One can only say that this happens, especially in cases such as the present in which the authors appear to be specialists in brain function rather than molecular biology, are being obliged to write in a language other than their native one; and this is compounded by journals with inadequate editorial supervision.
Even worse, is the fact that mistake in citing the length of the transcript in base-pairs appears in the ENSEMBL entry for this gene, although not in that from NCBI, which gives the lengths in nucleotides (nt). I would, however, take issue with NCBI’s use of the term encoded in “The protein encoded by this gene…”, as a protein is encoded by a mRNA, not a gene, and the primary transcript of one gene can result in several different mRNAs, with different protein products — as in this case. I would recommend the use of the word specify rather encode in this case.
One must remember, however, that both ENSEMBL and NCBI employ temporary staff with qualification outside of molecular biology to compile these gene descriptions.
How to find gene details oneself
There are standard genomic resources where one can fairly easily find the details of any gene oneself, especially, as in this case, human genes. The two main sites are NCBI and ENSEMBL, for which the links to this gene are already posted above. To understand the data, one needs the basic knowledge of gene structure, transcription, splicing and translation of mRNA expected of those posting questions of this sort. From these sources I would list the salient information about ALDH7A1 as follows.

The human gene ALDH7A1, aldehyde dehydrogenase 7 family member A1, is located on chromosome 5.
It runs from nt 126,541,841 to 126,595,219 on the reverse strand, and hence it encompases 53,379 bp and its initial transcript are 53,379 nt.
The initial transcript contains 18 exons, which constitute a mature mRNA of 4765 nt (not 4964) after the introns are spliced out.
This mRNA is translated into (or “decoded to”, if you wish) a protein of 539 amino acids, the difference between the 1620 nt coding sequence (including the termination codon) and the 4765 nt of the mRNA being the untranslated 3′ and 5′ regions of the mRNA.

This is illustrated in the diagram of the gene below in which the vertical bars or boxes are the exons, with the translate regions solid and the untranslated regions blank.

Is this really the gene?
It seems to me that calling this the ALDH7A1 gene is rather dubious — or misleading, at least. The gene that gives rise to the transcript described above also specifies 36 other transcripts, many of which appear to be translated to different variants of the alcohol dehydrogenase protein. (See the transcript map in the page cited above.)


text:
Why are GC-rich regions less condensed than GC-poor regions?
As far as I know, chromatin consists of two kinds:
Heterochromatin is more condensed so translational factors have less access to this region, and this region is poor in GC.
Euchromatin is less condensed so translational factors have more access to this region, and this region is rich in GC.
I wonder how GC content affects the condensation status of the chromosome? What is the mechanism behind this relationship?
It is well known that GC and AT pairs differ in the number of their hydrogen bonds. Does this hydrogen bonding play the key role in condensation of chromosomes?

@ThoH.Ho and @Thawn. When banding chromosomes they are first treated with trypsin before staining with Giemsa dye. My understanding, and I have worked in the field of cytogenetics for quite a while, is that chromatin condensation due to gene content IS the reason for differential banding patterns. Gene rich/ high GC content areas, with more open chromatin, are more readily digested by the trypsin enzyme and therefore less protein is then present to stain with Giemsa. Vice versa for the gene poor/ low GC content regions. This is why non coding regions such as heterochromatin stain very dark and gene rich chromosomes such as chromosome 19 are pale. So although chromosomes may be at their most condensed stage of the cell cycle in pro metaphase, there is obviously still a relative difference between chromatin condensation of the GC rich and GC poor regions.

Chromosome condensation seems to be primarily driven by epigenetic factors like methylation and histone modifications, not GC content. However, high GC content is associated with gene rich regions and gene expression generally requires open chromatin. In other words high GC content correlates with genes, and genes being expressed correlate with open chromatin, so high GC content correlates with open chromatin, but isn't necessarily causal.

Thank you. I highly appreciate your point of view. There's only one thing, I'd like to hear your opinion on this, that the reason I asked this question is because of the G-banding. When people stain the chromosome using Giemsa solution, the cell is mostly in prometaphase or metaphase. Expression regulation should be very low at this stage, chromosomes should be condensed at a same level. So why they are stained differently while they are all condensed (metaphase)?

@ThoH.Ho The question you ask in the comment is a completely different one from the question you originally posted. I suggest you ask a new question and specifically mention the giemsa stain. The dye used for the giemsa stain specifically binds to AT base pairs and this creates the banding. This has nothing to do with chromatin condensation.


text:
THYROGLOBULIN (19S) comes to a heavier position than ferritin (51S). Why?
Sedimentation values of thyroglobulin and ferritin containing iron are 19S
[1] and 51S [2], respectively. But, by density gradient centrifuge, it seems thyroglobulin (19S) migrates faster than ferritin (51S). Could anyone explain this?
Figure 3 in this article shows a migration pattern of GE High molecular weight marker containing ferritin and thyroglobulin. Thyroglobulin comes almost at the bottom but ferritin, in the middle, which I did not expect.
PS
I asked GE and confirmed ferritin in the marker contains Fe ions.

Ferritin and iron-containing ferritin are different and the latter
would of course be heavier; it will therefore sediment faster.
Figure 3 of the third article uses thyroglobulin and ferritin as molecular weight markers. For your information thyroglobulin is 650kDa whereas ferritin is 440kDa. Also note that apoferritin i.e. ferritin that is not bound with iron has a sedimentation rate of 18S (from the same article that measures the sedimentation rate of iron bound ferritin - ref#2).

There seems to be some confusion regarding the sedimentation rate of ferritin. From this article:

One molecule of ferritin can bind up to 4500 Fe2+ ions.
  When fully loaded with iron, the ferritin can increase in mass up to
  ca 900 kDa; it then has a sedimentation coefficient of 24S (Chasteen &
  Harrison 1999).

55S for ferritin seems dubious.

I confirmed that ferritin they used contains iron. I directly asked GE because the marker is their product. (I accidentally sent wrong message before.)

@243 There is some confusion with the sedimentation rate measurement of ferritin. See the edit.


text:
What is the biological mechanism linking temperature and probability to be infected with a virus?
It is common knowledge that when you're cold you could get a cold.
What is the mechanism linking temperature and viral infection?

There's some information on that in this question on Skeptics.SE

Wow that seems like a really bad idea for a stackexchange site.

@Uri What do you mean by that? “a really bad idea for a stackexchange site”

skeptics stack exchange overlapping with everything

It is common knowledge that when you're cold you could get a cold.

This may be a nice illustration why we need to be wary of “common knowledge”.

What is the mechanism linking temperature and viral infection?

This isn’t clear. There are a few proposed mechanisms but a likely explanation is: “there is no mechanism” – and the assumed correlation between cold temperature and catching a cold might be nothing more than an illusion – a form of confirmation bias.
In fact, we don’t even know for sure that the cold season coincides with cold temperatures.
On the other hand, a 2007 review [1] found that

… most of the available evidence from laboratory and clinical studies suggests that inhaled cold air, cooling of the body surface and cold stress induced by lowering the core body temperature cause pathophysiological responses such as vasoconstriction in the respiratory tract mucosa and suppression of immune responses, which are responsible for increased susceptibility to infections.
   [emphasis mine]

So according to their results, potential mechanisms which link temperatures and viral infection are indirect:

The lowered core body temperature would imply, in my interpretation, that the body has to expend more energy to maintain its temperature, and hence less energy to power its immune system (which is expensive).
Lack of respiratory tract mucosa removes an important physical barrier between the environment and the body, and allows pathogens to enter the body with much less resistance.

[1] Mourtzoukou & Falagas: Exposure to Cold and respiratory tract infections, in Int J Tuberc Lung Dis. (2007), pp 938–943

The John Tesh Radio Show (not sure how credible) also mentions that communicable disease, such as a cold, tends to spread easier because we tend to pack more densily in warmer places like homes and buildings.


text:
Do human neurons in a petri dish do different things from chimpanzee neurons
I want to know if qualitative experiments have been done growing chimpanzee neurons and human neurons in vitro and have any differences emerged, such as the amount of connections per neuron or anything else.

it is not a single neuron per se that makes the difference.. it is the neural network. The basic neuron structure is same in humans and hydra (just that hydra has smaller repertoire of neurotransmitters)

The claim that it is not a single neuron has nothing to do with what I'm asking (and is also not consensus AFAIK). I'm asking whether there are global differences, such as amount of connections, which are discernable in vitro.

I have came across several studies indicating large similarities between chimpanzee and humans. A study by Bianchi et al., 2013 used immunohistochemistry, electron microscopy, and Golgi staining to characterise synaptic density and dendritic morphology of pyramidal neurons in primary somatosensory (area 3b), primary motor (area 4), prestriate visual (area 18), and prefrontal (area 10) cortices of developing chimpanzees (Pan troglodytes). They found that synaptogenesis occurs synchronously across cortical areas, with a peak of synapse density during the juvenile period (3–5 y). Moreover, similar to findings in humans, dendrites of prefrontal pyramidal neurons developed later than sensorimotor areas. These results suggest that evolutionary changes to neocortical development promoting greater neuronal plasticity early in postnatal life preceded the divergence of the human and chimpanzee lineages. This study however does note that

Despite sharing these neurodevelopmental similarities, it is important to note that cognitive ontogeny in chimpanzees differs from humans in several respects. Behavioral studies suggest that the different social and environmental contexts in which humans and chimpanzee develop may have also been important in the evolution of human-specific socio-cognitive abilities. For example, whereas young chimpanzees do not fully wean until 4–5 y of age and remain closely attached to their mothers during the early years of development, human infants often interact with multiple caregivers and engage in joint attention.

In another study by Bianchi et al., also published in 2013 regional variation in the morphology of pyramidal neurons in the cerebral cortex of great apes, humans' closest living relatives were investigated. The study used the rapid Golgi stain to quantify the dendritic structure of layer III pyramidal neurons in 4 areas of the chimpanzee cerebral cortex: Primary somatosensory (area 3b), primary motor (area 4), prestriate visual (area 18), and prefrontal (area 10) cortex. The study showed that

Consistent with previous studies in humans and macaque monkeys, pyramidal neurons in the prefrontal cortex of chimpanzees exhibit greater dendritic complexity than those in other cortical regions, suggesting that prefrontal cortical evolution in primates is characterized by increased potential for integrative connectivity.

However

Compared with chimpanzees, the pyramidal neurons of humans had significantly longer and more branched dendritic arbors in all cortical regions.

These studies show that despite significant morphological and developmental similarities between human and chimpanzee neurons, there are still notable observable differences.


text:
Comparing SIFT and PolyPhen to other methods
I'm looking for a database of nsSNP (non synonymous single nucleotide polymorphisms) and their effects. As I understand, the common methods to predict this are SIFT and PolyPhen, and I want to compare them to other methods.
The database needs to list the old sequence and the new one (or that I'd be able to infer that somehow), and their effect (whether harmful or not).
What are my options?

I will strongly suggest you:
PredictSNP: It's the best tool for nsSNP detection as it compares and throw out result from all the tools available.
http://loschmidt.chemi.muni.cz/predictsnp/
Paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3894168/


text:
Alternatives to trypsin for cell detachment?
I have ran out of trypsin and need to passage my cells (immortalized chondrocytes, C28/I2) today or tomorrow. I have been out of town and forgot to order more trypsin.
I was wondering if there are any alternative, "homemade" ways to detach cells. Googling this results in a lot of commercially available detachment solutions. I may or may not have a cell scraper available, but I have never tried it. I have hyaluronidase and I was thinking that might work.

Do you use flasks or plates? And how strong do your cells attach?

My cells are in a T75 flask. They attach moderately strongly.

You could try to knock them off the plastic. To do so, you take the flask with medium in one hand and knock it gently 4 or 5 times against the palm of the other hand. The cells should come off then and can be centrifuged down to separate from the medium. Alternatively you could replace the medium first and then knock them off.

It is simple - and more gentle (even though the handling seems a bit rough) for some cell lines than trypsination.

EDTA can work for some cells. I forget what concentration to use.

Most chealating agents will work. Important to rinse off your cells in Ca and Mg free buffer

Lets make this a proper answer: There are a few possibilities to detach adherent cells without Trypsin.
PBS/EDTA: Integrins and Cadherins play an important role in the adhesion and also in maintaining cell-cell contacts. These function of these proteins depends on Calcium2+ ions, so EDTA will chelate them and make them unavailable. First remove the culture media, rinse the cells with warm PBS to get rid of most ions and then incubate them for 5 min (the time needs to be optimized for each cells line) in PBS with 10mM EDTA in it. The cells either detach themself, can be washed of the surface with a pipette or can be gently knocked off the surface (this works only in tightly closing flasks). Centrifuge the cells shortly to pellet them and get rid of the PBS/EDTA and take them up in fresh medium.
Wash cells of the surface: Some cell lines are so loosely attached (which makes working with them pretty hard), that they can simply be washed off the surface. To do so, use the pipetboy to get some medium and then pump it out again against the cell layer. You can see the cells disappearing from the surface and the medium (or the PBS) get more cloudy.
Knock off cells: To do so, you take the flask with medium in one hand and knock it gently 4 or 5 times against the palm of the other hand. The cells should come off then and can be centrifuged down to separate from the medium. Alternatively you could replace the medium first and then knock them off. This method is not recommended for very sensitive cell lines.
Besides these methods, there are a number of commercial products available which claim to be better than the classical Trypsin/EDTA method and to be less harmful for the cells. Since I haven't tested them, I cannot say anything about them. In my experience Trypsin and the methods described above work perfectly.

Addition to what Chris already said:
Papain can be used for cells sensitive to trypsin (neurons etc)
Collagenase  can be used for certain cells where trypsin is ineffective (Accutase is a commercially available enzyme mix(?) which has collagenase activity)
Hyaluronidase - I don't know where it is specifically preferred but it is used.
Pronase and Proteinase K - Can be used to disrupt tough tissues. I have used them mostly to dechorionate zebrafish embryos.
See this documentation by Sigma-Aldrich on cell disruption enzymes.


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How many organisms have ever lived on Earth?
I've looked for some information on this, but couldn't find anything useful. Has there been any noteworthy attempt to estimate the sum amount of individuals of all species that have ever lived on Earth?

it is impossible to know the exact number so here is my gross ballpark estimate of an upper bound -  i.e. the maximum number of organisms that could have lived on earth in the extreme best case scenario. in practice it is probably much less, but this is to get an idea of what kind of numbers we are dealing with.
The earth's volume is about 1.08321 * 10^12 cubic kilometers =  1.08321 * 10^21 cubic meters
The crust of the earth is 4-8km and the radius is about 6,353km giving around 1% of the total volume available for life.
Hence, the volume available, i.e. the volume of the crust is about 1.1 x 10^19 Meters.
An average-size bacterium such as the rod-shaped E-coli is about 2 micrometers long and 0.5 micrometers in diameter. Hence, the volume is roughly:
(2*10^-6)*(0.5*10^-6)*(0.5*10^-6) = 0.5*10^-18 meters
Hence, if the entire volume of the crust of the earth were entirely filled with e-coli bacteria, there would be:
(1.1 x 10^19 meters)/(0.5*10^-18 meters) = 1.3*10^36 bacteria on the earth.
Bacteria take time until they reproduce. If they reproduce faster than they grow, they will become reduced to zero size, so there must be a balance between growth and reproduction.
Under ideal conditions the E-coli bacterium would divide every twenty minutes. source
Let's say we have the maximum number of bacteria on earth dividing every twenty minutes. Somehow, they divide and then one dies so that the population is stable. (hypothetically)
The age of the earth is roughly 4.5 Billion years. Much of that time, it was not colonised, but just to give an upper bound let's assume it was colonized the whole time.
There are 525600 minutes in a year so this give
4.5 ^ 10^9 * 5.3* 10^5 = 2.385 * 10^15 minutes
Dividing by twenty minutes gives 1.1925 * 10^14 total reproductions.
Hence, the number of organisms that ever lived if the entire volume of the crust of the earth were entirely filled with e-coli bacteria reproducing at the maximum of every 20 minutes would be:
(1.2*10^14) *  1.3*10^36 bacteria = 1.56 * 10^50 bacteria
This is an highly exaggerated gross estimate of the maximum number of organisms that ever lived in the extreme best case scenario. In practice it is probably 5-15 orders of magnitude less than this but we get an idea of the kind of numbers we are dealing with.
UPDATE: A more realistic number
The number of bacteria currently on earth is about 5*10^30 forming a biomass which exceeds that of all plants and animals. source.
According to this source cited by the previous wikipedia article:

Most of the earth’s prokaryotes (bacteria) occur in the open ocean, in soil, and
  in oceanic and terrestrial subsurfaces, where the numbers of cells are
  1.2 × 10^29, 2.6 × 10^29, 3.5 × 10^30, and 0.25–2.5 × 10^30, respectively. The numbers of heterotrophic prokaryotes in the upper
  200 m of the open ocean, the ocean below 200 m, and soil are
  consistent with average turnover times of 6–25 days, 0.8 yr, and 2.5
  yr, respectively. Although subject to a great deal of uncertainty, the
  estimate for the average turnover time of prokaryotes in the
  subsurface is on the order of 1–2 × 10^3 yr. The cellular production
  rate for all prokaryotes on earth is estimated at 1.7 × 10^30 cells/yr
  and is highest in the open ocean.

Hence we have about 1.7 x 10^30 New Cells/year
Multiply this by the estimated 3.5 Billion years (3.5*10^9) when the earth was colonized and we get

5.95 * 10^39 Bacteria that ever lived. of course there were other organisms, but as above even the biomass of bacteria exceeds that of
  all plants and animals combined so their effect on this number is
  negligible. Likewise, the life conditions were surely not ideal at all
  times, so this number may be lower still.

For some perspective, the estimated number of atoms comprising all of planet earth is about 1.33 * 10^50 according to this source.
ESTIMATE OF NUMBER OF MAMMALS THAT EVER EXISTED
The upper bound for mammals is as follows.
The surface area of the land of the earth is 149 million square kilometers.
Let us consider if the entire land area of the earth was completely covered with mice.
A mouse is typically 10cm from nose to base of tail and about 5 cm wide=0.1*.05=0.005 square meters. So we get 200 mice per square meter.
Hence, if the entire land area of the earth were covered with mice the world population of mice would be:
149*10^12 square meters * 200 mice per square meter = 1.788 * 10^15 mice
Mice typically produce a litter of 6-8 young and a female can have 5-10 litters per year. source
Let's say we have this maximum population reproducing in a stable manner. i.e. for every new mouse, an old one dies.
Hence the total number of new mice per year would be:
1.8 * 10^15 * 8 young * 10 litters = 1.44*10^17 new mice per year.
Mammals appeared around 200 million years ago (source), so that makes
1.44*10^17 new mice per year * 200 million years
= 2.88 * 10^25 total mice.
In practice mice need space and resources and compete with other mammals which take up space and which reproduce less frequently. Likewise, deserts and polar regions are less inhabitable, and sometimes there are periods of droughts, and they don't always reproduce at the maximum rate etc. so the total number is probably about around 4-10 orders of magnitude less than this.
So it is probably something like 10^20 total mammals ever existed.

Sorry, but this estimation makes no sense. First, the earth wasn't colonized from the very beginning, as far as I remember the oldest estimates for life go back as far as 3.5 billion years. Then life was different at that point (for example was not dependent on oxygen) and the life conditions were surely not ideal at all time. Not to mention the changes in atmosphere (and biosphere), when the oxygen concentration went up. It also assumes that all organims where from one kind of bacteria, which they were not.

@Chris I am trying to give an upper bound - i.e. a maximum number of organisms that could have lived on earth. this is the best we can do. I updated the answer with your point. primitive organisms were more or less the size of e-coli give or take an order of magnitude or two or three. do you think the upper bound number is higher? if yes, what would you change to increase this number?

20 min for generation time is way, way off. In natural conditions, like for example in soil, your average bacterium reproduces maybe once a week. I imagine generation times are still much longer in e.g. seawater.

@5heikki thank you for the clarification. yes, I wrote in the end, it is probably at least 5-15 orders of magnitude less. this is just an exaggerated upper bound best-case scenario. I updated it with a more realistic number. It's probably still less than this though.

When looking at these numbers, did you happen to see anything similar about viruses?

@Brannon viruses need hosts, so their number is far less than this

This is a hard problem - estimates of total living things in an given environment are usually created by looking at the number of species and individuals found in a sample area and extrapolating.  As far as estimating the number of living things in the world, there are still lots of species which are not known, making this number still unknown for the world today as it is.  Doing a similar survey into past ages adds another layer of problems to the estimate.
EO Wilson has, among others I'm sure, made a serious effort to understand how many species are currently alive on Earth.  Its pretty clear that currently we don't know how many species are currently alive - that would make it nearly impossible to answer your question historically.

About 1.9 million species have been discovered and given scientific names, though the actual number may exceed 10 million. Bacteria and archeans could comprise tens of millions species—once taxonomic units are precisely defined. Knowledge about species and extinction rates remains very poor, and species disappear before we know they existed. We propose that, as scientists are better able to assess the conservation status of the species that compose an ecosystem, the more they will understand the health of that ecosystem. It is time to accelerate taxonomy and scientific natural history, two of the most vital but neglected disciplines of biology.

from "The barometer of Life" Stuart, Wilson, McNeely, Mittermeier & Rodriguez, emphasis mine.
As you can see there are some important technical obstacles to even the question of how many species there are. Bacteria and free living eukaryotes have rules for speciation that are fairly difficult to define, esp since many can transfer just a few genes with many near relatives and do not require sexual reproduction.
Another obstacle is that the animal and plant surveys are not really done yet either.  Plants animals and insects are still being discovered in jungles, deep underwater and at rest stops.  As far as the microbial record goes, an average glass of water from a pond or river probably has undocumented species.
The encyclopedia of life is a resource worth mentioning here. It is self admittedly only a partial record.
For past speciation records, the geographical sampling is not strong - digging down in selected spots where fossil records remain is bound to miss many of the species which had existed.
In 1990, Peter Dodson wrote this review in PNAS holding forth on the taxonomical difficulties in estimating the number of dinosaur species which included a founding period which was as much circus as science as well as the incredibly sparse sampling of prehistoric surveys over time and history. As recently as this year the count of dinosaurs has continued to vary wildly. A pubmed citation list to Dodson's paper shows 7 citing works, mostly from the past 3 years.

I tried to amend this... but you're right Paul I did misread this. I guess my eyes misled me because the question seems even more impossible. Estimates of bacteria living deep into the earth's crust have seriously multiplied in the past decade or two since they have been discovered and is still being discovered..newscientist.com/article/… Although the question of how many living animals would be more likely, they are hard since only select environments can be surveyed via fossil records. still many dinosaurs, etc to discover.


text:
What is Chronic immobilization stress (CIS)?
I am trying to self study BNDF a little bit when I found this article:

Abstract Stress impacts multiple systems within the CNS, including the
  hippocampus. A key molecular mediator in hippocampal functions,
  including learning and memory, is brain-derived neurotrophic factor
  (BDNF). BDNF mRNA is reported to be decreased following chronic (every
  day) immobilization stress (CIS) in the rat, however the effect on
  protein is unknown. Utilizing a mouse model of CIS, the hypothesis
  that total hippocampal BDNF protein, in addition to BDNF mRNA, would
  be decreased was tested. The effects of intermittent (alternating day)
  immobilization and cold stress on hippocampal BDNF protein levels was
  also examined.
In this study it was demonstrated that CIS results in a small (8 per
  cent decrease relative to non-stressed controls), but significant (p =
  0.0013) decrease in the exon coding for mature BDNF (exon VI). In addition, there was a significant (34 per cent, p = 0.005) decrease in
  the mRNA coding for exon I in the stressed animals. Contrary to
  expectations, however, CIS resulted in a significant (116 per cent, p
  = 0.0087) increase in hippocampal BDNF protein levels. Furthermore, both intermittent immobilization and chronic cold stress both
  increased BDNF protein levels. Chronic stress, therefore,
  differentially regulates BDNF mRNA and protein levels in the
  hippocampus. Copyright © 2004 John Wiley & Sons, Ltd.

I'm really curious what they mean with CIS: Chronic immobilization stress.
I can't find anything on the internet that actually explains what this is.

There are >1200 articles tagged "chronic immobilization stress" on pubmed.
From Hennebelle et al. (2012):

Half of the 6-month old male rats from each dietary group were subjected to a validated chronic stress procedure (Buyntsky and Mostosky, 2009) based on a restraint stress procedure adapted from Veena et al, [32]. Rats were placed in wire mesh restrainers for 6 h a day (fom 10 am to 16 pm) for 21 days (5 days a week) over a period of 4 weeks. Unstressed rats were handled weekly. The unstressed and stressed animals were housed in different rooms.

Hennebelle, H., et al. 2012. Influence of Omega-3 Fatty Acid Status on the Way Rats Adapt to Chronic Restraint Stress. PLoSOne 7: e42142.

So Chronic Immmobilization Stress means they don't allow (the rats in most cases) to move freely ?

Yes for certain period of time.


text:
Where can I find disease diagnosis datasets?
For an epidemiological study, I'm looking for datasets for any kind of vector-borne disease (i.e. West Nile Virus, Malaria, etc.), or any parasites that are dependent on intermediate hosts (i.e. Schistosoma spp., which have snails as intermediate hosts).
The data should include day or week and location of each diagnosis. I have been able to find diagnosis data for individual countries for each year, but I'm looking for daily or weekly data for city-wide resolution or at least smaller regions inside countries.
Additionally, it does not matter what country/continent the data is for, as long as there are many data points (i.e. at least 10,000). For example, if there is a lot of good data for Brazil, that's fine.
Does anyone know if such information exists, and if so, where I can find it? I've been searching for it for the past month but have had little luck with finding anything useful. Any help and guidance is appreciated!

Can you reveal some typical keywords to help with the search?

@Jan Maybe things like: "malaria outbreak dataset" or "malaria diagnosis dataset"? I'm not entirely sure what the best way to word this Google search is, either, which is severely limiting what I can find

I was thinking about synonyms for dataset and other keywords that help to find the type of data you are looking for. I'm very familiar with the medical terminology, but not with statistical one. Also can you show an example you've already found?

Is this close: https://data.gov.in/keywords/malaria ?

@Jan Hi again Jan, sorry for the late reply. That website's great! I didn't bookmark any of the sites I searched thorugh, so I'm having a hard time finding them again to share with you - but they weren't as good as yours; the best one contained monthly data for countries, not regions. Do you know if this kind of data is available for other countries (not just India)? I'm also looking for it, but in case you already have them. Lastly, add this as an answer :)

NIAID has released a new open data discovery portal and you can search or filter by disease, host species, etc. https://data.niaid.nih.gov/

CDC Wonder, a health database of the US Center of Disease Control and Prevention (CDC), has weekly data for Nationally Notifiable Infectious Diseases and Conditions, United States: Weekly Tables from 1996 to 2020 on the state level for antrax, brucellosis, dengue fever, leptospirosis, malaria, meningococcal disease, Q fever, rabies, etc.
Weekly tables since 2014 are available on Data.CDC.gov.
Weekly tables for 1952-2017 published in the MMWR are available at CDC Stacks MMWR and weekly tables starting in 2018 are available at CDC Stacks NNDSS.
HealthData.gov has two weekly datasets for malaria by US states - here is one.
Open Government Data (OGD) Platform India has data on a district or state level, for example, for malaria.
Keywords that can help in further search:

infectious disease
week or weekly report or data
MMWR (Morbidity and Mortality Weekly Report)
surveillance

Keywords, like diagnosis or outbreak, can limit your search too much.


text:
What is this species of tree?

In my city, there is a unique tree, with thorns all over it. I would like to know - what species is this?

Which city is it?

If you google the name of the place where this tree is found you might well found information.

Thank you, but this is a unique tree, there are not many trees like this in the area. Also, there is not that much information about this city's flora in google.

Can you please give us the name of the city?

Modii'n Maccabim Reut, Israel.

Found it! The tree is Ceiba insignis, כוריזיה בקבוקית, planted in many cities in Israel. Its origin is from South America, and it grows to a height of 10-15 meters.

I am not a botanist but looking at the flower in the second picture and the thorny trunk and pods it is likely to be part of the Ceiba genus. I cannot however be sure of the exact species.


text:
Western blot extrange band
I performed a WB using plasma rats and monkeys samples with anti ubiquitin K-48 antibody. In every sample the antibody binds something and it appears a specific band that seems to be 71kDa. When I used anti-ubiquitin unspecific antibody(just to see if I get the same results) same bands appears. It cannot be ubiquitination because the molecular weight. How can I explain the both antibodies bind something that I dont know?
Thanks

I can not see the reason why you deny ubiquitination. In addition, Ubiquitin K-48 ligated products can be recognized by anti-ubiquitin antibody. But, usually you could get multiple bands from cells and as a result, a whole lane is stained and smeary.

thanks for your answer. I see it strange because I am using several plasma samples of different animals, and it appears exaclty the same in all of them with the same molecular weight. So I dont know what is it. Because if there is poly-ub as  you say it should appears smears, but no a clear band of specific molecular weight in all the animals right? I am a litle confuse.

Plasma contains cells but also lots of extracellular proteins such as albumin, immunoglobulin, etc., right?  So, signals from cells can be very weak.

Yes but Im using as a control cells which I know they accumulated poly-ub K48, so the control looks as smear, however, plasma cells it does not look like that, it looks as a clear band of specific molecular weight that it does not correspond with the weight of the ubiquitin but is not a smear either. I am still confuse :/


text:
Why does the pET- expression vector contain a LacI gene additionally to the one in the genome?
The pET plasmid is used for protein expression with T7 promotor in expression strains, such as E.coli BL21(DE3)
It contains a lacI gene which codes for the lac repressor protein, a protein of interest under the control of a T7 promoter for T7 RNA polymerase and a lac operator which can block transcription, directly behind the promotor. The lac operon is another control of transcription of the protein of interest.
Furthermore, T7 polymerase is located in the genome as well under the control of the lac operon.
When IPTG is added, the lac repressor is inactivated -> T7 polymerase and therefore the protein of interest will be expressed.
The Lac I gene is already present in the genome of the expression strain used, why is it also cloned into the pET vectors?

Because you can then use this system in bacterial strains which do not have LacI.

Thanks for you comment @Chris. Are there strains that have the T7 RNA polymerase but do not have lacI? Or are those then just infected with T7 phage to express the protein? Could you find a reference for your statement and post it as an answer?

I don'T know about all strains - sorry. But you could co-express it from another plasmid.

Another possibility (and probably more likely) is that the construct is less leaky that way.

According to this article, a single lacI gene copy gives rise to about 10 copies of lacI protein per cell, and we can conclude, therefore, that this is the amount required to keep a single lac operon repressed.  The article also mentions the lacIQ mutation in the promoter of lacI that results in a ten-fold increase in the level of lacI protein.
If a lac expression construct is present at more than 100 copies per cell the result will be leaky repression, and this can result in selection for mutations in the gene of interest if it has deleterious effects on the host bacteria. The easiest way around this problem is to put a lacI (or lacIQ) gene on the expression plasmid so that repressor levels are commensurate with the number of copies of the lac operator, as in the pET vectors.


text:
What is the recommended culture volume for HeLa cells and seeding number for 384 well plate wells?
For 24 well plate wells, thermofischer recommends to seed 0.05E6 cells with 0.5 to 1 ml of medium. What are recommended numbers for a 384 well plate well?

The Privalsky Lab@ UCDavis writes:
Growth Area of Tissue Culture Plates and Dishes
    Growth Area (cm2)   Media Volume (ml)   Maximum Volume (ml)
Plates
 35 mm            8          1.6- 2.4
 60 mm           21          4.2- 6.3
100 mm           44          11 -16.5
150 mm          148          30 -45
245 mm (square) 500         100-150

Dishes
  6 well        9.5         1.9  -2.0       16.8
 12 well        3.8         0.76 -1.14       6.9
 24 well        1.9         0.38 -0.57       3.4
 48 well        0.95        0.19 -0.28       1.6
 96 well        0.32        0.1  -0.2        0.36
384 well        0.056       0.025-0.05       0.125

Flasks
 T25             25          5- 7.5
 T75             75         15-22.5
T150            150         30-45


text:
Causes of Misophonia
Whether it's snacking on chips, munching on salad, or simply chewing gum, when I hear someone do it within an earshot, it drives me completely bonkers!
It doesn't matter if it's my girlfriend, my mom, someone sitting next to me at the office, or random stranger on the train, it bothers me just as much. The "mouth open" chewing type makes me want to get violent, and I often find myself in a blind rage. I also notice the slower, and more "deliberate" the chewing/munching is, the more I get tense and more it bothers me.
Sometimes I feel like they are doing it on purpose, and completely fake, sort of like a commercial where they exaggerate the act of eating.
I want to know more about Misophonia or "Hatred of Sound"?

Misophonia

Misophonia is a relatively unexplored chronic condition in which a
person experiences autonomic arousal (analogous to an involuntary
“fight-or-flight” response) to certain innocuous or repetitive sounds
such as chewing, pen clicking, and lip smacking. Misophonics report
anxiety, panic, and rage when exposed to trigger sounds, compromising
their ability to complete everyday tasks and engage in healthy and
normal social interactions.1

Physiology
The auditory pathways may be functioning normally, but there is an abnormally strong reaction of the limbic (emotional system) and autonomic nervous system (body control system) to which the auditory system is intimately connected.
Several definitions are listed for the disorder, including:

“Abnormally strong negative reactions of the autonomic and limbic systems to specific sounds resulting from enhanced functional connections between the auditory and limbic systems for these sounds.  The auditory system works in a normal manner, without abnormally high activation.  At the behavioral level, sounds specific for a given patient evoke strong negative reactions.  This situation may cause general negative attitude to sound as well.  When fear is dominant emotion (patient is afraid of sound) phonophobia occurs (phobia – fear).  Phonophobia is a specific case of misophonia.”

“Selective sound sensitivity should be considered a type of misophonia, where soft sounds (typically eating and breathing sounds made by emotional attachment figures) are the focus, and the quality of those sounds causes annoyance and rage in the listener.”

“Pre-puberty seems to be a very common age of onset for the majority of those with misophonia, with lifetime persistence for most cases, and there appears to be a genetic component.”

“Misophonia can be considered abnormally strong connections between the autonomic and limbic resulting from enhanced connections between the auditory and limbic systems.  These connections encompass both a high level of cortical level loop with involvement with cognition as well as subconscious connections, most probably involving the link between the medial geniculate body and the amygdale. The functions of these connections are governed by the principles of conditioned reflexes.”

(source: wordpress.com)

(source: wordpress.com)

source:
1 Misophonia: physiological investigations and case descriptions
[2] MISOPHONIA 4S Provider Network USA
Great Site: http://lifewithmisophonia.wordpress.com/


text:
Simple protein graphics software for stick models
Anybody know of a good free molecular graphics system that allows PDB file input? I prefer that it does not use Java. I also prefer that it is online, although I would consider recommended software with a simple download process.
I am looking into trying to display a stick version of one of the chains of a protein, and want a program that can help me easily do this.
I have tried using FirstGlance and Protein Workshop, but FirstGlance is difficult to navigate through and the Protein Workshop doesn’t do stick models.

Have a look at Pymol and Chimera...

There are inofficial Windows builds of Pymol, those are free. Compiling Pymol yourself on Windows is very difficult, it's pretty doable on Linux.

There's also UnityMol, reads PDBs,  Cytoscape networks, OpenDX potential maps, and Wavefront OBJ.

VMD is very powerful.

which capabilities do you expect to have?

Comments are not for extended discussion; this conversation has been moved to chat.

Another good alternative is Swiss-PDB viewer. It is free, small, easy to install/use and is available for different OS (I had used it in Windows XP with 256MB RAM! Some features don't work well with low RAM but nonetheless it is not very resource hungry). It is good for the kind of tasks you are interested in. But it is not online (Actually I fail to understand why you need an "online" viewer).

This is an answer simply because I can't fit it all in a comment, or several...
To install and run PyMOL, you'll need a few extras. They are all free and open-source:

Python 2.7.10: Make sure you choose to install pip during the setup process, and also choose to add Python to your PATH, if that option is given. Also, note whether you installed the 32-bit version (x86 MSI installer) or the 64-bit one (x86_64). Which you choose depends on your operating system - if you have a 32-bit OS, you only have one choice. If you have 64-bit Windows, you can do either one - there's no real difference to the casual user. I like 64-bit, but I'm a nerd :)
The numpy+mkl package: I'd get version 1.9.2, as 1.10.0b1 is a beta version. Make sure it's not one of the "unoptimized" builds! You want the cp27 (stands for CPython 2.7) package, either 32- or 64-bit, matching your choice above.
From the same page, the PMW package (choose the py2 version).
Finally, PyMOL itself (both pymol and pymol_launcher packages for cp27).

Once you have everything downloaded and Python installed, open the command prompt by hitting WinR, typing cmd into the box, and hitting Enter. Use the cd command to change to the directory where you downloaded the .whl files (paths with spaces in them should be completely enclosed in double quotes: cd "C:\Users\John Smith\Downloads"). Next, type pip -V to ensure pip works. If it doesn't, just use the whole path: C:\Python27\Scripts\pip -V. Once you get the version statement, you're good to go. For each filename, type pip install really_long_filename.whl to install it. Remember that you can start typing a long name, then hit Tab to complete it. Do this for all four wheels - numpy+mkl, pmw, pymol, and pymol_launcher - in that order.
Once you do that, you should be all set. I'm not on Windows at the moment, so I can't tell you whether you'll get an icon or not, but if you don't, then open Windows Explorer and browse to the C:\Python27\Scripts directory - there may be a PyMOL script there you can run.
If you have any questions, please ask on Stack Overflow, tagging the question with [python] and [pymol]. People are generally very quick with comments and/or answers, so please stick around on the question's page for 5 or 10 minutes to assist those who would help you.
Good luck!

Is the MKL part important? I have numy but not MKL..

I'd recommend it, as the MKL can offer quite significant improvement in some numerical calculations over standard math libraries, and since PyMOL is completely based on very computationally-intensive work (displaying molecules and proteins in 3D), I'd strongly suggest getting it. To install over your current version of numpy, just run pip install -U numpy-1.9.2+mkl-blah-blah-blah.whl. The -U flag means "upgrade".


text:
How do we sneeze?
When a stimulus triggers the sneezing pathway, known as the trigenimal nerve network, how do the droplets from a sneeze get created within the nose? What affects the size of these droplets?


text:
Role of calcium chloride during competent cell preparation
I am aware of the fact that $CaCl_2$ settles down on the cell wall making it less negative may be by forming bond with Teichoic acid. Also due to the positive charge it attracts DNA (DNA is negatively charged due to phosphate group). But is there anything else the $CaCl_2$ does? Also if its the work of $CaCl_2$ why we are adding $MgCl_2$ first in the standard protocol of the making competent cell preparation chemically?

Even after so many years, nobody really knows what CaCl₂ does.

@WYSIWYG That's really true. Exact mechanism is not really known. Everybody hypothesis that this may be the reason. But what exactly happen maybe few people knows.

Please run a spelling check before posting a question. Whatever your first language, you can set it to English. We expect posters to be "comeptent" enough to do that.

Although we do not have any conclusive proof about how $CaCl_2$ works, the suggested mechanism is much similar to what you have suggested. When $CaCl_2$ dissociates in aqeous solution, $Ca^{2+}$ ions bind to the phosphate groups in DNA as well as the inner core of lipopolysaccharides in cell membrane (Dagert et al, 1979), neutralizing them. After this, heat shock allows uptake of this DNA into the host (how heat shock works is also not known; it is suggested that increased temperature creates pores in cell membrane, see this answer). For visual representation, see this diagram (from here):

Regarding $MgCl_2$, the role of $Mg^{2+}$ is not completely understood either. However, $Mg^{2+}$ is known to promote cell growth (Hanahan et al, 1983). It might be because $Mg^{2+}$ is an important factor required for functioning of ribosomes (Nierhaus et al, 2014). Anyhow, its role in increasing competence seems to be lesser than that of $Ca^{2+}$.
P.S.: during the experiment, $Mn^{2+}$, $Rb^+$ and $K^+$ also work effectively along with $Ca^{2+}$ (Hanahan et al, 1983).
References:

Dagert, M.; Ehrlich, S. (1979). "Prolonged incubation in calcium chloride improves the competence of Escherichia coli cells". Gene. 6 (1): 23–28. doi:10.1016/0378-1119(79)90082-9. PMID 383576
Douglas Hanahan, Studies on transformation of Escherichia coli with plasmids, Journal of Molecular Biology, Volume 166, Issue 4, 1983, Pages 557-580, ISSN 0022-2836, http://dx.doi.org/10.1016/S0022-2836(83)80284-8.
Nierhaus K.H. $Mg^{2+}$, $K^+$, and the ribosome J. Bacteriol.  2014 196 3817-3819


text:
Proteins that give color (without fluorescence)
Are there proteins that have strong color, that could be seen without the need of UV and with naked eyes (with white light) - in mammalian cells?
Searching for reporter, something like GFP, but that we could see it without UV (not fluorescence).
Like chromoprotein - but it is problematic in mammalian cells because most chromoproteins need a prosthetic group.

You've read the wikipedia page I assume? It has some examples.

Yes. I searching for something that may be used like GFP (reporter), but that we could see it without fluorescence and it's not chromoprotein - because like I mention it not perfect in mammalian cells, as far as I know.

The problem with these chromoproteins is that the color comes from a prosthetic group that is added to the protein later. If the cells can't produce the prosthetic group, or can't attach it to the protein, it won't be colored. I know you're not looking for fluorescent proteins, but I have seen E. coli express Red Fluorescent Protein and make reddish colonies, clearly visible on an agar gel. I can't say if mammalian cells would also make visibly red colonies.

I think it would help to add a cell type (e.g., red blood cells have red hemoglobin) or tissue (e.g. pigment epithelium in the retina is colored). As of now this question is quite brood as there are many colored proteins.

@AliceD Something universal - I wrote, like GFP.

with universal you mean occurring in any cell?

"E. coli express Red Fluorescent Protein and make reddish colonies" Because they absorb almost all light from daylight (~white) spectrum

@aandreev Yes, the colonies that had the RFP gene were reddish under visible light, the colonies without the gene were normal E coli color. Made it easy to pick the transformed colonies off the plate. When using GFP, we had to put the plate on a UV light to see the green.

@VGranin I think we should clarify what you want to do with this reporter. Do you want to see color with the naked eye? Are you looking under a microscope? Is this some sort of absorbance assay?

Check out Steve Boxer's papers on engineering single chain myoglobin in prokaryotes. As I recall it describes blood red colonies.

@user137,  with naked eye without UV and without microscope. If it's possible ..

@VGranin Many RFPs have their absorption maxima at around 500nm (green light) and therefore they can fluoresce even under white light. Since red scatters less it is easier to observe too. But the colouration is not very deep. So you can observe reddish colonies.

Have a look at this paper. They have isolated a chromoprotein similar to GFP, and like the latter it does not have any prosthetic group.
This protein — asFP595 (because it was isolated from the anemone  Anemonia sulcata.), is purple coloured under white light and also exhibits a little fluorescent emission in the red region  (λmax = 595 nm).
Also have a look at these two papers:

GFP-like chromoproteins as a source of far-red fluorescent proteins
Major colour patterns of reef-building corals are due to a family of GFP-like proteins

You are looking for light-emitting proteins. They gather energy from either absorption of photon (fluorescence) or via random thermal fluctuations. Problem is that fluorescence might be considered forced emission, whereas what you looking for is results of spontaneous transitions. That means that number of photons per second you can expect from latter proteins is $10^4$ times less (I don't have reference for that statement). You need very sensitive detectors and microscopy (sub- or just cellular) is almost impossible at that rate.
You should look into phosphorescence. Also, such thing as GFP-aeqorin might be of interest. That is a calcium-sensistive construct, might give you starting point in searching for reviews.
Another keyword is bioluminescence. See here for more: http://www.olympusconfocal.com/applications/fluorescentproteins.html

The question clearly specifies "that could be seen without fluorescence"

phosphorescence is relaxation pathway from states with much longer life-time (ms versus ns for fluorescence). Fluorescence persists after "exciting source has been removed" too, relaxation is just much faster

@nico Can you elaborate? My guess is that OP wants to see proteins without any harsh excitation light/in complete darkness, and I support OP in that endeavour

@aandreev the OP says "something like GFP, but that we could see it without UV (not fluorescence)." so giving him information about GFP-related proteins does not really seem a good answer to me... My guess is he's after something like Bacteriorhodopsin which is purple (albeit I'm not sure it's a good idea to use it as a reporter...)

@nico are you talking about GFP-aeqorin? it does not require any excitation, you can observe emitted light in complete darkness. Aeqorin is bioluminesce in presence of high Ca concentration, GFP is just a relay here. http://www.pnas.org/content/97/13/7260.fullhttp://www.pnas.org/content/97/13/7260.full

I was more referring to the link... The way I understand the question he is talking about a chromophore you can see with white light, not in the dark, maybe the OP should clarify...

@nico, right, in white light. I wrote like chromoproteins, and we can see them in white light. I added this point to the question. Thank you.

GFP-like non-fluorescent chromoproteins are colored and non-fluorescent.
A handful of them - Rtms 5, HcRed, cgCP, gtCP and zFP538 - have reviewed pages on Uniprot.
This paper from Nature describes the use of Rtms 5 to make hair dye: https://www.nature.com/articles/s41598-019-50283-0

Whilst true, it's not clear that this answers the question as written, which asks about non-fluorescent proteins found in human cells. Please take our [tour] and refer to the [help] for guidance as to our ways.


text:
Why do mice have a higher metabolic rate than humans?
Mice and other small animals have higher metabolic rate than humans.
How does that happen on cellular level, if we look on one cell in the mouse body?
What is it in this cell that will be different?
How is that regulated inside mouse cell?

I have changed the title. "higher" in  the original title is meaningless without a comparator. Let's keep science precise please.

In endothermic and ectothermic animals, ie. warm and cold blooded animals, metabolic rates are inversely proportional to size of the organism.

Quoting from https://www.biog1445.org/demo/04/metabolicrate.html
This is because smaller animals have a higher surface-to-volume ratio,
  thus a larger relative heat loss to the environment per unit time. To
  maintain a constant body temperature despite rapid heat loss across a
  body surface, a small animal must oxidize food at a high rate. Because
  the relative amount of food consumed and the pace of digestion,
  respiration, and so on must rise with decreasing body size, there is a
  lower limit on the size of endotherms. The smallest mammals are
  shrews, which weigh only about 4 grams. They must eat nearly their own
  body weight of food every day, and starve to death is just a few hours
  if deprived of food.

This is shows that smaller animals, like mice have a much faster metabolic rate than that of larger animals like humans or elephants.
When talking of within the cell, the mitochondrial content of a muscle cell of a mouse would be increased to produce more energy from one feeding than that of a human. This is because cells themselves increase the number of mitochondria based on the requirement of the body, thus a muscle cell of a human has more mitochondria than a neuron, since muscle cells have to utilize much more ATP to function. This phenomenon, known as mitochondrial biogenesis would be observed in mice vs human cells.
In mice, having more mitochondria would be an evolutionary advantage, as only those producing the optimal amount of energy would be able to survive the loss of energy to the surroundings and the process of natural selection would leave mice with relatively larger numbers of mitochondria in their cells.
(For more info)
https://en.wikipedia.org/wiki/Metabolic_theory_of_ecology
http://www.sciencedirect.com/science/article/pii/S0378111900005825

This basically re-states the background of the question, without actually answering it.  The question asks if the difference in metabolism extends to intracellular processes.

I'm sorry, I didn't quite pick up on that. I will do some more research then edit this answer