text:
Can E. coli make pyruvate from acetate?
What pathway would E. coli use to make pyruvate from acetate? I have found several papers that refer to a possible mechanism that could move acetate to pyruvate via a three-step process:
Step 1: Acetate Kinase (EC 2.7.2.1)
Step 2: Phosphate acetyltransferase (EC 2.3.1.8)
Step 3: Ferredoxin oxidoreductase (EC 1.2.7.1)
Is this the pathway that would be used in an E. coli system?

This is definitely not homework. I am asking because the pathway is not listed on MetCyc. No one has answered yet because it is a hard question and acetate-pyruvate flux pathways are beyond most biochem classes. Anyway, I assume it could be done in three steps for most prokaryotes and impossible for eukaryotes.

But what provoked your question? And why pyruvate particularly? It's too late at this side of the Atlantic, but I would reckon a few more than three steps. Also remember plants are eukaryotes. Perhaps tomorrow.

OK. Your mention of MetCyc convinces me, so I have taken the opportunity to provide a detailed explanation of the glyoxylate shunt. The reason you didn't find anything iin MetCyc is that acetate to pyruvate (or even PEP) is not regarded as a single "pathway" per se. This is also the case for other conversions that may utilize certain reactions of the TCA cycle itself.

I have just added a section regarding the suggestion you made in response for my request that you show you have searched for the answer yourself. Fine, I have withdrawn my close vote and deleted my comment about homework. Having looked at your bio I am still puzzled as to why you are interested in E. coli converting acetate to pyruvate. Is it anything to do with the 'metabolomics' tag, which seems inappropriate. Are you trying to explain metabolomics experiments that show increase in pyruvate, for example? Knowing the context would help us to help you.

Summary
Several pathways/metabolic reactions are required for bacteria to convert acetate to pyruvate — or more pertinently to the gluconeogenic pathway — but the key is the glyoxylate cycle or shunt. The sequence of reactions is:

2 acetate → 2 acetyl CoA (acetyl CoA synthetase)
1 acetyl CoA + oxaloacetate → citrate → isocitrate (entry to Krebs TCA cycle)
isocitrate → glyoxylate + succinate (glyoxylate shunt)
succinate → oxaloacetate (Krebs TCA cycle)
1 acetyl CoA + glyoxylate → malate (glyoxylate shunt)
malate → oxaloacetate (Krebs TCA cycle)

Thus, the two molecules of acetate replenish the original molecule of oxaloacetate used for one of them to enter the tricarboxylic acid (TCA) cycle, with — in addition — a second molecule of oxaloacetate. This is available for:

oxaloacetate → phosphoenolpyruvate (PEP carboxykinase of gluconeogenesis)

The phosphoenolpyruvate (PEP) could, in principle, be converted to pyruvate:

phosphoenolpyruvate → pyruvate (pyruvate kinase of glycolysis)

Although this sequence of reactions would normally be used to generate glucose etc via gluconeogenesis.
The link betweeen the TCA cycle and glucose metabolism
In addition to oxidizing acetyl CoA, the Krebs tricarboxylic acid cycle (TCA cycle) can act as source of certain metabolic intermediates for other pathways. As shown below, oxaloacetate (OAA) can be converted to phosophoenol pyruvate (PEP), in a reaction that is part of the gluconeogenic conversion of pyruvate to PEP.

Although certain bacteria can convert acetate into acetyl CoA in a reaction catalysed by acetyl CoA synthetase the TCA cycle per se does not perform a net conversion acetyl CoA to OAA, because a molecule of OAA is needed for acetylCoA to enter the TCA cycle and must be regenerated. The TCA cycle, in effect, oxidizes acetyl CoA to carbon dioxide. The TCA cycle, per se, can only convert to OAA and PEP those intermediates that enter the cycle directly after the acetyl CoA stage.
The glyoxylate shunt
The foregoing explains why most animals cannot convert fat to glucose. (Acetyl CoA cannot be converted to pyruvate by pyruvate dehydrogenase is this reaction is effectively irreversible.) However plant and certain bacteria (including Escherichia coli) can overcome this limitation by means of the glyoxylate shunt. A text available online that explains this is Berg et al., in a section entitled ‘The Glyoxylate Cycle Enables Plants and Bacteria to Grow on Acetate’. To help clarify this I have prepared my own diagram, below.

This involves the conversion:
oxaloacetate + 2 acetyl CoA → 2 oxaloacetate

i.e. the net conversion of
2 acetyl CoA → oxaloacetate

The glyoxylate shunt reactions are imposed on the TCA cycle with a pink overlay. One molecule of acetyl CoA condenses with OAA to enter the TCA cycle in the normal manner. However the isocitrate formed from citrate, instead of being decarboxylated, is converted to glyoxylate and succinate. The succinate — a dicarboxylic acid — regenerates the original molecule of OAA used to allow acetyl CoA to enter the TCA cycle.
What of the glycoxylate produced in the isocitrate lyase reaction? It reacts with a second molecule of acetyl CoA to produce the dicarboxylic acid malate in a reaction catalysed by malate synthase, the second unique enzyme of the shunt. This TCA cycle intermediate is converted to OAA. This second OAA is a net gain from the metabolism and can be converted to PEP, as indicated in the first diagram.
The poster asks about production of pyruvate from acetate. This is technically possible through the pyruvate kinase reaction. However I do not quite see the point of this. I would normally expect PEP to be channeled allong the gluconeogenic pathway towards glucose.
Coda: Pyruvate:ferredoxin oxidoreductase
The poster suggests a series of reactions to convert acetate to pyruvate, the final one being that catalysed by pyruvate:ferredoxin oxidoreductase. Although the pyruvate:ferredoxin oxidoreductase (EC 1.2.7.1) reaction is reversible, it generally functions to oxidize pyruvate to acetyl CoA. It is used as an alternative to pyruvate dehydrogenase by bacteria under anaerobic conditions (as it does not require NAD+), and this is regarded as its role in E. coli, and to an even greater extent in obligate anaerobes such as Clostridium.
The reverse reaction suggested by the poster, involving the synthesis of pyruvate from acetyl CoA, is restricted to autotrophs


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Why is pepsin able to operate at low pH?
Pepsin is a protease that operates in the acid pH of the stomach. Many proteins are denatured at low pH, and most enzymes — whether or not they denature — require a higher pH for activity.
Why is pepsin not denatured at low pH, and has catalytic activity at low pH, but not at higher pH?

Are you confusing inactivity with denaturation? Have you investigated how high and low pH can denature proteins (or inactivate enzymes without denaturing them)? Don't just say "if this happens to X why doesn't it happen to Y?", but show you understand why it happens to Y.

I think i may be referring to inactivity, why does pepsin become more inactive in more basic environments?

OK. I have edited your question so that it does not mix up activity and structural native state, and focussed particularly on pepsin so perhaps it is no longer a duplicate. You can revert if you wish.

The aspects of this question relating to the effect of pH on enzyme activity have been dealt with previously on SE Biology questions and answers:

Why does pH have an effect on enzymes?
How can ionized amino acid form be important for the catalytic activity?

Their relevance to the situatio of pepsin can be summarized:

The forces stabilizing the native three-dimensional (tertiary) structure of proteins include ionic and partial ionic (hydrogen-) bonds. It is thought that high concentrations of charged hydrogen ions or hydroxyl ions compete for the ionic or polar residues involved in these interactions disrupting the structure — denaturing it.
The effect of such ions will vary from protein to protein depending on the number and strength of these interactions. One presumes pepsin has evolved a structure with interactions that are less susceptible to a high concentration of hydrogen ions and therefore does not denature at low pH.
Catalysis often involves ionization of groups on the enzyme, not merely to bind substrates, but also to participate in the reaction. Typically the reaction mechanism involves flipping from ionized to deionized state or vice versa. Hence, the optimum pH for an enzymic reaction is often at the pKa of the ionizing group (in the environment of the protein), as this is the pH of half ionization.
The reaction mechanism of pepsin, an aspartic protease, involves two aspartate residues, each of which has a low pKa, explaining why pepsin works optimally at low pH.

The catalytic mechanisms of other proteases (serine proteases and cysteine proteases) do not involve ionization changes in aspartic acid, which is why they operate at higher pHs.

A good question. As you have accurately described, pepsin is indeed a protein, more specifically, a protease enzyme - a catalyst which assists the break-down of protein at certain amino-acid markers such as tryptophan and phenylalanine. As you are likely aware, proteins are composed from approximately 20 amino-acids, as shown below.

However, the chemical properties of a protein are constituted by its folding - its three-dimensional shape. This answer describes some superficial differences between protein families and the mechanism and function whereby pepsin is capable of functioning at a low pH.

Disregarding any post-translational modifications - the alterations made to a protein following translation from mRNA - proteins are made from a determined sequence of amino-acids, named its primary structure. Different classes of proteins shall have a different sequence and proportion of various amino-acids. For example, collagen fibrils are composed from a greater proportion of the amino-acids glycine-proline-hydroxyproline.
A sample of pepsin extracted from a pig (Porcine pepsin) demonstrated a higher yield of asparagine.
Secondary structure - the inter-molecular bonding between amino-acid side-chains including hydrogen-bonding and disulfide bridge. As you correctly described a protein denaturing, it is these bonds which are broken, thereby altering the protein's shape.
Although there be four principal protein structures - primary, secondary, tertiary and quaternary - the first two are most critical to understanding the ability for pepsin to withstand low pH. Pepsin is originally secreted into the stomach as a proenzyme - an inactive precursor to an enzyme - called pepsinogen. When food is ingested, both pepsinogen and hydrochloric acid are released into the stomach. Returning to our primary structure, pepsinogen possesses 44 additional amino-acids compared with the active enzyme. During acidic conditions, the pepsinogen auto-catalyses its own cleavage from the additional strand, folding into the correct form.
Therefore, other proteins in high acidic conditions lose their unique three-dimensional structure due to the breaking of these inter-molecular bonds. In a sense, denaturing only specifies a transformation into an inactive protein but could be stated for pepsinogen which is 'denatured' into pepsin which attains its activity in this 'denatured' form.
For more information regarding pepsin, I would advise the following Wikipedia page as an initial resource: https://en.wikipedia.org/wiki/Pepsin
For information regarding collagen and porcine-pepsin composition, the following sources respectively may help: https://www.ncbi.nlm.nih.gov/books/NBK21582/ and https://www.ncbi.nlm.nih.gov/pmc/articles/PMC427253/?page=2
I wish you good digestion!

So after all that I have indigestion because I don't see any answer to the question in what you have written. Can you summarize in one or two sentences?

@David It appeared that the Original Poster needed to discriminate digested proteins from the enzyme pepsin itself. So, proteins have primary and secondary structure which provide the protein with its shape. Dietary proteins are denatured because of the breaking of secondary structure while pepsin (pepsinogen) is activated at low pH. Admittedly, because I did not explicitly refer to high pH, I will edit the post and insert this additional response. Thank you.

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Oxygen in the earth’s atmosphere
If CO2 only makes up about 0.04% of the earth’s atmosphere how do trees and organisms in the ocean produce oxygen to 10% of the earth’s atmosphere?

Short answer: They had a very long head start

Some places the atmospheric Oxygen is nearly 20 %.

A very long head start
To elaborate on Drake Johnson’s comment, CO2 used to be much higher in concentration. During the Great Oxygenation event, when cyanobacteria (ancestors) began photosynthesizing, they converted much of the CO2 into O2, driving CO2 concentrations down as they drove O2 up.

When was this and what temperature was the atmosphere in then? Good sources?

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text:
What proportion of proteins require chaperone-assisted folding?
I am new to the field of biochemistry (I am a chemist, actually).
I have long known the process of folding as the process that leads to the minimum energy conformation of a protein.
Now, I am introduced to the chaperones, that I didn't know before.
What I am wondering is: my previous view of folding, as a proces of "self-assembly" (the protein folds without external assistance as it is assembled by the ribosome) is real, or any folding process is assisted by chaperones?
If both processes exist, how frequent is the "assisted" folding, compared to the spontaneous process?

I've edited your title to remove the word "frequent" as what you are asking is not a temporal question (how many proteins per minute are folded with chaperones) but one of proportion or description (do all proteins are just some fold in this way). Do revert or modify if you don't like my change.

I'm reminded of a lovely review in Trends in Biochemical Sciences that discusses chaperone independent, partially dependent, and fully dependent proteins in prokaryotes.  The conclusion was that smaller polypeptides are less likely to require chaperone assistance. This is their figure:

That principle still holds to a certain extent (in prokaryotes), but folding assistance is now more broadly understood to include much more than just specific proteins identified as molecular chaperones. The Anfinsen postulate (that the final tertiary structure of a protein depends only on its primary structure) may still hold for small globular proteins, but folding in vivo is almost certainly always assisted. Since you're coming from the perspective of a chemist, don't think of it as a reaction between two molecules in solution. It's a reaction in a gel packed with complex sugars, lipids, proteins, and nucleic acids.
If you're skeptical of the perspective of a crowded cytoplasm, read the review I linked. It's an important but often under-appreciated aspect of in vivo biochemistry. There is much more to read about it. You might try looking up Allen Minton (AP Minton) and macromolecular crowding in your favorite database.

I would upvote your answer, but for the last two sentences. If the cytoplasm is "a gel completely packed with things" how do tRNAs, protein synthesis factors etc. diffuse to the ribosomes, and the released proteins distribute themselves in the cytoplasm. And what precisely has this to do with the protein folding? This is a serious, not a rhetorical, question.

@David did you read the serious, not rhetorical paper I referenced?

@David on re-reading, i may have phrased it a little stronger than I should have in order to emphasize the difference between dilute in-vitro biochemistry and the gel-like phase where protein biochemistry (including folding) occurs in-vivo. I removed the word completely, and added a comment about it.

— I'll check your reference out. I'm traveling in a foreign country where I'm being charged a £7 per Mb for data, so I'm dependent on rather flaky wifi reception.

Ok, I've looked at both the TIBS review and the 2012 Int J Mol Sci review. I see that the latter makes the point that the results in vitro are not always borne out by those in vitro (e.g. with mutants in the chaperones) and the authors suggest that (non-specific?) interactions with other molecules may be important. That's all I see that relates to your "gel" remark, which I now see you've clarified in your answer. The general impression I get is that it's difficult to answer the question posted with any precision, although assisted folding cetainly exists.

@David they review the good deal of evidence for the importance of other macromolecules in folding assistance. You seem unconvinced :) Read some of Allen Minton's work.

I don't doubt the role of other molecules in folding. It just seems to me from the review that the field is still in flux. That's no criticism, just an impression.


text:
How do anaerobic bacteria produce ATP for their own cellular activities?
Anaerobic bacteria utilise glycolysis:
Glucose + 2 P + 2 NAD+ => 2 ATP + 2 H + 2 NADH + 2 H2O + 2 Pyruvate
followed by fermentation:
Pyruvate + NADH => Lactate + NAD+
The resultant NAD+ formed can then be used again to break down more glucose molecules in glycolysis to produce ATP.
However, besides NAD+, glycolysis also requires an input of 2 ATP at the beginning (for the phosphorylation of glucose to glucose 6P, and fructose 6P to fructose 1,6 BP)
Since only 2 ATP is produced from glycolysis initially, would these 2 ATP be reused in another round of glycolysis?
If so, how do anaerobic bacteria produce a net amount of ATP for cell activities and growth?

Please go back and check your sums and re-read the chapter in your text book, taking particular account of the fact that two molecules of triose are produced from one hexose.

That was already accounted for in the balanced equation above. 4 ATP - 2 ATP invested is a net of 2 ATP from glycolysis.

Your response to my comment is incorrect. As I said, please go back to your text book and look at the pathway of glycolysis and the actual reactions where ATP is generated and whether the substrate is triose or hexose and if it is triose how many trioses came from the original hexose.

@user1136 — The equation given by OP is not quite right. It lacks ADP and appears to involve phosphorus and molecular hydrogen. If the OP recognized that there was a net yield of 2ATP he would have included 2ATP on the left-hand side of the equation and 4ATP on the right. Indeed, if he had recognized there was a net yield of ATP he would not have entitled his question as he has. He obviously thinks there is no net yield because he has forgotten to multiply by 2 after aldolase. Perhaps that's why he has kept a low profile in the month since he posted. He may even have taken my original advice.

@user1136 NAD+ is regenerated in the NAD+ regeneration reaction that follows glycolysis in which the pyruvate products of glycolysis breaks down into lactate or alcohol depending on which organism you are talking about.

@user1136 you asked how NAD+ regenerates.

The product is 4 ATP not 2, 2 is the net product because two are used to start the reaction.
Looking at the complete glycolysis reaction helps.

ATP can be used to start another round of glycolysis which yields 4 ATP which can then start 2 rounds of glycolysis which yields 8 ATP, rinse, repeat. It is an exponential process, ATP can be taken from this for other processes since as long as you still have 2ATP around to can restart the exponential cascade. For example from the yielded 8 if you take half for other uses, you still get 8 ATP from the next round of glycolysis reactions.

During the reactions, the resultant molecules are dispersed in the cytosol, and it is a bulk phenomenon rather discrete and independent event. The calculations are mainly based on in vitro experiments, so the reuse of the energy transporter molecules (ATP), totally depend on it's quick availability.
The NET production of ATP cannot be determined in precised manner as pathways may show reuse of the formed energy bags (ATPs) or may use already present molecule or molecules from some other reaction.

@VishalKumarSahu Can you please provide some references to support your answer?

There is a lot of theory and scientific articles available through google. If this is a scientific (not for general people) forum, please let me know, I would not use researchgate, pubmed...

Anaerobic respiration, which is used by some Bacteria and some Archaea, is not glycolysis+fermentation. Anaerobic respiration is like aerobic respiration which includes ETC (electron transport chain). Basic difference is the terminal electron acceptor. In aerobic respiration the terminal electron acceptor is oxygen. On anaerobic respiration the terminal electron acceptors are various materials, for example hydrogen sulfide. Read this or research similar sources.
In Turkey, we were teaching anaerobic respiration and fermentation as the same things in high school biology lesson until a couple of years ago. May be you are asking in this regard. If so, rename your question.


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What determines the metabolic pathways that a biological cell is able to carry?
For example:

human cells (eukaryotes) can utilize the Krebs cycle pathway to generate more
ATP after glycolysis, but most bacteria cannot utilise the Krebs
cycle
plant cells can utilise the Calvin's cycle for
photosynthesis but human cells cannot.
yeast can utilise the ethanol fermentation pathway but human cells can only utilise the lactic acid fermentation pathway.

Why can't humans use the Calvin's cycle? Or why can't yeast use the lactic acid fermentation pathway instead? What determines the metabolic pathways that a biological cell is able to utilise?

It is fortunate that many bacteria can utilize the Krebs cycle and oxidative phosphorylation or eukaryotes would never have acquired this capacity through their endosymbiotic capture to produce of mitochondria. And the answer is trivial — evolution. Metabolic pathways are no different in this respect from the elephant's trunk, the giraffe's neck, the birds wings or the fishes' fins. All are a result of evolution of the genome under environmental pressure.

Is it possible to genetically engineer new pathways in bacteria cells the

Yes, it is possible to genetically engineer new pathways in bacteria — this is called Synthetic Biology and you can search for articles about it. Putting in the genes for a pathway is not enough, though, you need to consider how they will be induced and regulated etc.

The determining factor is the hereditary traits that are passed on to the organism. Metabolic pathways require protein catalysts of which the instructions to make are stored in DNA. In other words humans can't use the Calvin cycle because our parents can't/couldn't, but plants can because their parents can/could.
In the long run though, very slowly organisms can gain or lose the ability to use pathways that their ancestors had.

By protein catalysts, do you mean enzymes?

That's right. Enzymes are catalytic proteins.

In that case, if the enzymes were manually added to the cells in a bioreactor environment, would the reaction be possible? For example, human cells cannot utilise the carboxylation pathway that converts PEP into oxaloacetate since the instructions to make the enzyme PEP carboxylase is not stored in our DNA. However if we isolate and manually add PEP carboxylase to a human cell, would the carboxylation reaction be possible?

If by "manually" you mean to purify the enzyme and literally add the powder in the reactor then probably no. Because the cells will likely not transport it in and the enzyme will likely get denatured. If you add the gene for that enzyme then probably yes. There are other factors too like if the gene is expressed properly and the enzyme goes to where it needs to go. Modifying metabolic pathways is something people do right now. For example researchers are genetically modifying fungi to ferment all the sugars in plant biomass and inhibitors in the medium. This involves adding new genes.

Thank you. So the only way to make new metabolic pathways is to genetically modify the cell, and more specifically, isolate the desired gene and insert it into a cell plasmid? (making recombinant DNA)


text:
Menstrual cycle and luteinizing hormone (LH)
What is the effect of increased concentration of LH on the follicle at the start of the menstrual cycle?
I know that increased levels of FSH at the beginning causes follicles to mature and release estrogen, but I cannot seem to be able to find what the effect of increased levels of Luteinizing Hormone at the beginning of the cycle would have.

Do you mean the preovulatory LH surge?

If the preovulatory LH surge occurs at the beginning of the menstrual cycle, then yes that may be what the question is referring ro.

Luteinizing hormone (LH): A hormone released by the pituitary gland in response to luteinizing hormone- releasing hormone. It controls the length and sequence of the female menstrual cycle, including ovulation, preparation of the uterus for implantation of a fertilized egg, and ovarian production of both estrogen and progesterone. Theca cells in the ovary respond to LH stimulation by secretion of testosterone, which is converted into estrogen by adjacent granulosa cells. In women, ovulation of mature follicles on the ovary is induced by a large burst of LH secretion - the preovulatory LH surge. Residual cells within ovulated follicles proliferate to form corpora lutea, which secrete the steroid hormones - progesterone and estradiol. Progesterone is necessary for the maintenance of pregnancy, and, in most mammals, LH is required for continued development and function of corpora lutea.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3136063/

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What causes cells to inactivate one X-chromosome?
Normally, when a cell has two X-chromosomes (female genome), one is randomly inactivated. How does the cell detect that there are two X-chromosomes in the first place?
Is there some kind of protein that's coded in the X-chromosome, such that having two X's increases the protein concentration and a dosage effect causes one to become inactivated? I can't find any information about it in my textbook, nor on Google. A citation would be appreciated - especially for peer-reviewed research.

Even a male cell can count the number of X chromosomes. (Lee et al. 1996; Cell 86: 83-84)
When X inactivation is getting started the two chromosomes "kiss" - a process that lasts for a couple of hours (first shown by Jeannie Lee in 1996). The physical contact between two X chromosomes is over a small fraction of the chromosome but it's essential for triggering inactivation. (Xu et al. 2006: Science 311: 1149-52)
If it doesn't happen then the X chromosome assumes it's alone which would mean that Xist never gets switched on and inactivation never happens (a key stage in chromosome counting).

Chromosome counting is a process in which cells determine somehow
  their intrinsic chromosome number(s). The best-studied cellular
  mechanism that involves chromosome counting is 'chromosome-kissing'
  and X-chromosome inactivation (XCI) mechanism. It is necessary for the
  well-known dosage compensation between the genders in mammals to
  balance the number of active X-chromosomes (Xa) with regard to diploid
  set of autosomes. At the onset of XCI, two X-chromosomes are coming in
  close proximity and pair physically by a specific segment denominated
  X-pairing region (Xpr) that involves the SLC16A2 gene.

Take a look at Xist and Tsix. Some more papers worth taking a look at:
Xist regulation and function eXplored
Mechanism of regulation of ‘chromosome kissing’ induced by Fob1 and its physiological significance

Please note that this only applies to placental mammals. Drosophila, for example, has a different method for compensating for the two copies of the XX chromosome in females.


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What determines the direction in which motor proteins go?
I know that kinesin motor proteins move towards the positive (beta) end of the microtubule, while dyenin motor proteins move towards the negative (alpha) end of the microtubule. However, because the microtubule is composed of repeating alpha and beta units in ABABABABAB fashion (as shown in the picture below), what causes motor proteins to move to the positive rather than the negative pole?
For example, if one "leg" of the kinesin is bound to a beta tubulin while the other leg is up and ready to bind again, what determines which alpha tubulin it binds to (since there is alpha in front and in back of the beta tubilin it is bound to)?

While you're entirely correct that the ABABAB sequence is symmetric to a motor protein cruising along, the individual $\alpha$ and $\beta$ monomers themselves are not symmetric along the axis of movement (or any axis at all, as far as I can tell). This produces a polarity that can be seen in the figure below, from the original 1998 paper describing it.

The figure you use above to display the microtubule is slightly misleading in this way; it shows the subunits as blobby spheres. However, the motor proteins are able to distinguish the top of these molecules from the bottom, seeking a unique set of loops and helices to attach to. As it walks, then, the motor protein can only bind to one side (pole) of the subunit and is unable to walk backwards.


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Why is there such in interest in antibiotics against Pseudomonas?
I keep finding information on anti-pseudomonal antibiotics, or information specifying the antibiotic has anti-pseudomonal activity. Is there anything peculiar to this bacterium when compared with other gram negative bacteria?

Indeed Pseudomonas is a very peculiar (and concerning) genus in clinical microbiology, specially P. aeruginosa. The reason why you keep finding emphasis on antibiotics that have pseudomonal activity is because this organism is the model of bacterial antibiotic resistance. It is often considered more deathly than other important multi-resistant bacteria such as S. aureus, Acinetobacter or Enterobacter.
P. aeruginosa is responsible for multi-resistant nosocomial diseases (a basic definition of nosocomial is an infection acquired inside a hospital) that have really high mortality rates. It is not uncommon to see hospital antibiogram results for this bacteria informing about resistance for all the commmonly used classes of antibiotics for Pseudomonas infections including 3rd and 4th generation cephalosporins, fluoroquinolones and carbapenems.
Reference: Evolution of Pseudomonas aeruginosa Antimicrobial Resistance and Fitness under Low and High Mutation Rates
There are LOADS of articles and info to read about P. aeruginosa antibiotic resistance, but I like this one since it tries to explain how the problem appeared from a genomic point of view.


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Does Herpes Simplex Virus induce antibodies which last a lifetime?
Herpes simplex virus (HSV-1) is a virus which produces both lytic and latent infection. In the latter case it persists in a quiescent form in the neural ganglia for the lifetime of its host.
My question is whether the antibodies raised against the virus persist for the lifetime of the individual.
I understand that exposure to the virus again would activate the memory B cells and lead to the elicitation of these antibodies. But in general, what is the scenario with the circulating antibodies?
I found some websites stating that the antibodies persist for the lifetime of the individual, but I could not find any research publications to support this.

@MattDMo Thank you for your response. After the 3-4 weeks, the level of antibodies will deplete unless there is a reinfection. However, it is known that plasma cells residing in bone marrow can secrete antibodies for a long time even after the clearance of the virus. Not sure if it applies to herpes virus infection as well.

Which Herpesvirus are you talking about? Human Herpes Virus Type 1 (HSV1) or what? Until you tell us, nobody can answer your question, and anyone who has has made the same mistake as you.

@David I guess it does not matter as all herpes virus remain in our body for the rest of our life after infection. However, to be specific HSV-1 can be used.

Human herpesviruses range from alpha (HSV1 and 2, varicella zoster), beta (cytomegalovirus) to gamma (Epstein-Barr virus). So I think scientifically it is best to specify. I have edited your question accordingly. It would be helpful if you could give links to the sites you quote as saying that antibodies stay a lifetime.

For the vast majority of a herpesvirus infection, the virus genome is only present in the nucleus of latently-infected neuronal cells; there are no virus particles in the body. My understanding is that there will therefore be no circulating antibodies unless the latently infected neurons reactivate and begin producing viral particles. However, in this 2005 review, "Immunity in latent Herpes simplex virus infection", mouse studies found that infected neurons had CD8+T cells stuck to them that stayed there and secreted interferons for the lifetime of the animal:

In mice, CD8+T cells invade TG ~7 days after HSV-1
infection, reach maximum ~4 days p.i. and are then retained
in a significant number seemingly for the life-time of the
animal. Significantly, HSV-1-specific CD8+T cells are
persistently stimulated within the latently infected TG. ... The steady expression of IFN-γ and TNF-α in latently
infected TG suggests continuous stimulation of the cells
producing these cytokines. Expression of these cytokines is
tightly regulated and subsides within two hours of
withdrawal of the stimulant. Since IFN-γ can block HSV-1
reactivation from latency in sensory neurons, such a CD8+T
cell population is ideally suited to the function of long-term
protection with minimal tissue destruction (Kodukula et al.,
1999; Liu et al., 2000, 2001; Mueller et al., 2003; Stuart et
al., 2004).

So this implies it's the presence of T-cells in the trigeminal ganglion (TG in the above quote) that keeps infected neurons from reactivating and producing new virus. Since the T-cells are apparently being continuously stimulated, it seems possible that B-cells could also be getting stimulated and secrete antibodies, but I haven't seen that possibility addressed anywhere. Also, this continuous stimulation of the immune cells may only happen in mice, not in human infections:

In contrast to latently HSV-1-infected mice,
the frequent reactivation of HSV-1 in human TG may reflect
a less efficient CD8+T cell recognition. This would be
compatible with the fact that HSV-1 ICP47 protein inhibits
TAP-mediated transport of antigenic peptides more
efficiently in human than in mouse cells.

Mice with suppressed B-cells were not found to be less effective at preventing reactivation of latent HSV-1 infections.
Finally, the viral antigen that most of the reactivation-inhibiting T-cells were found to be going after was a fragment of gB, an envelope glycoprotein somewhat similar to the famous coronavirus spike protein. I would expect this antigen to also be a major target for antibodies.

Thank you for your response. Here is the a publication: http://dx.doi.org/10.1128/mBio.00678-17
Like T cells in trigeminal ganglion (TG) gets stimulated, the antibodies also increases after infection and persisted 8 months after infection (latest time studied). IgG concentrations were significantly increased in the TG and brain but not in the lung or liver. They persisted for long in human and murine TG.
The data in the paper shows that TG IgG originates both from locally antibody-secreting cells and from circulation.


text:
Exclusion Limit and permeability of outer membrane
According to this textbook:

P aeruginosa, for example, which is extremely resistant to antibacterial agents, the outer membrane is 100 times less permeable than that of E coli.[pg.no 27]

and then on the same page:

The porins of diferent species have diferent exclusion limits, ranging from molecular weights of about 600 in E coli and S typhimurium to more than 3000 in P aeruginosa.

How can P. aeruginosa have lesser permeability than E. coli, if its exclusion limit is greater than that of E.coli?

My Attempt:
This source claims that

OprF provides P. aeruginosa outer membrane with an exclusion limit of 500 Da.

This( 500 Da.) is near than that of E. coli's 600 Da., so how is it exteremely resistant?

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


text:
What happens during fixation of Nucleic acids on nylon membrane
In Southern blotting technique, fixation of DNA to nylon membrane is a step prior to hybridisation with probe. It is done by baking at 80ºC and according to this cross linking between DNA and nylon takes place.
What I am unable to understand is, if there is cross linking between DNA and nylon then, how does the probe bind complimentarily to the DNA? Isn't cross linking may mask the sites which may form hydrogen bonds?


text:
Pressure change in atria
Background:It is said that during the phase of isovolumetric contraction , due to sharp rise in the ventricular pressure, there occurs bulging of AV valves into the atria producing a small but sharp rise in the intra-atrial pressure called c-wave.( in the second cycle of diagram).

Question: I am unable to understand why is then pressure in atria falling after the end of isovolumetric phase, even though the pressure in the ventricles is rising, so this should further bulge the AV valve or atleast( due to action of papillary muscles) have same pressure, So why is pressure falling?

The curve you are talking about is JVPJuglar Venous Pressure Curve.
You are talking avoit x-decent after c pulse.
The downward deflections of x decent is produced by the atrium relaxation and the downward movement tricuspid valve.
This causes decrease in atrial pressure.
A new fascinating question could be why x-decent is greater than y-decent.
Good luck.


text:
Rationale behind different classification of nerve fibres
Two main types of classification of nerve fibres are numerical and Erlanger-Gasser classification, based on diameter and conduction properties.
In numerical classification group Ia and Ib both have same conduction velocity and diameter, then on what basis are they different ,is it just because they are innervating different structures, then why this criteria is not followed further?
Also in Erlanger and Gasser classification both A and B types are myelinated and C is unmyelinated, then why is B not clubbed as subgroup of A? How is B different from A(delta) even though both are myelinated and have same conduction speed?

Source :https://en.wikipedia.org/wiki/Axon

Why downvote??? Where I am going wrong?

There are a bunch of different questions here, for one thing.

If I ask them separately then the main question can't be asked.


text:
How colon resist to bile
There is a disease called bile reflux which can make damage to the stomach. I just don't know how the stomach can be damaged by bile but the colon (small intestine) can resist with it?


text:
Can you identify this climbing plant?
In my house there's a strange plant that I see growing for years now. I believe it is a climbing plant. Do you know how is this plant named? Is it poisonous?
Location: Greece
Altitude: 800m.

if you don't get answers here, this question would also be on topic on Gardening: https://gardening.stackexchange.com/

Do you have any idea what the flowers look like? A picture would be fantastic, but color, size and/or number of petals would also help a great deal.

we have this all over the place in france. it tends to wilt as the summer goes on, it has annoyingly hairy leaves which are a bit weird. red briony https://upload.wikimedia.org/wikipedia/commons/2/23/Bryonia_dioica_%282144983672%29.jpg they used to put it on the bandages of lepers, you know those who lose fingers and limbs to consumption.

Based on the fruits, leaves and tendrils, it looks quite like Bryonia dioica (which is toxic). It is almost certainly something from the same family (Cucurbitaceae, which often make such tendrils and usually have similar leaf shapes) and could even be the same genus, Bryonia, which is present in the Mediterranean region (there's even a cretica species). Based on images found on the internet, leaf shape seems variable (more or less indented).


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How EGDS (endurance genetic distance score) is calculated?
Can anybody please make me understand how EGDS5 has been calculated to 40.8 in this paper at page#31?
The formula has been described in this paper but when i tried the same, I am not getting the same results.
According to paper describing the formula:
$EGDS = 100 - \frac {100\cdot d} { n \cdot w }$
where
$n =$ number of studied polymorphisms
$w =$ score given to worst genotype
$d =$ euclidean distance calculated as follows
$d = \sqrt{ \sum_{i = 1}^{n} (2 - x_i)^2}$
$x_i =$ genotype score of corresponding polymorphism
$2 =$ optimal genotype score
here is what I tried. Given below is the genotype score of 5 genes:
$ x = (1,1,1,1,0)$
$d = \sqrt { (2-1)^2 + (2-1)^2 + (2-1)^2 + (2-1)^2 + (2-0)^2 }$
$= \sqrt { 1 + 1 + 1 + 1 + 4}$
$= \sqrt 8 \approx 2.82$
Now, $EGDS5 = 100 - \frac{ 100 }{ 5 \cdot 4 } \cdot 2.82$
$= 100 -  5  \cdot 2.82 $
$= 85.9$
which is not equal to 40.8.

In my opinion, there must be something wrong with the formula given in the paper. The rationale behind the conversion of $d$ into the range 0-100 is stated in the papera as follows:

An EGDS9 of 100 represents an “optimal” endurance genetic profile,
  that is, all GS’s are 2. In contrast, an EGDS9 of 0 represents the
  “worst” possible profile for endurance genetic profile, that is, all
  GS’s are 0.

So what they are basically saying is that they want
$d_{max} = \sqrt{\sum_{i=1}^n(2-0)^2} = \sqrt{4n} = 2\sqrt{n} \Longrightarrow EDGS_n \stackrel{!}{=}
 0$
$d_{min} = \sqrt{\sum_{i=1}^n(2-2)^2} = \sqrt{0} = 0 \Longrightarrow EGDS_n \stackrel{!}{=}
 100$
So let's just define EGSD as the percentage of reaching the minimum possible distance:
$EGDS_n =100 \cdot \frac{2\sqrt{n} - d}{2\sqrt{n}} = 100 \cdot \left(1 -\frac  d {2\sqrt{n}} \right) = 100 - \frac {100\cdot d}{2\sqrt{n}}$
Which gives us a formula very similar to the given. (Actually their formula is just missing the squre root in the denominator).
Let's apply this formula now to the case of the other paperb in discussion:
$EGDS_5 =100 \cdot \frac{2\sqrt{5} - \sqrt{8}}{2\sqrt{5}} \approx 36.754$
Not quite 40.8, but closer. Now, what if we assume the people in the other paper used this formula but made a mistake when calculating d, getting $d = \sqrt{7}$?
$EGDS_5 =100 \cdot \frac{2\sqrt{5} - \sqrt{7}}{2\sqrt{5}} \approx 40.839$
Interestingly, the other score 33.8 comes from apparently calculating
$EGDS_4 =100 \cdot \frac{2\sqrt{4} - \sqrt{7}}{2\sqrt{4}} \approx 33.856$
In their table, there are actually five rows but the last row has no value in its column?
I would say these are just bad papers, IMHO.
References
a Meckel, Yoav, et al. "Practical uses of genetic profile assessment in athletic training–an illustrative case study." Acta Kinesiologiae Universitatis Tartuensis 20 (2014): 25-39. (http://ojs.utlib.ee/index.php/AKUT/article/view/11961)
b Ben-Zaken, Sigal, et al. "Genetic profiles and prediction of the success of young athletes’ transition from middle-to long-distance runs: an exploratory study." Pediatric exercise science 25.3 (2013): 435-447. (https://www.ncbi.nlm.nih.gov/pubmed/23877193)

Thank you! I've been trying to make sense of this for over an hour. Now I have to spend an hour forgetting about it.


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How can myoglobin be responsible for the red color of meat if it is located in the cytoplasm?
How can myoglobin be responsible for the red color of meat if it is located in the cytoplasm, as the visible part of muscle cells is the membrane (at least as I believe)?
Sources:
https://en.wikipedia.org/wiki/Myoglobin
http://jeb.biologists.org/content/207/20/3441

Presumably for the same reason that red cells are, well, red.

— I am not a moderator. As a retired educator I believe that students learn better if they are asked to think about their questions. The additional examples I provided should suggest to you that cell membranes are effectively transparent — think about any other pigmented cell. So your question becomes one of the optical physics of biological membranes. I suggest you phrase it in those terms and submit it to a more appropriate list.

+David I don't see any example you've provided, maybe due to a server error. Secondly, I didn't know that cell membranes were transparent; in any case it would have been better if you had answered normally and not only by letting a comment. Thanks!

I am not a physicist, which is why I phrased the comment the way I did. I presume cell membranes must be transparent from examples such as haemoglobin but I cannot answer the question why, which presumably lies in the realm of biophysical optics.


text:
Is it possible that there are two people in the world who belong to a different species?
There're over 7 billion people in the world and every one of them is different from everyone else. Is it possible that there are two people so different that they belong to different species (in the sense that they cannot reproduce to produce fertile offspring)?
This doesn't have to mean that there's someone in the world who's completely unable to reproduce with everyone else, just that these two individuals are so different that they can't reproduce with each other (they can still reproduce with other people who can reproduce with the other individual - a ring species system).
I'm particularly interested in an answer based on how much the genome varies between people vs. how much they vary against our closest relatives (such as Neanderthals). For example if humans and Neanderthals share 99% of their genes, and the largest variation among current humans is 0.001% of genes, then the answer to this question would be "no".

though not an answer, you might be interested in ring species

Yes, I was originally going to phrase the question in terms of that but then forget about it. Let me edit.

I have edited your question to change genetic code to genome. If you do not understand why, please read e.g. the Wikipedia entry on the genetic code.

Your question is basically interesting, although the idea that people can belong to a different species and that mere % difference in the genome will determine the fertility of offspring seems to me naive. I think a more scientifically productive approach would be to consider known examples of interspecies crosses like that between the horse and the donkey. Then you can ask how different the genomes have to be for viable offspring and what causes offspring to be sterile. I don't know the answer but would encourage anyone who does to respond.

The question boils down to the following things:

Whether arbitrary mutations are possible. Yes, they are. (A simple proof: any rearrangements of matter that follow physical laws are possible - that's a direct consequence of physics and probability theory.) But most mutations have very low probability.
Whether further speciation is possible for humans. Yes, it is. (The proof is an unlikely and trivial example: mutating (see above) to become any other species that has existed, for example the ancestor species. We know that these species can exist. And probably an enormous number of new species are conceivable.)

From the above it follows that mutations towards speciation are possible (but improbable). So the answer is: yes, there is a very small statistical probability. (Even though some people like to claim that very small probability equals zero, but that is not correct.)
And by the way, we don't know what mutations are out there. Even if we would, we still wouldn't know much, because some speciation-relevant properties are not obvious just by looking at genotypes.

At SE we're looking for answers that provide some explanation and context. You need to explain why your answer is right, ideally with citations. Otherwise how can the poster or anyone else know whether or not you are correct? Assertions of the type you have made just don't cut it. See the Help for "how do I write a good answer?".

Edited to add proofs based on mathematics and physics.

OK. You support your premises now. I just do not agree that it boils down to the two things you mention. I think it boils down to the what determines separate species as defined by the poster "cannot reproduce to produce fertile offspring". It is my gut feeling that the variation in modern humans is less than that between humans and neanderthals or denisovians, and so the answer to his question is no. But I don't have the numbers. You might also argue that the neanderthals were different enough from us to be regarded as a separate species, but that's another question.

You are talking about how low the probability is. Yes, it is very low. But note that very low probability is not the same as zero probability. Poster asks "is it possible", i.e. is probability above zero. My proof works for any definition of "species".

At the beginning, the population of the parents who we are talking about should be made more specific. Let's limit it to adult, healthy individuals (let's skip pathologies, various kinds of random body injuries, personal sexual preferences and close relatives).
From the descendants group, let's also exclude children who would die from random causes, body injuries (unintentional :-( and intended :-((( ), genetic diseases, etc.In addition to the genetic variation (A global reference for human genetic variation), epigenetic variability (Worldwide patterns of human epigenetic variation) should also be taken into account.
If we give the most popular definition of a species (and there are very many of them), as individuals capable of giving fertile offspring, of course all humans belong to one species. Contrary to popular opinion, we are similar to one another like drops of water.

I'm not sure that I think the first two paragraphs of your answer are particularly pertinent, but at least you provide some sort of references. However your final sentence is obviously untrue: "Contrary to popular opinion, we are similar to one another like drops of water." Like it or not, some populations are very different from one another in appearance, a difference that has a genetic basis. Asserting otherwise betrays a political agenda and discredits your argument. In the context of the question all that is important is that different populations can mate and produce fertile offspring.

It is obvious that every population has a certain variation, but our impression of human diversity is illusory. It results from our perspective. Identical to us other individuals (eg penguins) are perfectly able to recognize each other. From their point of view, each penguin is different and unique. A similar situation occurs when a resident of Europe, Asia or Africa goes to another place where a different type of appearance prevails. At the beginning, everyone seems the same and only after some time begins to notice differences.

I happen to believe that we should live in racial harmony, but my points are (1) that this is a biology list, so that we should be careful to restrict ourselves to a discussion of biological facts in answer to a question that may or may not be loaded, (2) by making well-meaning but weak assertions you risk undermining the credibility of a position that may be correct/just. An example is the "like two drops of water". It would be easy for a racist to reply "No, like oil and water, which don't mix". So it is really best if social, religious and political opinions are kept off the list.

I assume that we are conducting a substantive discussion, not a worldview dispute. Hence the works cited earlier and now: How Humans Differ from Other Animals in Their Levels of Morphological Variation. I maintain my opinion: people are more similar to one another (less changeable) than most animals.


text:
DNA or enzymes — which came first?
Considering that the DNA needs enzymes, to be formed, however enzymes need DNA to be formed too. What biomolecule was created first?

If one is scientifically rigorous, the answer to this question is:

Nobody knows.

If one accepts the most commonly accepted (although not proven) view of the evolution of genomes and catalysis, the answer is:

Enzymes

Explanation
The ‘RNA world’ hypothesis, mentioned by @vkehayas, postulates that the first genome was RNA, not DNA, and the first enzymes were also RNA. DNA genomes arose later (as did protein enzymes, although the timing of that event is irrelevant to the question as originally written).
Alternative Question
If one was not aware that RNA is thought to have preceded DNA as genome, and had not been aware of catalytic RNA, then one might have asked:

Which came first, RNA or protein?

And in fact, this question was originally asked by Francis Crick in the restricted context of  the synthesis of proteins by ribosomes on mRNA and led him to remark.

“It is thus not impossible to imagine that the primitive machinery had
  no protein at all and consisted entirely of RNA.”

The later discovery of catalytic RNA provided a mechanistic basis for an original world in which RNA was a self-replicating genome.
(So the answer to the alternative question is that ‘RNA’ preceded protein.)
Supporting citations
I have kept this answer brief and only provide a single general reference because @vkehayas provides links to other questions about this topic on this list.


text:
Mutate from non-GM to GM?
Would non-GM crops such as Grains, Fruits, & Vegitables retain their non-GM make up if they were to be re-planted in soils that have been made entirely of composted GM plants and GM plant matter?
Or would the GM plant matter still retain those properties enough mutate the transplanted or planted crop?

Can you please rephrase Or would composted GM plant and non organic plant matters still retain those properties enough mutate the transplanted or planted crop?. It is unclear to me

I am not sure I understand the question, but it appears to me as the question is about labelling and therefore is a question of policy and not biology. I am therefore voting to close.

You've rephrased the sentence I asked you too but I still don't get it. Maybe you misunderstand the concept of mutation. Note by the way, the in a single reproductive event, several mutations will typically happen. See for example estimates in humans from this question

I have reworded your question to relate solely to genetic manipulation (GM) as your question relates to mutation. Organic is a subjective concept, and this site is not about labels on food, which in any case vary between countries.

@Remi.b I modified the question so it is no longer about food labelling. I assume the poster knows nothing about genetic transformation, but you could interpret this as a question whether DNA from dead plants in the soil could transform growing plants, perhaps with the aid of soil bacteria. I'd still be happy to close under the portmanteau homework/lack of research heading.

@Remi.b  Tough crowd. Yes i'm very new and i'm keen on learning new things. obviously i'm behind the curve. i do appreciate assistance with the edit.  this is a Q&A site and i believe the question to be a valid one.
[eartheasy.com guide to compost][1]
[wisegeeks.org definition of flash freezing][2]
[wikipedia.org/wiki/Food_fortification][3]

@JeffreyBoettger Don't worry. It is not easy to ask a clear question, esp. as a new user. Do you think your question could be rephrased as Can plants absorb DNA from the soil and integrate it into their genome?. If you think it is not a goo reformulation, can you explain why?

@jamesqf no need to be rude. How is this related to religion? And, anyway, there isn't a "Religion SE", there are at least 4 I can think of for various different religions. Yes, the OP is showing ignorance, but there's nothing wrong with that! Not everyone is a biologist and, sadly, given the misinformation spread about what GM actually is, this sort of confusion is reasonable from a lay person.

@terdon: I don't see any rudeness.  WRT to religion, that is what most of the objections to GMO are based on.  Not reason or logic, but just the faith-based belief that GMOs are somehow "unclean".

@jamesqf the rudeness lies in ascribing motives with no evidence. Yes, some people object to GM based on religion. Many object for socioeconomic reasons. Others because the idea of fiddling with things we don't understand perfectly scares them.  What bothered me was your off-hand dismissal of "go ask on 'religion SE'" (a site which doesn't even exist). You are unlikely to find anyone who objects to religion as vehemently as I do, which might be part of why I found it insulting, but I don't think it's polite or fair to make such assumptions with not evidence.

The process of genetically modifying crops is performed in a lab. Genes would not leak into planted organic crops from compost any more than they would move from decomposing soil nematodes, earthworms, or manure. So no, organic plants would not be genetically modified. However, the labeling of a crop as "organic" is not always standardized, so it could be a cause of concern for some people who do not understand the process.

This is called horizontal gene transfer. In general, it's quite difficult to get a plant or animal to pick up foreign DNA and integrate it into its own genome, requiring special reagents and laboratory conditions. That's why we didn't have GMO fifty years ago. Note that you will spend your entire life consuming plants and animals for food, but you won't integrate cow, apple, or potato DNA into your own genome.
However, some viruses and bacteria can and do swap DNA with each other, and with their host organisms. In particular viruses can carry DNA into eukaryotic cells, and can even integrate the DNA into the host genome. Specially engineered bacteria and viruses are typically used as the vectors to create GMO in the first place. There has been concern about horizontal gene transfer from GMO organisms, but it's widely thought that it would be rare enough to not be a significant hazard. As far as I know there in nothing about GMO that would make them more susceptible to horizontal gene transfer in your compost pile than non-GMO.

It has been brought to my attention through further research on this subject matter that it is possible to obtain " DNA into your own genome"    http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.503.7552&rep=rep1&type=pdf.                                                    As specified from minute 23:00 to 23:38 https://www.youtube.com/watch?v=gjNtyFtJdho " the aleuts are so dependant & so integrated with the marine ecosystem that in fact their  tissues the same carbon 14 molecule reservoir as the sea lion."

Neither of those references say anything about integrating non-human DNA from food into human DNA. The thesis by Rubicz is just tracing the influences of surrounding human populations on Aleut genetics, that is, determining to what degree they are intermarrying with Russian and other neighboring native populations. The YouTube video doesn't say anything about integrating DNA either. Integrating carbon molecules from your food into your body tissue is very different from integrating their DNA into your genome. Carbon in itself doesn't carry any genetic information.

Should I remove comment and question all together? And ask the question of “How do carbon molecules enter human body tissue from a food source.”

That's up to you. That's certainly a very different question from the one you originally asked here.


text:
Why is it possible to calculate the equilibrium potential of an ion using the Nernst equation from empirical measurements in the cell at rest?
In trying to understand the Nernst and GHK equations, I've hit upon a snag somewhere deep in my understanding of the subject matter.
Scenario 1: when calculating the membrane potential of a living cell at rest we use the Goldman equation. This requires us to measure both the concentrations of the ions and the membrane's permeability to said ions, at rest (at least for the concentrations).
Scenario 2: given two cells separated by a membrane (as in Figure 3 here), with a different concentration of KCl in each cell, and having the membrane permeable only to K ions, we can compute the equilibrium membrane potential using the concentrations of the K ions - after the system has reached equilibrium.
So far so good. Here's my question:
Given a living cell at rest with all its ion concentrations, the Nernst equation is used to compute the equilibrium potential of a single ion, using the concentrations at rest. Why is this allowed? As I understand it, the concentrations as measured are what the cell "decides" them to be - it can change the permeabilities of the channels, or create more pumps, etc. - and then we'll measure different ion concentrations at rest. And these concentrations will change if a cell decides to open or close some channels (which is what happens to create the action potential). But the concentrations that are used as input for Nernst's equations should be measured at the actual, not just the steady state, equilibrium (right?).
So, why can we use the steady state measurements to derive the equilibrium potentials?

Excellent question! The answer is actually a really cool and crucially important detail about membrane potentials and the movement of ions. Basically, the electric force is very strong. You don't actually need to move many ions for the membrane potential to fluctuate dramatically. The number of ions that "move" to establish equilibrium is tiny compared to the actual concentrations. That's why the Nernst and GHK equations are so powerful: what really matters is the relative permeability of different ions and the gross concentration differences, not the changes in their concentration that occur when, for example, voltage-gated channels open during an action potential.
You can calculate just how many ions have to move, which depends on the size of the cell. Here is a nice example from the reference I have linked below:

For a typical cell, 1 microcoulomb of charge (6 × 10^12 monovalent ions) per square centimeter of membrane, transferred from one side of the membrane to the other, changes the membrane potential by roughly 1 V. This means, for example, that in a spherical cell of diameter 10 μm, the number of K+ ions that have to flow out to alter the membrane potential by 100 mV is only about 1/100,000 of the total number of K+ ions in the cytosol.

Therefore to answer your question: why is it allowed to use the resting concentrations? Because the concentrations of the ions don't change by more than 1/100,000 fold with a 100mV swing in potential, and there isn't much impact on the GHK/Nernst equation from a change this small. For example, as the voltage goes from ~-70mV when a fairly typical neuron is at rest (and the membrane is most permeable to K+), up to maybe +30mV at the peak of an action potential (and the membrane is most permeable to Na+), only a "few" sodium ions actually cross the membrane, so maybe the internal sodium concentration changes from 10mM to 10.0001mM. The thing that changes most during an action potential is not the actual concentrations, only the permeability to different ions.
Maybe an additional misconception you have is about the cell "deciding" what the concentrations are. Indeed, if the concentrations of particular ions changed dramatically, it would be necessary to recompute equilibrium potentials. The key concept is that those concentrations don't change much during normal functioning of the cell, and they don't have to change much to observe big changes in membrane potential. An excitable cell uses those swings in membrane potential as the signal, rather than the concentrations of the ions. One exception is calcium, see the note at the end.
Reference:
Alberts, B., Johnson, A., Lewis, J., Raff, M., Roberts, K., & Walter, P. (2002). Ion channels and the electrical properties of membranes.
(as a side note, movement of ions does matter over a longer time scale, which is why it is necessary for the Na+/K+ pump to constantly operate to keep the membrane potential steady, and some ions like Ca2+ are at such low concentrations normally that the influx of calcium can be substantial relative to the resting concentration, which is partly why calcium is so powerful as a second messenger and why calcium chelating components of the cell are important)

Thank you for your prompt response, but unfortunately I don't understand how this relates to the question. Can you elaborate more, please?

@VladimirGritsenko I made an edit to try to connect it more explicitly to your original question. Does this make sense? If not, perhaps I am misunderstanding your question, can you clarify?

I think I understand now - since the factor that most affects membrane potential are permeabilities, not concentrations, (and thus concentrations change very little during an AP), we can treat the steady state as a very close approximation to equilibrium?

@VladimirGritsenko Mostly right - steady state and equilibrium are the same thing, but you are probably thinking about "rest" or a cell in the absence of external input. There is a new steady state/equilibrium voltage any time something happens to change the permeabilities. Ions will flow until that new equilibrium is reached, but it doesn't take the movement of very many ions and it isn't enough to appreciably change the concentrations.


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In myosin II are regulatory and essential light chains calcium binding proteins or sites of phosphorylation?
According to my medical physiology by Rhodes and Bell their description is as follows:

the essential light chain is necessary for myosin stability, and the other chain called the regulatory light chain is phosphorylated during muscle activity and serves to modulate muscle function*

However, according to molecular biology 4th edition:
it states that the light chains both exert their function via Calcium binding, they make no mention of phosphorylation.
So do light chains regulate myosin by calcium binding, phosphorylation or both ?

The answer is both, the regulatory light chains , regulate myosin by phosphorylation which  can be dependent or independent of $\ce{Ca^2+}$.
Medical Physiology:

The activity of the myosin regulatory light chain is in turn regulated through phosphorylation by $\ce{Ca^2+}$ -dependent and $\ce{Ca^2+}$ -independent kinases.

Source claiming calcium is essential for phosphorylation in tarantula skeletal muscle:

Contraction is modulated in many striated muscles by $\ce{Ca^2+}$-calmodulin dependent phosphorylation of the myosin regulatory light chain (RLC) by myosin light chain kinase.

Calcium independent phosphorylation of regulatory protein by MLCK4:

We find that MLCK4 is also expressed abundantly in cardiac muscle, and structural analyses indicate that it is a $\ce{Ca^2+}$/calmodulin (CaM)-independent kinase, in contrast to $\ce{Ca^2+}$/CaM-stimulated cMLCK.

thank you for the answer! Does the calcium binding and/ or phosphorylation change the confirmation so as to modify the ATPase or the actin binding site ?

Read the section below figure 11.27 at https://www.ncbi.nlm.nih.gov/books/NBK9961/


text:
What does it mean for sodium and water reabsorption to be "coupled" in the nephron?
If sodium is transported across the tubule membrane down the concentration gradient established via the $Na^+$/$K^+$ exchanger via symport with glucose and antiport with hydrogen, and water is transported via aquaporins...how is this coupled? They don't have the same transporter. This seems like they are independent.
Is this related to concentration gradients (more $Na^+$ in epithelial cells --> water wants to follow osmotically)? If so, why is $Na^+$ controlling whether water is reabsorbed or secreted, and not some other ion?


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

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

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

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

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

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


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What is the brain's preferred energy source? Glucose or ketones?
As with all cells in our body, I know that the brain can get fed from both glucose and ketones, so my question is, given both of them, which one would the brain prefer to utilize first?

Can you explain what you mean by "preferred"? The brain mostly metabolizes glucose only.

By preferred, I mean, given the choice for either, which one would it use first  @BryanKrause

"The brain gets a portion of its fuel requirements from ketone bodies when glucose is less available than normal (e.g., during fasting, strenuous exercise, low carbohydrate, ketogenic diet and in neonates)" from https://en.wikipedia.org/wiki/Ketone_bodies @BryanKrause

Exactly - it is only during those special cases that ketones are even available for metabolism, and the reason ketones are made available is a drop in blood glucose below sufficient levels.

My question comes from learning about https://en.wikipedia.org/wiki/Caprylic_acid which apparently increases ketone bodies in your body even if you aren't in one of those states @BryanKrause

First of all, for those readers with less knowledge of the general principles of biology, I want to state an important, even if obvious, point: The brain doesn't
"prefer" anything. Despite being the smartest organ in the body, it is subjected (like any other biological system) to changes in the concentrations of the substances in question, that is, glucose and ketone bodies.
According to a study in rats from 2010, it seems that ketone bodies suppress glucose metabolism in order to conserve glucose when its concentration is too low for the body to be used regularly. Therefore, the ketone bodies are regarded as neuroprotective, since their metabolism prevents the brain cells from starving.
Another study in rats from 2013 emphasizes this point further. Please note the following excerpt from the discussion section:
The brain's ability to switch from glucose oxidation towards ketone bodies requires a type of ‘cerebral metabolic adaptation'. This process is not well understood but is thought to be highly associated with the duration and level of ketosis. Ketones are considered to supply up to 70% of the total energy demands once maximal metabolic adaptation occurs. Blood ketones become elevated during prolonged fasting or with a ketogenic diet reaching a state [of] ketosis and glucose sparing. During this process, monoca[r]boxylic transporters upregulate at the blood–brain barrier with increasing demand for ketone utilization by brain. Recently, investigators have recognized additional therapeutic properties of ketosis, such as neuroprotection after stroke or injury. What remains unclear is whether the neuroprotective or therapeutic properties of ketosis is as a result of changes in the regulation of metabolic signaling pathways...
This means that when the balance of concentrations shifts toward the ketone bodies, they will have precedence over glucose in order to conserve the latter. The mechanism is probably upregulation of ketone bodies receptors and transporters that increase its transport into the brain, as stated above.
Therefore, when the brain is given both ketone bodies and glucose (which actually happens in the fasted state - ketone bodies transport and metabolism in the brain begins when blood glucose is low, not zero), there will be "preference" for the ketone bodies, but this depends on the glucose concentration. If it shifts back, above a certain glucose concentration glucose metabolism is supposed to be renewed.

Thanks for your answer, I guess this partly answers my question. What's left to know is how much of a difference in concentration does it need to be in order for the brain to use ketones, like someone doing low-carb and consuming Caprylic-Acid, how low carb does that person need to go to get the brain consuming ketone bodies.

Long story short. Burning glucose it’s the easiest, most « efficient » and laziest way your body supply energy to your brain. Fat on the other hand is harder to break for the body. But, the ketones produced during the combustion of the fat cells have unsuspected properties making them of a much greater benefit to the brain health, with benefits that includes: better decision making, acute intuition and sereinity.
I hope this helps.
YO
P.s; Fat is the preferred source of energy but the body will use glucose first (Fast for 3 days, enter ketosis, maintains carb intake under 50g and enjoy feeding u brain ketones for as long as you can). Plus, while writing I remembered that the brain is made out of fat to start with. What is more natural, intuitive and logic than feeding the brain with what look alike?!

Welcome to Biology.SE. We're looking for long factual answers that provide explanation, context, and references to reliable sources. Don't just give your opinion — instead explain why your answer is right with appropriate citations. Answers that don't include explanations may be removed especially when they are a poor duplicate of an already existing answer. Please take the [tour] and then consult the [help] pages for additional advice on [Answer] effectively on this site and then delete or [edit] your answer accordingly.


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Is there human Anatomy software that provides great detail?
Is there Anatomy software that is exact representation of human body, like let's say virtual reality tour inside human body from head to foot, detailing all organs even small, covering all systems, nervous, blood vessels, muscular, skeleton systems, could be zoomed even to deepest skin layers, neurons,  that can be applied unapplied like layers in Photoshop?
If this does not exist, then which is the most advanced human Anatomy software?

try this page https://www.google.fr/search?q=very+detailed+human+Anatomy+software%3F&oq=very+detailed+human+Anatomy+software%3F&aqs=chrome..69i57j69i60&sourceid=chrome&ie=UTF-8

In English the indefinite article "a" is never used with the word "software". (The definite article can be used in appropriate circumstances.) I have corrected your question accordingly.

Isn't the question off topic?

My favorite is this one and it is quite detailed and interactive. It does not use virtual reality technology, but it is a good resource for anatomy students. Then there is this one, but it is more virtually animated and less real. Hope this helps!


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Secondary structure and function in mRNA and single-stranded virus RNA
Although some mRNAs and the RNA of single-stranded RNA viruses do have some secondary structure, this is much less than in rRNA, tRNA etc.
Why is this so? What prevents their folding to the extent of the RNAs mentioned?
And surely mRNA cannot have very much secondary structure. It enters the ribosome in a linear fashion, so if it bound to itself, wouldn’t that stop translation?

To the best of my knowledge all RNA has secondary structure. Some conformations are stablized by RNA binding proteins.

Welcome to SE Biology. As a new user we expect you to read the Tour and take a moment to find out how the site operates. An appropriate place to start is the Help on "How do I ask a good question?" where you will read "Have you thoroughly searched for an answer before asking your question? ...Tell us what you found and why it didn’t meet your needs." If you had researched you would have found that mRNA has secondary structure. What have you read about viral RNA?

I didn't assert anything, I am just clueless, because if it self bound, wouldn't it stop the translation if it entered the ribosome? As far as I know, there is no mechanism to unbind mRNA.

The details of how viruses function are not agreed on. If you ask any questions about HIV, such as basic things like what it looks like, what genes it has, or the mechanism of action, you will get dozens of conflicting answers even if you ask the most senior PhD biologists. So there is no scientific answer to your questions.

I have modified your question to remove the false premise I criticized. I think this rescues it to the extent I shall post a brief answer myself. I have withdrawn my close vote. You are free to roll back the edit if you really wish.

"As far as I know there is no mechanism to unbind mRNA". I am afraid your knowledge is deficient.  I assume that by "unbind" you mean break the hydrogen bonds that are responsible for base pairing in mRNA. Even the DNA double-helix with long stretches of perfect base pairing can be unwound by DNA polymerase, RNA ploymerase, restriction enzymes, transcription factors etc. The essence of life is that it is dynamic, and at the molecular level this is contributed to by the weak interactions responsible for the higher order structure of proteins and nucleic acids. These can be made, and broken.

Well, for me unbinding or breaking a hydrogen bomb means, for me, exciting the system such that there is no more binding. The strength, for me, should not matter for the naming of the reaction. But, if you say so I have to accept, as it might be a practice in the field. And the answer is exactly what I was looking for. Now, I can research things further.

Summary

Both mRNA and the RNA of ssRNA viruses can have secondary structure, which is often important in regulating translation
The extent of secondary structure of RNAs depends on the base composition and sequence, so that RNAs of various degrees of folding are possible.
Weak RNA–RNA hydrogen bonding can be competed for by weak RNA–protein interactions, so that a dynamic situation is possible — secondary structure in some circumstances which is unwound in others.

Evidence for Secondary Structure in mRNA and viral RNAs
Work in the late 1960s and early 1970s on the translation of the polycistronic single-stranded virus RNAs (MS2, R17,Qβ etc.) provided evidence for their secondary structure. The extent of masking of the ribosome binding sites (Shine and Dalgarno regions) of different cistrons affected their translation, and treatments and mutations that destroyed the secondary structure stimulated translation. This 1980 paper by Iserentant and Fiers and this 1982 paper by Hall et al. provide entries to that literature.
Eukaryotic mRNAs do not normally have ribosome binding sites, although those of certain RNA viruses like polio do, and these have distinctive secondary structure (ribosome landing pad) — see e.g. this paper from Sonenberg’s group. However the majority of eukaryotic mRNAs have extensive secondary structure at their 5'-ends, which requires a specific helicase — initiation factor eIF4A — in conjunction with eIF4B and eIF4H to unwind — see e.g. Svitkin et al., RNA (2001).
Secondary Structure varies with Sequence
A little reflection is enough to convince oneself that the extent of self-folding of a single-stranded RNA depends on its nucleotide sequence. The extent of hydrogen bonding of, for example, an (AG)n polymer (A does not base-pair with G in a Watson–Crick helix) would be expected to be much less than that of an (AU)n polymer where A–U base pairing can occur. Likewise, continuous stretches of complementary bases are likely to result in extra stabilization by base stacking, and hence in a more stable secondary structure than the same number of interspersed base pairs. The fact that the secondary structure of a mRNA can be altered by changing the nucleotide sequence without changing the amino acid sequence of the protein product is illustrated by the algorithm described in this paper by Gaspar et al., Nucleic Acids Research, (2013).
Competition by Proteins
It has already been mentioned that proteins (eIF4A and other initiation factors) are involved in unwinding eukaryotic mRNA, and there are numerous examples of the interaction of proteins with specific nucleic acid structures (including the ribosomal landing pad (aka internal ribosome entry site — IRES), previously mentioned above and shown below).

[IRES for Hepatitis C virus RNA, showing areas of interaction with various proteins. From Hellen and Sarnow, Genes and Development (2001)]
The general concern that mRNA secondary structure would impede secondary structure has some basis, but the movement of the ribosome can disrupt secondary structure, as the initial RNA phage experiments indicated. One should remember that after each peptide bond is formed, the ribosome causes the translocation of the mRNA by three nucleotides with respect to the A and P sites, so that it is continuously applying a motive force to the mRNA.
Turning to viruses, tobacco mosaic virus (TMV) — a positive single-stranded RNA virus — was the first virus the structure of which was determined by X-ray crystallography. There is, therefore, a wealth of detail as to the organization of RNA and protein in its virion — this PDB ‘Molecule of the Month’ article (illustrated below with the RNA in red) is quite accessible (in both senses). (A schematic of the virion of a different virus — vesicular stomatitis virus — VSV — is also shown.)

The assembly of the TMV virion involves initial protein self-assembly followed by the looped RNA (secondary structure) being fed in and winding round the inner core. The secondary structure origin of assembly of the TMV RNA is shown below.


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Frequency of nucleotide sequences of specific length in DNA

How frequently would you find the nucleotide sequence GGATATCCGC (5' to 3' direction) by chance in a DNA molecule?
On average, how many times do you expect to find a specific 20 nucleotide sequence in a genome with a total size of 4 x 109 base pairs?

Since that probability of finding each base pair in its given position is 1 in 4, thus the total probability of finding that particular sequence would be $0.25^{10}$
But how do I approach the second problem?
TIA

While the 'background' of this question is biology, it's actually a pure combinatorics & statistics question. I'd recommend asking this on a different SE site.

Apply the frequency you calculated in the first part (reworked for a 20mer) to an actual length. May be easier if you work it as 1 in x, then all you have to do divide the genome length l by x. Try my teaching site: https://www.mvls.gla.ac.uk/Teaching/SLS-GMC/ren.html.


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Why do sparrows jump instead of walk when they are not flying?
I want to talk about sparrows, one of the most common birds around the world. I noticed that when one slowly walks into them (so that they are not frightened enough to fly away), these tiny birds would jump away, rather than walk away, as if they are not able to walk.
Why?

That’s the way God made them.

As pointed out by @jamesqf in the comment below, there exist many birds like quail and pheasants that run and walk rather than hop. Also, there are several flightless birds like  ostriches, emus, rheas that do the same. But it is also true that sparrows don't walk or run but hop. The question now is- why?
There is an interesting fact- both Quail and Pheasant are ground nesting birds.
Now, the reason why we do not see sparrows running like pheasants is because sparrows rely more on their ability to fly for survival and getting around. So, a sparrow will rather fly the distance than run. The reason for this might be its smaller size which makes it more efficient and safe during flight.
But the question is- why don't sparrows walk? Why do they hop? Quails (video) and Pheasants(video) certainly walk even for short distance.
Just before a flight, all birds jump to power their flight. So, if a sparrow hops around rather than walking around, it can convert any of these jumps into a full flight in the case of an unexpected need. This again comes down to sparrow's heavy reliance on flight to escape danger. Because of their light weight, hopping rather than walking is less costly for a sparrows.
Whereas in a normal situation, Quails and Pheasants would rather run to build the necessary  momentum to initiate a flight. But they walk even for shorter distance because they are heavier than a sparrow, and walking for them is more efficient than hopping. But in worst case scenario, even birds like Quails can simply jump into a flight, as can be seen in this video if you watch it in slow motion.
Edit: another factor that might influence whether a certain bird hops or walks is the irregularity of the terrain with respect to the size of the bird. The terrain is relatively more irregular for smaller birds (there are obstacles like twigs, stones, grass etc), hence making hopping a better option than walking.
There are many kinds of birds that each choose whether to walk or hop. Here i present a small categorization with video evidence to bring out some pattern if any. You might need to watch some of the videos in slow motion.
Birds that hop:

sparrows
American robin
blue jays

Birds that walk

Crow
magpie
Quail
Pheasant
an unknown small bird that the video title says is American robin but which walks

You have a very long answer, but very little of it answers the main question. This is ok, except that your actual answer is not supported by any citations or links to sources. Please [edit] your post to include support. Thank you

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

An avian researcher states that birds with short necks hop as it allows them to turn around faster and benefits their 360' field of vision so it aids their agility and perception, wheras walking birds have longer necks and can see around them while walking.
https://www.researchgate.net/publication/264193094_Biped_gait_in_birds_some_observations
https://www.researchgate.net/publication/233934125_Hopping_in_Birds_is_The_Choice_of_Gait_Influenced_by_Cervical_Mobility_and_Field_of_Vision
Perhaps walking distracts vision for animals that can't bob their heads like pigeons, the stiller the eyes are, the clearer the peripheral vision.
As pro ornithologists states that birds that are adapted for tree life and constant branch hopping also hop around on the ground, however birds that spend a lot of time on the ground save energy by walking.
https://ww2.rspb.org.uk/birds-and-wildlife/bird-and-wildlife-guides/ask-an-expert/previous/hop_or_run.aspx


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Cellular respiration and membrane surface protons
The final product of cellular respiration is the proton motive force, formed by protons pumped out of the membrane and by the voltage due to all charges. While Mitchell’s original theory considered pumped protons released immediately to the bulk external medium, that has been criticized. Today there is a good amount of research showing that protons tend to remain confined in 2D in proximity with the membrane (one review can be found here). This would explain how certain extremophiles can survive in very basic niches (poor in protons), where the proton motive force, defined from the bulk pH, cannot sustain ATP synthesis.
As far as I have been able to discover, the existence of such “surface protons” has only been shown in vitro (e.g. in a sustained lipid bilayer).
Is there any experimental evidence of such “surface protons” in intact cells, i.e. in vivo?

I have take the liberty to edit question (you can always revert it if you disagree) to give it more focus. I particularly dislike questions asking for the "consensus in the field", and this is not necessary — all that will serve is evidence, and that is assumed to include citations. Remember, at one time the consensus here was squiggle-X! In fact, this is a biophysics question, although of considerable interest, I think is likely beyond the scope of all but one or two of the members of this list. You are probably as well doing your own search for papers citing the one you mentioned.


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Are vacuum centrifuges the same as normal centrifuges?
I came across a method that used a vacuum centrifuge:
Carvalho et al. 2012. The diversity, antimicrobial and anticancer activity of endophytic fungi associated with the medicinal plant Stryphnodendron adstringens (Mart.) Coville (Fabaceae) from the Brazilian savannah. Symbiosis 57(2):95-107

Five-millimetre-diameter plugs of each filamentous endophytic fungus were inoculated into the centres of Petri dishes (60 mm diameter, 20 ml PDA). The plates were incubated at 25±2 °C for 15 days. The culture materials from each Petri dish were cut and transferred to 50-ml vial tubes containing 35 ml of ethanol (PA, ≥99.8 %, Vetec, Brazil). After 48 h at 10°C, the organic phase was decanted and the solvent was removed under a vacuum centrifuge at 35°C

I couldn't find information online as to whether a vacuum centrifuge is the same as a normal centrifuge. Is there a difference?

It would be helpful if you shared a link or citation to the study

Also, we would need to know what model centrifuge you have in your lab to definitively say whether it is the same as what is being described.

I presume they're trying to use a non-brand name for what everyone I know calls a SpeedVac.

A "normal" centrifuge = piece of laboratory equipment, driven by a motor, which spins liquid samples at high speed to allow centripetal acceleration to separate substances of greater and lesser density.
Without further information regarding the method you read, a "vacuum" centrifuge might be a reference to one of the following:

Ultracentrifuge

a centrifuge optimized for spinning a rotor at very high speeds.

The vacuum ultracentrifuge was invented by Edward Greydon Pickels in the Physics Department at the University of Virginia. It was his contribution of the vacuum which allowed a reduction in friction generated at high speeds. Vacuum systems also enabled the maintenance of constant temperature across the sample, eliminating convection currents that interfered with the interpretation of sedimentation results

Centrifugal evaporator

device used in chemical and biochemical laboratories for the efficient and gentle evaporation of solvents from many samples at the same time.

The system works by lowering the pressure in the centrifuge system [via a vacuum pump] - as the pressure drops so does the boiling point of the solvent(s) in the system.
The centrifugal force generated by spinning the centrifuge rotor creates a pressure gradient within the solvent contained in the tubes or vials, this means that the samples boil from the top down, helping to prevent "bumping".

"Vacuum Concentrators"

Use a combination of centrifugal force, vacuum and heat to speed evaporation of multiple small samples. They offer maximum throughput required by biology, microbiology, biochemistry, pharmaceutical research and analytical chemistry laboratories

UPDATE: Based on updated info from the OP quoting the method of the paper, it sounds like they're most likely talking about using a centrifugal evaporator to remove solvent.

"Five-millimetre-diameter plugs of each filamentous endophytic fungus were inoculated into the centres of Petri dishes (60 mm diameter, 20 ml PDA). The plates were incubated at 25±2 °C for 15 days. The culture materials from each Petri dish were cut and transferred to 50-ml vial tubes containing 35 ml of ethanol (PA, ≥99.8 %, Vetec, Brazil). After 48 h at 10 °C, the organic phase was decanted and the solvent was removed under a vacuum centrifuge at 35 °C (Santiago et al. 2012)."

from "The diversity, antimicrobial and anticancer activity of endophytic fungi associated with the medicinal plant Stryphnodendron adstringens (Mart.) Coville (Fabaceae) from the Brazilian Savannah." 2012 paper by Carvalho et al.

@Emil Thanks. So follow these steps: 1. Add the pertinent parts of this info to your question (not just in the comments). 2. Go to the references section of  Carvalho paper; Locate Santiago et al. 2012 citation, search for it on Google Scholar, and see if they have more info. Update w/ that too.

@tomd thanks for the info! I really knew little about the history of centrifuges before writing this answer (and now seeing your references). I also found a good "story" that walks through the history of the centrifuge. I'll paraphrase some major quotes from it in a subsequent comment.

"In 1926 Svedberg received a Nobel Prize for the invention of the ultracentrifuge. Svedbergs ultracentrifuge, however, was essentially an analytical instrument. The transition from these analytical instruments to modern preparative ultracentrifuges came through the efforts of Emile Henriot, who achieved high rotation speeds using a bearingless top, driven & supported by compressed air. Edward Pickels & Johannes Bauer build the first high-speed vacuum centrifuge suitable for the study of filterable viruses. Later, Pickels developed the more convenient, electrically driven ultracentrifuge.


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Where can I get fungal extracts?
Does anyone know how I can get fungal extracts from fungal isolates? I have isolates in PDA slants and I'm gonna need to get their respective extracts to impregnate in sterile discs. I'm a novice in the field and all the help I can get will be greatly appreciated.