texts: Why can't we find a broad spectrum antiviral drug to viruses like antibiotics to bacteria?

texts:
Antibiotics have a very broad spectrum because they attack the metabolism pathways many bacteria share. For example, penicillin inhibits peptidoglycan synthesis, which is vital for formation of cell wall of gram-positive bacteria, so penicillin can be used to treat gram-positive bacteria infections. Streptomycin inhibits protein synthesis of bacteria. Because all the bacteria need protein synthesis, streptomycin has a very broad spectrum.

Why doesn't such strategy work on viruses? For example, nucleos(t)ide analogues can inhibit the RNA synthesis of RdRp. Most riboviruses (except hepatitis D virus) require a viral RdRp to replicate their genome. But why can't nucleos(t)ide analogues be used as broad spectrum anti-riboviral drugs even we have found very good drugs such as Sovaldi?


texts: Do model species evolve away from Batesian mimics?

texts: Batesian mimics - palatable mimics of a poisonous species - are detrimental to the species they imitate. Predators learn which species are unpalatable by tasting some. If Batesian mimics are rare or nonexistent, few if any of these samples will be tasty and predators'll quickly learn to leave this species alone.  But if Batesian mimics are common, predators have good chance of being rewarded for attacking things that resemble the model species.  It would seem that an overabundance of mimics would create a condition for the model species to evolve to visually differenciate itself: is there any evidence that this occurs?


texts: Why do living fossils like crocodiles remain so constant and not evolve?

texts: Crocodiles have supposedly remained unchanged for millions of years, and several other species are considered as "living fossils". How do such species remain so constant over time given that they will have had so much time to accumulate new mutations?


texts: Pregnancy from two parents with incompatible blood types, can it lead to complications?

texts:
Let's take Alice and Bob, both healthy adult human specimens. Alice is (A-). Bob is (B+).

If they decide to have a child, would Alice's pregnancy involve any additional risk or complications compared with, say, Abraham and Abigail's pregnancy (both AB+)?

Background

I overheard claims that pregnancies from parents with different blood groups can lead to complications in pregnancy due to interactions between the mother and the child's blood. (These claims were not officially backed, otherwise I would have brought them up on Skeptics.SE). The explanations and my Google browsing went beyond my biology knowledge. I know these pregnancies must be viable, since the AB group exists, but I do not know if there are edge cases that lead to complications that would not happen with same blood type parents.

Related question

Can the mating of a couple with Rhesus positive and negative blood types result in miscarriage? This question only asks about Rh+ and only if it leads to miscarriage.


texts: Is there any free software similar to CellDesigner that allows me to represent large networks of biochemical reactions in the human body?

texts: I continually have to review multiple articles, in multiple journals. These articles present how various enzymes, proteins, lipids, carbohydrates, etc. intervene in the processes that lead to certain pathologies (generally neurodegenerative). I have used Celldesigner and Freeplane, but Freeplane is very general software and CellDesigner provides reduced work spaces. I would like to know if there is any other free software that works for this purpose (I usually work in Linux).


texts: There is a problem of devastating mold in ventilation of old buildings in Europe. I guess tardigrades might be better solution because chemicals is not a good idea for ventilation because people are breathing with this air.


texts: Are there sterilisation methods that do not denature proteins as heat does?

texts:
Context:
Most countries require milk to be sterilised through radiation or heat to remove possible harmful bacteria. Both of these processes denature the proteins in the milk (ref).

Are there methods of sterilisation that will not denature proteins?


texts: What is the surface area to volume (SA:V) ratio of a red blood cell?

texts: According to this author, red blood cells (RBCs) are biconcave to allow easier bending. The standard explanation in biology for higher surface area to volume ratios is that it improves reaction rates. When a RBC squeezes through narrow veins I imagine that it gets deformed. Considering that a RBC's function is to exchange oxygen in narrow capillaries, I was wondering whether it is appropriate to reason that the biconcave shape promotes gas exchange. So what is the SA:V of a biconcave RBC and by how much does the SA:V change depending on where in the body the RBC is traveling?


texts: What concentration of sugar is optimal for baker's yeast fermentation?

texts: I'd like to do an experiment on what concentration of sugar would be best for fastest yeast fermentation. I'm thinking to put some active dry yeast into different concentrations of sugar water and measure the fermentation activity after a certain amount of time (like 15 minutes or so). I know at a certain concentration the yeast will effectively die as the sugar solution becomes hypertonic, but I don't really know what range would be most effective right now. Any papers I've found are on yeast for alcohol.


texts: What is the half-life of dNTPs at 95 °C?

texts: I'm looking for the half-life of dNTPs, either as a whole or broken into individual bases, at 95 °C (or similar). A titration would be great if that exists. I can provide more specifics if need be, but broadly the idea would be 'able to polymerize' vs. 'unable'.


texts: Pipetting: do human experimenters need liquid class information?

texts:
I've been working on a protocol standardization project where, among other things, we want protocols to be able to be run equivalently by both humans and robots.
Something that I've noticed in doing so is that there's a radically different amount of information typically assumed needed by a human vs. a robot when it comes to pipetting.
With a robot, it is generally recommended to understand the nature of the liquid thoroughly, specify the liquid class (which includes information on viscosity, volatility, polarity, etc), and do quite a bit of quality control to make sure than when you want to pipette 100 µL you actually get 100 µL. A typical example is shown on this page by Hamilton.
With a human experimenter, however, the protocol pretty much always just says "pipette 100 µL" and assumes that the human can figure out all of the potential issues that we have to be so careful for with robots.
Is this actually a safe assumption, or just something that we don't typically check during protocol development for humans? Is it really intuitively obvious for nearly all liquids, or should our protocols be providing more guidance for humans as well?


texts: Flexor/extensor group in lower arm and limb bud rotation

texts: Have the flexor and extensor groups in the lower arm have rotated laterally 90° towards the humerus epicondyles independently of the rest of the lower arm? The pre-axial and post-axial veins are still in aligned with their segments in the upper arm, so I assume that the muscle mass that forms the flexor group was initially located on the anterior side aligned with the flexors in the upper arm. The other option is the entire lower arm rotating relative to the upper arm but it seems less likely.


texts: What is the derivation of the rules of proportionality between axon conduction velocity and diameter?

texts:
We have been told that in myelinated fibres, conduction velocity is proportional to the diameter of the axon. In unmyelinated fibres, velocity is proportional to the square root of the diameter.

Can this be derived from use of the length constant? The length constant being the distance over which the voltage drops to 37% (1/e) of its original value.

length constant = sq.root(transmembrane resistance/longitudinal resistance)

I understand that longitudinal resistance would (if analogous to electrical resistance in a wire) be inversely proportional to the cross-sectional area, which would lead to being inversely proportional to the square of the diameter (from area = pi.r^2).


texts: Exactly which amino acids are phosphorylated in higher plants during state transitions?

texts: I know it is usually stated as the threonine residue near the N-terminus of either light harvesting complex (lhc) b1 or lhcb2, but if this is somehow lost, say in a mutant, is the system flexible enough to compensate by phosphorylation at another site such as a serine residue or will state transitions just cease?


texts: Why is the 3'UTR region highly methylated in most of the human genes?

texts: Most of the human genes are found to be highly methylated in their 3'UTR region (0.8-0.9%). I was wondering if there is any specific reason for this?


texts: Why do neutrophils need to die after pathogen phagocytosis?

texts:
From referenced article below, neutrophils need to be removed because its granule contents and oxygen metabolites (used for killing phagocytosed pathogen) are harmful to the surrounding tissue. Thus, the process used for this is that neutrophils undergo apoptosis, then are phagocytosed by macrophages.

However, I do not see why neutrophils need to first die to be phagocytosed by macrophages. Do macrophages not phagocytose living cells?

Source: http://www.sciencebrainwaves.com/the-immune-cell-the-neutrophil-the-good-the-bad-or-the-ugly/

  Once the pathogens have been dealt with, and to completely resolve inflammation, neutrophils need to be cleared from the tissue... For removal, neutrophils firstly need to die.


texts: Can hair follicle miniaturisation affect hair color?

texts: We all know that follicle miniaturisation affects hair texture, making it look thinner(the hair shaft/root itself will be thinner), but does it affect hair color as well? So if an individual has thick mid brown hair in his/her 20s, hair follicle miniaturisation kicks in in the 40s. Does this person's hair look light brownish due to hair follicles being thinner, fewer, and they reflect light better? Is my hypothesis right? A thinner hair shaft/follicle reflects light better, ie becomes more transparent? Is this broscience on my part, or am I right? I have a hard time believing that a person's hair color doesn't look lighter/more frail if you will, after miniaturisation kicks in.


texts: During blood pressure measurement, when the flow within the arteries of the arm is interrupted, how is blood flow redistributed to the rest of the circulatory system? Is it possible that more blood enters the carotid arteries and therefore causes an increase in blood flow in the brain?


texts: What makes tones sufficiently useful that it would lead to the evolution of tonal processing?

texts:
I will define a "tone" as  a steady periodic sound. As an example, I consider a sinusoidal wave to be a tone. By "tonal processing", I mean ratio relationships between the notes. For instance, if I play 220Hz sine wave then a 440Hz wave will be perceived as an octave higher.

I don't understand why humans have the ability to perceive frequency relationships between tones. I have read several evolutionary anthropology books like The Singing Neanderthal and Finding Our Tongues and, between these two books, they suggest that the obvious evolutionary purpose of music is for communication. Each author takes a slightly different approach but the basic underlying point remains that tonal processing exists because it gives us advantageous communication abilities. But even accepting this hypothesis, it doesn't explain why humans have a tonal processing mechanism that is specific enough to perceive ratio differences between notes. The tonotopic organization of both the basilar membrane and the precortical auditory pathways might partially account for the machinery used for tonal processing and why the advanced forms in music could have developed. But this still leaves us with the question as to why would such information be useful?

I remember reading somewhere one person hypothesized that the purpose of perceiving these differences was to identify "relative pitch", i.e. the ability to identify or re-create a given musical note by comparing it to a reference note and identifying the interval between those two notes. But this hypothesis doesn't really make complete sense to me because it doesn't explain why the brin can have such specificity when identifying the ratio between two notes.

Another phenomena that seems pertinent is the idea of a "drifting reference point" which Glimcher discusses in Foundations of Neuroeconomic  Analysis. In Chapter 12, he explains how our perception of color isn't fixed but depends on context and in this sense drifts. IIRC, there is a literature that discusses possible neural mechanisms for this. Perhaps something similar would be relevant here for explaining why humans can process tones so precisely.

My Question:

What are the accepted arguments for why would ratios between tones would be be useful information for social communication?

Just to clarify, I am expecting the answer to this question to involve a discussion of the physical properties of tones and why a hominid brain would find this useful information for communication purposes.


texts: Does digestion require hydrochloric acid?

texts:
Would our digestion function any differently if we secreted something else, like sulfuric or nitric acid, instead? I'd assume an acidic environment may be required, but not sure if chloride is also required as well!

Perhaps we just use it out of convenience—e.g., presumably blood serum $$\left[\ce{SO4^2-}\right] + \left[\ce{NO3-}\right] \ll \left[\ce{Cl-}\right]$$ and channeling polyatomic ions across the membrane may be significantly more difficult than doing the same for chloride as well!

*Edit: In fact, Wikipedia states

  In the stomach, chief cells release pepsinogen. This zymogen is activated by hydrochloric acid (HCl), which is released from parietal cells in the stomach lining. The hormone gastrin and the vagus nerve trigger the release of both pepsinogen and HCl from the stomach lining when food is ingested. Hydrochloric acid creates an acidic environment, which allows pepsinogen to unfold and cleave itself in an autocatalytic fashion, thereby generating pepsin (the active form). Pepsin cleaves the 44 amino acids from pepsinogen to create more pepsin.

So, while maybe something like $\ce{H2SO4}$ or $\ce{HNO3}$ could work too, hydrochloric acid is just more convenient to use?


texts: Why oxLDL accumulate to form foam cells?

texts:
In atherosclerosis, why macrophage store all the cholesterol from oxLDL inside, and turns to foam cell, and not just degrade it and going back to blood? (there are some amount that leave the plaque, but much more stay (J Clin Invest. 2011 May;121(5):2025-36. doi: 10.1172/JCI43802. Epub 2011 Apr 18.))

Reading a lot about atherosclerosis, but no explanation about why macrophages stay there and form a plaque, instead leave or at least break the cholesterol.


texts:
How is photosynthesis observed?

Say I have plants A and B, and I want to find how fast they are able to turn carbon dioxide into oxygen. How would I experiment this?
Say I have one plant A, which has two kinds of leafs B and C. I hypothesize the B-leafs produce oxygen faster than the C-leafs. What kind of experiment could I set up to test this?


texts: Can a stationary eye with a moving pupil exist?

texts: I am making a sci-fi web-comic set on an alien world and I thought up an idea for an eye that works much like an eye from a mammal, but instead of moving the whole eye, only the pupil moves. This idea sprouted from the eyes of mantis, though their moving pupil is possible because of their compound eyes, I would like to know if my idea could be physically possible. (And yes I know this is a strange question compared to others on this site).


texts: How many genes does D. melanogaster have?

texts: Obviously there is no 100% exact number, but I came across this on flybase, the gold standard for annotation. I am confused now. "Genes located to the genome", is that what I am looking for? If so, what does "Genes not located to the genome" mean?


texts: Explanation of protocol in DNA extraction experiment

texts:
In the Materials and Methods section of this paper on DNA extraction and analysis from hair I do not understand some parts of their protocol methods. In particular:

  "The digested hair solution was then extracted twice with two volumes of phenol saturated by Tris-EDTA (TE) buffer (Sigma), and once with two volumes of chloroform. "

How do the volumes of phenol and chloroform come into play? I know they are used for an organic-solvent extraction, but what was the actual procedure used, i.e., the steps for adding each chemical?

Another question I had was on the buffer they used:

  "0.01 M Tris-HCL(ph8), 0.005 M EDTA, 0.1 M NaC1, 0.039 M DTT, 2% SDS"

That whole combination would be the "Tris buffer" then yes? And the proteinase K would then be added to some of this buffer to digest the hair?


texts: Has a mammalian species that cannot interbreed with another ever been selectively bred in isolation from it so that it can?

texts: Take two mammalian species that cannot interbreed by any means. Has one ever been selectively bred in isolation from the other so that eventually it can?


texts: Can androgen-insensitive genetic-males get pregnant?

texts:
According to the linked report, people with androgen insensitivity syndrome appear as male, but have both feminine and masculine outer genitalia.

However, I was not able to find out whether their internal reproductive system is functional, i.e., if these people have a functional uterus.

Is it possible for such a person to get pregnant?


texts:
I was going through this paper, but did not understand a term.
What is the meaning of functional screen?

(I am not a biology student, I don't understand much, and a small simple explanation would be enough)


texts: How many dinosaur genes are in a chicken genome?

texts:
I read recently that we can "work back" to a dinosaur by selectively turning off certain genes in chickens, and we were able to create a chicken with a snout instead of a beak.

How many dinosaur genes are still hanging around in a chicken genome? I understand there is a lot of overlap for vertebrates, but shouldn't these genes have shuffled out over time?

Otherwise, couldn't we work back to worm or even earlier life forms? Is the whole history of a creature's evolution contained in its genome?

Edit This was a news story about a month ago. Here's excerpts from the BBC's write-up: "Chicken grows face of dinosaur: A chicken embryo with a dinosaur-like snout instead of a beak has been developed by scientists"

  To understand how one changed into another, a team has been tampering
  with the molecular processes that make up a beak in chickens.

  By doing so, they have managed to create a chicken embryo with a
  dinosaur-like snout and palate, similar to that of small feathered
  dinosaurs like Velociraptor. The results are published in the journal
  Evolution.

Link to Evolution paper included.

Also this piece from about a year ago: "Paleontologist Jack Horner is hard at work trying to turn a chicken into a dinosaur"

  In 2009, the world’s most famous paleontologist made a bold claim. In
  “How to Build a Dinosaur,” Jack Horner proposed re-creating a small
  dinosaur by reactivating ancient DNA found in its descendants,
  chickens.

  The toothy snout is already here. At his lab at Harvard Medical
  School, Matthew Harris has made chicken embryos that express ancient
  genes for the growth of conical, crocodile-like teeth.


texts:
I recall learning that humans have 5 senses, but that may have been an over-simplification to focus on the most notable ones, or simply that no others were known about at the time. Wikipedia says:

Although traditionally around five human senses were known (namely sight, smell, touch, taste, and hearing), it is now recognized that there are many more.

Is there a known, discrete number of senses (and, if so, how many are there)?
Note: If there's disagreement in the scientific community about the answer it would be interesting to learn what most biologists consider most plausible.


texts: Terrarium Compatibility: Millipedes with Carnivorous Plants?

texts:
I have a child that loves his large millipedes (Desert Millipedes) and Venus Fly Traps.  He's also been wanting to get some Sundew Savages.  Given this little collection and his real enjoyment of terrariums, we're curious if we could consolidate his millipedes into a terrarium with these carnivorous plants without causing harm to either of them.

We keep the millipedes fed well with decomposing plant material, but weren't sure if they'd go wild after the fresh plants... and then of course if they would try to do that, could these plants harm the millipedes?

In the end I fear there will be some problems here and wanted to check to see if anyone knows about this compatibility before we dive in and have our hopes dashed.


texts: Large plasmid ligation: do I need alkaline phosphatase?

texts: I have a doubt about a protocol I'm using for a ligation of a very large plasmid (15kbp circa) with an insert: after digestion with a single-cut enzyme (sticky ends), the protocol passes directly to the purification of the plasmid without making any alkaline phosphatase. My doubt is during the ligation, the plasmid will self-ligated without accepting the insert?. Am I mistaken or the protocol is incorrect?


texts: Do leaves grow larger by adding cells at the centre or at the edge?

texts:
I'm writing a paper on wrinkling of plant leaves. For biological and physical background information, I would like to know whether leaves grow by adding cells at the edge, at the center or in a completely different way. Since I need to confirm any information I get, please do not write opinions or guesses. It would be great if someone could find a reliable source with link since all my researches didn't lead to a good answer to this question.
Thanks in advance!


texts: Which organisms have their cell wall made of polysaccharides and amino acids?

texts:
I came across a question which somewhat goes like

  In which of the following kingdom, most of the members have a cell wall made of polysaccharide and amino acids ? - Monera or Fungi.

To me it looks like both are correct answers because both are having hetero polymers of glucose and amine. Please enlighten me if I am wrong.


texts: Role of non-inflammation in H.Pylori positive people

texts:
Quoted from Saudi J Gastroenterol. 2009 Jul; 15(3): 201–207 publication :

  Approximately 50% (over 3 billion) of the world populations are known
  to be infected with Helicobacter pylori, mainly in the developing
  countries. Among those, hundreds of millions of people develop peptic
  ulceration during their lifetime ....

I know that many people have H. pylori in their stomach, however, just a small percentage of them develop peptic ulceration. Does anyone know the role of this? Why don't more people develop any symptoms?


texts: What is the difference between abiogenesis and spontaneous generation?

texts:
As we all should know, abiogenesis and spontaneous generation are far from identical. For one, spontaneous generation was disproven with Pasteur, and abiogenesis seems to be a solid scientific theory. However, one can loosely summarize both as "the emergence of life from non-living materials" which, at the very least, is confusing for the layman.

My question is: What truly differentiates abiogenesis from spontaneous generation? For example, if abiogenesis were to happen again, how would we differentiate the two terms?

Is time the most contributing factor (abiogenesis happened over hundreds of millions of years)? Or the fact that abiogenesis generates "primitive organisms", while spontaneous generation assumes the generation of evolved, complex organisms?


texts: Are There Rules for How Proteins Are Formed?

texts:
Proteins are formed by stringing together different amino acids.  Different amino acids have different properties (such as being attracted to or repelled by water, positively or negatively charged, large, small, etc.).

What I would like to know is if there are any rules or principles which determine how amino acids are strung together to form proteins?  If so, what are those rules and can anyone recommend any resources where I can learn more about this subject?

Thanks.

MORE DETAILS

Let me try and explain what I am trying to ask.  I understand that there are rules of grammar that I need to follow in order to put together a well formed English sentence.  I am wondering if there is something akin to that for stringing together amino acids in order to create a 'well-formed' protein. (I am NOT referring to how DNA codes for amino acids).

For instance, imagine that I wanted to create a new protein and I had a pile of amino acids at my disposal.  It seems to me that if I understood the principles and rules by which amino acid chains work then I could know which amino acids to string together and the order in which to string them together in order to create the particular type of protein that I wish to create.

This is similar to how I can string together letters and words to form well formed sentences or how I can string together well-formed sentences to create logical arguments.  There's a logic to how to form a sentence and a different logic for how to form an argument -- and it is possible to discern that logic by studying syntax and reasonable arguments.

I assume the same is true for proteins.  There must be some sort of logic or system for how amino acids are strung together -- some sort of connection between the 3-dimension, functional protein and the nature of the properties of the individual amino acids and how they are organized together.  What I am wondering is whether or not we have any idea what that system of logic is.


texts: Hydrogen peroxide decomposition and catalase uses

texts:
All google searches have simply returned more info on catalase. I'm looking for a catalyst that isn't found inside living organisms which  can break down H2O2. Looking for any resources to look at, or just examples of other catalysts.

Side question since I don't want to clutter with a new thread.
Can catalase be used for anything other than the decomposition of h2o2?


texts: How does the immune system distinguish between a TH1 and a TH2 response?

texts:
Hello and thanks for taking the time to read my post.

I know that naive T-Cells (T0) can be induced to become mature T-Helper cells (TH1 or TH2)
by induction with either IL2 or IL4.

IL2+  TH0 -> TH1   Humoral (antibody-mediated)
IL4+  TH0 -> TH2   Cell Mediated response

But what I would like to know is the causal chain that creates the IL2 and IL4 cytokines.

The reason I ask is because one clinician has reported that Azythromycin(an anti biotic) is useful in treating COVID-19(a virus) disease and was wondering if the immune system might become confused about whether should develop a TH1 or TH2 response.

If you can provide me with any help I would greatly appreciate it

Thanks in Advance
Michael Mckeon


texts: Is it possible to sequence rRNA directly, that is, using the ribosome rather than the DNA from the nucleus? For example, this paper, Complete nucleotide sequence of a 16s rRNA gene from E. coli,  suggests that it uses DNA to find the sequence. Would it be possible to isolate the rRNA and derive the sequence from that?


texts: Camera and the eye (filtering information)

texts:
How does a camera recreate a very similar perceptual stimulus (through the photo) for us to see compared to the person directly viewing the object of interest with their eye?

My questions stems from what I've already learned about the visual system:

1) The retina receives information from the external world, but not 100% of the photons (the form of this information).

2) This information is then passed to the superior colliculus where further filtering, and changes to this information occurs.

3) It is next passed to the thalamus and then relays it to the occiptal lobe which interprets this information (another filtering process) causing us to perceive the external world in a particular way.

Is it that the camera captures the light information on the film that would otherwise have made contact with our retina? And then upon seeing the photo, that same information (or similar since the camera would not exactly capture it, but enough for us to notice that we are seeing what we expected to see) finally makes contact with the retina and then the process occurs as described in the points above?

If so, how does the camera do this!? Because I thought the camera would also be selective in which light it uses to recreate these images. And I'm incredibly doubtful that a camera simulates the filtering processes of the human brain. Moreover, it doesn't make sense that we would perceive the expected image in the photo if it was already based on the filtered information.

I am very curious and very confused. :)

-N


texts: Does DNA influence death (e.g. by cell aging)

texts:
I know that we age because of errors in the cell replication process and these errors eventually leads to death.

If we exclude environmental factors, are there any other factors that can cause these errors? Is there for instance some kind of "programming" in our DNA of our death?


texts: What are known methods of non-surgically disabling neural tracts/pathways (esp. Corpus Callosum)?

texts:
I think I've read something about usage of TTX and optogenetics, but I cannot find the papers for either anymore. Any reference would be much appreciated, especially those concerning mice and the Corpus Callosum.

Edit: By surgical, I mean to say methods that are based on actually cutting through the tract using a surgical knife (or lasers etcetera), as is commonly found in literature.


texts: Batch several sequences for absent restriction sites

texts:
I have a collection of about 120 7kB sequences I would like to check for ether a list of specific restriction sites, or what restriction sites might be absent in all of them.

Is there a app or library that can do this?

So far I've only found systems that can do 1 or 2 sequences at a time.

Possible workaround:
Right now I'm trying to concatenate all the sequences together (about 850Mb) and then using Bio.Restrictions methods of the Biopython libraries.  As I kept running into memory overflow problems, I'm refining the search make a new RestrictionBatch based on 4-5 enzymes that are absent and introduce-able into 3-4 test sequences.

Even then I'm running into crashes, which will probably mean that I take the complete set and test over five or so combined strings.

Before I completely go re-inventing the wheel, can anyone let me know of something that already does this?  I don't really care about the language, we have Python, .Net, Java, R, and MatLab "covered" across the lab.


texts: How does the inability to produce vitamin C helped weight gain?

texts:
I recently wondered how do dogs cope without vitamin C intake like us.

A few Wikipedia pages later, I learned that our dry-nosed ancestors lost about two-thirds of the gene responsible for vitamin C synthesis some 63 millions years ago. And then this passage:

  Johnson et al. have hypothesized that the mutation of the GULOP (pseudogene that produces L-gulonolactone oxidase) so that it stopped producing GULO may have been of benefit to early primates by increasing uric acid levels and enhancing fructose effects on weight gain and fat accumulation. With a shortage of food supplies this gave mutants survival advantage.

(Wikipedia: L-gulonolactone oxidase)

I'm curious about the interaction (GULO/uric acid/fructose effects/fat storage) quoted above.


texts: Supposedly (consciouss) movement is started in the cerebral cortex. But some time ago I've read a research which stated it might be possible some movements (not specified which ones, probably mean automated ones) start in the brain stem. That research was in one of those research file websites, it wasnt an article and it didnt have any mainstream visibility. Then I didnt hear anything more in this line, but you hear many times about these babies "born without a brain" who lacks most of its brain, 80% of its brain or who lacks cerebral cortex yet they move. Where are those movements started? Can motor neurons in the brain stem start movements?


texts:
Can someone please let me know what insect this is?

This may be something very common, but this is the first time I have seen them and that too suddenly in a large number.

They were mostly on plants, but the only clear image I got was of the one sitting on this bike. Image captured in Vasai, India

(Brought into Biology SE from https://i.stack.imgur.com/RHcrg.jpg)


texts: What does (G+) (G++) in terms of male mutation rate and male-heterogametic XY-system?

texts:
What's the expression for $\alpha_m$ in case of male-heterogametic XY systems (G+)?

Derive the corresponding $\alpha_m$ expression of for (sic) male-heterogametic XY systems (G++)

I have absolutely no idea what they mean with G+ and G++ in the exercises. I have searched the whole Internet and the lecture slides for this but I think I am going crazy. Has it something to do with the gametes? Anyone who knows?
Thanks in advance!


texts: Why do mammals produce more carbon dioxide than insects?

texts: I understand that mammals produce more carbon dioxide than insects on a gram per gram basis, but why is that? I'm thinking it might be because mammals are warm-blooded, which require more energy consumption. Could it also be due to the fact that insects are less active than mammals? AKA they do less work?


texts: Do primitive streak cells remain with us?

texts:
Is there any evidence or experiments to show, that cells from the primitive streak in humans remain in us in a super low quantity? For example I've read of teratomas https://www.healthline.com/health/teratoma#causes
Is it possible for these cells to still be within all of us in our tail bones yet cause no problems for the majority? Do we still have these 'primitive streak cells' in other areas of our body that don't cause problems?
Also, where does the primitive streak end at in the human body? Does a small part of it stay with us in a tiny place somewhere?


texts:
I found this (mite?) on my head skin close to hair. Is it a common dust mite or something else? Photographs under a simple microscope (10x objective) are below. Size is in the order of tenths of mm. Some of the hair sticking out are as long as the body. It was not that translucent enough to be well visible in bright field, only as a black spot.

Also, what could be the large round white object on the back an the brown spot to the left and right in the first picture?

Note: One month ago I was treated for scabies and my head is still itching (although scabies is supposed to not affect heads of adults). But I do not think this is Sarcoptes and I think it likely does not cause the itching.


texts: Using an analytical balance (0.0000 precision) to measure µg (micrograms)?

texts: If i needed to prepare 200µg/ml of proteinase K, and the proteinase K  was in a solid powder form, would I  have to weight out 200 µg using an analytical balance, and if so, is it possible with a balance that only goes up to four decimal places? (i.e. 0.0000) I assumed 1 microgram is 1×10-6 gram and therefore 0.000001 gram.


texts: Why do some white blood cells have lobed nuclei?

texts: Several types of white blood cells (eg Neutrophils) have lobed nuclei.  Is this for a functional reason?  I have seen people refer to structural differences in the lobes as indicative of problems, but I have not been able to find why the nuclei form into lobes in the first place.  Is this known?


texts: Biological meaning of Lotka-Volterra Jacobian matrices

texts:
In a book about community ecology, I learned about Lotka-Volterra models and dynamic food web models (I am not an ecologist in the first place).

In one of the chapters, a Jacobian matrix of partial derivatives of the Lotka-Volterra model at equilibrium densities is given:
\begin{bmatrix}-&-&0&0\\+&0&-&0\\0&+&0&-\\0&0&+&0\end{bmatrix}
where + and – represent positive or negative values.

This matrix is later interpreted in terms of direction of trophic links in a food web, but the reasoning allowing to jump form one to the other is not detailed.
So what is the biological meaning of these values?


texts: Why we aren't making Darwin's theory a Law

texts:
I was wandering about darwin's theory which is controversial theory and there are no enough evidence to prove it right or falsify it, since I'm a biology student so i studied basic way of a hypothesis going to be a law ,the last thing to be a law is theory...am i right?
Hmmm if yes then it's been about more than 130 years since darwin died and there is still no response to his theory?why this taking so long? Are we supporting Darwin because if we don't then we gonna recreate our basic embryology and evolution? If no then why we aren't making it a scientific law?


texts:
Vitamin D acts in a way which to me is counterintuitive. It functionally supplemets Parathormone. It in the intestinal tract steps up calcium absorption by altering nuclear gene expression and also prevents calcium excretion in kidneys. All of this is understandable. But it also, like parathormone, steps up osteoclast action in bone (actually steps up both osteoclast and osteoblast, but the osteoclast action is increased more to result in net bone resorption). This means that Vitamin D increases blood calcium level by increasing bone resorption.

Then how does Vitamin D help in improving bone density, bone strength and prevent rickets or osteoporosis? All of these would require bone deposition rather than resorption.


texts: Neuron activity on body parts measurable?

texts:
Is it possible to measure the neuron activity on body parts like the back or the arm? Or is this done already?

Of course neuron activity can be measured on the scalp using an EEG. I wonder if similar technology could be used to do the same on other parts of the body.

I know there is EMG which measures muscle activity and  that's also easier to measure as the voltages are multiple orders of magnitude higher. But I imagine that one could get much richer data by directly sampling neuron activity.


texts: With radiation therapy, could some of the radiation used cause new mutations in non-cancerous cells that are near the tumour that is being irradiated? If so could these new mutations lead to new cancerous cell colonies (which might later metastasize)?


texts: Why eukaryotes have three different types of cytoskeleton filaments?

texts: Ok: IF, microtubules and microfilaments serve different purposes. But whats the biological advantage of having these three types over other organisms? I don't know if I'm being clear.


texts:
I stumbled upon a birch growing in sandy soil in a coniferous forest in central Russia.
It looks like over time the tree trunk got bent towards the trail and one of the branches became the new trunk as it now grows straight up, whereas the old trunk is pointing sideways.1

The tree isn't dead, I visited that place during summer time and it was covered with green foliage.

I'm wondering what's the name of such phenomena, how common it is and what usually causes the tree "to change it's mind"?

1. I apologize in advance if the terminology I'm using is inaccurate, so feel free to edit my question.


texts: Is DNA actually like source code repository?

texts:
So after reading articles like "People Use Just 8.2% of Their DNA" etc., and thinking a bit... I got this idea:

What if DNA is actually like a software source code repository? You know, it has "master" branch - which is most stable and up-to-date version of program but also it has other branches, experimental ones and of course it has huge amount of "junk" - i.e. backed up version of files from previous changes to code that is not used in any way in actual program.

So what if first primitive single-cellar organisms had super primitive and very short DNA, then it got improved, but original DNA was not erased, but backed up every time new mutation (commit in software SCCS) appeared.

Theoretically, the more primitive organism is, the shorter DNA it should have. For example, some very old sharks that still survive from Mesozoic era should have shorter DNA than modern sharks... Is this confirmed by actual experiments?

This explains why human DNA is mostly so similar to dog DNA, fish DNA etc. Because we all evolved from same primitive cells! Base of our "repository" was same!

Also this explains why human embryo come though all this steps of been single cell, multi-cell, fish, amphibian, mammal etc.

I'm no expert in biology by any means, and I suspect that this idea was around for long time, but I'm not sure... What do you think?


texts: What are the chemicals present in body of paddle worm which makes it show biolumniscence

texts:
Paddle worm is the light emitting species i want to know that
1. What are the chemicals which produce this light?
2. For what purpose it needs this light?


texts: Does neural network in brain form cycles?

texts:
In other words is it possible for dendrite of neuron A to be connected with axon of neuron B and at the same time dendrite of neuron B to be connections with axon of neuron A (or similarly for any larger number of neurons)?

If so, are there any statistical data on number of such cycles in average human brain?


texts:
There is the common belief that

  Chewing gum takes 7 years to digest

But is this actually true? Does it really stick to your intestines for 7 years, or is it processed like all foods, except it isn't broken down and is excreted soon after digestion?


texts: Does playing music during sleep actually suppress rather than rouse the brain?

texts:
I've long been interested in the effect of music/sound on dreaming, and even built 2 apps that play music during REM period. Now I'm looking at this article about FMRI studies of a sleeping brain, and I see that it mentions:

  During wakefulness, acoustic stimulation elicits activation of the
  auditory cortex (red). Similar stimulation during light NREM sleep
  stage 2 evokes transient downregulation of widespread cortical areas
  (blue), supposedly a sleep protective mechanism.

and

  Acoustic stimulation in REM (rapid eye movement) sleep revealed a
  different brain activation pattern during phasic and tonic REM
  periods, with strongest suppression of cortical reactivity during
  phasic REM sleep periods.

Can I interpret information on that site to suggest that auditory stimulation during sleep actually makes the brain less active? Can one assume that playing audio during REM would disrupt dreaming due to transient downregulation?


texts: Brain regeneration - book recommendation

texts:
Searching for an up-to-date book on regenerative brain medicine with a focus on stem cell therapy.
Also interesting in genetic engineering of neuronal stem cells for this purpose.

Alternatively, a comprehensive review article is welcomed too.


texts: Is there any evidence that soft tissue can be preserved for 65m+ years and if not what hypotheses exist to explain it?

texts: I read an article on howstuffworks.com and they mentioned how we have found soft tissue in dinosaurs. According to the article even Mummies and Mammoths have no soft tissue left. Is there any evidence that soft tissue can remain intact this long even under perfect conditions? and if not what are some hypotheses that could explain it?


texts:
A seizure is basically a synchronized firing of neurons as opposed to the more common unsynchronized firing taking place during normal neural activities. However, I am uncertain if the exact technical definition of a seizure restricts this synchronized nerve activity to the brain only .

I wonder whether a wave of synchronized firing can propagate up to or occur in the area of brain controlling the blood pressure level and hence affect the blood pressure of the individual going through a seizure? Or can the impact of a seizure propagate to other areas and hence affect other functions like cardio-vascular system and hence the blood pressure? Or can neurons connected to heart, but not necessarily present in brain, exhibit synchronization as in a seizure and thereby affect the blood pressure of an individual undergoing seizure?

Summarizing my question is: can seizures affect blood pressure?


texts: Facial uniqueness of some animals of the same species

texts:
Do birds of the same species ,such as each pigeon that we see in cities, have unique facial geometries (facial phenotypes) regardless of their feather ,colors, spots etc? Sometimes it is almost impossible to distinguish two pigeons between each other just looking at their facial structure and curvature of their heads.

Human face has evolved with countless of varieties such as shape of nose, distance between the eyes, proportion of mouth and the nose etc.
Billions of humans have existed so far and billions of humans will ever exist each have unique facial features.

However some animals of the same species (birds like pigeons, baby chicks, fish species like sardines and sea bream etc) look like sharing a limited amount of variations in their facial geometries therefore they become distinguishable only because of their colors, patterns etc. I know that mammals such as apes or dogs have unique faces almost  as distinctive as humans. I also know that human brain is already attuned to distinguish differences in human faces more than any other animal.

What I would like to understand whether all pigeons have existed so far and will exist furthermore have unique facial geometries like humans? Or do they all differ in millimetric level which cannot be captured by naked human eyes? Can two pigeons(or sardines) of the same species share exact same facial geometries unlike humans?  I couldn't have satisfactory answers in this subject so far. Can you please explain?


texts: What is this plant with distinctive leaves?

texts:
Location: Vienna, Austria

Leaf size: two big thumbnails

Plant height: large thumb

I assumed it might have come from the seeds of some fruit I ate.  I consulted these websites:

https://www.baumkunde.de/baumbestimmung/

http://www.blattbestimmung.de/blattform-herzfoermig

but found nothing. Perhaps it is neither shrub nor tree.

Edit:
This is how it looks now, ten days later:


texts: At how low a temperature can a snake like a copperhead survive in winter /

texts: Copperheads were very common here, less so now that more people have moved into the subdivision. My yard is sort of an oasis for them . E. TX is expecting record cold in spite of climate change so I was covering a few things; damn ground orchids are already blooming. I let the camellias take care of themselves; there are too many to cover. I lifted a large plastic tub that was inverted on the ground , a smallish ,dormant copperhead fell out on the leaf covered ground. He did not move so I built a well insulated enclosure over him ( with an exit). Temp is now 40 F but 30 is expected tonight and mid 20's the next two nights. I am wondering at his chances of survival ; I estimate his body temperature will get to mid 30's F. I had thought they went deep into animal boroughs; we have many voles and some moles ( because there are not enough copperheads left to keep them under control). I have a well insulated garden shed that will probably not go below 50 F but I don't want to move him unless it is an emergency.


texts: What did we learn with Nazi human experimentation?

texts:
Was there actually any useful knowledge gained from the Nazi experiments on human test subjects? Wikipedia cites freezing and phosphine gas reactions, but I would like to know other potential results from the Nazis.

At a first glance, it looks like the problem is that, in addition to the obvious ethical issues, there was also a lack if scientific rigor. Is this true or can some results actually be of some use?


texts: There are numerous examples of sessile animals (sponges, barnacles etc.) but are there any examples of motile plants? If not, why not? Surely mobility would have conferred an evolutionary advantage to some plant species. I am specifically thinking of locomotion here.


texts: If evolution is not about increased complexity, why does so much complexity evolve?

texts:
In my last question I asked why we don't see increased complexity in artificial life simulations of evolution. It seems I had fallen for a common misconception, that evolution was about improvement by increasing complexity. One comment discussing that post read

  "... he [David Deutsch] is falling for one of the biggest
  misconceptions about evolution that you can, that evolution is about
  improvement. Evolution has simply only ever been about change..."

However, when you look at the history of life you see increases in complexity. You see this increasing complexity evolving over billions of years, suggesting that it requires an explanation.

My question
If evolution is not about increasing complexity then how does so much complexity evolve?


texts: Do Fatty Acid Synthase Inhibitors Selectively induce Apoptosis in Cancer cells without inducing the same in healthy human cells?

texts: Do Fatty Acid Synthase (FAS) Inhibitors (e.g. cerulenin) selectively induce apoptosis in cancer cells without inducing the same in healthy human cells?


texts:
We are probably all familiar with the dangers of asbestos in your rooftop or in various pieces of old equipment as it has been shown that the microscopic asbestos particles reach our lungs and can then potentially cause lung cancer.

Now smoking (for example) can cause cancer because of various carcinogens chemically interacting with DNA, but how can these asbestos particles, specifically prized for being quite unreactive, damage DNA to the point of triggering cancer?


texts: How do receptors lose their sensitivity?

texts:
Recently, I learned that one of the causes of Type II diabetes is that insulin receptors on cell surfaces lose their sensitivity due to long-term high exposure to insulin (which occurs as a result of high blood sugar).

How do receptors (like that for insulin) become more resistant to ligands? Is the receptor itself getting damaged? If so, how, and why don't other frequently activated proteins/receptors (like GPCR's) also get damaged? If not, then how does the cell become more "resistant" to insulin?


texts: Is it correct that the nicotinic acetylcholine receptor has nothing to do with Dopamin?

texts:
As I know Dopamine is almost exclusively produced via metabotropic receptors, is it possible for a nicotinic ACH receptor to influence a dopamineric neuron?
Can a nicotinic ACH receptor cause a dopamineric synapse to create dopamine?

Unfortunately I can't find anything about it.

Edit: rephrasing my question:  Do 2-neural systems exist where neuron A has a nACH-R and neuron B has a dopamineric receptor? And do dopamineric nikotinic ACH-R exist (receptors which react to dopamine)?


texts:
There are heterotrophic prokaryotes, and there are autotrophic prokaryotes. In the autotrophic prokaryotes category, there are photoautotrophic prokaryotes and chemotrophic prokaryotes.

Are there chemotrophic eukaryotes?


texts:
I am trying to better understand the relationship between the placement of EEG electrodes and the quality of the "brainwave" signals they produce.

There is the standard 10-20 system which has me wondering a few things:

Is the 10-20 system just a standard based on uniform distribution of the electrodes (so as to maximize brain signal collection)? Is it safe to assume one could increase the "density" of electrodes (again, in uniform distribution) and receive better quality signals? In other words, how does the placement & quantity of electrodes affect the quality of the information that can be obtain via EEG?
Is electrode gel strictly necessary? Is the gel used for adhesion, conductivity or both? I can't imagine it helps much with conductivity seeing the most of the scalp is (typically) covered with hair?


texts: Are some non-coding RNA spliced like mRNA? I tried to find some information but I don't find anything...


texts: Evolution: Can the genotype frequencies change, but the allele frequencies remain constant?

texts:
If a population isn't evolving because it's in Hardy-Weinberg (HW) equilibrium, then I know that both genotype and allele frequencies must stay constant.
My question is, can evolution still not occur even if Hardy-Weinberg conditions aren't met? In all of my books, the conclusion seems to be that if HW conditions are met, then evolution doesn't occur. However, they don't clarify if HW conditions being met is both a necessary and sufficient condition for evolution to not occur (they only imply that it's sufficient).
Any thoughts?


texts:
I have a plasmid with the P15A origin which apparently has a low copy number (see here). This would explain why my purification yeilds for subsequent digestion are low (gel shows the plasmid after digestion and clean-up with 5µl being loaded). I am currently growing my E. coli containing plasmid up in 5mls overnight before doing a miniprep. My question is should I grow my 5ml cultures up for longer (2 days) or just give it up and do a larger amount for Midiprep.

I am also curious as to what actually controls the plasmid copy number inside cells. An explanation of the regulation of plasmid copy number would be much appreciated.


texts:
Viruses at this period of time do not fit the current definition of life.

Much of the reasoning behind this is that we currently believe that all life must be made up of cells.

Also, many biologist/scientists say that viruses are not living because all they are is just chemicals carrying out their predefined chemistry.

Has anyone every considered the fact that cells, the supposed building blocks of life, themselves simply only carry out predefined chemical actions? All actions cells carry out are chemically driven, not consciously or spiritually driven. Cells do not make choices, they follow chemical directions present in their DNA and RNA. Viruses act very similarly, following the action transcribed in their DNA or RNA.

How can we really even draw a defined line of what life is?


texts: How should you choose from the various methods of constrained ordination?

texts:
I have a bacterial OTU matrix from various sample points and times. So for each sample I have the sequence counts across the various OTUs that they were assigned to.

I also have a corresponding matrix of abiotic variables including temperature, pH and the concentrations of a range of nutrient compounds. This data was collected at the same time as the bacterial OTUs.

This is a tutorial written by the people behind the R package 'vegan', it offers three separate types of constrained ordination. I just don't understand what the differences are between these and what would suit my data-set best. There is not much advice out there at all for this sort of thing so any help would be appreciated.


texts: Do we understand how (some) proteins work?

texts:
Are there proteins whose operation we can describe from first principles using chemistry or physics?

I've had introductory college courses in biology, and some classes in neuroscience, so I know that the behavior or purpose of many proteins is well characterized. But the descriptions of how proteins work—at least in what I've read—are always sort of similar and vague, “X binds to Y and the shape of the protein changes, which does Z”. At the level of the material I'm reading, I wouldn't necessarily expect much more, but I am curious whether researchers actually have a more detailed understanding of how proteins work. Can we describe the way that (some) proteins work in the same way that an engineer can describe how an internal combustion engine works?


texts: Why there is no neurovascular drug-eluting stent?

texts: I'm researching on neurovascular stents and I'm wondering why there is not much about drug-eluting neurovascular flow diverters in the literature? I read in an article that it's because of complex shape of cerebral arteries in comparison to cardiovascular system. But it doesn't look satisfactory to me. Any suggestion or idea is appreciated.


texts:
Technically brain is composed of billions of neurons for abstract computation of the world around us. I am bit confused that how does emotions such as fear/anger gets simulated by amygdala, which is nothing more then bunch of specialized neurons but we feel it as penalty. What part of the brain senses response from amygdala and determines ok, thats fear/penalty? What exactly is penalty?
How does human comprehend reward and penalty (fear/anger/sorrow)?


texts: Troubleshooting SDS-PAGE of trypsin-treated BSA

texts: I am currently working on SDS-PAGE technique having 20% acrylamide concentration for hydrolyzed BSA protein. Here I attached a gel photo for trypsin hydrolyzed BSA. I don't know , is it a good result and how do I interpreted this result?


texts: What instances are there in which two species share the same binomial name?

texts:
Since binomials are required to be unique only within a kingdom, two species can share the same binomial name if they are in different kingdoms. I know of one instance of this, Orestias elegans: this name denotes a species of fish (kingdom Animalia) as well as a species of orchid (kingdom Plantae).

Are there other instances where one binomial name validly refers to two (or more!) species?


texts: What is the effect of antibiotic chloramphenicol on bacterial size?

texts: When low amounts of antibiotics like Chloramphenicol is added in a bacterial culture, the steady-state growth rate decreases but what happens to the steady-state size? Can anybody please refer me to any paper that comments about the effect of these antibiotics on the size of bacteria (or yeast)?


texts:
This seems counter intuitive: dry hands mean low humidity, so why when humidity is increased, by washing hands, they become even more dry, eventually?

In particular, why such hand dryness is usually observed in a dry climate?


texts:
Location is South India.

Behavior: It is not moving.

Month: May,

Place: No people come. (Actually species chooses the place on my next door, where neighbors left 2 months ago)


texts: What are the major evolutionary pressures for Bioluminescence?


texts: Why plants (eg. parsley) can keep vitamin C despite all the sun?

texts: I have read that vitamin C is highly sensitive to light. So, how could parsley, for instance keep its vitamin C as it's flooded with sunlight?


texts: Mushroom Identification: Small conical light-brown mushroom

texts:
I found a small single mushroom growing on grass and I decided to try to identify it.

Characteristics:

Region: Brazil southeast coast, state of São Paulo, predominantly Atlantic forest
Gilled mushroom
Substract of growth: Grass
Dark coloured spores (I'd say yellow-brown. Picture Below)
Gills either free or adnexed (My mistake this time, the cap was conical and small, so I couldn't have a clear view of the end of the gills. Should have cut it)
Cap 1.6cm in diameter, conical shaped
Height of about 6cm
Very fragile, specially stipe. Dry texture
Cap color: Like a faded orange or very light brown. Stipe color: Light cream

I tried to follow some identification keys (mostly this one, but that one also seemed to go the same direction) and it pointed me towards the Conocybe genus, possibly Conocybe apala (item 45a on the key from the link, you can follow back to the beginning going to the item on the parenthesis).

However, from what I read it's very hard to identify Conocybe mushrooms to the species level, because some are only differentiated by some microscopic features. They are also sometimes confused with mushrooms of Bolbitius or Galerina genus. Most mushrooms pictures I found from Bolbitius and Galerina give the impression they are a little more "fleshy" (not sure that's the word), and mine had this dry-fragile texture, which most pictures of Conocybe apala seem to align with.

Below are some pictures:

Is it likely a Conocybe apala or are there any other possible candidates?


texts: What kind of larva is this? (Southern CA, USA)

texts:
I need help identifying this larva:

(Click images for full size versions).

There's about a dozen of them in my parents' bathtub and I'm not sure what they are or where they are coming from.

They are about a centimeter long, maybe a little less. They look flat and are hardly noticeable. When they are upside down they look more like a maggot.

My parents didn't even notice until I pointed them out. They move around very little and stay at the bottom of the tub. I haven't seen them anywhere else.


texts: How long do melanocytes and melanosomes continue to protect DNA after UV exposure? Basically, if skin is tanned, then over the next month it is shed, will melanocytes continue to produce high levels of melanin to keep the new skin tanned without requiring more UV exposure? The cells react by producing more melanin after exposure but will they continue to do this in new skin cells?


texts: How do short polypeptide chains serve as identifiable antigens?

texts: My understanding is that MHC class I and II bind to relatively short polypeptide chains (~ 20ish amino acids). I'm surprised that a non-self protein fragment that short would be distinctive enough to target for an immune response. Also, how does expressing one polypeptide chain help the immune system identify the source? Isn't it quite likely that the presented polypeptide is in the interior of a protein and would never actually be exposed to the environment until after it's been lysed? Or is it hydrophilic peptides that bind?


texts: If mutations are random, why do antibiotics 'cause' resistance?

texts:
Full disclosure: I am not a biologist and this is more of a general question about understanding antibiotic resistance of bacteria.

We are always told that careless antibiotics use is the cause of new more resistant bacteria, which can obviously devastate huge societies and even have global impact. At the same time from my knowledge it seems that bacteria mutates in a purely random fashion.

So, thinking about this concept probabilistically, the virus mutating and antibiotic consumption seem to be completely disjoint events such as:

$$P(M|A) = \dfrac{P(M \cap A)}{P(A)} =\dfrac{P(M) P(A)}{P(A)} = P(M)$$

Where $M$ is the event that the bacteria mutates and $A$ is the event of taking an antibiotic. I couldn't find any research online as to how $P(M)$ is actually modelled or what probability distribution it even roughly follows, but intuitively it would depend on time as the longer the bacteria spends inside the host the higher the probability of mutation would be. So from this train of thought it would seem that taking antibiotics would actually be a good idea as to eradicate the bacteria quicker and give it less chance to mutate down the line.

I am obviously not trying to discredit hundreds of years of research and understand that there must be a gap in my thinking somewhere. My question is, why are we told that antibiotics cause antibiotic resistance even though the mutations are described as 'random'?

(ELI5 explanations are preferred as I said I don't come from a biology background)


texts: What is the relatedness of sisters in a haplodiploid system if you mate virgin queens with 1 of their sons

texts:
So I'm having trouble wrapping my head around this. In haplodiploid insects, sisters are related by 75% on average due to all sharing 100% of dad's genetics and 1/2 of mom's. (males are produced from haploid eggs)
The question I have is, if you take a son of a queen and mate her with her own son, what is the genetic relatedness of her resulting daughters to one another?
Here is an illustration of the haplodiploid system in insects.

Thanks in advance!
source: https://en.wikipedia.org/wiki/Haplodiploidy


texts:
In essence - to make a sourdough starter:

Put flour and water in a jar, and leave it in a warm place overnight
Divide the remaining mixture in half, throw out half, add half as much flour and water again.
Repeat for 7 days.

I don't see why you couldn't just add all the ingredients required at the start, open it once a day to let more yeast drop in and give it a stir, and keep in a warm place every day.

The vague idea comes to me that throwing out half the mixture every day has a Darwinian element, but it doesn't involve any 'selection', you're simply casting out half, regardless of adaptability.

My question is: Does the process of making a sourdough starter involve Darwinian selection?

EDIT: There is no 'choice' involved in throwing out half the sourdough. It is entirely arbitrary - and both halves look equally the same.


texts: The Relationship between Copper and Alzheimer's Disease

texts:
I've been reading up about the research concerning the etiological factors behind Alzheimer's and I came across two papers - "Studies on Copper induced stability changes in DNA fragment (GCA ATC TAA TCC CTA): Relevance to Alzheimer’s disease" and "Copper interactions with DNA of chromatin and its role in neurodegenerative disorders." The issue I'm having is that the papers suggest that copper causes the DNA's double helix to unwind in some parts, and it causes it to coil more tightly in others (the fluorescence and circular dichroism research supports the latter).
My question is this: do high concentrations of copper cause DNA to unwind or coil more tightly?
If you could provide any help, I'd be very grateful, as I feel like I'm be missing something obvious.


texts: Does hypokalemia increase sodium concentration in cells?

texts: In hypokalemia, when intracellular potassium is low, does intracellular sodium increase?


texts:
I read that blood clot reduces blood flow from few website and from doing an A level biology question; and if this blood clot is formed in pulmonary thrombosis, this can reduce gas exchange in lung.

However, how are we so certain this is true? If there is a blood clot, then blood pressure around that region increases I believe thus implying the blood will travel faster in that region? If so, then we can't firmly conclude blood clot will reduce blood flow as although blood clot will reduce the lumen of the vessel, the blood will also be travelling faster.


texts:
When media, such as this site wants to explain just how dangerous large animals are, they often quote bite-forces as pounds per square inch (psi).
However, it appears that they mixed up the units, as the numbers they give are the total force in pounds.
But what animals have the strongest bite force per unit area? There is no obvious scaling law here: scale up an animal 2 fold and the cross-sections of both the muscles and the teeth and jaws both quadruple. This puts tiny insect mandibles are on a level playing field with our largest beasts.
Instead, bite-pressure will be niche-dependent as well as the details of the animal's anatomy (such as mechanics of the jaws). It may be somewhat hard to define contact area given the complex shape of teeth and mouthparts in general; maybe one could measure the indented area in a tough material that the animal chomps down on.
Given that our strongest biomaterial found yet is microscopic teeth and that microscopic materials tend to be stronger than bulk materials, it seems likely to be a small animal. Is there any data to support this?


texts: Reptiles are a paraphyletic group because?

texts:
Here is a question I am trying to find the answer to

Reptiles are a paraphyletic group because... ?
A) They include worm lizards, which have no limbs
B) The group doesn’t include birds
C) The group doesn’t include mammals
D) Not all of them have three- chambered hearts

I’m a bit confused about the reasoning. I know a paraphyletic group does not have all of its descendants so if birds were to be included it would become monophyletic. So is B the answer? Could anyone help explain it better?


texts:
Given an in vivo sample from an experimental infection, I would like to see if a bacterial protein is present.

I've been thinking about Western Blot using sera from animals infected with the bacteria. However, this strategy needs a positive control that requires prior gene cloning and expression.

There is maybe a shorter path.

Thanks


texts: Implications of what the discovery of Naia means

texts:
Recently a discovery was made of a ~12,000 year old girl in Hoyo Negro in Mexico.

This has been covered by many different news agencies.

I'm confused however by many of the reports.  Does it strengthen the hypothesis that the ancestors to the Native Americans came over the Bering Strait?  Or is there still some doubt on the matter?

Additionally, what are the arguments against the Bering Strait migration?


texts:
I'm a bit confused what prevents our organs from not collapsing into a heap or putting pressure on each other. I have a 3D anatomy app and have been studying the relationship between the organs. According to the models, the organs are remarkably complementary in geometry and compact, but this still doesn't explain what prevents gravity from distorting them or squishing them.

My Question

What keeps organs suspended in the body?


texts: What is this bizarre looking animal we found in the forest? Bug identification

texts:
Please can someone identify this?

I can't find anything on the Internet like it. 2 cm long. North Bohemian mountains (Czech Republic).


texts: How can promoter binding sites be determined?

texts:
I have been trying to find out which sigma factor is responsible for the transcription of RNA polymerase subunits $\alpha$ (rpoA) and $\beta ^{\prime}$ (rpoC) in Bacillus subtilis. I would expect it to be the housekeeping $\sigma^A$. However I have found out from the Bacillus subtilis transcription factor database, that $\sigma^A$ binding sites have been found in the promoters of $\beta$ (rpoB) and $\delta$ (rpoE) subunits, and a whole bunch of alternative $\sigma$ factors, but it says nothing about $\alpha$ or $\beta ^{\prime}$.

So I want to know if there is a way for me to find out, without entering a wet lab!

Firstly; how do we know that something is a transcription/sigma factor binding site? What is it about the region? And how do we know which TF/SF it is a binding site for? Could the same transcription/sigma factor have multiple different binding site motifs?

Secondly; Since the genome for B. subtilis is available, would I be able to find out binding site motifs for all the sigma factors, and then determine which is/are contained within the promoter for the $\alpha$ subunit? I.e. if I know the TF/SF sequence, is there a way of finding out which promoters it can bind to?

Finally; the main purpose of this question is to find out how rpoA is transcribed, and I know that in general sigma factors are required in bacteria for specific transcription initiation, but could it be that rpoA transcription is non-specific, and that the sigma factor is just not involved in its transcription?

Please let me know if there is anything I can do to improve my question, I can provide references if it would be a good idea. Thanks!


texts: How do circulating androgens contribute to higher rates of hirsuteness in some women?

texts:
I was reading up on ethnic groups in which the women are naturally more hirsute (such as South Asian women) in the context of evolving standards of beauty. I came across this statement on a forum:

  Hirsutism is much more common in South Asian women (particularly North Indians such as Punjabi Sikhs) asymptomatically because they tend to have higher levels of circulating androgens than your typical [North or Western European ethnic group]. This is also true of Eastern European women to an extent.

Per Wikipedia, I learned:

  Circulating levels of androgens can influence human behavior because some neurons are sensitive to steroid hormones. Androgen levels have been implicated in the regulation of human aggression and libido. Indeed, androgens are capable of altering the structure of the brain in several species, including mice, rats, and primates, producing sex differences.

So: do circulating androgens trigger higher testosterone production in some women? Is this what yields higher instances of "hirsutism" among certain populations? How are some women more prone to this than others? (That is, per the forum post, why are South Asian women more likely to have this than Western European women?)


texts: Is it possible to intentionally limit bacteria's lifespan?

texts: Say I have a species of bacteria. I want this species to only persist for a set number of generations, after which it simply stops reproducing. Is it possible to do this at all (with known genetic engineering techniques), and if so, how do you prevent bacteria from evolving against it?


texts: What is the difference between chrysophytes and protozoa?

texts: Amoeba is present both as a protozoa and as a chrysophytes.How to understand ,with which defining feature to which group to classify into?


texts:
I want to understand how a motif is present or not, can be deduced from a PDB file. Are there any rule of thumb for forming 3D motifs? Like a series of helices and sheets in some direction will lead to a particular 3D motif? Are there any such rules? If so, any resources that you can provide me with?

For example, beta-hairpin. What should be the sequence of amino acids or helix/sheet that would result in the formation of beta-hairpin motif?


texts: What is the minimum length required for a circular DNA ligation?

texts: What is the minimum length of a DNA molecule for the ends to come in close enough contact that they can ligate. Assume there are free divalent cations in solution. Does anyone have any idea?


texts: Two different sized colonies from the same species of bacteria. What does it mean?

texts:
I have got two different sized colonies in a plate of Salmonella Paratyphi, identified by biochemical methods. What does two different sized colonies mean? What kind of question can I investigate in this regard?

Protocol followed:

Positivity of serum sample was checked in BacT/Alert blood culture system. Bacteria was subcultured from the positive result giving culture bottle from the BacT/Alert system and incubated overnight at 35 degree celsius. Two different sized colonies were found and they were subjected to biochemical and antisera tests and both identified as Salmonella Paratyphi.


texts:
Might be a stupid question, but I'm quite curious about finding out ^^

If someone looses his ear, or for example cuts it of, just as Van Gogh did. Would he still be able to hear, since the actual organs that are responsible for hearing are on the inside of your ear canal? The ear itself more or less is just flesh, right?


texts: I heard that animals cannot get Down syndrome or trisomy. Is that true and why can't they get it? They also have chromosomes.


texts: Why would it be beneficial for cortisol and corticosterone to exhibit pronounced anti-inflammatory activity?

texts:
These questions are always a little silly (as we will never truly know), but it always struck me as odd that corticosterone and cortisol exhibit pronounced anti-inflammatory activity.

Because these compounds are released during fight-or-flight episodes, it seems almost counter-intuitive for an organism to promote "anti-inflammatory activity" during an event that is most likely coincident with injury (i.e. wounds from fighting / escaping).

Anti-inflammatory activity, I believe, is fairly synonymous with anti-coagulation activity. If wounds are most likely to occur during periods of fight-or-flight (which is a reasonable intuition), why would organisms select for a glucocorticoid that has additional effects such as reducing acute clotting capacity?

The only thing that I can think of is there is an energetic cost to initiating the coagulation cascade, which would siphon energy away from skeletal muscle. Any thoughts / hypotheses?

Cheers~


texts: What is the evidence that australopithecines were bipedal?

texts:
Before the discovery of Australopithecus afarensis in the 1970s, most anthropologists believed that an increase in brain capacity had preceded bipedal locomotion. However, this reconstruction of the Lucy skeleton shows that the A. afarensis was bipedal even with a brain size of around 400 cc.

But the actual Lucy skeleton does not include feet, and only has two partial leg bones.

How do anthropologists determine, based on the bones preserved, that A. afarensis was bipedal?


texts: What actually happens to the human body during fasting/starvation?

texts:
I recently came across a UN study which advocated that controlled fasting can be beneficial for the the human body and I am fascinated by stories of wilderness survival against the odds.

It piqued my interest to ask; what exactly happens to a human body during fasting and ultimately starvation?

I understand that there is a period of glycogen use/exhaustion and functioning becomes impaired but what medically happens to the human body (organs, muscles, protein, body fat, cognitive processes etc) and over what timeline (24 hours to death).  I read that halitosis is an interesting side-effect etc.

Assume the human body has ample access to water and can avoid dehydration.


texts: Which grows slower: the thumb nail or the pinky nail?

texts: I notice that thumb nails and pinky nails grow slower than the 3 other fingers in the middle. But which one is slower, the thumb nail or the pinky nail?


texts:
When I do a Google search, most of the results are about whether or not people can get HIV / AIDS from getting a tattoo through dirt needles. I am, however, curious whether or not it is possible to get a tattoo if you have AIDS.

Quoting wikipedia's entry on tattoos:

  Tattooing involves the placement of pigment into the skin's dermis,
  the layer of dermal tissue underlying the epidermis. After initial
  injection, pigment is dispersed throughout a homogenized damaged layer
  down through the epidermis and upper dermis, in both of which the
  presence of foreign material activates the immune system's phagocytes
  to engulf the pigment particles.

If your immune system is not working properly, I can imagine that the phagocytes might never respond to the tattoo ink and that the pigment might not ever enter the fibroblasts?


texts:
Source

Source

Source

Acetoacetyl-CoA is a C3 unit.

3-Hydroxybutyryl-CoA / Butyryl is a C4 unit.

Where does the additional C atom come from? I'm suspecting it's another Acetyl-CoA -> CoA reaction, but I don't see it in the images.


texts:
What is the E coli transformation efficiency for 2 plasmids? Are any studies that have looked at the correlation between number of plasmids transformed and transformation efficiency? Is there a commercial E coli strain that is better at co-transformation?

For example, electroporation with single plasmid yields around 1 × 10^10 cfu/μg. I would like to know what is the limit for co-transformation and whether it can be or has been improved.


texts: Is there a stem cell dye for education purposes?

texts:
I need a dye that will stain stem cells (for this purpose the stem cells will proquired from chicken bone marrow).

This will be an educational hands on activity for young teenagers so ideally the dye should be:

Safe
Easy to handle
Stain quickly
Be relatively cheap
Present an obvious colour change under a low zoom microscope or the naked eye

I vaguely remember using a dye years ago that fits this bill, but cannot recall the name or company.


texts: What is the exact principle of capillary isotachophoresis?

texts: I know it's a type of capillary electrophoresis, but I don't get how does the separation happen exactly.


texts: Why can a zygote develop into all different types of cell, whereas a differentiated cell cannot?

texts: A cell formed by the fertilization between two gametes has all the DNA and can lead the development of a human person (or other animals in other species). But other cells in a human person has also all the DNA (like skin cells), yet they don't lead the development of organs, bones, etc. What is the difference between the zygote and cells from any part of the body from a developed person that one can lead to the development of a person and the others can't in spite of all of them have all the DNA? Does it have to do with the enviroment/surrounding those cells are in, is there any structural difference between the zygote and the other cells or how is it?


texts: What exactly does the phrase "chimerical sharing" mean in this abstract?

texts:
The Gizmodo article Australian Siblings Are Semi-Identical Twins, Some of the Rarest Humans Ever links to the new paper in NEJM Molecular Support for Heterogonesis Resulting in Sesquizygotic Twinning Gabbett et al. N Engl J Med 2019; 380:842-849 DOI: 10.1056/NEJMoa1701313.
The abstract of this paper says:

Sesquizygotic multiple pregnancy is an exceptional intermediate between monozygotic and dizygotic twinning. We report a monochorionic twin pregnancy with fetal sex discordance. Genotyping of amniotic fluid from each sac showed that the twins were maternally identical but chimerically shared 78% of their paternal genome, which makes them genetically in between monozygotic and dizygotic; they are sesquizygotic. We observed no evidence of sesquizygosis in 968 dizygotic twin pairs whom we screened by means of pangenome single-nucleotide polymorphism genotyping. Data from published repositories also show that sesquizygosis is a rare event. Detailed genotyping implicates chimerism arising at the juncture of zygotic division, termed heterogonesis, as the likely initial step in the causation of sesquizygosis.

There are several terms I am trying to understand here:

sesquizygosis and sesquizygosity: A postulated form of twinship, in which individuals share between 50 and 100% of genetic identity by state (number of shared alleles).
heterogonesis: The assortment of two or more paternal genomes into distinct cell lineages after polyspermic fertilization of an ovum.
juncture of zygotic division (?)
chimerism

So far I understand that the chimerism means for each fetus, some cells have a distinct genome from other cells, and sesquizygosity means (at least) that there is DNA present from more than one sperm.
But I don't understand what "...chimerically shared 78% of their paternal genome..." means exactly when speaking about twins. What does chimerical sharing mean in this case? Are we talking about four genomes (two genomes in each of two fetuses)? If so, how does that comparison reduce to a single value of 78%?

Heterogonesis \ he-tə-rō-gō-ˈnē-səs \
The assortment of two or more paternal genomes into distinct cell lineages after polyspermic fertilization of an ovum.

Visual Representation:


texts: Is there a vertical measure of appearance of a genotype over generations?

texts:
Is there some kind of a vertical measure of appearance of a genotype $g$ throughout ancestry, i.e. a measure of how many ancestors of $g$ had genotype $g$. Like for example in saying that on average each member of a population $P$ have 60% of its ancestors having genotype $g$ over 20 prior generations.

A clarifying example, lets take some genetic trait like color, suppose we have a population $P$, and suppose we know all of the ancestry of each individual $x$ in that population up to say six generations, i.e. we know specifically the color of each mother and father of $x$, the grandmothers and grandfathers of $x$, the first great grandmothers and the first great grandfathers of $x$, up to .. the fourth great grandparents, call the set of all those as $Ancestry^6(x)$, lets denote the set of all individuals of $Ancestry^6(x)$ that are $a$ colored as $Ancestry^6_a$, let's denote the total number of members of any set $y$ by $|y|$,

Now what I'm looking at is the proportion $p^6_a(x)$ of all $a$ colored members of the 6 generations ancestry of $x$, from that ancestry.

$$p^6_a(x)=|Ancestry^6_a(x)|/|Ancestry^6(x)|=|Ancestry^6_a(x)|/(2+2^2+..+2^6)$$

Now for population $P$ we'll look for average $p^6_a(x)$: $x \in P$, symbolized as $\mu^P(p^6_a)$ which is $$\mu^P(p^6_a) = \big{(}\sum^P p^6_a(x)\big{)}/|P| $$

In general the measure is $\mu^P(p^m_a)$, where $P$ is the population, $m$ the total number of generations in the ancestry of each member of $P$, $a$ is the genotype, and $\mu$ signify average, and $p$ for proportion. So $\mu^P(p^m_a)$ is: the average proportion of genotype $a$ in ancestry of each member of $P$ up to $m$ generations.

  Question: is that measure directly proportional to fitness?

The idea is that if genotype $a$ is more fit than others, then it would appear more frequently in the ancestry of each member in the population.


texts: Vision: what is the difference between on-off ganglion cells and lateral inhibition?

texts:
Is 'lateral inhibition' just a term for the biological basis of the functioning of the on-center (or off-center) ganglion cells?
Or do these terms describe separate processes?


texts: Evolutionary elimination of recessive gene

texts: As recessive gene is suppressed, why over millions of year of evolution have not wiped them away completely, why don't they just go extinct, as people with those genes go extinct?


texts: Literature about putative epigenetic state changes in mammal sequences after cloning steps in Escherichia coli

texts:
I would like you to point me out some literature about putative epigenetic state changes in mouse/mammal sequences after cloning steps in Escherichia coli.

This are the last search details I used in NCBI PubMed:

  "epigenomics"[MeSH Terms] AND "cloning, molecular"[MeSH Terms] OR
  "molecular cloning"[All Fields] AND "sequence"[All Fields] AND
  ("escherichia coli"[All Fields] OR "e. coli"[All Fields])


texts: Alternatives to trypsin for cell detachment?

texts:
I have ran out of trypsin and need to passage my cells (immortalized chondrocytes, C28/I2) today or tomorrow. I have been out of town and forgot to order more trypsin.

I was wondering if there are any alternative, "homemade" ways to detach cells. Googling this results in a lot of commercially available detachment solutions. I may or may not have a cell scraper available, but I have never tried it. I have hyaluronidase and I was thinking that might work.


texts: Formal definition of a 'genetic trait reservoir'?

texts: I've read the tomato genome paper in Nature published recently, and they describe the tomato genetic resource as a rich trait reservoir that will provide biological knowledge and empower biodiversity-based breeding. What would be a formal definition of trait reservoir in this context?


texts: How does formaldehyde/PBS or methanol fixation of cells affect lysosomal pH?

texts:
The question is fairly simple - does formaldehyde or methanol fixation in preparation for immunocytochemistry/immunofluorescent staining affect the pH of the lysosomes?

Some background: I'm trying to look at the intracellular trafficking of a fluorescently-labeled lysosomal enzyme. Cells are grown in vitro and treated with the labeled protein, which is taken up into the cells via receptor-mediated endocytosis. The protein-receptor complex targets the late endosome-lysosome pathway, where eventually the acidic pH of the lysosome causes the two to dissociate and the receptor to recycle, while the enzyme stays and does its thing. I've labeled the enzyme with two different dyes - Alexa Fluor 488, which is supposedly pH-insensitive between 4 and 10, and pHrodo Red, which has greatly-increased fluorescence as the pH drops. Alexa488 is the brightest of the Alexa dyes, and is widely used in all sorts of applications. pHrodo is not as bright (as far as I can tell, it's been difficult to find comparisons), but its pH-dependence helps lower the effect of non-specific extracellular binding, and it seems to work in my system so far.

So what's the problem? I'm developing an assay that will measure the ability of certain substances to block the uptake of this enzyme into the cell. Since I'll be measuring a lack of signal, the higher I can get the uninhibited signal to be, the better. Like I said, pHrodo works OK, but it could be better. The problem is that my Alexa-labeled protein has an extremely low signal to noise ratio, when I would have expected the exact opposite. I'm wondering if, in my system, the Alexa dye really is somewhat pH-sensitive, and is not fluorescing as well when in the acidic lysosome. I'm encountering a few other issues as well, and while before I was performing live-cell imaging, I'm starting to toy with the idea of fixing the cells first, as that will positively impact some other things I want to try.

Hence my question: Will fixing the cells with 4% formaldehyde in PBS (standard ICC/IF protocol) affect the pH of the lysosomes? Would methanol fixation do the same thing? Any other suggestions for increasing signal?


texts: Did human hairs actually evolve from scales?

texts: What is the evolution of hairs? Did they evolve from scales?


texts:
I am working in the field of neuroscience with a background in computer science. I try to find new ways of analyzing brain imaging data (mostly MRI, EEG, MEG, fMRI) with modern machine learning methods.

I would like to take a step up by adding genetics to the data arsenal. My work this far has found connections between some X and Y but not really shed insight to why things should be like that. I hope I could get a partial answer from biology.

To get started, I would need some good material to read. It does not matter if the content would be difficult in mathematical/statistical/technical aspects, but it should be approachable with limited knowledge in biology and/or chemistry and physics.

Suggestions?


texts: If the stomata close during the night to conserve water, how does the plant get oxygen for respiration when they are closed? Do they not fully close? Does the plant's metabolism slow down to accommodate for the lack of oxygen?


texts: Why are abiogenesis and evolution considered unrelated?

texts:
When a discussion about evolution comes across abiogenesis - the typical reaction is that they are unrelated (see the headline at http://www.factsnotfantasy.com/abiogenesis.php).

It seems to be that both are stochastic processes in which less ordered structures become ordered.  It seems that, in general, abiogenesis is the process of forming of life (whatever that is) whereas evolution is the process in which life would develop into more complex forms.  In other words, it seems that it's really just two phases of the same type of process and I'm wondering why they are considered as such isolated fields.


texts:
I am currently digging in some books to understand the three major metabolic pathways involved in physical training. The most difficult one for me is the glycolytic non-oxidative pathway (also more commonly known as the anaerobic lactic pathway) and I would like some help from people versed in this field.

In this pathway, as far as I understand, glycolysis produces pyruvate. In this process, NADH and H+ ions are produced along the way.

Then, if there is still a high energy demand (i.e. glycolysis is still necessary); NADH binds with pyruvate to form lactate and free up NAD+ which is necessary to sustain the glycolysis (otherwhise, pyruvate would be consumed via an oxidative pathway i.e. oxidative glycosis or slow glycolysis). This can theoretically continue until glycogen is depleted or severely diminished as far as I understand.

The problem comes then from the H+ ions produced during the glycolysis. These ions cause acidosis of the muscles if not removed. However, they can be removed if sufficient oxygen is present to form water. And here is my main question :

Why, during high intensity exercise, would oxygen be insufficient to take care of the H+ ions produced by the glycolysis ? Is it because muscles used during high intensity are not the best ones for using/transporting oxygen? Is it also because these H+ ions cannot be transported towards neighbouring muscles able to oxidise H+ ions ?

I understand this is a difficult question and maybe there is no precise answer at the moment. If you could point me toward a good ressource that deals with this question, I would be glad. I currently base myself on McArdle book on exercise physiology.


texts:
Short question:
where can I find what F and J and < and - and 7 mean in a Sequence file?
Longer version:
I was looking at this sequence file I got from NCBI (it's an sra file? if that is the correct terminology) and I used the sratoolkit to print out a few spots
looking at them I expected to see ACGU (this was meant to be an RNA sequence), but what I see are like

AAFFFJJJFJJJJJJJJJJJJJJJJJJJJJFJJF<JJ77AJJJJ-JJJJJFF7FA--F7FAJJ7<AJ-FJA<J<JJFA<<77F-JJJJJJF<JF<7-FF-A-----A-77JJ7FJJF-FFFAJ<<-FJJFAJAFFAFFFFF<7A7JFJJ7AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJFJJJJJJJJJJJJAA<JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJAAFFJJFJJJJJJJJJJJJJJFJ-FJF

Where can I find a reference to help me "understand" this?
I mean I assume - means missed or unknown? or is it meant to be already aligned and these are deletions?
I appreciate any pointer to get started. as you must have observed I am a total noob.
I got the file from: https://www.ncbi.nlm.nih.gov/sra/SRX8156420[accn]


texts: How does blood pressure substantially drop in the capillaries and arterioles?

texts: Is this due to increased frictional resistance which decreases the velocity of the blood? You would think using Bernoulli's principle that the velocity of blood in the capillaries would increase due to the decrease in pressure but the inverse is true.


texts: How long a dog can remember its owner's smell?

texts: Can dog remember multiple smells? and how long it can remember a smell?


texts: Consensus codon optimization by organism

texts: Does a public database exist that contains this information? I'm trying to make a simple gene annotation program that will let me input a DNA sequence and then optimize it based on one of these tables using the E. coli preferences, for example.


texts: Characteristics of Araneus hui (an orb-weaving spider)

texts:
What are the characteristics of Araneus hui? Neither thematic literature nor photos was found.
Mentioned in RU Wikipedia, reference wasn't found.
https://ru.wikipedia.org/wiki/%D0%9A%D1%80%D0%B5%D1%81%D1%82%D0%BE%D0%B2%D0%B8%D0%BA%D0%B8


texts: Transverse diffusion of lipids in red blood cells

texts:
The membrane of a human erythrocyte has polarity:

Phosphatidylethanolamine and phosphatidylserine are predominantly on the inner side.
Phosphatidylcholine and sphingomyelin are predominantly on the outer side.

Although these can diffuse in the lipid bilayer, they stay on only one side of it. How is this sidedness preserved?


texts: Why are there six reading frames if only one strand of DNA is referred to as the ‘coding strand’?

texts:
We need to consider six reading frames when considering the potential of DNA to encode protein (three frames for each strand). But only one strand is transcribed into RNA — the so-called coding strand. It would therefore seem to me that there are actually only three reading frames to consider. Why, then, do people refer to six?

Another point concerning reading frames is the definition of Open Reading Frame — ORF. One text defines ORF as:

  “An ORF is a continuous stretch of codons beginning with a start codon
  (usually AUG) and ending with a stop codon”

whereas another text defines it as

  “An ORF is a continuous stretch of codons that do not contain a stop
  codon (usually UAA, UAG or UGA)”

It seems to me that the first definition is correct. Which is the generally accepted definition for ORF?


texts: I am studying chaperon proteins DnaK, DnaJ etc. This question sounds trivial but I would like to know what the acronym stands for. I have looked on google/google scholar. My best guess is that the name comes from the fact that these are genes whose products are necessary for bacteriophage DNA replication. Can this be confirmed? The full name of GroES and GroEL may also be helpful. Thanks!


texts: Could miniaturization be used to protect endangered large species?

texts:
In some animals (like dogs) size seems like it's controlled mostly by just a few genes (IGF1, and the genes that repress it). I'm curious:

(1) Does other miniaturization takes a similar route (for example, with pygmy hippos).

(2) Do we have the technology / knowledge to deliberately create "pygmy" animals?

(3) Is it possible that miniaturization could be a way to protect endangered large species? For example, we shrink them down so they need less room but they could still breed and preserve biodiversity. Also, later on there's always the possibility that we could gradually un-shrink the species if we get our act together and free up more habitat.

Note: I realize that they wouldn't be able to fill the same ecological niche at half the size.


texts:
What are the names of the parts A, B, C and D?

This is not homework. I am not a biology specialist. Looked through books for than 30 min. Most of them are schematic diagrams, not photos. Furthermore, the vascular bundle is normally shaped like a cone but this one is crescent shaped.


texts: What kind of objects can be qualified as artifacts? How do we distinguish such objects?


texts:
The canonical definition of action potentials found in textbooks states that action potentials are all alike in shape.
From techniques such as spike sorting which are used to attribute electrophysiological recordings to individual cells, we know, however, that shapes and amplitudes of action potentials vary.
Synaptic strength is defined as the average amplitude of postsynaptic potential evoked following a presynaptic action potential.
Given that the incoming action potentials might differ for different synapses (and for instance lead to more or less vesicles being released), how can we hence have a uniform definition of synaptic strength?


texts: Agarose vs agar? Why do DNA gels use agarose only and how do you obtain agarose from agar?

texts:
Agar is a relatively cheap substance from red algae.  And it contains a saccharide agarose as well as a small amount of pectin.

Agar is used for culture plates as is, but for DNA gels a grade of agarose, I guess with the pectin removed.  What happens when a gel is run in agar?  i.e. why remove the pectin?

If you can guess, how is the pectin removed?  I know there are enzymes that might do it, but not sure what's really used.