texts: Protein half-life regulating gene expression

texts:
Are there any instances in real life of protein half-life regulating gene expression? For example, in a cell, Gene A produces a starting population of protein P, after which the expression of the gene is turned off. The starting population then degrades over time. When the numbers of protein P are reduced to roughly half, the transcription of Gene B, which had been repressed until then, is turned on (perhaps a byproduct of the protein degradation acts as a transcription factor for Gene B?)

My apologies if the question does not make sense. I am a sci-fi author, trying to design a synthetic virus for my novel - a bioweapon of sorts. The scenario is that the viral genome, upon making its way into the nucleus of a human cell, goes into a lysogenic phase, where the genes for its replication are turned off.  The virus needs to initiate its replication only after a certain amount of time has elapsed, say X days. X is the half-life of protein P, which is produced by the viral genome while lysogenic. After X days, transcription of the rest of the viral genome is turned on, and the virus starts making copies of itself. Only this time, the copies go straight into lytic mode upon infecting a cell and start multiplying exponentially. My fictional virus has mechanisms to suppress interferon signalling and evade the immune system (for some time at least, until it gets out of control in the host body).

I am aware that some real-life viruses that infect bacteria can switch between the two phases, but the trigger for the switch is always an external event - like UV damage - and not something controlled by the virus itself. In my scenario, I want the virus to behave like a programmed timer, turning itself on after a fixed elapsed time.


texts: How much mice red blood cells should I dilute before counting?

texts: I am wondering how much red blood cells I should dilute with how much PBS before counting on hemocytometer with trypan blue


texts:
I've seen several websites claim the amount of hair cycles a follicle will go through is predetermined at around 25-30 complete cycles. Is there any genetic evidence to validate this claim? How can this even be determined apart from observationally seeing people lose hair as they age?

Here's a link referring to what I'm talking about:

  The number of hair growth cycles is limited: our hair will experience about 25 to 30 cycles like this during our lifetime.


texts:
I am aligning a large number of ESTs. It seems poly-A tails show in many different ways. In addition to occurring at the very end, they can be flanked by the cloning sequence one one end, or have mismatches/errors. What is a good rule or available tools that will handle the usual cases?

A few examples of the non-trivial cases I found, with their Genbank Accs:

>EE409337
... AAAAAAAAAAAAAAAAAAAAAAAAAGGAAAAAAAAAAAAAAAAAAAAAAAAAAAACCTTGTC
>EE409340
... TTTCTACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACTTGTC
>EE409361
... TTGTTAAACTGAAAAAAAAAAAAAAAAAAAAAAAAAAAACCATGTCGGC
TTACTGAATTGAA
>EE420306
.... AAAAAAAGTTATGTTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGGGAAAAAAA
AAAAAAAAAAAAAAAAA

Cross-posted on SeqAnswers,Biostars.


texts: I saw this insect near a beach in Corsica France:


texts: Found in Alexandria MN, on sidewalk. Small, fast little spider.


texts: A molecular marker for global protein synthesis

texts:
I know that protein synthesis is governed by a lot of factors (I'm mostly studying the mTOR pathway), but I'm looking for some kind of marker that will indicate the global protein synthesis rates.

I know there are tissue-specific markers (like actin/myosin in muscle) but I'd like something more that is ubiquitous and is proportional to global protein production (maybe a muscle can make more or less myosin depending on whether there are some factors).

I assume protein synthesis factors (like mTOR, S6K1 etc.) are quickly regulated, so they cannot be used as markers.

So, what would serve as the best molecular marker?


texts: How can frogs tolerate freezing while humans cannot?

texts:
A wood frog can tolerate the freezing of their blood and other tissues. (wiki, news2), but human beings can not.

Some people plan to freeze their bodies/brains after death, and some of them have done that.

Can wood frogs help us learn how to freeze our brains safely?


texts: What is the best alignment definition for the Multiple Sequence Alignment (MSA) problem?

texts:
For simplicity, suppose that I am penalising mismatches and gaps with -1 and adding a score +100 for each match.
Does the optimum alignment of the three DNA sequences

AAATTT

AAAGGG

GGGAAC

equal to:

AAATTT---

AAAGGG---

---GGGAAC

with the total score S =  294 + 294 - 6 = 586? In this case I sum the alignment score for each of the three pairs.

Or does it equal to:

---AAATTT

---AAAGGG

GGGAAC---

with the score 200 - 7 = 193? In this case I am rewarding only the matches that occured across all three sequences at the same time.

Which of the two scores are the common Multiple Sequence Alignment algorithms trying to optimise for? Or if both are valid, then which optimal alignment (i.e. with respect to which definition) is preferred if realistic reward/penalise values were used?


texts:
How do cellular conditions change the Gibbs free energy of a reaction?
Taking glycolysis as an example, how exactly would cellular conditions affect the free energy released from this reaction?


texts:
It is quoted in wikipedia that:

  Following the EC number classification, they belong to the group of ligases , with lyases catalysing the reverse reaction.

And we all know that enzymes are biocatalysts which catalyses reaction in both forward and backward directions.

So my question is that how can the reaction in one direction catalysed by one enzyme and in reverse direction catalysed by other enzyme? If we assume that they are telling that one direction synthase acts as ligase and in other direction it acts as lyase then how can lyases have more than one substrate for reaction? Because products(more than one) of ligase acts substrate for reverse
reaction.(taking for example a ligase, glutamine synthetase as synthase)

It is also quoted from wikipedia

  Lyases differ from other enzymes in that they require only one substrate for the reaction in one direction, but two substrates for the reverse reaction.


texts: What enzymes I shall use for preparing single cell suspension from cardiac tissue for flow cytometry?

texts: Can anyone suggest which enzymes I shall use for preparing single cell suspension from cardiac tissue. I will be looking at both cell surface and intracellular antigens involving cardiomyocytes and fibroblasts.


texts: Is DNA sequencing coverage a function of sample purity?

texts: How is coverage affected by the purity of a sample? And can coverage for a sample be affected by other things, like the library preparation or manner in which the sample was stored?


texts: Eating rarely but a lot, or often but little

texts:
I wonder if it matters if an average person eats the same amount of food distributed between a few (2-3) meals during the day, or constantly having small snacks.

I'm interested in several aspects of such food consumption:

How does it affect appetite?
How does it affect fat accumulation?
Are there any notable side effects caused by either way of eating?


texts: What is the meaning of pygo and pagus in the word pygopagus?

texts: I know definition of the disease pygopagus but I want to know the meaning of separate parts of it, in fact what's the meaning of pygo- and -pagus in terminology?


texts: Why do Proteins store energy when the body already contains Carbohydrates and Lipids?

texts:
We already know that lipids are a source of long term energy and carbohydrates are much faster energy releasing sources. So why do we need specific proteins within the body to store energy?
Are proteins some sort of much quicker sources of energy?
I really can't understand.
Thanks for answering.


texts: Do electron microscopy change the structure of the specimen due to the vacuum step?

texts: Since specimens have to be prepared using the vacuum, would the pressure change affect the structures of the specimen?


texts:
I understand that in many isolated islands, such as the Galapagos, there are no large predators. I find this observation interesting because it has been suggested that the lack of predators unleashes the evolution of new and bizarre species.

However, as new species evolved there (and increase their size, with respect their ancestors), why no small predator species evolved into a large predator species? Or can new predators evolve from herbivorous animals?

This may be a difficult question, because we may not  know the natural history in such great details. More specifically, I wonder if, in general, there is some pressure against the selection of predators or if there are counter examples which show that small isolated islands evolved their own apex predator.


texts: Is the binding of androgen to androgen receptor in prostate cancer cells a requirement for the production of prostate-specific antigen?

texts: The binding of androgen to the androgen receptor results in the transcription of androgen-regulated genes, which signals the proliferation of prostate cancer cells. This process also produces prostate-specific antigens (PSA). Does it mean the activation of the androgen receptor (via binding to androgen) is a requirement for PSA to be formed?


texts: What is measured by electroencephalograms and local field potentials?

texts:
In the Scholarpedia article on local field potentials (2013), I read:

  The current view is that EEG and LFPs are generated by synchronized
  synaptic currents arising on cortical neurons, possibly through the
  formation of dipoles (Niedermeyer and Lopes da Silva, 1998; Nunez and
  Srinivasan, 2005).

There are three things I do not understand:

What does "on neurons" mean? Why not "in" or "around neurons"?
I assume that what is measured is the electric potential in an electric field that is generated by charges (the ions). So only the changes of the measured potential are due to currents, the potential itself (at any given point in time) is only due to the distribution of charges. Is that view correct? Independent of the nature of the charges.
What exactly are the above mentioned dipoles? Of which are they formed and what is their size? (At least, the article says "possibly generated through the formation of dipoles".)

Does all this sum up to the picture that it is all and only about the ions that pass through the ligand-gated channels at a synapse and the electric field and potential generated by them, the contribution of all other charges being cancelled and filtered out?


texts:
What purpose does reticulate venation in dorsiventral leaf or parallel venation in isobilateral leaf serve?

Does it have any relation with unequal transpiration in dorsiventral leaf or equal transpiration in isobilateral leaf?


texts: Making penicillin using animals - specifically, a goat

texts:
In the scifi novel Lucifer's Hammer, one of the characters (a biologist, if I remember correctly) finds himself in a post-apocalyptic world and tries to make penicillin to save his own life. To do this, he repeatedly states that he needs "a goat" - for some reason which is never explained.

I know that penicillin (in its various forms) is a byproduct of some types of fungi (see Wikipedia), but I can't make sense of the statement "I need a goat to make it". Assuming you don't have a chemical lab at your disposal (think "post-apocalyptic world"), does this requirement make any sense to any of you (apart from "I need to eat the goat to stay alive long enough to find a deserted biochemical lab" :-) )?

If not, how would you go about finding or making penicillin in such an environment?


texts: Would an enrichment of pyrimidine runs of two of more nucleotides be an early indicator of DNA to be damaged?

texts: I am analysing two categories of protein coding genes comparing their relative characteristics. What I am observing is that one of these, in comparison to the other, is enriched in pyrimidine runs (two ore more consecutive pyrimidines). I have counted the number of these runs (I do not call them dimers because I have no data underlining a cross-link between two or more pyrimidine bases) per protein coding-gene performing then a Mann Whitney test that indicates that one of these two group of genes is enriched with respect to the other. I am hypothesising that this enrichment could be an early indicator of DNA to undergo local conformation changes. By your experience, could this hypothesis be reliable or I am totally misleading what I am observing?


texts: What is the current status of the taxon Crocodylus raninus?

texts:
What is the current status of the taxon Crocodylus raninus, the Borneo Crocodile? See Wikipedia Is it now a valid species, a subspecies of Crocodylus porosus (The Saltwater Crocodile) or merely a synonym of the later?

As for Colin Stevenson, "Crocodiles of the World, Reed New Holland 2019", it is not listed as a (valid) species, nor in the IUCN Crocodile Specialist Group.


texts: How far can parrots fly without needing to land?

texts:
This is for a story I'm writing.  I can't find any information on how far various parrot species can travel without needing to land-- the closest I could find is this page saying that a macaw flies up to 15 miles looking for food.  Intuitively I would think that larger birds, like macaws and African greys, would be able to fly farther than smaller ones due to having stronger wings, but the nonstop-flight record-holder is about the size of a robin so I guess that's not necessarily true.

Can anyone tell me how far various parrots can fly in a stretch, or at least the farthest that any parrot species can fly?


texts: Why do people feel pleasure when using roller coasters / centrifuges?

texts:
The feeling when using an amusement park unit is usually a pleasure. Why is it not a pain instead?

Are there advantages, from an evolutionary point of view, in loving this potentially dangerous activity?

Is it related to the liking for extreme sports?


texts: How do multiple replication forks function without 'colliding', and what is the benefit of this method?

texts:
I'm currently reading a little about DNA replication, and have come accross the following statement;

  Replication starts from a fixed point and is bi-directional ... In Eukaryotes, there are multiple replication forks, each progressing in a bi-directional fashion.

If there is a single, long strand of DNA in a Eukaryotic cell, I see potential problems with this:

These forks involve opening up a section of double-stranded DNA, and each strand becoming a double strand in a newly synthesised piece of DNA. At some point, before any single fork has become two new double-stranded molecules, another fork could 'collide' with this, causing it to attempt to replicate the non-finished section.

Simply, how can one replication fork meet another without either exponentially increasing the number of strands being replicated?

Also, on a more general level, I would be quite interested to know the actual benefit of this, when, typically, only a single copy of the double-stranded molecule needs making.


texts:
What response of cellular immunity would appear after complementary protein activation to keep pathogenic bacteria away from our body?

Notes: I do appreciate your explanation. Though I am facing multiple choices:

(a) wrapping the bacteria cell (b) immobilize the bacteria cell (c)    destroying the bacteria cell by enzyme (d) creating pores on the bacteria cell

The key answer is (c) but then I do not know what enzymes make this happens. Any Idea?


texts:
There's undoubtedly more than one way to do this, but if a DIY biologist were to attempt to detect food fraud (e.g. as done by students from Stanford University and Trinity School, Manhattan with respect to fish samples from markets and sushi restaurants), then what would be the minimum steps and equipment?

(I know barely anything about molecular genetics, but have been reading about DremelFuge, OpenPCR, and Blue Transilluminator, and wondered whether they - or things like them - might get such an investigator some of the way towards the goal above; and what else would be required.)


texts: Can I sterilize the equipment for experiments without an autoclave?

texts: If I don't have access to an autoclave, can I sterilize my equipment in a regular pot. If so, what time is needed at about 110°C (I measured inside) for a proper sterilization?


texts: How are oranges in the US or anywhere made seedless? Please explain the broad principles and not the technicalities.


texts: The first species having circle of Willis (circulus arteriosus cerebri)?

texts:
I know mammals are not the only species that have this anatomical unit (i.e. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3982101/).

But I was wondering what was the first species that had a similar structure in their brain (or brain-like organ). Do we know this?


texts: How will changing the concentration of a Tris buffer affect amylase enzyme activity?

texts: For instance if you increase the amount of Tris but pH still does not change then will the enzyme activity still proceed normally?  If it does change the pH will it change enzyme structure and why?


texts: How exactly does heterozygous sickle trait help patients survive malaria

texts: Heterozygous sickle cell anaemia trait is known to increase the survival rate of carriers to malaria attacks. How does a recessive gene not expressed in the phenotype allow for such an advantage? Is the red blood cell of a recessive carrier structurally different from that of a non-carrier?


texts: What makes iodine an effective antiseptic?

texts:
I'm thinking about tincture of iodine, potassium iodide (Lugol's), and povidone-iodine (PVP-I) specifically, which, as is my understanding, work by solubilizing elemental iodine in an aqueous solution. These solutions slowly release free iodine, and it is ultimately the free iodine that does the biochemical damage that kills microorganisms.

But how, specifically, does free iodine cause this damage? The Wikipedia page on povidone-iodine says that free iodine:

  kills eukaryotic or prokaryotic cells through iodination of lipids and oxidation of cytoplasmic and membrane compounds.

and that:

  Slow release of iodine from the PVP-I complex in solution minimizes iodine toxicity towards mammalian cells.

I understand that elemental iodine strips electrons from all kinds of stuff because it is such a strong oxidizing agent, being so close to neutral valency, and obviously that's bad for important macromolecules, but I guess I'm looking for a bit more detail on how it works (or doesn't work) in other respects, with answers to questions such as:

Why does iodination of lipids cause the lipid membrane to fail?
Why does "slow release" make a difference for mammalian cells - are eukaryotic cells somehow better able to handle the damage caused by low concentrations of free iodine than prokaryotic cells?
What makes bacterial spores and protozoan parasites such as Giardia resistant to iodine's antiseptic properties?

Sorry that that's more than one question. But if anyone is able to elaborate on any of these concepts, I'd greatly appreciate it!


texts:
Is the blood test result for the P1 cat is logical?

Because, it shows that even the card containing no antibody, has undergone aggluntination!


texts: Does Sympaticus and lymphatic circulation cause feeling of thirsty after short shower?

texts:
I have been reading blogs, Guyton and Pocock about what triggers the feeling of thirsty.
I am not convinced that is the fact of

warm water
time is short so not much water lost

Assume that the water's temperature is the same as body's temperature.
Of course, there is little temperature change caused by air and water, but I think it is not that much.
I think more important is the steady, continous irritation of skin as a mechanism.

I wrote my suggestion for the answer below.

Do sympaticus and stimulation of lymphatic circulation cause feeling of thirsty?


texts: Is a nucleus more dense than the rest of the cell?

texts:
On the one hand, it seems like there's a higher density of 'stuff' in a nucleus, so it should be more dense. On the other hand, if it was more dense, I'd imagine that nuclei would 'settle' to the bottom of a cell, which would be rather surprising.

Update:
http://www.eng.umd.edu/~nsw/ench485/lab10.htm reports nucleic density of 1.4 g/cm3.

https://books.google.com/books?id=t4ZQRWvr510C&pg=PA85&lpg=PA85&dq=cytoplasm%20density%20g%2Fcm3&source=bl&ots=rEkcu0HzZE&sig=Bs4MVad_pbS7vWY2pRv6ALWf-bc&hl=en&sa=X&ved=0ahUKEwj2rLXVnLbJAhVSlogKHUjAAS8Q6AEIMTAD#v=onepage&q=cytoplasm%20density%20g%2Fcm3&f=false
reports a density of 1.03 - 1.1 g/cm3 for cytoplasm, so less dense.

do nuclei sink then? or is ICF too viscous / there too much disturbance through movement for nucleus to sink?


texts: I found these skulls in a old bottle in the woods. Can you tell me what they are?

texts: Can you help me identify these skulls I found in an old bottle in the woods?


texts: Which of Perutz et al's protein structures other than 3₁₀ helix were correct?

texts:
In 1950, Bragg, Kendrew and Perutz published "Polypeptide chain configurations in crystalline proteins" (open access) and were famously 'proved wrong' by Pauling, Corey and Branson the following year, in the paper that documented the alpha and gamma helices, "Two Hydrogen-Bonded Helical Configurations of the Polypeptide Chain" (also OA)

I'm reading about this (as reviewed here for example) where the idea is that Bragg et al were disproved - in the words of the Pauling paper:

  None of these authors propose either our 3.7-residue [α] helix or our 5.1- residue [γ] helix. On the other hand, we would eliminate by our basic postulates all of the structures proposed by them. The reason for the difference in results obtained by other investigators and by us through essentially similar arguments is that both Bragg and his collaborators . . . discussed in detail only helical structures with an integral number of residues per turn, and moreover assume only a rough approximation to the requirements about interatomic distances bond angles, and planarity of the conjugated amide group, as given by our investigations of simpler substances. We contend that these stereochemical features must be very closely retained in stable configurations of polypeptide chains in proteins, and that there is no special stability associated with an integral number of residues per turn in the helical molecule.

There was one however, the 310 helix which was correctly identified by Perutz's group in 1950. I don't have any access to library facilities at present and online resources aren't quite the same as a solid textbook. I'm wondering if any of the other forms described were in fact correct?

To list, these were:

27a
27b
28
213
214
38
( 310 )
411
413
213

I'll continue looking in the meantime but it's hard to search when there are subscripts in names, and I would think more experienced protein scientists could give me a quicker answer (or just direct me to where I should be reading)


texts: How can I use this data to make a function?

texts:
I'm currently in high school biology (final year) and am currently working on an assignment. I need to create some sort of interactive model, so I've decided to make a simulation-type program.

I've looked a bunch at lots of papers and journals and I was wondering how I could take the data and make a function out of it.

Here is one example (Pleasants & Oberhauser, 2012):

In particular, I want to know how to make sense of the values F_1,11; r^2; and P. I am finding a lot of these values in the papers I'm looking at so it would be awesome if one of you guys could point me in the right direction.

Thanks!


texts: Are human chromosomes connected or separate molecules?

texts:
Do the 46 human chromosomes form a single unbroken DNA helix?  Or is it rather that a human's genome consists of 46 disconnected helices?

If it is the former, does the common numbering scheme for the chromosomes have any correlation to their actual ordering in the one large strand?

If is the latter, is there a convention on how the chromosomes are ordered in genomic datasets?  Also, is there a clear understanding of how sister chromosomes "find" each other in Meiosis I?

Generally, during periods when Mitosis/Meiosis are not occurring,  what's a good physical picture for how the chromosomes are physically arranged (e.g. a bowl of 46 spaghetti noodles, or maybe the sister chromosomes always stay close together, etc)

thanks!


texts: What culturing process / experiment needs a "grid" petri dish (one with a vertical division)

texts:
You can buy petri dishes with separations in them like this:

I have studied biology and biochemistry and never come across one of these before.  What cell culturing / experiment would this be used in?

** Edit: **

Perhaps it's not cell culturing but instead used for containing different macroscopic organisms like woodlice or something?  But then I'd have thought they'd climb over the divisions.


texts: Please help identify insect found indoor in Malaysia, south east Asia

texts: Found this insect in my home. About half an inch long. Would appreciate it if any of you could help me identify it. Thanks.


texts: Can 1.5 gigabytes encoded in the human genome really account for the complexity of a human being?

texts:
I read the human genome is 1.5 gigabytes in size. Thats actually not a lot; Photoshop probably takes more space. Mac OS takes 10+ gigabytes of space. Also, the genome is 1.5 gigabytes when counting base pairs as the alphabet, but the actual unit of information is a codon, which is made of 3 base pairs. That means that if the 64 codons are the alphabet, then the amount of information is (top of the hat calculation) 0.5 gigabytes. This is analogous to a "byte" in computer memory, composed of 8 bits. Byte -> codon, bit -> base pair.

Nevermind that some codons are start/stop signals and not part of a protein defining instruction. You can go further and say that the next level, formed by all the known proteins/chains of aminoacids, is a subset of all possible combinations of aminoacids, and forms a new alphabet. The language of proteins.

Anyway, a cell has 100 trillion atoms, and that structure is controlled by DNA containing 1.5 (or 0.5 depending on taste) gigabytes of instructions. That right there is pretty impressive. But then, the human body has 37.2 trillion cells, and you are telling me those 37.2 trillion cells, each containing 100 trillion atoms, are controlled by ~1 gigabytes of instructions? That doesn't add up.

In computers everything is 0 or 1, but after many layers that simple alphabet of {0, 1} can represent complex structures. I guess the same is possible with DNA, but I feel you'd need way more instructions to represent even the most basic of organs. So, I think I am missing something here. For basic structures, like tissue, veins, eyes, blood, hair; things that we share with animals, is that all encoded in DNA?

The complexity is rather enormous for a rather tiny amount of instructions, so there must be something else controlling organ and bone structure.


texts: What could make a person get ill from not eating often enough?

texts:
Say a person needs to eat every 3 hours, or s\he gets physically ill with fatigue and cold sweating, and this is the case every day.

What could cause this?


texts: Is it true that oral sex exists in non-human animals?

texts:
For example, outside of humans, do other species of animals engage in oral sex, or any oral stimulation of others' genitals purely for pleasure, not any cleansing habits, etc.?

Basically, what I am saying is, is it true that oral sex, like in humans, exists in non-human animals?


texts: Why are genes expressed as proteins rather than other types of bio-molecules?

texts:
I guess, we could infer that the structure of an amino acid has the same functional units as RNA is used to synthesise it. Therefore, from a logical point of view it would make sense that genes are expressed as proteins.
However, why is this the case; why are genes expressed as proteins rather than any other type of bio molecules? Also, from what are other bio molecules expressed if not for genes?


texts:
So I was wondering if consciousness is continous and I found out it might not be the case. But in that case it begs a question, what if in every frame of consciousness my old me dies and new is reborn or rather there is nothing as consciousness but its just a reaction?

What I mean is if I clone a person, the clone would think its the original and we would be unable to determinate it either (if by clone i mean literall copy on the atomic level and with exclusion of any effect of quantum mechanics). If we would annihilate original and put clone into its place noone would be able to tell and to him it would look like everything is continous and nothing happened.

So can it be just illusion in our minds that we are continous sentient beings because we have access to our memory which tells us its like that, same as a clone but as the perception lost focus we die - frame stops to exists?

Can someone clarify this to me or point me to some interesting literature/article on this topic?


texts: What is the name of the smallest self-replicating thing?

texts:
Some time last year, I found an article on Wikipedia about the smallest something to be able to reproduce.

I don't remember exactly what it was, but I am fairly certain that after the initial discovery another of the previous organism (this one slightly smaller) was discovered.

I think that the smallest something might have been the smallest self-replicating protein, or smallest self-replicating molecule, or something like that.

It was not mentioned in this thread: Which organism has the smallest genome length?

It had a strange, stand-out name and I believe it was discovered in the 90s.


texts: When was the purpose of bone marrow discovered?

texts:
I'm currently reading William Cheselden's book Osteographia or The Anatomy of the Bones, which was published in 1733 (for the pretty pictures, naturally; not up to date anatomy). When he addresses the topic of bone marrow, he says,

  Every cylindrical bone has a large middle cavity, which contains an oily marrow, and a great number of lesser cells towards their extremities, which contain a bloody marrow. [...] The bloody marrow is also found in all spongy cells of the bones. [...] The use of the first kind of marrow I imagine is to soften, and render less brittle, the harder fibres of bones near which it is seated; and that the other marrow is of the same use to the less compact fibres, which the more oily marrow might have made to soft; and that for this reason, there is less of the oily marrow, and more of the bloody in young bones than in old ones.

Which strikes me as completely incorrect -- though correct me if I'm wrong. So, when was the purpose of marrow in hematopoiesis discovered, and by whom?


texts: Why does shaving dehydrate the skin? Is there an hormonal effect involved?

texts: I want to understand why the face becomes dry after shaving and if shaving affects hormones? I've heard that after shaving, hair grows back faster, why? Shaving damages hair follicles and they become inflamed. One could get an infection JUST by shaving because tissue is ripped from the hair follicles. So maybe the increase in hair growth can be attributed to the natural blood rush that brings nutrients to the damaged follicles when they are inflamed after shaving....


texts: How are drugs distributed in regards to bone marrow?

texts: I know that as volumes of distribution increase they correspond to the blood, then the vascular rich group (heart, kidneys, liver, brain if BBB permeable), then muscle then adipose. But things like flow should also be taken into account. So are drugs usually distributed in a similar manner to blood, vascular rich group, etc?


texts:
What is the meaning of this poor sequencing result? What is the problem?
Can anyone guide me, please. Thank you.


texts: Do we know how animals refer to us, humans?

texts:
In human languages, we have "sounds" (or words) to refer to animals. For example, in English, we denominate a dog using the vocal sound dɒɡ. So, from the perspective of dogs, if they knew that the sound dɒɡ refers to them, then they "could deduce" that a human emitting the following collection of sounds is referring to them:

  lʊk, ðæt ɪz ə kjuːt dɒg. aɪ ˈwʌndə ˈwɛðər ɪt ɪz lɒst?

Now, what about the reverse? Do scientists know of a particular sound (or maybe a sign, a movement, or related form of communication) used by any animal which signifies "human"? In case the current answer is no, is this ever possible to know? Maybe for animals where studies are more advances, like primates?


texts: What do the haploinsufficiency scores in the clinVar database represent?

texts:
I understand that haploinsufficiency occurs when one of the two copies of a gene is mutated to the point of being unusable, and the single copy remaining is unable to cope with the cell's demands for a given peptide, resulting in a phenotypic deficiency.

In the clinVar database, there is a "haploinsufficiency score" (example here) which seems to range from 0 to 3 (though that is anecdotal only; based on the genes that I've looked at).  I assume it refers to how phenotypic or how deficient the cell is.  However, I fail to find a place where this is clearly outlined...

Am I correct in this assumption, and if so, what does a score of 3 (for example) represent?


texts:
Wikipedia just says...

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

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


texts: What are those huge plants / fungi on trees called?

texts:
I've seen them in Scotland in August 2015:

The plants / fungi were quite high (over 2m) on the tree. They are almost circular if you view them from the top, I guess (except for the part where they are connected to the tree). I guess the diameter of them might be over 14cm.

What are they called?


texts: Is there any complex organism that is both autotroph and heterotroph?

texts: Possibility also include "adaptation mode" if such exist. I don't discern whether autotrophic/heterotrophic part play only minor role either.


texts:
All I know about adaptor is that it is a device that converts attributes of one electrical device or system to those of an otherwise incompatible device or system.
Thank you.


texts: Why do bananas turn black after some time? Please don't just give hypotheses but concrete references to experiments


texts: What is the neural coding of rod and cone cells?

texts:
In Rushton's paper on the Principle of Univariance, he states:

  Thus, though the rod input has two variables, wave-length and energy, the output differs only in one respect, namely 'brightness'.

However, as far as I understand, a photon can only vary according to one dimension, namely wavelength (vibrational energy), because the wavelength and energy of a photon are interdependent.

This suggests then that the input to a cone cell, for brightness to be perceived (i.e. the intensity of light), must be a beam of photons, so that the input can vary in wavelength and amplitude (does this equate to the number of quanta being absorbed by the photopigment per unit of time?).

My question, then, is how can a discrete event (the changing of shape of a photopigment) encode a continuous value (i.e. intensity)?


texts: Most fish have largish bones which support the core muscles.  Around the abdomen, they act as a sort of framework protecting the organs.  With herring, the bones are really fine: almost thread like and there are lots of them: more than on any other fish I've eaten.  I would like to know why herring have such fine bones.


texts: Are immunosuppressors necessary after a bone marrow transplant for Bubble Boy Syndrome?

texts:
I know that under normal circumstances, immunosuppressors are needed to mitigate the host body's immune reaction to the graft. However, people suffering Bubble Boy Syndrome have pretty much no immune system to begin with. Graft versus host disease does occur in some cases, but not all. So, in these other cases, are immunosupressors required?

Thanks to all!


texts: There are people who completely blind or deaf. Are there people who are completely blind to touch in a particular area or in the entirety of their body? If not, are there people in whom the temperature modality of touch or the pressure modality of touch is completely absent? It seems that this might be related to congenital insensitivity to pain, but it is not quite the same thing.


texts: What evidence do we have that dinosaurs were mesotherms?

texts: They went extinct millions of years ago, so what is the evidence supporting the claim that they were mesotherms? And are there any examples of modern-day mesotherms?


texts:
How do crickets get away with being so loud without getting eaten? There are a number of bugs that reproduce by blatantly advertising their location. For instance fireflies advertise their location with physical light and are extremely easy to catch.
How is this evolutionary selected for?


texts: Why do predatory mites have to be introduced multiple times?

texts: I'm combating spider mite infestation using either Phytoseiulus persimilis or Amblyseius californicus. After extensive study of the literature, I'm still unsure why the producers of these predatory mites suggest that they have to be introduced several times (2-3 times depending on manufacturer). I know that adult predatory mites are very agile and scout for new prey. Phytoseiulus is also known to wipe out spider mite populations. So as long as spider mites are present, why should one introduce them at intervals rather than just introduce a large number of predatory mites at the beginning?


texts: Woodpecker pecking, an effective evolution?

texts: I was sitting out on my balcony earlier and saw a woodpecker land on a tree nearby. It began pecking at the tree, and did so about five times, in intervals of about four pecks each time, before finally giving up and flying away. My question is quite simple, were woodpeckers gifted(did probability glean favorably upon) with a positive form of evolution? Does the reward justify the amount of energy they have to exert for food? Were they given an improper and doomed form of evolution?


texts: Is there an advantage to antibacterial soap?

texts:
There are plenty of different hand soaps out there, as well as hand sanitizers. Is there an advantage to soaps that claim that they're antibacterial vs soaps that just say soap?

In particular I'm looking at Softsoap who offers normal soap and antibacterial soap.

Examples:

Normal:

Antibacterial:


texts: Why Didn't Evolution Cause the Human Body to become Streamlined?

texts: If streamlining makes movement/locomotion quicker and easier, why didn't the apes evolve into life-forms that had streamlined bodies (much like fish)?


texts: How exactly does long-term tension (over months) build up in the ligaments, tendons, muscles?

texts: And is there any basis for believing that massage relieves that tension?


texts: gene expression of tumor with different percentage of infiltrates

texts:
I'm performing differential gene expression analysis on rnaseq of  tumor samples that might have different amounts of immune infiltrate.
Tumors are extracted from patients that respond/not respond to immunotherapy

In my lists I found several immune response related genes significantly modulated but i suspect that this could be related to the different amount of immune infiltrate.
In order to highlight the genes that are induced by the tumors and not by the different amount of immune cells... it could be appropriate to normalize the raw reads counts (on which is based my analysis) on the basis of CD3 gene?


texts: Questions regarding transformation in bacterial cells

texts:
First off, in transformation the donor DNA aligns itself with the complementary bases in the recipient DNA.
Now a "perfect" alignment of the donor DNA ( Sorry if my terminologies are incorrect ) would mean that an exact replica of the donor DNA fragment already exists in the recipient DNA. If such is the case no genetic recombination will take place but genetic recombination is observed, this is the part where I get confused.
If the DNA fragment is aligning itself with the donor DNA and and causing a genetic recombination, then obviously the donor DNA fragment should contain some variation from the recipient's DNA. This would mean that the alignment of the DNA fragment isn't perfect and not every base in DNA fragment can form a complementary base pairs with the recipient DNA. ( Again sorry for usage of improper terminology as I'm a new student who just started an introductory course pertaining to microbiology ).
Now the problem is -

Shouldn't it be energetically unfavorable for the donor DNA fragment to replace the original DNA as the original one should be able to form complementary base pairs with the entirety of the recipient DNA while the donor DNA can do so only with a part of the recipient DNA.
After thinking about this, I thought of an assumption to explain this. The RecA protein involved in transformation is somehow forcing this process to happen. The thing is how? I have zero knowledge of enzyme chemistry and can't understand how this could possibly happen?
So is this assumption correct? If so is there any reference material explaining how RecA protein could be doing this?

This brings me to the second issue. This newly created DNA should now have many irregularities, how are they fixed?
After some thinking, I came to the conclusion that as RecA proteins are involved in DNA repair, the RecA protein simply fixes the irregularities. Is this line of thinking correct?

In short, I have assumed that a RecA protein is causing a DNA fragment which can not form complementary base pairs with the entirety of recipient DNA to be accepted in the recipient DNA, following which the irregularities that arise are also fixed by RecA. Is this line of thinking correct?


texts: Would somebody born 'reversed' (e.g. heart on their right side, etc.) be completely healthy?

texts: By reversed I mean their body is a complete mirror image of a normal human's.


texts: What is the aqueous solution for DNA immobilization?

texts:
This paper
Electric-field assisted immobilization and hybridization of DNA oligomers on thin-film microchips

Which is talking about how the electric field improve the DNA immobilization process.

Unfortunately, I have no biology background, I could only understand about 50%  contents.

In the section 2.3.1, its says "the chip was exposed to a aqueous solution of the DNA probe".

What is the aqueous solution of the DNA probe?
Is it DD water (DI water) + DNA? or it is some kind of buffer solution + DNA?


texts: Comparion between machine vision & human vision

texts:
I hope this is the correct Stackexchange to ask this question.

I am trying to know : What is the current status of knowledge regarding human vision and pattern recognition.

More specifically,

How does the human eye read signals from  the cone cells? Is it row
by row, column by column like a computer? or or there other things
happening ?
When detecting, say, an edge, or a connected component - does the human eye continue searching row by row? or does it jumpimmediately to the next neighbor? Are human cone cells arranged in arectangular gird with 8 neighbors per cone besides for the edges?(my guess is no). Then how are the neighbors addressed? Does somerace condition occur?

As you can see, I am not a biologist, I am a physicist working with computer vision. I have moderate knowledge of anatomy, but I am willing to learn.

Thank you


texts: X Linked Hardy Weinberg Equilibrium Problem

texts:
In a given population under Hardy Weinberg equilibrium, 40.0% of men have hemophilia. What is the probability that a random man and random woman will have a daughter with haemophilia?

I think the answer is 16%, but the answer given is 9.6%. According to  Hardy-Weinberg principle, p2 + 2pq + q2 = 1. In order to inherit the disease, the mother must either be a carrier of have the disease, which occurs with probability 1-q2 = 0.72

Therefore, the odds of having a child with the disease is (0.84)(0.4). Since it asks for the probability of a girl, the total must be divided by two, so the answer is 0.168

Where am I wrong?


texts: How does symbiogenesis explain reproduction of organelles along with the cell?

texts:
Symbiogenesis is an evolutionary theory that says that prokaryotes eventually evolved into eukaryotes (having multiple organelles and better structure) by forming symbiotic relationships with other bacteria that have been absorbed, or have entered the cell in an initially parasitic way.

My question is that when the individual bacteria have become organelles, what happens when the cell reproduces? The bacteria were individual entities with their own reproduction mechanisms before they became organelles. Do they still divide in their own way inside a cell (and are subsequently present in both halves of the cell when it is dividing itself), or does their division somehow get incorporated into the cell's own DNA?


texts: In theory, would it be possible to create an injection of Vitamins, Minerals, sugars etc so that eating was no longer necessary?

texts:
I am wondering, out of pure curiosity, whether with current medical & biological science, (or indeed with accepted probable future developments in those areas), in theory, would it be possible to create an injection of vitamins, minerals, sugars etc so that eating was no longer necessary, and in fact, an average life with average energy usage could be continued?

I am not a biological professional nor academic, so apologies if this is on the wrong Stack Exchange site, however I thought this was closest to the mark. If there is somewhere more appropriate please direct me, and I shall delete the question and post it there.

Also, if no, would there be certain parts that you couldn't replicate in an injection or something of the like?

NB: This doesn't have to be an injection, any simple method of ingesting or attaining everything the body needs. This could be a pill, or anything. I simply used an injection as an example.

Thank-you very much.

Edit:
Having found this question,
Has there ever been an attempt to create nutritionally tailored food for adult human consumption?
I would like clarify. This has given me a lot of information, however, I am looking for any method APART from food. Thanks.


texts: Why can't plain water be used in dialysis? Why is buffer used?

texts: I read that buffer is used in dialysis because usage of water could cause precipitation of proteins but I don't really understand why and how water can cause precipitation of proteins and buffer cannot.


texts:
This article in ThoughtCo.com claims we have a resting stomach pH of 4-5.

Unfortunately, there are no references, so I can't verify what it says.

I am slightly confused, however. The study says
"Results are given as medians and interquartile ranges: fasted gastric pH, 1.3 (1.1-1.6); gastric pH during the meal, 4.9 (3.9-5.5)"

This other one says
"In the fasted state, the median gastric pH was 1.7"

This article in UCSB Scienceline says "The normal human stomach has a pH which can range from approximately 1-3 but is usually closer to 2.". Unfortunately, they too don't provide any references, so I can't check their claim.

So what is the pH of a human stomach at rest? If it is about 2, then did the article in ThoughtCo.com get it wrong? If it is about 4-5, then what did I misunderstand in the two studies I cited?


texts: Does sympathetic nervous system acts bilaterally for pupil dilation or other two sided organs?

texts: The question might seem weird. Does sympathetic nervous system acts 'bilaterally' meaning if you shout to a person's left ear a loud noise (e.g. by headphones), will it activate sympathetic system just on the left or on the both sides. For example it will only dilate left pupil or dilate both ?


texts: Why is it necessary to have both cone and rod cells in the eye?

texts:
Our eyes have both cone and rod cells. Rod cells measure the intensity of light whereas cone cells identify the colour of the image formed in the eyes. So cone cells must also be able to identify white, black and grey and also their shades.

So it wouldn't have been that much trouble to just have cone cells cells as identifying black and white would have been the same as measuring the intensity of light. Wouldn't it?


texts:
I have isolated RNA from cell culture (T25 flask, mouse cells) with trizol. I've measured the sample on Nanodrop, and this is what I've got:
A260 (10mm): 16.408
A260/A280: 1.98
656.3 ng/ul
How is this possible? What could go wrong here?
Thank you!


texts:
Are all aposematic insects chemically defended? Can there be insects that mimic chemically defended insects that are also aposematic?

Any ideas?


texts: Why does evolution not make our life longer?

texts:
Why does evolution not make life longer for humans or any other species?

Wouldn't evolution favour a long life?


texts: Text Book Recommendation: Organic Evolution

texts:
I was wondering if anyone could point me in the direction of any text books on organic evolution? I have recently become interested in the subject and would like to know more. I think an undergrad level book would be a good place to start, but if you would like to recommend any graduate level books it could also be helpful.

I have a background in mathematics and modeling using mathematics. I have also taken a genetics class and an intro to cell biology class as well as read some papers on both subjects. Any help would be nice.

update

I was looking for a higher level discussion on the mechanisms of evolution. A better term to use might be evolutionary biology.

Sorry for the confusion I was under the impression that "organic evolution" was a common term.

Thank you for your time.


texts: Why exactly does UMN lesion cause hypertonia?

texts: The corticospinal tracts are excitatory in nature (Glutaminergic). So damage of the CST would mean less excitatory input to the LMN. By this logic, there should not be hypertonia. What is the mechanism behind this spastic (hypertonic) state of the muscle in UMN type of lesion?


texts:
Feeling the hardened tissue of a scar on my head I wondered what the purpose of that scarring is, such skin scars are pretty harmless but from what I understand internal scarring can cause major problems if internal organs get damaged.

An extreme example I vaguely remember is the scarring following nerve damage, the new scar tissue can't transmit signals and so the nerve stops functioning properly.

Why does scarring occur when it seems so detrimental, why don't we rebuild the old tissue?


texts: I caught a scorpion in my house and wondering if it is a deathstalker? This was caught in Central Asia Northern Tajikistan.


texts: Salbutamol's Pathways of Interaction and Classification

texts:
Salbutamol is a very commonly used direct-acting β2-agonist.
This suggests me that it is sympatholytic.
However, it has sympathomimetic pathways, see PubChem for Sympathomimetic.

I am trying to think the group of Salbutamol.
Sympathomimetic or sympatholytic.

How can you classify Salbutamol into a group?


texts: Can the eye determine which type of defocus is presented to it?

texts:
I have a question regarding myopic and hyperopic defocus.
My question is, is the eye able to determine which type of defocus is presented to it and if so what mechanisms allow it to distinguish between the two types of defocus. This question was thought of after reading a study which showed that the eye's AL could change temporality based on which type of defocus was presented to it and I was unable to find a definitive answer on to why this happens.
As well as this, I saw numerous reports on how different lenses can slow the progression of myopia by presenting peripheral myopic defocus onto the retina without an explanation on why this occurs.
Thank you for taking the time to read my question and I look forward to your response!


texts: Fruit colour related to the dissolving of pectin

texts: What does the dissolving of pectin have to do with the colour of a fruit?


texts: A day in Beijing is like smoking Only one sixth of a cigarette

texts:
This is the title of this blog post followed by this other good post.
I'm particularly anti-tobacco-smoke, at the point of not always considering other pollution, and this article shows how this kind of domestic pollution (main domestic pollution is usually heating) is probably no insignificant in the global air pollution.

The weight of this pollution is also maybe increased since people tend to be nearer from potential smokers than from cars (e.g. near entrances).
I've not known the period of the past, without the smoke-free laws in buildings, but it seems in my country, that it has just moved the problem, possibly reinforced smokers reflex to smoke when outside

The author shows useful references, that all measure second-hand smoking in terms of PM2.5 which is the common indicator with PM10 for air pollution [car traffic,domestic heating,industry,coal combustion,construction,quarry,waste treatment].
The results are interesting showing the important rate of PM2.5 in second-hand smoke, it would even be very useful to indicate air pollution levels in terms of cigarette inhalation. 0.17 cigarette/day is quite more insightful than 150μm of PM2.5, at least to me.

But I'm still skeptic and think the effects of second-hand smoke are more important (second-hand smoke is smaller in size than 1μm, considering not only cigarette from manufacturers which include many brute carcinogens and poisons (arsenic, hydrogen cyanide,..), but other tobacco/or drug smoking that are different but considerably noxious too)) and this study is quite informative too, comparing diesel car exhaust to cigarette combustion.

I'm wondering:

is the pollution from cigarettes as volatile as the rest of air pollution?
is the concentration of second-hand cigarette global pollution not insignificant compared to the rest of pollution (in countries with high smoking rates)?
does it go in higher layers of the atmosphere, lower layers (more critical), or does it blend uniformly?
can air pollution mask (with PM2.5, and PM10 reduction filter) protect as well from it?

particles size in micrometer, from http://en.wikipedia.org/wiki/Particulates

edit: this http://ash.org/CAEPAProposal.pdf report is particularly interesting


texts: Resting and action membrane potential..?

texts: In the resting membrane potential of neurons the inside of membrane is kept negative and outside of membrane is kept positive by the utilization of energy through Na-K Atpase pump, While during action membrane potential through the opening of specific gated ion channels inside of membrane is made positive while outside is made negative, What is the significance of specific charges across the membrane, does these specific charges across the membrane play any role in the passage of neurotransmitters ? or these charges are just arbitrary ?does this can happen that during resting membrane potential the inside will become positive and outside will become negative and vice versa, I want to know that what is the significance of these specific charges across the membrane ..?


texts: What is Mendelian Segregation and how is it related to the Hardy-Weinberg equilibrium?

texts: I can't find the exact definition of Mendelian segregation. In addition, I am wondering how it is related to the Hardy-Weinberg equilibrium?


texts:
Location: Germany
While cleaning the windows today, I realized some dirt falling off the top of the window frame. By looking further, it seemed to be some kind of cocoon. (The first picture is very bad, I'm sorry)

Those cocoons were about 2-3cm long. There was a total of 6 cocoons.
Two were damaged by falling down.

The last picture shows the inner part of the second picture I think. The larvae(?) was about 0.8cm to 1cm long.
Not sure if it matters, but the window is an attic window, located at the third floor.
Do you have any idea, what kind of larvae it is?


texts:
Paracetamol overdose is one of the most common drug toxicities. It may be treated by intravenous N-acetylcysteine which replaces the glutathione that is used up in paracetamol metabolism to prevent the harmful effects of NAQBI.

Why can glutathione, NAC nor an inhibitor of the alternate cytochrome metabolism be added to paracetamol to prevent the possibility of acute liver failure? I imagine there is a reason as this is too obvious a solution.


texts:
I was reading a paper in the journal Molecular Basis of Disease, which stated:

The ORFs are arranged as replicase, and protease and major S, E, M,
and N proteins which follows a typical 5’—3’ order of appearance, are
considered are as considered as major drug/vaccine targets.

(Naqvi, et al., 2020)
I'd like to know what the " ' " means; if it means inch, or something else like minute. I am doing research so I don't know what units are being used.
Source
Naqvi, A. A. T. et al., 2020. Insights into SARS-CoV-2 genome, structure, evolution, pathogenesis and therapies: Structural genomics approach. Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease, Volume 1866, p. 165878.


texts: How do plants take in only carbon dioxide?

texts:
There are only 400 molecules of CO2 in 1 million molecules of air.

How do plants only take in CO2 but not the other gases?

My teacher told me that's because there is less concentration of CO2 in the leaves than the air and the CO2 rushes in the leaves.But, then how does the leaf maintain the concentration of CO2 and other gases?


texts: How did people's liking of ceremonies evolve?

texts:
Habitual group activities are prevalent across many animal species, particularly in mammals, especially in primates.

However, I do not see any evolutionary benefit of this. 'Ceremonies' take time, and in many cases seem to exert more energy than they reap. Note at this point I am not talking about hunting groups, but rather about group activities that serve a purely social purpose (mourning is a  good example of this and is present in elephants, chimpanzees, bonobos, and probably more). This costs significant amounts of resources, time, and energy which apparently could be better spent hunting, foraging, traveling, mating, or grazing.

I'm interested in finding a timeline, and explanation, of why and how this phenomenon of higher social rituals (perhaps using mourning as an example) evolved throughout the mammalian kingdom.

A cursory google revealed nothing about how this 'liking' of interaction evolved.


texts: How to decide which is the correct scientific name for a particular species

texts:
To start with, I am not a person having sound knowledge in biology. When I started my search for phyto-chemicals in a particular family in the plant kingdom, I got confused. The scientific papers use a particular name, and when I searched in these 2 websites, (just to name it) I got the message that some of the names are  "not resolved"  or "synonyms".

My questions are

Biologists do they accept  the names mentioned in  website 1? If not where can I find authentic names?
Who controls / monitors the name of these plant species?


texts: Alternatives to commercially available flow cytometric analysis software for use in cell cycle analysis?

texts:
I know that many labs use either FlowJo or FCS Express to plot and analyze their flow data. These seem like the two standards for most labs (and I have used FlowJo before). However, my current funding does not cover software licenses and I'm not keen to pay $500-2000 out-of-pocket for a license.

Are there alternatives that approach the quality of FlowJo/FCS Express but are open-source/free with an academic license? I'm looking for an approach which will allow me to fit G1/S/G2-M curves to my data.


texts:
A closed wound is one where skin is intact and underlying tissue is not exposed to the environment.

Abrasion is an erosion of skin usually due to sheering force. In most cases the dermis is intact and the injury is superficial limited to epidermis. Abrasions heal without scarring by epithelialization.

Are abrasions considered closed wounds? I would think they are open wounds as the underlying tissue (which would be dermis in this case) are exposed to the environment. Please state the reason why they are classified into whatever group.


texts: What are in common between transcription factors?

texts:
In terms of their structures (primary to tertiary) and locations?

Why do they have these commonalities? Or are any of these commonalities critical to their functions?


texts: According to the Wikipedia article on swans, swans are mostly monogamous but may sometimes separate, particularly after a "nesting failure". What "nesting failure" may mean is not entirely clear to me. Does it mean that they they have literally failed to build a physical nest? Or is it that they have failed to produce offspring? Or is it something else entirely?


texts: What is the "lifecycle" of an average eschar and what types of cells are involved in each stage?

texts:
(after some deliberation in the comments, I've decided to make the question more general)

An eschar or "dry scab" often forms at a site of injury over a large cut or sore.

It seems as though the healing scab portion binds more strongly to the other scab cells than to those of the surrounding healthy tissue initially, as evidenced by the ability to remove the scab en masse without disturbing the edges of the actual wound (in surgical debridement or when the area is "picked" at).  Then, the eschar bonds then bonds more strongly with the edges of the wounds (so it's more difficult to remove), and then finally, the underlying newly formed skin seems to push it off completely.

Does this accurately describe the "lifecycle" of a common dry scab, or are there other well defined stages in the process?  What types of cells (platelets in the beginning?  epithelials at the end?) are involved with each stage of the process?


texts: What is the potential function of ultra-conserved elements in the genome?

texts:
If selection pressure results in conservation of DNA sequences, what is the most plausible explanation for the existence of ultra-conserved elements (refs here and here) given that there hasn't been any significant validation of the functional significance of these elements other than a lot of bioinformatic analyses across different genome datasets? If these are of such high significance, does this mean that there is still some significant gap in our understanding of fundamental biology or is there another explanation? The second reference in particular show that there are UCEs shared between plants and animals, but are not syntenic (which is not necessarily a surprise) so it might suggest that at least a class of UCEs are associated with structural rather than functional elements.

It appears that there are at least several different 'classes' of ultra-conserved elements, based on the number of matching/identical bps, their spatial distribution across the genome and the species in which they exist. Even though there is probably no single explanation that would account for all the possible functions they can have, it is surprising that they are difficult to test functionally. This is again probably due to a lack of understanding about their properties and therefore no real method to validate their function. I think this is where we need to think outside the box to come up with the answer.

What would be the most obvious (and possibly not so obvious) function for UCEs?


texts: What accounts for size variation in breeds of dogs?

texts: My assumption is that dogs vary so much in size because of artificial selection pressures coming from human breeders, but are there genetic loci that roughly determine approximate size?  Do other feral species of animals exhibit such a wide range in sizes or is this something that only occurs when breeders intervene?


texts: Mysterious spherical mass of feathers (Reddit)

texts:
Original posting from Reddit

I am posting this here in the hopes that an ornithologist might be able to shed some light on this unusual finding.  Locality is Boise, Idaho.

This appears to be a roughly spherical mass approximately 6 cm diameter, most of which comprises tightly packed feathers with a central core of dermal tissue.  The mass has been parasitized by maggots.

I speculate that this is some kind of tumor, which detached from the afflicted organism, and the decaying tissue attracted flies after detachment.  But that's just a guess.  If anyone has seen such a phenomenon before, please feel free to enlighten me!

Note, I am not the individual who found this object.  I am merely relaying the question to this forum.


texts: Can cell mediated immune response be transferred via blood transfusion

texts: I read that human body can develop cell mediated immunity to viral infections and subsequently clear the virus. For example, people clear warts through cell mediated immune response against the wart virus. Is it then possible to transfer the blood from one person to another to transfer the type of immune cells that kill the virus?


texts: Is it possible to simulate tetrachromatic vision in a trichromat?

texts:
Suppose we are able to stimulate the whole matrix of cones of a human retina, targeting each cone individually¹. Normally we would project an image in the LMS color space onto the cones, in such a way that each sub-image of particular color channel would get to cones of corresponding type. As the eye moves, this image would be adjusted so as to create an illusion of real surrounding (similarly to a VR headset).

Suppose now we think up a new spectral sensitivity function $P(\lambda)$. We choose a subset of e.g. M cones to represent this type of sensitivity, making sure that this set is scattered enough around the M cones so as to avoid clumping the same color channel cones. And then we try to simulate tetrachromatic vision by replacing the M-channel sub-image in the projection by a special sub-image that an actual sensor with $P(\lambda)$ would capture.

Would this result in a sensation of a new color having appeared in the image, or would this be simply a lot of noise in the visual field?

¹The technology is not quite there, but on the way: see e.g. this answer.


texts: Nocturnal Animals whose Eyes Don't Shine

texts:
Are there any classes of animals which are mostly nocturnal and rely on their eyesight to a non-negligible degree whose eyes still don't shine during the night?

In other words, are there animals which have decent night vision without having a tapetum lucidum?


texts: What are the side-effects of long-term liquid breathing?

texts: I just saw a recent Physics question that mentioned liquid breathing (which I had never heard of before) and I started to wonder about its long-term effects. Let's imagine a person underwent liquid breathing for some wacky reason - see the Wikipedia page for some starters - for a long time, maybe a month. What would begin to happen to them? Would any effects be reversible?


texts: How does an ant know about Earthquake is it because of an organ or due to other factors?


texts: What are the criteria for determining the influence of epigenetic factors?

texts: Isolating a gene or sets of genes in diseases sometimes isn't enough to determine penetrance - epigenetic factors can have a significant effect. What are the criteria in determining whether epigenetic factors are significant?


texts: Do dead cells always contain no nucleus?

texts:
If I examine a dead cell, can I be sure that it has not a nucleus?

And what about the other organelles?


texts: What happens if the Nematode epidermis becomes damaged?

texts: This animal has a hydrostatic skeleton which lets it move. If we damage the epidermis and fluids come out, can the nematode still move ?


texts: What happens after the purification step in Hi-C sequencing?

texts:
I am a statistician reading an article on Hi-C, and I am trying to better understand one of the steps in the DNA isolation and sequencing process.

Since I'm a statistician, please try to avoid too much jargon in your answers, and if you must use jargon, please define/explain it.

Specifically, I am confused about the isolation and shearing step.  To explain myself, I will make reference to the following images, labeled 1 through 4.

Image 1)

Image 2)

(source: nature.com)

Image 3)

(source: babraham.ac.uk)

Image 4)

(source: nature.com)

I understand that the DNA is cut up with restriction enzymes, producing a cloud of DNA fragments, some crosslinked and other not. When these pieces are attached with biotin and ligated in a dilute mixture, it is highly likely that these pieces will ligate with themselves, resulting in either; 1) a ring from strands that were NOT crosslinked (as in the third drawing in Image 3 marked "self-ligation"), or 2) figure-eights from strands that ARE crosslinked (as in the fourth drawing in Image 1).

Now, the following is what I find confusing:

The pull-down step draws down the rings containing biotin, but Image 1 and Image 4 make it seem as though only the crosslinked bits are pulled down, and not the solo rings. Don't both have biotin?  And thus would both be drawn into the pulled-down sample?  Or does the pull-down process rely on a molecule having 2 biotins?  If not, can one discern whether a pulled-down piece of DNA is the result of a cross-linked or solo piece of DNA?
Why aren't all of the loose ends of the DNA ligated in Image 2?  Incomplete digestion?  Does this affect the biotin linkage?
My next question.  Assuming that the pull-down process only selects the figure-eights that are crosslinked, then purified (i.e. the cross-linking protein or formaldehyde is removed) forming a ring that is composed of two strands of ligated DNA (as in the upper-right corner of Image 4).  The process then records a genome-wide contact matrix $m_{ij}$, the number of "ligation products" between locus $i$ and locus $j$.  What is a "ligation product"?

Sorry, I know the above is a lot, but I want to understand the nature of the data before I analyze it.  Thank you for your help.


texts: Who compared developmental biology to crystallography?

texts: I need to find out the name of a nineteenth century biologist who compared developmental biology to crystallography. His idea was that crystals are formed from 'cells' (defined molecular units) that bond together to form arrays. In living organisms cells are bound together but the rules that form the structures change as the organism grows, especially in animals, which is why we have different organs. In both cases you have units that coalesce undirected but according to rules to form structures. I remember finding out about this biologist from a documentary which also showed illustrations from the book he wrote on the subject. I can't find his name or that of his book using a web search because it's too obscure and that would only work with the correct terms. Does anyone know anything about this?


texts: Why does smoking change the human voice?

texts:
What happens to the biology of the voicebox of smokers?
Women's voices can change to croaky men's voices, and vaper's voices develop "white noise" content, like a TV set to static, compared to their original voice which is closer to an oboe reed. I am curious why the white noise content and What happens to the voicebox and what happens to the sound of humans that smoke?


texts: Simple and inexpensive geobiochemical studies

texts:
I plan to write a research proposal for conducting a small experiment related to geobiochemistry. I aim to make the experiment:

1) Simple (middle school aged students could comprehend its main ideas),

2) Inexpensive (less than $500 of science equipment is needed),

3) Fast (can be done by one person within 2 weeks of full dedication).

As a side note, the station does have a microscope that I could use.

I would have access to the surrounding areas and can collect soil, rock, shell fossils, etc. Previous groups have discovered methanogens in the soil and endoliths in the rocks. However, without much background in astrobiology, I am uncertain how much expensive equipment and time was needed for these experiments.

I am mostly hoping for ideas on how I could conduct a simple and feasible  experiment that could be shared with middle school students. Such as searching for life, biosignatures, etc. As I do not have experience searching for life and biosignatures in the field, I am truly unsure of how to approach this in a reasonable manner. Any suggestions greatly appreciated!


texts: Are there any fungi that can digest humic acids?

texts: Humic acids are a complex group of organic substances, that are generally known to be hardly biodegradable. Fungi as agroup are known for breaking down complex organic matter like cellulose or lignin. But are there any that beak down humic acids as a major contributor to their energy needs?


texts: How did the nucleus of eukaryotic cells evolve?

texts:
What is/are the most popular theory/theories on how the nucleus evolved?
I know mitochondria came from alpha-proteobacteria, chloroplasts from cyanobacteria and that eukaryotes evolved directly from archaea, but what about the nucleus?


texts: What does it mean to share similarities among living organisms "both horizontally and vertically"?

texts:
I came across the following lines in a textbook (NCERT biology for class 11).

  Systematic and monumental description of life forms, brought in, out of necessity, detailed systems of identification, nomenclature and classification. The biggest spin off of such studies was the recognition of the sharing of similarities among living organisms both horizontally and vertically

What does "both horizontally and vertically" mean?


texts: Thickness / size / volume of a macrophage

texts: What is the thickness of a macrophage? From some available literature it looks like a macrophage has a 'circular' shape of radius ~10 microns. But I need the thickness to calculate its volume.


texts: They were attached to a tree in a black-water inundated forest (igapó) near Manaus, Amazonas, Brazil. The photo was taken in mid June, the water level was already high, and the eggs were about one metre above the water (not sure if they had been or would be under water at some point). It's been many years now, but I think the whole group was about 5 to 10 cm long (about 2–4 inches).


texts: Base Substitution Probabilities Derivation

texts:
In Felsenstein's 1981 Paper Evolutionary Trees from DNA Sequences: A Maximum Likelihood Approach, he describes (in equations (6) and (7)) a derivation of the equation of the probability of a particular base substitution.  I am having trouble making the connection between equations 6 and 7.  That is, going from

$$P_{ij}(dt) = (1- u\  dt)\ \delta_{ij} + u\ dt \ \pi_j \quad\quad [6]$$

to

$$P_{ij}(t) = e^{-ut}\ \delta_{ij} + (1- e^{-ut}) \pi_j \quad\quad [7]$$

where $u$ is the rate of base substitution per unit time, $\pi_j$ is the probabiltiy of observing a particular base and $\delta_{ij}$ is the Kronecker delta function (1 if i=j, 0 if i != j).

In the paragraph that follows these equations there is an explanation as to why the exponential term makes sense (if you already know thats what it is), but I'm not understanding how to get from the first equation to the second. Any insights?

In case anyone is ever interested (or perhaps if I eventually forget), it appears that Felsenstein is using a Poisson Process approximation for equation [7], although even with this new information I still do no see the connection between equations [6] and [7].

Page 9 of this thesis had a pretty good explanation of this.


texts: Does the cell release the empty capsids?

texts:
The virus via the spike of the capsid connects to a receptor in a cell, then the DNA enters the cell wall.
My question is what happens to the capsid - does it stay connected to the receptor or is getting loose.
(e.g disconnected from the cell).


texts: What determines the reversibility of cell of G0 phase in cell cycle?

texts:
From Weinberg's The Biology of Cancer: A cell that has been recently formed by mitosis must decide whether it will once again initiate a new round of active growth and division or retreat into non-growing state G0. This decision is strongly influenced by mitogenic growth factors in the cell's surroundings. Their absence or presence of anti-mitogenic growth factors will trigger the default decision to proceed from mitosis into the G0 quiescent state.
Withdrawal from the cell cycle into G0 is often reversible (cell can re-enter into active growth and division), however some cells irreversibly leave the cell cycle (such as neurons).

Here comes my question : What determines in the cell whether the cell will go to reversible (quiescent) or irreversible (senescent) state of G0? I have found that it has something to do with the amount of RNA (low RNA content in reversible), but I do not understand why low RNA content means that the cell should proliferate again. And are there any other criteria that determine whether the cell will go to quiescent or irreversible state? (I am looking for exact molecules and mechanisms, the more into detail the better !)


texts: Where do gut bacteria come from in different organisms

texts:
We know that some of the bacteria in our gut come from the food we eat and our environment. I want to know if there is evidence of bacteria being transferred from the mother to her fetus or from the mother to the eggs.

I'm currently working with insects that have plastic-eating bacteria in their gut. They are raised in isolated spaces so those bacteria would have to come from the bran they eat or from their mother. I'm a physics student interested in biophysics so my biology knowledge is still a work in progress. Thank you.


texts: When I was about 5 or 6 years old, a tiny yellow puffball with 2 black spots which I think are eyes landed on my finger. I didn't dare breath, and after a few moments it flew away. Is there any such species that is similar to my description?


texts: What is this insect flying in my Los Angeles bathroom?

texts:
We live in the Los Angeles area. This insect has been very common in our bathrooms recently:

They're about 1/4" long, and can often be found resting on our towels. In the months leading up to December, we've been seeing them more and more.

Do they cause any harm?
Could they be responsible for the holes I've
been finding in my shirts?
Even if they're just a nuisance, how can
we get rid of them?


texts: is it possible for Cougars and Cheetahs to reproduce

texts: I know that many big cat hybrids exist ie ligers, but I always thought it these hybrids were limited to members of the Panthera genus till I came across a cross between a leopard and a cougar. Now since cougars and cheetahs are more closely related to each other than to leopards could these two successfully reproduce?


texts: Can anyone suggest a dye which specifically targets DNA, but is not fluorescent? We plan to mark DNA before observing it with RAMAN-Spectroscopy. Because of the weak signal, even a low emission would disturb the reading.


texts: Proteins: Post translational modification

texts:
I am a physicist and trying to understand some protein chemistry for a small project. Basically, amino acids combine to form proteins and after forming the primary structure, some chemical modification may occur, such as phosphorylation or glycosylation (post translational modification). In case of the enzyme carbonic anhydrase a zinc ion is added post-translationally as a cofactor. (The amino acid sequence can be seen here (scroll down to 'sequence' title).

Is the attachment of zinc regarded as a type of post-translational modification?
When carbonic anhydrase is denatured, is the zinc ion released in the medium?
Will the amino acid sequence (primary structure) be changed after denaturation? If yes, are amino acids removed after denaturation, if yes, which?
I guess Zinc will be removed after denaturation. Is the remaining structure the primary protein structure?


texts: I found this in Russia. It is approximately 2cm long.


texts:
Found this on the carpet in our office(North Carolina), no idea how it got there.
It is at between 8 and 12 inches long.


texts: What is the silencing mechanism of AGO1,AGO3 and AGO4?

texts: I read that this proteins lack of slicer activity, so what mechanism do they use to perform gene regulation?


texts: Is there a biological explanation for perceived altered cognition whilst on cannabis?

texts:
Cannabis has been associated with literature, arts, and culture for centuries. There are a few features of the drugs affect on the human mind that account for this, however it remains illegal in most countries.
In a very tangible way, cannabis causes a few alterations of perception, such as an altered sense of time and this is often exploited by police to see if a potential felon is intoxicated. Other psychoactive alterations that are attributed to a cannabis (AKA marijuana or weed) include a temporary sense of deeper metacognition, depersonalization, & derealization.
Whilst I'm aware that this is probably the result of the active compound THC, it's unclear how is this deeper feeling of cognition achieved from a physiological perspective? What is this process in the brain that changes the perception of reality?
Ideally studies mirroring the recent Cahart-Harris et al., 2016 paper would be ideal (but focused on THC rather than LSD). That paper identified key physiological features that correlated with the feelings of being "high" such as changes in brain blood flow, electrical activity, and network communication patterns.
Note I am not talking about long term IQ alteration, but rather the temporary affect the drug has on the brain's cognition.


texts:
As I understand during anaerobic respiration, the electrons received from the decomposition of glucose are transferred to nicotinamide adenine dinucleotide and flavin adenine dinucleotide. As there is no oxygen the electrons are then transferred to something else, either Lactic Acid or Ethanol (in the case of yeast).

So why do animals produce Lactic Acid and not Ethanol?

Also, (I know this is silly, but) what would happen if they did?


texts: How to track bacteria/ protozoa, unicellular algae in big volumes?

texts: Is there any special cameras and dyes? If I want to track migration/motion of them in 0.1-0.5 cubic metres.


texts: What is the probability that there are no substitution between an ancestor and a modern individual?

texts:
What is the probability that there are no differences if you compare the DNA
of the ancient sample to a single DNA sequence from a modern individual? Assuming the individual was diploid and lived T generations ago.

How would you go about finding this probability? I would assume that drift and maybe selection would change the sequence and the probability of no change over time would be extremely low.


texts: Exclusion Limit and permeability of outer membrane

texts:
According to this textbook:

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

and then on the same page:

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

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

My Attempt:

This source claims that

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

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


texts: How can a coldblooded animal make an egg hatch?

texts:
I have chickens at home, and yesterday while removing the eggs I felt that they were quite warm. This seems to make sense, because the chicken has been brooding on it in order to make it hatch.

However now I wonder: next to chickens and/or other birds, there are other animals who are coldblooded and who are having eggs. Brooding on an egg means that the animal is delivering body temperature to the egg in order for the egg to grow and eventually produce a young animal. Now how can a coldblooded animal deliver body temperature if by definition, such an animal does not have body temperature?


texts: Question on compatibility of blood groups

texts:
How come a person with blood group O can donate to a person with blood group AB? Since there are A and B antibodies in the O blood group blood surely this would cause agglutination in the blood of the recipient?

My first hypothesis was that the antibodies and red blood cells were separated through use of a centrifuge or something but blood transfusion has been used for hundreds of years before this machine was even invented? What is going on here? Or was it just that before blood types were discovered only people with identical blood groups could donate/recieve from one another?


texts: Why do mints make your mouth feel cold?  And specifically, why does your mouth feel so cold if you eat a few mints and then drink a glass of cold water afterwards?


texts:
One of my friend was saying that her aunt (father's sibling sister) was having polydactyly but none of her cousins (her aunt has two daughters) is having it.

What is the chance that my friend's children inherit polydactyly?

(considering that her partner nor anyone in his generation exhibit polydactyly)


texts: What characteristics do living organisms (like humans or plants) have that viruses don't?

texts:
I am not too sure if viruses are considered living organisms.

I learned that living organism:

-Change their size
-Reproduce
-Heal themselves
-Need energy (by eating)
-React to the environment
-Have a lifespan
-Made of at least 1 cell (some exceptions)

Which features that are listed are not in viruses?

If I need to be more clear, please tell me as I'm not very good at explaining.


texts: Creating BLAST database with nucleotide "place holder"

texts:
I have a set of nucleotide sequences that contain some special characters with multiple meanings:

H -> C, A or T
K -> G or T
M -> C or A
R -> G or A
S -> C or G
W -> A or T
Y -> c or T

I would like to create a BLAST database with that sequences.

The "place holders" seem to be a known vocabulary (at least for the query sequence).

It is also possible to create a database (using makeblastdb), with sequences containing the "place holder" characters. However, the characters are always recognized as mismatch.

Is there a way to tell BLAST recognizing the characters above as match if the query sequence fits?

If not, I could imagine to "expand" all combinations for each sequences by replacing the "place holder" with it's concrete nucleotide, but that may grow up the database... Or is there another solution to face that problem?


texts:
Can anyone please help me identify these horns?
I guess they belonged to either European or Asian species. I don't know anything about their history -- they are my grandparents' who are from Moscow, Russia. The horns are at least 20 years old, I guess even more.

The length from the tip of each horn to its base (straight line) is about 35 cm = 13.7 inches.

A friend of mine suggested those might be a cow's horns, but I'm not sure.

Maybe someone can recommend a resource where it's possible to find it out?

Thanks in advance!


texts: How might IV-saline cause kidney damage that seems to be less likely with "balanced fluids" IVs instead?

texts:
The ABC News article What's in the IV bag? Studies show safer option than saline includes:

Saline — salt dissolved in water — has been the most widely used fluid in the U.S. for more than a century even as evidence has emerged that it can harm kidneys, especially when used a lot.
Other IV solutions called balanced fluids include saline but also contain potassium and other things that make them more like plasma, the clear part of blood. They're widely used in Europe and Australia.
The studies involved 28,000 patients at Vanderbilt University who were given IVs of saline or a balanced fluid. For every 100 people on balanced fluids, there was one fewer death or severe kidney problem.

and refers to research "...which were discussed Tuesday at a critical care conference in San Antonio and published by the New England Journal of Medicine."
Presumably the traditional saline solution does not contain a "wrong" or dangerous concentration of salt, but it seems that it's now conclusive that a balanced combination of ingredients beyond NaCl is safer.
Is there any understanding of the particular mechanism by which saline alone lead to issues with kidneys that seems to be alleviated by the addition of other natural constituents of blood plasma?
At first I thought the issue may be connected to "...especially when used a lot." by itself, but (also presumably) the study would have accounted for this.


texts:
I would appreciate if someone could identify this plant. It's tall, but not very difficult to pull from the ground, and it has yellow flowers in large groups. I was told it's not mustard. Is it wild cabbage, and if so, what variety?
Location: western Illinois, in a garden.
Season: it's late April, and their roots are now rotting.
Height: I think they were around 3 feet.

More pictures:


texts: If you recreated intermediate species between every species on the evolutionary tree, would every species be able to reproduce with each other through a series of intermediates? Would this blur the concept of "species"?


texts: Why only heterogeneous SNVs for validation using genotyping arrays?

texts:
I am trying to validate the variants I found using whole genome sequencing . The standard practice, I have seen in the two publications below were to check for the number of heterozygous SNPs called by the SNP array.

1) Performance comparison of whole-genome sequencing platforms

  To further assess the accuracy of the variant calling, ... Of the 260,112 heterozygous calls detected with the Omni array, 99.5% were present in the entire SNV data set, 99.34% were concordant calls and only 0.16% were platform-specific SNVs. This demonstrates that both platforms are sensitive to known SNVs and that few known single-nucleotide polymorphisms (SNPs) are detected by only one platform.

2) Optimised filtering reduces the error rate in detecting genomic variants by short-read sequencing

  To confirm that shared SNVs are indeed true variants, we used Illumina single-nucleotide polymorphism (SNP) arrays and selected all SNPs heterozygous on the SNP array.

My question is - why are only heterozygous SNPs chosen for validation when using Illumina Omni arrays?


texts: Are there yearly variations in HIOMT (HydroxyIndole-O-MethylTransferase) availability?

texts:
I'm reading a booklet on melatonin published in 1996, titled "Melatonin and the Biological Clock". And see the following statement:

  HIOMT (HydroxyIndole-O-MethylTransferase), one of enzymes of melatonin
  synthesis, rises and falls in an annual rhythm, with troughs in March
  and October and peaks in January and July.

Seeing how HIOMT is the last methyltransferase involved in Melatonin synthesis in humans, I'm interested in learning if there's indeed a yearly variation in this MT production in humans, and if it is regulated by genetics or photoperiod duration.

Thank you for your input!


texts: Do Squirrels have 4 legs OR 2 arms and 2 legs?

texts:
Do squirrels have four legs, or two arms and two legs?

I first asked this question many years ago, and it has since unearthed a whole array of conundrums and questions that I have struggled to get a conclusive answer to.

See a squirrel (often described as a quadruped, 4 feet, which implies 4 legs) can stand on its back two legs and hold a nut in the paws of its front two legs - but those front legs are jointed in a very similar way to arms, look like arms and are being used as arms.

When a squirrel runs, it uses all four limbs - but then so does a gorilla, and that definitely has arms.

So in trying to answer this seemingly simple question I ended up lost in a world of definitions and further questions - questions like "what is an arm anyway?"  "what is the difference between a paw and a hand or foot?" - and after trying to find out the answers to those questions I ended up in a much stranger world.  Octopuses have arms, but no hands - bats have hands, but no arms (I will spare you one of the resulting conversations which wanted to know how long a nose has to be until it's a trunk, especially concerning anteaters).

I could be wrong but it seems to me that if your front paws are called hands, then you have two arms and two legs.  Koalas, for instance, are often described as having hands despite also being described as quadrupeds.  Perhaps the differences are merely linguistic choices rather than anything relating to the biological nature of these limbs.  I just don't know anymore, and at this stage, I am starting to wonder if I have given this question way too much thought, time and energy.

Can anyone help me out?

Very sorry if this question isn't appropriate here - if there is a better group for this question on Stack Exchange please let me know.


texts: I need some forearm bone motion pictures

texts:
I would like to know how my forearm bones move inside my forearm when I'm twisting my hand. (Also, it would help to see the hand bones action too). "twisting hand" means to me the motion in which the rest of the body is in place except the hand which turns from upside up to downside.

I have the intuition that the bones inside my forearm move between themselves to make my hand twist, but am not sure if that is true.

I would like pictures of the forearm bones before and after twisting. Animations would also be great of course.


texts:
What are the dominant plant and animal species in the tundra biome?
I searched this up and I found the following:
Herbivorous mammals: lemmings, voles, caribou, arctic hares and squirrels. Carnivorous mammals: arctic foxes, wolves, and polar bears. Migratory birds: ravens, snow buntings, falcons, loons, sandpipers, terns, snow birds, and various species of gulls.
But which one is the dominant species predatorily and which one is the dominant species population-wise?


texts: What about a bat's immune system protects them from Ebola?

texts:
Current evidence indicates that fruit bats are a reservoir host for Ebola. Has any research established what is different about their cell biology or immune system that reduces virulence for them?
Failing research on this particular system, do you have an example in another system of how virulence is reduced in the reservoir host?

I'm teaching a cell biology class, so actual examples of modified proteins or enzymes or inflammatory molecules in the reservoir is preferred.


texts: How likely is it that through dog breeding, tail-wagging has been disassociated with happiness?

texts:
I am not a biologist, so sorry to anybody for misinformation in this post.

If I understand correctly, dogs evolved the ability to show emotions through various sounds and tail-wagging in order to better communicate with their symbiotic partners, humans. Is it possible that recently, dog breeding has disassociated this with the communication of emotions due to the fact that humans like dogs which are more naturally happy? Considering that they have been tamed, and therefore their actions wouldn't be a good indicator, it seems plausible to me.

Please correct me on misinformation.


texts: How does the shoulder joint stay in place?

texts: I read that a human shoulder is a ball and socket joint, but when looking at a picture of a shoulder the socket part seemed way too small to hold the ball in place like a ball and socket joint. Usually the socket covers a little over half the ball and the shoulder socket covers almost none. How does the shoulder stay connected? Are the illustrations wrong?


texts: How can an infection of lower respiratory tract lead to a skin infection?

texts:
I am interested in the multifactorial process about infectious diseases of the lower respiratory system and their progression to a skin infection.
Possible agens are zwitterions, viruses, fungi, amoebas, bacteria and/or parasites.

Zwitterions

Small protein segments, much unknown but their importance is much greater than known.

Viruses

Parvovirus B19

Example of a case: 5 children develop a bright red rash on the face and turns violet after a few days and then disappears. Then maculopapular rash appears on the trunk, buttocks and extremities. It soon fades from the trunk but persists on the thights and forearms. Two children have also had a slight fever and a sore throat, but all were not terribly sick. What is the genetic material of the most likely causative agent?
It is a skin infection. Not so severe. Little upper respiratory infection but not necessary caused by the agent. Infects many so spread probably by respiratory droplets. **But how a respiratory infection can lead to a skin infection?*

Bacteria

....

Amoebas

...

Fungi

....

Parasites

...


texts: What are Antihistamines doing in a baby?

texts:
In his song Lullaby, Tim Minchin sings:

  Your nappy is dry and your tummy is full
  Of enough antihistamine to chill out a bull
  Yet still all this gringing

According to Wikipedia, antihistamines are used against allergies.

So, why is there antihistamine in his baby's tummy and why is it supposed to make her sleepy?


texts: Small black slow-moving insect showing up in the home

texts:
In the past few weeks (winter) I've started to notice these insects crawling about various places of the home.

Slow-moving like a beetle.
Black all over.
Hard to see but they have two prongs sticking out of the front.
I own dogs and cats.
I live in Tel-Aviv, Israel.
I live on the second floor.

Very hard to capture in an image so I tried a video. Here's a Gif:

What is this species?


texts:
A gout attack typically causes pain, swelling, redness, and warmth (inflammation) in a single joint, most often the big toe.

What makes big toe more susceptible for gout?

Also I was said that it mostly occurs in right big toe, if this is correct then what could be the reason for its right sidedness?

Source : http://www.webmd.com/arthritis/gouty-big-toe


texts: Does anybody knows name of this bird I found in my backyard in India?

texts: I found this bird in my backyard in India. I checked several websites but wasn't able to identify it. Any help would be appreciated.