text:
How does the choice of blood draw site influence the possible specificity of a serological test?
The news has reported that a new serological test for the presence of anti-SARS-CoV-2 antibodies has received an emergency use authorization from the FDA, and notably has a higher specificity than other tests (99.8%).
The new test requires blood to be drawn from a vein, rather than a finger prick, and a quote from the test's manufacturer reads, "If you take blood from a finger prick, you will never be able to achieve the same level of specificity that you will achieve … when you take blood from the vein" (non-scientific news outlet source). Although the question is prompted by news related to COVID-19, I'm interested in the general case as well.
It is unclear to me why this would be the case, since antibodies should be present in capillary blood taken from the fingertip. I would suspect one of two reasons, but I don't have enough of a biology background to verify whether they make sense:
1) The volume of blood which can be drawn from a vein is much larger. This would make sense if it improved the sensitivity to a low-concentration antibody of interest, since there may not be enough antibodies in a fingertip sample to bind to antigens in the test. However, it's not clear why having a larger sample would help with specificity.
2) Fingertip blood samples are contaminated with lymph, matter from the skin surface, and so on. I'm not sure how it would affect the specificity of the test. In my naive understanding of serology tests, the reagent would consist of a synthetic antigen of interest, plus either anti-human-Ig or a second moonoclonal antibody for the antigen that would be used to detect any bound antibodies from the sample. It's not clear to me how these sorts of contamination could cause false positives for this sort of binding.

This ref, https://academic.oup.com/ajcp/article/144/6/885/1761216
show that drops of finger prick blood vary more than venous blood.
The main reason for using venous blood is licensing. A test is licensed only for an exact procedure and materials. If you vary any conditions the license is invalid.
However, I would not expect a test for antibodies (present vs. absent) to show much variation except for detecting the lowest levels of antibodies. (Sorry I cannot find a ref for this).

Thanks. I'm still a bit confused by the licensing aspect: it makes sense that a test is licensed for a certain procedure, but here the choice of procedure was justified by a difference in specificity. The reference about fingertip sample variation is nice, and I'm still trying to wrap my head around any mechanisms by which it can affect specificity.


text:
Are black panthers the same as jaguars?
I google the scientific name for black panthers. I get panthera onca. I google panthera onca, and I get jaguar. Can someone explain what is going on? Are they the same? What is the real scientific names for them? Because panthers are black and jaguars are yellow with black spots.

Black panther refers to melanistic examples of either leopards (Panthera pardus):

or jaguars (Panthera onca):

It is not typically used to refer to (the rare/historic/unconfirmed) examples of melanism or pseudo-melanism in other species of Panthera (e.g. black tigers).

So they are basically black leopards or black jaguars?

@Asadefa yep.

It can also refer to black puma as well. It doesn't help that puma have more than a dozen common names. including panther in the southern US.

@John "Despite anecdotes to the contrary, all-black coloring (melanism) has never been documented in cougars." https://en.wikipedia.org/wiki/Puma_(species)#Characteristics

Really, interesting, now I want to look and see if any Pumapard ever exhibit it. But it still might be worth mentioning since we don't know what context the OP is asking the question for, they could be referring to reported sightings

source: Stack Exchange

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

sort: votes


text:
When a 'v' letter should be changed to 'w' in botanical nomenclature?
When should be 'v' changed to 'w' in botanical names? (especially ones derived from names originally written in cyrillics).
The International Code of Nomenclature for algae, fungi, and plants says that

The letters w and y, foreign to classical Latin, and k, rare in that
  language, are permissible in scientific names
When the original publication of a name adopted a use of the letters
  u, v or i, j in any way incompatible with modern nomenclatural
  practices, those letters are to be transcribed in conformity with
  modern nomenclatural usage.

Where should I look for the rules on such usage?

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


text:
How do PARPs counteract coronaviruses?
I read that

[SARS-CoV-2 has] a nonstructural protein called NSP3, a component of which blocks the host’s efforts to fight off the virus. In particular, this protein shuts down host enzymes called PARPs, which prevent viruses from replicating, and interferes with cellular calls for the release of virus-fighting immune proteins called interferons.

I'm somewhat acquainted with interferons, but I'm trying to better understand the part about PARPs. Alas the Wikipedia page on these does not mention an anti-viral-[replication] function. So, how do PARPs stop viruses from replicating? (Is it by triggering cell death?)

Nsp3 is the other protease and it is also characterized as 'inducing with nsp4 & nsp6 the formation of double membrane vesicles' (where the replicase complex (nsp7 to 15) comes anchoring and doing the genome and mRNA synthesis)

I think this is an interesting question, but I have altered your title to make it less specific to mechanism (replication). Although the quotation mentions this, there is no evidence that replication is specifically targeted by PARPs in coronavirus infection (just as there is nothing I have read to support the contention that nsp3 "shuts down" PARPs). Better, I think, just to say "counteracts" and let the evidence do the talking about mechanism.

Summary
The poster’s answer to his own question focuses on the end results of the anti-viral action of poly- and mono- ADP-ribosyl transferases — PARPs. The references he provided stimulated me to read about the molecular aspects of this topic, which is where my own interests lie. The ‘answer’ emerging from this reading is somewhat extensive, but can be summarized as:

The molecular details of the way in which PARPs act as anti-virals against
  coronaviruses, and in particular whether and how they antagonize viral
  protein NSP3, are still unknown. There is indirect evidence to
  implicate PARP9, PARP14 and PARP15, which — like NSP3 — share a
  structural feature known as a macrodomain, although their mode of
  action is complicated by the fact that PARP9 does not catalyse
  ADP-ribosylation. The viral NSP3 protein has the ability to remove
  ADP-ribose from proteins in vitro, but whether this is its mode of
  action in the cell is yet to be established.

The role of PARPs in the cell (1)
The name PARP is an acronym for poly-ADP-ribosyl transferase, although the 17 human PARPs are defined, not by this catalytic activity, but by the possession of a domain homologous the catalytic domain of the founder member, PARP1 (2). On the basis of assaying the cloned, expressed proteins for self-ribosylation activity most of these (eleven) have only mono-ADP-ribosyl transferase activity, and two (PARP1 and PARP13) are inactive — a conclusion consistent with the substitution of a key catalytic residue at the active site (3).
   One can consider three stages in the involvement of catalytically active PARPs in cellular metabolism: activation, catalytic action and effect.

A common feature of activation seems to be the response to some stress signal, which may result in increased transcription of PARP genes or activation of an inactive form, for example by combination with an accessory protein (4).
   Catalytically active PARPs covalently attach one or more ADP-ribose groups most commonly to specific glutamate residues (less frequently to asp, arg, or ser residues) of target proteins (or in some cases themselves) using NAD+ as a donor:

For those PARPs that catalyse poly-ADP ribosylation (PARP1, -2, -5a and -5b)) linear or branched chains are formed by glycosidic bonds between the 2′ and 1″ positions of ribose rings.
   Although all PARPs — by definition — contain the PARP domain, they vary considerably in the other domains they possess, and this would be expected to be the basis for different substrate specificities. However for many PARPs these substrates have not been identified — only the processes they affect, the main processes (other than anti-viral action) appearing to be DNA integrity, telomere homeostasis, RNA transcription, regulation of mRNA translation by cytoplasmic stress granules and degradation of proteins through the ubiquitin pathway. Most effort has been directed at the substrates of PARP1, which include histones H1 and H2B and  the chromatin insulator binding protein, CTCF (in response to DNA strand breakage) and the transcription factors NELF and C/EBPβ.
   The effect of modification of the substrate protein may be a change in its activity (as exemplified by the inhibition of translation EF-2 by diphtheria toxin) or more generally interaction with some other protein that recognizes the ADP-ribose moiety. One feature of this recognition — particularly significant in the context of virus–host interaction — is that it often involves a specific domain called the macrodomain (5), named after the C-terminal domain of the histone H2A variant, MacroH2A.

Macrodomain from Archaeoglobus fulgidus protein AF1521 showing binding of ADP-ribose (red)
The macrodomain is found in certain classes of enzyme responsible for the turnover of the reversible modification of proteins by ADP-ribose. These include the polyADP-ribose glycohydrolases — which cleave ribose–ribose glycosidic bonds — and MacroD1 and MacroD2 — which hydrolyse the ester bond between the amino acid and the terminal ribose.
   Also of interest is the fact that, several macrodomains are found in three PARPs: PARP9, PARP14 and PARP15.
PARPs in cellular anti-viral responses and viral anti-PARP proteins (6)
   In different classes of viruses PARPs can act in a pro-viral or anti-viral manner. In coronaviruses (human SARS-CoV has been the subject of most study) they exert an anti-viral effect, as indicated by the effect of inhibitors of PARPs. Furthermore certain PARPs (-9, -12, -13 and -14) are induced in response to interferon, itself a consequence of viral infection. As mentioned by the poster, PARP13 binds directly to viral RNA resulting in its eventual destruction. However in most cases it is unclear which PARPs are involved, what their targets are, and whether their anti-viral action is a result of their catalytic activity — clearly not in the cases of PARP9 and PARP13. This is an important proviso to what follows.
   A study of the evolutionary conservation of the all 17 PARPs in different primate species showed that five of these underwent rapid evolution, typical of proteins involved in host–viral conflict (7).
   One of these was the catalytically inactive PARP13, which before its assignment to the PARP family had been shown to have anti-retroviral properties and was termed ‘ZAP’ (Zinc-finger Antiviral Protein).  The zinc-finger domain binds directly to a long stretch of viral RNA (8), but the details of the recognition and how binding leads to the destruction of the viral RNA (is the PARP domain involved?) remain to be elucidated.
   More relevant to coronaviruses, perhaps, is the positive selection of PARP9, PARP14 and PARP15, which all contain the ADP-ribose binding macrodomain. In contrast to PARP13, the mutations in these PARPs are found throughout the proteins, including the macrodomain, where they are found distributed in surface patches, rather than in the ADP-ribose pocket. The relevance of this to anti-viral action is that there is a virulence protein, NSP3, in SARS-CoV which posses three macrodomains, one of which (MAC1) is structurally homologous to the macrodomain of the PARPs. (This macrodomain is also found in the virulence protein of hepeviruses and togaviruses.)

Structure of SARS-CoV genome and domains in gene nsp3 (from (6))
This macrodomain has been shown to bind ADP-ribose, and mutations in the macrodomain of nsp3 have been generated at key residues at the binding site. Using these mutants it has been established first, that such mutants have reduced virulence compared with the wild-type virus, but that this difference is abolished when infection was in cells with knockdowns in the gene for macrodomain-containing PARP14  (although also in PARP12 knockdowns) (9).
   It has been demonstrated that NSP3 can remove ADP-ribose from proteins in vitro, suggesting that this catalytic activity may be the basis of its virulence (6). However evidence for such action during infection is lacking.
   If indeed the continual mutation of the macrodomain of PARP9, -14 and -15 is part of an “evolutionary arms race” with NSP3, the nature of the postulated interaction or antagonism between these proteins remains to be determined.
References
   1. Gupte et al. (2020) Genes & Development 31, 101–126.
   2. Schreiber et al. (2006) Nature Reviews: Molecular Cell Biology 7, 517-528.
   3. Vyas et al. (2014) Nature Communications 5, 1–13
   4. Suskiewicz et al. (2020) Nature 579, 598–605
   5. Leung et al. (2018) PLOS Pathogens 14(3): e1006864
   6. Fehr et al. (2018) Trends in Microbiology 26 598–610
   7. Daugherty et al. (2014) PLoS Genetics 10(5): e1004403
   8. Guo et al. (2004) Journal of Virology 78, 12781-12787
   9. Grunewald et al. (2019) PLoS Pathogens 15 (5): e1007756.

From one of the review papers of the author/prof (mentioned in that article) it looks like (table 1) PARP12 and 13 have direct anti-viral activity at least against some viruses; PARP12 was shown to have some activity against the Zika virus by binding the viral RNA and blocking translation, while PARP13 binds and degrades some influenza proteins like PB2 and PA.
There are quite a few paper cited in that review, which probably have a lot more details.
Basically type I interferon is not directly an anti-viral compound but rather activates/enhances a series of downstream mechanisms (interferon-stimulated genes) which translate into anti-viral compounds that regulate translation initiation and elongation... and among these are some PARPs (12 and 13, the latter actually seems to have two splice variants.)

the best-characterized antiviral protein is PARP13 or zinc finger antiviral protein (ZAP), which is encoded by the zinc finger CCCH-type, antiviral 1 (ZC3HAV1) gene. [...] ZAP is transcriptionally upregulated by type I IFN signaling and directly induced by phosphorylated IRF3 in virus-infected cells. [...] ZAP was first discovered as a potent antiviral factor against the retrovirus Moloney murine leukemia virus (MLV) in a cDNA library screen. Since then, it has been shown to inhibit a broad range of RNA and DNA viruses, including other retroviruses, alphaviruses, filoviruses, and hepatitis B virus. It is not understood what determines the broad yet specific antiviral activity of ZAP. It binds viral RNA via its N-terminal zinc fingers, and ZAP-responsive sequence elements in MLV and Sindbis virus have been mapped. ZAP recruits the exosome to target retroviral and specific host mRNAs for degradation but also acts to block viral genome translation. ZAP dramatically reduces Sindbis virus production, and experiments utilizing temperature-sensitive Sindbis virus mutants that are unable to replicate the RNA genome at nonpermissive temperatures support a mechanism in which ZAP represses translation of the incoming viral genome. [...]
In addition to ZAP, other members of the PARP family are upregulated by IFN and have also been shown to inhibit alphaviruses. Murine PARP7, PARP10, and the long isoform of PARP12 (mPARP12L) block cellular translation and inhibit replication of Venezuelan equine encephalitis virus (VEEV), another member of the alphavirus genus 20, 21. mPARP12L also blocks infection of a variety of RNA viruses from other families, such as vesicular stomatitis virus (VSV), encephalomyocarditis virus (EMCV), and Rift Valley fever virus (RVFV). Similar to ZAP, mPARP12L affects protein translation, and the tethering of mPARP12L to a renilla luciferase reporter mRNA inhibits its translation. Furthermore, mass spectrometry identified ribosomal proteins and proteins involved in translation as interacting partners of mPARP12L. mPARP12L interacts with ribosomes in the polysome-containing fractions at 4 hours post-infection (pi) with VEEV but facilitates disassembly of polysomes at later times of infection (12 h pi), which is dependent on its RNA-binding and PARP catalytic activities.

Weirdly enough Wikipedia has a page on antiviral protein which discusses ZAP, but fails to identify it as PARP13...
And a 2019 paper found that there are four ZAP isoforms, with varying degrees of effectiveness against different viruses.

Regarding the lack of mention in the Wikipedia article that ZAP is PARP13: the "weirdness"  reflects the scientific history and the way Wikipedia works. The history is that ZAP was discovered — and the article written — before it had been shown to have a PARP homology domain (and which is catalytically inactive). Anyone can write an article for Wikipedia, and presumably the original author was interested in anti-viral proteins in general, made a general survey, wrote a short piece on each, but has not bothered to update it since. Anyone can update it, so I probably will. Caveat emptor.

I've just edited the Wikipedia page on anti-viral proteins, so, assuming that my edit is not removed, your comment about Wikipedia needs removing or updating. In fact that particular page is of quite low quality in general. Someone had the idea of grouping anti-viral proteins together and started a few entries for examples he was familiar with, hoping others would expand it (you can see that in the Talk section). However that section hasn't been touched for ages. I see some of the PARPs have their own Wikipedia entries, but not PARP-13. Only those of known protein structures.


text:
Mercury intoxication in cats
I was not sure if this question is more appropriated to be here or in Pets Exchange. I'm posting here first.
I accidentally broke a thermometer in my bedroom and, by my lack of attention, have spread mercury along the house. I cleaned the most part before the spread, so what I found after was only really tiny drops of mercury. However, I have four cats and I'm afraid that one of these tiny beads could possible be stuck in them paws while they are walking and they possible lick it, swallowing the beads.
I'm maintain the house ventilated most part of day (except when I go sleep) to minimize mercury vapors and I already search for possible symptoms of mercury intoxication in cats and found weakness, vomiting, diarrhea and difficult walking. Until now, I didn't observe any of these symptoms, but I would like to know what I should to if I notice some of them.
Because COVID-19, reach my veterinarian maybe will be difficult.
PS: I live in a country which doesn't have a service to come to my house to check the mercury amount in the ar neither get rid of it.

Unlikely that you have a mercury problem. I have had about 6 mercury thermometers broken in my house over a few years ( the places I kept them were not safe from a housekeeper).I don't know if she did anything to clean up; I except only sweep up broken glass. These were laboratory thermometers ,so typically over 12 in. long. No cats but dogs, no symptoms yet.

I don't have sure if your case applies to mine because, as much as I know, dogs don't lick themselves. If the drops of mercury were sufficient tiny, I guess the dogs and cats were not even be able to seen it. My worries about my cats is exactly because they lick them paws.

@Mycroft The oral toxicity of elemental mercury (the kind in thermometers) is very low in humans and laboratory animals, and it is likely not of much concern in your case. Liquid mercury is very poorly absorbed across the GI epithelium, so your cat's licking behavior isn't going to contribute much to overall risk of toxicity. The main health concern with elemental mercury exposure is inhalation of the vapors.

@MikeyC Could you send the source or reference? I would appreciate that.

It is soluble mercury compounds that are harmful if ingested.


text:
Are there any known consequences of the right-handedness of the DNA double helix?
In this article it is suggested (without evidence) that the right-handedness of DNA may be the cause that "kick[s] off asymmetry in the early embryo [of snails]".
On the one hand we know that symmetry breaking in an organism's development happens at multiple levels, from molecular to larger structural levels (see this). On the other hand we also know that right-handed DNA double helix does have many notably distinct properties from their left-handed cousins (see this). Are there any visible macroscopic asymmetries in some organisms that are known to be ultimately traceable back to DNA's handedness? More generally, what could be some consequences of the right-handedness of DNA double helix?

The short answer is no, there currently aren't any visible macroscopic asymmetries in some organisms traceable to DNA's handedness.
The long answer is still no, but I want to clarify that this "no" is more of a "not really". This is because there can be potentially drastic consequences when left-handed DNA is present in a cell in addition to the traditional right-handed DNA.
Let me explain. First, left-handed DNA is officially called Z-DNA. Right-handed DNA, which is the normal DNA configuration, is named B-DNA. There's a third type of DNA, which is also right-handed, that is called A-DNA. A-DNA is essentially super-coiled B-DNA.
Z-DNA isn't that unusual, and it is regularly found in human cells in addition to B-DNA. One study, done in yeast, found that Z-DNA can act as a nucleosome boundary element. Another study, by Kwon and Rich, found that the consequences of Z-DNA weren't as benign. The vaccinia virus requires Z-DNA to bind to a key protein that has anti-apoptosis activity. When Z-DNA does this, apoptosis is effectively blocked.
Furthermore, Z-DNA has been found in patients suffering with Alzheimer's Disease. Suram, et al., found that the hippocampus of severely affected AD patients used Z-DNA instead of B-DNA. This change in the DNA coil has potentially drastic consequences with regards to gene expression.
Finally, the presence of Z-DNA antibodies were found in patients that suffered from Systemic Lupus Erythematosus (SLE). Lafer, et al., describes how non-SLE patients do not have these antibodies, which suggests that Z-DNA is involved in the clinical manifestation of SLE.
So, with those thoughts in mind, yes, there can be visible asymmetries traceable to DNA handedness. In fact, some tumors depend on genes that have Z-DNA domains (one study by Alan Herbert found that it was about 40% of tumors on their panel). While this isn't really what I think you're asking, it's technically true as tumors do qualify as visible asymmetrical phenotypes traceable to DNA handedness. Diseases associated with Z-DNA could also technically qualify as since they're diagnosable, they're visible in that manner.
Regardless, there is currently no proof that the handedness of our DNA actually causes any real macroscopic phenotypic effect in the developmental stages of life. The reason why left-right asymmetry happens in organisms is due to asymmetric gene expression, not the direction of the DNA coil. This review by Michael Levin talks explicitly about how the left-right borders are established in embryonic development, and there is nothing regarding the direction of DNA's double helix.
Nonetheless, DNA handedness is still a rapidly developing field. I anticipate that more research on these subjects will quickly become available. But as of now, no. Snails shells are not right-handed because of the right-handedness of their DNA.

The review link by M Levin is corrupted. Can you fix it?

Just fixed the review link. It should be working now.


text:
A book about the palmaceae
I hope this isn't inappropriate for the forum - I'm trying to find a book that I read several decades ago, possibly 40 years or so. As I recall, it was a systematic treatment of the whole of the palmaceae. The title was fairly brief, possible just the word 'Palms'; however, I don't think it was this one Martius: The Book of Palms. (I could be wrong, though.) Any ideas?


text:
Ways to identify/distinguish individual coyotes?
Are there any methods to distinguish individual coyotes from a distance (with a binocular or telephoto lens)? Are there marks or patterns we could be looking for?
Similarly, if I have seen a coyote at the same location multiple times, what should I look for to see if it has been the same coyote?
I've been searching about it and only found ways to distinguish individual wolves.
Thanks!

Is there some reason you think the approaches that you found for wolves wouldn't work?

According to a colleague that dabbles in tracking coyotes and other mammals in the San Diego area, "it is difficult to do unless you see them a lot. People may do it based on color of the tip of the tail, chunks taken out of ears, or gender if you get a good look". Apparently people do this for mountain lions based on their tracks (morphology/size), see here and here.

The Wikipedia entry for subspecies of coyotes has a very useful chart here (click [show]) that gives a description, range, and other information for each of the 19 subspecies of coyotes. Since I presume you are from the California area, I would focus on the descriptions of coyote subspecies that could exist around your area, such as the San Pedro Martir coyote, which has "reddish summer fur and a short, broad skull" to differentiate among the various coyotes you many encounter. Generally, the coyotes differ in color, teeth, tail size, fur, ears, and other such factors. As for determining if you've seen a coyote already, I suppose there's no real way of knowing unless there is a unique marker on the coyote's fur or appendages that differentiates itself from the others; however, examining the coyote's scats and comparing them may be a viable option for this, but that would require you to examine close to the coyotes rather than from afar.

I don't think OP is concerned with subspecies of coyotes, but rather distinguishing individuals, the way one might differentiate and name wolves in the same pack even if they are all related. Accuracy is likely to be suspect, but for some species there are patterns of variation that can be useful for this.


text:
Do pinhole glasses help reduce eye strain?
I've noticed that I can read about 10x longer at screens and books without my eyes tiring using the "pinhole trick" - where you curl your fingers and look through the hole (great explanation here https://www.youtube.com/watch?v=OydqR_7_DjI)
Pinhole glasses (shown below) have been advertised as being healthy for your eyes, although there seems to be no strong supporting evidence.
If not for long term affects, would these glasses use the same pinhole principle to reduce eye strain and allow you to stare at close objects for longer?

The pinhole glasses improved visual acuity, DOF [depth of focus], and accommodative amplitude; however, they resulted in decreased visual quality including general reduction of VF [visual field] sensitivity, CS [contrast sensitivity], and stereopsis.

https://iovs.arvojournals.org/article.aspx?articleid=2166618

One (out of many) cause of eye strain is accommodative demand (the muscle effort required to make an object appear sharp on the retina). As pointed out by the paper you cite:

That is, the pseudoaccommodative power induced by pinhole glasses was 3.99 D. This effect may be explained by the small aperture of the pinhole glasses requiring less accommodative power for the same stimulus.

So if the source of eye strain is solely accommodative demand then yes, you would assume pinhole glasses to reduce it. However, again as pointed out by the paper you cite, this is not without tradeoffs. These tradeoffs could very well be the source of other types of strain. In particular the main source of eye strain is related to binocular vision (ref below), and stereoacuity was strongly reduced by the pinhole glasses. This is speculative but I wouldn't be surprised if pinhole glasses cause far more eye strain because of that. I also doubt there is any research on the long term effect of pinhole glasses.
Steinman, B. A., & Garzia, R. P. (2000). Foundations of binocular vision: A clinical perspective. McGraw Hill Professional.


text:
What would happen to organisms if stem cells didn't differentiate?
I've tried to research this online and looked through my textbooks as well. This is something that has been on my mind for a bit. Will it just mean that the organism is more simple? Or would it mean they are less efficient? I'm not sure.

What would you expect to happen if stem cells didn't change into other kinds of cells? Can you think of any organisms that don't have cell differentiation? What do they do?

The organism would be unlikely to grow any "useful" tissues, and if the appropriate growth factors were still present (with differentiation blocked) there would be a higher chance of cancer.

If we consider a mammalian organism, it would eventually die, and one can presume that it would not take too long. In mammals, a lot of tissues are primarily constituted by specialized cells that cannot divide. Some of these cells have a tremendous lifetime (e.g. neurons), but others have a much shorter lifetime (e.g. erythrocytes). In tissues that are composed of the latter type of cells, certain stem cells are actively differentiating in order to maintain an adequate number of such cells in the organism. If such differentiation suddenly stopped, the concentration of such cells would progressively drop as time goes by, until the functions carried out by such cells are not executed. At this point, without these functions (e.g. oxygen transport carried out by erythrocytes), where some are essential, the organism would quickly die.

Then you'd have lumps of unspecialized stem cells. Differentiation means that most of the genome has been turned off and only a subset of the genes is active. Makes IMHO sense in the light that different cells make use of the same signalling pathways downstream of different receptors to elicit cell type specific responses.


text:
Doubt related to nerve impulse transmission
Naturally, the extracellular fluid has more sodium ions and the axoplasm has more potassium ions. Since there are more potassium leakage channels than sodium leakage channels on axoplasm, it is more permeable to potassium ions moving out into the extracellular fluid.
Is it correct to assume, due to this huge outflux of potassium ions into the extracellular fluid, there are more potassium ions than sodium ions in the extracellular fluid now?

You can look up any table of the intracellular composition of nerve cells, and actually any other cell, that K+ is always high inside. You should attempt to include some of your prior research and specifically tell us what you don't understand.

The question is different but see if this answer clears it up for you https://biology.stackexchange.com/a/57066/27148 tldr: very very few ions move to change a cells' voltage.

@AliveD I know K+ is always high inside (axoplasm), but the thing I wanted to know is, at that particular region and time, after the leakage channels do their job, is the concentration of K+ in extracellular fluid more than Na+?

Check the answer I linked to.

@BryanKrause Thanks a lot! I got the answer (similar) to what I was looking for.

One friendly correction. The Indian English usage of the word “doubt” to mean “query” or “question” is not standard US or British English. It’s difficult, I know, but you should try not to use it Internationally. It can be misleading as it suggests that you do not believe some person or idea.

@David Okay! I'll take care of that.


text:
Identify this insect seen in a rural area in North India
During my stay at a village in Haryana, India, I noticed many of these grey-brown insects in my room. They spend most of their time crawling but occasionally fly too (for short distances—one metre to a few metres). Here are some photographs—the spacing between the ruled lines is about 7 mm:

I am curious to know what species they are. Any help would be appreciated.


text:
Histone Deacetylase Inhibition
So I am trying to brush up on my knowledge of HATs and HDACs.
I am reading the just the 1st paragraph of the background of this study
I remember learning that HATs turn things on on, and HDACs turn things off.
It says that sodium phenylbutyrate (PB), can epigenetically regulate gene expression by inhibiting histone deacetylase.
Does this mean that one of the effects this drug can have is turning the thing that turns things off to produce the effect of turning it back on? Similar to that of a double negative?
Thanks.

Yes, Sodium phenylbutyrate can upregulate the transcription of silenced genes by inhibiting the activity of Histone deacetylases (HDACs).
Histone acetylation performed by Histone acetyltransferases (HATs) helps in activation of genes, while deacetylation performed by HDACs is responsible for gene silencing. This makes HDACs a potent drug target to treat malignancies.
The inhibitors of HDAC regulate the chromatin structure which loosens the chromatin and hence effect the binding of transcription factors to DNA.  This binding modulates the expression of genes playing role in cell cycle and apoptosis, thus effecting cell growth and differentiation. (Reference)
But this is not similar to double negative. Double negative is term used in embryogenesis, where a particular repressor gene is activated in specific regulatory state. (Reference)

Just for clarification - you are agreeing that PB acts as a negative feedback mechanism? (Not sure if that a better terminology than double negative?) Because when I used double negative I meant it in the sense that two negative processes could create a positive "constitutive on" for binding of TFs and hence turning gene expression?

yes.. you are right, but I think that term can't be used in this case.

Sort of. Histone deacetylases act on a particular region on the chromatin fiber to decrease or even silence the expression of the genes in such region. According to the study, PB has the capacity to inhibit the activity of histone deacetylases, which implies that the effect of PB, is to the make the cell less able to decrease the expression of certain genes, so one could crudely say that PB is turning off the thing that turns off the expression of certain genes, but this does not imply that it will turn the genes back on.


text:
Profile of a human foot
I am not sure if this is the right place to ask this question, so please let me know in case it is not. My question is just out of curiosity.
What is the reason for curved human foot profile?
First a bit of clarification in layman terms. When looking at a human foot sideways on the inside, you see an arch along the foot length, however there is no such arch when looking from the other side (imagine a footprint and how it has a curve on the inside and is flat on other side).
I looked on Google to find the answer. Pardon my lack in knowledge of biology vernacular/terminologies. Reading through wiki article on Arches of the foot, they do describe the two arches - longitudinal arch and transverse arch. In the laymen explanation I gave earlier, if I understand the anatomy right, the transverse arch is what leads to the footprint shaped that way. As I understand, they explain how the arches are responsible for the stiffness of the foot, akin to how arches of a building help support more weight will lower deflection compared to other configurations. Also the space under the dome enable the elastic soft tissue to spread and provide enough contact surface for the body weight to be effectively distributed. On transverse arch, they say it creates a half dome and the two foot together form the complete dome. However, structurally, they will not fulfill the same role as a full dome, far from it in my humble opinion. Can someone explain the structural benefit of the half dome of the transverse arch?


text:
How many proteins could participate in a complex
Disclaimer: I’m a computer science student with minimum knowledge of biology.
I’m working on an algorithm to cluster proteins in Protein-Protein-Interaction Networks to find protein-complexes. While working on that I stumbled upon the question how many different proteins can be part of a protein complex. (I'll call this the size of the complex from this point.)
I started by counting the the participants from all Corum complexes.
I got sizes ranging from 1 to 143:
[1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 36, 37, 38, 40, 44, 45, 47, 48, 62, 68, 78, 80, 104, 143]
The distribution is skewed to smaller sizes with 3 participants counted 1465 times and most of the bigger sizes from around 30 counted 1 or 2 times.
{44: 1, 36: 1, 32: 1, 47: 1, 78: 1, 48: 1, 31: 1, 143: 1, 40: 1, 26: 1, 38: 1, 62: 1, 104: 1, 23: 1, 20: 2, 22: 2, 33: 2, 80: 2, 37: 2, 45: 2, 28: 2, 68: 2, 27: 2, 30: 3, 19: 3, 24: 4, 25: 4, 18: 6, 17: 11, 15: 19, 1 6: 21, 14: 23, 11: 25, 12: 28, 13: 30, 10: 55, 9: 57, 8: 72, 7: 83, 6: 100, 1: 127, 5: 237, 4: 499, 2: 1370, 3: 1465}[Sorry for not sorting...]
My main question from this first dip into data is, are there any assumptions to make about the size of complexes? Are these big complexes for example special cases and normally complexes are limited to a size of around n?
Is there maybe even an upper limit of participants in a complex?
Anything would be helpful for me to minimize runtime.

This is suggestion as to how you could clarify the question to help us help you, without your having to resort to socializing, as per my answer. Could you sort the non-redundant list by number of participants and then present us with say 20 entries that span your putative cut-off, just showing the number of participants and the name of the complex? That way the question becomes, can we apply some different descriptor to complexes above the cut-off, which you can use in your report. Btw. I downloaded one of the files. I would advise having only one instance of a complex, e.g. not mice and man.

Hi. At first thanks for the answer. I can do that, but it'll probably take me some time as I'm right now working at several different spots concerning this project.

[Was to slow to edit...]
Still I want to clarify more what my project is. The Idea is can we find protein complex candidates just by looking at the structure of PPI's. I'm especially working with quasi-cliques. So I try to find a configuration where my algorithm finds all known complexes and more. These extra findings are then seen as candidates. That's my reasoning for asking this question. The project itself is more like "Let's see what happens and if we want to further work in this direction" Also it's my bachelor thesis, so the scope is definitively limited.

The problem with coming into bioinformatics from a non-biological background is all too apparent in your question, and very real. You are dealing with a category of object called a protein complex, you suspect that it will be reasonable to exclude a proportion of them, but as you don’t really know what they are (other than at a basic level) you don’t understand the implications of doing so. As generally in such cases, you need to find an appropriate biologist to help you.
All I can do is try to make an analogy. Consider an entity that the biologist who knows nothing about computing calls a ‘program’. As a surrogate for the number of components, let us consider that it is written in Java and so that one can judge its complexity by counting the number of classes. (I know that the examples I am giving are not all normally written in Java, but in theory they could be.) I could write a simple program that just parses a file and outputs a second file in a different format. That would use very few classes (especially without a GUI interface). Then I might write a modest web application to query a database and return biological information to the user. That could have perhaps two dozen classes. A more sophisticated commercial web application would have more. And then we get into commercial desktop applications from the relatively modest utilities to the monsters like Microsoft Word.
But just classifying computer programs on the number of Java classes would have severe limitations, just as would an alternative approach such as programming language (python for scripts, C++ for large applications). What I would really need to decide is what kind of program to include or exclude.
Likewise with protein complexes. I am not familiar with Corum (I just checked the website on my phone) but one might assume that the protein complexes it contains range from basic enzymes and proteins with two different subunits (perhaps in two or more copies, generally in a regular structure) like haemoglobin or immunoglobulin G, through proteins that interact with several species and posses half a dozen different subunits, to what are in effect machines of greater or lesser complexity, like the ribosome, the two subunits of which may together have 70 to 80 proteins.
So, yes, it would be reasonable to exclude the relatively small number of very large complexes which constitute a class of “machines” (and your size distribution suggests where the cut-off might be). But for your work to be valid you need to know specifically what class of complex you are excluding so as to be able to state that you had deliberately decided to ignore large complexes like ribosomes, splicesomes etc. And name them.
It’s tough at the moment, I know, but in my opinion you do need to sit down with a biologist and have this explained in more detail, reviewing the names of the complexes in the Corum list that you are considering excluding.


text:
umbrella term for microtiter plate, petri dish, cell culture flask etc
I'm looking for a term I can use in a software user interface that includes anything that may carry cell cultures or similar biological imaging samples (ie that may conceivably go into an automated microscope).
Since it's for a user interface, the term should be short and intuitive.  It should not depend on context.
Examples:

vessel, carrier, dish --- often used for what I mean, but not intuitive out of context.
cell culture carrier --- too long, also potentially too specific.

A flask or petri dish do not go into a microscope. Can you specify what you are exactly after? Are you after containers to grow cells? Or are you after plates to do repetitive stuff with cells (add substrate, coloring agents etc), or are you after carriers that go under a microscope?

@AliceD: anything you might grow cells in, potentially adding reagents, potentially fixate, and then image, for example these plates.  And yes, we do image cultures in flasks like this one

Thanks for the clarification. I left the field some 20 years ago, so I'll not even bother trying to answer this question, but it may help others to answer your Q. Good luck programming!

This sort of question is not really about biology. It may be a better fit for English Language & Usage with the tag “technical” (or the like). There are technical people there who delight in this sort of thing (as well as people who know nothing about the subject but can’t stop themselves answering every question in a comment).

@AliceD No problem. Just a suggestion, anyway.

@David thanks for your understanding.

@David I know of EL&U (and I've posted there in the past), and you're right, this is a single-word-request (one of the tags there).  The reason I posted on biology SE is that I thought the chances of the right person seeing the question here are vastly higher.

Could be. You never know.


text:
Can mutation take place in G1 and G2 phases during the cell cycle?
We know that the DNA replicates during the S phase in Interphase. There it might undergo a number of mutations. We also know that the forward half strands are more susceptible to undergoing a mutation since they live most of their lives single-stranded. But can mutation take place anytime before or after the replication? It is weird that the strands "wait" to open up in the S phase and only then undergo a mutation.

Yes, it can. A mutation can potentially occur at any given moment in the cell cycle, not only in S phase, which is why revision mechanisms remain alert during the whole cycle. Such mechanisms not only make sure every important event in the cycle takes place adequately (e.g. DNA replication, chromosome segregation) but also repair any damage associated with DNA (e.g. AP sites, single strand breaks, double strand breaks, to name a few). Once DNA damage takes place, specialized sensors detect such events and activate several mechanisms. One of these will pause the progression of the cell in the cell cycle, and another will repair the DNA-associated damage, in case that it can actually be repaired [1].
[1] Karp, G. (2009). Molecular and Cellular Biology: Methods and Concepts. Wiley. New York.


text:
What exactly happens to hydrogen atoms in step 4 of citric acid cycle?

It seems that there are four hydrogen atoms in alpha-ketoglutarate and one in HS-CoA (not counting the ones in CoA), five in total. Two of them go to NADH and H+, so there should be three atoms in succynyl-CoA instead of four. What am I missing here?
picture taken from Molecular Biology of the Cell, 6th ed., by Alberts et al.

Where are you getting "Two of them go to NADH and H+" from? Count the carbons on each side of the reaction, including CO2.

There are 5 of them on each side (not including the ones in CoA). But there is one more proton (H+) on the right side of reaction, and that's what seems problematic to me, that is, reaction would make more sense to me if the product contained NADH, not NADH + H+.

Oops, for some reason I read "hydrogen" as "carbon"- my bad.

Short answer:
There should have been an additional $\text{H}^+$ on the left-hand side.
Long answer:
You have rightly observed that the left side of the equation is deficient in one hydrogen atom. Let me draw your attention to another issue: the charges on both sides are different too. The left side has one negative charge too many. This gives us a clue: possibly there is a missing $\text{H}^+$ on the left.
This reaction is actually the sum of three reactions catalysed by a multi-enzyme complex. If you add the balanced equations for the reactions of $\alpha$-ketoglutarate dehydrogenase, dihydrolipoyl transsuccinylase and dihydrolipoyl dehydrogenase, you will see that there is indeed an additional $\text{H}^+$ on the left-hand side, which is omitted in your textbook.
But that is the case with most biochemistry/molecular biology texts. Biologists are very bad at balancing their equations, especially when it comes to $\text{H}^+$ and $\text{H}_2 \text{O}$. They balance out only the major reactants and products. The rest is often, er, left as an exercise to the reader.

Lodish is a Molecular Biology book. Berg et al., which is a biochemistry book, has it right (i.e. no hydrogen ions at all). However, heaven preserve us from chemistry students who can’t see what’s important in biochemical pathways because all they understand about chemistry is balancing equations.

Sorry Alberts — molecular or cellular biology. But not biochemistry.

NAD+ accepts only one hydrogen ion (H+) and two electrons (2e−), to form NADH + H+.  So only one Hydrogen is used by NAD+, and remaining four are present in Succinyl CoA.
The reaction mentioned in your question is a three step reaction involving decarboxylation of α-ketoglutarate, reduction of NAD+ to NADH, and at last formation of Succinyl CoA. Last step also uses FADH2.

Reference:
http://www.phschool.com/science/biology_place/biocoach/cellresp/closer2.html
https://www.elysiumhealth.com/en-us/science-101/whats-the-difference-between-nad-and-nadh

I am confused. In your second reference the illustration "NAD+ to NADH redox reaction" clearly shows that NAD+ together with 2e- and H+ forms NADH, not NADH and H+, as you claim in your answer.

As this is an redox reaction the two electrons balances out the reaction, which is normally shown, but here they have not shown the electrons.

And this is a multistep reaction using FADH2 also.

Yes, FADH2 is produced in step 6 and there doesn't seem any problem. But I still have problem with the fact that there isn't equal number of protons before reaction and after reaction in the picture I posted, and I don't feel your answer addressed this concern.

I am not talking about citric acid cycle's 6th step. But this alpha ketoglutarate dehydrogenase enzyme complex's 3rd enzyme. Now I added the picture in my answer

So, as far as I understood, this extra H+ appeared from other reactions taking place in alpha-ketoglutarate dehydrogenase complex and which are not explicitly mentioned in the picture I posted?


text:
What causes paresthesia from compression?
Compression of a nerve causes loss of afferent and efferent information in it. What is the physiological basis of this?

Seems like it results from a loss of blood flow as the Vasa Nervorum is compressed. Vessels, like arteries or tubules within the kidney, are compressible since they have a vacuous lumen, while an axon is cellular and resists compression. I was thrown off a bit by an answer by a Bryan Krause to this question here, Neurons during Numb feeling, "the feeling of paresthesia is not from loss of blood flow", but, seems like that person was wrong.

Another commenter noted my comment was mentioned here; it was made in haste and probably misleading, probably I should have added a word and said "complete loss of blood flow". I was referring to the article linked in the question there that implied that blood flow to entire limbs is cut off; if this would happen there would certainly be tissue damage in short order. The distinction I meant to make was between compressing major blood vessels versus compressing nerves themselves.

It can likely happen if vessels proximal to vasa nervorum are compressed too. Loss of blood flow to vasa nervorum does cause tissue damage, but increases in severity with time. And for the axon conductance to shut down (however it is axons actually do conduct signals), likely very deplete of oxygen, glucose, or whatever it is lacking that makes it not signal anymore.

@BryanKrause if its caused by oxygen/glucose deprivation, that proves the saltatory conduction theory that the action potential has to "boost" itself at the nodes of Ranvier. do you happen to know if electrolyte exchange is in any way stifled in the peripheral nervous system where the nodes of ranvier are a bit "covered" with projections from the myelin cell?


text:
Why is prothrombin time used to monitor warfarin and not activated partial thromboplastin time?
Warfarin is said to change prothrombin time (PT) but not activated partial thromboplastin time (aPTT) (for practical purposes at least anyways, not really sure). But looking at the mechanism of action of warfarin, I dont see why that is.
Warfarin works by inhibiting vitamin K, or more specifically, vitamin K-mediated post-transnational modifications of certain clotting factors (X, IX, VII and II) which are important for the activity of said clotting factors. Warfarin affects factors in both the extrinsic and intrinsic pathway (and maybe a bit silly and irrelevant, but the same number of factors in each too; 3 by 3!). So, why is it that PT is affected by warfarin but aPPT isnt? I looked alot and couldnt really find any satisfactory answer (there werent many answers to begin with either). What I've found and have gotten from my professor are the following points:

Warfarin's effect is more pronounced on PT because factor VII (the first factor in the extrinsic pathway) has the shortest half-life and is therefore the quickest to get depleted. But in that case, warfarin usually takes a few days to be considered effective enough to stop administering patients heparin with it; wouldnt all the affected factors be depleted enough by that time to also affect aPTT?
Warfarin affects factor VII, which is the initiating factor (tissue factor aside) for the extrinsic pathway, which is why it affects PT more? Honestly I don't know how these tests work exactly so I'm not sure if this would matter. This was what my professor answered with when a student asked (or at least it's what I recall).

This article tells that warfarin can prolong aPTT too.
Now look at the image below

It is almost 5 days and some extra hours when anticoagulant effects start, during which we give heparin, also called as heparin bridge.

But in that case, warfarin usually takes a few days to be considered effective enough to stop administering patients heparin with it; wouldnt all the affected factors be depleted enough by that time to also affect aPTT?

PT is used as a standard measure not just for initiating but also for monitoring  warfarin therapy using the INR(international normalised ratio) because it gives the earliest result(as half life of factor VII is shortest) to start another treatment according to guidelines, when INR is altered beyond normal range

Warfarin affects factor VII, which is the initiating factor (tissue factor aside) for the extrinsic pathway, which is why it affects PT more?

Well I might not have any sources to answer that, but I can try to deduce answer by some logical arguments. In intrinsic pathway there is multiplication of factors, for eg. Factor XII activate factor XI and factor XI activate factor IX but by this time more and more factor XI are getting activated thus causing more interaction with whatever factor IX is left in blood(factor IX is less here due to warfarin) so no relative profound anticoagulant effect of warfarin is present. But in case of extrinsic pathway factor VII is the intiating factor and is already less due to warfarin, and there is no such factors multiplying before that to cause their maximum interaction and therefore activation of factor VII so relatively more profound anticoagulant effect is present.


text:
What fraction of human cells gets infected during a viral infection?
As I understand, if a cell gets infected during a viral infection then it eventually dies. If an individual does not die of an infection, the percentage of cells that gets infected in the course of the infection must be quite low.
Are there any estimates available on how many cells get infected during a viral infection? (say, an influenza infection)?
(A very similar question was asked five years ago but unfortunately received no answers.)

After trying to answer this for a while, I've reached the conclusion that the information needed to answer it satisfactorily doesn't exist. I'll go ahead and summarize my findings here for you though, hopefully it's informative.
Different viruses infect different cells, and different people's immune systems are more or less successful at limiting infection, so the number of cells that get infected also varies a lot. A useful way to narrow your question might be "What is the maximum fraction of virally infected cells that can be survived?". All infections will vary between this maximum and 0%, with milder disease being associated with lower % cells infected.
I looked at Ebola as a candidate because it can infect a wide variety of cell types and a lot of research has been published on it.
From J Virol. 2004 Apr; 78(8): 4330–4341.:

Notably, 20 (91%) of 22 nonsurvivors had viral loads that reached ≥10^8 RNA copies/ml within the first 8 days after the onset of symptoms, thus suggesting that 10^8 RNA copies/ml can be considered an approximate threshold that predicts a fatal outcome with a positive predictive capability of >90%.

So, for about 3 L of blood serum in a person, that's 3 * 10^11 copies of the viral genome in the blood as a threshold for survival. I couldn't find useful information about viral load in organs and other tissue, but since blood has been claimed to have much higher concentration of virus than saliva or other fluids, we can assume this number is a significant portion of the total load. I'll assume about a third, so we get 10 ^ 12 genome copies. Some or even most of these RNA genomes might not be incorporated into viral particles but counting actual viral particles is very difficult, so no-one has published a correlation between Q-RT-PCR results and infectious particle counts as far as I could find.
Next, we need to estimate the number of progeny viruses that each infected cell produces. In Clin Diagn Lab Immunol. 2002 Jan; 9(1): 19–27. , researchers got about 2 * 10^4 PFU from wells containing 2-4 * 10^6 alveolar macrophage cells each. In these wells, 50-60% of the cells had detached from the walls, compared to 0 in non-infected wells. This implies that, for macrophages at least, about 100 infected cells make enough virus to create one plaque in the assay they used. In J Virol. 2015 Jul 1; 89(13): 6773–6781. about 1000 particles per PFU are reported for the 12th passage of virus in their Vero cell assay system, so 10 virus particles per infected cell. We estimated 10^12 virus particles earlier, so that implies about 10^11 cells were infected. That's a similar number as estimated for HIV in the comments of that question you linked. At about 3 * 10^13 human cells in the body, that's about 0.3 % of all cells.
Each of the studies I've linked here is quite different from the other, so plugging results from one into the other is introducing a lot of error, but hopefully the process was informative.

Thank you for this answer!


text:
Why isn't there T2 thyroid hormone?
The follicles in the thyroid, intake iodine and bind them onto the tyrosine rings (attached to the thyroglobulin). This produces either MIT or DIT (tyrosine rings with 1 or 2 iodines attached respectively).
Then the DIT joins with either another DIT or a MIT to form T3 or T4. This makes sense.
But it seems to me, that there could be a MIT attaching to another MIT, forming T2. Why doesn't T2 get created?

What makes you think that T2 doesn't exist? I did a search for "T2 thyroid hormone" and got several papers as hits ...

I think you've already answered your own question. DIT = 'T2', so yes, it gets produced.

ok so it appears T0, T1, T2, T3, T4 actually all exist, except T0, T1, T2 are simply byproducts of synthesis and don't do anything.

In fact, there are two T2 hormones, depending on the position of iodine atoms on the thyronine backbone molecule [5].
One of them, 3,5-diiodothyronine (3,5-T2) is the most active of all thyroid hormones with a relative T4 potency of 8 to 15. Thereby, it is 2 to 5 times as potent as T3. Its plasma concentration is rather low, however, being 0.2 to 0.37 nmol/l [1–3]. It is weakly bound to plasma proteins and has a short half-life [7, 8]. 3,5-T2 seems to be a risk factor for atrial fibrillation [3], and it is able to suppress pituitary thyrotropin (TSH) secretion [4]. It is upregulated in critical illness (NTIS/TACITUS) [1, 3, 6].
The second isomer, 3’,5’-T2 is an inhibiting thyroid agent that is able to block the activity of deiodinases and receptors for thyroid hormones, similar to reverse-T3 (rT3) [5].

References

Pinna G, Meinhold H, Hiedra L, Thoma R, Hoell T, Gräf KJ, Stoltenburg-Didinger G, Eravci M, Prengel H, Brödel O, Finke R, Baumgartner A. Elevated 3,5-diiodothyronine concentrations in the sera of patients with nonthyroidal illnesses and brain tumors. J Clin Endocrinol Metab. 1997 May;82(5):1535-42. PMID 9141546. https://pubmed.ncbi.nlm.nih.gov/9141546/
Lehmphul I, Brabant G, Wallaschofski H, Ruchala M, Strasburger CJ, Köhrle J, Wu Z. Detection of 3,5-diiodothyronine in sera of patients with altered thyroid status using a new monoclonal antibody-based chemiluminescence immunoassay. Thyroid. 2014 Sep;24(9):1350-60. doi: 10.1089/thy.2013.0688. Epub 2014 Aug 1. PMID: 24967815. https://pubmed.ncbi.nlm.nih.gov/24967815/
Dietrich JW, Müller P, Schiedat F, Schlömicher M, Strauch J, Chatzitomaris A, Klein HH, Mügge A, Köhrle J, Rijntjes E, Lehmphul I. Nonthyroidal Illness Syndrome in Cardiac Illness Involves Elevated Concentrations of 3,5-Diiodothyronine and Correlates with Atrial Remodeling. Eur Thyroid J. 2015 Jun;4(2):129-37. doi: 10.1159/000381543. PMID 26279999. https://pubmed.ncbi.nlm.nih.gov/26279999/
Pietzner M, Lehmphul I, Friedrich N, Schurmann C, Ittermann T, Dörr M, Nauck M, Laqua R, Völker U, Brabant G, Völzke H, Köhrle J, Homuth G, Wallaschofski H. Translating pharmacological findings from hypothyroid rodents to euthyroid humans: is there a functional role of endogenous 3,5-T2? Thyroid. 2015 Feb;25(2):188-97. doi: 10.1089/thy.2014.0262. PMID 25343227. https://pubmed.ncbi.nlm.nih.gov/25343227/
Hoermann R, Midgley JE, Larisch R, Dietrich JW. Homeostatic Control of the Thyroid-Pituitary Axis: Perspectives for Diagnosis and Treatment. Front Endocrinol (Lausanne). 2015 Nov 20;6:177. doi: 10.3389/fendo.2015.00177. PMID: 26635726; PMCID: PMC4653296. https://pubmed.ncbi.nlm.nih.gov/26635726/
Langouche L, Lehmphul I, Perre SV, Köhrle J, Van den Berghe G. Circulating 3-T1AM and 3,5-T2 in Critically Ill Patients: A Cross-Sectional Observational Study. Thyroid. 2016 Dec;26(12):1674-1680. PMID 27676423. https://pubmed.ncbi.nlm.nih.gov/27676423/
Louzada RA, Carvalho DP. Similarities and Differences in the Peripheral Actions of Thyroid Hormones and Their Metabolites. Front Endocrinol (Lausanne). 2018 Jul 19;9:394. doi: 10.3389/fendo.2018.00394. PMID: 30072951. https://pubmed.ncbi.nlm.nih.gov/30072951/
Köhrle J, Lehmphul I, Pietzner M, Renko K, Rijntjes E, Richards K, Anselmo J, Danielsen M, Jonklaas J. 3,5-T2-A Janus-Faced Thyroid Hormone Metabolite Exerts Both Canonical T3-Mimetic Endocrine and Intracrine Hepatic Action. Front Endocrinol (Lausanne). 2020 Jan 8;10:787. doi: 10.3389/fendo.2019.00787. PMID: 31969860; PMCID: PMC6960127. https://pubmed.ncbi.nlm.nih.gov/31969860/


text:
Effect of soap on the survival of non-enveloped viruses
As I understand it, non-enveloped viruses are not annihilated by alcohol or have lipid layers to get soluble in soap micelle.
Does soap remove non-enveloped viruses and does hand wash help in their spread?

Yes, hand washing with soap is effective at removing non-enveloped viruses. Here is a study showing that washing with soap is effective at disinfecting norovirus, which is a non-enveloped virus: https://aem.asm.org/content/76/2/394


text:
Why do birds legs' not get frostbite?
In a nature documentary I watched a while ago, there was a scene where a flock of flamingos slept in a lake that froze overnight. Each morning they just had to wait until the lake defrosted sufficiently to release them so they could get on with their day.
How do they not get tissue damage etc doing this?

Birds have a few adaptations and behaviors to keep their legs warm in cold weather:

Blood vessels (veins and arteries) run very close together or are intertwined:

The arteries and veins intertwine in the legs, so heat can be transferred from arteries
back to veins before reaching the feet. Such a mechanism is called countercurrent exchange. Gulls can open a shunt between these vessels, turning back the bloodstream above the foot, and constrict the vessels in the foot. This reduces heat loss by more than 90 percent. (Wikipedia)

Birds have specialized scales on their feet and legs which act as an insulator.

Birds often alternately tuck their legs into their body feathers to minimize heat loss. (Audubon)

Other survival mechanisms such as shivering and torpor come into play with extreme cold.

Other sources: Mother Nature Network. I don't have my texts handy, but can highly recommend Manual of Ornithology: Avian Structure and Function by Noble S. Proctor and Patrick J. Lynch.

Left this open for a bit just in case of further answers with additional info, but marking this as the answer as it is perfect, thanks!


text:
Difference between stem cell "expansion", "repopulation", and "self-renewal"?
From this paper (link:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4130805/), I read "Thus G-CSF results in the expansion of phenotypic HSCs in the bone marrow with reduced repopulating activity and self-renewal capacity."
If expansion meant population-expansion, then would that not mean the same thing as repopulation? Likewise, self-renewal occurs through asymmetric cell-division in which a parent cell divides into two daughter cells; or it can occur through symmetric cell-division in which a parent cell divides into a progenitor cell and a daughter cell. In essence, both types of cell-division maintain or increases the population of stem cells; hence, "self-renew" or "expand". Clearly, I am missing something here with the terminologies. Please help! Lastly, I thought phenotype is a noun, then what does phenotypic even mean?

will you be still interested in a few days time?

@PolypipeWrangler: Yes! Please help! I need this.

I will read paper this weekend

After an hour of reading the paper (from 2014), if you can I recommend instead reading the below review article (from 2020). the 2014 article uses difficult to understand language.
Eric M. Pietras; Inflammation: a key regulator of hematopoietic stem cell fate in health and disease. Blood 2017; 130 (15): 1693–1698. doi: https://doi.org/10.1182/blood-2017-06-780882
https://ashpublications.org/blood/article/130/15/1693/36384/Inflammation-a-key-regulator-of-hematopoietic-stem
I found this by pasting your article's title into google scholar, hitting "cited by", sorting by date, and browsing until I found a review article.
The point of treating with G-CSF is that the stems cells divide, and can be recovered from the blood for stem cell treatments.
"expansion" . Here means an increase in the numbers of cells. But in plant biology it has the literal meaning of cells growing larger.
"phenotypic HSCs". Using the adjective phenotypic, the cells express the phenotype of HSCs. So the cells behave like HSCs
By itself, G-CSF makes the the HSCs divide for a while, then they stop dividing. That is, they become "quiescent".
This state of quiesence can then be interrupted. If the mice are treated with antibiotics to kill intestinal flora (or if mice are used that are germ-free), then the HSCs continue to divide.
The article calls this process of getting the HSCs to divide again "mitigating the G-CSF-mediated HSC repopulating defect"

So to paraphrase the in-quotes from the 2014 paper, G-CSF causes the expansion of bone marrow HSCs with the phenotype of low repopulating or self-renewal capacity? Since G-CSF causes BM niche HSCs to exit quiescence. I am assuming that the 2014 paper distinguishes BM niche HSCs from BM HSCs.

Perhaps say "eventual phenotype". The HSCs that divide after treatment with G-CSF, seem like normal HSC but eventually stop dividing and become insensitive to G-CSF.


text:
What insect is this? Looks like a spider but with six legs and long antennae
I've been spotting some of these insects in my house lately, they look like spiders but it seems like they have six legs and antennae instead of eight legs.
Can someone tell me what insect is this? Is it dangerous? I don't mind having them in my house but if they're dangerous I might have to do something.
A photo of the insect:

Their body seems to be relatively flat when you look at it from a side, the location is Costa Rica, we are in the wet season (no winter,summer,etc. here) but I'm almost sure I've seen them during the dry season as well, also, the insect's body size (ignoring legs) is similar to a thumb. In case that helps to indentify it.

In general, it looks like it could be a cricket of some type.  They typically have long antennae.

Welcome to Biology.SE! Please [edit] your post to include an estimate of the size (e.g. around 5 cm long) — thumbs are highly variable and it isn't clear which part(s) of a thumb you might mean anyway! Also, could you try to get clearer pictures and, if possible, include one from the side and another from the front? Thanks!

https://biology.stackexchange.com/questions/112103/what-kind-of-insect-is-this-it-looks-like-a-huge-spider-with-one-long-antenna-a

I am think that I have narrowed it down to either Amblypygi (i.e., whips spiders, tailless whip scorpions), or Solifugae (i.e., camel spiders, wind scorpions, sun spiders). The thing is, in part due to the quality of the photo, I find both clues for and against each option. Long thin antenna-like appendages suggest Amblypygi, but the pedipalps aren't quite right. If it weren't for the think anterior legs, I would say it's a Solifugae. There's also the unidentified appendage that cast shadows don't explain.

My perspective, annotated photo
Rights belong to the initial poster/creator of this post.

This creature is an amblypygid (aka, whip spider, or tailless whip scorpion). Amblypygids are arachnids, but not spiders, and they are not venomous. Like other arachnids, they have eight legs, however the anterior legs have been modified into very long antennae-like limbs used to feel for prey. Anterior to the antennae-legs are the pedipalps, which have been modified to be long and spiny, used for capturing prey.


text:
Which beetle is this?
I'm curious to find out what kind of beetle this is. Google lens search suggested a type of longhorn beetle, but I am not convinced.
The photo is taken in Karnataka, in India
Thanks!!

Welcome to Biology.SE! Please [edit] your post to include habitat information and an estimate of the size of the organism. This information may be essential for an accurate identification. ——— If possible clear, closeup photos of the creature from multiple angles would also be helpful. ——— You may also benefit from taking the [tour] and then going through the help pages starting with [Ask] questions effectively on this site. Thanks!

This is a beetle from the family of the "longhorned beetles", since you found this beetle in India, I think this is Acanthophorus serraticornis
See the images for comparision (from here and here):

There is not much information online, but some can be found here and especially  here in this scientific article. The larvae of this beetles are considered a pest, as the bore into wood.


text:
Regarding different nucleotides on a DNA strand
I am not a biologist therefore, it might seem as an elementary question. I retrieved rodent sequences from UTR database:
http://utrdb.ba.itb.cnr.it
And I know there are supposed to be four nucleotides namely: A,G,C, and T. However, on this database I get sequences that have 'n' nucleotide in several locations, 'm' and 'k' as well. What does these letters mean? I haven't been able to find anything regarding it. Does it mean these positions in UTR are undefined or they are some 'intermediate' nucleotides if there are any?

These are IUPAC codes for so-called "degenerate" or ambiguous bases, alternatives to the usual A, T, C, and G nucleotides (for DNA). The N code represents any base, while M and K map to A or C, and G or T, respectively.

Okay. Thanks. That makes much more sense to me now.


text:
When is it viable to remove old graves?
Societal considerations aside, when all the remaining relatives of a particular gravesite have all disappeared or forgotten about a certain grave, is it viable/hygienic to remove or repurpose old gravesites as something new?
Not all burial traditions use airtight coffins that wouldn't let the body decompose — Muslim burial tradition would wrap the body in a plain sheet of cloth and then bury.

I think it's a really interesting question, but I also struggle to see the biology in the question... religions and societies can decide on things but if you want to evoke biology you're probably going to have to come up with an operational definition for the thresholds you are asking about.

@BryanKrause I'm asking from the perspective of hygiene, mostly. I'm really nothing related to biology, but I sent this question to a bio graduate friend of mine and she mentioned soil ecology, for example.

If the question is really asking "how long under [some set of environmental conditions] does a human corpse take to decay fully?", then I think it's biology.

@kmm How does one define "fully"?

Not to speak for the OP, but I would suggests when it is "viable/hygienic to remove or repurpose old gravesites as something new".

To weigh in on this: it totally depends on soil type, moisture, and oxygen levels of medium (not tomention burial practices as you mention). See bog bodies as an extreme example -- preserved bodies after 10k years!

Also, I personally think it to be very inappropriate both socially/religiously and regarding simple decency/respect for the dead to be considering disturbing their grave sites. In many places, it is also unlawful. So I encourage you to reflect very intently on any purposes you have for gaining this information.

8-10 years
Keep in mind digging up bodies once they are nothing but bones was common practice at one time, look up the catacombs of Paris or just Ossuary.
Human remains are not actually considered infectious once they have rotted away, not that they have much risk before that, but the smell of a corpse that still has soft flesh is remarkable unpleasant, which is why waiting until they are dry bone was common.
How long it takes to reduce a body to a skeleton is controlled by the site of burial and climate. Forensics uses a baseline of 8-10 years for a six foot deep burial in most temperate soils, much longer if buried in a casket. Note changing the conditions of burial can change this time from a few weeks to never because it mummifies.
source

I think the answer to this question is open for debate, as it depends on a lot of factors.
To start with an extreme, King Tutankhamun died about 3,000 years ago. The opening of its burial grounds was attended by Lord Carnarvon, a British sponsor of archaeology in Egypt, who died shortly after attending the tomb's opening. While at first it spawned superstitious beliefs like 'Tut's curse', nowadays researchers believe it was, perhaps, caused by various bugs found in the tomb, namely Aspergillus niger and Aspergillus flavus. These molds can cause allergic reactions, including lung bleedings. The toxins can be particularly harmful for people with a weakened immune system. Other bugs, like the respiratory-assaulting bacteria, Pseudomonas and Staphylococcus have been found as well on the walls of the tomb (source: National Geographic).
However, food items were stored alongside a host of other sacramental stuff, so Tit's tomb was anything but  a 'clean' grave. A normal grave hence may, or may not lack these contents and hence its bugs. However, there are many, many more variables in play, among them the type of coffin used to bury the corpse, the type of grave, type of soil, humidity, temperature etc. etc., which all interact and can affect the duration of the various stages of decomposition (source: Wikiepdia). Up until the last phase (skeletal phase), active decomposition is taking place, and hence many bugs are around, which would raise hygienic issues.
Lastly,cleaning up graves is quite regularly performed, and a period of four decades is used on a regular basis (source: BurialPlanning.com).
In all, I guess a definitive answer to this question doesn't exist, other than longer than 3,000 years....

People do remove graves much, much sooner than that, for example: https://www.thisamericanlife.org/689/digging-up-the-bones/act-one-6 but I don't really think this is a "biology" question per se. I won't use my close vote but I do think the OP needs some clarification to make this anywhere near biology.

@BryanKrause yes wasn't done yet. The Q needs clarification, which my answer hints at. Close away. Up to you. It's a broad question, but an interesting one imo.

Oh indeed, lots of interesting concepts here but...harder to frame it in biology :) I find it really fascinating from an anthropological and archaeological perspective that different human societies have completely different ideas of what "complete" burial and decomposition means. In Greece it seems the timeline has been shrunk down to <3 years, and is driven by mostly practical concerns.

@BryanKrause wow, that's really short! Note that I'm pretty biased in my close- and answer-behavior to the type of question. Questions on sensory systems I practically never close, I'm only human. So feel free to let that mod hammer swing...

Oh definitely - I suggest listening to the linked podcast which is fun regardless :) the lack of decomposition seems pretty central to the overall experience...and yet it is all pretty separate from the ideas expressed in OP here :)


text:
Does the process of making a sourdough starter involve Darwinian selection?
In essence - to make a sourdough starter:

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

I don't see why you couldn't just add all the ingredients required at the start, open it once a day to let more yeast drop in and give it a stir, and keep in a warm place every day.
The vague idea comes to me that throwing out half the mixture every day has a Darwinian element, but it doesn't involve any 'selection', you're simply casting out half, regardless of adaptability.
My question is: Does the process of making a sourdough starter involve Darwinian selection?
EDIT: There is no 'choice' involved in throwing out half the sourdough. It is entirely arbitrary - and both halves look equally the same.

How does the half you cast out compare to the half you retain?

Dividing it would be closer to genetic drift since nothing the bacteria do has any impact on which half you throw out. Note you don't actually have to throw out any of it is just that the process produces a lot of bulk which is usually too impractical to use unless you own a bakery.

Yes, continually diluting the mix like this encourages the organisms (bacteria, yeasts, fungi) to have more constant conditions (maximum nutrients, fewer waste products) and be in log phase growth. The mix selects for particular faster-growing organisms. if you did not dilute, the nutrient levels would change (lower) and waste products accumulate much faster. Then the conditions would be more different day-to-day.
Practically, the dilution adds more nutrients while still allowing the pH to fall. Without the dilution, particular bacteria tend to take over and lactic-acid producers dont get a chance.
refs
https://en.wikipedia.org/wiki/Bacterial_growth
https://en.wikipedia.org/wiki/Sourdough

How is that "Darwinian selection"?

I abbreviated the term to selection

so step 1 is Darwinian but dividing the culture is not.

There absolutly is selection involved. First, you create a selective environment to culture a subset of environmental organisms (yeasts). Then, by infusing fresh media (flour/water) into the cultures each day, you are essentially passaging a live culture or organisms. It's not rational selection, like that practiced by plant breeders, since you aren't hand picking the lineages you want to passage, but it does allow for natural selection to occur in this environment which would otherwise be stunted in a simple batch culture if you didn't add new flour/water mix each day. This passaging allows for more reproductive growth to occur, increasing the probability of adaptive mutations and creating the conditions for such mutation expands via competative exclusion with other clonal lineages. With more generations, organisms in the starter should become more and more specialized to the unique selective pressures in that environment over time. In theory, as they become more adapted to this environment, it will be less and less likely that any new wild strains or spoilage agents will take up residence in the starter. Richard Lenski has been conducting a series of long term E. coli evolution experiments describing how cultured organisms evolve over many (many) generations. Since people are known to keep sourdough cultures alive for years, decades, or even centuries, it seems like an analagous experimental system.

That is not Darwinian selection, because you are not selecting anything. As you mention yourself, it doesn't matter which half you discard and which half you keep. In fact, you can keep the entire thing. Discarding just makes it more practical.
If all conditions are fine, yeast will grow exponentially, meaning your amount of yeast will double every 2 hours or so. By discarding half of your mix, you simply reduce the volume you are working with. Otherwise you would have to add double the ingredients every time. For example, let's assume by adding fresh ingredients you double your volume. Starting with 250ml you would have 500ml the next day, 1l the day after, 2..4..8.. 16 liters and soon you have a bucket full of yeast.
Handling that volume to avoid overgrowth and insufficient nutrient/oxygen supply is way harder than a small volume. In the lab we grow yeast preferentially on shakers, mixing the solution to ensure all cells get the right amount of nutrients. Otherwise the yeast would die once the nutrients are depleted. So, how do you do that in your yeast bucket? ;) Just stirring it once won't do the job. The yeast would settle and die.
You could keep the halfs in separate smaller containers, but how much space do you have to store these? Here is a video where this issue is explained and what you can do with the discarded half: https://youtu.be/Ye4A2judXck
In the end, what would you do with all that starter? Once you have your sourdough starter ready, you can take half and use it for baking and keep growing the other half. How much bread do you want to bake? Do you need a bucket full of sourdough starter?
Sure, some of the yeast will die and the cells best adapted to the growing conditions will remain. This is a selection process, but it's independent from discarding half of it.

Natural selection does not require that a person is rationally selecting something, only that selection is occuring. Taking any group of environmental organisms and placing them in a new environment will absolutly involve selection. Not just initial colonization selection, but also adaptive selection over increasing reproductive generations. It's the same reason lab strains of bacteria or yeast often lack certain phenotypic traits of their environmental ancestors, while environmental organisms sometimes grow poorly in laboratory conditions at first.

The question was if discarding half of the starter involves a "Darwinian element". As I mention in the last paragraph, there is of course always adaptation/selection happening, but that's completely independent of the fact that you are discarding parts of it or not..


text:
Protein-coding introns in mitochondrial genomes
I am studying the mitochondrial genome and have read that some contain introns. However, these introns code for proteins. I cannot really understand this. Could someone tell me what intron in which mitochondria genome this refers to?

Can you please share the exact sentence and the reference to the paper/textbook mentioning this? I tend to think that introns are by definition the portion of genes that does not cod for proteins (although some exception may apply, such as intron retention). I would therefore be curios to investigate the issue.

unfortunately my references are in Greek, so not helpful I guess. if i translate it says sth like that: ORFs inside introns of group I and II. ORFs usually encode for GIY-YIG or LAGLI-DADG  endonucleases

Pehaps the mitochondrial proteins are encoded (with introns) in the nuclear genome, and then transported to the mitochondria?

Mitochondrial genomes differ greatly in size, coding potential and even whether they are circular or linear. Mammalian mitochondrial DNA is small (11–28 kbp) and intronless. However the mitochondria of certain other organisms range up to 1000 kbp in size.
Certain sponges (demosponges) with large mitochondrial genomes contain type I introns and type II introns.  Although introns were initially thought to have no other function than to separate exons, the introns of certain nuclear genes have been found themselves to contain genes. This turns out also to be true of some of the mitochondrial introns. To quote from then introduction to a paper I found through an internet search:

Most Group I introns encode homing endonuclease genes (HEG) and/or
  maturase of the LAGIDADG † family, while most Group II introns encode a
  reverse transcriptase (RT).

These introns are found in genes such as that encoding cytochrome oxidase subunit 1 (COI).

† This appears to be a misprint for the LAGLIDAD mutases, which are also endonucleases, and are involved in splicing the introns in which they reside.


text:
Is hair made of protein or dead cells or both?
Some sources say hair is made of dead cells:

it's mentioned in many titles of Google searches, so I'm linking the Google search search

Other sources say hair is a protein filament:

Protein filament that grows from follicles found in the dermis, or skin

I don't think protein and dead cells are the same thing. Where am I mistaken?

I found the answer while trying to write the question. Hopefully this helps others

We usually say that hair is “made” of a protein called keratin—that’s a bit of a simplification. As hairs become part of the shaft, they undergo a process called keratinization, in which they become filled with keratin. So, technically, instead of being made up of pure keratin, hair is made up of dead cells that are filled with and surrounded by keratin.

Source
I'd say some visualisation would be helpful, please add a new answer or propose edits to this answer


text:
Is this may-flowering grass an Echinochloa (barnyard grass)?
There's a grass growing in my thyme pot on my balcony, that's currently flowering (end of May, Paris region, France, southern exposure, windy conditions), and I'm wondering what species it is:

Here are a picture where details of the flower and leaves may be more visible:

I tried to search using my old determination key for French flora (G. Bonnier / G. De Layens), and after much hesitations, I guess it could be what is called "Oplismenus Grus-galli" in this book.
Internet tells me it is now called Echinochloa crus-galli. The base of the plant indeed has a similar way of growing, and the flowers are a bit similar.
Does this look plausible? Do you see a better match?
Can I use the seeds when they are ripe (for instance to put in home-made bread)?


text:
What is the name of this insect? Is it venomous or possess any threat to human life if someone gets stung?
I found it in Northern part of India, on a mango tree. When I intended to move it away from home, it seems to bite like a snake with front part lifting like a king cobra.
This insect is 6-7 inches long, 1-2 inches wide, and appeared during summers.

That looks like some kind of lappet moth caterpillar. Although I am no expert in them, especially not species that would appear in India. But hopefully my answer gives you the right direction of research.
You can see some visually similar observations on iNaturalist:

https://www.inaturalist.org/observations/42382365
https://www.inaturalist.org/observations/40958993
https://www.inaturalist.org/observations/40137289


text:
What is this snail? (Location: Bangkok, Thailan; size: 3 cm long, 5 mm wide; color: mostly black)
What is this snail? (Location: Bangkok, Thailan; size: 3 cm long, 5 mm wide; color: mostly black)

Video:  https://youtu.be/vxig5QOSoss

Possibly Macrochlamys indica or another species in the same genus, based on shell morphology.

Source

Thanks, looks similar indeed!


text:
Crickets with live babies
From what I understand of Crickets, they lay their eggs in dirt and hop away and that is their parenthood.
But in the past month (since I moved into this apartment) I have found 1 adult cricket and half a dozen tiny baby crickets in my bathtub on THREE SEPARATE OCCASIONS.
There have been times I have found other adult crickets in the tub, I have never found a baby cricket in the tub alone.
Something is going on here that doesn't track, an adult cricket could easily get into the standard 18 inch-ish high bathtub, but these baby crickets are about 2mm long and can jump upwards of about 3 inches from my testing.
Why/How are they traveling together?  What is the gestation on crickets?  Is it short enough that she lays the eggs at night and they hatch by mid morning?   Are they coming up the drain?  Carrying their brood on their backs because this is Arizona and they learned it by watching scorpions?  I need answers! This is the weirdest mystery of quarantine, and it must be solved.


text:
Is there any animal database or website that classifies animals as wild / domestic?
Is there any animal database or website that classifies animals wild / domestic?
Or.. the site that I can get the wild / domestic information of animal list...

That’s a hard one. For many species, there are individuals that are wild/feral, and individuals that are domestic: cats, dogs, birds, snakes, lizards. iNaturalist has an option to indicate whether each observation is captive or cultivated, and that’s about it.

If we knew the purpose of the question we might be able to offer more help. There is a lot of grey area with domestication.

I need the list of wild animals for the project.. so I tried to get the database of the animal list which classifies wild / domestic.