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If silver nanoparticles kill bacteria by penetrating the cell membrane, why don't they also kill human cells on contact?
Apparently, the silver from the nanoparticles can penetrate the cell wall of bacteria and kill them from the inside. Why, then, doesn't the same happen to human cells, e.g. the skin on my foot when I wear nanosilver-coated antibacterial socks, or the stomach lining when people drink nanosilver-treated water? Is it because the cell wall is different in bacteria than in multicellular organisms?

The nanoparticles from your sock will most certainly not reach to your foots cell membrane (Walls are for plants/fungi)  because of the thick layer of dead skin, oils, than about 30 cell thick cornified layer (stratum corneum) build up from practically dead cells (with no nuclei or organelles) but lots of filamentous keratine. This is the most outer shell of your epidermis followed by layers and layers of 4 other tissue types , then comes the "actual" skin dermis and the hypodermis beneath.

If some of the silver-sock -nanoparticles would actually make it through there to basal tissue and reach the cells plasmamembrane, they enter via endocytosis, and start to release Ag+ they break all kinds of things, because Ag+ is cytotoxic it induces ROS, damages you Mitochondira, disturb some pathways... you get the point.

However this was proven to happen within human in vitro celllines.

a few in vivo studies showed that Ag-NPs cause adverse effects on reproduction, malformations, and morphological deformities indifferent non-mammalian animal model.

Says "Review: A systematic review on silver nanoparticles-induced cytotoxicity: Physicochemical properties and perspectives
https://doi.org/10.1016/j.jare.2017.10.008

conclusion, definitely enough evidence to be suspicious, but don't freak out, just change socks daily, wash feet and don't drink dubious solutions or liquids. (sunscreen could be a factor )

I'm not freaking out, just wondering. :)
So, in the case of skin contact, I'm protected by a layer of dead skin, OK.
But there are disinfectant sprays with nanosilver, meant to be applied to open wounds. And disinfected water that goes to your stomach.
Is it actually killing both bacteria and your cells, but you're fine because your cells get replaced? Or what's the idea?


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How do birds eliminate oxygen free radicals
Birds breathe in a lot. Do they produce a lot more of oxygen free radicals than mammals? And how do they cope with oxydative stress?
Thanks!

Did you check on google scholar? There are a few papers there

“Birds breath a lot”! Me too.

@user438383 That is not scientific wording. better results from: https://scholar.google.com/scholar?hl=en&as_sdt=0%2C5&q=avian+oxidative+free+radicals+&btnG=

There is some info on that here:
Oxidative stress in ecology and evolution: lessons from avian studies
The article cites enzymes, antioxidants, brood size, serum analysis, body temperature, food types, membrane fatty acid composition, Vitamine E, carotenoids, and many other considerations. Perhaps you can read it and write an answer for us? Here is a summary:

Possible explanations for the higher longevity of birds compared to their mammalian counterparts are that birds have (1) a lower ratio of oxygen radical production and oxygen consumption, (2) an exceptional cellular resistance to oxidative stress, (3) a lower mitochondrial and nuclear DNA oxidative damage, (4) a lower cell membrane unsaturation and (5) a slower life history for a given body size

thanks, this table is wonderful! I will try to find an answer, the article you shared seems to be more complete than what i had found so far. i will share my findings

take it with a big grain of salt "aging rate" is not a well defined thing. There are also big extraneous factors like mammals can run out of new teeth and starve becasue they can't feed, which is a common cause of death among mammals and nothing else. becasue mammals are basically the only group with limited numbers of teeth. and mammals can develop more in utero becasue of the advantage live birth has over eggs.

source: Stack Exchange

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

sort: votes


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What global habitat classification systems are there?
I am an IT guy, not a biologist or ecologist, but have ended up with (roughly) the task "given this Latitude/Longitude pair, return the 'habitat' at that location". The points of interest in practice are likely to come from Europe or North America, but could come from anywhere. All data points will be terrestrial, not marine. What habitat means isn't fully defined, and I'm looking for a best-practice answer.
At this point I thus have a question: "what are the well-regarded global habitat classification systems?". A basic search leads me to the IUCN Red List Habitat classification 3.1. From there, I find some nice recent research work by Jung et al that attempts to map the world onto an IUCN habitat type by combining data from a Koppen-Geiger climate classification system, from Copernicus land-cover data and from an ecoregion+biome classification coming from the WWF. This classification has had a number of iterations, but currently seems to have 867 ecoregions in 14 biomes. The resulting map is at approx. 100m resolution and maps on to 47 of the IUCN habitats.
To my amateur, all of this seems great, but is it the state-of-the-art? Or are there other habitat classification schemes out there? Where should I be reading?
Many thanks indeed for any help and apologies in advance if I have broken any rules of the site - this is my first post.

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


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Does hydrolysis of carbohydrates, proteins, and fats occur in the small intestine?
Does the hydrolysis of carbohydrates, proteins, and fats occur in the small intestine? I have researched this and just cannot seem to get a clear-cut answer. Perhaps I am misunderstanding something?
Any help and/or links to resources are appreciated! I just want to make sure that I understand this concept before moving on with other biology topics that I am learning.

Can you explain more about what you've learned and where exactly your understanding is lacking?

@BryanKrause I am not sure if I am lacking any understanding. I am taking high school bio, and I have been learning about the digestive system. So, I am not sure if hydrolysis of carbohydrates, proteins, and fats occur in the small intestine.

That's fine, but according to our homework policy we require that questions show their own research effort (not just state that the effort happened). This is part of how we avoid people asking questions here to just fill in the answers on their assignments, which we feel damages rather than assists learning.

@BryanKrause You know, I really appreciate that. I am so over the cheating nowadays because now I have to show proof of my research rather than just you trusting me (one bad apple spoils the bunch). Then again, I appreciate you taking the precautions. :) This is where I was finding my information, but I did not find what I was looking for...

digestion doesn't only happen in small intestine, but also in stomach and mouth even. search for what hydrolysis exactly means, then search for where do hydrolysis reactions happen in body, then search for digestion of carbohydrates, lipids and proteins and how do they happen.

@manidattas Thank you for your help! After some other research, I feel like hydrolysis of all three compounds does occur in the small intestine. I hope that I am understanding everything correctly; appreciate it. :)

This article section should give you enough terms and anatomy to answer your question the way you asked it. Once you know some names, look up the enzymes in other sources - you can use Wikipedia, but you can't trust it.  (Then try submitting an answer to your own question to help solidify your knowledge!)


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Recommendations for a haemocytometer (phase-contrast)
I'm looking for recommendations for a haemocytometer that can be used with a phase-contrast microscope. I want to use it to quantify the vegetative and spore fraction in my samples. Can I use any haemocytometer, or should the counting chamber be reduced in overall thickness?


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Does anyone have a tutorial or some guide to get started with Rosetta protein modeling and design tool? (I am a Mac user)
I have been trying to get started with Rosetta protein modeling and design software bundle. I searched online but the tutorials in the Rosetta website are difficult follow. I have the binaries already downloaded.
I would highly appreciate if someone could help me out with this.
My initial goal is to model a few proteins structures and to design basic backbone structures.
Thanks in advance

I don't think this is really the place for this kind if question. You might be better off going to   biostars or reddit bioinformatics if you have a specific question. Good luck.

You give no link to the software you are enquiring about, so we cannot check what sort of support they provide, but you should certainly check yourself. If there is no such support, I suggest SE Bioinformatics would be a better bet.

Welcome to Bio stackexchange! I edited your question to make it more specific, and detailed. I found through a youtube search that meiler lab has some nice tutorials for rosetta, like this video on protein design


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Can someone identify this jellyfish?
Recently, I saw this video but I couldn't find out if it's CGI or if it's an actual jellyfish. If it's real, what explains its beautiful bioluminescence pattern? And could the output from the ROV thrusters rip it apart (in the video description it says so)?
Photo:

Location: off the East coast of Africa.
Size: unknown, but it can be compared to the objects in the surroundings.
Additional info: footage taken in 2013.

The video you linked to, and from which you got the still shot. is real.  There are  hundreds of such videos now that Underwater Remotely Operated Vehicles (ROV) are more commonplace.

...could the output from the ROV thrusters rip it apart(?)

A working class ROV needed for deep ocean floor exploration can be the size of an SUV. There's no reason to believe its thrusters can't generate the shear forces needed to (sadly) tear a delicate jelly apart.

...I couldn't find out if it's CGI or if it's an actual jellyfish.

Although not a jellyfish, it is similar in being delicate; it's a ctenophore or comb jelly. The refraction/bioluminescence pattern is common in ctenophores.

And what dazzling colors these creatures display! The cilia of the ctenophores refract light in iridescent waves. Certain species are even capable of producing light, like fireflies of the sea!

For more information and videos, this short Youtube video might help. Or for a written explanation, this article, Introduction to Ctenophora  (https://ucmp.berkeley.edu/cnidaria/ctenophora.html) is good.


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Can apes have schizophrenia?
Many animals can become mentally ill, but I could not find any account of animals showing schizophrenia, not even apes. I could only find this, but it seems very vague.
Is there any evolutionary explanation of why only humans have schizophrenia?

Makes me wander how would you verify the animal has halucinations, delusions or disorganized thoughts.

@BagiM - You don't need to ask a Great Ape (or a mouse) if they're having hallucinations. If schizophrenia is genetic and the sites responsible for it are known, we need only to sequence DNA to know. If it is morphologic, we need only to do histological studies. And yes, both of these types of studies have been done on humans and great apes, looking specifically at schizophrenia as a uniquely human disease. I an not a neuroscientist, so will not comment on the findings, as they are kinda beyond my ability to judge competently. But a neuroscientist should be able to answer.

I really like this question (so +1), but I’m voting to close it because it might be a better fit on Psychology & Neuroscience.SE

@anongoodnurse: Re "If schizophrenia is genetic...", but is it purely genetic?  Or is it a case of the genetic variants being necessary but not sufficient?  In the same way that having certain genetic variants predisposes one to various cancers, but doesn't guarantee that you're going develop that cancer.

@jamesqf - (I hope you know what I'm going to respond...) Schizoprenia, like most mental illnesses showing a genetic component, is very likely multifactorial, with different factors having different weights/influences on expression. I do believe that the genetic component(s) is/are heavily weighted. My comment was to someone who doubted on the basis of asking an animal questions. A nuanced response would be kinda inappropriate to that user. I was pointing out that there is more to science than asking an animal if it's having, say, flight of ideas, or if their cat is giving them commands.

Like hearing voices? that's a characteristic symptom of one form of schizophrenia. or multiple personalities, which is the original meaning? you have to clarify. your question is a bit dull for effort at the moment. You can try this though https://scholar.google.com/scholar?hl=en&as_sdt=0%2C5&q=psychosis+chimpanzee&btnG= and https://scholar.google.com/scholar?hl=en&as_sdt=0%2C5&q=schizophrena+chimpanzee&btnG=


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Can animals speak like humans?
I know some animals don't have the required vocals. But, I do think that some like parrots, etc may have the capability to produce speech and talk just as we do.
My question is that if an animal is trained from birth, spending all the time around only humans, in the initial years of growth when their brains are much into learning everything, can they learn to talk just as we do?

Have you read about Alex the African Grey parrot? https://en.wikipedia.org/wiki/Alex_(parrot)  Or Washoe the chimpanzee? https://en.wikipedia.org/wiki/Washoe_(chimpanzee)

I think the smartest could understand sign language

It depends on what is understood by speaking.
Anatomy  If by speaking one means producing sounds similar to those produced by humans, than the ability to speak is largely determined by the anatomy of the speech organs - whether they can produce the same type of sound as human does. There are very few animals capable of this (I will find the reference), and this notably excludes some rather close human relatives, such as the great apes.
Neurology Language is a more complex phenomenon than speaking. The most notable difference between the animal and the human communication is that the former typically uses a set of signals with hard-coded meanings, whereas the humans can construct an infinite number of phrases coveying complex meaning. The study of language from this angle has been traditionally carried out by linguists and computer scientists rather than biologists, under the general name of universal grammar (but may also appear under such terms as transformational grammar, generative grammar, etc. ) However, these studies have a direct biological implication that humans possess a genetically coded set of rules for sentence/phrase structure, which is independent on their native language. This clearly requires certain degree of neural development, which the language-less animals do not necessarily possess.
Psychology  Finally, language requires significant psychological development - even in humans. Feral children often fail to acquire language competences. Similarly, the extensive studies on small chidlren in care homes (starting from the works by Anna Freud and Melanie Klein from more than a hundred years ago) demoinstrated that children deprieved of normal human contact have significantly diminished speaking abilities. Getting back to the OP - one can therefore question whether an animal could concievably be exposed to normal human environment to facilitae development of linguistic ability similar to that of a human.
See here and here for more background.


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Why do nearby cells have similar meiosis periods?
A few days ago, I conducted an experiment to observe the meiosis of rye ears. During the experiment, I observed that cells in similar locations have similar meiosis period. Can anybody tell me why does this happen? Does the checkpoint of a single cell affects the checkpoint of nearby cells?


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DNA replication and Protein synthesis
Is DNA replication required for Protein Synthesis or can proteins be synthesized without DNA being replicated?

Sounds like you may not be be very familiar with the basics of DNA and protein synthesis. I suggest you check out Khan Academy, they have some very good videos explaining many aspects of biology (and other subjects)

If you have a file on your computer hard drive, a document, and you want to translate that document into a different language, do you need to make a copy of the original file before you translate it?
Making a copy of a file is duplicating it, like replicating the DNA in a chromosome.  Translating the document into a different language is “sort of” like translating a messenger RNA into a protein.

DNA replication and protein synthesis are very very different processes. The key thing to remember about protein synthesis is that DNA is not directly used; RNA is. When DNA is replicated, it is for reproduction. When it is transcribed, it is copied, with certain changes, into RNA instead. RNA is then "read" by protein synthesis machinery to produce the proteins.
To directly answer your question, no, replication is not required. If you inject some RNA which codes for a protein into a cell, it will be translated into a protein. There are many viruses which exclusively use RNA for their genetic makeup. The RNA is replicated at some point by the host cell's machinery but the RNA can be directly translated into a protein by the host cell as soon as the RNA enters the cell.


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How much Kanamycin is too much for selection in dh5α E. coli?
I'm using Kanamycin for selection after electroporation of my plasmid containing a kanamycin-resistance gene at a concentration of 50mg/L prepared in 1000x stock that is usually kept in frozen aliquots.
When preparing LB plates for selection, I usually prepare a 300ul dilution of the 1000x stock (30ul kan + 250ul h20) and spread that onto my plates evenly. This usually works fine.
However, on some occasions, if I let the plates sit for a week or so, I'll go ahead and reapply more antibiotic just in case.
Is there an amount of kanamycin that is toxic to the E. coli, even if they've been successfully transformed? Are there any side effects I should be aware?

Can't answer for what is too much, but kanamycin is a highly stable antibiotic. No need to replenish after only two weeks:
https://bitesizebio.com/10252/ye-olde-antibiotic-plates/
https://bitesizebio.com/9655/antibiotic-stability-keep-your-gunpowder-dry/


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Can I use TBE to elute a plasmid shipped on filter paper?
I'm receiving a plasmid shipped to me dried on sterile filter paper, as described in this question. This protocol and many others like it call for eluting the DNA from the paper using TE buffer.
My question is can I also use TBE to elute, as I already have a bunch on-hand? And in general, what concentration should the buffer be as I never see that mentioned in any of the protocols (including the AddGene version).

In my experience it does not matter if you use water, TBE or TE buffer. Even with a little EDTA in it, it will not mess up enzymatic reactions as the concentration is way too low. TBE/TE buffer usually contains 1mM of EDTA which can chelate 1mM of bivalent cations.
Since you not use the DNA undiluted (which also binds a lot of magnesium needed for most enzymes btw.) this really doesn't affect you in reality (been there, done that multiple times).
Additionally, I would recommend not using this DNA directly but transform it into bacteria first and then do a proper miniprep so you have enough material to work with (maybe even do a few restriction cuts and run it on a gel, to ensure the right identity) and a stock you can go back to if something goes wrong.

This is not exactly an answer to your question, i.e., how borate ions affect storage of your plasmid DNA.
But I would recommend you to use neither TBE nor TE, as they contain EDTA that might interfere with downstream enzymatic reactions. Use water (ddH2O) instead. As long as you store your plasmid DNA at -20°C it will be perfectly stable for many years. Alternatively, use a simple Tris buffer.
Addgene has a good article on this.

It really depends on the downstream applications, but the concentration of EDTA present in 1X TE (1 mM) is generally not enough to interfere with enzymatic reactions like restriction digestion, since the buffers used in those reactions supply Mg2+ at a final concentration of 10 mM or greater. EDTA chelates Mg2+ at a 1:1 stoichiometric ratio and prevents the activity of contaminating nucleases by sopping up the trace amounts of metal ions that those nucleases need as cofactors, greatly increasing the stability of DNA in aqueous solution.

Yes, you're right, the final EDTA concentration in an enzymatic reactions ends up being incredibly low. Also, as @Chris points out, you would most likely want to transform the eluted plasmid in bacteria and prepare new plasmid before any downstream enzymatic reactions.


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How to replace intron region in a plasmid?
I'm considering working with the plasmid pRFHUE-eGFP and would like to replace the gpdA intron (which is the eGFP promoter region) with a promoter from another organism.
What would be a good strategy for replacing the intron if I already have the other gene in-hand?
Would I cut out the fragment between the SalI and SmaI restriction sites and then insert the new promoter with compatible overhangs there?

Your strategy would work, but if possible you might be better off using XmaI rather than SmaI, as the latter is a blunt-end cutting enzyme.
Furthermore, your strategy would not replace the entire gpdA promoter, if that's what you're after. You might wanna refer to their paper, where it's clear from Fig. 1 that the promoter region is much longer than the region between SalI and SmaI:

I've been appreciating your on-point synthetic biology answers! Want to support the proposal for a dedicated SynBio StackExchange site? https://area51.stackexchange.com/proposals/125068/synthetic-biology

Thanks @jakebeal, but I'm of the humble opinion that Synthetic Biology questions should remain part of SE Biology. :)

Your call, of course; my own reasoning is spelled out in https://area51.meta.stackexchange.com/a/32413/211190

Your answer has pointed out that the plasmid on AddGene and the one referenced in the paper are different. The directionality is reversed,  they vary by 8bp in size and the annotations don't match. I wonder why this might be.

For what it's worth, I'm self-learning synbio. There aren't any focused places on the web for me to get support (diybio forums maybe?). I see pros/cons for a dedicated SE, pro: draw-in synbio focused expertise to central place, con: I appear to be getting my answers from SE Bio already.

Note that what you refer to as directionality here is irrelevant: one map is simply displayed as the reverse complement of the other. Second, annotations might differ because the authors chose a certain vocabulary for the paper, whereas the plasmid map you got from AddGene might be automatically annotated based on the DNA sequence (just guessing). And I wouldn't pay too much attention to the 8 bp difference in size.


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What was the evolutionary advantage of having seeds so large that they could only be dispersed by megafauna?
I understand that fruits like the avocado and the osange orange are so large and unwieldy that their evolutionary "intent" was to be consumed whole by megafauna that are now extinct. What I don't understand is why there was selection pressure for such a relationship to develop. Wouldn't it be to the plant's advantage if its seeds could be dispersed by more types of animals? What advantage does the plant get by limiting seed dispersal to a small set of large animals?

There are a few advantages to megafauna:

they travel large distances and are hence are likely to be able to
spread your seeds widely.
They also eat large amounts, so can carry a lot of seeds and
distribute those around widely.
Large fruit capable of being eaten only by the largest fauna might have the seeds survive by not being eaten and destroyed by smaller animals
Large animals have large guts, so the more of the seeds might survive undamaged

Another significant factor is that a megafauna animal also produces mega-feces, literally a large pile of nice warm fertilizer for the new plants to grow in.

You may be focusing too much on the megafauna. If there are selective advantages to making a big seed, some seeds at least will get bigger and bigger until there is no animal that will disperse them. If you've ever sprouted an avocado seed, its shoot and first leaves grow very high very quickly. Smaller seeds may have more dispersal routes, but if they end up near an avocado seed, they will have to grow in its shade.
Seeds may continue to get bigger past the point that they can be swallowed whole by an animal, if simply dropping the seeds is viable (Quercus insignis acorns can be up to 8 cm in diameter), but then there will be selective pressure to reduce the energy spent on the fruit coating the seed.


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Unknown pentatomid from India
I found this bug last year in August in Bharatpur, Rajasthan, India. The scale at the bottom of the picture is in mm and the size of the bug seem to be about 1.5 cm.
It looks a bit like Halyomorpha halys, but all the pictures of H. halys I've seen show white markings and sometimes more colour and not the dark markings as shown here.

Oh, and it was feeding on the bird dropping shown in the upper left corner.

For me it does not look like Halyomorpha halys because as you said the white marking but also there are some white sections in the antennas (see here). We have also this specie in Europe and considered as invasive.

Also the head is more squared on the Halyomorpha halys as shown in this picture from the same site, yours has a triangle/sharp head.


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Using Height and Area for plotting histogram of each marker in FACS
I had a flow cytometry experiment. After normal filter with cell debris and doublet cells, I would like to gate the cells by different markers. However, I get confused to use which parameter to plot out the histogram/ scattered dot plot. More specifically, for each fluorescent channel, there are 3 options: height, width, and area. I know that width is only related to the cell size while height and area both correlate with the signal intensity. I would like to know which measurement (i.e. height or area) should I use to plot the graph?
Someone suggested that if I am analyzing different cell populations with different shapes/sizes, I should use the height. I wonder whether this is true.
Thanks!

Height is most typically used for fluorescent channels, but not necessarily for forward and side scatter. For example, you'll look at a plot and see FL2-H vs FL1-H. Experiment by substituting the different options and see how your plots change, if at all.


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How to correct the different (background) fluorescence for different cell types?
I am differentiating mouse bone marrow macrophages in vitro. However, I found that the differentiated macrophages have higher background fluorescence (the unstained sample) in all channels, which includes both BV421 and AF-647. I also test this in single-stained cells and got similar results (therefore, I believe is not because of failed compensation).
I have these specific questions:

Is it common to see cells having different background fluorescence?
Are there any tools or algorithms to be used to correct such differences?
For publication/ presentation purposes, is it common to omit the plot of unstained control? I would like to know what is the convention.

I hope this is not caused by my experiment's failure. I found this thread, but the hyperlink does not work. Therefore, it would be great if you can also comment on what are the potential causes of this observation if you found that relevant.
Thanks!

Far from an expert here but I believe that there are many tools that can help you correct background fluorescence, here is one such.


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Is deleting two or three consecutive nucleotides and inserting exactly two or three back more common than two or three consecutive SNP?
I am looking at cancer mutations. I found that some of the mutations are e.g.

c.1251_1252delGGinsTT
c.151_152delGGinsTC
c.351_352delCAinsTT

I wonder if these are indeed two consecutive single nucleotide polymorphisms, such that they are indeed:

G>T, G>T
G>T, G>C
C>T, A>T

I would like to know which scenario is more biochemically plausible. I would like to distinguish them because I am looking for grouping them into mutation categories. I am not sure if I should treat these as indels or SNPs.
Thanks!

I believe it is SNPs, though they can be di-nucleotide polymorphism (DNP) or TNP. I saw this on some common oncogenes, e.g. TP53.

Thanks for your clarification,  I think you'd better include all the information and ask again in bioinformatics stack exchange ( , you will receive immediate feedbacks).

Please also refer to SNP and indel definitions:  https://genome.sph.umich.edu/wiki/Variant_classification, (https://snp.gs.washington.edu/SeattleSeqAnnotation154/HelpIndelAnnotation.jsp)


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Why there is Cp/Ct (crossing point) value for negative sample in COVID-19 RT-PCR?
I am from IT/ Engineering background and have some confusion in RT-PCR. So far my understanding we extract RNA from test specimens and transcribed it into complementary DNA (cDNA), and inside PCR DNA double helix is separated. Then primer a short nucleic acid sequence that provides a starting point for DNA synthesis with the target sequence and multiples the target DNA.
Since a higher cp value indicates a negative result but why negative results have cp value? Why it cross the threshold when it does have any target sequence (viral DNA)? Fluorescence is the measure of target DNA right??
In extraction, RNA is extracted does only COVID viral RNA is deducted? What happens to other viral and human RNA?
I have seen result were we have low cp value and test result is negative, the reason for this was because curve do not have Sigmoid function. I need more explanation on it.

I do research on these tests for a living, and I've never found a good explanation for why some PCR reactions produce these linear amplification artifacts, even amongst my clinical diagnostics colleagues. You could try running the product of them out on an agarose gel to see if you see the expected band (or bands). But I agree with the Chris's answer that, if you're unsure about a result because of a strange shape to the amplification curve, I would re-test the sample, probably doing a fresh RNA extraction, rather than simply making a negative determination.

PCR is highly specific (meaning it amplifies only the DNA the primers bind to), so the results in general are good. But: Due to the exponential nature of amplification, even very small mispairings can lead to the amplification of a very small amount of DNA and subsequently to a fluorescent signal. There are basically two ways of getting this amplification (except from the desired one): Contaminations and primer self-amplification. The first one should be clear, the second one happens when primers are able to bind to themself (or the complimentary one). This usually shows up late in the PCR, which is the reason why you assign a Ct-value to it after which you do not expect any meaningful amplification result anymore.

Depending on the method, you extract all RNA from your sample and translate it into cDNA. However, for the amplification in the PCR you need primers that fit to this cDNA. And since these primers have been proven to be highly specific (meaning: they bind absolutely no other sequence, not even from closely related viral species) we can be sure that any signal which is about the criteria mentioned in 1. comes from viral RNA and shows an infection. See the reference for one of the often used PCR tests.

Without seeing the curve, I cannot say anything specific about it. In general a real-time PCR curve follows a sigmoid shape. This gives some information about the way the reaction progressed over time. If it looks differently, something may have either happened to the reaction or to the sample. It may contain a PCR inhibitor, the sample can be contaminated or something else. I wouldn't trust such a result and repeat it with a new sample.

Reference
Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR

Just a side comment, but for diagnostic purposes it's often not the case that All RNA is reverse transcribed into cDNA. Most nucleic acid tests for SARS-COV2 (and other RNA pathogens) use a target specific RT step, so that only regions containing the PCR targets are reverse transcribed, helping improve specificity and reducing RT bias. Since the reverse primer for the PCR will generally perform this function well, these tests often use a 1-pot (or 1-step) RT-PCR, which is faster and also slightly more sensitive since you don't dilute the cDNA when adding it to the PCR mix.

While @Chris's answer is correct, there is a complication that comes into it:
The principle behind quantitative PCR (qPCR) is that you have a reaction which, if your reaction is 100% efficient, doubles the number of DNA strands produced at each cycle. In theory, you can start from one strand and get 2, then 4, then 8 in a 2n style equation, where n is the cycle number.
However, in reality this rarely happens, most reactions are not 100% efficient; generally in the 90% range is considered acceptable, so if you do the maths, it doesn't quite work out at a doubling each cycle.
The qPCR tests run on COVID-19 samples are generally run out to 45 cycles, which if you work out the maths, means that if a sample is showing some amplification at this point, then there is less than 1 copy of the RNA (actually cDNA) in each reaction, so the signal is likely to be non-specific amplification or spurious signals from other products in the reaction, such as primer-dimers (shouldn't be the case in these tests though, they use a system that all-but eliminates this problem).
Non-specific amplification can be detected by looking at the reaction and comparing the melt-curves of the products of the PCR. Specific products will have melt-curves that meet certain criteria (all with a peak at the same point), while non-specific products will have different melting points/curves.


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Is there a simple incision that would render a man impotent?
I’m writing a novel in which two women (one of whom is a doctor) take revenge on a rapist by performing surgery on him.
What would be the simplest but most effective way of causing permanent and total erectile dysfunction?
I assume cutting one or more nerves but there are several up for contention:
The Dorsal nerve
Pudendal nerve
Inferior rectal nerve
Perineal nerve
Posterior scrotal nerves
Ideally, I’d like the surgery to be so minimally invasive that he wouldn’t even be aware that it had been done to him.

Snake Bite. There is a cobra in Thailand/Asia whose venom interferes with the male pituitary or some deep brain hormone regulation, and the result of enough venom is that he stops growing a beard, his testosterone drops, and he becomes like a 8 year old boy again.

@com.prehensible Thanks! My novel is set in a small English village so getting cobra venom may be a bit difficult, but I may use that for a future novel! Out of interest, why would a question like this get voted down with no explanation as to why? Have I not phrased it correctly? Thanks!

I think the downvotes are from people who might not think this stack is most appropriate for your question. I see the biological relevance, but future questions like these might be better answered in the medicalsciences stack or the writing stack.

Thanks Bruce. On the writing stack we generally migrate questions and explain why rather than just downvote them. But they're a cheery bunch over there. Glad I made the mistake of picking this stack, if I hadn't, I wouldn't have found you!

I'm voting to close this question as off-topic because it's better suited for health.

You want to somehow damage the cavernous nerves of the penis. If you damage the preganglionic root of the cavernous nerves (the pelvic splanchnic nerve), you'll create all kinds of other problems.
You might also  consider using a chemical agent instead of surgery; this will allow for increased discretion and ease of administration. I discuss this after the break in my answer.
Erection is driven by the parasympathetic nervous system; ejaculation is driven by the sympathetic nervous system. Since you're looking for "permanent and total erectile dysfunction," you want to disrupt parasympathetic innervation to the penis. The candidates you've mentioned (dorsal nerve, pudendal nerve, inferior rectal nerve, perineal nerve, posterior scrotal nerves) won't work since none of them provide parasympathetic innervation to the penis. Rather, the dorsal nerve of the penis is a branch of the pudendal nerve and provides sympathetic (ejaculation) and sensory innervation; the inferior rectal nerves are also branches of the pudendal nerve and provide purely somatic innervation to the anus (these lie below the pectinate line, which marks the boundary we use to define internal and external hemorrhoids); the posterior scrotal nerves are a sensory branch of the perineal nerve, which itself is a branch of the pudendal nerve. This plate from Gray's will help you visualize these relationships.

"The Epidemiology and Pathophysiology of Erectile Dysfunction." Melman et al. The Journal of Urology. 1999.
Erectile  dysfunction
is
a
common
condition  associated
with  aging,
chronic
illnesses
and
various
modifiable
risk
factors. Normal penile erection
is a hemodynamic
process
that
is
dependent
on
corporal  smooth
muscle relaxation mediated
by
parasympathetic neurotransmission, nitric
oxide,
and
possibly
other
regulatory factors
and
electrophysiological
events.
As
more
knowledge
is
gained
of
the
physiology
and
regulatory factors
that
mediate
normal
erectile
function,
the
mechanisms
involved
in
the
pathophysiology
of
erectile
dysfunction
should
be
further
elucidated.

So, let's say you want to go after the parasympathetic nerves to the penis – the cavernous nerves. These are postganglionic, meaning they've already synapsed in the cell bodies of their target organ. Here's another plate from Gray's to make clear the parasympathetic (blue) vs. sympathetic (red) innervation in the body:

As you can see, the preganglionic pelvic splanchnic nerve might be an easier target than the postganglionic cavernous nerves, which will be running all over the tissue of the penis, making them difficult to quickly and directly target. However, you risk disrupting other hindgut functions as you move closer to the sacral spine.

"The actions of parasympathetic and sympathetic nerves in human micturition, erection and seminal emission, and their restoration in paraplegic patients by implanted electrical stimulators." Brindley. The Royal Society. 1988.
Appropriate stimulation of the S2 roots causes the erectile tissue of the penis to swell... Implants that stimulate the S2, S3, and S4 anterior roots improve micturition, defaecation, and penile erection in many patients with spinal-cord injuries.

Your desired discretion will go out the window if your antagonist wakes up unable to normally urinate or defecate, so you might target the prostatic plexus, where the branches of the cavernous nerves arise, but this is a relatively deep structure (bound within the prostatic sheath) that you won't be able to discretely injure. When scientists test cavernous nerve injuries, they use a variety of techniques, but none of them are particularly non-invasive:

"Functional Sequelae of Cavernous Nerve Injury in the Rat: Is There Model Dependency." Mullerad et al. The Journal of Sexual Medicine. 2006.
Nerve Manipulation Techniques
(1)  Control  group  (C):  underwent  a  laparotomy
only  to  control  for  the  effect  of  anesthesia.  The
pelvic  organs  were  not  disturbed  and  thus  the
result was no visualization of the CN. (2) Exposure
group (E): laparotomy and dissection of the pros-
tate to enable visualization of the CNs bilaterally
without any direct CN manipulation. (3) Neurot-
omy  (N):  the  CNs  were  transected  bilaterally,
5  mm  distal  from  the  ganglion,  with  as  much  of
the overlying fascia preserved to allow approxima-
tion  of  the  nerve  ends.  (4)  Bulldog  clamp  crush
group  (B):  a  vascular  bulldog  clamp  (60  g/mm
2
,
Fine Science Tools, USA) was applied to each CN,
5  mm  distal  to  the  ganglion.  It  was  applied  for
30  seconds,  removed  for  30  seconds,  and  then
reapplied  for  a  further  30  seconds.  (5)  Hemostat
crush group (H): an ultra fine hemostat (12.5 cm, nonserrated, Fine Science Tools) was applied with
full  tip  closure  in  the  same  manner  as  for  the  B
group.

Understanding the anatomy of the penis will help you decide how to proceed. I think you're on the right track with a neurovascular or nerve injury. "The Physiology of Human Penile Erection" (Weiss, Annals of Internal Medicine, 1972) includes this great figure, where each labelled letter in the pathway relates to a specific site of erectile dysfunction-causing injury:

You're most focused on sites F, G, and H. Here, F is caused by long-term illness and G is caused by, once again, invasive surgery:

SITE  F The  incidence  of  erectile  dysfunction  in  diabetes  mellitus   exceeds   that   in   diabetic   retinopathy   or   nephropathy.  In a random study  of 200  diabetic  men,    59%   were  impotent.   The  incidence  of  impotence  does  not  correlate  with  the  duration  of  the  diabetes,  the  severity  of  the  imbalance  in  carbohydrate  metabolism,  or  the  degree  of  diabetic  control.   Impotence   is   occasionally   the   initial   clinical   manifestation  of  diabetes,  and  diabetes  should  be  considered  as  a  possible  cause  whenever  a  man  complains  of  impotence.  Ellenberg   found  a high correlation between  neurogenic  bladder  abnormalities  and  impotence  and  thereby  postulated  that  an  autonomic   neuropathy   was  the  cause   of   impotence  in  diabetes  mellitus.  Other  causes  of  autonomic  neuropathies  are also frequently  associated with impotence. Simpson   speculated  that  a  diabetic  angiopathy  involving   the   small   vessels   of   the   erectile   tissues   might impede  the blood flow and lead to impotence in some  cases.
SITE  G Radical   surgical   procedures,   such  as  abdominoperineal  extirpation  of  the  rectum,  frequently  destroy  the  nerve  plexuses  from  both  spinal  erection  centers,  resulting   in   complete   impotence.   The   effects    of    sympathectomy  on  potency,  if  any,  have  been  discussed   earlier.   Other   surgical   procedures,   such   as   transurethral   prostate   resection,   that  do  not  interfere  with  the  neural  or  vascular  structures  mediating  erection   usually   do   not   alter   penile   potency.
SITE  H Drugs  that  inhibit  the  action  of  acetylcholine  on structures   innervated   by   postganglionic   autonomic   nerves  (for  example,  methantheline  bromide)  occasionally   cause  impotence.   This   effect   is  consistent  with  the  role  that  cholinergic  fibers  play  in  opening the polsters  and initiating erection.

Alternative method: chemical agent
Site H caught my attention most, since the author mentions inhibitory drugs causing impotence. This might be the non-invasive, discrete route you've wanted.

"Pharmacology of Penile Erection." Andersson. Pharmacological Reviews. 2001.
Phosphodiesterase Inhibitors. The L-arginine/NO/GC/cGMP pathway seems to be the most important for penile erection in some species (see above), and recent results with sildenafil, a selective inhibitor of the cGMP-specific PDE5, further support the view that this may be the case also in humans. Sildenafil is 4000 times more selective for PDE5 than for PDE3, 70 times more selective for PDE5 than PDE4, but only 10 times more selective for PDE5 than for PDE6. Sildenafil is rapidly absorbed after oral administration (bioavailability 41%) and has a plasma half-life of 3 to 5 h.

PDE5 degrades cGMP, which is required for an erection. PDE5 inhibitors (Viagra, Levitra, etc.) prevent cGMP degradation. You might have your protagonist culture PDE5-overexpressing cells and isolate the enzyme (or, she could buy a bunch from Sigma) and sneakily inject the isolate into your villain. This probably wouldn't really work, but I think it might be a better (more plausible) fictional solution than a surgery, which you won't be able to cover up without some other kind of trauma to the area. (Plus, at that point, why not just use the cover-up trauma to create the erectile injury in the first place?)

Bruce, I had no idea erection was so complex! You’re an absolute star for giving up so much of your time, thank you. I should name one of the characters after you but since the only male character available is the rapist, I’m sure you’d prefer I didn’t!

There is a reason I’d like to use surgery: another character will train to be a nurse after assisting with this surgery.
So, if nerves aren’t an option, how about we target blood flow to cause vasculogenic erectile dysfunction?
I found an article on Laparoscopically assisted penile revascularization for vasculogenic impotence, so couldn’t she perform the same operation to cause instead of cure impotence? What if she were to sever either the inferior epigastric artery, the dorsal artery, or the interior pudendal artery?

Long story, but I got to watch a vasectomy and through two tiny incisions, he was able to pull out, cut and cauterise the vas deferens tubes. It would be great if she could do something similar with one of these arteries? Or, failing that, a small incision and cauterise the artery. But I have a feeling you’re going to tell me severing arteries isn’t as simple as severing the vas deferens?

You can definitely sever arteries quickly, but you’ll have two problems: (1) blood is going to want to go somewhere, so you’ll need to cauterize (like you saw with the accompanying vasculature on the vas defrens) or otherwise ligate those vessels; (2) blood is bringing oxygen to those tissues – if you deprive them of blood (to prevent an erection), you risk ischemic necrosis and subsequent amputation. To cause erectile instability, you’ll want to damage the deep artery of the penis, which supplies the corpus cavernosum (the erectile body). As the name suggests, it’s deep!

No need to thank me! If you think my answer was sufficient for your question, you can mark it “correct” and it’ll come off of SE’s unanswered board.

Have marked it!

Bruce, I found some diagrams, you’re right, it’s too deep, impractical. But, I also read that an erection is maintained because, “as the tunica stretches, it blocks off the veins that take blood away from the corpora cavernosa” (sounds like a Harry Potter spell). So, what if she were to stent either the circumflex vein or the deep dorsal vein (which despite its name appears to run along the top surface of the penis)? Would the stent prevent blood from staying in the penis while avoiding necrosis due to blood deprivation?

Obviously, this doesn’t need to be a 100% solution, as a surgeon, she could admit that she’s not sure it will work, nobody’s ever done this before, just as long as there’s a chance it could work. That’s really all you need for fiction!  Thanks!

That's very clever! Ensuring venous drainage is a great, discrete solution – you could place a stent by entering a different vessel (further down the leg, for example) to obscure your work even more (although this stretches realism a little since you'd need to pass through the prostatic venous plexus – easier to go in directly). Venous stripping can treat ED – doing the opposite (stenting/shunting) should work!

BRILLIANT!!  I was hoping you'd say that! But I wouldn't have reached that solution if it wasn't for all your pointers. Going in through the leg would be awesome in terms of discretion, but looking at the diagrams, the deep dorsal vein runs along the top of the penis. I guess, if she does it up high enough where it's buried in his pubic hair, he won't notice the incision. And one of his colleagues will be slipping him pain killers for a few days. Excellent! One impotent rapist! All in a day's work! Thanks!

A minimally invasive surgery could be accomplished with insertion of a thin blade or needle through the penis shaft into each of the corpora cavernosa chambers and rotated in a circular fashion around the interior walls. This motion would destroy the spongy tissue within the corpora cavernosa making erection impossible. Another effect would be the eventual retraction of the penis to a small stub. I have had a similar surgery for penile implant placement and I can assure you that natural erection reflex is totally and permanently destroyed.


text:
Water absorption plant physiology
Can the movement of water in plant outside xylem be multidirectional ,like in case of sucrose transport?

Do mean bulk flow? If not then yes. As in osmosis during transport of organic substances in phloem at source and sink.

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


text:
Are there any known examples of animals with air-conditioner type cooling?
Sweating is often poor at cooling, particularly on humans and animals with a lot of hair or fur because it collects on clothes and other coverings, trapping heat in while promoting the growth of potentially pathogenic bacteria. Additionally, sweating leaks out important electrolytes and water.
With that in mind, are there any known examples of animals that mimic an air conditioner's heat pump? In particular, consider a special channel where blood (or even better: a specialized cooling fluid) is pressurized (almost similar to inflammation) and pumped through a fin, then depressurized on the way out.

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


text:
Tumor-suppression, cell differentiation, and apoptosis: How do macroevolutionists justify dismissing such strong evidence for intelligent design?
Consider the 20 kilobase TP53 gene named for its massive initially-believed 53 kilodalton protein product (later found to be 43 kilodaltons - see https://en.wikipedia.org/wiki/TP53).
Something that complex and of that length doesn't just "happen" on its own. Considering there are 2^40K unique DNA strings of that length (enumerating every permutation), you could easily spend orders of magnitude more than the age of the universe waiting. Simply put, the odds of randomly generating that are none for all practical purposes.
Also consider apoptosis - where a cell recycles itself when it detects too much damage.
The principle of "survival of the fittest" would intuitively rule out the development of apoptosis - there's no reason for a cell or species to develop that feature on its own because that would damage its ability to replicate. Survival of the fittest would actually encourage cells to proliferate as tumors, because they're preserving their genomes and eating everything else out of existence.
The only logical conclusion is that apoptosis and tumor-prevention was purposefully built-in through intelligent design. There's no way that mutations alone could "figure out" that self-recycling (taking one for the team) would increase fitness. Even if 1 pre-tumor cell in a complex life form suddenly decides to recycle itself, chances are that dozens of other pre-tumor cells disagree (sinking the whole life-form). In the absence of that, the pre-tumor cell that recycles itself never survives to hand that ability on.
Additionally, it's even more implausible for mutations alone to "invent" apoptosis mechanisms and 20 kilobase mutation/damage scanners purpose-built for them.
Then you have cell differentiation. Take for example a simple 2-cell system where both cells are joined together and are specific-purposed for different tasks. If 1 of them cells breaks, the other one can't survive on its own. Obviously, decreasing a cell's survivability wouldn't increase its fitness, considering all the types of disasters and damage that could split the 2-cell system.
From a fitness perspective, you would expect any cell to retain the ability to take over the tasks of a different cell type suddenly found to be in short supply, however that often doesn't happen in more complex life forms. Mammals in particular are notorious for relative inability to regenerate large amounts of damage. The only logical conclusion is that the different cell types were purpose-built (read: intelligently designed) to work that way.
With that mountain of evidence for intelligent design, how do macroevolutionists continue to justify fooling themselves?

"The principle of "survival of the fittest" would intuitively rule out the development of apoptosis" - Apoptosis is a normal part of development of multicellular organisms, and is entirely consistent with the concept of selection. For multicellular organisms, selection does not act only at the single-cell level but at the level of the entire organism. There is a mountain of evidence for evolution, not for intelligent design, and arguments for intelligent design, including yours, are either based entirely on religion or based on a misunderstanding of evolution.

umm.... why am I being accused of basing my argument on religion? considering I never even mentioned religion in the original post. All of my arguments were based on basic arithmetic and logic, something that most computers and STEM majors would be proud of.

I'm voting to close this question as off-topic because it is not a question in the terms of SE Biology but an opinion/rant pretending to be a question. It is a clear abuse of this site.

@user1258361 No, your argument falls under the latter of misunderstanding evolution. See Remi.b's answer which is making exactly the same point.

@David I disagree that the post should be closed, because posts like this can often generate good responses, like the one Remi.b posted. I fear that closing posts like this without a robust refutation seems a bit like censorship and there is benefit to engaging to some extent. Not all such posts are acceptable, of course, but this one contains many easily refuted points and demonstrates a clear misunderstanding of selection and evolution as a whole.

@BryanKrause — Please re-read the introduction to SE Biology to refresh your understanding of its purpose and what constitutes a good question. That is what determines whether a question is off-topic, not whether you think someone has made a good point feeding the trolls.

@David "general questions about biological concepts" - Isn't evolution and selection a biological concept? I know, my first reaction to these types of posts is a face-palm, but it's nice to have good answers to point to in the future to refute these types of arguments. That's my opinion, I understand yours, and I disagree. There has been disagreement in the community as a whole, too.

@BryanKrause — I am away from my desktop, so chapter and verse will be delayed. But it cuts no ice to say "there is disagreement" when the purpose and mores of the list are perfectly clear.

@BryanKrause — for the record (as you already know) I have expressed my arguments on meta

@BryanKrause Questions about biology and evolution are of course not off-topic. Troll questions spreading intelligent design and which are obviously not interested in the answer (see the comment on Remi.B's answer) are off-topic, should be closed and not answered.

You are mixing up a bunch of different subjects so that your question is very broad. The post should be closed as too broad.. I will just briefly say a few words about each misunderstanding and hopefully you'll be curious to further your understanding in each of these subjects.

The principle of "survival of the fittest" would intuitively rule out the development of apoptosis

Yes, there is. You are confusing germ lines with soma line.
A cell does not proliferate. It will just do whatever it has to do to all cells in the testes and ovaries (if we're talking about a mammal) to proliferate. Just like a worker ant can commit suicide, a cell can commit suicide. There is no contradiction between the existence of cell apoptosis and the theory of evolution.

Additionally, it's even more implausible for mutations alone to "invent" apoptosis mechanisms and 20 kilobase mutation/damage scanners purpose-built for them.

Clearly, life does not explore all of these possibilities. It only explore a little subset of it. But it does not do that by randomly picking sequence from this gigantic set of possible sequences. New sequences are created via "small modification" (actually such modification can be rather important in reality) of previously existing sequences.

Obviously, decreasing a cell's survivability wouldn't increase its fitness, considering all the types of disasters and damage that could split the 2-cell system

Same issue as above, you need to learn about the soma line germ line differentiation. It will then bring you to the field of social evolution (evolution of traits that affect other's fitness) but you'll probably have to start with an intro to evolutionary biology before going into the field of social evolution.

From a fitness perspective, you would expect any cell to retain the ability to take over the tasks of a different cell type suddenly found to be in short supply

Just google why do cells specialize, you'll get tons of hits.

With that mountain of evidence for intelligent design,

There exist no evidence for Inteligent Design mainly because Intelligent Design does not do any falsifiable and testable claims

how do macroevolutionists [..]?

The macroevolution / microevolution distinction is not used very often in evolutionary biology actually. Today, it is a distinction mainly done by religious extremists to attack the theory of evolution based on a logical fallacy called argument from incredulity

how do macroevolutionists continue to justify fooling themselves?

Maybe you should learn a little bit about science and evolutionary biology before calling scientists fool :)
This sentence suggests that you have an opinion and will not reconsider it based on evidence but I might be wrong here. Maybe you'll be able to rethink your representation of the world based on what observation of this world are being made. Good luck!
Want to learn about evolutionary biology
Understanding Evolution by UC Berkeley is a short very introductory course to evolutionary biology. You should have a look at it.
On Biology.SE, you might want to have a look at the post Is evolution a fact?.

Please don't feed the trolls.

Your post has more holes in it than a rag. The original question specifies 2^40K strings (K=1000) which you obviously failed to read. "A cell doesn't proliferate" -> that already violates the principle of survival and replication. A non-intelligent cell has no way of knowing the consequences of unlimited exponential replication. "Life only explores a subset of possibilities" Weakest argument ever. There is no way for a blind random process to selectively explore a subset of possibilities short of failing everything else - in fact the existence of such a subset implies intelligent design.

Indeed, I missed the K but you could remain polite when pointing it. For the rest, obviously, you are opinion-based and will refuse any evidence, so there is really no point about talking any further. I will be happy to help you learn about evolutionary biology when you'll be ready to learn. FYI, I (like several other users of this website) am researcher in evolutionary genetics and know a thing or two about evolutionary processes. Following @David's advice, I will not react any further unless you show good will to learn. Cheers,

@user1258361 I've actually never seen a rag with a hole in it.


text:
Why hasn't there been a serious effort to develop an anti-inflammatory that blocks the responsible genes?
After numerous years of reading about how to disable inflammation and related treatments, it appears that the common existing approaches are fundamentally wrong.
The most popular over-the-counter treatments target cyclooxegenase (COX) - see:
https://en.wikipedia.org/wiki/Paracetamol#Mechanism_of_action
https://en.wikipedia.org/wiki/Aspirin#Mechanism_of_action
https://en.wikipedia.org/wiki/Ibuprofen#Mechanism_of_action
COX inhibitors have been known to have a wide range of side effects (with even more recently reported, I forget what specifically). They are generally weak and only decrease rather than eliminate inflammation completely at the recommended dose.
The common prescription approach is largely topical steroid creams such as hydrocortisone - another crude and bad approach due to increased risk of infection among other side effects
The most recent and promising novel approach appears to be peptide chains that manipulate the immune system:
https://en.wikipedia.org/wiki/Immune-selective_anti-inflammatory_derivative
The main question: Why hasn't there been visible progress on a gene-blocking approach? There are all sorts of ways to block them - find all the proteins and other products that promote or cause inflammation, then consider all sorts of options to stop them. Options including blocking transcription, blocking translation, stopping the protein/product from exiting its cell, blocking its receptor, blocking intermediates.
Future "last resort" treatment for chronic debilitating inflammatory diseases could include "nonsense mutation" gene edits that permanently disable inflammation in specific cell types.
The end result would be a new generation of anti-inflammatory treatment guaranteed to block known mechanisms of inflammation at the source, instead of the largely ineffective and side-effect ridden standard approaches.
The cost might be prohibitive with today's technology although it would almost certainly become feasible with biochemical 3D printing.

Your question is very complex, so for now I'll focus on a few points and answer these first:

Why hasn't there been visible progress on a gene-blocking approach? There are all sorts of ways to block them - find all the proteins and other products that promote or cause inflammation, then consider all sorts of options to stop them. Options including blocking transcription, blocking translation, stopping the protein/product from exiting its cell, blocking its receptor, blocking intermediates.

You are right that all of these options to block genes exist for laboratory or research purposes. Using them on humans as medicine is a lot more complex in a lot of ways though. One main factor I'm not going to discuss much is the cost of all these techniques - which generally a lot more compared to making a simple chemical drug.
Blocking translation
This is a almost a standard experiment for research labs and can usually be done quite specifically (without side effect on most other genes). In oder to achieve a transient (short lasing) effect you usually use RNA knockdown: The introduction of small RNAs, that specifically target the mRNA of the gene you want to knock down, into a given cell with stop transcription in that cells. There are two problems with using this in patients: 1) transformation efficiency: you need to bring RNA into to the cells, which is not a very efficient process. You'll need even higher doses of the stuff to get a strong enough effect in the immune cells you want to target, since it's very hard to specifically target them. 2) The transformation process itself requires either potentially toxic chemicals or viruses to get the RNA into cells, both of which a costly to make and no one wants to take them unless they have to. Taken together this makes RNA knockdown a very bad drug / treatment strategy.
Blocking transcription
The only way to block transcription of a gene permanently is gene editing - which you really don't want to as a short term treatment against inflammation. To make it work transiently you'd have to bring proteins into the cell that bind to and block the genes you want to suppress - inactive transcription factors would do the trick. One (almost minor) problem is that they wouldn't be very specific, so you'd get lots of side effects. The bigger problem is that it's very hard the get a lot of proteins into cells. You'd need large scale transformation and there are many problems with that, which I discussed above.
Stopping the protein/product from exiting its cell
This is an interesting idea, which might actually work - given a few additional years of research. It's probably not possible to this specifically, so you'd generally block the release of proteins from cells. However if you find a drug that only lasts for a few hours it might work. One important caveat is, that the same (or at least a very similar) mechanism is used, when synapses release neurotransmitters - which you definitely do not want to mess with.
There seems to be active research in this area
Blocking its receptor / blocking intermediates
This strategy is very viable in the immune system, where many soluble factors like cytokines with respective receptors are important. Blocking of receptors or soluble proteins can be done by antibodies and there are many people working on this, some antibodies are already licensed by the FDA as drugs for humans. In most cases these are however intended for use in cancer or other more severe diseases, as all of these are immensely expensive.

Future "last resort" treatment for chronic debilitating inflammatory diseases could include "nonsense mutation" gene edits that permanently disable inflammation in specific cell types.

You do not want to this. Inflammation is an important process that keeps your body healthy and permanently disabling it would basically make you immune deficient, which is not a good thing.

The cost might be prohibitive with today's technology although it would almost certainly become feasible with biochemical 3D printing.

Biochemical 3D printing will likely never be a thing. It's possible to print e.g. organs with cells, but printing proteins requires molecular construction and it's unlikely we're ever ging to find a system that's better than what nature came up with during a few million years of evolution.
In general though technological advancements should decrease the cost of all these strategies.

Lots of good answers, some parts are wrong though. You can block DNA -> RNA transcription through obstruction of the promoter or the transcription start site (similar to preventing a file from downloading properly through obstructing the first few bits). Biochemical 3D printing is already in experimental practice - developed at a university somewhere in Illinois a few years back, according to a somewhat old news article. I forget where exactly though.

@user1258361The way to block transcription (which is always DNA-RNA) is excatly what I described, I only didn't specifially mention the promoter. I also know that printing with biochemical materials is possible, but you can't '3D print' a protein.


text:
Identify this organism I found in my food
I found this thing floating in my orange juice this morning.
I pulled it out and it appears to be some sort of protozoa or something. It's about a quarter the size of my pinky nail. Was not moving at all.
Should I be worried about this? Either way I will be notifying the store. Location is Okinawa, Japan.

A flatworm (Planaria) perhaps?

This appears to be the same organism, and is (also) unanswered.

See my comment on this question

See this SO question for an answer to a related question, which points to Chironomous egg masses.


text:
are there any species that we can identify as being 'mid-way'though an evolutionary change?
I have just learned that dolphins evolved from a dog/cat like land mammal (Mesonix) that became ever-more water venturing. I understand and can visualise how the arms legs and tail slowly evolved into the fish-like ones of dolphins. The necessary transformation appears complete, with no benefit to further change of these limbs. So, I'm wondering if when you look at a seal, are they at a sort of intermediary stage, with the tail kind of like two little feet, which might 'improve' over time? Eitherway, when I read that the nostrils of Mesonix 'slowly moved' upward to the top of the head, I wonder why is there no sea-mammal that is only part way on this evolution, with a nostril between its eyes or something? (Is that even possible?) Or has evolution tended to happen in relatively short periods of accelerated  rates relating to climate changes as opposed to arbitrary and consistant rates, and we are now in a 'dormant' period? Also, surely there are some evolved biological characteristics that are only beneficial once 100% arrived at (eg nostril on top of head) and any intermediary form/position has no benefit and so cant be assumed to have been a natural/obvious path for evolution to have followed, yet how else do we explain how the transformation occurred?

you mean like the pygmy right whale, who's nostrils are about half way down its snout? http://rspb.royalsocietypublishing.org/content/280/1753/20122645 and http://scienceblogs.com/tetrapodzoology/2010/11/08/caperea-alive/

Also that seal's "tail" IS its feet, you can even see the seperate tail in many species, https://biologicalmarginalia.wordpress.com/tag/pinnipeds/. You seem interested in marine mammals you would do well to actually learn something about their anatomy before speculating.

I think there are a couple of issues that make this hard to answer. I find it very hard to think of a "half" evolved animal since it is a tree of life rather than a linear scale. This is close to an offshoot of "why didn't a beneficial trait evolve?"

Every species in existence is "midway through its evolution"
This is because evolution is a never ending process. Technically, we humans are still evolving. Evolution only ends when the species dies out.
Evolution is a very long process spanning countless generations. In a way its also an incredibly democratic process with voting in the form of reproduction. The populace tends to vote for things that increase survival or looks good.
The main cycle of evolution involves mutation and selection.
Selection is in my opinion the most misunderstood part of it. In order for a select trait to gain adoption by a populace it has to push out inferior traits. This normally means inferior members dying off by various means.
Let me give a scenario that starts to tie into your question:
Imagine a dog like creature that can only hunt on land, we'll call them a scruffy. Say one day a scruffy is born with webbed feet which makes it able to swim better allowing it obtain food from water. Now say something kills off ALL of the scruffies land based food sources. The scruffy with webbed feet can obtain food and provide for his progeny while the normal scruffies die off from starvation. Flash forward a few generations and now say a scruffy is born with longer toes (more like fins) which makes him an even better swimmer. That scruffy can be a better provider to his family making him a more desirable mate.
Flash forward MORE generations and the scruffies have become mostly aquatic since that's been their best food source.
One last distinction, it's considered a breed until one breed cannot successfully reproduce with another breed, that's when technically it becomes a new species (or so I've heard the argument). This is also the current great ambiguity with evolution because we don't know when or where this has happened for any species. Not to mention I read somewhere that Neanderthals did successfully copulate with humans which bares the question of whether they were a breed or a species (is a great Dane compared to Chihuahua a breed or species).

Also, surely there are some evolved biological characteristics that are only beneficial once 100% arrived at (eg nostril on top of head) and any intermediary form/position has no benefit and so cant be assumed to have been a natural/obvious path for evolution to have followed, yet how else do we explain how the transformation occurred?

Trait development is a very complex process. Things as arbitrary as sexual attraction play in. Mutation alone is incredibly random and can sometimes be dramatic. Something like a nostril on a snout could have migrated up the head over generations as a quality that was deemed sexually appealing. Or a mutation could have created a hole on the back that decoupled breathing from situational awareness and over time that hole was refined to be a more effective breathing apparatus.
NOTE: to all whom want to debate the breed vs species aspect. Lets not and just agree that it is an ongoing debate to be settled by doctoral thesis.
Clarification: In my opinion, as well as others, the biological classification system is not a very defined or very concrete with various cases breaking the system. This is especially the case with the category known as species where one begins or becomes another. The common, yet still fallible definition of a species, is members of group who are capable of producing reproductively viable offspring. There are many cases where this categorization breaks down or becomes blurred.

Thank you for taking the time to answer this. I did also find a helpful post title "where are all the evolutionary inbetweeners". I still find it amazing that the mutations coincide with the opportunities. Its seems like a child being potentially born gifted in some activity, but that activity actually hasn't been invented yet! and then if by chance they did coincide, the child would have to successfully procreate, and the gene successfully be carried on?

"since no one has actually recorded an evolution" ...this statement makes no sense. I also don't find this answer treats the issue of what a 'species' is correctly. -1. That said, the overall answer "Every species in existence is "midway through its evolution" is correct.

Sigh, and so the species debate begins, even though the hole biological classification system is continuously being challenged at various levels.

@BryanKrause how would you describe what a species "is".

@anon Species are just labels we put on a group of similar organisms that can breed with one another. There is no line where a species becomes another.

@BryanKrause that's abstractly part of my argument. Except the part where you say there is no line because there is and your own definition even hints to it. If we go far enough back into our ancestry we could not mate with whatever we were related to that was hiding from the dinosaurs. So there is a line its just ambiguous much like the sticker we call 'species'.

@Bryan Krause: Re "since no one has actually recorded an evolution", it not only makes no sense, it's (arguably, anyway) no longer true.  See e.g. https://www.bbc.com/news/science-environment-42103058 where scientists have recorded the evolution of a new finch species in the Galapagos.

@jamesqf Agreed. The obvious falsehood of the statement in one of the possibly poor ways you could try to interpret it is part of what means it makes no sense, especially because "an evolution" is not a unitary thing. "Evolution" broadly is observed constantly.

No, because that assumes evolution has some "end goal" which of course is not the case.
The statement "surely there are some evolved biological characteristics that are only beneficial once 100% arrived at..." is a fallacy.  I would recommend checking out Dawkin's The Blind Watchmaker and/or Climbing Mount Improbable for some very nice elaboration on this exact topic.


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Human's capacity to withstand extreme heat in dry air
What is the maximum temperature a human can withstand for short periods of time in an environment with dry air (e.g. oven @+300F, other confined spaces) and what would be the immediate risk of being in such environment be (lung damage, core temperature, etc.).


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How does DNA encode high level features like animal behaviour and language?
We know there are complex features which animals supposed to develop based on their genes as opposed to learning from the environment and the collective, also sometimes being very specific to certain species:

Concepts how to build homes
Animal languages including social insect interactions responsible for information transmission (or do they have to learn them through an acquisition process, let's exclude languages of ape tribes where "term" creation has been demonstrated?)

Valid answer: if already known, one or to examples to corresponding research.
Constraint: we are not talking about genes responsible for some sort of tendencies in behaviour but situations where there seems to be a more or less complex "blue print".

I suppose we are yet very far from understanding these things. Relation of genotype to phenotype is teh subject of much contemporary research, but it is mainly limited to simple phenotypic features, explainable by action of a few genes, such as the colors of zebra fish mutants: see, e.g., this paper and the related publications by Nüsseln-Vollhardt group. Perhaps closer to your question is circadian rythms, which also have genetic determinants.
The complex behaviors are likely a result of the complex interactions of many genes, which are a very interesting, but also a very difficult problem to solve.


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Which mushroom could be this?

Collected in northern West Europe in autumn 2017

It's a shelf mushroom (pores or tubes on the underside) or polyspore (are also called bracket fungi.) How specific an answer do you want? Some are edible (e.g. 'chicken of the woods'), some are lethal.

By a hint from a FB forum, it should be meripilus giganteus and I have to agree.


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Is there any species that cannot reproduce without its symbiont?
I was thinking about humans and machines being symbiotic "species".
So I wonder if there exists in biology a species that could not reproduce without its symbiont.

I don't know why you are bringing up humans and machines but this is a pretty trivial question: yes of course, there are tons of examples.

@BryanKrause While I agree the human/machine bit is superfluous to the question (though it gives background in what the questioner was thinking), if you have "tons of examples", you can (and should) pick some illustrative ones and write up an answer, rather than snarking about its triviality.

@R.M. I meant merely to explain the reason for my downvote, because, as the alt-text for the downvote button notes: "This question does not show any research effort." Poor effort questions should not be answered.

To the exception of many Monocercomonoides (thanks @canadianer for pointing the exception), all eukaryote (incl. animals, plants, fungi and others but excl. bacteria) all have one or more types of endosymbionte (e.g. mitochondria) and cannot function without it. So yes, any eukaryote is an example.

The question of whether at this point mitochondria/chloroplasts/etc. count as separate organisms (and full symbionts) or rather they just originated as an endosymiont but are now just a part of the cell (and thus not technically a symbiont anymore) is one of perspective and thus whether it "counts" is a little fuzzy.

Tell this to Monocercomonoides.

Any obligate parasite would be an example.

An obligate parasite or holoparasite, is a parasitic organism that cannot complete its life-cycle without exploiting a suitable host. If an obligate parasite cannot obtain a host it will fail to reproduce.

How about Leishmania?


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How do brains find the peak/valley point on a curve?
It costs O(n) time if we find the max/min value in a number sequence with the length n. However, if we convert this sequence into a curve and find the peak/valley point with our eyes, it will use much less time.
How do brains complete this computation? I guess the visual nerve process it in divide-and-merge, like breaking down the curve into small segments and comparing them in parallel. If this is correct, what is the size of the smallest segments?

You might read about orientation selectivity in V1. Receptive field size is a function of distance from the fovea.

The question is not very precise: e.g., if we know that there is only one minimum, and the sequence is sorted as it is for plotting a curve, then finding its minimum is trivial and rather quick. If there are multiple minima, then indeed we need to go element by element and we will find a minimum in $O(n)$... but we can do it in $O(n)$ for sequence of any length, whereas the eyes can do it only for finite resolution and finite picture size.


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What is the point of calculating extinction coefficients of a protein without Cys residues?
ProtParam computes various physico-chemical properties that can be deduced from a protein sequence. One of these parameters are "Extinction coefficients". They provide two values. One value considers that all pairs of Cys residues form cystines. The other considers they are reduced.
What is the point of giving two values? Is it to provide the upper and lower bounds?

Cystine absorbs 280 nm light due to the disulfide bond (ε = 125 M-1cm-1) whereas cysteine does not (appreciably). Thus the extinction coefficient of a protein as a whole depends on the redox state of its cysteine residues. Cysteine residues in a protein may or may not form a disulfide bond and the sequence alone does not contain that information.
You can read about this in the ProtParam documentation.


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Ways to predict the preservation of functional domains in fusion proteins
My lab is synthetically creating fusion proteins consisting of an enzyme attached to a zinc finger through a linker. We can attach the zinc finger to the enzyme at either its N-terminus or its C-terminus, but are unsure how to decide which terminus order to use. Have there been any attempts to predict the preservation of proteins' functional domains when they are combined into fusion proteins or, more specifically, to assess the relative qualities of different fusion protein orderings?

Naively I would think that if either domain binds with/interacts with large molecules in the cytosol, it might be better to place that downstream to minimize any effect on translation. Why not just try it both ways and see what happens in terms of synthesis yield and functionality?

A quick non-specialized search for "fusion protein zinc finger" brings up several papers dating back over 20 years. Have you looked at these papers to see where the fusions were made and whether the DNA binding activity was maintained? It would seem more appropriate to consider experience rather than prediction. And please note that you are expected to do your "homework" before posting here and to indicate in a post that you have done so and what you have found. (And, personally, I find it strange that any lab funded to undertake such studies is not aware of previous work.)


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What is the structure of PduK in the Pdu BMC?
My lab is creating 1,2-propanediol utilization bacterial microcompartments (Pdu BMCs) with an operon containing genes for PduA, PduB, PduJ, PduK, PduN, PduU, and PduT. According to Mayer et al., all of these Pdu proteins form homohexamers, except for PduN, which forms homopentamers. Additionally, all of these Pdu proteins, except for PduK, can be found in the Protein Data Bank. Where can I find information on the structure of PduK in the Pdu BMC? Is there a reason for this apparent lack of PduK crystallography data online?

If the structures of all the other Pdu gene products are in PDB, then presumably the structure of PduK has not been determined for Lactobacillus reuteri. Why this is so is anyone’s guess. May be difficult to crystallize, group run out of money, in progress etc.  Best to email the lead author, Yeates, and enquire. (And thanks to @acvill for pointing out  that I'd got  the genes confused in my answer, now deleted.)


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What is this liriope looking plant?
They look like monkey grass, in the midst, a tall, skinny stem with bright orange flowers on top.
One of the plants, although it looks just like the others, has pink, purplish flowers instead of orange.
I would like to know what these are so I can start to take care of them properly.

Your question' better suited to Gardening SE where members can identify plants. As it is, I'm an active member there and the identity of these flowers are straightforward. They're all different cultivars of the daylily (plants in the Hemerocallis genus). If you use Google image search, you'll see photos of various cultivars. Basic structure:

Notice the flowers on a branched (or unbranched) scape (tall stem); leaves arise from the base of the plant. Flowers can be single or double (sometimes more); single flowers (as in your lower left photo) have six petals.
While Asian and Oriental lilies are toxic to pets (even the pollen is toxic to cats if they lick it off their fur), daylilies aren't. They're easy to tell apart as the daylily has long narrow strap-like leaves with flowers on stems with no leaves. Asian and Oriental lily have small leaves continue up the length of the stem like this -

This includes Easter lilies.
Daylilies are named for the reason individual flowers lasts only one day. But each stem has many buds on it that continue to mature over a few weeks so will produce flowers for about a month (as some stems don't have open flowers yet when the first stems start flowering).

Hi. I added a picture of a daylily as is customary on this site when identifying. Hope that's ok. If not, please feel free to roll back. :)

Again, I'm thankful for your extra help! I'm still learning what the protocol is (even though I've read through the Help section twice). I don't remember it all so your example helps me to remember.


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Why did ALL dinosaurs go extinct?
Why did all dinosaurs, rather than just some of them, go extinct during the K-T extinction event? Birds are an exception, but being able to fly, they are also a very special kind of creature, and specalization doesn't usually help with resilience.
My understanding is that dinosaurs filled a very broad and diverse set of ecological niches. In view of this diversity, it is counterintuitive to me that all members of such a diverse set of species would disappear, rather than just a fraction of them.
Did they have (or lack) a common set of features that distinguished them from mammals and birds and made them particularly susceptible to whatever caused the extinction? Did their niches cease to exists temporarily? (It couldn't be the case for all of their niches, could it?) Did mammals already have superior potential which could finally be realized because something upset the global ecological balance?
To sum up, my question is why a large and diverse group disappeared completely rather than partially. There must be some ecological principles that could illuminate it.
Please excuse this naive question from an ignorant but interested layman.

They didn't. Birds exist today: https://biology.stackexchange.com/questions/17546/were-there-any-flying-dinosaurs?rq=1

Most dinosaurs were bigger than most K-T survivors. A quick-and-dirty answer would be a sudden lack of sufficient foodstuffs induced by global cooling post-impact. That would off non-small herbivores, which in turn would cause most carnivores to starve

Here's a good place to start your research: https://en.wikipedia.org/wiki/Cretaceous%E2%80%93Paleogene_extinction_event  It gives a good overview with references about different species groups and the extinction event and its aftermath. Remember that although it is thought to be a single impact, the size and location of the impact led to blast effects, thermal effects, steam/cloud effects, worldwide chemical changes to oceans and land, "impact winter" temperature and sunlight decreases, etc.

@Armand Summarize and make your comment an answer.


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Is the Orca a Whale?
I've read that "all dolphins are whales". I've also read that "the killer whale (orca) is a type of dolphin" and that "orcas are not whales, they're dolphins."
But if the orca is a dolphin and all dolphins are whales, aren't orcas whales?

Where are you quoting from? Please provide your sources. Also, we ask that all posters provide evidence of trying to answer their own question. Please update with additional info to avoid having your post closed. Thanks!

When common names are misleading, it can help to look at the taxonomy. Cetaceans include both MYSTICETES (baleen whales) and ODONTOCETES (toothed whales). Odontocetes include the family Delphinidae (dolphins), which includes the orca species (Orcinus orca).
I think your confusion might stem from the common use of the word "whale" to sometimes refer to mysticetes in particular (baleen whales) and sometimes refer to cetaceans as a whole (including both mysticetes and odontocetes). And to be extra confusing, the common name of Orcinus orca is "killer whale", but it is a "whale" (in the sense of a cetacean) in the dolphin family.
Does that help?
Here is another article from the International Fund for Animal Welfare that dives into this question quite nicely.

All dolphins are whales but all whales are not dolphins.
Orca, the killer whale is the largest member of oceanic dolphin family.
https://en.m.wikipedia.org/wiki/Killer_whale


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Are there any bacteria, virus or mold that can withstand ozone?
Ozonation is often promoted as one of the most effective disinfection procedures. There are numerous reports on how ozone effectively kills bacteria and molds, and disarms viruses within seconds due to its exceptional oxidative activity and small size.
Still, there are examples of thermophilic bacteria existing in volcanoes, as well as viruses in arctic ice, so they both can adapt to extreme conditions. Are there any examples of bacteria, viruses or molds (not necessarily pathogens) that cannot be killed by ozone, or at least show significantly higher resistance to oxidation?


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What is the preferred way to abbreviate amino acids?
Amino acids are often denoted using either a 3-letter abbreviation or a 1-letter notation, e.g. Glutamine  is denoted via $\mathrm{Gln}$ or $\mathrm{Q}$.
When one notation should be preferred over the other and what are the reasons behind?
P. S. This is a follow-up to my question on Chemistry.SE Proper common notation for a ligand, where the problem of distinction between $\mathrm{L}$ notation for "ligand" and for "leucine" occured.

In my experience neither is preferred.
When simply presenting a protein sequence, e.g. in the context of a database of proteins encoded by a genome, then the one-letter code tends to be used.
When showing an alignment of a DNA sequence with the encoded protein sequence both can be used, although personally I prefer the one-letter code for this too because I don't like squished-together text like LysAlaTrpLeu.
In papers referring to an individual residue in a protein I would say that the three-letter code would be more likely to be used.
When referring to a mutation (or,  rather, an amino acid substitution) you might see Leu129Gln or L129Q.
And, by the way, I use L for ligand and have never found it to be confusing. If the reader of your text is sophisticated enough to know that L is leucine then I think they would be able to tell from the context that you were using L for ligand.


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Should I relocate the Raphigaster that tries to winter in my house
In mid October a shieldbug entered my house. After 3 days, it found a very small hole inside one of the veneers under my bedroom window. It stayed there for days, so I did a quick search and was sure it would like to try and hibernate (I'm unsure if this is the correct term) there.
Temperature's outside have only recently (15 days or so) hit winterly levels. I have started to turn on more heating. My house has pretty high temperature fluctuations, especially in the bedroom area.
Yesterday the bug emerged from the hole, waited 2 inches from the entry for an hour or so, then went in again. It emerged again today and is still sitting outside of the hole.
I'm afraid the fluctuations are confusing it.
Can someone explain to me if Raphigaster needs constant "sleep" to winter and would it be better to leave it alone and figure something out by itself or should I place it outside, even though temperatures are below freezing?

You might want to get a positive ID on it, not all shield bugs are Raphigaster genus and some are invasive pests, such as the Brown Marmorated Stink Bug.

@bob1I'm 90% percent sure it's Rhaphigaster nebulosa but will try to get a picture if it emerges again; the bug has reentered its home.

@bob1 my initial thought went straight to H. halys, too. Based on OP's name (German), R nebulosa is an option (the native) , but so is H. halys (invaded as of 2011). Both are similarly colored, and both may find their way inside. Differentiatibg between them would be possible, but I'm not sure IDing to species here necessarily changes OP's question or a likely answer (though possibly, so Wottensprels please take photo if possible)


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Do amphibians feel pain?
It seems strange, but I always hear that toads and frogs don't feel pain.
Is this a true assumption? Do this species can feel pain?

Welcome to Biology.SE! What research have you done before asking it here?

Did you read the Wikipedia article... pain in aphibians? https://en.wikipedia.org/wiki/Pain_in_amphibians

Keep in mind that perception of pain is a higher nervous system response that protects the organism from further damage. Amphibians have different responses for protection. Such as receptors for vision, hearing and touch. If they do feel pain they do not seem to indicate that they do so. If a fish on a hook cried out in pain most people would never go fishing. It would seem that pain response is confined to mammals

According the the Wikipedia article, It is widely accepted by scientists that they feel pain, based on their opioid receptors and sensory physiology.
"Amphibians, particularly anurans, fulfill several physiological and behavioural criteria proposed as indicating that non-human animals may experience pain. These fulfilled criteria include a suitable nervous system and sensory receptors, opioid receptors and reduced responses to noxious stimuli when given analgesics and local anaesthetics, physiological changes to noxious stimuli, displaying protective motor reactions, exhibiting avoidance learning and making trade-offs between noxious stimulus avoidance and other motivational requirements."
en.wikipedia.org/wiki/Pain_in_amphibians


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What is the current accepted taxonomy of the Citrus genus, and how do common cultivated fruits fit into it?
I want to learn about the taxonomy of Citrus, and how cultivated fruits fit into it. I know that the history of cultivated citrus fruits is full of hybridisation and that the taxonomic classifications have changed extensively over time, but I'm looking for the most up-to-date and currently accepted classifications.
Kew (Plants of the World Online) has information about which species names are currently accepted and which are synonyms. But there is no information about ancestry or about how cultivated plants fit into those species. Horticulture/agriculture widely use common names, and botany widely uses scientific names, but I'm looking for information that bridges these two areas.
I want to be able to write a full binomial and cultivar (if applicable) name for common citrus fruits. For example:

"Meyer lemon". Is it Citrus × meyeri? Citrus × limon 'Meyer'? Citrus × limon var. meyeri?
"Satsuma". Is it Citrus unshiu? Citrus deliciosa? Citrus × deliciosa? Citrus aurantium var. unshiu? Citrus reticulata?
"Seville orange". Is it Citrus × aurantium? Citrus aurantium var. aurantium? Citrus aurantium 'Seville'?

Researching individual species or cultivars turns up some answers, but they often don't match each other because there are so many different sources. I want a cohesive summary of the current classification for the entire genus. Is there a book or article that can help me?

I don't have any sources for you, but I can tell you you're very likely going to find disagreement about classification,  taxonomy, and naming. Certainly some judgement calls will need to be made on your part, so make sure you're citing your sources and jotting down brief explanations why you choose one over the other. Ideally, you'd find 1 (maybe 2) sources to pull from to mitigate this problem, but if that's the case, then you'd probably not be tackling this project to begin with. Anyways, I'll keep my eyes open for helpful sources. Good luck!