text:
Why hypothyroidism causes body ache?
In the condition of hypothyroidism the Thyroid Stimulating Hormone level is high in individuals. What signalling/metabolic pathway mediates this sensation of pain which is mostly experienced in feet and joints.

This isn't my field, and I'd love to see my answer surpassed by someone with expert knowledge.  But I should say a recent case report (Pantazis, 2016), though it dealt with an unusual situation, discusses some of the current thinking:

hypothyroidism is characterized by decreased synthesis and degeneration of collagen. Hypothyroidism also inhibits epimerase, which results in reduced chondroitin sulfate and elevated hyaluronic acid, hence weakening the matrix. Moreover, it causes accumulation of glycosaminoglycans (GAGs) in the extracellular matrix (ECM), being involved in the pathogenesis of carpal tunnel syndrome during hypothyroidism and predisposing patients to tendon calcification

THs have known effects at the cellular level on the proliferation and differentiation of bone and cartilage. The hypothyroid state appears to induce abnormalities in these tissues, which results in such clinical manifestations as epiphyseal dysgenesis, aseptic necrosis, possibly crystal-induced arthritis, and an arthropathy characterized by highly viscous non-inflammatory joint effusions primarily affecting the knees, wrists, and hands. Neuropathic and myopathic symptoms accompanying hypothyroidism may manifest as joint region abnormalities when in fact there is no underlying arthropathy.

These paragraphs cite three much older sources.  I don't see a tremendous amount of activity on this narrow issue in PubMed - the broader issue that this case illustrates is whether there are better ways of diagnosing and treating hypothyroidism to restore the balance more effectively; see Midgeley, 2019 for example.

Thank you so much :)


text:
How does salicylic acid work on acne?
There are claims that salicylic acid has an effect on acne. I have done preliminary research and found multiple sources saying:

"Salicylic acid [can] help prevent future breakouts." - https://www.healthline.com/health/skin/salicylic-acid-for-acne
"Salicylic acid penetrates into your skin and works to dissolve the dead skin cells clogging your pores." - https://www.healthline.com/health/skin/salicylic-acid-for-acne
"Salicylic Acid works by opening the pores and killing the bacteria inside." - https://www.reddit.com/r/askscience/comments/tuqt2/how_do_things_like_salicylic_acid_and_topical/
Pointing out that salicylic acid is used to treat acne, but no explanation as to how. - https://en.wikipedia.org/wiki/Medical_uses_of_salicylic_acid
"Salicylic acid modulates COX2 gene expression to decrease the formation of pro-inflammatory prostaglandins. Salicylate may competitively inhibit prostaglandin formation. Salicylate's antirheumatic (nonsteroidal anti-inflammatory) actions are a result of its analgesic and anti-inflammatory mechanisms. Salicylic acid works by causing the cells of the epidermis to slough off more readily, preventing pores from clogging up, and allowing room for new cell growth. Salicylic acid inhibits the oxidation of uridine-5-diphosphoglucose (UDPG) competitively with nicotinamide adenosine dinucleotide (NAD) and noncompetitively with UDPG. It also competitively inhibits the transferring of glucuronyl group of uridine-5-phosphoglucuronic acid (UDPGA) to the phenolic acceptor.", again, with no source. - https://en.wikipedia.org/wiki/Salicylic_acid
"Because BHAs [specifically salicylic acid] are oil soluble, they’ll be able to penetrate deep into the sebum filling up your pores, loosening the gunk to make it easier to remove" - https://fiftyshadesofsnail.com/2015/03/28/how-to-shrink-pores-temporarily-plus-3-pore-myths/
"Salicylic acid dissolves well in vegetable oils." - https://chemistscorner.com/cosmeticsciencetalk/discussion/2514/how-to-dissolve-salicylic-acid-or-aha-acid-in-oil
"Salicylic acid helps ... by dissolving the type of skin debris that clogs pores and causes acne" - https://www.huffpost.com/entry/heres-exactly-what-salicylic-acid-does-to-your-skin_b_578cff25e4b07cc1115aa329

Therefore, the sum of claims add up to that salicylic acid

Penetrates skin.
Dissolves dead skin and skin debris.
Separates skin.
Opens pores.
Reduces inflammation.

If I suppose the anti-inflammatory properties of salicylic acid is well-documented by virtue of being similar to acetylsalicylic acid, then 5) can be intuitive. My remaining questions are as follows.

How does salicylic acid penetrate skin? Which part of the skin? What does it do there? How does it penetrate skin better than other amphiphilic molecules?
How does an acid dissolve dead skin and skin debris? How much acid, at what concentration, at what temperature, and for how long?
Through what mechanism does salicylic acid "open pores"? Additionally, if opening pores is one of its selling points, is it not true that ordinary soap also removes dirt from pores?

Most of the claims above are from unreliable sources. https://scholar.google.com/ might be a better place to search. Since this is a medical topic, https://pubmed.ncbi.nlm.nih.gov/ would also be a good choice. Apart from these, you could look up the references in the Wikipedia article.

source: Stack Exchange

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

sort: votes


text:
How big can a colony/society get?
I hope this is the appropiate place for this question, asked from a math/physics perspective with little to no training in biology.
Bacteria are very small and live in huge colonies, ants are bigger (but also very small) and live in smaller colonies (but also very big). Ignoring the human species, I can't think of any big animal living in big colonies
Is there any name for this relation? I want to study it from two perspectives: first, why? (this may be easy to explain in terms of resource supply or energy available) and second, what is the precise relation? (clearly inverse, but linear, logarithmic...?)
Thanks!

You should know the word "colony" means different things when referring to ants and bacteria. Bacterial colonies arise because bacteria divide faster than they can move (if they can even move). An ant colony is more of a social structure. Not really comparable.

It is not trivial to define a "colony/society". Sure, you can say "this bacterial blob is a colony", or "this ant nest is a colony", and so on, but these would be your own definitions. These systems you mention don't have definite boundaries (temporal or spatial). Although physicists like to do gross approximations to things in nature (and I'm pretty sure there is already some paper 'answering' your question), I'm not sure anyone can get a "precise relation" for a concept that even biologists struggle with (that of a "colony"). This is because at core, what you are really asking, is what is a biological individual and how can I measure it? (the individual ant, the individual colony, etc); and that's something we have no answer for. For what is worth, I recommend you read about the problem of biological individuality, which will give you no answer to your question but at least can tell you why you can't really answer it: https://link.springer.com/article/10.1162/BIOT_a_00068

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


text:
What’s the function of introns
As far as i know, introns do not encode protein products, but living creatures still have them. So what’s their function ?
P/s: Sorry for my grammar

Welcome to SE Biology. As you will see, this question has been asked before. You can find out whether your question has already been covered by searching for a term of interest like "intron". If you are on a desktop or laptop you will any case see a list of related questions in the right-hand sidebar. Also see How to ask good questions in the Help.

Eukaryotic  organisms possess introns for few purposes. One of them which i know is protein isoform formation, where different combinations of exons can give rise to different forms of the same protein  which wouldn't have been  possible otherwise , if  we only had exons. Also introns code for SiRNAs  and few other RNAs.

Welcome to Biology.SE! Your answers will be much more likely to receive a favorable response if you include supporting references (primary literature is best). In addition, please don't answer questions that have been marked as duplicates — if you have new material to contribute please post that as an answer to the older question. ——— Please also take the [tour] and then consult the help pages for additional advice on [Answer] effectively. Thanks!


text:
Folded stem on apples - does it have a name?
I have some Newton Wonder apple trees. One feature of the apples it bears is that the flesh around the stalk is occasionally elongated out of the calyx. Below is a picture that shows this on the near side.

Is there a specific name for this feature in apples?


text:
How can i count my E. coli colonies?
I did a test which involved growing e. coli on a petri dish. I did not dilute the sample, and this resulted in growing hundreds of small, overlapping colonies. However, they still can be counted, but it has been tedious work. Does anyone have tricks for counting small colonies? Also, I've read people will just write >300 if their colony count is too large. Is this data sufficient? I need to compare the colony count for several petri dishes and they all have quite a lot. If i just write ">300" for 80% of my data, it won't be a very good comparison. Can anyone help me out here?

I had once learned of a method where you can observe through a microscope and do a calculation. However, I can't remember the exact procedure over the top of my head. Do a google.

Read this on why people report >300. It’s acceotable depending on what you are doing. If you need an actual count, you need to dilute the original culture.

I'm seeing an opportunity for some image analysis here. Sounds like you could tweak some basic segmentation methods to at least approximate the number of seeds on your plate, but you'll need to work yourself into FIJI (https://fiji.sc/) or a similar image analysis software. Might be able to get help at the forum at https://forum.image.sc/tags/fiji

Actually, Cell Profiler (http://cellprofiler.org/) might have out-of-the box functions that could count your dots, but the image format might need some adjusting.

Divide the plate into equal sectors. Count one sector as accurately as you can then multiply that number by the number of sectors. This assumes the colonies are roughly equally distributed.


text:
Gluconeogenesis in the liver
Glycolysis yields 2 net ATPs. However, gluconeogenesis (lactate->pyruvate->glucose) costs 6 ATP, with a total net loss of 4 ATP.
Does the body not care about the net loss because of the potential energy from glucose to yield up to 38 ATP?

Welcome to SE Biology. As a new contributor you should do some research before posting here, as outlined in the Help on Asking Questions. In this case you might like to ask yourself (1) Why do cells make ATP if not to use it? (2) What is the purpose of gluconeogenesis by the liver — what is the product, for what tissues is it destined, and what would happen if it did not occur? Even if you cannot answer the question for yourself completely it would allow you to construct a more focussed question.

The brain and also the erythrocytes need glucose to survive.
Gluconeogenesis is one of the possibilities of the body to keep the glucose levels stable and to avoid hypoglycemia. The precursors needed come from amino acid and lipid metabolism, and is turned on, when the body has no energy sources available which can release glucose, like carbohydrates in the food or the degradation of glycogen.
As you said, it comes at a price, making glucose itself costs a lot of energy. This process is available to maintain the level of glucose, which shows the importance of it.

One point worth mentioning. Lactate produced by anaerobic utilization of glucose in erythrocytes can be recycled so there is little or no net requirement for glucose. The need of the brain is for net glucose as this is completely oxidized and no lactate is excreted from the tissue.

On another note- you might wish to reference this answer, or I'll banner it ;-)


text:
How can we quantify the effect of pancreatin (biological enzyme) on the clarification of milk powder
Alright so I'm trying to quantify the rate at which casein (protein constituent of milk powder) is converted into a product (I am unaware of) by pancreatin (a biological enzyme that speeds up the reaction). I've attempted researching what the product of the reaction is erroneously given I couldn't quite determine the answer.
All I know is that this enzyme essentially allows casein to convert into whatever thus clarifying any water it would be poured into. Casein remains in suspension (opaque) and then progressively reacts and clarifies the water. How to quantify it on the other hand, I haven't merely got a conceivable clue.
Yes, this question is broad, perhaps you could inform me of any other notions that pertain to this experiment and thereby aid me in my pursuit of an answer.

Google immediately tells us that pancreatin is not an enzyme, but a mixture of enzymes.  Data on conversion rates, if it exists, would likely be reported for individual enzymes, not a mixture.


text:
Is the zygote the only totipotent cell?
I’ve been told that the unfertilized egg contains cytoplasmic determinants (e.g. proteins, transcription factors, mRNAs) that are divided unevenly during the early stages of cell division in an embryo. Thus, each embryonic cell has a different cytoplasmic composition with a different set of transcription activators, allowing the expression of only certain genes.
By this token, it seems to me that this uneven partitioning of cytoplasmic determinants occurs in the very first division of the zygote. Thus, the first blastomeres are already no longer totipotent. Is that correct?

Search on fraternal/ maternal twins

Initial 3 divisions are equal.

Can you explain why my reasoning is incorrect? What really happens to maintain the totipotency of the first few cells?

Did you search on fraternal twins? Well I know this much only.

As I also said , first few are equal and unequal partition does not lead permanent differentiation and it matters only at later stages.

If this were actually the case, identical twins would be impossible (yet they are far from rare.) There may be a bit of confusion regarding the identicality of two blastomeres (they are not always - maybe even never - completely identical), but totipotentiality means they have everything needed to develop into complete beings. Also, the zona pellucida plays a role in survival of divided blastomeres (e.g. 8 cell stage cells have been seperated, and have developed into normal mammals (horses, cows) if supplied with a zona pellucida.

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


text:
Do hydrogen ions contribute to water potential?
I was thinking about lysosomes and how they maintain an acidic pH inside themselves by pumping H+ ions from the cytosol. Do hydrogen ions set up a concentration gradient that causes water to move by osmosis? If so, why doesn’t water rush in to the lysosomes to raise their internal pH?

Osmosis is prevented by cell membrane.

Why would that be the case? If osmosis couldn’t occur across phospholipid bilayers, we would be dead.

We have special pores like aquapores which enable osmosis only when required. Did not you read it in class 11?

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


text:
Are all genes transcribed in differentiated cells?
My textbook tells me that it’s specific transcription factors that allow for a different set of genes to be expressed in different cells (differential gene expression). My book gives the example of liver and lens cells—liver cells contain the specific transcription factors (STFs) to activate the enhancer for the albumin gene, while lens cells contain the STFs to activate the enhancer for the crystallin gene. Liver cells do not have the STFs to activate the crystallin gene, and lens cells cannot activate the album gene.
However, my book also tells me that there is a basal level of transcription that arises from the binding of general transcription factors. Enhancers only increase the rate of transcription on top of that basal rate. Does this mean that in differentiated cells, all genes are indeed transcribed? I.e. a lens cell does transcribe the gene for albumin and the liver cell does transcribe the gene for crystallin?
(The wording of my book dissuades me: "Liver cell: The albumin gene is expressed, and the crystallin gene is not. Lens cell: The crystallin gene is expressed, and the albumin gene is not.”)

Theoretically, yes. They are all transcribed, but in trace amounts. And because hepatocytes do not need crystallin, it might get degenerated by proteases or processed into another protein by ER and golgi bodies.

No, there are genes that are completely turned off. As in, our current technology cannot amplify any transcripts to detect in sequencing. If you do full high sensitivity RNA-seq in different cell types, you will find some transcripts for which there are zero reads (above noise) in each type, and they will be a different overall set based on cell type.  In addition, some genes are silenced after development.  This silencing is usually through histone modifications that completely abrogate the ability for transcription factors to even bind to the DNA.

This answer and the paper referenced therein may answer your question, if you still care after all these years.

No
Not all genes are transcribed, repressor proteins and nuclear receptors can bind the DNA preventing transcription of particular genes. Even things like histone regulation can prevent transcription. There may even be epigenetic regulation of transcription.
Source 1
Source 2

I think genes are transcribed but either mRNA is not transcloated (moved) into the cytoplasm or they are not translated (maybe degraded).I think if you do RNA screening you will get same positive results in both liver and lens cells (as transcription occurred and if your procedure is not having any error) but if you do a western blot, the result will change as now we are seeing the things at the protein level.
So even though all of our cells have same gene composition depending upon the tissue and organ they have differential RNA selection so that they will not waste resources in making unwanted proteins.

A source would be important, especially for an "I think" answer.

Sorry, yes I should have given the proof. You could read it in Developmental Biology Gilberts 6th edition, here is the link of the book from NCBI https://www.ncbi.nlm.nih.gov/books/NBK10112/

You should add that is not the answer, I can't change my vote unless you edit it anyway.


text:
Does a zygote express all genes?
If a zygote has all the cytoplasmic determinants and all the specific transcription factors, does that mean that all genes in the genome are expressed?

There are some obvious counter examples: myelin, immunoglobins, keratin, crystallin, haemoglobin.. you could just go on....

The short answer is that no, a zygote doesn't express all genes simultaneously.
A zygote is like any other cell, in that it represents a distinct phenotype. And like any other cell, this phenotype is maintained by tight regulation of gene expression patterns. Check out this paper, for a nice description of the process of embryonic gene activation.
An important way in which the zygote differs from other cells, and which might be what drives your question, is that the zygote has the potential to differentiate into all the other cell types found in the body. This process of differentiation is also very tightly controlled in terms of gene expression.


text:
How does salt concentration affect chromatin compaction?
I've read that the primary obstacle to the compaction of chromatin is the negative charge on the DNA phosphate-sugar backbone. This negative charge is slightly stabilized by the positive charges on histone proteins. In solutions with high salt concentrations, chromatin adopts a more condensed state, whereas in solutions of low salt concentration, chromatin is less condensed. The explanation I found was that cations from the salt help provide additional stabilization to the negative charges on the DNA molecules—thus, solutions with higher cation concentration promote greater condensation of chromatin.
But what about the anions in the solution? A solution must be electrically neutral; when salt concentration increases, the concentrations of both cations and anions increase. Even if the salt cations stabilize the DNA's negative charge, won't this be perfectly offset by electrostatic repulsions between the DNA and the salt anions?

I think the 'whereas' part is excessive and misleading - I'd say "Higher concentration results to more condensed state".
So charge of DNA + solution will be the same but it will be distributed differently:
$$ D^{-} + nK^{+} + nA^{-} \rightarrow (D^{-}+mK^{+}) + (n-m)K^{+} +nA^{-} $$

Could you explain what the symbols in your formula mean?

D - DNA, K - cation, A - anion, n - number of water molecules, m - number of attached to DNA cations.


text:
How exactly does mitotic recombination help repair damaged DNA?
I understand the utility in crossovers during meiosis, but how exactly is mitotic recombination useful for dealing with DNA damage? If one sister chromatid is damaged, the other can supply a functional replacement for the defect part, sure, but then the donor chromatid will lack that section. Isn't that a zero-sum game? What am I missing?

Note: the technical term is homologous recombination (as DNA repair is actually its primary function), and this answer focusses on lesions affecting both strands at approximately the same level (as a lesion affecting only one strand at a particular location can easily be repaired by using the clean strand as a template), such as symmetrical double-strand breaks (where both strands of the double helix are severed at the same level; commonly caused by [and responsible for the main lethal effects of] overexposure to ionising radiation; used as the example type of damage for the purposes of this answer).
Short answer
The homologous DNA serves as a template for synthesis of new DNA to repair the damaged area.
Long answer (paraphrased from here)
If both strands of a chromosome are severed at or near the same location, special enzymes unwind the broken ends, and other enzymes then clip off a length of one of the strands from each end (the strand that gets clipped off is always the one with the exposed 5-prime end, in case you were wondering), leaving an exposed single-stranded flap on each side of the break.
At this point, other special proteins grab onto these flaps, and take them looking for an intact homologous piece of DNA (that's why it's called homologous recombination), which can be either a sister chromatid (which is guaranteed to be either identical or very nearly so, and is, thus, the preferred solution when possible) or a homologous chromosome (which is always available, except for haploid cells [such as human gametes], but is virtually guaranteed to be not-quite-identical, and, thus, is a less-optimal solution).
With the help of the aforementioned special proteins, one of the flaps then butts into the homologous double helix, base-pairs with the strand it's complementary to (forming a structure known as a Holliday junction [well, technically, seven-eighths of a Holliday junction, as one of the junction's four arms has only a single strand, rather than two]), and kicks the other strand out of formation.  The displaced strand forms a single-stranded loop hanging off to the side (known, unsurprisingly, as a displacement loop, or D-loop), while a DNA polymerase latches onto the bare 3-prime end of the invading strand and lengthens it, using the homologous DNA as a template.1
At this point, things can go in either one of two ways:

In the simpler pathway (the synthesis-dependent strand annealing, or SDSA, pathway), the polymerase simply continues to lengthen the invading strand until enough DNA has been added to the end to bridge the gap between the two broken ends and base-pair securely to the flap on the other end; at this point, the invading strand backs out, allowing the invaded DNA to reassume its double-helical dignity, and the newly-lengthened flap grabs onto the complementary flap on the other broken end.  More DNA polymerases fill the remaining gaps, and a ligase seals the helix back up.  The SDSA pathway is the major homologous-recombination pathway for cells not planning on undergoing meiosis.
In the more complicated double-strand-break repair (DSBR) pathway, the exposed flap on the other broken end also gets in on the action, base-pairing to the exposed D-loop and likewise being lengthened by a DNA polymerase.  When enough new DNA has been synthesised to completely fill the single-stranded gaps, the exposed ends are joined together by ligases, forming a structure with no exposed ends and two complete Holliday junctions.  To turn this back into a pair of separate bog-standard double helices, two of the four strands in each Holliday junction are cut by endonucleases, causing the two DNAs to separate.  (There are rules as to which two strands are cut; either both of the two strands that cross over in a given Holliday junction, or else both of the two strands that don't cross over in said junction, but never one crossing and one non-crossing strand [as this would merely create a new double-strand break at the location of the junction].)  Depending on how the Holliday junctions are severed, the portions of the two chrom[atid/osome]s distal to the original break may or may not be exchanged between the chrom[atid/osome]s; if both junctions are severed on their crossing strands, or both on their non-crossing strands, this distal DNA will not be exchanged, while, if one junction is cut on its crossing strands and the other on its non-crossing strands, said DNA will be exchanged.  Due to its possibilities for swapping bits of genetic material, this is the preferred pathway for cells that are planning on undergoing meiosis (although it also occurs to some degree even in somatic cells).

Here's an image to illustrate the process:

(Image by Emw at Wikimedia Commons.  Blame them for the typo in "Strand invasion", not me.)

1: This is why the 5-prime strand got pruned back, and not the 3-prime strand; all DNA polymerases known to science lengthen DNA strands in exclusively the 5-prime→3-prime direction, and can only add nucleotides to exposed 3-prime ends (exposed 5-prime ends need not apply).


text:
What are these tiny dark red insects?
I found these creatures stuck to a leaf on my tomato plant in the greenhouse/glasshouse, in early June, in south Oxfordshire in the United Kingdom.
They are each about 1-2mm in size. They didn't move much, even when gently nudged, although some did crawl tentatively.
I would be very interested to know what these are, especially if they are a beneficial species or a pest!

These little creatures look a lot like White-margined Burrowing Bug or Sehirus cinctus nymphs.

Very interesting thing about the Sehirus cinctus is their brooding behavior. The female watches the eggs and even feeds the young for a few days. Have a look around. You might see it.

AFAIK they don't harm your plants.
More info:
http://polyploid.net/bugs/bugs.html
https://en.wikipedia.org/wiki/Sehirus_cinctus


text:
Why are sequencing reads shorter than PCR products?
I have desinged and tested primers for RT-PCR, then purified the PCR products from the gels and send them to sequence at GATC (SUPREMERUN) using the forward primers.
After blasting the reads to refseq, I see that they are ~30% shorter than the PCR product. Example:
PCR expected length = 182 bp
Read length = 133 bp
I must mention that in the gels the expected PCR sizes were ok.
Does anyone have an idea what is the reason for this decrease in length?
Thanks

https://www.researchgate.net/post/My_PCR_product_is_163_bp_but_when_it_was_sequenced_multiple_samples_used_it_appeared_like_it_is_133_bp_what_could_be_the_problem

Reliable sequencing reads start usually 50bp downstream from start of primers. Which means that 180bp-band (on the gel) sequenced with one primer will yield readable sequence in region 50-180bp (130bp length). Also I notice that sequences usually reported somewhat before reliable data, i.e. clean data starts after 52-55bp, but sequencing reports basepairs downstream from 48bp after primer start.
If you need whole-band sequence, you will have to sequence with set of two primers, each in different direction. Since you PCR this band, you already have your sequencing primers.


text:
Lysosomal Storage Disease
In my biochemistry class today we did a problem detailing two lysosomal storage diseases.
In the first scenario, a cell line for I-cell disease can synthesize lysosomal hydrolases that are perfectly functional which are then secreted outside of the cell instead of being sort to the lysosome. However there is a mutation that inhibits the the kinase domain that normally phosphorylates Mannose-6-Phosphate (M6P), so there is no M6P-labeling in these cells.
In the second scenario, a cell line for Hurler's disease has a mutation that eliminates one lysosomal glycosidase so that it cannot degradte certain classes of oligosaccharides. This results in the cells of this mutant cell line to have engorged / bloated lysosomes.
Now when these two cell lines are co-cultured in the same flask, it is observed the I-cell culture correctys the defect in the Hurler cell culture, while the Hurler cell culture was not able to correct the defect in the I-cell culture.
My question is how can this phenomenon be explain? And why are the Hurler cells still growing?

While you explained the problem quite well, please note that homework questions are considered off-topic on this site unless you show your own effort in solving the question (Please edit your question instead of just commenting).

I-cells produce the normal functional lysosomal hydrolases, however they are secreted outside of the lysosome.
The Hurler cells lack a functional lysosomal hydrolase to degrade the certain oligosaccharides.
When the two cell lines are mixed together in the same media, through non-specific endocytosis, the Hurler cells will simply arbitrarily want to endocytose things such as nutrients from the media into the cell, and some of the times, the Hurler cells may endocytose the functional enzymes secreted outside of the extracellular matrix / membrane from the I-cell.
Thus, the Hurler cell's lysosomal contents can then be degraded to some extend and restore the defect exhibited in normal Hurler Cells.


text:
Exocytosis of synaptic vesicles
I'm reading the following paper:
http://jcs.biologists.org/content/123/6/819
The part I am really confused about is when they say:

Exocytosis appears to use two alternative pathways: clathrin-mediated endocytosis (CME), which is well established by numerous lines of evidence, and the more controversial ‘kiss-and-run’ pathway, which involves direct retrieval of a vesicle at the site of fusion

My question is .. How can exocytosis (contents inside of cell are transported to outside of cell) use clathrin mediated endocytosis?
I thought endocytosis is the opposite of exocytosis, so why do synaptic vesicles use clathrin mediated endocytosis as a method of exocytosis?

That sentence is located in a paragraph titled "Stages 5-7: Endocytosis and recycling": it's talking about recycling exocytosed membrane which is necessary for making vesicles for further exocytosis.
The sentences before the part you quoted are:

Synapses possess highly efficient mechanisms for retrieving SVs from the plasma membrane of the presynaptic terminal after exocytosis. Fast regeneration of functional SVs is a prerequisite for synapses to function during prolonged activity.

I think the passage is just somewhat confusingly worded, in that "exocytosis" is used as the subject of the sentence which is strange in this context. You could rewrite that sentence:

There appear to be two alternative pathways to recycle membrane for exocytosis: clathrin-mediated...

The author likely intended the word "exocytosis" in the original sentence to mean "the entire process of releasing synaptic vesicles, including formation of those vesicles" rather than the specific event of vesicle fusion with the membrane. Kind of like if I referred to "planting trees" as part of "logging" - you typically think of "logging" as cutting down trees, but in the right context it can make sense to refer to the process: you need to have a tree there to be able to cut it down. I could say "Trees are necessary for logging. Logging uses two alternative pathways: planting trees directly as saplings, or leaving land to grow new forest naturally over a number of years."


text:
Neuronal membrane resting potential for large cells
I'm reading Medical Physiology by Boron and Boulpaep (a really terrific book). In the chapter Electrophysiology of the Cell Membrane, section Membrane Potential Is Generated by Ion Gradients, Not Directly by Ion Pumps, the text reads:

It may seem that the inside negative Vm originates from the continuous pumping of positive charges out of the cell by the electrogenic Na-K pump. The resting potential of large cells -- whose surface-to-volume ratio is so large that ion gradients run down slowly -- is maintained for a long time even when metabolic poisons block ATP-dependent energy metabolism. This finding implies that an ATP-dependent pump is not the immediate energy source underlying the membrane potential.

I totally get the main takeaway, that Vm results from the net accumulation of ion gradients, rather than the immediate consequences of the ion pumps. But I'm unclear on the phrase large cells -- whose surface-to-volume is so large that ion gradients run down slowly.
Presumably a cell with a large surface-to-volume ratio, like a long thin neuron, would have many ion channels which leak constitutively. So I'd expect the net ion conductance to be high, and gradients would run down quickly. But that contradicts the book's run down slowly point, so I'm confused.
Does passive diffusion play a role here? A long, thin cell would have slow passive ion diffusion, so is that why Vm would run down slowly?
Am I overthinking this?
What is the authors' point here?

In a typical neuron at rest, potassium is high inside the cell and low outside, with the opposite true for sodium. The membrane is mostly permeable to potassium. Let's ignore the other ions.
The resting potential in this situation will be something like -70 mV. Rest means that the net current flow is zero; however, there is still current: potassium is flowing out of the cell and sodium is flowing in. Therefore, if we turn off the sodium-potassium pump, over time, the concentration gradients will slowly equalize.
The authors are making an assumption that the current is roughly a function of membrane surface area: more membrane = more current. However, the "reservoir" of concentration imbalance is a function of volume: a bigger cell has more total potassium ions than a smaller cell.
Therefore, in a large cell, if the membrane potential is mostly driven by the concentration gradient, and it takes a long time for the concentration inside to equalize with the outside because the current is small relative to the volume, the membrane potential will only change slowly if you use a toxin to stop the sodium-potassium pump.
I don't think the authors are really intending to say anything special about large cells versus small ones, they are just setting up some assumptions under which their argument about the resting potential is going to be most evident. This is a bit like in a physics textbook where you read something like "assume a uniform spherical baseball."
The claim they are making: "the membrane potential is because of the concentration gradient, not the action of the pump itself" is true for all cellular membranes, not just in large cells. This particular piece of evidence they are referring to, however, is going to be most obvious in a large cell. That's all.
If you tried to do this experiment in a very small cell by turning off the pumps and watching the membrane potential, you might erroneously conclude that the pump was responsible for the membrane potential, but this would be a false conclusion caused by the concentration gradient equalizing too quickly. Instead you should test it in a big cell to see the effect more clearly.
In my personal opinion, this is not the best evidence to explain this feature, but it's a hard concept for many people to grasp and I suspect the authors of your text approach it in several different ways to find one that sticks.

I also thought about a large spherical cell, and had the authors stopped there, the point would have been clear. Given that spherical area grows at $O(r^2)$ and volume grows at $O(r^3)$, the resting dynamics of a large cell would be rate-limited by the small number of open membrane channels compared the huge number of intracellular ions. And if that's correct, they probably meant to write, "whose surface-to-volume ratio is so small"... Might just be a typo.

@user50080 Oops, I hadn't even read the quoted passage clearly. Yes there is definitely a typo, they mean to say "whose surface-to-volume ratio is so small" or conversely "whose volume-to-surface ratio is so large", I think they caught up with the cell being large and the ordinary way to arrange these things is "surface-to-volume ratio" and made a mistake. The meaning is more clear from the rest of the text.


text:
If every person between 15-60 had an immune system equal to the healthiest people, would this affect the spread of coronavirus?
Has anyone calculated the speed or breadth of the spread of something like coronavirus (or any cold, flu, airborne pathogen) based on how well the population can master the virus with their immune system? Just as a simple example, let's say you shortened the window of contagiousness by 2 days. Would that have a significant impact on the spread of the virus?

SE Biology is a question and answer site — not a discussion site or a site for floating ideas. It is concerned with the mechanisms of biological processes, not medical or social aspects of biology. For one of these reasons I think  that your question on the coronavirus outbreak is off-topic here. Question of a medical nature might be on-topic at SE Medical Sciences. Otherwise you are advised to consult more appropriate reputable sources for such information, some of which are listed here.


text:
Could a virus produce prions, leading to prion disease?
Viruses can make cells produce proteins that are not a part of the new viruses themselves, but are used to help with replication. However in the case of rotavirus, one of these proteins (NSP4) is actually a toxin that causes diarrhoea. Prion diseases like Creutzfeldt–Jakob disease are caused by misfolded proteins that make normal versions of the protein also misfold, causing a chain reaction.
While this might not actually have been observed in real life, is there a biological basis for a virus containing genetic code for producing a prion, that after infecting an organism will cause the production of prions inside of infected cells (or perhaps proteins that cause the production of prions in the body), leading to a prion disease - in a similar way to how rotavirus causes the production the the NSP4 toxin? Since these prion diseases often have 100% fatality, would this mean a virus like the common cold could arise, that spreads quickly and non-fatally, but then triggers a fatal neurodegenerative disease in its victims by causing the production of prions in the host?

Perhaps not prions themselves, but viruses may possibly contain "pieces" or domains of proteins with prion-like chemical activity, which can catalyse refolding of prions from normal to disease state.
Mutation rates put limits on the size of RNA viruses. There is a higher cost for the average RNA virus to allot precious genomic space on encoding a normal protein that would take decades to be pathogenic, and which does not seem to help make copies of the virus.
Because DNA is a more stable molecule, and DNA polymerase has a higher fidelity rate than RNA polymerase, DNA viruses can have a larger genome. They could more easily carry code for encoding prion-like domains inside proteins.
There's a recent paper from George and Victor Tetz that looks for these so-called "prionogenic domains" (regions which encode portions of another protein that could potentially have prion-like behavior) in a catalog of viral genomes, and they find approximately three times more such domains in DNA viruses than in RNA viruses:

We determined that more PrDs can be found in the DNA-viruses compared with their numbers in the RNA-viruses, and in the enveloped viruses, compared with that in the non-enveloped ones. This may be partially explained by the larger genome size and protein numbers in DNA-viruses.

While the domains themselves are usually part of proteins that are not themselves prions, infection could lead to expression of those proteins, which in turn provides the domain templates that invoke misfolding in the host of normal prions into pathogenic (disease-causing) prions:

Some viruses may be implicated in the prion misfolding in humans since it was observed that the de novo appearance of prions can be facilitated by another PrD-containing protein

Also! There are retroviruses that have integrated themselves in our genome over millions of years. These are called "endogenous retroviruses" or ERVs, and have been called "junk DNA" by some biologists. However, some get expressed along with our normal genes:

Although a large percentage of ERVs are replication-defective or are suppressed by host defense mechanisms, some ERVs can be expressed and replicated. The activation of an ERV gene can bring positive co-opted functions to the host, which may be evolutionarily maintained [13,20]. For instance, some ERV proteins may provide important functions during normal development; for example, human protein syncytine-1, which is an ERV Env protein, is involved in the formation of the syncytial layer in the placenta [30,31]. Moreover, the expression of Env proteins encoded by ERVs has been suggested to mediate host resistance to exogenous pathogens [32,33]. However, because of their analogy to exogenous retroviruses, the activation of certain ERVs has been frequently implicated in disease.

The authors observed that some people who develop Creutzfeldt–Jakob disease (CJD) have ERVs that get overexpressed:

To evaluate the possible relationship between HERVs and human prion disease, we examined the retroviral sequences in cerebrospinal fluid (CSF) obtained from individuals with sporadic CJD. The frequencies of several HERV families, including HERV-W, HERV-L, FRD and ERV-9, were significantly increased in the CSF of individuals with sporadic CJD compared to the frequencies observed in normal control CSF. In addition, when compared to individuals with other neurodegenerative diseases that exhibit similar symptoms to CJD, such as dementia, the incidence rate of HERV-W and HERV-L were significantly higher in the CSF of sporadic CJD patients. Moreover, the frequency of increased HERV-W and HERV-L in the same samples was much higher in sporadic CJD than in either normal or other neurodegenerative diseases CSF samples, and there was no correlation between individual parameters, such as sex and age [61].

The cause may not be expression of proteins with PrD, but with the triggering of signaling pathways that lead to inflammation of tissues, which sets up conditions for normal prions to malform into disease-causing prions:

According to these studies, ERV proteins may be closely implicated in the pathogenesis of inflammatory diseases, such as multiple sclerosis and rheumatoid arthritis (RA) [51,54,68]. In prion diseases, a correlation between the inflammatory process and neurodegeneration has been suggested because of the activation of large numbers of glial cells and the up-regulated expression of proinflammatory cytokines, which are pathological features of prion diseases [69,70].

Life is complicated.

So is it possible that a DNA virus of some sort could spread without killing people, but then trigger prion misfolding that does? Has this ever been observed?

"Some viruses may be implicated in the prion misfolding in humans since it was observed that the de novo appearance of prions can be facilitated by another PrD-containing protein"


text:
Do multiple axons innervate a single skeletal muscle fiber?
The typical text-book illustration of innervation of muscle fibers shows branches at a single position along the fiber. Does any given muscle fiber have more axons that innervate it though, given that muscle cells can be quite long, up to half a meter in Sartorius?

Until a better educated person contributes a more detailed answer, Hunt's article here from 1954 will likely be the best source,

studies have shown that muscle fibres in the frog's sartorius are innervated in two major zones and most of the fibres receive motor
  endings at at least two regions along their length (Katz & Kuffler,
  1941). In this case a multiply-innervated muscle fibre may derive its
  several end-plates from the same motor nerve fibre. The possibility
  also exists that a muscle fibre may receive end-plates from more than
  one nerve fibre, i.e. polyneuronal innervation.

HUNT CC, KUFFLER SW. Motor innervation of skeletal muscle: multiple innervation of individual muscle fibres and motor unit function. J Physiol. 1954;126(2):293–303. doi:10.1113/jphysiol.1954.sp005210
He in turn references an article by Kats and Kuffler from 1941,
KATZ, B. & KUFFLER, S. W. (1941). Multiple motor innervation of the frog's sartorius muscle. J. Neurophysiol. 4, 209-223.
As those are both 70 years old, it is likely that more documentation has been produced, and that it could contribute to a competent answer to the question.


text:
In phospho/pan analysis in Western blots, what is best way to normalise to an internal loading control?
I am analysing the expression of a protein kinase X that is a phosphoprotein through Western blots. I have labelled the membrane for both the phosphorylated form of the protein and also for the total target protein. I am comparing the expression of my phosphorylated protein between different experimental conditions.
For each sample, I have calculated the proportion of protein that is phosphorylated by dividing the phosphorylated protein signal by the total target protein signal. I have also done this to ensure that the differences in phosphorylated protein between samples is not due to variations in total protein levels under different experimental conditions.
However, I want to normalise this ratio to an internal loading control, since I think that it would be incorrect to assume that the expression of the total target protein is uniform between the different experimental conditions. I have read when comparing the expression of a protein amongst different experimental conditions, you need to use an internal loading control.
I have used a total protein stain (Ponceau S) instead of a housekeeping protein as my internal loading control, since studies have shown that expression of housekeeping proteins can vary between different experimental conditions and that the level of total protein between different experimental conditions is more consistent.
I am currently debating between the following two methods of normalisation:
(1) (phosphorylated protein X/Ponceau)/(total protein X/Ponceau)
(2) ((phosphorylated protein X)/(total protein X))/Ponceau
I think that method (1) is the more correct way to normalise the phospho/total protein X ratio, since you would want to obtain the relative abundance (to Ponceau) of both phosphorylated protein X and total protein X before calculating the phospho/total protein X ratio.
However, I would was wondering if anyone knows whether this reasoning is correct? Any insights are appreciated.


text:
Is there a reference brain sample for the RNA-Seq data in the Developmental Transcriptome tool from the Allen Brain Atlas?
I am using the Developmental Transcriptome tool from the Allen Brain Atlas to determine at what stages of development a specific gene is expressed in the human brain.

I have read the official documentation as to how the RNA-Seq data for the Developmental Transcriptome was generated and analysed. In the documentation, it says that they used postmortem human brain specimens from a range of different developmental stages (embryonic, early prenatal, early mid-prenatal, late mid-prenatal, late prenatal, early infancy, late infancy, childhood, adulthood).
The heatmap showing the gene expression levels across the different brain samples was generated from the RNA-Seq data. I know that heatmaps show the gene expression levels in a number of samples (e.g. treatments, disease) relative to a control sample.
However, when showing the gene expression levels across the different brain samples they used, I was wondering if there is a reference brain sample that was used? E.g. they are comparing gene expression in other brain samples relative to the reference brain sample. I have read the documentation and there is nothing mentioned regarding this.
I was wondering if anyone who has used the Developmental Transcriptome tool before knows whether the gene expression levels are compared against a reference brain sample? Any insights are appreciated.


text:
What test to apply to detect genomic signatures of selection?
I would like to ask you for your sugestions for selecting a test to detect signatures of selection in the following mouse model:
We have three groups: animals exhibiting trait A, trait B and controls. These animals were selected over the last 4 decades (controls were mated randomly and do not show any of the traits). That is total 170 generations (~4 generations per year).
We want to detect the genomic signatures of selection for trait A and B.
I am new in population genomics, but according to this paper (http://www.ncbi.nlm.nih.gov/pubmed/21218185), showing a desition tree (fig 1). I should apply a the Fst and a Linckage 'Desequilibrium test, given that the time scale would be short (40 years, 170 generations) and there are multiple populations.
Could you corroborate if this is the correct approach?
Thanks

Do you assume you know what loci are affecting the trait? What kind of data do you have? There are a number of different approaches. Here, here and there are some papers that should help you.

Thanks. I have no clue about the loci affecting the trait. The purpose of the study is to define that. We will do resequencing.

Ok. You really have a number of different existing algorithm for that. I am not able here to make a good list and comparison of these algorithm but the aforementioned papers should help. One other set of question, you must ask yourself is "Do I know in which environment the individuals are selected in?", "Are the individuals occurring over a continuum of environmental gradient or are they occurring in either of two different environments?".

I hope I got the question right: The mouse lines have been artificially selected in the same lab facility. From a founder population, animals were grouped by trait A or B. Within this groups, animals were mated over ~170 generation, avoiding inbreeding. A control line was kept, mated randomly and does not exhibit neither of the traits.

Where is the selection process? Only the separation according to their trait value?

Yes, they were separated according to their trait value. Trait A and B increased steadily over the ~170 generations.

I am assuming in this answer that you do not have any information about what environment is affecting the selection pressure so that methods like Bayenv2 can't be used.
The standard algorithms are:

Lewontin-Krakauer test
fdist
BayeScan
FLK
PCAdapt

Whitlock and Lotterhos 2014 showed that most often FLK and Bayenv2 perform better than the the three others. A number of articles (Meirmans 2012, Bierne et al 2013, De Mita et al 2013 and Fourcade et al 2013) have also shown that fdist and BayeScan suffer from high false positive rate. I would therefore recommend to go with FLK but I am probably not good enough to give very good advice.
Note that you should learn a bit about how these algorithms work and not using them blindly.


text:
why selecting cells after gene editing with CRISPR Cas9?
I am new to the CRISPR Cas9 genome editing system and I have the above basic question.
Another way to think about this: what would happen if after cells are transfected, the cultures are left to grow without any selection. Thus, if a mutation disrupts a cell cycle gene (e.g. p53), such cells will proliferate more and the culutre will be populated by those cells rather than healthy cells.
Is this a valid reasoning?

Your suggestion of using CRISPR to disrupt P53 and hope for selecting cells that grow out of control isn't what most CRISPR experiments aim to do. CRISPR is used to get precise mutations, but doesn't always work. Only a small percent of cells will be successfully edited, so you have to screen for them and find a good one. This is what makes CRISPR so hard to use in vivo, where you can't just kill off 99.99% of cells and let the good ones grow back.

user137 is correct. Screening for successful CRISPR/CAS9 mutation is a headache. You typically need to either titrate your cells down to 1 cell/well of a 96-well plate, let them expand and genotype, or something more rigorous like this:  http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-15-1002


text:
Validation by PCR of a lowly expressed gene in microarray
I am interested in validating the precence of a gene (FETUB) whose expression is in the lower quartile of the microarray (see figure in link).
https://drive.google.com/open?id=0B82aQne0d_mYWlFiMjRlb05CUVU
Do you think this gene would be detectable by PCR?
Thanks

If your lab is lacking specific expertise on qPCR, and you need a sensitive and quantitative readout of transcripts, branched DNA single-molecule FISH may be less work than PCR ( while also being more sensitive and quantitative than RNAseq etc. )

If it was detectable in a microarray, the odds are very good for RT-rtPCR. If you are designing your own primers, make sure they span an exon junction, or if the gene is intronless, then span the UTR to exon junction to avoid amplifying DNA.


text:
Why is it so hard to find the amount of biotin in food?
According to the WHO publications biotin is a thing we need. Although its non toxic, so you can't get too much.
However, excluding a few (small) lists that deal exclusively with biotin content there doesn't generally seem to be any information on how much of it given foods contain. For instance this page gives a very impressive summary of a kiwi, but there is no mention of biotin.
If this is something we need, why is it not normally listed?

Hello, and welcome to Biology Stack exchange. Unfortunately this seems to be a primarily opinion based question and won't result in good quality answers.

Biotin is also called vitamin H or vitamin B7. You might try searching for those.

I'm voting to close this question as off-topic

Apparently, it's really hard to measure biotin levels in food accurately.
From "Determination of the biotin content of select foods using accurate
and sensitive HPLC/avidin binding" (2004, emphasis added):

Total biotin content of 87 foods was determined using acid
  hydrolysis and the HPLC/avidin-binding assay. These values are consistent with published values
  in that meat, fish, poultry, egg, dairy, and some vegetables are relatively rich sources of biotin.
  However, these biotin values disagreed substantially with published values for many foods. Assay
  values varied between 247 times greater than published values for a given food to as much as 36%
  less than the published biotin value. Among 51 foods assayed for which published values were
  available, only seven agreed within analytical variability (720%). We conclude that published values
  for biotin content of foods are likely to be inaccurate.


text:
What is this long cylindrical white fruit called?

Location: West Bengal, India
Temperature: 27 °C
Weather: Survive all seasons, although it was raining today
Length: 35 cm (although it can be small or big typically 10 to 40 cm length), girth:10 cm
Weight: 1 kg (estimate)
Appearance: Cylindrical in shape, the outer shell is very hard, color  of shell is typically white to pale yellow(the dark patches is due to mud and dirt). It is really tough to crack the shell but the inside (I believe) is pulpy and fibrous but dry.
Extra information: Not edible (never tried to eat), no smell emitted, colloquially called "monkey's club"(in native language), typically hangs on branches of trees in groups (typically 4 to 6 together)

is it the same as these white things in the foreground of the picture? https://www.thestatesman.com/wp-content/uploads/2020/01/QT-vegetable-production.jpg

Could it be Kigelia? https://en.wikipedia.org/wiki/Kigelia#/media/File:Kigelia-Africana-Fruit.JPG Native to africa, but seems to grow in a lot of places including mexico and india: https://inaturalist.ca/taxa/81491-Kigelia-africana/browse_photos?term_id=12&term_value_id=14

@JimN you are almost certainly correct, make it an answer!

It appears this is a Kigela (and commonly referred to as a "Sausage tree" in English).

It is - as you suspected - considered inedible and even poisonous in its fresh form (but apparently it can be dried or fermented). It has, as you said, a hard shell which can make this fruit usable as a container after it is hollowed-out.
The wikipedia article on this tree says it grows throughout tropical Africa, but looking at iNaturalist, it has been observed growing all over the world:

It's nice to have another naturalist here. There are a few of us, but I haven't been around much lately to have seen your answers. Very nice!


text:
How does a cell identify itself?
In embryological development, undifferentiated cells developed into specific types.  As far as I understand, a key differentiating factor is the regulation of gene expression via transcription factors.
However, if all cells have identical genomes and, therefore, identical transcription factors, what is the source of difference in their morphogenesis? Does it rely on some element of randomness in external factors?

This is essentially asking 'How does (embryo) development work?' which is even after decades of research and several nobel prizes not a fully solved question. I don't think its possible to write even a general answer here that doesn't omit tons of important factors.

I think you can ask the basic question and get an answer. In fact, there are two good ones below. I particularly like @swbarnes2's answer because, well, that's the answer to the basic question. If you have asymmetry in the initial cell, you can establish different lineages. Re: "this is not a fully solved question", no field in biology is complete (thankfully), but we know an extraordinary amount about this in several important model organisms.

This has been studied this in Drosophila, and a lot of development hinges on where the cell is in the body.  An initial asymmetry of mRNA in the pre-fertilized ovum leads to the establishment of the anterior-posterior axis (which end is the head, which is the tail)  So cells are told what to develop into based on what mRNA signals they receive which depends on where they are along that axis.
https://en.wikipedia.org/wiki/Drosophila_embryogenesis

yes. the most simple answer to this is gradients (established initially by an asymmetrical cell)

If all cells have identical genomes and, therefore, identical transcription factors

Important comment: all cells do indeed have identical genomes, and all cells are therefore equipped with DNA that codes for transcription factors, but that does not mean that all cells have the same state of the genome. It is well understood that different cell types have different chromatin accessibility ('DNA open and closed for enzyme access'), and this is dependent on the modification of histones which DNA is wound around. It is not a complete image to simply visualize DNA as a strand; it is in fact a complicated 3-dimensional structure, and each region or 'neighborhood' of a DNA location is different from other regions. The below image helps in visualizing the levels of ordering. The ordering is very specific based on the current state of the cell and its history (i.e. which progenitors it came from).

Currently, we have a few ways in which we can study DNA conformation and epigenetics (study of things 'on top of DNA') with a few methods, each limited to probing a certain aspect. Among many others, we use:

ChIP-seq and related methods to determine which proteins occupy positions on the DNA (most often we look for polymerases, or histone modifications),
DNase hypersensitivity assays to determine which regions of chromatin are accessible to cutting enzymes, and thus are open for transcription,
3C-based methods to determine which regions of DNA are in close proximity with  other regions (via e.g. looping of the DNA strand to bring distal enhancer or silencer elements to promoter regions)

How do cells differentiate into specific types?

Factors that cause differences in morphogenesis are called morphogens. There is an incredible wealth of information on the topic, and it's difficult to find a good place to start. Indeed, transcription factors are central players. The best known family of morphogenic TFs are homeotic genes that are crucial for patterning the body. They give rise to the body plan, determine which cells are the head and which are the opposite end, they determine where organs arise, how segmentation proceeds, and how organs form. The field of evo-devo is the principal field that studies how body morphogenesis is determined at the cellular and molecular levels.
Here is a simplified image that illustrates how the same conserved elements (a handful of Hox genes) determine body patterning even across species:

For the layman, I think there is an outstanding engaging and mandatory video on the topic. It does a good job at summarizing and depicting exactly what you are asking, without going into the painful details that would do the science justice.


text:
Maximum recombination frequency
During the process of crossing over, Why is the maximum possible recombination frequency between two genes equal to 50% and not more than that?

Statistically, this is that the maximum mean recombination frequency is 50%.
Recombination defined this way means that Gene A and Gene B from one chromosome are not 'together' on the same chromosome after recombination. That means that the recombination frequency is the probability of an odd number of recombination events between the loci. If there is an even number of recombination events, Gene A and Gene B end up back together again (with some rearrangement between them).
Recombination events can be modeled by a Poisson distribution: that is, recombination events are discrete (you either get an event or you don't) and they don't depend on each other. The rate can be expressed in terms of base pairs, e.g. "mean number of recombinations per base pair" or "mean number of recombinations for 'distance' X."
The probability of getting an "odd" result from a Poisson distribution is always <0.5. See for example this Q&A from Math.SE.
Spoken in plain language, let's start from two loci that are very close where the recombination rate is very low. In most cases, then, we get 0 recombination events so the genes stay together. Now, as we increase the distance, we will get more cases where 1 event occurs. However, as we increase the distance further, we will also start to get cases where 2 events occur. 2 events has the same end result as 0 events: the genes stay together. It turns out mathematically that there is no rate that you can choose where the number of "1"s is more than the combined number of "0"s and "2"s; therefore, the frequency must be <0.5, but will approach 0.5 as the rate approaches infinity. If this doesn't seem intuitive, check the math from Math.SE!


text:
What the name of this fish?
Well saw this on a fish group on facebook. Noone can give a decent answer so I came to you guys hoping you can help us? The one who posted lives in the Philippines and he said he caught it in the river that is somewhat connected to sea.

This fish called neon velvet damsel fish (Neoglyphidodon oxyodon)
Check wikipedia

I don't think this is right. The asker's fish has a brown tail, no golden spot/stripe on its back and very different "fluoro" markings. The asker's fish was caught in a river but yours lives in the sea.

@DavidRicherby maybe if the asker added many pictures from different sides, I can see the blue color under the fish eyes which says everything ..

There's only one photo available and it already shows significant differences from your suggestion. Having more photographs of the unknown fish can't make it look more like a neon velvet damselfish.


text:
Why don't most life forms show uniqueness in progeny?
I guess everyone must have observed this. Dogs, cats, and most of all insects (including mosquitoes) appear more or less the same.
Why is there so little variation in their offspring, unlike humans, where you rarely find two humans showing even a little resemblence.
Is it the large size of the human genome that allows infinite combination of traits? (seems unlikely, as even small flies like drosophila melanogaster have somewhat large genomes, but show very little variation).

@iayork I'd searched but couldn't find. Thanks.


text:
What is this lightning-fast tiny spider?
Saw this spider as I was taking a shower. It moves really fast. This I noticed when it moved away (from the center of this splendid pattern) to repair its web.
Location: West Bengal, India.
It appears to be almost 1.5 cm in length.

Many web-dwelling spiders are lightning-quick in their own web (even if they are slow/clumsy walkers outside of their web) so that doesn't help in identification.
Hard to tell from the photo, but it appears to be Cyclosa ginnaga
A better image of the specimen would help identify.
edit after comment:
Here is a gallery of observations (currently 50 of them) of cyclosa ginnaga: https://inaturalist.ca/observations?place_id=any&subview=grid&taxon_id=360502
All those observations were made in South-East Asia or Australia.
You could also look at Cyclosa Insulana with similar range:
https://inaturalist.ca/taxa/560706-Cyclosa-insulana/browse_photos?quality_grade=any
But I think the length of abdomen in your photo more closely resembles C.ginnaga, and also the observations of C.ginnaga more consistently show a spiral in the thick webbing while C.insulana tends to be more random.
And here is a breakdown of the cyclosa genus broken down into specific species if you want to browse other possibilities:
https://inaturalist.ca/taxa/127360-Cyclosa/browse_photos?quality_grade=any&grouping=taxon_id

Welcome to SE Biology. This answer would be improved by a picture of Cyclosa ginnaga.


text:
Parameters that determines the thermal stability of DNA
Why a DNA with a high GC content more stable than one with a less GC content? Is it because of the three hydrogen bonds in GC base pair which is one more than a AT base pair or is it because of the more stable base stacking of GC base pairs?
In my book it is given that it is due to the hydrogen bonds but in a research article I found it is saying that base stacking solely determines thermal stability. enter link description here

Although taken in isolation GC bonds should be more stable than AT bonds, due to their higher binding energy (three hydrogen bodns versus two), it is the stacking energy that is considered the stabilizing factor of the DNA:

We find that temperature and salt dependences of the stacking term
fully determine the temperature and the salt dependence of DNA
stability parameters. For all temperatures and salt concentrations
employed in present study, base-stacking is the main stabilizing
factor in the DNA double helix. A•T pairing is always destabilizing
and G•C pairing contributes almost no stabilization. Base-stacking
interaction dominates not only in the duplex overall stability but
also significantly contributes into the dependence of the duplex
stability on its sequence.

The reason for that is that one can have the same number of pairs under many different configurations of strands, which means high entropy and instability, unless there are stacking interactions. This is why most models of DNA and RNA helices are based on adding the stacking energies, although there are some additional contributions, particularly in the case of RNA - initiation energy, energies associated to the inner loops, etc.


text:
Do birds require cilia for left/right symmetry during their embryological stages?
I know that in humans ciliary dyskenisia can lead to a Situs inversus, is this also the case for birds and reptilians?

Here is a paper that talks about left-right patterning across bilateral organisms, discussing both Xenopus (frog) and chicken.
It looks like it may be hard to generalize, but the answer appears to be "yes" for Xenopus and "no" for chicken (see e.g. Figure 2, and text immediately following).
However, it looks like the question of what exactly is going on in chicken is not well understood, according to this other paper. Chickens do have lethal ciliopathy mutants homologous to mutants causing left-right defects in other organisms, but these mutants appear to have normal left-right asymmetry development in chicken.
It is also not clear that the requirement of motile cilia for left-right asymmetry is generalizable within clades though, as pigs have apparently also lost the dependence on cilia for L-R, whereas mice and humans do require cilia for L-R. It appears that pig and chicken have dispensed with cilia by the same histological mechanism (see image below, Figure 7 of first paper).
I do not know whether the mechanism has been investigated in other birds.
Hope that helps.


text:
What is the gene for height?
Height doesn't seem to be linked to sex, which is surprising. I have seen ways to predict children's height and it involves taking the average of both parents height. Upon my search, I did not find the actual gene for height.

No single gene determines the height (a polygenic trait) of an individual. In fact, height is coded for by over 700 genes. Also, I'm caught quite off guard by your suggestion that height isn't linked to sex, which is obviously not true. One gene that is associated with a shorter height (to put it simply), ITM2A, is expressed more strongly in women and so helps explain a small (though not inconsequential) fraction of the height difference between men and women.


text:
What happens with the nitrogen in blood in membrane oxygenators?
The air we breathe consists of about 80% nitrogen and 20% oxygen. The oxygen gets diffused into the blood and CO2 out of it, the nitrogen does mostly nothing, as there isn't a partial pressure of nitrogen between the air and your blood.
In membrane oxygenators the blood flows arround small tubes which contain pure oxygen. The oxygen diffuses in your blood en the CO2 diffuses in the tubes, basically doing the same thing lungs does. However, since it's pure oxygen that flows through those tubes, the nitrogen in your blood should get diffused into the tubes.
So is this what happens? Does the nitrogen simply diffuse untill there's nothing left? Isn't that then bad for your body if all the nitrogen is out? Or can't nitrogen pass through the membrane the tubes are made of? Or does it differ wether you use 'true' membrane of microporous membrane?

You are not considering the fact that nitrogen has low solubility in blood. There isn't a lot of nitrogen in the blood anyway and it performs no physiological function. I don't understand why you assume that loss of nitrogen will have any negative effect on the body?

I was actually asking what happens with the nitrogen in your blood in membrane oxygenators, wether it gets diffused in the tubes or stays in the blood or... The "isn't that bad for your body" is more of a side question which you now answered, for which thank you.

It gets diffused out, like you expected.  Grist (2013) writes about this in relation to "the bends," which has already been mentioned by user1136.  He writes:

Cavitation of blood containing normal oxygen and nitrogen levels by mechanical heart valves after implantation generates bubbles that can be detected in the brain using transcranial Doppler ultrasound (2). These bubbles are mainly nitrogenous. Nitrogen is less soluble in water than oxygen. So during excessive turbulence, temperature changes, or pressure changes, nitrogen is the first gas to come out of the solution. (Ask any knowledgeable diver about the physiology of the bends.) We know these bubbles are mainly nitrogen because when the nitrogen in the patient’s blood is off-gassed by breathing 100% oxygen, the cavitated bubbles go away. In one study, the administration of 100% oxygen by facemask reduced the cavitation generation of GME by 98% (3). [Emphasis added]

Can't say it a lot better than that and the rest of the article.  When people are breathing de-nitrogenated air, it simply results in nitrogen being diffused out of the blood.  So yeah, basically the amount of N2 goes down to 0, at least if they are on it for long enough.
As for it being bad for you, not really, at least not perceptibly: though nitrogen is critical for body function, it's practically useless to the body in the N2 form; it has to be "fixed" to a more reactive form such as ammonia / other nitrogen oxide.

Sources

Grist G. 2013. Oxygen or Nitrogen: Which Is the Lesser of Two Evils? J Extra Corpor Technol 45(1): 61-63.

Sprent JI, Sprent P. 1990. Nitrogen fixing organisms: Pure and applied aspects.


text:
Does a severed limb/finger experience pain after its separated?
If a person ends up with a severed finger will that finger, after falling off, experience any pain and start writhing? Can a limb kind of have a mind of its own for a few more seconds after separating from the body like for instance the tail of a lizard?

haha, that's hilarious though, but no, your severed finger will not have/gain own mind nor will "feel" the pain :) however, it may twitch on its own for few seconds/minutes

@cell0 So why will it twitch for a few seconds/minutes? It should lay still right after getting seperated from the body because the connection with brain is lost....am trying to know how it's able to twitch in the absence of life force

Twitching does not require contact from brain. The muscles can respond to local triggers. Anyway, that should be a new question altogether.

@user221238 its due to muscle contraction and fyi human body can twitch even days after being dead. guys from morgue could tell stories...

@cell0 am aware of muscle contractions occurring hours after death as rigor mortis sets in....I was curious wondering if limbs have their own local sensation mechanism, much like the tail of the lizard

@user221238 Just any sensation is different from pain sensation. Pain is not merely a sensation but an "emotional" response. Of course, severed body parts can contain neurons that continue to fire. However, these signals are not reaching spinal cord or the brain and hence there won't be any response.

@WYSIWYG thanks. That's just what I was looking to confirm.

Pain is a signal emitted from a nervous pain receptor cell (called a nociceptor) to the central nervous system (CNS, i.e. the brain). If I hurt myself causing a small cut in my finger, nociceptors around the cut will send the pain signal to the CNS, which in turn processes it and causes the physical feeling of pain in that region.
If a finger is severed, nociceptors just above the cut will be extremely active, interacting with the CNS and causing a lot of pain. On the other hand, nociceptors in the finger itself have nowhere to "push" the pain signal to, so in this sense they cannot measure any pain - there's not a CNS connected to the finger anymore that is able to process the signal emitted by any nociceptors in the finger.


text:
Mass spectrometry: What is meant by the 'most intense peptide ions' in data dependent acquisition (DDA) mode?
I am learning about data dependent acquisition (DDA) mode in mass spectrometry from this online resource. I have come across the following statement:
In DDA mode, the mass spectrometer selects the most intense peptide ions in a first stage of tandem mass spectrometry, and then they are fragmented and analyzed in a second stage of tandem mass spectrometry.
I am not sure what is meant by the "most intense peptide ions". Does most intense refer to the most abundant peptide ions? Any insights are appreciated.

I don't have a source at the moment (and hence a comment instead of an answer), but I would imagine the authors of that resource are referring to the most intense peptide ion m/z (mass/charge ratio) signal as measured by area under the curve (AUC). The software picks the largest peak(s) and targets them for further analysis during the second mass spec run. This can also be done manually.

This is a good question. If we are making an "apple-to-apple" comparison, the answer is yes, meaning that for the same peptide ion, the peak intensity is positively correlated with the abundance of the peptide.
However, in the case of the DDA mode acquisition, where the mass spectrometer selects the most intense peaks (from different peptide ions) from the MS1 scan for fragmentation in MS2, the most intense ions are not necessarily the most abundant. This situation is more like an "apple-to-orange" comparison. The peak intensity is related to the ionization efficiency of the peptide. Some peptides may have higher peak intensities than others despite their lower abundances, simply because they "fly" better in the mass spectrometer.
Ionization efficiency depends on the peptide sequence. For example, in positive mode acquisition, if the peptide sequence has basic residues such as lysine or arginine that can carry the positive charge, the peptide will "fly" well, resulting in an intense peak. Conversely, the peptide with mostly acidic residues, e.g., glutamic acid or aspartic acid residues, will not be ionized, leading to low or no signal.
In a nutshell, depending on the instrument speed and sample complexity, DDA mode acquisition typically selects the top 5–20 most intense peptide ions for MS2 fragmentation. For proteomics analysis, the general rule of thumb is to use two or more unique peptides for protein identification and the top three most intense peptide ions for protein quantitation.

this looks like a good answer overall, but you might consider adding references, figures, or links to support it.


text:
What is the purpose of interkinetic nuclear migration during neurogenesis?
I am reading about neurogenesis and I am learning about the different types of neural stem and progenitor cells (neuroepithelial cells, radial glial cells and basal progenitors). I have read that these cells exhibit  interkinetic nuclear migration.
For example in neuroepithelial cells, the nucleus migrates to the basal side during G1 phase, is at the basal side during S phase, migrates back to the apical side during G2 phase, with mitosis occuring at the apical surface.
I am wondering if there is a clear purpose for interkinetic nuclear migration during neurogenesis? From some papers that I have read about the topic, it seems to me that the exact reason why this occurs in cells during neurogenesis is unknown, even though the molecules that are involved in the process have been identified.
Thanks.


text:
What are protein iBAQ abundance values in SWATH mass spectrometry?
I am reading a journal paper where they used SWATH mass spectrometry to quantify the abundance of proteins in synaptosomes isolated from different species. I am trying to determine whether some proteins of interest are present in synaptosomes.
I have looked at the supplementary material of this paper, and they have a table called "Protein iBAQ abundance values for discovery proteomics (DDA) measurements of mouse, rat, marmoset and human synaptosomes used for the spectral library."
I am not very familiar with SWATH mass spectrometry. In the context of SWATH mass spectrometry, what are protein iBAQ abundance values and what do they represent? Would it be correct of me to say that they represent the abundance of a protein present in the synaptosome?
Any insights are appreciated.


text:
Can potassium ions depolarise neuron membranes?
I am reading a journal paper about the cell adhesion molecule NCAM2 and I have come across the following statement:

To confirm the functionality of the reporters, neurons were time-lapse
recorded before and after application of 90mM K+ used to depolarize
membranes and induce Ca2+ influx via VDCCs.

I know that depolarisation is when the membrane potential of a neuron becomes more positive. I have read that the opening of channels that let positive ions flow into the cell causes depolarisation, such as the opening of channels that let Na+ into the cell.
However, the above statement in the paper seems to imply that extracellular K+ ions can also cause membrane depolarisation. I am not sure what the relationship between potassium ions and membrane depolarisation is and I have not found anything about it online. Any insights are appreciated.

Yes, this is a very basic neuroscience question, something that would probably come up in the first week of a neurophysiology class or unit.
The polarization of the membrane at rest is due to cells being primarily permeable to potassium at rest, and due to a concentration difference of potassium inside vs. outside the membrane. Inside, potassium is high, outside potassium is low.
Therefore, there is a concentration gradient such that if a cell were at 0 mV, potassium would be flowing out of the cell. There is a membrane voltage where this net flow would stop. We refer to this as the "reversal potential" or "equilibrium potential" for an ion. For potassium in a typical cell, this tends to be around -90mV. The larger the ratio of concentrations in versus out, the larger the potential. You can calculate this potential with the Nernst equation if you know the concentrations (image from Wikipedia):

From this equation you can see that the reversal potential is negative for a positive ion if [outside] is small compared to [inside]. By applying higher potassium outside than usual, the ratio of [outside]/[inside] gets closer to 1, so the reversal potential for potassium is closer to 0mV, and typical neurons that are mainly permeable to potassium at rest will depolarize.


text:
Cellular respiration, why double membrane in mitochondria and not bacteria?
Bacteria perform cellular respiration across a single membrane, their plasma membrane. What are the benefits of having double membranes in eukaryotes (in the mitochondria), and, how do bacteria achieve the proton gradient?

This is incorrect. Mitochondria are derived from bacteria and their two membranes correspond to the inner and outer membranes of bacteria as pictured and described in this Wikipedia article on oxidative phosphorylation.

OK. Should have thought of that (that bacteria tend to have double membranes. ) The endosymbiont theory is beautiful, one bacteria sacrificing the other symbiont to oxidative stress. Taking one for the team :)

@David What about bacteria with a single membrane?

@canadianer — I know nothing about them. I suggest that if you are interested you do some research and then ask a specific question on that subject or edit this one, which certainly was not formulated with that in mind.

@David My question was rhetorical. The original question though clearly was formulated with that in mind given that it explicitly mentions bacteria having a single membrane.

@canadianer — Formulated with that in mind? Did you read the poster’s response?

As @canadianer implies, there are bacteria — gram-positive bacteria — that do not have an outer membrane. I have now found a previous specific question about oxidative phosphorylation in gram-positive bacteria, so I suggest this one should be closed. The answer given there is that it is not necessary to generate a pH gradient as it is the proton motive force that drives the ATP synthase, and that can consist solely of a membrane potential produced by the movement of protons.

I was unaware that bacteria have double membranes (or, I've heard it, but, did not make the connection), so Davids answer cleared it out for me. It is still relevant though how bacteria with a different structure do cellular respiration. Then another factor, new discoveries from the past decades, here published in 2009, show that a proton-gradient is part of the equilibrium phases of water in cells or in nature overall, water polarizes at contact-zones. This drives osmosis. http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.618.291&rep=rep1&type=pdf.


text:
Protein content in chemical composition of different phyla?
The protein content in the human body is roughly 15%, what are the percentages for other organisms? Bacteria, plants, fungi, protozoa, etc.

It can vary greatly and what you are asking is a shopping list of different values.
A spore is very high in protein. Bacillus subtilis (you may have seen slime on old bacon?) is by weight mostly carbohydrate (i.e. slime). etc.

Also, 'Bacteria, plants, fungi, protozoa, etc.' are not phyla. A phyla is a rank between kingdom and class. What you mean is clade or phylogenetic group —'protozoa' are not a clade (polyphyletic).

phylogenetic group and phyla are interchangeable, depending on semantic framework you use (they describe large clades, if you prefer word clade), but clade works as word. yes protozoa are polyphyletic.


text:
How far can free radicals from UV radiation diffuse through the skin?
UV radiation damages DNA through two separate mechanisms. Direct damage occurs when a photon is absorbed by DNA. Indirect damage occurs when a photon is absorbed by a chromophore, and the excited chromophore then reacts with DNA, or reacts with other molecules, forming free radicals and causing harm via an oxydative stress mechanism.  How far can these free radicals travel?  The Wikipedia article on indirect DNA damage states

Unlike direct DNA damage, which occurs in areas directly exposed to UV-B light, free radicals can travel through the body and affect other areas—possibly even inner organs. The traveling nature of the indirect DNA damage can be seen in the fact that the malignant melanoma can occur in places that are not directly illuminated by the sun.

This seems extremely dubious to me, but I know very little about the topic and can't find any more reputable sources discussing the question. Can indirect damage occur in adjacent non-illuminated cells?  Can it occur millimeters away from the illuminated area? Centimeters?  Can UV light harm inner organs?

The part about melanoma vs basal cell carcinoma is nonsensical.  All types of skin cancer can occur in any area of the skin since things other than UV radiation can damage DNA.

The life of the radicals decides how far they move.
This paper https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4310837/#!po=6.92308 has a table of half lives of radicals, the longest lasting ones (the radical of nitrous oxide and nitrogen dioxide) have half lives of seconds.
Diffusion theough the skin would be slow
Technically the problem is "reactive oxygen species" (ROS) and "reactive nitrogen species" (RNS) that are the damaging chemicals that includes free radicals. The reactive species that are not radicals have a longer half-life or are even fairly stable and so could diffuse further before making mischief.
The wikipedia article has problems - that is mentioned on the talk page.


text:
Can far-UVC light be safely used as germicide? (help understanding a paper)
I've been trying to familiarize myself with the literature on far UVC light as a germicide.  My question mostly pertains to figure 4 of this paper. The paper investigates the efficacy of 207 nm light for killing MRSA without damaging human cells.  Figure 4 shows that you can get 4 logs of cell kill for MRSA with relatively little damage to human cells.  The authors treat this as a very promising result.  This is where I'm confused:  Yes 207 nm light kills MRSA selectively, but it still kills a lot of human cells: to get 4 logs of MRSA cell kill, you need a fluence that kills 80% of human cells.  Killing 99.99% of bacterial cells while also killing 80% of human cells seems obviously not good enough.  But the authors don't touch on this point: They just point out that it kills 5000x more MRSA cells than human, and interpret the result as promising.  What am I missing here?

This is a great biological question! It asks a lot about how empirical science is done in the field of modern biology! I'm glad we encourage such questions from curious people who want to learn more.
There is another paper here that discusses using a similar frequency range of UVC radiation (207-222 nm) as a biocide:

The biophysical reason is that, due to its strong absorbance in biological materials, far-UVC light does not have sufficient range to penetrate through even the outer layer (stratum corneum) on the surface of human skin, nor the outer tear layer on the outer surface of the eye, neither of which contain living cells; however, because bacteria and viruses are typically of micron or smaller dimensions, far-UVC light can still efficiently traverse and inactivate them.

Safety perhaps derives from the relatively exponential damage that far-UVC light can do to bacteria and viruses, while the layers and types of human cells that would get exposed are surface cells and mostly already dead or expendable. A 20% constant survival rate of vulnerable cells may be an acceptable trade-off, as those cells which are vulnerable would not typically be exposed (short of a wound or other exposed tissue, maybe), while the figure you cite suggests that you can raise the intensity of UV light linearly and kill exponentially more MRSA (or other disease-causing bacteria).

First of all a disclaimer, I am not an expert in this subject, but I have read these studies and came to this understanding. There might be a chance I get a lot of stuff wrong.
From another paper by the same authors, this time regarding 222nm UVC:

We have previously shown that 207-nm light emitted by a filtered krypton-bromine (Kr-Br) excilamp has bactericidal efficacy while being minimally cytotoxic to human cells in a 3D skin tissue model in vitro (7) and in a hairless mouse skin model in vivo (8). Thus, continuous exposure of the wound to far-UVC light during surgery may inactivate the microbes alighting directly onto the surgical wound from the air.

This shows the limited scope of its use presented by the paper as a way to sterilize the air immediately around the surgical site instead of sterilizing the surface of the patient, though it might also mean that further uses are not researched enough.
Also, it is important to analyze how the far-UVC affects human cells. In the 2013 paper you mentioned, Buonanno's team tested 2 methods of irradiating human cells with 207nm far-UVC. The figure you quoted is the dosage response curve of normal human skin fibroblasts, which are located in the dermis of human skin. In the experiment, these cells were cultivated on petri dishes and irradiated directly with UV light. This is not what you would normally expect when a person is exposed to UV, as the epidermis covers these cells and shields them from far-UVC radiation.

Normal human diploid skin fibroblasts (AG1522) were obtained from the American Type Culture Collection (Manassas, VA, USA) ... Briefly, cells were trypsinized within 5–10 min of exposure, suspended in growth medium, counted, diluted and seeded in 100-mm dishes with numbers resulting in ∼100 clonogenic cells per dish.

This brings us to the other method of measuring the effect of irradiance on human cells, which is the use of a 3-D human skin model, aka lab-grown human skin. The skin sample was then irradiated, after which they measured the amount of by-products caused by UV degradation present inside the nuclei of the epidermis. The results show almost undetectable levels of UV damage by-products, even at 150 mJ/cm^2, the dose which resulted in a 4.7-log reduction of MRSA and a 0.9-log reduction of dermal cells. These results are consistent with the cited literature that far-UVC will not penetrate the epidermis far enough to reach the cell nuclei of the first layer of skin.

In terms of the safety of 207-nm UV light, the lack of induction of typical UV-associated pre-mutagenic DNA lesions in the epidermis of a 3-D skin model is again consistent with biophysical expectations based on the limited penetration of 207-nm UV light, and consistent with earlier studies using 193-nm laser light [23].

So there you go, it turns out the far-UVC might kill 88% of non-skin human cells on the first layer, but the same dose will kill 99.998% of MRSA bacteria. The same team behind this paper has since went on to test 222nm UVC, live mice, as well as against H1N1 aerosol, and the studies show even more promise in this regard in requiring far lower irradiances to achieve a 4-log reduction in those microbes.

What a great contribution to the site!


text:
Do proteins contain phosphorous? If its true then how alfred hershey and martha chase used the statement that proteins do not contain phosphorous?
I hv heard about phosphorus that it is a constituent of certain protein, although we know that no amino acids have phosphorus... and if its true then how Alfred hershey and Martha chase experiment got acclaimed whose base of the experiment was that "protein doesn't have phosphorus"??

This should answer part of your question.

Yes some of the proteins contain phosphorus but in the experiment (Hershey and chase experiment) they used bacteriophage it's protein sheath contains carbon,hydrogen,nitrogen and sulphur while the DNA in the bacteriophage contains carbon,hydrogen,nitrogen and phosphorus(in the acid) so they selected this for that experiment moreover sulphur is absent in the DNA but phosphorus is not so one can conclude that DNA is the thing that was transferred
Reference:NCERT

Yes, None of the amino acid contain phosphorus in its side chain, but it is introduced during Post translational modification. This helps in stability and proper functioning of proteins. (Via:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3415839/.
As, phosphorus is main building block of nucleic acid not proteins, so its usage in production of new bacteriophage will represent utilization of phosphorus in nucleic acid synthesis.Further using the blender experiment, Hershey and Chase separated the protein coat of bacteriophage  from its nuclei. And then introduced this nucleic acid into the bacteria,
 and found that it can reproduce to synthesize new viruses. And this proved that nucleic acid is responsible for transmission of genetic information.
 (Via: https://embryo.asu.edu/pages/hershey-chase-experiments-1952-alfred-hershey-and-martha-chase)

It is true that no amino acids contain phosphorus, but due to post-translational modifications some proteins can be phosphorylated. In addition, there are enzymatic proteins such as glycogen phosphorylase b, which are relatively inactive protein, and the change to the active forms (glycogen phosphorylase a) can be carried out by the action of phosphorylase kinase (Lehninger. Principles of Biochemistry. 5th Ed.)

Your first sentence suggest that all amino acids contain phosphorous — is that what you intended?


text:
Does the Abbott ID NOW coronavirus test return a positive result if you take it while you're still in the incubation period?
It seems like Abbott's ID Now test works by detecting the virus directly as opposed to checking for antibodies? If the test result is negative does that mean you don't have the virus? Or does that not rule out a recent infection with the virus that has not yet reached a level high enough to be detected?

Welcome to Biology.SE! Please take the [tour] and then go through the help pages starting with [Ask] questions effectively on this site and [edit] your question accordingly. In particular note that personal medical questions are not appropriate for this site. ——— We also encourage you to do some research on your own and then, informed by what you have learned, ask any questions you still have (ideally with references to reliable sources). Thanks!

This is a great biological question! It asks a lot about how empirical science is done in the field of modern biology! I'm glad we encourage such questions from curious people who want to learn more.

It seems like Abbott's ID Now test works by detecting the virus directly as opposed to checking for antibodies?

Yes, the ID NOW test performs a quantitative real-time RT-PCR assay to amplify reverse-transcribed viral RNA, specifically targeting the SARS-CoV-2 RdRp gene.
The product insert for the COVID-19 test for the Abbott ID NOW product describes the "analytical sensitivity" or "limit of detection" (LOD), which describes the true positive rate.
The LOD described in the product insert is the lowest amount of viral genome in the collected sample that you need to get a true positive in 95% or more of administered tests, in units of "genome equivalents per mL".
This is effectively the minimum number of copies of viral genome per mL of assayed sample needed to give a true positive in 95% or more tests. Its LOD (125 copies/mL) is comparable with other tests (example).
A false negative can result if there is insufficient virus copies in the sample, or if there is test material contamination or the test is not performed correctly.
This assay includes positive and negative controls, which help to identify potential problems with how the assay was performed. Controls are important, given the many millions of tests that will be done to identify infected carriers of SARS-CoV-2 — the assay must be done correctly and without contaminants, in order to give the best statistical odds for the correct diagnosis of those who will be tested.