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Why can early embryos survive freezing?
According to this
Blastocyst & Embryo Freezing in IVF

Embryos can be frozen at the pronuclear stage (one cell), or at any stage after that up to and including the blastocyst stage (5-7 days after fertilization).

Given that freezing normally destroys mammalian cells1 why can early stage embryos survive being frozen?
Reference:
1: Shier, W. T. (1988). Studies on the mechanisms of mammalian cell killing by a freeze-thaw cycle: conditions that prevent cell killing using nucleated freezing. Cryobiology, 25(2), 110-120.

I think you might find this answer to a somewhat related question of interest:
https://biology.stackexchange.com/questions/43077/could-a-single-cell-be-brought-to-life/43092#43092 ——— Since freezing usually kills tissues unless they are specially treated, I think a better question would be why early embryos can survive freezing! Based on this, I've suggested edits to your question.

The reason why cells (and tissues) die during freezing is that ice crystals rupture the cell membranes1,2, so to me it seems the question is actually why early embryos can survive this process.
The answer depends on the technique used, but it comes down to size.  Small tissues (or cells) have a large surface area to volume ratio.
In techniques that use cryoprotectants (compounds that suppress ice crystal formation), the small size allows efficient replacement of water by cryoprotectant prior to freezing (and the reverse after thawing) so that the cells don't have time to die1,2.
In flash freezing (vitrification), the small size allows the entire tissue to be frozen instantaneously, which also suppresses ice crystal formation1,2.
This Scientific American article is very relevant as well.

References:
 1: Konc, J., Kanyó, K., Kriston, R., Somoskői, B., & Cseh, S. (2014). Cryopreservation of embryos and oocytes in human assisted reproduction. BioMed research international, 2014.

2: Loutradi, K. E., Kolibianakis, E. M., Venetis, C. A., Papanikolaou, E. G., Pados, G., Bontis, I., & Tarlatzis, B. C. (2008). Cryopreservation of human embryos by vitrification or slow freezing: a systematic review and meta-analysis. Fertility and sterility, 90(1), 186-193.


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Do cells not grow during mitotic S phase (synthesis phase of interphase of the cell cycle)?
Both these links mention cell growth during G1 and G2 phase, but not during synthesis phase (only DNA replication is mentioned). Is replication all that happens and is there no cell growth during S phase?
https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/interphase
https://bio.libretexts.org/Bookshelves/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/10%3A_Cell_Reproduction/10.02%3A_The_Cell_Cycle/10.2A%3A_Interphase

Welcome to Biology.SE. Please take the [tour] and then go through the [help] pages starting with [Ask] questions effectively on this site. This will help you ask good questions and avoid some of the pitfalls that new users can experience using this site.

Also note that each post should only have one question, so I've focused on the question of "growth" as that seems the most central to what you are asking. There are of course many other processes that occur throughout the cell cycle, but that is beyond the scope of a single question (or this site in general) so I've removed those.

By growth I'm assuming you mean something like an increase in cell mass/volume.
This can likely vary depending on the organism and cell type (biology is riddled with exceptions), but in budding yeast (Saccharomyces cerevisiae) cell mass increases during mitotic S phase1.
The following is a quote from the introduction to reference 1:

Typical pie chart representation of the cell cycle (Figure 1A) stresses the discontinuous events that have to take place only once per cell cycle (i.e., S and M phases), but fails to show that proliferating somatic cells are continuously increasing in their mass throughout the cell cycle (Figure 1B). As pointed out as early as 1971 by Mitchinson2, the “continuous events of the growth cycle” (i.e., increase in cell mass) and the “discontinuous events of the DNA division cycle” (i.e., DNA replication, mitosis, and cell division) need to be tightly coordinated in order to maintain cell size homeostasis.

Main Events That Occur during the Yeast Cell Cycle
(A) General representation of the cell cycle showing the discontinuous events that have to take place only once per cell cycle, namely the S phase and the M phase, spaced with G1 and G2 phases that allow increase of the cell size before DNA replication and cell division, respectively.
(B) During the dynamics of the cell cycle, RNA and proteins increase exponentially, while the DNA content show a typical doubling amount until the cell divides to generate a newborn daughter. From G1 to M phases, the cell increases continuously in mass.

References:

Barberis, M., Klipp, E., Vanoni, M., & Alberghina, L. (2007). Cell size at S phase initiation: an emergent property of the G1/S network. PLoS computational biology, 3(4), e64.
Mitchison, J. M. (1971). Biology of the cell cycle.

thank you very much

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Has anyone seen/read interspecies competition that is different at spatial scale for the same group of animals?
I work at a highly fragmented wildlife sanctuary in North Borneo, Malaysia. We have 8 species of hornbills here and from our observation they've grown to be less territorial in terms of where they forage for food. Our friends in the mainland of Malaysia have observed differently - these hornbills are territorial even in the areas they forage, rather than just during breeding season or around their nesting trees.
Do you think the limited resources for space and food where I work force them to be less territorial than their counterparts that live in areas with more forest cover (thus more space and food)?
I'd love to hear or read more observations like this from different areas, if any of you have anything to share.

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Which species of bumblebee(?) is this?

I observed this beautiful insect near a forest in northern Switzerland. What is it?

To me that looks like a "hover fly" — specifically the Pellucid Fly (Volucella pellucens).
Compare with:

This species is present throughout Europe according to the wikipedia article (first link).


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Can viruses stabilize and increase the shelf life of wine and other foods?
When you make wine, you use the yeast Saccharomyces cerevisiae to ferment sugary juices. After you're done, you want to avoid them doing anything by using some chemicals etc. There are also other living things (especially bacteria) that can ruin your wine or food during storage. For example, there are bacteria that would turn your wine into vinegar.
Have viruses been identified that infect and kill the bacteria that spoil wine or other foods?

For an example of background reading that could help you improve your questions I found this freely available paper.

There is at least one bacteriophage ("phage") that targets bacteria that spoil wine:

The Gluconobacter phage GC1 is a novel member of the Tectiviridae family isolated from a juice sample collected during dry white wine making. The bacteriophage infects Gluconobacter cerinus, an acetic acid bacterium which represents a spoilage microorganism during wine making, mainly because it is able to produce ethyl alcohol and transform it into acetic acid.

This particular linked paper does not say anything about usage of bacteriophages as a food preservative or for food safety, but there is interest in using bacteriophages for this general application, as an alternative to the use of antibiotics in food production.
Phages are everywhere. Craig Venter went out on his yacht and scooped up a bunch for one of his papers. Phage therapy may end up augmenting or replacing antibiotics, which would be good for us humans as many disease-causing bacteria have developed or are developing resistance to them.

Phage are quite specific though. It would be difficult putting together a cocktail that could kill all of the many bacteria that might spoil a particular food.


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Gibson assembley for small fragments?
I am new to the Gibson assembly, I know how I need my plasmid but main problem is I don't have short tags and linker so I wanted to do Gibson assembly?
5'-TCACTCTCGGCATGGACGAGCTGTACAAGcagcggcagcgaaaccccgggcaccagcgaaagcgcgaccccggaaagcgaaaacctgtactttcagtccgactacaaggaccacgacggtg

Capital letters - my plasmid backbone
Italics - 3xtag
Bold - TEV site

I have plasmid backbone but I dont have 3xtag and TEV site so how can I design the primer so that i can do Gibson assembly to incorporate the sequence?

I assume that your backbone is supposed to continue after the TEV site?

Yes, but due to MCS limitations i decided to go on another plasmid and it is 21nt length so difficult to extract by agarose

Gibson Assembly is not ideal for short fragments; chances are that the T5 Exonuclease will digest your entire fragment before it has the chance to hybridize with the backbone. For fragments shorter than 200 bp NEB recommends a 5-fold excess to compensate for this, but in your case the fragment would only be around 130 bp long. It might work, but efficiency will be very low.
Either way, based on my understanding that you don't have the 3xtag-TEV sequence available as PCR template, what you would need is two long primers designed such that they overlap by 20-25 nt at their 3' ends (orange), and with the backbone at their 5' ends (blue) as shown below:

You would then run PCR cycles with the primers alone to generate your double-stranded fragment, which you can then use in the Gibson Assembly reaction.
If you're not using a commercial Gibson Assembly kit, but instead add the enzymes yourself, you can also try an alternative method called TEDA cloning. The procedure is practically the same as that of Gibson Assembly, but TEDA uses only T5 Exonuclease. Instead of relying on (very expensive!) Phusion DNA Polymerase and Taq DNA Ligase for sealing the plasmid, plasmid repair in TEDA happens after transformation into bacteria, taking advantage of E. coli's own DNA repair machinery.
In your case, the advantage with TEDA is that you can try different incubation times with T5 Exonuclease to find a short enough incubation time such that single-stranded 5' homology ends are generated without digesting your entire fragment; or even incubate your backbone first and add your short fragment later in the TEDA reaction. As an extra bonus, TEDA cloning costs a fraction of the price of a Gibson Assembly reaction.

Great. I will go for long primers which seems to be reliable. In case if i have time i will give a try to TEDA cloning also.


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What kind of parasite is this?
I found this strange disease on the leaves of a pear tree. I don't know the tree's species but I found it in South Turkey, 150 km from the Mediterranean. What causes this disease?

Welcome to Biology.SE! If you know this a pear tree then you do know the genus (Pyrus).

Related: https://biology.stackexchange.com/q/10002/16866

This is pear rust (Gymnosporangium sabinae).

It is fairly widespread in the northern hemisphere:

It is a fungal infection and affects pear trees from junipers. Pruning the affected nearby junipers can help control its spread.


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Are these springtails and isopods?
G'day!
I'm based in Victoria, Australia.
I'm hoping to culture springtails for my terrariums, so I went out and tried to collect some. I found them underneath a rock, which was sitting on damp ground. They certainly look like springtails, and gee they're tiny! 1-2mm. But they don't jump at all.
My first question is -- is this little fella a springtail?

Fast forward a few weeks, and these little critters still seem to be alive in a jar. However, what I believe are isopods appear to have joined them. They're super tiny though, < 2mm. And they're always hovering around what appears to be eggs.
Here's two pictures:

I read online about the lifecycle of isopods. They don't lay eggs; rather, the mother keeps them in a pouch on her underside. I also read that, absent better food sources, they can feed on the eggs of other insects.
So what I suspect is, that these are springtail eggs, and the isopods are eating them. Is that a correct assessment? And are these indeed isopods?
Thank you in advance for your help!
TLDR

Is the first picture of a springtail?
Are the second/third pictures of isopods eating springtail eggs?

Look in thick, damp, leaf mulch for springtails

Thank you! The rock I found them underneath was nestled among a fair bit of damp leaf litter and mulch, so I'm hoping they're springtails (other than the fact they don't jump).

All three photos feature springtails (two different families, though).  The last photo shows only three pairs of legs, eliminating Isopoda.

It seems like they're both springtail species, as suggested by Arthur's comment.
The white one appears to be a type of folsomia, which is easy enough to guess from the appearance (mine don't jump though, I guess ruling out folsomia candida?).
You can compare it to this image of one, from Wikipedia:

I purchased a cheap USB microscope to inspect the second one further. Indeed, as Arthur suggested, it only has three sets of legs:

Additionally, I turned it around and got a look at the underside. I can only guess this is the furcula (though, interestingly, this one doesn't jump either!)?

I'm not sure what the genus is. Could be folsomia, or perhaps hypogastruridae? Either way, they're both springtails! Great news!


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Antimicrobial susceptibility testing
To learn the Kirby-Bauer method, I've been looking at youtube videos where a bacteria's susceptibility is tested.
In this video, the researcher places the discs (containing antibiotics) right after she inoculates the lawn on the agar disk. Shouldn't you wait until the bacteria has grown before adding the disk containing antibiotics?

That's "a fungus" or plural "fungi"; I can't tell if the rest of your question also has the same type of error for "bacteria" or what you are actually trying to ask.

No; antimicrobial discs are almost always added at the time of plating. The antimicrobials will prevent growth. This covers both bacteriostatic and bacteriocidal antimicrobial agents. If you were trying to differentiate between bacteriostatic and bacteriocidal, I suppose you could treat with the antimicrobial only after growth. What are you actually trying to test? What is the purpose of your experiment? Can you give us more details?

Rarely do you have a single bacterium, @tripleee; multiple colonies, even of the same species, are typically referred to in plural.

@CodyGray I'm trying to test the susceptibility of the fungi M.furfur against different concentrations of neem extract. If I added the disks right after the inoculation, wouldn't the bacteria be killed even before it has grown? How would zone of inhibition occur if it has already been killed?

Yes, that's precisely the idea. The bacteria is not able to grow around the disc, because the antibacterial is inhibiting its growth. The zone of inhibition shows how effective the antibacterial is at inhibiting growth of the bacteria. Because a lawn was plated, the bacteria will be able to grow everywhere else that it is not being exposed to the antibacterial agent from the disc. Google for "disk diffusion test" or "Kirby-Bauer test" for more details; e.g., this Wikipedia article.

A more useful question to ask would be, Why do you place the disc on the plate before the bacteria have grown up? This test allows us to infer which antibiotics an organism is susceptible and resistant to by observing whether or not they grow in the presence of that given antibiotic.
But there's a good reason we don't wait until the bacteria are already grown and see which antibiotics kill it. The metabolic activity of bacteria growing on a plate will slow as their population grows and available nutrients are locally depleted. However, the most common modes of antibiotic action only function well when the target organism is metabolically active. So we apply the antibiotics at the same time the culture is inoculated to ensure some level of metabolic activity is going to be happening.
For example, Betalactams disrupt cell-wall synthesis but don't destroy existing cell walls. If the target population is largely dormant, there will be minimal cell-wall synthesis occurring, and any bactericidal effects would be difficult to detect, if not completely absent. The same goes for antibiotics that disrupt translation (aminoglycosides and tetracyclines), prevent nucleic acid synthesis (Quinolones), or interfere with synthesis of specific metabolites (Sulfonamides). Those are all disruptions of metabolic activity that are necessary during growth and reproduction, but largely shut down during dormancy. Some bacterial populations even take advantage of this loop-hole by maintaining a small proportion of their population as metabolically inactive "persister" cells.


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Can you help identify this bird in Louisville Kentucky?
This bird shows up in my back yard every night.  It is calling and sometimes I hear a bird in the distance calling back.  I think its an owl but I haven't seen it yet.  Any ideas what it is?

To me that sounds like the distinctive "who cooks for you" call of the Barred owl.
Compare with the recordings available from the Audubon Society, Cornell's All About Birds, and many others such as this YouTube video from a Cornell Lab Bird Cam of a Barred owl calling from its nest.

That it!  Thanks.  Now got to find a way to get a camera on this bird...

My Gravitar is from one we observed that was hunting around mid-day so this is definitely possible. Looking for owl pellets around largish trees in your neighborhood may help you identify where it roosts or nests.

@tyersome I agree that this is definitively a barred owl. Very distinct call. As my wife always says when I imitate the call: "you do!!" :p


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Help identifying this bird skull
The skull is 4 to 6 inches long and still has tendons attached. I found this on a beach in central California, which leads me to think it's probably from a seabird. I believe this is from a smaller scavenger bird.

I don't think the photos came through.

Welcome to Biology.SE! Can you please measure the skull and [edit] your post to include the more accurate estimate. 4-6 inches is a very large range and a more precise value may be critical for getting a correct identification. In the future please also proofread your posts and makes sure that the image has been uploaded. Thanks!

Certainly a seabird, with the tubenose. Possibly a giant petrel or one of the other Procellariidae. Please post an exact size.


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Did the old world have relatives of plants which were brought after the discovery of Americas?
When the Americas were discovered many plants were brought back to Europe. For example: potato, tomato, strawberries, chilies etc. At the same time many animals were brought to the Americas including: horses, cattle, sheep, and camels. It seems from the records that there were relatives of these animals in the Americas — for example llamas are in the same family (Camelidae) as camels. I wonder if there were relatives of these vegetables from the Americas already present in Europe or anywhere else in the old world.

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 asking about "related" leads to a trivial answer (Yes) since all known life on earth is related! ——— We also expect 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). E.g. the wikipedia article on strawberries has links to its genus, from which you can find "old world" species. Thanks!

Three of your examples: potato, tomato, and chilies, are from the genus Solanum. Along with the rest of the Solanaceae family, they are most diverse in the Americas but some species are found worldwide.
Species that would be found originally in the 'old world' from the Solanum genus and Solanaceae family include the black nightshade, bittersweet nightshade, and deadly nightshade. There is also at least one cultivated plant variously known as eggplant, aubergine, or brinjal (Solanum melongena) that is thought to have been domesticated in Asia.
The strawberry genus, Fragaria, also has species world-wide.
Of course, because all life on Earth is related, the answer to the general question "are there relatives of X found in some place" will always be "yes" as long as there is life there, it's only a matter of the extent of relation.

Thank you so much, could you give any resources I can refer?

@FrkEr I've linked to a variety of Wikipedia pages, all of which contain pretty substantial taxonomy. If you want to get more scientific references to dig deeper than basic phylogeny you're probably best off doing it at a species level rather than systematically. You could also ask more specific, detailed questions here at Biology.SE, but you'll have to make them specific.


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What's the name of this colorful tiny spider?
Found this colorful spider yesterday in my study. Couldn't find exact match over internet. Does anyone know what spider is this? Is it harmful?

Welcome to Biology.SE! Identifications questions should also include: 1) the species-identification tag; 2) the location where you observed this organism (e.g. country and region — the more specific the better); 3) habitat information; and 4) an estimate of the size of the organism. Please [edit] your post to include this essential information. ——— Please also take the [tour] and then go through the help pages starting with [Ask] questions effectively on this site. Thanks!

It seems a lot like the 'jade jumping spider'.
The jade jumping spider scientifically known as Siler semiglaucus has been observed primarily in Asia. I notice that the legs and abdomen have similar patterns to this species. As for the feelers and head I'm not so sure, but the dark hair on the front legs makes me more convinced of my guess. Perhaps look at different species that share the same genus to see if there is any other species that looks more similar to your observation.

If you're still not convinced, as a last resort, perhaps take a look at the peacock spider also known as Maratus volans. It's a long shot but maybe you see connections that I couldn't catch from the photo :).

Thank you for the details, Ark.


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Air bubble in addled egg
I'm a complete novice in biology. This is just a question that arose during Saturday night warmup and there is no better place to get answers :)
So, as probably most of you know, if you want to decide whether an egg is rotten/gone bad/addled you just put it in a bowl filled up with cold water and some salt.
If the egg stays on the bottom of the bowl then it is good.
If it floats to the top of the water then it is rotten/addled.
I imagine the egg is floating because there is an air bubble in the rotten egg.
But how would that air bubble get in the egg?

Egg shells look as if they're solid, but in fact they're filled with tiny pores through which air can and does diffuse.

...up to the time when internal pipping takes place, when pulmonary ventilation is initiated, about 20 liters (O2 + CO2 + water vapor) have passed through 10,000 pores of an 80 gm egg.

--Pores and gas exchange of avian eggs: a review.

A typical 60-g chicken egg has about 10,000 pores, each with a functional cross section of 150–200 μm^2; therefore, the total pore area is about 1.5–2 mm^2.

--Gas exchange in avian embryos and hatchlings
You only asked about chicken eggs, but chickens have it pretty easy compared to many other avian species.  For example, ostrich eggs have a much larger volume-to-surface area, meaning that exchange is less effective. One way ostriches may compensate is by incubating eggs at lower temperatures, reducing oxygen requirements; more significantly and related, incubation time is relatively slower for birds with large eggs.   Birds at high altitudes have larger total pore size, adapting to the reduced O2 pressure.
Actually, a more serious problem than oxygen exchange is water exchange.  The egg needs to manage water loss (not too much, not too little), and the more gas exchange the more water loss.  Accordingly, birds adapted to different humidities lay eggs with different gas exchange capacities (changing pore densities for the most part); birds in very arid environments, like gulls in Chile's Atacama Desert, have very low gas and water exchange, to the point where their developing chicks are relatively hypoxic:
--Reduced oxygen diffusion across the shell of Gray gull (Larus modestus) eggs.

As an egg ages, it becomes progressively less dense and this is a natural consequence of the development of the embryo. If an egg becomes contaminated by bacteria, then it will also become less dense. The reason for this is that as the contents of the egg develop (or decompose, as the case may be) gases are produced. These gases dissolve into fluids of the egg and then migrate out of the egg into the surrounding environment.

I would not use the terms "rotten/addled". The test you describe is a simple kitchen test to determine if eggs are "old" vs "fresh" (before the days of refrigeration).  Fresh eggs will sink while old eggs will tend to float. This is because all eggs have a "bubble of air" at the blunt end (presumably for the chick to breath while hatching). As the egg gets older, this bubble will increase in size due to simple desiccation (moisture loss) over time.
You can try the test using fresh vs. expired eggs from the market.  You will find that many more of them will float when they are weeks past their expiration date, but they are definitely not rotten/addled and some people will still use them. It is more a test for the cautious person to avoid possible health risks from older eggs. A rotten/addled egg will give off the characteristic "rotten egg" smell due to bacterial growth.


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Why are embryonic germ cells considered stem cells?
In a class that I'm taking we were presented 3 types of stem cells.

Adult stem cells which come from bone marrow
Embryonic stem cells which come from embryos
Embryonic germ cells which come from testes

I understand that adult stem cells are a bit more specialized than embryonic stem cells, but I'm confused why embryonic germ cells are considered stem cells. From Wikipedia, the definition of stem cells is:

Undifferentiated biological cells that can differentiate into
  specialized cells and can divide (through mitosis) to produce more
  stem cells

But from my limited understanding of biology embryonic germ cells can't specialize into any other cells unless they fuse with another gamete, so why would they be considered stem cells? What am I missing here?

You are confusing germ cells, sperm and oocytes with Embryonic Germ Cells. EG Cells are diploid, while gametes are haploid. I explain what EG cells are in my answer below.

The difference in designation is the timing of the foundation of the cell line and the tissue that it was sourced from.
Embryonic Stem Cells are harvested from the inner cell mass of a Blastocyst around day 5 post fertilization. This is the first or second generation of cells to have started to differentiate, but they still have Pluripotency, which means that they can differentiate into any one of the three germ line cell types. [1][2]
Those  three germ cell types are:

Endoderm
Mesoderm
Ectoderm

Embryonic Germ Cells are "cultured from primordial germ cells obtained from the gonadal ridge and mesenchyma of 5- to 9-week fetal tissue...." [1] These cells are multipotent, meaning that they will usually only be able to give rise to mesenchymal derived cell lines.[3][4]
There are also differences in replicative ability. ES cells are for the most part immortal cells able to be maintained in in-vitro culture for long periods of time, while EG cells have a life cycle of about 70 to 80 cell divisions before they reach quiescence.[1] If I had to venture a guess as to why this was the case, I would say that EG cells have likely already reached a stage of differentiation where they are repressing or down regulating the expression of Telomerase. ES cells will be expressing telomerase, so they will not experience telomere shorting due to the 3' end replication problem during DNA synthesis in S phase of mitosis.
There are other cell types of Adult Stem Cells other than Hemopoietic Stem Cells, so I am not sure why your course is making the distinction. It could be that in practice, we have only really successfully used Hemopoietic Stem Cells in treatments for diseases by doing bone marrow transplants. You would likely have to have your instructor clarify this point for you.

Stem cells in embryos are the basis for the development of the organism i.e once the gametes are fused you have a produced a cell that will replicate and differentiate into every cell that body is composed
Any cell that differentiates into another cell can be defined as a stem cell. Yes, the testes only produced sperm cells but a localized group of stem cells will almost always be differentiated into the same type of cell over the course of the organisms lifetime.
In reality a stem cell is no different than any other stem cell as they are all pluripotent. What makes stem cells different are the location in the body and the differentiation signals that are prevalent there.
For example the hematopoietic stem cells in bone are responsible for producing all types of blood cells due, while the stem cells in the crypt of the villi lining the intestinal tract differentiate into absorptive epithelial cells and mucus secreting goblet cells.
To summarize, a stem cell's differentiation is based on signals. The type of signals are ultimately determined by the function of the particular location that the stem cells reside in. (It is more complex than just "signals" but if you decide to delve into a bit of genetics and biochemistry it will make more sense).

Adult stem cells are considered multipotent, not pluripotent. They have differentiated to the point where they can no longer give rise to other cell lines. HPSCs will not give rise to neurons. There are laboratory techniques that will induce cells back into pluripotency, but those do not take place within the organism, that we know of. ES cells are really the only pluripotent stem cells, and they arise early in development, and differentiate into the three different cell lineages. I would also hesitate to say that any cell that differentiates into another cell is a stem cell...

Monocytes are partially differentiated cells that can give rise to macrophages. Activate B and T-Cells can differentiate into effector cells and memory cells. There is also a temporal aspect to signaling and how it effects cell differentiation.

Stem cells are defined as having two properties: self-renewal and differentiation. This definition applies to hematopoietic stem cells just as well. As such, the substance of this response is incomplete.

Adult stem cells don't always come from bone marrow. In any or most adult tissues still have stem cells exist. Stem cell doesn't only mean it can specialize into other cells. Any cell, if it has self-renew ability and never grows old, can be called stem cells. So, for men's germ-line, even it has limit differentiation ability, maybe just could turn into sperm, but it has self-renew ability and never grows old. The is the reason that some old man, over 100 years old, they still can have a newborn....

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How much does the nutritional value of insects depend on what they're fed?
Insects are often touted as being the food of the future due to their nutritional value and small amount of resources required to raise them. However, how dependent is the nutritional value of an insect on what they are consuming. How many vitamins and amino acids are they able to synthesize?

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Evolutionary motivation behind number of neurons in DCMMP
I'm studying neuro-anatomy right now and I was surprised to learn that there are only three neurons along the Dorsal Column Medial Lemniscal Pathway (DMLP) which relays mechanical sensations from the limbs to the brain. Is this the same across all mammals? Is there an evolutionary motivation behind having exactly three neurons, instead of 4 or 2?

The species you want to look at for this are giraffes and, to some extent, elephants.  This article is talking about information flow in the other direction (corticospinal tract) but it might have some insights into the sensory pathways.  I did not read it yet, though.


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What's the evolutionary reason behind decussation?
A bunch of stuff in the human nervous system decussates. Optical information inputs from the eyes cross over in the optical chiasm. Multiple sensory and motor pathways cross-over before ascending the spinal chord or within the brain stem.
What's the current hypotheses being explored for justifying this anatomical phenomena?

Related: http://biology.stackexchange.com/questions/3807/why-do-the-two-hemispheres-of-the-brain-control-the-opposite-sides-of-the-body/3835#3835

I don't think it is a clever thing to group all types of decussation and look for a general explanations. I would tend to think that different decussation have different explanations. It is like asking what are the hypothesis to explain evolution of body size. There is no general answer to that but only a list of case specific impact of different factors on body size (see this post). Consider the two case-studies 1) "why does left brain controls the right part of the body" and 2) "Torsion in gastropoda" as examples of how different explanation applies to different decussation.
why does left brain controls the right part of the body?
See @shigeta's answer to this post. It is very interesting.
Torsion in Gastropoda
Torsion in Gastropoda is an interesting case. In this lineage individuals undergo some torsion during their development. This wikipedia articles say:

Snails are distinguished by an anatomical process known as torsion, where the visceral mass of the animal rotates 180° to one side during development, such that the anus is situated more or less above the head. This process is unrelated to the coiling of the shell, which is a separate phenomenon. Torsion is present in all gastropods, but the opisthobranch gastropods are secondarily detorted to various degrees.[13][14]
Torsion occurs in two mechanistic stages. The first is muscular and the second is mutagenetic. The effects of torsion are primarily physiological - the organism develops an asymmetrical nature with the majority of growth occurring on the left side. This leads to the loss of right-paired appendages (e.g., ctenidia (comb-like respiratory apparatus), gonads, nephridia, etc.). Furthermore, the anus becomes redirected to the same space as the head. This is speculated to have some evolutionary function, as prior to torsion, when retracting into the shell, first the posterior end would get pulled in, and then the anterior. Now, the front can be retracted more easily, perhaps suggesting a defensive purpose.
However, this "rotation hypothesis" is being challenged by the "asymmetry hypothesis" in which the gastropod mantle cavity originated from one side only of a bilateral set of mantle cavities.[15]
Gastropods typically have a well-defined head with two or four sensory tentacles with eyes, and a ventral foot, which gives them their name (Greek gaster, stomach, and poda, feet). The foremost division of the foot is called the propodium. Its function is to push away sediment as the snail crawls. The larval shell of a gastropod is called a protoconch.

You can find more information there


text:
What is the purpose of an siRNA screen in drug discovery?
In the paper "A genome-wide siRNA screen identifies a druggable host pathway essential for the Ebola virus life cycle" by Martin et al. the authors try to disrupt the Ebola life-cycle by screening which human genes participate in it's replications:

In order to identify host factors involved in the EBOV life cycle, we performed a genome-wide siRNA screen comprising 64,755 individual siRNAs against 21,566 human genes to assess their activity in EBOV genome replication and transcription. As a screening platform, we used reverse genetics-based life cycle modelling systems that recapitulate these processes without the need for a BSL4 laboratory.

This helped them find a pathway.
What is siRNA screening and how does it help find a pathway?
The tag [rna-interference] references siRNA:

A post-transcriptional mechanism of gene-regulation/silencing mediated by small RNAs (siRNA)

However, I can't tell if siRNA refers to "small RNAs" or the whole process.

According to the Labome article "siRNAs and shRNAs: Tools for Protein Knockdown by Gene Silencing" siRNA does stand for small interfering RNA.
siRNA is used to silence genes via mRNA degredation:

NA interference (RNAi) is the process by which the expression of a target gene is effectively silenced or knocked down by the selective inactivation of its corresponding mRNA
[...]
The silencing mechanisms can either lead to the degradation of a target mRNA, as induced by small interfering RNAs (siRNAs) or short hairpin RNAs (shRNAs), or the suppression of translation of specific mRNAs, as induced by microRNA (miRNA).

There are also Wikipedia articles discussing these concepts that didn't come up in my search somehow, but a colleague linked me to:

Gene knockdown
Small interfering RNAs


text:
Which bacteria takes the longest to double?
Currently I am writing a lab report on the enumeration of bacteria.
E.coli takes about 30 mins to double. That is going from 1 bacteria to 2 bacteria.
I want to know which bacteria takes the longest to double? Do some bacteria take a day to double?
Thank you for the help.

3000 years plus seems a little longer than 15 hours.

There is no answer to your question
The doubling time of a bacterium is dependent on the conditions: primarily on the temperature and the availability of nutrients, but other factors can apply. Because of this, the doubling time of any particular bacterial strain cannot be considered in the abstract, thus to give a single number  we can consider the optimum doubling time for a strain instead - i.e. how fast it will double under the perfect (for it) temperature and nutritional conditions. For the E. coli strain you worked with, this is likely 37 degrees and in a rich media such as Lysogeny Broth. But for the staggeringly vast array of bacteria out there, we simply don't know what the optimum conditions are much less have actually measured growth under them. In fact, there are many bacteria which are known about, but currently uncultured so we haven't even begun to understand their growth dynamics.
So even the simplified question of longest optimal doubling time cannot be answered because we don't have the data for so, so many bacteria. The question of the maximum time between divisions is even less clear: there are bacteria that live under conditions of extreme nutritional limitation that can take thousands of years to double, and strains that can exist as spores for at least 100,000 years and maybe even tens of millions. Do we consider their doubling time to be a 100,000 years? 25 million years? Without specifying the conditions under which the doubling takes place, the question is poorly defined.


text:
Spider Identification in Miami, FL
These two spiders were found at the Fairchild Gardens in Miami, FL.
What spiders are these?

Please [edit] to separate this into two questions and include size estimates for both species. Please also consult the "species-identification" tag (click on the tag I added to your post) for more information on how to best ask this kind of question. Thanks!

The second one is called the golden silk spider commonly found in forests.

@JossieCalderon If you are certain about that post it as an answer. It's OK to answer your own question.

@aminabzz Terrible moderating removed it. This answer is hidden. This answer was deleted and converted to a comment last month by AliceD♦

@AliceD terrible.


text:
Need help identifying what looks to be a skull
  ( BOTTOM VIEW )I was given this skull(?) by someone a few years ago, it was found washed up on a beach in Panama. I collect bones so usually I’m really good at IDing skulls and I’ve spent some time trying to just generally research skulls that look the same. I’ve looked at snake, fish, mammal, and bird skulls but none of them seem to match, it’s just a very odd shape. I researched on animals that live in the water in Panama but none of them matched up. I could just not be looking hard enough or looking at the wrong things. It doesn’t have a lower jaw and the eye sockets or at least I think they are, are very deep inside the skull. It does seem to have a base for vertebrae. Which is why I assume it’s a skull along with the general structure. The top part of the piece is completely flat with a small incline.
This is my first question so please tell me if I’m missing anything.

I don’t know if it’s just my view of the app, but I don’t see a photo of the specimen, which would be helpful. Could you upload one? Thanks!

I apologize I forgot to add the images I’m so sorry

Im having a problem with my post, It won’t let me paste the pictures I wanted to add. I’m sorry for any inconvenience I thought they were part of the post.

@Jacob You might try from desktop if you are using a phone. Or if a phone is the only option, at least use the browser version and not an app.

thank you! using the desktop version worked.

Welcome to Biology.SE! Please [edit] your post to include the size and if possible pictures from other angles. Thanks!

Probably not a skull. It's probably part of a bird's synsacrum


text:
How can Chronic myeloid Leukaemic drugs reduce the production of the Philadelphia genotype?
How can Chronic Myeloid Leukaemic drugs (Tyrosine kinase inhibitors, e.g. imatinib, etc.) that act by inhibiting bind of ATP to the active site of the BCR-ABL1 protein actually reduce the prevalence of the Philadelphia chromosome? (For example, optimal response to TKIs in 3 months would be Ph+ <35% and/or BCR-ABL1 <10%.) What I am actually asking is how a drug that targets the result of the oncogene (the BCR-ABL1 protein) can have an effect on the source (ie. genotype of the cells), as CML is a clonal haematopoietic stem cell disorder?
An example Reference paper: Apperley JF. Chronic myeloid leukaemia. Lancet. 2015 Apr 11;385(9976):1447-59. doi: 10.1016/S0140-6736(13)62120-0. Epub 2014 Dec 5. PMID: 25484026.

Very interesting question! Could you cite a paper too? thanks

@EvanP Just added. Thanks!

The key is that TKIs, such as Imatinib, are a therapy rather than a cure
Per Wikipedia, Imatinib acts as a competitive inhibitor of the otherwise constitutively-active BCR-ABL fusion protein, rather than the fusion gene.  By binding the kinase domain, BCR-ABL is unable to phosphorylate downstream effectors that result in unchecked proliferation.  As long as a patient continues to take Imatinib, BCR-ABL activity should be blocked.

In the past few years (i.e, long after imatinib's discovery) there has been a lot of research into exactly how hematopoetic stem cells, which reside in the marrow and create leukemic blasts, work. Most HSCs remain in a quiescent state, but it's not particularly well-known how frequently they turn over.  Recent CML studies have shown that after ~5 years, a large portion of CML patients can safely taper the the drug.  Presumably this is related to HSC turnover, but frankly as a leukemia molecular biologist rather than a physician, I'm not the best font of clinical knowledge.


text:
Is there a chemical reaction that blocks two cysteines by reacting with a third molecule?
The idea is to block the two cysteines so they can't react in the future. We need the reaction to remove the -SH groups of the two cysteines, or modify them.
Also important, the reaction should not make cross-link between the two cysteines.

To explain briefly my motivation: I am a PhD student and I do optical tweezer experiments. We can hold and manipulate two micrometer beads in two optical traps. We have a process to tether one protein using two DNA linkers to the two beads. I need to block two of the three cysteines of my trimer to properly couple the protein to both beads.

Welcome to Biology.SE! Please take the [tour] and then go through the help pages starting with [Ask] questions effectively on this site. In particular, I've voted to close this question because it is primarily about chemistry rather than biology. While this might be a better fit for [Chemistry.SE], please don't repost (instead request migration). ———— In addition, we 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). I would start by looking into peptide synthesis. Thanks!


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What type of insect is this found near Mountain View California?

This was taken in a hotel room in the Mountain View area of California. Size wise, it was pretty small, perhaps somewhere around an inch from left to right (not including antennae). My first instinct was cockroach, but, on further inspection, it doesn't look like a German or a field cockroach, as it doesn't seem to have wings. Is anyone familiar with this insect?

It looks pretty difficult to identify, it's been crushed beyond recognition.

That specimen is pretty squished, but I'm guessing it's a cave cricket or spider cricket (order Orthoptera; family Rhaphidophoridae).  They're very common invaders of cool damp places like basements or air conditioning units.  Harmless, but can be quite startling, as most species can jump several feet in one leap.

This would likely be a nymph, not an adult, right? I don't know too much about these types of things, but it was quite small (0.5-1.0 in).

Welcome to Biology.SE! You are likely to get a more positive response to your answer if you explain why your identification is correct. Specifically, please [edit] your answer to add discussion of key features that led you to this conclusion and supporting references or at least validated images. Without this your answer is indistinguishable from opinion. ——— You may also wish to take the [tour] and then consult the help pages for additional advice on [Answer] effectively on this site. Thank you!

Assuming Alan is right about the ID (which would be problematic in any case, due to Chris' probable reaction to seeing the subject--I'm assuming the OP also did it in) the specimen may well be an adult (ALL Rhaphidophorid crickets are wingless at that stage); with a few notable exceptions (see for example Tropidischia xanthostoma on bugguide) most species of this family need to be identified from intact adult males, and much unpublished work has been done (for a preview, see the article here, the author of which has since died).


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What morphological traits can be used to diagnose members of the Eucalypteae?
I read the Wikipedia article on Eucalypteae and it doesn't actually say what these plants have in common.
(I am now reading through https://bsapubs.onlinelibrary.wiley.com/doi/pdf/10.3732/ajb.1200025 and I think I've found the answer to this question.)

Welcome to Biology.SE. The Biology.SE community has agreed that questions that show little or no prior research effort are off-topic on this site as are "homework" questions unless you have shown your attempt at an answer. Please [edit] your question and tell us where you've looked for answers, what you do know about the topic, and where exactly you still have questions. Under researched questions may be subject to down-voting and closure. Please take the [tour] and consult the [help] starting with [ask] for details.

In particular, what all taxonomic groupings have in common is an ancestor — however, this definitely falls under the category of "trivial to biology professionals" and so is a "homework" question. If that isn't the question you are trying to ask, please [edit] to clarify what you do want to know and to demonstrate your prior research effort.

Wouldn't that be all clades? With taxonomic groupings also being on the basis of traits?

Well, I'd say it is more a matter of inference  — what we care about is the evolutionary history. If we were to find that one group of eucalypts had a different ancestor, then those plants would be moved into a new group. The traits (now primarily based on DNA sequences) are the evidence used to determine relatedness — my understanding is morphological traits are now primarily field marks for diagnosing to what group an organism belongs. ——— At any rate, it seems your question is more about common traits, so I think it would be helpful to edit your question's title and body to emphasize that.

I've edited your title to something that seems clearer to me — please make additional changes if I'm still not understanding you correctly, or if you prefer a different wording.

If you're reading now the article that you link to in your question and you think it answers your question, then perhaps you might consider accepting my answer which linked to and quoted the same article (before you edited it into your link).

Couldn't find the place to click it. Much appreciated.

Have you had a look at the APG website ? http://www.mobot.org/mobot/research/APweb/orders/myrtalesweb2.htm#Eucalypteae it may give some interesting information ...

It's a slightly tough question that can't be answered with a simple "they share X characteristic in common". It's more that some of them share a characteristic, and some of those share a characteristic with another load of species within the same sub-clade, and some of the characteristics they have are shared with some more... etc.
The American Journal of Botany puts it:
(Synapomorphy: a shared trait believed to have been present in a common ancestor.)

Currently, no unambiguous morphological synapomorphies have been confidently  identified as defining the Eucalypteae in comparison to other
Myrtaceae (however, see Wilson et al., 2001 , for some possibilities).
Within the Eucalypteae, however, subclades are defined by
synapomorphies. For instance, Angophora Cav., Corymbia , and
Eucalyptus share several possible synapomorphies, such as presence of
oil glands that protrude above the surface of the epidermis (“emergent
oil glands” of Ladiges, 1984 ).

These are modified into distinctive
bristle glands in Angophora and Corymbia ( Johnson, 1972 ; Ladiges,
1984 ), which are a unique synapomorphy for the Angophora - Corymbia
clade ( Ladiges et al., 1995 ; Wilson et al., 2001 ). Angophora ,
Corymbia , and Eucalyptus are also characterized by having compound
petals and, in Eucalyptus, a portion of the compound petal is usually
modified into a staminophore, or stamen-bearing tissue ( Drinnan and
Ladiges, 1988 , 1989a , b ,  1991a ).

Other characters are apomorphic
but are likely homoplasious, having arisen more than once within
Eucalypteae. For example, some Corymbia and Eucalyptus species are
characterized by the presence of calycine and/or corolline opercula,
or cap-like perianth whorls that are deciduous from the flower at or
prior to anthesis (e.g., Johnson, 1972 ; Hill and Johnson, 1995 ;
Boland et al., 2006 ). Opercula likely have separate origins in these
genera ( Ladiges et al., 1995 ; Parra-O. et al., 2009 ). A caducous
calyx that usually leaves a scar on the flower bud (see Johnson, 1972
; Boland et al., 2006 ) is also an apomorphic but homoplastic
character within Eucalypteae, being a synapomorphy for a clade within
Corymbia ( Ladiges et al., 1995 ;  Parra-O. et al., 2009 ) and having
arisen at least once on the stem of Eucalyptus subgenus Symphyomyrtus
( Fig. 1B ).


text:
Can COVID-19 affect a person a second time?
I keep hearing people are recovering from COVID-19 virus. Is there any chance that same person can become infected with COVID-19 for a second time?

Please see here.

Does this answer your question? Human Immune Response to COVID-19 Virus

Short answer: Although there are some reports on this, it is pretty unlikely. It is more likely that patients where released too early from hospital, developed further symptoms later on and got worse, was re-hospitalized, tested again for SARS-CoV2, which was positive and counted as re-infected.
Another possibility is that a false negative test happened, when people got re-tested later the test was positive again and the patient was counted as re-infected. Given the rising number of cases worldwide this should become evident pretty soon, if this is a real problem and not an artefact. For the moment, I don't think there is enough evidence for the re-infection of the same patient in such a short time period. If this holds, future will tell.
Long answer: There is now an experimental paper, which infected rhesus macaques with SARS-CoV2, tested if the infection was similar to humans happening in the upper airways (which it was), and re-infected the animals after 28 days with a really high dose of virus (which is much higher than what comes around in our environment), with none of the macaques getting re-infected or showing pathological signs of the infection. See reference 1 for details.
This article has its limitations with small sample size and the general questions if the chosen animal model is really comparable with human.
Additionally it looks very much like that patients who are recovering don't shed infectious virus anymore. The PCR test however does not discriminate between infectious virus and plain virus RNA, so it is most like much longer positive than people are infectious. They also show the rapid appearance of specific antibodies, which would at least temporarily protect against a re-infection. See reference 2 for a nice summary and reference 3 for the original article.
References

Reinfection could notoccur in SARS-CoV-2 infected rhesus macaques
People ‘shed’ high levels of coronavirus, study finds, but most are
likely not infectious after recovery begins
Clinical presentation and virological assessment of hospitalized
cases of coronavirus disease 2019 in a travel-associated
transmission cluster

Edit (24.11.2021):
Being 1,5 years further into this pandemic there are clear signs now that reinfections are possible, although it was first thought it should not be a concern. There are a few reasons for this, mainly the occurence of new, much more infectious viral strains (Delta variant), waning of the immune respone (in vaccinated and also people who got infected), weak immune responses at all (reinfection probably occurs in connection with the Delta variant). Following reference 4 (thanks to @bob1 for the hint) below, it seems that reinfections are less severe than primary infections.
For more information please have a look into the additional references below. This shows very well the problem with an unknown pathogen and the rapidly ongoing research on it.
Added references (24.11.2021):

Risk of SARS-CoV-2 reinfection after natural infection
The durability of immunity against reinfection by SARS-CoV-2: a
comparative evolutionary study
Prospects for durable immune control of SARS-CoV-2 and prevention of
reinfection
Severity of SARS-CoV-2 Reinfections as Compared with Primary
Infections

Update: Coronavirus reinfection has been reported in India for the first time. See this news: https://www.google.com/amp/s/www.timesnownews.com/amp/india/article/first-case-of-coronavirus-reinfection-reported-from-bengaluru-27-year-old-woman-affected/648563

And in US: https://indianexpress.com/article/coronavirus/first-us-covid-19-reinfection-case-identified-in-nevada-study-6574428/

@NilayGhosh I have read newspaper articles about this as well, but I would like to see a scientific paper first, before I update this answer. I am following this :-)

Good answer.  There's an interesting paper in NEJM today on severity of infection in re-infected patients, that might be worth including.

@bob1 Thanks for the hint, this looks indeed interesting. I will include this as well.


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Does the SARS-CoV2 spike protein passively diffuse through the nuclear pore complex?
I found this thread which is worth reviewing as context to my question(s) since there is some overlap in potential discussion, although it's concern is with mRNA ingress rather than spike protein.
Does the mRNA of the covid19 spike protein contain any nuclear localization signals
It focuses on nuclear localization signals, but there are other mechanisms by which proteins or small enough macromolecules may ingress through NPC's (nuclear pore complexes)
First, see:
Which is bigger, mRNA or the protein it codes for?
http://book.bionumbers.org/which-is-bigger-mrna-or-the-protein-it-codes-for/
mRNA is, somewhat paradoxically (although not really) larger, mass wise, than the proteins it codes for.  And passive diffusion is influenced by molecular weight (a fair model,) so before being concerned about the larger mRNA sequence, we should first be concerned about the manufactured spike protein (either by wild type SARS-CoV2 or vaccine) both produced at the ribosomes of the ER.  An additional concern though could be the geometry / spatial extent of the mRNA or spike protein (in both it's conformations); ex: since mRNA may typically be more linear than globular, passive diffusion curves will be substantially modified as most NPC diffusion curves I've perused all consider globular macromolecules.
Second, see for proof of concept where an accessory protein on SARS-CoV is found to ingress via passive diffusion:
SARS-CoV 9b Protein Diffuses into Nucleus, Undergoes Active Crm1 Mediated Nucleocytoplasmic Export and Triggers Apoptosis When Retained in the Nucleus (2011)
https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0019436

Background 9b is an accessory protein of the SARS-CoV. It is a small protein of 98 amino acids and its structure has been solved recently. 9b is known to localize in the extra-nuclear region and has been postulated to possess a nuclear export signal (NES), however the role of NES in 9b functioning is not well understood. Principal Findings/Methodology In this report, we demonstrate that 9b in the absence of any nuclear localization signal (NLS) enters the nucleus by passive transport. Using various cell cycle inhibitors, we have shown that the nuclear entry of 9b is independent of the cell cycle. Further, we found that 9b interacts with the cellular protein Crm1 and gets exported out of the… Show more

Simple rules for passive diffusion through the nuclear pore complex (2016)
https://rupress.org/jcb/article/215/1/57/38760/Simple-rules-for-passive-diffusion-through-the

Recent in vitro studies over the last two decades also suggested a relatively sharp threshold of 30–60 kD (Keminer and Peters, 1999; Ribbeck and Görlich, 2001; Mohr et al., 2009; Ma et al., 2012), although such in vitro systems have recently been shown to be quite sensitive to the precise experimental conditions (e.g., the concentration of transport receptors and the nuclear factor Ran; Ma et al., 2012; Lowe et al., 2015). Larger molecules up to 230 kD in size have also been observed to permeate the NPCs in vivo on the time scale of many minutes to hours (Wang and Brattain, 2007; Popken et al., 2015).

SARS-CoV-2 spike protein: pathogenesis, vaccines, and potential therapies (2021)
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8326314/

SARS-CoV-2 S protein is a class I fusion transmembrane structural glycoprotein that is composed of S1 and S2 subunits [ 71 ]. It is a homotrimer with a size of 180-200 kDa

Back to a quote from Rockefeller University press paper above, I found this very interesting:

Nonetheless, the prevailing functional model of passive transport, which we term the “rigid barrier” model, is that of a barrier with a firm size threshold of 40 kD for passive diffusion (Christie et al., 2016; Knockenhauer and Schwartz, 2016; Musser and Grünwald, 2016; Schmidt and Görlich, 2016). According to this prevailing view, the slow permeation of larger macromolecules across the NPC is regarded as residual leakage beyond such a firm threshold (Kirli et al., 2015; Fig. 1 A, red curve). However, this supposed “leakage” may be also interpreted by an alternative “soft barrier” model of transport. In this model, passive transport rates are expected to decrease much more gradually with increasing molecular mass than previously realized (Fig. 1 A, black curve).

Note that last part, which is somewhat telling (and the curve in the paper)
So invoking:

Larger molecules up to 230 kD in size have also been observed to permeate the NPCs in vivo on the time scale of many minutes to hours

And

It is a homotrimer with a size of 180-200 kDa

Could spike protein manufactured at the endoplasmic reticulum ingress by way of passive diffusion into the nucleus or not?  If so, has this been studied?
Is it possible to be unconcerned because such a small 'negligible' quantity would ingress as such (without a NLS)?
Does the geometry / spatial extent of the spike protein (or secondarily, mRNA) itself augment how it would passive diffuse through a normally protected protein complex?

Welcome to the site. What would be your concern if the protein was capable of entering the nucleus?

Thanks bob1.  I'm not sure.  I'm just trying to understand the mechanism and validity of the idea (summarized by the title of the post) before hypothesizing potential outcomes if it were possible.

Ok, was just trying to see if there was some motive behind the question. Generally proteins of the spike sort aren't freely floating and are actively transported to the surface of the cell for virion assembly. However, if it were free-floating I don't see that it couldn't occur via passive diffusion,  but I'll let a better cell biologist answer.

Fair enough on diffusion.  "Generally proteins of the spike sort aren't freely floating".  Have a source for this?  What is different about 9b accessory protein as described in the paper cited in my original question?  Yes, all of the sub-unit proteins are 'expected' to be shuttled for virion assembly, but it appears this doesnt always happen.  Also, according to, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7112327/, the earlier studies theorized assembly at intracellular membrane, but later ones suggest the tubes between ER and Golgi Apparatus as the location of coronavirus morphogenesis.

On that last bit, its definitely more complicated, as some sub units also appear to be assembled elsewhere, for instance, in the cytoplasm, which would be where passive diffusion through NPC becomes more possible.  Depending on the protein, this would naturally vary.  That particular paper describes S protein migration oddly, at least in my opinion: "During its transport to the cell surface, either alone or as part of virions, the S protein undergoes further modifications".  So it could be either?

What I meant by "not free-floating" is that they are generated at the ribosomes and directly transported on the RER; but I see that ribosomes can be not associated with the RER, so that could be a source. Of interest: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC249107/ https://link.springer.com/chapter/10.1007/978-1-4684-5823-7_3.

9b is tiny - only 98 aa (~17 kDa), vs the ~1270 (180-200 kDa) of spike, so much much smaller and therefore more easily diffused and small enough to pass through passive transporters.

The crux of the concern stems from me running into this statement in the paper and  comparing to the approximate size of SARS spike protein: "Larger molecules up to 230 kD in size have also been observed to permeate the NPCs in vivo on the time scale of many minutes to hours".  This would suggest a lower concentration gradient through the NPC, but it appears at least theoretically possible.  The molecular mass simplification doesnt account for spatial extent, and the full length spike protein is suggested to be more axial / rod-like so this also may allow for more permeability.

With small enough molecules (ex: 9b or maybe smaller), concentration in the cytoplasm versus nucelus may reach equilibrium.  For larger masses (and the 'more' globular), equilibrium wouldnt reached, but the question still remains: is it theoretically or experimentally possible for any amount of S protein to passively diffuse through, of course, without a NLS? (Noting the paper with the 230 kD upper bound might need to be recreated / observed in-vivo)

Welcome to Biology.SE. Could questions are problematic since you can often find (or hypothesize) biologically irrelevant conditions under which the answer is "yes". I've therefore modified your question title — if you dislike this change feel free to revert it, but if so please clarify why and what conditions are of interest.


text:
Help Identifying this small spider (Tennessee)
This small spider, about .75" when legs spread, has a distinct "teddy bear" image on its cephalothorax. Help with identity please.

Welcome to Biology.SE. Please [edit] your post to include as much of the following essential information as possible to improve your chances of getting a good answer: 1) photos from multiple angles if possible; 2) the location (e.g. country and region — the more specific the better) where you observed this organism; 3) habitat information; and 4) any behavior you observed. Detailed tag info page. ——— Please also take the [tour] and then go through the [help] pages starting with [Ask] questions effectively on this site.

This is a ground crab spider from the family thomisidae. The general identifiers for this family are that the front legs rotate outward (crab-like), the two hind legs are much shorter than the front two legs (about half the length), and there is a fairly distinctively wide eye arrangement, which is hard to make out in this photo.
I don't know if anyone will be able to narrow it down to genus from this pic alone... from its features and the geography, the possible genera are: Modysticus, Ozyptila, Xysticus.
You can browse some galleries of these here: https://bugguide.net/node/view/1957/bgpage


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Solid mouse (C57BL/6) WT primers
I am trying to get a good pair (or better yet, library of pairs) of primers that give me one band in WT mice (C57BL/6). Do you know where I could find such a thing?
Alternatively, I thought of just designing a few sets of primers myself for highly-conserved regions. But that's quite a bit of guessing work (what regions, what pairs from what eprimer3 will calculate for me etc.).
So:

Do you know where such a database could be found?
If not, could you help me get started with creating it myself? What specific regions would in your opinion be particularly good for this purpose?

One band of what? Just a random genome segment, or are you looking to amplify something more specific?

Something I can rely on is there in all WT and most if not all transgenes.

This is impossible to be done. You can make primers to distinguish between mice which are mutated and wildtype mice (at least for one gene or locus), but you cannot do this for the whole genome. Here you could sequence your mouse and compare it to the reference sequence. What is your gene of interest?

I just want a pair (or library of pairs) of primers that will ~always work. As a positive control.

then use actin, or tubulin, or GAPDH, or one of a thousand other genes.

As @MattDMo mentioned use one of the so called housekeeping genes.

I have settled for two GAPDH primers with a short amplicon (~50bp):
>gapdh_rv3 <unknown description>
GAGACCTGAATGCTGCTTCC

>gapdh_fw3 <unknown description>
CTCCATTTCCCCTGTTCTCC

They provide consistent and good controls, as seen here (lower bands):

how do you know those aren't primer-dimers?  you should aim to amplify >= 100bp

Because my primers aren't complementary, and the band only appears if there is sufficient mouse DNA in the sample


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Epinephrine vs. Adrenaline
Both names are widely used, with what appears to me as a slight prevalence of “epinephrine” in scientific literature and an overwhelming prevalence of “adrenaline” in popular media.
Are there any well-documented and/or well-motivated guidelines for the usage of these terms?

epinephrine is common in medical practice.. in general biology the molecule is usually referred to as adrenaline. and the receptors are also called adrenergic receptors.

@WYSIWYG epinephrine is certainly common in American medical practice, it's not universal across the entire profession however.

AFAIK, they're the same molecule, so the nomenclature is interchangeable. Despite the answer by @TheChymera, I see Epinephrine used more often nowadays in publications.

Apparently I asked too soon. Summarizing my recent findings, I conclude that adrenaline is the better term.
To be more explicit, here is why:

The US National Library of Medicine recommends “epinephrine”, this is however mainly due to historical reasons (adrenaline used to be a trademark name in the USA).
This quite comprehensive paper on the issue presents a series of arguments for the use of “adrenaline”. These include: Better compatibility with other languages (where epinephrine is not at all in use); Better integration with other biological terms (adrenergic receptors, adrenal gland, adrenectomy, etc.); Better historical accuracy (epinephrine used to be the name for a neurochemically inactive crude extract from the adrenal glands).

I find the arguments of the referenced publication convincing, though I would recomend you read them in full.

Epinephrine and norepinephrine is used in the US mainly. This is where the term epi-pen comes from. Everywhere else we tend to use Adrenaline and noradrenaline. Epinephrine is typically only used in literature arising from the US or US English speaking countries. In most countries they use adrenaline and also include Epinephrine so our American cousins don't miss our publications. Adrenaline is the better term as it is more widely understood by scientists, health professionals and the public. However at the end of the day they're the same thing.


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What kind of spider is this (East Texas)?
My wife has seen this spider in a shower in Texas:

What kind of spider is it?
I could not identify it by comparing it to pictures of common spiders in Texas.
Size: It is sitting on corrugated sheet iron in the picture. The legs span from the "top of one wave to the next". The body is "between" the waves.

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This is a fishing spider, Dolomedes genus, from the tenebrossus group (i.e. not Dolmedes Triton).
The picture is not clear enough to reliably choose a species, but it is probably Dolomedes tenebrosus (dark fishing spider) or Dolomedes vittatus (banded fishing spider), both of which are in Texas.


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I found this bug on my washer please help identify it
The bug was a light brown
It had like 4 legs and two antennas

Welcome to Biology.SE! For identification questions please [edit] your post to include the location (e.g. country and region — the more specific the better) where you observed this creature. The location can be an essential clue for identifications. ——— If possible clear, closeup photos of the creature from multiple angles would also be helpful. ——— Please see the [tour] and then go through the [help] pages starting with [Ask] questions effectively on this site as well as clicking on the species-identification tag for details. Thanks!

I live in northwestern Pennsylvania and I only got on picture but haven’t seen any more of them and oh boy I have been looking


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What coastal creature leaves braid-like trace that has clear landing and take off points?
6/29 around 8 PM EST (within 40 minutes after downpour) the depicted trace was found in swash zone at Jacob Riis Park in NY. For reference the boot size is 12.


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Anyone can identify this moth?
Found on the ceiling of my flat.
Place: London, UK
Date: 9th of August
Size I would say slightly more than inch and inch and half (3-4cm) wingspan
Suspect on the photo:

That looks very much like a brown color morph of the Box tree moth (Cydalima perspectalis), which has been seen in the UK since 2008. The size is about right (around 4.0-4.5 cm wingspan).
This species is an invasive pest outside of its native range (Asia).

By Nagy Sándor (NagySandor.EU) CC BY 3.0, Link
According to the Royal Horticultural Society this species has been invading the UK from the southeast with London a likely place to find them.


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What is this insect? 6 legs and red body
I'm in Brazil, southeast region, urban area. I've found these 6 legged insects with red bodies and black heads. They have long antennae (about as long as their limbs) and they walk around like ants, but slower. Their bodies are about 1.5mm in length.
I have also found a cluster of what I imagine are eggs they laid or got out from (there were 5 or so next to them last night).
Can someone identify them?

Welcome to Biology.SE! If possible please try to get clearer pictures and then [edit] them] into your question — closeups from multiple angles will improve your chances of getting a definitive answer.

These appear to be the nymphs of the red-shouldered bug (Jadera hematoloma), which eat the seeds of the Sapindaceae family (Soapberry family) throughout South America, Central America and the southern parts of North America.
There is a close-up picture of one of these at bugguide.net, and further images here on the same website.


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What kind of soil-dwelling flying insect is this?
In the UK. They are roughly 1.5mm long, appear to crawl much more than fly, and seem to live in the soil of indoor potted plants. They are fast and tiny, so apologies for very shallow DOF. The first is on an aloe, the second is on a pot. They really like the soil around some capsicum plants.

Those look to me like fungus gnats. If you're looking to get rid of them, I've heard that putting a layer of rice hulls on top of the soil keeps them from reproducing. From what little I've read my identification doesn't go much deeper than superfamily, taxonomically, but it's a least a common name to work from.

Some kind of Sciarid does seem plausible, thanks!

Agreed that we're looking at a Sciarid ("Dark-winged" or "Black" fungus gnat, depending on the side of the Atlantic), in which case going deeper won't be possible without dissection and slide-mounting (see here for an abstract of the most recent Palaearctic monograph; it might be possible to download it for free from researchgate.net [look for the author Menzel], but use will require fluency in German).


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Surface Area to Volume Ratio and Ice Baths
Hi I was taking a practice test and stumbled across this question. I couldn't find information about this on the internet. Does anyone know why B is the answer? Thanks

Please [edit] your question to include the full text of the image you posted. Images are not searchable, and are incompatible with screen readers for those with visual impairments.

At present there's insufficient information to determine if b. has merit, you would need to specify a timescale for measurement. As MattDMo says, please provide us with the full information.

Welcome to Biology.SE. This is not simply an answer site, but instead a site that promotes self-learning with some expert help. Consequently, questions that show little or no prior research effort are off-topic on this site as are "homework" questions unless you have shown your attempt at an answer. Please [edit] your question and tell us where you've looked for answers, what you do know about the topic, and where exactly you still have questions. Please take the [tour] and consult the [help] starting with [ask] for details.

look up the square cube law in reference to heat.

@ARogueAnt. - I don't understand your comment either. Why do you need a timescale for measurement for this very basic Physics question? (Please answer me; when I ask you something in comments, I can't remember you ever answering me.)

@anongoodnurse This is the first time I recall you asking me anything. Apologies if I've been unintentionally rude. 1) We don't know what organisms are being referred to and if metabolic processes continue at ice-bath temperatures, 2) the square cube law's effect will be short-lived in such small organisms if their metabolism ceases for temperature/lack of energy as they will quickly asymptote to ambient temperature (timescale). We need more info to answer without making assumptions that may be unwarranted. That's it.

@anongoodnurse I agree that a. c. and d. are impossible (assuming sphericity), but the practice-test is not a good one if the "correct" answer is only findable by exclusion of other answers - as opposed to findable by deduction from the information supplied, i.e. b. must be right, but there's only the evidence that the others are wrong to support it - e. or f. might be a better answer, but the nature of the multiple choice format is such that often it's not a good teaching aid.  I believe my concern was valid.

BTW. I had previously (mosquito hearing), but the comment was deleted. Just because something is common and seems "common sense" - doesn't inherently make it good quality. I've seen the same thing here (UK). Perhaps it might make a useful question on another site, [academia.se] or [psychology.se] regarding effective teaching/assessment.

Last comment on the issue, @ARogueAnt: I never said I liked the question or that it was good. I said it was common, and the fact that it's not a good question does not give validity to your request for more information. I use logic, and that it's common = it's good is a fallacy. It is common and it does not test all understanding; it tests the ability to deduce the correct answer using the information at hand, that's all it does. Well, also basic principles of Physics in this case.


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What is this small brown arthropod?
Does anyone have an idea what this arthropod is? I first found one in the bath but have since noticed them on the walls, ceiling and on linen around the house. They are 1mm long, look brown in colour and I think they have 6 legs. Couldn't get a better pic than the one attached.
Size: 1mm
Location: Sussex, UK

Wood framed house by any chance? Sort of looks termite-ish from that angle. I'll let the experts answer though.

It's timber framed, covered with brick. Plasterboard on the inside. Built this year.

Looks more like an insect than a mite.

Welcome to Biology.SE. Six legs is inconsistent with mites (which have eight legs) so I've edited your question to use the more general term arthropod. Please borrow something with better close-up capability and see if you can get better photos — the current photo is so tiny and unfocused I doubt anyone will be able to give you a definitive id.

Thanks for correcting my poor terminology! I'll see if I can get my hands on something with better magnification!

This appears to be a booklouse (psocid). They are tiny, harmless insects that are common in buildings. It is normal to have small numbers of them.

Nice first post neville, welcome to Biology.

Thank you! I have been active over on Reddit's bug ID forums and it only recently occurred to me to check out what's on StackExchange. I am mostly interested in arachnids, but can ID a lot of common insects people find around the house.

Thanks Neville. Yes that looks spot on! Had rather a lot of them! A few hundred. Think we've got a humidity issue so that would make sense based on what I've just read about them.


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The role of PCA (Principal Component Analysis) in recording neurons
I am reviewing the recording methods from an experiment that tracked neuronal activity on the prefrontal cortex of a monkey.
From the method description in Nieder, Andreas, David J. Freedman, and Earl K. Miller. "Representation of the quantity of visual items in the primate prefrontal cortex." Science 297.5587 (2002): 1708-1711.:

Recordings were made from three hemispheres of the PFC [prefrontal cortex] of two adult rhesus monkeys. [...] Arrays of eight to twelve tungsten microelectrodes (FHC) were inserted using a grid (Crist Instruments) with 1-mm spacing. [...] Neurons were selected at random; no attempt was made to search for task-related activity. Waveform separation was performed off-line applying principal component analysis (Plexon Systems).

Does anyone know what PCA (Principal Component Analysis) is exactly used for here? My guess would be that it is used to cluster "significant" waveforms, i.e. to identify neurons. But I could not really find reliable resources online.
The role is unfortunately not included somewhere in the paper quoted :(

Welcome to Biology.SE. 1) Please always define abbreviations and acronyms before using them (you use two PCA and PFC). 2) When you include a quotation you must include the citation. 3) The role should be included somewhere in the paper you quote — please don't expect us to read and interpret papers for you. 4) Please don't include "thanks" and "signatures" in you posts. Please take the [tour] and consult the [help] starting with [ask] and then the section on "homework" for details about expectations for users and their questions.

PCA is the simplest way to perform spike sorting, which is necessary when the experimenter has no way of verifying that recordings are coming from single neurons.

Like vkehayas mentions in a comment, they're using it for spike sorting, as you've guessed. This involves both identifying signals from putative neurons (vs noise) and separating different source neurons, when possible.
Plexon's website mentions "Manual cluster selection in 3D feature space using principal component projections, voltage slices in time, or more than 20 other waveform features such as peak, valley, full-width at half maximum, etc." for their software.
There are many, many different ways to sort spikes, some supervised some unsupervised, some using PCA, some using the original waveforms, some using other types of decomposition.
David Redish's MClust is one example which is open source if you'd like to look at some similar software; I assume Plexon's is proprietary but they'll be using similar approaches.


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Identification of the bug on the curry leaf- Delhi, India

I found this bug on my curry leaf in early morning. Which bug is this?
Size- 1-2 cm
Habitat- Delhi, India.
The bug was on one of the curry leaf of the curry plant pot in my residential balcony
Time- 7:00 am

Identifications questions should also include an estimate of the size of the organism and as much habitat information as possible. Please [edit] your post to include this essential information. ——— Please also consider taking the [tour] and going through the help pages starting with [Ask] questions effectively on this site. Thanks!

@tyresome I have edited. Thanks for your advice!

You're welcome! That looks like what is commonly known as a shield or stink bug (a large and very diverse group of beetles) . If you don't get a more specific answer you might try submitting your observation to a site like iNaturalist, which specializes in species identifications.


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Interpretation of Pangenome: high number of accessory genes
I performed a pangenomic analysis on a collection of 52 strains belonging to the same genus (some 5-6 different species). All the strains were isolated from the same environment: interior compartment of surface-sterilized plant root.
Now, the results of my analysis (I used the R package FindMyFriends) indicated a total of 32911 gene groups divided as follow:

581 core (present in 95% or more of the genomes)
6116 shell (present in 15 to 95% of the genomes)
26214 cloud (present in up to 15% of the genomes)

This results are quite unexpected. Even though it is typical that most gene groups get labeled as cloud or accessory, it surprises me that the percentage is so high! Especially given the common origin of those strains.
Other software I tried (Roary, BPGA, microPAN) gave similar or more extreme results, so I can exclude a technical error.
Therefore, if anyone has some experience with pangenomic data, some input on how to interpret this data would be greatly appreciated.

Don't know this area, but have you considered the possible presence of other organisms' DNA from contamination or the presence of eukaryotic (e.g. fungal) or prokaryotic cells inside the root tissue sample?

Welcome to Biology.SE! I did an [edit] that I think improves the readability of your question (e.g.s: your use of "begets" didn't make sense to me, and "worst" means most negative, which feels ... unnecessarily subjective) . Feel free to make more changes if you feel I've altered your meaning.  ——— Please also take the [tour] and then go through the help pages starting with [Ask] questions effectively on this site. Thanks!

@Rob, I'm unfamiliar with BGPA and microPAN, but I've used Roary and PanPhlAn. Some questions so that I can better understand your system: What is the average size (+deviation) of these 52 genomes?  Are these draft or finished genomes?  If draft genomes, how fragmented are they (how many scaffolds, on average)?

@mgkrebbs I would exclude that as the process of binning during the assembly should have taken care of that

@Dirigible The average size is 5.7 MB with SD of 1.2. I did not process them myself, but they are drafts, with an average of 76 scaffolds. However one of the genomes is almost double in size compared to the others and I believe I should probably discard it.


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What is the difference between floral primordia and floral buds?
As we know an axillary bud differentiates to form a floral bud, but what is a floral primodium?

Welcome to Biology.SE! I made some changes in your wording — please [edit] if you think that I've changed your meaning. Please note that we 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). ——— Finally, please take the [tour] and then go through the help pages starting with [Ask] questions effectively on this site. Thanks!

A primordium (plural: primordia) is the first recognizable manifestation of a biological structure. In the case of a flower this will be a small meristematic bump typically at the periphery of a shoot apical meristem.
In contrast, a flower bud is generally used to describe the entire structure including the meristem and any associated structures (such as bracts) that can develop into a flower. This structure often goes through a period of dormancy.
Another way of saying this is that, in the context of a flower, a primordium is a group of meristematic cells that has not yet formed any lateral structures, while a bud contains a meristem and its associated lateral structures. Note however, that I believe I've seen bud used as a synonym for primodium in some cases.
Another difference is that primordia are (usually) microscopic structures, while buds are (usually) macroscopic (visible to the unaided eye) structures.


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What is the name of this insect? It is from Punjab, India
What is the name of this insect? It is from Punjab, India.

It seems to be a bug that belongs the family Rhyparochrominae from the tribe Myodochini.
https://species.wikimedia.org/wiki/Myodochini
There are too many species for an inexperienced person like myself to know which particular one this photo belongs to.
These species I believe are known as seed bugs.

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

I found a number of images via Google Image Search

@MattDMo none of those photos in your Google Image search were A.hui (at least in the first few hundred) There were all Araneus diadematus or A.clerk or other common Araneus species.

@Noah It would help to know what characteristics you might be looking for, and maybe a 'why' would help. We don't know if you are interested in, say, the what colour they mainly have, or whether it is has genetic similarity to another species, or its evolutionary phylogeny, or something else.

@JimN I apologize for not specifying in advance. The initial interest was precisely in the appearance, including it's color. That is why I initially tried to find photographs.

Welcome to Biology.SE! In the future please [edit] your question rather than clarifying in the comments — comments are ephemeral and not read by everyone so essential information should not be included here. Please also check to make sure the changes I made are consistent with what you intended and make changes as needed. ——— You may also benefit from taking the [tour] and then going through the help pages starting with [Ask] questions effectively on this site. Thanks!

These pages cite papers that mention A.hui:
https://www.gbif.org/species/2160156
https://wsc.nmbe.ch/species/2910/Araneus_hui
The World Spider Catalog (WSC) offers papers to their users for free, and it is a free registration.
Browsing through the second pdf on the WSC, here is a sketch of the dorsal (top) view of the species:

The paper is primarily written in a language I cannot read.
The specific paper (book?) is:
Hu, J. L. (2001). Spiders in Qinghai-Tibet Plateau of China. Henan Science and Technology Publishing House, 658 pp.
658 pages is quite volumnous. The title of the paper suggests we limit our search to Tibet. Searching for Araneus images on iNaturalist in Tibet, there is a picture of one Araneus that has not been identified to species level, but it resembles the abdominal shape as in the drawing in the paper:
https://inaturalist.ca/observations/51273647
But the abdominal markings do not match at all. If you expand the geographical bounding box of the search around Tibet, you can browse a gallery of hundreds of possible pictures.

If anyone can translate the chinese characters in the 1. 2. 3. points in the footnote of the image, that would be great!

Female back view .  2. external female organ  3.  external female organ dissection

@PolypipeWrangler Great, thanks!


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What is this strange sea creature we found on the beach?
We found this on a beach in North Devon, UK. I've never seen anything like it.
There's a yellowy-ball in the middle with 5 pointed shells attached to it, each of which seems to have a single "leg" coming out of the bottom. It almost looks like it's 5 separate creatures feeding on something, but they're pretty firmly attached. Perhaps it's some sort of egg-sac that they're growing from?
Does anyone know what this is?

You have a Dosima: Also known as a Buoy Barnacle. A gallery of observations of these can be found here:
https://inaturalist.ca/taxa/462188-Dosima/browse_photos
They are found in the coastal UK and Spain area, New Zealand, and east and west N.America:

(source: iNaturalist observations)
These barnacles attach themselves to things that float, and if they don't have access to one, they will grow one themselves. Your image looks like five individuals attached to a central float that one of them (or a dead relative) constructed.

Wow these things are fascinating!


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What are the advantages of long read sequencing for cancer oncogenomic research?
Currently I am using whole genome nanopore sequencing, Illumina short read and 10x linked read to study oncogenesis mechanisms of certain types of rare cancer. I am wondering about the advantages of nanopore sequencing in this field, e.g. fusion gene discovery, detection of large structural variants and copy number alterations (SV/CNA), as compared to Illumina and 10x?
I am struggling with generating my doctoral thesis proposal, so any advice will be appreciated!

https://www.nature.com/articles/s10038-019-0658-5

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Why is there a notch in the Na curve for an action potential?
Just out of curiosity, why does the Na curve dip down like in the figure below? I can't seem to find an explanation!

AP? Please do not use non-standard abbreviations in questions, especially in titles as they defy the indexing system this site relies on and confuse readers.

Please [edit] your post to include the source of your figures — you should always include reference information for quotes and images. Also, are you asking about the left panel or the right panel ? ——— I made what I believe to be corrections to your title (nudge makes no sense in this context) — please check that the new wording is consistent with what you were trying to ask.


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How can Southern blotting be used to establish gene copy number?
I am reading a paper on a certain marine microorganism that can eat alkanes and therefore might be useful for cleaning up oil spills, etc. This sentence struck me as odd (although I am sure that the answer is pretty simple):

Using the same probe, Southern blotting analysis showed that there was only one copy of alkB1 in the B-5 chromosome.

I realized that I don't know how Southern blotting can tell you about copy number. Can someone help me on this?

please [edit] your question to include a link to the paper, so we can see everything in context.

This method is commonly practiced. Atleast I see the people working with zebrafish transgenics using it.
When you shear the genomic DNA or do a restriction digestion, you are likely to get fragments of different sizes.
It is highly probable that the two (or more) locations harboring a copy of the DNA element are a part of fragments with different sizes. So on the blot you'll get two bands.
But as I said this test relies on probability that the two fragments are dissimilar in length. Therefore, southern blot should not be considered as an absolute test to determine copy number. Inverse PCR, FISH, etc can be used to determine copy number.


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Do lysogenic viruses only infect bacteria?
In the video sent by my teacher on viruses, the example he used for lysogenic viruses was a bacteriophage infecting a bacteria. When he was describing how the genetic material was incorporated into the host cell's genetic material, he said something along the lines of:

Now the genetic material is incorporated into the cell's chromosome.

My question is, did he describe it as one main chromosome because that was the example being used? Or do lysogenic viruses only infect bacteria?
I guess a better way of phrasing this would be, are bacteriophages the only type of lysogenic viruses?
Thanks!
evamvid

Bacteriophages are the only viruses where this phenomenon is called lytic and lysogenic cycle. There is a similiar phenomenon in humans (and other mammals as well) which is called "endogenous retrovirus" and is pretty common.
For humans, there are estimations that something between 5 and 8% of the human genome are made of endogeneous retroviruses. See these two references:

Long-term reinfection of the human genome by endogenous retroviruses.
Endogenous Retroviruses and Human Evolution

Otherwise I can recommend reading the article on "Endogeneous retroviruses" in the Wikipedia, it is pretty extensive and has a lot of references.

This is really a question of semantics. Yes there are endogenous viruses in eukaryotic cells, but is the term lysogeny used to describe this situation in practice? (I don't think it is.)

Now that you ask direct, no I don't think so. I think this was discovered with the Phage Lambda in bacteria. I will edit the answer.

I'm confused -- the terms 'lytic' and 'lysogenic' don't apply if the host cell isn't a bacteria?

Obviously it is not used outside the context of phage-bacteria. Although endogenous viruses in our genome are more or less the same.