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Mathematical periodic turns in DNA
Today our college professor gave us a mathematical biological challenge in DNA. He challenged us to find the pattern in which DNA follows the following equation in its periodic turn. How can we crack this? Also,  forgive me if I have gone against community guidelines; it’s my first time posting a question.
Here is the equation:
$$2 \sum_{n=0}^\infty \frac{(-1)^n}{(2n+1)^2}$$

Welcome to Biology StackExchange! Can you please elaborate more on the context of your question? What is the overall topic in which you've encountered this expression? Was it DNA sequencing, X-ray crystallography ...? What is a "periodic turn in DNA"?

A hint is that you don't have an equation, you have an expression. So you could rephrase your question as, what does this expression equal to, in the context of DNA structural biology? (I say it's a hint but to be clear; I haven't figured out the answer. Is it actually related to sequencing as you tag?)

My personal opinion is that we'd need a bit more context for this to be on-topic here; we're not after solving riddles and puzzles but about understanding biology. So, if you want to understand why a particular expression is used in some particular biological context, that would be very much on topic.

Thank you, @Domen, The topic at the instance was DNA sequencing; that is why I tagged DNA- sequencing, though the challenge is out of unit course work, as the college professor indicated. It is an expression. I have rephrased the question to English as a secondary language. At that instance, he described how a mathematical transformation can describe the turn from a set of base pair nucleotides to another and inverse periodically; he talked about a sinusoidal wave pattern as an example; he wrote the expression.

I would start by plotting the expression as a function of n if you don't have an intrinsic intuition of what it would look like. Then I'd check your language and terminology carefully, it seems like a lot is being lost in the translation. Phrases I'd check carefully would include "in its periodic turn" and "DNA follows".

If it's of any help $(-1)^n$ will flip-flop between $+1$ and $-1$. Is there anything in DNA that cycles back and forth like that? $-1 \leq \sin \theta \leq +1$. The denominator has $2n + 1$ which always evaluates to an odd number. The first term in the series is $1$. The second is $-1/9$. The third is $1/25$. The fourth is $-1/49$. We're, it seems, converging to "something".

To anyone wondering, the value of the expression is $2K\approx 1.832$, where $K$ is the Catalan's constant.

@Domen, while researching the Catalan’s constant I found out that it is used in calculating of volume of the complement of the Borromean rings. where else physical instances of the Borromean rings have been made from linked DNA molecules.


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Can someone recommend a recent book on cytoskeletal proteins? Most preferably similar to "Guidebook to the Cytoskeletal and Motor Proteins" from 1998
As in the question, I'm looking for such a book, that will give an overview of the topic from general perspective, with some "branching ideas", and references to literature about them. As for the book I mentioned, I accesed some fragments of it by uni network, and I hope it can serve as a reference of what I'm looking for.

source: Stack Exchange

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

sort: votes


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How fast could the Amazon rainforest regrow after deforestation?
We hear a lot about clear-cutting of the Amazon rainforest and how that affects climate change. However, are there any studies on how fast areas of rainforest can regrow or the ecosystem can recover if left alone after logging or slash and burn agriculture? It is often discussed how many ecosystems can rapidly recover after human exploitation stops (e.g., temperate forests). However I don't know if that would apply to the Amazon because rainforest soils are so nutrient-poor after slash and burn agriculture.

depending on the type of deforestation possibly never. slash and burn rainforests often don't recover.

Plants can regrow in a matter of weeks, months, years, depending on species. However, I encourage you to review secondary succession as well as second growth forests vs old-growth forests. All forests are not created equal. Just b/c plants regrow, doesn't equate to the Amazon "forest" (in its current state) having returned. Its current (perhaps already former) state will likely never regrow (in fact, there is almost 0 chance). But any similar analog would take 100s or more likely thousands of years to establish.

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Will diffusible protein aggregates coated in cell-free nucleic acids near a depolarizing neuron's soma diffuse along the axon to synapsing neurons?
Edit in response to feedback in comments requesting specific details, etc.: Will aqueously diffusible protein oligomers and protofibrils coated in cell-free nucleic acids in the aqueous interstitial space near the neural soma of a cluster of long-projecting hippocampal pyramidal neurons diffuse along the length of their axons (i.e., parallel to the velocity of the axon potential) if the neurons depolarize, causing them to migrate from near the cluster of hippocampal pyramidal neurons proximal to the group of neurons their axons are synapsing with in a neocortical association cortex as part of the default-mode network?
To clarify a commment, we already have evidence (most of it already published) that these aqueously soluble and diffusible nucleic acid-coated protein oligomers and protofibrils do accumulate significantly in the cerebral cortices (and probably the hippocampi and entorhinal cortices too) of patients with the disorder we study  compared to those of control individuals who passed away without this disorder. However, we do not know if these particles diffuse stochastically with no net vector, or whether they might migrate in specific directions under some circumstances, which could promote inter-regional seeding of these aggregates. This is not something we intend to build.
I think nucleic acids (and proteins) diffuse in a partially charge-density dependent manner through aqueous spaces in a voltage gradient. For example, Bass and Weintraub found that RNA duplexes migrated further than their constituent RNA monomers did on native 4% polyacrylamide gel electrophoresis (PAGE) (1). RNA duplexes have a higher mass than monomers, but they have approximately twice as much charge density. As they wrote, "RNA was extracted from these oocytes and embryos and analyzed by electrophoresis in a native 4% polyacrylamide gel. This gel system
easily resolves the faster migrating duplex RNA (D) resulting from the hydridization of sense and antisense CAT RNA from nonhybridized
monomer RNA (M) (Figure 1)." Below is their Figure 1 (A) showing the gel in question, with the legend stating it is a native gel.
As far as I understand it, native (i.e., non-denaturing) PAGE is a somewhat ideal model of the aqueous diffusion of small charged particles. Polyacrylamide mixed with water forms a gel with small holes in it. Molecules are free to diffuse in the aqueous phase, but they have to pass through these holes to migrate far. Negatively charged particles are pulled  towards the positively charged electrode (anode). SDS-PAGE is a common variant of PAGE wherein proteins migrate according to their size, because they're denatured and coated evenly with the negatively charged chaotrope SDS, making their charge roughly proportional to their size.
Here is a GIF of a depolarizing neuron to help visualize the question:

As a simplifying assumption, let's say it's improbable that the nucleic acid-coated protein aggregates will cross the plasma membrane. In reality, oligomers of this particular protein, and structurally and functionally analogous virus-like particles, can cross the plasma membrane primarily via heparan sulfate proteoglycan-mediated macropinocytosis, and secondarily via clathrin-mediated endocytosis. Whereas, soluble fibrils of this particularly protein do not get taken up by cells (at least the larger fibrils). I would rather not provide citations to these claims, as it's not necessary to understand or answer the question, and doing so would give away what I'm working on specifically, which I would rather not do publicly yet.

Bass, B. L. & Weintraub, H. A developmentally regulated activity that unwinds RNA duplexes. Cell 48, 607–613 (1987).

Original post: Let's say there's a small, densely negatively charged object just outside the cell body of a neuron. It is freely diffusible in the aqueous interstitial space. Let's say it's improbable that it will cross the plasma membrane to enter the neuron. Then the neuron depolarizes. Is enough of a voltage gradient (and electromagnetic field) created by deplarization that it will cause the negatively charged object to diffuse? If so, in what direction? Will it diffuse down the length of the neural axon as it depolarizes?
What if the object can cross the plasma membrane? Then will it likely do so?
This object diffuses far in a native polyacrylamide gel electrophoresis (PAGE).

Welcome Odin. Please take our [tour] and read-up in the [help] particularly the [ask] section. We require one single clear question per post, and for you to show your research when posting. At the moment you've several vague questions - can you please [edit] to clarify what "object" you might be referring to, what you mean by "diffuse down the length of the neural axon as it depolarizes" and why you think electromagnetism might be a major factor, then add your research.

This is purely hypothetical, ions travel through specialized channels and pumps and typically 'objects' whatever that may be don't travel passively across the membrane. I suggest to focus the post into one specific question (and not a bunch of unrelated ones) and use a relevant, plausible situation instead of talking about hypothetical objects with ill defined characteristics

Hi Jiminy and Alice, thanks for the feedback. I have updated the post accordingly. Please let me know if you have any further feedback.

My short answer would be "no I don't think whatever you are planning will work". The longer answer is, if you want to engineer something new, you have to be prepared to build and test it, and if you don't know what you're doing you have to be prepared to hire people who do, not ask on StackExchange.

@BryanKrause This is naturally occuring, not something I plan to build. We know that these aqueously soluble and diffusible nucleic acid-coated protein oligomers and protofibrils do accumulate to some extent in the cerebral cortices and probably hippocampi and entorhinal cortices of patients with the disease I study. The question is simply, will they diffuse randomly, or in particular overall direction, e.g., when outside a cluster of long-projecting pyramidal hippocampal neurons with axons synapsing with distant neurons in a neortical association cortex as part of the default-mode network?

Okay, do you know that if the neuron in your diagram is a pyramidal cell you've drawn the depolarization along a dendrite?

@BryanKrause That's just a GIF of a depolarizing neuron I found online to help visualize the voltages created by an action potential. It's not of a pyramidal neuron.
We do not know that pyramidal neurons would be involved in this specifically. It just seems somewhat likely since they appear to degenerate especially severely in this disease, and they often synapse relatively long distances. Commenters seemed to want more specific details, so I added that in too in hopes of making it clearer.


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Can anyone identify this please?
I found this in a toilet in the UK. Any ideas what it is please?
Thanks

A Flat-Backed Millipede.
The Woodland Trust has an article that's much more informative than the Wikipedia page:

Via Wikipedia, CC By-SA 3.0, Ratingen, Germany.
They're:

This species has a long, flat, segmented body with a large number of
legs. It is orangey-brown in colour and measures around 2cm in length.

Herbivores, normally found in woodland where they live under leaf-litter.
Widespread throughout the UK.


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Correlation of Meselson and Stahl with “multifork” replication in E.coli
Because of the limiting value of the rate of DNA replication, rapidly dividing E.coli use multiple replication forks [1][2]. Thus, DNA replication of one generation has already begun in the previous generation.
To me, this poses a problem in understanding the results of the Meselson and Stahl experiment[3]:

Source Biology, Textbook for Class XII National Council of Educational Research and Training (https://ncert.nic.in), NCERT Publications (version: November 2021 Agrahayana 1943) https://ncert.nic.in/textbook/pdf/lebo105.pdf
Shouldn’t the DNA from generation I have somewhat more of 15N DNA, as its replication started when the E.coli was still in the 15N medium? Is that the case or is there another mechanism?

J. Mol. Biol. (1968) 31, 519–540

The EMBO Journal (2007) 26, 4514–4522

Proc. Nat. Acad. Sci. (1958) 44, 671–682

It is sometimes considered that the result was an artifact for a reason similar to that which you mention. However, it happened to be correct in its conceptual outcome, and was not rejected by subsequent better-controlled experimental tests.  This is pretty standard for experimental science. The result would not have been so widely believed if it were not that everyone else's data agreed.

Interesting the paper you reference. However it is not clear to me what you mean by "everyone else's data agreed"? "Subsequent results confirmed or were consistent with"?

@David yes, more or less that. If we are getting into the philosophy of science, we could say that their results were paradigmatic, or that the results were subjected to confirmation by various other experiments. But I think that going into epistemology of science is probably more than we require to say that the scientific community is more likely to accept results that are consistent with everyone's own private data.

What evidence is there that such private data existed?

I voted for this answer on the basis that it linked to an article (actually a book review) that suggests that the result is an artifact of shearing when the DNA was forced through a syringe before ultracentrifugation. However I disagree with the social/historical remarks. 1. There was no reason to disbelieve the results on the basis of multiple replication forks because this was 1958 and nothing was known about them and certainly not the rate of DNA replication. 2. They were certainly  not consistent with conservative replication. 3. They fitted with the Watson/Crick model.


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In the context of GWAS we have an alternate allele and a reference allele. Why do we only have one possible alternate instead of three?
I recently started analyzing a GWAS summary dataset. It has a column for the reference allele in which it mentions the base in the reference genome.
There is another column for the alternate allele (or the SNP). Each reference allele always has one alternate instead of three. I have read responses to this question on other forums and the answer usually goes like this:

The other two alternate alleles are very rare so not seen in the population that often.

I find this hard to believe.
On average every person has 3,000,000 SNPs (1 in 1000 bps). Does that mean in all the 3 million cases the individual always has that one alternate allele? Let's take a million individuals, do all those 3 million million SNPs always have that one alternate allele?
This just seems very unlikely, even if those alleles are very rare we have so many occurrences that we should be seeing them.
I am new to GWAS and have taken genetics courses during my undergrad. Could someone provide a satisfactory explanation? Sometimes I feel we are doing this as an approximation to make further statistical/computational analyses easier.
Edit: Although I am asking this in the context of GWAS, I have seen it in many other situations. It is sometimes referred to as the minor allele.

Estimates seem to be around 45-60 de novo mutations in an individual, e.g.: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9550265/
That means the other 2999950 mutations are inherited, they're shared with a parent and their parent and possibly siblings, cousins, so on. They won't have inherited just some random base pair at that location, they will have inherited exactly the same one as all those other people share with them.
Additionally, there are some SNPs that are going to be selected against. Any SNPs that are lethal will never be inherited, for example.
So, overall, I don't find it that surprising. Less common SNPs that haven't spread in the population are unlikely to be found in any sample of thousands or hundreds of thousands of humans in a population of billions. So, they may be out there but never observed. And unless they are observed they aren't very useful for the things people want to use SNPs for.


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Multispectral photography and biology
I recently made a post to the Photography site at StackExchange and I was told this might be a better forum.
My original post can be found here. From a high level I have a friend who is beginning a research project and I suggested possibly using ultraviolet light to identify individual specimens of fish similar to what is done here.
The question I asked there had to do with using multispectral images to try and mimic mantis shrimp vision to see if there was any biological signal that is invisible to the human eye. The hope would be to filter out individual wavelengths to see if there are 'outlines' that are visible to the shrimp but invisible to humans and parse out any potential signals.
I found this paper discussing a proof of concept that mimics this vision but I was also curious to see if there has been any research done already to take multispectral imaging to match color hues that are visible to certain species that are not visible to humans. I've been able to find to some resources for multispectral image data files but I have not been able to find much research done in a context similar to what is described above, i.e. trying to capture images that would be visible to certain animals but invisible to humans.
Does anyone here have any good resources or leads to investigate work that's already been done?
Any feedback is appreciated!

You kind of got your answer there; It's doable and it's being done. Is this actually something you want to do or are you just curious? Do you have the funds to do this? Are you ready to carry out this research and with whom would you do it? Seems to me you need to speak with the folks who are actually doing this with something fairly concrete in mind, but that's only one opinion.

Say it's curiously for now but it could change into something actionable later.
I'm not actively involved in research at the moment but I could be doing some consulting and assistance for one particular project. It would almost certainly not use be using multispectral photography. After reading a bit deeper about photography and having it brought to my attention that cameras can capture light that would match frequencies certain animal eyes are attuned to but not human I was hoping to check in and see if anyone has good resources on work that's been done. I hope you can forgive the naivety.

It's not naivety at all nor is it a bad question (I upvoted it); lots of people are just genuinely curious about Biology, and that you've done some searching yourself says a lot that's positive. My thoughts (fwiw) I'm not familiar with anyone here doing that kind of research, or having a deep interest in it. I hope someone answers, but I kinda doubt anyone will, because we - well, most of us - have jobs, and mere curiosity questions get left behind because searches take time. If there's someone who's knowledgeable or excited about the field, you'll get an answer. If you don't, you'll know why.

Having said that, there are some neurobiologists here who might be able to answer, and one of them seems particularly interested in sight, so who knows? In advising you to talk to those who are already doing this, if it's just curiosity, you may or may not get an answer. If it were a collaboration you wanted to do, you would be taken more seriously. (When I was in research, it was pretty cut-throat, and people kept their methods close to their chests, but that was ages ago.) Also, people at conferences/profs are generally more generous and helpful. Sorry I can't help; my field is medicine.

*neuroscientists, duh.

It seems like there are two pretty different things here; one is imaging into the UV (or infrared) relative to human vision; those things are pretty common by themselves for various purposes. Then there's oversampling the visual range, which doesn't actually reveal any "new" or invisible colors as in new wavelengths, but does add to the ability to resolve similar wavelengths as clearly distinct, which might help draw out certain patterns.


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Who demonstrated that phage lamba is integrated into the host chromosome?
In the 1950s, the Lederbergs (Esther and Joshua) demonstrated the presence of phage lamba in Escherichia coli K-12.
But who demonstrated that this virus is integrated into the host's genome? Is there a paper related to this discovery?
Thank you

This may work better on our [hsm.se] site than here, but see what others say.

@JiminyCricket — In principle you are probably correct, but looking at SE HoS for the first time I was not impressed by the biological content, eg Crick & Watson discovering DNA, in a title left unchallenged for years. I have tried in my answer to indicate the science as well as the man, so it falls better within our remit. I should have perhaps extended my answer, but would need more time to read round the subject. Fascinating stuff, though .

Allan McCulloch Campbell (1929–2018)
In brief, Campbell was responsible for the hypothesis that lysogenic phages physically integrate into the DNA of host bacteria (rather than being laterally ‘attached’ or ‘synapsed’, as was the prevailing view at the time) — part of his “Campbell Model” — and he was responsible for identifying a particular gene, h, as necessary for the integration of bacteriophage lambda. This relied to a large extent on observations on mutant phage incapable of lysogeny, and bacterial strains that were resistant to phage.
An excellent place to read about how he established this is his own account in Annual Review in Genetics (2007) 41 1–11 (subscription required). This shows how ideas in science often develop as a result of many experiments and their interpretation within new intellectual frameworks, rather than a single ‘historic clincher’.

If there is anyone who is unable to obtain institutional access to the review and is very keen to read it, I suggest they post a comment and I'll see what can be done to help.

Thank you for your in-depth answer.

Thank you for the hint. I have read the paper, but it states that the Cmpbell model is a model. IS there experimental evidence for the integration of lambda? Southern blot perhaps? or microphotographs?

@Gigiux — Southern published his blotting method in 1975. The Campbell model dates from 1962. The methodology of molecular genetics was initially genetic, with the molecular aspects added only gradually. When direct methods were not available science advanced through the interpretation of indirect experiments.This is not easy for younger scientists to appreciate, but the intellectual beauty of such experiments often makes a stark contrast to contemporary brute-force science. I won't have time to go into this in more detail for about a month, as I shall be away, but I may return to it anon.

thank you, I'll be waiting. In the paper, Campbell stated that Jacob and Wollman proposed a synaptic model where the phage chromosome was closely associated but separate from that of the host, like that of EBV. The question is: who gave the final proof that lambda was indeed integrated?


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Chains of ganglia on each side of the nerve cord belongs to the spinal cord
One of my textbook says this: "A double chain of ganglia on each side of the nerve cord belongs to the spinal cord."
But the diagrams I saw on internet depict only one dorsal root ganglion.
I am unclear which is wrong my textbook or the diagram.

There are only single dorsal root ganglia on each side of the spinal cord, within the dorsal (sensory) root of the spinal nerves.  If it is specifically referring to dorsal root spinal ganglia, the textbook is presumably describing the bilateral anatomy as a 'double chain'.
In addition, the dorsal root ganglia develop in the embryo from neural crest cells, as opposed to neural tube cells. Thus, the spinal ganglia can be considered grey matter of the spinal cord that is translocated to the periphery: that is, they 'belong to the spinal cord'.
Alternatively, the textbook may be referring to the Sympathetic Chain of Ganglia, a 'double chain' whose two components lie either side of the vertebral column and spinal cord, and consist of nerve fibres emanating from its ventral roots.  Any decent textbook of Anatomy should be pretty clear about this.
For your interest, 'Wikipedia' describes the latter in part as follows:
Sympathetic Chain Ganglia.
The bilaterally symmetric sympathetic chain ganglia, also called the paravertebral ganglia, are located just ventral and lateral to the spinal cord. The chain extends from the upper neck down to the coccyx, forming the unpaired coccygeal ganglion. Each ganglion within this chain is either cervical, thoracic, lumbar, or sacral. Preganglionic nerves from the spinal cord synapse at one of the chain ganglia, and the postganglionic fiber extends to an effector, a visceral organ in the thoracic cavity, abdominal cavity, or pelvic cavity.
There are usually 22–23 pairs of these ganglia (which is interesting number in view of chromosomal numbers): 3 in the cervical region (cervical ganglia), 11 in the thoracic region (including the stellate cervicothoracic ganglia), 4 in the lumbar region and 4–5 in the sacral region, collectively known as the 'Sympathetic Trunk'.

I hope this helps to clarify things in an area which is clearly problematic to describe without a precise anatomical diagram.

Can someone please explain the down-vote: is the answer incorrect or incomplete?  And voting like that without explanation is akin to assaulting someone on a public street for no apparent reason.  Very cowardly.  State your case sir.


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Doubt in Pedigree chart : why can't the attached pic be autosomal recessive?

Why is the attached Pedigree chart can't be called as autosomal recessive also?

Pretty similar to this one: https://biology.stackexchange.com/q/114172/27148

But in there they speak about 2 families, And it's more detailed. My question is simple.

Not really, it's exactly the same. What assumptions need to happen exactly out of the things unknown for this pedigree to result from an autosomal recessive trait? What assumptions are necessary for it to result from an X-linked trait?

The premise of your question is wrong. This pedigree can very well be explained also with the autosomal recessive inheritance, and there is no way of knowing whether it is autosomal recessive or X-linked recessive purely from this pedigree.

Indian English “doubt” does not work in International English, and is not generally understood. Use “question” or “problem”.

@domen can't we decide by writing and seeing out the possibile genotype and finding out the progeny. If I am wrong ,can you correct my ideology?

@david can you say in which part you can't understand the question? I can clarify

I am not interested in the science of your question, I am only trying to help you communicate it in International English. I have suggested words to replace it and suggest you consult an online dictionary such as Merriam-Webster that will give examples of usage of "doubt": https://www.merriam-webster.com/dictionary/doubt.

@SanjayS, try it yourself! Write down the genotypes, and you will find out that the pedigree can be explained by either of the two aforementioned inheritance patterns.

@domen yeah doman I have done that , and let me attach my image in the question

Great, you've find one possible set of genotypes (not the only one though) which is compatible with the hypothesis that the inheritance is autosomal recessive. So you've answered the question yourself :)

According to me this chart applicable for both autosomal recessive and x linked recessive. I just wanna confirm you guys whether this is correct or not?

Yes, but consider what initial unknowns have to be for that to be the case and how reasonable/likely that is. In this case your autosomal recessive chart only works if the two unknowns (numbered 2 and 3) happen to be carriers. If carriers are rare in the population, that might not be reasonable.

Ok Bryan thanks for your reply


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Is there a continuum between analogous and homologous traits?
How closely-related do two species need to be for a trait they share (say, bipedalism in mammals) to count as homologous (divergently-evolved) as opposed to analogous (convergently-evolved)?
In other words, is there a sharp dichotomy between analogous vs homologous traits (and if so, how is the cut-off criterion defined)? Or is there a continuum among them, and if so, again, on what bases is this defined?
Does said trait need to maybe "skip" a given number of intervening species on the tree of life for it to count as convergently evolved (in the example above: there being many mammals species in between humans and kangaroos, both bipedal)? Or is this somehow all about (continuously expressed) phylogenetic distance? Googling/chatGPTing didn’t really enlight me, hence this question.

The wings of bats and the wings of birds are analogous; their shared ancestor had no wings, their other close relatives have no wings, etc. They are quite different in form and structure despite each being used for flight. But, they also both evolved from homologous vertebrate forelimbs. Their common ancestor has forelimbs, all of their close relatives have forelimbs, etc. Is this the sort of thing you're asking about?

It is, but since it is a rather classical example of convergent evolution, I'm still not clear I understand what is the hard criterion that enables one to classify a trait as being homologous OR analogous between two species in more border-line cases where perhaps less is known about whether the LCA shared that trait or not.

I think the "close relatives" (as you note above) having or not having that trait gets us closer to the answer I was looking for, as it essentially invokes philogenetic distance, although, again, it's unclear just how many related species one has to count.

If nothing is known about the common ancestor I don't think anyone would bother claiming a trait as homologous or analogous, but you can often infer things about the common ancestor from just two species you are looking at plus a member of an outgroup. If, for example, some mutation conferring a different function of a protein is present in two species and absent in an outgroup species that doesn't have that trait or mutation, you'd infer it's more likely that the common ancestor of those two species also had the mutation rather than the identical mutation happening twice.

Do you have some specific example to consider?

One example I had in mind (though maybe not the best) was the one mentioned in the question: bipedalism. One can find this trait in animals closely related to humans (e.g. other great apes; and thus argue it to be homologous in the context of that comparison); but one can also encounter it in distantly related animals, and thus argue it to be analogous. Am I making sense? (I'm no evolutionary biologist - and it shows!)

In that example I think you'd say that bipedalism (to the extent that other great apes are bipedal; some would argue they are not even if they occasionally go up on two limbs) is homologous among apes and analogous with, say, theropods. There's no conflict in saying that. Just like wings in birds and bats are analogous, but wings are also homologous among birds. I wouldn't describe that as a "continuum".

I still can't seem to express what exactly my doubt was, but in any case I think I'm clearer now on the topic. Thanks again!


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What's the difference between a mitogen and a cell cycle stimulant substance?
It's been a week since I got this question asked and I still have no clue. I have thought that the main difference would be that the mitogen induces mitosis, and the cell cycle stimulant substance accelerates the cell cycle. I don't really know, to be honest.

What do you mean "got this question asked"? Was it part of an assignment for a course? In that case I'd look at the course materials or ask your instructor. If not, why do you need this answer? Where are you seeing these terms used and where are those usages in conflict? We expect questions to include some background information necessary to identify the specific question asked and the level of understanding it is asked with. "Cell cycle stimulant" is not something I find many hits for on e.g. Google Scholar, is this a translation?

Yes, it is part of an assignment, we don't really have course material, and the question was asked precisely by my instructor. The use of these terms is in the cell cycle topic. I am sorry that I did not give enough context to answer my question. The concrete question was "What is the difference between a mitogenic substance and a cell cycle stimulating substance?"

You have an instructor and a course and no materials? That doesn't really seem to set you up for success. I'd ask your instructor what they mean by this. It doesn't seem to be a phrase other people use.

Yeah, I noticed that too while searching about those terms. I'm gonna ask him tomorrow about this, because it's really confusing. I really appreciate you for taking part of your time to answer my question.

Sounds good, curious to hear what you find.


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How to falsify claim that 2 samples are from different individuals?
Given 2 sealed, air-tight vials1 containing approximately 200 grams each of dried mammal blood.  Task is to prove they are (or are not) from the same individual.
What steps would you take?
Note:

Vials have been stored in the dark and at a relatively constant temperature between 16C and 23C.
Vials have been stored for many decades.
Money is no object.
You have 1 year's time.
If there is more information you want regarding the samples, please comment with your question.

Edits to respond to questions:

My sincere apologies; I was unaware one needed to show their prior work before asking a question.  I've read numerous articles on forensic DNA profiling, human genome sequencing, and several
companies' websites who provide DNA sequencing services.  Yes, clearly it's easier to prove a difference.  Forensic DNA profiling frequently uses a tiny fraction of genome, such as measuring restriction fragment length polymorphism (RFLP) or short tandem repeats (STR).  RFLP appears to be about 95% reliable.  My goal is closer to 99.999% reliable.
For my purposes, I'd like the proof to be extremely good, much better than the 95% reliability of RFLP.  Indeed, identical twins would be a problem in general. In my specific case identical births won't be a factor.
Thank you for mentioning spurious results in whole genome sequencing. It's something I hadn't read anything about. Agreed, blood type first, etc.  But imagine:  all simple tests like blood type match perfectly.  Now we're down to DNA and anything else (I admit ignorance) that might differentiate.  As above, forensic RFLP DNA fingerprinting is only 95% reliable; not good enough for the imaginary billion dollar bet I'm making on the results, if that helps?

Possible answer:  As a non-biologist, I imagine being able to extract complete2 DNA from both samples, fully sequencing it3, and then comparing4 the results of the sequencing.  Is this even close to correct?

Footnotes:

The blood samples were taken, dried and sealed with proper caution to avoid contamination and ensure long-term storage.
I have no idea how this might be done, but it appears that DNA can be extracted from some kinds of dried blood from what I've read.
Sequencing DNA appears to be nearly a commodity lab product these days from Google searching.  Correct or no?
I assume there is some viable way to compare the completed sequences' data once obtained, but have only found articles mentioning techniques for doing so with small segments of the larger full sequence.

Resources I've read:

https://en.wikipedia.org/wiki/DNA_profiling
https://en.wikipedia.org/wiki/Microsatellite
https://www.findlaw.com/criminal/criminal-procedure/how-dna-evidence-works.html
https://sequencing.com/
https://med.stanford.edu/news/all-news/2022/01/dna-sequencing-technique.html
https://www.genome.gov/genetics-glossary/DNA-Fingerprinting
https://www.nature.com/scitable/topicpage/forensics-dna-fingerprinting-and-codis-736/

Your question got a few downvotes, likely because you haven't presented any prior research (which is expected on this site). As a start, you can read DNA profiling. Note that full-genome sequencing is very expensive and labourous, and most of the times unnecessary. Also note that it is significantly easier to prove that the samples belong to two different individuals (you just have to find an observable genetic difference), while it is more difficult to reliably show the samples belong to the same individual.

What are the standards of "proof" that you're looking for? (Identical twins could scupper your plans, as in many murder mysteries)

Whole genome sequencing is likely overkill, and also has potential to generate spurious results, depending on how it's analyzed. You might want to spend a little time googling forensic DNA testing methodologies, including their statistical probabilities of generating a false match (or mismatch) under different scenarios. You could also take a progressive testing approach, starting with some simple tests to eliminate any obvious clues. Do they belong to the same blood type group? If so, what's the next test you would perform?


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Best reference book for basic concepts when working with bioinformatics
I'm starting to study Bioinformatics, I already have basic knowledge of Biochemistry and Genetics, but I want to buy a reference book, to use when I forget a concept (I'm a Computer Science student, not a Biotechnologist).
I have already had contact with the following two books (for basic concepts):

Molecular Biology of the Cell, Alberts;
Principles of Biochemistry, Lehninger.

Which is better for my use or do you have another recommendation?
I prefer a generalist book, which covers the basic concepts, and not a Bioinformatics book, which covers basic concepts in one chapter.

bioinformatics has its own stackexchange fyi. 2. bioinformatics is a huge field. what is the part of it that you want to know about? sequence alignment/assembly? structural modeling? biostatistics/clinincal trials? population genomics? generic data analysis in a biology context? pharmacology and drug development? high-dimensional data analysis./ multi-omic data integration? metabolomics? theoretical biology? energetics? imaging? microscopy? each of these might have its own foundational text! specificity is super important.


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What does it mean when observed genotype frequency is different from expected genotype frequency in Hardy-Weinberg equilibrium?
As I understand it, if a population is at Hardy-Weinberg equilibrium, then the genotype frequencies should be $$p^2 + 2pq + q^2 = 1,$$ given the allele frequencies of $p$ and $q$, which you can figure out if given the number of homozygous recessive individuals in a population (such as 1/10,000 babies are born with PKU, so $q = \sqrt{1/10000} = 0.01$).
What I don't understand is what does it mean if your expected genotype frequencies do not match your expected frequencies. For example, here is a textbook problem where there are two alleles, $V$ and $v$. There are 16 $VV$, 92 $Vv$, and 12 $vv$ individuals.
If I did this right, that means

$V = (16\times 2 + 92)/240 = 0.516$
$v = (92 + 12\times2)/240 = 0.483$

and then the expected frequencies are:

$VV = 0.516\times0.516 = 0.266$
$Vv = 2\times0.516\times0.483 = 0.498$
$vv = 0.483\times0.483 = 0.233$

which are different from the observed frequencies:

$VV = 16/(120) = 0.133$
$Vv = 92/(120) = 0.766$
$vv = 12/(120) = 0.1$

The book says that the population is evolving because the observed frequencies are different from the expected frequencies. What exactly does that mean though? How can you tell if the population is evolving if you don't even know the allele frequencies or the genotype frequencies of the next generation? The reason I ask is because I thought to disrupt the Hardy-Weinberg equilibrium means that the allele frequencies would change over generations, so could you say the population is evolving is you're only given the data for one single generation? I mean, you can get the same allele frequencies from both the expected and the observed genotype frequencies, so I don't know if the population can be said to be evolving. Maybe I'm understanding this wrong. Please help. Thank you all.
My related question is: Can you have no change in allele frequencies across generations, while in each generation, the observed genotype frequency is different from the expected genotype frequency. If so, does this still mean the population is evolving?

From Wikipedia, bold added by me:

In population genetics, the Hardy–Weinberg principle, also known as the Hardy–Weinberg equilibrium, model, theorem, or law, states that allele and genotype frequencies in a population will remain constant from generation to generation in the absence of other evolutionary influences. These influences include genetic drift, mate choice, assortative mating, natural selection, sexual selection, mutation, gene flow, meiotic drive, genetic hitchhiking, population bottleneck, founder effect, inbreeding and outbreeding depression.

Therefore, if you observe allele frequencies that do not match what Hardy-Weinberg would suggest, that means one of those other things is happening. Think of Hardy-Weinberg a bit like the "null hypothesis". You can't tell directly which of these is occurring, and multiple evolutionary influences can occur simultaneously.
We can think about a particular example, though. Let's say you have a case with a recessive trait where the phenotype of vv individuals makes them more likely to die. You would expect when you look at genotype frequencies to find them out of equilibrium with respect to Hardy-Weinberg: you'll find fewer vv individuals than you'd otherwise expect based on the overall rate of v alleles in the population.
It's important to consider sampling effects in your measurement, too. Your estimates will rarely match the Hardy-Weinberg frequencies perfectly just from noise in your sampling. You'll want some estimate of how likely it is that, assuming the population actually does follow Hardy-Weinberg, you'd get a deviation as large as the one you observe. That is achieved by performing a chi-squared test.

How can you tell if the population is evolving if you don't even know the allele frequencies or the genotype frequencies of the next generation?

You can tell because if the population isn't evolving (this statement means exactly that the allele frequencies stay the same) and mating is random then the allele frequencies would be equal to the Hardy-Weinberg frequencies. A bit like if you park your bicycle, go inside, and come back outside and see no bicycle there, you can infer that your bicycle has moved even though you didn't actually observe it moving. You may not be able to conclude whether it was ridden away, was blown by the wind, or picked up and placed in a truck and driven off, but just the fact that it's not where you left it provides information that something is happening besides the "null hypothesis" that bicycles left in a place stay there.


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In search of motivation (Examples from nature) for reaction-diffusion systems with a conservation law
I'm an applied mathematician with a huge interest in mathematical biology. While looking at  this paper, I came across with the following:

Examples of reaction-diffusion systems (1)-(2), falling into the class
of systems we are interested in, are for instance the Brusselator, the
Schnakenberg, the Gray-Scott and the Gierer-Meinhardt model coupled to
a conservation law coming for instance from ecology.

Although I googled a lot, I couldn't find any example/reference from ecology which satisfies the above. Since at the end of the day, I am simply a mathematician, I thought to ask the experts of that forum. Having a motivation can help someone gain easier intuition on the expected results, which is really important.
Question: What are some examples of reaction-diffusion systems, coupled to a conservation law, coming from biology? I'm looking for a rather simple reference or examples from daily life (if any).
Any help will be much appreciated. Thanks in advance!

Please try to use a descriptive title that makes it easy for interested people to recognize they'd be interested in your question.

Paper, Chapter

@BryanKrause You're absolutely right. I edited my title, hope that it's better now

@RoniSaiba thank you very much, I'll check that!

There is a whole book here from spatial ecology. there appear to also be some applications in biochemistry involving adsorption or consumption across a spatial gradient.


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Overlapping atomic radii in data of experimentally observed protein assemblies
I am looking at experimentally observed configurations of viral capsid proteins like that of the tobacco mosaic virus. https://www.rcsb.org/structure/6R7M
When taking the atom centers of a monomer and applying the transformations specified in the .pdb file, I get a structure where the VDW radii of different proteins overlap. I have tested a variety of sets of radii and it happens for all of them. I tested with Bondis radii, ProtOr radii and several radii taken from popular force fields (AMBER, PARSE, CHARMM).
I am wondering:

What is the least wrong set of radii to choose here and why?
Is there a popular way to resolve this?
The Clashscore depends on overlaps within a protein right? What radii are chosen for this measure?

Thank you in advance
Ivan

can you give us the chain ID, residue number, and atomID for the atoms in the .pdb file that are overlapping in the linked TMV structure? Is this something you've noticed in other structures as well, or just this one?

In the example behind the link, the chain ID is 'A' and considering two adjacent monomers transformed by the specified BIOMTs we get an overlap between Atom IDs 164 and 72 by 0.3 Angström for example, when choosing Bondis VDW radii for the atoms. There are around 20 of these overlaps in total.
So far every assembled TMV structure I checked has these overlaps.

Looking at the validation report for model 6R7M, we see that there are no symmetry-related clashes listed. (Although there are two clashes within the asymmetric unit, HA of ASP20 - HD3 of PRO21 and HG13 of ILE95 - HB2 of ALA111)
The relevant portion of the PDB's validation explanation page is here:

All-atom contacts within the ASU are calculated by the Reduce and Probe programs within MolProbity (Word et al., 1999; Chen et al., 2010). This method was developed to quantify the detailed non-covalent fit of atomic interactions within or between molecules (H-bonds, favorable van der Waals, and steric clashes). Since most such interactions involve H atoms on one or both sides, all hydrogens must be present or added (Reduce optimizes rotation of OH, SH, NH3, etc. within H-bond networks, but methyls stay staggered). At present, in order to ensure comparable scores between NMR and X-ray, hydrogen atoms are removed from the analysed structure, and replaced by a different set placed by Reduce in idealised and optimized nuclear-H positions. All-atom unfavorable overlaps ≥0.4Å are then identified as clashes, using van der Waals radii tuned for the nuclear H positions suitable for NMR (rather than the electron-cloud H positions suitable for X-ray).).

(bolding mine)
The main takeaway is that MolProbity does not consider that amount of overlap to be a problem. So to your second bullet point, I don't think anything needs to be resolved.
As for which radii should be used, I don't have good advice. It looks like that is still being debated. However, looking up the original paper for the MolProbity tools used by the PDB for validation, the radii for O and non-carbonyl C are 1.4 and 1.75 Angströms, respectively. That sums to 3.15, I measure 2.92 between the atomic centers, so slightly less overlap than you got.
My initial assumption was that these would be poorly-resolved residues near the edge of the macromolecule and that the VDW overlap would be due to fitting errors, but it looks pretty good to me:


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Why is phloem parenchyma absent in most monocots?
What evolutionary advantage did monocots get by losing this tissue that just seems to be storing food and metabolites?
I think this question has been asked before, but I didn't see an answer for that one


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How do you find the template strand for a sequence where start codon is in both strands?
Maybe I'm missing something very obvious but I can't seem to understand how to find the template strand given a sequence and its complementary strand if both strands contain ATG from 5' -> 3'. Consider the following example of a DNA sequence:
5′ TCAATGAGCTGCCTTCATTAA 3′
3′ AGTTACTCGACGGAAGTAATT 5′
I can find ATG in the top strand from 5' -> 3' but also in the bottom strand when reading it 5' -> 3'. I usually try to find the start and then know that it will have to be the coding strand, but I'm lost in this scenario.
The sequence is originally from an exercise where the given sequence has a mismatched A - A mutation. This is the original sequence:
5′ TCAATGAGCTGCCTTCATTAA 3′
3′ AGTTACACGACGGAAGTAATT 5′
If we check what would happen if either the top or bottom Adenine was replaced with a Thymine, we would get different types of mutations. This was just an example sequence I thought would be alright to set the stage for a start codon on both the top and bottom.

Welcome to Biology StackExchange! Can you please explain a bit more what these sequences are? Do you have a DNA sequence or mRNA sequence? Note that the coding/template strand identity is determined by the promotor for each gene separately! Without knowing the location (direction) of the promotor, you cannot determine which of the two strands is the coding one.

I see you edited the question and added "DNA". But still: Where did you get this sequences from? Have you read my comment about the promotor?

Is this some sort of contrived homework problem?

Maybe I'm misunderstanding something or the exercise was a bad example, but just in general, I have trouble identifying the template strand, and all the answers I can find tell me to look at directionality. But my question is: what if both strands have a start codon when reading from 5' -> 3'? Doesn't that mean both have 'correct' directionality? So how would I know which to pick? And in regard to Domen's comment, the location of the promoter is unknown for these problems, but we were told to identify an ORF for which I need to know which is the template or coding strand, right...?

In real life, you can't predict the start of a protein by looking for ATG.  in organisms, the shape of the DNA (which is based in part on sequence) determines where transcription or translations begins, because the shape of the DNA molecule determines where those proteins can bind.  This is not perfectly predictable.  In real life, you'd need to have some kind of verified annotation to know where translation will begin.  You'd have to be empirical.  You can't just look at a DNA sequence and know for sure.


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Why is the retention of ability to synthesize non essential amino acids of negative survival value?
In my textbook "Harper's illustrated biochemistry" chapter 27 it is written that

The existence of nutritional requirements suggests that dependence on an external source of a specific nutrient can be of greater survival value than ability to biosynthesize it. Why?
Because if the diet contains ample quantities of a nutrient, retention of the ability to biosynthesize it represents information of negative survival value, because ATP and nutrients not required to synthesize “unnecessary” DNA-even if specific encoded genes are no longer expressed.

I could not understand the part that I have emboldened.

Seems like a simple word substitution error in editing, and it should read ATP and nutrients are required to replicate the DNA even if that DNA is not expressed. That doesn't fix the argument, but maybe makes it easier to follow.

It’s a very dubious argument in my opinion.
Whenever I see a question on this list arguing that higher organisms could save energy and DNA by such-and-such a hypothetical construct I want to scream. Think ‘junk’ DNA, introns, gene duplication, plant polyploidy and goodness knows how many other apparently inefficient and wasteful aspects of higher organisms that should never have appeared if these arguments held true. And the invalidity of the underlying assumption — that higher animals are competing like bacteria for the most efficient growth — never seems to occur to the proponents.
I‘m no geneticist, but I gather that it is thought that genetic changes can spread in a population even if they convey no advantage, as long as they are not deleterious.
The more I see of Harper, the less I like it. Not a biochemistry book for biochemists, and too many authors with only narrow expertise, lacking editing on what they write.

I totally agree, it's a spurious argument easily disproved by things like loss of ability to synthesize vitamin C - only found in anthropoid apes, guinea pigs, some bats, some birds and teleost fish. If it were about energy it would be much more widespread among frugivorous species.

Good answer. Yes, the argument exaggerates the power of natural selection on things that don't matter any more. There is essentially no selection for or against junk DNA, for instance. The loss of unimportant abilities (like synthesizing vitamin C) is accounted for by genetic drift: "genetic changes can spread in a population even if they convey no advantage, as long as they are not deleterious."

The argument also strongly implies that evolution is a smart, thinking process. When it's far more likely that the ability was just lost because it didn't matter enough (because those nutrients were available in the diets)

The passage is saying that if you get enough of a nutrient in your diet, you don't need to synthesize it.
If you don't need to synthesize a nutrient, you don't need to waste energy on the machinery to synthesize it.
Even if you switch off the process that makes the machinery, even just keeping and copying the instructions for making that machinery is a waste.

I don't see the cost of the synthetization machinery as relevant (in this case), either. There is selection pressure to turn off the production if it's not needed, since leaving it running would consume resources to produce something of which there is enough which thus are not available to produce something that is missing, leaving the next processes which rely on the products unable to run, since it is missing all other raw materials except one being overabundant. This may well make several percent of difference in fitness.
However, the cost of replicating the extra gene just in case someone might need it is an additional burden somewhere around a percent of a percent of a percent of cost: a selection pressure exists, but it is significantly lower. It will still lead to loss of the gene, but it will take thousands of times the number of generations to lose an useless gene compared to a detrimental gene, so it's not a significant effect.
Also consider that a mutation usually changes the gene, it does not remove it, so the cost remains unchanged: the change that makes humans unable to synthetisize vitamin C is merely due to a defective gene, not due to a lost gene.
It's more of a case of "use it or lose it": a mutation that causes loss of the ability to synthesize it would be a disadvantage if the product is not available otherwise. But if it is available from food then there is no deletrious effect: the organism can survive in spite of losing this gene, so there is no selection pressure requiring to retain it. Therefore, a mutation that stops it from working may spread through the population.
Still, the food situation can regularly change (for example, the source being seasonal), so the disadvantage is merely mitigated, thus a selection pressure against it still exists: if during the long time it takes to select against the useless gene a situation occurs where it is useful (like a year with bad weather), it will be strongly enough selected in favor to offset its uselessness.
What is additionally required is a bottleneck in which the population shrinks so significantly that the survivors coincidentally lack that gene to produce it. Since losing the gene was not harmful, lacking it could spread to a sufficient proportion in the population.
Then the founder effect in a subpopulation isolated from the main population would make that gene exceptionless in that subpopulation, coupled with the extinction of the remaining population or speciation of the new subpopulation leads to the species universally lacking that gene.


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Why can't the fructose monomer in sucrose be α-fructose?
In all academic sources, sucrose is identified as α−glucose (1-->2) β−fructose. However, I cannot find any explanation anywhere as to why the fructose monomer has to be in the β configuration. Maltose has both α and β anomers, same for lactose. Even trehalose, another non-reducing disaccharide with glycosidic linkage between two anomeric carbons, has α-α, α-β, and even β-β anomers. Why is sucrose special? And is there a disaccharide out there that has α−glucose (1-->2) α−fructose configuration?

Welcome to SE Biology. Please finish reading the [Tour] to learn how this site works. We allow just one question at a time, and if you wish to know whether a particular molecule exists it should be easy enough to determine its systematic name and do an internet search. As for the why question, why questions in biology can relate to either function or mechanics. In the case of disaccharides that function of which is nutrition, the answer is probably mechanical, and I imagine lies in enzyme structure and specificity. Check the structures of the synthases for these disaccharides.


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Is Regenerative Brain Tissue Technology In The Near Future?
I got 99% of my information from articles I found in NIH's library; I can't cite anything now because I am on a timed session in a public library.
I've been reading material from research papers in NIH's search engine, I'm no expert in this field but there's this cell called an Embryonic Stem Cell and there are 2 proteins of which I think there could be a probable chance we could utilize them to initiate and halt Stem Cell Differentiation into Neurons and Glial Cells. The 2 proteins are called Fibroblast Growth Factor-2 and Laminin-521, in the NIH article I was reading earlier today it said (paraphrase) that the suppression of FGF-2 expression resulted in ESCs (Embryonic Stem Cells) differentiating into neurons. I also read that FGF-2 maintains the pluripotent nature of stem cells and tends to prevent them from differentiating. I also infer that Laminin-521 could also be important because its important to the health of ESCs.

Laminin 521 Stabilizes the Pluripotency Expression Pattern of Human Embryonic Stem Cells NIH Article

I do not think we are far away from curing things like Alzheimer's or Parkinson's disease, it's possible to reprogram adult cells into Embryonic Stem Cells, that is what the Harvard Stem Cell Institute did.

In order to turn adult cells back into pluripotent or embryonic-like stem cells, scientists use viruses to insert four genes – Sox2, Oct4, Klf4, and cMyc – into the cells.  Harvard Stem Cell Institute

What I am saying is completely hypothetical and speculative but what if we took samples of tissue from other areas of the bodies of patients with nervous system conditions and reprogrammed them back into Embryonic Stem Cells then differentiated them into Neural and Glial Cells to make artificial brain tissue we could somehow transplant into them, or we could somehow get the stem cells to differentiate inside their brains. Anyways the reason I wrote this question is to get a reality check and see how plausible this actually is.

PubMed is an NIH website but things there aren't from the NIH, it's a library site that indexes journals. It would be like saying that Google wrote something because you found the article using Google search, or your local librarian wrote The Adventures of Huckleberry Finn because you checked that book out from the library.

@BryanKrause Oh yeah your right, I'll get that fixed.


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For Cytotox studies of anticancer compounds: What cell line can I use to check if my compounds will also damage healthy cells?
I am about to perform cytotox studies on cells with my synthesized compounds.
I want to test my structures against MCF7 cells (breast cancer) as well as a melanoma cell line. MCF7 should be vunerable against my compound.
In the best case, the drug like compounds be especially effective against cancer cells but spare healthy cells.
I read that HeLa cells are used as a test subject, to see if chemicals are toxic to human tissue, especially when cosmetics etc. are tested. Could I use Hela cells therefore as a cell line to see if my compounds show off target effect against healthy, not overproliferating cells? Or what cells are used usually for this purpose and are they immortalized?

HeLa are highly abnormal and very very proliferative. Most cell lines are proliferative in some manner. This sounds like a question that would be best suited to your advisor as they should know the details of your project and what is available for you to use or what is normally done in your lab.

I am wondering what people are normally do, to explore off target effects? I am not the first person who is testing cm against cancer cells. I assume they just use cells from actually patients that are not cancerogenic?

There are a few options which depend on the stage of your project. You could try a line which isn't a breast cancer line (normal breast), you could try one missing receptors for your compounds (KO/KD or natural) , you could try another tissue type (e.g. ovarian), another cell type (fibroblast instead of epidermal), you could try normal human primary cells, cells derived from directly from biopsy. All are possibilities... Like I said earlier, it's a question for your supervisor, there is no "normally do" in this, it's something that is project specific.


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What sort of social structure might *Homo floresiensis* have had?
I've found limited info on how they may have lived.
Physically, we've deduced the so-called "hobbits" used stone tools and hunted dwarf elephants in the Liang Bua cave, in hilly terrain 600 m/2000 ft. 50-100 years ago the region saw grasslands expand but rain forest persisted, maybe around the cave.
Physically they were small with long arms, short legs, and long feet and stood upright but they might have been partly arboreal. Very small brains suggest limited intelligence but they made tools etc.
Homo luzonensis, a possible sister species, was active in the Philippines in the same era, and also left remains in a cave alongside game it may have hunted with stone tools. Its curved fingers suggest it was more arboreal.
Both may have descended from H. erectus in the region and undergone island dwarfing. But to reach their respective islands both would have had to cross deep ocean straits, whether by accident on natural rafts of debris, by boat technology, or some other method, and many islands and long distances lay in between.
H. sapiens and chimpanzees have fission-fusion societies. Different baboon species vary. Orangutans are more solitary, bonobos more gregarious and peaceful.
Are there any clues, hypotheses, etc. to suggest if how the social structure or hobbits might have been?
Can you suggest a better forum?

Welcome to the Biology Stack Exchange. Please take the [tour] and visit the [help] for more information on this site and how it works. Please note we expect some evidence of you having done some homework - simply saying you haven't found anything isn't enough - tell us where you looked and what you know already. Small brain size doesn't correlate with intelligence - it's due to the folds on the brain, which can be seen in the shape of the skull when scanned. H. floresiensis has these folds and was likely quite intelligent.

Most anthropologists will tell you that it's incredibly difficult to know anything about social structures so far into the past. We can, at this time, only make limited inferences based on evidence that survives (typically more hardy materials).

Almost universally, there is little evidence for the social structures of early hominids. Such things simply do not survive in the fossil record.
You may be able to glean some idea of homo floresiensis social structure by researching the societies of hunter gather people who still exist today and have histories going back tens of thousands of years. They tend to live in groups of families, and have relationships with other groups, some friendly, some adversarial, who's territories border on theirs. Those borders they protect.
For example Australia’s original inhabitants:
The leaders of society are the elders – the most senior men and women who are respected by others. Important decisions are made by a council of elders, which include clan leaders and the most respected elders of the tribe. Australian tribes were not ruled by chiefs, but they had senior men who might be regarded as the best warrior, the best spear-maker, a medicine man, or being particularly wise.
Aboriginal society has separate names for up to seventy family relationship terms in some tribes. That is, far more than the European terms “father/mother”, “grandfather/grandmother”, “uncle/aunt” etc. Under their family and society rules, people have obligations towards certain relatives, and these obligations are reciprocated.extract from
Or the bushmen of the Kalahari (San)
Traditionally, the San were an egalitarian society. Although they had hereditary chiefs, their authority was limited. The San made decisions among themselves by consensus, with women treated as relative equals in decision making. San economy was a gift economy, based on giving each other gifts regularly rather than on trading or purchasing goods and services.
Most San are monogamous, but if a hunter is able to obtain enough food, he can afford to have a second wife as well. wikipedia
As you suggest in your question, the social structures of chimpanzees and other apes may give some indications of how these people lived. Jane Goodall says that chimpanzee behavior is very similar to human, even to the extent of having wars.
From Jane Goodall’s expositions on the life of chimpanzees:
Much of a chimpanzee’s life, especially male chimpanzees, is dedicated to climbing up or being knocked down the chimpanzee social ladder. Those on top need to fight to stay at the top, and those at the bottom need to find a way to improve their lot if they want a chance at fathering offspring and access to the best resources. This, however, is only one component of the complexity of chimpanzee behavior, as they also demonstrate altruism, share resources and knowledge with one another, and build strong friendships. It seems there is always more to learn about these perplexing primates! Goodall
Or here for a rigorous mathematical approach :
Chimpanzees organize their social relationships like humans  Nature
It can be seen from the last two references that chimpanzee social relationship echo that of humans and so may be a good indicator of some of the basic relationships that might have existed among homo floresiensis.


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Are humans unusual, compared to other animals, in not understanding the mechanics of sex instinctively?
To begin with a personal anecdote: there was a period in my childhood, which I can remember clearly, in which I was aware of sexual reproduction as a fact, but the mechanics of it remained a fascinating mystery. From conversations with friends - both at the time and later, recalling earlier times - and also from looking at popular culture, my experience seems pretty typical.
There are numerous instances from history of adults who were ignorant of sex to a degree which - from the perspective of our own time, where graphic content is ubiquitous and sex education mandatory - is quite baffling. A couple of royal examples:

Anne of Cleves seems to have believed, from a conversation with the Countess of Rutland in February 1640, that her husband kissing her goodnight was sufficient to impregnate her.
Louis XVI famously took seven years to consummate his marriage with Marie Antoinette. The rumours about there being an anatomical problem, i.e. phimosis, seem to have been discredited. Neither does there seem to have been any emotional barrier; the two always seemed to like each other, and eventually had four children together. But there was no consummation until Joseph II gave his brother-in-law some practical advice on the matter, after which he described Louis and Marie Antoinette as 'a couple of complete blunderers'.

Looking at the topic more systematically, this article summarises several scholarly sources. Said page discusses one book in particular called The Facts of Life: Creation of Sexual Knowledge in Britain 1650-1950 (1995) by Roy Porter and Leslie Hall. Although I have not read this book myself, the article I mentioned states:

Imagine a wedding night where neither party had any idea how the mechanics of sex functioned. Imagine a new bride so terrified of the “rude” action her husband tried to commit, she runs home to her parents and asks for an annulment the next day[...] These terrifying circumstances where women had no reproductive or sexual knowledge prior to real-life experience were all a reality, according to Roy Porter and Leslie Hall

So that's my case for humans lacking an instinctive understanding of the mechanics of sex. What about other animals? To the best of my knowledge, humans do seem to be unlike other mammals, at the very least. Any dog-owner can testify to the naturalness with which both male and female dogs play their respective parts. I remember a sheep farmer once telling me grimly that, in some breeds of sheep, it was a struggle to keep the male lambs from impregnating their mothers.
And what about other species of ape? With humans, there is a stock character in literature of the midwife/cunning woman/duenna/etc who advises the bride what to expect on her wedding night, and this character seems to have at least some basis in reality. There are also male equivalents to such a figure, e.g. the advice Joseph II gave to Louis XVI I mentioned above. Do we see any comparable roles being played among other species of ape? If so, could this be considered an example of epigenetic inheritance - analogous to the famous example of a rat mother licking her pups - and/or animal culture?

Absent sufficient sex education, teenagers get each other pregnant quite efficiently whether or not they intend to, suggesting they figure it out as well as any other animals. I question how you'd ask a dog, sheep, etc whether they understand the motions they're going through or are just following their instinctual programming.

only humans is weird societies that don't let children see adults have sex have this problem. humans learn about sex the way they learn about almost everything watching adults.

Giant pandas have been purported to benefit from instructional videos, but I found that to be not well attested when I looked for references for an answer.


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Can bacterial DNA solutions, which include other cellular components, be stored without compromising DNA stability?"
Question
Can bacterial DNA solutions, which include other cellular components, be stored without compromising DNA stability?"
Details
I'm using the boiling extraction method to extract acinetobacter bacteria's DNA, as following:

The bacterial deoxynucleic acid (DNA) was extracted by the Boiling
method of Chen et al., (2020). About 3-5 colonies of each
Acinetobacter isolate were emulsified in 100 µl of sterile dist.
water, incubated at 95 °C on a heat block (Thermo Fisher Scientific,
UK) for 15 min., and centrifuged at 10.000 rpm for 10 min. The
extracted DNA was stored at -20°C for amplification of the target
genes using PCR.
https://nrmj.journals.ekb.eg/article_276319.html

It works as the reading of the spectrophotometer are:

dsDNA conc (microgram/millilitre): 113.26
Ratio A260/A280: 1.77

Today the centrifuge stopped working. To keep to a timeline and to not waste the opportunity of having over night cultures (that were cultured for another purpose) at hand , can I store the suspension after the boiling step, then when the centrifuge device gets fixed, I can go on as usual?

It would depend on which variant of the method you are using. What's in your lysis buffer?

No lysis buffer, just 95 Celsius water bath. Tbh i haven't tested the long term stability of the product i get because i haven't done this method for a long time. I have a dummy sample that i'm have been keeping intentionally at room temperature to for 10 days compensate for the time factor, i'm going to measure it.

Normally this process is done in the presence of a buffer of some sort - it helps keep the DNA stable; i.e. pellet bacteria,  resuspend in lysis buffer, boil... Measuring the concentration is no indication of stability. You need to measure degradation using a gel or similar method. Also what sort of DNA are you after - plasmids are different to chromosomal.

Chromosomal, sorry I'm a beginner. I got this method from a published article. My downstream purpose is conventional pcr-amplification of partial gene (350 bp)

The article didn't mention any buffer, but it didn't mention how they stored their DNA,maybe they just extracted it in distilled water then added the buffer after that?

A link to the protocol would be useful as an edit in the question - unanswerable in this state. Most likely it will depend on the bacterial species too, so would be helpful to add this to the question too.

Done this part .


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Potassium Permeability in Cardiac Muscle Cells
From my research it seems as though there's a difference between cardiac and skeletal muscle cells in that during depolarisation, the permeability of potassium actually decreases for cardiac muscle cells. How does this occur? I imagine it would be due to the closure of potassium channels but if this is the case, then how is the inwards current of calcium balanced during the plateau phase?

In skeletal muscles, depolarization occurs via opening of voltage-gated sodium channels, leading to influx of sodium ions, and opening of potassium channels. However, in the case of cardiac muscles, during depolarization, voltage-gated sodium channels open, and influx of sodium ions leads to closure of potassium channels, which eventually leads to the long action potential and plateau phase. In cardiac muscles, co-occurrence of calcium channels also occurs.
You can find more details here


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Do right-handed helices bind to right-handed helices, and vice versa?
I know that B-conformation DNA is a right-handed helix, and most proteins that form helices form right-handed, not left-handed, helices (1). Furthermore, "Many transcription factors have an alpha-helix that binds to DNA bases in a specific fashion" (2), indicating that it is common for right-handed protein helices to bind to right-handed B-DNA helices.
Does this mean that, generally speaking, from the perspective of basic geometry, do right-handed helices bind to right- (but not left-)handed helices? And, vice versa, that left-handed helices generally bind to left- (but not right-)handed helices?
References

Novotny, M., & Kleywegt, G. J. (2005). A Survey of Left-handed Helices in Protein Structures. Journal of Molecular Biology, 347(2), 231–241. https://doi.org/10.1016/J.JMB.2005.01.037
Suzuki, M., & Gerstein, M. (1995). Binding geometry of alpha-helices that recognize DNA. Proteins, 23(4), 525–535. https://doi.org/10.1002/PROT.340230407

But the paper you quote shows that left-handed helices in proteins only span a single turn, so fair comparison with right-handed helices is not possible. The question seems to be a case of “if left-handed helices existed”, in which case it would seem a mathematical question.

My understanding is that protein and DNA helices show the handedness that they do due largely to the intrinsic chirality of their components. Note that in natural biomolecules L-amino acids and D-sugars predominate. This apparently leads to a subsequent bias in their respective polymers.
I believe that it has been demonstrated that artificial alpha helices constructed of achiral amino acids demonstrate inversions between left and right handed forms- these then need to be stapled with extra molecular bridges to hold left or right handed orientation.
Thus, I don't think that there is a right-to-right or left-to-left association. In all cases, I think it's just that the biased handedness is baked into the structure of natural amino acids.

Thanks, @Maximilian Press. What you're saying is true, but that's not really my question. I am NOT asking whether nuceic acids and proteins usually adopt right-handed helices because this makes it easier for them to bind to each other (nor am I suggesting this). I am simply asking, do right-handed helices bind more easily with other right-handed helices, and do left-handed helices tend to bind more readily and tightly with other left-handed helices? I'm being a bit coy because I don't want to give away my hypothesis, but I'm more interested in the LEFT-handed nucleic acid and protein helices.

@OdinTheDO I see. I would be interested in whether anyone had any data either way, but my guess on this is a solid "no". I think that the secondary structure of helical geometry of DNA and protein with respect to each other is probably low/no relevance for binding compared to the tertiary and quaternary structures. But that's purely a guess.


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Can a stereo microscope be used for mycology?
I have a need for a stereo microscope to do electronics work. I also have a strong desire for a stereo microscope to do mycology. I would like to be able to,

Clearly identify mycelium, from bacterial contamination (no interest in bacteria).
Be able to isolate spores of mycelium.
Identify dikaryon, from monokaryon
Ideally, but not required be able to identify different types of mycelium that are undesirable (mold).

Could I take a trinocular stereo microscope and add a barrow lens that increases the zoom and decreases the focal length, and use it for biology as desired above? Some stereomicroscopes that have 2x Barlow advertise 225x, like the AmScope ZM2225NT.
What would the downsides of this approach be?


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What is the difference between myoblasts, myotubes and myocytes
I am struggling to grasp the difference between myoblasts, myotubes and myocytes.
If I am right, myoblasts are mononucleated and differentiate into myotubes which are muscle fibers.
Are myocytes the mature muscle cell? I can't find a good definition for this.
Thank you for your help!

Please share what prior research you've done here?

On request I'm providing helpful explanation of the picture i have added for those who are new in learning
Myoblasts - focus on 'blast' which means related to early stage of cell which has not yet differentiated such cells are also called stem cells, once differentiated their fate is decided very much what they are going to be.
Myocyte - [cyte:cell] they are already differentiated, hence are fully specific about themselves what constituent they are going to become.
Myotubes - myocytes condense as a mass, also besides that they undergo elongation as well, which ultimately results into formation of bundle like structure. Now at this stage idea of a singular cell is lost, we can't pick up a part of it and say this is one cell.
May myotubes coalese and form few myofibril (imagine 1000 myotubes make 100 myofibril)
And bundle of 100 myofibril makes one myofibre/muscle fibre which has sneath covering called sarcolemma. Many such muscle fibres together (with the help of endomysium as connective tissue/glue) make muscle fascia which in turn with the help of perimysium(connective tissue/glue) and covering called epimysium makes up Muscle.

Source:
https://www.researchgate.net/publication/347023906_Effects_of_External_Stimulators_on_Engineered_Skeletal_Muscle_Tissue_Maturation
Mueller, Claudia & Trujillo Miranda, Mairon & Maier, Michael & Heath, Daniel & O'Connor, Andrea & Salehi-Müller, Sahar. (2020). Effects of External Stimulators on Engineered Skeletal Muscle Tissue Maturation. Advanced Materials Interfaces. 8. 2001167. 10.1002/admi.202001167.


text:
How is the "global pLDDT" score in the Protein Data Bank calculated?
Consider this list of entries for the Tobacco Mosaic Virus (TMV). I selected to sort by 'Global pLDDT' from best to worst. It is my understanding that pLDDT is usually calculated per residue for a given prediction of a protein structure by comparing it to some 'true protein structure' (taken from PDB for example?).
I assume the 'Global pLDDT' is some form of aggregate of these per residue values? But what is the 'true protein structure' it is compared to? Other entries in the PDB?

pLDDT is a measure of confidence that ML models like AlphaFold provide for predictions of protein structures. The entries you are sorting here are not predictions, they are all experimental structures. As such, none of them have any pLDDT assigned. Notice that the order of your list does not change if you switch from 'Best to Worst' to 'Worst to Best' while sorting on Global pLDDT.
In the query builder for your link, notice the 'Include Computed Structure Models (CSM)' switch. It is set to not include predicted structures, although it appears the CSM providers RCSB integrates don't have any for TMV anyway. Here's RCSB's documentation for CSMs.
For experimental structures you probably want to sort by resolution, but the most important thing is to make sure the structure is exactly the molecule you think it is, e.g. not a mutant or a cleaved fragment, etc.


text:
Why does my cell subculture have these black dots like appearance?
I tried to subculture cells(hek293 cells) for the first time for a Cell Biology experiment, and here are the steps I followed:-
Cell subculture
(*the media is a mix of 10:1:0.1 of DMEM:FBS:Pen/Strep)

If cells are 70-80% confluency, please subculture the cells
Remove media
Add 5ml of PBS and wash the cells by tilting the culture dish few times
Remove PBS
Add 2ml of Trypsin/EDTA and mix well by tilting the culture dish few times
Incubate the cells for ~2min at RT (until cells are detached)
Add 5ml of media and resuspend well by pipetting
Transfer 7ml of Cells/meida/Trypsin/EDTA into a 15ml of conical tube
Centrifuge 300xg for 2min at RT
Remove supernatant
Resuspend cell pellet by tapping the tube 5 times.
Add 5ml of media and resuspend by pipetting
Add 10ml of media into a new 10cm culture dish
Add 1ml of resuspended cells into the culture dish (containing 10ml of media) (1:5 dilution)
Check the cells by a microscope
Put the culture dish into 37oC, 5% CO2 humidified incubator
Check the cells every day, and when cells are 80~90% confluency, do subculture.

I followed all the steps above to a T, and here is the cell culture under a microscope prior to culturing-

And the culture under a microscope post subculturing-

I don't really know what the numerous black dots are in the post-subculture cell culture. I also can't quite understand if I can see any of the cells in the post-subculturing culture. So, I wanted some advice on what the black dots might be, and if the subculturing appears to have been performed correctly. Thank you in advance!

Welcome to the Biology Stack Exchange. Please take the [tour] and visit the [help] for more information on this site and how it works. Please edit into your question which cell type this is, as that may help provide useful information on the effect you are seeing here.

Thanks a lot for your warm welcome and your suggestions! I have edited the question accordingly.

How long after subculturing is the second picture taken?

It was taken immediately after subculturing.

Were both images taken in similar conditions? The 'before subculturing' image on top looks like a dark-field image while the 'after' image below it looks to be bright-field

I'm thinking you are very new to cell culture - your first step should be to ask people in your lab.
You have a couple of problems here - it takes time for cells to settle and attach and start to spread out. Often several hours after seeding is needed for them to return to looking normal. Have a look at your cells now, as I've answered this ~24 h after you asked it. They should look more normal.
However, a lot of what you are seeing there is cellular debris. This indicates that you probably over treated your cells with trypsin and/or were very rough with your pipetting. It is normal to see some debris after seeding, but not too much.
In addition, your first photo shows massively over confluent cells, they are all tightly packed together and there are absolutely no gaps in the monolayer. This stresses the cells (even if they are not contact inhibited - HEK293 aren't contact inhibited), so they tend to attach more firmly than they should. This means that you end up treating them with trypsin for too long and then a lot of them die. You should be subculturing much earlier - there should still be about 20-30% of the culture area free of cells. The large, blobby areas in the top third of the first picture are not gaps in the monolayer - some of them look like senescent cells, and some are gaps left by dying/dead cells that haven't quite filled in yet.
HEK293 are a weakly attached cell line; in many instances you can tap the side of the flask firmly to detach them, you can even wash them off by pipetting. In my experience, you should only need a minute or less to detach them from cell culture vessel.
It might pay you to check the concentration of your trypsin/EDTA - often stocks are 10x or 100x rather than the 1x you need. Adding the wrong concentration will result in a lot of cell death as it is very hard to neutralize the trypsin.


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Cynobacteria vs. BGA
I am really confused. On google and other places(though very old) it is mentioned that Cynobacteria are the same as BGA(Blue-Green Algae) and are technically bacteria and are places under the kingdom monera. However, in some places is it mentioned that they are not the same and so does my teacher. It is mentioned that Cynobacteria, being a unicellular prokaryote is placed under Monera.
So, I have 3 Questions -

Are Cynobacteria and BGA the same?
Is Cynobacteria a monera or protista ? is it a prokaryote or euakryote ?
Is BGA a monera or protista ? is it a prokaryote or eukaryote ?

Is it true that later it was believed that Cynobacteria and BGA were the same, and now it has been discovered that they are different?
What is the true fact?
I believe this community has experienced biologists, hence I have reached out here.
Please understand that I am a student and this question might sound amateur, so please ignore that and please help clear my confusion.
Any help would be appreciated !

Cyanobacteria are oxygenic photosynthic prokariotes, historically known as "blue-green algae" until their prokariotic nature was unambiguously confirmed. (So, yes, Cyanobacteria and blue-green algae are the same, but they are not algae.)

Since their prokaryotic nature has unambiguously been proven, the term “cyanobacteria” (or occasionally “cyanoprokaryotes”) has been adopted in the scientific literature. ... the taxon Oxyphotobacteria is proposed for cyanobacteria in a strict sense.

Taxonomy has been a big problem for this/these organism(s); there are entire papers arguing the case for various taxonomic classifications.
It cannot be in the kingdom Protista as it is not a eukaryote. (So, they are in the kingdom Monera.)

Is BGA a monera or protista ? is it a prokaryote or eukaryote ?

Blue-green algae is a historical term and incorrectly describes what is now called Cyanobacteria. The question is not answerable as written, but if it has to have an answer, I'd go with "monera" and "prokaryote".
Chorus, I, Welker M; eds. 2021. Toxic Cyanobacteria in Water, 2nd edition. CRC Press, Boca Raton(FL), on behalf of the World Health Organization, Geneva, CH.


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Insect ID from sound in video
Can you please help identify what insect this might be based on the noise it makes? Video below.
The noise is regular tapping, and can be heard especially at night when everything is quiet. When approached or my footsteps can be heard, the noise stops and starts again when it’s quiet again. I’ve never managed to see what it looks like.
It is only a single source of noise, and on different days comes from different parts of the room. Often can be heard from wooden window frames. This time when I recorded the video it was most likely somewhere in the bag.
I live in Sydney, Australia.
I listened to a number of different bugs (in videos) and can confirm it is not:

Termite
Deathwatch beetle
click beetle

https://youtube.com/shorts/5wf-UhwSEgk?feature=shared

I think that the most likely culprit are the so-called booklice (Psocoptera and Psocodea). These have a world-wide distribution and are a common household pest, eating dust and plant material (including paper)
These are small whitish/transparent insects that you might see scurrying around on recently disturbed surfaces - particularly books, stored boxes or in cupboards where you store flour or similar foods. They are quite small - in the order of 1-2 mm (~1-3/16th inches) long. Some of these species make quiet tapping sounds and they are very common in households - which might explain them being in a bag.
However, I wouldn't be so sure of ruling out deathwatch beetles - there are quite a few species in the group, besides "the" deathwatch beetle (Xestobium rufovillosum), some of which  I believe also make clicking/tapping sounds, though I'm not sure of the species which do and whether they might be present in Australia.

Booklice are tiny! I can't imagine one making this type of sound. I'm not convinced :p.

@theforestecologist  Surprisingly audible though - I've heard them a few times. I'm guessing it's a drumming effect on a thin surface.

Thanks for the answer. I have in fact seen book lice a few times in the house, however, as mentioned in the comment above, they really are tiny so I can’t imagine them being so loud. It might be though.


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Problems reading my gel electrophoresis result
This is an image of my gel electrophoresis result.
I used the alkaline lysis method to extract E. coli plasmid and put it on gel electrophoresis. Based on what I had learned, I expected to see a band of nicked plasmid, a band of supercoiled plasmid and a smear at the positive end due to DNAse that was not completely removed.
However, I can't identify which band is which in my result and the smear from 200 to 1000bp having 3 bright bands is confusing me.
Could you please help me identify the forms of plasmid present in this result?

What plasmid are you trying to isolate, which size do you expect?


text:
Binding modes of a protein on a planar surface graphene
Can a protein have different binding modes on a flat even surface like graphene? For a surface like Graphene oxide I can understand, since it has several oxygenated groups on its surface that makes it easier for a protein to have different binding modes, but what for a homogenous aromatic surface like graphene?

Proteins tend to denature on hydrophobic surfaces, which "changes" the binding modes in that it abolishes them completely. I found a study on BSA binding affinity when adsorbed to reduced graphene oxide (rGO), which should have very similar behavior to graphene itself.

The biochemical functionality of adsorbed BSA was investigated through the interaction with its anti-BSA antibody counterpart. BSA on GO can retain its binding sites while, in contrast, a denatured ad-layer of BSA forms on the rGO followed by further binding of active BSA molecules, depending on the concentration of the protein.


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What is meant by longitudinal splitting of chromosomes?
My textbook says that during prophase, the chromosome longitudinally splits (except at the centromere) into two sister chromatids. But what does this mean? The DNA is already duplicated in the S phase. So does this mean the uncoiling of the plectonemic coil formed by the sister chromatids? Perhaps the degradation of cohesin(I think unlikely)? I am a grade 10 student unable to find the answer(although this is not a homework question) so  please try to keep things simple.

The duplicated set of DNA in each chromosome(formed at replication in s phase ) gets separated and repacked as a new chromatids that we call as sisters, which are held together at centromere by COHESISNS & CATANANES(mechanically interlocked DNA) But the arms are seperated from each other by further condensation of the DNA, DECATANATION by TOPOISOMERASE & SELECTIVE BREAKUP OF COHESISNS at NON CENTROMERIC REGIONS (ARMS) from late S PHASE to PROPHASE & PROMETAPHASE through a CLEAVAGE INDEPENDENT PATHWAY (which is REVERSIBLE). But the complete seperation of sister chromatids at the centromere is due to the additional action of SEPARASE through CLEAVAGE DEPENDENT PATHWAY (QUICK, IRREVERSIBLE) which occurs from LATE METAPHASE TO ANAPHASE.


text:
Is this snake hazardous around children?
This snake lives in a small rock dam in a residential retention pond in Chattanooga, TN.  Children play in the area at times.  It is approximately 30 inches in length. Is this snake a hazard or can it be ignored?

This appears to be a northern water snake.

 TN.gov
Nonvenomous. Not dangerous if left alone, From tn.gov:

When threatened Northern Watersnakes will make a silent retreat, but are aggressive when captured. They will flatten their head and neck, try to strike and bite, and discharge a foul-smelling musk from glands at the base of their tail.

See https://www.tn.gov/twra/wildlife/reptiles/snakes/northern-watersnake.html

The fat body is quite reminiscent of a cottonmouth, but it doesn't have the mottling I associate with them.


text:
What is the minimum Ct value that you would consider indicates no gene expression?
I am doing relative quantification to compare gene expression between a control with several mutant backgrounds using qPCR.
Looking online I find several different sources suggesting different values that indicate high, low, and no gene expression. Some say that Ct > 35 = no expression, others say > 40 = no expression.
Where do you draw the line with Ct values and why?

Can't you just do a negative control and use that to calibrate?
Alternately, run the DNA from your PCR on a gel with a positive control indicating expression. Literally zero expression should mean that the correct band never comes up even after 40 cycles or whatever. And if you do see a band even in a negative control lane, that means that you have contamination and you should probably do something about that!
I think it's also reasonable to use those thresholds that you mention.
Overall, what I'd say is that PCR (and particularly Ct type values) are finicky and while the basic amplification is robust, there are tons of factors that affect the kinetics of your amplification curves. That's why it's so important to run controls in every qPCR run- you are correcting for all the weird batch effects of your reagents, primers, etc. in your master mix.
Every primer set will have slightly different kinetics, and so will every enzyme, so if you want to be really rigorous you would establish a threshold for every possible methodological permutation and reaction setup. However, that's a lot of work. I'd rather just run the final product on a gel and say yup or nope- it should be pretty obvious.

Thanks for your response. You're right, I definitely should have used a negative control. Unfortunately its too late now (I was doing an undergrad project and my time in the lab is up so i'm just left with the data).


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Improving contrast between dot and paper in dot blot
Currently using dot blot to attempt to determine if a serum contains antibodies for some reagents I am testing.

I pipetted samples as 10-5ul dots on whatman paper.
Incubation steps were for 1 hour with light shaking.
Blocking solution is composed of 1mg/ml BSA in PBS.
Wash steps were 3X PBS for 10 minute each.
Solution for incubating the blot in primary antibody was 1ml of serum per 9ml of blocking solution.
Solution for incubating the blot in secondary antibody was 100ul of IgG in 10ml of blocking solution.
Then a 1:10 DAB substrate mix was used to develop the blot. Products used for the test listed below.

Currently, the whatman paper is a light brown with vague outlines of the dots where the samples were pipetted. Samples that should trigger more antibodies than others (like serum positive control) tend to be a bit darker, but it's not nearly as clear as we'd hope for.
I have also blotted the IgG which usually forms a darker smudge, rather than a clean, dark dot. Does anyone have any advice on how to improve the developing process? I have also tried using TBS, adding Tween to the PBS or TBS as well as trying nitrocellulose instead, but none of these have impacted the results.
Reagents:

secondary antibody
DAB kit

In the absence of another answer, I'll transition my comments to an answer.

Please label your images.
Both an Abcam guide and a Thermo troubleshooting document suggest using a kit or DAB protocol including metals such as nickel or cobalt to intensify signal. I notice that the kit spec that you link doesn't seem to have these. Have you tried different DAB kits?
They also recommend carefully monitoring staining over time under a scope and removing as early as possible. This may help to reduce background.
I'd try a few different combinations of conditions, stain + wash times, to see if any have an effect. I don't have a great sense of where your protocol came from, I'd suggest clicking through those documents above or searching the literature to find more DAB protocols that you might try.