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Neuron connectivity- how are they connected physically
If Neurons are only connected through synapse and there is no physical connection,  how are they just suspended in brain layers?

Neurons are suspended, as you say, in an extracellular matrix. Brain tissues are a little bit more specific. Here I quote a few summaries from literature to answer and give your a perspective on your basic question. In bold I highlight important statements which differentiate the brain's ECM from the ECM found elsewhere in the body.

Barros, Franco & Müller, 2011: An astonishing number of extracellular matrix glycoproteins are
  expressed in dynamic patterns in the developing and adult nervous
  system. Neural stem cells, neurons, and glia express receptors that
  mediate interactions with specific extracellular matrix molecules.
  Functional studies in vitro and genetic studies in mice have provided
  evidence that the extracellular matrix affects virtually all aspects
  of nervous system development and function. Here we will summarize
  recent findings that have shed light on the specific functions of
  defined extracellular matrix molecules on such diverse processes as
  neural stem cell differentiation, neuronal migration, the formation of
  axonal tracts, and the maturation and function of synapses in the
  peripheral and central nervous system.
Ruoslahti, 1996: The extracellular matrix of the adult brain
  tissue has a unique composition. The striking feature of this matrix
  is the prominence of lecticans, proteoglycans that contain a lectin
  domain and a hyaluronic acid-binding domain. Hyaluronic acid and
  tenascin family adhesive/anti-adhesive proteins are also abundant.
  Matrix proteins common in other tissues are nearly absent in adult
  brain. The brain extracellular matrix appears to have trophic effects
  on neuronal cells and affect neurite outgrowth. The unique composition
  of this matrix may be responsible for the resistance of brain tissue
  toward invasion by tumors of non-neuronal origin.
Dityatev et al. 2010: The extracellular matrix (ECM) of the
  central nervous system is well recognized as a migration and diffusion
  barrier that allows for the trapping and presentation of growth
  factors to their receptors at the cell surface. Recent data highlight
  the importance of ECM molecules as synaptic and perisynaptic scaffolds
  that direct the clustering of neurotransmitter receptors in the
  postsynaptic compartment and that present barriers to reduce the
  lateral diffusion of membrane proteins away from synapses. The ECM
  also contributes to the migration and differentiation of stem cells in
  the neurogenic niche and organizes the polarized localization of ion
  channels and transporters at contacts between astrocytic processes and
  blood vessels. Thus, the ECM contributes to functional
  compartmentalization in the brain.

Neurons are also contained within a matrix of glia cells, which outnumber neurons by a considerable margin: https://en.wikipedia.org/wiki/Neuroglia https://www.scientificamerican.com/article/the-root-of-thought-what/

@jamesqf This idea of glia vastly outnumbering neurons has been challenged and refuted. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5063692/

@Bryan Krause: Perhaps so  - I'm only going by what I've read in texts - but regardless of absolute numbers, glia cells do form a significant part of the matrix in which neurons are embedded.

@jamesqf Yeah that's fair, just challenging the 10x number that is often repeated and rarely supported. The non-somatic components of neurons are also very important and probably more likely to be overlooked.

It's true, neurons in the brain are really sparse within an extracellular matrix. But I would like to say that there exist several type of synapsis.
The first one, to which you referred is the chemical synapse connecting the synaptic button of first neuron with the post-synaptic membrane of the second neuron. Thus in that case, you think there isn't a direct contact of pre and post synaptic membranes but the electrical signal is converted and transmitted as neurotransmitter through the synaptic cleft. To note, both axons and synaptic cleft are "covered" by other cell types, a particular type of glial cells, the Schwann cell that causes the saltatory nature of the electric signal across the axon and, at level of the synapsis, acts in order to reuptake the released neurotrasmitters.
The second type is the electrical synapse. In this one, post and pre-synaptic compartments of neurons are phisicaly connected by gap junction: these are structurally made by two hemi-channels called connexons and makes the cytoplasms to communicate and thus the electrical signals continue to diffuse thanks these connections. In that case the connection between such cells approach within about 3.8 nm of each other creating a mechanical and electrical continuity (Sheriar G.Hormuzdia et al., 2004)
Thus, when you say "neurons are only connected through synapse and there is no physical connection" it's quite simplistic. In reality, also the chemical synapsis are "connected" mechanically by a large number of cell adhesion molecules that acts in order to make and modulate the connection between neurons. For instance these include neurexins and neuroligins or Ig-domain proteins etc (Missler M, et al. Cold Spring Harb Perspect Biol. 2012). Indeed, the pivotal differences between electrical and chemical s. is the ways by which neuronal cells communicate. In the latter, the distance between pre and post synaptic membranes is wider with respect to the electrical one.

Welcome. Can you mention your sources such that other users can background read on your material?

Absolutely yes. I will improve the answer with some bibliography.

I just noticed the inline reference. Best practice is to add a subsection with literature and include the link (e.g., to pubmed or the pdf). +1

I understand. The next time I will change strategy. However I added another reference inline. I hope it will be useful for the other  users. Thanks for the suggestion.

Have you seen histology of brain tissue? Neurons are not "sparse" at all in the brain. Space is a serious constraint for the nervous system. Your points about the physical connections of a chemical synapse are very important though, thank you for that part of your answer.

Yes, you're right. What I mean is that extracellular matrix and glial cells outnumber neurons. I used "sparse" instead of "immersed" to simplify. However connection molucules between chemical neuron's synapses is strong important inorder to allow synaptic plasticity (for instance glutamatergic synapses long term potentiation and/or depressions or synaptic selection/deletion during development of neuromuscular junctions)


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How to find out the when we had a common ancestor with a particular animal
For example, Jordan Peterson claims that human and lobsters have a common ancestor X million year ago. I wonder, how does he know it?
I'd be so delighted to visit a website, where I could select two currently existing species and it'd show me how many years ago they had had a common ancestor. Does anything like this exist? Do we at least have a database, so I, as a web programmer, could create this kind of website?

This post will interest you: The best free and most up to date phylogenetic tree on the internet?

TimeTree [http://www.timetree.org] is one site that allows you to look at times from divergence of various taxa. Their FAQ describes how they calculate the times by pointing to this paper: Tree of Life Reveals Clock-Like Speciation and Diversification, but in general they used standard molecular clock approaches. You ask about downloading their database: they say

The TimeTree Database data is currently not available for download. Methods for making these data available in the future are currently under discussion.

source: Stack Exchange

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sort: votes


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How to recover all protein ses into refseq database
I'm actually trying to download all the virus protein sequences available in the NCBI database.
I guess the link is this one: ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/viral/
How could I get all the protein sequences in fasta format into one file ? Does someone have codes to do that easily?
Thank you very much.

I believe that this question belongs to StackOverflow, as it's not about biology or related interdisciplinary subjects. Also for such tasks I recommend using Scrapy for Python

@MaximKuleshov — Better on SE Bioinformatics than Stack Overflow as nobody on SO will know anything about the file format of Genbank files. And leave it at that. Recommending a package in a particular language is not appropriate in a comment and not much use anyway if the poster doesn't use the language.

As with most things, there are multiple ways to do this. Here are two of them:
Download from the NCBI Assembly portal

Go to https://www.ncbi.nlm.nih.gov/assembly/ and search for 'Viruses[Organism]'. For our purposes, I am going to restrict this search to Virus assemblies that are latest RefSeq and reference genomes. The query for this will be: "Viruses"[Organism] AND "latest refseq"[filter] AND "reference genome"[filter]. It will return 46 results.
To download the protein FASTA sequences for all of these, click on the big blue Download Assemblies button, choose RefSeq as source and Protein FASTA as File Type.
Click the Download button and a tarball with FASTA files - one for each assembly - will be created for you to download. You will then have to combine them all into a single file.

Download using wget

Go to ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/viral and download the assembly_summary.txt file. This is a tab-delimited file with information about every RefSeq viral assembly located in that FTP path. Column 20 has the FTP path for the assembly which you can parse out and use wget to download the protein FASTA file for each assembly, followed by combining them into a single gzipped file as shown below:
## download the assembly_summary.txt file
wget ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/viral/assembly_summary.txt
## download the protein FASTA files
grep -v '^#' assembly_summary.txt \
    | cut -f20 \
    | while read -r url ; do wget $url/*_protein.faa.gz ; done
## combine all files into a single one
zcat *_protein.faa.gz | gzip > all_viral_proteins.faa.gz

Hi, thank you for your help, it did work. Unfortunalty when I try zcat *_protein.faa.gz | gzip > all_viral_proteins.faa.gz I get : -bash: /usr/bin/zcat: Argument list too long

Finally I found I way by doing : for i in $(ls | grep "_protein.faa.gz");do cat $i >> all_viral_proteins.faa.gz;done

Interesting. I never had to concatenate so many files! Is there a reason why you want such a large number of sequences in a single file? Can you not work with multiple files? Presumably, the single file would be very big and may not be the easiest to handle for downstream usage.

It is because I'll make a blast with those sequences as queries, so I'll make a blast database with them.

Maybe you can help me again, I would like to download a list of genomes, I have their ID number (list with one ID number by line) and I would like to get all the genomes in .fa format do you know if it is possible with the same script?

What kind of IDs do you have? Can you give me a couple of examples?

Yes of course:
'Genome ID:  12051
Genome ID:  39971
Genome ID:  44840
Genome ID:  55512
Genome ID:  39899
Genome ID:  65382'

Where did you get these IDs from? They don't seem to be the NCBI Assembly UIDs because when I search for 12051[All UIDs] in the NCBI Assembly I don't see any results. Would it be possible to get GCF or GCA accessions for these genomes?

Let us continue this discussion in chat.

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Does diamond tblastn exist?
I actually want to use diamond instead of blast because it is faster with small sequences and big genomes, but I actually want to make a tblastn with several protein sequences as queries and the database which will be the genome transformed by makedb.
Do you know if diamond have the tblastn option? I cannot find it.
Thank you.

We welcome new posters to SE Biology, but I must say that the obvious place to ask such a detailed technical question about software that few people will have heard of is on the website or documentation for that software. Failing that, I would email the authors of the paper cited on the website. (If you must post on SE you would be better trying SE Bioinformatics.)

Biostars.org is another very helpful Q/A site for bioinformatics.

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From refseq ids to Go term Ids
I have a list of Refseq accession numbers such as :
YP_009448812
YP_009448725
YP_009448701
NP_659591
around 10 000 acc_numbers...

and I'm looking for a tools in R or Python in order to get the corresponding Go term ids.
I tried the packages (org.Mm.eg.db) and (GO.db) but it does not work.
> Term(names(get(get("YP_009165174", org.Mm.egREFSEQ2EG), org.Mm.egGO)))
Error in .checkKeys(value, Rkeys(x), x@ifnotfound) :
  value for "YP_009165174" not found
> Term(names(get(get("YP_009448701", org.Mm.egREFSEQ2EG), org.Mm.egGO)))
Error in .checkKeys(value, Rkeys(x), x@ifnotfound) :
  value for "YP_009448701" not found
> Term(names(get(get("NP_659591", org.Mm.egREFSEQ2EG), org.Mm.egGO)))
Error in .checkKeys(value, Rkeys(x), x@ifnotfound) :
  value for "NP_659591" not found
> Term(names(get(get("YP_009448812", org.Mm.egREFSEQ2EG), org.Mm.egGO)))
Error in .checkKeys(value, Rkeys(x), x@ifnotfound) :
  value for "YP_009448812" not found

Does anyone have an idea? Thank you for your time. I cannot find a egREFSEQ2EG for viruses.

I've had very good experience with the biomaRt package (R, bioconductor) when it comes to mapping of different databases. If I don't forget about it, I can post an answer with code tomorrow.

Ok thank you for your time then. The proteins are from Acc_number  types and from virus organisms. The idea is to get the corresponding Go terms Id of these refseq Acc_numbers IDs in order to perform a Go term analysis.

So, I've looked a bit into this and the way you want to do your analysis won't work as you planned it. The main reason for this is that the GO database does not contain any virus species (as fas as I could see). The existence of the species you want to analyse in the database is important, because you need to have a background or reference gene set in order to perform enrichment analysis. Even if you're just interested in the IDs and want to perform the analysis by yourself, this means that you're unlikely to find anything for your genes/proteins in the GO databases.
Your best alternative is to use other annotation databases and either rely on their annotation or map their annotation to GO term ids (here is a list of all databases that allow this).
Your best bet for this is probably the UniProt database, since that should have entries for most of your proteins (though not all will have annotated GO terms). UniProt also offers an ID mapping tool that should be able to convert your RefSeq IDs to uniprot IDs, and also comes with an API for python. Do note that some of your IDs (the YP_ ones) are provisional RefSeq entries and the webpage tool only finds them in the 'UniParc' database (not UniProt KB).
Once you have the the UniProt IDs you should be able to map the available GO terms from there (see the last entries of the first link above).

Allright, thank you very much for all these informations!! It will be very useful for my project. Have a lovely day.


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Recombination frequency
From Campbell Biology 2017, unit 15, test your understanding question 5:
Using the information from problem 4, scientists do a further testcross using a heterozygote for height and nose morphology. The offspring are tall upturned snout, 40; dwarf upturned snout, 9; dwarf downturned snout, 42; tall downturned snout, 9. Calculate the recombination frequency from these data.
Why is the correct answer 18% and not 22%? My reasoning is that you should do a 9 + 9 = 18 and 40 + 42 = 82, and then do an 18/42 = 22%.

If you post this sort of question, like any other question, it must be self-contained. This question refers to a problem in a text book, so is only comprehensible to someone with that text. Hence it is off-topic here and I have voted to close. Please take the tour and read the help on asking questions before posting again.

For recombination frequency you have to consider the whole population of the offspring (not just the offspring that got not recombinated), means 40 + 42 + 9 + 9 = 100. Then you have 18 recombinants, and your recombination frequency goes with 18/100 = 18%.

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Are highly-polyploid organisms more resistant to ionising-radiation-induced DNA damage?
Homologous recombination, although most famous for its use to mix together maternal and paternal alleles during meiosis, is most commonly used as a DNA-repair mechanism, allowing cells to repair double-strand breaks (lesions where both strands of the DNA double helix are severed at the same, or nearly the same, level), such as those produced by (and responsible for the main lethal effects of) overexposure to ionising radiation.  In this process, the broken ends are cut back asymmetrically, producing single-stranded flaps at the ends; at least one of the flaps engages and base-pairs with a strand at the same level on a sister chromatid (if available) or a homologous chromosome (if we’re still in G1 and no sister chromatids are yet available), producing either one or two Holliday junctions; new DNA is synthesised to fill the remaining single-stranded gaps; and ligases and (sometimes) endonucleases complete the repair and separate the two pairs of strands.1
Although eukaryotic cells have two other methods of repairing double-strand breaks (non-homologous end joining [NHEJ] and microhomology-mediated end joining [MMEJ]), homologous recombination is, when possible, the highest-fidelity repair method:

NHEJ consists of a DNA ligase grabbing the loose ends (taking advantage of the fact that the two strands usually aren't broken at exactly the same level, leaving short complementary single-stranded flaps on each side of the break) and gluing them together; if the cell’s DNA contains multiple double-strand breaks, there is no guarantee that the ligase will join the ends with their correct partners (especially if the strands didn't break cleanly, and a few nucleotides or bases were damaged or snapped off), and, if the wrong loose ends are joined together, various severe chromosomal aberrations can occur (such as fusion of chromosomes, translocations of material between non-homologous chromosomes, deletion of segments of chromosomes, production of ring chromosomes, etc.).  In contrast, since homologous recombination relies on the cut-back broken ends recognising their counterparts in the same location on a sister chromatid or homologous chromosome, it is impossible for the wrong ends to be joined together; the worst that can happen is that material is exchanged symmetrically between homologous chromosomes, an essentially-completely-benign occurrence.
MMEJ relies on the presence, sprinkled liberally throughout the genome, of numerous repeated short identical DNA sequences; when a double-strand break occurs, each of the broken ends is cut back to the nearest one of these repeats, one strand is cut away from the repeat on each end, leaving a pair of complementary single-stranded flaps, one on each broken end, and these flaps are then stuck together and the whole thing stitched up by a ligase.  This process, by its very nature, always results in the loss of the segments of DNA immediately adjacent to the break; if the break occurs between two repeat sequences, one of the two repeats will be lost, as will the entire unique segment between them, while, if the break cuts through a repeat, the bisected repeat will be lost, as will both of the unique segments flanking it, as will one of the pair of nearest undamaged repeats upstream and downstream of the original break.  Homologous recombination, in contrast, results in no loss of genetic material.

The main drawback of homologous recombination is that it requires an identical, or near-identical, template; if - say - double-strand breaks occur at near the same level on both examples of a particular chromosome in a diploid cell in G1, or if any double-strand breaks occur in a haploid cell in G1, the damage cannot be repaired by homologous recombination, and repair (if possible at all) must be carried out via one of the two aforementioned lower-fidelity methods.
One would, thus, intuitively expect (at least so far as concerns double-strand breaks and the repair thereof) that in DNA repair, as in data recovery, the more homologous copies (even if damaged) that are available, the better the chance of successfully rebuilding a working genome or boot drive; i.e., the greater the organism’s ploidy (its number of homologous copies of each chromosome), the greater its ability to repair DNA damage involving numerous double-strand breaks, such as that produced by ionising radiation; e.g., a diploid organism would be less able to repair radiation-damaged DNA than a tetraploid organism, which would itself be more vulnerable to radiation-induced damage than an octaploid organism, which would still be less resilient than a hexadecaploid organism, which would, in turn, have a harder time piecing its genome back together than a dotriacontaploid organism.2
Is this actually the case in practice?

1: There are two variants of this pathway.  In the double-strand-break repair (DSBR) pathway, both single-stranded flaps engage with the homologous chromatid/chromosome, producing two Holliday junctions; all DNA synthesis, and the first pair of ligations, occur prior to the junctions being cleaved; and the portions of the chrom(atids/osomes) distal to the junctions are sometimes exchanged between the two, depending on how, exactly, the Holliday junctions are cleaved.  In the synthesis-dependent strand annealing (SDSA) pathway, only one flap engages, producing but a single Holliday junction; the homologous DNA serves purely as a template, with the intruding strand disengaging once it has acquired enough additional length to bridge the gap; and the balance of the new DNA is synthesised after the two ends have already stuck back together.  (Alternatively, see Wikipedia.)
2: This assumes an autopolyploid organism (one where all however-many chromosome sets are from the same source and equivalent to each other), such as any of the extant sturgeons (all of which are either autotetraploid, autooctaploid, or autododecaploid); for an allopolyploid organism (one produced by putting the entireties of two [or more] genomes from two [or more] related organisms into a single cell and letting that develop into an organism), such as bread wheat (allohexaploid), the chromosomes from (say) genome A refuse to hang out with those from (say) genome C, and the organism is functionally merely diploid (albeit with a greatly-increased monoploid number).


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Is prokaryotic chromosome really a chromosome?
As far as i know, chromosome is a highly compacted version of chromatin during mitosis. And chromatin is a complex consisting of DNA strand and histones for more effective storage of DNA.
And I'm heard(not actually 'learn' it) that chromatin is only found in eukaryotic cells and prokaryotic cells have a different organization of their DNA.
Taken together, prokaryotes don't have chromatin and don't have chromosome either since chromosome is a upgraded version of chromatin.
But many medium including books and internet sites call prokaryotic organization of DNA chromosome(especially E.coli chromosome)
Hence, my question is:
Is it just a wide use of chromosome term in prokaryotes? or my knowledge of chromatin and chromosome wrong?
*plus, I searched about this problem previously and am heard that the prokaryotic chromosome equivalent is called genophore. How about genophore?

Initially, chromosomes got their name from the ability of eukaryotic metaphase chromosomes to bind certain dyes. The word chromosome is Greek for "colored body".
Nowadays, the term chromosome refers broadly to a single DNA molecule, no matter the organism. Hence the term "E. coli chromosome".


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Pathophysiology of pink frothy sputum in pulmonary edema
Pulmonary edema is a condition where fluid leaks into the alveolar spaces. This can be due to to hemodynamic causes like left heart failure and pulmonary venous obstruction or microvascular injury or increased capillary permeability.
Clinically we are taught to differentiate between various types of sputum. The sputum in pulmonary edema is characteristically pink and frothy.
It is important to mention here that the fluid that leaks into the alveolar spaces is a transudate and not blood. Hence it is by no means that the pink is due to blood. Otherwise it would be called hemoptysis.
My question is, why is the sputum pink if blood has no role to play?

Please don't migrate this question to health.se since pathophysiology pertains more to biology than health. Thanks.

Even though the fluid in pulmonary edema is a transudate, there is blood in it. This is substantiated by the fact that there are microhemorrhages in acute lung congestion and hemosiderin laden macrophages or 'heart failure cells' in long standing pulmonary congestion on histology. These signify that RBCs have escaped the vasculature to enter the tissue (and failed to get back to the blood), while the macrophages have consumed them later on.
Since the blood loss isn't very high, the color is pink rather than red as seen in hemoptysis.
The reason for this is likely due to the significant differences in hydrostatic and oncotic pressures when compared with the rest of the body. In the Lung, one edge of the capillary is up against a single, extremely thin alveolar cell that provides very little pressure to counterbalance the increased forces present in pulmonary edema. Without this inward pressure to stabilize the capillary wall, you end up with a situation in which small ruptures occur at weak points in the AC membrane, unlike elsewhere in the body where pressures are more equalized and change is an osmotic process rather than one of cellular disruption.
Although hemosiderin laden macrophages can be a proof that RBCs leave the vasculature, it is important to note that they can be found in other organs too. One example is the chronic venous congestion of the liver, where the hypoxia (due to congestion) can lead to endothelial damage letting out the RBC, which later get engulfed by macrophages.


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Why are vegetations in Infective endocarditis common on the atrial side?
Robbin's Pathology says that vegetations of IE are more common on the atrial side in AV valves. In Liebmann Sack's Endocarditis, which is a sterile (non bacterial) type of endocarditis, the underside of the valve also has vegetations. Why is it so? If its just colonization of bacteria in IE, how does it matter where?
Does gravity matter in colonisation of bacteria!! ?

Infective endocarditis generally develops when there is a pre-existing valvular lesion. The location where the vegetation in infective endocarditis develops is based on the pressure of the surroundings. Bacteria tend to colonise places where the pressure is low.
'Where the pressure is low', depends upon what kind of a valve deformity is already present.
In mitral regurgitation, blood when pumped from the left ventricle enters the atria due to the patent bicuspid valve. Naturally, the pressure is more on the ventricular side than the atrial side. Hence, the bacteria settle on the top of the leaf. Moreover, the do so at the edges of the leaves. This is because, since the blood has to squeeze through, according to to bernoulli's theorem (Venturi effect). Hence they form on the edges of the atrial side of the valves

In case of an aortic regurgitation, since there is a backflow of blood from the aorta to the ventricles, the vegetations are found on the underside of the aortic valves.
Liebmann Sacks (which is non infective and happens in lupus) is common in the mitral valve though it can happen anywhere. I assume, since bacteria are living cells, the pressure constraint applies to them but not to sterile vegetations like the one in lupus.
I implore you to have a look at this wonderful video which explains it all.
Picture credits and reference : Endocarditis by osmosis.org

With the bacterial IE, it would look like the vegetations tend to colonize the lower pressure sides of the valve structure (REF1). Something that was made clear that distinguishes the IE vegetations frm the Libman-Sacks vegetations was overall motility. Specifically, Libman-Sacks vegetations exhibit no independent motion and are largely sessile, whereas IE vegetations can be motile (REF2). In terms of where they attach I think this makes sense, the more motile vegetations colonize the less turbulent area, and the sessile vegetations seem to hold up in either scenario. Reference 1 also rather usefully points out that IE vegetations may be located anywhere on the valve structure as well, they just tend to be on the low-pressure side.
So being said i would argue that the motility of the organisms is a deciding factor.

Robbins classifies IE as acute or subacute. Subacute IE is the one where flowing viridans bacteria stick to already damaged valves. Arrhythmia isn't mentioned as a risk factor or a predisposing factor. Rather valve damage/ prosthetics are. Could you suggest a further read regarding the Afib leading to endocarditis thing?

I'll be honest, I don't like that answer that I initially posted, so i'm going to rehaul it here

Thanks for the answer. Could you pls explain what 'motility' means in this context? The vegetations don't move themselves right? Like move with the valve??

Motility meaning "are they capable of moving on their own or are they for the most part adhered to the structure?", in essence.

The Cleveland Cardiology review mentions Mural thrombi as a risk factor for bacterial endocarditis :)


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How is monoclonality or polyclonality determined?
I was reading up Kaposi sarcoma and Robbins Pathology says,

..many features suggest that KS is not a malignant tumor despite the ominous name ...spindle cells in many KS lesions are polyclonal or oligoclonal

This is also seen in multinodular goiter where the lesions are polyclonal, but some monoclonal nodules are found.
My question is, how are these determined? By sequencing, is it not that, in cancerous growth there are myriad mutations, how can you map whether the mutations present are due to monoclonal expansion or polyclonal expansion? In non cancerous growths, wouldn't all cells have the same genotype?
Polyclonal and monoclonal expansion in B-cells is clear to me since a polyclonal lineage would have different vdj recombs while monoclonal would have the same. Here also, is it decided by genomic sequencing or the Ig sequence?

There are a few ways to determine clonality. Sequencing-based methods are probably the cheapest, given the current costs of either sequencing, or the even cheaper PCR-based clonality assay. Other methods might include histomorphology, looking for known chromosomal aberrations and/or immunophenotyping, among others. Here's a nice review of some of the clonality testing methods.
Sequencing and PCR would be the most definitive ways to determine clonality of a tumor, since they provide information on the exact sequences of sets of cells.
Exome sequencing would be a good way to determine clonality in a large group of cells, where you don't necessarily know what to look for a priori. PCR is a lot cheaper and more focused and might make a better choice when you do have a specific target to sequence, such as highly polymorphic genes like some androgen receptors and the genes involved in VDJ recombination.


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What is the function of the Moderator band?
The moderator band in the right ventricle is a band sorts of muscle which consists of a significant branch of the AV bundle. Does it mean it delivers impulses to the anterior papillary muscle faster? If it does, how does this help? and why only the anterior papillary muscle? What makes it special to have a moderator band?

Does it mean it delivers impulses to the anterior papillary muscle faster?

Yes.

If it does, how does this help?

To facilitate the conduction time thereby allowing coordinated contraction of the anterior papillary muscle.

and why only the anterior papillary muscle?

This is because its chordae tendineae insert into anterior and posterior tricuspid valve leaflets, so only their contraction before systole would be optimum.

What makes it special to have a moderator band?

For effective Cardiac Output because it helps in coordinated contraction of ventricular cells. The ventricles must maximize systolic pressure to force blood through the circulation, so all the ventricular cells must work together.

Could you add some reputable support/citations for your answer? Thanks!


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Why do anaerobic bacteria require a low redox potential for their culture media?
I'm reading Clostridium ,which is an anaerobic bacteria in my microbiology text and it says,

of more importance than the absence of oxygen is the provision of a sufficiently low redox potential in the medium. Third can be achieved by adding unsaturated fatty acids, ascorbic acid, glutathione, cysteine, etc.

Why? Do they reduce oxygen free radicals or something? Well, are these present in Clostridium's natural habitat?

The higher the redox potential is, the higher the oxygen dissolved in the media will be. Lowering this potential insure that the oxygen concentration is lower and that the anaerobe will be able to grow easily.
Several steps can be done while preparing the media such as boiling to remove oxygen and adding chemical which reduces this redox potential to dissolve oxygen back into the medium.
As for the natural habitat, they naturally have no or really really low amounts of oxygen. If the habitats containing little oxygen have other molecules able to reduce redox potential is a good question.
Lowering the redox potential is mainly important for the medium since there is oxygen involved (hard to remove 100% while preparing media).
I hope my answer helps.

Thanks! Also on further reading I found out that the pathophysiology of gas gangrene cause by anaerobes is also related to the reduction of redox potential and hypoxia.


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What is this marine creature? Is this a fossil?
Found this on a beach on the East coast of India - Vishakhapatnam, India
Is this a fossil? A coral?

Its small enough to fit in my hand

These tunnel-like structures are hard like rock/calcified

Obverse

Obverse

Doesn't look like a fossil because doesn't look rock-like enough and not buried. Maybe this? https://gohiking.ca/animals/fish/marine-worms/calcareous-tube-worm/

Its not a fossil.
It is just shells of various marine invertebrates that get stuck together as they grow. It looks like worm-snails on a a large piece of clam shell. the little holes in the clam shell are bored by sea snails and erosion.

there are whole blogs devoted to finding interesting examples. https://natureinfocus.blog/2010/01/13/calcareous-worm-tubes-on-flat-oyster-shells/


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Is there any way to tell if a gene is functional for an individual with only a reference sequence and the individual's sequence of the gene?
I have gene sequence of a ton of individuals within a subspecies from cdna and the ncbi IDed sequence as well. Is there any way to tell using just the sequence that the gene for an individual is non-function or only partially functional?

In general, no.  There might be specific cases where you can, like if there is a stop codon, or a frameshift mutation early on, or someone else has seen your exact variant and experimentally proved that it has no function.
But in general, you cannot predict function from in silico data alone.

It is possible to get a prediction of the change caused by a mutation using programs like Sift or polyphen(only for human proteins), but these are only rough estimates

I don't know your level of knowledge, so this may seem very obvious to you, but...

Translating it into the six frames gives you some hints. If the sequence has degenerated and is full of stop codon, then it's nonfunctional.
Align the sequences with Mega or AliView or whatever, then translate them. If there is a frameshift mutation in your sequence, it becomes very visible within the alignment and chances are that the sequence isn't functional anymore.
Find information about the protein's domain in Pfam and look closely to the alignments in the functional domain. If otherwise conserved residues are mutated, this should ring a bell. (Since all your sequences will be very similar to each other, you may want to add some sequences of the protein of other species, so that you can find more easily the active residues within a domain)


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Why does Cyan appear bluish rather than greenish, when the phototopic eye sensitivity is highest in green (and Cyan contains blue and green equally)?
Cyan contains blue and green equally.
Phototopic eye sensitivity is highest in green.
Why, then, does Cyan appear bluish to most of us, rather than greenish?


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What is this? In Florida. Found in plant bed under rosemary tree that gecko' enjoy hiding aloe plants also growing.

Species identification of round soft outer shell

Could you please add the size/diameter of this object?

Possible duplicate of Is this a plant or a fungus?

I only know this because I have seen them before in the tropics, but this is probably Clathrus ruber (Wikipedia).  So interesting!
EDIT: Also mentioned in these questions 1 and 2 so perhaps this will get marked as a duplicate.

Clathrus spp. is a good call but Clathrus crispus  is common in Florida. Still an up-vote.


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are clones siblings to the original?
i have a question about cloning, if a person had his/her DNA sample like hair or blood used to make a clone wouldn't that clone be that same person's brother or sister since they share the same genetic makeup? also, what if a person had heterozygous genes and had two clones? but the clones had their alleles swapped making one clone have most of that person's dominant genes while the other had that person's recessive genes making the clones homozygous, would that make the person a father of mother to those clones or a blood related brother or sister?

This actually isn't a biology question, it's a moral, legal and semantic question. "Siblings", biologically, are offspring of the same parent(s). A clone, as developed through human technology, isn't the offspring of any parent in the usual sense. It was not generated from a pair of gametes that came from two different parents; it came about via a completely different biological process, one that doesn't really occur in nature (there are many natural processes that result in identical copies we call "clones", but none of these does exactly the same thing as technological process we call "cloning").
Biologically, a clone is a clone, siblings are siblings, and they come about via very different processes.
None of this means that legally, or morally, or by the dictionary definition, we cannot redefine "sibling" to include clones. And it makes perfect sense to do so. It could also make sense to define clones as "offspring" instead. This could be based on genetic similarity, or on other things.
The thing is, there isn't an obvious single answer to how they should be redefined if human cloning were a thing. This isn't an issue human society has had to deal with yet so none of these redefinitions have happened.
For an idea of what they could look like though, I'm reminded of Lois McMaster Bujold's science-fiction Vorkosigan series, that deals with cloning (in books like Brothers in Arms in particular). Different societies in her books deal with cloning in different ways, and human clones have different statuses. One of those societies (one of the more sensible ones) considers a clone to be the child of the cloned person if it's an adult cloning themselves to make a baby, but to be the sibling of the cloned person if the person's parents decided to clone their child. Basically, in that society the people who decided to make the clone would be considered its parents, and the clone's genetics would have nothing to do with it.
Note that even in our society, siblings and parents aren't only defined by genetic similarity or any biological process, but by a legal relationship, shared history and responsibilities. Adoptive parents and siblings are considered in many (most? all?) countries to be legally equivalent to biological parents and siblings.

but you just said "A clone, as developed through human technology, isn't the offspring of any parent in the usual sense." then said "It could also make sense to define clones as "offspring" instead." so would a clone be a sibling or offspring to the original? also, to be a sibling to a clone is exactly what i meant if someone was cloned off of since it's that same person's DNA being replicated.

@sarahdan I am saying that right now, there is no definition of "sibling" or "offspring" that includes clones. My second paragraph was about how we might change the definitions to include clones, but I can't tell you in advance what the governments, ethics commissions, supreme courts and people of the world will change them to if human cloning happens, because that hasn't happened yet. Do you understand what I mean by this not being a biological question? Adoptive siblings are siblings but that has nothing to do with biology, wouldn't you agree?

i agree, but i can't help but feel that if you were cloned you and your clone would be siblings since you share the same genetic code.

@sarahdan to put my answer differently, your question seems to assume that "siblings" and "parents" are defined by genetic similarity. But this is not true. Parents and siblings are defined by how an individual came to exist. If it was formed from the union of two gametes, the organisms the gametes came from are its parents. If other organisms came from the union of gametes from those same parents, they are siblings. All other systems for making new organisms involve extending the definitions or using new words.

@sarahsan in nature plenty of organisms reproduce by making copies that share the exact same genetic code, and those are usually referred to as "parent" and "offspring" but it depends on context. They are also sometimes seen as parts of a same, larger clonal organism. So you see "same genetic code" doesn't mean "siblings". You assume that because in humans, the only people with identical genes are twins, who are siblings by the standard definition (children of the same parents). But humans don't reproduce by cloning, so we have no words or definitions for the relationships between clones.

@sarahdan and the fact that twins are the only humans that have identical genes, and happen to be siblings, is pure coincidence. If humans could reproduce asexually we might think it normal for children to have the exact same genes as their parents.

but that would be kinda weird to define something that has the same genetic makeup as you as your kid. i mean, if the two pair of chromosomes you have was used to create another being, surely the product of that would be your sibling like how you explained if a parent were to clone a kid they already have their current kid would have a sibling that was cloned off him/her.

@sarahsan why would it be weird? It's exactly what we do with aphids when they reproduce through parthogenesis. When we talk about a cell asexually splitting into two cells, we talk about the new cells being daughter cells, not sister cells. Why would it make sense for something that has the same genetic makeup as you to be your sibling? Human siblings don't typically have the same genetic makeup, anymore than human parents and children do.

yeah i know asexual is normal but cloning like ding somatic cell transfer seems to come off more as something where your genetic material such as hair, skin, or blood consisting of your entire two chromosomes to make a clone would be the end result of you and your clone come off as siblings, thats what i wonder.

@sarahsan ...why would cloning make people more like siblings than asexual reproduction does? I mean, do you actually "wonder" here or do you think the answer is "yes" and you're just fishing for confirmation? If not, how exactly have I not answered your question here? Just repeating the question won't help.

i said somatic cell transfer, in other words, EX: you take hair from a person named tom and a egg from a person named samantha who donates her egg but has her sex cells removed from it making it be a nucleus that holds tom's hair to make a clone, after undergoing the process, an embryo is formed and placed in samantha to give birth to the said clone. (this is what i'm talking about wondering if the clone is an actual sibling of tom)

and just to be clear, you did say in order for a clone to be a sibling to the original the original has to be cloned by the parents, but isn't this the same thing?

@sarahsan again, why does somatic cell transfer say "sibling" to you? Human siblings don't come from somatic cell transfer. Please answer my questions instead of just repeating yourself. And I did NOT say that "in order for a clone to be a sibling of the original the original has to be cloned from the parents". Please read what I write more carefully. It sounds like you're confusing something I said about an IMAGINARY law in a SCIENCE-FICTION book with an actual statement about reality, and that's not even what the imaginary law I mentioned said.

@sarahsan actually for a direct example of somatic cell transfer not resulting in something people called "siblings", Dolly the sheep's DNA donor was generally referred to as her mother.

i already gave my answer as to why somatic cell transfer is saying "sibling" to me you should read carefully, and i'll say it again more clearly, the reason why i see somatic cell transfer as a cloning process to where the original being cloned off of is a sibling, it's cause like identical twins they themselves are close to that of being clones, but naturally different from cloning, but most of all in this case, it's because of two beings sharing the EXACT DNA structure should/could be that of siblings since there are no shared 23 chromosomes/sex cells between two people.

@sarahsan that is true, all those are things you've said, and not only did I read them at the time, I addressed every one of them so I don't know what you are looking for here. Except for the twins thing, which you haven't brought up before but I also addressed (though I could add that one difference between twins and clones that affects how they "come off" is that twins are always the same age & from the same pregnancy, clones not). Do you still have a biological question that needs to be answered here, or do you just have an opinion on how words should be used that you want me to agree with?


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Why does the iron content differ in different species on seeds?
Iron can be affected by pH of the soil but why does each species actually have a different iron content. What causes it? What genes cause it?

I don't think there is some single omnipresent gene in plants that says what the iron content of their seeds are. I think different genes in different species plays a role as well as environment.

Why would you expect different species to have the same iron content?  Or anything else, FTM.


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What Snake is this? (Found at my door in Raebareli, North India)
Found this snake at my door in Raebareli, North India. We of course allowed it to go away peacefully.
Could someone please identify it for me?

It is the venomous Common Krait (Bungarus caeruleus), one of the Big Four Indian Snakes,  responsible for the highest number of snake bites in India.

How close was it to humans when it was noticed? Are these aggressive snakes?


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How is SARS-CoV-2 'deactivated' for some Covid vaccines (for example Covaxin)?
Some Covid vaccines like Covaxin employ a 'Whole-Virion Inactivated Vero Cell'.
How is the virion 'deactivated' for the vaccine?

For Covaxin (BBV152), SARS-CoV-2 was inactivated by treatment with β-propiolactone [1]. β-propiolactone reacts with and modifies, among other things, nucleic acids, thus preventing their replication [2].
[1] Yadav P, Ella R, Kumar S, et al. 2020. Remarkable immunogenicity and protective efficacy of BBV152, an inactivated SARS-CoV-2 vaccine in rhesus macaques. Preprint.
[2] Perrin P, Morgeaux S. 1995. Inactivation of DNA by β-propiolactone. Biologicals 23(3):207-211.


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Please help me identify this tree/fruit. Is it edible?
When free, could the experts here please help me identify this tree.
Location: Delhi, India
Height: 20-30 feet
Date: October
Is the hanging green colored fruit edible?
Thank you for all the kindness in Biology SE.

This looks like Catalpa bignonioides, aka the Indian bean tree and is commonly used as a garden or street tree.¹ The plant is  native to the southeastern United States but was introduced in northern India later.²
Regarding edibility:
No,  I would not recommend eating any part of it as multiple websites list it to have no edible uses, and the roots are highly poisonous³ ⁴

References:

https://en.wikipedia.org/wiki/Catalpa_bignonioides
https://powo.science.kew.org/taxon/urn:lsid:ipni.org:names:30194969-2
https://pfaf.org/user/Plant.aspx?LatinName=Catalpa+bignonioides
https://homeguides.sfgate.com/catalpa-edible-90090.html


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What is this insect found in Malaysia?
Found in Malaysia, South East Asia. Small insect with wingspan of around 1 centimetre. Its back legs and abdomen are pointed away from the wall.
Front View:

Diagonal View:

That is a moth, (Lepidoptera), in the family Pterophoridae. It looks very much like Stenodacma wahlbergi.  https://en.wikipedia.org/wiki/Stenodacma_wahlbergi


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Is there gas exchange in the fingers?
I saw A documentary many years ago that said that hemoglobin will take in O2 in the fingers and toes. I have Not been able to find any information on this. But it would seem that being so close to the surface some gas exchange would occur, and more so in the fingers and toes than the teunk.

At first I was skeptical about this question but then I did some researching and apparently, a certain amount of oxygen is indeed taken up from the surroundings through the upper layers of our skin. In fact, the paper titled "The cutaneous uptake of atmospheric oxygen contributes significantly to the oxygen supply of human dermis and epidermis. states that

the upper skin layers to a depth of of 0.25-0.40 mm are almost
  exclusively supplied by external oxygen, whereas the oxygen transport
  of the blood has a minor influence.

Here is another paper that you would find interesting. In short, I would say that its not just the fingers but O2 diffusion into cells take place over the whole body.


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Does the brain always enter alpha/beta waves upon brief awakenings during the night?
If you realize you are awake briefly before falling back asleep, have you necessarily exited REM sleep or another stage? That is, is the experience of waking briefly (tossing and turning, etc.) always tied to conscious beta wave patterns?


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Lipid Diffusion
Epithelial cells in the small intestine absorb lipids through simple diffusion but how does diffusion of lipids occur in the first place if they are insoluble in water? I thought that substances need to be dissolved in order to have concentration and therefore a concentration gradient?

Insolubility means they don't dissolve in water and may self-associate. That doesn't mean they cannot exist in aqueous environments. I'm not sure this question is clear enough to answer accurately.

Do you actually have a reference that supports your understanding as being correct?

http://www.vivo.colostate.edu/hbooks/pathphys/digestion/smallgut/absorb_lipids.html     "The major products of lipid digestion - fatty acids and 2-monoglycerides - enter the enterocyte by simple diffusion across the plasma membrane. A considerable fraction of the fatty acids also enter the enterocyte via a specific fatty acid transporter protein in the membrane." Essentially I would like to know if a non-soluble substance could diffuse in water because my current understanding is that only dissolved substances can.


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Can anybody identify this flower for me?

One single flower on small 2 year old tree with alternate leaf arrangement

What is your location?  Do you know if this is an ornamental specimen, or something native?  The flower strongly suggests the family Malvaceae (think hibiscus).


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What type of spider is this?
What kind of spjder is this? It was found in nova Scotia

The rounded carapace of the cephalothorax, and the relatively slim, banded legs indicate that this is one of the terrestrial Dolomedes fishing spiders.  The 'w' stripes on the abdominal pattern have white markings on the margins, but are not 'underlined' completely across in white, which rules out Dolomedes scriptus, in my experience.  Also (although I think this can be somewhat variable in these particular Dolomedes), this spider does not have the familiar white rim to the cephalothorax and abdomen.  Accordingly, I'll go with a rather light-colored individual of the fairly variable Dolomedes tenebrosus.
The links I enclose allow you to explore images of these spiders for your own interest:
https://bugguide.net/node/view/38828
https://bugguide.net/node/view/2011
Oh, yes - almost forgot.  Although these spiders can give a noticeable bite, the venom is less trouble than the standard Polistes paper wasp sting.  I have been bitten only once despite handling numerous females, and had almost no effects beyond a bit of pain and a small red bump.  Like most spiders, these can control the amount of venom they inject, so mine might have been a 'dry bite', but I've heard nothing about bad effects from bites by this very common spider.  I think it's safe to assume that this is a harmless spider - to us.  They love beetles and other large arthropods.


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How are the helices of MscL gating "attached"?
I'm attempting to model the mechanosensitive channels of large conductance (MscL) in E. coli for finite element analysis purposes. I have a number of papers where this has been done, and one shows the modelling with van der Waals forces (as seems logical), but is it known how/where these forces exist?
For references, two papers I'm using have videos and pictures:
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0183822#sec013 (see the movies S1 & S2)
https://www.cell.com/action/showFullTextImages?pii=S0006-3495%2806%2971838-0

Well, the N-terminus is connected to the TM1, which is connected to the TM2, which is connected to the C-terminus... how are they connected?

Thank you @MartinKlvana, if you put that as an answer I'll vote it. It's exactly what I was looking for.


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Why can humans tolerate eating onions but other mammals like dogs and cats cannot?
Onions are one of the many foods we shouldn't feed our pets. Looking it up, I learned that onions cause hemolytic anemia in MANY species: cattle, sheep, horses, dogs, cats, and even some primates. If anything, WE'RE the odd ones out. A few sulfur-containing organic compounds found in onions were fingered as the causative agents, and oxidative damage to red blood cells following decreased activity of glucose-6-phosphate dehydrogenase was the most mentioned mechanism. How do humans avoid this?


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Why aren't all strongly self-recognizing T cells made into regulatory T cells?
Negative selection in T cell development is often simply described as preventing effector T cells from recognizing self-antigens. This is complicated by regulatory T cells developing from T cells with moderate affinity for self-antigens. If recognition of self is useful for immune tolerance, why don't T-cells with strong affinity for self-antigens also become regulatory T cells?

The selection is based upon the strength of the binding. A strong bond causes a signal in the T-cell to self destruct (apoptosis).
Wikipedia has a post on T cells. Perhaps the moderate bonding become regulatory cells, because these cells have to recognize those T cells that survive negative selection, which are most likely to cause autoimmune responses over a long period of time.
Strong affinity to self means the immune response will become a danger to the host.

I understand that effector cells should have a weak affinity for self so that they do not attack the host, but why shouldn't regulatory cells? If moderate affinity for self is used by regulatory cells for tolerance, why wouldn't strong affinity for self do the job better?

@BatWannaBe To my knowledge the strength of the self-reactivity of Tregs can differ by subset, and those cells have different roles. The problem, and some evidence here, is that high self-reactivity is associated with autoimmunity.

@CKM The article you linked seems to claim that higher self-reactivity makes Tregs better at SUPPRESSING autoimmunity. See the discussion paragraph starting with "Our study showed that the level of TCR self-reactivity alone can be used to identify superiorly functional Tregs in preventing tissue-specific autoimmunity."

@BatWannaBe Sorry, I was unclear and that comment was less helpful than when I was typing it up. They do state that clearly in the discussion. There are also some tidbits that continuous TCR signaling can potentially make the Tregs dysfunctional and ablate their ability to control the autoimmunity.


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What does the decline of serum antibodies after infection mean for B cell immunity, exactly?
About a month ago there was a small media blip about a report in the New England Journal of Medicine that neutralizing antibodies to SARS-CoV-2 decline significantly within a matter of months. Published op-eds ranged from "a vaccine won't work, why God WHY" to "actually this isn't that weird, stop freaking out." Some key details from the articles I read at the time:

We still got T-cell immunity, and there are some signs this could last longer for COVID-19
Antibodies decline as infections clear for other illnesses.
Remaining memory B cells are (usually) primed to churn out more antibodies upon reinfection.
Nevertheless, the decline of antibodies is less protective and raises concerns of decay of immunity (an opinion in the original report)

I want to ask about the B cell side of this in order to better understand the somewhat conflicting messages and opinions.

If memory B cells worked as advertised, how would serum antibody levels even be a measure of immunity? It would seem that antibodies dropping to negligible levels wouldn't matter if your memory B cells can make them on demand.
Is there some benefit to having antibodies in your blood independent of your memory B cell function? Is it somehow quicker or vital to prevent reinfection or recurrence of serious illness?

The decline in serum antibody level after vaccination means the level of spike protein specific T cells declines, in another word, the virus is eliminated [1]. When the vaccine introduced a viral particle or mRNA into the cell, SARS-CoV-2-specific CDH4+ T cells recognize 2 variant spike proteins, helping B cells to secrete antibodies and activating cytotoxic T cells to destroy the infected cells [2]. After infected cells are destroyed, antibody level will gradually decline because the virus is eliminated from the body [3]. But this doesn't necessarily mean an absence of immune memory because

Memory T and B cells remain, however, and maintain a heightened ability to mount a response to a recurrence of infection with the same pathogen.

Otherwise, it's wasteful to have antibodies synthesized and maintained independent of B cells function.
References:

Cox, R.J., Brokstad, K.A. Not just antibodies: B cells and T cells mediate immunity to COVID-19. Nat Rev Immunol 20, 581–582 (2020). https://doi.org/10.1038/s41577-020-00436-4

Alberts B, Johnson A, Lewis J, et al. Molecular Biology of the Cell. 4th edition. New York: Garland Science; 2002. Helper T Cells and Lymphocyte Activation. Available from: https://www.ncbi.nlm.nih.gov/books/NBK26827/

Janeway CA Jr, Travers P, Walport M, et al. Immunobiology: The Immune System in Health and Disease. 5th edition. New York: Garland Science; 2001. Immunological memory. Available from: https://www.ncbi.nlm.nih.gov/books/NBK27158/

First sentence: "B cells", not "T cells"?


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What is this trilobite-like creature?
This was found under a rock in a freshwater creek in Maryland. Stayed like this for while, then stretched out long, then contracted, and then JUMPED off the rock back into the water. Looks like a trilobite. Rock-colored.

well I don't know of any freshwater chitons, so I'm going with a leech. In fact, if by "stretched out long" you mean it literally became long like a ribbon, then this is almost certainly a leech.

Yes, a leech. I don't know the species, or even family.

Very nice image of a leech (probably of family Glossiphoniidae). Please consider sharing a cropped version somewhere like iNaturalist.org

Thanks, everyone. Never seen a leech before. I always assumed they were more squishy-looking!


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What's the difference between a lymphocyte and a plasma cell?
According to my understanding, lymphocytes is the broad terminology for both T lymphocytes as well as B lymphocytes, while plasma cells refers to mature B cells which produce antibodies. But then why are they mentioned separately, doesn't a plasma cell come under category of lymphocyte?

But then why are they mentioned separately, where are they mentioned separately? If you are referring to a specific text or quote that raises this question, it would be best to include that reference here. right now your question is a bit confusing.

Yes, in Robbin's Basic Pathology, while describing inflammatory process of several diseases, it is mentioned that there is presence of both plasma cells as well as lymphocytes in the affected tissue. So that raises the question, why are plasma cells and lymphocytes mentioned separately? Why not just mention that there was infiltrate of lymphocytes (assuming that plasma cells come under a category of lymphocytes)?


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Why is there low hepcidin levels in hemochromatosis?
If hemochromatosis is iron overload and there is excess iron in the blood, why does the liver reduce hepcidin secretion (which increases the iron uptake) furthering the worsening of hemochromatosis?

From what I remember it all depends on which type of hemochromatosis we are talking about. There are several types depending on the cause and some of those like the hemojuvelin gene mutation-related have low levels of hepcidin as the CAUSE of the hemochromatosis (since like you mentioned, seeing it as a consequence wouldn't make much sense)
The first 4 pages of this paper should clear things up a little bit https://www.aasld.org/sites/default/files/guideline_documents/Hemochromatosis2011.pdf


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What is the difference between cytokine and chemokine?
I often see these terms being used in inflammation, and I'd like to know, are they synonymous with each other or do they mean different things? Also could someone provide an example of each?


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Why is beta thalassemia major not lethal while alpha thalassemia with loss of all 4 genes lethal?
So why is beta thalassemia major with two B0 alleles not fatal in utero (despite the hemoglobin not having any B chains), while alpha thalassemia with deletion of all 4 genes encoding for the alpha chain fatal? Is the alpha chain more important than the beta chain?

This has to do with the fact that fetal hemoglobin (HbF) isn't made of the same chains as adult hemoglobin. The latter comes with 2 alpha chains and 2 beta chains while the main fetal hemoglobin is made of 2 alpha chains and 2 gamma chains. Hence any disease affecting the quality or quantity of beta chains won't have nearly as much impact on a fetus as it does on an adult.
Reference: https://www.uptodate.com/contents/fetal-hemoglobin-hemoglobin-f-in-health-and-disease

In essence, yes, the alpha chain is more important than the beta chain, because there are alternative forms of hemoglobin that can deliver oxygen without beta chains, but the hemoglobin forms without alpha chains cannot.
Hemoglobin has a bunch of different forms, depending on which four globin chains make up the protein. While there are even more, here's an overview of the most important forms:

Hemoglobin A is α2β2, this is the normal form, and in adults this makes up 95% of our hemoglobin.
Hemoglobin A2 is α2δ2, with 2 delta chains instead of beta chains. It normally makes up about 2-3% of hemoglobin, and its properties are nearly identical to HbA.
Hemoglobin F is α2γ2, with 2 gamma chains instead of beta chains. This is the primary form in utero, because it has a higher affinity for oxygen, and thus can extract oxygen from the maternal circulation. It normally decreases after birth, and makes up <1% of adult hemoglobin.
Hemoglobin H (β4) and Hemoglobin Bart's (γ4) are defective forms of hemoglobin that occur without alpha chains. Both of these are unstable molecules, and are poor at delivering oxygen because their affinity for oxygen is too high (not allowing it to be released in the tissues).

What you'll notice from the above is that there are functional hemoglobin variants that don't have beta chains, but no functional variants without alpha chains.
If someone has beta thalassemia major, with loss of both β alleles, the body compensates by ramping up production of HbA2 (with delta chains) and HbF (with gamma chains), which compensate for not having HbA. That's not to say that everything is okay... it's still a very serious condition, and usually progresses to death before age 20 if untreated. But, the hemoglobin variants are sufficient enough to allow people to live.
If someone loses all 4 alpha alleles, the only hemoglobin they produce is Hb Bart's, which isn't functional. There are no alternatives to the alpha chain like there are with beta thalassemia, so there's no mechanism to compensate for this loss. Because forming HbF isn't possible without alpha alleles, this condition is fatal in utero.


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Why is melanin black?
I understand that the function of melanin is to protect individuals from sunlight, and that people living in sun exposed areas are darker due to increased production of melanin. But why is the melanin pigment black in color? Wouldn't it have been more useful if melanin was white?
From my understanding, black absorbs more sunlight than white, so if melanin is black, it will tend to absorb more heat (which isn't a good thing in areas with a lot of sun exposure). This will lead to production of more melanin (tanning).
Instead, evolutionarily wouldn't it have made more sense if melanin were white, since not only would the pigment protect the person from sun exposure, but also prevent more sunlight from being absorbed?

As phrased, the question is not a biological one, but one for chemistry or physics: melanin is black because of the way its chemical structure interacts with photons.  Perhaps you meant to ask how mammals evolved to produce melanin, and how humans (among others) have evolved to use it as protection against the harmful effects of intense sunlight?

Let's do a quick mind experiment. Imagine a ray of UV light hitting a white molecule in the skin. White generally reflects light, so that UV light would bounce off, and potentially could hit something much more critical. Black, on the other hand, absorbs light, so the energy in the UV light would be absorbed by melanin rather than other, more sensitive molecules. According to this article:

eumelanins are capable of dissipating >99.9% of absorbed UV and
  visible radiation through nonradiative means.

Eumelanins are the most commmon type of melanin. Incidentally, not all melanin is black.
Another quick note, somewhat relevant: Try not to think of evolution as having a goal or purpose. Melanin being black is a result of random changes that happened to result in a beneficial phenotype. It didn't conclude that something was needed to counteract UV light and try to reach that goal.


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DNA test to prove that two grand-grand-children descend from same grand-grandparents
Can DNA test prove that two persons descend from same great-grandparents (or test where one great-grandchild and grand-child are tested)?

Yes testing for relatedness of grand-grand children is possible. (Ignoring some very unlikely, but theoretically possible cases.)
Grand-grand children are still highly related genetically, and this degree of relation is also shown in standard consumer grade commercial DNA testing kits (such as 23andme, where you could link to other people and see their degree of relatedness to you – even further beyond grand-grand children - or where you could even search for relatives, whom you may not know personally).


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How much energy is in a human brain's electromagnetic activity?
Lately there has been an increased interest on worldbuilding.se about a realistic depiction of fictional creatures who would feed off thoughts and dreams, with some answers proposing feeding off the electromagnetic emissions of the brain.
As a first guess I would think the energy in those emissions is very small. However, has there been any study to give an approximate amount? Most information a quick search provides stems from sensationalist articles which don't look too trustworthy.
The brain does use up almost 20% of the whole body's energy balance, but I would guess most of it is turned into heat.
If one could extract useful work out of the electromagnetic field generated by an average human brain with 100% efficiency, without any physical intrusion (so, the energy potentially available outside of our head), how much would it approximately be? An order of magnitude approximation would be enough.

EEGs pick up about 0.5 to 100 µV on the scalp and about and about 1-2 mV when measured on the surface of the brain, it's about 100 times lower than ECG (heart) signals.
Brain waves have been categorized into four basic groups

beta (>13 Hz),
alpha (8-13 Hz),
theta (4-8 Hz),
delta (0.5-4 Hz).

Votage times current = power. In this case, the amount of current would be/is hypothetical as it would be based on a "salt water" bridge; neurons contain Na+, K+, Ca++, and Cl- ions which are the basis of the current.
EEG measurements must be amplified simply to be seen. An amplifier has to provide a gain of 100 - 100,000 in order to move a delicate needle (and draw the EEG). So, using the amplifier gain as a indication of the amount of current, let's suppose you need as much force to move a pen back and forth as would be required to accelerate a feather one inch in one second.
A feather weighs 0.0082 grams and an inch is 2.54cm. That's about 2 newtons or 2 watts. So, since the current from the brain is amplified 100 - 10,000 times then the wattage picted up by an EEG would be between 0.2 to 20 milliwatts. Supposing that an EEG was only 1% efficient at absorbing the power, then the wattage could be on the order of 20 milliwatts and 2 watts. Altogether brain power might possibly enough to accelerate a feather one inch per second... at around 100% harvesting efficiency.


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Can I get 1% of my one of my great great grandparents genes?
I basically took a 23andme test and found out genetically I was 1% African. The weird part though is that family records shows that my father's mother's grandmother was African, making me 1/16 African. Shouldn't it be closer to 6%?

hi Ray. Nice question. I would suggest you think about some additional question (and maybe 23andme explains it or you might have to search internet). For example, what doe it mean to be 1% African? Technically, all people are from what is currently known as Africa. Also, for example, a lot of people from South Africa have predominantly European ancestry. Finally, when someone says 1%, what is the uncertainty of this number? There is no precise measurement in science, it is always 15.5±0.3 or something

it's a bit like shuffling 16 packs of cards into 1 as far as I know...  That should have a quantitative answer giving the probability of having less than 50% of a parents, less than 25% of a grandparents and less than 6% of a great great GP's genes.  After 4 generations I expect there's a 20% chance that one grandparent has only 1% of genes in an offspring.

The science behind "being X % from a certain place" based on genetic analyses is... approximative at best. It relies on the assumption that some genetic traits are only found in certain (narrow) regions of the planet - which for most of them, is not really true.
Additionally, did your test provide any confidence metric for this result? If not, it may mean that it may be derived from a statistically unsignificant number of traits (and the number could therefore mean anything) or maybe it's simply something like 1% with a confidence interval of several points, in which case the result could be a compatibe the mathematical truth. Genomes are large and have complex dynamics, it it probably difficult to get a precise estimate.
On a side note, there is more genetic diversity in native African populations than on any other continent (for reasons pertaining to Homo sapiens history) so "African" does not describe a homogeneous population.
Source: https://www.nature.com/articles/nature13997 doi:10.1038/nature13997


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Cortisol in sharks
Is there an established method for measuring stress hormone levels, like cortisal, in sharks? If so, is it known what levels of such hormones create significant detrimental effects like decreased immunity?

This is not simply an answer site, but instead a site that promotes self-learning with some expert help. Consequently, questions that show little or no prior research effort are off-topic on this site — have you tried searching for "stress hormone levels sharks"? Please [edit] your question and tell us where you've looked for answers, what you do know about the topic, and where exactly you still have questions. Please take the [tour] and consult the [help] starting with [ask] for details.

https://pubmed.ncbi.nlm.nih.gov/17977765/


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In electron transport system the final acceptor of proton is?
My lecture notes say that the answer to this is inorganic phosphate  (iP)..and the question is about proton not electron so the answer can't be oxygen. But I don't understand how is the answer iP

Hint: what's the overall chemical formula for respiration?

I still didn't get it..how is the answer iP?

Let’s see . . . loss of electrons is oxidation, and gain of electrons is reduction.  Respiration involves oxidation of carbon, and oxygen is the terminal electron acceptor in this process.  So carbon is oxidized, and oxygen is reduced.  And in the process the electron transport chain generates a proton motive gradient to generate ATP.  The Hydrogen ions (protons) move across the membrane, but do they need an acceptor?


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Element of promoter responsible for expression power of gene
I know that there is a classification of promoters like: strong, medium and weak. This shows how a promoter affects gene expression levels. So my question is: what part of the promoter affects it?
For example I want to raise or lower the expression of some gene, so, what part of promoter I need to edit or maeby I can just replace it with another promoter?

Tldr; In an in vivo context the answer is going to be dependent on DNA sequence and context.
Simplistically, Eukaryotic genes promoters can be segmented in to several parts. The first, a core promoter region where RNA pol II will bind. This isn't capable of a robust transcriptional response on its own and relies on proximal promoter regions, or more specifically transcription factor binding to the proximal promoters. Proximal promoters are usually 100 or so base pairs upstream of the transcription start site and will bind proteins that will assist in Pol II binding and activation (or silencing). Enhancers (and Silencers) are conceptually similar to proximal promoter regions with the exception that they can be a looooooooooong way away from the transcription start site in sequence space. See here:1.
So, if you just wanted to drive expression of a transgene in a cell line in the lab there are plenty of established cloned promoters and enhancer regions known to work such as SV40 or Gal4. This would be an example of "replacing the promoter". That's exactly what it is and why these sequences were chosen to be cloned.
If you are asking which regions are specific to activate or repress a gene in vivo and/or in context then it will be, of course, context dependent and you'll have to find out yourself if someone hasn't already. Generally, these regions of effect will be binding sites for sequence specific transcription factors  which interact with the core transcriptional machinery (or bind other proteins that do) to effect the rate of transcription. So, if the sequence is what can induce an effect, how can you find it? You can search for these sequence specific sites by analyzing your sequence of interest with a slew of computational tools for potential binding sites and directly assess any hits ability to increase/decrease expression as isolated units when cloned upstream of an appropriate reporter construct. I guess you could even go as far to CRISPR single base pairs in or out to "edit" any hits. Alternately, you could use a purely wet bench technique such as promoter bashing to similar effect - performing serial deletions to find out which part of your promoter is important for strong/medium/weak effects or activation/repression.
The Stark Lab developed a cool genome-wide approach looking at the ability of DNA to drive expression. Although, something worth bearing in mind is that in a normal in vivo situation everything is context dependent - one piece of sequence may be reliant on another close by (like the core promoter requires proximal promoters) or it may require one or more pieces of DNA that are distant in sequence space to be close by in 3D space (like distal enhancers).
People have also taken completely synthetic approaches to making promoters .
This would be easier to answer if your question was more specific.
HTH.


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RNA contains Uracil in place of Thymine
Thymine does not present in RNA but DNA containing thymine why


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Could the protein dystrophin be artificially synthesised?
Could the protein dystrophin be artificially synthesised and if so could patients with DMD (Duchenne Muscular Dystrophy) benefit from it?
//Now I don't have much scientific background other than a high school biology qualification
I met someone the other day the same age as me who suffers from DMD, so I did some research and curiosity led to this question.
Sorry if I used the wrong tags or/and this question isn't allowed. \

Great question.
Yes, it is almost certainly possible to artificially synthesize just about any protein. There can be difficulties with certain proteins, but these are more engineering problems rather than true limits to artificial synthesis.
The problem is getting the protein where it needs to be to be functional!
A great comparison is insulin. Insulin is an important regulatory protein that floats around in the bloodstream. That makes insulin therapy a relatively straightforward solution to a problem of not enough insulin: all you have to do is make or isolate some insulin and inject it into the bloodstream.
Dystrophin, however, is a structural protein that acts inside cells. Proteins are really big, and they can't be simply taken up by cells. There's no mechanism to get an arbitrary protein inside: any proteins that can be taken up by cells need to do so via some specialized mechanism.
If you wanted to replace a defective allele for dystrophin, then, the most feasible approach would be gene therapy: getting a patient's own cells to produce a functional copy of the protein. Efforts to entirely or partially replace dystrophin via gene therapy are a current area of research, but there are still many challenges to gene therapy approaches in general.

References
Harper, S. Q., Hauser, M. A., DelloRusso, C., Duan, D., Crawford, R. W., Phelps, S. F., ... & Chamberlain, J. S. (2002). Modular flexibility of dystrophin: implications for gene therapy of Duchenne muscular dystrophy. Nature medicine, 8(3), 253.
McGreevy, J. W., Hakim, C. H., McIntosh, M. A., & Duan, D. (2015). Animal models of Duchenne muscular dystrophy: from basic mechanisms to gene therapy. Disease models & mechanisms, 8(3), 195-213.
Pichavant, C., Aartsma-Rus, A., Clemens, P. R., Davies, K. E., Dickson, G., Takeda, S. I., ... & Tremblay, J. P. (2011). Current status of pharmaceutical and genetic therapeutic approaches to treat DMD. Molecular Therapy, 19(5), 830-840.
Verhaart, I. E., & Aartsma-Rus, A. (2012). Gene therapy for Duchenne muscular dystrophy. Current opinion in neurology, 25(5), 588-596.


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Are drones from one honey bee queen all clones?
The Honey Bee queen lays eggs that develop into worker bees (female) if she fertilizes the egg.  If she does not fertilize the egg, it will develop into a drone (male).
The drone only has the queen's DNA so are all drones exact copies of each other, ie clones, or is there some other mechanism that will make each brother slightly different?

The queen is diploid; the drones are haploid. Meaning the queen has two copies of each chromosome, and the drones have only one. So for each gene, the queen has two copies and passes one of those copies on to the drone.
This means the drones are different for exactly the same reason female bee siblings, or human siblings, are different: because every parent has two copies of a gene, that are often different, and passes only one of those to their offspring.
If the queen were homozygous for every allele, i.e. the two copies of all her genes were identical, then the drones would indeed be genetically identical. But this is true as well of the children of two completely homozygous parents.
See this page on inbred laboratory strains of animals (animals which are inbred to the point they and their offspring are genetically identical to each other):
http://isogenic.info/html/inbreeding___it_s_effects.html

F1 hybrids, i.e.  the first-generation cross between two inbred strains, are isogenic but not homozygous.

In other words, if you have two parents who are genetically different, but have two identical copies for all of their chromosomes, their children will be isogenic (have exactly the same genes); they all have two copies of their genes, got one copy from their father and one from their mother, and those two copies might be different from each other (their mother and father have different alleles), but all the children got those same two copies because they're the only copies their mother and father have.


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Can varied temperature while sleeping help quality of sleep?
I read an interesting article which is about relations between body temperature and quality of sleep.
I'm interested in the phrase from the article.

Other experiments that varied the ambient temperature—decreasing it early in the night and increasing it in the morning—have shown similar benefits for improving and maintaining sleep.

So I tried to find papers and experiments but it seems my searching ability is pretty poor. I can't find it. Is there someone knows the latest knowledge or papers about this?
plus) In the article, why increasing skin temperature by 0.4 Celsius make core temperature low?


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What is the protocol for extracting Protease Onion?
I am Investigating the protease concentration in certain fruits and vegetables. I am unable to find the protocols for the extraction from onions. I want to purify my protein using the ammonium sulphate (salting out) followed by dialysis. I am specifically concerned about the mass of ammonium sulphate that is required and the amount of water I should dissolve it in.

If no protocol exists, you would typically increase ammonium sulfate in stepwise amounts and assay for activity. You can somewhat purify your protein this way. Or you could just add some arbitrary amount like 75% and see what happens. I use this calculator.


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Why do red muscle fibres have more mitochondria than white muscle fibre but less ATP than White muscle fibres?
This is a question given in my Anatomy book and I am really confused because logically the substance which have more mitochondria should have more ATP as mitochondria is the power house of cell.But the question contrast the logic.

It would be good to see some figures to support the assertion in the question. What is really needed is ATP/ADP ratios. I appreciate that you trust your book, but anatomy isn’t biochemistry.

This is because of the difference in mitochondrial protein expression of red and white muscle fibres. There is difference in posttranslational modification, which leads to functional difference as red muscle contraction is slow, and white muscle contraction is rapid.
Metabolic control in mitochondria contributes in speed of activity and cellular energy production. So, these differences effect the cellular energy levels in both white and red muscle fibres.
Following factors also contribute to the ATP production:
White muscle mitochondria have higher proton leak.
Red muscle contain high palmitic acid and oleic acid, but white muscle possess more phosphate ions.
Collagen and elastic fibers are largely distributed in red muscle mitochondria, whereas high titin levels and densely packed sarcomeres are present in white muscles. Whereas high levels of long sarcomeres are present in red muscles.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3118618/
https://www.hindawi.com/journals/bmri/2018/5816875/

MacIntosh, Brian R.; Gardiner, Phillip F.; McComas, Alan J. (2006). Skeletal Muscle: Form and Function. Human Kinetics. ISBN 978-0-7360-4517-9.
[https://en.m.wikipedia.org/wiki/Myocyte?wprov=sfla1 ][1]
[1]: https://en.m.wikipedia.org/wiki/Myocyte?wprov=sfla1
Good question,  I guess that high production could be linked to higher relative consume of ATP which could depend of necessity of energy and ATPase effectivity/ concentration of ATPase.
I suggest you to investigate the reference cited above.

Please do not post text as images. It discriminates against those sight impediments and need to use screen readers.


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What are the coverings of femoral hernia?
It was my Viva question and I was really puzzled.I know what is femoral hernia and it route like the abdominal content moves down the femoral canal and further through the saphenous opening and all but I have no idea about it's coverings.Can anyone please help me

Femoral hernia coverings (from inside out):

Peritoneum
Femoral septum (extraperitoneal fatty, connective and lymphoid tissue)
Tranversalis fascia
Cribriform fascia
Superficial fascia
Skin

Image source: SurgWiki, Creative Commons Licence
Sources:

SurgWiki: Hernias
SlideShare: Femoral hernia, p. 12
EarthsLab: Femoral canal
Textbook of Anatomy Abdomen and Lower Limb;, Volume 2, By Vishram Singh, p.45


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What did Francis Crick and James Watson discover that Rosalind Franklin didn't?
I've recently been introduced to the history of DNA research from Miescher to Franklin, Crick, and Watson, and I've found that Franklin had figured out a great many number of things out that Crick and Watson are popularly credited for when they 'acquired' her photo, including that:

DNA has a helical shape
The distance between two base pairs is 0.34nm, and each helical turn is made up of 10 bases at 3.4nm
Nitrogenous bases protrude inwards and the sugar-phosphate backbone is on the outside

On that note, did the paper written by Crick and Watson in 1953 result in any information that Franklin herself hadn't figured out? Or were Crick and Watson redundant when it comes to the current model of DNA?

Check out the story of "photo 51" one of the first photos of DNA taken under the supervision of Franklin. There is the background information there: https://en.wikipedia.org/wiki/Photo_51 ... you can say that there were some staff migrations, and personality issues. Antibiotics were discovered in France may years previously in a chance experiment, and the thesis was handed in 10 days before christmas and not followed up. Hunger for recognition and for a fight is something males have more of.

There were staff migrations and personality issues, information leaks between researchers and other factors. Her boss annoyed her. Watson and Crick used her geometry of a helix with previously known DNA nucleotides and phosphate from other researchers. She actually had discovered and photographed the helices.
Franklin had obtained the basic structure, shape and measurements of DNA.
Franklin:
She used careful hydration from 75-90% in order to obtain her best pictures. Hydration makes the DNA expand into a visible helical configuration. She used cylindrical Patterson map calculations to determing DNA's density, unit cell size and water content. From this she deduced the basic dimensions of DNA strands, and that the phosphates were on the outside of what was probably a helical structure. Her research was briefed/presented in an internal meeting/seminar at the college and was published officially in 1953 in support of Watson and Crick's presentation.
Watson and Crick:
Watson and Crick suggested a basic framework of a helical molecule for DNA,  Without elaborating precisely. Watson and Crick combine all the findings of other scientists, for the bases and acids of DNA, with Franklin's helix into a synopsis into a correct helical molecular structure. The phosphate and CAGT were already known, and they arranged it into a helix.
Judge for yourself if their research was brilliant research, if it is a discovery, or if it is laying the last pieces of a puzzle assembled by other researchers.
Watson and Crick stayed friends with Franklin after 1954 and shared friendly correspondence and some road trips, and helped with her health issue.
full pdf at .edu source here

If you check that publication, what may seem dishonest is that they iamge a photo by Franklin in support of their work, but only as a blurred photo, when they actually had access to all of her best photos. I haven't been able to find if Franklin published her photos independently in Nature or another magazine.

It was obviously not her best work.
Franklin obtained undenatured DNA gel from a Swiss researcher at Berne university, Rudolf Signer.
She used careful hydration from 75-90% in order to obtain her best pictures. Hydration makes the DNA expand into a visible helical configuration. She used cylindrical Patterson map calculations to determing DNA's density, unit cell size and water content. From this she deduced the basic dimensions of DNA strands, and that the phosphates were on the outside of what was probably a helical structure.
Her research was briefed/presented in an internal meeting/seminar at the college and was published officially in 1953 in support of Watson and Crick's presentation.

The Nobel Prize in Physiology or Medicine was awarded to Watson, Crick and Wilkins in 1962. The prize was not awarded to Franklin; she had died in 1958, and although there was not yet a rule against posthumous awards, the Nobel Committee generally does not make posthumous nominations. Watson suggested that she should have won the nobel prize for chemistry in his book, and Franklin is known through his distorting lenses. Ideally it would be interesting to know what Franklins personal letters and documents told of her research. Perhaps there is an autobiography of franklin? if not there should be one! She had differences with the lab director, professional or personal, we don't know, so she changed labs after only 2 years, leaving Watson and Creek and the research at King's. In july 25,2020 it will be the centenarian of her birth... She is older than Watson and Crick and would be 99 today. Perhaps she was not fond of helices?

This is a statement, but I'm not sure it is an answer to the well-articulated question asked.

Hey thanks, when I read the title to that paper I thought it was about sodium thymonucleate, I failed to add it to the answer information.

"Watson and Crick used her geometry of a helix with previously known DNA amino-acids and phosphate from other researchers." What are 'DNA amino-acids'?

sorry, corrected to nucleic acids.

Please could you correct/clarify two points in your answer. 1. The link http://www.sns.ias.edu/~tlusty/courses/landmark/WatsonCrick1953.pdf is dead. Could you replace it by a permanent link to the paper in the journal. I am not clear what it refers to. The May 30th 1953 paper shown? 2. You seem to imply that the X-ray fibre image entitled "Fig. 1 Fibre diagram..." is of Franklin's work presented in a W&C paper (the one shown?). It is in fact Wilkins' X-ray photo from Nature 171 p.738 (1953). W&C could not and did not publish Franklin's photos, so remarks on that score need removing.

I think that this answer leaves out the Chargaff's rules component, which was crucial to forming the structural model (David's answer gets it about right). However the degree of historical perspective here is appreciated.

None of the answers emphasizes the key concrete point:

The Watson–Crick model of DNA included specific base-pairing between
A–T and G–C, which they ‘discovered’ — postulated for the first time —
on the basis of model-building, informed by the overall structure of
the helix and Chargaff’s observations. In contrast, her notebooks and a draft manuscript showed that Franklin’s ideas at that time
did not include the conformation of the bases, primarily because she
had been concentrating on the interpretation of her X-ray diffraction
data, which did not address this question.

Of course, this was of major importance as it suggested a basis for the semi-conservative replication of the genetic material, mentioned in the answer from @sourcebug.
The evidence on which this assertion is based can be found in Appendix I of my answer to a more recent question on SE History of Science and Mathematics.

The astounding takeaway from the Watson-Crick paper was their understated recognition that the structure of DNA suggested a scheme for making copies of itself.  This had not been stated before by anyone.  Whether they were in the right place at the right time or had actively prevented Franklin from sharing in the discovery can be debated, but their brilliant deduction clearly contributed a new idea to our understanding of molecular genetics.

Some of the information contained in this post requires additional references. Please [edit] to add citations to reliable sources that support the assertions made here. Unsourced material may be disputed or deleted.

Well, they did win a Nobel Prize.


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How many electrons does the b6-f complex need to pump one proton into the thylakoid lumen?
In photosynthesis, photons are used through photolysis to split water molecules and retrieve their hydrogen ions and electrons in the water-splitting complex. For each four photons, two water molecules are split and four electrons are retrieved.
The electrons will go on to pass into chlorophyll a in photosystem II and after being excited by another photon, pass through a series of electron carriers and drop energy along the way. One of these electron carriers is the cytochrome b6-f complex which uses some of this energy to help pump hydrogen ions from the chloroplasts stroma and into the thylakoids lumen.
However, I'm unsure of exactly how many electrons the b6-f complex needs to pump each hydrogen ion across the membrane. Is it 2? 4? I've been unable to find an answer anywhere so far.


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If black absorbs light, then why did Africans evolve black skin? Wouldn't that make the heat worse?
Wouldn't it have been more adaptive to develop light skin and so reflect incoming light?

First, I think you have things backwards.  Africans came first: lighter skin is an evolutionary adaption to living in more northerly climates.
Second, evolution works with what it has, not necessarily what's best.  Mammals had the genes for melanin production long, long before hominids came on the scene, so it's fairly easy to apply selection to increase or decrease melanin production in a population.  The classic example is the British peppered moth: https://en.wikipedia.org/wiki/Peppered_moth_evolution  (Note: I'm not clear whether the moth pigment is melanin or something else, but the principle holds.)
For a white blocking pigment (or transparent to visible light - think sunscreen) or a reflective skin to be evolved, we'd have to wait around until some mutation happened that would allow the body to produce the right sort of chemical.  AFAIK, mammals don't actually produce white pigments: white fur is due to the scattering of light in the absence of pigment.  (Just as snow is white.)  So animals in sunny climes might evolve white fur, but that makes the animal conspicuous.

Check out this page on skin color adaptation —

Nature has selected for people with darker skin in tropical latitudes, especially in nonforested regions, where ultraviolet radiation from the sun is usually the most intense.  Melanin acts as a protective biological shield against ultraviolet radiation.  By doing this, it helps to prevent sunburn damage that could result in DNA changes and, subsequently, several kinds of malignant skin cancers.