Clarification on the "orientation" of chromosomal rearrangements I need some clarifications on the concept of "orientation" in case of chromosomal rearrangements.
Given a deletion event on a chromosome for example, is the resulting DNA at the breakpoint always in TH (Tail to Head) orientation? Do all duplications lead to HT orientation? And in case of translocations, inversions, etc..?

Can someone give a clear definition of "orientation", and make some examples?

Here some specific examples found in the Cosmic database:

CRC-3  large_intestine  NS  carcinoma  adenocarcinoma  intrachromosomal inversion  28066  0  2  53774826  53774826  +  2  53775947  53775947  +    21892161

CRC-3  large_intestine  NS  carcinoma  adenocarcinoma  intrachromosomal inversion  28072  0  2  60783417  60783417  -  2  60786447  60786447  -    21892161

0006_CRUK_PC_0006_T1_DNA  prostate  NS  carcinoma  adenocarcinoma  intrachromosomal inversion  113193  0  18  60375963  60375963  +  18  77010169  77010169  -      538

0006_CRUK_PC_0006_T1_DNA  prostate  NS  carcinoma  adenocarcinoma  intrachromosomal inversion  113314  0  7  153608258  153608258  -  7  153610727  153610727  +      538

As you can see, they have inversions having all of the possible strand orientations, '++','--','+-','-+'.
How is this even possible?! How to convert to H/T orientation in this case?

P.S. This is the description of the header of the data:

               HEADER[IDX] : IDX : DATA[IDX]
               Sample name :   0 : 0006_CRUK_PC_0006_T1_DNA
              Primary site :   1 : prostate
              Site subtype :   2 : NS
         Primary histology :   3 : carcinoma
         Histology subtype :   4 : adenocarcinoma
             Mutation Type :   5 : Interchromosomal unknown type
               Mutation ID :   6 : 113196
          Breakpoint Order :   7 : 0
         GRCh37 Chrom From :   8 : 6
  GRCh37 Location From min :   9 : 129148581
  GRCh37 Location From max :  10 : 129148581
        GRCh37 Strand From :  11 : -
           GRCh37 Chrom To :  12 : 7
    GRCh37 Location To min :  13 : 153610712
    GRCh37 Location To max :  14 : 153610712
          GRCh37 Strand To :  15 : -
     Non-templated ins seq :  16 :
                 Pubmed ID :  17 :
                  ID_STUDY :  18 : 538

I think the picture will help you. In fact, to determine which kind of rearrangement for the chromosomal, we need to define an "orientation". However, this orientation is not fixed. It is a definition compared with the two chromosomes before and after the rearrangement. As the picture shows, the duplicated sequence after rearrangement should be in the same orientation, if one of them not, it should be described as "inversion after duplication". For deletion, there is no difference in the orientation if the remain parts still in their previous pattern. The key point to understand,  is to check the sequence before and after the rearrangement and find difference(s) between them, then compare to this picture(which is the definition of rearrangement) to find if the chromosome has one or multiple rearrangements.
Hope this could help you.


Are there any papers arguing against vaccination in French? Disclaimer: This question is NOT about challenging the safety or efficacy of vaccines. It is only asking for tips on providing credible references that may show harmful effects of vaccination, if any.

In my French class, we were asked to debate an issue in current events. My topic is vaccines in children or adults.

The challenging part is that I was assigned to argue against vaccination, and I have to back up my arguments with credible sources (not blogs) that are in French. Hopefully some of you could point me towards some links to articles or research papers in French.

Please avoid discussion on safety and efficacy of vaccines, including local and global policies on their use. I just need help with this topic for my French class

I wish you good luck, as 99.99% of the anecdotal claims out there that conclude vaccination is bad are based on unfounded rumors.

Note that much of the negative public opinion is based on a fraudulent (and retracted) paper by Wakefield in The Lancet (1998). Unfortunately for you, however, it is in English.

My French is a bit rusty, but if you go to Google Scholar and type in a search term like vaccination results in autism (les résultats de la vaccination dans l'autisme) or Wakefield vaccination autisme something might pop up in French that advocates against vaccination.


Gene distance and Recombination Frequency: Mechanism Why is the recombination frequency higher if the genes are farther apart?

The genetic phenomenon referred to as recombination reflects the process of crossing over which occurs during meiosis. Crossing over creates an exchange of genetic information between homologous chromosomes. To a first approximation cossing over events take place at random positions along the aligned chromosomes. Consequently the further two loci are apart, the more likely that there will be a crossing over event between them. Thus the recombination frequency can be used to measure the distance between two genetic loci (or genes).

Supplement added in response to comment from OP

An analogy

Imagine a piece of string. It has 6 marks on it (1-6 on the diagram) which divide it into 7 intervals (A-G). We are going to cut the string at one of the marks. We throw a die to decide which position to cut.

What is the probability that our cut will separate A and G? It's 100% since all single cuts will do this.

What is the probability that our cut will separate A and D? It's 50% since single cuts at 1,2 or 3 will do this.

What is the probability that our cut will separate A and B? It's 16.7% (1/6) since only a cut at position 1 will do this and the probability of throwing a 1 on our die is 1/6.

Think of the intervals (A-G) as genes and the cut sites (1-6) as possible crossing over events. If two homologous chromosomes are going to undergo a single crossover somewhere at random, then the closer together are the genes (intervals), the less likely is it that the crossover (cut) will take place between them. This assumes of course that the site of crossing over is chosen at random.

In the model presented here, if the order of the letters was scrambled and didn't know what it was but we were told the frequencies of occurrence of the separation of the intervals with random cutting we could deduce the order of the letters.


What happens to the human brain when unconscious? What part of the brain gets affected and does it harm the brain? Thank you I just needed some extra info for a video I'm making.

We don't know. Disruption of cortex, thalamus, or brainstem structures (someone mentioned ascending reticular activation system) all can cause loss of consciousness. Different drugs have different mechanisms of action and some might cause different "types" of loss of consciousness - for example, ketamine and propofol seem very different, and trauma is a completely different issue.

The reason this is such a hard problem is that these structures are all interconnected, and there are likely proximate and distal causes of loss of consciousness. For an analogy, imagine you starve to death. You could make a convincing case that lack of food did it - so conclude food keeps you alive. But you weren't declared dead when you stopped eating; you were probably declared dead when your heart stopped. So conclude your heart keeps you alive. But in the middle somewhere, you had changes in ion concentrations in your blood, loss of glucose. So salts and sugars keep you alive. I can prove these are all true - take out your heart, you die. Stop feeding you, you die. Fill your arteries with KCl, you die.


Identifying a shrub with unusual "many shoots" growth behavior While recently hiking in the southern mountains of New Hampshire, we came across a plant, and some of them were exhibiting what we interpreted to be a disease, or least unusual growth. On some of the nodes, there were a large number of extra stalks:

On each plant, the number and locations of these things varied, and not all of them had it. And we first assumed it was some ivy, or parasite, or separate plant, but it seemed pretty clear to us that it was coming right from the same branch.

We soon saw there were dead versions of this plant, and all of them had this "extra shoot" variation:

So we reasoned that no matter what this thing was -- natural variation or some kind of disease -- it was killing the plants.

Google image search was no help. It possibly identified the plant as a "viburnum", but was unable to help with the growth.

Anyone know what plant this is, or what this growth behavior is the result of?

Possibly an example of a "Witch's Broom."

Witch's Broom is a deformity in plants (typically woody species) which typically causes dense patches of stems/shoots to grow from a single point on the plant. The name comes from the broom-like appearance of the stems.1

Witch's broom may be caused by many different types of organisms, including fungi, oomycetes, insects, mistletoe, dwarf mistletoes, mites, nematodes, phytoplasmas, or viruses.2

Sources:
1. Wikipedia
2. Book of the British Countryside. Pub. London : Drive Publications, (1973). p. 519
 Image1. Gardeningknowhow.com
Image2. Iowa state University


Does Remdesivir interfere with human transcription? Remdesivir is metabolized into a nucleotide analogue. It is incorporated in the viral genomes causing either termination of transcription or a dysfunctional genome. Thus, the new viral particles produces within infected cells are dysfunctional.

However, how does Remdesivir intefere with human transcription, or does it? I'd imagine that a nucleotide analogue could be incorporated into a human mRNA. Can it?

edit: The mithocondria are discussed below. I would also be interested in usual, i.e. nucleic transcription. Is Remdesivir transported into the nucleus? Does human RNA polymerase accept it?

However, how does Remdesivir intefere with human transcription, or does it?
Via https://www.ncbi.nlm.nih.gov/books/NBK548938/:

Nucleoside analogues can cause liver injury by several mechanisms. Most characteristic is a mitochondrial type of hepatic injury that is probably caused by the nucleoside analogue becoming incorporated into or blocking mitochondrial DNA synthesis by the mitochondrial gamma polymerase, leading to a depletion of mitochondria or decrease in their function. Mitochondrial injury can affect multiple tissues thereby causing myopathy, neuropathy, pancreatitis, bone marrow suppression and/or hepatic injury.

Remdesivir trials for treatment of Ebola virus infections included in vitro studies of hepato- or liver toxicity. Via https://www.who.int/ebola/drc-2018/summaries-of-evidence-experimental-therapeutics.pdf?ua=1:

Remdesivir and the parent nucleoside analog GS-441524 were extensively profiled for in vitro cytotoxicity and mitochondrial toxicity in multiple relevant cell types. Both remdesivir and GS-441524 exhibited > 3.5-fold margins in most in vitro toxicity assays. Data from in vitro studies with liver cell culture systems demonstrated that human hepatocytes are susceptible to remdesivir mediated toxicity, likely due to high cellular permeability and effective intracellular metabolism of the drug. Systemic metabolites of remdesivir detected in vivo in plasma do not exhibit any in vitro hepatotoxicity at pharmacologically relevant levels.

However, treatments in vivo did not show much in the way of negative effects:

Single dose of remdesivir IV infusion from 3 to 225 mg was well tolerated with no dose limiting toxicity observed. No treatment emergent AEs were observed in more than 1 subject per arm. No evidence of renal or liver toxicity was observed. All AEs were Grade 1 or 2.
Multiple-dose IV administration of remdesivir 150 mg once-daily for 7 or 14 days was generally well tolerated. No subjects had a Grade 3 or 4 treatment- emergent laboratory abnormality during the study. Reversible Grade 1 or 2 ALT or AST elevations were observed in several subjects without abnormalities in total bilirubin, alkaline phosphatase (ALP), or albumin. There was no abnormality or clinically significant change in international normalized ratio (INR) in any subjects. Remdesivir did not show any effects on renal function in the multiple-dose study.

Stereochemistry of the active portion of remdesivir may help make it less toxic.
Human DNA polymerase selects for or preferentially incorporates right-handed or "D" nucleosides. Nucleosides that are of the left-handed ("L") enantiomeric form will still be incorporated by RNA polymerase and have clinical effect from blocking viral replication, but will less likely be used by the machinery in human cells.
Here is another paper that explores how DNA polymerase selects for the D-enantiomer: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4121797/
Other nucleoside antiviral drugs appear to have L-stereochemistry (ibid.) for this reason, to reduce toxicity, so I'd assume the same about remdesivir, as well. I tried looking through a paper on the organic chemistry of remdesivir synthesis, but I don't know enough about that subject to see whether there was a specific step or steps along the drug's synthesis, which involve separation and purification of enantiomers. Perhaps someone with more expertise there can comment.


Is there any natural blue rose? I had recently read an article that the possibility of having natural blue rose is extremely rare because of the absence of delphinidin in most roses. Are all blue roses just a product of cross-breeding?

There are no roses (that is, flowers of genus Rosa species) that naturally express a "true" blue color. Through cross-breeding, there are lilac-mauve rose horticultural varieties ("Blue Nile","Blue Moon","Lady X", etc.), and through genetic engineering (actually inserting delphinidin-producing genes) there are mauve-lavender varieties ("Applause"). The insertion of delphinidin-producing genes did not yield blue colour roses as hoped is due to the acidity of the rose petals, which itself changed the delphinidin blue to mauve-lavender instead. The next breakthrough will be to switch off the acidity of the rose petals to create a true blue rose.

More info

Wikipedia article Blue Rose gives good coverage.

Here's a nice scientific bibliography of rose pigments with some good information on blues.


Where can I obtain the sequence of the E. coli ribosomal RNA precursor? I have found separate sequences for 16S rRNA (from the small subunit) and 23S rRNA and 5S rRNA (from the large subunit). I need the full precursor rRNA sequence, which I cannot find.

However the complete annotated sequence of the E. coil genome is available:

https://www.ncbi.nlm.nih.gov/nuccore/U00096.3?report=fasta

Does changing the T to U of this sequence give me the complete rRNA sequence?

Generally most organisms have multiple copies of the genes/regions coding for ribosomal RNA (since it's needed quite a lot). Additionally these regions can be repetitive or otherwise similar to sequence or place correctly in the genome, therefore it's generally harder to find good genomic sequences for rRNA compared to other genes.

Based on your link, it seems that you are looking for the rRNA of E.coli; the GeneBank entry corresponding to the fasta file you linked contains the annotation of the full genome and has 7 entries for sets of ribosomal RNA (named rr[slf][A-H]*).
If you take any of the sequences spanning one of these regions you should get the sequence of the full precursor. However, there are things you should be aware of:

there will likely be minor sequence differences between all 7 regions
Apparently most of the e.coli rRNA operons also have tRNA genes mixed into them (these are different for all 7 operons)
replacing the genomic T with U will make the sequence look like RNA, however ribosomal RNA is often also edited post-transcriptionally, so the sequence you get may not fully match the mature rRNA sequence.

Another website that gives a better readable overlook over the rRNA operons in e.coli is this, it also contains source links & seems to match the genbank entry from what I can see.

  Example on how to find rRNA region from the geneBank entry:

  This is a (shortened) part of the annotation of the GeneBank entry, which shows the 'A' ribosomal genes :

gene  4035531..4037072
  /gene="rrsA"
rRNA  4035531..4037072
  /gene="rrsA"
gene  4037141..4037217
  /gene="ileT"
tRNA  4037141..4037217
  /gene="ileT"
gene  4037260..4037335
  /gene="alaT"
tRNA  4037260..4037335
  /gene="alaT"
gene  4037519..4040423
  /gene="rrlA"
rRNA  4037519..4040423
  /gene="rrlA"
gene  4040517..4040636
  /gene="rrfA"
rRNA  4040517..4040636
  /gene="rrfA"

  As you can see the genes in the region/opernoccur in order rrsA, ileT, >alaT, rrlA, rrF (the fact that this is an operon can not be inferred from the GeneBank entry) and if you take the corresponding region of the fasta sequence (nucleotides/characters 4035531 to 4040636) you'll get (most of) the primary transcript sequence.
  Since promoter & terminator Sequences are not annotated in GeneBank (or any/most other genome assemblies), you can't easily get the sequence before the first and after the last gene. One  potential source for these might be the other ressource I linked, which lists some sources for terminator sites.

* This is expressing all names as regex. i.e. for rRNA operon A there are rrlA, rrsA & rrfA; same for B,C,...


Are there any organisms that are made of more than one (~5-12) cell? Prokaryotes and eukaryotes are unicellular, made of one cell. Great. Eukaryotes are unicellular or multicellular. But the typical examples of multicellular eukaryotes we have are made of, often, trillions of cells, like us humans. Ants must still be made of many millions of cells. Are there known eukaryotes with very few cells that make them up? Like, 5, or something? Or maybe a dozen cells making up the whole organism in its fully developed state?

There's Trichoplax adhaerens, a Placozoa, made of a few thousand cells. Then there is Dicyema japonicum, a simple mesozoan, made up of 9 to 41 cells. Arguably, the simplest multicellular organism is the algae Tetrabaena socialis, whose body consists of 4 cells. Then, there's the parasitic Myxozoa which have 7 cells.


why finger of hands and feet become wrinkled due to to water? Mostly due to bathing or washing clothes our finger become wrinkled what was the reason behind it??

There are a few hypothesis around it, but it is known that its associated with the function of distal nerves of the hands and feet. I suggest reading this short case for a glimpse at this - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2464382/

Also another tip I can give is that professional swimming athletes for example, eventually experiment an adaptation process in which this wrinkling reaction diminishes due to being exposed to the same stimuli repeatedly and for long periods of time.


What factors affect the rate of transpiration in plant leaves? I'm trying to get my head around factors which affect transpiration in leaves.

For example, how would applying petroleum jelly to the surface of plant leaves affect their rate of transpiration?

I get that it's basically going to decrease the trasnpiration rate because the stomata will be covered, but I'm not sure about these parts:

How would it affect the rate of transpiration if only the top surface was covered?
How would it affect the rate of transpiration if only the bottom surface was covered?

Also, I think I'm right in saying that increasing wind / applying a fan to plant leaves will increase the transpiration rate, but why?

The rate of transpiration is very closely linked with the rate of evaporation from the leaf surface.  Increased air movement across the surface of the leaf (e.g. from a fan) increases the rate of evaporation of water from the leaf surface. This happens because water saturated air is moved away; making the osmotic gradient more pronounced.

As for the relative changes from adding an impermeable substance like petroleum jelly to the top and bottom surfaces of leaves, it's a question of plant-anatomy.  In the majority of plants, stomata are only located on the bottom surface of the leaf.  This is to prevent them getting 'clogged' during rainfall and to keep them out of the sun to minimise water loss (again more sunlight on the stomata would increase the rate of evaporation).  Therefore a plant with the underside covered would have a much slower rate of transpiration than one with the top surface of the leaf covered.

Other factors that would affect the rate of transpiration:

Temperature (Positive Correlation)
Humidity (Negative Correlation)
Light Availability Excluding CAM photosynthesis pathway plants (Positive Correlation - the stomata are in the main only open when photosynthesis is occurring, so transpiration is less at night or on a cloudy day in addition to light  heating the leaf surface)
Water content of soil (Positive Correlation)

amount of salt in soil (negative correlation)


Does melanin protect humans from gamma radiation? It is known that radiotrophic fungi use melanin to make use of gamma radiation. It is also known that melanin protects human skin from UV radiation.

Thus I wonder whether melanin protects humans from gamma radiation as well?

Are the black people and tanned white people less vulnerable to gamma radiation?

http://web.archive.org/web/20080424001002/http://www.sciencenews.org/articles/20070526/fob5.asp

Since it is clear from the source in your question that melanin can absorb energy from gamma rays, yes higher concentrations of it would reduce the energy of gamma rays getting through the skin.  However this would not provide any real relative protection, the gamma rays are still going to go right through your skin and start damaging DNA.

Gamma rays are three orders of magnitude higher frequency and therefore carry much more energy than UV.  Of course there are energy transfer inefficiencies but since the fungus are not growing at even an order of magnitude faster, it's fair to say that melanin is not absorbing all of the energy in a gamma ray.

Since the gamma rays are not fully absorbed by melanin, they will still go through the skin and will still be able to do significant DNA damage.

So yes, but not enough to really matter.

Frequency Differences
http://www.davidterr.com/science-articles/electromagnetic_spectrum.html


X linked traits expression in females We all know that females have an inactivated X chromosome (Most of its genes are inactivated).
Consider a female who is a heterozygous carrier of an X linked abnormality,
If the inactivated X was that carrying the normal gene, shouldn't the abnormality be expressed in this female? Why is it not expressed even though the other X is inactivated?

Because in different cells different copies of the X chromosome might be inactivated.
So, in (approximately) 50% of the cells you will have the X carrying the normal gene activated, and in the remaining 50% you will have the other.
You might start reading something here, and then go in further detail to understand. A nice article is here


What pattern can be learned from the data of RNA seq counts and HiC matrix? I now have some data on the RNA seq counts and related Hi-C matrix of gene segment on a chromosome. My concern is, basically, what can we do with these data so as to establish the connection between the two types of data such as the level of expression of gene segment and the interaction of the gene segment, since it seems that they are correlated. Thanks

This seems to me to be two independent pieces of data. mRNA seq allows one (in case of linear amplification) to quantify message RNA transcripts of genes of interest. that is, how many copies of mRNA for given gene are in the cell at the moment. It is ultimately, how active this gene is. In neurons different genes will be more active, than in epithelial cells, and vice versa. Genetic expression pattern provides identity of the cell.

Hi-C method, closely related to chromosome conformation capture answers question: what genes are physically interact in the nucleus via stabilizing proteins (e.g. enhcancers). There is more in the video, but general idea is that it allows you to see how genes positioned inside intricate chromatin. Since many genetic elements might physically interact via, for example, enhancers, 3C/Hi-C allows detection of such interactions. Or, at least, quantification of correlation between physical positions of two genes.

Now, the only direct connection between mRNA seq and Hi-C that I can draw is following logic: actively transcribed genes are located in expanded, less tense regions of chromatin. Hence, it will be hard to crosslink genes in such regions and correlation going to be low. Silent genes, if they are located closely in nucleus will be cross-linked with high probability, because chromatin is denser around non-transcribed genes.


A Hadeeth on the fly I think most biologists here on this site will not  consider my question below to be unfit for posting on Biology SE.

I came across this article about the hadeeth (a hadeeth is a saying of the Prophet Muhammad (peace be upon him)) on a fly:

  "If a housefly falls in the drink of anyone of you, he should dip it (in the
  drink), for the one of its wings has a disease and the other has the cure of
  the disease." [Bukhari, vol. 4: 537].

where an attempt is made to show the truthfulness of the hadeeth with an experiment: they dip a fly into water in a petri dish wholly and partially in another petri dish and different kinds of bacteria appear in each petri dish. This experiment is carried out 3 times and results are different in each round. (Please, read that article thoroughly before answering) I want to know biologists' point of view on that experiment, i.e.

Do you believe this hadeeth based on the experiment? (i. e. do you consider it to be pseudoscience or not? If yes, please provide your proofs.)

Can pathogenic bacteria arise in such an impressive quantity in water just by dipping fly into water? If yes, could you explain how?

Do you agree with the notion in the hadeeth 'he should dip it (in the drink)?

Thanks very much for your answers in advance!

Rephrasing your question
Allow me to start by saying that I barely know the term Hadeeth / Hadith mean. Of course I have checked on wikipedia but its definition is vastly unrelated to any concept in science. I think it won't be necessary for me to use this term, I will use a more classical, scientific terminology. As I barely understand the term, I do not really understand your question phrased as

Do you believe this hadeeth based on the experiment?

I can however answer to the questions

Is this document a fair description of a natural phenomenon?
Is this document contribute to our understanding of a scientific phenomenon?

The answer to both of these questions are "absolutely not"!
Lack of methodology and definition of the expectation
The document is extremely unclear, provides a very poor description of the methods and does not provide any suggested interpretation of the results. After reading it several times, I have little idea what the treatments are.
Note that this document is not peer reviewed and does not follow an appropriate format (no introduction, no method section, just a religious quotes, a citation from the Quran and images with a vague legend). It is just a document that someone wrote and uploaded online.
As @BryanKrause perfeclty said in the comment below

[I]n science the burden is on the person making a claim to defend it and provide appropriate support - there is no point in proving a claim true or false if it lacks documentation of the methodology. Being poorly written in terms of lacking adequate description is hardly better than lacking any experiment at all

In short, this document does not make any contribution to our understanding of a natural phenomenon.
The claim is very unlikely to be true
The expectation implicitly suggested to be tested is something like (my own phrasing)

If a fly barely touch (with one wing only) the media, then the media will be full bacteria but if the whole fly (with both wings) touch the media then the media will remain clean.

This expectation is highly unlikely to be true. If it were to be true, it would probably lead to a major revision of our understanding of microbiology or of the biology of flies (whichever species is considered)! Also, there is no reason to expect that in some petri dish only one bacterial species would have invaded, while in another only another bacterial species. Also, the pictures don't really match what the species described IMO. Hence, if the authors claim that this document report the results of a scientific experiment (I am not saying they make this claim), then I very much think this is a case of scientific dishonesty or at least a case of very poor understanding of how to perform a scientific experiment.


Reason for specific location of a gnat swarm? While checking on my yard trees, I noticed a tiny swarm of gnats above one small maple that has a metal cup holder stake used to help train the trunk straighter. Approximate swarm size of 20 - 30 gnats and they hovered about 6 inches above the top of the cup holder.

I know there's studies on the phenomena of swarm behavior, and out of curiosity as to what they would do I put my hand a couple inches above the cup holder. The little swarm repeatedly moved straight upwards 3-4 inches then returned to the original spot as soon as I removed my hand. When I raised my hand up towards the swarm they would move higher and higher and also follow my hand back down as I lowered it. No matter how high I raised my hands if I removed it quickly they returned immediately to the original location. I checked back a half hour later and they are still there and acted the same way.

What might be the reason for that specific preferred location of the swarm? I has been cloudy and humid all morning and I wonder if the metal of the cup holder is changing the air temperature or some other quality that far above itself? I did also notice a stronger sweet smell of the clover in that location but do have clover all over the yard. My other trees, including a very similar sized young maple but without any support next to it, have no swarms so the metal cup holder perhaps is a correlating factor?

I tried adding a picture for reference but can't get it to upload.

'Gnat' is the common name for a number of species of tiny flying insects in the Dipterid suborder Nematocera (https://entomology.ca.uky.edu/ef632), including Ceratopogonidae (biting midges), Chironomid midges (non-biting midges) and Simuliidae (blackflies). Like many other Diptera, a lot of these species mate aerially in swarms: the males gather using visual cues to determine swarm location. I'll try to add more detail to this later on why they go for specific locations, but in the meantime here are some papers on mating swarms in some of the groups normally called 'gnats':

General papers on swarming behaviour in Diptera:

Downes, J. A. 1969. The swarming and mating flight of Diptera. Annu.
Rev. Entomol. 14: 271–298.

Swarming behaviour of the family Ceratopogonidae:

Downes, J. A. 1955. Observations on the swarming flight and mating of
Culicoides (Diptera: Ceratopogonidae). Trans. R. Entomol. Soc. London
106: 213–236.
Campbell, M. M., and Kettle, D. S. 1979. Swarming of Culicoides
brevitarsis Kieffer (Diptera: Ceratopogonidae) with reference to
markers, swarm size, proximity of cattle, and weather. Australian. J.
Zool. 27: 17–30
Zimmerman, R. H., Barker, S. J., and Turner, E. C. 1982. Swarming and
mating behavior of a natural population of Culicoides variipennis
(Diptera: Ceratopogonidae). J. Med. Entomol. 19: 151–156.
Blackwell, A., Mordue, A. J., Young, M. R., and Mordue, W. 1992. The
swarming behavior of the scottish biting midge, Culicoides
impunctatus (Diptera, Ceratopogonidae). Ecol. Entomol. 17: 319–325.

Swarming behaviour of the family Chironomidae:

Gibson, N. H. E. 1945. On the mating swarms of certain Chironomidae
(Diptera). Trans. R. Entomol. Soc. London 95: 263–294.
Oliver, D. R. 1971. Life history of the Chironomidae. Annu. Rev.
Entomol. 16: 211–230.
Fyodorova, M. V., and Azovsky, A. I. 2003. Interactions between
swarming Chironomus annularius (Diptera: Chironomidae) males: role of
acoustic behavior. J. Insect Behav. 16: 295–306.

Swarming behaviour of the family Simuliidae:

Moorhouse, D. E., and Colbo, M. H. 1973. On the swarming of
Austrosimulium pestilens MacKerras and MacKerras (Diptera: Simuliidae). Australian J. Entomol. 12: 127–130
Hunter, D. M. 1979 Swarming, mating and resting behaviour of three species of black fly (Diptera: Simuliidae). Australian J. Entomol. 18: 1–6


Leptin and fat mass? I am interested in the relationship between blood leptin concentration and fat mass.  It is well known that as fat mass increases, leptin increases.

Have there been studies that look into whether the relationship is linear, or perhaps as fat mass increases, the level of leptin increases at a decreasing rate (e.g. logarithmic relationship) or an increasing rate (exponential) etc.

Furthermore, for two individuals with identical fat mass, is there a high variance of leptin concentration?

The obese gene (OB gene) secretes a protein that functions in the signaling pathway of adipose tissue and adipocytes (fat cells) produce the hormone leptin (reference).

  When the amount of fat in the body increases, the amount of leptin
  released into the blood also increases and signals to the brain that
  the body has enough to eat (reference). Inversely, studies in rodents suggest
  that a reduction in leptin level during weight loss signals to the brain
  to increase feeding and decrease energy expenditure (reference).

Other molecules have a role to play in the ratio of BMI to leptin like the ghrelin hormone (reference). The genetic and environmental factors other than overall adiposity may also regulate leptin concentrations (reference) which is why individuals with the same weight may have different leptin concentrations.

A study has reported finding a strong exponential relationship for leptin levels with body mass index (BMI) (reference). Hope that answers both your questions.


How to isolate host cell RNA (tRNA,mRNA,rRNA) from viral RNA? A retrovirus with RNA genome infected a host cell. You would like to isolate the host cell’s RNA (rRNA, tRNA, and mRNA) from the virus RNA. What properties can you rely on to determine the three types of host cell RNA- for example, in terms of their size, complexity, GC content, or abundance in the cell? The undetermined RNA can be identified as the virus RNA.

Thermo Fisher has a protocol for the separation of host mammalian RNA from prokaryotic RNA, optimized for E. coli vs human, mouse or rat sequences. Capture oligonucleotides bind portions of the mammalian RNA and hybridize. These hybridized oligo/RNA are then removed from solution via "oligonucleotide-derivatized magnetic beads," after which the remaining RNA assumed to be from whatever prokaryote can be precipitated out w/ ethanol. If you know enough about your virus and your host, I don't see why a similar assay can't be created. Otherwise, Thermo Fisher has additional links to RNA isolation protocol.. most of the viral assays, however, utilize serum, plasma, etc. because host DNA/RNA will elute along with the viral RNA if they're present, as in samples containing cells.


What makes a strong polyadenylation signal a strong signal? I was wondering why is it that "AAUAAA" is a strong Polyadenylation signal whereas the rest of the polyadenylation signals show reduced cleavage and polyadenylation efficiency?

Just expanding on aandreev's comment.

Polyadenylation is initiated by binding of CPSF (Cleavage and Polyadenylation specificity factor) after its binding to the AAUAAA motif.
From the introduction of this article:

  CPSF (cleavage and polyadenylation specificityfactor) binds to the
  AAUAAA hexamer via its 160-kDa subunit and possibly its 30-kDa subunit
  (Keller et al., 1991; Murthy & Manley,1992; Jenny et al.,1994;
  Barabino et al.,1997). CstF (cleavage  stimulation  factor) binds to
  the U- or G/U-rich element downstream of the cleavage site, and
  stabilizes the binding of CPSF to the AAUAAA sequence of the pre-mRNA
  (reviewed in Colgan & Manley,1997; Wahle & Kuhn,1997).

Any alteration in the CPSF binding site will lead to reduced polyadenylation efficiency. Polyadenylation efficiency also depends on other factors such as secondary structure and presence of proximal CstF sites.


Insect identification Colorado We found this bug in our house today. So far have not been able to identify it after past hour online. Its pincers look way larger than most normal beetles I can find. Can someone help us finger out more about this critter? Thank you

That is a cottonwood stage beetle. Lucanidae, Lucanus mazama https://bugguide.net/node/view/666700/bgimage


Which organs do cats not eat on their prey? My female cat is a very active hunter and brings me her prey daily. Except for shrews and birds, she always eats them entirely.

This afternoon she brought me this:

It was quite large (maybe between half and two thirds of the length of a mole), and I couldn't identify it (I'm in Europe if that matters).

The prey was already dead when my cat brought it to me, and she quickly started eating it. I noticed that she didn't eat this part:

I'm not a biologist, but I guess this is the stomach of an herbivorous animal?  What's inside looked like wasabi.

Why didn't she eat it? She is not so picky with smaller animals. Is it because of the size of this one?

Are there some organs or parts of the prey that cats usually don't eat ?

That looks like some sort of rodent.  The rodent stomach, while not as acidic as the human one, is still strongly acidic:

  The mouse stomach pH was 3.0 (fed) and 4.0 (fasted), and the corresponding values in the rat were 3.2 (fed) and 3.9 (fasted).

From this article

Since it's clear from the picture that the organism had just eaten (the stomach had not yet emptied), the pH would be on the lower end of that spectrum.

In humans, acidic foods often taste sour, so it may be that the cat ran into a terrible taste at the base of the esophagus that caused her to stop there, but I don't know whether the taste buds on the cat are comparable to those in a human.


Is endoderm visible in the germ layer? This picture is my drawing about germ layer - not embryonic folding as I wrote initially.

Where exactly is the endoderm here in the picture?

The known things

Ectoderm
Neural tube
Notochord
Endoderm - Where is this?
Somite
Somite leg
Intraembryonic coelom
Embryonic somatopleura
Embryonic splanchopleura (lateral mesoderm)
Endoderm
Mesoderm (intraembryonic)

I think you're going for a view of tube formation, in which case, here's a good image:

Lateral plate mesoderm
Intermediate mesoderm
Somite mesoderm
Chorda
Endoderm

(Reference)

Again in your drawing I think you correctly have it labeled as 10, and don't really need to put it twice.


Re-solidify disturbed agar plates I am stuck in trouble while pouring LB agar onto my petri dishes. I had to add kanamycin to my plates just before it started to solidify, out of forgetfulness, which I tried to mix using the tip. The plate was such a disaster! Is there a way to melt the agar in the plate and re-solidify it evenly.
I use falcon sterile plastic petri dish.

Yes. It is quite simple actually. Do this inside a clean laminar hood:

Take a clean sterile scalpel blade or any other sterile long object. 1ml pipette tip would also do.
Cut the agar on your plate. Scrape off cleanly.
Put it in a sterile glass bottle.
Heat in microwave
Add kanamycin
Pour back

Another solution is to coat the agar surface with kanamycin just like spread plating. Check the appropriate concentrations.


If someone A has lung cancer and the lung cancer has not spreaded to other parts of A, does transplant help to remove cancer?

If someone B transplants a lung 'contaminated' by cancer, does B necessarily get cancer too? His body may kill cancer?

To the best of my knowledge, the only solid organ neoplasm routinely treated by Tx, at the moment, is hepatocellular carcinoma (liver), and even that under very strict conditions. For the rest, transplantation is currently not a standard therapy because of the very real possibility of accelerated growth of micrometastases under severe imunosuppression after the transplant.

And yes... a tumour transplanted into a person would grow, and fast, again because of immunosuppression.

If you're asking this for a practical reason, I'd advise you to talk to the oncologist involved in treatment for a thorough explanation of why this wouldn't work / referral to an applicable study, if there is one.


Function of ER in reviewing mutated proteins At least in the case of Cystic Fibrosis it happens that a mutant protein (which could actually function!) is held in the ER because the ER detects it as misfolded. Does this happen in every type of mutant protein?

If so, should I conclude that such genetic disorders are caused because of the total absence of a protein rather than because of a misfolded protein? If not, why would the ER or anything else in the cell allow some mutated proteins to do any job (Like in the case of Sickle cell anaemia, where an amino acid substitution happens)?

How do scientists conclude that a misfolded protein could have done a good enough job (Like in the case of cystic fibrosis)?

Membrane proteins have to go to the ER from where they are transported to the Golgi apparatus. Usually these proteins are translocated into the ER while translation is still going on. There are chaperones (such as calbindin) in ER which help in translocation and also catalyze initial steps of folding. ER is also involved in unfolded protein response. Unless the protein is properly folded it is not transported to Golgi. However, this process is regulated at many steps and I wont add a detailed explanation of the mechanism, in this answer.

To conclude ER is involved in this case because the protein considered is a membrane protein.


Behavioral change in dolphins during different hemispheres activity periods? It is known that dolphins never sleep in the sense that we do, instead they have one hemisphere of the brain sleeping while the other one is awake. I wonder, do they show observable changes in behavior in regard to this, depending on which hemisphere is active? Do their hemispheres even have a specification similar to ours (logic and emotion)?

Sleeping is a biological stage which we presume as a relaxation period but its really a highly functional stage for brain. Most of the memory related processing such as management of working memory and cognitive functions such as decision making, reasoning, and episodic memory are closely related with sleep.

Dolphins never sleep in the sense that we do, CORRECT, because we close our both eyes and enter into a stage of decreased ability to react to a stimuli. But in the case of dolphins they need to breath, so by fully entering into a sleep stage like us is suicidal in their case.
Dolphins have a specialised way of dealing with this problem, they do a "unihemispheric slow-wave sleep". They only sleep with one hemisphere of the brain while the other being active, when the right hemisphere is sleeping the left eye is closed and vice-verse, as the right hemisphere controls the left part of the body. The observable change in their behavior is visible from the closed single eye.

Humans and dolphins had a common ancestor that lived 95 million years ago. During the last 50 million years dolphins have been evolving in water and their brain evolution had taken a different route. The neocortex, the outer most layer of brain which is considered as the recent evolved part of brain. The neocortex is actively developing in both humans and dolphins, one of the most striking features among them is that human neocortex is having large thickness and dolphins are having thin one with more folds than ours. The folding in neocortex is a technique to increase its surface area. This substantial difference is due to the evolutionary divergent way both the species took.

Dolphins have a complex echolocation system and binocular eyes, they need to create the visual and sonar image of their surroundings and studies shown that their increased brain size is due to the tremendous volume of data they need to process for these purposes. Also being a social animal their neocortex consists of connections like us but as we both are evolutionary separated for about 95 million years ago most of the brain areas are diversified and evolved.

  Dolphins showed that they can understand a symbolic, human-based
  language, where the words are either whistles or hand gestures. And
  the dolphins could easily understand that we use different word orders
  to mean different things. So they understand syntax. The dolphin brain
  is arranged in a completely different way from ours, and yet they can
  still understand what we are trying to teach them. Lou Herman also
  showed that dolphins are right up there with humans and chimpanzees in
  being able to understand that when we point at something or look at
  something, we’re meaning “Don’t look at me; look at what I’m looking
  at.” He’s done all kinds of really fascinating things, and his work
  has contributed the most to our understanding of what these animals
  can do.Reference


is it possible to visualize coronavirus infection and what type of assays are routinely used? There has been some electron micrograph of SARS-COV-2 published; but are there any fluorescent/ confocal-fluorescent image of them? or is it possible to do them?  I know that viruses are usually much smaller than capacity of light microscope but I think by using any immunofluorescent probe or FISH technique it is possible to visualise the locations occurance of the virus in cell or tissue. At least one website says it is possible to visualise viral infections using fluorescence techniques.

Now is there any such image for SARS-COV-2, and is it possible to take?

If you have an antibody against the viral proteins you can do an immuno staining followed by fluorescence imaging. For this type of technique you would need a very specific antibody. I am not aware that this exist at the moment and I don't think anyone had the time to do it for immunostaining purposes.

For FISH it would depend on the genomic nature of the virus (ssRNA, ssDNA, dsRNA, dsDNA), again you would need specific probes to capture it. Again specific is key.

EDIT 01.04.2020: This group says they have found specific antibodies https://www.centivax.com/covid19


Why don't we have hair on palms? We have hair all over the body except palms.
What is the biological reason behind this?

The main functional reason is we need to be able to grip things with our hands (and feet, which are also hairless), and hair would interfere with that. Physiologically, the epidermis in these parts of the body is very thick and highly keratinized, and when combined with the thick underlaying layer of dermis, this results in skin that does not support the growth and maturation of hair follicles.


Cross-integration of puma subspecies populations A major concern of conservationists  in south Florida is the population of native Pumas, the Florida Panther.

Until recently, it was thought that the Pumas were a genetically distinct subspecies, but some genetic studies have shown that they may not be, and so their subspecies status is disputed.

If the population of Pumas in Florida is genetically distinct from other populations in North America, is there any precedent for using a distinct subspecies to bolster populations of an endangered subspecies?

If the population of Pumas in Florida is not genetically distinct from other populations in North America, would there be any behavioral issues (hunting, etc.) in animals brought from other biomes to south Florida, either as adults or offspring of transplanted adults?

The study you are referring to is probably a study by Culver et al. (2000). They performed a genetic analysis of 315 individuals of the American Puma (Puma concolor), also known as the cougar. Their thorough analysis (especially for the late 1990s) showed that the Florida panther and the western North American pumas were the same subspecies, Puma concolor couguar (note the proper spelling of the subpecies). All individuals north of Nicaragua are this subspecies. From Nicaragua south into South America, they recognized five additional subspecies of American Puma.  The distribution of the subspecies, as well as the sample locations, are shown in the figure below, taken from Culver et al. (2000).

Notice in the figure above that the American Puma used to occupy most of North America but now is restricted to the the region west of the Rocky Mountains, except for the isolated Florida population. Because the genetics of the Florida Panther and the western American Puma are effectively the same, individuals from the western US can be introduced into southern Florida. This idea was first proposed (to my knowledge) by Hedrick (1995) as a conservation measure by introducing genetic variation and reduce the effects of inbreeding. In that same year, eight female pumas were transferred to Florida from Texas, which had the population of panthers closest to Florida. Introducing pumas from outside of Florida has pros and cons, reviewed by Pimm et al. (2005), from both a short-term conservation perspective as well as long-term evolutionary perspectives.

Several years after the Texas pumas were introduced, Johnson et al. (2010) performed a genetic analysis of the Florida population. They showed that the Texas females were indeed reproducing in Florida. The release of Texas panthers did introduce more genetic variation into the Florida population and reduce the effects of inbreeding. The net effect was that more Florida panthers were surviving. The downside is that habitat loss continues and the effective population size is still very small. That means that inbreeding is still very much an issue.

The studies to date have focused on genetic integration and overall recovery due to the introduction of genetic variation but I did not find any studies that reported any behavioral changes since the 1995 introduction. Given that it was only 8 females, I would not expect any significantly different behaviors to be introduced into the Florida population.

Introducing more genetic variation from Texas (and perhaps populations farther west) may be helpful but ultimately preservation of habitat and improving ability of individuals to move among available habitat fragments via corridors is necessary to protect the species long term.

Citations

Culver, M. et al. 2000. Genetic ancestry of the American Puma (Puma concolor). Journal of Heredity 91: 186-197. (open access)

Hedrick, P.W. 1995. Gene flow and genetic restoration: The Florida panther as a case study. Journal of Conservation Biology 9: 996-1007.

Johnson, W.E. et al. 2010. Genetic restoration of the Florida Panther. Science 329: 1641-1645.

Pimm, S.L. et al. 2005. The genetic rescue of the Florida panther. Animal Conservatation 9: 115-122. This issue of Animal Conservation has a few articles dedicated to the Florida Panther.


Are axons capable of endocytosis? There is evidence for the uptake of toxic substances like prions from the cell bodies of neurons via endocytosis.  There is also evidence for prion deposition in white matter.  But I haven't been able to find a discussion of whether or not endocytosis is possible from axons.  Does anybody know if this is possible?

Short answer
In hippocampal neurons, endocytosis does occur in the axon, but only at the synapse and at varicosities.

Background
In cultured rat hippocampal neurons, Parton et al. (1992) showed that the cell body and dendritic regions are indeed capable of endyctosis. They used horse-radish peroxidase dissolved in an internalization medium. In the axon, endocytosis was only found to occur in the pre-synaptic region and in varicosities. Varicosities are points of synaptic release from the axon, outside the synapse proper.

Hence, axonal endocytosis is limited to regions where neurotransmitters are released. Presynaptic terminals often engage actively in neurotransmitter reuptake mechanisms to recycle released neurotransmitters.

Reference
- Parton et al., J Cell Biol (1992); 119(1): 123–37


What is the scientific name of this evergreen plant? This plant is found in India. It is an evergreen plant. Would love to know the scientific name.

The tree in question belongs to the Araucariaceae family,

There are multiple species of Genus Araucaria,

I'd place Araucaria araucana on the first place, but there are multiple others:

Araucaria araucana

Araucaria luxurians

Araucaria columnaris

Araucaria subulata


Skin (epithelial) stem cells: unipotent or multipotent? In a video on the Khan platform on stem cells, epithelial stem cells are described as unipotent stem cells, i.e. only producing one kind of specialised cell: epithelialor skin cells.
However, on a website describing the hierarchy of [stem] cell potency, skin cells are shown to be the product of multipotent stem cells:

Which category is correct for skin stem cells - unipotent or multipotent?
UPDATE

In this article on sciencedirect.com epithelial skin cells are described as the products of epithelial multipotent stem cells and/or unipotent "progenitor" cells (which I presume is a way of describing a stem cell that only produces one type of cell - in this case an epithelialor skin cell). The epithelial multipotent stem cells can produce a variety of cells.

Most epithelial tissues self-renew throughout adult life due to the
presence of multipotent stem cells and/or unipotent progenitor cells [emphases mine].
Epithelial Stem Cells and Their Lineages Epithelial stem cells can generate tissues that display a fascinating array of cellular
architectures, each of which are specifically tailored for distinct
functions. In this review, we will focus on four well-characterized
epithelial stem cells whose tissues possess diverse architectural
designs and physiology: intestine, epidermis, mammary gland, and
cornea.

So it seems the answer to my question is: both.


Hydrogen Peroxide on Open Wounds I know that H2O2 is a chemical with high oxidative potential. It can deliver nascent oxygen which can destroy bacteria.

I understand that open wounds have cells that are dividing at a fast rate to effect healing. Is it good to add a substance that can cause damage to cell membrane and possibly cause mutation in the DNA of these fast growing tissues?

Can H2O2 be safely used to sterilize wounds?

There will be few rapidly-dividing cells in a fresh wound (which is the wound to which H2O2 is applied). In general, it is a good idea to avoid applying irritants to rapidly dividing tissue.

Hydrogen peroxide is a weak mutagen. It is produced in many body tissues, ingested in drinks, produced by mouth bacteria, etc. It may well cause some cancers. Some OSHA-mandated literature does warn that it is a mutagen and must be handled with care, but these are warnings to people who work with concentrated solutions.

However, a relatively weak hydrogen peroxide solution, even if it is mutagenic, would need to be left in place and active (or renewed) for a long period of time to produce skin cancer. As it has been a staple of first aid kits for decades, and this association has never been made clinically, my best guess is that the benefit (as a bacterocidal agent) far outweighs the risk in the treatment of minor wounds. As in all things, however, prudence is advised. (I myself don't use it because soap and a lot of water is quite effective. Nor is it used in the care of wounds in Emergency Rooms where it is considered to be detrimental to wound healing. If I were in a country where clean water and soap were in short supply, I might well use it if necessary.)

Because it is an irritant (and many irritants can be considered mutagenic), it is actually used to treat precancerous skin lesions, the finding being that it affects the more rapidly dividing pre-cancerous cells than the rest of the epithelium.

Far more potent peroxides have been used topically, which may increase the risk of skin cancer.

Interestingly, one of the responses of skin cells to H2O2 is the generation of an oxygenase to fight the effects.

Topical sulindac combined with hydrogen peroxide in the treatment of actinic keratoses
Effects of Peroxides on Rodent Skin: Epidermal Hyperplasia and Tumor Promotion
Heme oxygenase is the major 32-kDa stress protein induced in human skin fibroblasts by UVA radiation, hydrogen peroxide, and sodium arsenite
Recent Advances in Wound Care, Michael K. Abraham, MD, MS, and Jason S. Oh, MD


Why is the swelling of bread when placed in water not considered to be caused by osmosis? Why is bread swelling up when placed in water not considered to be caused by osmosis?

Is there a property of water that should make it leave the bread instead of enter?

The phenomena that you are describing, where bread, which is a porous material, similar to a sponge, absorbs water, is the absorption of water by capillary action.

As @Joel mentioned, osmosis is specifically the flow of a fluid across a semipermeable membrane, such as the plasma membrane of a cell or dialysis tubing, that occurs in such a way as to cause a flow from an area of low concentration to an area of high concentration. This flow eventually leads to a state of equilibrium when the concentration on both sides of the membrane is the same.

The wikipedia article on Osmosis gives this definition:

  Osmosis is the spontaneous net movement of solvent molecules through a semi-permeable membrane into a region of higher solute concentration, in the direction that tends to equalize the solute concentrations on the two sides. It may also be used to describe a physical process in which any solvent moves across a semipermeable membrane (permeable to the solvent, but not the solute) separating two solutions of different concentrations. Osmosis can be made to do work.
  - Wikipedia: Osmosis

- By OpenStax College [CC BY 3.0 (http://creativecommons.org/licenses/by/3.0)], via Wikimedia Commons

The bread is not selectively permeable, and it will continue to absorb liquid until it is fully saturated. This isn't actually an equilibrium, because additional water would do nothing to change the concentration on one side of the bread or the other. If you added more water to one side of a semipermeable membrane in equilibrium, by Le Chatelier's principle, you are will force the reaction (in this case, you change the concentration) to one side, then the liquid would again flow from the area of low concentration to the area of high concentration.

Capillary action is the result of water flowing into the small spaces, such as the air bubble that form in bread when it bakes, in the absence of a force "pushing" it into those spaces, or against the force of gravity. The liquid accomplishes this through intermolecular forces that cause adhesion of the molecule to the surface of the material that is absorbing it and cohesion of the molecules in the liquid keep them associated to one another, and as the liquid moves into the spaces, it is able to pull the other liquid molecules along into the space.


Can spike protein induced cell fusion be triggered by the mRNA vaccine? The mRNA-based vaccines cannot lead to COVID-19 or its symptoms since they only lead to the production of the spike protein in the cell.
However, the spike protein itself can lead to cell fusion:
Quantitative assays reveal cell fusion at minimal levels of SARS-CoV-2 spike protein and fusion from without
Is this a potential risk of the mRNA vaccine ?
I could imagine, that the spike protein needs to be bound to the virus to induce this effect ?
I could not find any literature where the effect of the unbound spike protein is tested.

The mRNA vaccines encode a mutant version of the spike protein in which the structural transition needed to to fuse membranes is blocked. This was done to make the immune response focus on the pre-fusion state, which is much better for neutralizing the virus.
From https://cen.acs.org/pharmaceuticals/vaccines/tiny-tweak-behind-COVID-19/98/i38:

Fortuitously, Graham and a former postdoc, Jason McLellan, devised a solution to this problem before the pandemic. Through a bit of structural biology and persistent protein engineering, McLellan discovered that adding two prolines—the most rigid of the 20 amino acids—to a key joint of a vaccine’s spike protein could stabilize the structure’s prefusion shape. This 2P mutation worked in preclinical studies of Graham and Moderna’s MERS vaccine, so they applied it to Moderna’s COVID-19 vaccine.

I don't know if cells expressing wild-type spike protein would fuse into syncytia, but it seems very unlikely to happen with the vaccine spike.


Probability of carrying an autosomal recessive trait given both parents are carriers I recently came across a question that asked for the probability of having a child with an autosomal recessive trait, namely cystic fibrosis. From various parts of the question, we can conclude that the father is definitely a heterozygous carrier and that the mother's parents are both heterozygous carriers. In this situation, the only way to produce a child with cystic fibrosis is if both parents are heterozygous carriers, and this will happen with a probability of $\frac{1}{4}$.

The part that causes confusion is figuring out the probability that the mother is a carrier.

One student reasoned that a cross between two heterozygous parents will produce a 1:2:1 genotypic ratio, so $\frac{1}{2}$ of the progeny will be heterozygous carriers. Therefore, the probability that the mother is a carrier is $\frac{1}{2}$ and the probability of producing a child with cystic fibrosis is $\frac{1}{2}*\frac{1}{4}=\frac{1}{8}$

Another student also referenced the 1:2:1 ratio but reasoned that since the mother is phenotypically normal, that the ratio is actually just 1:2 because there is no chance of being homozygous recessive. Therefore, the probability that the mother is a carrier is $\frac{2}{3}$ and the probability of producing a child with cystic fibrosis is $\frac{2}{3}*\frac{1}{4}=\frac{1}{6}$

These two answers are also found at this other question.

The last solution proposed is the most interesting. This student referenced the Monty Hall Problem, which is indeed somewhat related to this problem (read more about the Monty Hall Problem). Using the same ratio as above, we can conclude that there is a $\frac{1}{4}$ chance that the mother carries no alleles for cystic fibrosis and a $\frac{3}{4}$ chance that she does. The fact that she definitely does not carry two alleles does not change this probability. Therefore, the probability that the mother is a carrier is $\frac{3}{4}$ and the probability of producing a child with cystic fibrosis is $\frac{3}{4}*\frac{1}{4}=\frac{3}{16}$.

Out of these proposed solutions, which one is correct? And why are the others incorrect?

EDIT: To be clear, the solution I initially considered to be correct was the second one.

Monty Hall does not apply here because there is no decision point past where information is given: the information is already known that the mother is normal phenotype, and the probability for each child of the mother's parents is independent; in the Monty Hall problem, it is known that exactly 1 of the doors contains the prize. Because this sum is known (that only 1 door has the prize), if you know the contents of one door it changes the probability of the others. That is, the occurrence of the prize/goat is sampled without replacement: the thing behind each door is dependent on what is behind the other doors.

2/3 is the correct probability for the normal phenotype mother to be a carrier. Therefore the probability for a child to be homozygous recessive is (2/3) * (1/2) * (1/2) = 1/6.


What is the difference between gene expression and protein synthesis? I have no idea what I'm supposed to do. Can someone please help me? What is the difference between gene expression and protein synthesis?

According to the homonymous article of Wikipedia

Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product.
These products are often proteins, but in non-protein coding genes such as transfer RNA (tRNA) or small nuclear RNA (snRNA) genes, the product is a functional RNA.

As shown by this picture, gene expression consist of genetic transcription, that results in a mRNA, maturation of the mRNA (splicing, incorporation of a poly(A) tail, capping, ...) and finally protein synthesis by means of translation of the mature mRNA.
Again, the homonymous Wikipedia article tells us what is protein synthesis:

Protein synthesis is the process whereby biological cells generate new proteins [...]. Translation, the assembly of amino acids by ribosomes, is an essential part of the biosynthetic pathway, along with generation of messenger RNA (mRNA), aminoacylation of transfer RNA (tRNA), co-translational transport, and post-translational modification.

The following picture describes the process of mRNA translation by ribosomes that results in a polypeptide.

Once folded in its proper 3D structure, the polypeptide becomes a functional protein.
In order to work properly, some proteins need post-translational modifications, which is (citing Wikipedia again) the covalent modification of proteins following protein biosynthesis and goes beyond the scope of this answer.


How do fish maintain razor sharp teeth? I was watching a program about Barracuda - they have a front tooth that is supposed to be razor sharp.  My kitchen knife goes blunt if I use it for long periods without sharpening.  Sharks keep on growing new teeth but barracuda don't.

How do fish like Barracuda maintain a tooth that is razor sharp?

Edit News article on how sharp the tooth is

http://www.dailymail.co.uk/news/article-1348152/Barracuda-attack-breaks-womans-ribs-forces-boyfriend-seal-punctured-lung-hand.html

Fish replace their teeth over time as needed. Thus, they don't maintain the sharpness of individual tooth, they just replace it. This is a passive process not a conscious process.

Source: Barton, M., & Bond, C. E. (2007). Bond's biology of fishes. Thomson.Pg. 414-415.


How do minute changes in an organism, as a result of evolution, get carried over to next generation The theory of evolution states that random variations in organisms occur to better suit their surroundings. We take for example a bacteria's flagella. There's a bacteria who has a tube kind of structure that it uses to inject toxins in other cells. Structure of flagella and this tubular structure is very similar. So biologists state that this is clear evidence for evolutionary process wherein this tubular structure underwent gradual changes that resulted into a flagella.

Now my question is, minute changes did occur to this tubular structure, but how do those changes get carried over to the next generation? Almost all components of a cell are created as per the instructions coded into DNA. So does it mean that every minute changes that occur to an organism get recorded into DNA so that they can be carried over? In above example, assume, that a few proteins got accidentally attached to the tubular structure that will help the structure to rotate. Now when this temporarily changed bacteria gets divided into a new one it will have lost that change. So to actually carry over this "beneficial" change would the bacteria have changed its genome? How does this happen? What is the basal mechanism that supports evolutionary changes?

As populations expand, generation by generation, they will inevitably
  run into limits on resources. Not all individuals in a population are
  exactly alike as some will have traits that give them an advantage in
  survival. A change in any aspect of the environment can suddenly turn
  what had been just another variation or variant into either an
  advantage or a disadvantage  If a selective pressure (i.e. change in
  the environment), acts against or upon the differences between the
  individuals in a population, you get natural selection, which, through
  time, can cause a population to evolve

http://rmitchellbioanthro.weebly.com/uploads/2/3/7/6/23767919/natselinanutshell.pdf

Evolution consists of two essential things:

Random mutagenesis (in this case a slight change that occurs in the DNA, that causes a slight change in the protein to show up)

The second stage of evolution is natural selection. After the mutagenesis event, nature rigorously selects for the mutation. If the mutation has a fitness cost to the organism, it gets removed (the organism doesn't survive). By removing all things that are more costly than beneficial, nature selects for the fittest.

Take the examples of beetels here (http://evolution.berkeley.edu/evolibrary/article/evo_25)

Very rarely does the external environment directly change the DNA code (you can argue about epigenetics, but that's a different can of worms). Changes in the environment usually dictate the survival of organisms with different traits. In fact what usually happens is a change in the DNA code occurs naturally due to mutagenesis and that change undergoes the rigours of natural selection.

So in you case what might have happened is (I am postulating here, I would recommend a literature search to verify this), your bacteria had a tubular structure that it used to inject toxins in other cells. Some bacteria (due to genetic variation in sexual reproduction) had mutations that allowed it to move this tubular structure. This allowed it to survive more efficiently, and hence reproduce more. Eventually this population of bacteria, slowly replaced the bacteria who had no locomotor control on their "tube", and hence one stage of natural selection has occurred. Now this happens again and again, till the efficiency of the locomotion is optimal.

Might I suggest you read this book ?

Bonner, John Tyler. The evolution of complexity by means of natural selection. Princeton University Press, 1988.


Factors That Would Promote Eusocial Development In Mammals? What would cause mammals to evolve to be more eusocial, like the naked mole rat did? What advantages does eusociality give in such scenarios?

What?
Eusociality in mammals can be defined by the following criteria:

reproductive altruism (which involves reproductive division of labor and cooperative alloparental brood care);
overlap of adult generations;
and permanent (lifelong) philopatry (stays (or returns) at (to) breeding ground).

Why?
Burdo et al. (2000) state that eusociality in mammals is a special case of monogamy, involving prolonged pair bonding for more than one breeding period. They argue that eusociality in mole-rats evolved from a monogamous mating system where cooperative brood care was already established. A tendency for group living is considered to be an ancestral trait in some genera of mole rats. The solitary lifestyle seen in some other genera is assumed to be a derived trait.

The aridity food-distribution hypothesis (AFDH) suggests a causal relationship between cooperative foraging for patchily distributed resources and the origin of eusociality. This theory states that limited nest sites or patchy resources leads to benefits of staying within the natal group, including reduced dispersal risk, and the possibility of inheriting the natal nest (Plowes, 2010).

How?
In proximate terms, in eusocial mole-rats either puberty is assumed to be developmentally delayed so that under natural conditions most animals die before dispersal is triggered. If genetic relatedness among siblings is high, then philopatry would not invoke an appreciable loss of fitness, especially if the cost of dispersing is higher than staying within the natal group. High genetic relatedness is more likely in a monogamous mating system or a highly inbred population (Burdo et al., 2000).

References
- Burda et al., Behav Ecol Sociobiol (2000); 47(5): 293–303
- Plowes, Nature Education Knowledge (1010); 3(10): 7


Is Homo sapiens the only species capable of prioritization? Just what the title states--given an absurdly large number of assignments to perform in a limited time-frame we usually attempt to do the most important ones first. Is this ability to define and execute by priority a universal feature in all sentients, or is it a socially learnt behaviour of us Homo sapiens?

There is a very simple experiment you can do that will demonstrate that animals prioritize. Give a dog two bones. Preferably one which is more tasty than the other. Say one has more meat on it. The dog cannot eat both at once and you will observe it choosing one over the other. This is a clear example of prioritization.

Again with a dog, try observing one greeting two people it is fond of. If you and a friend stand a few meters apart when the dog comes up to you, the animal will choose to greet one of the humans first. Prioritization.

Any animal, or plant, fungus, bacterium or archaeon for that matter, that is ever presented with a choice between two actions during its lifetime, will have to be able to prioritize in order to chose between them. Clearly they can as our world is not strewn with, for example, panicked, confused looking squirrels trying desperately to chose which tree to climb.


How many ion channels on average must there be in one µm2 of neuronal membranes? If the conductance of a single ion channel is 1pS and its capacitance per cm2 is 1uF and the time constant for a human neuron is 1ms

How many ion channels on average must there be in one µm2 of neuronal membranes?

How is it possible to know how many ion channels with only these information? would you be able to explain it?

Thank you

I expect your homework was already due, so...

You're supposed to remember what a membrane time constant is. I'll quote from page 12 of my (by now quite old) copy of "Ion channels of excitable membranes", by Hille:

  For biological membranes the product, RmCm, of membrane resistance and capacitance is often called the membrane time constant, taum.

Since you know tau and C, your goal is then to determine the membrane resistance. You also need to convert the capacitance to square microns (1e-14F per square micron). In this case: 1ms/1e-14F = 1e11Ohms, or 1e-11S, or 10pS. So on average there are 10 channels per square micron, assuming I didn't make any silly mistakes.


What causes DNA gel electrophoresis bands to swirl? I recently ran a gel on a new system and came out with something I've never seen before.

I loaded the first three wells with a ladder in the first and an uncut plasmid in the next two. There are no bands, just swirls all over the gel.

It's a 10 cm gel, 0.7%, and I ran it at 80 v for 1.5 hours. Part of the new system is the buffer, lithium borate,  which I've never worked with before.

Any ideas as to why this is happening?

Edit: thank you for your answers. I followed the regular protocol closely and used the same bottle of buffer for both making and running the gel. I did this twice and got similar results both times.

I had the power supply tested and discovered that the voltage may have been fluctuating between 77 and 83 volts during the run. Could this have caused it?

It can possibly be one of two problems:

Either the gel poorly prepared, in that it was cooled for too long, resulting in parts that solidified before pouring it into the mold.
This I have seen before, the pH of the electrophoresis buffer and the buffer used to make the gel was not the same. It has to be the same throughout the gel to ensure that the DNA moves evenly to the positive electrode.

Do you perhaps have a gel image of the bio-transilluminator? It could provide more insight.

Hope this helps


How do animals know who their child is? This may be a strange question, but really it's something I've always wondered.
Recently I was watching a documentary of penguins and how a mother penguin lost its child. Then it went looking for it, and among a horde of penguins, it was able to find it's child and take it.
What really intrigued me is that the penguins looked exactly the same. Animals don't have "as much"
distinctive features as we humans do, such as significally different hair color, skin color, they don't really look very different. Rather animals of the same species look very similar.
Just consider the following image:

How can one even differentiate between all these penguin children? Even the parents look very similar.
That's just what I'm wondering. How can parents spot their child between all of these penguins that look almost identical.

Penguins (and many birds) recognize their offspring and mate thanks to vocalizations.
It's called individual vocal recognition, it's like when you recognize your friend voice among a group of chatting people.
Scientific article references for penguins:
http://www.sciencedirect.com/science/article/pii/S0003347299910862
http://rspb.royalsocietypublishing.org/content/267/1448/1081.short


How does Isoxaben kill newly germinating seeds, with almost no effects on established ones? Isoxaben (N-[3-(1-ethyl-1-methylpropyl)-1,2-oxazol-5-yl]-2,6-dimethoxybenzamide) is a pre-emergent herbicide used in landscape beds before the application of mulch (my use for it, anyway). It kills the weeds as they germinate, while not harming most established plants.

Here's the mode of action, as stated by Dow AgroSciences:

  Isoxaben belongs to the Benzamide family of herbicides and inhibits cellulose biosynthesis in the cell walls of susceptible
  weeds (WSSA group 21). This means that cells cannot divide during the reproductive cycle; therefore, they cannot grow,
  causing death. While cell division does not occur, this mode of action should not be confused with mitotic inhibition that
  occurs with dinitroaniline herbicides.

How does this only affect germinating weeds, while not noticeably affecting weeds that have emerged from the soil (I have to hit those with another herbicide)?

As with your other question on mitotic inhibitors ("How does Trifluralin kill newly germinating seeds, with almost no effects on established ones?"), inhibiting cellulose synthesis will inhibit growth. Hence, an established plant will stand its ground, but newly germinating plants cannot grow without cellulose synthesis and hence will fail to germinate.


What are the small lumps in the mouth of the fish, and what is its function? Today I was performing a fish head dissection to investigate the gas exchange process in biology. Then when I opened the mouth I noticed these small hard structures at the base, I assume they may be a form of teeth that allows the fish to grind hard shells of invertebrates and plant matter. Yet I was curious as to why some fish have this and others don't and what exactly it's function is. Also if you have a name I would highly appreciate it as I can label it in my lab book. Thank you so much for your time.

Yes those are teeth and some have them and some do not for the same reason some have sharp teeth wile others have flat scrapper teeth, it depends on their diet.

this kind of teeth are called molariform, and are used for crushing shellfish more than anything else. This slide show will help you, https://www.ru.ac.za/media/rhodesuniversity/content/ichthyology/documents/Anatomy%20Lecture%207.pdf


What does the hornet do on the ivy blossoms? We've got blooming ivy growing around a tree. Since several weeks lots of hornets have been whirring in the foliage and I wonder whether they want to feed on insects that are lured by the blossoms or whether they come for anything they get from the ivy plant.

Hornets, just like wasp in general, hunt insects to feed their larvae but feed themselves with carbohydrates like nectar (or lemonade). So it is quite probable that the hornets are feeding on the nectar of your ivy. wikipedia


How can Pyridostigmine have the indication of Myasthenia? I am thinking how pyridostigmine can be used in the treatment of myasthenia gravis.
Its similar compound (neostigmine) is also anticholine esterase.
This compound has the indication of myasthenia gravis but with the stimulation of the nicotinic receptor.

I cannot understand how pyridostigmine is causing the effect.
Probably, pyridostigmine is similar to neostigmine in structure, which can be why more pieces of information is about neostigmine than pyridostigmine.

How can pyridostigmine have the indication of myasthenia gravis?

Pyridostigmine is an analog of neostigmine, so has the same basic mechanism of action. Please forgive me for repeating information you may already know.

There are two main families of acetylcholine receptors: muscarinic and nicotinic. Acetylcholine receptors at the neuromuscular junction (NMJ) are exclusively nicotinic (N1 or NM), so that's the only receptor I'll address.

Myasthenia Gravis is caused by an immune response to nicotinic postsynaptic receptors on skeletal muscle. An antibody can either destroy or block the receptor site. The antibodies destroy the receptor sites more rapidly than the body can replace them. In MG, there can be as much as an 80% reduction in the number of these receptor sites.

Acetylcholinesterase (AChE) is an enzyme that breaks down acetylcholine (ACh) at the synaptic cleft. AChE has a remarkably high specific catalytic activity: each molecule of AChE degrades about 25000 molecules of ACh per second. Any drug which serves to inhibit AChE will increase ACh concentration at the N1 receptor. AChE inhibitors can be irreversible or reversible. Reversible inhibitors, (competitive or noncompetitive) have therapeutic applications; irreversible AChE  modulators are toxic.

Carbamates are organic compounds derived from carbamic acid (NH2COOH). They are reversible AChE inhibitors. This group includes neostigmine, pyridostigmine and physostigmine. Pyridostigmine is an analog of neostigmine, so has the same basic mechanism of action. Because they are not lipid soluble, they are selective for the NMJ; both also have direct action on Nm Receptors. The major difference between them is that pyridostigmine has a slight but significantly longer duration of action.

Drug Bank: Pyridostigmine
NeuroLex.org (get's it's info from PubChem)


Calculating sequence divergence score for a protein from identity or similarity score? I have % identity and % similarity scores for ~50K protein alignments, that I fetched from Ensembl Compara database. The issue is that I wanted to have divergence scores instead. So in order to calculate divergence scores, I first looked for the conventional method to calculate divergence score from protein alignments. But turns out, most of the methods/tools calculate % identity and % similarity scores instead of divergence scores.
(1) So I wonder what is the conventional method to calculate divergence scores from protein alignments.
(2) Could I simply calculate % sequence divergence as 100 - % identity or 100- % similarity score? If that's ok, should I prefer 100 - % identity or 100- % similarity?
Any suggestions from experts are welcome.
Update: As suggested in a comment below, I should mention that the average % identity score is more than 70. I hope this information would be helpful.

This is a very tentative answer as I haven't done anything like this, but it's a learning experience for me and I hope it could be helpful to get a more knowledgeable response started.
I don't think you can do this.  Per Wang, 2009 and Yona, 2002, divergence scores could be Kullback-Leibler divergence or Jensen-Shannon divergence, but both papers opt for the latter.  Divergence scores are based on "empirical probability distributions between the 20 amino acids".  BLOSUM or PAM matrices may be used.  Simply counting the identical or similar residues wouldn't contain as much information.  Wang, 2004 compared JensenShannon to numerous other scoring methods in the context of PSI-BLAST.
The similarity score is related to the divergence score:  Score = 0.5(1-D)(1+S) where D is the divergence score and S is the significance score. It is equation #15 in Wang, 2009 paper.  If you could safely assume the significance score for some alignments was near 1 (no chance similarities) then maybe you could say D = 1 - similarity score.  Unfortunately, judging by the glossary because I haven't downloaded any of the datasets, for the Ensembl data similarity is merely "How well one sequence matches another determined by calculation by an alignment program of identical and conserved residues/nucleotides."  So from that I take it they may just be counting up the "conserved" amino acids in the old fashioned way, but don't know that.


Is there enough vitamin B12 in lakes, rivers and ponds, for humans not to need to take supplements? Vegans will often say that having an animal-free diet is best for our health and is actually the diet that humans should be eating to function optimally. To which meat eaters will raise the issue of B12, and how (they believe) it is only to be found in animal products [thus vouching for an evolutionary need to eat meat and eggs). These days, with all our water being treated to remove pathogens, it is obviously best to take b12 supplements, but the question remains: do vegans have a point? Is there actually enough b12 in water for humans to not develop an insufficiency?

Of course there is no evidence for the superiority of the vegan diet claim to begin with, so there is that, and there are plenty of vegan foods fortified with B12, even some from non-animal sources.

No, there is not enough B12 in treated water nor well water for a human. There can be enough B12 in untreated river/lake water because it contains high levels of fecal matter or algae which is high in B12 (b12 is manufactured by anaerobes).  Of course these are the things you want removed from your drinking water so reducing B12 is inevitable. Also can contain enough being the key phrase it depends on the water source, cleaner river contain less.

Evolutionarily speaking humans eat animals for the same reason every omnivore and many herbivores (deer, ect) do, because we can, it is generally a superior nutritional substrate which is more than enough for evolution to favor it.

source 1

Source 2

source 3


How long will a typical bacterial strain keep in a -80°C freezer? I know that a -80°C freezer is the recommended means of long-term cell-line storage, and that cells will typically not last long in a -20°C freezer.  But how long will a typical bacterial strain (e.g., E. coli DH5-alpha) actually stay good in a -80?
Searching around via Google, I'm finding a wide range of answers, anywhere from only 3 months to indefinitely, so I'd like to try to get a better grounded way of estimating longevity.

Richard Lenski's lab at Michigan State university has been doing long-term evolutionary research on E. coli and maintaining a "frozen fossil record" of their experimental populations every 500 generations since 1988. They still periodically release research papers comparing the physiology of evolved and ancestral populations. For example, this recent paper looks at populations collected at 2000, 10000, and 50000 generations. According to this timeline, they used populations frozen over 3 decades ago.
This doesn't guarantee that your specific organism will last that long, but it does show that freezer stocks can remain viable for longer than some research labs will even exist. Most of their protocols are on the website. I've had lunch with Dr. Lenski, and he's a pretty approachable guy. I'm sure if you emailed him with specific questions that aren't covered on the website, he'd try to find an answer for you.
References:
Changes in Cell Size and Shape During 50,000 Generations of Experimental Evolution with Escherichia coli. Nkrumah A. Grant, Ali Abdel Magid, Joshua Franklin, Yann Dufour, Richard E. Lenski, Journal of Bacteriology Mar 2021, JB.00469-20; DOI: 10.1128/JB.00469-20
Lenski Lab homepage: http://myxo.css.msu.edu


Is there a limit to acceptable brightness for plants? Can overly bright artificial light harm plants? Is it possible to achieve a level of brightness so high that it does more harm than good to plants?

If sunlight can be filtered of infrared light spectrum, so the plants don't burn from high temperature, but if it's possible, then that too.

The wikipedia page on photosynthetic efficiency has some useful insight here:

  Photosynthesis increases linearly with light intensity at low intensity, but at higher intensity this is no longer the case. Above about 10,000 lux or ~100 watts/square meter the rate no longer increases. Thus, most plants can only utilize ~10% of full mid-day sunlight intensity. (5)

and

  If photosynthesis is inefficient, excess light energy must be dissipated to avoid damaging the photosynthetic apparatus. Energy can be dissipated as heat (non-photochemical quenching), or emitted as chlorophyll fluorescence.

So, briefly, yes. Too much light can harm plants.

To answer the second question: yes, there exist filters for a large variety of wavelengths of light. You could certainly filter out infrared light, just as most sunglasses filter out some UV light wavelengths. However, just filtering out infrared light would not filter out all photons that could cause damage; likewise, all wavelengths of light have the capacity to heat up what they hit, not just infrared wavelengths.


Why is gel used in electrophoresis? In analysing amino acids content in a protein through gel electrophoresis, What's the purpose of the gel? Wouldn't putting the amino acid in the gel prohibit the amino acid from dissolving into the buffer solution (which its pH controls the protonation and de-protonation of the amino acid)?

In gel electrophoresis, the gel is the mechanism by which macromolecules of different sizes are separated. By loading the gel with amino acids (or proteins or DNA), you start all of the samples equally, and then push them through a gel using a salty buffer solution that is electrified.

The gel has a certain concentration of a polymer (commonly agarose or polyacrylamide) that acts as a mesh that slows your macromolecules down. So, after running a gel for a certain amount of time, molecules of different sizes will have traveled different distances. This can be visualized by different methods (ethidium bromide for DNA and antibodies for proteins, commonly) after further preparation.

So, the amino acids in question should not be dissolved in buffer, as this would result in loss of sample.

Edit:

Regarding the last point: when loading samples on a gel, they must first be dissolved in some loading buffer that will help the sample settle into the well and not diffuse out. I took your mention of "buffer" in the original question to be the running buffer for electrophoresis, which you should not dissolve your sample in. I am also unfamiliar with analyzing amino acids by electrophoresis, and I do not know if there is a specialized loading buffer that kind of analysis would require. A quick look didn't uncover anything, but you might be in a better position to answer the loading buffer issue.


Difference between genetic engineering and synthetic biology I've recently seen the term synthetic biology being used to describe research involving genetic modification of organisms. What is the difference between synthetic biology and genetic engineering?

Is it just a new term for the same thing, or is it something different? Does one of the two terms encompass the other?

My understanding is that synthetic biology is genetic engineering 2.0. The difference is in the approach. Whereas genetic engineering projects are usually ad hoc, synthetic biology aims to apply proper engineering principles such as standardisation, modularisation, and reusability. Synthetic biologists create and use libraries of standard parts that are characterised, so they can be easily reused in projects. A part could be a gene, a terminator, a promoter, etc.

Synthetic biology also has greater ambitions. The focus is on creating whole systems/circuits of genetic regulation. This means there is a need for computational modelling and understanding of how biological systems work. In this aspect synthetic biology is a sister of systems biology a bit like synthetic chemistry (engineering) is a sister of chemistry (science).

You could of course argue that it's just a marketing ploy to invent a new name for something that is just the next step in genetic engineering, but the differences in approach are quite large and a new name signifies it.

With regards to synthesised vs. PCRed DNA: It doesn't really matter which you use in synthetic biology. However, cheap synthesis is one of the technologies that enable easier synthetic biology. The idea for the future is that you will be able to synthesise whole plasmids and chromosomes instead of having to "cut and paste" DNA. When that happens physical parts repositories will be obsolete, but they will remain crucial in silico. Cheap synthesis is nice, but doesn't make or brake synthetic biology.


Rampant low Vitamin D Why have people inadequate vitamin D status? Is it just (the lack of) sun exposure, or is it related to hormone and thyroid function?

Here in Australia there are more cases of vitamin D shortage than in England. Given the double amount of sun hours per annum here in Down Under, that's quite counter intuitive. In fact, an estimated 31% of adults in Australia have inadequate vitamin D status, increasing to more than 50% in women during winter–spring and in people residing in southern states (Nowsen et al., 2012).

It turns out that in Australia people are, rightfully, careful of sun exposure due to the thin ozone layer and the resulting high incidence of skin cancer. As a result, people here wear long-sleeves on the beach, use high-factor sunscreens, wear sun hats, use umbrellas to evade the sun etcetera. The Australian  Cancer Council supports the famous "slip, slop, slap" slogan:

  Slip on a shirt, slop on sunscreen and slap on a hat, Slip, Slop, Slap! You can stop skin cancer [..]!

Hence, folks here in fact often take vitamin D supplements, despite the large amounts of sun hours.

Reference
- Nowsen et al., MJA (2012); 196(11): 686-7


How does vasodilation slow blood flow? During inflammation, cytokines and histamine cause vasodilation to increase blood flow to the inflamed area. However, it is also said that vasodilation slows blood flow which facilitates the adhesion and movement of leucocytes through the blood vessels and into extravascular tissue. My question is how does it slow blood flow? To me it would seem that there would be less drag force for a given volume of blood which would increase the speed of flow. There would also be less resistance.

The measurement that decreases during vasodilation is flow velocity, $v$, or a change in distance over change in time $\frac{\Delta x}{\Delta t}$. Prior to a reflex response, the same rate of flow, $Q$, or $\frac{\Delta V}{\Delta t}$ enters the capillary bed (here we use a capital V to represent volume, where $\Delta V$ is a change in volume, and $\frac{\Delta V}{\Delta t}$ is the change in volume over change in time. Because volume is area times a third distance dimension (e.g., if we say area is height times width, then volume is area times depth or thickness), we can describe flow as flow velocity times cross sectional area ($Q = A \cdot v$, or  $Q = A \cdot \frac{\Delta x}{\Delta t}$). If you increase the cross sectional area, $A$, and maintain the same flow, $Q$, then flow velocity, $v$, has to decrease.

A more intuitive explanation would involve turning on a garden hose and covering part of the end with your thumb. The smaller the opening you allow, the greater the flow velocity through the end of the garden hose. The same volume of water leaves the hose per unit time. It's just moving at a faster flow velocity if you decrease the cross sectional area (and at a slower flow velocity if you increase the cross sectional area).

This is discussed in Chapter 4 of Costanzo Physiology, in the section on hemodynamics.

The actual physical measurements end up being more difficult to predict in a situation with parallel capillary beds and reflex responses. $Q$ does not stay constant, for both the specific capillary bed, and for the entire circulatory system. However, you can say that, as a general rule flow velocity, or $v$, will decrease when cross sectional area, $A$, increases. As @BryanKrause points out in particular, provided the series resistance for a capillary bed doesn't change, the initial $Q$ for the capillary bed won't change, which means this caveat isn't relevant.


Lobed Nuclei still count as One nucleus? Do the Lobed Nuclei of immune cells (such as Megakaryocytes) still count as one nucleus?

Yes. Lobation is when a nucleus deforms, but it is still a single compartment. How the nucleus deforms can be helpful in roughly determining the cell type by visual inspection.