texts: Spermatogenesis in humans - timing of phases and chromatin modifications

texts:
I'm interested in the timing of events during human spermatogenesis, ideally with some references I can build off of. Specifically, I am trying to pin down the number of days for:

Spermatogenesis, beginning to end (I have come across 65, 75, and 100).
Leptotene stage
Zygotene stage
Pachytene stage
Spermatozoa maturation and histone-protamine transition
Time in epididymis (I have come across 12 days)

Again, I want to know the timing of these events in humans, not mice or rats. Specifically, I am trying to pin down the major epigenetic reprogramming stages, with a focus on those occurring in mature males.


texts: Does testosterone weaken the immune system?

texts:
I was reading this articles here that states that the higher the blood level of testosterone is, the weaker the immune system gets.

I read another article about testosterone here that focuses on the positive side of high testosterone blood levels and avoids the effects on the immune system.

So my questions is: Does testosterone really weaken the immune system?


texts: Do babies conceived naturally or artificially have any differences in long-term health?

texts: Are there any long-term differences in children conceived via artificial insemination or sexual intercourse, pending that the mother successfully delivers the child?


texts: Is "cell proper" considered a biology term / well defined concept?

texts:
I am asking this question after writing an answer on English Language & Usage sent me on an expedition through the internet. The originating question asked about the meaning of the word proper after the word cell.

At first I was certain that it was a biology term, describing some sort of cell. I am not a biologist. After some pushback, I researched a bit and found what seems to be the original definition in a book from 1853.

  It is a mistake to apply the word cell sometimes to the cell with a membrane, sometimes to the cell without a membrane, and sometimes to the membrane without the cell. Since the contents of the cell constitute the essential part of it (see p. 155), since it forms, before the secretion of the (cellulose-) membrane (pp. 156-167), a separate entity, possessing its own, essentially proper, membranous boundary (the primordial utricle, pp. 169-173), we must call this internal body the cell proper, unless we restrict the term cell to the enclosing wall or chamber, and give the internal body another name. If the name is restricted to the internal body, we cannot, in the great majority of cases, say that new cells are formed in the old, but merely that they are formed out of the old, for even the primordial utricle shares in the division, in the propagation of cells by division. Therefore when daughter-cells are said to be formed in the mother-cells, or to slip out from the mother-cells, or mother-cells are said to be dissolved and absorbed, these phrases must be admitted only as conveniently abbreviated expressions, "mother-cell" being here used instead of maternal cell-membrane.
  (bold emphasis added)

My question is: Is cell proper considered a biology term or concept that would be understood by an expert of cellular structures?


texts: How diverse are species in remote, isolated areas on Earth?

texts:
If we consider land areas that have been largely isolated from each other from a human point of view, but with a similar climate – for example, a part of Europe and a part of Americas with a similar climate before the time of Columbus – generally how different can one expect the flora and fauna to be between the places?

I realize there can be quite different approaches to measuring the biological differences. Not being a biologist, I probably miss some quite important metrics. Some ideas that come to my mind:

How distinct are the species in each environment? For example, can we expect to see the same ant species? Same grass species? Same bacteria?
DNA difference based approaches: How much of the DNA material in each environment does not exist in the other one? How large a proportion of organisms in one environment does not have a close relative on the other, given some threshold closeness value?
Historical approach (probably overlaps the DNA approach quite a bit): How long ago (alternatively: how many generations ago) did the common ancestor of similar organisms in each environment live? Do the organisms share this number, i.e. is the common ancestor of, say, humans in Europe and America as ancient as that of ants and grasses?


texts:
I found this on my back while looking in the mirror.It took me 10 minutes to kill it.I hit it well at least 5 times before it died.It kept flying to me every time i tried to hit it,trying to go under my shorts

Is this a TseTse fly?

what fly is this?


texts: Can someone identify this tree from the Pacific Northwest?

texts: A tree at my house in Seattle, Washington, USA has these leaves. Can someone tell me what it is?


texts: Difference between infectivity and cell fusion abillity of Virus. (COVID 19)

texts:
I'm a computational chemist who have interest in COVID-19.

As a physical chemist, I'm lack of basic knowledge for biology.

What is the difference between 'infectivity' and 'membrane fusion activity'?

I thought that, for corona virus, infection is equal to membrane(cell) fusion, but it seems wrong idea.

Thank you for reading!


texts: Trying to extract DNA with an incomplete kit

texts:
I'm wanting to run a DNA extraction on soil and root samples using a 96-well plate kit.

My problem is that someone has gone through the kit and taken the Sealing Tape. This tape it used to seal the plates so they can be vortexed and centrifuged.
I have considered using a similar tape from our qPCR reactions, but this would be a very expensive last resort. I've tried filling a plate with water and covering it with strips of label tape, but the tape doesn't provide a good enough seal for the vortex.

I'm wondering if anyone has run into a similar situation, and if they were able to find a solution. This particular kit is this PowerSoil kit from MoBio, which no longer exists after being bought out by Qiagen. I called Qiagen and they do not sell the Sealing Tape individually.

Thank you


texts:
I have run an in vitro transcription reaction and produced some RNA of a single species and definite size. I would like to visualize it to check if the reaction worked.

Can I do this on an agarose gel? Is it sufficient to simply make a 1% TAE-agarose gel with EtBR that you would use for routine DNA electrophoresis, and run this? Is it necessary to take special measures against possible RNAses in the gel or the running buffer?


texts: What is a "noninvasive" biomarker for a disease? I know what a biomarker is, but what makes it noninvasive?


texts: Why are high levels of epinephrine and low levels of cortisol signs of stress?

texts: According to my psychology textbook (Psychological Science: Modeling Scientific Literacy), high levels of epinephrine and low levels of cortisol are signs of stress. However, earlier in the textbook it is shown that the autonomic response of the human body releases norepinephrine and epinephrine, while the hypothalamic pituitary adrenal (HPA) axis pathway releases cortisol. So it seems to me that signs of stress would be high levels of both of these things. Is my textbook wrong or am I just understanding what stage of stress it's describing?


texts: How do I interpret this depiction of dopamine neuron signaling?

texts:
I am studying the work of Wolfram Schultz on reward signals. He depicts dopamine reward signals as shown below, which I do not know how to interpret. Each dot represents an action potential in a dopamine neuron, but is each row a different trial of the same neuron, or is each row the activation pattern of a different neuron? And are the bars at the top showing a sum of the count of the action potentials at each time step?

Schultz, W. (1999). The reward signal of midbrain dopamine neurons. Physiology, 14(6), 249-255.


texts:
The E. coli has a genome with approximately 5×106 bp. The main DNA polymerase involved in its chromosome duplication (DNA pol III , the one with highest processivity) can polymerize ~103 nucleotides per second.
By a simple calculation, we would conclude that the whole chromosome duplication would take ~ 5000 seconds ( about 80 minutes, so more than an hour). The whole cell duplication would probably take much more than that, considering not only DNA Pol III is involved.
However, in optimal conditions, E. coli can actually duplicate in ~30 minutes.
How could that be possible?

OBS.: all the numbers used here are aproximate, but sufficient to account for the correct orders of magnitude.


texts: Was lactose present in the environment before the evolution of mammals?

texts: Are there lactose sources other than dairy products in nature? I tried to search for it but I did not find anything. The question arose because I was wondering whether lactose-utilising enzymes in bacteria evolved only after the appearance of mammals.


texts: In insects like the cockroach the brain is distributed, i.e. some parts lie in the head and some in the abdominal cavity. Which part is responsible for controlling locomotion?


texts: What does "developmentally programmed" mean?

texts:
What does the term "developmentally programmed" mean? I can't seem to find a definition anywhere.

What would the alternative (i.e. not developmentally programmed) imply?


texts: How did the cardiovascular system evolve?

texts:
How has evolution created our blood, lungs and the heart?

We can't exist without blood, which transports the oxygen to all areas of our body. However, the blood needs a lung, which gives it the oxygen to transport. The blood also needs something which lets it flow through the whole body, which are our veins. And in order to allow the blood to flow through our veins, an organ is needed to pump the blood, which is our heart. We also need a brain which controls all that, and the brain in turn needs the blood in order to function right.

Evolution makes very slow steps....."it just doesn't jump". So, How did evolution manage to create all that?


texts: What does the hominin phylogenetic tree look like?

texts:
I'm no biologist, but I'm curious what the rough phylogenetic tree looks like for Hominin.  Could you create a rough sketch that includes:

Homo rudolfensis
Homo ergaster
H. georgicus
H. antecessor
H. cepranensis
H. rhodesiensis
Homo neanderthalensis
Denisova hominin
Homo floresiensis
H. heidelbergensis
H. neanderthalensis
H. sapiens
H. erectus
H. habilus
any others I may have missed

Feel free to correct any incorrect assumptions I may have made here, or clarify anything that could be instructive.


texts: Is oxygen's paramagnetism biologically relevant?

texts:
It seems our most common everyday O2 molecule happens to be a paramagnetic one (see https://en.wikipedia.org/wiki/Oxygen).

But, does this have a biological relevance as well? In other words, Do any chemical processes occurring within the physical volume of any entity considered "living" depend in any way, shape, or form on oxygen's paramagnetic properties?

(It seems to me the answer would be "no", but I am no expert in this field!)


texts:
Is there a database where I can find an affinity estimate if I provide a given antibody and a given antigen sequence ?

Input : antibody + antigen sequence
Output : quantitative binding/affinity estimate

Many thanks.


texts: What is the difference between contig- and read-based sequence alignment?

texts: I am trying to understand the difference between read based and contig based alignment. Is contig based alignment refer to de novo assembly and then it is align to a reference genome. I am confused that if you have read based alignment then what is the importance of aligning contigs on the reference.


texts: Why do brain cells use shuttles that pass electrons from NADH to FAD?

texts: Brain cells are cells require one of the highest amount of energy of any cell of body. So why do they use a shuttle which will transfer electrons from NADH produced in glycolysis to FAD(and there by reduce the no of ATP that can be made ) ?


texts: How does the white blood cell ‘hunt’ the bacterium?

texts:
There's this mildly viral video which reportedly shows a white blood cell hunting a bacterium:

https://www.youtube.com/watch?v=JnlULOjUhSQ

What I don't understand is - at this scale, how does the white blood cell "know" to chase the bacterium and where to go? How does the bacterium "know" to run? Are they constantly shedding some bacterium-specific molecules that the white blood cell reacts to? Wouldn't the bacterium soon run out of molecules that way? Is there some other mechanism? What's going on here?

Note - I'm a total newbie; my own biology/chemistry knowledge is high-school level at best (and even then I graduated 16 years ago), so please try to explain it simply. :) I'm OK with looking up unknown terms on Wikipedia, but I probably won't be able to comprehend too much jargon. Thanks! :)


texts: Are these claims of "revolutionising" understanding of human vision and hearing valid?

texts:
I've started a hobby machine vision project (and posted some questions to this end on other SE sites) and on a side track, also been looking at relevant research in human vision (and partly, hearing).

I came across the work of one "James T Fulton" through an excerpt of a book which claims to have "revolutionised" our understanding of human vision and hearing.

Here are the respective links:

http://neuronresearch.net/vision/

http://www.neuronresearch.net/hearing/

I tried cross-verifying these claims via Google, but nothing turned up on searching either for the author or the book (apart from some Amazon links and very obscure references).

Considering the controversial natural of the claims made here, I would have imagined some level of debate, but the silence I found on the Internet is puzzling. Puzzling, because the sheer level of DETAIL in these books, prevents me from dismissing the claims altogether as well.

Can someone validate some of the content from these books so I can get an idea of the overall legitimacy of the work (and decide if I should continue reading, or not). Below might be a good link to start from:
http://neuronresearch.net/vision/pdf/11Biophenom.pdf

Adding a few examples:

The simplest one - is that the Principle of Univariance is not entirely correct. This is examined on pages 15 through 17 at this link (where I read it):
http://neuronresearch.net/vision/pdf/11Biophenom.pdf
There is this claim quoted verbatim from the site:
"The theory shows that the ARCHITECTURE OF ALL VISION IS TETRACHROMATIC. Although traditionally called trichromats, it is shown that HUMANS ARE BLOCKED TETRACHROMATS"
Caps in original. I just pasted it here to give an idea of the tone of some of the text.
This specific claim is "proven" here (in short):
http://neuronresearch.net/vision/files/tetracomparison.htm

And a longer form of the text is linked in the same page
There is also a theory proposed on why cochlea are coiled:
http://neuronresearch.net/hearing/pdf/coiledcochlea.pdf

Thanks!


texts: Why would yeast grow but not produce alcohol?

texts:
I'm studying for my intro to microbiology test and I have a question asking why a culture of yeast responsible for producing alcohol would be growing, but not producing alcohol?

The multiple choice answers are:
a) the maltose is toxic
b) O2 is in the medium
c) Not enough protein is available in the agar
d) The temperature is too low
e) The temperature is too high

EDIT: There is not much more context that what I gave here. The question simply asks me to assume the position of a scientist at a wine production company, and then asks the question I posed above - nothing too specific.

I think it is (b) because the presence of O2 would cause the yeast to respire aerobically, but I can't eliminate (d) and (e)

I figure it probably isn't (a) because a toxic chemical would inhibit the growth of the yeast. I don't believe protein is relevant so I don't think it is (c).


texts: How the pattern of fertilization path is determined before the cell division to form the blastocyst? Is it individually specific?

texts: After sperm meets ovum,the inactive nucleus starts following a particular path inside the zygote rather chase a path.This path is biologically known as fertilization path (as mentioned in an article of a local magazine named "science reporter"). But my question is how the pattern of the path is determined?  I came to know from the article that for every individual this particular path is very specific. Is it true?  If so then what does that specific path determine and why is it specific for every individual?


texts: How T-Cell recognizes a cell infected by a virus?

texts:
According to few articles I read (like BBC about The people with hidden immunity against Covid-19 ):

starting out about four or five days after infection, you begin to see T cells getting activated, and indications they are specifically recognising cells infected with the virus,” says Hayday. These unlucky cells are then dispatched quickly and brutally – either directly by the T cells themselves, or by other parts of the immune system they recruit to do the unpleasant task for them – before the virus has a chance to turn them into factories that churn out more copies of itself.

When virus just entered a cell, but had no chance to churn more copies: Is surface of the cell any different? How T-cell can distinguish infected cell from non-infected?
I am no biologist, but I am fascinated about biology now, and curious to learn more. Sorry if I am not using proper terminology.
I found How do T-cells determine which cells they've already inspected? , but T-cell activation is mentioned only in the context of dendritic cells and lymph nodes. IIUC, T-cells should attack lungs cells to eliminate cells infected by covid-19 there.


texts: What attaches plant cells to the cell wall?

texts: In animal cells integrins span the plasma membrane and attach the cell membrane to the extracellular matrix. I was wondering how are plant cells attached to the cell wall? Is it just the middle lamella holding them in place or is there something else (i.e proteins)?


texts: Does the genome make sense without knowledge of the ovum?

texts:
Much of the literature for laypeople seems to consider (and to spread
the idea) that an animal (or a plant, I guess) is characterised by its
genome. I do not know whether the same goes for more professional
literature. Even on this site, the tag genomes is defined as The
entirety of an organism's hereditary information, which seems to imply
that it contains a description of all that can be be inherited.

It seems to me that attempting to define an animal with the sole
knowledge of its genome (let alone recreate it as envisioned by some people) does not
really make sense, without the complementary knowledge of the cell
structure of the ovum that has to interpret this genome.

This question seems never to be seriously addressed in lay literature.

Is it the case that this decoding machinery evolves much less than the
genome itself? This could be expected, since changing the decoder has
usually more important, global and drastic effects than changing the
genome, which may result in a very localized effect. Hence, changes to
this machinery are less likely to give a viable being.

To refine that question (unless the moderator prefers this to be a
separate question):

Is there any study of the diachronic evolution of that genome decoding machinery in a
given species, or of the synchronic differences between species, which
would probably give a measure of the speed of diachronic evolution of
that machinery?

When two close species cannot mate, is it analysed (for some cases) whether it is due
to difficulties in combining the two genomes, or to the fact that the
ovum of one cannot properly interpret the genome of the other?


texts: How is knowledge about farming transfered between generations in farming ants

texts:
There are some varieties of ants capable of "agriculture", e.g. dairing ants farming aphids and leaf-cutting ants farming fungus.
How is the knowledge about the techniques involved passed between generations (in the case of dairing aphids I mean e.g. milking the the aphids to get honeydew, and protecting the aphids)? In short, is it more "genetic" (so that lab-cloned ants are capable of it) or is it more part of "culture", i.e. younger ants mimicking the older ones? I'd be mostly interested in answers with references to relevant experimental research.


texts: What genetic distance model should be used when calculating genetic differences in Arelquin?

texts:
I'm using Arelquin to look at the genetic structure between a number of different populations. I  want to compare the populations by producing pairwise FST values, however I don't know what model for the genetic distances I should use.

The two models provided are Slatkin's distance or Reynold's distance. They both aim to linearize the FST values by transforming them [Slatkin's = FST/(1-FST), Reynold's = -ln(1-FST)].

How do I know if the FST values need to be transformed, and if they do need to be transformed, what model should I use?


texts: What controls leaf senescence in deciduous tree species, and how can I predict it?

texts:
If I want to predict litterfall, what data do I need to collect, and what statistical model might I use?

For example, I might use the following coding to record phenological stage every other day, or perhaps once per week:

|value| description
|-----|--------------
| 0   | all leaves fallen
| 0.5 | most leaves fallen
| 1   | no more green in canopy half of leaves have fallen
| 2   | most leaves yellow or red few leaves have fallen
| 3   | noticeable reddening or yellowing, green still present
| 4   | summer condition

Once I have these data, I can also collect weather data. Now, say I want to predict the day on which each of the transitions ($4\rightarrow 3$, $3\rightarrow 2$, etc) occur.

Many studies use a temperature metric of growing degree days $GDD = (T_{max}+T_{min})/2-T_{base}$, but I have also seen chiling days and photoperiod used to predict changes in phenological stage. I would like to develop a function (statistical model) $f$ that would allow me to predict a date of state change from environemental variables, such as $$D_{4\rightarrow 3} = f(GDD)$$

My questions:

what controls litterfall? Is it photoperiod, temperature, other?
do the controls vary by species?
is there a "standard" approach to modelling senescence?


texts: Why are $\beta_2$ receptors present on bronchial smooth muscles , considering that they have only parasympathetic innervation?

texts: It is well known that the bronchial muscles have only parasympathetic innervation. But they still express $\beta_2$ receptors. How does this system still cause bronchial relaxation? What is the exact mechanism?


texts: There is a question in my textbook which asks: "What does the glucose produced from photosynthesis form?" However one of the answers said that glucose forms protein.  But I'm quite sure that amino acids form protein, don't they?  I would be grateful if anyone out there could help me out.


texts: What is the most genetically complex organism?

texts:
I understand that new genomes are being sequenced ever day and these answers replace themselves often; although as of today, what has been proven to be the most genetically complex organism (Other than a human of course)? I keep getting a multitude of different answers like Daphnia pulex, Axolotl, Paris japonica or Adder’s Tongue all from different dates and sources so it becomes difficult to tell what is the right answer here if any. If this question is not specific enough I would be happy to revise.

Edit: I would define genetic complexity as either genome size or number of genes. Either answer  would work. If you would like give other information like chromosomes or isoforms from any other definition, that would be helpful. Whatever is the best of the best.


texts: Why do the two sexes have different reproductive costs and capabilities?

texts:
Is there an evolutionary explanation that shows why the reproductive costs are mostly on the female sex?
And therefore, why do males can potentially have more offspring?
Does that happen to create more competition in sexual selection?


texts: Why are the granules of pancreatic beta cells larger than those of alpha cells?

texts:
Why are the granules (insulin) of β cells larger than the granules (glucagon) in α cells in pancreatic islets of Langerhans?

Also is there any size difference between alpha cells and beta cells?

Source: Inderbir Singh , Text book of Human Histology. Ed 8. Ch-16. Pg 202.


texts: Why do haemophillic females $X^hX^h$ die before birth?

texts: I just came across a statement in my book , while reading genetics, that haemophiliac females do not survive till birth (the reason not mentioned here why) . Before posting this question here I conducted quite a bit searching on the net but couldnt find any document on this. Can anyone tell me the reason why don't haemophiliac foetus make till birth ? I mean where is the problem, when a haemophiliac male having XhY can survive why not an XhXh  female ?


texts: Does drinking coffee have negative effects?

texts: From what I collected, coffee is a magical potion that lets you feel energetic, and essentially not-sleepy. But are there any tradeoffs? I mean, if it was so beneficial, wouldn't the human body produce caffeine naturally?


texts: Is there a word for the length of time an animal stays with parents before going off on their own?

texts:
Gestation is a word describing the pregnancy for animals, and you can use 'gestation period' to describe how long a pregnancy generally takes for a species. I'd like to know if there's a corollary word for the time an animal stays with its parents before leaving.

For example, after birds are hatched, they stay in the nest for a while, but they eventually leave the nest. Is there a single word or phrase that is used to describe the time between hatching and leaving the nest? I imagine different bird species have different periods, and other animals (that don't stay within families their whole life) can also be describe in a similar matter. Perhaps 'puberty', though I'm guessing there's a more specific word.


texts: How to calculate the occurrence of a stretch of nucleotides in a genome?

texts:
I have seen that the formula to calculate the number of times a given sequence of nucleotides occur in a target genome is derived from that to calculate the expected frequency of restriction sites:
a = (g/2)^G+C × ((1-g)/2)^A+T,

where:
a = probability
g = G+C content of the target genome
C+G = number of G and C in the stretch
A+T = number of A and T in the stretch.

An example was given for the mitochondrial genome and the restriction site for EcoRI (GAATTC). I calculated, based on the example:
a = (0.44/2)^2 × (1-0.44)^4 = 0.0005

given that the length m of the mitochndrial genome is 16 000 bp, the number of occurrences is:
n = am = 0.0005 × 16 000 = 4.92 (against 4.80 reported in the paper).

I then tried to calculate the occurrence of a primer based targeting E. coli: GTGTCCATTTATACGGACATCCATG.
The GC content of E. coli is 50.8%, thus:
a = (0.58/2)^11 × (0.42)^14 = 1.22×10^-6 * 3.24×10^-10 = 3.95×10^-16

and the number of occurrences is:
n = 3.95×10^-16 × 16*10^6 = 6.32×10-9

Looks to me, that the primer should not occur at all in the E. coli genome.
Are the formula and its application correct? Also, I don't like the fact that one needs to know the CG content beforehand (although, one can assume 50% content) and an exponent at the 11th power; is there an alternative formula?
Thank you.


texts: What's the percentage similarity between human individuals (and other primates) when comparing only exons?

texts:
In popular science books and articles, I often see it stated that humans are >99 % similar to each other (wikipedia has it a 99.5 %, referencing Craig Venter and this PLOS Biology article) and ~96-99 % similar to chimpanzees or bonobos (Smithsonian Institute, National geographic). I have previously thought that this referred to the entire genome, but the wording on the Smithsonian Institute page I linked, makes it appear that it might refer to genes only, which also seems to be the case according to the answers to this post Do apes and humans share 99% of DNA or 99% of genes? What is the difference?.

How big are these percentages when comparing only the coding regions (exons) instead of entire genes, both within our species and compared to other species, such as primates? And, not as importantly, what are these numbers when including the entire genome with all non-coding DNA?


texts: What is the use of an antibody that is non-neutralizing?

texts:
When we generally speak of the immune response to viral infections, we talk of neutralising antibodies. These are antibodies that can neutralise the effect of the virus and reduce its load.

My question is, what do the rest of the antibodies produced, which are not neutralising, even do?

Is it a failure of the immune response of the body to produce antibodies that are not neutralising? But isn't binding enough for opsonisation?

How is 'neutralising' even defined? Are such antibodies neutralising just based on binding (since I assume neutralisation assays are in-vitro) or do even these antibodies require downstream antibody effector mechanisms like complement, opsonisation, ADCC etc. for neutralisation?


texts: Using serotonin for relief from allergies

texts:
When someone suffers from an allergy, due some allergens they are given drugs like anti-histamine, adrenaline or serotonin. How does serotonin affects the body to give a relieve from the action of allergents?
What is the physiology behind this?


texts:
I usually find substances that activates proteins, like ApoA-I, but I don't find substances that inhibit it.

So in an experimental design, could I consider the absence of a drug that directly acts on the increase of a protein could be considered an inhibitory process?


texts: What is delayed compliance in blood vessels?

texts: What I understand is it is a permanent stretch of the vessel wall. Is this true or does it mean something else?


texts: Why is the 4.4 kb band barely visible in this HindIII digest of lambda DNA?

texts:
Why is the 4.4 kb band barely visible?

Also, what is the mass (ng) of DNA in band X if lane S contains 250 ng of digested lambda phage DNA?


texts: Understanding Genetic Dynamics of Specific Problem

texts:
The following questions comes from International Biology Olympiad 2014, theoretical part B.

It states:

  Earlier research suggested that the red flower pigment of plant species was the result of a
  chemical pathway including multiple steps and that all intermediate pigments were white. Three
  pure-bred lines with white flowers (White 1, 2 and 3) of this species were crossed with each other
  and the following ratio of colors were obtained among the progeny:

The question was how many genes control flower color. I completely botched it. Here are my thoughts:

Looking at F2 generation, there are 9 reds + 7 whites = 16 total. (I know it's a ratio.) Generally, having 16 suggests at 2 genes controlling the phenotypes. For example, cross AaBb x AaBb, you'll get 16 phenotypes.

Turns out 2 is incorrect, and I have no clue as to how colors are inherited in this problem. Any suggestions?


texts: Frequency of nucleotide sequences of specific length in DNA

texts:
How frequently would you find the nucleotide sequence GGATATCCGC (5' to 3' direction) by chance in a DNA molecule?
On average, how many times do you expect to find a specific 20 nucleotide sequence in a genome with a total size of 4 x 109 base pairs?

Since that probability of finding each base pair in its given position is 1 in 4, thus the total probability of finding that particular sequence would be $0.25^{10}$

But how do I approach the second problem?

TIA


texts: I am troubleshooting a PCR reaction that gives me no product, and there are a lot of different approaches that I can find in books and just in google searching (things like running a gradient, increasing cycle number, etc.). But it would be really nice if somebody could list out in order the steps they take to troubleshoot a PCR reaction. Thanks.


texts: Is RNA polymerase affected by proteins bound to the coding sequence of a gene?

texts:
I am designing a synthetic gene construct to express genes in E. coli driven by either Ptet or PLacO. The construct would look like:

-Ptet-(Gene1)-PLacO-(Gene2)-

I want to express each gene using either aTc or IPTG, but I want to make sure that the transcription of each gene can be controlled independently.

Let say I only add aTc and transcription is initiated at the Ptet location, would RNA polymerase bump into LacI bound to the PLacO promoter and stop transcribing? Or would it knock-off LacI transcribe (Gene 2)? I am not sure whether or not need to include terminator sequence to make sure the expression of each gene is decoupled.


texts: Why did a lot of common insects evolve such a thin waist?

texts:
Something that doesn't quite make sense to me is why lots of insects like ants, bees and wasps have a such a small petiole when it connects many major organs to the rest of their body from a suddenly much wider abdomen.

Normally from an engineering standpoint, you don't increase the width of a cantilever from a joint because the torque applied to a joint already increases with the length of an overhanging segment, so increasing the width would only multiply the torque that joint or opposing segment needs to balance.

It could have something to do with ants being so small that large  torque isn't an issue in proportion to their body size, but if it wasn't, then why do their legs also get thinner as they measure further in length from their body?


texts:
When we create new cells, how come they are of the 'right' type at the 'right' place?
For example, when I make a new cell on my lips, it's obviously not the same as a new one in my kidneys.

Is the differentiation done by using a different part of the DNA each cell has?
How does the mechanism of growing specific types of cells at a specific place work?


texts: What is the diameter of each type of deoxyribonucleotide (if the types are significantly different in diameter, if they are fairly similar one value would suffice)? I.e., if a hole was to be created through which only a single deoxyribonucleotide could pass at a time, how small would it have to be?


texts: A silly question. A few days ago I observed a very vocal bird with impressive vocal variety. It was rapidly switching from one tune to the next. After sometime I realized that the bird might be mimicking the 6-8 tone car alarm (the one that rapidly changes). Is this my imagination, or are birds really know to mimic/compete with car alarms?


texts:
I am studying nursing and have a question regarding the physiological response to shock (decreased perfusion).  In lecture notes supplied by the lecturer, he indicates that there is a neural, hormonal and immune response to shock that is compensatory.

The neural component is the activation of the sympathetic nervous system, and hormonal response is through RAAS, etc.  This makes sense, as these mechanisms attempt to increase blood pressure and blood volume

I don't understand the immune response, though, which is described as the release of pro-inflammatory mediators, which lead to endothelial cell damage, making the vessels leaky, leading to oedema.  So how is the compensatory, it seems disruptive?  And why exactly would pro-inflammatory mediators be released in response to shock in the first place?


texts: My question is whether translation can be done, either naturally or artificially, through a ribosome reading (single-stranded) DNA directly. If not, I would like to know what allows ssRNA to be translated but not ssDNA.


texts:
I have come across many articles which seem to suggest (but do not explicitly state) that limbs refer to arms and legs. My confusion stems from the fact that does the term vertebrate limb also include vertebrate wings and vertebrate fins or only refer to arms and legs of vertebrates. I would be grateful for clarification.

A simple google definition states that it does include the wings of birds however I would like to know if this is also the case in evolutionary biology or not.

I also refer you to this article
Yano, T., & Tamura, K. (2013). The making of differences between fins and limbs. Journal of Anatomy, 222(1), 100–113.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3552418/

Are vertebrate wings and fins considered vertebrate limbs?

Based on other articles I have read wings are included in the definition of limbs but I am not sure whether fins are included.


texts: What is the perisomatic region of a neuron?

texts:
In the scholarpedia page on interneurons I encountered the following passage:

  The perisomatic domain is responsible for the summation of postsynaptic potentials arriving from all dendritic branches [...]. Thus, the perisomatic region - and particularly the axon initial segment [...] plays a crucial role in the generation of output.

The page, however, does not define what the perisomatic region really is. What comprises the perisomatic region of an interneuron?


texts: Would a plant survive if it was watered using hard-water?

texts:
Hard water is water with high mineral/salt content. I'm told that a potted plant watered with a salt solution dries out sooner or later. Is this true?

If so, would a plant survive if watered using hard-water?


texts: What´s the role or function of the homologous arms in a donor template in a knockout/knock edition via Crispr-cas9?

texts:
I have to make an exposition in my university about Crispr-cas9 edition and I have some questions about the method. In the knock out/knock in technique is used a plasmid containing the DNA that codifies for the Cas9 protein and guideRNA and a Donor template that has a gene for puromicine resistance, and a DNA that codifies for a fluorescent protein and "left homologous arm" and "right homologous arms". My questions is What's the fuction of the homologous arms?Furthermore what's the role of the Loxp(look at the image)?
The method is described here   http://www.origene.com/assets/documents/CRISPR-CAS9/CRISPR_manual.pdf   (page 5-10)


texts: How does the human body extract energy from ethanol?

texts:
I was talking about alcohol and obesity with a colleague. I always thought the only cause of that is the sugar that is found in most alcoholic beverages. But my colleague pointed out that ethanol itself provides calories to human body.

I checked that and it seems to be the case. What I don’t understand is how is it possible. On wikipedia I found following statement:

  If catabolism of alcohol goes all the way to completion, then, we have a very exothermic event yielding some 1325 kJ/mol of energy. If the reaction stops part way through the metabolic pathways, which happens because acetic acid is excreted in the urine after drinking, then not nearly as much energy can be derived from alcohol, indeed, only 215.1 kJ/mol.

The statement relates to these reactions:

$$C_2H_6O (ethanol) → C_2H_4O (acetaldehyde) → C_2H_4O_2(acetic acid) → acetyl-CoA → 3H_2O + 2CO_2$$

Now note that the wikipedia calls the pathway "exothermic". However, I don’t think that human body can derive energy from heat. Or can it?

Since most articles claim that ethanol alone has positive caloric value, how exactly is this energy extracted and used or stored as fat?


texts: Is there a name for this principle in biological contexts?

texts:
This is mostly a question about usage.

There is a probability-related idea that has been used in at least two biological contexts. The idea is that if something happened, it was probably likely to do so.

This has been used in discussions about evolution, in which it is said that while we have trouble imagining circumstances in which self-replicating forms arise, the odds were probably in favor of their emergence when it actually occurred. And in discussions of the existence of intelligent life--it may be prevalent if we make the somewhat natural assumption (among others) that our own emergence was not highly improbable, given the existence of a suitable planet and so on.

Is there a name for this principle? I am familiar with the idea in the context of probability but have thought of it as an 'argument from likelihood' in biology. Also if there is a good description of the idea in a biological context a reference would be appreciated.

The tag is a little arbitrary. Thanks for any suggestions.


texts: What step of the cloning process requires an egg cell? Have alternatives been attempted?

texts:
In the famous Dolly the sheep an egg cell was required. Why was specifically an egg cell required compared to say sperm cells or any other cell types?

Given that egg cells are not trivially harvested and culturable, have clones from alternatives been attempted?


texts: Is it possible for any animals today to have more than one brain?

texts: Is it possible for any organisms in the animal kingdom to have more than one brain?


texts: History of ideas about the form of the genetic code

texts:
In preparing a lecture on mRNA translation and the genetic code, I remembered a talk given at a symposium where they mentioned the origin of the code and how, before the code was established, various other mathematical possibilities were proposed that turned out to be incorrect.

Does anyone know about these alternative proposals?


texts: Is There An Initiative To Sequence The Genomes Of Critically Endangered Species?

texts: I realize that there are many isolated efforts to sequence the genome of a particular endangered species such as the orangutan or the snow leopard. However is there a concerted effort to sequence the genomes of every species on the brink of extinction? Also, is there an effort to sequence the genetic diversity of the surviving populations, since it would be very difficult to re-create alleles that would be needed if the species were to ever be resurrected.


texts: How would you find and cultivate specific forms of algae?

texts: Knowing how simple and efficient it is to grow algae, I started wondering how a person would specifically isolate and grow different strands of algae. Say I walk to the closest body of water and took a sample of water. How would I prepare it so that I only got a specific strain of algae, say a green algae?


texts:
While eating sour food or candy, I start to sweat if it's sour enough. My body feels much hotter although my actual temperature is the same, my forehead starts sweating a lot and I feel like it just got twice as hot wherever I am.

Is this a biological phenomena or is my DNA just stupid? Is it somehow related to the digestive system, that sour food is harder to digest?


texts: I've seen snakes get captured in sacks and I've wondered if the snake would get dizzy if the sack were twirled around.  I have not done any tests (and don't plan to) because snakes scare me.


texts:
We live on the shore of Kentucky Lake in Middle Tennessee and kayak often.  A common snake here is the Northern watersnake.  Observing several of these snakes over a period of ten years, I am puzzled by their behaviour in several respects.

The snakes appear in March when it's still cold, much earlier than other snakes.  They repeatedly return to the dock or the pontoon boat even after being forcibly removed. The other snakes here are shy and usually don't return once frightened away.  This year, twice, Northern watersnakes have followed my kayak.  They change course towards me and speed up to keep up.

My basic question is, Why would a snake follow a kayak?


texts: Its been quite a while since my Daphnis Nerii has passed its eating phase, now its just a sort of recluse and is curled up in one corner and sleeps the whole day. It's a bit brownish in colour now. Although when I check on it, by lifting the container and moving it about, it starts jumping oddly. Like a jumpstart,  everytime it gets provoked. It maybe is the last phase of its instar period. Is it getting ready to pupate? Or is it not well?


texts:
I'm doing conceptual questions in preparation for a Western Blott and needed clarification on a specific question:

Is it possible/ will your Western blot work if you use a primary antibody (say generated in mice) and use a secondary antibody (generated in goats)? Would this combination still work with the western blot? At first glance, I'd say no but I'm still looking into it. Any clarification would be greatly appreciated!


texts: What is this fuzzy, black fungus that grew on my plates in the 4⁰C room?

texts:
I often find the fungus below growing on my (ostensibly) sterile plates in the 4⁰C room. Presumably it takes a few days to reach this size.

The colony looks puffy and dimpled in the middle, like a chocolate cake. The colony is actually black, but looks grey because of what I assume are hyphae and/or spores on top.

It looks like if I disturb the colony physically spores will be released (I haven't tried this because I don't want to contaminate the whole lab with aggressive spores). I notice that the center of the mass curves upward over time, and after a few more days of growth this colony will probably tear itself apart, leaving a gaping hole in the middle (based observation of similar contaminants on other plates, not pictured).

I suspect this is a very common lab contaminant. It grew to this size in less than 2 weeks, and was at 4C the entire time. I noticed many plates in the same batch/sleeve were contaminated, but each plate had only one colony, so it somehow spreads from plate to plate but not within the plate. What is it?

If anyone has any suggestions for simple but informative, classical microbiological techniques that would help identification (common stains, inexpensive selective media) I would be happy to try them - although it would be hard to justify very involved experiments since this doesn't pertain to my main research (in other words, if this was bacteria, sequencing the 16S would probably be out but a Gram stain is fine - this is very likely not bacteria, but I don't know the equivalents of those methods for fungi). Since identifying species is not really my strong suit, I'd appreciate if you link to a protocol when suggesting methods.

Update: I have found 4 more plates, all LB-Ampicillin, with what I suspect to be the same contaminant. With regard to Alan Boyd's comments, the colony morphology seems to be uniform in several aspects. It is not necessarily flower-shaped as I have claimed, but on the other hand, it never has a halo of satellites (dots) around it either.

Photos of the plates:

View from the top (agar side close to the benchtop) - shows round colony morphology and various stages of growth. Bottom left colony shows small dimple as the mass begins to swell. Top right shows cracks (actually tears) appearing as the mass is distorted by growth. Note that there is never two colonies on the same plate. The plates all came from the same sleeve in a cold room storage.
View of same colonies from the bottom - note star-shaped inward creases which form as the colonies grow and distort the surface.


texts: The human brain in numbers II: synaptic connections

texts:
The overall number of synapses in the human brain is roughly 1,000 trillion, i.e. 10,000 synapses per neuron.

My question here is three-fold:

I assume that each structural type of neuron (basket, pyramidal, ...) has a somehow characteristic average number of in-coming and out-going synaptic connections, i.e. not every type of neuron will have about 10,000 in-coming and 10,000 out-going synaptic connections. I am looking for a thorough overview of these characteristic numbers by structural type.
I assume that for some functional groups of neurons (see The human brain in numbers I: neurons) there are characteristic average numbers of in-coming and out-going synaptic connections per neuron. I am looking for a thorough overview of these characteristic numbers by functional group.
Finally, for some functional groups there are presumably characteristic ratios of inner and outer synaptic connections: "x % of the in-coming synaptic connections of a neuron in group X come from other neurons in this group, the rest comes from the outside. y % of the out-going synaptic connections of a neuron in group X go to other neurons in this group, the rest goes to the outside".  I am looking for a thorough overview of these characteristic ratios by functional group.


texts: How does our body produce new antibodies?

texts:
My professor said that in human body nearly 10$^9$-10$^1$$^2$  antibodies are produced by VDJ recombination and all the antigens that a person encounters in his lifetime are dealt by antibodies already present in his body. But he didn't explain what if the body in infected by a new mutated microbe(antigen) whose corresponding antibody is not present in the body.

My question is does our body have the mechanism to judge the epitope of the new antigen and synthesise an antibody with completely new paratope? If so what is it?

After reading the following I was forced to wonder whether the specificity of the antibodies improve(improve by synthesising new paratopes) after encountering antigens in the course of response.


texts: What are the survival limitations of alcohol?

texts:
This question was inspired by watching one of the Pirates of the Caribbean movies; particularly where Jack Sparrow allegedly survives on a desert island by finding an unlimited supply of rum. I've heard alcoholic drinks dehydrate you more than hydrate you, so this seems like an unsustainable strategy.

My question is threefold.

How long can a human survive by drinking hard liquor (40%
alcohol by volume) for their sole water intake (ignoring food)?
If it's unsustainable, what will finally take you down?
If the hard-liquor approach isn't viable, what % alcohol can
keep you hydrated (beer, wine, etc.)?

Related:
1. Question on dehydration studies
2. Question on what dehydrates


texts: How should one interpret heritability? Is it related to $R^2$?

texts:
From Wiki:

  Heritability estimates are often misinterpreted if it is not understood that they refer to the proportion of variation between individuals on a trait that is due to genetic factors. It does not indicate the degree of genetic influence on the development of a trait of an individual. For example, it is incorrect to say that since the heritability of personality traits is about .6, that means that 60% of your personality is inherited from your parents and 40% comes from the environment.

So what is the plain english interpretation of heritability?

Is it supposed to be the genetics version of $R^2$? If so, please explain it to me anyway because I forgot my statistics.

I found this so from what I understand, one might say:

  If height is estimated to be 80% heritable, and if we get 10 people, get their heights and then compute the variance, we say that around 80% of that variance is likely due to genetic factors while the remaining 20% is due to other things.

Such interpretation of heritability seems to work for non-categorical traits. What about categorical or binary traits?

Hair and eye colour is categorical (I think?). So what, we assign a number for each colour and then compute the variance?

ADHD is binary (I think?). Do we assign 0 for not having and 1 for having then compute variance?

I seem to recall regressing binary or categorical variables needs some kind of adjustments and hence interpretations of estimates (such as intercepts or slopes) may be different.

Also, the book linked above says

  heritability represents the degree to which the variance in a trait is attributable to genetics in the population on average

Combining that with the Wiki paragraph above, I don't think someone saying

  Eye colour is around 98% heritable. I have brown eyes. Therefore, around 98% of the reason why I have brown eyes is genetics.

is far off from saying

  If we have a million people who near-identically flip a million near-identical coins a hundred times, and we compute the average of the coin flips that turn out to be heads to be 58.6, then the probability that you will flip heads when you near-identically flip this near-identical coin is around 58.6%.

Is it? (Of course 'near', 'around', etc are not always used similarly...lol)

So yeah, technically the 60/40 interpretation in the Wiki example is technically wrong but practically it's around 60% $\pm$ some standard deviation?


texts:
Are there (global, country, etc.) data of COVID-19 deaths (or hospitalization) by year of birth? I was able to found them only by "age group", the meaning of this being usually an interval of 5 to 15 years, but I'm interested in smaller intervals.
Why I am interested? We know that the severity of this illness increases with age, and in fact increases a lot with ages around 70. If this increasing is more o less locally constant (that is, the first derivetive does not vary much in any interval of a few years) or at least the second derivative is more o less locally constant, we can think that maybe age on its own is a factor risk. But if there is a rapid increasing in one, two or three (consecutive) years and then a smaller slope (that is, a sort of "jump"), it is possible that there are (instead/also) other factors: maybe an exposition of this aged people to something during their lives that younger people don't lived, or some other thing that we don't know yet. So we need to know with more detail ages of hospitalization, deaths, or other sign of severity.


texts: Why do plants produce and store both amylose and amylopectin?

texts: Since both forms of starch has its primary purpose of storing glucose and hence releasing energy, why are there 2 variations of this sugar? Is it possible for an organism to contain/depend only on 1 but not the other?


texts: How are physiological reversal potentials (or ion concentrations) of neurons measured?

texts:
Patch clamp electrophysiology experiments typically use an intracellular solution that mimics the ionic concentrations of neuronal cytosol. At the same time, the extracellular solution is meant to mimic cerebrospinal fluid. If these two sets of ion concentrations are similar to their in vivo physiological values, then one might expect a patch-clamped neuron to also have physiological ionic reversal potentials. If, on the other hand, they are dissimilar, then we might expect the behavior of the patched neuron (for example its intrinsic excitability or synaptic currents) to be different from the behavior of the same neuron in vivo. In principle, one would like to use solutions that are as close as possible to physiological for this type of experiment.

My question is: how do we know what these physiological values (concentrations or reversal potentials) really are? It is easy to find these values in a textbook, but I would like to know what original research was performed to determine these values in the first place.

In many patch clamp experiments, the solutions are designed to set the reversal potentials to non-physiological values, or are otherwise constrained by the practicalities of the experiment. Let's consider these issues to be outside the scope of this question.


texts: Are carbohydrates an essential component of human diet?

texts:
Are people able to satisfy all the needs of a healthy diet without consuming carbohydrates?

My question includes the assumption that a person has no health condition that would prevent them from meeting their caloric needs with only fat and protein.

I'm also not asking about the practicality of eliminating all carbohydrates.  If a person could consume no carbohydrates whatsoever, this other question would clearly matter a lot, but I'm not asking it.

If there are essential dietary components that happen to be carbohydrates, but are not converted into glucose, I'll say up front that it wouldn't satisfy what I"m asking.  However, it would be interesting footnote on an otherwise correct answer.


texts: I've searched for some time now, but I can't find a definitive answer. The closest I have gotten is "knowledge about peptidoglycan structures dates back to the 1970s–80s" from this paper.


texts: What are the effects of oxygen toxicity in human blood?

texts:
I was reading some text on deep sea Physiology, and for to know that diving to do could cause oxygen toxicity in the blood. This was the exact text from the book Textbook of Medical Physiology by Arthur Guyton and John E. Hall:

A  column  of seawater  33  feet  (10.1  meters)  deep  exerts  the  same  pressure  at  its  bottom  as  the  pressure  of  the  atmosphere  above the  sea.  Therefore,  a  person  33  feet  beneath  the  ocean surface  is  exposed  to  2  atmospheres  pressure,  with  1  atmosphere  of  pressure  caused  by  the  weight  of  the  air  above the  water  and  the  second  atmosphere caused by the weight of  the  water.
When  the  PO2  in  the  blood  rises  above  100  mm  Hg, the  amount  of  O2  dissolved  in  the  water  of  the  blood increases  markedly. Note  that in  the  normal  range  of  alveolar  PO2  (below  120  mm  Hg), almost  none  of  the  total  O2  in  the  blood  is  accounted  for by  dissolved  O2,  but  as  the  O2  pressure  rises  into  the thousands  of  millimeters  of  mercury,  a  large  portion  of the  total  O2  is  then  dissolved  in  the  water  of  the  blood,  in addition  to  that  bound  with  hemoglobin.

I understand that high pressure causes more oxygen to dissolve in blood, but cannot figure out how excess dissolved oxygen in the blood disturbs the normal physiological balance of the body.
I'd be grateful if someone knowing the answer can help me.


texts: Relative roles of ATP and NADPH in anabolic and other processes

texts:
Chemistry isn’t my strong point, but I’m trying to understand why NADPH is said to be the main agent necessary for anabolic reactions, and if NADPH is used for anabolic reactions what is ATP used for? Movement?

An example of what I'm wondering: When skin cells are exposed to sunlight, to synthesize melanin is the free energy of ATP hydrolysis sufficient? For example by catabolizing some protein in the cell and using the amino acids to synthesize melanin? Or is NADPH always necessary?

I have not been able to find an explanation on-line that addresses this, so suggestions of a suitable book would be appreciated.


texts: Are PVC&PET bacteria found inside homes?

texts:
I am interested in weather PVC and PET eating bacteria can be found inside people's homes. The PET consuming ones were found in or near plastic waste dumps or in the ocean, but would they also have adequate conditions in people's domiciles or they require specific things like the plastic being constantly in contact with water or earth?

I am mainly interested in the probability/possibility of PET eating bacteria being found in domestic spaces.


texts: Which DNA sequence will have higher melting temperature: CCCCCC... or GCGCGC...?

texts: I tried this service to calculate temperatures. The nearest neighbour method consistently gives larger results for sequences like GCGCGC over sequences like CCCCC or GGGGG, while other methods don't give a difference. Is it nearest neighbour's feature or is there indeed a difference in melting temperatures?


texts: Voltage-gated Potassium channels in the action potential of cardiomyocyte?

texts:
There is one type of potassium voltage-gated channels open in Phase 1 too.
Some call them early repolarization channels.

I am not convinced that the channels are different in different phases: 0, 2, 3 and 4.

I think all these potassium channels are voltage-gated.
However, they probably differ in some places.
I am not sure if one type of channel can be open in all these five phases.

Which types of potassium channels are open during the action potential of cardiomyocyte?


texts: Query regarding calculation of survival analysis

texts:
According to this tutorial, for table to find the survival estimates, the square root of the 6th column is multiplied with the 4th column, which is Survival probability. The value that should come for the 7th column for the 2nd row is 0.052((square root of 0.003)*0.950=0.052) but in the tutorial it is given 0.049. Am I making any mistake with the calculation?
Many of the values in the table does not match with the calculations given.


texts: If we put a meal into the food storage container, does it produce methane gas while it is getting rotten or what else types of gases it produce?


texts: Transcription of Genes: Are Specific Transcription Factors + Enhancers Necessary?

texts:
I learned about transcription in my AP Biology class and we discussed how transcription occurs, but I was wondering whether transcription always requires the enhancers, activators (specific transcription factors), DNA-bending proteins, etc. to be present, or if this is only used for higher-level production of RNA transcripts?

Can transcription occur if only the RNA Polymerase (I, II, or III) and the General Transcription Factors are present?

Thanks!


texts: Nitrogen deficiency and chloroplast function

texts:
Q. The formation of which of the following in the chloroplast is affected by a deficiency in nitrogen?

(a) Glyceraldehyde 3-phosphate
(b) Starch
(c) Enzymes
(d) Carbohydrates

My thoughts:

Nitrogen is used in both of chlorophyll and in converting carbohydrates into proteins so I am puzzled between glyceraldehyde 3-phosphate and enzymes.

However, glyceraldehyde 3-phosphate, starch and carbohydrates are nearly identical in this context and enzymes aren’t produced in the chloroplast either.


texts: How fast can our skin recuperate from sunlight?

texts: Imagine that you get burned in the sun after half an hour. But a quarter and another quarter is also a half hour. So if you go into the sun 15 minutes and after one hour another 15 minutes do you get equally burned? Or what in case you pause half an hour etc. Is there a kind of schedule for recuperation times/pauses?


texts: Why is cancer not a communicable disease?

texts: I read another question where the author is asking about the infectivity of viruses. In the same vein, I am curious why cancer is not a communicable disease.


texts: Why do we have wrinkly fingers after swimming?

texts: I found an explanation for my question here http://www.pitara.com/science-for-kids/5ws-and-h/why-do-we-have-wrinkly-fingers-after-swimming/, which suggests that water washes out sebum (special oil, which covers our skin) and water gets into outer layer of now unprotected skin by osmosis. This article also suggests that fingers are not really shriveled - they are water-logged. But is this right? I think I observed many times my wrinkly fingers after swimming, but I never felt that they are water-logged. Any thought on this matter would be highly appreciated.


texts: Do electromagnetic waves outside the visible spectrum have any role in photosynthesis?

texts:
Does photosynthesis occur only in the visible spectrum? If there is a way to completely remove all other electromagnetic bands from the sunlight, including infrared (IR), will photosynthesis continue to occur?

Is there any known plant (algae, fungi, bryophytes, pteridophytes, gymnosperms and angiosperms) that utilises the other wavelengths for photosynthesis?


texts:
Usually DNA sample manipulation is realized with an ice box at hand in order to avoid degradation, and also its storage is set at -20ºC. Nevertheless, DNA has been obtained from really ancient samples that were not in a cold environment and even our DNA is at 36ºC. Furthermore, when performing PCR, samples are put into a massive heat shock and at high temperatures.
Then how needed are those protocols in order to grant correct DNA quality? how much can a sample be left without need to worry? and how does this degradation happen (DNAse free environment)


texts: Why can't we use plasmids to add genes to ourselves?

texts: Reading these answers I wonder, why doesn't "gene therapy" use self-contained plasmids instead of trying to splice a length into a chromosome?


texts: What is the role pyruvate carboxylase in lipogenesis?

texts: I just know that Acetyl-CoA is a positive allosteric modulator for pyruvate carboxylase, but I cannot find anything else.


texts: Concerning Rabies can an animal feeding on rabid bat transmit right away?

texts:
Playful kitten found biting and toying with a dead bat. Lets say the kitten nips and plays rough with a human right after biting and toying with the bat.

Will a potential rabies virus transmit from the mouth of the kitten into the human being that it may still harbor the virus from the bat?

Putting aside the fact that the rabies virus takes days to weeks to infect the kitten, can the virus cross contaminate from the mouth or nails of the cat if the feline was playing with the corpse?


texts: What is (roughly) the net charge of the DNA in an average human cell?

texts: I was wondering about what general range for the net charge of DNA in human cells is in Coulombs.  I imagine that kind of thing would be hard to measure but could be approximately calculated/estimated.  Could you approximate it by taking the average number of base pairs in the human genome and multiplying it by the charge of a phosphate group?  Would you have to multiply by two as well because there are two phosphate groups attached to each base pair?


texts: Enzyme inhibitor leads to higher turnover rate?

texts:
I'm currently working on a project where I have to deal with enzyme inhibition.
The purified enzyme shows a good substrate turnover. When I try to inhibit it with different inhibitors described in literature, however, I receive quite awkward results.
I have now tested 3 different inhibitor compounds. One showed good results (it reduced the substrate turnover), while the other two compounds instead led to increased substrate turnover?!
I know it sounds ridiculous, but has someone experienced something like this before? The measurements of the "working" and "not working" compounds take place on the same plate.
How can it be that widely described inhibitors lead to such results?


texts: How to find a model organism's standard data about proteome size and genome size?

texts:
I want to know proteome size(the number of proteins not length) and genome size(length) of model organisms like Caenorhabditis elegans, Saccharomyces cerevisiae etc.
I found www.uiprot.org
and I made a table which is wrong according to my prof.

for example, I searched "Saccharomyces cerevisiae" on the site.
https://www.uniprot.org/proteomes/UP000002311

I wrote 6,049 on protein. and clicked the link "GCA_000146045.2 from ENA/EMBL" on Genome assembly and annotation.
https://www.ebi.ac.uk/ena/browser/view/GCA_000146045.2

I clicked "Assembly Statistics" on the right box and wrote the total length.
where am I wrong?
It seems there are so many samples about a species. I don't know which is standard reference for the model organism. I want data as a general knowledge like on the text book
and I found model organism database sites on wiki
https://en.wikipedia.org/wiki/Model_organism_database
I don't know how to use these sites. they give me complicated sequence browsing but I only want just proteome, genome size. what should I do?

EDIT.
professor didn't tell us about strains. he just gave the table at the top of this post with data about E.coli by red text as a example.

this is what professor showed on his next lecture, which is other student's answer.
professor didn't mention which is correct or wrong, he asked if the student is sure about the source(Yu Nie) and if the source is reliable.
anyway, comparing this to my table, Mus musculus and Drosophila have significant difference.
Mus musculus other: 39,412, mine: 55,474
Drosophila other: 30,443, mine: 22,117
I searched again about these.

Mus musculus have only two result, it seems I should have chosen standard rather than close to standard.

but about drosphila, they have no standard. (I chose random one)
https://www.uniprot.org/proteomes/?query=drosophila+melanogaster&sort=busco&desc=no
where can I find about Drosophila?


texts: Does electrotonic spread/conduction occur in saltatory conduction?

texts:
Even as textbooks, and almost all web pages I've seen so far, explain electrotonic spread/conduction as the passive current flow along an axon, they do so with continuous conduction only. Apart from myelin sheaths which enwrap axons leaving only the Nodes of Ranvier exposed, and of course, the energy requirement and speed of conduction differences, I can't see how else continuous conduction differs from saltatory.
My question then is why electrotonic spread is never mentioned in saltatory conduction.


texts: How much light can pass through the human eyelid?

texts:
My sister tells me that at night when the lights in the room are off that she can see the ambient outdoor light from neighboring buildigns and streetlights through her eyelids (i.e., when her eyes are closed). I, on the other hand, can't see anything. I can easily fall asleep even when the lights in the room are on; my sister can too, but when I tell her to sleep with the lights on because I have work to do, she just stares at the light and says that she can't sleep.
So, quantitatively, how much light would be able to pass through a normal human being's eyelids. And would ambient outside light be enough to pass through?


texts: Why are so many recreational drugs serotonin 5-HT1A partial agonists?

texts:
I found out that many psychoactive drugs partially activate the 5HT1A receptor. Looking at Wikipedia, these include MDMA, LSD, CBD, Psliocybin/Psilocin, amphetamine and various other psychedelics, and they appear to all be serotonin 5-HT1A partial agonists.

Why is this receptor so popular for recreational drugs? Why are all these partial instead of full agonists? I looked at 5-HT1B and there weren't any recreational drugs that used this listed. I looked at other 5-HT receptors, and only 5-HT2A had other recreational drugs as agonists.

Why do so many recreational drugs affect these two 5-HT receptors?


texts: Is there an evolutionary reason for the 5 electron transport complexes in plants and animals?

texts:
The electron transport chains of both the light reactions of photosynthesis (in plants) and oxidative phosphorylation (in animals) both contain 5 complexes including ATP synthase, as shown below.

Image Source

Image Source

Is this coincidence, or does this possibly suggest that both chloroplast and mitochondrion precursors derived their energy-obtaining mechanisms via an ancient evolutionarily-related metabolic pathway which diverged?


texts: What is the mechanism of monofunctional glycosylases?

texts:
I am learning about the base excision repair mechanism. I understand generally how glycosylases work, but I am trying to understand this with much more detail. I found a paper where they write:

  Monofunctional glycosylases catalyze the single-step displacement of damaged base via attack of an activated water molecule on c1' of the substrate.

I am not sure what an activated water molecule is and how, for example, an aspartate residue is making a water molecule 'activated'. Furthermore, how is this activated water molecule hydrolyzing the N-glycosyl bond to remove the damaged base. Thank you for any help.


texts:
I heard that Actinia Equina normally eats what it can catch, but this clownfish here doesn't care much about that:

https://www.youtube.com/watch?v=Ughm4mnZ1ls

Since the actinia obviously can't hold the clownfish, clownfish does whatever it wants with actinia swimming all over it. Is the clownfish having some sort of fish fun, or is there a purpose behind this playing with actinia?


texts: Is the phrase "transmembrane segment" equivalent to the transmembrane domain of a protein?

texts:
I am reading the Handbook of Neurochemistry and Molecular Neurobiology  and I am learning about the cell adhesion molecule NCAM2 and I have come across the following:

The overall structure of NCAM2 is similar to that of NCAM. Thus, NCAM2
consists of five Ig‐modules (supposedly of the C2‐type) followed by
two Fn3‐modules. The protein exists in a GPI‐anchored isoform and in a
transmembrane isoform that contains a 20–25 amino acid transmembrane
segment followed by a 106–119‐amino acid cytoplasmic tail (Alenius and
Bohm, 1997; Yoshihara et al., 1997).

I know that NCAM2 is located at the cell membrane and has an extracellular, transmembrane and intracellular domain. However, for the above statement: The protein exists in a GPI‐anchored isoform and in a transmembrane isoform that contains a 20–25 amino acid transmembrane segment followed by a 106–119‐amino acid cytoplasmic tail, is the term 'transmembrane segment' equivalent to the transmembrane domain? Further is the term 'cytoplasmic tail' equivalent to the intracellular domain? Any insights are appreciated.


texts: Suppose we've collected a big (hundreds of thousands) library of different protein sequences with certain features. Then we want to use this data base to train a classifier. And for several statistical reasons we want different functional domains to have somewhat equal frequencies in the data base to reduce domain-specific bias. The straightforward way to achieve this is to use structural information from UniProt and the like, but many proteins don't have any verified structures and de-novo structure prediction might take ages to compute. Alternatively we can perform sequence clustering and pick an even number of sequences out of each cluster. We can either apply a local-alignment based clustering algorithm with ~35% identity threshold or use some sort of hidden Markov model to cluster by profile. What do you think? How biologically relevant this might be? Can this simple clustering based approach help normalise the library to some extent?


texts: How do you convert mtDNA sequences in FASTA to FSTAT format?

texts:
I've got control region sequence data from a population of shark and I'm looking to convert this from FASTA to FSTAT in order to calculated the effective population size of females. The software I want to use only accepts FSTAT or Genepop files.

Is it possible to convert FASTA to FSTAT or even Genepop?


texts:
With respect to the following paper:

Automated identification of protein-ligand interaction features using Inductive Logic Programming: a hexose binding case study

I have a few questions:

in page 2, in the table, what does 501 mean in GLC-501(I searched for GLC-501 in PDB,couldnt find anything)
in page 3, in the table, the cavity center column has got two entries, what does that mean? does one entry belong to the protein and another entry to the ligand(left for protein and right for ligand)??


texts: Is the knee locking mechanism present in animals?

texts:
We study in human anatomy that when the knee is in full extension, the femur slightly medially rotates on the tibia to lock the knee joint in place. This reduces the work required to be done by the hefty thigh muscles. This happens in the knees in humans since they are the weight bearing joints.

So, is the mechanism of locking present in other animals? If yes, is it even in the fore limbs or just the hind limbs?


texts: Element of promoter responsible for expression power of gene

texts:
I know that there is a classification of promoters like: strong, medium and weak. This shows how a promoter affects gene expression levels. So my question is: what part of the promoter affects it?

For example I want to raise or lower the expression of some gene, so, what part of promoter I need to edit or maeby I can just replace it with another promoter?


texts: Using Chi-squared analysis to confirm expected phenotypic ratios of offspring

texts:
In a recent question the original poster was faced with deciding which ratios to use in a Chi-squared analysis. They were supposed to decide on, "logically", what test-ratio to use.

Example question:

A supplied sample contains four types of seeds and the total number is 64. The
types of seeds are large red 42, large white 8, small red 10 and small white 4. Calculate goodness of fit.

My initial assumption was that in order to solve the problem, you would need to think about the genotype of each parent.

Lets say:
L = large seeds;
s = small seeds;
R = red seeds;
w = white seeds

If both parents were LsRw, the phenotype-distribution of the offspring would follow a 9:3:3:1 ratio.

If one parent was LsRw, and one parent was ssww, you would have a 1:1:1:1 ratio.

And if one parent was LsRw, and the other parent was Lsww or ssRw, you would have a 2:2:1:1 ratio.

Obviously, out of all of these ratios, the example question follows most closely with the 9:3:3:1 ratio.

So, to solve this question statistically, would you make the null hypothesis There is no difference between the observed and expected ratios?

While the alternative hypothesis would be There is a different between the observation and the expected ratios?

And would a statistically significant result indicate that the null hypothesis must be rejected in favour of the alternative hypothesis, thus the parents are unlikely to be heterozygotic for both traits?


texts: What are the criteria for determining the origin and end of muscle anatomically?

texts: For example the pectoralis muscle starts from sternum region and ends on the acromion or coracoid process. Why you can't say that it starts acromion process and ends on the sternum?


texts: what's the species identification of that camponotus queen

texts:
City: Antalya, Turkey

Date: July 27 night

Specific location: I found it in the middle of the city


texts: What makes the neurons of the auditory nerve with such high-speed? So the most labile are the fibers of the auditory nerve, in which the frequency of the generation of PD reaches 1000 Hz, while for skeletal muscles, it corresponds to 200 pulp / s, for smooth - 10-20 imp / s.  Motor nervous ending can be transferred to the skeletal muscle and at all no more than 100-150 excitations in 1 s


texts:
Coming from a non-biology background, I've realised many academic papers on experiments use DMSO as like a control. This is an example:

  KN-93, a specific inhibitor of CaMKII inhibits human hepatic stellate cell proliferation in vitro

What make DMSO so special that so many scientists use it for their experiment and report their results? Why do we need it in the first place?


texts:
I am a student of Mathematics.Since I found no better place to ask my question I post it here.

I was looking for some classes of graphs which are used in biology.

I came across this particular class of graphs called kite graphs whose link can be found here https://rpubs.com/thoughtfulbloke/kitegraph.

I found it interesting because graphs are mathematical objects and finding them useful in biology is naturally very interesting.

I also find research papers in Mathematics involving kite graphs.

My question is what are some classes of graphs like the kite graphs which are used in biology.
Where can I find them?

In case someone helps,I will be grateful to them.


texts: How do GPCRs transmit a signal across the plasma membrane?

texts:
How do G-coupled protein receptors (GPCR) transmit signals through the plasma membrane?

Links containing information about this and pictures will be very helpful.


texts: I am wondering how DNA glycosylase works from the chemical point of view. Sometimes in papers I can see that they are doing activity assays with 1M NaOH and I am trying to understand why using 1M NaOH is more factual? Thank you for any help.


texts: Darwin's first sketch of a phylogenetic tree

texts:
Coming from Darwin's notebook this first sketch of a phylogenetic tree became one of the most emblematic image from Darwin's work.

I have a hard time to read what is written on it.

What is written on this page?


texts: Counting the number of hydrogen bonds of multiple PDB files

texts:
I've been trying to figure out a systematic way to count the number of hydrogen bonds for multiple PDB files.

DSSP shows me the total number of hydrogen bonds when I make dssp.exe 1A11.pdb, giving me the total number of 24 (am I correct, ok?)

24 96.0   TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(J)  , SAME NUMBER PER 100 RESIDUES

But when I run this command in R:

> require(biod3d)
> x=dssp(read.pdb("1A11"), full=T)

it doesn't look to have the number of hydrogen bonds. It shows this:

> x$hbonds
     BP1 BP2 NH-O.1   E1 O-HN.1   E2 NH-O.2   E3 O-HN.2   E4 ChainBP1 ChainBP2 Chain1 Chain2 Chain3 Chain4
1-A   NA  NA     NA  0.0      5 -2.1     NA  0.0      4 -0.3     <NA>     <NA>   <NA>      A   <NA>      A
2-A   NA  NA      3 -0.2      6 -1.5      4 -0.2      7 -0.2     <NA>     <NA>      A      A      A      A
3-A   NA  NA      4 -0.2      7 -1.8      5 -0.2      2 -0.2     <NA>     <NA>      A      A      A      A
4-A   NA  NA      1 -0.3      8 -1.5      6 -0.2      7 -0.6     <NA>     <NA>      A      A      A      A
5-A   NA  NA      1 -2.1      9 -1.9      6 -0.2     10 -0.2     <NA>     <NA>      A      A      A      A
6-A   NA  NA      2 -1.5     10 -1.3      1 -0.3      5 -0.2     <NA>     <NA>      A      A      A      A
7-A   NA  NA      3 -1.8     11 -1.3      4 -0.6      5 -0.2     <NA>     <NA>      A      A      A      A
8-A   NA  NA      4 -1.5     12 -1.2      3 -0.2      6 -0.2     <NA>     <NA>      A      A      A      A
9-A   NA  NA      5 -1.9     13 -1.1      4 -0.2      7 -0.2     <NA>     <NA>      A      A      A      A
10-A  NA  NA      6 -1.3     14 -2.3      5 -0.2     13 -0.4     <NA>     <NA>      A      A      A      A
11-A  NA  NA      7 -1.3     15 -1.8     12 -0.2     16 -0.3     <NA>     <NA>      A      A      A      A
12-A  NA  NA      8 -1.2     16 -1.8     13 -0.2     11 -0.2     <NA>     <NA>      A      A      A      A
13-A  NA  NA      9 -1.1     17 -2.4     10 -0.4     18 -0.5     <NA>     <NA>      A      A      A      A
14-A  NA  NA     10 -2.3     18 -1.6     15 -0.2     13 -0.2     <NA>     <NA>      A      A      A      A
15-A  NA  NA     11 -1.8     19 -1.8     17 -0.2     20 -0.5     <NA>     <NA>      A      A      A      A
16-A  NA  NA     12 -1.8     20 -0.8     17 -0.3     14 -0.2     <NA>     <NA>      A      A      A      A
17-A  NA  NA     13 -2.4     21 -1.9     19 -0.2     16 -0.3     <NA>     <NA>      A      A      A      A
18-A  NA  NA     14 -1.6     22 -2.0     13 -0.5     21 -1.0     <NA>     <NA>      A      A      A      A
19-A  NA  NA     15 -1.8     23 -2.0     20 -0.3     24 -0.3     <NA>     <NA>      A      A      A      A
20-A  NA  NA     16 -0.8     24 -1.5     15 -0.5     19 -0.3     <NA>     <NA>      A      A      A      A
21-A  NA  NA     17 -1.9     25 -1.0     18 -1.0     19 -0.2     <NA>     <NA>      A      A      A      A
22-A  NA  NA     18 -2.0     25 -0.3     23 -0.2     20 -0.2     <NA>     <NA>      A      A      A      A
23-A  NA  NA     19 -2.0     22 -0.2     18 -0.3     21 -0.2     <NA>     <NA>      A      A      A      A
24-A  NA  NA     20 -1.5     23 -0.2     19 -0.3     22 -0.2     <NA>     <NA>      A      A      A      A
25-A  NA  NA     21 -1.0     23 -0.2     22 -0.3     24 -0.2     <NA>     <NA>      A      A      A      A

So, my question: Is the total number of hydrogen bonds hidden somewhere in this output or somewhere else (or doesn't exist)?

If I manage to count the number of hydrogen bonds in a single PDB using Bio3D and R, then I can create a loop and iterate over all remainder PDB files.

Thanks for all!


texts: Cells scatter light in solution. Do they refract?

texts: For part of an exam question, "why do cells grown in liquid cause turbidity?" I answered that cells refract light. The correct answer was that cells scatter light. Isn't the light scattering ultimately caused by lots of refraction events? Is the grader correct to take off full points?


texts: Excretion of monovalent and divalent ions in sharks

texts: I have heard that sharks excrete $\ce{Na+}$ and $\ce{Cl-}$ by their gill surfaces but divalent ions like magnesium are excreted through feces. What could be the reason behind this?


texts: Why do we feel numbness and an electric sensation in our legs after standing for too long?

texts:
We have all felt that numbness while standing immobile for a while.It gets difficult to walk.It can also happen if we are just putting some pressure on our legs
Why does this happen?

I'd like to know what specifically happens in the muscular tissue(if that's the origin of this sensation) for us to feel like this


texts: Reason for partially double-stranded DNA of Hepatitis B virus

texts:
According to my school biology textbook and also Wikipedia, hepatitis B is the only Hepatitis virus to possess partially double-stranded DNA.
I found an image from here
What is the reason for the partially double-stranded DNA?
(It seems that it can be triple-stranded as well.)
I found this information in this research about duck hepatitis B virus

Similar to classical retroviruses, viral assembly begins with the formation of intracellular nucleocapsid particles that specifically package the pgRNA. However, all hepadnaviruses undergo a maturation phase during their morphogenesis that is characterized by the reverse transcription of the pgRNA prior to membrane envelopment and secretion as extracellular virions, rather than subsequent to entry into new target cells, as is the case for classical retroviruses (for a review, see reference 20). Thus, secreted hepadnaviral virions contain only the “mature” ds DNA, whereas intracellular pools of nucleocapsids contain nucleic acid species from all the intermediate stages of reverse transcription ranging from only pgRNA to single (minus)-stranded (ss) DNA as well as ds DNA, a fundamental observation made by Summers and Mason 2 decades ago (22)

What is the special advantage of having such a genome?

are there any other organisms with partially double stranded DNA or partially double stranded RNA as well?


texts: Do alleles, by definition, code for the same trait?

texts:
A trait is defined as an inherited characteristic, like eye color and height.
A phenotype is defined as the specific physical manifestation of a trait, like blue eyes and 6 feet, respectively.

Now, genes code for traits. And because alleles are different versions of the SAME gene, they must code for the same trait. Let's say gene A codes for hair color (trait). Gene A(1) (allele) codes for brown hair (phenotype) while gene A(2) codes for blonde hair. Therefore, alleles code for the same TRAIT, but differing PHENOTYPES.

Here is the problem. When I google: "heterozygous", I get a bunch of websites defining it as "referring to a gene pair in which the two alleles do not code for the same trait"

This is not correct because a gene-pair refers to genes located at the same locus on a chromosome. In other words, they are alleles of the SAME gene and code for the SAME trait. They only code for different phenotypes associated with that trait.

So. Either my definition of traits is wrong. My definition of alleles is wrong. My understanding of alleles being different versions of the same gene is wrong. OR. The internet loves to be imprecise with their language and interchangeably use terms that mean different things.

Which is it?


texts:
I want to know what is the smallest viviparus known at this time.

I was Googling, but I can discover this animal.

Thanks.


texts: What is the minimum-volume : neutral-volume : maximum-volume of the molecules that make up the SARS-Cov-2 virus-fusion machine?

texts:
The "neutral-volume" is the over-lapping volume between minimum-volume & maximum-volume of the molecules that make up the SARS-Cov-2-fusion machine. Those identifying potential differences that support particle-flow inside the SARS-Cov-2-fusion machine-molecule have certain degree's of freedom. The best description of the structural dynamics of the Sars-COV-2-fusion machine that I have found was in "Scientific American", July-2020-issue/page 34,.
A base understanding of the "open-loop & closed-looped" particle-flow-symmetry is needed to explain the action of why the fusion machine of the SARS-Cov-2 virus binds to a lung-cell. The way I understand it, there is an exchange of particle-mass, starting with disorganizing lung-cell-mass by this virus at point of attachment, then re-organization occurs between the lung-cell and the SARS-Cov-2-fusion machines particle-flow grid. The SARS-Cov-2-fusion-machine may in fact accelerate into the lung cell, (to-push & bend/in the act of causing mass to dis-organize) and then deaccelerates, causing the act of organizing particle-flow between the two cells (to pull-straight/in the act of synchronizing & organizing), producing a certain closed-looped function between the virus-cell & the lung-cell. What are those unseen differentials between what is seen and what is not seen? Covalent bonding is straight-forward and well understood, except for the fact that there are other molecular actions involved. Would this be a function of two under-square vortexes, Van Der Wall-forces, Brownian motion, the action of dipoles, or something else? ALL of which may in fact contribute to an exchange of mass of which brings on those pulling forces that bind. There is a certain working-mass having a certain energy efficiency per location per time that changes the squareness of the SARS-Cov-2-fusion machine. Volume displacement of heavenly bodies plays a critical roll as to the way particles move around and through them, i.e. outer-space becoming inner-space & inner-space becoming outer-space per location per time.


texts: What do the qualifiers used in botanical species names mean?

texts:
These are all the qualifiers I've come across so far. The first 3 were quite easy to google, but the other 4 have me stumped.

I also can't say I'm completely clear on the nuances of s.s. vs. s.l..

agg.
s.s.
s.l.
cf.
cv.
auct.
ined.


texts: How far in can non-extremophiles live, in Earth?

texts:
I am a high school student. I'm doing a project where I need to find a planet in our galaxy that might be habitable. Then I need to create an organism that could live on that planet and justify everything about it Ex: Sight, whether or not it can see and why or why not / Touch / Smell / Respiration / Central Nervous System / Cell Count... My final outcome must have these and a lot more.

I just need to justify and explain where it lives on the planet I have chosen. I found a planet (Kepler-422b) which was described as being one of the most Earth-like planets, in terms of size and temperature, yet found. Since it is very Earth-like, it made my job a bit easier. But the planet orbits a red dwarf star that is cooler than our star, and this planet is -40 degrees Fahrenheit (80 degrees cooler than earth) so my organism will have to live in the ground of the planet and rely on the core for warmth. But I do not know how deep organisms can go into the Earth. Can someone please help me? I have done a lot of research and spent a lot of time trying to find this but extremophiles are the only organisms listed.

Thank you so much for helping me.

An extremophile is defined as a microorganism, especially an archaean, that lives in conditions of extreme temperature, acidity, alkalinity, or chemical concentration. Like the Tardigrade. Im sorry I did not make this clear initialy


texts:
I'm a CNA and I just got home from a very long day at work. I just started this job and I got hurt at work last night which made me wonder can enough pain cause death (without suicide)?

I think the answer is yes, but I'd like to know how/why.


texts:
I'll have few questions about passing out and dreaming. English is not my native language, and my biology knowledge is very limited. So bear with me.

What exactly is blackout? (in a really simple way)
Are there different types of blackout? (see below)
Do fainting, passing out, and blacking out mean the same thing?
Can someone have a dream/vision after loosing consciousness? (during blackout?)

I'm asking these because I had a similar experience and I'm trying to make sense of it.

We were goofing around and a friend of mine had me in an arm triangle. I suspect he choked me, because I lost consciousness for a few seconds, max 3. While in that state, I kind of had a dream or vision, whatever it is called. It felt like hours. This was a long time ago and I still remember the dream, but can't make sense of it. What I've seen was really interesting and I couldn't just let it go.

I'm not asking for dream analysis or anything, but the biological/neurological aspect of what happened, so don't get me wrong.

I'm also new in here, though not to stackexchange, so the tags might need a modification.


texts: Meta-analysis of fruits in blocking Cytochrome family

texts:
My professor says that some drugs cannot be used with grapefruit.
I am trying to search a list of cytochromes and their effect to block members in the cytochrome family. Some in Cyt P450.

What is the main meta-analysis of fruits in blocking cytochrome family?


texts: If fever is a natural immune defense, why do people take drugs to lower it?

texts: If fever is a natural defense against pathogens, why do sick people take NSAIDs to reduce the fever?


texts: how to extract promoter regions given a TF binding site

texts:
I have constructed a PWM and want to test its accuracy. Scanning an entire chromosome (chr3, hg18) yields very high false positives (magnitudes higher than the true positives). Scanning the entire genome is much worse.

From some literature and biostars posts, its recommended that I only scan sections of the genome to get an understanding of the accuracy of my PWM. Some posts talked about just scanning the promoter regions with my PWM (or say, a 1000bp neighbourhood around the promoter region).

So, is there a database or some sort of annotation that tells me where the promoter regions are?

I have a feeling that this question may not be well formed because to get "promoter" regions, I need to be talking about genes. Since I am only working with the MEF2 family of transcription factors, is there a way to retrieve promoter regions in which these transcription factors bind?

My idea: Since the TF binds upstream of the gene, usually in a promoter region, AND I know the true binding sites, would it be sufficient to just extract a 2000bp neighbourhood around the binding site?

Here is what my data (only the first couple of lines) looks like:

>chr1:6585537-6585547(-)
------ctatttatag-------
>chr1:228916512-228916522(+)
------ctatttatag-------
>chr12:50731227-50731237(+)
------ctatttatag-------
>chr13:49597702-49597712(+)
------ctatttatag-------
>chr14:103058980-103058990(+)
------ctatttatag-------

So again, is it sufficient to take chr1:6585537-6585547(-), extract a 2000bp neighbourhood around it, and scan this neighbourhood with my PWM. Clearly, I know there is one true binding site and I'll compare it with the number of false postives it gives me.

edit: Background

I have information (coordinates) for a total of 1875 binding sites. From these, only about 140 coordinates to binding sites on chromosome 3. These are my "true binding sites". If I scan chromosome 3 with my PWM, it gets around 85,000 hits.. ie, 85000 sequences that have scored very high that could be potential binding sites. They are, for all intents and purposes, false positives unless they fall (or overlap) the true binding site. Out of 85000 hits, only a very overlap the true binding region.

Now, literature recommends that instead of scanning an entire chromosome (or the entire genome), its better just to scan promoter regions. I guess there is confusion here, because the question can be "promoter regions for what gene?"

But I guess we have bonafide promoter regions if we take say 1000bp neighbourhoods about our true binding sites.


texts: What species is this grey insect with red antennae and mouthparts?

texts: I’m very curious to know whether this is a type of ant or not, I only see 6 legs. Found in Tampa, Florida near Tarpon Springs.


texts:
Many solvents can be used for mutagen X (3-chloro-4-(dichloromethyl)-5-hydroxy-5H-furan-2-one), however, long-term stability is not specified. Which would be the best solvent for long-term storage? Once dissolved, can it be stored at RT or -20ºC?

Thanks


texts: Why do some grasshoppers have a black exoskeleton?

texts: What species of grasshoppers have black exoskeletons? Is there a scientific difference in species between field crickets and grasshoppers?


texts: Which is a good methodology to find out a domestication process?

texts: I just started with my course in genomics and I'm working with domesticated animals (cows, chickens, pigs, etc) and I would like to know which methodology is better to trace the process of domestication since the origin of these species. I'm thinking of using SNPs of a particular gene to identify punctual traits that were selected, but also I was suggested to do a complete screen analysis and identify all the polymorphisms present in each variant and compare them with the species that gave them origin.