texts: Why do scary situations make our skin crawl? Why do we have goosebumps in such situations?

texts: I do not see why should scary situations make our skin "crawl". In scary situations, we supply less blood to our skin (which makes it paler), so shouldn't its activities reduce? Goosebumps should take up some energy to raise the hairs. Shouldn't that energy be conserved?


texts:
I'm preparing myself for the GRE. The quantitative stuff has all been going well. I'm aiming for a geology grad scheme. In the event of having to take subject specific tests, I'm teaching myself a few "out there" things in science.

I'm going through biology and looking at genetics for the first time since high school(!)

I just had a question here really to do with genetic crosses. I've been looking at Mendel and the experiments he carried out. One specifically looking at short pea plants. I'm looking at an example where all F1 plants are tall (F1 being the generation of plants). In the example the F2 generation are created in selfing the F1 plants.

Now, I've got my head around the science involved, but I just basically wondered if any biologists here could show me how to make a genetic cross of F2 in order that I could show the genotypes and phenotypes of the offspring.

This isn't necessary but I feel as though it would help my understanding.

At the moment I'm drawing a two by two grid. I suppose I need to fill it with the appropriate alleles?

Thanks.


texts: Why is atropine a CNS stimulant, although it blocks the muscarinic receptors in the brain?

texts: I know that atropine is a muscarinic  antagonist, so why does atropine have excitatory actions on the brain while it is blocking muscarinic receptors?


texts:
My Campbell's Biology textbook discusses photoperiodism of plants and introduces us to short-day and long-day plants. What I don't understand is why short day plants will not flower if they are exposed to a very brief flash of light during the night, even if that brief period + the actual day's length is still less than their critical day length? Or, put more concisely:

Length of Flash + Length of Day < Critical Period    <-- Why does the short-day plant not flower?

The following diagram is from Campbell's and makes no sense to me, because it also seems like a long-day plant which is exposed to a brief period of light during the dark will flower even if that period of brief light + its actual day's length is not greater than its critical period (i.e. it never fulfilled the pre-requisite for flowering).


texts: Can swarming locusts act as a vector for any human pathogens?

texts:
What human pathogens can the locusts currently swarming in Africa act as a vector for?

E.g. can the locust swarm 'become a reservoir for' SARS-CoV-2? Measles? Ebola?


texts:
G proteins consist of an alpha subunit and a beta/gamma subunit. These proteins are involved in various cellular signalling process.
From what I have understood, the alpha and gamma subunits have covalently bound lipid tails. That is, they seem to be directly connected to the cellular membrane. If this is the case, how do these protein subunits move?
I understand that the cellular membrane is flexible but I'm currently imagining a flying fox type scenario. This is where the alpha subunit is covalently bonded to one phospholipid and is now gliding down a cell membrane. I kind of find this hard to believe because it seems ridiculous (but fun!).
How do alpha and gamma protein subunits move if they are covalently bonded to the cellular membrane?


texts: How is it possible for only one in five children to have brown eyes when their parents both have brown eyes?

texts:
I have observed that parents having brown eyes had three female offspring with blue eyes, one son with green eyes, while only the youngest daughter had brown eyes.

How can they produce so many blue-eyed offspring?


texts:
A population given inhabiting an area. I can trace every individual and I've got the hypothesis there is a break in distribution like individuals born in the upper half of the area will rarely move to the lower half and vice versa.

Tracking each individual how can I determine the line/border which divides the population in a upper and lower half. What's the math or algorithm behind to draw this imaginary line?


texts: Are flowers / flowering plants vital to all life on Earth?

texts:
Not a biology student so forgive me if this is a very basic question. Are flowering plants (angiosperms) vital to all (or most) life on Earth?

In other words, if flowering plants disappeared, would all (or most) life on this planet be gone as a result?

To give a bit more context, I'm arguing with a friend who claims (from a biblical perspective) that without flowering plants life couldn't exist.


texts: Can low temperatures induce a withdrawal reflex?

texts:
I read in "Essentials of Pathophysiology: Concepts of Altered Health States
By Carol Porth" that

  "The thermal pain receptors are stimulated only by extremes of temperature such as "freezing cold" below 5°C and "burning hot" above 45°C."

Also in "The Journal of Neuroscience, April 7, 2010 • 30(14):4933– 4942 • 4933" it states:

  "In lightly anesthetized rats, hindpaw cooling with ethyl chloride, but not acetone, was sufficiently noxious to evoke withdrawal reflexes"

We know, 'burning-hot'-receptors induce a withdrawal reflex when we touch a very hot object, say hot frying pan.

But does this mean if we touch a very cold object (temperatures below 5°C), the 'freezing-cold'-receptors would induce a withdrawal reflex in humans?


texts: Is complete linkage found in all four chromosomes or only Y-chromosome of Drosophila?

texts: Male Drosophila shows complete linkage. Is it observed for all four chromosomes or only the Y chromosome?


texts: Why is the inside of a cell negatively charged

texts:
So my teacher asked: "$[K^+]_i$ (k+ on the inside) is about forty times higher than $[K^+]_o$ (k- on the outside). With so many more positively charged potassium ions inside versus outside, why isn’t the interior of the cell positively charged compared to the exterior?"

My Thoughts: I am assuming that there must be enough negative charges inside the cell from other things like chlorine or ATP and proteins that the net coulombs on the inside is lower than the net coulombs on the outside. Does this seem like the correct answer? I am hesitant to use this because so far my teacher has only talked about potentials and not charges. I completely understand that the potential is negative, but potential and charge are two different things.

Edit: posted exact question from teacher as opposed to original summary of question


texts: How to predict a mRNA secondary structure with a large sequence?

texts: When I use some web servers to predict a mRNA secondary structure, I find they always required in a small size sequence. If I use a long sequence and cut it into small parts, do these small parts change the energy or thermodynamic data from the origin sequence when predicting? Is there any effective way to find the right sites when cutting the long sequence?


texts: is it necessary that every theca of an angiospermic anther must contain two microsporangia

texts:
i basically don't know the procedure or sequence of steps involved in the formation of anthers but i have read it somewhere it is formed from the dedifferentiation of shoot apical meristem of the axillary bud through mitotic divisions

so is it necessary that every theca of an anther of an angiosperm must contain two microsporangia, if yes then why are they two in number., can i get an account on the development of microsporangial lobes [here i am not asking about the process of development of pollen grains in them].

i am asking how the microsporangial lobes itself are formed

a diagrammatic answer would be highly appreciated


texts: What exactly happens to hydrogen atoms in step 4 of citric acid cycle?

texts:
It seems that there are four hydrogen atoms in alpha-ketoglutarate and one in HS-CoA (not counting the ones in CoA), five in total. Two of them go to NADH and H+, so there should be three atoms in succynyl-CoA instead of four. What am I missing here?
picture taken from Molecular Biology of the Cell, 6th ed., by Alberts et al.


texts: What's the name of this Heteroptera bug from Toronto, Canada?

texts:
My friend already identified it as belonging to the Heteroptera order, but I was wondering if anyone knows the name of the species.

Found in Toronto, Ontario, Canada, on July 21 2017, in a residential bathroom.


texts: Why do some viruses have only one serotype, but others have many?

texts: Some viruses, like the virus that causes mumps, have only a single serotype, meaning that variants of the disease are immunologically identical. However, other viruses, like the influenza virus family, has many different serotypes. Why is this?


texts: Is there a relationship between HDL-C and LDL-C?

texts:
For a gentle introduction to cholesterol and its functions, see a great answer on SE Biology

Whenever I read about how to deal with cholesterol level, the rule is to keep a low LDL fraction, ad a high HDL one.

How to achieve this usually falls into the categories of a healthy body (sport), a healthy diet and possibly medicamentation.

Since generally the advice is more or less the same for both goals (lowering one fraction and increasing the other one), I was wondering if there is a strong relationship between these fractions. In other words - is moving one in the right directions automatically drags the other one (also in the right direction)?

Anecdotally (and this is what triggered my question), I saw my LDL crash almost by 250% (not by chance but through a good diet, etc. - over a few months) and, surprisingly, the HDL go down by 30% as well.


texts: How does the "giant mosquito", Psorophora ciliata manifest it's "aggresive and vicious" behavior?

texts:
On Psorophora ciliata Wikipedia states:

Not only are these mosquitoes vicious and aggressive towards humans
and other animals as adults but, P. ciliata larvae are known for
preying on other mosquito species' larvae and even tadpoles. [2]

Emphasis mine.
Now every mosquito is kinda aggressive by drinking your blood and being generally annoying. So what makes Psorophora ciliata especially aggressive? Does it scream expletives or what does it do?


texts:
From my understanding, polymers are long chain molecules containing repeating units of monomers.

For example, proteins are polymers called polypeptides with repeating units of (different) amino acids. Therefore, a fatty acid, saturated or unsaturated, would classify as a polymer as they are long chain molecules with repeating units of alkyl monomers?


texts: Where does the 'C' in exhaled CO₂ mostly come from?

texts: When a human being exhales CO₂, what is, by the numbers, the main source of carbon atoms exiting the body in this way? I mean what class of cells, or which tissues are the biggest on a pie chart of where carbon atoms breathed out in the form of CO₂ molecules came from?


texts: Help me identify this animal from Bangladesh

texts:
I have come across this animal in a facebook group. After one group member identified it as Asian palm civet, I looked at some google images, I am not convinced. Judging from google images, this animal doesn't look like any of the common civet species found in Bangladesh.
Location: Noakhali, Bangladesh


texts: Which virus capsids consist of only one type of capsid protein?

texts:
The Tobacco Mosaic Virus (TMV) capsid consists of many copies of one protein (http://www.rcsb.org/pdb/101/motm.do?momID=109).

Which other viral capsids consist of only one kind of coat protein?

Does each copy of the protein in these also have the same tertiary structure?


texts: How much damage is caused by smoking 2-3 cigarettes on a healthy body?

texts:
I do not know how bad does 2-3  cigarettes on the average healthy body.

I do not want to include genetic factors on this issue.

So, maybe there is a study or something on this topic.

Does it cause a real damage, or to this quantities the body recovers.


texts: How much does the Hayflick limit/telomere length vary across taxa and within humans?

texts:
Since they seem to be quite connected, I'm curious if anyone knows of research comparing the Hayflick limit (and presumably by extension telomere length) between different taxa. I've heard the Hayflick limit numbers 40-50 thrown out repeatedly for humans (probably relating to the WI-38 tissue line), but how universal is this really? I Know there are particularly long lived species, but has research been done to correlate this with telomeric length, or do they simply have slower cell division?
I suppose it is worth mentioning that a Hayflick limit of 40 rounds of division is massively different from 50, since each round of division conceivably could double the number of cells...


texts: How does the emerson effect produce a higher rate of photosynthesis?

texts:
Can anyone explain how the emerson effect works to increase the rate of photosynthesis, and as the original studies were done over 50 years ago, how much research is still done into this area? Or is it well understood now as to not need further work?

I am obviously not a biologist but from what I have been reading, photosystem 2 absorbs light at 680nm due to the primary electron donor p680 and photosystem 1 at 700nm due to p700. The rate of photosynthesis when exposed to light at these 2 wavelengths simultaneously is greater than the sum of the rate of photosynthesis if exposed to these wavelengths separately. Sorry for any mistakes, I am just starting to try to learn about it. I'm interested to find out how this higher rate of photosynthesis occurs when using light in the red and far red end of the spectrum at the same time.


texts:
I am considering preserving the DNA of a family member who passed away. The funeral home offers a service called DNA Memories from a Canadian company (CG Labs). They have two options: Store the DNA in their secure temperature-controlled facility, or "home DNA banking", where they somehow preserve the DNA such that it can be stored without damage "indefinitely", at room temperature. This is how they describe the technology:

"The  DNA is bound to a substrate and sealed under nitrogen gas with out patent pending process. This process allows the DNA to remain in a state of suspended animation and if the vial remains sealed the DNA has an indefinite shelf life. The DNA Memorial Home Banking may be banked in non extreme conditions and room temperature for future testing at home."

My question is basically this: Is there any scientific merit to their claims (i.e. is there anything peer-reviewed on the subject of room-temperature DNA preservation for many years, using technology such as the one they describe)? Can DNA preserved in such a way really be tested later in regular DNA testing labs (or will I need a specialized lab that knows how to deal with this unique process)? Is there any possibility of a full sequencing later of DNA stored in such a fashion?


texts: Why is it easy to separate the cotton wool from the roots of young plants grown in cotton?

texts:
In my book it is said that if we grow Maize and Gram seeds in wet cotton, after the seeds are sprouted it is easy to separate the cotton wool from the roots of young plants.

My question is why is it comparatively harder to separate roots from soil while it is easy for cotton wool?


texts:
Except for the feces, which is more brownish, all the human wastes (urine, earwax, snivel, phlegm, and rheum) are usually yellowish. Why is that?
I heard that urine is yellow due to bilirubin(?). What about others?


texts: Why does the number of mutations per individuals follow a Poisson distribution?

texts:
I was reading this review. On page 11, left column, first paragraph, one can read:

  [..] there is a Poisson distribution of the equilibrium number of mutations per individual, if fitness effects are multiplicative.

with no further explanations. In other words, let the variable $X$ be the number of (deleterious) mutations found in one individual (irrespectively to whether the mutation occurred in the parents gonads or is older back in the lineage). The variable $X$ is Poisson distributed.

Why is this statement true? I suppose that the statement also assumes that all mutations have the same effect on fitness, is that true?


texts: How many mosquitoes would it take to "drain" enough blood to put a person into shock?

texts: I'm just curious, how many mosquito "bites" (mosquitoes which have removed blood from a person) would it take to remove enough blood to put a person into shock? (Putting aside all reasons why it wouldn't happen, how many would it take?)


texts:
Why exactly do eyes turn black when we die? (Or even change colour at all).
The source of inspiration to this question is due to this video https://www.youtube.com/watch?v=6mNs_TcUyHc&t=627s (it's a cow's eye being dissected). The man explained how the cornea is crystal clear in an actual cow but since it's been preserved, the preservative has denatured the protein causing it to turn cloudy.

So why does our eye change colour when we die when no preservative is used?
I know this is a pretty gruesome question to ask but curiosity has the best of me haha.


texts: Are there any examples of how to apply evolutionary models?

texts:
Apologies if this question it too open-ended; evolutionary biology is not my primary field.

I have been reading a lot about the use of statistical mechanics in analyzing evolutionary dynamics. As an example, consider this paper: http://www.pnas.org/content/102/27/9541.short.

The ideas are pretty straightforward. There is some genotype-fitness landscape and selection drives populations towards maximal fitness. However, genetic drift can pull these populations away from maximal fitness. These two concepts are analogous to minimization of internal energy and maximization of entropy in thermodynamics.

However, most of the papers that develop these models never properly explain how to apply them to observable phenomena. Is it because there is some disconnect between the parameters in the models and nature? For example, many of these models use the effective population size, which is unknown for most species.

I guess my main question is this: are there any demonstrations on how to use these toy models to predict something in nature, or are they simply for theoretical purposes.


texts: How do proteins and genes participate in learning?

texts:
I am a computer scientist that studies biology and bioinformatics.
In the last weeks, I have been trying to study new research directions, and I would like to deepen my knowledge on the role and behavior of genes and proteins in learning.

By learning, I mean the human process: the information I is absent at time T, and present at time T+1.

I would like to study more this problem, and I am wondering: how do proteins and genes behave during learning?
I have read that proteins that participate in learning are called marker proteins. Is it true? Which role do they have?

Where could I find some resources to study this fascinating problem?

Thank you very much!


texts: How does the matter that makes up the fat of your fat cells ultimately leave your body--following weight loss?

texts:
I'd like to get some clarification on specifically how the matter from the fat reserves of the Adipocyte physically leaves the body.

In other words, if you were to somehow follow every atom in the fat reserves of the cells of a dieting person, then, via what hole would these atoms ultimately exit the body?

Is the answer to this question merely "exhaling through the mouth"? Or do they come out in feces too?

Note 1: This question is not to be confused with the question: "How does mass leave your body in general?" For there are several ways to accomplish this. (e.g. shedding skin cells, cutting off your arm, cutting your hair, sweating, dehydration, liposuction, bleeding, spitting, blowing your nose, etc...)

Note 2: Please see this other similar StackExchange post here:

https://physics.stackexchange.com/questions/2605/how-does-mass-leave-the-body-when-you-lose-weight


texts: Why does the nerve action potential needs potassium?

texts:
When looking at the action potential generation I do not understand why potassium is needed. I know that potassium is used to repolarize the cell. But why are sodium channels and/or sodium pumps not used to push the cell back into its resting potential?

For example in this video at minute 2:00, sodium is pumped in, and potassium out of the cell. But both are positive ions. You get a less negative membrane potential but wouldn't it go faster if the potassium ions stayed in the cell?

Has potassium an extra property compared to sodium that makes it especially suitable for the repolarization step?


texts: Does some form of self organizing map exist in the brain?

texts:
Self organizing maps (SOM's) are an extremely interesting and powerful tool in the field of artificial neural networks. My question is: Does something similar exist in the brain? Or are these systems completely "man made"?
Also, if there are such things in the brain, how do they work?


texts: What is the biggest structure in nature for structural coloration?

texts:
I'm interested in the actual sizes behind structural coloration: I find it fascinating and I think it may have a couple very nice applications.

The problem is I couldn't find anything but vague references about the actual structures' dimensions. Like, the thickness of the walls, their diameter, the height...

I'm sorry about the tags but I couldn't find anything fitting. Is this, like the wrong stackexchange section?

Edit: For what I mean by structural coloration please refer to https://en.wikipedia.org/wiki/Structural_coloration.

  Structural coloration[a] is the production of colour by microscopically structured surfaces fine enough to interfere with visible light, sometimes in combination with pigments. For example, peacock tail feathers are pigmented brown, but their microscopic structure makes them also reflect blue, turquoise, and green light, and they are often iridescent.


texts: What is the use of ampulla in Scoliodon?

texts:
What exactly is the use of Ampulla of Lorenzi in Scolidon?
It posseses eyes for seeing prey, so what is the use of Ampulla?


texts:
I have something in my notes that doesn't seem right.

If I use restriction enzymes on a PCR product how many bands should I see provided I know the restriction enzimes will cut the DNA? If I use two restriction enzymes I expect two cuts then then gel should show three bands. Then, if I use just one enzyme and I know the enzyme will cut just once, then should I expect two bands? According to my notes one band is expected.


texts: Physiological effects of electrical shocks on human body depending on the energy

texts:
When discussing safety of electricity, one usually considers a constant DC or AC current with constant amplitude over a longer time. It is easy to find tables in books or in the web which lists different magnitudes of current and it's physiological effect on the human body. For example this (chest pathway):

If you consider a short time discharge, for example from a capacitor or an inductor, this description no longer applies. For example if you charge a small parallel plate capacitor with several thousands of volts and touch it, nothing dangerous will happen (just a slightly painful sensation). Initially the current through the body will be very high (such that it would be deadly if it was constant), but which decays exponentially in a very short time.

So one needs another scheme to evaluate the dangers to the human body in the case of a short discharge. One simple criterion is the energy criterion where one calculates the energy which may maximally deposited in the human body by the discharge. This is for example used in for electrical safety guidelines for German schools (http://publikationen.dguv.de/dguv/pdf/10002/si-8040.pdf, page 27), where for > 60 volts a discharge energy below 350 mJ is considered as safe.

My question is if there exists also an overview of the effects on the human body for short discharges depending on the energy (for the case of > 60 volt), or even a two dimensional map (one axis voltage, the other one energy).

If so, do you have a reference to the original papers.


texts: Is this statement in agreement with Darwin's theory of evolution?

texts:
Is the following statement in agreement with Darwin's theory of evolution?

  The number of offspring is not related to fitness.

If so, why? This is not a homework assignment, I just want to justify the reason for which this statment is in agreement (which I really hope it is).


texts:
What is the method to estimate the error rate in mtDNA sequencing?

E.g. we are given a profile like this:

16069T 16126C 73G 152C

Is there a method, a table of known values, or any other way to say that there is an x% chance of 16069T being incorrect?

I'm asking because I would like to have a method to estimate the probability of the profile being incorrect. Something like:

Perr = Perr(16069T) X Perr(16126C) X Perr(73G) X Perr(152C)


texts: How was the first ribosome theorized to have been made?

texts: Seeing as ribosomes are what help perform the act of translation itself, and the blueprints for they themselves are in nucleotide sequences, how was the first ribosome theorized to have been made? Also, before there were any ribosome, how was translation theorized to have taken place?


texts: Can growth rate be used as an indicator of fitness in fish populations?

texts:
I would like to calculate selection gradients in order to gain insight into the strength and type of selection influencing my study population.

(see here for review. http://jgking.web.unc.edu/files/2012/06/Kingsolveretal.AmNat_.Mar2001.pdf )

(see here for what I would like too do in the end. http://onlinelibrary.wiley.com/doi/10.1111/evo.12077/epdf).

For this I need an indication of fitness.

My question is this:

Does it make sense to use growth rates (in mm. per year or other) as a "proxy" for fitness?

Thanks in advance for your time


texts: Recombination fraction( frequency) in Homozygotes

texts:
I have a question about the recombination frequency I hope you have time to answer.

Background: If we look at homozygous individual A/A B/B which has been formed from the gametes AB and AB, this individual will in turn have the gametes AB, AB, AB, AB. These are the same as the gametes that were used to form the individual.

My question: Is the recombination frequency 0? Or should we consider the A's and B's as different, i.e like A$_1$, A$_2$, B$_1$, B$_2$. Then we get the possible gametes A$_1$B$_1$ (parental), A$_1$B$_2$ (recombinant),A$_2$B$_2$ (par), A$_2$B$_1$ (recomb). We then get that the recombination frequency is 50 percent (which it should be according to the source given at the bottom). Which interpretation is correct?

Definitions used in my question:

"Meiotic recombination is any meiotic process that generates a haploid product with new combinations of the alleles carried by the haploid genotypes that united to form the meiocyte." (Griffiths et. al, Introduction to Genetic Analysis, tenth edition, International Edition, p. 95)

Recombinants: "Recombinants are meiotic output different from meiotic input." (same book).

Recombination fraction: "Recombination fraction (also called recombination frequency) between two loci
is defined as the ratio of the number of recombined gametes to the total number
of gametes produced." (Shizhong Xu, Principles of Statistical Genomics, Springer, Chapter 2, page 11, 2013).

Furthermore: "When genes are unlinked, they have a recombination frequency of 0.5, which means 50 percent of offspring are recombinants and the other 50 percent are parental types." (Source: Boundless. “Genetic Linkage and Distances.” Boundless Biology. Boundless, 21 Jul. 2015. Retrieved 11 Sep. 2015 from https://www.boundless.com/biology/textbooks/boundless-biology-textbook/modern-understandings-of-inheritance-13/chromosomal-theory-and-genetic-linkage-97/genetic-linkage-and-distances-427-11654/)


texts:
I hope the picture is clear enough, I've found a worm like insect like the one below a little while ago in my shower, and today I found another one. I've never seen something like this. I would say it is slightly bigger than a centimeter.

Location: Netherlands

Why do they come in my shower ?


texts: How is the right amount of nucleotides synthesised during homologous recombination?

texts:
I'm reading about homologous recombination in the context of double-strand break repair. It seems like the trick is that around the break, homologous recombination uses a template duplex to generate some overlap between the broken parts so that the strands can just be complementarily repaired. However, when reading from the template, unbroken duplex, it seems like it's quite important exactly how many nucleotides are generated to form the overlap between the two broken strands. Too little, and no overlap is formed as the broken strands still form two disjoint sequences. Too much, and the broken pieces no longer fit together, there are parts doubled. It's like a puzzle where some pieces describe overlapping regions.

How does the polymerase know to add exactly the right amount of nucleotides?


texts: Can someone identify this snake? Photographed in a home in Los Lunas, NM, USA.


texts: By definition, will some children always be stunted?

texts:
I had a question about stunting i.e. height-for-age. The WHO defines at as any child whose height-for-age is 2 standard deviations below the median height-for-age.

Given this definition, wouldn't there always be stunted children? I must have misunderstood the definition because this seems like one of those challenges that needs to be "fixed" but my current understanding means its sort of unfixable.

Any insight is appreciated.


texts: Can a certain part of human dna can be replaced with other animals dna?

texts: Human DNA consists of adenine, thymine, guanine and cytosine. Can thymine of other animal can be placed with humans thymine?


texts: How is the number of mitochondria in a cell regulated?

texts: How does the cell regulate the number of mitochondria in a cell? What happens when there are too many or too few?


texts: Advice on type of database and software for research on genetic diversity of crops

texts:
for a research project I am evaluating the potential of Robusta coffee genetic resources in the tropic region of Africa. Different ex-situ genetic lines will be mapped as well as chemical, morphological and organoleptic analysis of the coffee beans.
I am looking for a type of database and software that would be well suited for this type of dataset. Are there any genetic database programs out there that allow you to merge other datasets (like plant descriptors or cupping profiles)? Or should I look the other way around and use a database that easily links with genetic fingerprint software?
Thank you,
Robrecht


texts: Can nervous disorders be cured? Will enough research be the answer?

texts:
I have searched every nook of the internet and I couldn't find a clear and to-the-point answer. Well my story is that I am a young BSc student who wants to do research on neurological conditions because as far as my knowledge goes neurologists cannot do anything about ANYTHING, things like dementia and brain damage lead the person to become completely destroyed and then eventual death is what every doctor has to see. As of current.

So I am asking if we can develop eventually effective treatments for let's say OCD or Alzheimer's? Or that will never happen because of other factors in the ecosystem and it's the rule of the nature that some people are just unfit to survive? If that's possible, and about to happen in my life time -- i.e., I can contribute -- I am in. I am gonna get a doctorate in one of the life sciences and start doing something. Like discovering genes, or understanding the pathophysiology, or discovering drugs, whatever I am competent in and able to. I just cannot see people suffer like that.


texts: What does the "cov" mean in a velvet assembler generated contig name?

texts:
A exmaple of a contig name generated by velvet assembler:

NODE_127_length_39203_cov_244.873016

What does cov_244.873016 mean?

It sounds like coverage. Does it mean reads coverage or other statistical description of the contig?


texts: How do insects such as crickets circulate blood through their antennae?

texts: Some insects, like the crickets pictured below, have such slender antennae it seems no blood could fit. How do they get blood through their antennae?


texts: How can a heart of human work if one of its valve is not working?

texts: Yesterday I went to a hospital and heard a doctor say that one of the heart valves of a patient is not working. However, the patient was still alive and was healthy; the patient could walk and talk too. I could not understand it because I have read that all valves of heart are extremely important. I have tried searching on google but all I could find was heart attack problems.


texts: In the vacuum of space would death be instantaneous?

texts:
I was arguing with my colleague about this matter (I'm not going to mention which side I fall on).

Would death be immediate in the vacuum of space? For example, if I was suddenly teleported into the vacuum of space would I die straight away? Or would I experience a suffocating sensation?


texts: What is the point at which abiogenesis is complete and evolution begins?

texts:
Is the minimum criterion for life a single cell?  It seems that self-replicating RNA is not enough, but I don't know.

What would be the most basic cell that could fit this criterion and what cells today would be most similar?


texts: Why is the relative expression in qPCR so low?

texts:
When analyzing different mutations through qPCR I found the $2^{-\Delta\Delta ct}$ value for each mutation. All the mutation have similar values compared to the wild type gene, however one of the mutation has an extremely $2^{-\Delta\Delta ct}$ value. Having $1$ for the wilde type, and an average of $0.9$ for some mutant genes, the exceptional case has a $0.05$ value.

I think one could argue that this mutation deletes a sequence from the wild type gene, but I believe other things can be suggested from this.


texts:
Can someone identify this white colour bird?

Location: unknown (image taken from someone's profile pic).


texts: Estimation of tissue-partition coefficients and clearance for liposomic nanoparticles

texts: I am working on developing a PBPK model for liposomic nanoparticles used to deliver drugs to fells in the bloodstream. However, I do not have any in vivo data or in vitro data. Given only chemical and physical properties like pKa or the octanol-water partition coefficient, how can a get a relatively accurate estimate of the tissue:blood partition coefficient, as well as the renal & metabolic clearance?


texts: What is the surface area of the cardiovascular system?

texts:
In this question says:

  An adult human has been estimated to have some 60,000 miles (96,560
  km) of capillaries with a total surface area of some 800–1000 m2 (an
  area greater than three tennis courts).

But the question is about the length and only mentions area in the body not the title, and the answers don't cite the area.


texts: What are the essential criteria for sleep in living organisms?

texts:
I was reading this fascinating article about how sleep evolved before brains, and it got me thinking "can plants sleep" and "what is sleep anyway".
A line in the article states:

Studies by a team in South Korea and Japan showed that the hydra
periodically drops into a rest state that meets the essential criteria
for sleep.

But after looking around I am unable to find the "essential criteria for sleep" - Before I am able to answer questions like "can plants sleep" I think I first need to understand what these essential criteria for sleep actually are.
Can anyone here help me out?  Many thanks in advance.


texts: Does the brain have a clock and can it be sped up?

texts:
Before i start, I'm an engineer and have very limited knowledge on biology and neuroscience. My question is, does the brain have a clock like a computer where it has a set processing speed?

Clocks in CPUs can be overclocked to increase processing speed and I am wondering if the brain has something similar. The average human reaction time is around 0.25ms, Is it possible to react faster to stimuli and not only react but perceive surroundings faster than others. What I mean is while everyone perceives 1 second to be 1 second long, Is it possible to focus and stretch 1 second out mentally to 3-5 seconds and move/think/react faster as a result?

How could this theoretically be achieved too? BCI headset, Chip implant in the brain, serum or chemically?


texts:
I live in Dayton, Ohio.  I've found large-ish ants in my kitchen, and I'm wondering if they're carpenter ants.
I realize there's been a few questions about carpenter ant identification, but in my defense, this one comes with video: https://youtu.be/HGWertws0oo
Picture, with penny for reference:

See the video for better shots (mixed in with bad shots, haha).
Is this a carpenter ant, or something more benign?


texts: Were dinosaurs 'hot-blooded' or 'cold-blooded'?

texts: Were dinosaurs hot-blooded or cold-blooded? NOTE: The popular term 'hot-blooded' means having an internally maintained average body temperature, which is generally more than that of the surroundings, despite the variation of the temperature outside.  And obviously 'cold-blooded' is the opposite of 'hot-blooded'.


texts: Help identifying a bug which looks like a housefly and mosquito hybrid

texts:
I'm from Kochi, India (southern part of India). I found this bug inside my house , it was about a centimeter long . But how can such an hybrid be possible. (It was raining before I found it).
1: https://i.stack.imgur.com/Dlyio.jpg


texts: Wondering what kind of bug this is found outside


texts: Is there anything that can tell me precisely how the cross sectional area/radius of a snake changes over length?

texts:
I am trying to 3D model a green anaconda which I thought would be simple, then I realized there is actually this very gradual change in thickness from a minimum around its neck to a maximum somewhere in the middle then to another minimum around its tail.

Is there some kind of specific terminology or archive I can look up to get precise measurements? Regular google searches aren't doing it and there is a high amount of variation in this thickness gradient between species.


texts: Braquio-abduction illusion explanation and references

texts:
Illusion: Lying down on a hard flat floor move arms up and down (as when doing a snow angel) while keeping them touching the floor. While repeating it a few times the floor begins to appear concave, with the deepest part where the arms as perpendicular to the rest of the body.

Questions: What is the origin of this illusion?

My guess: I think it might be related to the arms being harder to extend towards the back when they are perpendicular to the body than when they are at other angles.

Note: The name above is only the way I like to call it. I found this illusion when I was a kid, but I am sure others might have noticed it as well.


texts: Is there an evolutionary explanation for the black spots around a pandas eyes?

texts:
I couldn't seem to find one elsewhere, at least not with a scientific source.

It would seem as it's quite a striking feature there would be an advantage it would infer.


texts: What does fail-safe mean in transmission at electrical synapses?

texts:
I'm reading a book named Neuroscience:Exploring the Brain recently. And in the chapter about synaptic transmission, it says "Transmission at electrical synapses is very fast and, if the synapse is large, fail-safe." So what does fail-safe mean? And why is that transmission fail-safe when the synapse is large?
And when is comes to EPSP, it also mentions that "The neuromuscular junction has evolved to be fail-safe; it needs to work every time, and the best way to ensure this is to generate an EPSP of a huge size." I don't understand the meaning of the word and the whole sentence.


texts: How to estimate the DNA density in human sperm head?

texts: I have got an estimate of sperm head volume from internet.Like consider it as a disk of order 4-5µm. Now I wanted to find the DNA density in the sperm head. How to find that?


texts: Can a person's body produce enough electricity to break a wristwatch?

texts:
I know of someone who cannot seem to wear watches without the battery dying or something else about the watch going haywire. this person was told it is because their body is producing too much electricity and that by putting nail polish on the reverse of the watch to block the current the watch would work.
This was tried and it actually worked. My question is, is this a real thing? I couldn't find a legit discussion of this online.


texts:
This question is similar to a previous question, but is not the same.

I was told, you are born with a bacteria in your digestive track that are made by the body. Can a body in development create it's own bacteria from nothing? Also said by the teacher the first time you take an antibiotic it is gone forever?  Can a body in development create it own bacteria from stem cells? Is there such a bacteria, can it be cultured and re-introduced into the body?


texts: I have a knowledge that when you woke up and see green light it increases your sight power. How it does so?


texts:
Brief question:

I have performed a double digest with heat inactivated restriction enzymes with no star activity. I usually purify the DNA (PCR inserts and linearised vector) using a kit or gel electrophoresis but today I don't have time for it.

Is it okay to freeze (-20*C) the PCR inserts and linearised vector following heat inactivation of the enzymes? After a week, I will thaw, purify and perform ligation on these products.

Thanks!


texts: Mendelian genetics - How can we infer the number of genes in play in this scenario?

texts:
So this is a practice question I got from school but I kinda lost here. So the question is:

  In    Drosophila , four new recessive mutations have been found all
  of    which produce purple    eye colour.

  Mutations 1, 2 and 3 are all found to be X-linked whereas mutation
  4 segregates with one of  the autosomes.

  Crosses   between females heterozygous for either mutation 1 and
  mutation  2, OR mutation 1 and mutation 3, and wild-type males have
  been performed.

  1st cross:    no  wild-type   males were  observed in 7500
  male  progeny.

  2nd cross: two    wild-type males were recovered among 1510
  male  progeny.

  What is   the minimum and maximum number  of  genes   identified  by  these four mutations    given   the above   data? Explain your reasoning.

  How   would   you go  about   determining the actual  number  of  genes?

My best guess is either mutation 1 & 2 OR 1 & 3 must be allelic because we didn't observe any WT on the first cross. If it's not allelic, there should be complementation there and we will observe a WT phenotype.

I'm not sure what "OR" means.

I'm not sure why only 2 WT males were recovered among 1510 male progeny. I think it has something to do with recombination, but can't really find out what the gene configuration is to obtain that result.

And the way to determine the actual number of genes is by performing a complementation test, right?

Really appreciate if someone can help me / give me some hints here. I'm really lost!

Thanks in advance :)


texts: Can the sensory neuron network and the motor neuron network be considered separate networks?

texts:
I am reading up on the nervous system using wikipedia and trying to interpret one infographic on this page:

I've always thought of the human nervous system as a singular network of neurons. This diagram however makes a distinction between 'Motor neurons' and 'Sensory neurons'.

Can the sensory neuron network and the motor neuron network be considered seperate networks?

Indirectly they will definitely be interconnected (because of impulse-response relations), but physically, are they connected or disconnected?

Or are there more?

It is very well possible that I am missing some knowledge to make this question make sense.


texts: How many citric cycles are (can) working at the same time in one mitochondria?

texts: Does one mitochondria has a limit of how many acetyl-CoA it allowes within his inner membrane to produce NADHs? And if, lets say 100 acetyl-CoA are in a mitochondria are they simultaniously running through their citric acid cycle or has the mitochondria also a limit for the amount of running citric cycles at the same time?


texts:
I understand that muscles do anaerobic metabolism, specifically, "lactic acid fermentation", which I understand produces lactate. I'm not asking about that process.

What chemical conversions are involved , and what's the name for the process, when the muscles use lactate as an energy source?

I'm aware that it can happen as    This paper, is tellingly and usefully titled, "Lactate as a fuel for mitochondrial respiration"   (though I only have the abstract)

And aside from that paper i've also heard

  "lactate produced during exercise can be reused as fuel by the muscles
  by turning it into glucose".

But I'm interested in what chemical conversions are involved


texts: Difference between cytospin and metaphase spread protocol

texts:
I would like to know what exactly is the difference between cytospin and metaphase protocol. I'm a data scientist helping a medical lab and I receive images of cells with particular types of DNA. The DNA comes stained with DAPI. However, other times, if the scientists can pinpoint a particular gene in the DNA, they stain it with FISH. I asked the following: When I separate the image into the separate color signals (RGB),  will I see the DNA in both the green gray scale images and the blue gray scale images, I was told that you can but it won't be that clear since cytospin spread protocol has worse quality than metaphase spread protocol.

What exactly is the scientist referring to? I looked at some articles but the methodologies are a bit beyond me and it would be helpful if it can be answered in broader terms.


texts: What are these tiny, swarming, jumping bugs?

texts:
I built a small plywood box in my yard (on Long Island, NY, USA) for some stray cats about a year ago. I didn't bother waterproofing the box, and so over time the box has gotten damp.

About two weeks ago I started seeing small reddish brown bugs on the box, and in the food/water dishes near the box. Can anyone help identify them? Here are some details:

there are 100s of them
they're really small, the biggest ones are about the size of a sesame seed
they jump when disturbed, usually in an upwards direction
they don't seem to go on the cats
some venture 2-4 ft from the box to find food dishes on the ground (concrete patio)
they drown themselves in the water dish by the dozen
they're more active when it's warmer (~ 45°). When it's cold (25-35°) they mostly hide somewhere

All of this makes them sound like fleas,  but they're not fleas -- they don't jump as high or have the flat body of a flea. They actually look like arachnids. OK that makes them sound like baby jumping spiders - but I've seen baby jumping spiders at work, and these look different (they're reddish brown, not black, and they don't jump in an "across" direction, they jump upwards, kind of randomly). Maybe they're a different type of jumping spider, but why haven't they moved on? Why are they taking up residence on the box, instead of spreading out and going their separate ways like baby spiders usually do?

They're are about the size of a sesame seed so it's hard to get a good picture.

EDIT: new picture collage:


texts: Determination of Ageing by ECG inclusions/exclusions?

texts:
I am studying ageing and considering ECG signal because of its high sensitivity in theory (escardio). Some factors

Sensitivity
Gender
Medical treatment
...

Benchmark:
RTG dental + wrist uncertainty $\pm$2 years. Etc tooth washing, and hardness of drinking water affect much the dental health. Exposure to the ionisative radiation is problematic so less radiative approach would be nice.

ECG

Cardiac characteristics by ECG signal in power spectrum, having greater uncertainty than RTG dental 2016 because no sufficient exclusions/inclusions and too much exclusions covering data segments of autonomic nervous systems.
Processes to be excluded from the ECG signal

respiratory process
heart beat itself
some cellular-tissue processes

Some cellular-tissue processes

ROS determination ...
some genes about lipids and their characteristics with ageing in metabolic syndrome
decreased replication of cellular ageing
DNA replication stress, genome instability and aging
MICCAI 2012 Workshop on Novel Imaging Biomarkers for Alzheimer's Disease and Related Disorders

Low-Cost Targets

internal physiology of cardiac events in association with ...
cardiac and brain imaging makers related to substance use disorder, HIV, and aging (Stanford)

How can you determine aging by biochemical test and imaging?


texts: It stays the same color when ripe. It's about the same size as a pear. Grows in sub tropical climate of Meghalaya, India.


texts: Why are Ramachandran angles of first and the last amino acid not necessary to define the full 3D structure of a protein chain?

texts:
I have come across an online ppt slide of the bioinformatic algorithm where it is said that first and the last amino acid Ramachandran angle is not necessary to tell all its internal coordinates. Is it really not necessary for any simulations while predicting the 3D structure of proteins? For instance, if we have a protein chain of N amino acid sequence, there will be 2N dihedral angles. Of which we need to specify only the 2N-2 (apart from the first and the last amino acid dihedral angles) dihedral angles. Why the two angles are ignored? Let's assume all the bond angles and bond lengths are provided for the entire chain.
I have seen this statement in the following ppt, slide number -9, titled representation of internal coordinates, under bullet point 3.
https://www.cs.umb.edu/~nurith/cs612/Manipulation.pdf


texts: Evidence that Attention Deficit Hyperactivity Disorder (ADHD) is caused by too much cellular ATP?

texts:
The question is pretty simple — it's just a theory that I remember my biology teacher mentioned long ago and for years now I've wondered about it without ever asking.

Some people with attention deficit hyperactivity disorder (ADHD) report "energy bursts" with the feeling of needing to explode while sitting still. Further, they report that movement, like vibrating the legs, can help suppress this feeling.

Is there any reason to think that symptoms like these might come from too much ATP inside cells?


texts: What is the trigger of pollen tube formation when the pollen is on the stigma?

texts:
What is the mechanism of pollen tube formation when the pollen is close to the stigma ?

Is it because of chemotaxis? In other words, is the growth triggered by some chemical substance that is released by the stigma?

We have learnt that on a stigma of a flower, you can sometimes find pollen of other plant species. Would these pollen grains also form tubes in response to a possible signal from the stigma of a different species?

EDIT :

So in this experiment we put pollen grains in 2 bottles which contained all chemical substance required for the formation of pollen tube.

In bottle 2 we observe that all pollen tubes are oriented to the stigma! If it really is some kind of chemotaxis then what is the chemical substance that causes this?


texts:
How are shrimp and other animals able to not be crushed by the 1000x greater pressure at the bottom on the Mariana trench?

Wiki says the trench is home to "large living creatures such as a sole or flounder about 30 cm (1 ft) long, and shrimp"

I understand natural selection, but what features has evolution "selected" that enable soft flesh and bones to not be instantly crushed like our own skulls would be at that depth?


texts: Do all dicot seeds have endosperm? Will they be retain as they grow and what are the difference with its monocot counterpart?


texts: Maintaining purebred pedigrees and how to lessen chance of getting disease?

texts:
Many breeds of dogs are known for a high incidence of genetic disorders. German shepherd and Saint Bernard dogs are predisposed to developing a crippling condition called hip dysplasia.

Q: What advice would you give to dog breeders who want to maintain their dogs' purebred pedigrees, but also want their dogs to be as healthy as possible?


texts: In DNA repair, how is it determined which strand contains the error?

texts:
DNA replication is more accurate than transcription (or RNA replication) because mechanisms exist for proof-reading and repair of DNA, but not for RNA.
Consider a segment of a DNA strand, AGTC. Its complement is GACT. Now suppose its complement is mutated to TACT — the DNA repair system will replace the wrong T by G. Why isn’t A in the original strand replaced by C? How does the system determine that the first strand is correct and its complement is incorrect?


texts: Why don't humans typically drink human milk after infancy?

texts: Does any human culture routinely do this? Typically taboos have some evolutionary basis. So what would that be? Does any mammal drink the milk of its own species, besides nursing?


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


texts: How do you interpret the resulting bands of gel zymography?

texts: I would like to clear up some things for gel zymography. I understand that bright bands show proteolytic activity. But which molecular weight do these bands correspond to? Is it the weight of the active enzyme or is it the weight of the digested substrate?


texts:
I have encountered comparisons of the Michaelis-Menten constant ($K_m$) a few times. Generally speaking if the $K_m$ of an enzyme is higher, then its affinity to its substrate is lower. How does this make sense?

Maybe the maximum velocity ($V_{\mathrm{max}}$) of higher $K_m$ enzymes is higher? Then of course, $K_m$ can have a higher value. Because $K_m$ is the substrate concentration at half of the $V_{\mathrm{max}}$. But I think we cannot determine affinity with $K_m$.


texts: What are chemical candidates for replicator molecule?

texts:
I have read Selfish gene by Richard Dawkins and idea is that at random some molecule was synthesized that had a property if there is enough 'materials' to construct copy of itself - it would. And then it made bunch of it's copies and then copies started mutating and eventually we got to DNA in us.

In his book he never says what actual molecule is original replicator.

What are chemical candidates for original replicator molecule?


texts: Difference between protozoa, protists, protoctista?

texts: Are protozoa, protists, protoctista different classes of organisms or simply different names for the same?


texts: Why people have less hair than other primates?

texts: Well as you can figure out, most primates such as monkeys, gorillas and chimpanzees, have all their body covered with fur. As we know they are evolutional "relatives" to us humans, but we dont have much hair(only on the head,on the armpits, on the groin, etc.). I would like to know why this "evolution" happened in a such brief era and why.


texts:
I had a quick questions on the size limitations of a CRISPR guide. More specifically on the shorter end. Can I make a guide that is say 7-10bp and still have an active complex? I transfect using an RNP system.

Just curious.

Thanks in advance.


texts: Does animal based food contain molecules that behave like dietary fiber for humans?

texts:
I have read that dietary fiber is beneficial to human health in many ways, for example that it can help to reduce risk of colorectal cancer. However, when I look at nutrition labels on food it seems that only plant based food contains fiber; animal based food (meat) contains none.

What exactly is meant by fiber? I looked it up and found that there are actually a variety of definitions. The CODEX Alimentarius Commission has recently come up with an updated definition described in a paper by Jones. The definition states that “dietary fiber means carbohydrate (CHO) polymers with ten or more monomeric units, which are not hydrolyzed by the endogenous enzymes in the small intestine (SI) of humans”. Further more their definition "includes resistant oligosaccharides, resistant starch and resistant maltodextrins" when a footnote of the definition is included.

Jones points out that some definitions of dietary fiber do not explicitly rule out dietary fiber from animal sources. So does meat or animal based food contain any carbohydrate (CHO) polymers that are not hydrolyzed by the endogenous enzymes of the small intestine in humans?

An earlier version of this question was posted in my blog.


texts:
I was heard that this combination first Gonoline and other culture another culture on Euroline is good one.

What is the benefit of using Gonoline-Euroline in combination?


texts: What is it called when one human eye is seeing brighter color than the other?

texts:
What is the name of a phenomenon where one of the human eyes is seeing brighter/more saturated color than the other? I can observe the same object from the same position while alternating which eye is closed, and there's a visible difference in the saturation of color. Like one color is more pale than the other.

Here's an example of what the difference looks like between image perceived by two eyes:


texts: Basic Molecule Editor for use in journals / theses?

texts:
My background is Geosciences and Physics and I am going to study water and biomolecules in the Autumn.  I was reading a PhD thesis about peptides and peptoids by someone in my research group and I had a really basic question abouting the drawing program that they would have used to create molecular diagrams.  I found this link https://en.wikipedia.org/wiki/Molecule_editor and it looks like a good starting place but could someone recommend a default app for creating drawings like the ones below?

Thank you!


texts:
I received a gift that is a jug of Pure Mexican Vanilla. Having never dealt with large quantities of vanilla, it made me curious as to what would happen if a person had too much vanilla.

I understand that the alcohol has a higher toxicity rate and is probably more fatal than the actual vanilla itself, but I'm curious as to what ratio of mass of pure vanilla to mass of the human would be considered fatal.

Also, what is the physiological effect of a vanilla overdose as it pertains to inhibiting critical bodily functions? That is -- specifically what about a vanilla overdose would cause fatality?


texts: Will neurons die if they are inactive for a long time?

texts: We know that when muscles are not used they atrophy. Does something similar also happen in neurons if they do not receive any stimulus?


texts: Do findings on promoter methylation of the serotonin transporter gene and amygdala activity contradict the established view of serotonergic function?

texts:
In this article http://www.nature.com/neuro/journal/v17/n9/full/nn.3778.html it states that

  Increased promoter methylation of the serotonin transporter gene predicted increased threat related amygdala activity.

I'm finding this somewhat difficult to understand. Increased promoter methylation would imply that the serotonin transporter gene is less expressed, so less serotonin is taken up by the presynaptic neuron, leading to increased serotonin levels in the synaptic cleft. Surely the increased serotonin levels would lead to decreased amygdala response to threat? After all, selective serotonin reputable inhibitors (SSRIs) are used to treat anxiety disorders and depression by reducing uptake of serotonin and increasing serotonin levels as well. It seems like these two are suggesting two contrasting effects for the same cause?

I would be grateful if someone could point out where I have misunderstood. Thank you in advance :)


texts: Why are plants unable to take up Phosphorus directly in their organic form like Phytic Acid?

texts:
I am researching acquisition strategies of phosphorus by decidious trees. I am reading a lot that plants take up nutrients as their inorganic form. In the case of P according to literature this is mainly $H_2PO_4^{-}$ (Schachtmann et al. (1998), Hinsinger (2001), Buchanan (2015)). So far so good...

In forest soils for instance, Phosphorus is much more concentrated in the form of phytic acids (derivates of inositol hexaphosphate), which are organic acids. Not in any paper which I have read before, it is stated why organic P is not taken up directly, only that it is enzymatically cleaved before it is taken up as inorganic P. The best, which I have found so far is that

  Although organic P ($P_o$) is present in soil solution at higher concentrations than inorganic phosphate (Ron Vaz et al., 1993; Seeling and Jungk, 1996), direct uptake of ($P_o$) compounds by plants is considered unlikely. --Hayes et al. 2000

My problem - or rather limited understanding - is that I wonder, whether plants in fact do have the ability to take up nutrients directly as organic forms.  I would prefer not to take the presence of enzymes as a proof that organic P cannot be taken up directly by plants. Also phytate seems to be used in plant tissue for storage of P.

Unfortunately my understanding of biochemistry is limited, that's why I'm pretty sure that I am missing some basic facts, which could clarify the situation. My best guess so far is, that organic sources of P are simply too big to pass through the cell wall.

So my question is: are there certain structural or biochemical barriers or obstancles, which would prevent plant roots from absorbing organic P directly, or is it for some reason better to cleave phytates "outside" the cell?

I would be very happy if you could point me in the right direction. Thanks in advance

Sources:

Buchanan, Bob B.; Gruissem, Wilhelm; Jones, Russell L. (Hg.) (2015): Biochemistry & molecular biology of plants. 2. ed. Chichester, Rockville, Md.: Wiley Blackwell; American Society of Plant Biologists.

Hayes, Julie E.; Simpson, Richard J.; Richardson, Alan E. (2000): The growth and phosphorus utilisation of plants in sterile media when supplied with inositol hexaphosphate, glucose 1-phosphate or inorganic phosphate. In: Plant Soil 220 (1/2), S. 165–174. DOI: 10.1023/A:1004782324030.

Hinsinger, Philippe (2001): Bioavailability of soil inorganic P in the rhizosphere as affected by root-induced chemical changes: a review. In: Plant Soil (237), S. 173–195.

Schachtman, Daniel P.; Reid, Robert J.; Ayling, S. M. (1998): Phosphorous Uptake by Plants: From Soil to Cell. In: Plant Physiology (116), S. 447–453.

https://en.wikipedia.org/wiki/Phytic_acid


texts: Software recommendation for protein in electric field modeling?

texts:
I'd appreciate a suggestion for software to compare models of two proteins in an alternating electric field. The more detail, or perhaps direction towards an existing and similar paper, the better. Right now I'm particularly interested in comparing rotation of the proteins as a result of the field. The first protein, tubulin (1TUB), will be modeled as a dimer while the second, septin (2QAG), will be modeled as a trimer.

The electric field will consist of a 200Khz field at 1.5V/m with a spatial resolution of 300Ax300Ax300A. I believe that I will only need a temporal resolution of 1.5 milliseconds for 10 solutions(?) per cycle for 3 cycles in the 200Khz field (particularly unsure of this part).

In terms of computational power I have access to two 7870 Radeon GPUs, but am also interested in cloud computing if that's not enough.


texts: Non-cumbersome respiration sensor for sleep study?

texts:
I'm working on a project where I collect ECG signal from multiple volunteers, derive ECG derived respiration(EDR) from the timestamped ECG signal and calculate the cross correlation between EDR and Respiration signals collected from NeuLog device which is treated as reference respiration signal. The problem is that the NeuLog moniter, although widely in use for monitoring respiration, is very cumbersome and uncomfortable for the volunteers to wear and restricts breathing. Is there any alternative respiration monitering devices which doesn't have to be strapped around the chest and less cumbersome to wear?

The following are the other requirements.

Respiration signal should be time stamped(to synchronize with ECG signal).
Minimum Sampling rate of atleast 5sps.
Should collect data offline for atleast 10 hours in single charge of the battery.

I found this device which seems to be more comfortable than NeuLog but it is not clear whether it measures only respiration rate or can also log Respiration signals along with timestamps.

If anyone knows any alternative products meeting the above requirements, please do share the details.


texts: I'm having some trouble understanding the concept of ancestral allele. What exactly does it mean? What does it have to do with Identity by descent/state? What does it have to do(if anything) with SNP's? Also, how is the concept useful in genetics/evolution? I've tried reading these up on various websites, but I'm not satisfied with my understanding yet.


texts: If eukaryotic cells can survive in extreme conditions, then why are their still prokaryotic organisms?


texts: Why do we perceive colour? (i.e., distinct values?)

texts:
This is a question I often asked myself, but never really found a satisfactory answer to. It may be that I always went about it from a wrong starting point because the question is induced by physics. But I think an evolutionary perspective may be the most satisfactory one to explain this.

Humans and other animals had much to gain from differentiating not only dark and light but also colors to identify edible things, or threats etc. For this purpose we developed multiple types of cone cells. But what reason is there to not perceive light as we perceive sound, in a spectrum? We could easily distinguish said things by just knowing how high or low the light frequency is (or for that matter, what the spectral 'fingerprint' of specific objects is). Why differentiate between an - albeit big - array of colors?

Or, to go one step further, why did we need an extra type of cone in the middle, the yellow-green wavelength? Is there an evolutionary reason? I'd settle for using the three more or less distinct cone sensitivities as explanation that the brain just has enough information to arbitrarily differentiate these into very discrete cognitive signals.

But evolutionarily, there has to be a purpose, so that one of the questions is the right one. The colors must bring something to the table. Or not?

Thanks in advance. I am also grateful for anyone nitpicking my arguments, because it always helps.


texts: How to compare diversity between different ecosystems?

texts: I've used the Shannon Wiener Diversity Index for a single ecosystem (species as categorical variables). Do you know any alternative indices, especially ones that compare diversity between different samples/ecosystems ?


texts:
I have read in some papers about the layers L1-L5 of the brain (e.g. in this paper). I could not find a definition of these layers. I have found information about the layers V1-V5 in the visual cortex.

Where exactly are L1-L5? And do these definitions vary across mammals?


texts:
I collected some bladder snails several months ago. While checking them out one day, I noticed that they were now infested with worm-like ectoparasites.
Appearance and behavior
Here's a picture of a snail with a bunch of the worms hanging off of it's head, where they tend to congregate. I've also circled one of the worms crawling along the glass.

I sampled some of the worms and took a look at them under a microscope. Here's a video ("Video 1" below) I recorded of one of them crawling around. They have some notable characteristics.
First, they appear to have some sort of sucker mouth.

Second, they have some interesting "legs" tipped with hairs (?) at the ends of their tails. Here's a short video ("Video 2" below) of a worm writhing around that shows them off a little better than pictures do. They appear to be in pairs of two.

Animated clips from the linked videos:

 Video 1 (left) and Video 2 (right)
The length of the worms ranges from 1-5 mm (edit: they get larger; see below).
Update: After keeping infected snails for a while longer, I believe that these worms only parasitize bladder snails when the worms are young (within the aforementioned size range). Larger, adult worms appear to be free-living and growing up to 1-1.5cm, and will actually crawl away when snails disturb them. Here is a picture of an adult specimen (along with some smaller ones), no microscope required:

Here's a much better picture of the hair-like legs, of which this adult specimen has numerous pairs:

Lastly, here's a very interesting detail: These worms are highly specialized, and do not seem to affect ramshorn or pond snails, which I have numerous of in the same tank, in the slightest. It's only the bladder snails that end up infested.
Location
These snails were gathered in Canada, in a still-water area connected to the Oldman River. The river is accessible by cows and deer.
Reproduction
I have witnessed the snails shedding tons of cercariae into the water, which eventually disappear after a couple of hours (reinfect the snails?). I'm not sure if those are related to this worm, or if the snails are also infected with some other type of fluke.
Update: I now believe the aforementioned cercariae are unrelated to the worm in question. I managed to record an adult worm releasing numerous live young, which resemble tadpoles (trochophores?):

I've recorded a video of the worm giving birth that can be viewed here (left image below). The young seem to be stored in chambers inside of the parent, and then are pumped through the body and out the back end. While the young appear to be still in the video, some of them are quite active (right image below).

My theory at this point is that the young penetrate snails, grow inside of them, emerge and hang onto the host for a while, and then eventually dismount as free-living adults. Adult worms seem to be independent, while smaller worms hang off of the host the snail (feeding off of it?) until they're large enough to live freely.
Treatment
I would like to eliminate these worms if possible (I can't gather more snails any time soon, and they eventually kill off smaller snails). My first attempt was dosing with praziquantel, which is supposedly effective against flukes while being snail-friendly. Unfortunately, three days later, one of the snails died, and the worms appear to be unharmed.
Update: I gathered some more snails, and attempted praziquantel once again. While it did not harm the snails, it also continued to be ineffective against the worms. I have been experimenting with Seachem ParaGuard, and the results seem to be positive for minor infestations, but not against fully mature worms.
Conclusion
After some research, my best guess is that they're trematodes from the class Digenea-- They appear have sucker mouths, can parasitize snails exclusively, can have a free-swimming form, and can shed cercariae. That said, I'm not terribly confident, and would ideally like to be able to identify them more specifically.


texts: What is this spider spinning a bright green web?

texts:
Here is the picture of it I took with my phone while I was out working:

Here is a close up:

Location: Texas (winter).


texts: What is the identity of this fruit/tree found near Berkeley, California, USA?

texts:
Please help identify this fruit/tree found near Berkeley, California.

The tree had no leaves. The fruit looked like a pear from far. It has no flesh. When the outer skin is peeled, the seed looks like a large avocado seed. Very little smell from the fruit/seed not a bad smell and not an appetizing smell as well.

Could this be a Yellow Buckeye?


texts: Does your iris color have an effect on your vision?

texts:
I've always wondered if having different iris colors, (eye colors) may have any advantages or disadvantages on ones vision. Specifically regarding the effects of light.

Personally, I have troubles being out in the bright sun without sunglasses. My girlfriend on the other hand does not share this issue. Coincedentally my eyes are a light blue and hers are brown. After realizing this, I began to notice a trend when it comes to blue eyed people having this same issue.

So, on a bright day, does a person with blue eyes have a higher sensitivity to the light than their darker counterparts?  Thank you.


texts: Is it possible to identify a particular gene sequence from next gen sequencing techniques (especially RNA-seq )?

texts: I have to check the expression of a gene in a fish whose sequence is not known in the fish in question. Sequence is known in an another fish (zebrafish) but the gene has 10 isoforms. The genome of fish in question is not sequenced, however RNA-seq data is available. I have no knowledge of RNA seq data analysis. Is it possible to know the sequence of gene of interest from this RNA-seq information?


texts: Is the suicide of a moribund individual to be considered group selection?

texts: When a moribund individual commits suicide (e.g., Refardt, Bergmiller & Kummerli, 2013; http://rspb.royalsocietypublishing.org/content/royprsb/280/1759/20123035.full.pdf), is this to be considered group selection?  It could be considered costly to the individual, since the individual commits suicide and, therefore, loses reproductive opportunity.  And it occurs to the benefit of the group, by saving resources for the group and sparing it susceptibility to infection.  Is this group selection or does group selection require an intentional formation of a group?  If not, what else is necessary for this to be an example of group selection?  (Thank you.)


texts:
I just watched a video of a small desert fox (fennec) that toys and eats a scorpion. Although I am unsure of the exact type of scorpion, it is apparently quite able to sting. Another online instance of the same video states that the scorpion is Androctonus Australis. Not only is this breed severely venomous and claiming, as its name suggests, human lives every year, but it is also well armoured. You can hear it when the fennec chews on it...

Fennec Fox eats Scorpion

So, my question, which might be stupid: how can this fox take the scorpion in its snout again and again? I notice that it lets the scorpion go many times. Is it able to avoid being stung? Is it extremely resistant to venoms? I read in the Wikipedia article, that it eats insects, but was unable to find out more!

I was able to find some information about hedgehogs and snake venom, but nothing similar about canines. In the case of hedgehogs, a partial immunity is apparently due to a protein called erinacin in its muscles.

After a user kindly corrected my spelling, I found some comments beneath YouTube videos, claiming it was nearly immune to scorpion venom. Sadly without additional information.


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


texts: The genetic code and the effect of point mutations on proteins

texts:
I was asked a question, "Considering degenerate and non ambiguous nature of genetic code, Why is that certain mutations don't disturb the protein synthesis leading to synthesis of functional proteins where as certain mutations cause synthesis of non functional proteins or diseased proteins?"

My argument was that according to Wobble hypothesis, the tRNA carries anticodons that have A,U,G,C,I where I is inosine (sugar phosphate with hypoxanthine) that can bind with A,C,U of the codon and also G binding with U and vice versa is possible. Then, I gave the example of serine -AGU- whose anticodon is -UCI- for instance and after mutation say, -AGU- becomes -AGC-, it still codes for serine and -UCI- stills agrees to bind with -AGC- giving us serine as before and hence no disturbance is brought up leading to synthesis of functional protein. But suppose -AGU- got mutated to -CGU- , then the anticodon -UCI- no longer can bind with the codon and hence another tRNA molecule with anticodon of that of arginine gets attached and hence leading to interruption in the amino acid sequence which ultimately leads to non functional protein.

But my professor disagrees with my argument and says I am not clear with the concept. Can anyone please help with where I am going wrong ?


texts: Is the serum concentration of calcitriol different at different times in the day?

texts:
Given that calcitriol has a relatively short half-life in adults it would be possible that the serum concentration is at different times of the day different if it gets produced in different quantities at different times of the day.
Is this the case or is the level relatively constant over the day and doesn't follow a daily rhythm?


texts:
A search following a recent news item led me to a CDC Morbidity and Mortality Weekly Report for 23 March 2020 which says in part:

  SARS-CoV-2 RNA was identified on a variety of
  surfaces in cabins of both symptomatic and asymptomatic
  infected passengers up to 17 days after cabins were vacated
  on the Diamond Princess but before disinfection procedures
  had been conducted (Takuya Yamagishi, National Institute of
  Infectious Diseases, personal communication, 2020). Although
  these data cannot be used to determine whether transmission
  occurred from contaminated surfaces, further study of fomite
  transmission of SARS-CoV-2 aboard cruise ships is warranted.

Identifying bits of RNA does not imply a surface is infectious and that's not what I am asking about here.

This reminded me of answer(s) to Was 14,000+ year old DNA “laying around in cave dirt” protected from degradation, or is it just naturally this robust? which explain that small fragments of DNA can be quite stable in some environments; in some places on Earth the DNA in the soil can be ten thousand years old.

Question: Roughly speaking how stable are short sections of single-stranded RNA in exposed environments compared to double-stranded DNA?

The answer is likely to contain "It depends on..." as did the answer to the DNA stability question, I'm primarily interested in the differential stability between the two.


texts: What determines the sex of hybrid offspring?

texts:
I'm aware of the usual definition of Haldane's rule, which says that, if the offspring of inter-specific hybrid offspring are sterile, then the sterile offspring will be of the heterogametic sex. That is, for example, females in birds, and males in mammals. But I'm a bit confused. This implies that non-sterile hybrids are also produced, which rarely happens.

So, I have two questions, please:
 1. Does Haldane's Rule really mean that only offspring of the heterogametic sex are produced?

And 2. If so, please account for the exceptions. Crosses between Golden Pheasants and Lady Amherst's Pheasants regularly produce female as well as male offspring, as do crosses between Ring-necked Doves and Barbary Doves. Thanks!


texts: Why animals can move and plants cannot in general?

texts:
To clarify, I think the answer should be able to explain:

What are animals?
What are plants?
What's the difference between animals and plants (How do biologists differentiate them, if they differentiate them by moving ability of course it's simple, but we know they don't)?
How do those differences affect their evolutionary paths so that most animals can move around and most plants cannot? I know there are exceptions, but that's just the exceptions that show the rule.


texts: What is the pH of cytosol? And plastids?

texts:
My teacher ask this question, and I answered 7 to 7.4, but she said it's wrong.
I read a lot and found the same answer (wikipedia)
I'm here asking for confirmation of this and the pH inside & outside of the tilakoidal membrane.


texts: Is it correct that Green color gives rest to our eyes compare to other colors?


texts:
The NPR News article and podcast Getting Fire From A Tree Without Burning The Wood begins with

A scientist walks up to a cottonwood tree, sticks a hollow tube in the middle and then takes a lighter and flicks it. A jet of flame shoots out from the tube.
It seems like a magician's trick. Turns out, there's methane trapped in certain cottonwood trees. Methane is the gas in natural gas. It's also a powerful greenhouse gas.

and describes the discovery that quantities of methane have been observed to be produced within cottonwood trees.
There is a video of the methane tapped from a tree being set on fire.
The article continues:
"The wood in this particular species naturally has this condition called wetwood, where it's saturated within the trunk of the tree," says the lighter-flicking scientist, Oak Ridge environmental microbiologist Christopher Schadt.

This wetwood makes for a welcoming home for all sorts of microorganisms.
"You can't actually see a lot of the organisms because we can't grow a lot of these organisms," says Melissa Cregger, a staff scientist at Oak Ridge. "So we're able to identify them using their gene sequences."
Some of those organisms turned out to be species of archaea that are known methane producers. So it's not the trees themselves that are making the methane, it's the microbes living in the trees.

It's not clear to me if the use of "wetwood" refers to the natural condition of cottonwood trees, or if this is meant to refer to some kind of bacterial infection. For example, Mirriam-Webster defines wetwood as:

wood having a water-soaked or translucent appearance because of abnormally high water content sometimes due to bacteria and sometimes to physiological factors

Question: Is it unusual for populations of archaea to be found living inside trees? Is this something new and surprising or is this well documented?


texts: When is it unacceptable to measure dry mass in an experiment to measure growth of plants?

texts:
I'm an A level student (British high school final year) and I was doing an exam question which asked for the design of an experiment to test the effect of light intensity on the growth of a certain type of plant. Here is the paper; it is question 2(c). The marking scheme can be found here.

As my measured dependent variable, I picked dry mass. However, the marking scheme specifically says to 'ignore dry mass' and asks for use of 'mass'. We were always taught that dry mass is the most accurate measure for experiments where we are trying to measure the effect of a certain parameter on the growth of plant. So now I am wondering - when is it unacceptable to use dry mass as a measured dependent variable in such experiments?

As far as my attempts extend, I tried determining what conditions we should use dry mass under, but I could not find any source that talks about detailed use of dry mass (when to use it and when to not use it).

Perhaps a different way to phrase this question is to ask: when do we use mass rather than dry mass? And when do we use dry mass rather than mass? As far as my knowledge extends, dry mass is the most accurate determinant of growth that there is, given that the plants are genetically identical. This is because it ignores the possible fluctuations that may be present due to fluid mass within the plants.


texts: Are there any examples of viruses that have jumped from reptile to human?

texts:
I know that there are plenty of examples of zoonosis occurring from reptiles to humans that involve bacterial pathogens, (e.g. Salmonella) but are there any instances of viruses being transferred from reptiles to humans?
If applicable, for this question, I am only interested in reptilian viruses "jumping" from reptiles to humans, not the capacity of reptiles to serve as reservoirs for non-reptilian viruses that could potentially infect humans.


texts: How can a waterborne disease be transmitted

texts: If a disease is waterborne [as in it is based in the digestive tract], what ways can it be contracted other than the obvious drinking of infected water?


texts:
In Wilk et al. 2001 I saw that HIV has 3 open reading frames. In the Watts et al. 2009, I noticed they mentioned HIV has 9 open reading frames. I don't understand this very well.

e.g.

[ATG] GAT GTA AGT
A[TG G]AT GTA AGT
AT[G GA]T GTA AGT

Could anyone explain this to me?


texts: Evolution of the Redundancy of the Genetic Code

texts:
In short

Looking at the genetic code, it appears that most redundancy is on the third letter rather than on the first or the second letter of the codon. Why has it evolved this way?

Longer version

In order to compare the relative redundancy accounted by each letter of the codon, let's assume that that every codon occurs at equal frequency. It is probably wrong but useful for the sake of the calculations. Using observed frequencies of codon usage in a given population would change the following probabilities but the question of why some positions in the codon has more redundancy than some others still hold.

A substitution of the first letter of the codon has a probability of $\frac{1}{2048}≈0.00005$ (Stop codon) to be synonymous. A substitution of the second letter of the codon has a probability $\frac{3}{256}≈0.012$ (nucleobases U and G) to be synonymous. A substitution of the third letter has a probability of exactly $\frac{2}{3}$ to be synonymous.

Probability of a substitution to be synonymous given that it occurred on the...

First letter: $\frac{1}{2048}≈0.00005$
Second letter: $\frac{3}{256}≈0.012$
Third letter: $\frac{2}{3}$

Why are there more redundancy on the third position than on the second (which has more redundancy than the first position) in the codon?


texts:
I took it upon myself to research how methylation/acetylation affects histone tails via post-translational modifications. However, I find myself confused about how to "read" this histone code, specifically for the Euchromatin.

My problem is that there are both acetylations and methylations. Does that mean that the methylation of lysine 4 will cause that portion of the chromatin to be condensed, but the acetylation of the lysine 9 and so on will cause that portion to be decondensed?


texts: Without plant breeding and domestication, would most of the foods consumed by humans evolve to become inedible?

texts: Would this happen? Do species evolve to avoid being consumed, especially the animal species which have no need to leave seeds?


texts: Why is your taste affected due to sinuses?

texts:
I heard someone say "My sinuses are acting up, I can't taste the food." I don't think the person is lying, they probably believe this but I'm having trouble seeing how the sinuses would affect the taste buds. I realize smell helps identify foods, but it seems like not smelling a food wouldn't affect taste so severely as people make it sound.

I don't have sinus troubles much and haven't experienced this, so I'm not claiming it's fake, I'm just curious to understand how that works.


texts: What is this bird of prey with white belly?

texts:
This bird was around the house in northern Switzerland (alt: ~700 m) on January 17th 2016, and I am just wondering what kind of species it is.

The legs are yellow and the under (I do not have picture while flying, but saw it just before) is almost all white with just a black (or dark) stripe on the end of the tail.

For me it looks like a nordic species of Buteo buteo but can any specialist confirm it?


texts:
When I yawn I can't hear anything happening around me. I also feel some kind of muscles inside my head contract and hear a faint hum, but it is not loud enough to explain not hearing other sounds. I can force those muscles to contract even without yawning and it produces the same effect of humming and no other sound, so I suppose they cause this effect, but how?

What really happens? What muscles do I feel?


texts: Two subunits connected by only one disulfide bridge: quaternary structure?

texts:
I've always simply assumed quaternary structure to be characterized by non-covalent interactions such as hydrogen bonding, van der Waals interactions and whatnot. However, if two distinct polypeptides were only connected by one covalent disulfide bridge, would this be considered as quaternary structure, assuming that non-covalent interactions between the subunits are either negligible or even repulsive?

In other words, can a disulfide bridge, on its own, convey quaternary structure?

On a side note, are there any notable examples of this type of interaction?


texts: How does drinking 25 mg-50mg Viagra every night cure Erectile Disfunction permanently?

texts:
https://www.webmd.com/erectile-dysfunction/news/20040513/nightly-viagra-may-restore-normal-erections#2

This article says that people taking viagra once daily can have erection restored permanently again.

Those who take viagra only when they're about to have sex do not.

I do not understand their reasoning why?

They said it helps make Endothelial cells better.

If that's the case, how come people that take viagra only when they're about to have sex do not improve?


texts: Smallest unit on which selection can act

texts:
Traditionally, the individual was considered to be the smallest unit on which Natural Selection (NS) acts. Today, we usually consider the gene as being the unit of NS. Of course, we should also consider all sequences that affect the fitness even though they are not genes (even though the do not code for polypeptide). And theoretically, any sequence of DNA does have an effect on fitness because it influences the time and energy for DNA replication (although it might be negligible). The decision of considering the gene as the smallest unit of NS seems rather arbitrary to me. We might as well consider a group of genes or a given exon of even a smaller sequence.

Here are my questions:

What factors influence the minimal size of a sequence to be considered as a unit on which NS acts? Mutation rate, generation time, selection differential for this sequence, recombination rate, ...?
Could we consider a nucleotide as a unit of NS? Why?
How does the quasispecies model fit into the question of what is the smallest unit of NS? (for those interested, you will also find a very good explanation of this model in Martin Nowak's book called Evolutionnary Dynamic: exploring the equations of life)
Is it worth talking about that? Is this question biologically relevant? Or is it rather a question based on a choice of definition such as "Is a virus alive?"

As I asked several questions, let me know if I should split my post into several. Otherwise, please do not hesitate to answer only very partially to this post!

UPDATE

Terdon's answer makes sense to me. I should be a bit more accurate in the reas of my question.  I read The extended Phenotype from Richard Dawkins quite a long time ago and if I'm not mistaken, Dawkins says the following things

A unit on which selection acts has to be:

active
germ-line
replicator

A replicator has the 3 following properties:

fecundity
longevity
fidelity while being copied

Therefore for fidelity to be respected a unit of selection has to be a sequence which is not too long, so that it is not too often modified by recombination or mutation. He argues in this sense.

He also argues that nucleotides are not possible unit of selection. Indeed, it is hard to imagine a nucleotide being an active replicator. The word active means that it influences its not probability to be replicated. I don't think a nucleotide can do such a thing.

Unfortunately I don't have the book with me right now and I can't check what I have said, give you a citation nor a more accurate a reference. If anyone has some citations from this book, it will be welcome for the discussion!

Thank you!


texts: What are the structual differences between DNA and RNA?

texts: How is the structure of DNA different from that of RNA?


texts: When is Water Produced During Photosynthesis?

texts:
The formula for photosynthesis is: $$6CO_2+12H_2O \rightarrow C_6H_{12}O_6+6O_2+6H_2O$$

I can count the carbons, the waters on the reactant side, the oxygens, and the glucose, but I cannot seem to locate where in either light or dark reaction 6 water molecules were produced again. Where and when were they produced?


texts: Is it possible there were multiple origins of life? And, if so, why did the one which became the common ancestor between all organisms prevail?

texts: I have learned that all currently-living organisms come from a common ancestor, which I theoretically understand. However, my professor in a class mentioned that there is a chance that there were multiple origins of life, but that all the creatures living today all came from the same one and the others died. How can we be sure that before the other origins of life died, they didn't somewhat evolve, and the species from that origin didn't just evolve in convergence with those of this one since through natural selection both would need similar characteristics to survive on Earth?


texts: What is the number of mega pixels available in the human eye? It seems that newer camera models continuously keep increasing their pixel count. However, they never seem to be capable of reproducing what the eyes can see.


texts: How different is an introverts brain different from an extroverts?

texts:
How is an introverts brain wired differently than an extroverts? Just to give you an example. On an average, the processing that goes on in an introverts brain is greater than in an extroverts [citation needed].

What part of the brain affects personality traits such how introverted someone is? How is this part of the brain different in either it's physical entity or it's activity between extroverts and introverts?


texts: Reasons why people say that AIDS/HIV doesn't exist

texts: It's been recurrent when I hear people saying that AIDS doesn't exist. When I ask why, they give weird reasons like HIV is a virus created to control economy and to develop medicine, etc. Also when I try to watch videos on youtube about people that are infected with this virus, I see a lot of comments saying that AIDS is a lie and some of them base their opinions on a documentary called House of Numbers. So I would like to know scientific reasons if this a myth, or why this is true.


texts: It's easy to set the maximum E-value threshold in a BLAST request. I need to set the minimum E-value. Does anybody have any suggestions?


texts: Why not use SDS-PAGE as a method to detect viruses?

texts:
Recently, I have been researching about DNA and I know the most popular method for detecting viruses is based on DNA. After learning about proteins, I wonder why we do not detect viruses based on virus proteins?

If it becomes true we can save a lot of money, instead of doing a PCR reaction, we can detect more than one disease in a single reaction.

For example, when I have the sequence of a virus from NCBI Genebank, I can know how many proteins the target organism produces and I can calculate the molecular weight of each protein. Then running it in a SDS-PAGE gel to see what the bands look like, may be that I can know the target organism is present or not?

For example, HIV produces 9 proteins and the molecular weight of each protein is different.
So after doing electrophoresis, I have 9 bands. Based on the distance between each band and based on the molecular weight, it's possible to know HIV is present or not?


texts: Relation of conformational entropy and protein folding

texts:
I'm trying to figure out the relation between conformational entropy and protein folding.
I read the following in Lehninger, Principles of Biochemistry (6th edition):

  Most of the net change in free energy as weak interactions form within a protein is therefore derived from the increased entropy in the surrounding aqueous solution resulting from the burial of hydrophobic surfaces. This more than counterbalances the large loss of conformational entropy as a polypeptide is constrained into its folded conformation.

In this context the meaning of conformational entropy is that the higher the stability of the proteïn is the lower the conformational entropy is (I think).

Why does the surrounding entropy increases because of the burial of hydrophobic residues?

Why does the burial of those hydrophobic residus couterbalances the large loss of conformational entropy?

I think maybe because the unfolded protein has more conformation then the protein when it's folded because of the hydorphobic core, it lowers the possible conformation because the hydrophobic interaction restrict the possiblities. Am I right?


texts: How to create a collection of anonymous sequences for teaching and testing?

texts:
I am looking for a large collection (>1000) of sequence files (eg. FASTA) from any real organism or a tool to create such a collection.

The sequence files would be used for teaching and for testing automation methods.

Students would be assigned one unique sequence file and asked to look at it (eg. using gORF) and to identify it (using BLASTn).

The sequence file would thus need to contain only the sequence data (no meta data about species or gene).

I would need an associated answer sheet.


texts: Cracking sounds made by glowing plankton

texts:
Recently I had opportunity to swim in place with glowing plankton, it was amazing experience and it as well gave birth to few questions in my head.

I manged to google that they can glow thanks to chemical reaction called Bioluminescence.

Once submerged I could hear a cracking sounds, are these sounds as well effect of said chemical reaction?

Few more questions I am wondering:
How often can the plankton light up? Do they need to recharge or something?

Do they light up during the day as well but we can't see them because of daylight or do they act depending on how much light is there around them?


texts: What is this species of green frog found in store-bought flowers in France?

texts:
Today I found a frog in a big flower composition bought at a french shop (living in Grenoble, south of France).

It started snowing today, and I'd like to keep it until it's warmer outside.

So could someone tell me what species it is ? (To check what it eats and if it's legal to keep it)

Thanks !

(I'll edit with more pictures if it's needed and if she moves)

Edit :