texts: Why is an increase in the amount of oxygen in the atmosphere favorable for life?

texts:
I have followed the David Attenborough series on 'First life' and heard, that an increase in the amount of oxygen in the atmosphere, as it took place just before the Cambrium, is generally favorable for life and also enables the evolution of larger organisms.
Why is that so? Is it because aerobic respiration had a better conversion rate to energy?


texts: Can anyone help me identify this tiny larva I found in my cat's water dish and tell me how it got there?


texts:
I found this strange bur on a stray cat in my neighborhood.  I've never seen anything like it, and Google reverse image search thinks it's an earring.  Found in in northern California, just south of Clearlake.  (38.90 N, 122.60 W)

The spike structure is almost exactly one inch long.


texts: Could drugs promoting angiogenesis be used as a treatment for burn victims?

texts: From what I've learned from my textbooks and in class lecutures it seems that inducing angiogenesis for people with severe burns would be an excellent way to speed up the healing process. Is this already being done? If so or if not what are (if any) challenges that are presented to doctors and surgeons trying to use this self-healing method?


texts: During weight loss, do we inhale more oxygen?

texts: During weight loss, triglycerides which are composed of carbon, hydrogen and oxygen, are broken down. During respiration, the inhaled $O_2$ is bonded to a carbon atom to form $CO_2$ which we exhale. However this process happens anyway, even one isn’t trying to lose weight. So that suggests to me that during weight loss people must inhale more oxygen, otherwise where are all those extra carbon atoms that we now have going?


texts: Why haven't land animals evolved beyond urination?

texts: It occurred to me (while urinating) that this would seem to be selected against because water is a scarce resource.   Why are we constantly losing water we don't need to through urination?   What is it about the chemistry of urine and the waste products eliminated that make urination necessary as opposed to eliminating them through defecation and recovering the water on the way out?


texts: Why is the head/neck of the femur at that 120-150 degree angle?

texts: I'm just wondering why the femur is such that there is that head and neck sticking out of the top at an angle, why it isn't just straight up into the hips?


texts: Isopropanol precipitation of DNA - duration and magnitude of cold storage

texts:
DNA prep protocols often include a final precipitation step with alcohol, often isopropanol, where the DNA must be kept in the alcohol, at a low temperature such as -20C or -70C, often overnight.

What is the point of keeping it at low temperature? Is lower better? At what point do you see diminishing returns?

What about the time? Is overnight really necessary, or would, say, an hour suffice? Do lower temperatures result in quicker precipitation?


texts: Are there organisms that have incorporated plastic into their lives?

texts: Are there organisms that have incorporated (manmade) plastic into their lives in any way? Either in their diet, or as a part of their body?


texts: Relation between goose bumps and temperature

texts:
As we all know, cold weather will cause us to have goose bumps. I honestly don't know why (1), because our skin contracts?

Apart from that something quite contradicting happened this morning. I was taking a hot shower and it was so hot that I suddenly felt that I had goose bumps. Not because it was cold, but because it was so hot. How can this happen? Because of a sudden change in temperature the skin goes haywire? Or aren't goose bumps related to temperature in a way, but is a sort of safety reflex?


texts: Does LSD "stay" in your fat storage and then "returns" back?

texts:
This rumor was told me by a very anti-drug person. A stance I agree with only lightly.
The rumor was that when you take LSD, it stores itself in your fat storage, and then returns back in 3-6 months, returning back meaning there would be another series of effects of LSD (the trip).
Is this true? I highly doubt it. However, what I don't know, if the body is processing (burning?) fat and then processing substances (such as the rumoured LSD) found in fat stores.


texts: Does consuming sodium benzoate (preservative E211) cause problems during pregnancy?

texts:
There seems to be strong evidence to support the claim that sodium benzoate (E211) causes hyperactivity in young children, e.g. Bateman et al. (2004) and McCann et al. (2007).  This leads me to consider whether or not E211 is harmful during pregnancy.

A study by Mowafy et al. (2001) found a slight decrease in survival rates for pups of pregnant rats given sodium benzoate; they also found a more significant drop in mean weight of their pups.

Question: Could the consumption of sodium benzoate by the mother be harmful during human pregnancy? How would this be the case?

References:

Bateman, B., Warner, J.O., Hutchinson, E., Dean, T., Rowlandson, P., Gant, C., Grundy, J., Fitzgerald, C. & Stevenson, J. (2004) The effects of a double blind, placebo controlled, artificial food colourings and benzoate preservative challenge on hyperactivity in a general population sample of preschool children. Archives of Disease in Childhood. [Online] 89 (6), 506 –511.
McCann, D., Barrett, A., Cooper, A., Crumpler, D., Dalen, L., Grimshaw, K., Kitchin, E., Lok, K., Porteous, L., Prince, E., Sonuga-Barke, E., Warner, J.O. & Stevenson, J. (2007) Food additives and hyperactive behaviour in 3-year-old and 8/9-year-old children in the community: a randomised, double-blinded, placebo-controlled trial. The Lancet. [Online] 370 (9598), 1560–1567.
Mowafy, A.R., Darwish, A.M., El-Kholy, S.A. & Abdel-Mohsen, S.H. (2001) Effect of food preservatives on mother rats and survival of their offspring. The Journal of the Egyptian Public Health Association. 76 (3-4), 281–295.


texts: Why human endometrium doesn't stay constant?

texts: Is there any explanation or evolutionary advantage to the endometrium constantly cycling between the proliferative and menstrual cycle? Wouldn't it be more advantageous if it kept always fully thickened? I imagine it is less energetically expensive than to be always producing and losing all those cells, blood vessels, etc.


texts: Identification of Bird feather, probably from a predatory bird

texts:
Found in Berlin,Germany
Area of Charlottenburg
I want to know the species of this bird, someone please tell me.
Approximate size 19 cm


texts: Why does a lightsource postpone the time it takes for the leaves falling from a birch tree?

texts:
It is autumn and the leaves have already left their trees on all birch and other trees that has leaves, except one. This birch has a spotlight pointed to the tree and it is on 24/7. I have recognized that this birch have lost almost no leaves. And if we take a closer look at this birch, the back side of the birch, which is faced away from the spotlight have lost a noticeable amount more leaves than the front side which is directly hit by the light from the spotlight.

My conclusion is that having a lightsource pointing to a leafy tree will postpone the time from when it loses its leaves, relative to trees that does not have a lightsource pointerd at them.
 But I have no idea why this is happening. I do not know anything about trees, leaves, chloryphyll or the reason why trees drops their leaves in the autumn.

If any one is a expert in this field and might know why this is happening, or just have a hypothesis of why this is happening please provide it since I find this really interesting and I can't find anything on Google about this phenomenon.

You can make your anwer as complicated as you wish, I will understand it even if I might need to Google some of the things in the answer :).

Thanks!


texts: What is the name of this red and blue striped spider (?) - Brazil, Rio de Janeiro

texts:
Anyone knows the name of this thing? I found it in our bathroom. It is maybe 10-15 mm.

It looks like a spider but the colors left me puzzled


texts: Relation between trigeminal and facial nerve in sympathetic response

texts: In my neuro-anatomy course notes I found that the facial nerve "uses" the trigeminal nerve to reach its targets. However, I have yet to find any diagram or reference that indicates how this is done. How is the trigeminal nerve "used" by the facial nerve?


texts: What is the probability of an offspring sharing identical HLA typing as one of their parents?

texts:
DISCLAIMER: I have yet to thoroughly study HLA 100% to the bone, and hence I won't know everything about it at the back of the hand.

Recently I came across this information on a San Francisco hospital website claiming the chance of a full HLA match between 2 randomly selected people is 1/1,000,000 and the chance of a full HLA match between a child and one of their parents is 1/200.$^{[1]}$

What struck me as odd is the 1/200 chance of a parent matching their offspring's HLA, which seemed too high of an estimate. The immediate intuition is for a child to have identical HLA typing as one of their parents, their parents need to share some HLA haplotypes, which on its own should be a rare occurrence. Hence I decided to attempt verification of this number to confirm if it was within the realm of possibility

According to Stanford$^{[2]}$, the HLA cell surface receptors that mix during inheritance are HLA-A, HLA-B in MHC I, and HLA-DR in MHC II. A set of these 3 forms a haplotype. [HLA-C and HLA-DQ are probably involved too, but we'll omit them for simplicity's sake.]

For our estimation, we use data from the same Stanford source$^{[2]}$ and find there are 59 HLA-A serotypes, 118 HLA-B serotypes, and 124 HLA-DR serotypes. This gives us $59\times118\times124=863288$ different possible haplotypes.

To get the probability of 2 parents sharing at least 1 common haplotype, we do some math: $\frac{1}{863288} \times \frac{863287}{863288} + \frac{1}{863288} \times \frac{863287}{863288} + 2 \times \frac{1}{863288} \times \frac{1}{863288} = 1/431644$

The above is assuming the parents have met randomly in the world and no inbreeding has taken place. Inbreeding will pretty much ensure 2 parents share common HLA haplotypes.

This means the chance of an offspring to even possibly have the same HLA typing as one of their parents is 1 in 431,644, which is already way lower than the 1 in 200 chance stated on the hospital's website.

Just for calculation sake, the precise chance of an offspring sharing the same HLA typing with either one of their parents after accounting for different possible haplotype combinations produced by the parents would be: $100\% \times \frac{1}{863288}^2 \times 2 + 25\% \times \frac{1}{863288} \times \frac{863286}{863288} \times 2 + 50\% \times 2 \times \frac{1}{863288}^2 = 5.792 \times 10^{-7}$

An exceedingly small chance.

Issues with my estimation:

There were 2 assumptions made during this estimatey computation. I didn't take into account the weighted and uneven distribution of the haplotypes, and just assumed they are all statistically evenly distributed. Some haplotypes are more common than others, and this factor was not considered during the estimation. If existing data on haplotype occurrence is used, it will likely affect the estimation quite a bit, however, this is highly difficult as the data varies by region and ancestry.

I also did not take Genetic matchmaking into account, which is a factor that will lower the chance of 2 parents sharing common HLA haplotypes.

If exact computation for the probability proves to be difficult, what would be a reasonable estimation on the order of magnitude of said probability? Is 1/200 within the realm of possibility once you take into account the uneven distribution of haplotypes caused by certain more common ones?

Sources:

$^{[1]}$https://www.ucsfbenioffchildrens.org/education/types_of_bmt_donors/#2

$^{[2]}$http://web.stanford.edu/dept/HPST/transplant/html/hla.html


texts: Why did T cells have evolved to recognise self cells along with foreign antigent to generate a response?

texts: T cells have evolved to be strain specific. For a T cell to respond it has to identify not only the foreign antigen but the antigen must also be attached to a self cell. what is the significance of that? Isn't that the reason behind autoimmunity and hypersensitivity? I understand about foreign antigen, but why self cells? the experiment by Zinkernagel and Dorothy about MHC restriction shows that same antigen presented by a foreign cell will not be killed by sensitized T cells.


texts: Why do some animals and fungi prefer asexual reproduction?

texts: Animals like Sponges and Hydra and fungi like Yeast and Mushroom can reproduce both asexually and sexually. However, they only reproduce sexually if the 'circumstances' are 'bad'. Is there a specific reason for that?


texts: First genomic survey of human skin fungal diversity

texts:
"The researchers found that a single type of fungus, belonging to the genus Malassezia, is predominant on the head and trunk. Hands, which harbor a great diversity of bacteria, are home for relatively few types of fungi. In contrast, feet, including toenails, heels and toe webs contain tremendous diversity.

"Applying DNA sequencing to a study of the skin's fungi is the natural progression in understanding microbial life that co-exists on our bodies," said NHGRI Scientific Director Daniel Kastner, M.D., Ph.D. "Along with recent genome sequencing to define bacterial diversity, this analysis of fungal diversity provides a more complete human microbiome picture."

"Fungal communities occupy complex niches, even on the human body," said Heidi Kong, M.D., co-senior author and an investigator in the dermatology branch of NCI's Center for Cancer Research. "By gaining a more complete awareness of the fungal and bacterial ecosystems, we can better address associated skin diseases, including skin conditions which can be related to cancer treatments.""

Source

Is there another reference for this research please?


texts: Do genes play a role in the athleticism and shape of a person?

texts:
I am an Indian with a small thin stature with some deposition of fat around my belly.I was wondering if genes play a role in fat deposition in the body for Indian, Chinese, European or African people. Fat deposition may differ among all these people around the belly, thighs etc.
These people also differ in their stamina and speed naturally.

  For example here in India in the game of cricket there has been no
  fast bowler out of 1.2 billion people who can do fast bowling
  because it requires a lot of strength and stamina.Also on field
  athleticism is also very bad compared to Australian or South African
  players.I assume that may be its because of some cultural or genetic
  problem.


texts:
What is this insect? (Location: Hong Kong; size: 8 mm long, 4 mm wide, 2 mm thick; color: black with some brown at center on the top)

The insect in the picture was slightly damaged after an altercation with a human.


texts: Brain + ethanol experiment suggestions needed

texts:
I need to demonstrate the effects of ethanol on a human brain (or other brain with developed telencephalon) in vitro; ideally the effects on vigilance and/or memory.

Could you please suggest such an experiment?

What method would you suggest to demonstrate the effects of ethanol on NMDA receptors or membrane penetration by ethanol?

Edit in respose to the first comment by @MadScientist:

The point is to empirically demonstrate how ethanol affects the cognitive performance of brain (specifically vigilance and memory) and explain the biochemical nature of such an effect on an observable real example (not using computer simulations). It is aimed at mature layman audience.

The experiment has to be in vitro due to ethical and environmental limitations (well, I am not permitted to intoxicate mature students nor animals).

Demonstrating the effect of ethanol in the role of an NMDAR antagonist would be satisfactory as the chain of implications would be illustrated on a theoretical basis.

I have access to standard laboratory equipment on a university level, but the simpler it is, the better. As to the material, the same is true while a fresh brain slice will hopefully be available as well.


texts:
I've been growing plants in pots for several years, and in some of my pots a patch of green moss appears and steadily grows to fill the whole surface area of the soil. But that doesn't happen in other pots. I've used different bags of soil for different types of plants, but moss doesn't seem to appear only in one type of soil from the same bag.

How does moss appear in the first place? Or is it present in all soil and only grows to a visible size under certain conditions?


texts: Why eyes don't get heated while converging sunlight into retina?

texts:
It is a common observation that a magnifying glass when used to converge rays of sun to a fine point in paper, the paper burns due to intense heat.

Why doesn't this happen in our eyes? Our eyes are also doing the same, they are converging the sunlight into our retina but our eyes don't get burned, or to say get heated.

Is viterous or aqueous humor absorbing heat? If so, then the tiny amount of fluid present in the eye shouldn't be enough to cool the eye for a longer period of time, but we can spend the entire day at sunlight without any eye stress or pain.

Size of eye lens small compared to magnifying glass? However a magnifying glass of the size of eye lens should also be able to produce significant heating by converging sunlight.

As far as I know, the heating effect is due to Infrared rays not because of UV rays so we can safely ignore them in this case, right?


texts: How do I identify the protein with the highest Disulfide bond density? i.e protein with highest ratio of Disulphide bonds per Peptide bond?

texts:
I want to list all proteins in the protein database and list them by the ratio of number of disulphide bonds per peptide bond.
I am not particular about the reliability of identification of disulphide bond.

--EDIT 1
I've been doing some research on this topic, and heres what i've found.

The PDB structure file lists all the Disulphide bonds in each structure.(SSBOND)
The PBD structure file does not list the number of peptide bonds, however it does
mention the number of amino acids. And number of peptide bonds = [no. of amino acids - 1].
We can generate a list of all PDB structure IDs with atleast 1 disulphide bond, using PDB.org's advanced search feature. This gives a list of 22543 structures.
Downloading all the 22543 structures and then parsing them using any programming language would be easy, except for the difficulty of downloading all the 22543 sturctures.

So the question now is:
 How do I parse all the 22543 structures to output only the number of disulphide bonds and the number of amino acids in each chain, without downloading the PDB structure files?


texts: Why do tattoos persist if body cells are regularly renewed?

texts:
I am not quite sure if it is true, but I read somewhere that within 7 years all the body's cells are replaced with new ones. I am not quite sure if it is cells or atoms.

If it is then why do tattoos persist for so long? If the cells which were impregnated with the dye have been replaced, then why do the tattoos still remain?


texts: Is this "Sympathetic fight response" axis accurate?

texts: Peripheral sensory cell > Preganglionic cell > Dorsal root ganglia cell in the ''Sympathetic chain'' > Ventral root ganglia cell in the ''sympathetic chain'' > Post-ganglionic cell that activates an organ such as the pancreas (or a muscle).


texts:
I'm writing a thesis in biology and my supervisor asked me to find literature about beetles living under rocks - specifically she wants me to find something about hypolithial diversity. However Google doesn't even recognize the word 'hypolithial' so I'm kind of stranded without any references on where to start searching.

I know that hypo lithia comes from ancient greek and means below stones, but nobody mentioned it like that in the literature.

Has anybody heard of this term or knows a similar one which I could use for my research?


texts: Do bacteria with multiple flagella move faster than bacteria with a single flagella? Assuming the flagella are at the same length.


texts: Do adult humans exchange beneficial bacteria? If so, how?

texts:
Recently there has been increasing interest and research into symbiotic bacteria present in humans and human gut. I'm aware of two new discoveries:

humans are surrounded by a unique cloud of bacteria, similar to fingerprint, useful in forensics
human brain and cognition could be influenced by gut bacteria that produces up to 90% of serotonin and dopamine in the human body (not sure how, vagus nerve is implicated)

I've also heard that mothers pass a lot of beneficial bacteria to children during childbirth to jump start intestinal flora. Apparently this happens as the baby travels through the birth canal.

This makes me ask - do adult humans share/ pass along symbiotic or beneficial bacteria or other micro organisms?

I'm aware of viruses and diseases that can be passed via blood or be transmitted sexually, but does anything beneficial get transmitted this way?


texts: What kind of snake is this? Seen on Koh Lanta, Thailand

texts:
We had this snake in our bungalow on Koh Lanta, Thailand. From the reaction of the employees at the resort I can tell that it is venomous, but that's all I know. I am curious, does anybody know what species it is?

Thanks and cheers, Philip!


texts: Are there electron or proton receptors in our nose?

texts: We can easily smell chlorine gas and its irritating odour, but we cannot smell oxygen gas. Do few protons and electrons make such difference to our olfactory receptors?


texts: Simulating DNA sequences in R with a given value of $\theta = 4N_{e}\mu$

texts:
This might not be the most appropriate site to be asking such a question, but perhaps someone has a solution.

My question is: is there an R package or function for simulation of DNA sequences of a given basepair length generated according to a prespecified value of the population mutation rate $\theta = 4N_{e}\mu$, where $N_{e}$ is the effective population size and $\mu$ is the per-generation mutation rate

I have real sequence data from GenBank, but I would also like to simulate some random DNA sequences according to a coalescent process.

Essentially the function would output the generated aligned DNA sequences as a FASTA file.

I have been rather unsuccessful in tracking down a suitable package, as most only output generated phylogenies.


texts: Why do some herbivores like sheep, cow, and others excrete feces in a pellet (or biscuit or other) shape, while other species including humans do not do so? What is the reason for such an adaptation in herbivores? Is it beneficial to them, and if so, how?


texts: Food Intake versus ability to flee among birds, particularly the hummingbird?

texts:
Logically speaking, if a hummingbird drinks too much nectar, it will be temporarily overweight and less able or unable to fly to escape danger. However if the same hummingbird doesn't drink enough nectar, it will suffer the same problem of not being able to flee danger, but for the different reason of it wouldn't have enough energy to do so. Hummingbirds are incredibly small, so I would assume they would have the most problem with this issue due to the fact it would have very little margin for error. I am not sure how much that margin is though or the marginal percent of body weight, so I'll ask that question too.

What mechanisms do (humming)birds have to regulate and control their body weight and their energy needs and scouting and timing the acquisition of their next potential food source? What is their margin for error and how do they meet it and how did they meet it in the past?

EDIT: I want a more concise question, so hopefully this is answerable:

Alternatively and optionally, Can you describe to  me a general day in the life of a Hummingbird? I want to know what good decisions it makes over the course of its "perfectly average" day to survive. Such things as what it does to avoid dangers, and how it finds its time to eat and how much it eats and at what intervals, and what it does with the rest of its time?


texts: Sexual selection in cats or other animals

texts:
I was wondering if you could answer some of my questions regarding sexual selection in cats (or any other animals). I would like to apologize beforehand for my incorrect term use.

When it comes to mate choice, is mutual choice for both males and females the norm? If not, is it mostly a tomcat or a female cat who does the choosing?
Do female cats always have freedom to choose, or is it more like a rape or consensual sex?
How do cats choose their prospective partners in the wild, what are the mechanics of this process? Does a prospective partner come with the territory or are there any courtship rituals? I am interested in mate availability for female cats and sexual selection from a female cat perspective.

Thank you very much in advance.

P.S. Any other animals will do if they do not live in groups, prides or harems. I am interested in individual choices.


texts: If PAM-1 matrix refers to time or evolutionary event for 1% change in amino acid sequence of a protein then how come there is PAM250? shouldn't PAM 100 be the highest where the two concerned sequences are 100% different


texts: Richard Dawkins says evolution doesn't have any goal. But I think evolution has one. At the end evolution creates intelligent being. If we find another earth like planet evolution sould have the same pattern. Evolution is not a chaotic event. Am I wrong?


texts: Is Sinus node conduction necessary for heart beating?

texts:
Assume a patient with previous cardial infaction which SA node not possible to activate action potential anymore.
However, SA trying to beat unsuccessfully repeatedly waisting energy.
Therefore, I thought in this discussion about the possibility to stop Sinus node from trying to start action potential; which was deleted but the article about the SSS (sick SA) and remodelling is about its goal. The proposed treatment (laser ablation) of AF/AFL can backfire and cause SN (Sick Node) through remodeling. Assume there is no bypass of impulses through SA node.

Can the heart still beat through AV node and bundle? Yes.
Do you have any evidence that [heart] can "beat" properly on just the AVN? Yes, see article. Short-term mechanisms where electrical/metabolic remodeling. Long-term mechanisms where irregular rhythms and complete heart block can occur because of anatomical remodeling.

I want to know if these pacemakers are in series or parallel.
If they are in series, then laser operation can be dangerous to the SA node.
The series connection is however the idea which I get from many schematic drawings:


texts: Can someone please direct me to an e-resource or a book that will help a newbie like me learn in depth about Cloning using pET28a and Protein Expression in DH5alpha and BL21. Though I have done cloning using TA vectors, pET28a is very new to me. I need to design primers with restriction sites to insert my GOI into pET28a, so would like to learn how to choose these sites too.


texts: Specific numbers of nucleotides in Okazaki fragments

texts: Okazaki fragments are formed during replication of the lagging DNA strand. What determines the length of these fragments?


texts:
The organ we have to provide us with current acceleration information is quite complicated. Because an ant queen didn't seem to notice when I picked up the bottle she was in, I have a suspicion that ants don't really care about acceleration and therefore can't tell where it's up and where it's down.

Am I right? If not, how do they sense acceleration?


texts: Why does weight loss lower blood pressure?

texts:
I have read that weight loss is an effective lifestyle modification for people with hypertension, and systolic pressure may be reduced by up to 1-2 mmHg for every 1kg of weight lost.

What is the physiological reason for weight loss reducing blood pressure or weight gain increasing it?  Please provide a physiologically detailed response rather than simply saying that more weight means the body must work harder to pump blood.  I understand this but I want to know the mechanisms of how the body detects the increased weight and adjusts the blood pressure accordingly.  Thanks!


texts: Yeast Strain with squalene synthase / farnesyltransferase (ERG9) gene deleted

texts:
I was interested in obtaining a yeast strain without the enzyme farnesyltransferase (Which catalyses conversion of FPP to Squalene). The Euroscraf database has thousands of yeast strains with individual genes deleted but when I search for "farnesyltransferase" I get a couple of hits that I am not being able to interpret.

Here's the link: http://www.euroscarf.de/search.php?search=farnesyltransferase&project=

What are all these different strains? In particular how does one interpret notation like which seems to be describing a particular strain:

BY4743; MATa/MATα; ura3Δ0/ura3Δ0; leu2Δ0/leu2Δ0; his3Δ1/his3Δ1; met15Δ0/MET15; LYS2/lys2Δ0; YKL019w/YKL019w::kanMX4


texts: No genes' ID in peak annotations during ChiP-Seq with ChIPpeakAnno R package

texts:
I am trying to perfom Chip-Seq Analysis which is greatly described in that conversation: introduction to Chip Seq . The same as autor of mentioned question I am a student of Applied Mathematics and I am doing my best to enter bioinformatics fields.

I am basically at the moment where I would like to annotate peaks with genes' IDs. To do this I am using ChIPpeakAnno R package from Bioconductor. I used below  code to annotate my reads (outputs from MACS) with genes' ID's

> library(ChIPpeakAnno)
> # data(package = "ChIPpeakAnno")$results[,3]
> macsOutput <- toGRanges(data="example_peaks.bed",
+                                               format = "MACS")

> data(TSS.human.GRCh37)
> macs.anno <- annotatePeakInBatch(macsOutput,
+                                                                AnnotationData=TSS.human.GRCh37,
+                                                                output="overlapping", maxgap=5000L)
> library(org.Hs.eg.db)
> macs.anno <- addGeneIDs(annotatedPeak=macs.anno,
+                                               orgAnn="org.Hs.eg.db",
+                                               IDs2Add="symbol")
>
> # no annotations for some genes
> as.character(head(as.data.frame(macs.anno)$symbol))
[1] "PTCHD2" "PTCHD2" "PTGER3" NA       "HFM1"   NA

but there occures that there are no genes' annotations for some peaks. Can anyone tell me why this might happen? And how to avoid this? Does this refer to the maxgap=5000L parameter? When creating output from MACS I set a parameter for length to be 10 000.


texts:
Can someone please explain me the concept of Immunodominant peptide in simple language?? I did read the wiki article but did not understand it clearly. Please help!
(I have not studied biology since last 8 years and now I am going through it because I need it for my research. So if someone can describe it in simple language it would be very helpful)


texts: why and how multi allele gets reported during variant calling in vcf?

texts:
This might be a very basic question for many here. With the basic understanding of inheritance, eventhough there is a possibility of multiple genotypes due to multi alleles, the resulting genotype can only have two alleles(paternal and maternal) that way after variant calling, an allele at one position can be homozygous or heterozygous. So there can be max of two alleles, but why do we see multiple alleles at a given position in VCF. I am trying to understand the science behind this. Please help out. Thanks!

chr5    127640782   .   AG  A,AA    .   .   .   GT:AD:DP    1/2:0,28,409:437


texts: Why are introns called 'introns' when they are the actual ones who are getting spliced out from the pre-mRNA. Shouldn't exons be named introns as they are the ones that are 'in' and are not 'exiting'? On what criteria were they named like this?


texts: How should I feed and keep an ant queen?

texts:
I have captured wandering ant queen. I guess she was just fertilised and was looking for a place to start a hive.
I'd like to create my own ant hive in artificial environment.

I unfortunately only have a small clean chemical bottle (1.5 CM in radius) to keep her in. I was wondering how much space would she need to feel safe.

I'm also not sure what should I feed her. Every morning, I have dropped few sugar crystals in the bottle. She shows much more individuality than an ant, because she has immediately started to collect them. It seems that she ate almost everything. I have also dropped few tiny drops of water in the bottle. Although it's hot and she ate the dry sugar she doesn't seem to drink it at all.

So what does she need? (well, except of natural forest which I don't have in my room)


texts: Alternative protocol for evaluating RNA integrity, using a bleach gel

texts:
I hate having to run MOPS PFA agarose gels with DEPC and everything just to verify my RNA integrity. I came across an alternative protocol that uses ordinary household bleach in the gel to inhibit RNases and was wondering if anyone here has tried it and what the success was like? Or any helpful insight is welcomed also.

here's a protocol I put together based on what was done in that paper.

For a 50ml gel
IN a RNase-free 250ml Erlenmeyer flask
Mix:
5 mls of 10x TAE that I gave you
42.5mls ultra purified water
0.5g of the agarose I gave you
2.5mls of household bleach (6% sodium hypochlorite, use clorox)

Incubate 5-10 minutes.

Microwave for the minim amount of time on the lowest heat setting that’s needed to completely solubilize the agarose, you don’t want evaporation adjusting your solutions volume
Check your volume with a sterile 50ml serological pipette, if you have lost more than 5% volume I would redo, using less heat.

Add 3µl 10mg/ml ethidium bromide, swirl to mix.
Pour in casting frame, allow to cool, submerge in 1xTAE

Combine 1µg of your total RNA, 2µg RNase free 6x loading dye and q.s to 12µl in RNAse feree water, you can use the water from the qiagen kit for this.
Run at 100V, about 30 min, get  good scanned image of it and use Photoshop to assess the band intensity. The 28S should be twice the brightness  of the 18S in a sample with little to no fragmentation.


texts: Do we know the physical-nature of "senses" or qualia?

texts:
We have a peculiar property/ phenomenon called  having 'sense' or qualia, also sometimes called as consciousness.

Such as, if we see a red flower; we perceive a particular colour, "red". That is an example of sense.

Now scientists could tell, what was the wavelength of red light, which group of cone-cells responded, what group of nerve-fibres were sent message to which part of brain; and how the informations are being computed in brain, what gene-expression-pathways are working. They can describe the chemical reactions and other molecular interactions, even molecular-orbitals taking part.

But could science yet tell; what was that "red"? and why it was not perceived-as blue but was perceived-as red? Similarly, hot, cold, pain, tickle, joy, fear, hunger... whatever we "sense" in our mind; what are they made up of? Are they simply flow of information? doesn't seem.  Could chemical-reactions make-up sense? or what else they could be?

To avoid the answer from being too-broad; I can simplify it in following  alternatives:

qualia does not exist. It is just a myth.
qualia exists, but it is nothing more than information and computation.
qualia exists, but we do not know its nature.
qualia exists, we know its nature, and that is more than information and computation.

Which one is true on present scenario?


texts: Identifying type of inhibitor from $K_m$ and $V_{max}$

texts:
Apparently it is possible to identify whether an inhibitor is competitive or non-competitive from graphs of substrate concentration (x axis) and rate of reaction (y axis).

There needs to be a line for with inhibitor (constant concentration) and without inhibitor. The difference in $K_m$ and $V_{max}$ can then be interpreted to find out whether the inhibitor is competitive or not.

I know that if the effect of the inhibitor decreases with an increase in
substrate concentration then inhibitor is competitive.

However I don't understand how to tell from the graphs mentioned earlier and  $K_m$ and $V_{max}$. Could someone explain.

I have tried to google this but most of what comes up is scholarly articles which are beyond my level of understanding...


texts:
Everywhere I look describes how the 5 sacral vertebrae start fusing together during adolescence and are totally fused by the time you're 30 or so. But nobody seems to explain why this happens.

It seems like it would be disadvantageous for women, since presumably having a fused sacrum makes giving birth more difficult- apparently post-partum fractures are not uncommon (http://rheumatology.oxfordjournals.org/content/42/2/384.long). So why does it happen?

EDIT: Matthew McTernan gave a great answer, but I am greedy and would like to know more: Why does the sacrum only start fusing together in adolescence, and then finish in your late 20s - early 30s? Most major development ends in your early 20s. Does this have something to do with reproductive concerns? If so, why does it happen on the same timescale in men and women?


texts:
Is chlorophyll living or non living, and after boiling the water out of a chlorophyll extract would it still live, as in would it still maintain its properties after re-adding liquid to the dried chlorophyll?

Thank you for any help.


texts: Is excess of potassium as strenuous and harmful for kidneys as excess of sodium or worst?

texts:
I was wondering since channels of body's cell membranes deal with potassium and sodium ions differently and considering the fact that potassium lowers blood pressure and sodium raises it :

What is the most expensive in energy for kidneys between having to excrete an excess of potassium and an excess of sodium, for a healthy person and without considering blood pressure? Which process is the longest?
I know that insulin tends to make kidneys reabsorb sodium but does glucose help the kidneys to get rid of the excess potassium in any way?
On long term, what is the most harmful for the kidneys' circulatory system considering blood pressure and in the case of a kidney failure? For tubules and nephrons?


texts: Reference sequence for defining single nucleotide polymorphisms

texts:
Single nucleotide polymorphism (SNP) or genetic variation in general, by definition are relative to a reference sequence. When we talk about databases of SNP as in ("dbSNP—Database for Single Nucleotide Polymorphisms and Other Classes of Minor Genetic Variation", or "A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms" -- titles of well known research papers), what is the reference genome? Similarly for defining a "SNP Map/Profile" of a person (in medical genomics), what is the reference genome sequence? Is there a de facto reference, or is it context dependent? There is a sentence "Scientists are trying to identify all the different SNPs in the human genome" at http://www.cancer.gov/cancertopics/understandingcancer/geneticvariation/page36 -
what is the reference genome here?


texts: Why "Having chlorophyll without photosynthesis is actually very dangerous" and "like living with a bomb"?

texts:
The Phys.org article Scientists discover first organism with chlorophyll genes that doesn't photosynthesize says

"For the first time scientists have found an organism that can produce chlorophyll but does not engage in photosynthesis.

It is referring to the new paper in Nature A widespread coral-infecting apicomplexan with chlorophyll biosynthesis genes (paywalled).

"This is the second most abundant cohabitant of coral on the planet and it hasn't been seen until now," says Patrick Keeling, a University of British Columbia botanist and senior researcher overseeing the study published in Nature. "This organism poses completely new biochemical questions. It looks like a parasite, and it's definitely not photosynthetic. But it still makes chlorophyll."
[...]
Chlorophyll is the green pigment found in plants and algae that allows them to absorb energy from sunlight during photosynthesis.
"Having chlorophyll without photosynthesis is actually very dangerous because chlorophyll is very good at capturing energy, but without photosynthesis to release the energy slowly it is like living with a bomb in your cells," Keeling says.

Question: Why is it that "Having chlorophyll without photosynthesis is actually very dangerous" and "like living with a bomb"?


texts: Is it possible to move your arms above your head when handcuffed in the back?

texts:
This move was seen in Pitch Black and i wonder if it is possible at all. Say you are handcuffed to a pole, hands in the back, and the pôle is a little higher than your head. You just want to do a complete loop with your hands, going above your head, so they end up in front of you and you are free of the pole.
Now, putting horrible pain aside, is it possible to perform this move alone?
If not, maybe with a small surface to rely on, for a lever effect?
Would it cause minor / major damage at all or just pain ?
I am also curious if performing this move slightly turned sideways help ( as much as you could at least, considering the situation). In the movie he goes one shoulder at a time.
Anyway, i hope im clear enough !
Exactly what i mean is this video at 1:35


texts:
This answer to the question How to clean and preserve a cicada's molted exoskeleton (exuvia)? states:

  The exuvia is made of cross-liked chitin, and will not decay. You don't need any special preservatives as all. If you need to get the mud off, just rinse it as you said, in soapy water, let it dry, and you are done. Simple.

Wikipedia's Chitin says only:

  Chitin is a modified polysaccharide that contains nitrogen; it is synthesized from units of N-acetyl-D-glucosamine (to be precise, 2-(acetylamino)-2-deoxy-D-glucose). These units form covalent β-(1→4)-linkages (like the linkages between glucose units forming cellulose). Therefore, chitin may be described as cellulose with one hydroxyl group on each monomer replaced with an acetyl amine group. This allows for increased hydrogen bonding between adjacent polymers, giving the chitin-polymer matrix increased strength.

I'm not a chemist, but "increased hydrogen bonding between adjacent polymers" doesn't sound the same as cross-linked polymers. So I would like to ask for an answer based on sources other than Wikipedia:

Question: Is the chitin in an insect's exoskeleton cross-linked? If it depends on the type of insect, then the focus should be on "a cicada's molted exoskeleton (exuvia)" as discussed in the linked answer.


texts: Did dinosaurs have more than one brain? If so, why?

texts: I once remember reading (15 years ago) that dinosaurs had two brains. One for their head and another one for their digestive functions. What is the current opinion on this theory? Has more evidence become available?


texts: Confusion about the role of capping and polyadenylation in nuclear transport

texts:
Before termination stage of transcription a GMP cap is added to the 5' end and poly-A tail to 3' end of mRNA.

The link(http://sciencing.com/role-rna-polyadenylation-5434666.html) says:

  The poly(A) chain is important for transport of the mRNA from the nucleus where it is synthesized to the ribosomes where protein is translated.

I don't get this point. How does polyadenylation affcts the transportation of mRNA?

Wikipedia says abour capping's functions:

  Regulation of nuclear export;
  Prevention of degradation by exonucleases;
  Promotion of translation (see ribosome and translation);
  Promotion of 5′ proximal intron excision.

I don't get how it plays a role in nuclear export.


texts: Have skeletons of "failed" animals been found yet?

texts:
I don't know what the correct term for "failed animals" is, but I mean those animals which wheren't able to survive due to their "failed" evolution process. Because evolution, as we see it today, has gone through a lot of "this doesn't work" and "this does work" - so the "good" outcomes of mutation have survived and the others haven't.

This is for some an argument against evolution, but just because they don't know really why nothing has been found or that something has been found.

So I want to ask if skeletons of any of those "failed animals" have been found or not. So is there any evidence of animals who had a "really bad" mutation (not illness, but mutation) and haven't survived in the process of evolution?


texts: Where can I find a list of transcription factors that are used in somatic embryogenesis?

texts: Where can I find a list of TFs that are used in somatic embryogenesis or zygotic embryogenesis?


texts: What does saying a phylogenetic tree is 'well resolved' mean?

texts: I'm not sure what 'resolution' means in the context of phylogenies.


texts: How is pain induced by blunt and sharp objects?

texts: Normally, when something touch you, you won't feel pain. With a great force "touching" you, you will feel pain. However, if something that is spiky makes contact with you, you will feel pain. So, how much force should be exerted by a smooth/blunt object to make you feel pain? When and how does a spiky object make you feel pain?


texts:
Many times, when there is rain after a long time, snails come out afterwards, and you can see snails and slugs everywhere! I have two questions:

Why do they come out after the rain?
Where are they usually found, not after a rain?

Note that I do emphasize when there is a rain "after a long time"


texts:
When is a cell said to be flaccid and when is it called plasmolysed?
So far I found that there is a specific relation to osmosis.


texts: Enzymes extracted from diferent tissue, may have diferent $K_m$ values under the same conditions?

texts:
My laboratory team has been used succinate dehydrogenase (1.3.5.1) from Gallus gallus domesticus breast (the most meated part of the chicken, where you will obtain nuggets) to determine $K_{m}$ and $V_{max}$ under 3 linearization methods.

But, in BRENDA page, I found various values for many organisms, like Bos taurus, and they select other tissues like liver tissue.

Why the difference?

PD. Any reference about where to find this values for Gallus gallus mesticus will be very appreciated.

EDIT: The reaction consists on dehydrogenating succinate to fumarate, on the tricarborxilic acid cycle. Include the creation of a trans-double bond.

Describing my laboratory practice, we macerate the meat with glass sand, and divide this mixture on 2 kinds: one with methylene blue and trichloroacetic acid (TCA) and one without TCA. Now I know that TCA is a protein precipitant, and methylene blue is an indicator; the less blue, the less succinate. So, with absorbance tests, we can elucidate [Succinate] vs time plot, and approximate the ratio $V_{max}/K_m$ from the michaelian equation for substrate concentration decay:
$$S(t)=S_0 e^{-\frac{V_{max}}{K_m}t}$$
Also, i think it will be possible modeling instantaneous velocity with its derivate and make the linealization plots, but i'm not very sure of this.

EDIT2: Thanks for the help with my practice report (I really appreciate it), but I still wanna know if it's possible to have different $K_m$ values on the same enzyme, only changing the tissue for reaction.


texts: Alleles refer to duplicate genes, where one allele can be dominant over the other. What makes an allele dominant or recessive, given that both code for a single protein?.


texts: Can mitochondria be regenerated by the cell?

texts: In the cell, division of mitochondria takes place on a regular basis, but what if there are no mitochondria present in cell (suppose all of them died), then can the cell make new mitochondria on its own?


texts: Why is the "worm" body shape so prevalent in Eumetazoa?

texts:
What is the selection advantage, of this incredibly common body form? (long, cylindrical tube-like body with no limbs)

Is it just the body plan of the ancestral bilaterian and therefore remained prevalent due to absence of selective pressure against it? I.e. is it a neutral adaptation? Or is it actually a positive one?

Examples of "worms":
- Platyhelminthes
- Nematoda
- Annelida
- many kinds of insect larvae
- sea cucumbers
- lancelets, lampreys, eels, snakes, caecilians, ...
- Chaetognatha
- Hemichordata
- Acanthocephala
- Gastrotricha
- Gnathostomulida
- Nematomorpha
- Nemertea
- Priapulida
- Sipuncula


texts: Start codon AUG also codes for methionine and without start codon translation does not happen. And even the ambiguous codon GUG codes for methionine when it is first. So does this mean that all proteins start with methionine as the first amino acid.


texts: Recommendations for an exemplary presentation of statistics related to preclinical drug studies and cellular chemistry?

texts: I am reading Nature's recommendations for collecting and presenting statistics, but would like to also read a few exemplary articles with good charts and data presentation to learn what it looks like when done well. Would be grateful for recommendations -- thanks!


texts: What is the difference between hilum of the lung and root of the lung?

texts:
In my book they describe root of the lung like this:
In the region of vertebrae TV to TVII, the mediastinal pleura refects off the mediastinum as a tubular, sleeve-like covering for structures (i.e., airway, vessels, nerves, lym-phatics) that pass between the lung and mediastinum. This sleeve-like covering, and the structures it contains, forms the root of the lung.

And hilum of the lung like this:
The root joins the medial surface of the lung at an area referred to as the hilum of the lung. Here, the mediastinal pleura is continuous with the visceral pleura.

I dont see the difference between Root and hilum.
Can somebody please help me out?


texts: NF-κB activated, but IRF blocked - Rewiring of immune response

texts:
Rubela virus has the following PAMPs: ssRNA, which will activate the following PRRs: TLR7, TLR8, RIG-I, and possibly MDA5. Dendritic cells infected with Rubela virus are reported to produce very low levels of IL-12p70 and to produce weak activation of naïve T-cells. DC-SIGN is one C-type lectin receptor (CLR) reported to be targeted by surface glycans on Rubela virus. Please explain in a few lines, via the principle of pattern recognition receptor rewiring, how the immune suppression by Rubela virus could be mediated.
My teacher's answer:
Triggering of DC-SIGN along with e.g. TLR7/8 would activate NF-κB, but block IRF activation. This would lead to weak IL-12p70 induction, and instead propagate IL-23, and perhaps IL-10 levels in DC.
My question is, how is NF-κB activated, but IRF blocked? I would say that both will be activated, when the TLRs are triggered. Also, how does IL-23 get in the picture? I would say that TLR7/8 would give a type 1 response, and the DC-SIGN would give a regulatory T cell response.


texts:
Found in Phuket, Thailand. White flower, five petals, 5 stamens. Strings of flowers hanging down from red stems. Buds white, tear-drop shape.

RHA, Here are the leaves. The flowers hang from a bush about 6 foot (2 metres Tall)

Bli, thanks, but not honeysuckle. No scent.


texts: How does the strength of 3D printed tendons compare to original tendons?

texts:
There have been some attempts such as {1,2} to 3D-bioprint tendons. How does the strength of 3D-bioprinted tendons compare to original tendons? I am mostly interested in human tendons.

References:

{1} Ede, David, Nikki Davidoff, Alejandro Blitch, Niloofar Farhang, and Robby D. Bowles. "Microfluidic Flow Cell Array for Controlled Cell Deposition in Engineered Musculoskeletal Tissues." Tissue Engineering Part C: Methods 24, no. 9 (2018): 546-556. https://doi.org/10.1089/ten.tec.2018.0184
{2} Rimann, Markus, Sandra Laternser, Hansjörg Keller, Olivier Leupin, and Ursula Graf-Hausner. "3D bioprinted muscle and tendon tissues for drug development." CHIMIA International Journal for Chemistry 69, no. 1 (2015): 65-67. https://doi.org/10.2533/chimia.2015.65 (open access)


texts: How do scientists determine the nature of ions passing through a channel/carrier/pump?

texts:
The NCE (Sodium Calcium Exchanger) transports 3 Na+ inside the cell for 1 Ca2+ outside.
How did we figure this out, and other mechanisms of this sort?
If it were a protein, we could tag it with GFP. But they're ions.
Looking at potentials isnt very informative either I guess; both K+ and Na+ have the same charge.
What is done, experimentally?


texts: Does anyone know any statistics about the rate of cell division of malignant cells?

texts: I've tried to look online to find some statistical data about the rate of growth of any type of cancerous cells, but haven't been able to find any. Would anyone know an appropriate time period for a single cancer cell to divide? Obviously, this hugely varies with the stage of cancer and type etc., but I am looking for any acceptable figure correct to an order of magnitude.


texts: Question about Racemic Mixtures in Miller-Urey Experiment

texts:
I'm studying the Miller-Urey Experiment for my Biology class, and a significant point made by my professor was that Miller made a 50/50 racemic mixture of chiral monomers.

However, life is homochiral.

I'm trying to draw some significance out of Miller and Urey's experiment. Could life have started in multiple various places (because all you need for life to start is some organic molecules), so you could have developed various chiral forms of polymers (like amino acids), but one chiral form dominated and thus natural selection favoured that one form?

Thank you!


texts:
Please help identify this species found at home.  I think it's a moth. Size is about 1 cm.

Is it harmful if found at home?

Location: urban home in Hong Kong

 Click photo for full-size picture


texts: How could this molecule affect the body? (Lysergic acid derivative)

texts:
First of all, could you please help me name this molecule? I think the name of it is something like this: N,N-pentamethylene lysergic acid. Secondly, my main question is what could be the pharmacology / mechanism of action (eg the target receptors, etc.) of this molecule? I couldn't find any info on DrugBank, so I'm all ears to your ideas. Please help me on this; it is quite a burning question.

P.S.: If there are any mistakes in my English, please excuse me.


texts:
Do they form a peptide bond? Or is it just some affinity/van der Waals interaction?

Is the mechanism enzyme catalized?

Are the residues/moieties at the join site known? Could they be introduced to synthesized peptide fragments to achieve something like native chemical ligation?


texts: Fine permanent fluorescent marker for blue light

texts:
I am looking for a fine- (or small-)tipped permanent marker to write on Petri dishes that is visible under a blue light or a transilluminator. It would seem obvious, but it is a nuisance.

The Sharpie Neon series are too thick.
Highlighters and all the arts pens I have tried rub off the polycarbonate.
The red colour from Staedtler lumocolor (black body) shows up faintly —none of the other do— but too faintly.
The Neon series from Staedtler triplus fineliner (gray body, triangular) rub off

So I would like to find what solutions other have come up with or if there is a brand that works well.

EDIT. This is how the Sharpie series look:


texts:
Gene : HBA2? hemoglobin alpha 2 (Homo sapiens)

I don't find any tissues (or organs) in which the expression of this gene is strongest? What is the size of the gene (promoter off) encoding this sequence?


texts: Difference between going against and going down a concentration gradient

texts:
The difference between facilitated diffusion and active transport is that facilitated distribution occurs down a concentration gradient and active transport occurs against a concentration gradient. I understand that, as a result of these differences, active transport uses ATP so that it can bind to the carrier protein, however I don't know what is meant by going against a concentration gradient or down a concentration gradient.

In short, I would like to know the difference between going against and down a concentration gradient. A definition of what a concentration gradient is might clarify things a little further as well, since the definition I have doesn't help much.


texts: Just how light-sensitive is ethidium bromide?

texts: One lab I was in was paranoid about keeping it in a foil-wrapped conical tube; my current lab leaves it out on the bench (and it works fine for staining gels). It's the same company/concentration in both cases, but this second lab uses it up much faster.


texts:
The cell proper contains the cytoplasm in general and the cytosol in particular when referring to the fluid/gel without notable organelle.

Once we move inside the nucleus there is the nucleoplasm and the nucleosol.

My question is in the intervening void of the perinuclear space (between the inner and outer membrane of the nuclear envelope) what if any is the terminology used to refer to the internal chemistry in that space - and what is known about it's makeup?


texts: How does Sanger sequencing resolve two bands with equal size?

texts: In Sanger sequencing, how can we read the sequence if we have 2 bands with the same size?


texts: Kinetic binding / unbinding constants of protein + mRNA ⇌ mRNP

texts:
I wish to find an order of magnitude for the binding/unbinding constants of mRNA and RNA-binding proteins.

Suppose molecules A and B reversibly associate to give the complex C. Assuming the diffusion is large enough such that no concentration gradient exist, the reaction equation at equilibrium is:

➕[A][B] — ➖[C] = 0

with ➕ the binding constant (units: concentration-1.time-1), ➖ the unbinding constant (units: time-1), and [A], [B], [C] the concentrations of the molecules.

I found many papers assessing the equilibrium constant K = + / ➖ but I am interested in + and ➖ independently.


texts: Is secondary follicle or Graafian follicle arrested in the second metaphase of oogenesis?

texts:
My note about which I am not sure:

  Secondary oocyte is arrested in the metaphase II monthly after puberty until fertilization with sperm.

The following picture also satisfies my sentence: .

So you can see that the secondary oocyte that is arrested seems to be Graafian.

I know that Graafian develops during the second week.
I know that the secondary follicle is developing two days before ovulation.
It seems that the development of the secondary follicle ends and the formation of Graafian follicle occurs just before ovulation.
My lecture material suggests that Graafian follicle is arrested in metaphase II, since Graafian follicle is ovulated once in a month and waits sperm in tuba uterina infundibulum:

The answer to my question is not also clear from my previous thread:

  An oocyte completes meiosis I as its follicle matures (during ovulation) resulting in a secondary oocyte and the FIRST polar body. After ovulation, each oocyte continues to metaphase of meiosis II.

Which follicle is arrested in the metaphase II of oogenesis?


texts:
Why some seeds are mucilaginous (chia, rucola)?
It is not obvious what kind of preferences that can bring to them. What is a role of mucilage in seeds cultivation?

P.S. The cultivation in germination cup shows only "difficulties": more affected by micro-flora, harder consequences after become too dry...


texts:
When we assume that peripheral touch receptor densities are equal in tall and short people, then tall people should have more touch receptors than short people, given the larger amount of skin surface in the former. Hence my question:

Do taller people have larger somatosensory cortices than short people? And analogues to that, what about larger motor cortices in tall people? If tall people need larger somatosensory and motor areas, could this imply that they have less space devoted to other functions, like functions devoted to the prefrontal cortex?


texts: Plasmodium sp. does not have any locomotory organs. So, how does it move? What biochemical process allows it to move?


texts: Can plant fruit and seeds be albino like animals?

texts:
There are numerous examples of albino animals, including snakes, birds, fish, mammals---humans too. Apparently this comes from some a genetic defect that results in lack of pigment.

What about plants? Obviously a lack of chloraphyl would be fatal for a plant, so I'm imagining the seed or fruit being white. Does this exist in nature?

Edit: I'm thinking of fruit/seeds that are not normally white.

Note the wiki page I cited has only 2 paragraphs on this:

  In plants, albinism is characterised by partial or complete loss of chlorophyll pigments and incomplete differentiation of chloroplast membranes. Albinism in plants interferes with photosynthesis, which can reduce survivability.[4] Some plant variations may have white flowers or other parts. However, these plants are not totally devoid of chlorophyll. Terms associated with this phenomenon are "hypochromia" and "albiflora".[5]

That last part seems what I'm interested in, but the cite is a dead link.

Later in the article:

  The primary function of pigments in plants is photosynthesis, which uses the green pigment chlorophyll along with several red and yellow pigments including porphyrins, carotenoids, anthocyanins and betalains.

No cite there and not much info anyway.

So are white seeds or fruit found in nature?

If you're curious, I originally thought of this as an alternative way of getting white chocolate from an albino cocoa bean, and maybe even a white coffee bean too.


texts: How does RNA polymerase achieve higher processivity?

texts: DNA polymerase uses a sliding clamp in order to replicate DNA. RNA polymerase does not require one. What allows RNA polymerase to hold on to DNA just like DNA polymerase?


texts: Are some people more 'attractive' to mosquitos? If so, is that a hereditary trait?

texts: Mosquitos clearly love me-- but I have been told I am just more reactive to mosquito bites. Are some people more 'attractive' to mosquitos (get bit more)? Or is it just that they are more reactive? If it is an 'attractive' trait-- is this hereditary?


texts: What does reflected onto means in the text below?

texts: The pleura lines the thoracic wall and diaphragm, where it is known as the parietal pleura. It is reflected onto the lung, where it is called the visceral pleura.


texts: Anesthetics, specifically inhaled anesthetics

texts:
I have had a look at previous inhaled anesthetics and many of them appear to be fluorocarbons. What could be the mechanism behind fluorine's anesthetic properties? Is it the specific bonding pattern or the molecules involved?

I realize anesthetics are rather unknown I just wondered what people have as a hypothesis?


texts:
How long do sickle red blood cells "live" before being broken down in phagocytosis?

I had trouble doing a normal search as it brings up life span of those inflicted with the disease. Also, I have been doing a semester long assignment, where we are delving into all aspects of this disease, and I have 20 sources so far and still haven't come across the answer.


texts: Can galls be formed from mutualistic relationships?

texts:
According to Wikipedia, galls (cecidia) are formed by parasitic insects and mites like gall wasps (Neuroterus albipes). At some metamorphic stage, these organisms alter cell division processes in meristematic tissues of their host plants, which creates a tumour on (typically) the surface of leaves, branches or roots. These organisms use the galls as their habitat and/or food source (exploiting the sugars present).

However, I also know that bullhorn acacia and ants form an interspecific mutualistic relationship (with galls), so apparently galls don't need to be parasitic. Are there any other specific plant-insect pairs that have the same type of mutualistic gall relationship as the acacia-ant system?


texts: Why bipolar neurons in retina transfer information via graded potentials?

texts:
Why should bipolar cells prefer graded potentials to action potentials?

My attempt:
I know that graded potentials are better in processing information since stimulus is directly proportional to response generated unlike action potential where the response is always same.

Reasons:
But I don't understand its need in bipolar cells , because graded potentials  have already been generated in rods and cones. Also the final message coming out of eye is in the form of action potentials from ganglion cells. If graded potentials were of that importance then why they do stop at bipolar cells and continue as action potentials in the later pathway?

Finally, graded potentials are slower than action potentials so latter should be preferred in places like eyes where response is needed to be quick.


texts: Are “tremors” and “ tetanic contractions” the same thing?

texts:
Do these two expressions have the same meaning?
1- Tetanic contractions in the skeletal muscles
2- Rythmic shaking of the hands
(These two expressions are supposed to be two symptoms of Parkinson’s disease ,however I am told that this is repetition)


texts: What has caused life to choose this unfathomably tiny subset of all possible proteins?

texts:
I wonder why life uses the particular proteins that it does, about 10^6 different proteins, I think? Evolution cannot explain it because the number of possible proteins is far far too large to ever come into existence anywhere in the visible universe, let alone on Earth. And evolutionary selection only works on stuff that exists.

Is there some chemical or other explanation, or is this an unresolved paradox in biology?

The median number of amino acids in a human protein is 375. Most are longer than 200 and maybe all are longer than 100. The 20 different kinds of amino acids can be combined to 20^375 = 10^487 different proteins which have the length 375.

If the entire crust of the Earth consisted of proteins which all were 375 long and each protein mutated once every nanosecond during 5 billion years and each mutation resulted in a protein which is unique in time and space, and there exists 100 such "protein Earths" around every star and 1000 billion stars in each of 1000 billion galaxies in the visible universe, it still only adds up to something like 10^100 proteins. Adding 10^37 years until the last star remnant has cooled down to less than 1 Kelvin, doesn't change this picture, almost all of the possible proteins will literally never exist anywhere. Even if I'm off by a factor a million on each of those numbers, only one in 10^300 of all possible median length proteins could ever exist.

Since our mind-bendingly small subset of possible proteins supports life, shouldn't we expect that many many (as in 10^300) other potential subsets of different proteins would do so too? And can we conclude that if DNA/protein based life has originated somewhere else, it will not have even one single protein in common with us or with any other independent origin of life? Or is this focus on proteins somehow invalid?


texts: The effect of 3D structure and solubility of the binding site of enzyme on its affinity Km and maximum activity Vmax?

texts:
Could some one provide me with some resources or papers where I can read more about the following:

1- How can the 3D structure of an enzyme affect its Km and Vmax? (some papers, books or articles will be very neat).

2- How can the solubility of the amino acids of the binding site of an enzyme affect its Km and Vmax? (again some paper, books or articles will be very helpful).

Or maybe some description about that with some references? I spent some time in searching but unfortunately with no attractive results.

I just resay that I am inneed for some resources or papers about the two points in addition to some word explanation.

Thanks in advance!


texts:
Lead is known to be bad for your health for a long time, but I can't find a explanation why is it so.

In school they teach that heavy metals are poisonous, and they are trapped inside our bodies. I can just assume that the liver can't process those elements. But I still don't understand why this happens.

And finally why is lead different from, let's say, gold that is also a very dense metal, but is safe.


texts:
Can GHK equation be used to predict the membrane potential even if the cell is not at resting state?
To say it again, can we use GHK equation at every moment during Action potential?
I'm confused because GHK equation is derived at the situation with total ionic current is zero, but is that true also during AP?


texts: Why is there a compound highlighted in red in a KEGG Module search?

texts:
Considering the following module:
http://www.kegg.jp/kegg-bin/show_module?M00115+C00003
why is the compound C00003 marked in red?


texts: Bilirubin metabolism and UGT1A1 inhibition in human vs. monkey?

texts: In human UGT1A1 seems to be the only relevant enzyme to glucuronidate unconjugated bilirubin into excreted forms. Is the pathway the same for e.g. the Cynomolgus monkey (Macaca fascicularis) in vivo? In case UGT1A1 is potently inhibited are there any other potential enzyme to metabolise/glucuronidate unconjugated bilirubin in monkey? Furthermore, bilirubin is analytically challenging in UGT1A1 inhibition studies in vitro. Estradiol (3-glucuronidation) has been used as a specific substrate for human UGT1A1. Do you know any substrates known to be specific for monkey UGT1A1?  Any reference would be highly appreciated.


texts:
I've been transforming E. coli via heat shock in order to insert oligonucleotides (around 50 nt); however, none of my experiments have given positive results so far. I begin to question the efficiency of chemical transformation, especially for short DNA fragments. Is there such a notable difference between chemical and electro transformation?

EDIT: I'm checking for CRISPR array expansion, so my oligos have a protospacer length and structure. I'm using BL21(DE3) cells which have an IPTG-inducible T7 that I'm first transforming with a Cas1-Cas2 plasmid. Then, I induce the cells in order to express those proteins, make them competent, and transform then once again but with the oligos and an eGFP plasmid (for some sort of selection). To check for positive results, I'm amplifying the leader-repeat junction of the CRISPR array and compare its length (via electrophoresis) with a usual array that has no integrands.


texts: Is there biological evidence for self-awareness in animals?

texts:
I am conducting an investigation into the topic of the intelligence of
animals, in particular farm animals. I would be interested to hear a scientific and biologic perspective as to what is perceived to be self-awareness, whether it be in a human or
not. Specifically, I am interested in the high-level self-awareness that we as humans experience and that is only now, beginning to be theorised as possible in other mammals (e.g. Dolphins).

The question is framed in a robotic context, where a being (natural or artificial) is defined to be self-aware if it can approximate enough human behaviour and thought, that it becomes indistinguishable from a human. This term we could label sentience, but this is a subjective term, and so I will avoid using it for the purpose of this question. I will define a being as self-aware in the robot context, as a being capable of both conscious reflection of itself and of its own conciousness.

One of the problems I have found in my investigation, is a serious
misunderstanding about the nature of self-awareness, amongst
the general public.

It seems that many people incorrectly assume that self-awareness is a product of
a being having a soul. This is rather unfortunate for animals as orthodox
Christianity teaches that animals do not have souls, and therefore are
incapable of attaining self-awareness.

My investigation aims to bring to mainstream public attention, a new
definition of self-awareness, and to end the centuries-old misconception
that we are the only intelligent, self-aware creatures on the planet.


texts: Why we have just 2 teeth cycles, primary and secondary not more?

texts: After baby teeth go, secondary teeth grow, is there a scientific reason why they are just 2 sets not more?


texts:
I have been reading some literature on measurements related to biofilms.

In some articles the word "substrate" seems to stand for the material on which a biofilm is growing. In other articles, it seems to stand for the nutrients that are freely floating in (say water) where the biofilm is growing, and which then diffuse into the biofilm and which it uses to grow.

Have I misunderstood something or are both of these meanings in active use? Is there a disciplinary or some other difference that determines who uses which term?

The review article [1] uses substrate to mean freely floating nutrietnts. Also, searching for "substrate loading" or "substrate loading rate" or such (on Google scholar) gives examples of substrate as something that is fed to the biofilm.
For example Wikipedia uses the other meaning of substrate: https://en.wikipedia.org/wiki/Substrate . Scientific literature with this meaning can be related to how easily biofilms detach from a given material in the presence of shear forces.

[1] Harald Horn and Susanne Lackner. Modeling of biofilm systems: A review. In Kai Muffler and Roland Ulber, editors, Productive Biofilms, pages 53–76. Springer International Publishing, Cham, 2014.


texts: What are the short/long term effects of chloroquine on fundamental cell processes?

texts: Does chloroquine, which affects the endosomal membrane traffic pathway (by affecting the acid environment used for fundamental endosomal reactions), have short/long-term effects on cell growth/proliferation/signaling?


texts: Various Genetic Loads and their Definitions

texts:
In population genetics, we talk about several types of genetic loads (also called just loads). I am asking for a exhaustive list and a short definition.

Here are for example some genetic loads that come to my mind..

Mutation load
Segregation load
Drift load
Lag load


texts: What are the ESSs among hawks, doves, retaliators, bully and prober retaliators?

texts:
In his book "The Selfish Gene", Richard Dawkins says that retaliator emerges as an evolutionary stable strategy. But I think dove is also a kind of retaliator and so if dove increases,  the hawks and others can exploit them.

Is retaliator an ESS? If not, which strategy is ESS?

Definitions:

hawk : They always fight hard and retreat only when injured.
doves : They merely threaten in a dignified way and never hurt anyone.

If a hawk fights a dove, dove runs away. If dove meets dove they go on posturing until one of them is tired and retreats. If a hawk meets hawk they fight until someone gets seriously injured or dies.

retaliators : A retaliator plays dove at the beginning of every fight. If opponent attacks, he attacks , if opponent behave like a dove he behaves like a dove. When 2 retaliators meet they behave like doves.
bully : A bully behave like a hawk until someone hits back. Then, he runs away.
prober retaliator : He is like a retaliator but he tries a brief escalation of the contest. He is hawk like if opponent doesn't strike back. If opponent strikes back he behave like a dove. If he is attacked he retaliates.

The pay offs: 50 for winning, 0 for losing, -100 for being seriously injured. and -10 for wasting time in a long contest.

Source: The Selfish Gene


texts: Does a virus that spreads more rapidly have less chance to evolve?

texts:
Now that the COVID-19 pandemic has been going on for a while, there are reports of many new variants, which have presumably arisen in the past year through mutation and spread through natural selection.
I'll assume that the outcomes of COVID-19 infection are either death or a successful immuse , others would have developed antibodies. Suppose for the purposes of discussion that those are the two end consequences (or correct my answer in your thinking.)
If eighteen months ago, everyone in the planet had been infected with COVID-19 in one very bad day, then many people would die, and the others would end up with antibodies. That might stop the spread of the disease, which would stop its evolution. (Feel free to address Typhoid Mary-like scenarios in the answer; or of course any misconceptions in this paragraph.)
Is there a perspective from which—or set of circumstances under which—drawing out a pandemic can actually worsen the effect of a disease by giving it more chance to evolve?
(I've put the question in terms of COVID-19, but I think it's really a generally question, no less applicable to COVID-20 and above. :-) Please feel free to answer in general terms. I am not looking for a discussion about what public health measures may or not be appropriate to the current pandemic.)


texts: Clarification on Hatch and slack pathway

texts:
The following is a minor clarification that I want to make, since it is rarely addressed directly in most of the texts I have gone through.

In C₄ pathway, the chloroplasts are dimorphic, that is, the bundle sheath chloroplasts contain RuBisCO, but lack grana and can hence perform only the light-independent reactions. The mesophyll chloroplasts lack RuBisCO but contain the granal apparatus to perform light reactions for synthesis of ATP and NADPH. The bundle sheath cells are impervious to gaseous transport (to prevent the entry of O₂), but recieve the required CO₂ by the intake of an organic acid produced by CO₂ fixation by the mesophyll cells.

  But, to effect the Calvin cycle in the bundle sheath cells, it
  requires a high concentration of the light reaction products, i.e.,
  ATP and NADPH. Since they themselves lack grana, they must obtain the required share from elsewhere. Where do they obtain it
  from?

My guess is that NADPH enters the bundle sheath cell with the organic acid primarily produced in the mesophyll cells where light reaction occurs. ATP is met by a similar uptake plus the utilisation of the ATP produced by respiration. I need to confirm this as it is usually never addressed in texts.


texts: More than 1 washed up on a beach in Ireland..close to some big jellyfish


texts: What are some of the immediate challenges to break through before finding a cure for mad cow disease?

texts:
What are the immediate challenges to break through in seeking a cure for mad cow disease?

I know that mad cow disease has no treatment as of yet.


texts: Problem on Probabilty of a restriction enzyme cutting a random DNA sequence

texts:
I think its a silly question to ask here. When I came to this site all I could see were the questions which asked detailed explanation behind a phenomenon and reasoning was there at first place. I am bringing quite math here!!!

First, I am a beginner.

Second, I would like to mention some problems..

Genomic DNA is digested with AIU I, a resrtiction enzyme which is a four base pair cutter. What is the frequency with which it will cut a DNA assuming a random distribution of bases in genome?
Eco RI and Rsa I restriction endonucleases require 6 bp and 4 bp sequences respectively for cleavage. In a
10 kb DNA fragment how many probable cleavage sites are present for these enzymes?

These questions were solved by my teacher using some probability results or rules.
I would like to mention it here.. [you know already...!!! ;-)]

(1/4)^n *10,000 or simply (1/4)^n. By putting n = number of base pair cut by enzyme.

I get the frequency with which enzyme will cut a DNA assuming a random distribution of bases in genome by using (1/4)^n and I get probable cleavage sites are present for Eco RI and Rsa I in 10 kb DNA fragment.

But why do I do that? I mean why that formula? How to understand how it was derived? Can you explain me that?

Please suggest some good books containing concepts and numerical problems like these so that I can work on it.. [Please let me know your source]. Thank you.


texts: How can I change my buffer system for protein purification?

texts:
I have a protein that I purified in PBS buffer, pH 7. I will do dialysis to remove salt and will then further purify the protein with ion exchange chromatography.

I will need to use another buffer (Tris-HCl) with pH 8 in the chromatography, and so my question is: Can I change the buffer system for my protein in the dialysis step? Or would you recommend me to use the Tris-HCl buffer from the very start and then just adjust the pH for the chromatography?

Thanks in advance!


texts: What is the theoretical maximum height of a herbaceous plant stem?

texts:
Foreword: I'm posting this here instead of, say, Worldbuilding, because while it is based in a speculative concept, this is a question purely of biology as we know it instead of speculative biology under non-real conditions. I would address that later and elsewhere. And sorry if this is actually more physics than biology, I have trouble pinning these things down.

I'm trying to determine what the maximum height of a non-woody plant stem can be (i.e. I don't want the tallest flowers). I think the primary issue at hand is load-bearing and resistance to bending. So I found this 1997 paper by Schulgasser and Witzum that sort of discusses what I'm looking for. It suggests that the plant's ability to resist shear forces is a matter of how bundles of fiber are arranged inside the stem and of the plant's internal pressure, which affects how much weight it can stably bear. But I'm no biologist, so the paper is difficult to penetrate. I'm sure there are other issues limiting the height of non-woody plants, like the maximum height above the ground that capillary pressure can raise water. Considering all factors, what is the theoretical maximum height of a herbaceous plant?

I've found this question, which concerns the tallest real herbaceous plant, while my question concerns the theoretical. But I would like to extend that question - are there any examples of fossil herbaceous plants that are larger than the modern banana plant, and do they run up against the theoretical maximum?


texts: Yesterday I noticed an array of filament type structures, each with a bulbous feature at the end, hanging off my car door. As can be seen in the first image, these structures are quite small (comparing to door handle/key hole). I live in Kentucky, USA. What are they?


texts: What is the difference between HPLC and FPLC and why is FPLC preferable for protein purification?

texts:
I've used HPLC (high performance liquid chromatography) before (once, so I'm barely even qualified to know what it stands for) so I was surprised when my labmate told me she would be using an alternate technique to isolate a protein.

What exactly are differences in HPLC and FPLC (fast protein liquid chromatography) instruments, and why would FPLC be a better technique than HPLC to use with proteins? What situations make HPLC preferable?


texts:
Spider silk is pretty darn strong and all sorts of comparisons are made to steel. I'm more curious about the various moduli of spider silk and how it compares to other materials. What is the Young's modulus of spider silk? What is the bulk modulus of spider silk? What is the shear modulus of spider silk? In general how do those moduli describe the material properties of spider.

A simpler way to ask the question, what does it mean when it is said that spider silk is strong?


texts: Roles of creatine and bilirubin in foetus circulation

texts:
I think they are not inputs from maternal placenta.
I think they are the results of foetus metabolism.
However, I do not understand it how and where exactly.

What are the roles of creatine and bilirubin in foetus circulation?


texts:
What it the diffusion coefficient of blood in, e.g. water?
It is needed for microchannel length calculations

I have found a bit different nubmers: 0.94 and 1.66 microns^2/ms, but not sure


texts: What was the cause of some egg-laying animals evolution to animal-laying?

texts: Is there a specific reason for this evolution? Are no egg-laying animals more complex beings so their embryonic  development requires more time and better nutrition conditions?


texts:
From Giulia Enders, Gut: The Inside Story of Our Body’s Most Underrated Organ

  Mucins are proteins that form the main constituent of mucus. They help provide hours of fascination and fun for young children who have just found out they can blow bubbles with their own spit. A more useful function is their ability to envelop our teeth and gums in a protective mucin net. We shoot them out of our salivary papillae like Spider-Man shoots webs from his wrists. These microscopic nets can catch bacteria before they have a chance to harm us. While the bad bacteria are caught in the net, antibacterial substances in our saliva can kill them off.

What is the mucin net the author refers to? No result is found when googling it.


texts: Is it possible to have both type-1 (insulin-dependent) and type-2 (non-insulin-dependent) diabetes mellitus? That is, to have both insulin resistance and zero (or negligible) insulin production? If not, why not? And if so, then how common is this (among humans with each type of diabetes)? Any information on why the comorbidity may be high or low is also most welcome.


texts: Orange tipped plant found in Carden limestone plains of Ontario

texts:
What is species is this plant?

Found in the Carden limestone plains of Cameron Ranch (near Orillia, Ontario, Canada) on September 9th, 2017.

It is located in an old bog that seems to have sphagnum peat moss (to my untrained eye).


texts: Cells have mechanism to repair damaged DNA. So why don't the cells in moles (the spots), repair themselves and the moles dissappear?


texts: Is feeding wild pigeons really "weakening the entire species"?

texts:
While reading about what foods are healthy for pigeons, I came across the following paragraph: (Source)

  Human interaction and improper feeding of domestic and wild pigeons is believed to be one of the reasons for the birds' decline. While many urban areas claim that pigeon populations are out of control, the truth is that around 59 species are currently threatened by extinction, which is over 20 percent of the pigeon population. Since the 1600s, 10 species of pigeon have become extinct. While habitat loss and over-hunting are partly to blame, bird specialists believe that domestication and improper feeding has weakened the entire species.

There are no sources cited. What does "weakening the entire species" even mean? What evidence is there to support the claim that improper feeding is weakening entire species of pigeons? How would overfeeding by humans lead to extinction? And how would domestication be contributing?


texts: What kind of insect is this found in North America in April?

texts: I noticed this small insect that probably measured 5 mm in length on my coat lapel. Not sure whether or not it had been inside or landed outside on my coat. Photos were taken in Nashville, Tennessee, USA in April. It was alone and I have never seen an insect like this one before. Just trying to figure out whether this bug is harmless or something that could be a problem. . Here is another photo taken of the same insect.


texts: Is Brain Eye connections reversed in all animals or just Humans?

texts:
I know that Brain Eye connections are reversed in Humans,

Left Hemisphere controls the Right eye/Right side of the body
Right Hemisphere Controls the Left eye/Left side of the body

Is it true in other animals like Birds,Cephalopods and other creatures?
Are the optic nerves physically connected in reverse or is it internally mapped ?


texts: heart rate vs pulse strength when exercising

texts:
I have noticed, depending on the exercise I am doing, two different patterns (and probably every combination in between):

if I do an exercise like biking, I can feel I have a faster heart rate but the pulse (touching my neck) doesn't feel very strong.
in opposite, I have noticed that if I do an exercise like push-ups, the heart rate is not as high, but the pulse feels stronger.

why the difference?


texts: Why is liquefactive necrosis only seen in brain?

texts:
Liquefactive necrosis is a type of necrosis uniquely observed in brain. This occurs due to breakdown of cellular proteins by the action of hydrolytic enzymes.
In other parts of the body, usually a different form-coagulative necrosis is seen.

What makes the brain so unique that this form of necrosis is only limited to brain?


texts: Location of genes encoding ribosomal proteins

texts:
I have cited two sources below: the first, a textbook, says ribosomal proteins are imported into the nucleolus (from the cytoplasm) where initial ribosome assembly occurs.
The second is a journal which asserts, in the first paragraph, that ribosomal protein mRNA is processed in the nucleoplasm, distinct from the nucleolus.
I am therefore very curious about the location of ribosomal protein genes whose transcript is the mRNA; specifically whether these are located in the nucleolar region or not.
Sources:

"Histology a text and an atlas" by Michael H. Ross and Wojciech Paulina. 6th Edition; pg. 79.

"Nuclear and Nucleolar Targeting of Human Ribosomal Protein S6" (Carola Schmidt, Edgar Lipsius, and Joachim Kruppa) ; Vol. 6,1875-1885, December 1995.


texts:
Recently I saw this news trending, I never heard single
disadvantage regarding masturbation.

But China Army considering it has danger for army.
So How Excessive masturbation can make a person unfit for army?


texts:
There is an area of where there is a distinct line of only trees on one side and only shrubs on the other (right next to each other). What could cause this?

My attempt: I said there could be a difference in sunlight, but I'm not sure.


texts: Connectivity Relation between axon terminal synapses and dendrites

texts:
With regards to the synapses between axon terminals and dendrites, what is the relation between a given neuron's axon terminals and its neighbouring neurons' dendrites?

Does each axon synapse on only a single dendritic spine from another neuron, whereby all other connections that axon makes are with distinct neurons, or
Can multiple axon terminals from a given neuron end up connecting to a single neuron via multiple dendritic spines?


texts: Is it better to maximize sleep, or align to ~1.5 hr cycles

texts: What is better for the body, to sleep 6 hours (4 deep sleep cycles) or to sleep 7 hours, but interrupting the last sleep cycle. I know I feel a lot better with 6, but am curious as to its medical consequences. Does the brain have a chance to repair/clean itself properly with this lesser amount?


texts: Why do erythrocytes have no MHC1 but platelets do?

texts: Red blood cells do not have a considerable number of MHC1 through their membranes, and that's explained by them not having a nucleus. But why do platelets have MHC1s if they have no nucleus either? I don't think that lifespan is a good enough explanation since that would mean young red blood cells have MHC1s and old platelets don't, since the latter can last over a week in circulation. Megakaryocytes do have MHC1s, but that means nothing, since red blood cell percursors also have them.


texts: What is the difference between transpiration and evapotranspiration?

texts:
According to my point of view transpiration and evapotranspiration are different things, but i am confused about this topic. After great effort, I found a major difference between it.

Transpiration: The loss of water in the form of vapour from plants surface is called transpiration.

Evapotranspiration: The loss of water from any surface in the form of vapour is called evapotranspiration. Such as water surface, soil and any body surface.
By educationspot

Is it correct? Please explain.


texts: Which mammals cannot synthesize taurine?

texts: It is fairly common knowledge that domesticated cats cannot synthesize the compound taurine. Other mammals seem to be able to synthesize taurine from cysteine [source]. Are there other mammals that lack the ability to synthesize taurine?


texts: Cooperativity of haemoglobin and oxygen dissociation curve of haemoglobin

texts:
Haemoglobin shows positive cooperativity with oxygen. When an oxygen atom binds to one of hemoglobin's four binding sites, the affinity to oxygen of the three remaining available binding sites increases; i.e. oxygen is more likely to bind to a hemoglobin bound to one oxygen than to an unbound hemoglobin. This is referred to as cooperative binding.

Haemoglobin reaches 50% saturation when the partial pressure of oxygen reaches about 28 mm Hg. Now partial pressure had to be increased by about 70 mm Hg for haemoglobin to reach maximum saturation. If haemoglobin is a cooperative molecule, once haemoglobin reaches 50% saturation it should be easier to attain ~100% saturation. But it is taking a difference of 70 mm Hg. Whereas 50% saturation requires only 28 mm Hg.
Hope this makes sense.
Please answer this and correct my understanding.
Thank you


texts: The reason why researchers usually use cell lines from "blast cells"?

texts: What's the reason why researchers usually use cell lines from "blast cells" (so, immature, like lymphoblastoid cells) for measuring gene expression data? Is that they are growing up, which would make their expression data higher and more significant?


texts: What does myelin insulate against, exactly?

texts: I am aware of the saltatory conduction model, nodes of Ranvier and all that, and that myelin lets electrical signals "jump". What does not add up to me entirely is what the myelin sheath insulates against, why it improves conduction through axon. If the cell membrane is already impermeable to ions, why does a "thicker membrane" improve signal conduction? There are nearly infinite memes on the internet about action potentials through axons, have not really seen any answer this though. Some vaguely mention "less leakage", but isn't the cell membrane preventing that to begin with?


texts: How is energy stored in the cotransport of molecules down to its electrochemical gradient?

texts:
I am talking about symporters and antiporters, that transport usually an amino acid against its concentration gradient while at the same time transport another molecule down its electrochemical or concentration gradient or both. It is said that "cotransporters use the energy stored in electrochemical gradient", but I do not understand what do they refer to when talking about storing energy.

Thanks in advance.


texts: Over-consumption of water in a short period of time

texts:
With too much water consumption at once, the blood will become much more hypotonic. Therefore, a larger amount of water will remain in the blood as the kidneys cannot ultrafiltrate all water out from the blood.
Therefore, the blood will be diluted, hence the concentrations of electrolytes decreases.
I searched for the illnesses caused by the over-consumption of water. What I mainly found is only hyponatremia, which is low content of Na+ in blood, and the symptoms caused by hyponatremia. However, I am thinking about why seems only the concentration Na+ decreases, but not other electrolytes e.g. K+, Cl-, which are vital for metabolism and homeostasis?


texts: unsaturated fatty acids and hydrogenation

texts:
what is the need to hydrogenate unsaturated fats?

When we hydrogenate the unsaturated fatty acid, we eliminate double bonds by adding hydrogen atoms, and this straightens out the natural bent shape of the unsaturated fatty acids. But why would we choose to hydrogenate unsaturated fatty acids before consuming them?


texts: How does translational coupling work in prokaryotes?

texts: Today I heard about a phenomenon called "translational coupling", where the translation of one protein influences the translation of another protein. The messenger RNA levels don't seem influenced. How does this work? Do they need to be in the same operon?


texts:
As I know Plasmodium falciperum survive in either a host animal, human or mosquitoes.

But how does malaria come to infect either of them initially?
I am interested in knowing evolution of malaria. How it infected first mosquitoes when neither human nor any other mosquito was infected?


texts: Measure of relatedness between two animals

texts:
So I am aware there is such a thing as inbreeding coefficient which is a number allocated to an individual as a result of taking the average of it's parents' inbreeding coefficient.

(Note that I am working in terms of pedigree based relatedness, not genomic relatedness.)

Is there a number that quantifies the relationship level between 2 individuals?

If so how is this calculated? Can it be done in R using the pedigree package?

Where say a sire and ewe have a 0.5 value or something similar?


texts:
The classical definition of the Genetic Matrix

G = ZZ'/2p(1-p)

where Z = M - P

where P = 2(p-0.5)

I don't have a background in biology but understand Maths and Computer Science very well. I am trying to wrap my head around

1) Why do we define P the way we do?
2) Why do we subtract  P from M
3) How to interpret a negative entry in G?
4) Does the j,k element of G give me the genetic distance between j and k individuals?


texts:
I am currently studying DNA extraction from various bio-originated samples. I am new to this field, and have learned how commercial DNA extraction kits work for bacteria.

I understand that the very first step is called 'lysis', and that this is supposed to break cells to pull out all the stuff inside them, including DNA.

I am studying cell-free DNA extraction procedure from human blood, and I don't understand why the lysis step is necessary in this context.

If lysis is to break cells, and cell-free DNA is already out of the cell and freely circulating, such a step seems unnecessary.

Is my understanding about lysis right? Then, why is the lysis step necessary during cfDNA isolation?


texts: How does RCSB determine the origin of the Cartesian coordinate system utilized in all PDB files

texts:
When perusing through the text version of a PDB file, I noticed in records that begin with "ATOM," there are x, y, and z coordinates for these atoms.
How is the origin of each molecule's Cartesian coordinate system determined by RCSB?


texts:
I always wonder if rather than getting minerals from food, can I directly eat them and will they have same effect as in food,
e.g. can I eat iron filings for iron, magnesium and drink hard water for calcium?

Is there any difference between having minerals through food or directly eating metals?