texts: More *total* oxygen absorbed by breathing fast or slow?

texts:
I have heard that human lungs capture/absorb/process more oxygen by breathing slower.

A) Is the above true?

B) If so, if my primary concern was absorbing the most total oxygen (not most efficient), would it better to breathe deeply and quickly or deeply and slowly?

C) Are there any other considerations (e.g., will fast, inefficient breathing make me feel more tired even if I'm taking in more oxygen)?

D) Is there any "ideal" breathing rate (such as for sports) that is a good balance between volume of air intake and efficiency of absorption?

Thanks.


texts: What is the lower temperature limit for ion channels function?

texts: What is the cold-block temperature of ion channels? (not of nerves or axons)


texts: What could be the reason for the large difference between sodium and potassium blood concentrations?

texts:
Reference values for sodium and potassium concentrations in blood tests are usually in the range of 135-145 mEq/L and 3.5-5.1 mEq/L, respectively.

My question is what could be the reason for this (relatively) large difference in the blood concentrations of these two ions which are together responsible for cells function and communication? What other roles does sodium play outside of cells that require it to be a lot more abundant in the blood than potassium?

Also, a follow-up question: is this proportion more-or-less maintained in other animal species?


texts: What chemicals and structures control the *direction* of plant growth in leaves, stems and roots?

texts:
If you want a specific plant, let's say the snap peas I am growing that I bought at Agway. I noticed that they grow towards the light source through the nearby window. Also I think roots work the same way for water/minerals. also don't various kinds of ants find food conceptually identically?

How much of this is true? Please correct:

I think analogous to ant colonies, plants will attempt to grow every which way initially, and will only continue growing in directions that give the most/enough light/water/minerals. If a direction is or becomes unfruitful, that section withers. After the initial state the plant will start branching in directions off of locations on still growing sections of plants and that cycle continues until none of the plant can be supported and the whole thing withers (perennials) or slows its metabolism down to the point where it could survive those conditions until they picked up again (such as winter seasonal survival of tree species). Also, it is not as if they decide which direction to go in. that type of decision would forgo going in another direction. And not sure, but I don't think plants have decision capabilities anyways. they grow in directions they grow best.


texts: What is the meaning of Dimer Catastrophe?  I still don't understand it even I've already read the paper about it.  Here's the link to the paper origin NCBI


texts: What is ApoCas9 in the CRISPR-Cas9 system?

texts:
I am currently reading an article about a particular assay of Cas9 nucleases. In one of the experiments, they have used ApoCas9 (Apo variants of other CRISPR nucleases) as some sort of control.

But the whole article they have not defined ApoCas9? I did check online of definition and activity of ApoCas9, but came across without any fruitful results.

A universal method for sensitive and cell-free
detection of CRISPR-associated nucleases


texts: How is Na concentration re-established after action potential

texts: I understand that the repolarization is because some K+ chanels are opened with the action potential. But whats happens with the sodium chemical gradient that is needed for a new action potential? Are there further Na-K pumps in the axon membrane?


texts: Is Pork more prone to carrying higher loads of parasites than Beef?

texts:
My friend told me that pork is dangerous due to containing worms.
I told her that beef contains worms too and that's why we cook it.
We went to steak restaurant and ordered "medium" beef.
And that makes me think a lot. Why I can order medium beef? It's still rare inside.
I have never heard people ordering medium pork.
Is pork more prone to worm investation than beef/cows?
What sort of worm we have anyway?


texts: Do all fungi dislike acidic environments?

texts: I know that some fungi prefer mildly alkaline environments and dislike acidic environments. Is that true of all fungi, or do some fungi prefer acidic environments? If so, are such acidic fungi rare exceptions or is it common for there to be acid-loving fungi?


texts: What's the composition of Actinobacteria's hyphae?

texts:
I'd like to know which chemical compounds form hyphae in Actinobacteria. Is it the same structure of the cell wall?

Thank you


texts: What determines walking direction in humans?

texts:
I've wondered about this for a while, without being able to come up with an answer.
Is there a body part that single-handedly determines the direction we're walking in? Is it a group of body parts that make us "steer" when walking?
I took a look at the behavior of some body parts while walking, and I came to the conclusion that:

it's not the direction the feet are pointed to, as you can turn them in or out while maintaining your path
it's not your head, of course, as you can be looking at any direction while maintaining your path
it's not your hips either, as you can move them freely without changing path (although I wouldn't suggest trying that in front of people)

As much as this sounds like a silly question, I still haven't been able to get to an answer. Any input is appreciated.


texts: Testing a COVID-19 vaccine on a large sample space of population from different nationalities

texts:
I came across an article few days ago, while checking the number of canditates for vaccines about COVID-19 where Sinopharm's vaccine development's trial phase caught my eye. The article says that:

In mid-July, Sinopharm launched its phase three trial among 15,000 volunteers—aged 18 to 60, with no serious underlying conditions—in the United Arab Emirates. The company selected the UAE, as it has a diverse population with approximately 200 different nationalities, making it an ideal testing ground.

Now, my question is, why is a diverse population present in UAE or any country with 150+ nationalities ideal for the testing phase of COVID-19? Is it because of the presence of diverse gene pool among the canditates from so many different nationalities? I don't understand why does testing on a population with approx. 200 different nationalities matter. Since, everyone's DNA is different, wouldn't they get the same results if they test it on a large sample space of population whose nationality is the same (for 2-3 generations or more)?


texts:
Are there any introductory book to explain gene manipulation in yeast for non-biologist?

I had a look at this book and now I have some ideas. I like to read another book at the same level which is more applied/practical. I find this book chapter useful too, but I find it a bit more difficult to follow. Also video lectures are appreciated.


texts:
It seems betaine HCL is often recommended for those suffering from "low stomach acid" -- which, as I understand, is having too high stomach pH for proper digestion (especially for proteolysis via pepsin). However, I have a few questions then -- though I'm not sure if my reasoning is correct here:

Understandably, one wouldn't want to drink pure or highly concentrated HCl by itself to increase stomach acid! But then, what role does the betaine play?

I'm guessing betaine HCl probably does not dissolve in water to give the same pH as just straight (or concentrated) hydrochloric acid -- since then it would seem just as dangerous as drinking plain HCl!

In that case, if it doesn't decrease the pH as much, making it safe for oral consumption, what value does it bring for "lowering stomach pH" anyway? I mean, one could just drink a little vinegar or citric acid for the same effect?

Or, perhaps, is betaine-HCl just a means of some "delayed release" of HCl to lower stomach pH without hurting the mouth and esophagus during its initial consumption? Betaine may just be a useful carrier here, given it's quaternary ammonium and carboxylic acid groups (e.g., a zwitterionic carrier)

Alternatively, could the value of betaine HCl simply be in providing a source of Cl- anions, possibly for increased pepsin activity? (I'm not sure if pepsin requires merely low pH or specifically also needs Cl- anions as well) Betaine-HCl does seem to be often formulated with additional pepsin enzyme(s) as well...


texts: Lying on my bed, doing nothing I recently noticed flies usually fly in small circles, right under my ceiling lamp. Worth noting - the lamp was off as it was middle of a day. And those flies kept flying like this for hours, not moving anywhere else! Later I noticed it repeated every day, pretty much the same pattern. Why is that?


texts: Can a trait be too successful? Wouldn't overwhelmingly successful traits limit variability, which is one of the requirements of NS?

texts:
Can a trait be too successful?  Wouldn't an overwhelmingly successful trait soon limit the gene pool, and if so, how would the process of natural selection react to that?  If an individual is born with a trait that allows it to reproduce unimpeded, and it passes that trait on to its offspring, wouldn't the variability be quickly reduced in the population?  And if so, then would NS limit the trait so that it isn't overwhelming?
And thanks to everyone who contributed here, you have been very helpful and I am very grateful.


texts:
What species of crane is this?

Today afternoon, I found this crane among a group of white cranes that were moving around a herd of buffaloes. I live in West Bengal, India if it matters.

Is it an eastern cattle egret,Bubulcus ibis coromandus in breeding plumage?


texts: Why do humans hear better between 2kHz and 5kHz?

texts:
I've recently seen the following image:

Source: https://commons.wikimedia.org/wiki/File:Hoerflaeche.svg

Translation (from German):

The upper boundary (Schmerzgrenze) is where it starts to hurt
"Musikwahrnehmbarkeit" is where you can hear music
"Sprachwahrnehmbarkeit" is where you can recognize speech
"Hörschwelle" is absolute threshold of hearing (ATH)

While the ATH seems to be relatively smooth, there is a noticeable "gap" between 2kHz and 5kHz. Does anybody know why this is the case?

Some possible explanations I've heard are:

Evolution: Hearing a baby cry
Evolution: Hearing leafs rustling
Coincidence: There is no good reason for that.

The image is from wikipedia commons and has no references. It might be wrong. Do you know similar graphs? Do you eventually have this kind of information for other animals?


texts: What spider is this? Is it dangerous to humans?

texts:
What is the species? Is it dangerous to humans?

I chanced upon this beautiful one near our water well. It stood at a height where an adult could accidentally walk through the web and the spider would land on one's face.

As a test, I dropped a piece of leaf onto its web, and the spider jumped to action, checking what it was and it took out the leaf from its web.

Size: Web, almost circular 50 cm diameter. Spider, about 8cm.
Location: Malabar region, Kerala state, south of India


texts: Definitions of hermaphroditism, dioecious and monoecious?

texts:
What is the difference between these terms "monoecious","Hermaphrodite".
my lecturer says hermaphrodite is a zoological term and monoecious is botanical term, but in contrary to it, in my textbook both of these terms are used both botany and zoology.

So what is the actual difference?


texts: How do metal ions acting as enzyme cofactors "find" their respective enzymes?

texts:
Metalloproteins are metal-dependent proteins, i.e. they require certain metal ions (copper, magnesium, zinc, etc.) for their correct function in the body. Since proteins are manufactured inside cells by the ribosomes and metal ions are exogenous materials, i.e. are obtained from food, how would a metalloprotein and its respective metal ion find each other in the body? Are the metal ions taken inside all body cells? Does the meeting take place in the blood?

A quick Google search retrieved nothing useful.


texts: For allele frequency determination, is it good to take samples from a college/school or a hospital or any other technique?

texts: I am trying to determine allele frequency of a hla allele. Preliminary analysis shows the prevalence of the allele (homo or heterozygous both) is 3%. The allele is related to a disease (After exposure to risk factor). Taking samples from college or university can help reduce time and money. Taking samples from hospital may take time (the hospital I have contact to, has small sample size?). Though both ways may have ethnic diversity, college students are of a given generation only. What to do. Please suggest with references to read.


texts: I'm trying to identify this salamander-looking creature I found in my house today in Coos Bay, Oregon. It is about 2" long. What is it?

texts: This is about 2" long. It is white on its underside and looks like a small salamander, except for it being white underneath. It is about 1/8th inch wide.


texts: Why is proteinase K digestion performed at 50 °C?

texts: Many DNA isolation protocols use a Proteinase K digestion to remove proteins. This is often performed at 50 °C. Why is this?


texts: What is the best way to analyze non-quantitative mass spec hits from an immunoprecipitation pull down?

texts: I am studying a nuclear protein and want to come up with a list of potential proteins that it interacts with. From the nuclear fraction of 293T cells, I did an IP (immunoprecipitation) to pull down my protein and submitted whatever I pulled down for a mass spec analysis. I also did an IP with a non-specific antibody as a control. I got a huge list of hits, and I'm not sure how to prioritize them. I can manually remove the hits that also came down with the non-specific antibody, those are obviously just sticky proteins. I looked around Pubmed for ways to prioritize non-quantitative mass spec hits, but I'm not sure if any of them would work in my case. All of them require multiple mass spec repeats - I can do that if I need to, but would like a way to look at my initial data more intelligently.


texts: Measuring reverse transcriptase activity in E. coli

texts:
Goal: To quantify the HIV-1 reverse transcriptase (RT) activity for a number of mutated RTs.

Idea:

Put RT into a vector in E.coli.
Deliver GFP mRNA to E.coli.
RT will process the mRNA.
The resulting DNA will be integrated into E. coli.
RT activity correlates with the GFP we observe.

First question: Does this logic make sense?

Second question: An alternative procedure?


texts: In the picture above (Source: Amazon.com, United Scientific MCT001 Hand Microtome) we can see a microtome. How is it operated?


texts:
Apologies if this an obvious question - I am very new to this. I am, as of now, under the impression that multiple SNP variations interact to create multiple mutated proteins, which ultimately results in a variant phenotype.

I am wondering if the standard method of treating is this is by creating a drug that has a combination of all of the non-mutated versions of the proteins, or if drug makers simply use the protein that they believe has the biggest impact?

Thanks for the help!


texts:
There are number of virus which have animal as reservior and jump to human to cause disease. Why dont we use antibodies of animal to cure humans?
Like rabies in bats.


texts: Which modern methods of antibiotic production are there?

texts:
For my seminar paper in the field of biology, I have to collect modern methods of antibiotic production. The topic is a little overwhelming, but the work should also be quite extensive (approx. 18 pages).
I've already done some research, but most of the results don't help me. I would be very grateful for a few web links and keywords that I could research for in order to break down the topic.
I will visit the university library in the next few days. It would help me a lot if someone could recommend a few good books references.


texts: Chromosome naming convention: Why are there chromosomes named "1" and "1A"?

texts:
I've been stumbling on multiple genome of birds where there is a "1A" chromosome and a "1" chromosome. For example, the zebra finch has 1A and 4A. What does that mean?

Do you have any resource about naming conventions for chromosomes and if this naming convention is specific to birds?


texts:
Available resource but difficult for me to make scence

Relation about crime scene and identitas v1 forensics chip

Is the technology "identitas v1 forensics chip" related to microarray technology?

if true ,as I know, different combination of genes are expressed in different parts of our body which means a certain tissue only makes particular types of mRNA.

Then my question raised: How can a CSI crew reconstruct a person's virtual appearance (for example skin color, face structure) by a piece of microarray with limited tissue (for example cells from saliva) and mRNA?
I mean saliva cells don't make pigment of our body, so how can the eye color or skin color be presumed, for example?

Otherwise, what is the technique "identitas v1 forensics chip "which allow us  to detect several phenotype  simultaneously?

According to the information I Know,"identitas v1 forensics chip" it contains hundreds of thousands of short sequences of DNA that binds to SNPs,where the DNA from the crime scene binds to this chip can allow software to reconstruct the appearance of the person of interest.

the chip is the first to provide data on all these traits simultaneously. Other devices can determine at most two at a time – usually eye and hair colour.


texts:
I have thrown a dirty spoon after eating some pasta into one of my desk drawers (doesn't do me much honor). It stayed there for around a year. My house is warm and I think there is enough humidity for bacteria to multiply, however I have found it today with seemly same amount of food on it when I left it.

I assume given enough time all food should get converted into bacteria (bacteria would eat and multiply until food is there and stop when it is all consumed). Is this assumption incorrect?

Why didn't bacteria decomposed the food on my spoon?

EDIT: This question has nothing to do with fried McDonald foods and is referring to bacteria consuming 'ordinary' food, plus I am asking if food should disappear completely while the other question is about it being decomposed,  answers are completely different.


texts:
What is the good or stringent parameter for variant calling?
At present using the DP > 10 and Q > 30 for Variant calling. Is it ok?


texts: Why aren't mammals and reptiles considered amphibians?

texts:
We've all heard it: birds descend from dinosaurs, so they're dinosaurs too. But this got me thinking: doesn't this mean that, for instance, all terrestrial vertebrates – including humans – are technically fish? A recent video by MinuteEarth and the Wikipedia article for "Fish" confirmed my shower thought hypothesis.

Interesting. But... all amniotes, i.e. reptiles (and, by extension, birds) and mammals, descend from amphibians, right? If so, then why aren't they considered amphibians too?


texts: What prevents a pregnant woman's immune system from recognizing her fetus as nonself (and attacking)?

texts:
I'm familiar with the scenario of Rh- mother with Rh+ fetus having complications (more so after her first child), but that's not what I'm curious about. I want to know mechanistically why a pregnant woman's body does not display a reaction similar to what we see with rejection from a mismatched organ transplant. On the most basic level, I feel as though the fetus should be recognized as "nonself" due to paternal genetic contribution.

I feel as though if this mechanism could be understood, it could be harnessed for other situations (e.g., organ transplants).


texts: What is indirect vs direction selection of genes?

texts: As the title suggests, what is the direct and indirect selection of genes. Couldn't find a straightforward answer. Is it the same as direct and indirect fitness?


texts: Up to date, extensive documentary about dinosaurs?

texts:
I just finished reading the Wikipedia page about dinosaurs, and I very much enjoyed it. I knew that much of what I learned in the 80's as a child is (and was) incorrect, and now that I am a parent, I am excited to finally make some time to learn about this stuff.

It seems that a lot is known about ecosystems, socialization, and interactions between different species, herd behavior, and other interesting things.

Before I start reading books, I want to watch a good documentary.  A quick google search turned up some suggested documentaries, but in general they seem to be either old or focused on a particular dinosaur, and not on the era in particular.  All are short.

I watched the 10 hour documentary "The Life of Mammals" by David Attenborough a few years ago, and developed a much better understanding of how we as humans evolved, and how we are related to other mammals. I'd love it if there was something as extensive about Triassic/Jurassic/Cretaceous era dinosaurs. Is there something recent, extensive, and mostly correct?


texts: Is brain plasticity such that we can train ourself to see with our ears?

texts:
I am finishing writing some code which will parse a photo (eventually video) and use all the RGB information to synthesize an audio representation. I am wondering whether a typical person has sufficient neural plasticity to learn how to listen to this audio to understand an image in a general sense? I am not looking for perfection.  If the person has good vision they would do well to spend time listening to such synthesized audio while simultaneously viewing reality to give some training to enhance their interpretative abilities.  Once trained they could augment or supplant vision with its sonic equivalent.

  How plastic is our audio-visual brain? Is there hope this will work ?

PS.  Once working I will update this Q

For those wondering about the details :  I am traversing the image using a Hilbert Curve which tends to preserve spacial relations amongst pixels to minimize re-training upon change to pixel resolution.  This flattens the 2D photo into a 1D line sprinkled across from left to right with points storing respective pixel values (at a 1st approximation I collapse RGB into grayscale 0.21 R + 0.72 G + 0.07 B)

... to create the audio representation I visit each pixel position on this line and introduce an audio frequency oscillator per pixel at a unique frequency such that the beginning pixel at far left is given the lowest frequency in our range (say 200 hertz) on upward until the oscillator frequency at the far right pixel renders the highest frequency (say 10 khz) ... the grayscale value drives the volume of that pixel's oscillator

... further details at:  isomorphism between video and audio
                https://www.youtube.com/watch?v=DuiryHHTrjU

Beauty of this approach is it lends itself to performing this transformation in reverse (a bijection) - from audio to video we can use a Fourier analysis ( FFT ) of audio mapped into pixels - then back again to audio, rinse and repeat ...


texts: Why are sponges sometimes not considered multicellular?

texts:
I read somewhere (I can't find where) that there is no scientific consensus whether sponges should be considered multicellular organisms.

It seems I don't understand where is the line between unicellular and multicellular life.

I am not able to find a more elaborate explanation of that doubt. What are the reasons for it?


texts:
Do they just pass through the membrane? Is there some specific transporter or mechanism? Does it vary?

I've seen pictures if retroviruses outside the cell but no details


texts: Do viruses pickup new genetic sequences from the host cell?

texts:
Virus replication does not involve meiosis so the virus genome does not gain diversity from having two parents , so other than from mutation, do viruses obtain new genetic sequences from the host cell ?
Do virus genomes show evidence of containing base pair sequences which originated from host cell ?


texts:
I was reading Creation - Life and How to Make It by Steve Grand. (This is the book that inspired Jeff Bezos to start the AWS initiative. ) In it he makes the following statement:

  Anyhow, by now I hope you have thought of an experience from yoru childhood. Something you remember clearly, something you can see, feel, maybe even smell, as if you were really there. After all, you really were there at the time, weren't you? How else would you remember it? But here is the bombshell: you weren't there. Not a single atom that is in your body today was there when that event took place. Every bit of you has been replaced many times over (which is why you eat , of course)....

That didn't sound quite right to me. How could the atoms in your bones be replaced? Aren't your nerves pretty much fixed in place?

My question is: Are all the atoms in your body replaced with others over a 30 year period?


texts: Is there a karyotype database for human cell lines?

texts: I'm looking for the karyotype of a specific cell line. Some karyotypes are well known, such as HeLa or some carcinomas, but some are very hard to find, such as LG2 (B cells). Is there a database dedicated to karyotypes of human cell lines?


texts:
I found the following pictures of axon trees:

source

source (axons are red)

but didn't find a concise answer to the following question:

  Are there axon branches that go up to cortex layer 1 and spread there?
  (This is not indicated in the pictures above, maybe because there are no.)


texts: Are both (partial) copies of DNA transcribed in S and G2 phases of cell cycle?

texts: For a little less than half the cell cycle, a significant number of genes are represented twice (just before dividing).  Does the cell differentiate between these DNA in any way or are transcription rates limited by the amount of polymerase anyway?


texts:
Is the result of meiosis ONLY the sex gametes (male and female) which later meet to form a somatic cell?
Sometimes I feel as if my book is hinting towards meiosis is the process where sperm cells meet oocytes?? I'm a bit confused.


texts:
Till now I thought that embryonic stem cells have no epigenome as they are pluripotent. (I thought that since epigenome is what gives a cell its identity, no cellular identity means no epigenome) I saw something similar to this on this Wikipedia page. After fertilization, the paternal and maternal genomes are demethylated in order to erase their epigenetic signatures and acquire totipotency..
Other sources mention 'reset' in place of 'erase'.
This paper rather suggests that stem cells do have an epigenome. Specifically, genes associated with self-renewal are silenced, while cell-type-specific genes undergo transcriptional activation during differentiation..
I am not very literate in biology, please excuse me if I made a mistake.


texts: What makes synaptic vesicle release probabilistic?

texts:
The fusion of synaptic vesicles (SVs) with the plasma membrane of the active zone (AZ) upon arrival of an action potential (AP) at the presynaptic compartment is a tightly regulated probabilistic process crucial for information transfer (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4773589). In a typical forebrain synapse, only ~15% of APs arriving at the presynaptic terminal cause fusion of a synaptic vesicle.

My question is, what factors make this process probabilistic? What happens at the molecular/cellular level that an action potential can lead to the fusion of synaptic vesicles one time and not another time? Is it due to some differences between different synaptic vesicles, how the vesicles are positioned inside the synapse, variations in the synapse's environment, differences between action potentials, etc?


texts: What does this sentence about toxemia and Clostridium tetani mean?

texts:
I know that Cl tetani is not invasive and strictly localised.
I think toxemia means spread in the blood.
I am thinking this sentence

  The volume of infected tissue is small, and the disease is almost entirely a toxemia.

Cl tetani has spores.
This suggests me that these spores spread through blood.
They then open and become pathogenic in some tissues where they remain strictly locally (so small area/volume of infected tissue; I think area is better word, since the disease is not invasive) and pathogenic.

How do you understand the quoted sentence about pathogenesis of Cl tetani?


texts: Why is DNA polymerase added at the end of PCR reaction?

texts:
PCR reaction is used to amplify DNA fragment. Each reaction requires a DNA template, buffer, dNTP mix and a unique pair of primers, one ''forward'' primer and one ''reverse'' primer. The DNA polymerase should be added last to the reaction, just before starting the PCR programme.

My question is, why is DNA polymerase added right before the PCR starts? Is it because it can begin to amplify DNA before adding the reaction to the thermocycler? How could it amplify the DNA when the DNA is not denaturated until added to the thermocycler?


texts: Is there any evidence that any other species are "pre-intelligence"?

texts:
Is there any evidence regarding whether other species might, given time, evolve intelligence as humans have?

I realize "intelligence" is a vague word here, but I'm interested in throwing a wide net, since I imagine the small sample size of positive cases makes finding any evidence at all extremely difficult.

The only information I've been able to find so far seems vague and unscientific, but I'm expecting that is the best I'm going to be able to find.


texts: Obtaining a mapping of RefSeq ACs to Uniprot ACs

texts:
I am trying to obtain a mapping for RefSeq Accession Numbers to Uniprot Accession Numbers.

I can write a script to do this for a list of RefSeq ACs like this:

#!/usr/bin/python

"""
Derived from:
  http://www.uniprot.org/help/programmatic_access#id_mapping_python_example
"""

import urllib
import urllib2

url = 'http://www.uniprot.org/mapping/'

params = {
    'from':'P_REFSEQ_AC',
    'to':'ACC',
    'format':'tab',
    'query':'NP_511114.2 NP_004295.2 NP_031465.2 XP_004934106.1',
}

data = urllib.urlencode(params)
request = urllib2.Request(url, data)

# Please set your email address here to help us debug in case of problems.
contact = "email@example.com"
request.add_header('User-Agent', 'Python %s' % contact)
response = urllib2.urlopen(request)
page = response.read(200000)
print page

I am curious if there is a way to request the entire mapping of human genes to proteins.

I have tried to configure a query from the Uniprot resources, but I can't see how to get RefSeq data from this tool.

http://www.uniprot.org/uniprot/?query=reviewed:yes+AND+organism:9606#customize-columns

I am happy to use a resource other than Uniprot.


texts: Examples of healthy lifelong asymptomatic carrier of a severe infectious disease?

texts: I am curious, is there any known disease/infection that is very severe normally (patient suffers greatly and die easily without medical treatment), but ends up having little to no effect on the lives of asymptomatic carriers? I am asking this as I am thinking whether this means certain disease symptoms are mechanisms resulted from evolution to protect the "greater good", i.e. killing the patient to avoid transmission to another member of the species.


texts: Results of self-administration study about pain in honeybees?

texts:
There research on nih.gov about ability of bees feel pain. But I can't understand their conclusion. Could you provide necessary excerpts here from those study so it would be clear what conclusion they've got ?

And that research was granted by This research was funded by ARC Discovery Grant DP140100914. Does it mean that we shouldn't completely trust it ?


texts: I'm working on performing phylogentic footprinting to figure out how many TRE sequences there are in the TWIST1 gene. (Sequence motifs). I'm trying to use ENSEMBL to gather orthologues of species in which the gene twist1 is present, compile it into a FASTA file and upload it to MEME SUITE. However, I'm having trouble understanding how to compile the file. I also don't know how to read SEQUENCE LOGOS. If anyone can help me, I would appreciate it SOOOOO much.


texts: What exactly is the neural receptive field?

texts:
Neural receptive fields map the spatial or temporal distribution of the data to individual neuron excitation, if I understand correctly, but I do not understand if receptive fields (especially in the higher cognitive areas such as the various layers of the visual cortex, etc.) are:

Actual structural distributions of neurons that help map specific spatial or temporal properties of stimuli (such as concentric arrangement for contrast detection, rectangular arrangement for orientation detection, or movement detection, etc.), or,
Merely a mapping of the structure of the stimuli that can excite specific neurons.

If it's the latter, isn't it basically as simple as a pattern/feature/vector that individual neurons are sensitive to?


texts: Water-bird that can take off vertically from the water?

texts:
If you look at ducks taking off, they take off at a pretty flat angle, building up speed before they finally get some altitude. This takes a lot of distance, it seems, for them to get high in the air.

But this lead to a question. Are there water birds that, sitting on the water, take off at a more vertical angle without the long run-up?

The best I can think of are flamingos, who cheat by having their feet on the ground, in the shallow waters. Some birds will dive into the water, grab a fish, then fly out at a high angle, but that's a bit different from sitting on the water then taking off.

Many birds are able to perform a vertical or near-vertical takeoff, on dry ground. Can any birds do this while sitting on the water?


texts: Evolutionary support for parenting book "The happiest baby on the block"

texts:
The book by Dr Harvey Karp (MD) The Happiest Baby on the Block proposes that the duration of human gestation has evolved as a tradeoff between cranial size and development of the infant.  He hypothesizes that from an overall developmental perspective human babies are all premature and would benefit from additional time in their mother's womb; however, because humans have such big brains, and therefore our babies have big brains, the infant needs to be born earlier than would be developmentally ideal so that it doesn't get stuck in the birth canal.  The result is babies that have big brains but are highly vulnerable and dependent on their parents until their development progresses further.

I discussed this with some students in class as an example of the use of ideas from human evolutionary ecology and life history theory in the popular press, but with the disclaimer that I had no idea if any of Karp's ideas are backed up by any evolutionary or anthropological data.  Could anyone point me towards literature that support or contradicts Karp's claims?  For example, are human infants more dependent than those of other primates?

[The upshot of Karp's theories are that the best way to have a "happy" newborn is to mimic conditions that it would experience in the womb, such as swaddling.  Works for my child!]


texts: Genotypes in diploid/haploid cells under mitotic/meotic cell divisions

texts:
I am new to genetics , and am stuck with the following question at hand:

  If $2$ cells with genotypes $(A/a)$ and $(A/a,B/b)$ undergo mitotic and meotic cell divisions respectively, what will be the  genotypes/gene compositions in the resultant diploid and haploid cells with respect to the above mentioned alleles?

Can someone help me how to proceed?


texts: How does the Platypus grow before it eats?

texts:
From this fascinating documentary on monotremes it is mentioned that the Platypus is born less than 1 cm in length, but has doubled its size by day three when it begins to nurse. How does the animal grow before feeding?

Surely by conservation of mass there must be some alternate process by which materials are being processed and absorbed by the young animal. Does it absorb nutrients from the air or surrounding environment? Sucking on dirt? Osmosis?


texts:
Some people who get directly struck by lightning and some more than once (starts at 00:25) survive while others die instantly or later on due to complications/injuries.

Looking at a wiki page for Lightning injuries

  Lightning injuries are injuries caused by lightning strikes.

  They result from three factors:

  electrical damage.
  intense heat.
  the mechanical energy which these generate.

  While sudden death is common because of the huge voltage of a lightning strike, survivors often fare better than victims of other electrical injuries caused by a more prolonged application of lesser voltage.

Lightning can strike or injure humans in four different ways but I'm going to focus on direct strikes.

  Reported mortality rates range from 10–30 percent, depending on the source of data. Most people who are struck by lightning live to tell the story, but many suffer from long term injury or disability.
  Airforce medicine site

Is there a physiological reason why direct lightning strikes are not lethal for everyone or does it all come down to dumb luck?


texts: Are all of my ancestors from 400 million years ago fish?

texts:
Say you have your family tree for the last 400 million years or so, back to the Devonian, the age of fishes. You take the set of ancestors that are about 400 million years old (which will be across multiple generations). The question is are they all fish?

Or, is it more complex than that? Can there somehow be non-fish in that set?

Note added later: this question is not a duplicate of another question.
In the context of that other question, howewever, my question can be stated as "Is Dawkins correct in stating that my 185th million ancestor was definitely a fish, with no exceptions?"


texts: Negative association between habitat quality and reproductive success in birds

texts:
I'm looking for bird studies that have found either a negative correlation or no correlation between habitat quality and reproductive success.

Or in other words, bird studies that have found that reproductive success was lower in lower quality habitats. Or, that have found there was no difference in reproductive success between habitat classified as high quality and low quality.

Can anyone help?


texts: How does Hemocytoblast constantly get formed into so many blood cells and yet remains there in the bone marrow throughout the lifetime?

texts: I mean, Hemocytoblast is a stem cell which is constantly being differentiated into daughter cells and leads to formation of all the blood cells (having short and limited life spans), so how come those stem cells remain there and continue to function, even when we grow up and finally grow old (i.e for 70 years approx)? The no. of those stem cells gotta be limited.


texts: Major groups of photosynthetic prokaryotes

texts:
According to Stryer there are four major groups of photosynthetic prokaryotes, i.e. Table 19.1

Bacteria Photosynthetic electron donor $\ce{O2}$ use.

Green sulfur $\ce{H2}$, $\ce{H2S}$, $\ce{S}$ Anoxygenic.

Green nonsulfur Variety of amino acids and organic acids Anoxygenic.

Purple sulfur $\ce{H2}$, $\ce{H2S}$, $\ce{S}$ Anoxygenic.

Purple nonsulfur Usually organic molecules Anoxygenic.

Cyanobacteria $\ce{H2O}$ Oxygenic.

Do each groups belong to a different genus?


texts: Why do (almost) all energy carriers contain adenine?

texts:
Unlike this question which is specific to just ATP, this one includes all energy carriers.

When thinking of common energy carrying molecules, I can think of Adenosine triphosphate (ATP), Nicotinamide Adenine Dinucleotide (Phosphate) (NADH/NADPH), Flavin Adenine Dinucleotide (FADH2), S-adenosylmethionine, coenzyme-A (derived from cysteine, pantothenic acid and ATP), etc. Recalling exceptions, I can only think of biotin (carboxylated) and uridine diphosphate glucose. Just talking about ATP, we could have called its preference over others just a matter of chance. But when so many carriers contain adenine, there has to be some selection against other energy carriers (or adenine was so lucky?). Note that when saying 'common energy carriers', I exclude GTP, CTP, TTP and UTP since they are not very commonly used (or at least their use is confined to only some metabolic reactions, unlike ATP which finds its use in almost all metabolic reactions requiring energy).

Why do the majority of energy carrier molecules contain adenine (or its derivative) instead of any other nucleobase?

This question is open for discussion i.e. everybody is welcome to post their (scientifically backed-up) opinion as an answer while none of those answers will be selected because of lack of conclusive proofs, which are very likely to remain elusive forever.


texts: what is the characterization of mutant bacteria and how is it done?

texts: I have a task to characterize protease producing bacterial mutants but I have failed to understand what it is and how it is done


texts: What Effect Does Skin Redness Have On Underlying Tissue?

texts: When someone applies a rubefacient ( something that increases blood flow to the skin, turning it red), what effect does this have on the underlying tissue? Is blood supply increased radially from where the rubefacient was applied and thereby increasing blood flow to underlying tissue (I'm thinking up to a few centimeters of muscle) or is blood supply essentially being stolen locally in order to bring it to the skin?


texts: How did butterflies evolve to have eyes on their wings?

texts:
Some butterflies, such as the UK native Peacock butterfly (Google Image Search) have markings on their wings that look just like eyes, complete with a white fleck to imitate a convex, transparency effect, as though the "eye" is reflecting sunlight.

Presumably, this pattern is designed to deter prospective predators, because the predator will see a creature with massive eyes looking at them and think twice before attacking.

But how did the pattern evolve?  Was the first one a fluke / a genetic mutation that happened to work, or is there another explanation?

For possible bonus points, is there any way of telling when this occurred, and therefore making a guess as to which creature's eye is being imitated?


texts: Why does this genetic pedigree show an autosomal dominant allele at one generation but not another?

texts:
Questions 186-188 of the GRE Biology Practice Test are prefaced with this genetic pedigree:

  Questions 186-188 refer to the following pedigree for the inheritance of a very rare human disease over three generations.

It looks like the allele that caused the "affected" phenotype was dominant because Generation II showed a 3/4 probability of having the phenotype, and it looks like it was autosomal because it affected males and females roughly equally. This is confirmed by the answer to Question 186 ("Which of the following is the most likely mode of inheritance for the disease trait?") which is "(D) Autosomal dominant".

However, why don't the offspring 1, 2, 3, 4, and 5 in Generation III show a similar rate of expression?


texts: What is that? Dry brown fungus? See photo please

texts:
It has appeared two days in a row on my balcony, at exactly the same place. There's nothing near that can give me a hint of what it is. The birds can access the place easily. It's an inch in size, it's dry. In the photography you can see a eyelash and some hair, because has been taken after sweeping.

The place is Jerez de la Frontera (Cadiz, Spain).

What it could be? I'm curious and I would like to know why it appears.


texts:
I’ve noticed recently strange formations on the leaves of my flower.
No idea what could it be.
Could anyone help with the identification?


texts:
I was cooking rice this morning and was fascinated by the color and it's sweetness and began to ask...

How did fruits evolve?
Did they come from a single cell?
Which cell?
How did that cell branch off from  the cell that became animals? Is there any evidence for this kind of thinking or just a lotta theories? How did we get rice, mangoes, beans, orange, coconuts, peanuts, apples, bananas, if there is no "Designer", where did ALL these come from and how did they evolve?


texts:
I am thinking of making an aeroponics system.
But after i finished my primary design I though to myself how deep should I make the container for the roots of my plants? Since I want to make my system applicable to a range of plants image from microgreens to lettuce. I was thinking how can I determine the size of the roots of the desired plants? I there a way to determine this from the size of the plant or not?

This would be important since if the container is too small the spriklers my get covered my the roots of some plants. And if the container is too big some roots my not get enough water. Next to this a more space efficient container would be better (So it also looks a bit nice)

I am a complete newbie to this so please let me know if any clarification is needed :) And if this is even the right place to ask.


texts: Exact definition of single nucleotide polymorphism (SNP)

texts:
So, I know on a higher level what an SNP is but I'm a bit confused about the details.

Firstly, our professor said that an SNP has to have at least a prevalence of 1% in the general population to be considered an SNP and not just a mutation. Wikipedia says the prevalence needs to be 0.5%. Is this actually a strictly followed cutoff? And which of the two values is correct?

Secondly, he said that SNPs never cause a disease but can only predispose you to one. However, the wikipedia article mentions thier role in diseases that are clearly caused by single mutations (cystic fibrosis, sickel cell anemia, and beta thalassemia). So, can SNPs cause a disease or not?


texts: Why does tetracycline have such a broad spectrum of activity?

texts: What are the structural and chemical characteristics that make tetracycline uniquely broad spectrum? I understand it acts on the A-site of the prokaryotic ribosome, but there exist many ribosome-targeted drugs that are relatively narrow spectrum. I assume it has something to do with its permeability in several different classes of bacterial cell walls and/or membranes - but I can't find any literature that links some characteristic part of its structure to this permeability.


texts:
Please help to identify this shrub in Hong Kong:
- dark green fruit with white spot
- fruits cluster at top of stem
- upright growing of green leaves

The shrub was from Hong Kong MacLehose Country Park Trail in Tuen Mun (somewhere near a reservoir), route 10. The place was of an altitude about 200m (600 feet from sea level) hot and humid. Hong Kong weather is South of the tropic of Cancer which is equal to Hawaii in latitude.


texts: Can coronavirus contaminate public water systems?

texts:
It's been reported recently that people are panic-buying stuff as the coronavirus epidemic worsens. I've even noticed that the local grocery store is low on hand sanitizer, paper towels, and bottled water.

I did some reading and traced links back to the DHS's ready.gov website, and it recommended preparing a 2-week supply of food, water, medicine, and hygiene products for ISOLATION, though I expect if you're sick you're supposed to plan a trip to the hospital. Most of that makes sense to me. The exception is the supply of water. We have public water systems that send drinkable water to us, so why do we need to prepare a stash?

I tried finding an answer online, but I couldn't. The only guess I have is that coronavirus can contaminate the public water system, and it's not guaranteed water treatment will work. Who here has the know-how on waterborne viruses and water treatment to address this speculation?


texts: Are there animals that have evolved a resistance to human activity or encroachment?

texts:
There are countless sources, both peer-reviewed and popular, explaining how overuse and misuse of antibiotics is breeding a new generation of antibiotic-resistant "superbugs" such as MRSA (Methicillin-resistant Staphylococcus aureus) and MDR-TB (multidrug-resistant Tuberculosis). Over in the animal kingdom, the opposite seems to be happening - species after species is becoming endangered and/or extinct as humans destroy or alter their habitat through increased hunting, farming, construction, etc.

Are there any non-human animals that have been found to have evolved resistance to human encroachment into or alteration of their habitat in a way analogous to how bacteria have evolved resistance to human attempts to get rid of them? For example, this could consist of:

an animal that has adapted stronger bones to better survive collisions with vehicles
an animal that has significantly increased its blood coagulation rate to survive gunshot wounds from hunters
an animal that has developed better vision to see in urban environments
an animal that has evolved a skin pigment change that enables them to not take as much damage when they are sprayed with agricultural pesticides

One answer that came to mind is domestic animals - the horse and dog in prehistory, the cat in ancient Egypt, etc. That seems too obvious on one hand, and on the other hand may not really be an answer, as there seems to be no indication that pre-domestic animals were endangered by humans in any meaningful way. Are there animals that have significantly adapted themselves to surviving as wild animals in human-influenced environments?


texts: Standard Free energy of hydrolysis of phosphoenolpyruvate (PEP)

texts:
In ATP we have two anhydride bonds, each with a Standard Gibbs free energy of hydrolysis ~ -30 kJ / mol and one phosphoesterbond of ~ -20 kJ/ mol, if my notes are correct.

In phosphoenolpyruvate (PEP) we also have a phosphoester bond, but the Standard Gibbs free energy of hydrolysis is three times higher, at ~ -62 kJ / mol.

How does the double bond / enol form contribute to this high free energy of hydrolysis?


texts: How is monoclonality or polyclonality determined?

texts:
I was reading up Kaposi sarcoma and Robbins Pathology says,

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

This is also seen in multinodular goiter where the lesions are polyclonal, but some monoclonal nodules are found.

My question is, how are these determined? By sequencing, is it not that, in cancerous growth there are myriad mutations, how can you map whether the mutations present are due to monoclonal expansion or polyclonal expansion? In non cancerous growths, wouldn't all cells have the same genotype?

Polyclonal and monoclonal expansion in B-cells is clear to me since a polyclonal lineage would have different vdj recombs while monoclonal would have the same. Here also, is it decided by genomic sequencing or the Ig sequence?


texts: I am having troubles understanding the correlation between OD measurements and CFU/ml. What is the conversion factor between the two units, and does this conversion factor somehow compensate for dead cells OD might be reading? (Also lets say the OD is set at the standard 600nm).


texts: How does a baby deer stand the day it's born?

texts:
I know most creatures take time to learn some things.

Birds take some time to fly.
Human beings take some time walk or stand.

But in the case of the deer species, it's different. It can stand the same day it's born. Why is this so?


texts: Did most pandemics originate from Asia/China?

texts:
This question may be on the borderline of well-posed-ness. Let me ask it. Then please tell me if or where it can be improved.
Is it statistically true that the majority of the pandemics or epidemics originate from Asia particularly China? If not, is there a geographic concentration of the origin of pandemics? If so, why?


texts:
After vasectomy, where does the sperm go?

Vasectomy Procedure cuts only vas deferens, But Our Testes still produces sperm, if there is no output for sperm, where does it go?


texts: How do I improve expression using the GAL1 promoter in S. cerevisiae above the "leaky" level I'm currently seeing?

texts:
I am attempting to express GFP in S. cerevisiae using the GAL1 promoter.

I always grow an uninduced (in dextrose based SD medium) culture alongside my induced (in galactose based SD medium) culture. I see approximately the same very low level of fluoresence in both cultures, and also a band at 27kD on a PAGE gel. There is no overexpression of the GFP happening, the fluorescence is very weak by eye, and the cultures are not green in visible light, like E. coli cultures overexpressing GFP.

On the PAGE gel the amount of protein appears to be the same in both the uninduced and induced samples. I need to overexpress the protein, this leaky level of expression isn't acceptable. How do I go about fixing it? I am currently growing up a culture to do a plasmid prep to send for sequencing to make sure the promoter region of the plasmid is intact.


texts: Why antipyretics do not bring the body-temperature below normal?

texts:
Antipyretics like paracetamol are used to decrease the body-temperature in fever patients.

But some of them are also used as pain-killers in sprain or other injuries (where there's no fever). In that case they changes the body temperature very little (if any).

Why? Is there any molecular mechanism responsible for  this?


texts: Hybridization capture: Array-capture vs. in solution

texts:
If I wanted to utilize hybridization capture for capturing certain genomic regions, I could do it by utilizing complementary probes immobilized on an array or to use the probes in solution and then capture probes using biotin-streptavidin binding.
How do the two compare? Does in solution hybridization e.g. require more probes? What would I need to think about when making my choice?


texts: "50% of the variance in antisocial phenotypes is the result of genetic factors" means what?

texts:
How can i understand the following sentence:

  Overall, the conclusions reached by these studies have been highly consistent in showing that approximately 50% of the variance in antisocial phenotypes is the result of genetic factors.

Is it saying genetic factors have a weight of 50% in the total influences on antisocial behaviour?

Source: "Natural born killers: The genetic origins of extreme violence" by Christopher J. Ferguson , Kevin M. Beaver


texts: How do polygyne Carebara affinis or C. diversus (a.k.a. Pheidologeton affinis and P. diversus) colonies work?

texts:
I live in Hong Kong. Typhoon Hato hit yesterday and a whole bunch of Carebara queens decided to take their nuptial flight. I caught close to 20 of them within 15 minutes.

I'm pretty sure they are Carebara affinis, though they can also be Carebara diversa. They are also known by their old names Pheidologeton affinis and P. diversus, respectively.

In any case, I have read from multiple places that both Carebara affinis and Carebara diversa are polygyne, which means they can found a large colony with multiple egg-laying queens.

So I decided to temporarily put them into the same lunch-box-sized plastic container.

However, soon after I put them into the same container, I discover that some of them would get their legs and even their antennae bitten off. I thought maybe it's because they found the container too crowded and wanted to eliminate some competitors, so I added two layers of toilet paper to give them more surface to crawl around. That didn't really help. Tonight, after coming home from work, I found most of them have been completely amputated. They aren't dead yet though; they are just left there wiggling around without legs. A few of the queens come out intact so I suppose they are somehow dominant. The ones who get amputated tend to end up in a pile. I'm not sure if the "dominant" queens decided to drag them and pile them together.

Is that at all normal? Is that how Carebara ants start a polygyne colony? Basically one or a few dominant queens amputating their sisters to turn them into egg-laying slaves of some sort? If the dominant queens wanted to kill the weaker ones, why not bite their heads off? I'm pretty sure they had the jaw strength if they wanted to. So, supposing that the amputated queens do survive, I'm not sure I see how that helps in the evolutionary sense. Unless that's actually how it works: one or a few dominant ones amputating weaker ones to force them to lay eggs together?

Does anybody know how to properly start a polygyne Carebara diversa or affinis colony from scratch?


texts:
According to the recent research about Electromagnetic Signals from Bacterial DNA (A. Widom, J. Swain, Y. N. Srivastava, S. Sivasubramanian) it seems there is a possibility of a "wireless" version of intercellular communication which was found in bacterial communities.

The paper's abstract reports:

  Chemical reactions can be induced at a distance due to the propagation
  of electromagnetic signals during intermediate chemical stages.
  Although is is well known at optical frequencies, e.g. photosynthetic
  reactions, electromagnetic signals hold true for muck lower
  frequencies. In E. coli bacteria such electromagnetic signals can be
  generated by electric transitions between energy levels describing
  electrons moving around DNA loops.

The authors further note:

  There has been considerable interest in bacterial communities wherein
  a bacterium is connected to neighboring bacteria by means of narrow
  nanowires[5-7]. It is believed that the purpose of the nanowires is to
  allow for intercellular electronic communications. More advanced on
  the evolutionary scale are the more modern bacterial communities which
  are wireless. The electromagnetic signals sent from a bacterium to
  neighboring bacteria can be due to relatively low frequency electron
  level transitions within DNA.

Conclusions says:

  Although biochemical reactions are often described in terms of
  molecular contacts, electromagnetic signals can often be employed to
  allow chemical reaction control at a distance.

  ...

  The wireless broadcasts can in principle be of both the AM and FM
  variety due to the magnetic flux periodicity in electron energy
  spectra in bacterial DNA orbital motions. AM signals can arise from
  the Bohr transition frequencies between different electronic energy
  orbitals about the DNA loops.

Wired article Bacteria on the Radio: DNA Could Act as Antenna comments:

  Theoretical physicists have proposed an explanation for how bacteria
  might transmit electromagnetic signals: Chromosomes could act like
  antennae, with electrons traveling gene circuits to produce
  species-specific wavelengths.

  In Widom’s arXiv paper, he and other physicists calculate that as
  electrons flowed through loops of DNA in E. coli and Mycoplasma pirum,
  the species tested by Montagnier, they should generate wavelengths
  similar to what was recorded.

  “Different species have different lengths of DNA” in their
  chromosomes, he said. “These lengths probably determine frequency.”

  “This could be a wireless version,” said Widom. “Bacteria that set up
  nanowires are, on an evolutionary scale, fairly old. It’s occurred to
  me that more modern bacteria may use wireless.”

It seems that the concept of electromagnetic signal transmission in bacteria is not new and such an idea originates with Nobel Laureate virologist Luc Montagnier (2009), who detected electromagnetic signals after wrapping inductor coils around flasks of water, hooked up to an amplifier, which contained E. coli and Mycoplasma pirum. The frequency of the signals measured was about 1kHz.

That kind of communication could also explain the phenomenon of quorum sensing mechanism, where bacteria communicate with one another to establish the population density of micro-organisms of their own kind within their proximal environment.

Based on above, the question is, is there any possibility that the diseases can be transmitted wirelessly? Are there any further research around this topic?


texts: Under which conditions is human energy consumption minimized?

texts:
Including but not limited to:

body state

consumed food composition
state of the digestive tract
diseases
wounds
sleep
coma, etc.; death excluded

environment state

temperature
light
pressure, etc.

Merely curious. I do not expect to find complete answers, which seems impossible, but all insight is appretiated.


texts: Is it possible to have raw ngs data to practice

texts:
I'm looking for raw human ngs data to practice in bioinformatics. Better if it is from different machines (illumina, roche, pacsbio, etc). Panels, exomes and genomes.
Anyone knows something?


texts: Parasites with both plant and animal hosts?

texts:
Are there animals (or plants) that are parasitic on both animals and plants?

Especially such that they rely on their plant host being eaten by their animal host?


texts: What type of genetic changes occurs when ovaries or uterus are removed from female body?

texts:
I saw so many women which have present dermoid cysts in their ovaries or uteruses. Doctors operate and mostly the ovaries and uterus can not be saved and the doctors remove the ovaries or uterus.

Which type of genetic changes occur in such type of women?


texts: Is it possible for two creature in the same order and have odd haploid chromosome species to reproduce

texts:
Take the degu and the rat for example.
The degu has 29 chromosome pairs
Rats have 21 chromosome pairs.
They are only share the same order ( Rodentia )
Would it be possible for them to reproduce?

( also , before someone says " they're not the same species , so obviously not" allow me to remind you of the mule , and the europeans have 1 - 4 percent Neanderthal )


texts: Holder for 75 mm x 25 mm glass slides that can handle vibration

texts:
Hello Biology Stack Exchange,

I have an application where I have cells on a glass slide (dimensions: standard 75 mm length x 25 mm width  x 1 mm thick).  I want to vibrate/shake the cells rapidly while viewing through a microscope.

I have a piece of equipment that can produce vibrations, I just need to connect it to the glass slide somehow.

Are there any holders for glass slides out there that:

Firmly hold the glass slide
Enable me to somehow connect vibration equipment with the slide?  (Ex: screw into the holder, glue onto the holder, clamp onto the holder)
And still view the slides contents under a microscope?

Thank you in advance!


texts: Solvent Accessibility, the 20% cut-off method

texts:
I'm reading the papers linked below and all three of them mention a 20% cut-off for buried/exposed residues, by calculating a relative solvent accessibility (RSA) value.

I understand how the RSA is calculated, by dividing the calculated solvent accessibility against its total solvent accessibility values from paper 4 table 2.

RSA = calculated/total

e.g. if arginine is calculated to have a solvent accessibility of 55.43 and its total solvent accessibility is 241 then the RSA = 55.43/241 = 23%, so this arginine is considered exposed (see statement 1 below).

What leaves me confused is the definition or lack of the 20% method for defining an exposed or buried residue.

I am assuming it means one of the following:

If an amino acids RSA is below 20% it is buried and above 20% it is exposed. So for an amino acid with an RSA of 21% is considered exposed, this value seems a little low for me. I think statement 2 would make for sense.
If an amino acids RSA is below 20% it is buried and above 80% it is exposed.

Which statement if any is correct?

Paper 1 - see methods section first paragraph

Paper 2 - see figure 5 and table 3

Paper 3 - see abstract and dataset

Paper 4 - see table 2 for total values


texts: Why is the vermis of the cerebellum associated with speech?

texts:
I've found multiple sources claiming that damage or impairment as a result of alcohol to the vermis of the cerebellum results in speech impairment. I find this a bit surprising, since the only areas I know that are used for speech production are Broca's area. Additionally, I don't know of any way that the vermis influences this area or any other facial nerve that may need co-ordination to produce speech.

So why does damage/impairment of the vermis result in dysarthria?


texts: what is the difference between early blight of potato and late blight of potato?

texts: apart from different fungus causing these diseases in potato, how are Early Blight of potato and Late blight of potato different?


texts: What is the difference between prefrontal cortex and frontal lobe?

texts:
They are both in the front. Looks like they're the exact same thing.

Is one part of the other?

What?

Why is it called prefrontral cortex? What does pre before frontal mean? Before front?


texts: Functional role of voltage-gated potassium channels

texts:
Having better learned here how action potential creation works in some detail, I'd like to pin down the functional role of voltage-gated potassium channels: they mainly shorten the time it takes the neuron to get back to rest potential. Without potassium channels, the sodium ions that entered the neuron through a sodium channel would slowly diffuse away (electrotonically) and the sodium potassium pumps reset the potential. With potassium channels, this process is drastically accelerated (by quickly moving positively charged ions out of the neuron in situ). Without potassium channels, an action potential would be created nevertheless by the sodium channels alone, i.e. a peak of 40mV would be generated (equally fast!), but it would decay much slower, not yielding a pronounced peak.

  Would you agree that this is a correct description of the main
  "purpose" of potassium channels involved in producing action
  potentials?

In any case, potassium channels seem to  work equally well when their "closing" potential would not be -80mV, but e.g. -70mV, i.e. the resting potential. But because it's -80mV the potassium channels produce an afterhyperpolarization. My second question is:

  Does afterhyperpolarization play a ("positive") functional role,
  too, or is it just unavoidable? If so: Which "negative" and
  undesirable effects might it have? (In some respects it might
  have been better, if there was no afterhyperpolarization.)


texts: Is there an enzyme for the transformation of the hydroxyl group?

texts:
I would like to know, is there any enzyme which does the transformation of hydroxyl group to any other functional group using the enzyme.

The substrate is aromatic hydroxyl group. Product should not have hydroxyl group.

How should these types of queries be searched for?


texts: Okay so I know that night mode is supposed to filter out blue light that is bad for the eyes, but is it really more helpful than annoying? At night I do use it when I’m on the phone but it doesn’t make sense to keep it on during the day when it’s bright outside does it?


texts:
In a city, 4% of male population have color blindness. How many of the female are (a) color blind carrier, (b) color blind? Suppose the city holds Hardy Weinberg equilibrium.

My progress: 4% of male have color blind => $p=F(cb~allele)=0.04$ and therefore $q=F(not~cb)=0.96$. Since HW equilibrium stand, we get the allele frequency among female is the same as among male. Then (a) $2pq=2*0.04*0.96=0.0768=7.68\%$ and (b) $q^2=0.9216=92.16\%$.

Am I correct?


texts: How come that we "feel" it when someone's watching us

texts:
The question is relatively easy (the answer however..). We all know this feeling "being watched" and more often than not this is a real thing. If someone is staring at us from the side or from the back we sort-of "feel" it and we evenf eel the direction where it's coming from.

I can't seem to find a plausible answer for this though:

We actually see the people staring from the corner of our eyes - false, I tested this thoroughly and it also happens when your eyes are closed or someone's behind you.
Eyes don't send out energy (or "beams") as far as I know. They "receive" light but don't send any out, except for reflection.

So, what causes this strange phenomenon?


texts: To what extent do fossils change over time?

texts:
Fossils are formed over millions of years. How do scientists quantify the extent to which a particular fossil has changed in shape/relative tissue density/etc. over geological timescales (if at all)? I ask this (as a non-biologist) because we are often presented with fossils as being exact copies of the original species, as it was when it was alive. I wondered if this is indeed the case and imagine that the answer will vary for fossils of soft versus harder tissue composition.

If organisms do indeed retain their shape almost entirely, what experiments are carried out to mimic geologic timescales and processes to demonstrate this?


texts:
Why is histidine an essential amino acid for children but not for adults ? What changes in the body occur which lead to the formation of histidine in adults but not in children ? What causes these changes ?

UPDATE : Source : Campbell Biology


texts: Why is bacterial meningitis worse than viral meningitis?

texts:
My field is not biology related, but it is commonly said that bacterial meningitis is far more dangerous to the individual than the viral kind. It seems to be true even with antibiotic treatment. What is the biological reason for this?

If this question has already been addressed or this is the wrong stack exchange, feel free to redirect this question to the more appropriate place.


texts: few questions about active thylakoid isloation

texts:
I need to isolate active thylakoid, I have few questions regagrding:
why there is a need to do so in low temp enviormant? (3-5°C)
 im not sure if it is due to protease activity or something else.
why storing the thylakoids in ice will reduce elctron transfer activity?
why MgCl2 is so improtant? I know it affects granal destacking and proton motive force, but I'm not sure how. also, which enzyme/s need to use MgCl2 to mantain the granal stacking/PMF


texts:
I am looking at the PharmaPGKB database for SNPs and trying to understand what the following annotation means:

rs1801131 at 1:11854475 in CLCN6, MTHFR (VIP)

Ok, the SNP identified by rs1801131 occurs in the first chromosome, at position 11854475.

Then, the two genes' identifiers come. The position 11854475 is inside the gene MTHFR. Why do they also annotate the SNP to the gene CLCN6 (which is a "neighbour" of MTHFR) ?


texts:
I am aware of satiety only through experience, rules-of-thumb and possibly myths. For example: white bread is not filling, a pasta meal can be filling but because we "burn" carbs quickly pasta itself is not, and I personally find fruit in the melon family filling. (But that could be because I hate them ;) )

Is there a formal measure of satiety? How does it work?


texts: Effect of spaying on the female cat organism and health

texts: Veterinarians often recommend spaying a female cat if the owner does not want her to have kittens. What does biology know about the effect of spaying on female cats' organism and health (apart from lack of fertility, of course)?


texts: At small axon diameters (<1 µm), why does myelination not increase neuronal conduction velocity?

texts: As per the diagram below (and other graphs available online), why do unmyelinated fibres have a higher conduction velocity than myelinated fibres when the axon diameter is less than around 1 µm?


texts: How Do Acid and Base Loving Plants Get Enough PO4?

texts:
Acidic and Basic soils experience phosphate sequestration through binding with either calcium, aluminum, or iron. How do plant that thrive in acidic and basic soils obtain the necessary phosphate? Blueberries are an example that I particularly enjoy.

Thanks to the University of Hawaii for posting this picture.


texts: How does "inheritance of methylation" of DNA and/or histones work?

texts:
What are the current models/ideas describing the mechanisms explaining inheritance of methylation on DNA resp. histone level?

Is there evidance of this "setup" information being really duplicated/inherited during a cell division process?

Pointers? Articles? What is the current state of knowledge regarding this?


texts: Is life in the open ocean homogenously spread?

texts:
Obviously around land masses or in shallow water where reefs and coral may grow, life is diverse and numerous. But how spread out is sea life in the open ocean (for example, half-way between Hawaii and California) where there is no land mass or shallow depths for hundreds or thousands of miles?
Does life exist in clusters with large swaths of oceanic desert in between or is it relatively homogenously spread?


texts:
I have an ant queen in a jar. This is what she looks like:

Because I'm planning to start an artificial ant nest, I'd like to learn something about that specific species of ant. This particular queen is very common in the Czech Republic, central Europe. It's also very common in cities.

Could you tell what kind of queen is that?
Is there any image reference that would help me find out? Ideally with some location search possibility.


texts: Can you splice out the first and last exon from pre-mRNA?

texts: I think the answer is no because there are no introns before the first exon or after the last exon, although I am not sure if this assumption is correct. Thanks!


texts: Is it theoretically possible to treat filaggrin deficiency with a dietary supplement?

texts:
http://f1000.com/prime/reports/m/3/2/

  "Filaggrin is a highly abundant protein expressed in the uppermost part of the epidermis that is critical to the formation and hydration of the stratum corneum—the outermost dead cell layers responsible for the barrier function of the skin. Filaggrin deficiency leads to a 'leaky' skin barrier that allows higher than normal water loss (explaining the dry, scaly skin), as well as allowing entry of allergens through the epidermis where they trigger inflammatory and allergic immune responses (atopic eczema and allergies)."

Not that such a supplement exists, but is it biologically possible to treat filaggrin deficiency with something taken orally?


texts: Gradual slowing breath, its effect on health

texts:
I've written a computer program which beeps, then beeps after 10 sec, then beeps after 11 sec, then beeps after 12 sec, etc.

I tried the following "experiment" on myself: do only one breath between the beeps, so slowing breath until I can't do it.

After finishing this "training" and starting to breath normally again, I felt enormous "freshness".

Is this experiment safe for health? How does it influence health?


texts:
I am reading the paper: Pyramidal Cell-Interneuron Interactions Underlie Hippocampal Ripple Oscillations.
The authors use CAG::ChR2 rats (for example in Figure 2) and I don't know what it means.
I understand for example that in PV::ChR2 mice, parvalbumin neurons will be activated by light.
I am also familiar with types of other interneurons (Ivy, Martinotti, OLM, LTS, Bistratified, Mopp, VIP, Somatostatin...)
but I have never encountered CAG cells.

Is CAG represent a type of neuron? or, maybe it represents something else?

Thanks!


texts:
Q) A girl slipped and is falling. She puts out her arms to prevent falling. Which joints are most affected by her fall?

Fibrous and Synovial joints.
Cartilagenous and Synovial joints.
Fibrous and Cartilaginous joints.

The answer is 1.

Attempt:
Since it is the arms that will be affected, Synovial joints will be affected. But I don't remember there being any fibrous or cartilaginous in hands.

Are there any fibrous or cartilaginous joints in hand?


texts:
What causes an animal sperm cell to die? Does it die somehow from being outside its original environment?

I've studied the Wikipedia page
 on sperm and I see a lot of information on what makes up a sperm cell, but can't quite figure out its lifecycle and exactly how it dies.


texts:
Which of the following are usually identical between a lung cell and a brain cell, from the same person, assuming that they are normal (non-cancerous) cells?  Circle your choice(s).

a.  Size
b.  Shape
c.  Specific proteins found in the cell
d.  Specific genes in the cell’s genome
e.  Which genes are expressed
f.  Which parts of the DNA are methylated
g.  The specific DNA sequence of chromosome 12
h.  All of the above
i.  None of the above

I said only D and G because all cells have the full genome.  The difference between cells is how the these genes are expressed.  All of the other options are results of different amound of gene expression.  Is this the correct thinking?


texts: Are there antibiotics for all bacteria somewhere in the earth?

texts:
When I read about Penicillin, I found that it came from a green mold to protect itself.

If all bacteria and/or molds in competition to survive,
can we believe that there is an antibiotic for each bacterium somewhere in the earth?

In other words, just like bad bacteria change themselves to resist against the existing antibiotics, could good bacteria/molds produce antibiotics against the bad bacteria?

If so, can we use them like Penicillin, or should we still develop most of them?


texts: Do bacteria precipitate in static liquid culture media?

texts:
We performed 36h biofilm cultures and would like to know if this time is enough to planktonic bacteria to precipitate.
Since we observed biofilm formation one the surface of the microtiter plate. Were  biofilm bacteria derived from precipitation of suspended bacteria or rather replicated from some initial attached bacteria cells?

Specie: Haemophilus parasuis. A facultative anaerobe.


texts: What is this spider hunting in the tree in the night?

texts:
I took the following picture of this spider in northern Switzerland (alt: ~700m) with macro flash/lense.

The picture was taken during the night in a cedar tree (Thuja occidentalis).


texts: Why mosquito bite is confined to a certain shape?

texts:
I think this problem should be asked in a physiology forum rather than biology@ stackex but I'll give it a try.
So my question is simple - why a mosquito bite is usually confined to a certain shape (shape = red area) and not just disappearing continuously? Can our body cells tolerate some level of antigens without changing color from that?


texts: Local storage of NCBI database in MongoDB

texts: My short term goal in a project is to build a local database of the NCBI dbSNP database. The data and schema are available on the FTP site(). I was going to implement the database using MySQL, but I just learnt about MongoDB. Is it possible to somehow convert the sql schema code to mongoDB architecture? Also, are there any real advantages to implementing the dbSNP database as MongoDB?


texts: Why minimum infective dose of a virus is not just 1 particle?

texts:
I've stumbled upon a term "minimum infective dose" (for example, of HIV), but don't exactly understand what is it? Why it is not always equal to 1 virus particle? I expect 1 lucky virus to be able to start infection just like 1 lucky spark can start a fire.

The following options comes to mind:

Multiple particles of the same virus need to act in cooperation to trigger their reproduction;
There is some 100% working, but limited use immunity that knocks down first N viruses;
Infection probability lower than some theshold % is not considered by statistics.

In general, how infection probability and severity correlates with the number of particles? Is it linear (double the number of viruses => double probability or infection) or something trickier?


texts: What experiment for first time showed DNA is anti-parallel?

texts: Scientists how to prove DNA is anti-parallel?


texts: How are epigenetic marks transmitted during cell division?

texts: As far as I know, this is one of the biggest questions in the epigenetic field: how are the epigenetic marks like histone modifications propagated through cell division? A lot is already known about DNA methylation (e.g. as in How does “inheritance of methylation” of DNA and/or histones work?), but very little about histone modifications. What is the current state of knowledge?


texts: reason for "not for diagnostic use" advice in protocols

texts:
I read "not for diagnostic use" in every protocol i saw. why is it so?
which differences have the kits and material that are used for diagnostic purposes?


texts: Do antioxidants interfere with chemotherapy?

texts:
Since most of the chemotherapy drugs kill cancer cells by damaging their DNAs by means of free radicals. So antioxidants, which will detoxify free radicals, should theoretically decrease the efficacy of the chemotherapy.

However clinical trials are proving the opposite. Saying, antioxidants does not decrease chemotherapy efficacy but also make chemotherapy more effective, thus increase the survival rate.
http://www.ncbi.nlm.nih.gov/pubmed/17283738

The question is, why antioxidants do not interfere with chemo, while they are supposed to do ?


texts: What ways are there to determine how big genera are?

texts: I want to look at genera as a whole, across the animal kingdom to determine the range of sizes of genera. I have examined species richness and genetic diversity (pairwise distance from sequence data sets), but I am looking to find more ways to look at 'how big is a genus?' in terms of biodiversity. Any ideas or comments are greatly appreciated!


texts:
I'm trying to understand more about evolution theory.
(I am coming from a mathematical background)

What i understand till now is that the "improvement" of the dna is a purely random development and the Selection criteria if the improvement was not negative is by surviving.

The better the improvment was the higher the likelyhood of surviving is.

What i don't understand is that the likelyhood that something useful comes from random changes in the dna is very low?

This reminds me of the http://en.wikipedia.org/wiki/Infinite_monkey_theorem it has surely a finite likelyhood but considering the complexity i still doesn't understand how for example wings of birds evolve.

Consider a pre-bird without wings, to get wings it has to have interstage with some useless pre-wings and then it has to learn how to flight.

Maybe someone can help me solve these mysteries :)

The other thing i am wondering is the smallest living element is the cell.
How did the first cell evolve?

Thank you very much


texts:
I am extremely interested in science in general and in particular biology. Due to a different choice of career-path I probably will not be learning any more biology anytime soon.

So I would love to get my hands on a comprehensive textbook biology which hopefully will enable a goal in lifelong learning of biology.

What are some good recommendations? I looked up biology textbooks on Google and found candidates such as Campbell Biology by Reece and Biology by Brooker. But as there are so many of them, I have no clue which one to get.

So, biologists of stackexchange, can you help me out?


texts: Is there any definition of life which makes viruses undeterminable?

texts:
There are many different definitions of life (RNA, something that comes through evolution) but not one I have seen which could not determine wheter viruses are living things (even though there are many definitions both for YES and NO). Are there any such definitions (I'm looking for cases where it's really fundamental debate, not only struggling for the correct dictionary definition)?

Thank you.


texts: Why are smaller mammals more prone to cancer and tumors

texts:
especially rats and mice usually develop cancer and tumors very fast, reducing their life expectancy.
From an evolutionary point of view, how come that these mammals are so prone to cancer and tumors even though they reproduce at a very fast pace?
Shouldn't they develop a resistance towards these illnesses through natural selection?

Source: https://www.thesprucepets.com/rat-tumors-1238498


texts: Question About the Physiology of Seizures

texts:
Absence seizures usually occur in children between ages 4 to 14 (Hopkins Hospital). Spontaneous remission occurs in 65–70% of patients during adolescence (Medicine Central).

My question is what takes place biologically that allows you to 'grow out of them?' Is it synapse pruning in the brain or something? I have looked everywhere online but can't seem to understand the physiology of how one grows out of seizures.


texts: Any latest edition or successor of "Invertebrate zoology" by Ruppert & Barnes 2003?

texts: I have the 6th edition of the textbook "Invertebrate Zoology" by Ruppert and Barnes from 1993. I know there is a 7th edition from 2003, but is there and will there ever be a 8th edition? Assuming they should come every 10 years, shouldn't there have been one in 2013? So if Ruppert & Barnes retired, is there any more recent successor or alternative?


texts:
What happens to the mold spores we inhale?

I'm guessing when we exhale, many of them are expelled back out to the environment.

But given that disease can be caused by mold exposure, I'm also guessing that we do not immediately expel a percentage of them.

Molds can colonize in the lungs, causing detrimental effects.  Can they colonize elsewhere in the body?

For mold spores that do not colonize inside the body, what happens to them?  Are they expelled?  If so, by what mechanisms?  Are they alive or dead when they are expelled?


texts: What to look for when buying a light microscope?

texts:
I am a science lover and want to buy a microscope to explore things around me. Like studying cell structures, microorganisms, blood and plants. It would be great if there is way to photograph slides. Just curious to know and explore things around me.

I want to know which features I should consider while buying it?


texts: How does life change when you dig deeper?

texts:
I've just realized that I have no idea what life / biotopes / soil looks like when you dig deeper than a few meters.

I know that in the first meter of soil you can find all sorts of live animals (like moles and rabbits), insects (like ants, but many more), plants, and single-celled organisms, of course.

But how does that change when you get to the depth of a metro station (below 30m)? When you plan to build a metro, do you have to consider that you might destroy a biotope?

I guess there is a point from which you will quite certainly not find animal/plant life in the soil anymore. This will, of course, depend on where exactly you are. But can you give a rough estimate of how deep we're talking? 50m? 100m? 1km?


texts:
I'm getting started using ECG using a 3 lead system by iWorx. I have place the leads on my two wrists and the ground on my ankle and have recorded some data into the provided LabScribe 3 software using the ECG template. Can anyone help me interpret what I'm seeing?

It doesn't look like the standard QRS I see in my textbook, but it's so regular (this is just a snippet) that I don't believe I'm seeing artifacts.

Any insight would be greatly appreciated.

Thanks!


texts: Why are there exactly four nucleobases in DNA?

texts: Does someone know why DNA is composed of four nucleobases? In particular, is there an explanation for the number? Why four and not two, or eight?


texts: In what books can I find a detailed literature on the mechanism of function of different enzymes and proteins involved in DNA replication of E. coli ?


texts: What is the effect of temperature and carbon dioxide on the opening and closing of stomata?

texts: I am teaching biology in an academy. The question which I had asked above had been raised by on of my students. I tried my level best to search out the answer to this question but I could not find the answer. I had read a number of answers to different questions from this website. So that's why I thought to Post my question on your website


texts: What is the concentration of ATP in an average cell?

texts: Can someone give me some references showing the average concentration of ATP in a cell?


texts:
I would like to know how can i run a network analysis for identifying major OTUs hubs. I wish to build a network of co-occurring OTUs found in different soils samples.
I've started going through the VEGAN R package but i'm not sure it's what i'm looking for.
any recommendations network analysis packages ?
thank you!


texts: Why was disease transfer to the Americas one-way?

texts:
It is well known that the European colonists brought many infectious diseases to the Americas, and that these had a deadly effect on the native populations, because they had no immunity to them. Were there any local infectious diseases to which the colonists were not immune? I’ve never heard of such. I’m not aware that the colonists suffered any epidemics, or that they brought any new and unusual diseases back to Europe.

Why not? Is this merely an accident of history, that there were no infectious diseases in the Americas which did not already exist in Eurasia? Or is there some explanation?


texts: What exactly is meant by the expression "differentially expressed"?

texts: As far as I've seen, this expression is almost always used in relation to gene expression profiling. Unfortunately, I have no background in this area. Can someone please explain this in layman terms?


texts: Is there any possibility that gender is determined by Temperature?

texts:
One day I was watching TV show. It was based on Fire Dragon. They stated that if the dragon provide greater warmth to the egg, then a male Dragon will hatch. And if the Dragon provide less warmth to the egg it will be female Dragon.
This was totally Science Fiction!!

But is there any possibility that, the Temperature decides the Gender of progeny.


texts: What is the current consensus on the Loveheim Cube of Emotion

texts:
I recently encountered the Lovheim Cube of Emotion. I was wondering what level of supporting research there is to go with it and whether or not there is a concensus at this stage.

If I'm perfectly honest, I'm skeptical, the evidence that I've seen is uncompelling and the model over simplistic but maybe I've missed something.


texts: How Scientists sequence, assemble and annotate plant genomes?

texts:
I previously read this question and this paper and learned good things about this topic. my current question is that scientists use which tools, algorithms, soft wares... to sequence, assemble and annotate plant genomes?
For each genome project do they develop new tools and algorithms or there are some tools that are useful for (almost) all genome projects?
Are there any comprehensive site, book or paper that have plant genome sequencing and annotation protocols?


texts: What is the charge of (bacterial) ribosome?

texts:
Ribosomes are negatively charged and thus electrostaticaly repelled from DNA. However, I could not find a good reference that would allow me to estimate the magnitude of negative charge on a ribosome. Anyone could help with that?

This reference suggests it to be on the order of tens of e- or more.


texts: Storage of energy in muscles vs fat depos

texts:
How does the body control, where consumed energy (fat, glucose) is stored? And what is its strategy?

More specific:
1) How does the body control storing glucose in muscles and not as (subcutan) fat? (E.g. exercise lets more GLUT4 translocate in muscle cells; because of this, do muscles in total simply have more transporters to suck in glucose than all fat cells, or is there another mechanism? How does the liver refills its storage)

2) Same question as 1) but regarding FFA and not glucose.

3) What is the overall strategy for energy storing? (Can it be stated as simple as "Fill the liver and muscles until they reach full capacity and then store extra energy as fat?")


texts: Designing degenerate primers using alignment of protein sequences from other species

texts:
I am trying to design a PCR primer for a gene whose sequence is not known. Even the whole transcriptome sequencing done in our lab did not identify that particular gene. Hence, I guess I am left with only one option: to design the degenerate primers for this gene by performing sequence alignment of the given protein from several related species and designing primers based on conserved region. Could you please explain the process of primer design by this method. I know some steps which I have described below stepwise:

step 1: download sequence of protein in question from related species from NCBI in FASTA format

step 2: perform alignment using clustal omega

step 3: identify the conserved domains

I am not sure how to move forward from here. I tried J-codehop for next steps but it is asking many parameters for which I have no clue.
Thanks


texts: What's the maximum and minimum temperature a human can survive?

texts:
This is a question that has been in my mind since I was a kid. I'm not a doctor, nor even a biology student, just a curious person. What is the minimum and maximum temperature a human body can stand without dying or suffering severe consequences (eg. a burn or a freeze)? While at this subject, how much more global warming will the human body be able to take? Seeing as temperatures keep on rising, I'm just wondering how much longer until the temperature starts having drastic effects.

In my country the temperature is about 35-40-45 degrees Celsius in mid-summer (I live in Romania, eastern Europe, and the climate is supposedly ideal here) which is very unhealthy. Does the human body suffer more and more as the temperatures change?


texts:
Is it possible to identify this bug,,? Found in South Sinai  .in Egypt . Only seen crawling but maybe it can fly ? Black with 6 legs. 2 long black "strings " coming from back end
Thank you


texts: I have got some fungi on a polypore. Can it be a trichoderma?


texts:
This source here

  ...research has shown that it is STILL the males that compete for
  females.

says that male sea horses compete for mates but this source here

  Females exhibit a competitive behavior that's normally a male-type
  attribute, and males end up being choosy, which is normally a more
  female-type attribute.

.says that female sea horses compete for mates.

Can anyone provide me a trustable source regarding this ? I would also like to know if there are any recent papers exploring why males get pregnant in sea horses.


texts: Flower identification (England, late May)

texts: I took this photo near Stratford upon Avon by the side of a road. Can anyone identify this flower?


texts:
As far as I know, lipids are defined as biomolecules which are hydrophobic.

Triglycerides are composed of fatty acids and glycerol and are considered lipids but, are fatty acids alone or glycerol alone considered as lipids ?


texts:
I live in southern California, where the difference between seasons is mild, and the dominant limitation on agriculture is the lack of water. (Spring is whenever it rains, not a place on the calendar.)

In my early education, as is usual, I learned the growing season is shorter in more northern latitudes. The natural deduction is to expect less effective agriculture, further north.

Recently, I spent a week in early April in Vancouver (Canada). The weather was very (very!) nice, much warmer than I expected, and the hours of daylight longer. On reflection, all this was obvious ... but I was surprised at the time.

Northern latitudes may have shorter growing seasons, but the hours of daylight during that season are much(!) longer. What is the potential agricultural productivity of more northern latitudes?

Much of the past century of agricultural research was centered on the American mid-west. How much is possible if we further optimize agriculture for more northern latitudes, and higher levels of technology?

As the Earth warms, large expenses of Russia and Canada will thaw. Seedlings started early in artificially warmed and lit greenhouses could jump-start crops. (Or transported from more southern latitudes.) If we took full advantage of the longer hours of daylight in northern growing seasons ... what is the limit to agriculture?

With global warming, could Canada and Russia become the bread-basket of the world? Can agriculture as a technology be adapted to more northern latitudes, and take best advantage of a shorter season with longer daylight?

(In imagination, I see seedlings started in greenhouses, and robot-planters placing seedlings in just-warm fields, to capture every hour and day of longer sunlight.)

Do we know how to best take advantage of long northern days for agriculture?


texts: I read on Wikipedia that when the cell enters prophase during mitosis , the DNA has already been duplicated , that is the DNA is replicated in the chromatin form , but here I see the picture which shows the already condensed DNA ( now chromosome ) divide into sister chromatids. When does DNA divide actually ?link to wikipedia -https://en.wikipedia.org/wiki/Prophase


texts: Why should the pharyngeal cavity be essential for articulated speech?

texts: In a lecture, I've been told that one of the signs that homo habilis and homo erectus couldn't speak was that they probably lacked the distinction between oral and pharyngeal cavity. But do we really use it, apart from the nasal consonants?


texts: Can anyone identify this mystery caterpillar?

texts: I found this caterpillar in in El Cerrito, CA and was wondering what kind it is?


texts: Which kind of tick is this and what is that thing around its back?

texts:
I was recently bitten by a tick. After having removed it from my body, I put it in a glass. By now, it has stopped moving, so I put it under a microscope and looked at it. I was surprised about being unable to get a sharp image of its body (upper part in the images) – what could that be? And can someone help me identify it?

I found a picture of a tick with a somewhat transparent thing around its back here – maybe that's what made it hard for me to get a clear focus on the back? And maybe it's related to this one?

It was found in Oldenburg, Lower Saxony, Germany. Its length is between 1.2mm and 1.4mm (I don't have anything that's very usable for precise measurement of such small lengths).

If clearer focus on a particular part of that thing is needed for identification, please tell me.


texts: Currently we have many species which are "good enough" for current environment, some species emerge, another die. So let's say that they could be close to some local optima. Does the evolution head to some optimum that in future we will have only one species which will be superior to all other extinct form of life?