texts:
I read this article by Jeffrey Tomkins and Jerry Bergman claiming to debunk chromosome 2 fusion. Is there anything wrong with these conclusions?

" 1.The reputed fusion site is located in a peri-centric region with suppressed recombination and should exhibit a reasonable degree of tandem telomere motif conservation. Instead, the region is highly degenerate—a notable feature reported by a previous investigation.

In a 30 kb region surrounding the fusion site, there exists a paucity of intact telomere motifs (forward and reverse) and very few of them are in tandem or in frame.
Telomere motifs, both forward and reverse (TTAGGG and CCTAAA), populate both sides of the purported fusion site. Forward motifs should only be found on the left side of the fusion site and reverse motifs on the right side
The 798-base core fusion-site sequence is not unique to the purported fusion site, but found throughout the genome with 80% or greater identity internally on nearly every chromosome; indicating that it is some type of ubiquitous higher-order repeat.
No evidence of synteny with chimp for the purported fusion site was found. The 798-base core fusion-site sequence does not align to its predicted orthologous telomeric regions in the chimp genome on chromsomes 2A and 2B.
Queries against the chimp genome with the human alphoid sequences found at the purported cryptic centromere site on human 2qfus produced no homologous hits using two different algorithms (BLAT and BLASTN).
Alphoid sequences at the putative cryptic centromere site are diverse, form three separate sub-groups in alignment analyses, and do not cluster with known functional human centromeric alphoid elements."

I've also heard them say that there has to be a fusion in every living thing that evolved or evolution isn't true.  Is that true or not?

The article is here

Part one
Part two


texts: Does having a total gastrectomy (removal of the stomach) cause individuals to be more prone to infections?

texts:
If a patient has a complete removal of his/her stomach (i.e. a total gastrectomy), then does that cause a person to be more prone to infections from eating unsanitary food?

I'm asking this question because the stomach plays a role in sterilizing food and, hence, without a stomach it would follow that one might be more prone to getting intestinal infections.


texts: Small pink flower, started out as tiny buds, leaves look almost like Maple leaves..


texts: Why are there few quail any more in the Northeast of the US?

texts:
I currently live in southeast New Hampshire and was reading a history of my town and it describes the landscape as having a lot of quail and even partridges. The book said children going to school around 1920 would see lots of quail. The town itself has not changed much from 1920 except that there are fewer farms. The population is about the same. In fact, the population is probably lower now than it was in 1920.

I have never seen a single quail here, and certainly never seen a partridge. I have seen a pheasant on rare occasion. There are a lot of turkeys.

Is this like a Silent Spring thing, they all got killed off by DDT or something? Or is it because of insecticides killing all the crickets, maybe? I almost never hear crickets at night.


texts: What kind of soil-dwelling flying insect is this?

texts: In the UK. They are roughly 1.5mm long, appear to crawl much more than fly, and seem to live in the soil of indoor potted plants. They are fast and tiny, so apologies for very shallow DOF. The first is on an aloe, the second is on a pot. They really like the soil around some capsicum plants.


texts: Fst genetic distance: Autosomal vs. mtDNA

texts:
As far as I'm aware, mtDNA is only inherited from the mother. Hence, if I compute Fst from autosomal SNPs, then I'll get the actual genetic distance between two human populations.

If I compute the genetic distance Fst between two human populations based on mtDNA sequences, then it alone can't be used to draw conclusions on their genetic distance.

For example, an admixed population will score relatively low Fst value with its maternal ancestral population (assuming the admixture was caused by unisex migration) when computing based on mtDNA sequences. However, the Fst distance based on autosomal SNPs will be relatively higher (depending on proportion of admixture).

Is this correct?


texts: What animals have a blood-brain barrier?

texts: I am curious about how old the BBB is, in terms of evolution. Is it present in all vertebrates? or just mammals? or what?


texts: Is every part of a virus important for replication?

texts: Is every component of a virus absolutely essential for its infection and replication in a host cell? Or can you just have parts of it to cause infection?


texts: Why are Taurine and Arginine essential components of the feline diet?

texts: Taurine and arginine play a key role in the feline diet but I am unaware as to where exactly they fit in.


texts: What does it mean for Caenorhabditis species to be "pseudoparasitic"?

texts:
In this Wormbook chapter, Kiontke says that some Caenorhabditis species live "pseudoparasitically" on warm-blooded animals. What does it mean? What is a pseudoparasite? I understand a parasite to be in association with a host where the relationship is beneficial for the parasite and harmful for the host. How is pseudoparasitism defined?

I have found several definition:

Something in the blood that is mistaken for a parasite: not applicable to Ceanorhabditis as no Caenorhabditis has ever been found alive in blood
A false parasite; may be either a commensal or a temporary parasite (the latter is an organism accidentally ingested and surviving briefly in the intestine): could be this
an object or organism that resembles or is mistaken for a parasite: could be this
interpreted to be parasitic but not actually parasitic: could be this
This definition actually sounds like the definition of a parasite and only applies to invertebrates, so not applicable to Ceanorhabditis

In conclusion, I would say that some Caenorhabditis are pseudoparasitic of warm-blooded animals, which means they are commensal and cause no harm. However, I don't see the point of saying they are pseudoparasitic. I would rather just say commensal.


texts:
When I see fish in an aquarium, they never seem to stop swimming. This is in contrast to e.g. the penguins, who spend a lot more time just standing there.

Is this true in the wild or specific to aquariums for some reason? Is there a biological or evolutionary reason this is so? Is it a special case of some more general principle? (It occurs to me that fish are much smaller than penguins.)


texts:
I was reading in a book that in the process of neurogenesis - when new neurons are born -  neurons compete for survival. Or in other words they have to make themselves useful to the brain otherwise they die and become processed as brain food.

To what extent is this real and how often does this happen?

i think that in the book I was reading it the author mentions it happening in early life, but I'm not entirely sure.

Would be great to know.

Thank you!


texts: Why are bacteria and archaea in different domains?

texts: As I understand it, the main difference between the Bacteria and the Eucaryota domains are that eukaryotes have a nucleus and bacteria don't. I understand that bacteria and archaebacteria have enough of a genetic difference to be separate kingdoms, but why are they separate domains?


texts: On which DNA strand is TATA box present?

texts:
My book (Snustard and Simmons) mentions that TATA box is present on the non-coding DNA strand but that was for the promoter of mouse thymidine kinase gene.

I have tried to find out more information and stumbled upon these in wikipedia articles which actually said something else:

  The TATA box can be an AT-rich sequence "located at a fixed distance upstream of the transcription start site. (from a paper "The RNA Polymerase II Core Promoter'')

Then (from a book: Understanding bioinformatics),

  The Transcription start site is the location where transcription starts at the 5'-end of a gene sequence.

So my question is, on which strand is TATA box actually (or generally) present?


texts: Doubts regarding definition of upstream/downstream genes and cognate protein

texts:
With respect to the research paper, there are a few things I didn't understand:
1. What is upstream and downstream gene
2. This paper identifies proteins that help in secretion, but does not identify the originally secreted protein. Am I correct?
3. Does cognate protein here mean homologous protein(from common parents)?


texts: How do similar looking carps, but belonging to different species, differ from each other?

texts:
There are some carps which differ in colour, or has some easily noticeable morphological differences. But apart from that, most of the carps look "almost" the same. How does one differentiate one species from another?
Citing behavioral differences, differences in morphological characteristics (maybe subtle) and the likes which addresses this problem would be helpful. The characteristics with broader scope would be better.


texts: Can anyone identify this small shrub? Has white flowers

texts: Small shrub in adelaide south australia garden.


texts: What kind of changes "stays" in the neuron after the nervous impulse happened?

texts: I often see in neuroscience textbooks about how the brain controls everything in the body with different tracts and etc, and it seems that information is always being transmitted, like there's no fixed place in which they are stored. So after the depolarization and repolarization what happens to the neuron itself? Does it depend on which neurotransmitter stimulated it? And extending a bit the question, what is exactly the difference between being stimulated by two different neurotransmitters?(supposed that the neuron has receptors for both and the neurotransmitters are the excitatory type).


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


texts: Stopping the Gag Reflex: How and why does it work?

texts:
I was talking to some friends over the weekend, and one of them made a comment about gagging. He said that he read or watched that clenching your thumb with your other fingers (making a tight fist with your thumb in the middle) stops your gag reflex. So, naturally, as a bunch of stupid teenagers, all 7 of us proceed to do this while shoving our fingers down our throats as far as possible. None of us had a gag reflex.

Why does this work? it seems totally random and weird.


texts: Why do cells vary in shape and function when they have the same genome and the same organelles?

texts: Why do cells vary in shape and function when they have the same genome and the same organelles. For example: why do all cells have nuclei but red blood cell's don't; why can't the cells of a eye perform the function of the tongue; and the list goes on and on. If you say it is because of gene regulation, so then how does the RNA know to transcribe the specific genes that are necessary to that particular cell?


texts: What causes head hair to be different than body and face hair?

texts:
If you feel your head hair, it typically feels a lot softer and is easier to manage (comb, brush, fix) than a lot of other hair on your body - specifically I'm thinking about beard hair and pubic hair, which typically are a lot coarser than the hair on your head.

Why are these hairs thicker?

What causes them to grow differently than the hair on our head?


texts: How is it possible to even hope for an ebola epidemic of this current size to remain contained to a relatively small part of Africa?

texts:
As of 2014-09-14 at least 5347 cases of ebola have been identitied. Some estimates are much higher. While experts are sounding the alarm to try to get sufficient resources to contain the outbreak, some people are also speaking very hopefully about containment to roughly the current affected area. This article puts the risk of the outbreak reaching the United States as low as 3%. I'm not an expert in the field, but it seems like there are almost countless ways in which an increased number of cases increases the risk of further exponential growth. It's encouraging to hear that in countries with better healthcare, death rates would likely be much lower, but at this point, isn't it inevitable that the outbreak will run its course as a global pandemic?

For example, which of these possibilities is just my imagination, or likely so improbable that we don't need to worry about it?

Scared carriers not yet showing symptoms sneak or force their way across boarders to unaffected regions.
Objects, food, or water touched by the infected go unnoticed until they end up leaving the containment zone.
If it can jump from bats or monkeys, thousands of infected humans increase points of contact to create vectors into other species, perhaps one that will travel unnoticed far beyond the containment zone.
After months of the same security precautions day in and day out, airport checkpoints, and other points of entry become lazy, and let infected through.

With numbers as high as they are, and possibly higher than we even know, is this really containable at all?


texts: Is there any biological basis for the commonplace "eyes popping out" cartoon?

texts:
We might all be familiar with images like these below:

I see this clearly "works" in a cartoon context. It makes a point. That "eyeballs" hanging outside belong to the individual and can be shown next to him and not in the floor or so. But, is there any biological basis for this? Is something like this ever possible? Probably the answer is no, as the (optic) nerve connecting the brain with the "eyeball" surely cannot be extended like that. Would the eyeball actually hold its shape?

PS: for the sensitive among the crowd (including myself), please do not post gore-like pictures to show what actually happens. If want to provide some visuals, diagrams might suffice.


texts: I'm having a bit of trouble with searching for this piece of information. I'm doing a study related to phylogenetic susceptibility of hosts to pathogens (based on a recent Nature publication), specifically to flu. This requires knowing the reference 18S ribosomal DNA sequence for chickens, wild ducks, horses, pigs and humans (amongst others). Is there a resource that enables us to easily download these?


texts:
After searching "do antibiotics impact the immune system" I found out that antibiotics target prokaryotic cells. It all made a lot of sense thinking about all those yogurt recommendations you get after taking antibiotics: the collateral damage is on the prokaryotic cells that live with us, but are not "us" as such.

Except I remembered human red blood cells don't have nuclei, so where's my confusion?

(I'm only a biology enthusiast.)


texts: How does the counter current mechanism concentrate urine?

texts: The movement of ions like sodium into the interstitial space causes water to passively diffuse out the descending loop of Henle. How does this concentrate the urine? The solvent is removed at one place, and the solute at another. Shouldn't the concentration remain the same? Or does the removal of a little solute remove a lot of solvent? Why?


texts: Would prehistoric humans have been considered negroid or australoid by modern standards?

texts:
What are your thoughts about this?

For myself I think that the subject statement is rather obvious isn’t it, since Africans, & especially Australian Aboriginals, have the most archaic features & share the most traits with prehistoric humans & other primates within modern humanity? Africans have neotenized greatly, culminating with the khoisan people, whereas australoids don’t have any neotenous traits which the other races have been developing & don’t lack archaic traits which the other races have devolved.

Which of the great races, the highest general division of humanity, mongoloid, caucasoid, negroid, australoid, etc. would prehistoric humans have been considered both by layman’s perceptions, & classified as more scientifically, by contemporary standards, if the choice had to be made, or at least considered closest to or most resembling?

What we’re probably thinking of then are remains going really far back enough to not be of obvious contemporary racial categories aren’t we?

Since prehistoric humans are said to not resemble any modern race, this question may end up being more about opinions rather than hard answers, might it?

Please explain & fill in details regarding your opinion & knowledge. But please do answer the main question first before adding in more details, even if to explain how this subject statement has no merit!

Not sure how much merit this book holds, but do have a look at the tables in ‘Section II: Traits of Living Populations’ for a nice summary:
https://analyseeconomique.files.wordpress.com/2012/12/richard-d-fuerle-erectus-walks-amongst-us.pdf

Here’s the tables themselves. The site’s in French but you can translate it in google. You can also click on the images & save them:
https://analyseeconomique.wordpress.com/2011/11/20/erectus-walks-amongst-us-richard-d-fuerle-section-2/amp/


texts: I'm going to take a picture of a bacteria but I am unsure how large it is. What are the dimensions in angstrom of bacteria?


texts: Interpretation of agarose gel electrophoresis of a plasmid

texts:
I am performing agarose gel electrophoresis of plasmid which is 2.5-3 kb in size. I am getting more than 3 bands, after restriction I got single band at 3.5kb in size.
Electrophoresis conditions- 0.5X TBE, constant voltage 150V.
why am I getting more than 3 bands after agarose gel electrophoresis of plasmid?


texts: In my experiment I found that a GFP gene under T7 promotor in high copy number pTAC-2 vector is showing green fluorescence producing colonies of DH5 alpha under UV light. what could be the possible reason?


texts: Preprocessing microarray data to detect increased male expression variance due to dosage compensation?

texts:
I am currently working with a dataset from a large microarray experiment where one of the aims is to look for evidence of the predicted doubling of variance in expression on the X chromosome in hemizygous males relative to females due to dosage compensation.

Speaking broadly, the experiment uses a controlled breeding scheme in Drosophila to generate individuals that are heterozygous or hemizygous for different known X chromosomes (the autosomal genotype is also controlled). I then want to use a genewise linear modelling approach to estimate additive genetic variance for gene expression for each gene in males and females. The arrays involved are Affymetrix GeneST arrays.

My initial inclination was to preprocess the array data using RMA, in my case from the oligo package in R. A fundamental part of RMA preprocessing implementations is a log2 transformation, and of course this has desirable properties for most gene expression analyses. However, it is apparent that the variance-stabilizing properties of the transformation have some undesirable consequences when looking for the sex differences in expression variance across samples that I am interested in. A toy example showed that variance in log2 expression is the same whether or not males show dosage compensation, obscuring the very signal I am interested in.

I would like to retain the benefits of the preprocessing steps (e.g., background correction), but I wonder if anyone can weigh in on the best way to avoid the log2 transformation’s effect on estimates of variance. Is it appropriate to simply take the antilog of the expression matrix after RMA preprocessing or is there another approach/package I should look into instead?


texts: Are there any documented instances of coronaviruses being directly transmitted from bats to humans?

texts:
Many human coronaviruses have ancestral host origins in species of bat. However, all instances I am aware of identified other animals as intermediary vectors:

SARS-CoV: Human ← Palm Civet / Raccoon ← Bat
MERS-CoV: Human ← Dromedary Camel ← Bat
HCoV-229E: Human ← Alpaca ← Bat

Are there any known cases of direct bat to human transmission of coronavirus?

Source: Bats and Coronaviruses, Viruses (2019)


texts: What are the advantages of using interphase cells rather than metaphase cells for gene mapping purposes using FISH?

texts: I have been told that interphase cells are better for gene mapping purposes than metaphase cells but don't know why.


texts: will a plant grow faster if it is exposed to concentrated sunlight?

texts:
I know that plant grow faster depending on the hours of sunlight it has, but what happens if i put a giant mirror focusing light to the plant?.

Will the growth rate be limited by the damage the sunlight produces, or will it be limited by the speed of the photosythesis?


texts: Gland defined based on morphology or hormone secretion?

texts:
Is a gland defined by a visible morphology, or is anything that secretes a hormone a gland?

The answer does matter for the definition of histamine. Based on the answer I can conclude whether it's an hormone or not.


texts: Can the Staph streak method be used for culturing Neisseria on blood agar?

texts:
What I learned in class:
Normally chocolate agar is needed to grow Haemophilus and Neisseria. The Staph streak technique can be used for culturing Haemophilus on blood agar by allowing the Staph to hemolyze the blood so Haemophilus can grow around it.

My question:
Is there a reason this method couldn't be used for Neisseria as well?


texts: What software do I need to read-write cas9? and .dna files?

texts:
I am still a complete beginner to crispr and I am still trying to learn what it is and how to actually use it. I now realise that you have to order the crispr components after you have actually designed them yourself in software that lets you design and alter the components.

Am I correct so far?

I am wondering if anyone could help me find which software I should use to design and or alter .dna files . Preferably free and open-source software. Are there any good tutorials for someone who wants to get more into crispr?


texts: why don't antibiotics reduce our weight?

texts: I know that a significant weight of the human body (in Kgs) is contributed by microbiota. I also know that antibiotics can often be broad spectrum and kill all the bacterias regardless of them being good or bad for us. So why doesn't antibiotic courses reduce our weight as the microbial population must've been demolished?


texts: Are there any open plant databases (database/library/collection), containing species information and pictures?

texts: I would like to download a plant database containing photos and species details. Do you know if there are any openly available online?


texts: Can Serous inflammation on pleura pulmonalis cause dry cough and runny nouse?

texts:
I am interested in the mechanism between the dry cough and runny nose (serous inflammation) here.
I started to think how Acute respiratory viral infection is causing the dry cough.

The serous membrane, pleura pulmonalis, connects diaphragma to pars basalis pulmonalis.
It can be the source of the serous inflammatory response spreading to the nose probably.
There must be some source of inflammatory responses such that reflex arches can use them fast, thinking physically.

Assume medication Montelukast (stop asthmatic symptoms), codeine (to stop irritated dry cough) Flixotide (with Montelukast).
Assume that there is a diaphragm press on pars basalis pulmonalis.
Assume you breath mostly by abdomen 15 minutes in the supine position.
Assume opposite-astonic person in thorax.
You then feel that you exhale too much - the serous membrane pushing on pars basalis pulmonalis - serous inflammatory response in pleura pulmanalis.
The breathing process moves thoracic muscles and thoracic cavity gets shortly extended only little.
Negative tensor on lungs i.e. the volume of the lungs is getting smaller.
Consequently, a cough reflex arch and sympaticus start a deep dry cough to protect lungs.

Characteristics of the pathway against Acute respiratory viral infection

serous inflammation on pleura pulmonalis
serous membrane pleura pulmonalis presses on pars basalis pulmonalis
negative tensor on lungs
cough reflex arch and sympaticus
dry cough
positive gradient on the pleura spreads inflammatory response through the surrounding lymphatic system is sensed as dry in larynx
negative gradient is sensed on the nasal mucosa membranes as serous inflammation (runny nose)

Can the serous inflammation of plera pulmonalis cause a deep dry cough and runny nose?
The cause of this inflammatory response can then be Acute viral respiratory infection in some part of the lungs.


texts:
Autophagy and apoptosis are both necessary for survival of a multicellular organism. I have some information on evolution of autophagy and apoptosis.
However, the key difference between the pathways struck me as - autophagy is for self survival whereas apoptosis is for survival of the population. Given this, is it logical to assume that autophagy evolved earlier than apoptosis ?

Edit1:
I thought of a reason for autophagy to precede apoptosis. Since apoptosis requires mitochondria for its initiation and was acquired as endoymbiosis, I assume that:
$1)$ The primitive organisms taking up primitive mitochondria were eukaryotes.
$2)$ These were already sophisticated enough to have preliminary autophagy.


texts: Thoughts precede neuron firing or vise-verse?

texts: I am at the verge of submitting a paper on 'scientific explanation of reality' to an international philosophy body. First submitted draft was returned by the evaluation expert, asking me to re-submit it, after re-checking the validity of my  assertion that 'science (biology) believes that neuron firing always precedes thought'. Can any one provide answer on biology's clear stand on above question ?


texts: 'Terminal' and 'lateral' apical buds. Monopodial and sympodial branching

texts: Macroscopically, it seems to me that the difference between 'lateral' apical buds and 'terminal' apical buds and monopodial and sympodial branching is often rather superficial, if not random. Therefore I'm suprised that such things are sometimes used in identification keys (since in some shrubs and trees, there are no apical buds at all). Does anyone know if in Biology, there is an objective definition of those phenomena, e.g. based on inner workings of a plant or microscopy?


texts: Is there any knowledge of physics can be applied in to evolution?

texts: I have asked a similar question in Biology.SE (What physics knowledge can be applied to biology of organisms and ecosystems?), but it just about organisms and ecosystems, not evolution. After watching a clip that Richard Dawkin talks about applying Darwinian evolution to physics, I would like to ask a vice versa question: is there any knowledge of physics can be applied in to evolution?


texts:
I am going to perform some RT-qPCR tests to validate an experiment.

I'm currently in the process of ordering primers, and I would like to get them from the Harvard Primer Bank since these have been validated before.

However, I would like to get primer pairs that span an exon junction (i.e., one primer on one exon, the other primer on another exon.)

Currently, I have to do a lot of steps to figure this out, since the Primer Bank only gives the positions of the primers on the CDS, and not on the entire mRNA molecule.

Does anyone have a quick way to check on which exons the primers belong?

Thank you!

Is there a good site or software to see if a primer pair spans an exon junction?


texts: Why do we need to replicate incomplete DNA fragments by PCR from a crime scene?

texts: If the DNA from a crime scene is damaged, why would it be helpful to replicate it by PCR (polymerase  chain reaction)? Even if we get billions of those copies, it is still incomplete, isn't it? How can the PCR make the forensic process easier?


texts: Do insects with compound eyes have depth perception? They fly as if they do, but their eyes are so close together it seems like the image would be 2 dimensional.


texts: Is designing alien life still just science fiction?

texts:
As we continue to search for life in very different environments than the earth, it would make sense to me to think about and design lifeforms (theoretical) that could work in these environments. I know that we are searching for life in extreme environments, but are we thinking about lifeforms that could have evolved in such environments? (Even if we dont find any)

The idea of the atom comes from ancient greek philosophers long before one could find any evidence for it. Although their views on what atoms look like and how they behave were incorrect, one could later refine this model through evidence and experimentation.

I think some good thought could makes us learn what to look for in the first place.

Is this still just a field that science fiction thinks about, or are there any serious publications on this topic? If not, why not?

Clarification: I mean the theoretical design of lifeforms. Not just manipulating and editing existing lifeforms, I mean designing completely new theoreticaly plausible lifeforms, within the constraints of a given environment. On paper or simulation etc, not actually making them physically.

If you find any scientific papers on how and what kind of life could exist for example on Titan, Europa, below Earths crust etc... or any other environment, please link to them in your answer. Thanks!


texts: What types of archaea have been found in animals?

texts: I am curious as to the species or "types" of archaea that have been found to reside within animals symbiotically. One of the only ones I can think of off the top of my head are methanogens, which live in the gut of ruminants for example.


texts: Ways to identify that proteins are regulating different genes experimentally

texts:
As part of my study I have been given this hypothesis:

  HIF 1a and HIF 2a regulate different genes in multiple myeloma

What ways do we have to identify that these proteins are regulating different genes in multiple myeloma? I recall in lectures something being mentioned about using antibodies to isolate the regulatory elements, but can't find any specifics.

Any help is seriously appreciated!


texts: Why do polyneuropathies affect the extremities first?

texts:
Polyneuropathy is an anatomic pattern of nerve damage most commonly seen in Diabetes mellitus.

To quote Robbin's Pathology,

  In most polyneuropathies, axons are affected in a length dependent fashions leading to deficits that start in the feet and ascend with disease progression. The hands often start to show involvement by the time deficits extend to the level of the knee, resulting in a characteristic 'stocking and glove' distribution of sensory deficits

What is the reason behind longer neurons being preferentially affected?


texts: How can I search for and find specific biology topics in scientific journals?

texts:
I looked on google to find "scientific paper on biological explanation of homosexuality" but nothing comes up that appears reliable or from a journal. Then I looked up "scientific journals" and I found a directory for them, and searched through that directory, but of all the journals, I cant seem to find an efficient way to search for topics in these journals over the web.

Is there a way to efficiently search for specific scientific journal papers, specifically for biology?


texts:
The video below mentions whether the dendritic should call in a 'anti-virus force' or an 'army of bacteria killers'. The video goes on to talk about how bacteria is killed, using B-cells, but there's no mention of cytotoxic T-cells. Is the cytotoxic T-cells only for viral infections or is it for both?

https://youtu.be/zQGOcOUBi6s?t=2m42s   <-video is time stamped.

I don't study biology and the internet is confusing sometimes.


texts: Will bark-beetles infest the Methow Valley?

texts: What is the Methow Valley (esp. Winthrop, WA) area's susceptibility to bark beetles?  Did the 2014 Carlton Complex wildfires increase the vulnerability due to the large numbers of dead, dying, and stressed pine and fir species in the area.  Are there ways I can reduce the vulnerability of my property, which is already in open, park-like stands?


texts:
Richard Dawkins in one of his videos says that Evolution is a fact and not just a theory.

He goes on to say that man and chimpanzees both evolve from apes.
Is this correct (Is evolution a fact and did humans & chimps evolve from apes)?


texts: Does scratched Teflon coated frying pans contain carcinogens which can cause cancer?

texts:
Is it true that using scratched Teflon-coated pans contain carcinogens, and if so, can they be consumed through the food cooked in them?

E.g.

The deadly toxins from non-stick frying pans


texts: How does the MMR vaccine affect lymph nodes in preventing measles?

texts:
I am trying to understand this statement about the Measles part of the MMR (Mumps, Measles and Rubella) vaccine

  Measles prevention: MMR (AB protect during primary and secondary viremia)

Measles enters from respiratory tract, through mucosa of the upper respiratory tract. The virus passes into cervical lymph nodes. Now, starts first viremia (MMR somehow helping here) which lasts about 5 days. Then antibodies are secreted during 15 days which leads to rash lasting about 3 days.

I think this second viremia refers to the possible dissemination of the virus to other lymph nodes by blood.
This suggests me that the vaccine primarily have a mechanism that affects in the lymph nodes or generally in the lymphatic circulation.

How MMR vaccine affect lymph nodes in preventing measles?


texts: What is an accessible book about plant evolution for a non-biologist?

texts:
I have an acquaintance interested in learning about the evolution history of plants. This person has a wide knowledge on botanics, from personal reading and taking care of plants, but E is neither a biologist or a biology student.

Based on this, which is an accessible book to non-biologist that can be used to learn about the evolution of plants?


texts: Why do animals use glycogen for their polysaccharide storage whereas plants use starch?

texts:
The polysaccharide storage form of glucose in animals is glycogen, whereas in plants it is starch. Both of these are polymers of α-glucose with α-l,4 glycosidic linkages and α-l,6 glycosidic branch points (Wikipedia article on polysaccharides). The only difference that most sources mention (e.g. Berg et al.) is that glycogen contains more branches than starch.

It is not clear to me from this information what effect the different branching would have on the structures of the polysaccharides, nor why one rather than the other would be preferred in animals and plants.


texts: How is recruitment of multiunit smooth muscle cells fine tuned if they are innervated by varicosities?

texts:
In my physiology textbook (Silverthorn) and on wikipedia it says that:

  Multiunit smooth muscle tissues innervate individual cells; as such,
  they allow for fine control and gradual responses, much like motor
  unit recruitment in skeletal muscle.

However, that does not seem right to me. Although potentially each cell could be innervated, they are innervated by autonomic neurons. These neurons use the rather crude method of varicosity innervation. Such neurons recruit all the cells adjacent to its varicosities, not just a few. Hence, does this not mean that there is no 'fine' control of unit recruitment of smooth muscle cells?  Or is there an other way in which recruitment of smooth muscle cells is fine tuned?


texts:
Both fungi and algae have very small cells but so do most animals. Yet both of them are visible to naked eye just like other organisms.
Why do we call them as microorganisms then ?


texts: I am reading the paper "Activity of the bcr-abl kinase inhibitor PD180970" but I don't understand how IC50 works on table 1. Can you tell with simple words and give me an easy example?


texts: How to seek for available genetic data relevant to ecology and evolution?

texts:
I had a quick look online. There seems to exist many different website of database archiving. Some data might be free of charge while some others might not be. I found things such as Dryad, TreeBase, DataOne or GeneBank. I think that several journals (American Naturalist, Molecular Ecology, Science and Nature for examples) force their authors to make their data available

General Question

Can you make a short review of what different database exist, what are their properties (what kind of data, what license and fees) and how to seek for data (are datasets associated to keywords or do we have to look for a paper and then look for their data).

Case study

Imagine for example, you are looking for SNP data of a spatially explicit population that recently underwent a range expansion (might be too accurate, you may want to drop down some specifications). How would you go about to look for this kind of data? (No need to pull out data but only to describe a procedure).


texts: Falconer & Mackay population mean calculation & genotypic values

texts:
I am reading chapter 7 of Falconer and Mackay where they give a formula to calculate the population mean as a deviation from the heterozygote genotypic value.

As an example, imagine a one locus two allele trait, with alleles $A_1$ and $A_2$, with respective frequencies $p$ and $q$, and genotypic values ($\theta$) of $A_1A_1 = \theta_{1,1} = 0.5$, $A_1A_2 = \theta_{1,2} = 0.4$, and $A_2A_2 = \theta_{2,2} = 0.3$.

The mean is given by

$ M = a_1(p-q) + 2pqd$

where $a_1$ is the deviation between the genotypic value of $A_1$ homozygotes and genotypic value heterozygotes, and, because $d=0$ (the dominance deviation), this equation reduces to

$ M = a_1(p-q)$

For my above example, if $p = 0.7$ then $M = 0.04$ and the population mean should be

$\frac{1}{2} \theta_{1,1} + \frac{1}{2} \theta_{2,2} + M = 0.44$

$\frac{1}{2} \theta_{1,2} + M = 0.44$

Is this correct?

What is the correct term and notation for the genotypic values (which I termed $\theta$)


texts:
Why is it that snakes do not have eyelids?

Is it due to that fact that they are not as evolved as we humans and other organisms that have eye lids, or is there any other significance behind it if any?


texts: According to my understanding of the Wikipedia page on the stinging cells of the jellyfish, the mechanism of delivering the toxic missile is largely due to water pressure. Does that mean that a jellyfish on land (or brought out water) is unable to, or perhaps less efficient at, delivering its stings?


texts: Can untargeted metabolomics detect epigenomic changes such as methylation?

texts:
My main focus is transcriptomics analysis and very recently I have also started working on metabolomics. From my transcriptomic data it looks like there is a gene/protein that could potentially generate epigenetic modifications. I also have untargeted metabolomics data of equivalent experimental conditions that I plan to analyse soon hoping it will complete the picture. However, I have searched for publications linking specific metabolites with hyper/hypomethylation or chromatin structure and I have only been able to find a few references (see link below) and I got the feeling that untargeted metabolomics does not seem to be an obvious technique to observe epigenetic signatures.
https://www.ncbi.nlm.nih.gov/pubmed/30125527

What metabolites would be regulated under epigenetic circumstances?
Does anybody have any experience or know of any particular study that looks into this relationship between untargeted metabolomics and epigenetic modifications? Thank you very much for your help!


texts: How long does immunity to influenza last when contracting the disease vs vaccination

texts:
The long term efficacy of flu vaccines are well documented, however I cannot seem to find a good source showing how long immunity lasts when contracting the disease.

I suspect it can't be much longer than vaccines since the virus mutates so quickly.


texts:
I have reached the end of my Winogradsky Column experiment, but out of interest I have kept them for a little longer. I have noticed small bug- and worm-like organisms appearing in some of my columns. All mud and water was sourced from a nearby pond in Florida. The bug-like organisms are simply swimming/crawling around inside the column, while the worms are sticking up from the mud and wriggling. This pictured column was part of a group kept under a heat lamp.

Could anyone please provide an ID for these organisms? I think the worms are bloodworms, but I am not sure and I do not know what the small bug-like organisms could be, either.


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


texts: Starch vs Cellulose. What are the differences between Alpha and Beta glucose ring structure in them?

texts:
I'm studying "Campbell Biology, 10th Edition" and in chapter 5 page 71 there's a statement I can't understand. according to book:

  In starch, all the glucose monomers are in the α configuration.

and then says:

  In contrast, the glucose monomers of cellulose are all in the β
  configuration, making every glucose monomer “upside down” with respect
  to its neighbors.

My question is if all glucose monomers of cellulose are all in the β
configuration (according to figures) why each monomer in cellulose is “upside down” with respect to its neighbors and is not just all the same as in glucose monomers.


texts:
The novice often performs population calculations using
what is referred to as Mendelian Genetics. Soon after the
publication of Mendel's results; Hardy and Weinberg presented
their results after the interjection of a collection of axioms.

Is there a difference between Medelian genetics and the
Hardy-Weinberg model?


texts: How to use a published phylogenetic tree?

texts:
I would like to know how should I use a phylogenetic tree from an already published article, to put it on my own article so I can analyze the evolution of a trait. Is there any software I can use, or do I only have to "edit" the tree with a traditional image editing software?

I've seen that using trees from other authors is a common practice. Many times they summarize the trees. But no paper seems to tell you how they did it.

Thank you!!


texts: What is the another use of de Bruijn graphs in bioinformatics except DNA assembly?

texts:
I implemented own generic de Bruijn graph, which I use for DNA assembly (alphabet: A, C, G, T). I try to find purpose of de Bruijn graph for another bioinformatics problems, if some exists. I want use/modify my implementation to solve this.
Are there another problems in bioinformatics which we can solve with de Bruijn graphs?

I found only RNA assembly, which is similar to DNA assembly.


texts: Using coefficient of variation (CV) for GCaMP6 'synchronised episode' spikes, good idea or not?

texts: Using GCaMP6 we have recorded fluorescence activity of kisspeptin neurons that exhibit synchronised pulsatile firing activity. I measured the intervals between each episode, which are quite variable. However, I am unsure whether or not using the coefficient of variation to analyse their variability is a good idea (since most papers I read have applied it to individual neuronal firing to analyse variability between spike intervals but not to population spike activity). Also, do I need a minimum number of 'spikes' to use CV (since in my recordings there are only around 4-10 spikes in around 3 hours)?


texts: What is this small black insect with an orange stripe?

texts:
Sorry for the poor quality of the second image, but a slightly different perspective may be useful.

This was taken in South Africa, Western Cape during the day.
They're fairly small, maybe around 5mm in length.
They were huddled together on an ivy leaf. I found another group of about five also huddled close together on another plant.


texts: What is reaction time of a single c. elegans neuron?

texts:
What is the reaction time of a single c. elegans neuron?
Is sensory neuron reaction to stimulus is similar to intermediate neuron passing a signal to motor neuron? What about chemical and electrical synapses?

I want to make a simple real-time artificial network model using existing c. elegans connectome projects, but I can't find anything defining time scale.


texts: Could an ant colony have 2 or more "branches" located far from each other (i.e. physically separated but interconnected nests) ? If so, how far is the limit?


texts: What happens when the bacteria in the petri dish lack nutrients for long time?

texts: If I put some E.coli in a petri dish filled with limited nutrition in room temperature and forget them for months or years. What will happen in the final after they overgrowth and used all nutrition left? Will they die or just stop dividing?


texts:
In research paper Euphytica 135: 187–204, 2004 it is written that:

  434 mutant varieties of rice have been released with improved characters such as semi-dwarf height,
  early  maturity,  improved  grain  yield,  disease-  and
  cold-tolerance, and improved grain quality. Of these,
  225 (56%) were induced with gamma rays, 16 with X-
  rays, 7 with fast neutrons and 12 with other radiation
  sources

So I can see that irradiation may have positive effects on plants' genome.

Is there any information that mutations induced in this way in humans were beneficial for them? Can irradiation have positive effects on your body?


texts: How common is it to be pregnant with periods?

texts:
As you may know, some women claim that they have their period while they are pregnant. In the arab world they call it "Deer pregnancy", since when the deer gets pregnant, it still gets its' monthly cycle.

Their doctors do confirm that. The appearance of such: The bleeding comes at the times when the period is expected, but is usually without pain, or smell, and lasts for less days. It is also of different color. But many women (and doctors) still call it a period.

(Although we all know, a real period is impossible biologically).

How common is that?

This is, I think, different from implantation bleeding, since it mostly continues to three months and after that.


texts: Signaling through G protein Coupled Receptors?

texts: There are two different cell lines but we do not know that these cell lines have Gs or Gi proteins, associated with their G-protein coupled receptors. If we wants to know about this. Can we design a experiment through which we would be able to identify specific Gs or Gi proteins in cell lines?


texts:
Of the twelve well-known atomic constituents of our body eleven elements have specific properties obviously relevant to their rôle, making them indispensable. Oxygen (electronegativity and valence), carbon and hydrogen (both elements have virtually unique properties), nitrogen (amino group), calcium (calcium(II) is necessary for bones in vertebrates), phosphorus (use of phosphate in nucleotides and ATP), sulfur (–S–S– bridges), sodium (Na+ is a small cation), potassium (K+ is somewhat larger, together with its companion and presumed substitute Rb+), iron (used in hemoglobin because of properties of a transition metal), magnesium (Mg2+ takes part in the ATP cycle, if not anything else).
What about chlorine? A search resulted in

Chloride is involved in the exchange of oxygen and carbon dioxide in the red cells.
In this, chloride passes into the plasma (chloride shift) and bicarbonate into the cells.

(https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/chloride), certain use by muscle cells and also some mention of ligand-gated chloride ion channels in neurons. Chloride in stomach secretion may be dismissed because is used as a generic acid (that is, to complement H+), not for its own special properties. And no mention of biological chlorine compounds other than ionic (such as, having a C–Cl bound) can be quickly found.
Which cells absolutely need specifically Cl− to function? Is the anion mandatory for animals to live?


texts:
As far as I know, alternative sensation it's a sensation to distract people from the original stimuli, for example when you have to get an injection, the nurse will pinch you in the other arms so your brain is distracted and will not focus on the original pain in the arms that's got the injection.

But I also read here, alternative sensation refers to the brains that can process stimuli from multiple senses, for example when the eyesight is bad, the ears will take up and boost the visual system to help and stimulate the visual system (Visual + Auditory) .

Which one is exactly an 'alternative sensation'? Also, what is Time-Frequency in alternative sensation ? I would appreciate any references too.


texts:
Please consider the following question:

Genes A and B are located on the same chromosome. If two individuals with the genotype shown below are crossed, which genotype could be formed?

Let / represent the line in the image above.
a.)AB/ab
b.)Ab/Ab
c.)aB/aB
d.)AB/Ab

Why can't the answer to this question be all of the choices? I thought that recombination was completely randomized through the process of crossing over. Why is only one of the choices correct and how would I go about doing this on my own?


texts: I know that L-Citrulline enters in the second step of urea cycle in the liver mitochondria and I wonder if a person takes an overdose of L-Citrulline wouldn't that cause mild hyperammonemia or at least cause an increase in the glutamine amino acid?


texts:
This is not a duplicate of all the other 260/280 ratio questions, I already know that DNA is supposed to be 1.8 and RNA is supposed to be 2.0. However, this might be more appropriate for chemistry, and will move it if I have to.

My question has to do with the Poly A tails on mRNA. I've been doing in vitro transcription and tailing for a while now and have noticed that the untailed RNA has a 260/280 of about 2.0, like you'd expect, but successful tailing results in ratios from 2.15 to 2.45, with higher ratios correlating to better band shifts on agarose gels, implying a longer tail. I suspect the reason for this is because the adenine has a much higher 260/280 than the other bases, so if you add a lot of adenines to the 3' end of the RNA you add much more 260 absorbance than 280 absorbance.

After seeing this I tried to come up with a mathematical method to estimate tail length based on 260/280, since gels are annoying, while I can get the ratio directly from the nanodrop.

I started by using the 260/280 for each nucleotide, A: 4.50, G: 1.15, C: 1.51, U: 4.00, T: 1.47 source here: 1. I then took the sequence for the Luciferase gene I'm using for mRNA and counted the nucleotides, 449 A, 566 C, 470 G, 374 U. I tried to get the weighted average of the 260/280 for my RNA.

A: 449 x 4.50 = 2020.50
C: 566 x 1.51 =  854.60
G: 470 x 1.15 =  540.50
U: 374 x 4.00 = 1496.00
Sum:            4911.60

Nucleotides: 449 + 566 + 470 + 374 = 1859
Sum / Nucleotides : 4911.60 / 1859 = 2.64

2.64 is clearly not 2.0. Even accounting for the potential effect of pH and ionic strength on RNA 260/280 ( acidic solutions have lower ratios ) I can't explain why the calculated ratio is so high. Even if we assumed an RNA with 25% of each base, the weighted average is still (1.15 + 4.50 + 1.51 + 4.00)/4 = 2.79, even higher than for my real sequence.

Doing the same calculation for DNA, (1.15 + 4.50 + 1.51 + 1.47)/4 = 2.16.

So why don't my calculated ratios for RNA and DNA 260/280 match the "ideal" ratios of 2.0 and 1.8?


texts:
I have been tasked with writing a program for computing properties of a give set of peptides. These peptides are given as 1-letter amino acid sequences and I need to compute the following :

Length of peptide
Number of Each Amino Acid
Percent composition of each amino acid
Molecular weight
Net charge of peptide
Positive charge
Negative charge
Isoelectric point (pI)
Hydropathicity
Percent polar amino acids
Percent positive amino acids
Percent negative amino acids
Percent hydrophobic amino acids
Hydrophobicity
Lipophilicity
Amphiphilicity
Water-Octanol Partition Coefficient
Steric Bulk
Side chain bulk
Net donated hydrogen bonds
Percent \alpha helix
Percent random coil
Percent \beta sheet

While some of these properties are self explanatory ( eg. size, num. of amino acids, percentage of amino acids. ) and easy to compute. Other properties ( like Molecular weight, Net. charge, Positive charge, Hydorphobicity etc ) have been difficult for me.

I donot have Chemistry or Biology background and hence have found these difficult to compute. I would be appreciative if someone could point me in the correct direction ( I have already been through Wikipedia ) containing methods to compute the above mentioned properties or to a standard text which would explain the above mentioned properties and also provide methods to compute them. Thank you all.


texts: Is there variation in which olfactory receptor genes are functional in humans?

texts:
According to wikipedia humans have around 400 functional olfactory receptor genes and 600 pseudo genes. Most mammals have higher numbers of functional OR genes.

My question is whether it has been studied how the number or subset of these functional ORs varies between humans.


texts:
I recently saw the documentary series Blue Planet 2 and was mesmerised by it. Can someone recommend me some resources to learn about marine life? I am particularly looking for those that detail the habits and lifestyles of marine organisms.

P.S. - Hope this is the right stack exchange for this question


texts:
Why do human women have periods when most animals don't? It is known that the unfertilized egg needs to be shed from the uterus. But why shed the whole endometrium? Why didn't evolution put macrophages to work to simply digest the ovum and only the ovum, instead of the physiologically, energy-draining process of menstruation and accompanying blood loss? Also, are there any other purposes for menstruation, besides wiping out dead ova?

Sites I used for references:
 1. Jensen et al., Am J Reprod Immunol (2012); 68(5): 374–386 -                       Menstruation seems energy draining, in my perspective, given that 30-40 ml of blood is lost × 3-4 days × 12 months × 15 years on average - that is a lot of blood loss.
 2. Also see this Quora post.

Related question: Why is menstruation in wild animals not a disadvantage to organismal survival?.

My question is different from this related question because there the OP is concerned about the survival advantage of the menstruation with respect to the predators. Here I've asked why menstruation and why not phagocytosis as the former to me seems to be highly energy consuming process. Also as the fellow post writer had earlier suggested though the two questions  seem to be one and the same, they are subtly different and aimed for two different audiences as I emphasise more on the physiological aspects of menstruation and the related question's OP needs clarification about survival advantage and other ecological aspects of menstruation.


texts: Is this claim about equine anatomy true?

texts:
While bumping through obscure corners of the Internet, I encountered the following image posted somewhere.

  The horse anus is a marvel of evolutionary biology.

  Like most mammals, rhythmic contractions of the bowels move the feces up to the end of the gut to be expelled.

  What sets the horse anus apart is the bafflingly complex autonomic contractive motion of 4 muscular rings which function like sphinctoral guillotine. As the feces is squeezed out, the rings expand and the
  outermost ring is retracted into an interior skinfold resembling the human foreskin, leaving an interstital tissue fold to open air.

  The two inner rings then contract, and push apart, severing the horse feces cleanly, allowing to drop free as the outer ring folds back through the interstital flap, creating a intrinsic wiping motion with the fourth ring as it contracts back into the horses rectum.

  This advanced biological mechanism is so effective that many industrial companies have copied Nature's design for self-cleaning viscus liquid dispensers housed within complex machinery.

Quite interesting, but anyone who saw one, recognizes an imageboard post - probably the infamous 4chan, where each page bears the warning: "The stories and information posted here are artistic works of fiction and falsehood. Only a fool would take anything posted here as fact." Accordingly, I'm skeptical. So, a verification please?


texts:
When papers refer to traits as being sexually homologous do they refer to traits which are:

a) present in both sexes but can be dimorphic (e.g. body size is sexually homologous because both sexes have a measurable trait which has the same criteria in either sex, but this is frequently dimorphic)

Or

b) present in both sexes and not different between the sexes

I have always thought it is a, but I'm now using the term in a paper and want to check. I would have thought the latter would be "homologous homomorphic traits" or something like that.

If an answer could have an example of the use(s) which make it obvious from published work that would be great!


texts: How to prevent mold from building on food and how to kill it along with neurotoxins?

texts:
I have some food/fruits chopped in very small parts, whatever it is that needs to be conserved during long time, when it is given to me it can be somewhat wet or humid, after some time of keeping it in a plastic Sterilite it builds mold.

After reading a bit I've learned that an autoclave can kill mold at 100°C at 10psi (68.9kPa) for an hour, but it won't kill toxins. My All American pressure cooker with gauge says it can reach 120°C at 15psi (103.4kPa), however this is not much of a difference.

Vinegar, bleach and borax can all be used, but food becomes unusable.

So here are the two questions:

How can I safely keep that food without building mold?
If mold does appear, how do I exterminate it along with toxins safely for human health?


texts: How to tell if something is an organ or apparatus?

texts:
An apparatus is defined as

  Physiology. a group of structurally different organs working together in the performance of a particular function.

An organ is defined as:

  Biology. a grouping of tissues into a distinct structure, as a heart or kidney in animals or a leaf or stamen in plants, that performs a specialized task.

The below shows the Juxtaglomercular apparatus (JGA). Without knowing its name, how would I tell if it is an apparatus or an organ?

There is a question in my book (which asks: which organs are necessary for the continuation of the Renin-Angiotensin-Aldosteron-System) and to answer it correctly requires that we know that JGA is an apparatus and not an organ.

Is there any giveaways that show it is an apparatus and not an organ, based on the diagram alone?

I can't really tell based on the definitions above e.g. based on the diagram, I cannot tell if JGA performs "a specific task" or a "particular function".


texts: What happens to the molecules of the pathogens after phagocytosis?

texts: For example, what happens when a bacterium gets digested by a macrophage? I suppose that the macrophage produces the presented antigen from leftovers from the digested bacterial particles. What happens to the rest of the bacterium? Can the molecules from bacteria be used as a source of nutrients for the body? Or will they accumulate/get transported as waste products?


texts: Which human body hormonal systems exhibit 24 hour diurnal cyclical activity?

texts:
I'm researching the possible connection between the dream content and the activity of various organ or hormonal systems within the human body. I'm looking for information on biological cycles within the human body that occur on a 24 hour cycle and may influence the sleep cycle, dream content or the overall state of awareness.

So far I was able to find:
Adrenaline, cortisol, testesterone - circadian endogenous cycle.

leptin, glucose, insuline  -  peak with awakening, decline with bedtime

What else within the human body is functioning on a predictable 24 hour cycle?

Thank you for any information!


texts: How do adult differentiated somatic cells divide?

texts:
My textbook (which is Biotechnology by David P. Clark) states, when talking about fate-mapping potential stem-cells:

  "If the marked cell is not a stem cell, the marker will not be passed
  onto descendants since normal differentiated somatic cells do not
  divide by mitosis."

He then goes on to say:

  "Most adult differentiated cells do not divide at all and are
  considered postmitotic."

So there are some differentiated somatic cells which divide, but apparently not by mitosis? So what is the technical term for their division?

Here is a screenshot of the passage:


texts:
I noticed that all of the cellular energy production methods that I covered have a fixed ratio of ATP to NAD(P)H out. For example, in the combined process of glycolysis, pyruvate oxidization, and the Krebs cycle, 10 NADH, 2 FADH2, and 4 ATP are produced (based off of my high school's bio text book, if I'm adding that right). In this way, NADH and FADH2 can easily be exchanged for ATP through oxidative phosphorylation. That got me wondering what would happen if a cell was using so many electrons (from NADH and/or FADH2) that there is too much ATP. (Just as a hypothetical: It seems fairly unlikely to me)

I was looking for a way that oxidative phosphorylation could be reversed, but I didn't find much. I did find that anaerobic bacteria can oxidize nitrite in this way, but I couldn't find much evidence of an O2-forming version. Does such a thing exist?


texts: Book recommendation for studying biology for neuroscience

texts:
I will be starting a double degree in neuroscience and mathematics very soon, and I realised that an understanding of human biology can really help me out, and so I'm looking for an introductory level biology textbook that also covers things in great detail. I have no background in biology whatsoever.

Also, am I supposed to learn about the biology of plants for example before diving into human biology or can I just get started with human biology straightway.

By the way, I'm not looking for a biology textbook that has a mathematical approach, just the traditional approach can suffice.


texts: Identity and similarity for Multiple Sequence Alignment (MSA) of proteins

texts: I have to do homology modeling for a transmembrane protein (sodium channel) and right now I am in the process of aligning the sequences of the template with the homologous proteins I have found. I am using T-Coffee to do the alignment. I would like to have some numerical descriptors of the different sequences and I have been told to include the percentage of similarity and identity. How can I compute them? Is there an on-line tools to do this? Thank you.


texts: Will dissolved proteins pass through a 0.2 micron filter?

texts: Given that there may be exceptions, can you usually expect protein to pass through?


texts:
Which type of mushroom is this? Hope the image has enough quality to allow answering the question.

Following community rules...

Images: please find below
Location: West-Northern Germany
Size - about 7 cm height, 5 width
Prior research: very hard to undestand which species is this, therefore asking here. Maybe this could be a Gymnopus peronatus - but here the stem is darker.
Specific characteristic: hollow stem


texts:
Opponent process is a color theory that states that the human visual system interprets information about color by processing signals from cones and rods in an antagonistic manner (source).

What is the advantage of opponent color against RGB color? For example, in object recognition or edge detection?

Can we say that it provides some level of invariance to changes in brightness?


texts: Thermophilic yoghurt bacteria survivability in the gut

texts: Would they mostly not simply perish since they need much higher than body temperatures to thrive? Are mesophilic ones (such as kefir) much better at that and thus have better probiotic functions?


texts: What's the mixture of plasma and haemoglobin called

texts: I know of oxyhaemoglobin but the mixture of plasma and haemoglobin in the blood gives what?


texts: How to calculate the quantification of qPCR to the equivalent of the number of nuclei in fungi?

texts: I have a question about the quantification through qPCR. The my question is: if I made the qPCR of a fungal functional gene, how is possible to obtain from the quantification number (in nanogram) the equivalent number in number of nuclei?


texts: I was trailing through a local bird sanctuary yesterday (central Kentucky, USA) and came across this spider.. it's definitely dead, but what is hanging from the back part of its abdomen? Has some parasite taken home within it, and that is its "nest"?


texts:
Male red deer (Cervus elaphus) and Male Fallow deer (Dama dama) have a descended larynx, presumably for size exaggeration - to attract mates and intimidate other animals.

Does this descent occur after sexual maturation?
Do females of these species also have descended larynx?
In males, does this occur twice - just as it does with human males?
Do deer use size exaggeration to intimidate other animals, other male deer only or both?
Lastly, are there other typical behaviors associated with size exaggeration (i.e. standing on back legs)?

Thank you in advance. I attempted to search for these online but so far have not found any answers. Of course, any cite-able literature containing the answers would be ideal.


texts: If one of eyes is blind, can that eye still feel pain?

texts: I was wondering this when I touched my bare eye (my eye was open) and since I'm not blind I was wondering if an eye is blind, can it still feel pain?


texts: Does artificial high intensity light damage permanently dark ecosystems?

texts:
Popular science features on wildlife typically capture camera images using natural light, or high-speed exposures. This is not possible where the ambient light is extremely poor.
E.g. Caves, Undersea

For beings accustomed to the stygian dark, the high illumination for a video camera and/or the flash of a still camera could both be the equivalent of a 1" spanner wallop on the head or worse. Do we, inadvertently, injure the local ecosystem this way?


texts: How copy number variation thresholds are defined in GISTIC

texts:
I am having trouble trying to understand how GISTIC discretize copy number variation to values -2, -1, 0, 1, 2. I am using TCGA copy number variation for ColoRectal Adenocarcinoma.
In cBioPortal FAQ it is written that:

For TCGA studies, the table in all_thresholded.by_genes.txt (which is the part of the GISTIC output that is used to determine the copy-number status of each gene in each sample in cBioPortal) is obtained by applying both low- and high-level thresholds to to the gene copy levels of all the samples. The entries with value +/- 2 exceed the high-level thresholds for amps/dels, and those with +/- 1 exceed the low-level thresholds but not the high-level thresholds. The low-level thresholds are just the 'amp_thresh' and 'del_thresh' noise threshold input values to GISTIC (typically 0.1 or 0.3) and are the same for every thresholds.
By contrast, the high-level thresholds are calculated on a sample-by-sample basis and are based on the maximum (or minimum) median arm-level amplification (or deletion) copy number found in the sample. The idea, for deletions anyway, is that this level is a good approximation for hemizygous given the purity and ploidy of the sample.

The low-level thresholds are quite clear, while the high-level threshold not (the ones used to label +/-2 values).
I tried to reverse engineer the discretization function (the cutoffs are not available on firebrowse). The best solution I found is, for each sample, to:

split the copy number values in two groups (amplified - positive values, deleted - negative values)

for each group (amplified - deleted)

compute the median copy number value inside each chromosome arm
take the maximum (minimum for deleted group) median value across arms and use it as higher (lower) threshold

I tested it using the files:

all_data_by_genes.txt
all_thresholded.by_genes.txt

trying to get the correct discretized value (-2, -1, 0, 1, 2) of the second file from the first. However, a small part of the values are not correctly mapped. Am I missing something?


texts: Which caterpillar is this? It was found in mid Europe during this time (April). Size about 2cm in length.


texts: Converting unit/mg or unit/ml into ng/ml, or vice-versa

texts:
I am working with the enzyme Cu/Zn Superoxide (SOD1) and i am quantifying them in ng/ml.
However, most past studies has SOD1 quantified in unit/mg or unit/ml, and i need to compare the SOD1 level of my study with those past studies. Is there a way to standardize these units?

Thank you!


texts: ratio between heat transfer coefficient and thermal conductivity

texts:
Consider the Robin boundary condition for the diffusion/heat equation $\mathrm{u_t=a(t)u_{xx}+f(x,t)}$:

$$\mathrm{-k(t)u_x(0,t)=h(t)u(0,t)}$$

or

$$\mathrm{u_x(0,t)+\frac{h(t)}{k(t)}u(0,t)=0}$$

where $\mathrm{k(t)}$ thermal conductivity and $\mathrm{h(t)}$ heat tranfer coefficient.

My Question: Is it possible that the ratio $\mathrm{h(t)/k(t)}$ to be constant? Could anyone please help me? I have really no idea.


texts:
I had the impression that PSII (photosystem II) always has four Manganese atoms
(4 Mn). Is there any reason that these atoms are needed?

Is Mn or Fe also present in bacteria LH1 or LH2?


texts:
I have data (RNA expression values, obtained with in situ hybridization) collected from 1mio human cells. For each cell, I have the expression value of a negative control (non-human RNA) and single-cell measures for different RNA species. I know that the values from the negative control correlate in a linear fashion with all the other RNA species. For example, when a cell has a high expression value of the negative control, the signal for all other RNA species will also be high. I now want to detect the cells that express an RNA without having a high negative signal, e.g. the "real" expressing cells.

One thing to have in mind is that some RNA species are abundantly expressed in many cells, other are very rare and have a low expression value.

I tried to do this with a linear model (for each of the RNA species, negative control vs. single RNA), computing z-scores, infer p-values and correct for multiple testing. For some RNA species, it works just fine. As soon as I have many cells expressing a certain RNA, the thing gets more tricky because the slope of the linear model doesn't reflect the linear relationship of negative control vs. RNA species in non-expressing cells because it is more shifted towards the "real" expressing cells.

To visualize the problem, I attached two plots. One plot showing high RNA expression many cells (left plot) and one from an RNA species which is expressed on a very low level in few cells (right plot). Blue colored dots are considered as expressing cells according to the linear model. As you can see, for the scenario shown on the left side, many "real" expressing cells are not detected.

Any ideas which statistical model would better fit to detect those cells?

Thank you for your suggestions!


texts: How to tell if/how allele frequencies change (USABO question)

texts:
This is question number 34 from the 2014 USABO Open Exam:

Black and white mice live on an island and have allele frequencies of B=0.20, b=0.80. On the continent, there is a much large population of mice with allele frequencies B=0.80,b=0.20. Ships begin moving back and forth between the island and the continent. Occasionally, a mouse finds its way onto the ship and leaves the ship and breeds with
the mice of the other population. Equal numbers of mice ride in each direction. If the ships move continuously between the island and the continent, will the allele frequencies
ultimately stabilize? (Assume that no other forces are affecting allele frequencies.)

A. Both populations will end up at approximately B=0.80, b=0.20.

B. The island and continent populations will stabilize with an allele frequency of B=0.50, b=0.50.

C. Black mice will move to fixation in both populations, because the B allele is dominant.

D. Both populations will end up at B=0.20, b=0.80.

E. The continent's allele frequencies will not change; the island will settle at an equilibrium that is somewhere between the continent's and the island's original states.

The correct answer is A.
I guessed E, because I thought the difference in allele frequencies on the continent meant that the B allele was selected for there, and since the population was so big, I thought that the immigration and emigration wouldn't affect the allele frequency there so much, while the island's allele frequencies would change a little because of the smaller population.

Why is the answer A, why is E wrong (besides that A is right), and is there a math way or some sort of rule to solve this problem (or are you just supposed to reason it out)?

Thanks! :)


texts: Why does exhaled air still contain oxygen?

texts:
I am a high school student and I am a little confused in the concept of breathing:
My confusion is that, when we talk of exchange of gases we say that gases always diffuse from their high "PARTIAL PRESSURE" to their "LOW PARTIAL PRESSURE" and we know that partial pressure of oxygen in our alveoli is about 104mmHg and in our blood vessels it is about 95mmHg ,so we can see that this statement sounds true.
But partial pressure of oxygen in atmospheric air is about 159mmHg and in alveoli it is about 104mmHg then why the air that we exhale also have about 16% of oxygen in it? I think this statement is not correct oxygen don't have brain it will always move from the higher PRESSURE OF TOTAL MIXTURE TOWARDS THE LOWER PRESSURE OF TOTAL MIXTURE, e.g assume a balloon filled with different gases in it and total pressure of gases inside the balloon in much higher than the surrounding, but balloon has very less amount of Oxygen in it as compared to other gases so, its partial pressure is less then the surrounding so of course when you let it go all the air from balloon rushes out even oxygen, and its seems logical as oxygen doesn't know how is it different from other gases , how only oxygen can left inside the balloon?
I think beside this In exchange of gases we would talk in terms of partial pressure because we have to talk only about oxygen and carbon-dioxide ,not all gases, so just to represent their concentrations we talk in terms of partial pressures? But saying this statement that gases always diffuse from their high partial pressure to their low partial pressure this is wrong ,please correct me If I am going wrong somewhere and please give a logical explanation to it.
human-biology


texts: How to understand influenza strain designations?

texts:
What do the strain designations for flu mean?
For example avian flu is classified as H5N1, what do the letters H, N and numbers 5, 1 mean? Is it more than a simple string-identifier?


texts:
Scientists observe a newly established population of sexually reproducing plants growing on the shore of a small island. An observable trait of the plant has two possible phenotypes. It is determined by a single gene, with the dominant allele having complete dominance over the recessive allele. The first generation had 26 plants with the dominant trait and 25 with the recessive trait. The data below is from the first six generations of this population:

Use the data to explain the changes in phenotypic frequency from generation 1 to 3.  I'm not sure how to explain the increase in the recessive trait for generation $2$ to $3$. How would a population go from $p^2+2pq=1$ to $q^2 \simeq .2$?

Do you think this population is in Hardy-Weinberg equilibrium? Support your answer.  No, I don't believe so, since the population seems to change constantly in both the total number in the population, as well as the number of individuals with each trait.

Propose a possible explanation for the change in phenotype frequency from generation 5 to generation 6. Perhaps a climate change or the introduction of some new factor such as a  drought or new preadator?


texts: Can female Drosophila melanogaster lay eggs without males?

texts:
Can female Drosophila melanogaster lay egg without males?

I maintain our lab stock but find a line that seems to have all females (or all males). The flies have been in the vial for two weeks, but I don't see any eggs hatching or become larva.


texts: How is color information transmitted from the eye to the brain?

texts:
Is color information sent from the eye to the brain frequency-modulated, or are different colors transmitted by different axons?

I know that each ganglion cell is connected to multiple photoreceptors. How do ganglion cells tell the brain which photoreceptors were exactly activated and by what color?

Do ganglion cells correspond to particular colors?

Can one ganglion cell transmit different signals to the brain?

How does the brain know which color the light has, if signals of different receptors are mixed in the ganglion?


texts:
I stumbled upon this term in a section called Induced breeding of Carps in an Applied Zoogy book.

  Traditional practice is to collect seed from the natural riverine habitatwhich also contain uneconomic,unwanted and predator fish species.

What are seeds? Does it mean zygote ?


texts: What is the difference between abundance and dominance in an ecosystem?

texts:
I was reading Hydroperiods of created and natural vernal pools
in central Ohio: A comparison of depth and duration
of inundation by Debra L. Gamble and William J. Mitsch (2008), and I came across this statement:

  The dominant tree species in the vernal pool area were Acer saccharinum and Quercus palustris, while Ulmus americana, though smaller in diameter than the other trees listed, was the must abundant species...As at the New Albany, the most dominant tree species in the vernal pool area was Acer saccharinum, followed by Fraxinus pennsylvanica, while Fagus grandifolia was the most abundant species.

There seems to be a distinction between the terms dominance and abundance in the context of ecology. I've read some of the wikipedia articles on them, but I can't seem to find the difference in their meanings. They seem to both deal with the frequency that a species is in a population.

Any help is greatly appreciated.


texts: Can below-threshold potential changes of neurons convey information?

texts:
In neuroscience we learn that when the membrane potential of a neuron reaches a threshold (typically around -55mV) it "spikes": That is, it actively propagates a signal. I have two related questions with this respect:

The spike initiation zone is typically (e.g. for mammals) at the axon hillock - from there the action potential is actively (opening of ion channels..) propagated through the axon. But what happens then at and after the (chemical) synapse? Is the propagation after the synapse to the postsynaptic cell passive?

Newer imaging techniques (e.g. calcium imaging) can capture sub-threshold changes in the membrane potential. How are these sub-threshold potentials relevant for information processing? Are they propagated to postsynaptic cells, albeit again only in a passive manner?


texts:
Okay, so there is this weird creature, which has been crawling around our house.
I can hear it moving around, and it's especially active in the dark. I've however been able to take a picture of it.
If it helps, it's a carnivore (I've thrown some hot dogs and such).
This weird thing is 25-30cm long, and the picture of it was taken from a balcony on the second floor. I've only been able to photograph it once, but never came close to it otherwise. We live in central Europe, in a small town that somehow resembles a village. As for the ecosystem, I don't quite know. Fields, rivers and forests are all in proximity of our house.

Thank you for your anwsers,


texts: When collecting cell lysates for a Western blot, how do I induce di-sulfide bonds?

texts:
I would like to conduct a simple dimerization experiment for some protein I'm collecting from a cultured cells. My thought is, that if I'm running a non-reducing, denaturing PAGE gel, then removing beta-mercaptoethanol/DTT from the sample buffer should be enough to allow di-sulfide bonds to form.

I have seen several authors incubate the cells first with a drug called BSS that diffuses across membranes and creates protein cross-links. I may be wrong, but the use of this drug seems more appropriate when trying to follow up with an immunoprecipitation or a pull-down assay.

If anyone has any experience with this, could you please enlighten me?


texts: Are there any generic (not dependent on symptoms) ways to find parasite infections?

texts:
Are there any generic ways to determine if a person is infected with a parasite?

With "generic ways" I mean ways that do not rely on symptoms caused by a particular parasite. Also I am mainly concerned by parasites that are too large for the immune system to completely handle on its own (such as worms).

For example, can parasites be seen in x-rays, MRI scans, or through some body fluid samples?


texts: Do vitamins protect you from common cold?

texts: Do vitamins (taken as pills) boost your immune system, and make you less likely to contract diseases such as common cold or flu?


texts: A question about the intersection of evolution and thermodynamics

texts:
From this 2014 article in Quanta magazine by Natalie Wolchover there is a quote from a physicist with an intriguing idea about evolution:

“You start with a random clump of atoms, and if you shine light on it for long enough, it should not be so surprising that you get a plant.”

Jeremy England's idea is that the attributes associated with life have a lot to do with absorbing and dissipating energy. He insists he is not saying Darwin is wrong, and that his thermodynamics-based idea in some sense subsumes Darwinian evolution.

(The Quanta article links to a recent paper of England's which is somewhat technical, but deals with bacterial replication and thermodynamics. I include the link to give a sense of his ideas in his own words.)

My question is  whether his idea, taking it at face value, might furnish a better explanation of something already explained in Darwinian terms or fail to account for some detail of current evolutionary theory?

So if someone had a lot of examples of different aspects of evolution s/he might be able to say, "Here is a situation in which the thermodynamics do not work out as England suggests but which is explained in evolutionary terms," or conversely, "Here is something contrary to evolutionists' expectations that seems to be pretty well explained by the thermodynamics." I suspect that there are several candidates and England's paper gives a hint in one direction.

Thanks for any insights.

Some helpful reading:

Thermodynamics, Enrico Fermi (1936) [Dover reprint].
Understanding Thermodynamics, Ness (1969) [Dover reprint].
What is Life?, Schrodinger (1944).
Entropy Production..., Crooks (2008).
Schneider and Kay, Life as a manifestation of the Second Law of Thermodynamics, Math. and Computer Modeling 19 (6-8): 25-48 (1995).

The last paper is a very readable and non-technical introduction to this topic. If one works through the equations in Chapter 7 of Ness and ref. 4 the idea should be quite clear. Basically, systems (both nonliving and living) which are at some remove from equilibrium devise ways to dissipate energy that involve a decrease in entropy, increasing the entropy of the surrounding system.


texts: Open protocol for Ligase Independent Cloning

texts:
Ligase Independent Cloning is a protocol that allow an insert to be integrated into a vector without ligation.  It uses T4 DNA polymerase with only ATP to first chew back from blunt ends to create long sticky ends and then a polymerase treatment with full dNTP compliments to fill in the vector.

While there are several nice articles and resources that describe the procedure, I really would like a protocol with concentrations, temperatures and timing, which I'm having problems finding.  OpenWetWare for instance has only stub pages with no details.  Can anyone point to a full step by step recipe to make this work, once you have designed the primers?


texts: Does Pre replication complex sit on both strands?

texts:
In case of prokaryotes, the ori site have a definite nucleotide sequence. Each ori site have 5 9base-pair consensus sequences and 4 non-consensus sequences. DNAa binds to both types of sequences with different affinity. Does, it mean DNAa and thus the PRC form only on a portion of one strand and not on the complementary portion on the next strand?

Does PRC sit only on one strand and not on the other?

What about in eukaryotes?


texts: Reconstruction of wildlife distribution based on poorly-sampled data

texts:
cross-posted to Signal Processing, Cross Validated, and World Building Stack Exchange

Hi, I thought I'd also put this here in case there are any field biologists with ideas on the matter.

Problem: After reading a series of fantasy novels, I noticed that the biosphere in that world made no sense. To clarify, this is a world where despite magical occurrences, the world itself is almost entirely non-magical. 'Alternate history magical realism,' perhaps. i.e., unlike, for example, Harry Potter, in which almost all plant and animal species mentioned are fictitious and magical, this series uses real flora and fauna. This allows me to extract information about the fictional world's environment based on the distribution of these animals, by assuming that similar animals will live in similar climates on Earth and in the fictional world.

Ignoring the likelihood that the original author did not put enough thought into worldbuilding to make this a necessarily reasonable endeavor, my idea for how to proceed was as follows:

As maps exist of the fictional world, and the path of the characters can be plotted, I hoped to mark every mention of a specific plant or animal in the text, along with the location of the characters when it occurred, and from this reconstruct a plausible distribution for each species. I've created a theoretical example (in photoshop), for illustration:

where the red dotted line represents the paths of various characters, the orange, green, and blue splotches represent the true distribution of the species; the stars, triangles, and circles represent the locations at which a species is mentioned; and the brown, green, and blue lines represent the reconstructed contours of the distribution.

Is there a method to do such a reconstruction? It sounds a bit like a Monte Carlo analysis, but I figured I should check... (It also sounds rather like the magical programs detective shows use to plot serial killers' locations)

Note: It should be clear from the problem statement that just because a species is not mentioned at a specific location does not mean that it does not exist there. i.e., a sample at a specific location returning only 'A' - 'Bill and Jeff saw a lemur.' - does not exclude the possibility of 'B' and 'C' also at that location, but not sampled. Just because the text may specifically say that Bill and Jeff saw a lemur, and doesn't mention any other flora or fauna doesn't mean we should assume that they are in a universe devoid of anything but the occasional lemur.

Final Thoughts: Ideally, the analysis method would further:

take into account the coverage of the paths, and not assume that (in
the example above) nothing exists in Mexico or northern Canada, just
because there are no samples taken there. Remember that samples can
only be taken along paths.
take into account edges, in this case coastlines. If A, B, and C are
land animals, it does not make sense that a reconstruction of their
distribution would include water, even if their range surrounds a
lake or something.

Sorry for the long-winded explanation. Any thoughts?


texts: Can Biting Insects Detect Specific Places On A Host Body?

texts:
I'm gonna make a presumptive statement: It -seems- as though I get bitten by mosquitos and other biting insects in -exactly- the same places over and over. I mean within a few mm. Is that true?

If true, that implies that insects have a mechanism to detect certain preferred spots in order to get blood or whatever they want. (Location of blood vessels? Sweat glands?)

And if that is so, what -is- that mechanism? What are they going for? And how does this detection work?

IOW: How do they know to bite me exactly on the side of my right knee over and over and over... but never on other spots?


texts: Are the introns present in a nascent rna molecule removed simultaneously or are they removed in some sort of sequential fashion or is removal completely random?


texts: How does a sheep's fleece impact its tolerance for high temperatures?

texts:
I am interested in whether a sheep endures more stress when its environment is hot if it has a full fleece or if it is recently shorn.  Put another way, at the extremes, is a sheep more likely to die due to high temperatures if it has its fleece or if it does not?  If the answer depends on breed, what are the biological differences that cause one breed to interact with this element of its environment than others?
I am interested in temperatures around 90°F but if the answer differs at some temperature commonly experienced somewhere on Earth, that would be interesting to know as well.
I am interested in modest relative humidity values, in the 40%-60% range, but again if the answer differs outside of that range it would be interesting to know about.
I considered asking this question on a physics stack exchange (where a sheep might be modeled as, say, a radiator with or without insulation) but I'm particularly interested in the answer for real, actual sheep - biological processes and all - and not just a spherical sheep of radius r.


texts: Can suppression of the immune system help cure chronic diseases?

texts:
I am not a biologist, but recently while reading an article on Scholarpedia about self-organization I encountered a fascinating biological observation concerning immune response to infections.  To quote the article:

  Whether the resulting patterns are stable or oscillating depends on the relation of the time constants. If the antagonistic reaction has a longer time constant than the self-enhancing reaction, oscillations or burst-like activations will occur. An example is the time course of an infection: The infection with few viruses could be sufficient to trigger a sickness since the viruses replicate themselves (self-enhancement). The antagonistic reaction, mediated by the immune system, is much slower. It takes a day to become sick, but a week to become healthy again. (What appears on a first inspection as a disadvantage is in fact a good strategy. If the immune system would be much faster, an equilibrium between virus production and virus removal would be established. After a single infection we would fight for the rest of our life against the virus. However, due to the burst mode, we become sick for a short while but the virus is subsequently completely eliminated).

Since the quote may be hard to parse out of context, I'll recapitulate: The writer is asserting that the immune system's response to infections is slower than might be physically possible because such slowness actually makes the response more effective.  By waiting a few days, the patient is sick for longer than they might be happy about, but when the infection goes away, it's gone for good.  If the immune system responded immediately to an infection, it might result in a low-level infection that persists indefinitely.

This makes me wonder: For chronic diseases, is the reason they are chronic related to the time scale of the infection vs. that of the immune system's response?  Could such diseases possibly be cured by suppressing the immune system for a time so as to get the "burst" effect alluded to in the quote above?


texts: What is the difference between muscle fascicle and muscle bundle?

texts: In the photo above (given by Bio teacher), the muscle bundle is shown to be as a bundle of fascicles, but in most web definitions I've seen, the two terms are used interchangeably. What is the correct name for the part labeled "muscle bundle" if there are in fact no distinctions between bundle and fascicle?


texts: Why are some genomic regions sequenced more than the others?

texts:
We have to normalise read count data from RNA-Seq experiments in order to account for the fact that some genomic regions are mapped more than others. i.e. we get the tags per million reads (TPM). In other words, they have a higher sequencing depth/vertical coverage.

Why are some genomic regions mapped more than others; what is the reason for this non-uniform distribution of sequencing depth?


texts:
here is my question:

In certain plants, tall is dominant to short. If a heterozygous plant is crossed with a homozygous tall plant, what is the probability that the offspring will be short?

My Solution:

Let T be the allele for the tall phenotype and t be the allele for the short phenotype.

Then the parental cross would be Tt x TT = 100% tall phenotype (1/2 Tt, 1/2 TT).

Hence the probability of having short offspring should be $\fbox{0}$.

However, the answer key for this question says the answer is $\fbox{$\frac{1}{2}$}$. How can this be??? It really bothers me when the answer key is potentially incorrect because it makes me very unsure, and I end up wasting time trying to figure out if the key is wrong or if I am. Can somebody please let me know if what I did was correct/incorrect??

Thanks


texts: Why do skin and nail go blue in cyanosis?

texts: I have learned that Cyanosis presents with blue skin and nails. What is the reason for the blue coloration of the skin and nails? Why wont the skin and nails turn another color in the visible spectrum such as green for instance? How is this disease diagnosed?


texts: I read some papers about studies on metabolism in post-mortem tissues in human, but I do not exactly the reason about why our brain continues to have activity after death.


texts:
I would like to take an apparatus containing bacteria to another country (Bolivia) from the U.S.. How do I determine whether I am allowed to do this?

The bacteria are:
http://www.atcc.org/Products/All/49787.aspx,
http://www.atcc.org/Products/All/53774.aspx,
http://www.atcc.org/Products/All/51573.aspx,
http://www.atcc.org/Products/All/700550.aspx

Also... What is the best way of transporting bacteria from one country to another?


texts: SNPs in DNase hypersensitive and histone marks sites

texts:
I am investigating a role of SNPs in DNase hypersensitive sites and in the DNA regions of histone marks and have some questions about it.

SNPs in DNase hypersensitive sites might mean that those SNPs are in enhancer regions and might influence TF binding affinity what can influence a transcriptional output. Is it correct?

SNPs in histone marks sites
I have the number of SNPs that fall in the peaks (chip-seq) for the following histone modifications of healthy patients:
H3K27ac,H3K4me1,H3K4me3 (represent the active chromosome)
H3K27me3, H3K9me3 (represent the repressed chromosome)

Histone modifications represent if the chromosome is active or repressed. A SNP might change the binding affinity of a histone. It means that if I have a SNP in data for active chromosome (H3K27ac,H3K4me1,H3K4me3), it might change the status of a chromosome, namely turn it into a repressed one or it might induce a histone not to bind at all(it means that this region is still active,no?) Is it right? I am not sure I understand the possible influences of a SNP histone marks sites.


texts: How many various types of Memory B cells does an average person has in his body?

texts:
Memory B cells are a B cell sub-type that are formed within germinal centers following primary infection and are important in generating an accelerated and more robust antibody-mediated immune response in the case of re-infection.

Now there is an accumulation of cells of a single clone population which expresses many of the one same type of antibody and that these memory B cells survive for long periods of time in a body.

Disregarding the number of different cells applying for one and the same antibody, how many Memory B cells are there in average humans which relate to different antibodies?


texts: Which is the guideline to choose a molecular target to identify vertebrate hosts from arthropod bloodmeals?

texts: There are some molecular targets to identify vertebrate hosts from arthropod bloodmeals including the Cyt b gene and the COI gene. Which are the standards or characteristics that I have to bear in mind to choose a molecular target to identify host blood from mosquitoes? I would appreciate your help.


texts: How to get a list of kinases that phosphorylated a particular protein?

texts:
I am analysing the protein SF2 (also named as SRSF1). In the database, it is shown that this protein is often phosphorylated at the 189th tyrosine residue.

I want to know which proteins could have phosphorylated the protein at this site. Is there a way to figure this out using databases? What about getting a list of proteins that phosphorylated SF2 at any site?


texts: Single stranded DNA in gel electrophoresis

texts:
From http://www.nfstc.org/pdi/Subject05/pdi_s05_m01_01.htm :

  ... The separation medium contains a denaturant in order that the
  electrophoresis is conducted on single-stranded DNA fragments.
  Single-stranded DNA fragments are more similar to each other than
  double-stranded DNA fragments are to each other. Double-stranded DNA
  produces more electrophoretic diversity due to its three-dimensional
  structure.

Questions :

What is the denaturant they are talking about?
It's mentioned that double-stranded DNA
produces more electrophoretic diversity due to its three-dimensional
structure. Why should dsDNA have more 3-D structures than ssDNA? ssDNA can form hairpins and other structures. Which structures can dsDNA form?


texts:
What are the pros and cons of using electroporators (left) and gene guns (right) for transformation in terms of:

Price
Target organism
Efficacy
Ease of use
Maintenance