texts: Can scientists name themselves in the scientific name when they discover a new taxon?

texts: There are sometimes people names in taxonomy, like Myotis keenii was names after Mr. Keen who contributed to discover the species. So, if you discover a species and someone else is constructing the scientific name and names you, it's clear. But when you discover a species and you publish it in a paper, can you propose a scientific name that contains your name? Has it ever happened, or is it considered an unhealthy practice?


texts: How to use the law of diffusion in the presence of electric forces?

texts: Isn't the movement of ions affected by the electric field as well? For instance, when a sodium channel in a cell's membrane opens, the sodium ions are said to diffuse into the cell, from higher extracellular concentration to lower intracellular concentration. But what about the electric force fields? The negative ions within the cell attract the sodium ions outside the cell, while the potassium ions within the cell repel them, so why aren't such interactions mentioned and taken into account when discussing the direction or intensity of flow? It seems that the only factor considered by books is diffusion of sodium ions from higher to lower concentration.


texts: Which variables are controlled in the mammalian womb to ensure a healthy environment?

texts: Recently, researchers have had some success with artificial wombs. Which aspects of the womb are difficult to replicate through technology?


texts: Basic question about symbiosis( or about kinds of symbiosis)

texts:
Is there a type of symbiosis where an organism is harmed and the other is neither harmed nor helped?

If not, do you think there's a term for this sort of relation between two organisms?


texts:
Out of 10 steps in glycolysis, only one reaction- Glyceraldehyde 3-phosphate (G3P) to 1,3-bisphosphoglycerate (PGP), uses NAD+ and thereby producing NADH. Furthermore, this very step is solely responsible for net gain of 2ATP in glycolysis since here phosphorylation occurs without the expenditure of ATP.

Why is NAD+ used only in this step? Is it possible to predict by other information that this is the only step to require NAD+? Is it possible to make this reaction happen without the involvement of NAD(P)+? Is it possible to skip this step and directly produce 3-phosphoglycerate (Lets not worry even if we cannot produce ATP in this process). I am interested in this because, this step necessitates the ferementation for regeneration of NAD+ in anaerobic condition. E. coli produced acetate as a side effect, as expected during anaerobic situations, but also rather unexpectedly during aerobic and high-growth rate situation (acetate-swtich, overflow problem). Production of acetate is unwanted in many industrial applications.


texts: What are the sources of molecular hydrogen in human breath?

texts:
In the BBC News article CES 2019: Tech preview of the expo's hottest new gadgets there is a new product that one can use to measure the hydrogen in ones breath, and this is supposed to have some connection to diet:

By contrast, FoodMarble's Aire measures the hydrogen in your breath and combines this with a log of what you have eaten, to warn you of foods you should avoid and possible substitutions.
Aire is designed to discover which foods are being passed to the large intestine without being fully digested

There also exist air quality monitor chips that measure both TVOC (total volatile organic compounds) and "eCO2", where "eCO2" is really a measurement of H2 in the air, and via some electronic algorithm uses it to calculate the expected rate that people are exhaling CO2.
Question: Both of these are examples of interpreting the presence of molecular hydrogen as having some indication that we are alive, breathing and eating. Here I would like to understand the sources of hydrogen in human breath, and how that hydrogen makes it from source to breath.
potentially related: Where does molecular hydrogen in the atmosphere come from?


texts: Is there any possible way that hybrids can mate?

texts: I'm writing a book, and a a portion of it involves a society of humanzees. Now, is there any plausible way that a hybrid (such as a humanzee) could procreate either with one another, or with their father/mother species? I apologize for my lack of understanding of biology, any help would be much appreciated!


texts: How do electrons destroy DNA bonds in radiation?

texts:
Malignant tumors can be treated by radiation therapy. Most commonly it's radiotherapy with photons, or protons and so on. The common denominator for both types is that the radiation creates electrons inside the body via different effects.

What I haven't quite understood is how these electrons destroy the DNA bonds in the tumor and how this aids in killing off the cancer cells? Is it due to the generation of heat, or otherwise?


texts:
If there is no gravity in space how does the food enter the stomach?
My guess is that it is due to the movement of the esophagus.Am I correct?


texts:
I was taught in school that female is the default sex in humans based on the following logic:

Development into a human male requires the activation of the SRY gene in the foetus. If that doesn't happen (because there is no Y chromosome, or for some other reason) then development into a female occurs.

For historical context on the use of the term default, please see this article:

Female sexual development ... was thought to proceed as a “default” in the absence of Sry.
The English word, “default,” means “failure to act; neglect” or “a preselected option adopted […] when no alternative is specified” (Oxford English Dictionary, 2011). In the case of sex determination, “default” became the prevailing model for female pathways—i.e., an ovary results in the absence of other action...

Is it reasonable to say that female is the default sex in humans? If so, is the SRY gene all there is to it?


texts: Can someone please help with this question? I'm not so sure whether part A should be 11 inches or something else. Also, is part B correct


texts: Would I expect salt precipitate on fibres of DNA in a NaCl water solution?

texts:
I just recently conducted an experiment in my biochemistry class where we had to add DNA to distilled water, isotonic saline and 2.5M NaCl. I noticed different physical aspects depending on the solvent, but I'm not sure how I would categorize them. Here's what I saw:

Distilled: fibrous precipitate, cloudy liquid
Isotonic: Honestly barely noticed a change here? Maybe I wasn't looking hard enough
2.5M: salt precipitate at the bottom and fibres

I know DNA is polar so solubility should increase as the polarity of the solvent increases. But to my recollection what I saw in 2.5M saline vs distilled water did not differ much. However, there is always the possibility that I could have made some experimental errors that led to inaccurate observations.

So, can someone help me deduce the solubility of DNA (simply soluble/not soluble) in each of these solvents, or refer me to a paper I can read? Thanks in advance!


texts: Is a raised baseline between T and QRS normal in any ECG lead?

texts:
Here are excerpts from an unknown ECG lead. I find it weird that the "baseline" changes after the T wave and doesn't return until after the following QRS complex. Is that normal/expected for any lead?

Click for better resolution. I've got another 10 minutes of the ECG, if that would be helpful.


texts: Health benefits & enzymes different between Thermophilic and Mesophilic Probiotic cultures?

texts: Is there a difference between the Enzymes produced by Thermophilic vs Mesophilic Probiotic cultures ? are there any other differences in health benefits between the two types of cultures ?


texts: How do mutations come to be shared by all cells?

texts:
It's my understanding that various hazards can damage the DNA in our cells, causing mutations.

But whenever I picture this, I see the damage being done to one of our tissues (for example, our lungs due to smoking, or our skin due to UV rays).

When I think about this, I see that... many cells in a smoker's lungs, or many cells on the back of a beach-goer's neck, may have mutations in their DNA. But only the cells in that tissue have these mutations... the other cells in our body would not have the same mutations.

In particular, sperm and egg cells would not have the same mutations, so the mutations due to smoking and UV rays shouldn't pass on to children.

Are there instances where mutations that occur over the course of our life are spread to every cell, including sperm and egg cells, so that every cell reflects the mutation, and the mutation is passed onto our offspring?


texts: What is the difference between multiple allelism and polymorphism?

texts:
From the Scott Freeman textbook Biological Science 4th Edition:
https://www.amazon.com/Biological-Science-4th-Scott-Freeman/dp/0321598202,

Multiple allelism is defined as "the existence of more than two alleles of the same gene within a population."

Polymorphism is defined as "the occurrence of more than two distinct phenotypes of a trait in a population."

I don't really understand the difference - unless it means that two alleles may not result in two different phenotypes?

Additionally, another definition of polymorphism also in the textbook was "the existence of more than one allele at a certain genetic locus."

What does this mean? I was under the impression that all genes had at least two alleles.


texts: Usage of the terms: Enhancer, Upstream activating sequence and Downstream activating sequence

texts:
From wikipedia

  An upstream activating sequence or upstream activation sequence (UAS) is a cis-acting regulatory sequence. It is distinct from the promoter and increases the expression of a neighbouring gene.

Again,

  In genetics, an enhancer is a short (50-1500 bp) region of DNA that can be bound by proteins (activators) to increase the likelihood that transcription of a particular gene will occur.

I find no difference between them, are they synonymous ?

  Due to its essential role in activating transcription, the upstream activating sequence is often considered to be analogous to the function of the enhancer in multicellular eukaryotes.

There appears to exist another kind of regulatory sequence, downstream activating element.I think it's another synonym for enhancer located downstream the transcription start site.


texts: How can I measure bacterial alkaline phosphatase activity?

texts:
I want to measure alkaline phosphatase activity using PNPP in my mutant bacteria strains, but all the protocols I found involve purification of the phosphatase (which I have no need of).

Does anyone know a good protocol which involves using only the supernatant, without purification of the enzyme? What is the preferred buffer for the reaction?


texts: Why/How do Cyanobacteria Produce Toxins?

texts:
I've been doing some research on the versatility of nitrogen-fixing cyanobacteria, particularly of the genus Anabaena, and I often run into safety hazards and have to add extra steps to my procedures because of the toxins produced by the genus. After doing some reading, I've found that most cyanobacteria produce toxins (collectively dubbed "cyanotoxins"). The wide variety of different structures and mechanisms of the toxins across multiple genera is astounding, especially because some of them are carcinogens, which would logically affect the host unless a mechanism to prevent this had evolved. This tells me that a lot of evolutionary "effort" must have been put into the evolution of toxin production in cyanobacteria. Originally, I just thought that the toxins were a natural part of their metabolism that evolved normally because these compounds didn't affect them in the same way as they did us. Now that I see the Huge, variable trend throughout the class, I have begun to think otherwise. My questions are as follows:

What is the evolutionary basis for the production of cyanotoxins by cyanobacteria
Are the cyanotoxins a necessary part of the bacteria's metabolism, or can they be eliminated by way of genetic engineering without directly affecting the success of the organism?
How do cyanobacteria cope with the constant exposure to native carcinogens?

These questions are only the major ones that I have, so any extra information is greatly appreciated


texts: I have been trying to understand the phenomenon of lipid packing defect, but the resources in this subject are very limited. Well, I did find some papers, but before reading papers, I want to have some intuitive knowledge about it. Can anyone explain to me lipid packing defect in brief. Thanks


texts:
Is there any disulphide bond in a quaternary structured protein?
If yes, please provide examples.
In tertiary structured proteins, what is(are) the most important characteristic(s)  of tertiary structured proteins?
a) globular in shape
b) have both alpha helix and beta sheet
or, is there any characteristic that I do not mention?


texts: How does the lymphatic system filter blood?

texts:
One of the main functions of the lymphatic system is to filter blood. How exactly is it done?
Its quite hard to find an exact answer.


texts: Found under my bed. Looked and there was nothing else like it or eggs of any kind.


texts:
I read a lot about speciation. To my knowledge, a species is often defined as a group of individuals that actually or potentially interbreed in nature and produce fertile offspring. Speciation is a lineage-splitting event that produces two or more separate species.

Now, some creationists claim that there is no speciation, rather variation in the same species. As in "fruit fly experiment", I read that two groups of fruit flies don't interbreed after the evolution and speciation takes place. As per the definition of species (biological concept of species), they are supposed to be two separate species (reproductive isolation). Nevertheless, creationist claim they are still fruit flies and there is no speciation. They say that's just a variation in fruit flies, not speciation. I can't understand their claim.


texts:
Some biological features scale with the animal mass (see previous Q&A).

Assuming the same concentration of nociceptors on the skin surface, I'm wondering how painful a 1 cm wound will be perceived in mouse, human or elephant. Despite the same firing number of nociceptors, will the mouse feel more pain as a bigger percentage of the body has been injured? Is it known whether pain sensing follows allometric rules?


texts: How do animals with fur get enough sunlight to produce vitamin-D?

texts: How is vitamin D synthesized in animals with fur; how do the cells get enough sunlight? If vitamin-D cannot be synthesized because of limited sunlight reaching the skin, do these animals have to obtain the vitamin from the diet or are there any alternate mechanisms of synthesis?


texts: Photographed in Rocky Point, Mexico. Any ideas about this plant? Thank you!


texts: What is the maximum number of babies a human woman can have?

texts: I know you could divide the female fertility period (~40 years, right?) by 9 months which would give something like ~50 kids (with no multiple kids per pregnancy). The limiting factor in this calculation is time but is there a biological upper limit as well?


texts: How can two individuals of the same species have different chromosome numbers?

texts:
It is known that male drones develop by arrhenotoky, and have haploid chromosome constitution, whereas the queen bee and workers are diploid.

Thus we can see two different types of ploidy occurring in the same species. Sill the drones and queen bee are successful in mating and producing offsprings. This would require the queen to produce haploid gametes by meiosis and haploid gametes from haploid drones.

Doesn't this create a problem in defining species?


texts: Can botulinum toxin be grown or kept from denaturing in an UNWRAPPED 50 pound hay bale?

texts:
Botulinum toxin is the neurotoxin protein created when botulism spores grow. The requirements for growth and/or for keeping the toxin from denaturing would seem to be very difficult to create in bale of hay.

There are well documented incidents of botulism in horses who are eating hay, all the references I found were centered around hay in large plastic wrapped bales.

I have been involved in an event where the presumed DX is botulism secondary to ingestion from hay from last year.  In this case the hay is second cutting timothy hay (making it 6 plus months old), in rectangular 50 pound (22 kg) bales that are not wrapped, have been barn kept, and when purchased from the vendor where stacked in rows 4 feet wide, by 6 feet (2 meters) high. The bale then spent more then a week on an shelf (chrome platted heavy wire) with good air circulation.

Three pet house rabbits appear to have been effected. with 2 dead and one recovering from a case of descending paralysis.  Several tests are underway, but my understanding is that it may be difficult to conclusively show either the botulism in the rabbits, or significant presence of 'botulinum toxin' or 'clostridium botulinum' in the hay (samples from the mangers of effected animals are being tested).

Is it possible to logically conclude that Botulinum toxin could, or could not, be created and/or survive in a bale of hay meeting the above criteria?

Note

If there is an awareness of a plant based neurotoxin that would cause similar symptoms that may be growing in the hay field please offer that in an answer at Gardnening.


texts: Relationship of bases in a gene to amino acids

texts:
One of my study questions for a biology test was:

A gene contains 1200 bases. How many codons will be on the mRNA immediately after transcription?

My initial answer was 400 codons, because 1200 bases = 1200 nucleotides and 1200/3 = 400. But since DNA is double helix, and only one of the two strands is used in mRNA creation, would only 600 bases be used instead of the full 1200?


texts: What is the number of DNA strands per cell?

texts: I wonder if each cell possess only one strand of DNA which according to my book is more than "7 feet" long(if uncoiled), then why does human has 46 chromosomes which are actually coiled chromatin (DNA wrapped around histone proteins)? Does DNA break into parts and form 46 chromosomes during cell division (I am just guessing I am not sure about it)?


texts: I keep finding what I'm 99% sure are carpet beetle larvae on my walls, of all places. Yet when I look around and search thoroughly, I cannot find any signs of an(y) adult Beetle(s). Why/how is this happening and if it's not a carpet beetle larvae, then what is it?


texts: What is the biological significance of k-mer counting?

texts:
There are many tools developed to compute the counts of k-mers present in a gene sequence. Jellyfish, Bloom Filter Counter, DSK Kmer Counter, KAnalyze, KMC 2 etc are some efficient software developed in last decade to count k-mers.

But in what purpose, these tools are used?

How they are serving biological community?


texts: Tiny orange yellow bug in raspberries? What is it?

texts:
There's a tiny orange yellow bug in raspberries:

What is it? The fruit was sitting in the fridge for 3 days


texts: Are codons that map to the same amino acids interchangeable?

texts:
From wikipedia, in the section on the RNA codon table, I see a mapping between codons and amino acids. There, Valine is related to GUU, GUA, GUG, GUC.

Does it mean in the same context that these four codons are interchangeable? Could one replace GUU with GUG?


texts: How does the Sensitivity of Sokolow-Lyon indexes change by age?

texts:
I am studying the indicator and how diseases/age affect its sensitivity.
However, no publication about it in PubMed and no luck in Escardio.

How does the sensitivity of Sokolow-Lyon index and/or its derivates change by diseases/age?


texts: Help ID this plant with balloon-like feature containing seeds

texts:
I noticed this plant creeping over another Ipomoea quamoclit near my house in Kerala, South India. It has these balloon-like projections over them that break when popped. These projections do bear seeds. No visible flowers.

Leaves:

The balloons:

The seeds:

EDIT: This plant is a creeper, obviously.


texts: Understanding the use of English tenses in biological journal articles

texts:
My colleague and I (second language speakers) got in an argument in understanding the sentence:  " however, how this complexity and diversification have been achieved remains rather poorly understood.” in the context of the below Abstract’s report.
In short, the question is:
Does this sentence valid till the end of this report? i.e. the complexity problem continued and not solved in this study?
His understanding that this sentence stated in this report as a past context or past story, i.e. the abstract is telling us how our knowledge was? and this study solved and answered how this complexity happens and achieved.
Reference:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1852327/
I know these questions are mostly about understanding English rather than biology!
I appreciate your help.


texts: We know that RNA can get modified post transcriptionally (RNA modification). So when the RNA is degraded, is it possible for such modifications to still be present on the individual nucleotides -- such that when the nucleotides are recycled for constructing another RNA, those modifications persist?


texts: What fills the spaces between non-fused sacral vertebrae?

texts:
What is in between the sacral vertebrae before they are fused?
I have looked and found no specific descriptions. If it is simply cartilage, what type of cartilage?


texts: Why placental progesterone suppressed or drop before onset of labour?

texts:
As we know during pregnancy predominant hormone is progesterone which is at early pregnancy about first 3-4 months produce by corpus luteum  of pregnancy together with estrogen after that placenta can make its own progesterone with estrogen till birth but for initiation of labour estrogen go up and progesterone should go down because it prevents uterine contraction. Does anyone know mechanism of suppressing of progesterone and rising of estrogen before onset of labour ?
In other word mechanism of initiation of labour ?


texts: What sauropod genera had a double row of chevron bones in the tail?

texts: I know that Diplodocus is marked by the feature of having a double row of or "double-beamed" chevron bones in the tail, but how diagnostic is this feature if several other sauropods have it? I mean, if there are other genera with the feature, which ones are they, so I know not to confuse them with Diplodocus?


texts: What does it mean for the signals for transcription and translation to be "conserved"?

texts:
I was reading this article: "Overview of vector design for mammalian gene expression."  for an explanation of why mammalian cell lines are used for expressing cloned genes, and one of the reasons given is that "DNA cloned from higher eukaryotic cells is readily expressed since the signals for transcription, mRNA processing, and translation are conserved in higher eukaryotic systems." What does it mean for the signals to be "conserved," and why does this make mammalian cells a better host than other types of cells?

Follow-up question, in case the answer to that question doesn't make it clear: the article also says the machinery for protein folding and assembly are "conserved" - what does that mean (if not the same thing as in the first question) - and again, why does this make mammalian cells a superior choice of host for expressing cloned genes?


texts: Is there a defined non-trivial chromosome number distribution for a given kingdom?

texts:
I'm pretty aware of the mechanisms for chromosome number evolution in specific groups (e.g. inside a given genus). Nevertheless, looking at a broader scale (e.g. in the Metazoa kingdom), is there a well defined distribution for the frequency of occurrence of chromosome numbers?

For example, are species with small chromosome numbers more frequent than those with large chromosome numbers? If so, is there some sort of scaling relationship between number of species and number of chromosomes?


texts: What biotechnology can be used to treat lazy eye, and possibly cure lazy eye?

texts: I tried very hard researching and finding the root cause of amblyopia. It is mainly because of imbalance in eye muscle. But, there are a lot more complicated causes of this disease. Thus, I need some help in finding a biotechnology for treating lazy eye.


texts: Is there an optimal composition and length for protein linkers in FRET?

texts:
I'm designing a protein that I'd like to use in FRET reporting.  General idea on the shape is:
FRETprotein1--Linker--CleavageSite--Linker--FRETprotein2.  I would like to know what AA are best for the linker, or does it matter?  I have heard SSG is a good choice, but when I started a lit review I become unconvinced.  If it doesn't matter, I may try and put more convenient restriction sites there.

Is there a good way to theoretically determine optimal length?  I realize that may change depending on which FRET protein pair is chosen.  The cleavage sites are between 15-18 AA long.  Unfortunately, I don't think I can give any more detail than that on the cleavage sites.

Response to answer:
So far there have been no FRET systems or tests published with the cleavage sites I want to study.  In fact, I haven't even heard of anyone else trying.  If I'm forced into a positive FRET probe, which I'm worried that I am, does anyone have any FRET pairings that don't interfere with Texas-Red on the spectrum?  My first choices were Venus and Cerulean, but if I have to make a positive probe then I don't think they are a good choice.


texts: Is water vapour a product of fossil fuel oxidation?

texts:
In textbooks, while water vapour and carbon dioxide are said to be the greenhouses gases which are most abundant in the atmosphere, when a table is given showing the top greenhouse gases emitted by humans, water vapour is omitted (carbon dioxide and methane are the top two).

However, when methane is oxidised to release energy from fossil fuels, the products are carbon dioxide and water (i.e. water vapour), therefore, aren't humans responsible for the concentration of water vapour present in the atmosphere?
Why is water vapour generally omitted from the tables?


texts: Can I compare Shannon indices of metagenome gene data?

texts:
I'm comparing 12 Metagenomes. I'm using HMM counts of a number of proteins known to exists as groups within certain operons. I have grouped the HMM counts for each type of operon and calculated the Shannon-Weaver index for each Metagenome.

My question is: Can I compare these Indices? Is there a better test to use than Mann Whitney U test? I would like to do this on the ungrouped data, but I have many zeroes for some fields?


texts: What's the worst that can happen from eating too many spicy peppers? Can you die?

texts:
Some peppers, such as the habanero or Carolina reaper are extremely spicy, and when eaten in larger amounts than one is accustomed to, can cause some discomfort.

I've also heard anecdotes claiming that pepper spray, if applied with sufficient intensity, can cause death.

What if you were to eat as many spicy peppers as possible, despite the noxious taste? Is it possible to commit suicide in this way (and what would the cause of death)? Would you faint from excessive mouth pain? Would uncontrollable vomiting prevent you from consuming further peppers?


texts: Solubility of Amylopectin and Glycogen in water

texts: The only difference between the structures of Amylopectin and Glycogen is that Glycogen is more highly branched than Amylopectin. How this difference between their structures makes difference between their solubilities in water?


texts: Why do hot water baths affect only males' fertility? Why not females'?

texts:
Here is the link where urologists are warning men not to take hot water baths.

Why does it affect only males' fertility? Why not females also?


texts: How difficult is it to make a shRNA/miRNA/siRNA to silence/knockdown NaV1.7 voltage gated sodium channels in humans?

texts:
There have been various research projects that experimented with shRNA/miRNA/siRNA to specifically silence/knockdown NaV1.7 voltage gated sodium channels in small animals like rats & guinea pigs. (Example; my previous question: Is HSV-vector-mediated miRNA expression in dorsal root ganglia stable?

But I can't find any that's been done for humans... So I think it means scientists have not gotten to that stage (if they are interested in doing so), and I was wondering,

technically, how difficult do you think it is to make a shRNA/miRNA/siRNA that can silence/knockdown NaV1.7 in humans, given that they already know how to make it for NaV1.7 in small animals?
financially, how much money is needed to invent such a thing (and how hard to get a grant for it?)
if technically not too difficult, and not very expensive to invent just a sample, is this something not necessarily a professional researcher, but a student could try making as their research project?


texts: What is the reason behind that sometimes when I see new thing I feel that I have already seen them?

texts: I have googled it and I found that it is, because of good memory, but how it can be due to good memory as it didn't happen before. It happened to me many times, that I feel that the scene which is happening now, has already happened to me in my past. But it was a new scene in my life, so why does I feel like this? How is it possible that a same scene happens twice?. What is the reason behind it, that we feel something twice in our lives.


texts: How are single cells sorted in an scRNA-Seq protocol by FACS?

texts:
I am computational guy trying to understand how FACS sorting works in an scRNA-Seq protocol. About sorting single cells in each well of a 384-well plate, I have a question that would be grateful if you could answer it.

The protocol reads that cells are sorted in the wells based on their marker levels. For example it says:

  NK single cells were collected from the CD19-/TCR-β- events by gating
  for NK-1.1+ events in NK-1.1 vs. Gr1.

The part that I don't understand is that how it is possible to know positive/negative events or even to gate on events beforehand? I know that FACS first examines markers and then sorts them into positive, negative or waste collections. Here is my question:

  But how do we know what an expression level is acceptable for calling
  a cell positive, and also in more complicated case, how do we to gate
  on a subpopulation of cells (like top right quadrant) when no events
  have yet crossed the laser beam because we don't know the baseline of
  CD markers' expression levels yet?

For instance, It could be possible that in my panel setup a CD marker can never reach a value more than X, but in your setup it can never reach a value more than X/2.

N.B. As protocol says, subsampling of the main sample for FACS is not possible to infer these values beforehand because it is very likely that the populations of different cell types is not conserved in the subsample.


texts:
I'm curious about the origin of the neural network.

I'm thinking perhaps once life evolved beyond the single cell organism, it needed a simple neural network to coordinate those cells, and cell functions.

What were the first neural systems like?

More specifically: What kind of cell did the first neurons evolve from and how did they work at first? (assuming there were few, if any, neural connections in the first organisms to develop neurons of some sort)

From what I understand about a neural system, it needs a few neurons linked together to keep firing.

Perhaps the first neurons had triggers other than dendrite connections?


texts:
With respect to this paper:

Identification of Host Proteins Required
for HIV Infection Through a Functional
Genomic Screen

In the abstract, I found names such as Rab6 and Vps35 and TNPO3. So Rab6 and Vps35 are proteins and TNPO3 is a gene? So the strings written in full caps are the genes and those strings whose just first letter is capital and the rest of the letters are small is a protein?


texts: What is the field of view for the human eyes?

texts:
I'd like to know how much a person can see regarding the angles.

If it is a rectangle, I'd like to know it's height and width.

But if is another shape, I'd like to know which kind of shape and the angles.

I suppose that we can see something like this and if this is true I am curious about 4 dimensions:

"vertical" angle for both eyes
"horizontal" angle for both eyes
"vertical" angle for an eye
"horizontal" angle for an eye

It would be also nice if there will be some "areas" with percentages. I mean, something related to "central" vs "peripheral" view, because we see better something that is in front of us than something that is near us.


texts: instances of virus transmission-enhancing research approvals

texts:
In February 2019 this article by epidemiologist Marc Lipsitch and professor Tom Inglesby raised concern about secret virus research.
Washington Post article link.

In 2014, U.S. officials imposed a moratorium on experiments to enhance
some of the world’s most lethal viruses by making them transmissible
by air, responding to widespread concerns that a lab accident could
spark a global pandemic. Most infectious-disease studies pose modest
safety risks, but given that these proposed experiments intended to
create a highly contagious flu virus that could spread among humans,
the government concluded the work should not go on until it could be
approved through a specially created, rigorous review process that
considered the dangers.
Apparently, the government has decided the research should now move
ahead. In the past year, the U.S. government quietly greenlighted
funding for two groups of researchers, one in the United States and
the other in the Netherlands, to conduct transmission-enhancing
experiments on the bird flu virus as they were originally proposed
before the moratorium. Amazingly, despite the potential public-health
consequences of such work, neither the approval nor the deliberations
or judgments that supported it were announced publicly. The government
confirmed them only when a reporter learned about them through
non-official channels.

Have there been other instances of transmission-enhancing research approvals since the apparent end of the moratorium?


texts: What does it mean to be a fully human monoclonal antibody?

texts:
I somewhat understand that some monoclonal antibodies are developed from the cells of mice, or a fusion of human and mice genes.

When something is a fully human monoclonal antibody does that mean it came from some person? What type of human cell did it come from? Will the drug always be from that original human?

I read that they're derived from something called a phage display technique. I'm guessing this is another type of way to fuse genes together, but with all human cells.

Where do the cells come from?


texts: The mycobacterium of TB doesn't secrete any toxins. The cause of disease in the immunocompetent is the collateral damage due to the immune response against disseminated infection. But then, when HIV patients are immunocompromised, why should TB do any harm to them? There is an absence of the typical granuloma in HIV cases.


texts: Why is glycine considered a nonpolar amino acid but a polar molecule?

texts:
Glycine has a dipole moment, so why is it considered a nonpolar amino acid when discussing its occurrence in proteins?

Also, is the backbone of a protein nonpolar?


texts: Can epigenetic structures carry a trait?

texts: Can epigenetic structures cause a trait to manifest in a person if the trait is not already in the DNA? In all my readings I have yet to find a definitive statement that it is impossible.


texts: How much of the weight of yoghurt is due to bacteria?

texts:
I recently started making all kinds of bacteria-processed foods by myself (such as yoghurt, but also Sauerteig and so on), and I found myself wondering how much of the weight of these products is actually due to the bacteria themselves in the end. But I couldn't find anything useful on the internet.

So, specifically for yoghurt, how much of its weight is due to the bacteria, i.e. dead and/or living bacterial cells, but not including the products of their metabolism outside the cells?

I would also be happy about numbers on other bacteria- or fungi-processed foods, but I wanted to keep the question simple.


texts: Where do plants obtain the metal ions needed for biological processes?

texts:
Enzymes employ metal ions (e.g. Mg, Cr, Mn, Fe, Co, Ni, Cu, Zn) for catalysing certain reactions.

Let's consider planting a seed. Where will it obtain these metal ions from? Just from water?


texts:
I am doing CRISPR/Cas9 experiment on E. coli. I am introducing recombinant plasmid  BPK764 (which carries Cas9 + sgRNA designed and added later in that plasmid) into compentent E.coli cells which already carries another plasmid with GFP gene. sgRNA will be designed so that it corresponds to that GFP gene becouse my main point is to cut out GFP gene. The main result of this experiment will be E.coli cells that do/don't express GFP gene (depending on CRISPR/Cas9 efficacy), therefore, the resultant cells will or hoply won't light green. I will see that under UV lamp, and by fluorescent microscopy.

Now I'm getting to my question.
Is there something on those resultant cells (some trait, like membrane structure, youngs modulus, that differs from CRISPR untreated cells) that can be visualized on AFM (atomic force microscopy)? Something that changes on cells after inserting plasmid that can confirm efficacy of this experiment?

Or maybe some other idea on this experiment using AFM?


texts: Really specific question, but what is the average tensile strength of human collagen, type I? I've tried looking for it online, and either my google-fu skills are weak, or I'm just unlucky. Also, is there a specific database for mechanical protien data, or do I just have to look up each protien's tensile strength individually?


texts: What is the difference between phylogenetic tree "construction" and "reconstruction"?

texts:
When I look through papers, there are two terms

Phylogenetic tree construction
Phylogenetic tree "Re"construction

What is the difference between phylogenetic tree "construction" and "reconstruction" ?


texts: If the brain has no pain receptors, how come you can get a headache?

texts:
I've read many years ago in books, that the brain has no nerves on it, and if someone was touching your brain, you couldn't feel a thing.

Just two days before now, I had a very bad migraine, due to a cold. It's become better now, but when I had it I felt my head was going to literally split in half, as the pain was literally coming from my brain.

So it lead me to the question: How come people can get headaches if the brain has no nerves?


texts: Criteria for the numbering of human chromosomes

texts:
What were the criteria devised for the numbering convention employed in human chromosomes? When was it fixed?

Correct me if I am wrong; it appears that chromosome pairs 1 to 22 were originally ordered in terms of perceived structural size, which ended up fitting neatly with the quantity of base pairs (but not with the quantity of genes).

The sex chromosomes in turn were arbitrarily assigned as "pair 23".

Is this sound?

Thanks in advance.


texts: How much time does it take a human body to replace all of its atoms?

texts:
Mikel Vsauce (Vsauce youtube channel) said in his video that it takes about 5 years for the body replace all of its atoms, while in asapscience youtube channel they are claiming that it takes 10 years. I am confused and I can't find anywhere the precise time it takes.

Mikel's video (minute 1:14)
AsapScience video (minute 1:07)


texts: Propagating errors for percentage reduction

texts:
Need a bit of help for this particular problem.

I have three averages collected from three genotypes (A, B, and C) and their associated SD (a, b, and c). A is my control.

I have been asked to represent the data as a percentage reduction as compared to A. How do I propagate my error?

Calculation:

% Reduction for A = (1-A/A)100%
% Reduction for B = (1-B/A)100%
% Reduction for C = (1-C/A)*100%

Thanks a ton!


texts:
Eusociality, particularly focusing on the presence of certain altruistic sterile organisms within the social set-up creates questions as to why would the process of natural selection have favoured the persistence of such genes especially in hymenopteric species. One explanation (provided probably by Hamilton) pertains to very similar genetic constitutions of females of such species (owing to haploid nature of males), which increases genetic similarity between the female members of the social group. Thus it would be more "beneficial" (i.e., favourable for the persistence of similar genetic builds) for a female worker to help the fellow siblings, to which it bears greater genetic similarity, than its own offspring to which it bears a lesser genetic similarity. This might in a deeper way explain altruism in case of hymenopterans where the male is a parthenogenetic haploid and the female is diploid.

But why would the sterile condition of the workers in case of almost all eusocial groups be favoured by natural selection on grounds that it improves the 'fitness' of the 'genetic build' of the workers and ultimately the sterile altruists benefit the persistence of its genetic traits? Moreover the altruistic nature of the haploid males also goes unexplained.


texts: Wet weight measurements: Setting up cultures for measuring growth rate via wet weight

texts:
I have some isolates which I am trying to grow in some toxic leachate in order to measure their growth rate I also want to measure the growth rates of certain combinations of these bacteria.

I've tried a few ways to measure their growth rate in leachate (mostly turbidity), all of which have been unsuccessful. My supervisor has therefore recommended I try wet weight measurements.

I am a chemical engineering undergraduate, and I have never done wet weight measurements before, so please forgive my naivety!

My set up is as follows:

I have overnight cultures of the isolates which are being grown up
in leachate (themselves inoculated from agar plates) in falcon tubes
as an inoculum for my wet weight cultures.
I plan on having several (~20) 250ml conical flasks with leachate in them. I will innoculate these from my overnight cultures, so that different flasks contain different isolates
I want to take daily kinetic measurements in order to get the wet weight of the bacteria growing in leachate. This will be done over a period of 5 days.
I will take an aliquot each day for 5 days from the conical flasks, centrifuge in order to pellet the cells, then remove the supernatant and weigh the biomass.

So what I don't know are the specifics of how I might set this up.

I know that my isolates grow slowly in leachate, and therefore I will need a relatively large volume of liquid (around 5-10ml) in order to get a meaningful change in biomass.

So my queries are;

How many replicates is sensible for this sort of wet weight measurement? I know that they can be quite varied from replicate to replicate, but I have limited room in my incubator. I think 4 replicates might be too many, but I don't know the extent of the variability when it comes to wet weight measurements.
In 250ml conical flasks, what is the maximum volume of liquid I can put in them before there is not enough head-space remaining?
What volume of an inoculum would be sensible for this experiment? And if I am wanting to get a growth rate, then does it even matter? As I am only concerned with the rate of change of biomass over time and not the final amount.
I want to take large enough aliquots to demonstrate an increase in biomass, but obviously not too much that it begins to affect the culture growth. As this is destructive sampling, what volume of my culture can I afford to lose?
I have demonstrated that in a volume of 5ml of leachate, and given 72 hours, my isolates' biomass increases by approximately 8,000 μg - 10,000 μg. So by this logic, is it right to say for the daily measurements, aliquots might should be 15ml so that I can get meaninful readings?

I already know it is not feasible for me to do dry-weight measurements simply because of time and the system I'm working with.


texts: Why don't all my cell membranes "smush" when I fall?

texts:
I've read the question about cell membranes breaking apart, which is close to what I'm asking, though I'm trying to probe a bit deeper.

I understand that there are hydrophobic forces keeping the cell membrane together, and I'm roughly picturing the strength of something like water surface tension.  With this intuition, I tried to consider a few examples:

I've read the idea that the cytoskeleton can help give a cell structure.  But if a cell has some kinetic energy (say, red blood cells in the bloodstream) and runs into something else (say, the arterial wall), are the hydrophobic forces holding the cell membrane together strong enough to prevent the cytoskeleton from puncturing the membrane?
Similarly, there are videos of bacteria with their flagella traveling at what seem to be pretty significant speeds (relative to their size) - are hydrophobic forces truly enough to hold the cell membrane together in the face of that kinetic energy?  Are they a lot stronger than my intuition gives them credit for at the tiny scales of cells?
Hydrophobic forces also seem to require being in solution - the obvious counterexample would be our skin cells, which clearly are not fully in solution, but even if that were the case, if hydrophobic forces were the bulk of the forces, then wouldn't any two cells merge the moment they made physical contact with each other?

This train of thought leads to the titular question and thought experiment:

Dropping a glass of water will result in the water going everywhere.  If I were to jump up and then land, and hydrophobic forces are holding the cell membrane together, why doesn't my cell membrane fall apart from that application of kinetic energy?


texts: How can a mutator gene can cause a mutation when it is shut off?

texts:
defination of "Mutator" - a gene that increases the rate of mutation of one or more other genes.

However, in the book "Molecular Biology of the Cell" (bruce alberts) it states that when a mutator is shut down, then that shut down increases the rate of mutation. How does that process work? It seems to contradict its definition? If the mutator is shut down, then how can it create mutations?


texts: Long-term effects of antihistamines on mind and CNS

texts:
Can maybe someone share knowledge or guesses on the following questions:

Does the prolonged use of antihistamines cause long-term effects on mind or CNS?
Are there any known evidences of their influence of formation of CNS or personality when taken at a young age?
Generation-II antihistamines are said to be next to devoid of sedative effects since they selectively block just the H1-receptors. However, they are reportedly potentially mind-altering. How is this possible?


texts: Is it necessary to conduct a power analysis before beginning an experiment?

texts:
I know that power analysis is the statistically valid way to ensure you use the correct numer of samples or repeats in an experiment. But I have never seen any biologist actually conduct a power analysis. Mostly, researchers seems to use a rule of thumb (three technical, three biological replicates is a common one).

Should I be doing a power analysis each time I design an experiment, or can I just use one of the common biology rules of thumb? If not, what are the consequences for the validity of my results? And is there a situation where I will be required to use power analysis, which makes it advantageous to get used to doing it now?


texts:
I met with the following question in my masters course:

  What do different fermentation products have in common?

Thinking about this, I have difficulty in identifying the similarities between lactic acid and alcohol fermentation.


texts: What is the difference between "dysregulation" and "deregulation" of miRNA?

texts:
I've started to study the role of miRNA in cancer. Wikipedia says:

  Just as miRNA is involved in the normal functioning of eukaryotic
  cells, so has dysregulation of miRNA been associated with disease.

  The first human disease known to be associated with miRNA deregulation
  was chronic lymphocytic leukemia.

1- What is the difference between dysregulation and deregulation?

2- How are these concepts related to RNA degradation?


texts: How long does it take for cancer to be detectable if it grows from a single cell?

texts:
Assuming cancer has its origins at a single malfunctioning cell, how long would it take for that cell to grow from the point at which it is malfunctioning enough so that it can be detected by the immune system, to the point at which it be detected with:

Routine modern medical tests
Cancer specific blood test
Noticed by the host (symptoms)


texts: What is the best argument for maximum parsimony method in phylogenetic tree construction?

texts: Beside the fact that maximum parsimony is computationally cheap, what other good arguments are there for it? Is there any model behind this principle? Why would one expect this principle to provide right phylogeny in any situation at all ?


texts: Their are basically two types of dialysis: 1.peritoneal dialysis 2.hemodialysis, My Question is Why the peritoneal dialysis needs to be carried out on everyday BUT hemodialysis is carried out on only 3 days in a week?


texts: compute contact mixing matrix from partnership degree data

texts:
In a discussion of sexual partnering, we are given the following information on a momentary degree distribution (as percentages):

degree    0       1       2      3
men      32.3    53.2    12.4    2.
women    26.7    71.9     1.1    0.2

From this, the authors construct a "proportional mixing model", treating the data as providing the marginal effects.  (The rounding error is small, so I'm going to ignore it.)  I want to understand what this means.  I'll try to get started.

To begin, since this is heterosexual mixing, there cannot be the same number of men and women participating, since men and women must be in the same number of partnerships.  So if there are say 10000 individuals, we must have about 4707 men and 5923 women. From this (and the above percentages) we know the number men and women of each degree, and thereby how many total partnerships (3954).

degree    0          1         2        3
men    1520.36    2504.12    583.67    94.1399
women  1413.23    3805.67     58.22    10.586

I think (?) the challenge is first to find the number of partnerships of each type.  Obviously there are no partnerships with individuals of degree 0, so we are looking to fill a 3 x 3 matrix of partnership counts, so that each deflated row sums to a male total and each deflated column sums to a female total (as given by the table).  (By deflated, I mean divided by the degree.)  This does not seem too bad on the face of it: 9 variables with 6 equations looks to leave solutions to spare.  But the system appears to be inconsistent.  So, I must misunderstand.

I get the impression that this is very standard stuff, but I'm not finding it in the textbook I have at hand.  I'm happy to work through the math if pointed to a careful discussion.


texts: How would cloning affect conservation of rare species?

texts:
Many species are at risk of extinction, and cloning could be seen as a relatively quick method to produce large numbers of members of the species to aid in conservation efforts, especially if the species involved has low fecundity (such as the giant panda).

However, cloning results in the reduction of genetic diversity, which may lead to significant issues due to inbreeding and susceptibility to diseases. This can most clearly be observed in the Gros Michel banana cultivar, which was nearly wiped out by Panama disease due to the cloned banana cultivar not having any resistance to the disease.

What are the main positive and negative aspects of cloning when applied to conservation of rare species?

(This question is based in part on this question, which was closed for having not done any research, but has an interesting premise that I wish to see answered on this site.)


texts: Can single-cell organisms have through-holes? (Are donut-cells a thing?)

texts:
I've watched a YouTube video about microorganisms, which featured a shot (below) of a single-cell organism, that looked like it had several through-holes in its body. Somehow I have a pretty steady mental image of a single-cell organisms being basically blobs: a sphere, an ellipse, a branching tree-like structure, all seem like plausible single-cell creature shapes to me, but something like a donut just doesn't. Is my intuition wrong and this is just a normal thing cells do? If so, how do those holes form? And if not, why does this shot look like a cell with holes?

I thought that those holes might be just me wrongly interpreting the image. One idea was that this might be a result of the cell's complex 3D structure being projected on a 2D screen, but the movement of particles inside of the cell (which you can see in the video) seems to support the "cell with holes" interpretation. The other one, that was suggested in YouTube comments, is that those "holes" might be vacuoles inside of the cell. It seems that for that to be true, the image would have to be more like an MRI scan, revealing only a "slice" of the cell. But you can see some of 3D structure there, so it doesn't seem right either.


texts: What is this fruit found in a market in Uyuni, Bolivia at the end of December 2019? (orange skin, 4cm, white flesh)

texts:
What is this fruit found in a market in Uyuni, Bolivia at the end of December 2019?

Fruit diameter: ~4 cm. Seed: large, spherical, black. Flesh: white. Taste: sweet but not as sweet as a lychee.


texts: Why are nausea and dizziness such common side effects from medication?  If you go through your medicine cabinet and look at side effects, those might just be on every single bottle.  Is there some system in the human body that is very sensitive to any disturbance and causes nausea and dizziness?


texts: Is there a resource that has quantitative data about cell proteins?

texts:
I am a MSc student working in mathematical biology. In my thesis I am modelling diffusion of a protein that can bind to cell surface receptors. In order to simulate this I need some rough figures about the binding rates, degradation rates, diffusion rates etc. of components involved in this system. I have managed to find some information about these things, but they have all come from reading papers - biology papers where I only barely have enough knowledge to grasp the key concepts and (lets face facts) barely have the patience to read.

Is there a better way to find this quantitative data? Ideally I would love to come across a database that had this kind of data in it, but I'm not holding my breath.

What techniques do people in my position use to find this kind of information?(short of trawling through incredibly dense biology papers)


texts: When should I use cryofixation and chemical fixation?

texts:
We know that the technique used in TEM sample preparation involves multiple steps, one of the most important of them is fixation.
Fixation can be of two types:

Cryofixation, that suggests that the specimen are subjected to freezing temperature to perserve the cell's living material before we observe them.

Chemical fixation involves the use of certain chemicals, such as formalin, glutaraldehyde, etc. for almost same purpose.

The question is when it is mandatory to use one of them only? Such as, cryofixation or chemical one? At some instances, have the researchers ever need to use both of the techniques at the same time?


texts: How does hyperthyroidism cause diarrhea?

texts:
According to Robbin's Pathology, hyperthyroidism leads to an overactivity of the sympathetic system.

It also goes on to mention that this sympathetic hyperstimulation in the gut leads to increased motility leading to diarrhea and malabsorption.

How would sympathetic stimulation cause hypermotility? Isn't the parasympathetic system responsible for it?

Also, how does hyperthyroidism increase the sympathetic tone?


texts: Does the growth in size of hippocampus of London taxi drivers affect their net number of brain cells?

texts:
In the paper, London Taxi Drivers and Bus Drivers: A Structural MRI
and Neuropsychological Analysis in the Journal Hippocampus, the authors state that changes in the hippocampus of taxi drivers in London results from their specific occupation. The authors stated this was more pronounced than in bus-drivers.

What accounts for grey matter change? Do their brains have more brain cells than other people? Or the increased in size of the posterior hippocampus means some other region of their brain must have less brain cells to have enough to grow their hippocampus?


texts: Why do shed and brown poplar (Populus) leaves get an iridescent blueish colour when wet?

texts: When the brown leaves of poplars shed on the ground stay for a while under wet conditions (e.g. like in a puddle), they become a fascinating iridescent blueish colour, which is best seen when light shines on it. I tried to look this up, but did not get any results... any ideas?


texts: Cell proliferation limit and senescence of embryonic stem cells and fibroblasts

texts:
I am trying to understand the importance of proliferation limits and cell senescence. In particular, I would like to compare the proliferation limit of Embryonic Stem cells (ES) and fibroblasts (which would be trans-differentiated) and describe how this difference plays a role when thinking about engineering organs, for example a heart transplant.

How do ES cells and fibroblasts compare with regards to the Hayflick limit?


texts: When and How do pacemaker cells develop during the cell aggregation process of Dictyostelium discoideum?

texts:
I was reading a paper by Tang & Othmer about oscillations and waves in Dictyostelium discoideum. Under certain condition like starvation period in the life cycle of a Dictyostelium discoideum community, they evolve itself into a multicellular organism in a process of cellular aggregation. I have read about Pacemaker cells among these individuals which transmits periodic cAMP and attracts other cells towards them.

So I was wondering: When and How do these Pacemaker cells develop from a "normal" cell into a pacemaker cell excreting cAMP?

References, links or answers would be very helpful for me.


texts: How stable is in vivo whole cell patch clamping?

texts: For a head fixed animal, how stable is the current state-of-the-art whole cell recording from a cortical neuron? The animal's breathing, and heart beat must move the neuron relative to the recording device quite a bit, and I was wondering how stable the seal would be. How long can one hold a cell, and what is the typical quality of such recording?


texts: Genetic networks vs genetic architectures?

texts:
What is the difference between the terms genetic network and genetic architecture? I've heard both in a variety of contexts used by different people, so I am interested in what people think they mean, other than what is described in Wikipedia:

Genetic architecture refers to the underlying genetic basis of a phenotypic trait

Genetic regulatory network (GRN) is a collection of DNA segments in a cell which interact with each other indirectly and with other substances in the cell, thereby governing the rates at which genes in the network are transcribed into mRNA.

EDIT: so what I take from the answers so far is that a genetic network is the molecular wiring of all the interacting loci, whereas genetic architecture describes the phenotypic consequence(s) one would be able to see from that network. Then, trying to bring the two definitions together, if we would assume we knew all the molecular details of a genetic network, we would only need to add the other factors in the model, such as environmental perturbations, to end up with the description of the genetic architecture, right?


texts: Does the male and female always split evenly the genetic material given to their offspring?

texts:
Are there animals known to have a different percentage of splitting of genetic material, like the male give 75% and the female just 25%. I know that drone bees have only genetic material from their mothers, I would like to know if there are also instances in larger animals (mammals and reptiles).

If the answer is no, then do we know why it is always evenly split.


texts: How can I get accession numbers of bread wheat miRNAs by their sequences? What are the tools or website that can be used?


texts: Why are there 10 base pair steps, not 16?

texts:
In a biochemistry course I'm taking, the lecturer emphasised that there are 10 possible base pair steps; I've included a screenshot of a slide stating this. This confuses me, because I cannot work out why it's not 16; why are the 6 greyed out in the image not allowed (for example, CG stacked on CG counts, but GC stacked on GC doesn't)? TA|AT is listed as distinct from AT|TA, so it's not that the greyed ones are redundant.
I've found a couple of papers mentioning that there are 10 base steps, but not why. (I can't get hold of the lecturer.)
Thanks in advance!


texts: What does fluorogenic mean for fluorescent probes?

texts: Many fluorescent probes are described as being fluorogeninc as an advantage for fluorescence microscopy but what does fluorogenic mean? Dictionary definitions state that it means generating fluorescence, but i've read somewhere that it involves switching the fluorescence on or off for super resolution microscopy. I just want to understand the exact meaning in this context. Thanks in advance for the help.


texts:
I took a quiz today on cell structure basics, which included cell junction types. I disagree with the "correct answer" according to the teacher.

Here is the question:

Which cell type would have the most tight junctions?

a) Pancrease cells
b) Ovarian cells
c) Epithelial cells (in the intestine)
d) Muscle cells (skeletal)

According to my teacher, muscle cells is the correct answer.

I argued that the answer should be epithelial cells, as muscles cells (according to the text) primarily use desmosomes for cell-to-cell adhesion, while epithelial cells rely on tight junctions primarily.

I searched it up quickly on Google, and from what I have found, epithelial cells is the correct answer.

Is my teacher incorrect?


texts: Is this a shell operculum? If yes, can I get more info on operculum

texts:
I came across this strange shell some years ago and my research concluded that it was an Operculum (gastropod)(https://en.wikipedia.org/wiki/Operculum_(gastropod)) and I am interested in knowing more about the operculum.
What is its uses, how is it formed, will I fine something inside if I break it, how does the animal feed itself inside this, and so on.

Bottom View

Top View


texts: What is the reason for having an extra recognition site for a restriction enzyme?

texts:
Can the size of a supercoiled plasmid DNA be determined by using standard DNA size fragment electrophoresed in parallel? 2. An unknown DNA molecule was cleaved using several restriction enzymes individually and in various combinations. The DNA fragment sizes were determined by agarose gel electrophoresis and the restriction enzyme recognition sites were mapped. Subsequently, the DNA was sequenced and an extra recognition site was found for one of the enzymes. However, all the other mapping data was consistent, within experimental errors, with sequence data. What are the simplest explanations for this discrepancy? Assume the DNA sequence had no errors.

My answer:

the  extra enzyme recognition site was cut-off with the fragment due to partial digest that occurred because of insufficient enzyme was added or the rxn was stopped after a very short time.

Am i wrong? my logic here was such that they only found the extra recognition site after they sequenced the DNA thus it was not available during the rxn and thus it was either cut off unevenly in one of the fragments OR it could have had the complementary sequence to it that was methylated that hid it.

Detailed answers are appreciated!!


texts: What's the aim of genetically modifying of foods/organisms?

texts:
On news, articles etc. experts talking about Genetically Modified Foods and Organisms often mentions about their disadvantages like,

their potential to harm human health
allergies may become more intense, new allergy types may develop
possible damages to the environment

So I wonder, what's the aim of genetically modifying of foods/organisms? In other words, what are advantages of that?


texts: I live in the northeast US, and really enjoy firefly displays at dusk in the summer. However, when paying attention this summer, I noticed that the fireflies were not displaying every night, but somewhat irregularly, and only over a short period (both within an evening and across the season). I could not figure out what combination of environmental conditions were associated with their display behavior. What are the environmental conditions in which fireflies are most likely to engage in light displays in the temperate eastern US?


texts: How a pathologist would analyse this H&E image?

texts:
I am working on a project which involves writing computer software to analyse histological images. A typical image looks like this:

It is a Hematoxylin and Eosin stained biopsy of breast cancer tissue.
Being a programmer without biology background, I would like to get insight into how a pathologist analyses such images.

More specifically:

Which cells are cancer cells and which are regular cells?
Can an invasive margin (a curve marking the boundary of cancer invasion into the tissue) be seen in this image?
Can a pathologist provide a TNM classification looking at the image? If yes, what would be the T, N, M, G values for this image?


texts: Is there a reference for the composition of viral genomes?

texts:
First of all forgive me for the bad written question.

I'm not a biologist. I'm neither a doctor nor a virologist. I am a physicist actually, and I have this question in mind since a long while.

What I'm trying to ask is if there is a sort of text file or a website (or a book) where I may read about viruses "composition".

"Composition" means something like

"This is the rhinovirus, and it's genetic "composition" is ACTGCT" (of course I just invented...).

I don't know how to express myself with good terms because I am not familiar with this field, so please feel free to edit the question if it may appear unclear.

Again, what I'm asking is for a sort of database of genetic sequences about viruses and so on.

Thanks in advance!


texts: Do scars generally continue to undergo beneficial changes after maturation?

texts:
I understand that succumbing wound healing, a modulated scar would go through a process of scar healing which I understand to be remodulation and maturation.

Do scars generally continue to evolve in beneficial ways throughout the life of a human?
That is to ask; might it be that a scar's evolution could be comprised of two major stages "primary" and "secondary" and that the primary stage is consisted of remodulation and maturation and the secondary is comprised of "post maturation" evolution which could last during all life of a human?

In general, scars do get changed after being "healed", at least by general bodily changes from aging effecting all tissues in general (including the scar tissue), but there might also be a "post maturation evolution" as well.


texts: Where to download gene list of human genome?

texts:
I am looking for a place where I can download a full gene list of human genome. Either by HGNC symbol or ensemble ID as long as it is usable on the consensusPathdatabase. Up until this point I have only found fasta files which include a bit too much information and unfortunately not in the format I would like. I am not in the biology field myself so if I am asking for something unreasonable call me out on it!

Reason for this is I am trying to stress test an application that uses the output tabular forms from the gene set analysis tool on consensusPathbase. The stress test on the entire human genome seemed to be the best option as a bigger data set than that will probably not occur.

Thanks in advance


texts: Can this system of mutual promoting and repressing proteins be simulated using Gillespie algorithm?

texts:
Consider an axon of length $L$ with the soma located at $x=0$ and the tip located at $x=L$.

We assume that there is a constant input of Kinesin motors to location $x=0$ coming in from $x \le 0$.

Assuming that all Kinesin motors travel at the same speed $v$, the proteins reach the location $x=L$ after a time $\tau = \frac{L}{v}$.

At $x=L$, incoming Kinesin motors induce Dynein motors to travel from $x=L$ to $x=0$.

Assuming that all Dynein motors travel also at the same speed $v$, they reach the Location $x=0$ after a time $\tau = \frac{L}{v}$.

At $x=0$, incoming Dynein motors inhibit Kinesin motors from travelling to $x=L$.

Thus, we get a negative feedback.

My question:

Can this system of mutual promoting and repressing preoteins be simulated using Gillespie algorithm?

I already simulated it with a mathematical model of delay-differential equations, but as this model doesn' t show all effects, I would like to try using Gillespie algorithm.


texts: Why do we feel headache after ice cold drink?

texts: Whenever we drink ice cold drinks, after a couple of seconds, suddenly we feel intense pain rising from upper nose to forehead. What is reason behind this pain after too cold drink and why it's felt in that particular part of head?


texts: Why does dryness irritate mucosal surfaces, and what exactly is this "irritation"?

texts: The mucosal surfaces of the body function to moisten the epithelial linings and keep them from becoming dry. Why is this important? As an example, the respiratory tract moistens and warms the air that we inhale before it gets to the lungs, to protect it from damage and "irritation". How would cold, dry air cause those things?


texts: Why is western blotting used to confirm positive ELISA HIV tests?

texts:
I know that when an ELISA test indicates a positive result for HIV, a western blot is done to confirm. When I search online for the reason why, all that I see is that western blotting is "more specific" than ELISA. If they both use antibodies, shouldn't these procedures have similarly accurate results?

My only guess would be that the combination of Ab-Ag binding in addition to expecting your antigen to be a certain size is sort of a "double yes" and thus western blot results would possibly be taken as more accurate.


texts:
So, I did an experiment on the effect of sodium chloride on amylase. and I found out the higher the concentration, the slower the activity.

Therefore, is it valid to make the assumption that when we consume food with starch and high salt concentration, it can affect our digestion of starch? like slower break down of starch?


texts: How can the child and the mother have different blood types?

texts:
As far as I know the fetus is fed by the umbilical cord which basically connects his/her circulatory system with the mother's in order to supply oxygen and nutrients. But how is this possible if they (the mother and the fetus) have different incompatible blood types?

It is possible that the father has A blood type, the mother B and the child A and thus incompatible with the mother's.


texts: How does one experimentally obtain a hemoglobin-oxygen dissociation curve?

texts:
I've always wanted to do comparative eco-physiology studies looking at Hemoglobin-Oxygen affinity of populations in different environments, but I can't find a protocol to experimentally measure the relationship. Does anyone know where I can find a protocol, or know a protocol themselves?

I'm assuming an answer would include what the necessary instrumentation would be, what condition the blood needs to be in (fresh?), if the heme is isolated (and if so, how), and what an appropriate sampling scheme would look like.


texts: Why some parts of the human body have immune privilege?

texts:
Why have the eye and CNS have immune privilege? Why does the body not develop tolerance against their tissue and instead risk their damage in case an accidental immune cell infiltration?

Wiki:

  ...in immune privileged sites, tissue grafts can survive for extended periods of time without rejection occurring


texts: What species of three-tailed flying insect is this?

texts: What species of insect is this? Collected in spring in the United Kingdom near a river in an urban area during the late afternoon. They were flying up and down in the air.


texts: Spectrophotometric Values of Individual Nucleotides

texts:
All around the net you will find this list giving 260/280 ratios of individual nucleotides:

Guanine: 1.15
Adenine: 4.50
Cytosine: 1.51
Uracil: 4.00
Thymine: 1.47

Yet I cannot find a reliable source for these values. One source cites a 70s version of Leninger's Biochemistry but even though I got hold of a more recent edition, I cannot find that information in there.

Does anyone happen to know a quotable source for this?


texts:
I do not understand how skin color in humans work, even after taking a basic genetics course and reading some on wikipedia.

From what I understand, skin is color based on multiple genes that control melanin and other products that affect appearance of skin. So then their are multiple alleles for "skin color" and also some of these alleles can be varying in their expression/inheritance? based on the other alleles presence?(epistasis)

So then a black person and a white person could have various skin colors (phenotypes?) And the offspring of these children could then have varying offspring as well?

Diagrams would help me maybe in explaining the concept.


texts: How to annotate a .broadpeak file with 9 columns?


texts: Can memories intentionally be overwritten, or forgotten?

texts:
Over the years, I've come across studies (e.g., here, here, and here), and have watched documentaries (similar to this), that speak about memory retrieval, and how that, every time you recall a memory, that memory is subject to being distorted (less accurate). Of the different types of memory, it seems that this is most often spoken about when episodic memory is involved.

In pretty much every situation I've seen, the person with the memory is trying their best to most accurately recall that memory, with respect to the true event(s) that was originally experienced. However, would it be possible to intentionally cause memory distortion, perhaps by continuously recalling a memory and then deliberately thinking of false information? Or, can this process only happen subconsciously?

There is a movie that somewhat plays on this idea, Eternal Sunshine of the Spotless Mind. In this movie, a participant is alseep while wearing a kind of helmet that selectively targets and erases desired-to-be-forgotten memories. And though my initial curiosity did not arise from seeing this movie, and yes, I am aware that this movie is sci-fi, I do still wonder if this kind of overall effect could be achieved without technological/medical intervention. If not, why?


texts:
I have read that DNA(after recombination) is packaged in bacteriophages lambda only if it's between 40000 and 53000 bp long. This constraint can be used to ensure packaging of recombinant DNA.

I don't understand why shorter DNA can not be packaged.

Source : Lehninger Principles of Biochemistry


texts: Does the Plasma Membrane have a hydrophilic interior/exterior/contain vesicles?

texts:
I am very new to the study of biology, and have been unable to find information in other sources which could tell me whether the plasma membrane has the following traits:

has a hydrophilic interior
has a hydrophobic exterior
contains vesicles

Thank you!


texts:
Please correct me if my understanding is incorrect; I understand branch/stem, and root are composed of different types of cells. Yet in some plants (e.g. rose, bougainvillea) a cutting from the stem is capable of developing and taking root.

How does this transformation from stem to root come about?

As an aside - I believe such root-generation happens only in plant cuttings, and not in a tree branch. Why? Is it a matter of the volume of nutrition required?


texts: What is this white fluff growing in my basement?

texts:
I live in the countryside of Western Europe by the beach with a temperate climate. After a period of unusual humidity at 84%, I noted this white fluff in the basement floor:

The first picture is about 40 cm and the second 10 cm.

The basement is usually closed and keeps humidity. Temperatures average 18-20ºC, and humidity is now 77%. I assume it's a fungus since the floor was clear before and it seems to collapse when I rub my foot on it.

What is this species, and how can I prevent it?

Update: Following @anongoodnurse's suggestions, it's definitely a salt. I scraped the stuff, poured water, and it shriveled instantly. Here are photos before and after:

Here is a close-up of another piece, where the shards look like a crystal:

It did not smell indeed, and I did not taste it. I opened the basement door to ventilate the area, and I understand that it would accelerate the evaporation of the salty water.

I don't know if this growth has happened before, e.g. because of a leak in a pipe, or is a one-off occurrence, e.g. because of the unusual humidity in the last few weeks. I will check if the basement has any pipes.


texts: What to do if microarray t-test, ANOVA, SAM and LImma show various selected significant genes?

texts: Need advice: how to approach discrepancy in differential microarray gene expression test results: what to do if ANOVA, ttest, SAM and Limma procedures show different results and especially more discrepant when using log transformations and normalization operations?


texts:
Here is the creature I found on the glass lid of my light bulb. I guess they are attracted to light as they all concentrate on the light source. I live in Hong Kong. The brown things aren't moving (those might be eggs). The green creatures are about 0.6-0.7 cm long in body length (excluding appendages and antennae). They are sluggish in movement.

Can you help me to identify these tiny creatures?


texts: Cows milk protein transferability through breast milk

texts:
I understand that cow's milk protein(casein) transfers through breast milk via the mother's diet.

I'm looking for the process as in what hormone does it bind to to allow this process in some women and not others?


texts: Polyploidy, or why plants of different species can produce fertile offspring hybrids more frequently than animals?

texts:
This site says:

  Plants hybridize much more frequently and successfully than animals do. [...] Chromosomal doubling (polyploidy) occurs more frequently in plants and facilitates the fertility of the hybrid offspring.

Outcomes of the successful hybridization of different species of plants (i.e. yelding fertile offspring) can be easily observed in agriculture - for instance, Triticum aestivum is 6n, while Triticum durum is 4n. The latter comes from the hybridization of two plants from different genera (!). So it seems to me that not only can plants hybridize more easily, but also that the evolutionary distance between the parents can be greater than in animals.

As far as I know, the preferred animal strategy to have fertile hybrids is to go partheno/androgenic (for example in Phasmida).

My question is:

Why can plants produce fertile hybrids more often than animals? What constraints are present in animals and absent in plants?

To my knowledge, polyploidization is the main mechanism by which this is achieved. If this is true, then my previous question can be rephrased as why does animal polyploidization occur more rarely?

I'm not entirely sure about my assumptions, so feel free to correct me, of course with references.


texts: What is the advantage of indirect ELISA over direct one?

texts: I guess the answer is about indirect one giving less error due to selectivity but how exactly does that happen?


texts: Current Trend in Evolution of Human Intelligence

texts:
Up front, I am specifically not interested in philosophical or ethical considerations re Eugenics and related concepts. In an effort to receive a concise answer I'll post a narrowly defined question following this preamble to set the stage.

Preamble:
In the movie Idiocracy there is a montage at the beginning "explaining" how the human population degrades, vis-à-vis intelligence, to an alarming (and absurd?) extent due to unplanned differential breeding resulting from several generations of the intellectually "more capable" people limiting their number of progeny, through active and passive family planning, while the bulk of humanity leaves caution to the wind. This exponential social differentiation eventually makes for a global imbalance that degrades our species' overall intellectual fitness to a debilitation level.

Question:
Is the premise of this movie merely a gag or is our species already doing something very much like this?
If yes or no, how might one measure the impact of differential procreation of this sort? Since testing results are always relative to the population as a whole and computers along with the Internet of Things would tend to obfuscate the initial degradation of mental capacity.

EDIT:
Based on the brief discussion in the comments - a summary of fecundity and IQ would potentially answer my question but only if it accounted for the current selection process we see going on in modern technophile societies. That is, it must account for the effect of our most educated couples generally choosing not to procreate and here I'm assuming there is in fact an effect (cf. Idiocracy for the (absurd?) degree to which the present-day trend may work itself out).


texts: Do blood vessel walls have blood vessels in them?

texts: If so, do those blood vessels have no walls because they don't need them because they're in the same tissue as that of a blood vessel wall? Are the cells alligned diffently at the edge of the blood vessel than in the rest of the blood vessel wall? Do blood vessels in blood vessels have an outer wall defined a sudden change in orientation of the cells?


texts: What is this compound-leaf tree in Southern India?

texts:
I am staying in South India. I didn't find any flowers to this tree; just leaves.

Just seeing the leaf, I am guessing Arabian Jasmine, but my tree doesn't have flowers or seed buds like Arabian Jasmine has.


texts: Molecular Evolution: Mrbayes never stops?

texts:
When I use my own data to build Bayesian phylogenetic trees using the software Mrbayes, after many generations, it never reaches stopping status (namely, the average standard deviation of split frequencies below 0.01).

What should I do to get to this point?

The dtype is protein, 37 taxa were included, the model I used was as follows:

prset aamodel=fixed(wag);
lset rates=Invgamma;
mcmc ngen=100000 samplefreq=100


texts: Does using CRISPR/Cas9 knockout need to add donor DNA in the process?

texts: I am new to this technology and don't quite understand how it works. Hope someone can give some suggestions! Thank you.


texts: Does the yolk sac for Danio rerio form at the vegetal pole?

texts:
Does the yolk sac in general form always at the vegetal pole?
If so, is this the case for Danio rerio (the zebrafish)?


texts:
Is there a correlation between eating raw meat and aggressiveness in felines and canines?

Growing up, I was always told to cook the meat I gave to my dogs and cats so as not to give them the "taste for blood". Is there truth in this myth?

And if that's the case, wouldn't the same food have the same effect on "bigger cats" ? Wouldn't it safer to feed Zoo animals cooked meat ?


texts: Does the use of a Thiazide diuretic affect the ability of a hair follicle to absorb substances?

texts: Thiazide diuretics are on the World Anti Doping Agency's, as well as the International Olympic Committee, list of banned substances due to it ability to mask illegal substances in urine. The rapid expulsion of water from the body helps to achieve this. Additionally, with Thiazide diuretics blood levels decrease. The hair follicle is fed by blood, sweat, and sebum. Will the body's inability to retain or reabsorb water and decreased blood level prevent substances from being deposited into the hair cortex?


texts: Help Finding Specific BlaZ Gene Type Sequences on Genbank

texts:
I am doing an undergraduate research project that involves blaZ gene typing for different strain types of Staphylococcus aureus bacteria; for reference, here are some of papers on this topic that explore resistance abilities of the blaZ gene and four different beta-lactamases that can be produced:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3421557/
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC188454/
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC106017/
Right now, I need to be able to align blaZ gene sequences in plasmids (or chromosomal regions, when looking at type B blaZ genes) of different S. aureus strains to the four blaZ gene type (A, B, C, and D) reference strains as mentioned in the first paper. The first paper provides the following strains as "reference strains": type A, PC1; type B, 22260; type C, RN98; and type D, FAR19. However, I can only find the nucleotide sequence for PC1 and the partial sequence for 22260 on Genbank; when I search for RN98 or FAR19, no relevant results come up. Even though these gene type sequences should only be distinguishable by several SNPs, it's important that I have references for all four for the most accurate strain typing.
In the last paper, I noticed they provide some of the differences between all four blaZ gene type nucleotide sequences, but not in a "from start to finish" order (i.e. the numbering above the nucleotides is not sequential and the sequence comparison length overall is less than 846, which is the length of the PC1 coding regions). Please advise, as after countless searches on Genbank I still do not have the specific sequencing information I need for each blaZ type.


texts: How long can I store autoclaved disposables and reagents?

texts:
I want to stock up on autoclaved disposables, such as Eppendorf tubes, pasteur pipettes etc., and some buffers.

If I don't open the container after autoclaving, how long can I store autoclaved materials and consider them still sterile? Does it make a difference if the material is dry or if it is a liquid?


texts: How much time can a human survive only drinking water and eating sugar?

texts: If a person only drinks water and eats glucose, how long could they survive before getting any symptoms? When would the damage become irreversible? When would that person die from lack of minerals, proteins and vitamins? Also, can this "process" be sped up by drinking distilled (pure) water?


texts: Fibonacci sequence in nature, truth or just wishful thinking?

texts:
I'm reading a bit on the Fibonacci sequence in nature, be it the golden ratio or the golden spiral forming over and over again in biological structures, and then I came across this online article by Donald E. Simanek, refuting a lot of these observations as merely optimistic 'flim flam'.

So which is true?

Does the Fibonacci sequence have a place in nature or is it all just a case of vigorously looking for anything that resembles a correlation?


texts:
This is a native gel. Let's call the left 2 lanes protein A and the right 2 lanes protein B. B is the same as A except it has a FLAG tag. They are both homotetramers of about 65 kDa. After purification, both appeared as single bands on SDS-PAGE. However, these are relatively old samples and I expect multiple bands due to degradation (which I've observed with previous samples). Either way, I cannot for the life of me resolve them with native PAGE. B is somewhat workable, though still atrocious. For each of A and B, I've loaded 5 and 15 uL (hence why there are two lanes for each) with 5 uL of 5X loading buffer. Yes, I know that's not the correct ratio; I can't imagine that being my problem but I'm running it again with the correct ratio. The rest of the conditions are pretty standard:

The protein was in PBS (50 mM dibasic sodium phosphate, 75 mM NaCl, pH~7.3) prior to adding loading buffer; I've also used TBS (50 mM Tris, 7.5 mM NaCl, pH~7.4) with similar results
4% stacking gel, pH=6.8
6% resolving, pH=8.8
Tris-glycine running buffer, pH~8.3, ran at 4°C with 23 mA constant current. I've also ran at 30 mA with similar results.
Stained with Coomassie

Let me know if any other info is needed. Any advice will be greatly appreciated.


texts: If a 100 pound bucket is dropped on someone's hand, what will this do to the nerves, will they get crushed, will they die? And how will this affect that person's ability to feel or move their hand?


texts:
I live in Egypt, and I do want to perform CRISPR-Cas9 genome modification, but there are no reliable sources of Cas9. I can order some Cas9 online from the US, but not much. So... my question is, is there any way I can replicate a small amount of Cas9 to get a bigger amount? Or maybe extract some from S. Pyogens? I've been searching about this for quite some time, so any support would be really appreciated.

Note: I'm not really the "Biology" guy, so please tell me if I sound ridiculous.


texts: Recessiveness of allele for protection of organism

texts:
Heterozygous organisms profit from pairs of gene alleles. Harmful alleles when being recessive can be carried without any harm for the organism. Only when two harmful recessive alleles form a gene the negative effect is produced. As described in wiki article on allele:

  A number of genetic disorders are caused when an individual inherits two recessive alleles for a single-gene trait. Recessive genetic disorders include Albinism, Cystic Fibrosis, Galactosemia, Phenylketonuria (PKU), and Tay-Sachs Disease. Other disorders are also due to recessive alleles, but because the gene locus is located on the X chromosome, so that males have only one copy (that is, they are hemizygous), they are more frequent in males than in females. Examples include red-green color blindness and Fragile X syndrome.

But some illnesses are carried by dominant alleles (from the same article):

  Other disorders, such as Huntington disease, occur when an individual inherits only one dominant allele.

My questions are:

How does harm from alleles correlate with their recessiveness? Generally speaking, do harmful alleles tend to be more recessive?
How does benefits from alleles correlate with their dominance? Generally speaking, do "beneficial" alleles tend to be more dominant?


texts: Does culling badgers restrict the spread of bovine tuberculosis?

texts:
The British government has announced that it plans a large-scale badger cull which they argue are implicated in the spread of Mycobacterium bovis - so-called bovine tuberculosis. Any cattle that contract this disease need to be slaughtered under EU regulations.

However, the link between badgers and cattle doesn't seem that clear to me. What is the evidence that badgers spread tuberculosis to cattle? Also, what is the evidence that badger culling will have a significant effect on the spread of the disease to cattle?


texts: Is there a database of known riboswitches?

texts:
I'm looking for sequences and annotations of known riboswitches, but so far I haven't found a resource that actually fulfills my requirements. The best database I found so far is Rfam, which has entries for many riboswitch classes. The biggest drawbacks of Rfam for my case are that it doesn't contain any information about the expression platform, only about the aptamer. I'd like to know if a riboswitch is translational or transcriptional, and where the terminator/Shine-Dalgarno sequences that are regulated by the switch are. Another limitation of Rfam is that I can't easily see which sequences are validated biologically in some way, and which are just predicted.

Is there a database of riboswitches that also contains information about the expression platform?


texts:
I'm interested in learning about computational modeling in biophysics. I have heard some amount about people modeling proteins as a network of ideal springs to examine things like conformation switching. I was thinking it would be cool to try to make a very simple model of a small motif undergoing denaturation at certain temperatures while being stable at others.

Does anyone know of a good reference about protein modeling that would be understandable to someone who is decent with math/physics/programming but is in no way a mathematician/physicist/computer scientist?

Also, if you have a better idea of a simple project for me to practice computational modeling in biophysics (or even just any biology) I would appreciate hearing it.

Thanks


texts: Why are protein-coding regions rich in GC?

texts: I have been searching for an answer for this question and have some possible solutions, but I am not sure. GC regions are more stable as there are 3 hydrogen bonds instead of 2 with AT, however I am not sure if this would influence the number of protein-coding genes in GC regions? Protein-coding regions would have to be less condensed than noncoding regions so transcription factors could access them. Would a high GC content influence this as well?


texts:
Why does genome folding have such great interest?

For protein folding I could say that's important because protein's functionality closely depends on its folded state, since it affects its mechanical properties etc.

But genome? What does it even mean to be folded? Where does it happen? Any reference to papers would be appreciated.


texts: Deliberately choosing one nostril to breath through

texts:
James Nestor, on pp. 41-42 of his book Breath: the New Science of a Lost Art, claims the following.

The right nostril is a gas pedal. When you're inhaling primarily through this channel, circulation speeds up, your body gets hotter, and cortisol levels, blood pressue, and heart rate all increase. This happens because breathing through the right side of the nose activates the sympathetic nervous system, the "fight or flight" mechanism that puts the body in a more elevated state of alertness and readiness. Breathing through the right nostril will also feed more blood to the opposite hemisphere of the brain, specificially to the prefrontal cortex, which has been associated with logical decisions, language, and computing.

Inhaling through the left nostril has the opposite effect: it works as a kind of brake system to the right nostril's accelerator. The left nostril is more deeply connected to the parasympathetic nervous system, the rest-and-relax side that lowers temperature and blood pressue, cools the body, and reduces anxiety.

... Our bodies operate most efficiently in a state of balance, pivoting between action and relaxation, daydreaming and reasoned thought. This balance is influenced by the nasal cycle, and may even be controlled by it. It's a balance that can also be gamed.

A question on this site describes we only breathe out of one nostril at a time: at any given time, one of our nasal cavities will be more open than the other, and this switches back and forth every couple hours. For the most part, we are unaware of this. (At any rate, I was!)
I am very curious about Nestor's claim that the balance can be gamed. It seems that one could prepare effectively for a math exam by practicing right-nostril breathing, or for sleep by practicing left-nostril breathing. Is this the case?


texts: How is Glyceraldehyde 3-phosphate converted into glucose?

texts:
In the light-independent reaction of photosynthesis, one of the products is glyceraldehyde 3-phosphate, and the Wikipedia page on the light-independent reactions states that 6 of these can be used to form glucose.  However, the Wikipedia article on gluconeogenesis does not mention this, and the Wikibooks article on gluconeogenesis only mentions the molecule glycerinaldehyde 3-phosphate (which I'm not sure if it's a typo, because I can't find any information on glycerinaldehyde).

So how does G3P actually become glucose (and is there a good reason this information is not available on those Wikipedia pages, plus the page on G3P)?


texts:
What are the standard bio-safety protocols for preparing plant pathology herbarium specimina?

I searched google but I did not found anything relevant, nor in my textbooks. I want to know about what bio-safety precautions must be taken before preparing plant pathology herbarium specimena.

PS. It seems many teachers and students routinely prepare herbarium specimens of wild and agricultural specimens including notoriously contagious fungal plant pathogens, but they are basically pressing and drying the sample in classroom notebooks and pasting it on herbarium sheets just like ordinary herbarium specimen. Sometimes old and neglected herbarium specimens go into ordinary garbage or stray official papers.

But whenever I ask a question about it, nobody could yet mention references or protocols (I put apart the authoritative issue), sometimes they give vague reasons with buzzwords like the pathogenicity will reduce with time, or the "disease triangle" (optimal conditions) are unlikely to occur, etc.

I kindly request to provide me protocols and references about safe way for preparing plant pathology herbarium specimens