texts: How to correctly preserve organic matter with ethylene and polyethylene glycol?

texts:
I am trying to preserve and dye flowers, especially roses. Let me walk you through the process I am trying to optimize:

1) Soaking flowers in 96%-ethanol for a day to dehydrate them. This step removes a lot of the color from the petals - red roses for example become faint pink. The flower itself becomes brittle to the touch, since almost all water is removed.

2) Putting the dehydrated flower into a mix of 96%-ethanol, polyethylene glycol 400 and reactive dye which is used in textile industry. I am still experimenting with the ration of ethanol:PEG. Soaking duration is a couple of days. In theory, the PEG gets into the cells of the petals - this preserves the petals and gives them most of their flexibility back.

3) Removing the flower from the mix and rinsing it for a minute in 96%-ethanol. This should remove the excessive PEG on the surface of the petals. Otherwise it looks glossy and stays sticky.

My problem begins at step 1): If I remove a flower from the dehydrating ethanol-bath, the petals turn opaque in a weird way. Some connected areas of a petal start to change their appearance abruptly (some sort of bursting, cracking, rupturing)! This starts some seconds after removing the petal from the ethanol and after a couple of minutes, almost all of the petal has turned opaque. Usually the outer edges of the petals don't turn opaque. I am not sure about this, but could it be, that the ethanol somehow destroys the cells of the petals? Is this a behaviour that is to be expected or am I doing something wrong? I think I would benefit a lot if I could understand where this abrupt change of quality comes from.

it doesn't matter, if I remove the flower after step 1, 2 or 3, the result is always this abruptly turning opaque behaviour.

Since my goal is to dye them to look nice and pretty, I need to find the mistake I am making. I was hoping you experts could help me.

You find two pics of already dyed petals attached.

(I wouldn't mind if they stay all transparent. In that case the petals should not turn opaque. But I also wouldn't mind if they become opaque - but on 100% of their surface. Also at the outer edges. This actually may be better - I think it looks nice this way.)


texts: Understanding the genotype written in terms of two genes

texts:
I have some doubt in understanding the following genotypes: HCV-Tg/AID(+/+), HCV-Tg/AID(-/-) and HCV-Tg/AID(+/-), where HCV-Tg stands for "Hepatitis C Virus (HCV) core proteins" and AID for the gene "Activation-induced cytidine deaminase". So it is about two different genes. It is clear though what is meant by for example AID(+/+) in terms of ist alleles, but in the case I am talking about these are two different genes. In the case HCV-Tg/AID(+/-) it could for example mean that one allele is mutated at each of the two genes, but it could also mean that in the first gene (HCV-Tg) one allele is WT and in the second gene (AID) one allele is mutated. And lastly it could also mean that in the first gene both alleles are WT and in the second gene both alleles are mutated.

Can somebody help me understand what is exactly meant ?

Many thanks.


texts: Difference between morphogens and evocators in development?

texts:
I am specifically interested in this within the context of 1950's developmental biology (I presume the meaning and scope of usage of the terms has changed since then), as I am reading Alan Turing's paper on 'The chemical basis of Morphogenesis'. Turing first mentions evocators in the context of 'evocators of Waddington'. I have read some articles by Waddinton to try to see what he meant by 'evocator', but have not gained clarification from the articles available online. Turing cites Waddington's "Organisers and Genes", which is not available on the web and I do not have access to.

A more recent article here states

  The first element is the inducer (or evocator) defined as the signal emanating from a piece of tissue, such that when the tissue is transplanted to an ectopic position it elicits changes in the behavior of neighboring cells.13 Today, we understand that most of these inducers are secreted proteins and include morphogens belonging to the Wnt, Hedgehog (Hh), TGFβ, EGF, and FGF families.

Which seems to imply that most evocators are morphogens, although from the definition of evocator given I would say that this is exactly what a morphogen is!

Any insights would be much appreciated!


texts: I found this on the beach at Breamlea in Vic Australia and wondered if you could tell me what it is please

texts:
It is about 6.5 x 5 centimetres and semi transparent.
It has quite a tough skin and is hollow inside. Like a tight clear tooth shaped balloon. I have put a coin next to it for you to see the size.


texts: X-recessive disorders and genetic markers

texts:
Please observe the following pedigree of a family with a x-recessive disease (bleeder disease).

The A's are genetic markers so close to the disease gene that recombination is negligible.

I understand it like this: They place markers that cut the DNA at the locus of the diseased gene. If you have the disease, your gene snip will be different in size than someone who does NOT have the disease and this will be visible on a gel.
So if A1 is the disease marker, how come II:1 is not affected? He only has 1 X-chromosome and has the A1 marker?

EDIT: Another problem:

Is the coming child affected? Here I don't understand how the mother A1,A1 is NOT affected when the child A1 is?! Obviously A1 is the diseased marker and the mother has two of them...So she should be sick? Unless it's spontaneous?

Am I misunderstanding something fundamentally?


texts: How does the bladder transition from releasing urine at night to being able to hold urine at night?

texts: I wonder about this.  What's the biology of the transition from wetting the bed at night to holding urine at night?  Is there a chemical change with how the bladder muscles contract?


texts:
I am having some issues with transfer efficiency to nitrocellulose membranes. To get all the technical info out of the way:

Transfer method: Wet, tank transfer overnight at 30V with normal tris-glycine transfer buffer + 20% methanol. I do this at RT with stirring. Of note: I have not recently been equilibrating my gel in transfer buffer, as this was reported to decrease transfer of basic proteins due to the stripping of SDS (I can furnish this reference if anyone is interested).

Sample: In all cases these are in vitro reconstituted nucleosomes with or without certain enzymes--the main transfer issues are the core histones, which are highly basic (pI 10-11). There should be no more than about 100 ng of each histone being transferred per lane. The salt in the sample is <25 mM. They are boiled prior to loading. There is no noticeable precipitate in the samples before or after boiling, however the volume is quite small (20 ul) so I would not necessarily detect precipitation.

Nitrocellulose is 0.2 um and is pre-equilibrated in transfer buffer prior to transfer.

The gel: I use a 15% gel, 1.0-1.5 mm thick. The acrylamide I use is 37.5:1 acrylamide:bis. Some issues could arise here--the acrylamide solution is about 1 year old and has been stored at RT that entire time (which is what is recommended on the label). In addition, we typically keep a stock of 10% APS at 4C, so I cannot guarantee my APS has not gone bad.

I have been quite careful generally to ensure there are no bubbles between any components of the sandwich and filter paper/foam pads are soaked in transfer buffer.

Now to the issue. Attached are images of the membrane after transfer (and also after processing, thus the relatively high background from the blocking buffer) as well as the gel after transfer. As you can see from lane to lane I seem to have differing transfer efficiencies. This has occurred with my last three blots. My first thought was sample precipitation, but I have not had this issue before despite running essentially the same blot many many times over the past year.

Any thoughts? Quite frustrating, as it has appeared suddenly with identical protocols/reagents as before.


texts: The insect pictured below just flown into my room. I live in Central Europe (Poland), it is about evening now. The thing is about 1,5 cm in length (not sure about this, I was too focused on driving it out). Its white stripe on abdomen seemed to be translucent. What is this insect?


texts: Cells with no apoptosis mechanism and their 'byproducts'

texts: If a culture or sample of cells is such they all have no apoptosis mechanisms yet they have not been at present determined to be cancerous ; given such a cell culture is there a way to determine by their byproducts or how they signal themselves or other cells that they have no 'working' apoptosis mechanisms?


texts: What do nerves have to do with feeling nervous?

texts:
I was thinking about how when people say: "Nerve cells don't regenerate" (which is, apparently, not true at least for some kinds of nerves) and "You're making me nervous" they might not refer to the same "nerves".

What makes a person "feel nervous"? Does it have anything to do with nervous system?

Bonus question: How did people come up with the thought that nerve cells don't regenerate?


texts: Must one autoclave LB medium after it has been made?

texts: Is it necessary to autoclave LB medium after it has been made?


texts: How can dehydrogenation steps in some biochemical pathways produce ATP?

texts:
Dehydrogenation reaction of alkanes is inherently endothermic as one removes two thermodynamically more stable C-H bonds and replaces it with one less stable C=C. Although the product is conjugated with the carbonyl group, this stabilization should be negligible, shouldn't it?
How comes then according to the scheme below, the result of this reaction are two high-potential electrons capable of forming ATP from ADP? Is the reaction concerted with some other not shown here? Or is the enzyme regenerated afterwards with some input of energy?


texts: Source for Specific Models of Birds' Habitat Suitability

texts:
This source gives a very detailed analysis of what habitats are best suited for many different species. However, this is a government funded project and, to the best of my knowledge, not published in a peer-reviewed paper. In addition, this project has officially been depreciated for 18 years.
There are 2 features of this project that are very attractive to my own project. First, each habitat is ranked as a value between 0 and 1. Second, it ranks 31 habitats, each with very precise differences (e.g. a conifer palustrine forest habitat is ranked separately from a deciduous palustrine forest). Compare this to other sources, such as the IUCN Red List which only says 'Yes' or 'No' to whether a species has been observed in a habitat and only tracks 18 habitats that are very broad groups (e.g. all forests are ranked together).
Can anyone direct me to a more modern and/or peer-reviewed source that has one or both of these benefits?


texts: No digested product bands, but markers are visible. What could be the reasons?

texts:
I had to digest my insert containing plasmid and another vector into which my insert has to be ligated, each with BamHI and NotI.

Upon digestion, I ran the gel to check for results. The digestion seemed to be ok the first time with reasonably good bands. Since I needed more concentration I ran the gel with the same reaction setup (30microL) for the second time.

Well 1 - 100bp marker

Well 2 - Insert in a vector (820 ng/microL, 3microL)

Well 3- Plasmid vector into which the insert has to be ligated (1000 ng/microL, 2microL)

The marker bands were faint while there were absolutely no bands in the other wells. What could be the reason for failure during the second run? I've performed the second time digestion in a span of 40 min after the first one.


texts: How much nucleoside triphosphate is required to form one peptide bond during protein synthesis?

texts:
I'm trying to find out how many molecules of nucleoside triphosphates (ATP, GTP, UTP and/or CTP) it takes to release enough energy to link two amino acid monomers together with a peptide bond, specifically during the process of mRNA translation.

I've tried to do some research online, but I could not find a reputable source that will say definitely how much energy is consumed in the process. The best answer I could find is formulated based on 'Molecular Biology of the Cell' 4th edition by Alberts B, Johnson A, Lewis J, et al., which is that at least one molecule of ATP is consumed for every peptide linkage. Is this correct?

I've also read on a science forum that the amount of ATP consumed during translation is different for every amino acid, but I could not find a reliable source to back up that claim. Is this true?


texts: Are phylogenetic tree construction algorithms any different than general clustering algorithms?

texts: I suspect the answer is no. But I don't know enough to be sure that that is the case. Of course phylogenetic tree construction uses biological knowledge, e.g special distance metrics, but does it brings anything new at the level of clustering agorithm (e.g hierarchical, neighbor-joining etc).


texts: What is the best food to eat at this type of day since it is so vey very late?

texts: Best food to eat? In this time of the day because it's late very soon to be


texts: How much of the jejunum is bypassed during gastric bypass?

texts: There is both long and short limb gastric bypass surgeries (along with several other variations on intestinal bypass procedures). How much of the jejunum is bypassed with a long-limb and short-limb gastric bypass?


texts: How the electrons from electrode play a role in stimulating the neuron?

texts: I am trying to understand how a neuron fires action potential after being stimulated via electrode (extracellular stimulation). GHK equation gives the membrane potential,which is -70 mV when neuron is at rest. When the membrane potential increases to -55 mV, it fires AP. But then an electrode gives electrons, which do not appear in the equation. Then how the electrons from electrode play a role in stimulating the neuron? Also,   is there a way to calculate how many electrons or how much current would be required to stimulate a  neuron?


texts: Does immunity to CRISPR proteins limit their effectiveness?

texts: The use of crisper-cas systems is currently applied to cells cultivated in vitro. As control of the ‘off target’ effects of Crispr improves and Crispr is used in vivo, why won’t the immune system neutralize it?


texts:
On a random forum, a member speculated that their cirrhosis was caused by wearing tight-fitting clothing such as a girdle or corset.  This leads me to the following question:

  Question: Can cirrhosis be caused by physical compression of the body?

The list of causes on Wikipedia does not include this.  However, this may just be because the list is incomplete.  Alternatively, it may be because physical compression is unlikely to contribute to cirrhosis.

A plausible mechanism that springs to my mind is that physical compression leads to the constriction of hepatic veins, arteries and/or their tributaries.  But I suspect the rib cage would provide significant protection against this (see below).


texts: small cocooned caterpillar found on bathroom door - what is this creature?

texts:
This larvae / moth has what seems to be a smooth gray cocoon which looks like a piece of cement. It can carry this cocoon with it as it crawls, and it can come out from both ends of this cocoon.
Would really be interested of knowing what this creature is and how it ended up in my bathroom.

Cheers!

As asked my location is Israel (Mediterranean climate)


texts: What happens to colloidal particles in a liquid medium? And how to stabilize it?

texts:
Definition

    Colloid is a dispresion of small particles of one material in another.

  Definition 2 (Wikipedia)

    A colloidal system consists of two separate phases: a dispersed phase (or internal phase) and a continuous phase (or dispersion medium) in which the colloid is dispersed. A colloidal system may be solid, liquid, or gas.

I am trying to answer problem 2:

  Question

  "Colloidal particles: What are colloidal systems, give an example, what happens to colloidal particles in a liquid medium. How to stabilize colloidal systems in a liquid medium."

My lecture slides mention this about gel: "a continuous network extending throughout the sample formed by association of colloidal particles or molecules in a liquid", "formed in concentrated polymer solutions" and "formed by association of sol-gel particles". Next lecture slides is about "liquid crystals", now I am confused -- not sure whether gel or "liquid crystals" is something to look here.


texts:
After looking at Cori Cycle (from wikipedia)

I have a question about how the lactate can be produced in ketosis. According to this article:

  in a low-glucose state, where the body senses that dietary glucose might not be coming anytime soon, peripheral insulin resistance is triggered. This prevents the muscles from taking up “precious” glucose that the brain requires. The brain’s sensitivity to insulin is preserved, allowing it to grab what glucose it needs from the paltry – but sufficient – levels available to it.

it seems that the glucose is not even transfered into muscle cells. In spite of this fact, the lactate is still somehow created during hard exercise even in full ketosis when ketones are present in the bloodstream. How is it possible?


texts: How Do White Blood Cells Learn? Or Do They?

texts: So I get the concept that a vaccine is a weakened form of a virus so that the body can "learn" to fight it and make a person immune to that disease, but how exactly does this learning take place? What learns? The white blood cells? Do they have their own database or something and do they go from cell to cell informing them of what they learned? I read that they only last around 5 to 7 days so that means there's constantly new white blood cells that also need this information for all diseases ever encountered. How does this work? Thanks!


texts: Fisher's Method to melt p-values for CpG sites annotated to the same gene?

texts: I have some data I am working with, and I am curious if I am able to combine p-values from a paired t-test for CpG sites in the genome using Fisher's Method to get one p-value for each unique gene. Linked here is the Wikipedia page for Fisher's Method. I understand that an assumption of the method used is that each individual p-value being combined must be independent. I'm relatively new to biostatistics, so I'm curious if using CpGs from the same gene would violate this assumption.


texts: Function of an VEGF inhibitor in the treatment of macular degeneration

texts:
I'm working on a short presentation of treatments of macular degeneration for a biomedical
optics seminar on macular degeneration.

Since I don't have any relevant medical or biological background (B.Eng. Electrical Engineering, now M.Sc. Biomedical Engineering w. a major in Biophysics) I need some help with
understanding the function of VEGF inhibitors, and how they work.

It doesn't need to go into all details as it is one of three treatments that I'm supposed to present, but enough to explain how it works, in about roughly 5 minutes.

Could anyone help me please?


texts: Why don't all bacteria have F-plasmids by now?

texts:
Some bacteria can undergo gene transfer by conjugation. Conjugation is a form of horizontal gene transfer, meaning from one (unrelated) bacterium to another (in contrast to vertical gene transfer, which is from predecessor bacterial cell to successor (daughter) cells). Conjugation is initiated when one bacterium has an F-plasmid (Fertility plasmid) and forms an F-pilus, connecting the F+ bacterium with an F- bacterium, initiating transfer of the F-plasmid.

Why is it that during evolution not all bacteria have acquired this F-plasmid?


texts: Do uerotelic organisms save roughly 3/4ths water compared to ammonotelic?

texts:
My analysis based on Daniel Atkinsons work, professor in biochemistry (see references below), is that ureotelism is saving 3/4ths water compared to ammonotelism. Is this correct? What do people here think? Here is my analysis: https://telegra.ph/Urea-and-uric-acid-as-adaptation-to-conserve-water-08-27.
Summary,

Land living animals therefore neutralize the bicarbonate by deprotonating the NH4+, by turning it into a much weaker base, urea (or uric acid in the phylogenetic clade birds are in. ) This forces the proton onto the bicarbonate instead, and the bicarbonate is excreted as CO2 gas, using no water. The nitrogen is also excreted at a lower cost (osmotically) than with ammonia. Urea has two nitrogens per molecule, so, half the cost osmotically, and the uric acid vector forms a non-soluble paste that has no osmotic water cost. The water saved by ureotelic animals (those excreting nitrogen as urea) is therefore 3/4th, ureotelism removes the osmotic cost of excretion for all bicarbonate (100%), and half the ammonia (50%), 100%*1/2 + 50%*1/2 = 75% of those end products from protein catabolism, i.e., only 1/4th water needed.

Reference
Atkinson, D. E., & Bourke, E. (1987). Metabolic aspects of the regulation of systemic pH. American Journal of Physiology-Renal Physiology, 252(6), F947–F956. https://doi.org/10.1152/ajprenal.1987.252.6.f947


texts: What problems do invasive species cause ?

texts: Why do we value species?  What is so bad about invasive species?  Why value biodiversity?


texts: I've never seen this kind of thing happen. What might trigger this??


texts: Are there genetic similarity between humans and pigs that don't exist in chimps?

texts:
Chimps are our closer relative.

Any genetic similarity between humans and chimps must exist on the common ancestor.

Pig branch out sooner. So, any genetic similarity between humans and pigs must be on common ancestor between humans and pigs. That must be on common ancestor between humans and chimps.

But chimps may evolve differently.

Hmmm... I am confused.

Actually is there any?


texts: I am studying viruses and I have a question about antiviral drug strategies. Why haven't researchers tried finding small molecule drugs that will bind to receptors on the host cell, thereby preventing viral attachment to the host cell? I feel as though with this strategy, virus resistance and mutation wouldn't be an issue. Thoughts?


texts: Deterministic model of lambda-phage lysis/lysogeny [MATLAB]

texts:
Project 1 Base:

Can someone please help me understand what I need from Project 1 Base code to do questions 1 and 2 from the first image? I'm new to MATLAB so a thorough explanation would be great.


texts: How does the tRNA recognise the first methionine during translation?

texts:
The process of translation starts with the initiator tRNA identifying the codon coding for methionine (AUG). However my textbook also says that there are various untranslated regions present on the mRNA. It was then this question had occurred to me.How does the tRNA actually differentiate between the regions that are ought to be coded and that are not ?One may say that translation always start with the methionine; but my question is different.For example,if the code is
5'...GUAUGCAUGAUC...3'
then when the tRNA arrives it reads from which of them? Does it leave the first two nucleotides and read it as AUG CAU GAU and so on or does it leave out the first six nucleotides and read it as AUG AUC and so on?


texts: Why "broad" instead of "large" cross-immunoreactivity?

texts: From the articles I read, expressions like "broad cross-immunoreactivity" pops up a lot. So, I was wondering, why "broad" is used here instead of large? Is there a specific reason?


texts: Coagulation of blood in small intestine due to trypsin

texts: Trypsin is secreted in the small intestine to convert proteins into dipeptides i.e. to carry out digestion of proteins. However, it is also a coagulating agent which coagulates blood by hydrolysing fibrinogen into fibrin. My question is, why doesn't the blood in the small intestine coagulate?


texts: Sampling of Species counting same member of species twice

texts:
As part of the biology class, we performed a sample on the number of red squirrels in a forest a few miles away from the classroom to estimate its population.

When we returned to analyse our data, we were discussing about the validity of our sample, and I was wondering whether the idea that the same member of the species being sampled twice may have an effect.

The book I was reading stated:

  a sampling procedure does not have to uniquely identify each member of a population to gain an idea of relative numbers.

I'm slightly confused as to why sampling the same member of the species twice is not something that affects the validity of our final estimate for population size.

Can someone explain why the passage in the book is correct?


texts: Does learning increase the number of neurons in the brain?

texts: I am attempting to understand neurogenesis related to learning. Does learning increase the number of neurons in the human brain? What would be some good scientific publications to read?


texts: How does HIV know to attack specific immune system cells?

texts:
I'm no biologist, but curious of the answer to which I could not find online.
How are Human Immunodeficiency viruses able to detect and distinguish immune system cells with a CD4 receptor on the surface from other cells in the body, in particular other immune system cells without the receptor?
If I have asked the question on the wrong platform, please inform me otherwise.
Thanks


texts: What is difference between light harvesting complex , reaction centre and photosystem

texts:
my book says light harvesting Complex are made up of hundred of pigment molecule bound to protein. Is photosystem has all the pigment (except one molecule of chlorophyll A )forming light harvesting complex also called and dinner this pigment help to make photosynthesis more efficient by observing different wavelength of light the single chlorophyll A molecule forms reaction centre.

These things are very confusing for me . I doesn't understand is light harvesting complex is present inside the photosystem or the photosystem is present inside the light harvesting complex.
Is reaction centre not a part of photosystem?


texts: The probability meaning of Covid variants

texts:
In the CDC webpage about Covid-19's variants the next sentence appears:

This (the United Kingdom) variant spreads more easily and quickly
than other variants.

In the ECDC paper about Covid-19's variants we can see that:

Several modeling studies corroborate the postulated increased
transmissibility of VOC 202012/01 (the scientific name of the United
Kingdom variant)

In a Nature article from last week written:

Several research groups suggested that B.1.1.7, which was first identified in the United Kingdom, was spreading more quickly than previous variants...

The probabilistic meaning of these sentences is not clear to me. Does this mean that the risk to be infected by the British variant is X times greater? E.g. if I was exposed to the British variant for 10 minutes, my chance of contracting is equal to the chance of contagion the original variant for 10 * X minutes?
Is there any nuance I miss?


texts: In humans what is the last metabolic process to cease after death?

texts: After death which of our body's metabolic processes will continue functioning for the longest?


texts: Can anyone identify the plant below? It's in a backyard in Pennsylvania, and the photo was taken today.


texts:
I tried to word my question so it will be given serious consideration. Rather than ask in Pets SE (which doesn't have the brightest questions or answers), I feel it's better suited for Biology SE - specifically animal behaviour.

Generally, the play behaviour of adult cats mimic their interaction with siblings when young, and as adults, their hunting behaviour. It's in regard to play mimicking hunting that my question likely fits best.

The stealthy stalk and pounce while playing is almost identical to what's used in actual hunting but with far more playful abandon. Leaping in the air to grab an escaping bird is seen when they leap and grab at a feathered toy that's whipped about. Tossing a small fuzzy weighted toy about mimics how they act when they've caught a mouse. The same with chasing after a small rolling ball.

But there's one play behaviour I can't find an equivalent. It's cats' fascination with a simple dangling string or cord. A person doesn't even need to move it. As long as it hangs and dangles near the ground, many cats can't resist playing with it. (I'm referring to an average active cat, not one of the unfortunate inbred creatures that do little.)

Does anyone know, or can think of, an equivalent natural behaviour that explains this? It's not similar to a mother cat flicking the tip of her tail as that involves tempting movement. But it's the closest thing I can think of. I've given this a lot of thought for a long time. Hopefully, someone else has wondered too and found a reason.

(No tags really fit my question so only one given.)


texts: Does the octopus have an anus? What does it look like?

texts:
Octopuses are cephalopods, which have separate anal and oral openings. Indeed, descriptions of the cephalopod GI tract clearly depict an anal opening.

However, I am very confused about how this applies to the octopus. I don't think I've ever seen the anus depicted - where is it? What does it look like? Does anything much come out?

My first instinct would be to simply do a google image search for this. Unfortunately, those results are flooded with unrelated hits (apparently the octopus is a popular motif for tattoos... in a certain part of the body).


texts: How long can an octopus survive out of the water?

texts: I saw videos of octopuses crawling on the ground and I was wondering how long an octopus can survive when out of the water? Does it depend on either its size (i.e., does a big octopus from deep sea survive longer than a tiny octopus) or the species?


texts: Biological implementation of convolutional neural networks

texts:
In computer science, 'convolutional neural networks' are used, that are meant to be inspired by biological network structures like found in the human brain visual cortex.

In the computer implementation, the 'convolution' means that any neuron of a certain 'layer' is linked with several spatial adjacent neurons in the previous layer. When those networks are trained, the 'weights', which are analog to synaptic strength, of all neurons of one layer have an equivalent local topology, and thus can be mapped between the neurons, and finally unified. This way, only one 'weight' is trained for all equivalent synapses on all neurons of an layer.

Is there any biological mechanism found that may sport this feature? My guess would be that the vision cortex is partly organised by self structuring not depending on neural activation to achieve low level vision processing. Otherwise, all neurons in one 'layer' would need a way to exchange information to synchronize their synaptic structure.

However, I guess that the human brain would have some mechanism of this kind, as it would provide for example the ability to learn the detection of certain visual patterns or events independent of their retinal position, without learning the detection individually for every image location.

Is any such mechanism known or how could it work?


texts: How small does a nanobot have to be to "swim through the brain" and access any neuron it wants to?

texts:
I read on this question What is in the space between neurons in a brain? that there is actually not much empty space in a brain. But my question is slightly different. Is there a visual demonstration I can see of approximately how "packed full of cells" the brain actually is?

Obviously there wouldn't be a fixed answer as it is likely a continuum where the bigger you get the harder it is to swim through without being blocked by all the neurons/synapses. But what is a good ballpark size to be to swim through with relative ease?


texts:
"The recent technology is peptide–MHC microarray or artificial antigen-presenting chip.
  In this technique, recombinant peptide–MHC complexes and co-stimulatory molecules are immobilized on a surface, and population of T cells is incubated with the microarray. The T cell spots act as artificial antigen-presenting cells containing a defined MHC-restricted peptides. The advantage of using peptide–MHC is that it can map MHC-restricted T cell epitope."

These few lines are from Chapter 3 of Immunoinformatics, De, Rajat K., Tomar, Namrata (Eds.).

What is recombinant peptide MHC? What is MHC restricted peptide? How did the advantage get derived?


texts: Which server to use for volume and accessible surface area calculation of proteins

texts:
I want to find the accessible surface area and the volume of a protein, giving PDB file as the input for the protein. I used two servers, 3vee and Vadar. For the PDB id, 1LTM, the websites are giving me different volume and surface area measures as follows:
3vee (vol: 50951 A^3; Surface area: 10837 A^2)
Vadar(vol: 40937.8 A^3; Surface area: 14680.6 A^2)
Can anyone tell me which server to use, which server is more accurate? If you know of any other server giving accurate result, please let me know that too.

Note: Both the publications are from Nucleic Acids Research, I guess I do not need to validate them. 3vee has been published in 2010 with citation of 164 and Vadar was published in 2003 with citations of 416. Is it okay if I take 3vee since it is the latest tool?


texts: How does an excessive amount of beta carotene affect skin colour?

texts:
How much is the daily need of beta carotene and how many carrots have to be eaten in order for one's skin to turn "orange".

I found 2-4 mg/ day as basic need, 30 mg daily over three weeks turns white skin orange. Is this correct? And what is the reason behind this?


texts:
Would non-GM crops such as Grains, Fruits, & Vegitables retain their non-GM make up if they were to be re-planted in soils that have been made entirely of composted GM plants and GM plant matter?
Or would the GM plant matter still retain those properties enough mutate the transplanted or planted crop?


texts: Where can I find a list of medical conditions and their incidence rates?

texts:
Where can I find a list of diseases and their incidence rates? I'm giving a presentation on Long QT Syndrome, which affects 1 in 2000 people, or 50 per 100,000. I'm trying to find other, more well-known diseases with a similar incidence to give my audience a frame of reference.

(Note: This is not a duplicate of this question. That question is asking about very rare diseases, and the answers to that question reflect that)


texts:
An answer on another SE site mentions that sugar "at a certain level acts as a preservative". I've always been taught that microorganisms eat sugar and expel acids, that is why sugary food are damaging to teeth. How is it that sugar acts as a preservative, then?

Googling the question I've found conflicting answers though I don't credit the sources as being especially reputable. What is the real reason that sugar can act as a preservative?


texts: How do baby birds get fed when they are only a day or two old?

texts: The eggs belonging to the robin on my porch hatched. The baby birds are very tiny, just lumps. They are not opening their mouth and cannot even seem to lift their heads. How do they get fed when they are so helpless?


texts: What does "genetic correlations" mean as opposed to just correlations?

texts:
I'm reading the paper "Large-scale GWAS reveals insights into the genetic architecture of same-sex sexual behavior". In Fig. 4 shows "Genetic correlations of same-sex sexual behavior with various preselected traits". This sentence confuses me. I understand that you could do a standard statistical analysis to find correlations between same-sex sexual behavior and various traits. What makes the way they are doing the correlations "genetic"?

(Note: This may be more of a statistics question than a bio question. Feel free to move it to a more relevant SE site.)


texts: Why are trichromat cone cells unable to sense ultraviolet and infrared radiation?

texts: I understand that cone cells vary in the color they sense, is this because of wavelength, frequency, something else, or a combination of the previous? I also understand that tetrachromats can see an extended spectrum of color because they have four as opposed to three (for trichromats) color channels, hence, I believe, an extended variation of cone cells.


texts: How can I determine the purity of cells isolated from rat brains if I cannot use FACS, Immunohistochemistry or SEM anaysis?

texts:
Please help.

I know how to isolate the different cells (astrocytes, other glial cells, neurons and synaptosomes) from brain tissue using a Ficoll-based separation but how do I determine the purity of the fractions that I have isolated if I cannot use immunological techniques, FACS or SEM analysis.


texts:
Could someone please clarify what is protein secondary structure:
https://en.wikipedia.org/wiki/Protein_secondary_structure

I believe I understand the primary structure, I am not sure what's the difference between secondary and tertiary structure. Tertiary structure seems to be 3d structure of a polypeptide but I am not at all clear about the secondary structure.


texts:
Do (some) birds ever fly in fog or clouds so that they would not be able to see either the ground or the sun? Assuming the visibility is good enough so they can see obstacles in time to avoid them.

If they do, how do they maintain straight flight?

Inner ear is inadequate in the air, because it can only sense the sum of gravity and acceleration, which is just the (reaction to) aerodynamic forces and those are always orthogonal to the wings. To an extent, it can also detect rotation, but this is not good enough to keep precision for minutes and hours in cloud. So how do birds know where is up?


texts:
Acuity of one's sight is rated on the 20/20 scale. An online search appeared to indicate there is no comparable 'standard' to rate olfactory acuity.

How is acuity of the olfactory system rated?


texts:
The testes (at least in human males) are vascular organs, the vascularization extending even o the interstitial spaces of the seminiferous tubules. The function of the scrotal sac, is to isolate the testes from the abdominal cavity, and provide a lower temperature ($1-2^\circ \text C$ lower than normal body temperature of $37^\circ \text C$).

  But since the blood is the main temperature-buffer maintaining the
  normal body temperature and the scrotal (testicular) tissues are
  considerably vascularized, why doesn't the blood flow raise the
  scrotal temperature to normal body temperature?

If the reason is the location of scrotum external to the abdomen, then all limbs and limb-extremities are located in the similar way (and in those cases, heat dissipation would be faster than in case of scrotum due to less surrounding insulation by thighs and clothes), and hence the temperature of all parts except the interior of the head and abdomen must be at considerably lower temperature? Is this the case?


texts: Why the length of UTR in the genomic sequence of gene X is too much longer than the same region in the corresponding Refseq mRNA sequences?

texts:
I'm browsing in the UCSC genome browser and found that the UTRs length of KIAA0040
gene in the genomic sequences is too much longer than the corresponding the Refseq mRNA sequence. In fact, the total length of Refseq mRNA sequence is 4,721 and the length of its genomic sequence is about 36,107bp, of which the length of CDS is just 300 bp. How to explain this event?
This gene has 4 transcript variant and I know something about that UTR can span multiple exons, but I'm not sure about it and would like to hear more from you.


texts: I am trying to find an ID guide that I can use to identify macroalgae. I specifically want to differentiate between Ulva species.


texts: Why can't you just take a vitamin? Why you need a healthy diet on top of that?

texts: From what I understand, your body needs certain amounts of vitamins and minerals to maintain health. Why can't we just take enough pills to obtain these vitamins and minerals?


texts: Can solitary animals show extroverts traits?

texts:
So far as it is known there are solitary animals and social animals.

Does introversion exist among nonhuman primates? says that there are introverts among social animals:

  Recent studies have identified extraversion/introversion in great apes, including chimpanzees, gorillas and orangutans. Chimps exhibiting greater solitary and reserved behaviors are considered more introverted, whereas those that are more playful and interactive fall on the extraverted side of the spectrum. Extraversion/introversion behaviors, such as sociability, have also been identified in species of monkeys.

Are there extroverts among solitary animals? I mean those who seek union with others although the vast majority of animals of their species are solitary?


texts: Constant or variable number of chiasmata during recombination?

texts: During recombination, is the number of chiasmata consistent for each gamete and are the chiasmata regions consistent within a single organism?


texts:
In this documentary about a lioness and a leopard the leopard is in heat for months.

https://www.youtube.com/watch?v=MGqmylkOuKw

Usually a big cat would be in heat for 5 days and then not in heat for 27 more days. Doesn't matter if it is a lion, tiger, cheetah, jaguar, or leopard, they have a very similar estrus cycle.

Why then is this leopard in heat for months until she finally becomes pregnant? The lioness is only in heat for 2 days because after 48 hours she becomes pregnant. In fact the lioness has 2 litters in the same period of time as the leopard has 1 litter.


texts: When evaluating methylation status at various CpG sites after sequencing, how much consideration should one give to random single base pair insertions and deletions. Suppose there is a CA dinucleotide; can we assume that the CA is native to the sequence or results from a G deletion especially when the latter is suspect once comparing to other sequences. Is there really a set standard sequence to compare it?


texts: Why do some mammals have incomplete orbits?

texts: I've noticed that a lot of carnivorous/omnivorous mammals (most, if not all the members of carnivora and some ancestral cetaceans), as well as some herbivores (marsupials), have incomplete orbits that merge into the temple near the zygomatic arch. I'm wondering what the evolutionary purpose of this is, as well as why we would lack them.


texts: Are there any methods to quantify H2O2 (hydrogen peroxide) which don't rely on horseradish peroxidase?

texts: I can't use HRP since my substrates interfere with it and I need a real-time method because I want to measure kinetic parameters of some oxidases.


texts:
Assume a pure tone (single frequency) is listen, lets say 2 kHz. If I understand correctly the temporal theory (aka timing theory), in a cochlea neuron the action potentials create a signal that will have one spike for each single tone cycle with the exception of some gaps due to the minimal interval between neuron triggers.

Volley theory extends previous model to a set of neurons. The union of triggers in all neurons of the set will have at least one spike per cycle (with few exceptions). In other words, the base frequency of the signal composed as the union of triggers of all neurons in the set will be the same frequency than the one of the incoming sound.

My question is, if in this model the trigger intervals is used to encode the sound frequency, and taken into account that usual models for neuron activity only take into account intervals between action potentials (all-or-none), how sound amplitude (power) of the sound is translated to the nerve signals. That is, the differences in the nerve activity caused by two tones of same frequency but different amplitudes/powers, assuming frequency/volley model.


texts: For how long viruses survive in non-air moisture environments?

texts:
On the Internet there are plenty of information that viruses don't live long after they were exposed to air, after they starting to dry out.
But it's hard to find an information on how long viruses can survive in wet non-alive environments at a room temperature like food, oils, soap.
I understand that it varies from virus to virus, but there may be maximal (for the most survivable ones) or average values.


texts: Can genetic recombination yield mutation depending on the new DNA that is incorporated into the genome? I would say yes because when something foreign comes in, the genome is bound to not function properly.


texts: How can the melting temperature of PCR primers be so far below the extension temperature?

texts:
Since our primer TM is lower than the extension temperature by design, (and often by a significant amount) shouldn't the primers be released from the template at extension temperatures?

Now, I have done PCR experiments and know they work. I just want to justify what's actually going on molecularly to be at peace. The only thing I can think of is that as the temperature ramps up to the extension temp, the polymerase has already begun adding nucleotides, thus raising the effective TM, preventing dissociation.


texts: If the electrical signals from all the various organs throughout the body eventually connect to the nerves in the spinal column traveling up to the brain, how does the brain differentiate the different signals.  Is the nerve in the spinal column like an electrical conduit with many wires inside?


texts:
Can you use indirect immounofluoresence to verify if a vaccine will work against a virus?

Using the vaccine antibodies against the virus, plus a second antibody with fluorophore that will join the first.


texts: What is this marmot-like animal (Tigray, Ethiopia)?

texts:
I was searching what are the animals I frequently saw in the north of Ethiopia. I took some bad quality pictures.

For me it looked like a large squirrel, local people called it a rat, and on the internet I find rock hyraxes are quite frequent in the region, but they appear not to have a long tail like the animals I saw, and they don't have the white lateral line


texts: Quantitative comparison of rate of energy output when burning carbs compared to fat

texts:
I'm studying scientific models of endurance exercise such as the one in a paper by Rapoport (see references below, popularization here). If I'm understanding properly, fat burning is in some sense slower than burning glycogen, but I'm confused about how to quantify "slower." I was thinking that it should be quantified in terms of the amount of oxygen consumed. House and Johnston (p. 107) say,

The metabolism of the sugars that come from carbohydrates is called glycolysis. It is a faster process (about twice as fast) than the metabolism of fats.

But I'm not sure if I'm putting this together correctly, because maybe here they mean something different by "slower." Glycolysis doesn't require oxygen, but I guess after glycolysis produces ATP, we use oxygen to burn the ATP.
Can anyone clarify the following?

Why does the human body produce a lower power output in aerobic, endurance exercise when burning fats rather than carbs?

If you want to quantify this relative slowness, is it correct to do it in terms of stoichimetry and oxygen consumption, or is there something else that makes it slower?

Is the factor of 2 something that is universal and can be made more precise (as I would expect if it's a stoichiometry thing), or is it more vaguely defined and dependent on the individual?

References
House and Johnston, Training for the new alpinism, Patagonia Books, 2014
Rapoport, Metabolic Factors Limiting Performance in Marathon Runners, PLoS Comput Biol. 2010 Oct; 6(10): e1000960, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2958805/


texts:
As I understand human love fatty food as they taste good because it has more energy which was good when we were primitive and food was scarce and unreliable,
Is there same urge for protein food too? it doesn't give much energy.


texts: What could the etymology of Phallodriline be?

texts: I'm reading about a series of gutless worms described in several papers as phallodrilines. A search in the World Register of Marine Species shows that there is a subfamily called "Phallodrilinae", but then, in at least one paper this term is used to collectively describe gutless worms in several taxa including Oligochaeta, Annelida, and Clitellata. Since they're also described as club-headed I'm assuming that "Phallo-" is from the Latin for penis, but what would be the rest?


texts: What species of short plant is this in Iran?

texts: Anyone knows the name of this Iranian local species?


texts:
Wiki says

  DNA is a molecule that carries most of the genetic instructions used
  in the growth, development, functioning and reproduction of all known
  living organisms and many viruses.

What bugs me is the "most" there, it implies some of the genetic instructions are elsewhere, but where?


texts: Why can dogs hyperventilate without consequences like humans?

texts: During the heat of summer, dogs usually breathes very fast, like 100 times per minute or more. If humans do so, we will experience an array of negative effects like dizziness, finger tingling or losing consciousness, by the results of blood alkalosis and reduced oxygen level. The question is, why don't our canine buddies seem to experience the same consequences?


texts: Why is there not an immune response to injected immunoglobulins?

texts:
When you inject immunoglobulins as a treatment for certain diseases, the immunoglobulins are a foreign substance.
I can appreciate that maybe the constant region would be similar to the hosts as it is from another human and these don't change a lot.
However, in the variable regions, wouldn't there be the possibility that the antigen receptor region could be the complement to the patient's own antibodies? Wouldn't this trigger an immune response and destroy the injected Ig's? Yet we seem to do this procedure, so why doesn't this process occur?


texts: Why don't the female lions in a pride help their male lion to protect their children from other males?

texts:
I watched a dozen of videos taping the fights between male lions; none of them involve female lions assisting in the fight. It is also known that the male lion who take-over the pride will kill all the under-age lions.
Why don't the female lions help their male lion such that their offspring won't be eliminated?
From an evolutionary perspective, the female lions will surely fight for their children as raising a new child is costly. Though they will most likely not fight to death. Even if a lioness does not have any child yet, her older sisters might already have a child so help defending the entire pride is the optimal strategy, although the younger sister might only contribute half of their strength comparing the older sister, as the child is not her direct offspring.


texts: Why is the coremata of Creatonotos gangis huge?

texts: This Australian moth has been some kind of curse image online due to its scent organs (coremata). It is inflated to attract mates. However, why does the coremata have to be inflated for it to work, and why does it have to be so big?


texts: What is the standard protocol for creating permanent stocks from freeze-dried bacteria?

texts: I've received freeze-dried bacteria that I intend to use for a study I'm doing on slime mold; however, I've never dealt with freeze-dried, only frozen, bacterial cells. After reconstituting these cells in 6mL media, is it alright to split this in to halves and place one aliquot into DMSO or glycerol to make a permanent stock right away? Or is it best to plate, isolate, suspend, grow, and then make a permanent stock?


texts: Clarification on the "orientation" of chromosomal rearrangements

texts:
I need some clarifications on the concept of "orientation" in case of chromosomal rearrangements.
Given a deletion event on a chromosome for example, is the resulting DNA at the breakpoint always in TH (Tail to Head) orientation? Do all duplications lead to HT orientation? And in case of translocations, inversions, etc..?

Can someone give a clear definition of "orientation", and make some examples?

Here some specific examples found in the Cosmic database:

CRC-3  large_intestine  NS  carcinoma  adenocarcinoma  intrachromosomal inversion  28066  0  2  53774826  53774826  +  2  53775947  53775947  +    21892161

CRC-3  large_intestine  NS  carcinoma  adenocarcinoma  intrachromosomal inversion  28072  0  2  60783417  60783417  -  2  60786447  60786447  -    21892161

0006_CRUK_PC_0006_T1_DNA  prostate  NS  carcinoma  adenocarcinoma  intrachromosomal inversion  113193  0  18  60375963  60375963  +  18  77010169  77010169  -      538

0006_CRUK_PC_0006_T1_DNA  prostate  NS  carcinoma  adenocarcinoma  intrachromosomal inversion  113314  0  7  153608258  153608258  -  7  153610727  153610727  +      538

As you can see, they have inversions having all of the possible strand orientations, '++','--','+-','-+'.
How is this even possible?! How to convert to H/T orientation in this case?

P.S. This is the description of the header of the data:

               HEADER[IDX] : IDX : DATA[IDX]
               Sample name :   0 : 0006_CRUK_PC_0006_T1_DNA
              Primary site :   1 : prostate
              Site subtype :   2 : NS
         Primary histology :   3 : carcinoma
         Histology subtype :   4 : adenocarcinoma
             Mutation Type :   5 : Interchromosomal unknown type
               Mutation ID :   6 : 113196
          Breakpoint Order :   7 : 0
         GRCh37 Chrom From :   8 : 6
  GRCh37 Location From min :   9 : 129148581
  GRCh37 Location From max :  10 : 129148581
        GRCh37 Strand From :  11 : -
           GRCh37 Chrom To :  12 : 7
    GRCh37 Location To min :  13 : 153610712
    GRCh37 Location To max :  14 : 153610712
          GRCh37 Strand To :  15 : -
     Non-templated ins seq :  16 :
                 Pubmed ID :  17 :
                  ID_STUDY :  18 : 538


texts:
I have run a gradient PCR.. and band 6 after the ladder is clearly the brightest. But all bands appear below the ladder. What does that mean? It is extracted mDNA that was loaded.

Thank you in advance!


texts:
If I have a mutated colony containing the fusion protein, mCherry instead of the stop codon TAA, and an unmutated colony which does not contain the protein. Why will the PCR products of the two colonies have the same size?

I thought that since the mutated colony contains the protein instead of the stop codon, this would cause this product to be larger in size than the unmutated product. However, from experimental data it shows that both products are of same size. Could someone please explain why this is?

Thank you!


texts: For which taxonomic levels are xylotomical, embryological, and palynological evidence each most useful in determining species relationships?

texts:
From the 2010 USABO Semi:

  In plant systematics, three
  lines of evidence may be useful in determining relationships; xylotomical (wood anatomy),
  embryological and palynological. Match these three with the level for which they are most
  useful.

The options for the levels were order, family, and genus. The answers matched xylotomy to genus, embryology to order and family, and palynological to genus, but if anybody could provide some examples to explain that would be great. Thanks!


texts: Do bugs love light bulbs because they resemble the stars or is it the sun? How do they sense the bulb? What is the purpose of this "brightophilia" that has evolved in insects?


texts: Why structures of many proteins are still unknown?

texts:
https://www.learner.org/courses/biology/textbook/proteo/proteo_3.html
Despite advances in techniques for determining protein structure, the structures of many proteins are still unknown...

My question is why? We have many researchers all over the world. We know what our 3 billion DNA is. The governments invest billions of money into medical research. We should have sufficient human resources and technology.
What's stopping us determining structure for all proteins? We need more money? We need more people? We need better technology?


texts: DNA content in plant seeds vs. fruit flesh

texts:
Is there a publication comparing DNA yield and/or PCR-amplifiability after extraction from fruit flesh (like apples, oranges, cherries etc) in comparison to seeds of the same fruits?

I would prefer a reference, but your unpublished experience is also interesting to me.


texts: Why do cockroaches burst from soapy water?

texts:
(careful, disturbing!)

I was experimenting with some stray cockroaches that ended up falling in my bath tub overnight (there is currently an infestation undergoing in my apartment building) and I found out that they are very easily killed by simply soaking them in soapy water.

I read that soap blocks some pores in insects' bodies which leads to suffocation, which appears to be the cause of death for my test cockroaches. But what I don't get is why about a half of them died with their innards bursting from their tail end. The water wasn't too hot to make them boil. Is it that they suffocate so hard that attempting to breathe they blow out their insides? Or is it the soap's reaction with the cockroach's bodily materials? Or is something else causing this?

I remember watching a documentary on injecting various insects with hydrogen peroxide which caused much more dramatic explosions, but it's not like I was injecting cockroaches, I just sprinkled them with soap water.


texts: Melting point of animal fat and plant fat

texts: I notice in daily life that animal fat typically has a higher melting point than plant fat does. I wonder the reason why this happens. What exactly contributes to this difference? Is it because of the difference between molecular structure? I understand that substances have different melting point because the intermolecular forces are different. But how does intermolecular force vary between animal fat and plant fat. Is it possible for any animal fat to have lower melting point than plant fat?


texts: What is immunosuppression? Why would one use it?

texts:
What is immunosuppression? I know it is used in cancer patients, but why would one want to suppress the immune system?

Do homeopathic physicians ever use immunosuppression, or do only allopathic doctors practice this?


texts: What metric(s) is a good proxy for relatedness?

texts: In attempting to seed a simulation, where an individual foregoes resources that go r to same-type individuals and (1-r) to all members (including same-type individuals).  What commonly used metrics are a good proxy for r in this sense?  In other words, if I am seeing a simulation to replicate the parameters of the mean population for, for example, a zebra finch or a human or a house mouse, and I am looking in empirical reports of these species and r does not appear, are there other metrics that are convertible?


texts: How quickly are plants able to sense changes in light intensity?

texts:
Evidently due to the process of photosynthesis, plants are able to "sense" light (as demonstrated by the phototropic response). My question is, how quickly are plants able to perceive changes in light intensity?
I.e. if there is a strong light shining on a plant, and at t=0 the light is switched off, is there some delay τd before the plant exhibits a response to the change in light intensity?


texts: Why is sexual reproduction so much more common than asexual (in macroscopic organisms)? Fundamentally, what makes it better?

texts:
I'm experimenting with an evolutionary method of creating a neural network. I use an asexual approach, but I've seen others use sexual approaches.

So I'm interesting in learning what's better about sexual reproduction as apposed to asexual, and biology is probably the best way to approach that question. So, why is sexual reproduction so much more common than asexual (in macroscopic organisms)? Fundamentally, what makes it better?

I'm struggling to understand what the combination of two gene sets does that couldn't be achieved by mutations to a child of asexual reproduction.


texts:
This website here stating video of New born baby walking breaking the internet.

How can just new born baby can walk ?


texts:
I'm curious if HeLa cells are intrinsically poisonous or dangerous to ingest.

My understanding is that some of the contamination in HeLa cells such as HPVs are not readily expressed.

I have no plans to do so, but I'm trying to understand why they might or might not be.


texts: Understanding different genetic terminology - Genotype vs SNP

texts:
I recently came across a study that refereed to variations in genes like this:

IGF1 (CA)19/(CA)19, IGF1(CA)19/X, IGF1 X/X

(From this study: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3274549/)

I wanted to know, as a member of 23andme, how I could check these "markers" (?) against the SNP's listed in 23andme.

I would be very grateful for any help.

Thanks.


texts:
Could you please help me identify this plant. I think it grew from some seeds we brought from Cuba (I might be mistaken though).

The plant in the picture is about 1.5 years old; it stands about 50 cm/20 in. tall. The leaf shown seems pretty large compared to the plant height, it's about 20 cm/8 in. long.

Leafs though appear shiny are rough to the touch on both sides, like very fine sandpaper.


texts:
Observe: In some rows (Order, Family), the third column reveals a discerning physical characteristic or body type (Elongate, Slender).

What are the discerning characteristics, missing from the other rows (Superfamily, Subfamily, Genus, Species)?

Basically I want this knowledge so I can work towards being able to separate, categorize (catalogue) and/or identify new or unknown species, etc.

Imagery

Exhibit A

Entomobrya unostrigata
(aka. Cotton Springtail)

Taxonomy

Domain      | Eukaryota        | (Eukaryotes)
Kingdom     | Animalia         | (Animals)
Phylum      | Arthropoda       | (Arthropods)
Subphylum   | Hexapoda         | (Hexapods)
Class       | Collembola       | (Springtails)
Order       | Entomobryomorpha | (Elongate)
Superfamily | Entomobryoidea   |
Family      | Entomobryidae    | (Slender)
Subfamily   | Entomobryinae    |
Genus       | Entomobrya       |
Species     | Unostrigata      |

Sources:
Image; photographed by myself. Text; transcribed from my own hand-written notes. Most likely (originally) gleaned and adapted from publicly available, online information. It may contain errors or inaccuracies.

Resources: Check out Bugguide.net and Collembola.org.

Reprise

Okay, the question has been put on hold, preventing answers from being posted (very irritating and obstructionist policy for those seeking answers, I might add). So I will attempt to clarify.

Exhibit B

Orchesella cincta

Exhibit C

Willowsia nigromaculata

Exhibit D

Entomobrya multifasciata

Exhibit E

Seira bipunctata

The diversity of these specimens; span not only multiple species, but multiple genera. Yet, despite the fact that they each exhibit relatively distinctive combinations of patterns and colours across their cuticle (epidermis, surface epithelium), setae, scales, etc. they all look pretty much identical.

This seems to be the equivalent of declaring a homo sapiens of African descent; a different species to a homo sapiens of Irish descent, on account of their superficial aesthetic differences (most notably regarding melanin; the pigments that determine the colours of a human's skin, hair[s], and iride[s] (eye[s]), and so on). Which, at first seems absurd. But for those of you who disagree, observe the differences between (for instance): Exhibit X vs Exhibit B & Exhibit Y vs Exhibit E. Similar variations between individuals of the same species are not uncommon in the least.

Thus, my question: What are the discerning taxonomical differences between various species and genera of the Arthropoda known as Collembola (aka Springtails)?

Exhibit X

Orchesella cincta

Exhibit Y

Seira bipunctata


texts: Why does protein folding not depend on the order in which it is synthesized?

texts:
I read an article recently, written by researcher from Department of Biochemistry, University of Washington, which stated that:

  Similarly, success in de novo protein design bears on the question I get after every talk about the importance of the order of chain synthesis on the ribosome to protein folding; computational protein design calculations completely ignore the order of synthesis which hence cannot be critical to protein folding.

I was wondering, how could it be that the form that the protein is folded to, does not have anything to do with the amino-acid sequence that constitute this protein? What I mean, is in case I look at mirror image of a protein, would it fold the same? if I consider for example the sequencers: ser-gly-ala-glu-pro-asp and asp-pro-glu-ala-gly-ser, will they both fold the same? (I think those are d-protein and it's l-protein counterpart)

Can anyone provide evidence that this is, in fact, so. Or do I misunderstand the section quoted?

link to the paper: sci-hub.tw/10.1002/pro.3588


texts:
I have the two differential equations:

$$\frac{dN_1}{dt} = N_1(2 - N_1 - 2N_2)$$
$$\frac{dN_2}{dt} = N_2(3 - N_2 - 3N_1).$$

I worked out the equilibrium points to be at $N_1 = 0, \frac{4}{5}$ and $N_2 = 0, \frac{3}{5}$. I then calculated all the Jacobi matrices and worked out the eigenvalues (and eigenvectors). I now have to classify these equilibria. How do I do that? Is there a set of rules I follow to classify them?

Also, the next part says:

  Sketch the phase portrait of this system in the biologically sensible region: draw the the null- clines of the system and determine the crude directions of trajectories in parts of the phase plane cut by the null clines, designate the equilibria in the phase plane, and sketch a few typical trajectories.

I can do the null - clines and I think once I have found out the stability of the equilibria, I can determine the directions of trajectories of the bits cut by the null -cline, but how would I sketch the trajectories of the equilibria?


texts:
I was hoping to get some clarification on how drug response data (i.e. IC50) are presented. On publicly available datasets like Genomics of Drug Sensitivity in Cancer, area under the curve (AUC) values are also presented alongside IC50 values. How are these AUC values for a particular drug/cell line calculated and are they correlated with the IC50 values?  If I want to compare the potency and efficacy of many drugs for a cell line (i.e. rank the drugs from highest potentcy/efficacy to lowest) should I use the AUC or IC50 values?

Any help would be greatly appreciated!


texts:
I'm trying to figure out whether it is better for the plant to reproduce by planting its whole fruits with seeds inside them, or picking the seeds out and planting them without the fruit. In my case it's chili pepper, but I'm also interested in other plants that reproduce through fruits.

I heard that the whole fruit concept is about providing the seeds with some energy in form of their shell (the fruit) to give them a head start in terms of initial growth into a seedling. Is that true? Do all seeds benefit from growing from inside its fruit, or is it not very significant?


texts: Why do humans have irregular teeth and impacting wisdom teeth?

texts:
Imagine that horses, dogs, bears, and gorillas had teeth as unreliable as humans do, The interruption in behaviour and stress brought by teeth would cause them to be more prone to sinus infections, jaw abscesses, and general poor performance.

The stress from cavities and wisdom teeth growing sideways would affect their survival rates.

Humans have evolved slow maturation times, including teeth, have shortened jaws with compressed teeth, and errored, unvariable, DNA from inbreeding after near extinction 100k years ago (lake toba caldera) which makes us biologically quirky and unreliable.

Why does our jaw have to be so short that we could live with impacting wisdom teeth? because it places strain on the neck to have a long jaw?

Why didnt face infections and tooth misalignment cause humans to select each other strongly with straight teeth?

Are wonky teeth a feature of cold climates, where people dont have so much fruit, and in hot countries, ethnicities have straigher teeth?


texts: Do I have to use sucrose to induce a lac promoter?

texts:
I'd like to optimize the expression of a Fab fragment in Escherichia coli.
For induction of the lac promoter on the pAK400 vector I use IPTG and sucrose. Do I optimize the expression in case I would just add IPTG?


texts: Can toilet or sewage aerosol transfer eggs of human parasites?

texts:
Flushing a toilet produces hundreds of thousands of tiny droplets containing viruses and bacteria (source).
Additionally vomit and feces of infected people sometimes contain extremely high concentrations of viruses or bacteria.
Similarly, sewage water produces droplets and was proposed as the transmission mode in the SARS outbreak in Hong Kong in 2003.

Apart from viruses and bacteria being transferred through toilet and sewage aerosol, can human parasite eggs be transferred as well given the droplet size?
I'm interested in the aerosol, not the relatively large droplets that land on the toilet itself.


texts: The principle of homeostasis in biology says that living organisms try to maintain some sort of equilibrium. Doing that requires the use of feedback mechanisms to regulate things like temperature, salinity, etc. Are there any feedback mechanisms the body uses to regulate the output of the skin's sebaceous glands? If so, what are they, and on what timescale do they operate?


texts:
In a former question, as a side question, I asked a clarification about the "Spandrels" paper. Being not a biologist, it was the first time I encoutered it.

Subsequently I tried to collect some information, because I read that the paper is debated and deemed "wrong" by at least a part of the community.

Despite my efforts I have not fully grasped what the issue is:

is the incorrect reference to the architectural element? (i.e., the paper is wrong because it uses a not fully agreeable comparison)
are some (or all) the claims in it wrong? if yes, are there any suggested reading to understand why?

I ask specifically because the first reference I encountered points to Dawkins, and I would like to understand if this paper is a mere pawn in the big "gradualists versus punctuationists" debate or if it has merits on his own.


texts:
Please help me identify this tree and its fruits that have sweet taste and very small soft seeds:

It grows in the Mediterranean region.


texts: How do DNA, enzymes, hormones etc. reach their proper cellular locations?

texts:
I was trying to understand DNA transcription from this chapter, and there seems to be no explanation on how exactly the proteins, enzymes and other molecules manage to find each other inside the cell. How do they get attracted to each other in order to start reactions or transcriptions?

Same way, when the body secretes a Follicle Stimulating Hormone, how does it reach the follicle instead of losing its way in the bloodstream and ending up in a woman's feet or getting excreted out of the body? In minute 20 of this video, the person speaks of how medicines are first "sent" to the liver, but this MIT article says that medicines go all over the body.

At least for a wound it's an understandable process. An artery of vein is severed and any blood that was supposed to flow through it now can't, so there's an accumulation of white blood cells and antibodies there which can disable any intruders (though I'm sure they wouldn't be able to see an intruder and move toward it, but rather just probabilistically bump onto the intruder), and if the intruder enters the bloodstream it would probabilistically bump into other WBC's or antibodies and get killed. Else there's always fever to kill them.

Similarly, one study says sperm use heat sensors to find the egg. Another assumes it's a chemical signal.

I went through the information about cell signalling, signal transduction and allosteric regulation, but although they speak about receptors, they don't explain how the chemicals manage to find those receptors. It's like saying that I entered a huge college campus and found the secret place where my friends were meeting and they receive me when I met them, but there's no explanation on how I knew which way to travel in that huge campus to reach my friends. Given how accurately DNA transcription happens and how viruses know to shed their shell on entering a cell and make use of the cell's transcription mechanism, I believe there has to be a specific process through which these molecules "know" how to find these receptors. Is there any research that could throw light on it?


texts: Is it possible to isolate and analyse intermediates of protein folding?

texts:
I would like to know if there is an assay which could allow us to analyse a protein before it has assumed its 3D functional form.
While studying structural biology, I only came to know the forces that stabilize the structure, but not the gap between the original random coil and the protein in its native form.


texts:
I am trying to understand the analysis generated by STRING.
In analysis for biological processes table, there is a column titled "count in gene set." This gives a value for example "68 of 498".

What does this refer to?


texts: Why do the calicheamicins bind to DNA at the minor, rather than the major, groove?

texts:
I am trying to understand why some drugs bind only to the minor groove and not to the major groove. More specifically, I am interested in calicheamicins.

  They target DNA and cause strand scission. Calicheamicins bind with
  DNA in the minor groove, wherein they then undergo a reaction
  analogous to the Bergman cyclization to generate a diradical species.
  This diradical, 1,4-didehydrobenzene, then abstracts hydrogen atoms
  from the deoxyribose (sugar) backbone of DNA, which ultimately leads
  to strand scission.[7] The specificity of binding of calicheamicin to
  the minor groove of DNA has been demonstrated.


texts: I fixate bacteria on titanium coins for 1 h i 2.5 % Gluaraldehyde. Then wash 3 times in ddH2O. Then 10 min in each solution of Ethanol 10 %, 30 %, 50 %, 70 % 90%, 100%. Finally soaking in HMDS in 15 min, then take out the HMDS and let dry overnight. Sputtercoat with Ag/Pd. I know I have bacteria on the titanium surface from the beginning but I dont see anything in SEM. What am I doing wrong?


texts: Do we as humans develop tolerance to deodorants or antiperspirants? In particular when they contain isobutane, isopropyl, palmitate, isododecane, dimethicone, coconut oil, magnesium oxide, allantoin, dimethiconol, disteardimonium hectorite, propylene carbonate.


texts:
I have read many articles about how the brain is the most power-hungry organ in any living complex organism, requiring about 70% of it's oxygen supplies in the resting state.

Since the usual medium of oxygen delivery is through respiration, this should mean that a lot of blood is supplied to (and hence present in) the brain.

Why then is the color of the brain almost always white? There is usually a little red tainting on the exterior and that's it, you can see the interior is still white. Should it not be red? Presuming that for a higher surface area to volume ratio, most of the brain cells are in direct contact with the bloodstream.


texts: Why do the "most sensitive photoreceptors" of insects consume so much energy it exerts evolutionary pressure to minimize receptor number?

texts:
The video Wireless Steerable Vision for Live Insects and Insect-scale Robots from the University of Washington's Paul G. Allen School of Computer Science begins with the following:

Vision is an important sensory input for many insects, but their most sensitive photoreceptors can consume significant amounts of energy.  This has led many insects to develop high visual acuity in only small retinal regions and evolve instead to move their visual systems through head motion.

The robot mimics this by articulating a narrow field of view camera with a low-energy actuator.
Question: Why do insects' "most sensitive photoreceptors... consume significant amounts of energy" What is it about the most sensitive photoreceptors that consumes so much more energy than the less sensitive photoreceptors that it would exert evolutionary pressure to minimize their number?
See also (potentially helpful):

Science Robotics: Wireless steerable vision for live insects and insect-scale robots
UW News: A GoPro for beetles: Researchers create a robotic camera backpack for insects
BBC: Beetle-mounted camera streams insect adventures
How much energy does a small spider expend per day just waiting for its web to vibrate?


texts: How to determine externally that a whale is a mammal?

texts: Mammals have external qualifying characteristics like body hair, ear pinna, etc. But a whale has none of that. So, can it be identified as a mammal just by external observations?


texts: What is the reason for fear induced defecation?

texts:
I started to handle mice for my job and noticed that they tend to defecate and/or urinate when they are scared. The fear is induced by me, because I need a long time (due to inexperience) to grab the mice and then move them from one cage to a new one. My question is why?

I tried to look up literature for this behavior and there are different fear behaviors for different animals some shake in fear, some play dead but I could not find something for fear induced defecation. Therefore my question: What is the reason behind the "Fear induced defecation"?

I am especially interested into the neuroscience pathway behind it.


texts: Productive turnover and generations in the fruit fly

texts:
I was reading about the Lenski experiments on the evolution of E. coli bacterium and Dr. Elders's experiments on the evolution of the guppy.
These two experiments absolutely fascinated me, and seemed to happen relatively quickly by evolutionary standards. It was mentioned in the book that the fruit fly's productive turnover time is especially short.

I am extremely interested and would very much like to conduct an experiment into the evolution of the fruit fly, in much the same way as the Lenski and Elder experiments when I'm older.

Just so I can get a good idea, as I can find nothing on the internet, how long would it take for the fruit fly to get through, say, 10 generations?

Also, what would be the best way to go about beginning an experiment like this? Would there be certain people to contact? Would you need certain qualifications?


texts: Immediate cause of death due to dehydration

texts:
When we don't drink we get dehydrated and after some time we die. What is the cause of death on the lowest level?

I would assume the dielectric properties around/in the heart tissue get imbalanced and the heart stops beating.

Then lack of oxygen in the brain. Then...?


texts: What are some useful physical information of a protein?

texts: Beside energy and heat, I don't know any useful physical information of a protein. Can you help me list some of it. Somethings like Fourier-transform infrared spectroscopy to provide protein structure aren't what I'm looking for.


texts: What is the name of this brown, "flat hat", fungus?

texts:
I've seen this in October 2016 on Corsica (Island of France):

See https://commons.wikimedia.org/wiki/File:Gr-20-petra-piana-to-onda-08.jpg for more images and higher resolutions.


texts: Is the heterotroph hypothesis universally accepted?

texts:
I was wondering whether there are hypotheses that take a different approach that is contrary to the heterotroph hypothesis.
The heterotroph hypothesis states that autotrophs evolved from heterotrophs because of the lack of food.
Is this issue still debated by scientists or is the heterotroph universally accepted?


texts: totaling OTU from 2 or more observations and assign to new observation in OTU table from qiime

texts:
I am new to microbiome processing pipeline but I want to ask, How do I combine two observations and assign it to a new single observation in the OTU table resulted from QIIME.

Here is the situation. I am doing river microbiome analysis. I have water sample named A-P, P for particle-attached sample and A for its and A-F for free-living sample for the same site. They are just different in the filter size being used.

I extracted the DNA, sequenced, and processed the raw reads separately using QIIME for all the 110 samples. But now, I am doing analysis on "R" and i need to combine A-F and A-P as one observation, namely only A. It seems simple to do on "R" for only one observation. But, I have 110 observations needed to be merged to 55. Are there any simple ways doing that without doing it one by one either in "R" or QIIME

Thanks,
Bob Adyari


texts: Why do beta-1 and beta-2 adrenergic receptors result in two completely different effects (though both use Gs pathway)?

texts:
$\beta_2$ adrenergic Receptors are $G_s$-coupled 7-TM proteins. Considering that $G_s$ , by activation increases $[\text{cAMP}]_\text{cytosol}$ which inhibits MLCK of smooth muscles (and causes relaxation as in bronchial smooth muscles).
But at the same time, in cardiac myocytes ($\beta_1$), $G_s$ activation activates PK-A (through cAMP) which in-turn activates L-type $\ce{Ca^{2+}}$ channels. Thus there is prolonged plateau phase and positive inotropic and chronotropic effect.
I think these two results are contradictory. Why and how are these two seemingly completely opposite effects mediated through similar signal transduction pathways?

Madamanchi A. Beta-adrenergic receptor signaling in cardiac function
and heart failure. Mcgill J Med. 2007;10(2):99-104.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2323471/


texts: Do HEK293T cells express sufficient endogenous G-Proteins for calcium imaging?

texts: I want to transfect different GPCRs to HEK cells and then do calcium imaging. I was wondering if the endogenous expression levels of Gq are high enough.


texts:
According to the article How long do viruses live on surfaces: Plastic, stainless steel, fabric, and more:

  With fabrics, it's unclear how long viruses can last. But generally, they tend to last for a shorter amount of time on fabric compared to hard surfaces like stainless steel, according to the Mayo Clinic.

Can someone kindly explain why this is so?

What is it about fabrics that decreases virus viability?

I would like to point out here that in many cultures our ancestors had figured it out empirically.  In North India, where I hail from, many old people will eat bread, snacks etc. from a cloth (especially a woolen fabric) if their hands are dirty.  The simplistic explanation given is that this type of fabric "stays pure".


texts:
By "children" I mean young people at the age of 10 or lower.

I know that the adult brain cannot restore brain cells, but what about children? I mean, the brain must develop from a few cells to a 90 billion cells somehow, when do we lose this ability?

I'm also interested in cases when a child gets hit into the head (concussion). Can the damage  be fixed over time?


texts: Why do cells in meristematic tissues lack vacuoles?

texts:
Cells located in meristematic cells in plants lack vacuoles. However, this contradicts with the fact that plant cells have large vacuoles to store water and keep the plant in an upright position. I would also like to add that meristematic tissues are generally found in roots and stems of plants. Finally, I would like to ask why do meristems lack vacuoles?
Sources

Turgor pressure exerted by the vacuole is also essential in supporting plants in an upright position: Wikipedia

Apical mertisem is present at the growing tips of stems and roots and increases the length of the stem and the root. The girth of the stem or root increases due to lateral mertisem (cambium): Science for Class 9 by National Council of Educational Research & Training, page number 69

Cells of meristematic tissue are very active, they have dense cytoplasm, thin cellulose walls and prominent nuclei. They lack vacuoles: Science for Class 9 by National Council of Educational Research & Training, page number 70


texts: When doing minipreps, do "good" plasmids produce more DNA than "bad" plasmids?

texts:
I've been doing minipreps for close to 10 years using the standard qiagen kits and DH5a e. coli. I typically do 24 minipreps at a time and then identify the good plasmids by enzyme digestion, PCR, sequencing, etc. Something I've noticed is that the good plasmids often seemed to have higher DNA concentrations than the bad plasmids. I thought it was just superstition, but I looked back at a couple of recent miniprep batches and did statistics, and found that the good plasmids had a statistically significantly higher amount of DNA. I don't see this pattern all the time, but I have seen it when using InFusion based cloning and traditional restriction enzyme based cloning. I don't have access to all of my miniprep data, so I can't check everything for statistical significance.

So, why would "good" plasmids have better yields of DNA than "bad" plasmids? Has anyone else noticed this pattern?

As far as I knew, as long as the plasmid carried a working antibiotic resistance gene and the bacteria could replicate it efficiently, then the plasmid should be ok. Could the bad plasmids have been cases where the bacteria manages to ligate the vector backbone together but creates a sequence that doesn't replicate well? Could it be a timing issue, where the bad plasmid doesn't start replicating until later, so that the bacterial growth is delayed? I have not weighed the bacterial pellets, so I can't say anything about bacterial growth vs plasmid yield.


texts: Base-stacking interactions versus hydrogen bonds

texts:
Is it correct that the hyperchromic shift in DNA is a result of the disruption of the base-pairing hydrogen bonds, but the actual denaturation of dsDNA has more to do with the base-stacking interactions? Why does separating the strands have any effect on the stacking of the bases? Why wouldn't the bases in ssDNA still experience stacking interactions?

I really appreciate any help with this. Thanks!


texts: What flying insect is this? Resembles Wasp / Crane Fly / Moth?

texts:
What insect is this?

Found this in southern Bangalore, India. Looked dangerous, flew really slowly with its body upright and legs spread out and landed on a wall.

Size: about 1.5 inches tall, 1.5 inches wide, when spread.

These photos are zoomed in and rather dull colored, but the actual color was a bright orange, like #FF9050 and dark black.


texts: Can some prokaryotic cells be larger than eukaryotic cells?

texts: Can the sizes overlap in some bacterial species? My science teacher claims so. My research says the opposite. Can someone confirm?


texts: Why is peanut allergy often more dangerous then other allergies?

texts:
From reading public media I have the impression that while peanut allergy is not more common then pollen allergies, peanut allergy is often more problematic and sometimes even deadly.

The most common cause of food-induced anaphylaxis, peanuts, account
for 80 percent of such fatal or near-fatal allergic reactions.
Source

Why is peanut allergy so much more deadly then other allergies?
Is peanut allergy more deadly and if so, why is it more deadly?


texts: Is there a name for this phenomenon described in "Phylogenies and the Comparative Method"?

texts: The figures below are from Felsenstein's paper "Phylogenies and the Comparative Method". I was wondering if there was a specific name for this effect where there is an apparant correlation that is actually the result of the data being structured into two separate groups, where there is no correlation within groups but an apparent correlation between groups. "Phylogenetic non-independence" doesn't seem specific enough.


texts: DNA test to prove that two grand-grand-children descend from same grand-grandparents

texts: Can DNA test prove that two persons descend from same great-grandparents (or test where one great-grandchild and grand-child are tested)?


texts: How are mitochondrial diseases like MERRF inherited?

texts: I am doing a project on the disorder MERRF in Mitochondrial DNA. I have to make a pedigree and explain how it is transferred on from generation to generation. I know that it is inherited maternally, but I am confused about how it is inherited. Would it be inherited inherited like autosomal DNA in a Mendelian fashion? If so, would this gene be dominant or recessive? Or would the children just automatically inherit whatever gene their mothers have? Also, how would the genotypes for Mitochondrial DNA be displayed? Any other useful information on Mitochondrial DNA or MERRF would also greatly appreciated. Thanks.


texts: Found in southwest Michigan.  It appears to have fallen from a nest.


texts: Howthe body differentiate between foreign and native protein? How does it know when to create an immune response?

texts:
How the body differentiate between a foreign and a native protein?
Suppose there is a bacteria, it has lot's protein on its membrane, with specific structures. How does our body know it's the foreign protein? How does it know, the particular configuration is native or foreign?


texts: Examples of striking/pedagogic large dataset analysis in biology

texts:
This question belongs in "Cross-Validated" as well as "Biology"

I am looking for example datasets that I could use both for teaching and for my personal training, that would be good examples of very successful applications of in silico data analysis tools.

I am interested in tools like: k-means or hierachical clustering, principal component analysis, generalized linear models, or basic machine learning like class discovery & prediction.

Of course, if the data is available, that would be even better, but a simple figure in a paper would work as well.

What I mean by good is "fairly unambiguous and demonstrative", ie. the results could be, for example, a dichotomy of the dataset into two or three groups that make sense from a biological point of view (e.g. different tissues of the same organ, different times in cell development...).

A good example would be, for example, this figure:

(From Handschuh et al, Int J Oncol (2017) Copyright Spandidos Publications)

Rows are genes (microarray expression analysis) and columns are healthy (HV) or cancer patients (AML); clustering makes two large clusters appear.

It is a really good example because we can easily check that the two clusters match the two types of patient samples, which makes this clustering a good, pedagogic case study.

In other words I am looking for striking examples of how the visualized data makes perfect sense, if properly analyzed.


texts: Where did H2 come from at pyruvate oxidation?

texts:
After pyruvate oxidation, H2 come out by pyruvate dehydrogenase. Does this mean H2 is from C3H4O3 (pyruvate)?

But then it makes no sense that numbers of pyruvate (C3H4O3) 's H and acetic acid (C2H4O2) 's H is same.

How can this happen if H is from pyruvate?


texts: Should the length of the electrodes in the electrophoresis chamber be proportional to chamber's size?

texts:
I am trying to build a small horizontal electrophoresis chamber from scratch. I want to use it for comet assay and I will be using only 1 slide, so it's going to be about 3cm wide, 10cm long and 4cm high, just enough to fit the slide and a small amount of buffer. As far as I know such thing is not commercially available, so before I make it I want to make sure that it's going to work. The main issue is the cost of the electrode (has to be platinum wire). I don't want to spent that much money just to realize that it doesn't work.
My question is: is a 3cm electrode in a 60-70cm3 enough? Basically, are there any physical restrictions on the size and the position of the electrodes and the shape of the chamber?
Since I am a biologist and my knowledge in physics are quite limited, I would greatly appreciate any information about this.


texts: I am working with Next Generation Sequencing. I BLASTed the bovine de novo assembled contigs to the NCBI nucleotide database. I got a matching with a lot of species i.e. different kind of bacteria, viruses and mammals. I want them to group in a logical way i.e. all the bacteria in one group (bacteria group) similarly viruses and mammals. This is hard to arrange manually, can anybody help how I can arrange my vast number of species into some logical grouping. Thanking in anticipation.


texts: How is receptor production (recycling) regulated?

texts:
My understanding of receptor downregulation is that when activated, a receptor then gets absorbed into its cell, as shown in this weird video. It then gets either recycled or degraded. Tolerance presents when more degradation than usual happens.

Receptor activated (ligand binds to receptor)
Receptor-ligand complex internalized to cell
Some complexes recycled, others degraded
Tolerance = more degradation than usual, resulting in lower
receptor density at cell surface (called downregulation)

So, what is causing the higher degradation than usual? Is it the lack of the materials required to produce the receptor? If so, can this be compensated for via diet or supplementation (i.e. eating more dopamine precursors if you're trying to avoid dopamine receptor downregulation, for example?)


texts: What is the difference between a fixed substitution and a single nucleotide polymorphism (SNP)?

texts: I recently read a report that stated "We found 430 fixed substitutions […], with an additional 34 single nucleotide polymorphisms (SNPs) fixed within individual patients." What is the difference between both terms?


texts: Microorganisms in Louis Pasteur's experiment of beans

texts:
Louis Pasteur's experiment proves that microorganisms do not grow from non-living matter, he discovered that microbes can cause food spoilage.
So, where do microorganisms come from? Do they come from the environment?


texts: Does the zeta potential of a nanoparticle generally take into account ligand charge?

texts:
For example, if I had a quantum dot nanoparticle with conjugated linker peptides capped with polyarginine tracts.

Would the localization of negative charge from arginine change the zeta potential of the overall np-peptide complex?

Or does the polyarginine tract have its own stationary layer and its own zeta potential separate from that of the QD? Especially if it extends outside the slipping plane of the QD?


texts: Can CRISPR-Cas9 make changes on a living organism? What's the limit here? E.g. reversing/restoring hearing loss in a living adult mice.


texts: Are nucleic acids found in cell membranes?

texts: I've found various results online and I was recently marked in on an important test as wrong when I made the assumption they were not found in the cell membrane. Does anyone know what the correct answer is in this case?  Thanks in advance.


texts: How accurate are Illumina microarray chips for genotyping?

texts: What is the error rate for these machines in genotyping (like for 23&me)? What is the chance of a false positive or false negative?


texts:
Small populations of organisms may be exposed to the dangers of inbreeding. But if a small population manages to survive for many thousands or millions of years, would mutations eventually diversify the gene pool, rescuing the species from adverse genetic impacts?

For example, if the cheetah - a classic example of a genetic "bottleneck" - survived for a million years, would we expect the cheetahs of the future to be more diverse?

If you know of any studies that expand on this, I'd be interested in knowing about them. For example, what is the minimum number of breeding age individuals of a mammal species that would have to wash up on an isolated island to survive, and approximately how long would it be before the population is free of problems related to a lack of genetic diversity?


texts: Why does a high osmotic pressure pull water in, yet a high hydrostatic pressure pushes water out?

texts:
When I normally think of high pressure, I think of it as pushing something away from the zone of high pressure.

Yet for a high osmotic pressure, water is pulled IN to this high osmotic pressure region.

Why is this the case?


texts: Are neurons clustered? How do neurons make thousands of connections?

texts:
According to this source, a neuron can connect to up to 10,000 other neurons. Does this imply that neurons are clustered, that is, not evenly spaced? Argument:

Say axons are length $L$, and dendrites are length $D$. Say a neuron $N$ has 10,000 outgoing connections. Then there must be 10,000 neurons within distance $D$ of $N$'s axon terminal. Then each of those 10,000 neurons are within distance $2D$ of each other by the triangle inequality. Assuming $2D<L$, then all of those 10,000 neurons are less than an axon's distance from each other. But for this to be true, the 10,000 neurons must be closer to each other than they are to $N$. Since this argument holds for any neuron, we get the result that neurons must form clusters of around $10,000$ neurons, or their dendrites must be longer than half their axon length.

Similar to this question.


texts: Is self-fertilization in hermaphrodite animals an asexual or sexual reproduction?

texts:
There are various Hermaphrodite animals, which can self fertilize.

So can this be called sexual reproduction because  there is fusion of gametes though from the same individual
? Or asexual because the involvement of a single parent(characteristics of asexual reproduction)?

There is a similar question-
Can Self-Fertilization in flowers be called asexual reproduction?

Can I extend the same logic mentioned in the  @Hawkeye's answer to the given question link on the animal case above and say that it is a case of sexual reproduction?


texts: Do human neurons in a petri dish do different things from chimpanzee neurons

texts: I want to know if qualitative experiments have been done growing chimpanzee neurons and human neurons in vitro and have any differences emerged, such as the amount of connections per neuron or anything else.


texts:
In this photo, I know that the arrows pointing towards the M-line of sarcomere on actin filaments are due to the power strokes of myosin heads. However, what I don't understand are the arrows on the myosin filaments pointing away from the M-line.
Are they the reaction forces (action-reaction pair, where the action force is power stroke)? Also, will this force (pointing away from M-line) 'tear apart' the myosin filaments on M-line? If not, how can the filament withstand this force?