texts: Questions about insects eating flour and living in the cracks of a wooden cutting boards

texts:
I have a large wooden cutting board which is used in my kitchen mainly for preparing egg pasta. The wood type is Populus (poplar or aspen or cottonwood).

The main ingredients used with the cutting board are: flour (mainly soft wheat flour), hens' eggs, white sugar, butter, and baking powder.

After the food preparation, the cutting board is cleaned by scraping away the ingredients remains.

The board has some cracks and some small unknown insects are living inside the cracks.

The board has also a lot of holes due to woodboring beetles but I think the woodworms operated long time ago and they no longer live in the cutting board.

The unknown insect has an approximate length of 1 mm (along the direction of their movements) and a width of 0.3 mm. The unknown insects do not have wings, they just walk. I am not able to see how many pairs of legs they have.

The color of the insect is pale brown.

The cutting board was free from these unknown insects some months ago but then they appeared.

My questions:

What insects are they?
Are these insects poisonous to humans?
How can I get rid of them?

Update

The unknown insects could be Acarus siro, I will try to get a picture of the insects.

Update 2

Here is a picture. The bottom part of the image is a one Euro coin, the top part of the image is a caliper (each bright area is one mm tick).

Some more pictures:


texts: How do I score differential activity of cellular pathways in microarray data (not enrichment)?

texts: I would like to identify cellular pathways (KEGG) with discriminative changes in the average activity (expression levels) of their gene members in a two-condition microarray dataset. The goal is to use the average pathway activity for machine learning (sample classification), not to identify pathways enriched in differentially expressed genes (i.e. not performing a classical gene set enrichment analysis).


texts: Is there recent info about the hypothetical ancient two-codon genetic code?

texts:
Here is the latest I have found. link

This is the basic idea: Evolution does not look ahead and make plans. It would not create a system of mRNA with giant ribosomes to create proteins, until proteins were already useful. There must have been a simpler way to create useful proteins before, that got complexified after it was already useful.

Since enzymes can be made of RNA, presumably early life made just RNA enzymes and no proteins. It didn't matter whether RNA enzymes were as efficient as modern ones because protein competition hadn't evolved yet.

And since we now make peptides off an RNA template, probably early proteins were also made off an RNA template. It is hypothesized that particular amino acids would be attracted to particular RNA pairs, and they would be put in just the position that would help them link to neighboring amino acids. This could be slow and inefficient compared to modern protein production because again the competition was not stiff back then.

Between two pairs of coding bases, the RNA needed a noncoding base for spacing. Possibly the noncoding base might be particularly good for catalyzing the joining of amino acids.

The system did not have to use the same amino acids we use today. It could use amino acids that were good at attaching to RNA, and later after the system got changed around the modern list of 22 amino acids could have developed.

There are various ways this is a satisfying idea. For example, the machinery to make proteins is largely made of RNA. The mRNA carries the message. tRNAs decode the message. Ribosomes are giant machines which transcribe proteins efficiently, and they are largely made of RNA with a lot of little proteins that help them hold their shape etc. Presumably the first protein-building machinery was itself built entirely from RNA -- because that's what was there to build with -- and over time evolution found ways to improve that machine with protein scaffolding.

This 2005 paper link describes a reasonably plausible way it could have been once. They imagine a few alternate amino acids which might have once been part of the genetic code -- ornithine. Homoserine. 2,4-diaminobutyrate. They imagine ways that the crevices between pairs of bases could be like the binding sites of enzymes. They fit the ideas together.

Have there been advances since 2005?


texts: What is the rationale behind reverse cholesterol transport?

texts:
Reverse cholesterol transport is transport of cholesterol from the tissues back to liver/VLDL. My question is why do the tissues have this extra cholesterol in the first place?

Why would you synthesise extra cholesterol when excellent feedback mechanisms exist - eg. SREBP SCAP INSIG path??

Does this happen only in the case of an atheromatous plaque? Nowhere else?


texts:
I believe I may have misunderstood water solubility this entire time.

I assumed that water soluble meant that it would literally dissolve in water. It would break down into atoms. A sugar molecule would break its bonds and become something else...

However I must be mistaken because I'm reading about why DNA is spiral shaped and it says that it is to keep the hydrophobic bases inside the spiral to protect them from the water, but keeping the hydrophilic phosphate and sugar molecules on the outside.
I would assume that because these molecules are hydrophilic they would disassociate from each other but this has to be incorrect. What am I misunderstanding about water solubility and what would happen if the bases were exposed to water?


texts: How would one describe the R-factor in crystallography?

texts: Yes, there is the wikipedia definition, but how would one explain this concept to a non structural biologist?


texts: I have used DNAStar laser gene and VectorNTI in the past for cloning, primer design, sequence alignments, etc but no longer have access to these. Are there any comparable replacement suites or what stand alone packages would you now recommend?


texts:
Is there any reason why AUG is the initiation codon?
Can’t translation start with different codons?


texts:
I am equally disgusted and fascinated by the "Silverfish" (Lepisma saccharina) that we regularly find in our UK home. I tried searching for information on the internet but they seem poorly understood.

We only ever find them on the work surface in the kitchen when we switch on a light at night. They are presumably feeding off food residues - but they never seem to be found in the most obvious place, among the crumbs under the toaster.

When caught by the lights, they run for cover but never, ever climb. You would think them unable to climb at all but then how have they reached the work surface?

The other day there appeared a new twist; 2 "husks" hanging from silk threads between 2 containers, maybe 8cm from the surface. If they were caught and eaten by a spider, why did it take them to a rudimentary web when it (presumably) caught them on the surface? There was no sign of a spider around. The only other possibility I can see is that they somehow suspended THEMSELVES from the silk and this was a moulting behaviour. Thus they now CAN climb - and very well - and also produce silk!
Can anyone explain the mystery?


texts: How can I obtain a computer readable model of Dr. Gerhard Michal's biological pathways map?

texts: I want to run simulations of various metabolic pathways – the project could end up becoming quite large, and having a machine readable chart would make thing a lot easier. Does anyone know if there is a machine readable file of Dr. Gerhard Michal's famous metabolic pathways chart?


texts:
I found many of these nuts in a botanical garden in Sweden (outside, not in a greenhouse) but was unable to find the plant it belonged to. The garden has species from all over the world. I don't recognize it as a native plant, but I could be wrong on that.

I've tried to use various identification webpages to find it, but failed. I would love to know the species, so that I can get more info on the plant and its seeds! The Bic lighter is there for scale.

The nuts (or seeds, or whatever they are) are very hard, like a peach stone or other drupe stones.

This is a crosspost from Reddit where no-one has answered the post(yet).


texts: Is it possible that weak memory is due to interference between signals in the brain?

texts:
"Weak memory", as used in this question, refers to the inability to retrieve a memory that a person otherwise knows he has memorized earlier. An example of this is some fact snippet that the individual memorized as part of a training exercise 2 weeks earlier.

Is there scientific consensus for the cause of this type of weak memory? Or is the consensus that there are multiple causes?

Is it possible that this type of weak memory is caused by interference between various signals in the brain, or what does the known evidence say (if anything)?


texts: shRNA knockdown not showing with Western

texts:
I've recently been performing shRNA transfections and was hoping to get some advice on why I'm not seeing any knockdown via western blot

I transfected by MDAMB468 breast cancer cell lines with shRNA against PTEN from the pLKO.1 lentiviral vector. I selected for the transfected cells using 1ug/ml  puromycin for approximately 6 days. During this time there was very few cell death amongst the cells compared to my control plate (untransfected cells with 1ug/ml puromycin), suggesting that the transfection was successful.

After the 6 days I harvested my cells for protein and RNA extraction. I performed a western yesterday to assess knockdown, but noticed that there was hardly any differences (if any!) compared to my shGFP control. I haven't done a qpcr yet but I plan to this week.

I was wondering if anyone has experienced something similar, especially when working with PTEN? could it be that the cells need to be selected for a longer period (i.e. more than a week) before assessing protein knockdown?

Thanks!


texts: Why don't most animals have "heads" in the middle of their bodies?

texts: For example, humans. It would seem like, to me, if our brains and eyes, ears, etc. were situated in our stomach area they would be more protected from harm and more central than up at the top in and on a fragile skull. The same goes for other organisms. For example, horses have eyes on the sides of their heads; why wouldn't the eyes be near their stomach area? To me, it would seem like it would make it more safe and the horse could still see alot. I looked at this question, but it didn't fully answer my question.


texts:
My grandma is O- blood type, my grandpa is B+, but my mother is A+ and my aunt is AB+.

Is that possible?

I've just looked at different sources like this and all of them are saying that from O and B, comes only B or 0, and A and AB are forbidden.

How can my mother be a child of my grandparents and how my aunt can be a child of my grandma at all? Or can we 100% say that they are not the real children of those parents, assuming that all blood types are correct?


texts: Evolutionary explanation for hypoxia causing euphoria?

texts: Why would something potentially very dangerous, such as hypoxia induce something pleasurable like euphoria? Are there any evolutionary hypotheses for this link? I'm thinking that something like the "choking game" would actually select against it, but that's probably too new.


texts:
I have a FeCl3 tank that I use to dip spruce wood in. After 2–3 weeks a fungus appears in the tank and it keeps growing with time. The fungus has a white colour and is spread throughout the whole tank. It looks like mainly on the surface but its everywhere in the fluid.
The FeCl3 solution has pH 1 and that doesn't change with time.
Can anybody tell me what it might be? What's the best way to make sure it doesn't occur anymore?


texts: What's a good reference for learning about recombinant proteins?

texts: I'm looking for books and articles that can bring me up to speed on the design, expression, and purification of mammalian proteins in recombinant systems, both in E. coli and in more complex systems like CHO or Sf9 cells. I have a weak but functional background in general molecular biology.


texts: Is it possible to be allergic to the yolk of an egg but not the egg white?

texts: At lunch one day, my friend had a hard boiled Easter egg. When he pealed it he squeezed the yolk, or yellow part, of the egg out. I asked him what on earth he was doing and he said, "I'm allergic to the yellow part of the egg not the white." I was very confused by this, he also sad he was allergic to tomatoes but could still eat pizza with sauce on it, apples but only the skins, and some other strange things. I didn't think this was possible at all. Can anyone explain this and tell me if it's even possible to be allergic to one part of an egg and not the other, or is it all in his head. If this is possible, is there an actual name for this condition?


texts: Why didn't more muscles evolve the endurance of heart muscle?

texts: The heart is a muscle capable of both the quick contraction of white muscle cells, and also the endurance of red muscle cells. Why haven't more muscles in the body adapted the same combo of abilities? Is there a known weakness to the heart muscle? Excessive energy consumption, or something else?


texts: What is this dark brown organism growing on a door frame?

texts:
A few brown spots appeared on a door frame and within 1 week it has grown to this size (~15cm). I have no idea what it is. How do I remove it completely? I worry that if I just wipe it off, it will just regrow from within the door frame. I've attached 2 pictures to assist with the identification.
Edit: I poked it with a stick and tiny white insects (~2mm) came crawling out of the structure.
My location: South India


texts: Why does pink colour reduce aggressiveness?

texts:
According to this Wikipedia page, a shade of pink colour known as "Baker-Miller_Pink" has been known to reduce aggressive behaviour.

Is there any biochemical reaction responsible for this?

Specifically, are any hormones responsible for this?

If yes, then which ones?


texts: Small worm living in some kind of cocoon, what are these animals?

texts: I am curious what animal is this. It is/lives inside some kind of cocoon, about 1 cm in length. They are attached to walls and to the ceiling, but sometimes they fall off. Inside the structure there is a small worm that can come out at both ends alternatingly. It can then hold on to the ground to move the cocoon around. They are said to feed on paper.


texts: Why do flies leave dirty spots on shiny/glossy surfaces?

texts: I've seen flies leave dark spots on lacquered wood, mirrors, glass and monitors. Why do they do that? Is it some food stash or are they dumping waste in a single spot? Why pick a smooth surface?


texts:
The female drops a twig from high up on a tree and the males have to catch it midair. The female is checking if the males can catch things midair because this species nests on cliffs, and the chicks may fall to their deaths while learning to fly. Apparently, skilled males can catch the chicks midair.

Which species is it?


texts: Do single nucleotides spontaneously bind to ss DNA? AT. GC. I realize the rhibisome is usually needed for making a strand, but what about randomly hbonded base pairs? Does this occur?


texts: During bacterial protein synthesis, when ribosomes attach to the cytoplasmic membrane and form a polysome, to what molecule are the ribosomes attaching? Is the polysome held to the cytoplasmic membrane by just a single connection between one ribosome and the particular attachment molecule?


texts: Is there any record of an Albino (Not leucistic) peacock

texts: Wikipedia says there are, however gives no source to one. Does anyone know if an albino peacock was ever recorded?


texts: What type of flask should I use to culture NTERA2 embryonic cancer stem cells?

texts: I'm just starting my MSc research and I am in the process of making a list of equipments/consumables to order. Is there a specific flask in which I can culture NTERA2 (NTERA2/D1) cell line?


texts: Is there natural occurrence of induced pluripotency / expression of Yamanaka factors and what is the evolutionary explanation of that?

texts:
Is there natural biological processes in which the full (full reprogramming into pluripotent state) or partial (partial reprogramming, stopped before point-of-no-return, preserving the functional distinctiveness of the cell) induced pluripotency (https://en.wikipedia.org/wiki/Induced_pluripotent_stem_cell) and expression of Yamanaka factors occurrs? What is the evolutionary explanation of such rejuvenation factors? I would like to see the natural explanation otherwise it begs for the idea that the Universe is created with the human as the goal of it (anthropocentric hypothesis) and it is quite uneasy for me.

I guess, that natural reproduction processes can involve some kind of rejuvenation/induced pluripotency and they determined the existence of Yamanaka factors.


texts: Why are bacteria immune to snake poisons?

texts:
In a test I was asked why bacteria are insensitive to snake toxins.

Is it their membrane that provides a barrier to the toxins? Or do snake poisons have specific targets and thus cannot bind to bacteria?


texts: Can the heart generate its own rhythm independent to the SAN?

texts:
My textbook and a revision guide, which I believe is a reinterpretation of the textbook, state that:

  The SAN initiates waves of excitation that usually override the myogenic action of the cardiac muscle.
  From the textbook

The revision guide is more direct in its interpretation of the textbook:

  The heart muscle is myogenic, which means that it can generates its own rhythm. However, this rhythm is overriden by the sinoatrial node (SAN).

I wonder whether the textbook was interpreted incorrectly, or if in fact the heart can contract independent to the SAN?


texts: Can blood that has had an anticoagulant added to it be boiled without coagulating?

texts: If I understood the information I've found elsewhere correctly, you can't boil untreated blood without it coagulating, right? But what if you added an anticoagulant to it? Would it be possible to boil that blood or would it coagulate in spite of it? Thank you in advance!


texts: Why are GC-rich regions less condensed than GC-poor regions?

texts:
As far as I know, chromatin consists of two kinds:

Heterochromatin is more condensed so translational factors have less access to this region, and this region is poor in GC.

Euchromatin is less condensed so translational factors have more access to this region, and this region is rich in GC.

I wonder how GC content affects the condensation status of the chromosome? What is the mechanism behind this relationship?

It is well known that GC and AT pairs differ in the number of their hydrogen bonds. Does this hydrogen bonding play the key role in condensation of chromosomes?


texts: Can we produce sugar using chlorophyll dissolved in ethanol?

texts:
I can't find anything about this on the net.
I read in my (high-school) textbook that if plants get sunlight, water and carbon dioxide, and the catalyst called chlorophyll, they can make sugar.
I'm just thinking... We CAN extract chlorophyll by dissolving the boiled leaf in ethanol! So can't we just bubble CO2 in and let the sun shine on it and add some water? Shouldn't that make sugar in the solution?


texts: Found on a beach in Brisbane, Australia. Only a few cms of it was visible but I dug the rest of it out, it was about 20cm in length.


texts: What is the energy cost of an action potential?

texts: As I understand it, ions flow down their electrochemical potentials through ion channels during a neuron's action potential. Otherwise, ion pumps work to restore and maintain the resting membrane potential. What is the energy cost of a neuron's action potential? That is, how much work must the ion pumps perform to restore the resting membrane potential after an action potential occurs?


texts: What is the term for all of the RNA in a cell at any given time?


texts: The Wikipedia page for rDNA says "Ribosomal DNA (rDNA) is a DNA sequence that codes for ribosomal RNA" Also, the figure next to it says "The gene segment of eukaryotic rDNA contains 18S, 5.8S, and 28S tracts and forms a tandem repetitive cluster". So, it gave me the impression that rDNA codes for both rRNA and the structural proteins of ribosome. Is that right?


texts: Linkage Disequilibrium - What does it mean when D < 0?

texts: What does it mean when you have a situation where your D<0?


texts: Does common X-like picture represent one doubled chromosome or two homologous chromosomes?

texts:
What is on common X-like picture of chromosome?

Here is the image from Wikipedia:

Are (for example) lower petals homologous to each other?

If yes, then why (1) is entitled as chromatid: one-half of two identical threadlike strands of a replicated chromosome? Homologous parts are similar but not identical.

If no, then why does human chromosomes are often denoted by Xs:

Do we have 23 Xs (females) or 46 Xs?


texts: How much pressure can human withstand if inner and outer pressure is balanced?

texts:
I know human can't dive too deep because there's pressure difference between inside and outside of the body. But how much pressure can human withstand if human is breathing components that is surrounding him?

So I have two questions:
1.How much pressure can human handle if he is surrounded by regular air (also breathing air)? 2. How much pressure can human handle if he is floating in oxygen-rich liquid and breathing it at the same time (Liquid Breathing, Wikipedia)?

There's a similar question, but it doesn't have answer that fully satisfies me. Highest Pressure Human Body Can Survive In?


texts: How can GMO contaminate biologic plants?

texts:
Let consider two use cases :

I am the only farmer within a 200km radius. I first grow GMO plants. A few cycles later I decide to grow bio plants, so I uproot all of the GMO plants and plant fresh new bio plants.
I am surrounded with GMO plantations and I decide to grow bio plants.

In both cases, can we consider the plantation as bio or was it contaminated and how?


texts: What are names of the colon delimited fields in this FASTA header?

texts:
The human chromosome DNA data in Ensembl release 96, here is in FASTA format.

Reading the Wikipedia article on the FASTA format, I understand the first line, prefixed with >, is variously referred to as a "comment" or "sequence headers". However, looking at FASTA files from different sources, it appears this first line is quite variable in actual content.

What are the colon separated fields in this FASTA header (as found above on the Ensemble FTP site)?  Most fields are guessable, but an explanation of each field would be much appreciated.  I believe the 46709983 is the number of base-pairs in the chromosome.

>21 dna:chromosome chromosome:GRCh38:21:1:46709983:1 REF

Finally, how should I have figured out the meaning of the header notation for myself?  Is there a list of common or known header formats?


texts:
There is a succulent-looking weed growing in a crack in my driveway. What is it?

Conditions: Dry, full sun, asphalt & gravel, no competition.
Date: 2018-07-16
Location: Toronto, Ontario, Canada
Size: 40cm x 40cm x 2cm


texts: What does "molecular" mean in the context of anatomy, for example the molecular layer of cerebral cortex

texts:
The first apical layer of the cerebral cortex is also called as the molecular layer, I could not find the exact reason of the naming.

What I found:

Molecular alongside its primary meaning in chemistry can also mean:

of or relating to individual or small components

source

And if you only stain the neuron somas, you can only see some scattered neurons in this layer. Maybe this is the basis of to the naming.

What does molecular exactly mean in this context?

Is this adjective used widely in anatomy with the same meaning?


texts: Most accurate depiction of cortical homunculus?

texts:
I was looking at cortical homunculus and I realized there are several different pictures and they don't quite agree.  For instance:

http://wellbeing.media.mit.edu/2014/02/21/mindfulness-neuroimaging-and-neurofeedback/

http://nawrot.psych.ndsu.nodak.edu/Courses/465Projects11/PLS/4Thesomatosensoryandmotorcortices.htm

One area, for instance, are the feet, which I feel should have a fairly large (not as big as hands) area in the brain, mainly from the personal experience of having more sensations in feet, which like the hands has many nerve endings, though obviously much less fine motor ability.  But that's just my speculation, and I like an accurate depiction so I can start from there and make sense of this.  Thank you.


texts: Predicting and identifying microbes and enzymes DNA sequence with metabolic prediction

texts:
Presently I am working on metagenomics of coal biomethenation by bacterial consortium.

I have got the sequence result (Illumina). The sequence is huge and I can't predict anything from the sequence.
I have gone through different database like Metacyc, Biocyc etc.
Please help me that how can I draw an inference towards the metabolic enzyme that are involved in biomethenation of coal.


texts: What is known and what can be measured of biofilms?

texts:
Context for the question

I am a mathematics researcher working on the mathematics of imaging and parameter estimation (inverse problems). I found an interesting diffusion equation that models the growth of biofilms. A question I am interested in: Given some measurements of the biofilm, and assuming the mathematical model is accurate, can we deduce the coefficients in the model? This, however, is not the question I want to ask here.

Please pardon nonstandard use and misuse of biological terminology and gaps in knowledge; this is by no means my field. I have never done biological experiments in a laboratory, for example, or studied any university-level biology.

The model

Let us assume a simple scenario where we have a biofilm and some substrate it consumes to grow. We consider a surface where the model should tell how fast and to where the biofilm grows. The parameters in the model are:

$d_1$ substrate diffusion coefficient;
$d_2$ biomass diffusion coefficient;
$K_1$ maximum specific consumption rate;
$K_2$ biomass decay rate;
$K_3$ maximum specific growth rate;
$K_4$ Monod half saturation constant (relative to initial data $S_0$);
$a$, $b$ biomass spreading parameters.

The quantities that are solved from the equations are the following, both of them scaled so that $0 \le M, S \le 1$. Both of them are functions of space $x$ and time $t$, which I omit from the notation.

$S$ is the concentration of the substrate that the biofilm feeds on
$M$ is the biomass density

The governing equations are the following, with some boundary conditions I will not specify here:

$$
\begin{cases}
\partial_t S = d_1 \Delta_x S - K_1 \frac{SM}{K_4+S} \\
\partial_t M = d_2 \nabla_x \cdot \left( \frac{M^b}{(1-M)^a} \nabla_x M \right) - K_2 M + K_3 \frac{SM}{K_4+S}
\end{cases}
$$

The questions

Can both $M$ and $S$ be measured with fair accuracy in laboratory conditions? How is it done and how reliable is it? Can the experiments continue afterwards, or does the measurement significantly alter the experimental set-up in some way (by for example destroying the biofilm or mixing the entire thing etc.)?

Of the parameters in the model, which are well-known?

I suppose the answer to last question depends on whether the biofilm is of known or unknown nature, and in the case of an unknown substance, only $d_1$ might be known. What about a known kind of biofilm?


texts: Calculating number of amino acids in mRNA

texts:
Assuming there were 20 different amino acids and less than 40 types of different tRNAs found in this alien organism. How many amino acids would be found in the translational product of a 600-nucleotide mRNA?

I am very confused over how I should solve this question.

If we assume 1 codon = 1 nucleotide,

20 amino acids require 20 different codons = 20 different nucleotides < 40 different tRNAs.

If we assume 1 codon = 2 nucleotides,

20 amino acids require 20 different codons = 5 x 5 combination of nucleotides? (considering A, T, C, G, U)?

5 x 5 = 25 < 40 different tRNAs.

The correct answer is to consider 1 codon = 2 nucleotides.

My question,

Since both 1 codon = 1 nucleotide and 1 codon = 2 nucleotides fit the requirement of this question, why is 1 codon = 2 nucleotides the correct answer?


texts: What tool to use to map reads (samtools, sequencher,...)?

texts:
I am a beginner in Bioinformatics. I have 4 files:

2 fastq files (aln1.fastq and aln2.fastq)

2 bam files (aln.bam and aln.bam.bai)

I know that:

the raw file is aligned to hg19 human genome.
The sequenced file is pair-ended from Miseq sequencing platform.
This file is the result of an amplicon sequencing design.

I also have sequence information about the primers (4 forward and 4 reverse) and 2 adaptors.

And I have to answer these two questions:

What is the constitution of each read, for example (adaptor + primer + amplified
region) ?
Which gene region did those reads mapped to ?

My question is what kind of tool do I have to use to respond to these questions? samtools? sequencher? FastQC? Can anybody help me just to start because I am totally lost.

Thanks


texts: Do you know what this black spider-like insect is?

texts:
I have encountered these insects before, but I always assumed them to be spiders even though I always noticed they have 6 legs, as an exception. But slowly with time I ended up observing them more. One day I almost stepped on one of them, but thankfully didn't crush it and that was the day I realized they may not be spiders at all, Because I felt like I had stepped on a thorn or something. These insects are 6 legged and that rules them out as spiders but can't be sure. They don't seem to have distinguishable spinneret. If they don't belong to spider species then it is possible that the spider-like appearance is mostly a camouflage and a single spike on their back would be a defensive measure. They don't seem to behave aggressive like spiders.
I live in a rural area, State of Odisha, India


texts: Is there other unknown-compound in Blood?

texts:
Blood is made of red blood cells, platelets, plasma etc. Let's say, then, there are these $x$ known compounds in blood.
But how can one be sure that there is no other compound other than those $x$ compounds? Does present technology ensure that there is no other unknown compound in blood that can't be detected?


texts: How do omega-3 fatty acids reduce cholesterol at the molecular level?

texts:
I have heard that omega-3 fatty acids found in fish are a good way to prevent/reduce cholesterol problems.

My question is how do omega-3 fatty acids do that: what are they doing on a chemical level to produce this effect? And is there any way to maximize this effect through other substances, that may work in concert with them?


texts: When we talk of functional macromolecules (e.g. proteins as enzymes, hormones, receptors, antibodies etc), towards what are they evolving?�

texts: Actually this is a question which is given in a book and to be honest,it has baffled me.I'm not so much well versed with molecular evolution so my guess would be,say some sort of enzyme which could catalyse more than 1 reaction maybe coz then that 1 will be sufficient enough to do much more work,like it happens at organismic level,like reduction in legs of prawns and shrimps which has happened (earlier relatives has more legs but they were less effective as compared to their modern counterparts).So,my guess would be something like that but as I said earlier,I'm not so good in molecular evolution so please help me out.Or tell me about what were the characteristics or primitive macromolecules and those that occur today and via that,this question might be explained.Also,I've written the question as such given in the book i.e without any changes.


texts:
Wikipedia has this image titled "Pressure Chamber to measure Enzyme Activity under High Pressure"

Made me wonder why do we need to measure Enzyme Activity under high pressure?

Are there enzymes in nature that must work under variable pressure conditions? My impression from my knowledge of conventional chemical kinetics was that in the liquid phase the effect of pressure on chemical kinetics was typically very low simply because of incompressiblity of liquids. Unless Pressures were very very high. Is this not so with enzyme activity? Or are there enzymes that must work under very high pressures?

https://en.wikipedia.org/wiki/Enzyme_assay


texts: Why do fungi and bacteria have macroscopically distinct patterns of colonies?

texts:
Why do microbes, when incubated on an agar plate forms a distinct kind of appearance i.e., d shape of colony.
 Its kind of less unique in case of bacteria.

Bacterial colony
http://image.shutterstock.com/z/stock-photo-colonies-of-bacteria-from-sea-water-on-a-petri-dish-agar-plate-isolated-on-black-background-300465722.jpg

Fungal colony
http://textbookofbacteriology.net/penicillium_colonies.jpg
. But if we  consider fungi, an amazing kind of pattern is seen as compared to bacteria.
So, on a broad spectrum if we speak, what is the real or basic motive behind forming these specific shapes.
Does it serve any purpose in protection or any such particular reason why do they do so?
Even plant leaves do the same. I mean to say every leaf is different from eachother making itself unique..
Why is this particular pattern seen in d universe and what it has to do with the colony of microbes.


texts: Can NSAIDs impact negatively the healing of tendons?

texts:
There are a number of articles regarding nonsteroidal anti-inflammatory drugs
 (NSAIDs) having a negative effect on healing conditions like tendonosis and tendinitis. From what I understand the channel through which they reduce inflammation disrupts healing. In general, many of them constrict vessels, thus reducing bloodflow even further to tendons. Are there other reasons, or interactions they can have with  cells that may also disrupt healing?

Are there advantages of using NSAIDs to promote healing?


texts: Why are there no tree-like plants that grow in lakes?

texts:
Looking at aerial photos of boreal forests, with dense woods clear-cut by quiet lakes, I wondered why exactly are the woods so clear-cut at the edge of water? Why won't trees develop adaptations that will let them grow from a shallow lake bottom, with the lower part of the trunk in the water and the crown above the water?

It seems to me that this would give them some significant advantages. Lake bottoms are rich in organic nutrition, and insolation will also be plentiful above water, at least at first when there's little competition. So why are lakes' surfaces so clear and open, instead of overgrown? Of course there are aquatic and semi-aquatic plants like water lilies, Scirpus or Typha, but they are a far cry from the nearby terrestrial forests, in terms of biomass. Why don't they develop into large amphibian trees, or why don't terrestrial trees try to re-colonize lakes?


texts: How often does parthenogenesis in mammals happen?

texts:
Probably everyone knows that mammals can't produce viable offspring by parthenogenesis.

But there are reports of human chimeras (see: a human parthenogenetic chimaera) and it's known for mice to quite often develop parthenogenetic embryos that will not survive past the 10th day of gestation (see: birth of parthenogenetic mice that can develop to adulthood).

So, how often does parthenogenesis happen in mammals and how long do parthenogenetic embryos survive? I have heard an estimate that 0.01% of human blastocystes are parthenogenetic with gestations always ending in miscarriage before the 3rd month, but I couldn't find any source for this claim.


texts: Can a plate with incompletely filled LB agar be used?

texts: I am falling short of LB agar plates and I have a plate with less LB agar poured. I meant, the plate is not fully filled with the agar (it was the last plate I poured the medium into). Some part of plate is empty. Does this cause any contamination problems or moisture retention? Is it okay if I use this to streak a 5 cm line?


texts: Given a plant $P$, predict its height $H$ at time $t$ since planting given some environmental variables $E_1, \dots, E_n$. How accurate are the state-of-the-art models for such thing? What data is used to make the prediction?


texts: Would a colony with only one male and female collapse?

texts:
This is a thought experiment:

If we form a population with only a single founder pair, can this population survive? What would happen? Would this inbreeding cause the population to go extinct? Could such a population continue to exist indefinitely?


texts: Does exercising increase the rate at which UV rays are absorbed and cause affects?

texts: Does exercising while in sunlight affect the rate at which the human body absorbs and reacts to UV rays? As sunburn is the secretion of fluids, increased dilation of blood vessels and inflammation of skin would exercising (as it also increases blood vessel dilation for heat loss) accelerate the "sun-burn" process in skin?


texts: Could we detect GMO foods if there were no samples to compare with?

texts:
In my understanding, there’s nothing “special” in how a GMO product is composed inside compared to a “natural” product. I mean, still, same principles apply to both: some DNA that controls protein building, and so on.

Now, having read about all existing methods of GMO detection, I still can’t understand how it works: e.g., given two potatoes, one GMO and one natural, would you be able to detect which is which without having any samples or knowledge about what parts of DNA to consider engineered by humans?

Once you change someone’s DNA, does it contain any signs that it was changed? Or do we need a database of “natural” products’ DNA to compare with in order to be able to detect DNA ones? Or do we need a database of GMO products to compare with?


texts: How far does the diaphragm stretch when it contracts?

texts: I have been wondering about this for this entire day today and I can't seem to find an answer. How far, exactly, does the diaphragm stretch for tidal breathing and what is its maximum stretch length?


texts: Damaged proteins are broken down in cells by ubiquitin-proteasome pathway. Do cells experience excess of proteins? If yes,  how excess proteins are taken care of?


texts: Hello! I need help with this exercise question. I am not really sure which pedigree diagram is autosomal and which is not. But, is question b 1/2. Can someone give an explanation? Thanks very much in advance? Appreciate any help!!


texts: Do mRNA vaccines encoded proteins get glycosylated?

texts:
per recent hype around the new mRNA vaccine against COVID-19 (or sars-ncov-2) it got me thinking about the mRNA vaccine principle.
From my biochem education I've taken, that human proteins are usually glycosylated.
It got me thinking, that if the mRNA vaccine encoded proteins would be glycosylated by human post-translational machinery, would present different epitope then the not-glycosylated one.
While I understand that the polyclonal antibodies target a lot of different epitopes, it seem to me that the performance of antibody protection obtained in such way could be limited.
I've researched this a little bit and there seems to be techniques to avoid the glycosilation machinery.
My questions in essence are:

Would proteins encoded by mRNA vaccines get glycosylated (if not mitigated)?
If yes, then do the vaccine designers use some methods to bypass the glycosylation?
If yes and no mitigation has been implemented, do we just count on chance that at least some part of protein surface to present the same epitope as the original target protein?

Found sources:

https://www.nature.com/articles/s41581-019-0129-4
https://www.pnas.org/content/117/3/1280
https://en.wikipedia.org/wiki/Glycosylation

Please forgive me my English and any typos. :)


texts: Do bisexuals have  any evolutionary advantage over straights and gays? Bonobos exhibit bisexuality extensively. Why so?


texts: What is the consensus, if it exists, on the (absence of) biological effects of artificial sweeteners?

texts:
I tried to Google (and PubMed) the question, but it seems to be fairly polarized debate and there does not seem to be a consensus as to whether sweeteners like asparatme, acesulfame etc. have meaningful biological effects.

Some studies point to molecular effect with little to no explanations about their relevance for health, and since statistical significance and size effects are quite different things, question remains unanswered.


texts: Why are there sporadic lightly pigmented hairs in facial hair?

texts:
My body and scalp hair are entirely black. Until recently, I thought this was the case with my facial hair also, until I noticed a small handful of hairs that were anywhere from light brown to copper-orange to burgundy-red. There are hairs that are entirely pigmented like this and there are mixed along their length between different pigmentation colors (for example there are copper hairs that have black tips).

Can anyone explain why this is?

My own thoughts are that it is caused by some variation between individual hair follicles (different type/number of receptors on the melanocytes that color hair that cause them to respond differently to various amounts of hormones? But then what is causing the hormone shift in the first place? I am pretty sure that until recently all the hairs were black and only recently have these lightly pigmented hairs sprouted)


texts: My question is simple. Why is a virus considered a microbe? Considering a microbe is considered to be a "living" unit of life, which viruses are not.


texts: Lookup for transporter locations in humans

texts: I am interested in several transporters and cotransporters (eg SLC12A1/2 and many others), more precicely, in (human) organism that are made of cells containing those transporters. So does anyone know a lookup table or database where I can find information about that? My google search unfortunately left me in the dark :/ So I am thankfull about any hint!


texts:
I know that cut grass from a lawn or field can cause allergies in some people.
I also know that most plant allergies are due to plant pollen.

However, most people do not allow their lawn grass to flower, and therefore, any allergy from cut grass is likely not due to pollen.

So, what exactly in the grass is causing the allergy?

I did a google search but only found evidence and info for grass-pollen allergies.

Does anyone know what's going on here?


texts:
https://www.healthcentral.com/article/aging-can-take-major-toll-on-womens-tendons (mirror) claims that:

  There are about 4,000 tendons throughout the body.

This claim is echoed by a fair amount of websites but I couldn't find any
decently trustworthy source.

Where can I find the list of all tendons in the human body?

I have only been able to find a list of skeletal muscles of the human body so far. I'm surprised that there are 4000 tendons even though they are only ~640 muscles: most muscles that I am aware of are attached to fewer than six tendons (FYI: Why some muscles have more tendons than others?).


texts: What does it mean to say that the sympathetic nervous system is organized for diffuse activity?

texts:
"Sympathetic activities generally serve to mobilize the energy stores of the body, to increase the blood flow through certain regions (e.g., the heart) at the expense of other areas (e.g., the abdominal viscerae), and to exhibit the outward signs of alarm and excitement.

Because the sympathetically innervated effectors generally have a wide distribution, even when the sympathetic supply to only one type of effector (e.g., the vasomotor fibers to the cutaneous blood vessels) is stimulated, the bodily response is diffuse."

1-By 'mobilize the energy stores' they mean metabolize or use up ?

2-'The bodily response is diffuse' - does that mean several parts of the body participate in the response but with no major effect individually ?


texts:
Embryonic gene activation is a process by which the embryo begins to transcribe its newly formed genome.As the embryonic gene activation occurs during early stages the paternal genome may not have any influence at that stage.

Now,
My question is why does only the maternal genome play a role in embryonic gene activation?
Does paternal genome have a role in prior/post embryonic genome activation?


texts: What is the name for when genetic deviation results in an organism that doesn't work?

texts:
There is a word for this, and it's escaping me. I want to reaearch more papers on it, but I can't find them or what the word is called.

It's typically used in the context of fitness and evolution. If there is a dead individual, it doesn't have a fitness and the mutation is called _____. ?? ( in some models could be given a zero or neg inf)


texts: The fats in our body are stored in fat cells. When we over eat fats does the size of our fat cells increase, are more fat cells generated, or do we "throw out" excess fat?


texts: Using Q solution with ready made MasterMix

texts: I am exploring the possibility of using Q solution (5x) to get rid of non specific bands in PCR. I mostly use a MasterMix and not separate aliquots of dNTPs, Taq, buffer etc. In principle, adding Q solution to the reaction mixture when I use MM should be fine, but I just wanted to ask if someone has done so and had success (or failure?) before.


texts: Are there natural selection experiments that quantitatively agree with theoretical modeling?

texts:
Has anyone ever conducted an evolution experiment and quantitatively compared it to theory?  For example, has anyone ever put bacteria in a million petri dishes filled with antibiotics and calculated the number of petri dishes that should develop drug-resistant bacteria, and then compared that calculation with the experiment?

I imagine that both the experiment and theoretical modeling would be very difficult, but maybe someone has been ambitious enough to try it.


texts: Does the false positive covid-19 PCR % referred to by Surkova & Nikolayevskyy in The Lancet mean % of all tests, or % of positive tests?

texts:
In False-positive COVID-19 results: hidden problems and costs it is said:

The current rate of operational false-positive swab tests in the UK is
unknown; preliminary estimates show it could be somewhere between 0·8%
and 4·0%

My questions:

Are there any more accurate estimates or research done on the real false positive rate than what Surkova & Nikolayevskyy are referring to?
Is Surkova & Nikolayevskyy referring to a percentage of total tests done, or a percentage of positive tests?

To clarify. Let us, for the sake of example, say that the false positive rate they are talking about is 1%, and one day we test 100.000 people, and that we get 5000 positive results. Will that mean that:
A: 1% of the 100.000 are false positives, therefore there are 1000 false positives?
or that
B: 1% of the 5000 that tested positive are false positives. Therefore, 50 are false positives?


texts: There exist a co-ordinate system from chromosomes like "12p11.3". In this system, first integer range from 1 to 23 i.e it takes homologous chromosomes as a pair. If we want to distinguish among homologous chromosomes, how do we refer to each on of the pair? Is it possible to determine if one chromosome from a pair of homologous chromosomes is from father or mother?


texts: Cancer biology: Can tumors form from cells that are genetically identical to non-cancerous cells?

texts: Can a tumor begin to form without any genetic mutations? I'm specifically interested in a tumor which could later lead to cancer.


texts: How much ATP formed from oxidation of stearic fatty acid

texts:
Stearic fatty acid is a C18-molecule, so eventually 9 acetyl-CoA molecules will be formed. One acetyl-CoA molecule enters the citric acid cycle, resulting in 3 NADH & 1 FADH2. Because there are 9 acetyl-CoA molecules, 27 NADH & 9 FADH2 molecules are formed. 1 ATP is formed per acetyl-CoA molecule -> 9 ATP is formed. 1 NADH gives 3 ATP during oxidative phosphorylation & 1 FADH2 gives 2 ATP, so in total you have:
27 * 3 = 81 ATP
9 * 2 = 18 ATP
9 ATP
Total: 81+18+9 = 108 ATP
(-2 ATP because 2 high-energy bonds are used in the initial combination of CoA with the stearic acid molecule => 106 ATP)
However, my book says that 146 ATP molecules are formed. Some other sources say 106 (or 108) ATP as well, so what is the right answer? This really confused me.


texts: Why do antibody tests target different antibodies?

texts: I've noticed in various COVID-19 lateral flow assays, they seem to target different antibodies (S1, S2, NP). What are the benefits or downsides of choosing different antibodies? I know that some have a higher chance of cross-reactivity, but why wouldn't all tests just use the ones with the lowest cross-reactivity?


texts: Ion Chromatography System For Extracting Aminoacids from Microalgae

texts:
I am interested in extracting aminoacids from microalgae after having ruptured its membrane and carried out proteolysis. After some research, I came to the conclusion that ion exchange chromatography is the best for a medium scaled extraction of aminoacids. However, considering that the tool is quite prohibitive, I was wondering if it were possible to make a small scale DIY version of it, in order to, get a feeling of how it works and what parameters it needs. Even though, I am not sure this question can be asked here, I do wonder how I could make a DIY ion-exchange chromatography system. Even though, a straight-forward answer would be appreciated, I would really value just to hear small tips on it.
Other "side" doubts:

How can I "stick" the ionic resin to the tube's wall?
Do you know of any online sources that will help me give the system the correct pH parameters in order to achieve optimum net charge?
Am I not approaching this correctly, is ion exchange chromatography not the solution?

I do apologize if this question isn't meant to be here. If that is the case, I would be grateful to have the question migrated elsewhere. I will only need to extract these 20 aminoacids (which are, basically, the 20 aminoacids in human metabolism).


texts:
My understanding is that gene expression, in response to some stimulus, generally occurs on the order of minutes. I'm curious about the extremes...the quickest and the slowest cases.

What is(are) the fastest time(s) recorded for genes being expressed in response to a stimulus? What are the slowest times?


texts:
As mentioned here, tantrums are primarily observed in young children and often involve a loss of self-control, both physical control and the ability to calm after a demand has been met. What changes in neurobiology reduce the propensity for this as children age? (The cause may be partly neurochemical, partly structural.)

I am especially interested in whether the vulnerability to tantrums in the young brain are at least partly due to positive feedbacks. A self-enhancing mechanism for the distress could explain why self-control sometimes suffers. (Positive feedback is also consistent with a colleague's claim, for which I have no source, that the risk of loss of self-control is low if a demand is met quickly.)


texts: Regulation of LBD33 genes Arabidopsis. If LBD 33 gene is up-regulated by auxin then why does expression decrease when increasing auxin concentration?

texts:
I have a question regarding the regulation of lateral boundary domain genes in Arabidopsis (specifically LBD33). I am an undergraduate student trying to understand the results of a lab where I measure the regulation of gene activity by using GUS staining technique. I have included a photo of images taken of Arabidopsis under different treatments:

A) Wild type no auxin, the wild type has no GUS gene inserted thus no transcription of genes that code for GUS. This was our negative control.

B) Positive control CyclinB1 where the promoter has been fused upstream of the coding sequence for GUS. GUS staining always present.

C) LBD 16 mutant no auxin GUS promoter is fused downstream, without auxin genes GUS is not transcribed.

D) LBD 16 mutant exposed to 1um IBA, GUS staining on lateral roots.

E) LBD 16 mutant exposed to 10um IBA, even more GUS staining on lateral roots compared to D) treatment.

....So far I think I understand, below is where I am having problems interpreting my results.

F) LBD 33 mutant no auxin. staining in leaf and roots (all the literature I have found says LBD genes are only active in lateral roots but the stain is present in leaves)

In images G) LBD 33 mutant exposed to 1um IBA, and H) LBD 33 mutant exposed to 10um IBA, the expression of LBD 33 genes seems to decrease by adding more auxin, but when I read journal articles they all say that auxin up-regulates the transcription of LBD33 gene. I thought that if these genes are auxin induced shouldn't expression increase when more auxin is added?


texts: Can ovulation and menstruation occur simultaneously?

texts:
Is that possible that ovulation happens in the time of actual menstrual haemorrhage in human females - let say in a case that woman has 21 day cycle and her menstrual period is 7 days?

If yes, does it means that in this particular case the woman has lower chances to conceive?


texts:
This cool design was "tattooed" on this leaf.

I found it on the windshield of my car.

What's up with it?


texts: Separation of smaller DNA fragments and larger fragments without using gel electrophoresis?

texts:
For an upcoming experiment I would have two kinds of DNA fragments in a sample after a particular reaction step: First there would be fragments of a length of approx. 170 bps and then there would be Fragments of a length of approx. 270 bps or more.

I would like to maintain all fragments with a length of 270 bps or more and throw out all fragments with a length of 170 bps.

Of course, I could run everything on a gel and collect just those bands above 170 bps.
However, I am wondering whether there is something more elegant to reach that aim. For instance, we could use a filter that collects just those fragments with a size of 200 or 250 bps or more and those fragments with a smaller size flow through the filter.
Is such a thing possible and if so, how? Or would you suggest something else?

Many thanks for your support in advance!


texts: Why is the formation of an enzyme-substrate complex endergonic (induced fit model)?

texts:
In the section about the induced fit model for enzyme substrate binding, my MCAT textbook claims that "The substrate has induced a change in the shape of the enzyme. This interaction requires energy, and therefore, this part of the reaction is endergonic."

As a chemist, I am a bit confused here because induced fit suggests that some kind of bonding must be happening between the enzyme and substrate (hydrogen, ionic, covalent, etc) that would induce a change in structure of both enzyme and substrate. Any kind of bond formation is STRICTLY enthalpically exothermic, so why is the formation of an enzyme-substrate complex endergonic?

Am I missing an entropic component here? Or is my assumption wrong, regarding how the induced fit chemistry operates?

I would assume that it would TAKE energy to then cleave/break all the bonds that induced structural change and release the catalyzed substrate...


texts:
Animals can use their circadian clocks to determine direction from the
  position of the sun. In a particular experiment conducted in Iceland,
  a bird, kept in a cage open to the sky, was trained to seek food on
  the western side. Its circadian rhythm was then phase-delayed by 6
  hours and after phase shifting, the bird was returned to its open cage
  at 12.00 noon real time. It was observed to seek food in the:

  a. north.

  b. south.

  c. east.

  d. west.

I think that if its circadian rhythm was phase delayed by six hours, at noon, it will feel that it is still 6 a.m. So, the sun will be located in its "east" and it will try to seek food in the "west" but its"west" will be our south. So, answer should be south. Is my reasoning correct ?


texts: Breathing with Clogged Nose during Sleep

texts:
This just happened to me recently, I was trying to sleep with clogged nose, so I tried breathing through my mouth. As you can imagine it was hard, but I managed to sleep deeply.

So I became curious, how does our body know whether to breathe through the nose or the mouth especially when we have a clogged nose during the time when we are in deep sleep?

NOTE: I tried researching this, but most result just shows how to clear clogged nose before sleeping


texts: Caterpillar identification - found on a coffee plant inside a house

texts:
Today, I've found a twig-like caterpillar hanging down from my homegrown coffee plant (which explained why some of the plant's leaves appear to be eaten away). What specie is this insect? It was about 2 cm long, I live in Central Europe.
Image of the caterpillar is attached below, and here is the movie of me annoying it.


texts: Is there any research paper state the pros and cons for human to be taller?

texts:
Is there any research paper state the physical health pros and physical health cons for humans to be taller?

For example, shorter people seems to more likely to get involved in heart diseases and taller people to be more likely to be involved in cancer


texts: Which countries do not feature mosquitoes?

texts: Please, I am so itchy, I need to know: which countries are free of mosquitoes?


texts:
This question was posed in our endocrinology class, however I have no idea how to answer it:

The thyroid gland of a 5-year old boy is transplanted from its normal position in the neck to the abdomen (between the kidneys). Assume that the gland develops a good blood supply in its new position and that it remains alive.
List the abnormalities that will develop in this child:

after two months.

after 10 years.

Any help will be appreciated.


texts: Is there a limit to how much concise information a human can learn adequately?

texts:
Like, I am trying to learn more chemistry, but also computer programming from the higher-level programming methodologies, frameworks, languages, APIs, XML, web development, and I'm also hoping to improve especially with computer hardware/electrical engineering, and I am trying to improve my pixel art/graphic design/animation skills all at the same time, that is no set schedule for any, and just learning whatever I get my hands on.

Is it possible to learn this way for a human, or will this eventually become too much, and I'll have to sort them/order what I learn separately?

I have not been seeing very much success, but I do keep learning. The problem? Well, I can't get a good grasp on any subject because I am interchangeably attempting to learn all of the aforementioned subjects sporadically, interchangeably, and without any fine schedule. Is this a wrong way for a human to learn, or is the human brain capable of constantly & linearly learning anything in any order very well?


texts: Are there other mechanisms for mutation besides imperfect DNA replication?

texts:
I was reading http://www.askamathematician.com/2012/05/q-is-quantum-randomness-ever-large-enough-to-be-noticed/ and saw:

  [...] the evolution of entire species can be changed by a single
  mistake in the replication of a strand of DNA (this is one mechanism
  for mutation).

... implying other mechanisms for mutation exist. Do they?


texts: Is local equilibrium a reasonable assumption for evolutionary processes?

texts:
Whenever I look at discussions of fitness landscapes (in particular, Kauffman's NK model) the questions tend to resemble:

  The population is at a local equilibrium, but another equilibrium of higher fitness exists, how will the population cross the fitness valley between these equilibria?

These sort of statements assume that the population has reached a local equilibrium. Although, the local equilibria must exist, why do the people working in this field believe that they can be found before environmental (or other external events) change the fitness function? Are the timescales required to go from a random initial population to one that is at a local equilibrium compatible with the typical time-scales on which a fixed fitness landscape is an appropriate approximation?

If we switch to the polar opposite model of complete frequency-dependent selection (say replicator dynamics in evolutionary game theory) then limit-cycles (think rock-paper scissors game) and chaotic-attractors are common and it is possible for the population genetics to be constantly changing and never at equilibrium.

In an experimental setting, it also seems like although beneficial point-mutations are much more rare than deleterious, they do exist. This would suggest that experimentally, organisms are not at a local equilibrium. Do model organisms tend to be at local fitness equilibria?

In general, is the local equilibrium assumption in fitness landscapes research a reasonable assumption?


texts: Do white Australians have a distinct look?

texts:
Background
I've heard from many people working in tourism or similar industries that, white Australians can be recognized as Australian solely by their facial features. Being Australian myself I've heard variants of the claim quite often and lean towards the claim being at least, a possibility.
While it's true that people tend to see patterns when there are none or incorrectly attribute, why they correctly recognize something. I don't necessarily think that is the case here. Australians don't tend to dress in a distinguishing way when overseas, and people have recognized them before hearing them speak. Given the extent to which I hear this claim made, I can't completely dismiss it.
Examples of claims
This article from an Australian newspaper in 1943 interviews an artist who when asked if Australians have a racial type, says he thinks that it was generally possible to distinguish an Australian [from other Caucasians] due to differences in the nose and differences in the jaw.
Googling for terms like "look Australian" returns examples of the claims strewn around the internet, such as this forum thread and this blog.
Also of note is the art project to show the average face of Sydney, of which the following quote is relevant:

In many cases, however, the likeness is so strong that it's possible
to guess the nationality just by taking a cursory glance at the photo.

Reasons for thinking it may be possible
I'm fairly ignorant when it comes to biology, although there are a few reasons I think this might be possible. The (relatively) small gene pool from when Australia was colonized could have led to features from a small group being inherited in a large population.
There seems to be some evidence that environment can play a large role in influencing genetics more so than ethnicity. I can't find the paper investigating that, although will update this question if I am able to.
It seems possible to me that facial features belonging to the original colonists could have spread through subsequent populations, becoming a defining characteristic for some Australians.
I don't think most immigrants are relevant to this question as they will not have inherited distinguishing features (if they exist), nor will they or their parents/grandparents have been able to be influenced by the environment - if that is even a relevant factor.
So...
Do a significant number of white Australians, excluding 1st or 2nd generation immigrants, have distinct facial features unique or generally only found in Australia?
Is it reasonable that some white Australians could be recognized as Australian, going only by facial features?


texts:
Is the overall biomass decreasing over time, and if yes, has that trend started within the last say $200$ years (about when industrialization started)?

EDIT. Let me add some of my own attempts to answer this question.

Reasons that the biomass might be decreasing. Humans have such a big impact on the environment that the current era is called the Anthropocene. Species are disappearing in masses. We put a lot of artificial chemical substances like pesticides and herbicides into the ground. All this makes it plausible that the overall biomass is decreasing. However...

Reasons that the biomass might be increasing. Humans are big animals, bigger than most species (and host to many bacteria). Their number has increased sharply in the last $200$ years. The $\text{CO}_2$ that humans output might lead to increased plant growth, and the higher temperatures might make macroscopic life possible in areas with little life.

Bottom line. It might be the case that animal biomass is increasing (due to human population growth), but the total biomass is decreasing because of the intense deforestation in the Amazon basin and other places.


texts: Are there any alternatives to the Epicentre product Plasmid Safe?

texts:
I need to remove any traces of linear DNA (both single and double stranded) from a ligation reaction while keeping circular DNA intact. Up to now, I have used Epicentre's Plasmid Safe to do the job. I would like to try another solution (mostly because of the unreliability of our supplier: it takes weeks to get a batch!).

Has anyone replaced Plasmid Safe with other nucleases? Which one?
I have been looking at the NEB nucleases and I was thinking to use ExoV and T together to get rid of any linear DNA (both ssDNA and dsDNA). Does anyone have any other solution to propose?


texts: Do species ever go extinct by becoming too successful?

texts: Are there examples of species that have driven themselves into extinction by being too good at what they are doing? Like a predator that evolves to hunt so efficiently that it kills all it's prey and then goes extinct itself.


texts: Did all early mammals have fur? Is it possible to trace the origins, how early animals with fur looked like and how it evolved?


texts: How long does it take for animal dander to break down?

texts: If there are animal dander on an article of clothing, how long would it take under normal conditions (kept unused indoors) for the dander to decay enough so that a person allergic to the animal no longer has an allergic response to the item?


texts: Black bumps on the cut surface of an avocado

texts: I cut an underripe avocado in half and put half of it, without the pit but with the peel, in the refrigerator. A day later, I see very small black bumps along the cut surface. What are they? What causes them?


texts: What is the number of species known through paleontological evidence?

texts:
Essentially, this question could also be asked: how many species do all of the paleontological specimens in collections (or collections records) represent?

I recognize that species is a temporal concept when thinking about differentiation across time; but, natural history collection catalog specimens to species level, so there must be a reasonable basis to make this distinction.
Also, note that I'm not exactly interested in inferred species (i.e. if we have records of species A and species B, we might infer a last common ancestor, species C).


texts: The human has 46 double chromosomes or simple chromosomes?

texts:
What I mean: does the human cell have 46 of these:

or 46 of these:

Thank you in advance.


texts: Herbivorous plants that consume falling leaves

texts:
I've just seen a report about specialized herbivorous plants which build special traps to catch falling leaves from trees above them.

The only thing, which I'm missing is the correct name of this plant. Do you have any idea what plant(s) could this be?


texts: where to buy DNA sample kit? why isn't it easy to find online?

texts:
I guess you can say that it's a hobby of mine to research my ancestry and gather as much information from my family's history as I can. Being a student I can't afford to pay for mtDNA or Y DNA test of my relatives. For the first time I'll be doing it for myself fortunately :)
Now I came up with the idea of storing saliva samples of my oldest relatives just in case they pass away. I'm afraid that can happen at any time since they are getting very old. I guess it's a good plan for now. It still depends on how much a DNA sample kit costs. I'm not going to say any brand names here, but it'd be very nice if someone pointed me out where I can buy self-collecting saliva sample kits on the internet. I've found producers, but no online store.... I also wonder why this is the case.


texts: How would one calculate the availability of nucleotides to an enzyme?

texts:
How would one calculate the availability of nucleotides to an enzyme like a polymerase ?

I imagine an answer in units like nucleotides per second per enzyme, but I'm also imagining an answer that is not a simple rate of reaction. k_on calculations and k_off do not offer mechanistic explanation.

I'd like to know, specifically, if there is a theoretical approach to this question:  how does a polymerase reject an incorrect nucleotide?


texts:
As a protein denatured, it may lose its functions.
So theoretically if I heat some type of biological toxins like poisonous mushroom to 100 oC or higher temperature, will I able to eat it? (I know peoples still death after eat them even boiled to 100 oC, but why?)
Is there anyway to make them edible?

Update: i know some protein can survive in high temperature, for example: taq polymerase. Can i destroy it functions by boil it to higher temperature like 140-160 oC at higher atmosphere pressure and then return back to normal temperature?

Update2 : i found some information on the internet by searching keyword "toxin destroyed by heat" : http://aggie-horticulture.tamu.edu/food-technology/bacterial-food-poisoning/

The botulinum toxin is destroyed by boiling the food for 10 minutes.*
.
So it's depend on the type of protein, the heat and time.

So is there any way/formula to predict the temperature and time to destroy a protein? Or is there any absolute temperature and time to kill most type of protein ?


texts: Is it the theory of the 5 senses obsolete?

texts:
An enigmatic topic in traditional science was labelled as the mystery of the 5 senses, and how to best group senses by type.

Is that theory now meaningless?

Do Scientists still agree that that there are 5 types of sense, and no salient new 6th sense which can't be classed with the others?

There was widely accepted merit for that summary classification, because it was the best logical process to approach a complex subject.

The theory questioned the controversial logic of these groups: Soundwaves, Photons, Chemical scent of the air, chemical scent of taste and touch which represents any nerves found in the rest of the body.


texts:
Six restriction enzymes discussed in Sequence-specific cleavage of RNA by Type II restriction enzymes (Murray et al.) have the ability to detect and cut RNA strands with that enzyme's recognition sequence.

As you know, restriction enzymes come from a system carried by some bacteria referred to as a restriction-modification system.

With this fact in mind while reading the paper above, I wondered how the bacteria carrying one of these six systems protects it's own RNA from restriction. Do the corresponding methyltranferase in each system methylate DNA as well as RNA? Would this not greatly sacrifice gene expression rates seeing as the methyltranferase surely cannot methylate all the RNA sequences being produced?

Perhaps I misunderstood the paper somehow. Could it be only in some circumstances outside the cell that these restriction enzymes have this unique ability?


texts: Why can plants handle extra chromosomes much better than animals?

texts:
Why can plants handle being polyploid way better than animals, where it is almost always fatal?
I found a 2004 paper while searching about this topic, but I'm wondering if there have been any recent discoveries and if scientists are still actively looking for a definitive answer.


texts: Aloha, I live in Hawaii working with sharks and their sensitivity to magnetism but here we also have large cockroaches. Has anyone worked with cockroaches and magnetism?  I wonder if placing high magnetic fields near food and anywhere else, would repel cockroaches. Mahalo and aloha.


texts: Why are the walls of the bronchioles folded?

texts: The bronchiole shown in the section above has folded epithelium, why is this so?


texts: Calcium ions and bacterial transformation

texts: What is the mechanism by which calcium ions and heat treatment allow the bacterial membrane to become permeable, allowing the uptake of plasmids?


texts: How does gold chloride stain neuromuscular junctions?

texts: Gold chloride is used in muscle biopsies to stain the NMJ. What is the substrate that it binds to?


texts: Why can blood vessel contraction be described as a second order system?

texts:
Suppose that the x-axis represents time, and the y-axis vessel diameter.

Then this graph is claimed to roughly describe what happens when the blood pressure increases, then decreases.

When the blood pressure first increases, the vessel diameter expands to its maximum radius. Then it contracts. What I don't understand is why it keeps on expanding and contracting after its initial expansion - does this model still make sense after its initial expansion and contraction?

Can anyone explain?


texts: What is this flat dry stick-like leaf that rattles?

texts:
I googled those terms but came up empty, here are three photos with a ruler for scale:

The hole and scratches are my dog's teeth, so as you can tell, it is strong yet not brittle. When you shake it, it rattles, like maybe there are seeds in there.

It's from a public irrigated park in a Northern Hemisphere hot desert climate (BWh) region, and I picked it up today, so spring time if that will help.

My dog is usually the one to find it, and we play fetch with it.


texts: We're producing some membrane proteins and they aren't amenable to freeze thaws even when we add glycerol. The proteins are solubilized in detergent above the cmc so they should be in micelle form in solution. Currently, they are being held at 4C. I'm curious what is the best way to store them for long term use?


texts: What change would you expect in phospholipid orientation of the membrane if the enviornment were mostly heptane?

texts:
The external and internal environment of the cell is basically water, thus phospholipids organize themselves the way they do (bilayer). If the environment were to magically become mostly heptane, how would the phospholipid orientation change?

Phospholipids maintain their structure in the cell membrane because of the hydrophilic heads and the hydrophobic tails. Much unlike water, Heptane (CH3-CH2-CH2-CH2-CH2-CH2-CH3) is non polar and thus would not cause the heads to present themselves on the outer bilayer and the tails to tuck themselves away.

Because heptane is non polar, I wouldn't expect there to by any hydrogen-bonding going on, so I don't think that we would see an "inverted bilayer". I could be wrong though.

My thought - the cell membrane would cease to exist, I can't think of what would hold it together, but that seems a bit out there.
Thoughts?


texts: Are there dangers to Teflon and aluminium cookware?

texts:
I've been reading some articles on the internet about dangers of Teflon and aluminium to the body.

My family say I'm just exaggerating the situation, and maybe I am, though I'm not sure because not everything on the internet is true. They always tell me that if aluminium were dangerous then why would the government allow the use of aluminium bottles in drinks.

Are there strong references and facts to support dangers associated with aluminium or Teflon cookware? If aluminium or other chemicals enter the body from cookware, are they naturally eliminated, or do they remain in the body?


texts: How does vasoconstriction/vasodilation change blood pressure?

texts:
Background: I am coming at this question from an electrical engineering background, and I feel like I am missing certain assumptions that are going into the statement found in my physiology textbook, "vasoconstriction increases blood pressure"."

Consider a simple series circuit and a parallel circuit run by a battery/heart [you will find the parallel and series circuit in any physiology book description of the vasculature, yet I can't find any exploration of the assumptions made when applying these circuit models]:

In the series circuit, if I have an increase in resistance across
one of my resistors, this will basically redistribute the pressure
drops across the resistors, but it will not alter the total pressure
drop across all the resistors [fixed by the heart].
In the parallel circuit, if I have an increase in resistance across
    one of my resistors, this will redistribute the flow to different
    branches, but the pressure drop will not change as again this is
    fixed by the heart.

This analysis seems to suggest that if the resistance across an organ [branch of parallel circuit] changes, the flow changes, not the pressure. The heart, I would assume, then responds by increasing the pressure to increase flow ie actually injecting energy into the system.

Here is the problem with the circuit model though:

it assumes that the battery/heart is the only source of energy in
the system, and the resistors are passive re distributors of that
energy.

the controllers of vascular resistance are smooth muscle which must actively put energy into the system to vasoconstrict. This could be
a source of pressure increase as the smooth muscle would be actively
constricting against an incompressible fluid, but I am really not
sure.
it does not account for the compliance of the vasculature.

-the tubing the heart is hooked up to modifies the blood pressure the heart has to generate to inject fluid into that tube. If the tubing was stiff, the heart would have to generate very high systolic pressures that would then rapidly decrease during the diastolic phase. The more compliant the tubing, the less pressure the heart has to generate to inject fluid into the tube. Intuitively though, there would seem to some relationship between the ability of a fluid to flow and vessel compliance. A highly compliant vessel with a fluid injection will simply expand and hold the fluid while a less compliant vessel will maintain a pressure necessary to push the fluid along.

Sparknotes in the form of questions:

Is the only source of energy in the cardiac circuit the heart? Or
does artiole smooth muscle actually inject energy into the system,
        and result in systemic increases in the pressure available in the
        closed circuit.
I don't think vascular compliance ie expansion of the artery walls
due to volume filling results in any active injections of
        energy into the system..it should simply transfer the energy
        available to push fluid to elastic energy in the connective tissue
        of the artery walls. Is this correct?
Does vessel compliance partly determine the pressure the heart has to inject into the system?
What is the relationship between compliance and flow if there is one?


texts: How can twins be born months apart? What is the science behind it?


texts: Why can't we defibrillate the heart within 1 minute after ventricular fibrillation by electroshock?

texts:
We mostly can defibrillate the heart before 1 min of ventricular fibrillation by electroshock.Then we often can't do defibrillate it with electroshock.

What's the reason and What's the best way to defibrillate heart within 1 min after ventricular fibrillation?


texts: How exactly does a plant know where water and light are?

texts:
I actually researched on this, but nothing was found regarding this. The only thing I found is that auxins grow on the farthest side causing it to elongate. Yes, but how exactly do the plants know where the source is. In the case of water,  For example, the roots always grow toward the water but how do they know it is water?

How does a plant know where the water source is?

Some web pages regarding it, but my question has no answer:

tum.de
wow.osu.edu


texts: Evolutionary advantage of F plasmid in bacterial conjugation

texts:
Hi I would like to ask a question on bacterial DNA exchange, namely conjugation via F plasmid. It seems to me that all the F plasmid codes for is the sex pilus. What is the evolutionary advantage of the F plasmid? Does it code for anti-biotic resistance as well? Or enhances binary fission for reproductive success? Also, if conjugation transfers duplicated F plasmid from a F+ cell to an F- cell, why aren't all bacteria cells (that are capable of being F+/-) already F+? Is there a mechanism that somehow degrades your F plasmid?

Thank you in advance! I couldn't find the answers anywhere online.


texts:
According to some scientists, at one point in time in this planet's history cyanobacteria almost drove life to extinction by reducing it to a snowball as they captured vast quantities of carbon and locked it up.

Today we face a different challenge where we have excess carbon dioxide (and other greenhouse gases) in the atmosphere leading to a warmer planet which threatens its current inhabitants.

As someone who studied applied physics I have very little understanding of how cellular and molecular biology work. But is it a viable solution to build artificial sinks of cyanobacteria in controlled environments at various places on the planet to capture this excess carbon dioxide? If not then what stops us?

I could think of some challenges:

As cyanobacteria need sunlight to capture carbon so the reaction will be limited to the surface where we will have most sunlight. But one can improve the efficiency by building columns which have embedded light sources (using solar/renewable energy only) at various points within.
Maintenance of these pools/columns.
An economic model to make this a profitable venture for companies. Can the end products produced by these bacteria be sold for money? Can they serve as an ingredient into some other (profitable) reaction?


texts: These critters have taken up residence in standing water in a small terrarium. It is home to several frogs and lizards. If they will coexist peacefully, I have no objection. If they will harm plants or critters I'll have to evict them.


texts: What is the mass of a single erythrocyte?

texts:
I really have been searching through internet on different languages, but can’t find any article that answers on the question what is the single erythrocyte mass. I don’t know, I think it’s pretty easy to calculate experimentally, but I didn’t find anything.

Has anyone measured single erythrocyte mass, and if yes, what is the value?

My try

Experimentally

I am not biologist or medical student. What do I know: blood consists of liquid part(water, salt) and solid part(red blood cells, white blood cells and thrombocytes). If It is possible, the white cells and thrombocytes can be moved off the blood in some test tube, so that will left only erythrocytes. Then, there should be medical statistical value like erythrocyte density or number of erythrocytes per liter.

We have some blood with only erythrocytes, we know how many erythrocyte are there. We can measure that blood weight, substrate the liquid weight(somehow), divide by erythrocyte number and will get the mass of a single erythrocyte.

Theoretically

About 90% of erythrocyte mass is hemoglobin. Hemoglobin is a molecule. Molecule is a countable thing, so, perhaps there is information about how many hemoglobin molecules, in average, is in one erythrocyte.

According to Angelo D’Alessandro, Monika Dzieciatkowska, Travis Nemkov, and Kirk C. Hansen article Red blood cell proteomics update: is there more to discover? it is about 270 millions per red blood cell. Molecular mass of hemoglobin is about $64 kDa$, absolute mass equals $1.106*10^{-22} kg$.

If my assumptions are correct, then 90% of erythrocyte mass is about
$$2.97*10^{-14} kg$$


texts: Looking for a database of plant features

texts:
To perform some private data science experiments I am looking for accessible information on morphological plant features (tabular information would be best). Crawling the web I found many websites with limited more general description and a lot of information on location and population data.

Do you know a website, institute or person in possession of such data and willing to share it? Since I am located in Germany my main interest is in the local flora, but any other would also do the job.


texts:
Why has life evolved around oxygen? Many lifeforms require oxygen to breakdown bio-molecules and release energy. I think there are two possibilities:

Reactions with oxygen tend to release more energy, so it is profitable to use oxygen for metabolic activities.
It is chance that it got to be oxygen; it could have been anything.

Which is right? Or is there some other possibility?

Edit: Yes, it is true that there are organisms to which oxygen is toxic. But you can't ignore the large numbers of organisms to which it is absolutely necessary for living. Why could it not have been some other molecule? Which property of oxygen drives it to become the most useful in bio-processes?


texts:
Walking past the park today, I heard a cicada so loud I thought at first it must be some sort of large power tool. How is it that that very small animals like cicadas (crickets, etc.) can make such loud sounds? It seems intuitive that larger animals should be able to make louder sounds, but perhaps:

a) I just fundamentally misunderstand the physics involved

b) A theoretical larger animal should be able to make louder sounds, but cicadas are just extremely efficient, making up for their small size

c) ?


texts: Standard datasets for testing new multiple sequence alignment algorithms?

texts: Are there any open and freely distributed standard datasets for testing new algorithms for multiple sequence alignment?


texts:
I have watched a talk by Mikko Hypponen (CEO of the security company F-Secure) called Silicon Plague. There, roughly at minute 51 of the talk, he mentions a computer code that is supposed to be able to infect DNA.

I was googling and found the corresponding article posted ~2.5 years, and some c++ codes. Let me cite:

 The computer code, written in C++, hosts the DNA sequence of M.mycoides
 JCVI-syn1.0. At runtime it acts as follows:

 1) Preparing the DNA sequence of M.mycoides JCVI-syn1.0 in the memory,
    (with slightly modified watermarks).
 2) Encoding own file-content in base32. The base32 code is then encoded in
    JCVI's DNA-encoded alphabet.
 3) This representation of its digital form is then copied to a
    watermark of the bacteria's genome in memory. With this, a fully
    functional bacterial DNA sequence including the digital code is
    generated.
 4) Next, it searches for FASTA-files on the computer, which are text-based
    representations of DNA sequences, commonly used by many DNA sequence
    libraries.
 5) For each FASTA-file, it replaces the original DNA with the bacterial
    DNA containing the digital form of the computer code.

 The code has a classical self-replication mechanism as well, to eventually
 end up on a computer in a microbiology-laboratory with the ability of
 creating DNA out of digital genomes (such as laboratories by the JCVI).

As far as I understand, the program tries to go into biology-lab computers with genome files, and modify the content with some content of itself. This sounds scary. Unfortunately, I'm not at the level yet where I would understand whether that could work (undergraduate student), so my question is: Does that idea work? Could there really be a computer virus that infects DNA?


texts: What does it mean when you "extract the filtrate with ethyl acetate three times?"

texts: "The fermentation broth (600 mL) of each endophyte was filtered, and the filtrate was extracted three times with ethyl acetate at room temperature and further concentrated in vacuo to give dried residues prior to antimicrobial assays"


texts: Is there any system how genes are spread across chromosomes?

texts:
Every chromosome being a wrapped DNA molecule contains thousands or more genes.

Now, is there any system why a gene A goes to a chromosome K and gene B to chromosome J?


texts: What is the efficacy of Pertussis booster vaccine among different age groups?

texts:
The Murray Microbiology book says that it is prefentially 10 years, similarly Estonian and Finnish health associations.

However, my professor says that it can be 5-7 years.

I started to think if the age is affecting here to the result.

When should you take booster vaccination of Pertussis if you are
a) 25 years old,
b) 50 years old,
c) 70 years old, and
d) 90 years old?

My professor says that there is no significant studies about the efficacy of Pertussis booster vaccination among different age groups.
Is this true?


texts: How protozoa spawns in newly formed ponds?

texts:
How big protozoa like Paramecium caudatum, Amoeba proteus, Euglena viridis etc. appear in newly created ponds of water? Suppose there was rain, and pond was formed. Or earth, dead leaves, live leaves and wood was added to bottle like in this video:

https://www.youtube.com/watch?v=j2T__l7FgU4

She says in this video that paramecium "should spawn from the dirt", but this makes no sense to me... Do they magically recombine from inorganic elements? Doubtful. Or maybe they are just scattered in every grain of dirt, everywhere, in a form of microbial cyst? Seems not very realistic either...

P.S. I'm mostly interested how Paramecium caudatum get in there, but if other protozoa have some other means, that would be interesting too.


texts: What’s the reason for isovolumic contraction and isovolumic relaxation?

texts:
During cardiac cycle, there are two periods in which the heart volume doesn’t change, but there is a change in tension/pressure. It takes about 0.25-0.35 second to achieve this change.

I searched in Google and Wikipedia, but could not find the reason, so I decided to ask this question.


texts: Is it possible to process electrical signals from the brain and interpret the results as exact thoughts?

texts: If the brain uses extremely low voltage signals to communicate (from what I understand around 100 mV), what sort of breakthroughs would be necessary to intercept these signals and interpret them as exact thoughts? I know we interface with the brain's electrical field through already at a much higher level, but what is stopping us from being able to interpret it more precisely?


texts: What is this toad suffering from? Myiasis or chytridiomycosis?

texts:
I found this toad on Aug. 29th at this location: position on osm

I think it is a bufo bufo, approx. 10 cm long. The nostrils seemed to be completely filled with a grey matter and from the activity of the floor of the mouth it apparently tried to breathe againgst this obstruction. It probably had enough oxygen via its skin though.

I tried to remove the obstruction using a blade of grass but this seemed to produce some pain as the toad closed its eyes on contact, so I stopped. The skin looked fairly normal and the toad was able to walk away after a while.

I can think of two causes for this condition.

Batrachochytrium dendrobatidis infestation
Lucilia bufonivora larvae

I could not see properly, if there were any larvae or unhatched eggs inside the nostrils, but as the rest of the skin seemed unharmed I assume the latter.

Is my assumption valid or is there even a third possibility?


texts: I'm reading a paper that on a population genetics study where they sequence a number of genomes. The study states that 101 Singleton Variants per individual where found. What does Singleton mean?


texts: Elevated position effect on recovery times from upper respiratory infections at rest?

texts:
In nursing school, they advice for people with upper respiratory infections to be in a slightly elevated position at the head region when sleeping.
My intuition of the reason is that the lymphatic drainage to the venous arch works better; gravity helps to drain the lymph to the venous system; not only the heart.
Bacterial infection of the pharynx occurs in a prolonged exposure of the concentrated lymph.

I got today exact information about exact positions to relieve the body most when sleeping:

5-10 % angle to relieve body most, while gravity helping to suck the lymph from the throat; can be helped with the hormone motilium (domperidone)
more than 10 % is for other conditions

Is there any studies about the effect of elevated sleeping position on the recovery time from the upper respiratory infection?


texts: meaning of binding capacity and binding affinity

texts:
Actually, I am unfamiliar to biology, so when I read a thesis, the term "binding capacity" and "binding affinity" are really confusing.
Since my major is unrelated to biology, I don't know correct definition. Is there anyone who can explain differences between them clearly? Any references would be helpful, thanks!


texts:
You are studying cellular signalling through a newly identified GPCR.
   Specifically you’re working on a pair of newly identified GPCRs,
  GPCR-A and GPCR-B. Each binds the same small ligand, but activates different
  heterotrimeric G-proteins that act on adenylyl cyclase.
  Your grad student mentor explains that both the receptors and the
  Gα and Gβγ subunits of the heterotrimeric G-proteins are membrane associated.  You examine the sequences of the seven predicted
  transmembrane α-helices of GPCR-B. You’re surprised to find that there are
  hydrophilic amino acid residues in these helices. How can you explain this
  observation?

This was an MIT quiz question.I have my guesses. But I wanted to know the correct answer.

Well, since GPCRs are transmembrane proteins, normally the transmembrane helices have higher hydrophobic amino acids or only hydrophobic, non-polar aa . Here it says they saw some polar residues. Well my guess is that, since there are two GPCRs a and b that bind to the same ligand, it could be that one activates a stimulatory G protein and the other an inhibitory G protein Gi . So probably the polar amino acids which are in the transmembrane alpha helical segment of the stimulatory GPCR is slightly displaced and is in the intracellular region of the inhibitory GPCR (Gpcr that activates inhibitory G protein ). To be in the intracellular region, it has to be hydrophilic.
This is all I can think of.

Any help with this question is much appreciated. It is not a homework question for me. I don't go to MIT. I just wanted to reinforce my concepts.


texts: When did human and animal blood became distinguishable from each other as forensic evidence?

texts:
Since a few decades ago, DNA testing became an important tool in criminal forensics, and a lot of information can be gathered from a single drop of blood or from a few cells.

Even before that, blood type could be used even in the early 20th century, to at least exclude 3/4 of possible suspects.

However, when did it first became possible to distinguish between human and animal blood, and what method did they use? Is there information about the first time it was used as evidence in a trial for forensic purposes?

I would suspect it was not sooner, or not much sooner as the discovery of the ABO blood types at the beginning of the 20th century. There are modern, much more accurate methods, and the introductory parts of such papers likely mention the early history, but they are behind paywalls.


texts: To determine no beating cardiomyocytes from ECG or video recording

texts:
I am trying to find data and some method by which I can see and say that there are some cardiomyocytes not working.
I have reviewed many arrythmia data where I think I can see much cardiomyocetes there and there which are not beating at all.

Is there any method with available data for the recognisition of cardiomyocytes without beating?

I am particularly interested in the paediatric data.
I am using at the moment ECG data after cardiac infarction.

What is the name of this video record?
Picture from House season 3 episode 2:


texts: Have people in Africa already started evolving resistance to AIDS?

texts:
Are people living in areas where AIDS is rampant (for e.g. Africa), less likely to die from it than they once were because some of the people without genes/mutations that give them resistance already died off?

Is there any data on this?


texts: Why do chain identifiers in PDB have no standard starting chain id type?

texts:
At first I assumed that PDB chain identifiers are just uppercase letters (A, B, C,..) but found out there are protein chain ids that are numbers (0-9) and lowercase letters as well.

For example,

1NAL only has chain ids (1 - 4). It starts with chain '1' (number).
103L has chain identfier 'A'. It starts with chain 'A' (uppercase letter).
5afi's chain id's range from [a-zA-Z0-6] since it has 52 unique protein chains. It starts with chain 'a' (lowercase letter)

Can someone please explain? Or are id's just arbitrarily assigned?


texts: Why are there no endoparasitic mammals or reptiles or birds?

texts:
I am curious why there aren’t any endoparasitic mammals, reptiles or birds

Endoparasite being a parasite that live In the host whereas ectoparasite lives On the host

I hope this clears up confusion


texts:
Why do we feel sleepy, tired, and feel like we need to sleep more when we wake up? (Like, is there a special chemical in the brain that causes that?).

Are there any ways to wake up without feeling such things?


texts: How long can the average, healthy adult human survive with only water?


texts:
Is there a point where too much CO2 is bad for a plant? Basically when there is too much CO2 in the air can a plant get sick?

Since plants photosynthesize and need CO2 to generate glucose and store starch, and since chemical reactions are pushed toward their end product when the reagent concentrations are increased, one would expect that more CO2 would be better, at least lead to increased growth and survival rates.

Is there a ceiling where CO2 gets toxic?


texts:
Forgive me if this question is too trivial.

I have the gene IDs of the following type

EOG6STSR2
EOG60ZRJB
EOG6SBFJ2
EOG6P5KX3
EOG6B5PRW

from the first supplementary file in Comparative validation of the D. melanogaster modENCODE transcriptome annotation .

I'm not sure as to the type of the IDs. I learned that IDs beginning with EOG are Eukaryotic Orthologous Group IDs but I couldn't find these particular ones in any of the databases.

Is it possible to map them to Ensembl IDs or any of the other commonly used ones?


texts:
What does a geneticist mean when they write "genotype structure", e.g. the sentence "...represents continuous allele frequencies for both tumor and normal samples, while leveraging the expected genotype structure of the normal."

Citation: http://bioinformatics.oxfordjournals.org/content/28/14/1811.long