texts: Is there a 'crural' and 'costal' parts of the diaphragm as suggested in this paper or is it just a single muscle?


texts: Can the kidneys utilize ketone bodies for energy?

texts:
Ketone bodies are water-soluble and should pose no problem to the kidneys because of solubility. If the kidneys are able to utilize ketone bodies for energy, then they must express the enzyme 3-ketoacyl-CoA transferase, correct?

Do the kidneys express the enzyme 3-ketoacyl-CoA transferase?

Can kidneys use ketone bodies as fuel?


texts: Is there a way to know how many sodium channels are active (conducting) at a given time in the brain?

texts: I was doing some reading about anti-epileptic sodium channel blockers, then wondered how many sodium channels are actually conducting (actively passing ions) at any given time, that is, in an "average, awake" brain?


texts:
Exposure of native protein to heat leads to partial denaturation of the protein due to breaking of-
a. S-S bonds
b. H-bonds
c. Hydrophobic interactions
d. Peptide bonds

After a bit of surface googling I understand peptide bonds are not broken in the process of denaturation and di-sulphide bonds are not broken either (by heat) but by reducers like $\beta$- Mercaptoethanol. These reducers are added in experiments to ensure that the bonds which contribute largely to the tertiary structure are broken.
So either H-bonds or hydrophobic interactions are affected. I cannot make out which one would be the most affected/first one to be affected since the question says partial denaturation, meaning, it was not heated for long.


texts:
Is there a way to mass produce a certain species of bacteria?

Answers I am looking for should not involve a Petri dish: I am only interested in protocols involving, perhaps, more efficient mediums to grow the bacterium-in-question.

Is it done with any yet? In a factory or where etc?

How is it done?


texts: Why does my eyes see a red spot when over exposed to light?

texts: When I looked into my projector when it was on the blue screen it left a red spot in my vision. I should not have tried it but all the colors left a red spot. Why not a blue or yellow spot was left?


texts: What determines whether an action potential is inhibitory or excitatory? Is it determined by the receptors, the neurotransmitters, or some other mechanism?


texts: Finding Rna-Seq dataset for C. Elegans (Caenorhabditis elegans)

texts:
I want to find a RNA-Seq dataset for C. Elegans to use it in RNA-Skim software. For those who does not know RNA-Skim let me explain it a bit. It is a tool which is used to quantify RNA-Seq data using sig-mers(special kind of k-mer). Firstly RNA-Skim clusters protein coding genes and find substrings that are special to cluster of that gene. After this preperation stage, it takes an RNA-seq data as an input and tries to quantify transcripts in it. So, I need to find a dataset in fasta file format for this step. Since I'm pretty new in this area, is there anyone who could provide me information about how could I find it?
Complete information about RNA-skim can be found here : RNA_SKIM

EDIT
The type of a dataset I'm looking for is something like that: http://codepad.org/n3ioT3nj .This dataset is for mouse, I need to find such a dataset for C. elegans as I said before


texts:
This question might be silly but I need some clarification.

I'm slightly confused about if there are multiple PAM and BLOSUM matrices? Is there a different matrix for each sequence?

My understanding is that PAM and BLOSUM are substitution matrices that are used to demonstrate how similar a sequence is to other sequences by seeing how many iterations of the matrix multiplication are needed before being able to achieve a "similar primary composition". Is this correct?

As I've understood it this means that if I want to compare 2 sequences together I can just this iterative calculation until the relationship between my target sequence and my initial sequence is maximized and then see if that similarity is enough that I can say they are closely related.

This is all assuming there is one standard PAM250 and BLOSUM62 matrix which I'm assuming are calculated from information derived from all information collected on protein sequences.

So when using PSIBLAST to search for similar sequences using BLOSUM matrices does it calculate similarity scores using BLOSUM matrices and then if this score is above a certain threshold it returns that sequence. If you do this for multiple iterations then what is the next input that it uses?

Thanks

EDIT: I think some of the reason for my misunderstanding is that I'm not sure why there would be one single matrix which can be used to determine the "resilience" of a particular amino acid in general. Isn't the "usefulness" or that amino acid dependent on the function of the protein? In that case shouldn't there be different substitution matrices for different proteins? Is this why PAM matrices have difficulty and is this semi-solved by using BLOSUM matrices which use blocks and so can capture when certain "blocks" of amino acids correspond to particular functions and are therefore seen together a lot and are resilient to change in that way? It still seems a bit strange to lump them together in this case.


texts: DNA methylation on the forward vs reverse strand?

texts:
I'm wondering if there are meant to be differences in DNA methylation between the forward and the reverse strand of the gene? I'm wondering because in primer design for bisulfite pyrosequencing one might only design primers for the forward strand. Should this matter for human/mouse DNA?

cheers and thanks in advance for any advice.


texts: Which poison makes seastars inedible to possible predators?

texts:
In the new citizen science project (see: Sea Floor Explorer), numbers of seastars, scallops, crustaceans and other animals are counted. Already one can see a heavy bias in favor of seastars, both the fat and brittle kind.

I would be interested in why this creature is so succesful, especially if it is poisonous to e.g., crustaceans, and what poisons exactly are responsible.


texts: What gene targets associated with the new coronavirus (SARS-CoV-2) have been identified so far?

texts:
One hypothesis for which we have some supporting evidence is that the new virus (SARS-CoV-2) "enters human cells through an interaction with angiotensin-converting enzyme 2" see here. Although it is still unclear what genes to target in order to prevent the infection (entry or reproduction).

Is there empirical evidence suggesting what genes can be modulated to fight the infection?


texts:
Most sources I've seen say that about 90% of humans are right handed, and 10% are left handed. Why is this?

My only guess would be that it has something to do with different parts of the brain developing differently and causing right or left "handedness", but this is coming from my very little knowledge of the brain.

Furthermore, about 2/3 of people are right eye dominant, and more people are right ear dominant than left ear dominant.

Why the right side?!?


texts: If I squash an insect and it produces red "juice", does it always mean it is a blood-sucking type?

texts:
If I squash an insect and it produces red "juice", does it always mean it is a blood-sucking type of insect? Or do some insects have red "juice" themselves, so the color is red on its own and not caused by sucking higher animal's blood?

I squashed a small fly-like insect recently, it produced a red stain, so I am wondering if the stain come from the insect itself or if it has to be some other animal's blood.


texts: A chromosomal male is XY and a chromosomal female is XX. Now imagine if, one day, this world has only males - is it possible to "recreate" a female by using two X chromosomes from two different males?


texts: In chromatin, what are the differences among states, interactions, and structures?

texts:
I am new to the study of chromatin, and I am trying to understand what people mean when they write about chromatin states, chromatin interactions, and chromatin structures.

What are the difference among these?
Is there someone available to explain them to me clearly?

Are loops interactions or structures?


texts: Are the words biology and Ecology ever interchangeable?

texts:
I often hear people use the word "Ecology" when i think they mean "biology." This got me wondering: are the words ever interchangeable, or are these people really just that frequently using the wrong word?

My understanding is biology is the broader study of life while Ecology is the more specialized study of life interacting with other stuff (life + earth).


texts:
I am wondering how much ribose we ingest as food? (Deoxy)Ribose is found in the backbone of DNA and RNA. So, we eat ribose as part of the nucleic acid found in plant and animal foods. While protein, lipid, and sugar content is well analyzed for many staples we consume, I cannot find any numbers on ribose or DNA/RNA. Does anybody know of a reference to shed some light? For example, how many (milli)grams ribose is in a steak or a salad? I'm thinking about this since ribose is a more reactive sugar than glucose. It can thus cause more unhealthy additions (glycations) to other biomolecules when in circulation, so the quantity take up might matter.

PS: Maybe the lack of quantitative data leads people to the false belief that they don't eat DNA on a daily basis? ;-)


texts: What's the highest temperature that algae can survive at?

texts:
I know there are a lot of different species of algae and that each one has different environmental tolerances. I've seen data on different species:

brown alga Sargassum echinocarpum J. Agardh - grows well at 35°
Dictyopteris australis - grows poorly above 28°
halophilic blue-green algae A. fertilissima - temperatures of 47° stimulates germination

What's the highest temperature that growing algae or its spores can survive at? In other words, what temperature would guarantee that no algae could grow afterwards unless reintroduced?


texts: How can a child be blood type AB, if both of the parents are blood type A?

texts: Basically, both of my parents are blood type A (both are confirmed and it's also certain both of them are my biological parents). I recently found out my blood type is AB. How is this possible? I tried reading about different mutations in blood type, but I couldn't find anything that was similar to my case.


texts: What is the space between -10 promoter sites and start sites (+1)

texts:
Between the transcriptional start site of a gene and the -10 promoter region there is always a space of around 10 nucleotides, what is this space function and purpose?

Do you see the space between operator and promoter.. that is what I am referring to, even without an operator it is usually still there

Also, if I want to insert a specific promoter into a vector backbone, how much space should be between the promoter -10 and +1 transcription start site? Is it always 10 bp?


texts:
These photographs were taken today in Marseille, in the Mediterranean coast of France. My French friends inform me that these beasties are called cousins because they are "cousins" of mosquitoes (whatever that means).

The thing is, we are absolutely infested by them. They seem to be more active at dawn and dusk (like mosquitoes) but we have dozens flying around the house every evening. I would like to know the species' name to see if I can learn anything about them. Do they have cycles like cicadas? Are they linked to stagnant waters like mosquitoes? Why are there so many of them this year?

Here's one with my hand next to it to give you an indication of their size:


texts: Bug Identification: Tiny Bugs in Fairport NY

texts:
We have been finding a ton of these tiny bugs (pin head size or smaller) outside on our patios, outdoor tables, on the grill, etc.

What are they and how do we get rid of them?


texts: We know body surface temperature rises during fevers. Do the internal organs' temperature also rise during fevers? How do they (internal organs) maintain their temperature? Will there be a variance of temperature among them?


texts: Visual phototransduction, neurons depolarization when no light: why?

texts:
While reading into visual phototransduction I was surprised to learn that photoreceptor cells are actually depolarized when there is NO excitation (no light, i.e. when you see nothing, black) and hyperpolarized when there is light (I expected the opposite).

This got me thinking...

Let the collection of neurons located within the eye be referred-to as IEN (inside-eye neurons) and, similarly, the collection of neurons directly linked to the eye, yet external to it be referred-to as OEN (outside-eye neurons).

Let the collection of neurons directly getting input from the retina be referred-to as RN (retinal neurons). I'm assuming RN < IEN (subset of -
 correct me if I'm meaningfully-wrong).

And finally, let the collection of neurons that directly link to OENs but are part of IEN be referred-to as XN (eXporter-neurons, in the sense that they export visual information from the eye to the "listeners" outside of it).

So the path of visual stimulus would then be RN -> [...] -> XN -> OEN.

Now, if my eyes were to be completely popped-out I'm assuming that relative to OENs that would have the same effect as XNs not passing along any excitatory/inhibitory information at all. Also, since what I'd perceive would be pure black, that seems to imply that XNs also don't get activated at all when we actually see black (e.g. close our eyes in a very dark room).

So, when we perceive black => RNs get depolarized => they release glutamate continuously => XNs don't excite/inhibit OENs at all (seems to also imply that RNs don't intersect XNs). It is this inversion that intrigues me - why is it that for XNs to transmit NO information RNs have to continuously be excited? By that sense, this makes me think of the eye as if it was a big NOT gate.


texts: How effective is feces such as cows, chicken or horses for fertilizing the earth of a garden in order to grow crops.


texts: What's the effect of oxygen deficit on plants?

texts: As I know all cells require oxygen. So my question is how efficiently can plants operate in no-oxygen atmosphere? Do all plants produce enough oxygen for themselves? Can they consume their own oxygen or the oxygen will be quickly lost to the air? Is there a plant that consumes more oxygen than they produce?


texts: Problem involving selfing (inbreeding it with itself) a plant to generate purebred lines

texts:
I am working on a past exam problem where the first bit is as follows

  A plant is repeatably selfed to generate inbred lines. Let $\mathbb{P}(He|He)$ denote the probability that a heterozygous parent gives rise to a heterozygous offspring, and let $\mathbb{P}(Ho|He)$ denote the probability that a heterozygous parent gives rise to homozygous offspring.

I am asked to work out the two probabilities as well as an interpretation and state the value of $\mathbb{P}(Ho|Ho)$. The interpretation is obvious and I calculate the conditional probabilities to be

$$\mathbb{P}(He|He)=\frac12, \quad \mathbb{P}(Ho|He)=\frac12, \quad \mathbb{P}(Ho|Ho)=1$$

Next I am given the following

  The inbreeding protocol is carried out $i$ times in an effort to obtain representatives of all alleles that can occur at a locus of interest. Suppose that there are 3 alleles, equally prevalent in the population at large and not under selective pressure during the inbreeding experiment. Let $p_j(i)$ denote the probability that, after $i$ repetitions the lines share $j$ distinct alleles between them. Let $p(i) \in [0,1]^3$ be a vector whose $j$th element is $p_j(i)$. Consider the following equation: $$p(i+1) = M p(i)$$

I would like to calculate the transition matrix $M$ and explain the boundary condition $p(1) = [ 1, 0 ,0 ]^T$.

I am lost on how to do this, I'm given the answer for $M$ to be $$\begin{pmatrix} \frac13 & 0 & 0 \\ \frac23 & \frac23 & 0 \\ 0 & \frac13 & 1  \end{pmatrix}$$

But for example looking along the first line I would interpret this as $$\mathbb{P}(\text{There is 1 distinct allele between all lines at time t}) = \frac{1}{3} \mathbb{P}(\text{There is 1 distinct allele between all lines at time t-1})$$

However if there is a single allele between the lines at time $t-1$ then this means every line is homozygous for a single allele so why would that change at the next time step?!

As for the boundary condition, I would of thought it would be $[0, 0, 1]^T$ since is the alleles occur with equal chance and you select a large enough number of lines, you should find all $3$ alleles between them. I was thinking perhaps there is a mistake in the question/solution and the vectors are defined the wrong way round, but even then I would be confused. Surely the number of lines we have makes a large difference, if every line is of genotype $\alpha_1 \alpha_2$ and we would like the probability that there is a single allele between lines at the next selfing step, then every single line would need to become homozygous for the same allele, which seems unlikely if we have a massive number of lines.

Can someone help me work out what is going on here?


texts:
Theoretically, is it possible to obtain the original gene from the protein’s amino acid sequence as its “template”, as in, the reverse of how gene’s codons were “templates” for the amino acid sequence of the protein?
I’m curious to know if it’s possible to use enzymes such as reverse transcriptase to obtain DNA from a protein in a reversed central dogma model.


texts: Among xerophyte plants, which one grow faster and consume water the least?

texts:
In an effort to select for the most suitable plants to possibly colonise desert and stop its expansion,

what would be the xerophyte plants that grow the faster and expand on surface, while using the less water and produce a maximum of biomass?


texts: How to start studying dinosaurs and pre-historic mammals/sea creatures

texts:
I am new to and really interested in the field of dinosaurs. Are there any good books/websites/webpages to study the biology of pre-historic creatures?
Specifically, I am interested in dinosaurs, mammals, fishes; anything that is not alive anymore. Also, I would appreciate recommendations for any good books about the history and evolution of these groups.


texts:
I live in Northern Virginia, USA. As I am sitting here there is a large flock of small (blackish) birds in a tree. They are quite prevalent here. For the sake of brevity I will call these birds "sparrows." I don't believe it matters what they really are.

There are also several medium-sized blackish birds perched on the eaves of the townhouses. Again, I'll call these birds "crows". (We have a committee of large vultures (yes, really) in the neighborhood as well, which is why I call the crows medium-sized.)

The crows (tend to) lay their eggs in the sparrow's nests. Little crow hatchlings are then "raised by" the sparrow parents, along side thier smaller "siblings".

Does the now adult crow think it's just an oversized sparrow? (IOW, do all of the crows I see have identity issues and feelings of inadequacy due to their extreme gigantism? :) )


texts: Opposite results between Blomberg's K and phylogenetic signal in Phylocom (AOT)

texts:
I've been trying to test for significant phylogenetic conservatism in some plant traits. So far I used R-package picante (Blomberg's K) and AOT in Phylocom. So far these two methods yield completely opposite results for the same traits, and I'm confused. Is it possible to get such very contrasting outputs from these two methods?

For example, one trait shows Blomberg's K = 0.2892 (P = 0.001), suggesting that the evolution of this trait overall has not been greatly constrained by phylogenetic relatedness. In contrast, for the same trait AOT yields variance of standardized contrasts across tree = 0.006, significance of contrast variance relative to null model (low rank) = 1, and significance of contrast variance relative to null model (high rank) = 1000 (i.e., P = 0.002), suggesting that treewise phylogenetic conservatism is significantly greater than the expectations of random tip swapping.

I've just started looking at these phylogenetic signals, so I may be overlooking something critical. I will greatly appreciate if you could kindly give me directions, thank you very much!


texts: What is the relationship between Homocysteine and Norepinephrine metabolic cycles?

texts:
I've been researching neuromodulators and have taken a look at the Norepinephrine/Noradrenaline  system.

The diagram of biosynthesis of Norepinephrine is presented in the wikipedia article:

Catecholamines_biosynthesis

The diagram appears to state that Dopamine gets converted to Norepinephrine , which gets converted to Epinephrine, and as a side effect, Homocysteine cycle gets advanced too (or is it involved?).

This article describes the homocysteine biosynthesis

I would like to understand what this means when two biosynthesis cycles are related like that. If I envision two cycles as connected gears, then turning one would turn the other, and if one is malfunctioning, so will the other. Is this a correct analogy?

What are the implications of the Homocysteine and Norepinephrine cycles touching each other? As far as I understand, Epinephrine(Adrenaline) is a stress related hormone, does this mean that stress also results in elevating the levels of Homocysteine ?

Thank you for your clarification!


texts:
Is it possible to predict how proteins coded from mRNA will be cleaved?
The reason I was interested in this is because I did some initial work to translate the raw Coronavirus RNA sequences, which you can see here: https://github.com/imranq/coronavirus. The background section below has more information on my approach.
With the "naive" approach to translate coronavirus RNA, using AUG as the start codon, I am able to identify 7 out of 24 proteins from Zhang lab sequences. However, I also did some string matching between my amino acid sequences and the Zhang lab final amino acid sequences. After doing that comparison, I see I have 21 out of 24 protein sequences coded in uncleaved protein sequences.
It would be nice to get to the final 24 proteins straight from the mRNA strand. Please help. Thanks!
Background
Here is the series of steps I used to convert coronavirus RNA into proteins.
1. The raw RNA sequences are here (sourced from the NIH):
https://github.com/imranq/coronavirus/blob/main/data/rawrna.json

2. The script to translate the RNA is here (assumes AUG is the start
codon):
https://github.com/imranq/coronavirus/blob/main/scripts/translate.js

The translated protein sequences are here:
https://github.com/imranq/coronavirus/blob/main/data/processed/translatedProteins.json

3. The script used to generate a comparison between the translated
proteins and the known protein sequences is here (using levenshtein
distance as our difference metric):
https://github.com/imranq/coronavirus/blob/main/scripts/compareTranslated.js

The data generated from that script is here
https://github.com/imranq/coronavirus/blob/main/data/processed/translatedComparison.json

4. Then we detect cleavage in proteins by running a sliding window
across RNA segments between the known and translated proteins. The
script to do so is here:
https://github.com/imranq/coronavirus/blob/main/scripts/detectCleavage.js

4. Finally we merge the datasets we generated from translation and
protein complexes into one dataset, translated proteins and protein
complexes matched to known proteins.

The data generated from this algorithm is located here
https://github.com/imranq/coronavirus/blob/main/data/processed/mergedProteins.json

At the end of this pipeline, we get 21 out of the 24 proteins matched straight from RNA.
References:
Here are the papers / articles I researched to answer this question
Turning Genome Data into Proteins
Khan Academy Genetic Code: https://www.khanacademy.org/science/ap-biology/gene-expression-and-regulation/translation/a/the-genetic-code-discovery-and-properties
Zhan Lab - SARS CoV 2 - Nucleotide, Coding Region, and Protein sequences https://zhanglab.ccmb.med.umich.edu/COVID-19/
More in the readme here: https://github.com/imranq/coronavirus/blob/main/README.MD


texts:
I'm doing old exam assignments to prepare for my finals on Monday and I've stumbled on one assignment that I'm not sure how to tackle.

A family with 2 children is examined for cataracts using PCR with 4 markers, A, B, C and D. The results are seperated on a gel and the genotypes are as follow:

Where Far = father, Mor = mother, Barn = child.

Notice that there was an error with the analysis so child 2's alleles are undetermined.

The question states: Draw a pedigree with each of their haplotypes. What is the most likely haplotype of child 2?

I don't understand exactly what it's asking. I'm not sure what a HAPLOtype is. I know what a genotype is and that is what the answer seems to indicate.

The answer for the father is: 4 3, 1 2, 11 5, 7 4. Now the only difference between these numbers and the given numbers are the re-arrangement of 5 and 11 in marker C?


texts:
I first thought that this is because of prolonged depolarisations.
However, I am not sure anymore, because after reading PubChem, the only possible pathways are are Choline agonist.
So I would say that succinylcholine cause myorelaxation by some cholino-receptor agonists.
I do not think it is about depolarisation and how long it is.

How can succinylcholine cause myorelaxation?


texts: How are new people created from the DNA of an aged person. i.e. Why are we young?

texts:
The question "why do we age" has been asked numerous times. But why are we young? The cells of the adult human being are an age (time>0), but how can old cells create new cells that are younger than themselves?

I.e, how are young people made from the cells of old people?

I realize that senescence, the act of a cell aging, has to do with the shortening of telomerase over time which puts a limit (the Hayflick limit) on the life of an autosomal cell. So in theory, because cells only make direct copies of themselves but the telomerase shortens with every division, each new daughter pair would be as old as the parent and would continue aging. But how come new people start senescence at time t=0?


texts: How do macromolecules (large drugs) in the eye reach the bloodstream and what are the relative significances of these pathways?

texts:
I am considering the elimination pathways for antibodies (50-150 kDa) from the vitreous humour to the blood stream. My overarching question is what is the most significant route such antibodies could take to get there?

Elimination from the vitreous humour to the aqueous humour is known to be quite a substantial route of clearance, but does drug eliminated through passage into the aqueous humour travel to the blood stream? Notably there are two routes of exit from the aqueous humour, one is directly into the bloodstream and the other is through Schlemm's canal, but where does that lead?

Also for example is the choroid directly in contact with the hyaloid membrane of the vitreous play a significant role in elimination? We also also such drugs penetrate into (and through) the retina, at that point they reach vasculature, however they have to work quite hard to get there.


texts: Is there any example of living beings destroying their environment?

texts:
I had an argument with someone about mankind being the only being destroying its own environment. I don't think this is true, yet, I cannot provide any example of significant importance.

Are there any examples of a living being destroying its own environment, making it uninhabitable to them? (Bonus point if this event led to an environmental catastrophe or to their extinction.)


texts: How efficient is the sodium-potassium pump ?

texts:
I am reading about transportation of ions in a cell. It is necessary to transport sodium back out and potassium back in, against their electrochemical gradient. This task is carried out by sodium-potassium pump, which transports three sodium ions out across the cell membrane for every two potassium ions carried inward. The source of energy for this transport process was hydrolysis of ATP.
My question is the order of the efficiency of a sodium-potassium pump.


texts:
Expressed in number of Base Pairs or Bytes, about how large is the simplest eukaryotic genome?

How much of this is 'junk-DNA' (non-coding)?


texts: Why does Penicillin only affect bacterial cell walls

texts:
I was quite fascinated by the feature Should Science Pull the Trigger on Antiviral Drugs—That Can Blast the Common Cold? in this month's Wired magazine.

They explain that Penicillin is effective at killing bacteria because it interferes with the growth of bacterial cell walls.

How does Penicillin do that exactly? And why does it not dissolve human cells as well?


texts: Sometimes I have many consecutive "dreamfull" nights but sometimes there is no dream during week. Why? What determines whether I will have any dream or not?


texts: What happens when the conductance of a sodium channel increases?

texts: My intuition is that, since the concentration of sodium within a cell is higher than the extracellular concentration, when conductance increases, this corresponds to the channel being open and means sodium will enter the cell. Is this correct? And what impact will this have on the membrane potential?


texts: How do BCAA's promote faster muscle recovery?

texts: I am aware that ingesting Branched chain amino acids (BCAA's) prior, during, and after workouts has an effect on muscle recovery due to their difficulty of metabolism. However, how much more efficiently do they speed up recovery versus whey proteins for example?


texts: How does the brain immediately know when one's thirst has been quenched?

texts:
The question struck me the other day when I drank a glass of water. I understand that there are at least two conditions under which the brain signals thirst: extracellular thirst, when there's not enough fluid in the blood, and intracellular thirst, when the cells need more water to lower the concentration of osmolites.

However, it takes time for water to enter the bloodstream after it has been ingested, and it spends at least a little while in the stomach.

Why does the sensation of thirst disappear despite the water having not yet made it into my bloodstream?


texts:
So we all know that humans average blood pH is 7.4. But is it the same for the animals?
I need examples of animals with the same blood pH as humans and the ones with different blood pH.
I guess dogs and cats have almost the same pH am I right?


texts: Horned Mohawk looking insect. What is it?

texts:
Any ideas? I didn't know any other way to explain it.

I live in Indiana, USA if that helps.

Someone said it might be a "stink bug" but I'm not sure and not willing to find out!


texts: Is a DNA molecule a single strand of polynucleotide or two of them linked together?

texts:
Our molecular biology teacher told us that a double helix of DNA was composed of two DNA molecules linked together by hydrogen bonds. The thing is, until now, I always thought a DNA molecule was composed of two strands, those being polynucleotides, both of them being linked together. I can't find a link which is saying the same as my teacher, even if it seems technically correct to call a double helix a dimer of two DNA molecules.

I was curious to know what was the exact terminology.


texts: Is starch a better coagulant than cellulose?

texts:
In an experiment, I used plantain peels (with a very high starch content and very little cellulose) and grapefruit peels (with a very high cellulose content and no starch) as coagulants (ensuring that I used equal masses of each peel) to improve the turbidity of water contaminated with wood chips and kaolin. Although the grapefruit was able to remove turbidity, I found that the plantain worked better. By the way, the same amount of cellulose was present (50%) in the grapefruit peels as starch present (50%) in the plantain peels. However, I can't work out why a coagulant concentrated with starch is more effective at lowering the turbidity of water compared to a coagulant concentrated with cellulose? Essentially, I don't know why starch helps more than cellulose with coagulation. Help would be much appreciated :)

If you use this link, you will find the method I used under "Preparation of Bio-flocculant" to turn the peels into coagulants: akademiabaru.com/doc/progeeV1_P47_56.pdf. To summarize, I dried them in an oven and turned them into very fine powder.

Search this up and you'll find previous experiments using polysaccharides (i.e. starch and cellulose) for coagulation: Chapter 2 Mechanistic Insight into the Coagulation Efficiency of Polysaccharide-based Coagulants


texts: Tool for nucleotide alignment with all nucleotide codes (e.g. R, Y, W, S, etc.)?

texts:
I have a vector sequence and would like to find the following nucleotide sequence in it.

AASYWSRA

This query sequence uses several degenerate symbols, defined as:

S = C or G (Strong)
Y = C or T (pYrimidine)
W = A or T (Weak)
R = A or G (puRine)

(See this page for a complete description of the IUPAC nucleotide codes.)

Is there a tool to align this sequence with the vector and find all the possible sites?

EDIT: I found this website but couldn't find any of the resources helpful. Maybe one of these will work but I found most of them too complicated. If you know which one will work and explain how to use it I will be grateful.


texts: Why does dissociation of carbonic acid cause a decrease in pH?

texts:
When a molecule of carbonic acid (H2CO3) dissociates, the two products are a bicarbonate ion (HCO3-) and a hydrogen ion/proton (H+). Because of the addition of a hydrogen ion, this process causes a decrease in the pH of the blood, and if someone breathes too slowly and doesn't quickly remove CO2 from their body, respiratory acidosis will take place.

However, why is it the case that the addition of this hydrogen ion lowers pH? While this might sound like a stupid question, it's also the case that the dissociation of carbonic acid produces a bicarbonate ion, which is a weak base. Therefore, the dissociation produces both an acid and a base in a 1:1 ratio. Therefore, the concentration of hydrogen ions relative to bicarbonate ions doesn't actually change. Given this fact, wouldn't there be no change in pH at all?

I read a paper on carbon dioxide transport which addressed some of my other questions but didn't touch on this precise point.


texts: Why does SDS-PAGE use for protein, and agarose use for nucleic acid?

texts:
My question maybe very primary, but after I learned this part, questions always follow me.
SDS-PAGE gel works for detect protein, agarose gel works for detect nucleic acid, so here is my question:
1. Why does SDS-PAGE works for protein, and agarose gel works for nucleic acid? Is it any possible to use SDS-PAGE to detect DNA? Or use agarose to detect protein?

Why does the SDS-PAGE gel always runs vertically, and agarose gel runs horizontally? Are they necessary?
Is any other material could be use in gel electrophoresis?


texts: Are myosin microfilaments or intermediate filaments? Or are they simply motor proteins? Under which category should I put them? I am highly confused.


texts: How to design a permanent vaccine to cholera using CRISPR?

texts:
I know that Vibrio Cholerae infects the body through the GM1 ganglioside. So, would it be possible to engineer a CRISPR gene editing tool to prevent Vibrio Cholerae from getting into our cells?

Specifically, would it be possible to insert a piece of DNA into our genes that allow the synthesis of cholera toxin-suspressing protein shown  here (Pubmed link).

The reason I ask this question is that there are obvious benefits to being immune to cholera from birth. While I'm definitely not planning on being the next He Jiankui, I find the prospect of such a vaccine highly intriguing.

Edit: changed link because I posted the wrong link.


texts:
The intial step in the digestion of milk in humans is carried out by which of the following enzymes?

A) lipase.

B) trypsin.

C) rennin.

D) pepsin.

I'm confused between the C and D option. as it's not specified whether they're asking about adult humans only or humans in general (where infancy also included), which between pepsin or rennin will be the answer for this question?

I know that in infants the milk digestion is initiated by rennin and in case of adults due to its absence it's carried out by pepsin. Which is the correct option for that question?


texts: Does the use of "var", "x", and/or "ssp" in a scientific name provide specific information?

texts:
What exactly does it mean when a plant has a scientific name that specifies a vairety, for example  Nothofagus solandri var. cliffortioides, or when the name includes an "x", as in Populus maximowiczii Henry x trichocarpa, Populus xcanadensis, or "Crataegus x macrocarpa"?

All of these species are in the USDA Plants database (of plants that occur in the US). There are > 6000 occurences of the string " var. " ~500 occurances of " ssp. " and only a handful occurences of " x " in the database,

Does the x indicate that a plant is a hybrid, and are the varied uses indicate a different meaning?
Does the use of " var " mean that the plant is a variety?

Does it mean that each of these species has been cultivated and/or bred by a human?

Does "ssp"  mean that the plant is distinct yet compatible with others in the species?
is there a way to identify a that a plant is cultivated based on its scientific name?


texts: Can rapid eye blinking induce epileptic seizures?

texts: Photosensitive epilepsies are characterized by visually-induced seizures. Flashing-light stimuli are known to induce seizures in some (but not all) patients. My question is whether people with this type of epilepsy can self-induce seizures by rapid eye blinking?


texts: Does CoA always bind to organic molecules through a thiol bond? Sometimes I see it written as SCoA in textbooks but sometimes it's just written as CoA, are those actually chemically different, or just laziness on the part of the author?


texts: I am trying to find the full plasmid sequence for pMG101. I have been looking through other papers that have sequenced this plasmid. The GenBank access numbers I got are the following: AY009372–AY009396, ASRI00000000. However, when I go on genbank it gives me a result saying it is not there..... I am stuck and not sure how I am suppose to find this full plasmid sequence. Does anyone know another way to find it?


texts:
A double stranded DNA was denatured in a mixture that included mRNA from a gene in the segment. The mixture was then cooled to promote RNA and DNA hybridization. The following figure the results.

Which strand is DNA/RNA?
What is source of the genetic material (Prokaryotic/Eukaryotic)?
Which segment is exon/intron?


texts: What insect is this? Looks like a spider but with six legs and long antennae

texts:
I've been spotting some of these insects in my house lately, they look like spiders but it seems like they have six legs and antennae instead of eight legs.
Can someone tell me what insect is this? Is it dangerous? I don't mind having them in my house but if they're dangerous I might have to do something.

A photo of the insect:

Their body seems to be relatively flat when you look at it from a side, the location is Costa Rica, we are in the wet season (no winter,summer,etc. here) but I'm almost sure I've seen them during the dry season as well, also, the insect's body size (ignoring legs) is similar to a thumb. In case that helps to indentify it.


texts: Is it possible to still grow taller after growth plates have been closed?

texts:
In addition, when do we know we stop growing taller? Or we keep growing taller?
To the first question:
Recently, I went to a doctor to have a check up, he said that my growth plates are closed and cannot grow taller anymore. True or false? Is it possible to have a second growth spurt. I am about 16.


texts:
how does acetic acid induce pain? I am finding the whole mechanism of it but cannot find any papers or writings. please help.
If you have links that would be nice too.


texts: How can an enzyme favor even chained fatty acids?

texts:
If we look at text books for the human fatty acid metabolism (FA synthesis or β oxidation), they typically shows even length fatty acids (C8, C10, etc). Now, from a chemical perspective, I am wondering how the involved enzymes recognize that the fatty acid is an even number of carbons.

Can someone point me to (historic) experiments that have been done that show that these human pathways indeed only apply to even chain length fatty acids? Or do they also act on odd length fatty acids?


texts: T-cells recognize the MHC molecules and body's own peptides. When it doesn't, it alarms the immune system. But do T-cells express MHC molecules ? If so, how are they using it? If not, what happens when a virus infects T-cells? (Yes, I am confused about HIV infection mechanism too. They escape from immune response by altering their genes and disrupting the MHC-peptide bonding. I can see that this can work in macrophages. But what is the situation in T-cells ?)


texts:
Our bodies can repair quite a number of injuries very well. However, it takes time. For larger wounds, complete recovery can last many weeks. Why is this time so long, what is the most important limiting factor? The speed of cell division? I thought cell division was faster, and if necessary, cells could also be transported in the blood stream. Thrombocytes, as far as I know, are transported to the location of the emergency by the blood, and are not produced locally.

If the pure physics and chemistry allowed, for example, a 2x faster healing rate, wouldn't there be any evolutionary pressure for it?


texts:
First, we are located in Missouri. In between St. Louis and Cape Girardeau. St. Francois county to be precise.

We just walked outside and found this on the porch so we carried it off. Normally this wouldn't be a big deal, but we have a little one now and I didn't want to take any chances.

The snake, pictured below, was approximately 6 inches long. He seemed timid in nature, he didn't let us get very close to him before he started to slither away.

I assumed he was a juvenile black rat snake, from my highly deductive google searching, but I also know that snakes sometimes change color, shape and design as they get bigger. So I wanted to find out if my guess was correctly or completely mistaken. Thanks for you help!


texts: Performing PCR on samples whose DNA concentration is nul

texts: Is it vain to perform a PCR on samples whose DNA concentration was measured as nul by a NanoDrop?


texts: We know that the hepatitis C virus can live on surfaces for at least six weeks. Maybe longer. The infectivity study ended after just six weeks; why?

texts:
Background

A paper has found that the hepatitis C virus (HCV) can remain infective for at least six weeks on ordinary household surfaces. You can see the free full text, or a summary for busy clinicians.

Elsewhere, Brian Krause has added:

"They tested their samples for (up to) 6 weeks.  At the time of the 6th week they still found infectious virus.  They did not test samples beyond 6 weeks, so they can't say anything about infection past that time."

My question

So, at six weeks, they saw that the virus was still infective. Why might they have ended the study right away instead of continuing it for a few more months?


texts:
I live in Taipei, and these flying insects are about 2-4 millimeters long (body length). They are very active when it's over roughly 24C indoors, and will fly, land and run around randomly on interesting surfaces then fly again, all in one continuous motion.

Some have moved into my apartment again.

They are attracted to food, especially coffee grounds!, vinegar, bread, and dark, moist areas. I can use these attractants to catch them inside bottles or plastic bags, but can't ever seem to get the last one.

I see them fly around while mating end-to-end (twice as long as a single fly) and they often go right past my face while doing so as if to say "ha! there's more of us on the way!"

The heads seem smaller than in images of common fruit flies that I've seen.

Are these likely to be fruit flies, or something else? I don't need an exact species identification, I'd just like have some kind of classification to describe them with besides "little flies".

In this answer to a related but different question, it was proposed that they were something very different, but I don't think that's the case.

Photos: the best I cold do with my cell phone plus a magnifying lens.


texts:
What would be the Hardy-Weinberg equilibrium condition for a population of haploid organism?

Would it always be in Hardy-Weinberg equilibrium?


texts: Which DNA elements belong to the definition of a gene?

texts:
I see a lot of different DNA elements mentioned as part of a gene (talking about eukaryotes):

  The length of DNA following the promoter is a gene and it contains the
  recipe for a protein. (video)

This implies that the promotor is not part of the gene.

This actually defines a gene without enhancers/silencers

   (source)

Here the gene also includes the enhancers/silencers

Question
Is there an accepted gene definition regarding the DNA elements? Thus which sequences like promotors, enhancers, silencers etc. are considered part of the gene?


texts: Is there a proton gradient across the cell membrane, just like for the mitochondrial membrane?

texts: Mitochondria have a proton gradient, is there also a proton gradient between cells and the extracellular medium?


texts: What is the meaning of propensity score of amino acid? How is it calculated? (I have not studied biology since last 8 years and now I am going through it because I need it for my research. So if someone can describe it in simple language it would be very helpful)


texts: How to reduce edge effects in cell-based high-throughput experiments?

texts:
In high-throughput experiments where cells are cultured, treated, stained, and imaged in 384-well microplates, I frequently see significant edge effects. For instance, the following plot shows cell count (as measured by CellProfiler from images) for each well on such a plate:

How can I reduce these effects? I can try to correct for them statistically, but it would be so much nicer to reduce them at the wet-work stage.


texts: For Penicillin Binding Proteins, why is the enzyme-peptide complex less stable than the enzyme-β-lactam complex?

texts:
I'm trying to figure this out. I cannot find any publications that go into good detail about the chemistry of PBP inhibition by β-lactam antibiotics.

PBPs cross-link adjacent pentapeptides to form peptidoglycan. My understanding is that, in most bacteria, this pentapeptide has a terminal D-Ala-D-Ala dipeptide. The enzyme removes the terminal D-Ala and forms a D-Ala-Enzyme complex, where the enzyme is linked to the rest of the peptide via ester bond to the D-Ala.

However, when PBPs bind to β-lactams, they also form a β-lactam-ester-enzyme complex. However, this complex is more stable so the β-lactam remains in the active site. Why?

Any good publications are also very welcome.

I would also like to ask, is there any reason the "β-lactamoyl-enzyme" complex can't be hydrolysed?


texts: Once food has been properly cooked is it absolutely safe?

texts: If you properly cook food (let's say in the oven for 2 hours) will there be no risk left? no pathogen will survive this?


texts:
We use electromagnetic communication everywhere these days. Cell phones, wifi, old-school radio transmissions, television, deep space communication, etc.

I'm curious about some of the possible reasons we have never seen biological systems having evolved to use electromagnetic, i.e. radio, for communication. The one obvious exception to this are organisms that generate their own light, i.e. bioluminescence. Cuttlefish are masters of this, and many other species as well.

It seems like bio-radio could have offered all kinds of evolutionary advantages for animals capable of using it.

Are their basic physical limits in chemistry, or excess energy requirements or something that would basically have made this impossible? Or was this perhaps just something that life never evolved to use, but would otherwise be possible in evolution?


texts:
I accidently touched formaldehyde some days ago. Skin on my hand got dehydrated as if I had placed it in salt solution. I washed it with water and it returned to normal state after 5 minutes.
But now whenever I wash my hands with water my skin gets dehydrated again, but returns to normal state after some time .
What's the reason behind it getting dehydrated again when exposed to water ? Will it return to normal state when new skin grows back ?
By dehydration, I mean something like this.


texts: What is the difference between stomata in evergreen broadleaf trees and deciduous broadleaf trees?

texts: They must have some difference in their stomatal density /whether they are hypostomatous or amphistomatous/whatever, mustn't they?


texts:
I am familiar with adenosine diphosphate (ADP) and adenosine triphosphate (ATP), how one relates to the other, and how each is formed in cellular respiration and photosynthesis, but I am confused as to how regular adenosine is formed.

I was reading an article on caffeine which stated:

  Caffeine is structurally similar to adenosine, a neuromodulator, whose formation is dependent on the relative rates of ATP breakdown and synthesis.

From this I concluded that ATP can be changed to regular adenosine, and adenosine back to ATP, but I cannot find anything else on the internet to support my conclusion. I was also wondering when and why your body would change ADP into adenosine instead of ATP. I assume that AMP plays a role in all of this, and possibly ADA.

I only have a high school level education in biology, so please bear with me. If you do not mind, please include a source in your answer so I can further research on my own. Thanks!


texts: Species identification: 2.5mm (3/32" or 1.5/8") brownish ant in highrise apartment

texts:
Can anyone please identify this ant?

In case it helps, 3 attempts of using Ortho Ant Bgon Max gel and bait has not helped.  They 2 were administered 2 weeks apart.  Apparently, it's basically borax and sugar water.

A respondent at this DIY Stack Exchange page referred me to "Ant Identification Keys" section at this site.  It seems that it may be a 2-node Big-Headed Ant, but it's hard to be sure.

Photos:

Update:

Location: Ottawa, Ontario (Canada); latitude 45 degrees north. It's an urban centre, and my highrise is by a main city street, but also with a creek on one side. I first noticed the ants in the kitchen in July, at the height of our summer heat, or perhaps at the tail end of it. I'm rent a 1-bedroom apartment on the 9th floor, facing the creek side and the major street.

Of possible relevance: The neighbour on my kitchen side says that he has never seen an ant. My unit is quite clean, with the only exception that I generate so little garbage that I change it infrequently. I spray inside with alcohol several times a day so that I'm not ravishing the environment by changing bags frequently. Most of the content are fruit/veggy peels/cuttings (no meats/fats or starch), and mostly oranges, which ants apparently hate. I've recently sprayed and wiped down the garbage in order to not use it until I've solved my ant problem.

Since paying close attention, I notice the ants on the floor and upper cupboards, whereas I only saw them before when they crossed the counter. Back then, I thought the ants were attracted to water from a leak that I found under the kitchen sink, or the dampened particle board due to water seeping from the rim of the sink. The latter would suggest carpenter ants, which like sweet things, like the borax/sugar mix that my store-bought baits were apparently based on.  However, the 2.5mm size of my foraging ants are much smaller than the 6-25mm described by this local federal government site.  My ants' 3/32" is also much smaller than the 6/32"+ C. sayi carpenter ant described here.

The leak has been repaired for about 2 months, and I've taken care to wipe up around the sink. No apparent relief from the ants, and the bait is mostly untouched. I'm wondering if the ants may be coming from elsewhere.  Upon reflection, however, I do recall seeing what might bhe the calling card of carpenter ants for years -- fine wood chips under some of the bottom hinges of the cabinet and cupboard doors in the kitchen.  It literally took years for them to accumulate to the point of noticability.  Maybe carpenter ants been visiting for years, and only this summer decided to move in.


texts: Name and Behaviour of Arthropods near a Cactus

texts:
Background Story

I have a small, old cactus on my sunny, south-facing window sill in southern Germany. Since a few years, small black dots gathered around its pot. At first, I thought the dots were dust or sand and wiped them away. But the dots appeared again and again, so I had a closer look at them and saw that they were tiny insects or arachnids, probably lice or mites. We just call them arthropods from now on.

More information

The following picture shows my cactus with some of the arthropods around the pot. Click here for higher resolution.

Here are some close-ups.

The arthropods seem rather dead. They do not move and most of them lie on their back. However, they are not dead. Once they are picked up and set on a paper towel they start to move. If they get on their legs (with a little help) they walk around, which can also been observed by the naked eye.

I inspected some individuals using a detached camera objective as a magnifying glass. The arthropods are brown, shiny, somewhat translucent, and have 8 legs. I could recognize a small head without a neck (like most bugs have) but couldn't recognize a mouth or eyes – probably because of the size.
I couldn't take a picture, but tried to draw what I saw:

Later I got hold of a cheap microscope and took a few videos. The video quality is miserable. In reality, the arthropods are not that dark, see my drawing and the photographs.
Here's on individual laying on its back, flipping over, and walking away.

Here's another individual walking.

The Strange Part

As said, the arthropods keep on re-appearing around the plant pot. But in all those years, I never saw any of them on the pot, inside the pot, or on the cactus. I also have other cacti right next to the "infected" cactus, but their pots were never surrounded by the arthropods.

Question

What are these arthropods, where do they live, and why do they leave their habitat?

My Theory

I suspect the arthropods to live inside the dead and cracked part of the cactus. They could walk on the spikes of the cactus and jump from the ends of the spikes to the ground. If they land on their backs, they cannot get up and stop moving after some time.

I don't think that the arthropods live inside the soil. Two reasons for that:

The arthropods could have drowned often. From time to time I put too much water in the pot, such that all soil is fully covered by water, often for more than 8 hours (yes I know that can't be good for a cactus *cough*).
In order to get to the window sill, the arthropods would have to walk quite a while. Over time, I should have seen at least some of the arthropods on their way to the outside world.


texts:
I'm trying to label a protein with fluorescent dye (TMR succinimidyl ester), but having trouble getting the protocol to work.

The protein seems to be stable in distilled water at a the recommended concentration of about 2mg/ml (determined by OD280 with an absorption coefficient calculated from its sequence).

However, the protocol calls for the addition of 1:10 1M sodium bicarbonate to raise the pH to ~8.5. When I perform this step the solution immediately turns cloudy. I have also encountered this precipitation problem when dialyzing against PBS.

What steps can I take to get around this? I assume a lower concentration of protein might prevent precipitation, but I have read that the labeling reaction becomes very inefficient below 1mg/ml.


texts: Can one refer to pieces of proteins produced by enzymatic digestion as "enzymatic lysates"?

texts:
A Russian text I'm translating says this:

  The location of post-translational modification (PTM) sites was determined using the “bottom-up” approach commonly used in this field. In accordance with this approach, enzymatic lysates from each of the studied MAB batches were separated using a reversed-phase chromatography column at high pressure (UHPLC), and peptide maps were plotted.

Can one refer to pieces of proteins produced by enzymatic digestion as enzymatic lysates? Or will lysates always imply that a biological cell has been destroyed?

The text I'm translating does not refer to cells being destroyed. The proteins in question are monoclonal antibodies present in drugs (solutions, tablets), therefore no cell destruction is involved.

I'm unsure whether to retain this word, "lysates", or use "digests" instead.

Here's an excerpt from the original Russian text:

  Идентификация положений РТМ проводилось по общепринятому в отрасли подходу «снизу-вверх». В соответствии с этим подходом, ферментативные лизаты каждой исследуемой серии МАТ разделяли на обращенно-фазовой хроматографической колонке при высоком давление (УВЭЖХ) с получением пептидных карт.


texts: Is there in vivo evidence of Amyloid beta toxicity?

texts:
Amyloid beta is thought to be toxic, however from a brief search, this is based on (1) in vitro (2) measurements of some proxies of toxicity (e.g. Ultrasensitive Measurement of Ca2+ Influx into Lipid Vesicles Induced by Protein Aggregates referenced in Wikipedia).

My impression is that we do not have any high-quality evidence that amyloid beta is toxic in vivo and that there is significant circumstantial evidence against it being toxic (links below). Is this correct?

"30% of elderly people have #Alzheimers pathology (plaques &/or tangles) but no disease"
There's an elderly woman with large amounts of amyloid plaques but no symptoms of Alzheimer's
According to Derek Lowe "all of those amyloid-antibody trials have ended in grievous, expensive failures"


texts: Is there a reliable reproduction rate for adenoviruses?

texts:
I was trying to find a R0 for adenoviruses but the best I could find was a study done in a bootcamp in China that infected 375 people.
This states that the R0 was found to be 5.1:

The basic reproductive number was 5.1 (95% CI: 4.6 to 5.6)

Is there any other more reliable method that covers more data?


texts: Why is gastric lavage considered to be helpful only if a patient comes to a hospital within 1 hour of a toxic ingestion? How severe would the effects be if a patient came to the hospital after the recommended 1 hour time frame?


texts: Is the tomato a very very close relative of the pepper?

texts: I ask because if you look at a tomato, the way it grows on a vine, its color, the texture, and make up of its skin and internal structure it seems very much like a pepper.  The only thing I can think it lacks that a pepper has is any amount of spice.  I wouldn't be surprised to learn that it has trace amounts of capsaicin.


texts:
I found these crabs at the end of September, 2018. My family was vacationing on the coast of Lopez Island in the Pacific Ocean off of Washington State. I have been trying to figure out what they are ever since. I found two crabs, one that was orange and black, and another that was off-white and black. They are both about an inch and a half across and an inch from front to back. I did some research and the closest thing I could find are oyster crabs, which are found inside oysters on the East Coast of North America. (I found my information on oyster crabs here). However, I found these inside clams on the West Coast. Also, the pictures of oyster crabs I can find online (figure 1) do not look like my oyster crabs. I was wondering if anyone can identify these crabs. Sorry about the picture quality and thanks in advance!

[Figure 1: A picture of an oyster crab that I found online. There are not very many pictures of oyster crabs online, and they all look similar to this one.]

[Figure 2: The back of the two supposed oyster crabs I found. They are not fighting, I just put them close together for the picture.]

[Figure 3: The front of the off-white supposed oyster crab. In the picture, you can see its tiny eyes and small mouth, along with the claws.]

[Figure 4: The front of the orange supposed oyster crab. In the picture, you can see its tiny eyes, small mouth, and claws.]

[Figure 5: The back of the orange supposed oyster crab.]

[Figure 6: The back of the off-white supposed oyster crab.]

[Figure 7: The undersides of the two supposed oyster crabs. As you can see, they both have eight legs and two claws, making them crabs and part of the crustacean family.]


texts: Potentials between endolymph/cytoplasm and endolymph/perilymph

texts:
I am studying for an exam and there is something I can't seem to understand. My textbook says that the endolymph contains 150mM potassium, 2mM Na+ and 130mM Cl-. The perilymph contains 5mM potassium, 140mM Na+ and 110mM Cl-. "Thus" the electric potential between perilymph and endolymph is +80mV (endolymph being positive).

I can see that there are chemical gradients but why is the endolymph so much more positively charged than the perilymph?

I've already asked this question before and it was closed as a "homework question", which I would need to give suggestions on myself.
However, I seriously don't know what to suggest because I do not have the faintest idea how the endolymph can be +80mV as compared to perilymph, although the listed ions suggest that the surplus of positive charges is higher in the perilymph. I would love to make suggestions but I honestly don't have a clue.

Thank you in advance!


texts: Genetics: pedigree following a rare trait autosomal recessive

texts:
I have two questions pertaining to this pedigree
I believe it to be an  autosomal recessive trait.

The probability that individuals IV-1 and IV-2 would give rise to an affected individual would be:
A. 1/4 b. 1/2 c. 1/8 d. 1/12 e. 1/24
Suppose individual IV-2 was unaffected. The probability of his marriage giving rise to an affected child would be:
A. 1/4 b. 1/2 c. 1/8 d. 1/12 e. 1/24

I worked on this problem for the last hour or so and figured up question 1 to be 1/2 and question two to be 1/4. I don't feel this is correct. I feel like I am missing something. If you don't mind showing the calculations for how you came about an answer that would be greatly appreciated.


texts: History: Building a "Phylogenetic network" of famous evolutionary biologists

texts:
Seems like many of the famous evolutionary biologists are somehow related to each others. For example (and I might be mistaken), Ronald A. Fisher was mentored by a descendent of Charles Darwin. Joe Felsenstein did undergraduate research with James Crow and wrote his doctoral thesis under Richard Lewontin. Muller was mentored by Huxley, friend of Darwin. Brian Charlesworth was mentored by John Maynard Smith who was himself mentored by J.B.S Haldane.

Is there anyone who is crazy enough and interested in the history of evolutionary biology enough to draw a network of relationships between most famous evolutionary biologists since Charles Darwin?

An arrow between any two evolutionary biologist might represent a relationship of the kind family, PhD supervision or friendship. Of course there is no limit to the number of famous people to include and there is no good distinction of who should be included. But a network of the 20 (or 50 if you feel courageous) most famous evolutionary biologist would be awesome!


texts:
Southern California, US and less than 1cm
Please help identify this caterpillar.


texts: Can anyone identify this creature that looks like a stick?

texts: This thing was on me. I thought was a stick until it moved. It had a black worm like thing come out one end and stood up and thats how it moved. It would stick to fabric also. In Louisiana


texts: How does species diversity vs Earth total biomass relate?

texts:
Are there any laws/theoretical foundations about how diversity of species relate with total biomass on Earth?

While there is a lot of esoteric sort of talk "humanity dis-balances the live on the Earth", I thought, there are formally seen the following hard facts (correct me if I am wrong):

biomass of human species and species we need (plants/cattle etc) is increasing;
diversity of species is decreasing

So it looks like some sort of global system change (correct me if I am wrong), but how does biology science discuss them (in case my inquiry can be anyhow scientifically formulated)?


texts:
I actually want to use diamond instead of blast because it is faster with small sequences and big genomes, but I actually want to make a tblastn with several protein sequences as queries and the database which will be the genome transformed by makedb.

Do you know if diamond have the tblastn option? I cannot find it.

Thank you.


texts: Why does protein have 4 calories per gram?

texts: As I understand it, protien that isn't used for building and repairing the body is inefficiently converted into glucose in the liver (at a rate of roughly 3 grams of protein per gram of glucose produced). Glucose has 4 calories per gram. So does that mean that protien would provide 12 calories of energy if the body could convert it at a 1:1 ratio? If not, Where does the 4 calories per gram number come from?


texts: Where does new blood comes from when penis get erected?

texts:
In Humans, During sexual arousal in males, his penis will get erected with blood.

Where does this new blood coming to fill his penis which is required for erection ?


texts: Do immature fruits perform photosynthesis? Yes they have chlorophyll bodies. But do they have stomata through which they can absorb carbondioxide like the green leaves? Sincerely Ulrik


texts: Identify this mite from Rajasthan (India)

texts: Can anyone tell me the classification of this bug? I found it in Rajasthan after it rained.


texts: How would one identify cellular transcription factors associated with a viral protein in a treated cell line?

texts:
I've been working as the computer guy for a microbiology lab for the past few months. I've always been interested in bench work, but my wet lab experience is rather limited and thus so is my understanding of wet lab techniques.

The PI has expressed his support and given me the opportunity to conduct my own project from start to finish (generation of wet lab data and computational analysis) and write a paper in preparation for my Ph.D school applications.

I realize that coming up with an actual question is a long and thought out process so I want to do my homework before approaching him with a question. I've read quite a bit of literature and have come up with a question i'd like to answer, the computational stuff I can handle and explain in detail, but I'm having a hard time with the wet lab techniques I could use to generate some of the data i'm interested in.

Effectively I am looking to obtain a list of potential cellular transcription factors that are physically associated (bound) with/by a specific viral protein. Is there a lab technique that would allow me to generate such a list?

Links to papers, wikis, your own theories or anything will be greatly appreciated. Also any advice, or "this isn't possible" is all appreciated, as long as you can give me a bit of "this is why".

Thank you! (PS I'm not sure if this type of post is allowed here).

EDIT: It is important to note that I am looking for new binding partners.


texts: What would be the shortest and optimal method of extracting human cells for PCR? Is there a colony PCR like protocol for human cells?

texts:
I am trying to devise a quick method to extract genomic DNA from human cells for a PCR.

I first collected cells by centrifuging  saline mouthwash (0.9% NaCl) and extracted genomic DNA using kit followed by a PCR protocol which works fine but is a rather lengthy process.

I tried to cut short the method and removed the DNA extraction steps by using pelleted spit samples as templates for PCR and increased the initial denaturing step from 3 minutes to 5 minutes. However this method was not reliable as some of my samples were amplified and some were not.

Can anyone suggest me a reliable protocol here?

Thanks!


texts:
Why are our bodies not evolved to store only limited amounts of fat, which won't kill us with all diseases associated with obesity?
Wouldn't obese people die faster and clean the gene pool for people who are slim?


texts: Why HIS tag is not detected in WB or dot blot?

texts:
I would like to know why the recombinant protein with his tag at c terminus is not being detected neither in western blot or dot blot.

I'm trying to validate protein expression of four proteins. Three of the four proteins have no assigned protein family or domain (PFAM). The size of the proteins is small:

Locus   Nucleotide length   Protein size    Membrane features   Cloned  WB  Dot blot    Dot blot urea   COG
HPNK_06205  360 120 signal peptide  yes no  no  -   -
HPNK_09829  129 43  signal peptide  yes low low -   -
HPNK_10446  756 252 transmembrane   yes no  no  -   COG1175 ABC-type sugar transport systems, permease components
HPNK_11461  264 88  signal peptide  yes yes yes -   -

Next steps:

-Discard possible his tag hidding by adding urea to dot blot.

-Revise annotation for the proteins. Since all are annotated as hypothetical proteins, maybe there is an alternative annotation that could lead to longer proteins and maybe more stable products.


texts: Number of serotonergic neurons in mouse/rat DRN

texts: What is the (approximate) number of serotonergic neurons in the dorsal raphe nucleus (DRN) of mice and rats?


texts: What's the best source characterizing proteolysis cleavage sites in the phagolysosome?

texts:
I have found MEROPS and TopFIND via the survey paper Quantitative proteomics and terminomics to elucidate the role of ubiquitination and proteolysis in adaptive immunity. These look like a good start, but I'm wondering whether there's anything more specific.

Ideally, I'd like a list of human phagolysosomic enzymes and some sort of statistical characterization of their cleavage sites, such as position-specific scoring matrices.


texts: Does Lucid Dreaming decrease the regenerative effect of sleep?

texts:
After watching this SciShow video on sleep, I wonder about lucid dreaming.

Specifically: Does lucid dreaming and associated directed agency within Lucid Dreaming decrease the regenerative effect of sleep?

That is, if I gained the skill of lucid dreaming - would I be negatively tampering with the brain's autonomous healing processes for the period that I had conscious control or even simply objective awareness during sleep?


texts: When does DIFFUSION occur and not OSMOSIS, and the otherwise?

texts:
For example, I do know that red blood cells have both the Na+/Cl- co-transporter and Aquaporin (water channel) that allows both Na/Cl and water molecules to pass through. But why in biology textbooks they imply that osmosis occurs instead of the diffusion of Na/Cl molecules, though red blood cells have the channels for them, too? (that leads into crenation or lysis of the cells)

NOT ion PUMPS, but ion CHANNELS (those that don't require energy). The Na+/Cl- co-transporter works along with the gradient (not against!).

If an RBC is to put in a hypertonic solution, why wouldn't it absorb the excess NaCl using this channel instead of letting the water out?

I do know in the case when we put cells in a hypertonic/hypotonic glucose solution, osmosis will occur instead because the cells need insulin to allow glucose in (via GLUT4).

But when does exactly osmosis occurs instead of diffusion?


texts: Does a software exist to automatically design antibodies that target a given protein or antigen?

texts: I'm looking for software to automatically design antibodies that target a given protein or antigen.


texts: Identify this thin and strangely-shaped dragonfly, and understand why the shape looks so weird

texts:
I took these photos around noon in mid August in Hsinchu county Taiwan. I've seen many dragonfly varieties but I've never seen anything like this before.
Its body is about 5 cm long and very thin compared to the ones shown in the related questions below. The midsection looks strangely shaped to me, as if it is bent upwards in the back and suddenly ends, and a very thin "tail section" was then added below it.


texts: How closely correlated is the level of an snRNA with the level of its corresponding snRNP?

texts: Let's say I am growing cells under two conditions, and let's say I measure U1 snRNA levels in both using digital PCR.  If the U1 snRNA level is reduced in one sample, how safe is it to say that U1 snRNP is also reduced in that sample?


texts: Why would a plant evolve to produce an addictive chemical?

texts:
It seems kind of anti-productive in terms of survival for a plant to produce an addictive chemical as that plant will constantly be sought after by animals that ingest it. In this instance, I'm looking for a possible general & inclusive answer here that would describe most plants that make this. Not a specific instance (although if provided as an example would be a plus).

To appreciate the scope of this is terms of number of plants producing potentially addictive compounds - see this compendium:

compendium of botanicals reported to produce toxic, physchoactive or addictive compounds


texts: I saw this on my window couple of days ago. Does anyone know what it is? I have tried google image search with no luck.


texts: Cross section through the right arm question

texts:
Is the largest drawn vein on first attached pictue v. brachialis or did they make a mistake and it's actually v. basilica?

Picture 1: Cross section through the right arm (source: Thieme, General Anatomy and Musculoskeletal System, p. 296)

Location of sectional plane (picture 1):

Picture 2: A similar drawing from Sobotta (source: Sobotta, General Anatomy and Musculoskeletal System, p. 240) :


texts: Will "circus peanuts" biodegrade, and how?

texts:
I have a compost barrel, and it is currently staffed by black soldier fly larvae. They eat pretty much anything, which is very satisfying to observe. I put a handful of the candy known as "circus peanuts" in there, and they haven't touched them so far. As you can see following the link, the ingredients are:

  sugar, corn syrup, gelatin, pectin, soy protein, food coloring, and artificial flavor

I assume these things are biodegradable, being "food", but if my star decomposers won't eat them, then what will? What can I expect to happen to these items in the compost heap?

As a follow-up question, was this a bad idea? Should I take them out and throw them away, so they can rot in a landfill instead?


texts: How does mass spectrometry detect histone methylation?

texts: In this research paper they talk about the methylation of histone.  They use mass spectrometry to identify which peptide position is methylated. Does the number yielded by the spectrometer calculate the mass of the amino acid with and without the mass of methyl group? I wonder because I saw some introduction saying the number present the molecular mass of the molecular. I also would like to ask the mechanism of it and how you interpret this data? Thank you!


texts: Attaching suspension cells to coverslip during mycoplasma contamination detection

texts:
I am planing to screen my cell cultures for mycoplasma contamination using the Hoechst 33258 DNA staining method.

This method is suitable for adherent cultures. Is this method suitable for suspension cultures?

If yes, what is the procedure to attach my suspension culture on coverslip and prevent washout of cells during staining.


texts:
I am reading this review. In the first part, the author introduces Standing Genetic Variation, described as:

  STANDING GENETIC VARIATION Allelic variation that is currently
  segregating within a population; as opposed to alleles that appear by
  new mutation events

Does it mean that in adaptation the allelic variation is already present (not created by mutations) and in adaptation it prevails over the others?

Thanks


texts:
What are the bumps on this tomato stem? They are way off the ground so I doubt they are air roots.

What are they, what function do they have and why do they form?


texts:
What is the map unit distance between L and S allele ?

My working : If we take the normal ratio :9:3:3:1 , first one should be 9/16 = 0.5625
and then subtract 0.51 from it, we get 0.0525, similarly working we get 0.0525 difference for all 4 and so the distance is 0.0525 X 4 X 100 = 21

Is my working correct ?


texts: What does (deaths / (resolved + deaths)) describe in an emerging epidemic?

texts:
It would seem in a emerging epidemic, where the time to resolve a disease is long, an evaluation might be used such as:

(predictive mortality rate) =  (deaths) / (deaths + resolved)

Is this a standard metric?  And if so what is it called?

It would seem that this kind of metric would be a predictor as to the ultimate mortality rate, unadjusted for treatment advances. The intent is to describe the demonstrated mortality of those who have acquired the disease, without influencing of the number of people who have acquired the disease.  This would be helpful where R0 is large and/or Specific Interval is small. However I cannot find references to a metric similar to this.  Pointers appreciated.


texts: Why are organs not harvested from deceased cancer patients?

texts: From my understanding, cancer is not contagious, and if a cancerous cell from a patient is introduced to a healthy person, then the immune system of the latter can destroy this cell. In such a case, why are internal organs from cancer patients not used for donation? Is this because there is a small probability of the immune system failing? Isn't there any other way to make these organs usable again?


texts: What is the best way to orally administer a water insoluble powdered drug to macaque monkeys?

texts:
They typically need to be given ~150mg, once a day, and it'll last for two weeks. The drug is very water insoluble, becomes almost like a paste, not suitable for tube feeding. And yes, this is for for real lifesaving medical research.

The best we can come up with right now is putting them to sleep, mixing the powder into Nutella, and putting it under their tongue. The idea being they'll wake up and swallow the mixture.


texts:
The well-known cartoon imagery of porcupines shooting their quills at opponents in a fight is just that: a silly cartoon concept that isn't real.  But it makes me wonder, does that mechanism exist elsewhere in nature?
Are there any animals whose bodies produce solid projectiles that are used as launched/thrown weapons?  (Not looking for liquid ranged weapons such as skunk spray, bombardier beetles, etc.)


texts:
The carrots we buy from a supermarkets spoil very fast, albeit giving many consumers a false sense of preservability due to their structural rigidity. The answer extends to many other vegetables many of us eat:

 Larsinio (2006)- wikimedia, public domain, DOR 27/09/2012

The question is, why do well aerated carrots spoil in the matter of days, at room temperature?

Things to consider: a tuberous rhizome with rough and segmented skin / oxygen levels / levels of aeration / relatively high sugar content / differences in immediate microbiome / lack of possible synergies which the earth provides...the majority of antibiotics is extracted from soil microorganisms {1},{2}....


texts: Would tinnitus be explained by perpetually-bent/opened hairs in the cochlea?

texts:
When I look around for what causes tinnitus and the like, the usual response is "Well, loud sounds and hearing damage" but I feel like that's a little plain and I am curious about the underlying mechanism / explanation on a physiological level.
My previous understanding of how the ear works can be found in my previous question (with a terrific answer by AliceD).
So my question is this: Let's say a really loud, fierce sound occurs - the sort of thing that is said to cause tinnitus. This is equivalent to a really strong pressure wave approaching the eardrum. I imagine it would hit the eardrum, causing it to move violently / harshly, causing a similarly strong movement in the stapes, which is already providing something like a 20x pressure amplification to the cochlea.
So the stapes hammers hard on the oval window of the cochlea, causing a harsh pressure wave through the perilymph / endolymph, also causing the basilar membrane to move very harshly and violently. To me this would imply a fierce smashing/dragging of the hair cells against the tectorial membrane above, possibly causing sufficiently harsh wear-and-tear along the tops of the hair cells, leaving them bent or maybe even chopped, allowing their channels to remain perpetually open.
If these channels are always open, they're always accepting potassium, always creating the action potentials, always triggering the nerves underneath, which would mean the person is always hearing that particular tone all day, every day, 24/7.
Is this more or less what happens, or am I way off in my little thought experiment daydream here? Is this why tinnitus is difficult to cure, because it would require somehow rebuilding / closing up hair cells that are always open?


texts:
Evolution provides different myelin sheathing cells (Oligodendrocyte and Schwann cells) in mammalian CNS and PNS. Damaged neurons in the CNS have little chance of recovery whereas damaged neurons in the PNS have an excellent chance of recovery. When ruptured, olidodendrocytes release Nogo that signals the damaged neuron cell body to stop any attempt at regrowing its axonal stump. Ruptured Schwann cells in the PNS do not release Nogo. Why should nature behave like this? Is it because the wiring density of the CNS is orders of magnitude greater than that of the PNS?

Or could it be because in the PNS the nerve is encased in a perineurial sheath that can readily self-repair and provide a framework for axon regeneration? There doesn't appear to be any similar sheath in the tightly packed CNS. Therefore to prevent unstructured axon regrowth, that could cause chaos in the brain, such a possibility is actively prevented?


texts:
I'm familiar with the concept of hybrid infertility, but my question is: Are ALL hybrids infertile, or is it just so extremely unlikely that the chances are basically nil that they can actually produce a viable sperm/egg?

Thanks.


texts: What caused the Mesozoic-Cenozoic radiation?

texts: The Phanerozoic eon has had 5 major extinction events and 3 major radiation events. After the Cambrian and Ordovician radiations came all five of the major extinction events, the last of which (Cretaceous-Paleogene) occurred during the last major radiation event (Mesozoic-Cenozoic). This timeline suggests the freeing of previously occupied ecological niches isn't the primary driver of major radiations. (However, the Cretaceous-Palaeogene extinction freed niches during the Mesozoic-Cenozoic radiation, and this may be part of why it continued for so long rather than being a purely Mesozoic event.) Although Wikipedia generally gives a good account of suggested reasons for major extinctions, and also for the Cambrian and Ordovician radiation events, it provides no real such detail for the Mesozoic-Cenozoic radiation. What are its conjectured causes?


texts: I can't see anything at all in my microscope

texts: I just got the Amscope M102C microscope, and it is the first microscope I've operated. I decided to try to look at a fly leg at 40x magnification, but all I could see were the blobs in your eye you get from looking at something bright, as well as a few dots that appear to be on the lens. I tried focusing, cleaning (even though it was fresh out of its package), but I still couldn't see anything. It's so blurry I can't even make out any shapes. Could I please have some help?


texts: By what mechanism does penicillin resistance usually develop in Streptococcus pneumoniae?

texts:
There are three mechanisms:

  prevention of the interaction between antibiotic and the target PBP;
  modification of the binding of the antibiotic to the PBP;
  hydrolysis of the antibiotic by a beta-lactamase.

  Medical Microbiology, 6e, p. 200, Murray

PBP: penicillin-binding protein

It may be the case that the most common mechanism is not known.
It is just one of these three depending on the situation.

What is the most common mechanism by which penicillin resistance develops in S. pneumoniae?


texts: Does biotin affect downstream experiments, such as RT-qPCR?

texts: I have two biotins--one of which is binding my RNA with cleavable bonds, and the other with irreversible bonds. Does biotin have an effect if it keeps its bonds with RNA? If it does, why is this the case?


texts: On which amino-acids residue is the SDS acting on?

texts:
I would like to know exactly what is the mechanisme of the SDS, and I would like to know on which amino-acids residue the SDS is acting on.

Can you help me please ?

Thank you in advance !


texts: Can elements of one's environment act directly as hormones?

texts: Can pollution and things in an organism's environment serve as hormones?


texts:
I have been processing some ChIP-seq data with the R package spp. I looked through the literature (ENCODE uses it) and it seemed that spp is indicated as a good program to use.  I have found and adapted the two tutorials I found for using spp (first and second), and read the original paper. I have also e-mailed Prof. Karchencko and posted on the bioconductor listserv - all with no response. My question is about the MSER and the predicted sequencing depth - additional output of spp. So what I think the MSER is, is the score value above which a peak is authoritatively determined? When I look at peaks above this score value they are very well defined. Also, is the predicted sequencing depth is a prediction of the number of additional "tags" necessary so that the MSER and the FDR value coincide? It is hard to find decent information about this program.  Any advice or additional information is greatly appreciated!

TIA


texts: How did giant sauropods satisfy their daily energy needs, considering their relatively small mouths?

texts:
Gigantic sauropod dinosaurs had relatively small heads (and consequently small mouths) in comparison to their overall body mass.

In the book "Dinosaur Odyssey: Fossil Threads in the Web of Life" (by Scott D. Sampson) the author says (on pp. 218-219) that

  The sheer size of the biggest sauropods has long shrouded them in
  mystery. How could such gigantic animals with such small heads (at
  least compared to their body sizes) manage to consume enough food to
  sustain themselves? The mystery deepens when we look inside the
  mouths of sauropods. Cows are typical of big mammalian herbivores
  (e.g. elephants, deer, antelope, and the like) in possessing oversized
  teeth well suited for processing large amounts of fodder. Chewing
  serves not only to break food-items into bite-size chunks' it also
  grinds up the plant matter and begins the process of digestion by
  making the bits of vegetation more susceptible to chemical attack. By
  comparison, sauropods have puny teeth well suited to tearing or, at
  best, slicing, but not for grinding.

(emphasis added)

I don't remember Dr. Scott providing an explicit answer to the question "How could such gigantic animals with such small heads (at least compared to their body sizes) manage to consume enough food to sustain themselves?" but somewhere in the book he did mention that the earth's ecosystem may have been rather different back then.

However, since the book came out nearly a decade ago, I was curious on whether any other findings have been made since then.

How did sauropods manage to consume enough food to sustain themselves? Was it because of some differences in the ecosystem that are now lost?


texts: Can we attack viruses by attaching proteins and such to their shells?

texts:
Haven't looked into this to very long, but an initial search didn't return anything.

HIV uses certain co-receptors to enter our cells. Could we flood the blood stream with specially designed proteins that mimic cell receptors, either locking the virus out of vulnerable cells, or even causing the virus to release its genetic material (pre-mature ejc. for viruses... :|), so it can't accidentally get away and infect a cell anyway? It seems like an obvious idea, so the fact that it may not already be happening must mean there are a host of challenges to it? Basically we design a protein that acts like a strait jacket, with tags that allow our body to recognize it as a 'friendly' body. T-cells use the same receptor though, so are there ways to identify a T-cell compared to a HIV virion?

Obviously this wouldn't prevent some viruses managing to infect actual cells, but over time, if we can attack enough, say 2/3 of the virions, for each generation, we could seriously harm the population, and maybe keep it in check?


texts: From DNA to final traits of microorganisms?

texts: From the answer of this topic, could someone indicate me a book or article about how DNA set the phenotype of microorganisms? For example, showing how DNA changes the shape of such a cell or how DNA sets the concentration of a such mineral inside the cytoplasm.


texts: Spotted in Czech Republic. Our office was hit with cockroach infestation, so I'm afraid if I haven't carried one home.


texts: Why aren't genetic triplets roughly evenly found in DNA?

texts:
Sorry, the page I linked to is huge and you'll need to do a text search for "CG" to find the part I'm talking about.

I found a graph on this page (http://www.oftenpaper.net/sierpinski.htm) showing that the eight DNA sequences including CG, i.e. four *CG and four CG* sequences are much rarer than the others in a human X chromosome. I realise that this is only for one sample of a human X chromosome (not even all human chromosomes) but I was wondering why this is? Obviously, if *CG is rare CG* will be too.

From my limited understanding the equivalent RNA sequences would be *GC (redundant codes for four amino acids) and GC* (the only codes that produce Alanine). According to the Wikipedia page on Alanine it accounts for 7.8% of genetic amino acids, well over the average.

Is this representative across all DNA? Across all human DNA? What does DNA have against coding CG sequences, even if only in the X chromosome? Do other chromosomes have an abundance of CG sequences but are rare in others?


texts: Identifying a spider very similar to a brown recluse

texts:
I took this pic tonight when I saw what I thought to be a Loxosceles reclusa or brown recluse. But when I looked closer, the typical pattern on the back of its cephalothorax seems to be upside down! I tried to compare with lots of pics and I was not able to identify this one. Plus, its abdomen is kind of velvet greenish.
Could anyone help identifying this spider please? Last precision : the body size (excluding the legs) is around 1cm.
Thanks Folks!
Photo taken on June the 24th 2018 around 10pm in Toronto, South Ontario, Canada.
PS: Even if one of its leg is fully missing, it was still running very quickly...


texts: Parameters that determines the thermal stability of DNA

texts:
Why a DNA with a high GC content more stable than one with a less GC content? Is it because of the three hydrogen bonds in GC base pair which is one more than a AT base pair or is it because of the more stable base stacking of GC base pairs?
In my book it is given that it is due to the hydrogen bonds but in a research article I found it is saying that base stacking solely determines thermal stability. enter link description here


texts: Moth that resembles a leaf. What species is this?

texts:
Location: Urban area near the Western Ghats, Kerala, South India

Date: Sometime in September, 2016

Climatic Conditions: Humid, frequent rains.

Brief description:

Head isn't prominent from the dorsal view. Wings outstretched even when at rest. Antennae largely concealed under the fore wings. Also it...um...does a pretty good impression of a leaf.


texts:
Sperm swims through semen and reaches the haploid egg in the oviduct during fertilisation.

Once the sperm reaches the cervix, through what does the sperm swim through to reach the egg?
Is the uterus completely filled with a fluid that allows the movement of the sperm, or does the sperm only swim through the endometrium (uterine lining)?


texts:
I just was bitten by a bug!!! It is 3mm long and has large pincers. Here is a photo:

I live in Colorado. Any help identifying it would be great.


texts: Help identify this awesome climbing plant with velcro like stem

texts:
I got this plant sprouting in my window box this spring. Starting from a single seed, it has grown into an impressive array of branching climbing vines, reaching 6 feet tall. The stem turned red as it matured. The most awesome feature of this plant is that the stem is covered in micro hooks that cling to everything. I've seen it cling to a paint on a metal gutter pipe I can think of these hooks as velcro or gecko feet.

Can someone help me identify this plant?

climbing vine
stem is covered in tiny hooks that are very clingy
grows to 6 feet tall
stem turns to red as it matures
segmented leaves
leaves grow to palm size
new leaves sprout from stem where old leaves were connected
 -


texts: Why are victims of Covid19 being wrapped in plastic?

texts:
Several articles describe the unique ways Covid-19 patients are being buried.

For example, in this Reuters article about Israel:

  These included decontaminating and hermetically wrapping bodies in
  double layers of polyethylene. For Jewish dead, ritual washing of the
  body would be conducted in one of four special stations in the
  country, the document showed.

And this LA Times article about Iran:

  Nor are they wrapped in traditional white cloth. They are covered in
  hospital plastic, marking them as victims — both young and old — of
  the coronavirus.

People die from viruses all the time but I've never heard of victims being buried in this way. What is unique about Covid-19 ?


texts: Why is knowledge of bacterial pathogenesis important?

texts:
Why is knowledge of pathogenesis increased more and more for common bacterial pathogens? Most of these studies lack a near application in disease control such as vaccines or antibiotics.

Examples:

Studies on the interactions of Haemophilus parasuis with porcine
epithelial tracheal cells: Limited role of LOS in apoptosis and
pro-inflammatory cytokine release
Sialic acid in the lipopolysaccharide of Haemophilus influenzae:
strain distribution, influence on serum resistance and structural
characterization


texts: Type B Nerve fibres cause exactly what kind of autonomic sensation to the preganglionic neurons?

texts:
Ganong's Review of Medical Physiology (25th ed) presents the Erlanger and Gasser classification of mammalian Nerve Fibres as such:

Type B Fibres are concerned with Preganglionic autonomic sensations, but there is no mention of this being sympathetic or parasympathetic. Does it mean that it is both?
The table does specify it as sympathetic for the Type C Fibres, though.
(I have tried searching this on google, but I can't seem to find anything specific.)


texts: Genome-wide methylation analysis: sources of technical error?

texts:
We are doing a genome-wide analysis of methylation via bisulfite sequencing for an insect species. Previous experimental techniques have suggested the presence of methylation in this organism, including an AFLP analysis using methylation-sensitive restriction enzymes and a differential expression analysis using a methylation inhibitor.

Our bisulfite sequencing data, however, is giving us essentially no evidence of methylation. If this finding is true, it will be a pretty big deal. But before we go down that path, we want to make sure we've counted out all sources of technical error.

First, we wondered if the bisulfite treatment failed, but quickly determined that this would not explain the result. If the C --> T conversion had failed at an extremely high rate, you would expect to see methylation all over the place. That's the opposite of what we're seeing, which is essentially no methylation.
Second, we wondered if there was some kind of "overexposure" issue in the bisulfite treatment that caused even methylated Cs to convert to Ts. We found a paper describing this phenomenon[1], but reports we can find suggest this happens at a low (<10%) rate, which cannot explain our data.
Third, we wondered if perhaps there was an issue with the reads mapping to the genome, we got at least 70% mapping efficiency for each BS-seq sample, so that can't be it either.

Are there any other sources of technical error we should consider and check for before believing this result?

Genereux DP, Johnson WC, Burden AF, Stöger R, Laird CD (2008) Errors in the bisulfite conversion of DNA: modulating inappropriate- and failed-conversion frequencies. Nucleic Acids Research, 36(22):e150, doi:10.1093/nar/gkn691.


texts: Why does the blood not clump and result in death?

texts:
In this question's accepted answer, it is said that the blood type will slowly change to that of the donor's.

When the blood in the person is about 50% his own and 50% that of the donor's.
i.e, 50% A group blood (his own) and 50% O group (donors blood),won't the antibodies in the O group react with the A-antigens and clump?


texts: What is the very hard sphere inside the eye of many common fish made of and how is it called?

texts:
Inside the eye of many common fish, like tuna, scad, snapper, actually probably all fish I have eaten, is a small sphere made of some very tough substance. This sphere is even hard to crush with teeth, and seems to be made of homogeneous material. That is after the fish is cooked, not sure how it is uncooked. It is immersed inside a quite soft, almost liquid substance inside the eyeball.
Is that the lens, or is the whole soft semi-liquid tissue the lens?
What substance is the small tough sphere made of? I imagine some type of proteins, but what type of proteins exactly?


texts: What is this species of angiosperm from Morocco?

texts: The flowers are about 1 cm long. The plant is about 1 metre high. Photographed in spring. The plant was found in a ruderal environment.