texts: How to identify the GPD gene when the sequence varies between organisms?

texts:
I'm reading a paper on genetic transformation of a fungi and the plasmid used in the paper uses two forms of the same GPD (glyceraldehyde3-phosphate dehydrogenase) promoter to drive a GFP gene, one from Agaricus bisporus and one from Lentinula edodes (GenBank: GQ457137.1).
However, I noticed that the sequences for the aforementioned GPD promoters do not match the reference sequence in GenBank (NC_007251.2) which itself is derived from another organism.
Why are there different sequences for the same promoter? Furthermore, how would I identify the GPD gene in another organism if I'm unable to compare it to a known sequence?
The organism I wish to transform has had it's complete genome sequenced and my transformation would be much more effective if I could use a native promoter like GPD.


texts: Scaling down amount of DNA for transfection: what factor to consider?

texts:
I am interested in transfecting HEK293 cells with a BAC. One paper suggests using 24 ug of DNA to transfect a 55-cm^2/10 ml culture plate. I am using an assay optimimzed for a 96 well plate so I am interested in scaling down the amount of DNA.

If I consider by volume: I will be going from 10 mL to 100 uL, scaling down by a 1/100, suggesting 0.24 ug of DNA.

If I consider by cell number: I will be going from 10^7 cells to 10^4 cells, scaling down by 1/1000, suggesting 0.024 ug of DNA.

If I consider by cell concentration: I will be going from 10^6 cells/mL to 10^5 cells/mL, scaling down by 1/10, suggesting 2.4 ug of DNA.

What factor should I scale down by? I want to say that it's volume but I don't really know why.

Thank you for any help or suggestions!


texts:
I've screened a non-redundant set of GPCRs acquired from UniProt. I found a handful of examples of record IDs that contain more than the 7 TMHs. For example Q89609 and P20905, both of which have been manually reviewed to some extent.

For an idea of the variability in the GPCR family, below is a screenshot from a Clustal Omega alignment comparing P2095 to a bonafide human GPCR. There are ~16 indels of varying length.

Also, when blasting against SwissProt, the 2 hits that appear are also GPCRs with the same function from mammals but they have the expected 7 TMHs.

Is it possible for GPCRs to contain more than 7 TMHs, or is it a case that the annotation is incorrect?


texts: Do decibels matter if the sound is outside human hearing?

texts: I bought a dog training device that emits sound at 25K hertz and 130 dB. Can this damage anyone’s hearing since they can’t hear it?  Also is it possible for an infant to hear in the 25K hertz range?  Thanks


texts: Why do biologists judge intellect based on brain size?

texts:
I have seen many times, that scientists will say Species A is smarter than Species B due to a higher brain-to-body ratio.  I've even seen similar arguments made by comparing the sizes of specific regions of the brain.  For example, "Species A must have a more developed linguistic ability than Species B because it has a larger language center in its brain."

This doesn't make sense to me.  I don't think we can make these judgements because we don't know what "software" is being run in each brain.  I can run a merge sort algorithm on a weaker computer just as fast as a brute force sort on a stronger computer.  The raw computation ability of a computer doesn't necessarily correlate to how quickly it can solve problems.

What am I missing here?


texts: When I walk downhill I lose potential energy.  If I descend 100m in, say, 10 minutes I lose potential energy at a rate of about 114J/s (114W).  Where does the energy go?  Not into kinetic energy provided I don't run or fall, not into heat, for there is little friction to create such heat.  My leg muscles appear to be acting as very efficient brakes, absorbing the potential energy but turning it into what? Chemical energy?


texts: In what two ways is ATP used in coupled reactions?

texts: I already have down "A coupled reaction is when leftover energy from a reaction fuels a reaction that needs more energy. ATP can break apart to transform into something new and use the energy created by breaking a bond to fuel a reaction in need of more energy" I think that is one use but I am not sure and I still need another


texts: eye myopia power changes with brightness

texts: Is there a condition where myopic power changes with ambient brightness. When I drive in the morning in bright sunlight my power is -4.0; however when I wear the same -4.0 glass in the evening (dusk time and night) I cant see properly. The images are blurred. I have to change to -5.0 glass. However the same situation does not happen in my right eye which has a constant -5.0 power in both daylight and night. I have observed this for many years (15+).


texts: What is the name of this yellow bumble bee that I photographed in New York City?

texts: Does anybody know the name of this bumblebee? (For categorization on Wikipedia Commons: 1 and 2)


texts: How were the synaptic areas identified in the somatic sensation pathways?

texts: I'm studying the somatic sensation pathways in neuro-anatomy and I was wondering what was the experimental procedure for identifying the number and location of the synapses in these pathways? Additionally, how were they known to not branch anywhere? Did they use dyes or green fluorescent protein? These are the only visualization techniques I know.


texts: Books on machine learning applications in Biology

texts:
I have recently engaged with a collaboration, which requires me to construct, then train an unsupervised artificial neural network (ANN).

However, I have only a very coarse understanding of what machine-learning classifiers try to do, and how they work. For example, Chen et al.'s random forest (RF) classifier (ensemble of decision trees) for protein-protein interaction prediction. Additionally, I have very little idea about which types of machine-learning are useful to different classes of Biological problems.

So -if they exist- I would very much appreciate information on books that discuss applications of machine-learning classifiers in Biology/Bioinformatics. Preferable criteria are:

Intuitively introduces key concepts.
Illustrates a variety of Biological/Bioinformatics problems and their solutions by appropriate types of machine-learning (e.g. when is it appropriate to use ANNs versus RF classifiers?)
Relatively short (I'm planning to read from cover to cover).

Related

Stack Biology: Machine-learning for light microscopy problems to solve (I would consider this question a sub-class of the present question; personally, I am more interested in the sequence analysis / genetics domain of Bioinformatics problems)
Stack Biology: Historical connection between neuroscience and machine intelligence
Blogs about deep learning implementations in Biology
GitXiv: Collaborative on-going (and also published) computer science projects pertaining to machine-learning (search using relevant Biology-related queries to filter)


texts: GWAS terminology "Tag" vs "Lead" vs "Index" SNP

texts:
I'm trying to get my head round the correct GWAS terminology. I keep seeing the terms like "tag", "lead" and "index" SNP to be used almost interchangeably and I would like to get a clarification from someone inside the field.

My (limited) understanding is as follows:
Tag SNP - the SNP included on the genotyping microarray. Once we have a compendium of SNPs for a given sample we can use reference haplotypes to impute the rest of the SNPs.
Lead SNP = Index SNP - the SNP assigned the highest association significance after we've run association analysis for all the imputed SNP. The other SNPs in high LD with the lead SNP will form the associated locus.

Am I correct in my understanding? Any other / better terms I should be aware of?

Many thanks!


texts: If bacterial plasmid DNA is methylated then how do we digest it using restriction enzyme in cloning experiments?

texts: So, I was reading about how bacteria protects its own DNA by methylation against restriction enzyme. But if the plasmid DNA is also methylated then we can't cut plasmid using restriction enzyme for doing cloning. And if we are isolating this plasmid from Methylase deficient strain so that the plasmid is not methylated, won't it would be digested by the bacterial restriction enzyme. Do we isolate these plasmid from a strain that is also unable to produce restriction enzyme ?


texts:
If I use antibiotic on a specific type of bacteria, some will survive because it is resistant. Was this bacteria resistant to this antibiotic before it was even used, or did the bacteria develop resistance after the antibiotic is used?

How or why some bacteria can simply mutate to form beneficial alleles which will help in survival and others can't?


texts: What is the general term for tree-dwelling animals?

texts:
Many different types of animals live primarily in trees, from birds to monkeys and beyond.

Is there a general term that I can use to refer to all of them?

The closest I've been able to come is "arboreal", and I'm not sure that that particular term is appropriate for the broad range of animals encompassed by the casual usage of "tree-dwelling."


texts: Are all protein composed of all the amino acid (in animal) or are there less diverse protein?

texts: I have a question about amino acid composition of proteins: Are there proteins in animals that are made up only from a small subset of amino acids? So instead of all 20 amino acids let's say only 6-14 ( or any arbitrarily small subset) amino acids are used in a particular protein. Could you give me an example (or maybe a few examples) of such protein(s).


texts:
According to this graph (from here):

cysteine contributes to pheomelanogenesis, and having a high enough concentration of cysteine makes the shift towards pheomelanin instead of eumelanin. So my question is: theoretically, let's say I would feed my dog a cysteine supplement daily, would that change its coat color over time? If yes, how, and if no, then why not? What am I missing in this process?

Disclaimer: this is just an example, of course I do NOT intend to feed my dog anything at all, it's just a hypothesis. What I want to know is that raising cysteine/glutathione levels can really contribute to pheomelanin production? I know that theoretically, in lab tests a higher cysteine concentration means a higher pheomelanin production, but I am interested in actual living things. If this is possible, it can be a huge breakthrough. If you have the opinion that cysteine alone won't make the difference, than what will? According to the graph attached, that's the only thing making the difference.


texts: How does the immune system fight scabies mites?

texts:
After a distressing episode involving my elderly mother and a nursing home, I've been reading up on scabies. It seems that in healthy people, the immune system limits the mite population to around 10 of the creatures at any one time; elderly and immunocompromised people can be infested by many more - thousands, even millions of mites (shudder).

So my question is, given that the mites burrow in the top, dead, layer of the skin, how does the immune system detect them and suppress them at all?
Conversely, if the immune system can limit the mite population so effectively, why doesn't it wipe them out entirely?


texts: Does Antioxidant prevent oxidation that creates free radical?

texts:
I have already known that antioxidant can neutralize oxidant/free-radical, but i want to know if antioxidant can also prevent the oxidation or not. I want to know to how it works if antioxidant can prevent it.

By the way, my point in asking this question is actually to answer my final question: Does vitamin C (antioxidant) inhibit the oxidation in ripening fruits?

thank you!


texts: Which organs can be donated after clinical death?

texts:
The information I found about organ donation does not address clinical death. For example:

  The process of donation takes place only after physicians declare a
  person brain dead [...] cessation of brain function [...] is
  irreversible. However, the vital organs (heart, lungs, liver,
  pancreas, intestine and kidneys) can be kept viable for a few days, if supported by artificial mechanical means (i.e. a ventilator).
  (source)

However:

  Blood circulation can be stopped in the entire body below the heart
  for at least 30 minutes, with injury to the spinal cord being a
  limiting factor. Detached limbs may be successfully reattached after 6
  hours of no blood circulation at warm temperatures. Bone, tendon, and
  skin can survive as long as 8 to 12 hours. (source)

Assuming the organs were not damaged by the cause of death itself, are there any organs that can be transplanted after clinical death?


texts: How does a prophage leave the host cell's genome?

texts: I understand that, unlike a prophage, a provirus never leaves the genome, but I don't understand how the prophage "leaves".


texts: What is the point in the Neuromuscular Junction?

texts: Surely a direct connection (i.e. an electrical synapse) between motor neurone and the sarcolemma would allow for much faster neuromuscular transmission? It is my understanding that chemical synapses are only useful in facilitating spatial summation of action potentials from multiple presynaptic terminals... muscles have no need for this as they are innervated by a single motor neurone only?


texts: What causes the blue color seen in baboons?

texts:
Based off of this question from Worldbuilding SE.

In that question, I talked about how the scrotum and buttocks of various animals have a blue color because of thick deposits of collagen in those areas. I wanted to make a race of elves that used this mechanism to achieve blue skin all over their body.

Now, I thought that the thickness of the collagen layer was what was behind the structural coloration of animals like baboons and vervet monkeys. However, I have since learned that it is also the way the collagen is arranged that makes that color occur. That made me think that to achieve my desired effect, I wouldn't need to make the skin exceptionally thick. I could just rearrange the collagen humans already have and not change the thickness at all.

I'm having a hard time understanding the underlying mechanisms behind what makes the arrangements of collagen different, and why it wouldn't occur over the whole body.

Thus my question is twofold:

Is it the structure, or the thickness of this collagen layer that makes the structural color work?
Does the way the collagen is structured in these areas make the skin function differently than normal skin? (I.e. Is it less stretchy? Is it more fragile?)

(I'm sorry if this is off topic, I was thinking that since the focus of the question is on how the collagen works that it would be better suited here than on Worldbuilding)


texts:
I'm working on developing a model of ant foraging. To do this, I have simulated food morsels distributed randomly within an area, with the minimum distance between morsels being variable. I'm trying to get a good idea of the scale at which I should define the distances. This has to depend on ant walking speed and their usual foraging distance.
I'm not very species-specific in my approach. One study (1) shows a survey of foraging distance for different species. They found that most of the species had a maximal foraging distance of less than 1m. Some species did go upwards of 10m. I presume this distance would increase with the presence of trails, but to only focus on finding food by exploring, I can keep the distance between food morsels to be 2m-3m.
Now, I also want to figure out the time that it would take an ant to start from the nest and reach the food given its distance. This is where I'm stuck. I wasn't able to find any survey or study on walking speeds of different ant species. I need an approximate 'exploring speed' of ants, which is just time taken to reach a morsel after leaving the nest. Are there any references I could use to estimate this value for my model?
References:

Eguchi, K., Bui, T. V., & Yamane, S. (2004). A preliminary study on foraging distance and nesting sites of ants in Indo-Chinese lowland vegetation. Sociobiology, 43(3), 445-457.


texts: Why do certain ferns have roughened spore surface?

texts:
Ferns such as Anemia phyllitidis, Blotiella lindeniana, Ctenitis hirta, Cystopterix fragilis, Hemionitis palmata and many others have roughened splity spore surface.

I ask, why is it evolutionary so? Does it have something to do with Equisetales spores, which has long derivates to join up together to spread more effectively? Or more like a convergention with polen of Asteraceae, which is morphologically adapted to zoogamy?


texts: If bacterial resistance randomly occur, then why limit broad-spectrum antibiotic use?

texts:
If there is importance to study some discipline, then one of the main matters is its applications, so besides the primary goal of knowing the truth of the matter regarding what that discipline is investigating, applicability or usefulness of that study in other fields or in the field itself is a very important matter. I'll direct my attention here to Evolution, and its mechanisms. So accordingly if something that I personally want to come up with is application of that knowledge to the field of my work.

In reality we don't study evolution extensively at college level in medicine, since it doesn't have a direct clinical impact on the diagnosis and treatment of patients in most of the cases. However, one possible area of interaction is "bacterial resistance to antibiotics", since this is related to "mutations", and generally viewed as a mechanism whereby the bacterium adapts to its environment.

Now all of my life in medicine from college through specialty and academic teaching, we've never ceased being reminded about not dispensing antibiotics liberally, and the main concern outlined is "emergence of resistant strains of bacteria" due to this liberal use of antibiotics itself. There are other reasons of course, like side effects and cost, but they are not the main concern most of the times.

During my recent review of Evolution, looking at the introductory courses that were cited to me by many participants here, in particular this page of Evo101 titled "Mutations are Random" I was really shocked to know that even the mutations that resulted in bacterial resistance were not "directed mutations", i.e. it is not the case that the exposure to the antibiotic caused the bacteria to have that mutation in the first place, actually the page mentions Esther and Joshua Lederberg experiments showing that those resistant bacteria were already there before the population was exposed to the antibiotics?

So why have we been always reminded by bacteriologists of limiting our antibiotic usage if emergence of drug resistance is not due to exposure to it?

Actually, its not only that, many lectures we attend, which are pretty much delivered by official bodies, does mention of emergence of antibiotic resistance as a DIRECTED mutation response to exposure to the particular antibiotic, that almost most of us we clinicians became to think that this is a fact. For example hospital bacteria are of the most resistant ones, especially those in intensive care facilities. The association between exposure to antibiotics and emergence of drug resistant bacteria to them is almost hammered in our brains, that to discover that the mutation was already there before exposure to the antibiotic seems quite shocking, at least to me in person.

My question here is the following:

  Is it a scientific fact that emergence of bacterial resistance through mutations is always random, i.e. in the sense that it is not a directed response to exposure of the population to that antibiotic?

For instance this seems to be a counter-example.

If that is the case then why bother about liberal use of broad-spectrum antibiotics? I mean as far as emergence of bacterial resistance is concerned!

I mean its not the case that I'm going to eradicate the "useful bacterial" that could rival the pathogenic resistant bacteria, by that liberal use of broad-spectrum antibiotics. If that happens temporarily we can in principle replace them back, like with the use of probiotics.

During my surfing of the web I found that page addressing the same point, but the responses are not that explicit, and far from being convincing?


texts: Why only 6 water molecules are formed in the aerobic degradation of glucose?

texts:
I am studying the aerobic degradation of glucose and it seems that for every glucose molecule we should obtain $\ce{10H2O}$ molecules. However, it is known that we only obtain 6.

$\ce{C6H12O6 + 6O2 -> 6CO2 + 6H2O}$

(I am not going to focus in all products and reactants, but just in the important ones for the formation of water molecules)

First, in the glycolysis, for each molecule of glucose we obtain two water molecules, $\ce{2NADH+}$ and 2 pyruvate molecules. By the oxidation of two pyruvate molecules we obtain $\ce{2NADH+}$ and 2 acetyl Co-A molecules. So we are going to pass twice through the Krebs cycle, obtaining $\ce{6NADH+}$ and $\ce{2FADH2}$, and requiring 4 water molecules.

So, when we arrive to the electron transport chain, we have a negative balance of 2 water molecules, and we have $\ce{10NADH+}$ and $\ce{2FADH2}$. We have been told that for every of these molecules 2 electrons go to the electron transport chain, that means that a total of 24 electrons go to the system. The problem comes here:

$\ce{4e- + 4H+ + O2 = 2H2O}$

So, bearing in mind that we have $24e^-$, 12 water molecules should be formed, so at the end, we have gained 10 water molecules, but we know that the number of water molecules formed should be 6. So, clearly there is something wrong in my explanation. I would be very pleased if you could tell me what is wrong.

Thanks in advance.


texts: Does making yogurt from non-pasteurized milk work against possible disease bacteria?

texts:
In the past, when there was no pasteurization, could making yogurt from milk lower the chance of getting infected by bovine tuberculosis (or other diseases from infected milk)?

For example, would yogurt cultures reduce the amount of "bad" bacteria or create a less hospitable environment for them?


texts:
A ribosome is where amino acids are linked together by peptide bonds.
A virus is NOT considered prokaryotic because it does not have a membrane.
The nucleotide ATP is one of the most used energy molecules of a cell.
Sugar phosphates are the type of lipid moved through the blood.
A compound that lowers the pH is called an acid.
The cell wall is a carbohydrate covering of all cells.
The term cytosol is only applied to (blank) cells?
An A-U base pair is part of the (blank) found in RNA.
The major form of usable energy in animals is (what)?
A polypeptide is a subunit of a what?

This is what I said
1. True
2.True
3. True
4. False (cholesterol)
5. True less than 7 acidic
6. False
7. Don't know
8.complementary
9. ATP
10. Protein or amino acid? Don't know


texts: Can exposure to blood make pathogens resistant to the immune system?

texts:
If a drop of my blood is dropped into a pool of pathogens. Does that act as "reverse-vaccination" for said pathogens?

I see this it as a potential risk for bacteria/viruses to compete or get acclimated with the weakened/dormant/key-specific of the immune system.

Please correct me if I'm wrong.


texts: Is it possible to re-align of SAM/BAM files?

texts:
I am carrying out some metagenomic comparison using whole genome sequencing approach. I would like to filter out reads from my files in a sequential manner, thus I would like to align to a first reference genome, then use the generated SAM/BAM file to extract the mapped reads with samtols view -F4, re-generate fastq files and align those to another reference genome. This decreases the size of the input and speeds the procedure.
Using BWA, though, I get an error of file synchronization when doing the second alignment:

[mem_sam_pe] paired reads have different names:
"HISEQ:90:C3UNJACXX:1:1107:16388:61141",
"HISEQ:90:C3UNJACXX:3:1303:2008:58095"
[mem_sam_pe] [mem_sam_pe] paired reads have different names:
"HWI-ST1437:64:C3UM1ACXX:4:1214:3833:62731",
"HWI-ST1437:64:C3UM1ACXX:4:1202:18519:45906"

This is weird since the fastq files were generated by the filtered BAM file, samtools should have known how to keep the synchronization of the files.
My question is: is it possible to realign a BAM file? maybe not with BWA, at least with another tool?

Thank you.

The procedure I carried out is:

# align
bwa mem -R <read_group1> <ref.fa> <file1_1.fq> <file1_2.fq> -o <file_aln.sam>
# convert
samtools view -Sb <file_aln.sam> > <file_aln.bam> # sort samtools sort <file_aln.bam> -o <file_alnSRT.bam>
# select mapped
samtools view -h -F 4 <file_alnSRT.bam> -o <file_alnMAP.bam>
# convert to fastq
samtools fastq -1 <filemap_1.fq.gz> -2 <filemap_1.fq.gz> <file_alnMAP.bam>
# re-align
bwa mem -R <read_group> <ref2.fa> <filemap_1.fq.gz> <filemap_1.fq.gz> | samtools sort -o <file_realign.bam>


texts: What kind of spider is this and is it poisonous?

texts: A brown furry diamond shape on its back and brown joints all on black body. Caught entering my house in Trinidad (small island off South America) -- killed the first one, this is the second.


texts: Why is the prefrontal cortex called such?

texts:
Pre means before. Frontal means front.

What does cortex means? Brain?

Is it the front most part of the brain? Is it located at the most frontal part of the brain and that's why it's called prefrontal cortex?

Is morality processed at ventro medial pre frontal cortex or at anterior singular cortex?

My background: I am a programmer. I just want to understand humans brain the way a programmer understand computer. It seems that we don't have CPU. We have huge analog based memory. And we got registers instead of tons of abstract variables. Understanding why certain part of the brain is named under certain things will help me a lot in remembering where exactly that thing is and why. It's something very useful in my ways of learning math and programming.

Basically there are 2 theories.

Prefrontal cortex is named as such because it's before (or in front
of) prefrontal lobe.
It's because it's behind prefrontal bone (the
way other brain lobes are named)

Some people told me to just look that up on wikipedia. If you can show me something in wikipedia explaining the exact answer I am looking for I will be very happy.


texts: When do fireflies glow in their lifetime?

texts:
Does a firefly glow only when adult or larva? Or does it glow during its whole life. By glowing, I mean that they glow only when they require, not all the time.

Is there a reason (evolutionary reasoning) why they glow? Also, if the answer is all the time, then why, or if the answer is specific period in life then why?


texts: Which are the most important carcinogens in tobacco smoke?

texts:
I am researching the neoplastic effects of tobacco smoke and would like to measure a set of key molecules in the saliva of several study subjects after they have smoked.

Which are the most relevant carcinogens originating from tobacco smoke that are detectable in saliva? I don't think there will be time or room to measure metabolites, as the saliva samples will only reflect short-term (<60 minutes) exposure to tobacco smoking.


texts: Whats the difference between voltage gated and ligand gated neurons?

texts: How are they similar and how are they different?


texts: Why did ants and meliponine bees lose their sting? What's the evolutionary advantage in it?

texts:
We know Aculeata is the Hymenoptera’s lineage where the ovipositor evolved into a venomous sting. However, most ants have lost this sting, as well as meliponine and some other bees.
Kerr & Lello (1962) say that “there are at least thirteen ways in which stingless [meliponine] bees protect themselves, making stings obsolete”. Since this subject is being researched for more than 50 years, we hope that some advances have been made in the understanding of this specific evolutionary change.
What's the evolutionary advantage for these groups to lose this apparently awesome defense system?


texts: Carbon Dioxide, sea water, diatoms, and oxygen

texts:
I recently viewed a documentary called “Flying River Observed in Tallest Structure in South America, National Geographic”  (https://www.youtube.com/watch?v=HjpPsZTwsaM).  In this film, as an aside, it was mentioned that a major source (the major source?) for the oxygen required for life on earth are the diatoms in sea water.
It was mentioned that diatoms have shells.
In a separate article (whose source I do not remember) it was mentioned that the sea, because it is being  exposed to higher and higher atmospheric  carbon dioxide levels, was becoming more and more acidic. This high acidity was making it difficult for sealife to form shells.
Will this decrease the number of diatoms in sea water?
Will this affect the amount of oxygen available to life on earth?


texts: There is a disease called bile reflux which can make damage to the stomach. I just don't know how the stomach can be damaged by bile but the colon (small intestine) can resist with it?


texts: Can fruit be affected by antifreeze in soil?

texts:
Due to an accident about 2L of car antifreeze (ethylene glycol & corrosion inhibitors) was spilled around the soil at the base of a fig tree. I am wondering if there is any way the antifreeze can enter the fruit? Will soil bacteria break it down over the course of time? I did a web search that indicated that antifreexe can be harmful to plant roots and can stunt their growth. I could not find any information indicating whether it has any chance of actually entering fruit. I wonder if the ethane glycol (ethane 1, 2 diol) molecule is too large to enter the root system. Your advice would be appreciated.

Kind regards
Chris


texts: Is end-systolic volume (ESV) the same as residual volume?

texts:
I am reading this site and my study materials.
The end-systolic volume (ESV), 50-60 ml, is the volume of blood found in ventricles after systole and contraction of ventricles.

I think ESV is the same as residual volume because residual volume is always the volume found in ventricles.

Is ESV the same as residual volume in normal physiological situations?


texts: How to correlate the pattern by which CAP activator from E.coli binds to DNA and its mechanism of action?

texts:
The catabolite activator protein (CAP) activates the expression of more than 100 genes involved in secondary sugar metabolism in E.coli.
Apparently, it always binds in sites that are away from -10 and -35 elements of the promoter by multiples of 10 base pairs (-70 or -60, for example). How could this be related to its mechanism of action?

I've searched about this particular activator and I found that it acts mainly by recruiting RNAP to weak promoters, although it does alter the architecture of the DNA, introducing an abrupt bend (for some CAP-dependent genes, this favours conformational changes in RNAP involved in the initialization of transcription): here's the crystallographic data.

However, I did not find anything conclusive about the pattern of binding to distances which are usually multiple of 10 base pairs (which is close to the number of base pair in a complete turn of the double helix).


texts: Is there some genetic variance underlying music appreciation?

texts:
Is there any research done on the genetic variance for Music appreciation?

If not, why is there no genetic variance for this trait?


texts: Strange white strings on cherry tree leaves

texts:
What could be the cause of these white strings on the leaves of our sour cherry tree? Is it some kind of fungus or an insect?

Also, i don't know if it's related or not, but on the other side of the tree brown spots started to appear also on the leaves:

I live in Hungary, if the climate is relevant.


texts: What determined the evolution of different faces in humans?

texts:
The most distinctive characteristic of a human is it's face - it is unique among each individual (with the exception of identical twins). It is uncertain to me if whether we best identify other humans by their face due to special brain parts developed for this (there are people with disease that cannot recognize faces) or for actual very distinctive physical face forms; maybe it is a combination of this.

Anyway, the question is about evolution. Why would distinct faces (or ability to recognize distinct faces) be something useful that would be retained by evolution? How is this better at survival?


texts:
I am a statistician and I'd like to test my new method on biological data. For this I am looking for genotype data for a number of individuals. That is, I am looking for something like this:

                    | Individual 1 | Individual 2 | Individual 3 | Individual 4 | ....
Chromosome 1 SNP 1  | AA           | BA           | AB           | BB           |
Chromosome 1 SNP 2  | AB           | AA           | AB           | BA           |
Chromosome 2 SNP 1  | BB           | AB           | BB           | AB           |
etc.

I don't really care about the species. Ideally I'd like to have data for complex and less complex genotypes (different number of chromosomes and number of SNP's).

Are there any publicly available data sets like this? I have been searching the internet, but I can't find any.


texts: There are many information about viral hepatitis. But it is interesting for me, can bacteria cause the hepatitis too?


texts:
So I've been reading a lot of papers on the reward pathway. But since I'm not schooled in any relevant knowledge I'm having trouble grasping the chain of events. Most papers detail just bits and pieces, but not the full sequence of events.

I'm trying to grasp how the error prediction signal works.

This is my guess so far:

Players:

  Photosensitice cell A
  Light processing neuron B
  Dopamine neuron C
  Motorneuron D

Event:

  Light strikes A
  A triggers B
  B spikes after N triggers.
  B triggers C
  C spikes after N triggers.
  C keeps repeadetly spiking for as long as its internally coded reward size/duration expectation.
  D receives predecition triggers spikes causing action.
  Reward comes, neural connections are strengthened.
  If reward doesnt come in predicted time connection degrades.

Am I correct in this deduction or way off?

How does the actual reward get communicated? By dopamine release in blood?
By the same neurons that coded the reward prediction? If so, how do those exact neurons get triggered to release reward?


texts: Can viruses that normally infect eukaryotic cells also infect bacteria?

texts: Can standard viruses infect bacteria?  I'm not speaking of bacteriophage but typical RNA and DNA virus such as influenza and Ebola.


texts: What is the name of this plant I found in ROAD HIGHWAY?

texts:
Location of the plant is South India,

Plant stem looks like Banana.


texts:
I'd like to do chemical structure prediction using a known molecule formulas. I'm familiar with de novo protein structure prediction, but are there any programs which will go from formula to structure with optimal geometry of random small chemicals (say 30 atoms)? I found http://cccbdb.nist.gov/mdlmol1.asp but it selects mol files from a limited database. I need a command line UNIX program which computes mols from formulas.

Concise structural formulas popular during past ages are unable to describe every type of chemical structure like morphine. I found no software that supports csf (Smiles and inchi are popular but are encoded and not human readable). When the bonds of the structure are known geometric minimization (DG-AMMOS) orients the structure to a stable native like direction.
http://www.mti.univ-paris-diderot.fr/fr/downloads.html


texts: Does an allergic reaction kill body cells?

texts:
I have wondered what actually happens in an allergic reaction that causes the symptoms such as pain, rash etc.

Is it possible that the human body actually kills its own cells in the process?


texts:
I miss the definition of ammonite. In my opinion, many authors confuse the term "Ammonite" and "Ammonoid". Ammonoids (Ammonoidea) are large group of cephalopods including for example goniatites (Goniatitida), ceratites (Ceratitida) and ammonites (Ammonitida?).

But what do we call "true ammonite"? Is it an ammonoid with ammonitic suture? This way, many triassic, jurassic, creataceous and possibly paleogenic (danian) ammonoids could be called true ammonites, because they have complex (ammonitic) sutures.

Can you show me where ammonites are on phylogenetic tree? Can we call phylloceratina, psiloceratina, lytoceratina, ammonitina, haploceratina, perisphinctina and ancyloceratina ammonites? Can we call phylloceratina, psiloceratina, lytoceratina ammonoids, but not ammonites?


texts: How do two parents, recessive and dominant genes and two complimentary nucleotides end up in one DNA?

texts:
In the basic school, I was taught that half of genome is received from father and another half comes from mother in the form of double-helix DNA, whose first helix consists of dominant nucleotide bases and second helix is a kinda inverted copy of the first helix. I feel like 3 different concepts are mixed here into one DNA spiral and I cannot sort them out. Can you explain exactly how is every concept (parent material, recessive genes and complemenrary nucleotides) are represented in the DNA? The professional and wikipedia explanations are too full and I cannot extract this basic information from too much detail.

For instance, mother and father could donate non-overlapping sections of the double helix, e.g. you inherit a head of DNA from father and tail from mother. I can also guess that first helix consists of primary nucleotides whereas second helix is complimentary. I also understand that despite it is natural think that primary = dominant whereas complimentary nucleotide stands for recessive, it is unlikely coz dominant is a full gene rather than a single nucleotide and dominant is independent and can differ from recessive whereas complemntary implies deterministic relationship between two. Furthermore, receiving dominant from parent1 and recessive from parent2 contradicts the fact that only one of the parent alleles enters the offspring DNA. Probably both are inherited and only one is expressed in phenotype but I am not sure and ask to clarify this. In other words, I would like to know how both parent1 and parent2 chromosomes live in the child DNA if not in the form for helix1 + helix2. Particularly, what are these two chromosomes, next to every person, if not two helix of one DNA

and where are they located? Are these just two DNAs which exist only during meiosis, during first moments of fertilization? How do you end up with only one DNA in the end?

I would also like to know if individual's eggs DNA is coming from his own DNA or is formed in parallel, from his parents' DNA? That is, when individual's eggs' DNA is produced: during fetation of the parent, during his lifetime from his DNA or during fetation of the child?


texts: What is the significance of 9+2 arrangement in flagella?

texts: Why eukaryotic flagella have 9+2 arrangement .? What is the significance?  a 9+0  flagella should have worked the same way .


texts: Have there been any macro-evolution experiements?

texts:
I'd like to start first by saying that I don't believe in creationism at all, nor any non-Darwinian-evolution explanation of the diversity of life on Earth. The theory, the fossil record, and the genetic, morphologic, and biochemical evidence are more than overwhelming in support of it.

Also, I understand that the term 'macro-evolution' is a "weasel word" invented by creationists to make a bogus distinction of two supposed kinds of evolution.

But for this question, I think the term is useful. I'm happy to take any corrections or qualifications in comments or answers.

I wonder if there has been any long-term experiment performed to attempt to induce 'macro' changes in a species-- something that would make this lab-based population considered to be a subspecies, or even a different species, if it were found in the wild.

I'm aware of the long-term E. Coli experiment that resulted in bacteria that developed mutations that allowed them to completely metabolize citric acid. I understand that's a change of a few genes (amongst other recorded changes).

What I'm looking for is something a little larger, more than a new protein. I was thinking something like 1. a new organelle, 2. a new type of cell or tissue, 3. a new organ, or 4. a new type of limb or radically different limb use (something like reptilian jawbones re-purposed in mammalian ears_.

I understand there are numerous incidents of organisms losing useless features, such as eyeballs in dark caves, flight ability, etc. For this experiment I don't think it's enough to show the loss of something-- genes turning off, but novel characteristics must arise. To rebut creationists, I think it's necessary to show 'new' information, not just loss of information (I'm speaking of the genes responsible for morphology).

With my laypersons' imagination, I was thinking of a species with a relatively fast reproductive cycle, put in an environment that had some selective pressures. Perhaps one without much room to fly, not enough food, but plenty of food in a water area where they couldn't normally get to it. Something that might encourage them to adapt to taking to water to exploit a new food resource.


texts: Why do neurons loose the potential to regenerate and reproduce in adult animals?

texts: I have read in several books that neurons in the central nervous system loose the power to regenerate after some developmental stage but why do they? Can we artificially induce regeneration?


texts: A simple question (I could not find it on internet): What is Pan for in pan-caspase? Is it any different from the term 'caspase' ?


texts: Is it possible to be (briefly) aware you had been decapitated?

texts:
If a person's head was cleanly and rapidly decapitated by a sharp blade slicing through the neck, such as would happen on the guillotine, could that person remain conscious? If so for how long? Long enough to be aware of (the head) falling down and hitting the ground?

Obviously it would be brief due to lack of blood supply, but it seems plausible that it could be a few seconds.

Or is there some inherent neurological shock due to the severing the top of the spinal cord that would cause near instantaneous loss of conciousness?

Could Marie Antoinette have seen her own severed neck from the basket below the blade?


texts: Are the chemical constituents of human bodily fluids similar to sea water?

texts: I have heard a comparison of human bodily fluids to sea water from various sources in the past. The most notable was a teacher who claimed, if I remember correctly, embryonic fluid is comparable in chemical content to sea water. I am wondering if this claim has any scientific basis. If not, is there another bodily fluid known for this characteristic? I tried doing some google searches and did not find any supporting evidence. If this is a myth, has anyone else heard such a claim and how it may have begun?


texts: Was life less colorful before color vision evolved?

texts: According to Wikipedia, we know that color-vision photopigments appeared in the common ancestors of tetrapods and fish at least 360 MY ago.  Would life have been less colorful before the evolution of color vision?


texts: Why is glucose used in oral rehydration therapy?

texts: What is mechanism of action of glucose in the intestine to reduce the watery and electrolyte secretion?


texts: Do organisms have a mechanism to control how fast mutations occur?

texts:
Sometimes the environment and other species can change rapidly (climate changes, changes in terrains from erosion, new river paths, etc), and it seems like a regular slow mutation rate would be bad, and faster-mutating species would thrive. On the other hand, this fast mutation rate seems wasteful and inefficient when the environment is changing slowly, thus slower mutating species thrive with less waste in this situation.

Organisms capable of responding to the pace of environmental change would seemingly do well in both situations. Does such ability to modulate the rate of mutation/evolution exist in nature?


texts: What's the smallest flier that migrates?

texts:
Painted ladies and monarchs migrate hundreds of miles (~1.61 hundreds of kms).

Are there long distance fliers that are significantly smaller?

Dual question: Are fliers' migration distances strictly a function of size? Or are there any fly-sized 1000-mile migrators?


texts: Why does the gravity of Earth appear in this formula estimating speed?

texts:
I'm currently reading the wonderful book The Dinosaurs Rediscovered by Michael J. Benton. It contains the formula

$$v = 0.25 * g^{0.5} * SL^{1.67} * h^{-1.17}$$

where $v$ denotes velocity, $SL$ is stride length in $m$, $h$ is hip height in $m$ and $g$ is the gravity of earth. Not being a biologist (in fact not being really familiar with any natural science), I don't quite understand why gravity appears in this formula. I can't imagine this would hold in any meaningful way in circumstances where gravity where different from earth's, so why not simply express the term $0.25 * g^{0.5}$ as $0.78 m^{0.5}/s$, which I assume stems from some fitting of terms to observed speeds given stride length and hip height.


texts: Protoporphyrinogen (IX) formation in heme synthesis

texts:
This picture shows one of the steps of heme synthesis. In this step two propanoate groups of coproporphyrinogen III are decarboxylated to form protoporphyrinogen IX. The enzyme that catalyses this step is an oxidase. Oxidase enzymes catalyze the removal of hydrogen  in the presence of oxygen to form water or hydrogen peroxdide.

So, will a water molecule form in this step? 2H+ will come from the two carboxylate groups and oxygen will combine with it to form water. Will a water molecule form in this way?


texts: How does methamphetamine (meth) damage neurons?

texts:
Meth is considered to be neurotoxic by forming reactive oxygen species and oxidizing the neurons. But unlike dopamine, which, by the way, is neurotoxic due to ROS induced dopaminergic stress, meth does not have any oxygen atom, and thus cannot be the direct cause of ROS.

So, how exactly does meth exert its neurotoxic effects?


texts:
Background

The concept of mutational variance can be found in many articles including this one for example. The mutational variance of a trait number $i$ can be found in the M-matrix in position $m_{ii}$ (in the diagonal). Elements of the off-diagonal represent mutation covariance. For example element at position $m_{ij}$ of the M-maitrx is the mutational covariance between traits $i$ and $j$. More info about the M (and G) matrix can be found here.

Question

What does "Mutational Variance" mean? What does it mean for a population to have a high or a low mutational variance?

Does "mutational variance" refers to:

Average effect of new mutations on fitness (mutational effect) (parameter $s$)
Variance in the effect of new mutations on fitness (variance in $s$)
Average effect of new mutations on phenotype
Variance in the effect of new mutations on phenotype
The increase in genetic variance ($V_G$) due to a new mutation
The increase in additive genetic variance ($V_A$) due to a new mutation
Genetic variance in the population at mutation-selection-drift equilibrium.
Is it a concept that is opposed to genetic canalization?
...


texts:
What happens when someone takes an anti-venom for an animal they weren't bit by, either for incorrect identification of the animal they were bit by or if they weren't bit at all?

I am looking for the immune system reaction, and possibly why it reacts as it does.


texts: Chromosome 2 alternate explanation - apes gaining a set of chromosomes?

texts: I'm preparing for a debate (just between friends) on evolution (I'm in support), and one of the points I plan to bring up is the Chromosome 2 evidence.  I'm now trying to predict their potential rebuttals.  The common statement I've seen is that since the apes have 48 chromosomes and humans have 46, then there are two possibilities: either we "lost" a chromosome, which would be fatal, or there was fusion.  This, I believe, was an actual prediction prior to the answer of Chromosome 2 being identified.  But couldn't there have been a third possibility - that the apes gained a pair of chromosomes, perhaps thru splitting of some kind?  This seems reasonable to me due to the other claim that we didn't evolve from apes but that we share a common ancestor, and so the ape lineage could have acquired the extra chromosome after the split.  (Note I'm a total biology noob, so if this doesn't even make sense, then please tell me.)  I understand that this isn't the way it turned out, that Chr 2 looks exactly as we would expect from fusion, but prior to this discovery, couldn't the apes gaining a chromosome have been a possible reason?  TIA.


texts: How do plastic containers and other thrash end up in the ocean

texts:
There are many photos of the ocean, which in some parts is littered with all sorts of waste, often plastic bags, containers etc. But I just wonder - how do such large amounts land in the ocean/sea? Isn't waste disposed at secure sites - so such a bug would either be recycled or in the worst case end up on some landfill? Of course rogue companies or entities could occasionally dump some thrash into the ocean, but the massive amounts of it seem surprising to me.
Beside, often the argument is to not use plastic bags, containers etc. but simply USING them doesn't put them in the sea. So what does, and can it be stopped?


texts: Does class switching occur both in B cells and Plasma cells?

texts:
I understand that the cell class switches to change the type of immunoglobulin it is producing. The B-cell produces the membrane bound B-cell receptor (BCR) while the plasma cell produces the the secreted form of Ig, the antibody. Now, the isotypes are different in their constant regions and I'm assuming switching only matters if it is an antibody. (differences in avidity, permeability, antibody receptors, etc.)

How would a B-cell receptor (membrane bound Ig) even benefit from class switching? Does class switching even happen in activated B-cells? Or is it a process limited to plasma cells? I read up that BCR also has the 5 isotypes.

What are the specific chronological milestones at which class switching happens in plasma cells and B-cells (if it does)?


texts: Hill's function for translational regulation

texts:
Transcriptional regulation is generally modeled as a Hill's function (similar to Michaelis-Menten Kinetics):

$$\frac{dm_X}{dt}=\alpha _{m_X}.\frac{R}{K+R} -\beta _{m_X}.m_X$$

Where $m_X$ is the mRNA for some gene-$X$, $R$ is a Regulator $\alpha$ and $\beta$ are formation and degradation rate constants respectively. This equation denotes a saturation kinetics; increasing activator wont cause indefinite increase in transcription. Sounds logical because all promoter sites will be occupied at some point.

In case of a repression the equation looks like:

$$\frac{dm_X}{dt}=\alpha _{m_X}.\frac{K}{K+R} -\beta _{m_X}.m_X$$

I want to model repression of translation using a similar equation. However, the issue is that even though a single mRNA can be saturated by a regulator, increasing mRNA will require more regulators. So effectively the regulator available for a single mRNA molecule will be total regulator ÷ total mRNA.

My question is that whether in such a case the following equation is logical:

$$\frac{dX}{dt}=\alpha _{X}.m_X.\frac{K}{K+R/m_X} -\beta _{X}.X$$

Where $X$ is the protein.

Which means we are taking into consideration the effective concentration of a regulator per mRNA. In other words the Hill's constant $K'$ should scale with mRNA concentration. ($K'=K\times m_X$)

Assumptions:

Well mixed system
System at thermodynamic limit
Amino-acid pool infinite
Ribosomes infinite


texts: How to interpret figure on somatic mutation frequencies

texts:
In paper Mutational heterogeneity in cancer and the search for new cancer-associated genes, Figure 1 defines:

  Somatic mutation frequencies observed in exomes from 3,083 tumour–normal pairs. Each dot corresponds to a tumour–normal pair, with vertical position indicating the total frequency of somatic mutations in the exome.

Is the figure representing with each point a tumor/normal pair because somatic mutations (differently from germline mutations) are assumed to not be present in the normal sample?


texts: How are two species with similar phenotypes identified as different? Have two different individuals  that were thought to be different species ever been determined  to be from the same species ( or one a subspecies of the other's species ) ?


texts: Yeast transformation plate confluent with growth

texts:
I have problem with yeast transformation. I tried to transform pyes3-tryp(my insert inside) into INVsc1 yeast cell by following the protocol in the manual for few times but failed(confluent with growth). In the manual, it states :INVSc1 will not grow in SC
minimal medium that is deficient in histidine, leucine, tryptophan, or uracil.I tried 2 media: selective media+ amino acids except tryp and selective media + amino acids except the 4 amino acids. There are confluent growths, no single colony on both of the plates including on the negative control plate( only yeast cell no plasmid).However, the confluent growth is less severe in the plate without the 4 amino acid. Everything i used is sterile except the old DMSO in my lab which had been opened outside of the laminar before. So, is it due to contamination by bacteria or...??.


texts:
In my biochemistry class today we did a problem detailing two lysosomal storage diseases.

In the first scenario, a cell line for I-cell disease can synthesize lysosomal hydrolases that are perfectly functional which are then secreted outside of the cell instead of being sort to the lysosome. However there is a mutation that inhibits the the kinase domain that normally phosphorylates Mannose-6-Phosphate (M6P), so there is no M6P-labeling in these cells.

In the second scenario, a cell line for Hurler's disease has a mutation that eliminates one lysosomal glycosidase so that it cannot degradte certain classes of oligosaccharides. This results in the cells of this mutant cell line to have engorged / bloated lysosomes.

Now when these two cell lines are co-cultured in the same flask, it is observed the I-cell culture correctys the defect in the Hurler cell culture, while the Hurler cell culture was not able to correct the defect in the I-cell culture.

My question is how can this phenomenon be explain? And why are the Hurler cells still growing?


texts:
I looked at some small ferns under the microscope. The circular sori of the ferns I looked at were less than 2 mm in diameter. The microscope I used had rather weak magnification, so I didn't get to see lots of detail. Later, I came across an image of large sori Wikipedia:

Image source. License: public domain.
I am surprised by the size of the circular sori in the image. If I could obtain large sori such as these, I would probably be able to see more detail under weak magnification. I'm wondering:

How big in terms of diameter can circular sori be?

What are some species of ferns with large sori?


texts: I have read that mature red blood cells (MRBs)do not have DNA.  So I am curious why crime scene technicians collect blood. Is it to collect and amplify segments of white blood cells?


texts: What's the fastest legal way for the nutrients in a dead body to re-enter the ecosystem?

texts:
Apologies for weirdness.

Of the various legal methods of disposing of a human corpse, which one ensures the nutrients which compose the body get back into the wider ecosystem the fastest?

Unless I've overlooked something (which is likely) the answer would seem to boil down to:

Burial, in which case soil microbes have relatively free access to the body but will initially restrict their nutrients to the sub-soil ecosystem.
Cremation, in which case most of the nutrients are converted into heat and light energy by the furnace, although this energy, and the remaining nutrients, are then made available to the wider environment much more rapidly.


texts: Can someone identify this bird? It looks like it has a few deformities

texts:
All pictures taken at Lake Roberta in Tampa, FL.
All pictures depict the same bird.
(The wing deformities can be explained by the lake water being slightly highly toxic, but the neck I can only assume to be caused by the Muscovy ducks that live in the lake.)


texts:
I have in mind that evolution is not a constant / continuous process and that there are bursts of evolution.

Are there terms to refer to the concepts of fast vs slow evolution rates?


texts: How do we know if the folding@home project results are right?

texts:
Some of us are involved in the folding@home project, spending time, money, and resources.

I would like to know the answer to two main questions:

How do we know we fold it right? I mean, these models used in folding calculations. Is it probable that in a decade we will find that all these results are nil and void?
Do we have any example that these calculations were practically applied anywhere?


texts: How was the diversity between ethanol fermentation and lactic acid fermentation evolved?

texts:
Quite simply, some organisms metabolize glucose under anaerobic conditions via Glucose->(2) Pyruvic Acid->(2)Ethyl Alcohol. Some organisms, however, metabolize to lactic acid.

When did such a process (lactic acid) arise biochemically from its related (ethanol) fermentation, and how was it selected for? i.e What were the advantages?

Also, can someone create the glycolysis or fermentation tag?


texts:
The (male) Fiddler Crab is a famous example of an animal whose morphology exhibits neither mirror nor radial symmetry:

(Image source)

List of animals featuring external asymmetry is a Wikipedia article showcasing a few more animals with this property.

Is there a comprehensive list of all such animals that have been described?


texts: Are the genes for transcriptional factors close to their targets in the genome?

texts:
Transcriptional factors (activators and repressors) are proteins which regulate transcription. Being proteins, they themselves are also made from expression of certain DNA sequences/genes.

For example, the lac operon repressor is coded for by the lacI gene. Now, in the case of the lac operon, the gene for the transcriptional factor is next to the promoter sequence. It is, in fact, a part of the lac operon. Similarly, the trpR gene is a part of the trp operon.

Is this always the case? Is the gene coding for the transcriptional factor always present next to (or close to) the transcription unit?

The two mentioned operons are only in prokaryotes. Could it be that this fact is valid for prokaryotes only, and not eukaryotes' DNA?


texts: Can we remove impacted teeth by key hole surgery?

texts: Can we remove impacted teeth by key hole surgery, rather than an open technique, like lithotripsy?


texts: Is there a way to determine how many times a given cell divided?

texts: Do cells divide into exact duplicates? If not, is there a way to determine how many times a given cell divided?


texts: Why do seeds grow upwards?  Surely gravity would pull them towards the earth's core?  Can anyone shine any light on this? Do seeds that are planted deeper grow more quickly.


texts: Can dermatophytes (toenail fungus) survive without oxygen?

texts:
I read that fungi in general can switch to alcohol fermentation in the absence of oxygen (https://en.wikipedia.org/wiki/Anaerobic_organism). How about dermatophytes ? (https://en.wikipedia.org/wiki/Dermatophyte aka toenail fungus) I read an interesting comment here http://gizmodo.com/cold-plasma-could-be-used-to-freeze-out-toenail-fungus-1734825446 by bra55orchid that

  "Topical infections like nail fungus and warts require access to the
  open air. This is why they don't go systemic. Nail fungus progresses
  as it degrades the nail to allow air to pass through it. Pine sap is
  enough to kill them by sealing them off. Spores may survive in the
  case of fungus, so you must keep them sealed off until the spores are
  pushed out by nail growth."


texts: Can human change its morphology or anatomy due to ecological changes?

texts:
According to Charles Darwin, as the surrounding environment changes, so changes the anatomy or morphology of a specific organism.

But nowadays, humans have become very advanced in the technology and when the surrounding temperature changes, humans in turn change the surrounding temperature (e.g. the use of ACs), and maintain the surrounding as they like.

What I want to emphasize is can human being evolve with these scopes in mind?


texts: Does the brain process sound in "clips" or "frames"?

texts:
I've always been under the impression that our brains process images (relayed to it via the eyes) at a particular frequency or "framerate"; this is supported by lots of sources, such as this one.

I'm wondering how close this compares to the way our brains process sounds:

Do we sample "snippets"/clips of sound? If so, is there any evidence as to how long (duration-wise) these "clips" are? Do we "sample" at the millisecond level? Microsecond?; or...
Do we actually sample "sound frames" (much like we do with visual images)? If so, how does our brain process a "frame" that contains multiple noises occurring at the same time (say a dog is barking at the same time the television is on)? After all, a frame is all the input for an instantaneous point in time, versus a clip, which is all the input over a period of time.

Any ideas?


texts: What is R.ornitholytica? Is it a misspelling of R.ornithinolytica or a different species?

texts:
I'm trying to find out which of these is correct, or whether they are different organisms:

Raoultella ornithinolytica
Raoultella ornitholytica

I have come across both spellings in various articles, papers, etc.  They seem to be used interchangeably, but I'm not sure if they are the same thing, if one is a misspelling of the other, if they are equally acceptable spellings or if they are separate organisms.


texts:
At age of 6 I accidentally dipped my hand into a boiling indian curry(Sambar) which was in a large pot.
I got a Boiling Water Burn(Just like in the picture but with a little more radius) in my hand right away and my grandma applied some toothpaste on the area. It has been 11 years now and I still have that mark in my hand.

The question is why is the mark in the center(In circle form)  of my hand and not spread down the whole hand which was  completely submerged a little above the mark. The curry's temperature was pretty uniform around the whole mixture.


texts:
I have generated a list of Proteins using oncogeenes and suppressor genes of cancer.
I have 5827 mapping identifier for 3916 interactions using STRINGdb R package  .
How do I build a network of 200k protein?

Identifiers.csv

"","mapping_identifier"
"1","9606.ENSP00000003084"
"2","9606.ENSP00000003100"
"3","9606.ENSP00000004921"
"4","9606.ENSP00000004982"
"5","9606.ENSP00000005178"

and these are the interactions

"","from","to","neighborhood","neighborhood_transferred","fusion","cooccurence","homology","coexpression","coexpression_transferred","experiments","experiments_transferred","database","database_transferred","textmining","textmining_transferred","combined_score"
"1","9606.ENSP00000163416","9606.ENSP00000240851",0,0,0,0,0,0,0,0,0,0,0,481,0,481
"2","9606.ENSP00000163416","9606.ENSP00000263967",0,0,0,0,0,0,0,0,0,0,0,195,0,195
"3","9606.ENSP00000163416","9606.ENSP00000270202",0,0,0,0,0,0,0,0,0,0,0,163,0,163


texts: How do these triplets code for these proteins?

texts:
I am slightly confused by the diagram above.

The first codon of the unaltered DNA is AAG. During transcription, isn't this coverted to UUC (mRNA). So doesn't UUC code for phe and not Lys?

Likewise, how does TAG code for a stop codon? Isn't it transcibed to AUC, which codes for ile?

Also, is that the coding strand or template strand? If there is a mutation in the coding strand, is there any impact on the protein?


texts: Why is the upper respiratory tract so vulnerable to infections?

texts:
Wikipedia has the following statement on its Upper respiratory tract infection page:

  In United States URIs are the most common infectious illness in the
  general population.

What is it about the upper respiratory tract that makes it so vulnerable to infections?


texts:
I was wondering if there was a database or list of all hominin fossil specimens. I am doing my own personal research, and don’t need images but just names. I know of lists such as the one here, but this includes only the most prominent fossils and not a complete list of all specimens. I understand if there is none available, but any help, even an incomplete database or list, is extremely welcome and would help a lot in my research.
(I know questions like this have been asked, but mine differs because I do not need images of the fossils and it pertains only to hominins.)


texts: Do male animals visually perceive females as more/less attractive?

texts:
If we somehow remove pheromones, do animals experience a phenomenon similar to human "visual beauty" when looking at members of the opposite sex? For example, given a set of 20 female ducks observed through a glass panel, would male ducks attempt to court/mate with a small subset of female ducks first(more attractive ones), or is it based on some other criteria (most receptive, random, closest, fittest, pheromones, etc?)

If there is some "visual attractiveness selection criteria", is there a requirement of certain complexity of the brain and/or visual system for an animal before this phenomenon starts to occur?

I'm aware of the existence of this question: Why does sexual selection evolve beautiful features?, and my question deals with the members of the same generation, not long-term evolution.


texts: Does our brain really "flip" images perceived by our eyes?

texts: I know a similar question has been asked and this is closely related to cognitive science. However, I want to know whether is there any mechanism or structure in the visual cortex which is proved to be flipping the images upside down.


texts: Can you say "screening for a" in English?

texts:
I know this is not a "Correct Use of English Forum" but I'm afraid that people from outside the field won't be able to properly answer my question.

Would it be correct to say "screening for a long peptide capable of killing Gram-positive bacteria"? Or you just have to turn the word "screening" into a noun like: "preparing a screening for a long peptide capable of killing Gram-positive bacteria"?

The last one doesn't seem right to me at all, but I'm not sure since I'm not a native speaker :(

Thank you for your time!


texts: Why do we urinate more when we are nervous?

texts:
This question is a result of my personal experience... But I guess that is common for many of us.

My school timing is 8:00 am to 1:30 pm (usually). During normal school days I typically urinate one time - at most. Last month when we were having our practical exams. There was a fair amount pressure to score high marks and on top of that we did not have any experience with such exams.

On the day of the exam; I was a little nervous about it. The duration of the exam was 3 hours (from 9:00 am to noon) on this day I urinated 4 times.

Several of my friends also experienced the same thing.

I was nervous also because for two days before the exam I was afraid that I hadn't even touched any book. I was thinking that there was no way I could cover the whole book and so I didn't even touch them.

Now that I have final exams in about two weeks, I was revising my syllabus but for the last 4 days I'm not touching the books. Whenever I start solving problems from any chapter then I have to look back for the formulas. Questions in which reasoning is asked, I love to do that. I'm not very good at memorizing things and so when I compare myself to my classmates then I feel like I don't know anything and so I give up. I have never tried to memorize anything, but I understand the reasoning and the concepts.

Kindly give me the answer of the question.


texts: What happens when the parietal cells of gut epithelium becomes partially non-functional?

texts:
The options are

a) The pancreatic enzymes will not work properly
b) The pH of the stomach will fall abruptly
c) Steapsin will be more effective
d) Proteins will not be adequately hydrolysed by pepsin into proteoses and peptones.

The answer is D because pro enzyme pepsinogen gets converted to active pepsin in presence of HCl.

But, Why can't the answer be B ? Because if HCl is not secreted by perital cells then obviously pH of the stomach is going to fall down ?


texts: Can oil be used instead of water in preparing wet mounts for microscopy?

texts:
Is there a reason that oil (e.g., vegetable or clear mineral) is not used to make wet mounts in microscopy? I am not referring to oil immersion technique but substituting oil for water in wet mounts in bright field microscopy.

The question is mostly about moss or mold, things that appear plantlike on a slide. The optical properties may be good and the viscosity, as with glycerine, gives a little depth to the slide. Maybe it causes some sort of distortion? I don't see this listed as a suggestion on microscopy sites.

Thanks.


texts: What can cause the bloating in high protein diet of Whey proteins?

texts:
I am thinking what can cause the swelling of gastrointestinal system i.e. bloating after high protein diet of Whey proteins.
Liver does breaks those proteins to branched chain amino acids (BCAA), which can cause this swelling.

However, I am not sure if this is the reason.
It may be the carbohydrates which are broken to enable this BCAA synthesis.
If you take the protein diet with carbohydrates, there seem to be less swelling.
So apparently easier energy for BCAA synthesis.

The combination of proteins, carbohydrates and lipids seem to be important.
Creatine should also be mentioned.
Fat burner thing is also important here, I think.

What can cause the swelling of gastrointestinal system after high protein diet of Whey proteins?


texts: Genotypes of gametes produced by an F1 individual?

texts:
I have an urgent question as I have an exam tomorrow. I was skimming some past exam papers and one question came up which has me completely confused.

A cross was made between a pure breeding diploid pea plant with round, yellow seeds and a pure breeding diploid plant with wrinkled, green seeds.
R and r for round and wrinkled respectively, and Y and y for yellow and green respectively. Assume dominant allele of each gene is upper case, and that the two genes are on different chromosomes and so are independently assorting.
a) Give genotypes of two pure breeding parents
RRYY, rryy
b) Give the genotype of resultant F1 progeny
RrYy
c) Give the genotype and respective frequency of the gametes produced by the F1 individual and indicate whether the gametes are parental or recombinant.
This is the question I am having trouble with and confused about

The reason I am confused is primarily I do not understand what is being asked when referring to the "gametes produced". Is this an F1xF1 cross and the question is asking about the F2 generation? I assumed not as the next question is:

Two of the F1 individuals obtained from the above parental cross were crossed to obtain the F2 generation
d) Give the phenotypes of the F2 progeny and their ratios

If someone could please shed some light on this it would be much appreciated


texts: Are all plants capable of sexual reproduction? Some can do asexual reproduction as well but I haven't found any plants that aren't capable of sexual reproduction. Is it correct to say all plants are capable of sexual reproduction?


texts:
First off, Im not sure, whether to put this into Cognitive Science or Biology. So sorry, if this is the wrong place.

I wondered, whether it is efficent to think with language (of course its efficient for communication). When Im thinking with long words, it takes longer than thinking with short words. Maybe thinking without words would be even faster?

So, do babies, who didnt learn think faster because they dont immediately try to find words for their thoughts to tell someone about them?

In our everyday life, we almost always need to talk to others about our thoughts. This leads to us thinking with these words instead of just thinking and then finding words for it. Its like writing a manuscript just from front to end instead of first brainstorming and collecting ideas.

Main question: Is it possible to think in a two-step process(and would it be more efficient)? First, thinking with emotions(or whatever you want to call it) and then finding words for that to spread your idea?


texts: Why does Hunger lead to the aggressive behavior?

texts:
I have observed that frequently when people are hungry; they tend to get angry more easily on pointless issues. Does this mean that our fight or flight response is more active when a person is hungry? What is a possible reason for this? Is this phenomenon linked with our cell signaling pathways? If it is, then what would be the pathway that leads to the aggressive behavior?

To summarize the question:

When a person is hungry and they get angry, is it due to a cell signaling pathway? If so, what pathway?


texts: Question on the concept of mitochondrial Eve

texts:
My question is about the very definition of this common ancestor.

Why shouldn't be the mother of mitocondrial Eve the real Eva m (and so on to grand grand ...mother)? All I know on the subject comes from Wikipedia. My question comes from the idea that mitochondrial DNA is passed from mother to daughter. I do not see where to stop back in time.

Please consider that here I am not asking for details or controversies. Just the significance of mitochondrial Eve.


texts: How can I create R8 (homopolymer repeat) filter without using illumina pipeline?

texts:
illumina instruments have built-in -or online- analysis software for variant analysis (CASAVA). This software can filter out the false positive variants near the homopolymer repeats (AAAAAAAA) and filter them with "R8" tag.

Is it possible to make homopolymer repeat filter without using illumina's own pipeline? (with another software?)

P.S I noticed that, GATK have HomopolymerRun script that makes similar job. But it is no longer supported and recommended.


texts: How does the flow of ions along voltage-gated channels lead to nerve conduction along axons?

texts:
Let's say the axon lies along the x axis, and voltage-gated sodium channels lie parallel to the y axis. When a channel is opened, sodium ions will flow along the y direction into the cellular fluid. My question is, how does this flow of ions in the y direction cause a flow of electric current in an entirely different direction (i.e., the x direction along the axon)?

Both layman and technical explanation would be appreciated.


texts: Is sweating possible if surrounding temperature is below the body temperature? How the sweating occur due to the combustion of food?


texts: What constitutes as the death of a bacteria?

texts:
I've read that some bacteria can survive a long time without food.
What constitutes the death of a bacteria ?
What process needs to take place for it to be considered dead?


texts:
I am interested in understanding what "pain" and "hot/cold" look like, as far as waves signatures (signal processing) go.

My general understanding of how pain (nociceptive pathways) and hot/cold (thermoreceptive pathways) works are as follows:

A sensory receptor (nociceptor for pain and thermoreceptor for temperature) responds to analog stimuli, and synapses an appropriate signal onto a first-order neuron (the neuron it directly connects to); then
The signal travels up the nerve, neuron to neuron, through the spinal cord, up into the brainstem, and finally into the somatosensory cortex; then
That cortex decodes the signal and interprets it as "pain" or "hot/cold"

Further, my understanding is that these signals are electrochemical in nature:

While passing through a neuron (dendrite -> axon) the signal is of a purely electrical form, no different than the electricity racing around the motherboard of my laptop right now; but...
To synapse from the axon of one neuron to the dendrite of the next sequential neuron, the electrical signal is transformed (somehow, this is where I'm fuzzy) into a chemical signal, and essentially hormones/messenger chemicals ferry the preserved signal to the next neuron's dendrite. At that point, the dendrite converts the chemical signal back into electricity, and on and on this goes until we reach the cortex.

So, only because I am a total neophyte here, I have to preface my actual question by asking the greater community at large: is my general understanding here correct? If not, please begin by correcting me!

The question at hand

If everything I've currently stated is more or less correct, then this implies that, while traveling inside a neuron (dendrite -> axon), neurological signals such as pain or temperature exist as waves of electricity.

I'm wondering:

What do these waves look like? Do they have special names? Are they sinusoidal in nature? Do they travel with known periods/frequencies/amplitudes? Can I represent these waves as trigonometric functions?
I'm sure this differs based on genetics and all sorts of other factors, but what are the general power ratings for the central nervous system? How much Watts/Volts/Amps travel with these signals? Are there standard ranges?

Please note: This is not homework! I am a grown man who works as a software engineer by day and I migrated here from the Stack Overflow community. I am asking this question because I have absolutely zero background in biology, and after scouring the internet for an answer to this, I could find nothing.

Please don't hold back with lofty, low-level explanations. Give me science here! Though I am not a biologist, I'm certainly no dummy either.


texts: Many fruits (like apples, berries, citrus fruits etc.) contain high levels of organic acids, especially malic acid and citric acid. Are there any evolutionary functions of those acids in ripe fruits? In unripe fruits the sour taste may protect fruits from being eaten prematurely by herbivores, but why are those acids still present in ripe fruits? Are they there for increasing osmotic pressure so plants can make bigger fruits in a cheap way by just inserting more water in them? Or do organic acids perhaps play a role in pathogen protection? Or are they just a by-product of some other biochemical mechanism in fruit development?


texts: What to eat/drink to become unattractive for mosquitoes?

texts:
Is there any diet which would repel mosquitoes away from me?

The only article I found on the internet recommends eating:

1-2 prongs of garlic daily
lemonade
cauliflowers and broccoli
legumes

https://kuchnia.wp.pl/co-jesc-by-odstraszyc-komary-6128846068992129g

But this article says they "may be helpful" and it would be good reading opinion from somebody who is sure.


texts: Energy coupling between two spontaneous reactions?

texts:
This diagram describes energy coupling between a nonspontaneous reaction (the formation of glutamine from glutamic acid and ammonia) and a spontaneous reaction (the hydrolysis of ATP). I can see that if you add reaction 1 ($\ce{Glu + NH3->Glutamine}$) and reaction 2 (ATP hydrolysis), then the overall ∆G will be negative, and this reaction will be spontaneous.

My question is this: why can’t you add the reverse of reaction 1, which would on its own be spontaneous, to reaction 2? Would that not make an overall ∆G that is even more negative (more spontaneous)? This would be even more favorable than what we got from the energy coupling shown in the diagram. Yet it seems that energy coupling can produce the reaction presented in the diagram. How does the universe know to add the nonspontaneous reaction to the spontaneous reaction rather than the spontaneous reaction to another spontaneous reaction? It seems to me that the latter would be more probable.


texts: Are proteins a different shape in space?

texts:
Is the shape of a protein affected by gravity? In space, will the shape of a protein be different to what it is on Earth?

If the structure and shape is in fact affected, then would it be enough of a change to cause a change in protein function?

I've found studies from NASA saying that when protein crystals are grown in space, they are larger and form more perfect crystals than on Earth but I want to know about the effect of gravity on proteins that have already been formed.

Thanks!


texts: Can we take advantage of nanopore sequencing systematic errors to predict secondary structure motifs?

texts:
One of the methods of single-molecule sequencing, Nanopore sequencing, is based on traversal of DNA strand through a nanopore. Nucleotide is determined by measurement of ion current (when nucleotide passes through the pore, it decreases the current of ions through the pore, which can be measured).

The method is known for producing systematic errors. I.e. if you sequenced the same molecule twice and during the first run Adenine in 255th position was confused with Guanine, it will be confused again if you repeat the experiment.

I wonder, if it's possible to make use of information about location of errors to predict secondary structure of DNA/RNA etc.? It is natural to suppose that presence or absence of errors is determined by the context, where a nucleotide is located. If I want to validate the hypothesis that same errors are produced by the same motifs of secondary structure, where can I get the raw data to validate this theory?


texts: Import of H+ ions into the thylakoid space during photosynthesis in plants

texts: Why are H+ ions pumped into the thylakoid space as the electrons pass through the cytochrome complex from PS2 to PS1 during photosynthesis?


texts: Determine which seed will germinate first

texts:
I recently studied about plant physiology for a test. Strangely, there was this question which I had no idea how to approach.

The question is,
Which seed will germinate first?

a) Castor
b) Wheat
c) Mung( Vigna radiata )

The answer is (c). I want to know how do we determine if which seed will germinate first? Which factors does it depend upon?


texts: Do mammals and birds have a common warm-blooded ancestor?

texts: Is it homogeneous or did they converge?  Did we both evolve from warm-blooded reptiles that are extinct maybe?


texts: What is the distance between the insertion of the distal end of the bicep tendon and the head of the radius?

texts:
I was unable to find a source that could provide a measurement for the distance between the insertion of the distal end of the bicep tendon and the head of the radius.

Does anyone know a source that might be able to provide this data for the average adult human?


texts:
Today me and my friend were coming on motor bike and I was sitting opposite direction because I was holding something in my hand (and it was fun :P). When he started bike I felt very high acceleration. I asked him to go slow however he said he is going with regular speed. Then out of curiosity, me and him tried different velocities and different accelerations while me sitting on either direction of acceleration and opposite to it. To my surprise I 'perceived' more acceleration when I was sitting opposite to direction of acceleration. While searching how we perceive acceleration, surprisingly it is not very well known. I found following explanations,

We overestimate arrival time ( ref: this )
Endolymph from Vestibular system ( ref: Wiki ) [Not exactly acceleration but rather balance]
Interpolated motion segments ( ref: this )

My question, Is it just visual perception or special mechanism for detection of acceleration? In any of these cases, why I was feeling more acceleration while siting opposite than in direction of acceleration? [ My initial guess is because I didn't have any support and visual cues were messed up ]

Update:

I found this post but I didn't get any satisfactory answer from book referred in answer.


texts:
In computers, finding a single word is realized through serial attempts across all available connections to find a specified target.

How does the brain solve this? How does the whole process, from the command to recall some memory to actually "play" its algorithm look like?

By "recall" I mean literally, attempting to bring back an image, a word, a melody or any remembrance from memory.


texts:
Sharks breathe seawater. Seawater isn't 100% pure water, but mostly water. Pepsi (other colas are available) isn't 100% pure water, but mostly water.

How long would a shark be able to breathe if submerged in Pepsi (other colas are available) and what, precisely, would kill them?


texts: What does the 'V' stand for in ECG electrode names?

texts:
In electrocardiography, electrodes have the typical names of:

RA (Right Arm)
LA (Left Arm)
RL (Right Leg)
LL (Left Leg)
V1, V2, V3, V4, V5 and V6

What does the V stand for? Is it perhaps from vector, ventricular, or maybe from something else entirely?


texts: Growing up in Oregon I don't remember ever seeing these. There are different mushrooms growing all over my backyard right now, but these look way different than all the others and there was only a small cluster of them in the corner, which caught my eye. Searching online and trying to match pictures it keeps coming back to Psilocybe Semilanceata aka Liberty Caps, which apparently are hallucinogenic.  Like I said  I've never seen these before growing up in Oregon, so I'm curious as to what they really are. I tried to upload a better picture, but it was too big of a file, so hopefully this one is good enough. Thanks in advance.


texts: So I have a validated set of primers for rtPCR from Biorad that contains SYBR green.  If I do rtPCR, can I use the rtPCR product after purifying it with a Qiagen PCR purification kit?  Also, I'm under the impression that the sequencing company needs primers to do sequencing, do I just use the PCR primer or one of the "universal" primers the company has?


texts: Are there ontologies for the description of the look of plants?

texts:
Are there existing ontologies for the description of the look of plants?
I am looking for something formally defined giving me at least or better more information like in descriptions:

They are mainly deciduous shrubs and trees, often with brush-like foliage, often spiny to deter grazing, and masses of small, pea-like yellow blooms which are sometimes fragrant.

which I took from https://en.wikipedia.org/wiki/Genista .
The use case is to be able to procedurally generate 3D models of them, which are not too far away from the reality as far as an ordinary person would notice.


texts: Subtracting shared DNA with half-sibling

texts:
I want to note that I am not a biologist. I've been on a nearly 20-year search for the identity of the parents of my 4th great grandfather (not an easy task.)
I'm using ancestry.com DNA, GEDmatch, and family trees of my matches in hopes of using DNA triangulation to find my ancestors. In addition, I have a half-sibling who also had his DNA tested which allows me to find common ancestors on this side of the family.
I read the article "Relatedness" on the topic of inherited parental dna with two half-siblings and I'm not sure I understand what the writer means when she says:

In other words, you and your half-brother should be able to figure
out what part of your DNA came from your mom.  And if you subtract out
that shared DNA, what is left must have come from your dad!

My first thought was that a person and their half-sibling wouldn't inherit exactly the same DNA from their mother, could they? For example, the mother has two different alleles for some trait. Her son could get a copy of one and the daughter could get a copy of the other. Therefore, in the author's example, how could subtracting out the shared DNA with the brother give the girl the ability to identify exactly which DNA must have come from her dad?
I read on and the author addresses this by saying:

One brother inherited the green version of the mother’s chromosome 2, while the other brother inherited the blue version.  This means that none of the chromosomes match!  So testing wouldn’t tell the brothers which version of chromosome 2 came from which parent.
It turns out, though, that it’s really unlikely that siblings would
have two totally different versions of a chromosome.  This is because
of something called recombination.

She's talking on entire chromosomes here which is different, but it doesn't seem to address fully why the girl should be able to 100% identify what DNA came from her dad by subtracting the shared DNA with her brother. I read that half-siblings share 25% of the DNA, but the mother here surely contributed more than 25% to each of her children.
In practice, my half-sibling shows a genetic relationship to people on our shared parent's side that I do not (and likewise, I have genetic relationships to people on our shared parent's side that he does not.) Therefore, I'm positing that my brother and I each inherited some different DNA from our shared parent.
I would take the writer's word for it, but I'm confused. Where am I going wrong? (Sorry about the bad biology background.)


texts: This question on the function of introns in eukaryotic genes made me think: I know that more basal organisms have smaller introns and fewer alternatively spliced exons compared to mammals. But are there eukaryotes whose genomes have no introns at all?


texts: What are the various parts of an ant hill

texts: How can I identify the parts of an ant hill structure from a casting?  Specifically, if there is no real commonality between species, I would like to identify the various parts of a fire ant mound in Florida


texts:
The equation for photosynthesis is

$\ce{6CO2 + 6H2O + Energy -> C6H12O6 + 6O2}$

My confusion rests in the following: during the photolysis (water-splitting) step of the light reactions that occur in Photosystem II, water gets split into 2 H+ ions, 2 electrons (which enter the photosystem), and one Oxygen ion. But if Oxygen ($O_2$) is comprised of two oxygen ions covalently bonded to each other, doesn't this mean that

$\ce{6H2O -> 3O2}$  ?

Could someone please clarify this for me?


texts: Calories burn rate calculation — scientific studies

texts:
There are many online calculators for measuring walking/running/bicycling calories burn rate. They differ in input parameters like some might need my weight as well as height and some don't. Almost none take into account duration of the exercise (and this is crucial in my opinion).

So my question here is: Where are these formulas (used in these calculators) coming from? Any scientific studies perhaps? Are they reliable?

Also I would like to know what is the most accurate method available for measuring the burn rate (I'm only interested in the scientific part, not going to do this myself).


texts: How to map the N6-dimethyladenosine by primer extension?

texts:
I am trying to map N6-dimethyladenosine on rRNA using primer extension (low dNTPs assay) method. But i am not able to detect map my position. I went through some articles they mentioned like they hydrolysed the RNA but they did not mention exactly by which hydrolysis method (enzyme, alkaline). can you please help me?

Great. I used (10 g) of Total RNA for primer extension reaction with 100,000 cpm [- 32P]ATP-labeled oligonucleotide. After annealing at 55–60 °C for 15 min and chilling on ice for 2 min, 1 unit of reverse transcriptase (Expand RT, Roche) and 1 unit of RNase inhibitor were added and an extension reaction was performed at 42 °C for 90 min. The extension products were ethanol precipitated and analyzed on 6% polyacrylamide, 7 M urea gel. (DOI 10.1074/jbc.M308997200)

This method specialized for 2’o methylation on rRNA, my interest is N6-dimethyladenosine (M26-A). In the literature M26-A blocks the RT I did not get the extension. In this publication, they have mentioned the RNA was hydrolyzed but hydrolysis has many different types (alkaline, enzyme) (https://doi.org/10.1091/mbc.E15-02-0073)


texts: How to introduce predators to a simulated ecosystem?

texts:
I made an evolution simulator and observed that when a marginally competent predator appears, it quickly multiplies and hunts down all of the prey animals, which leads to their own extinction soon after. This seem unlike the real world.

About the simulator
The animals are controlled by neural networks, herbivores must consume spontaneously generated food particles to obtain energy, predators can sap energy out of a prey without killing it, but this significantly hinders the prey's well-being. Animals reproduce asexually with mutations.

There are about 50 animals when the predator appears. All herbivores tend to resemble one another.

The ideal result
This simulator was initially meant to explore the development of individual organism through evolution, but the phenomenon I observed made me aware of the importance of whole ecosystems. I want a modified simulator to produce a ecosystems with multiple niches and stable final state, in short, I want biodiversity.

Some proposed modification

Add different habitats: different habitats vary in naturally spawned food particle, and their difference can be detected by the animals
larger population
arbitrarily increase the reproductive period of predators (?)


texts: What happens to embedded membrane proteins after a vesicle is formed?

texts:
When an animal cell is going through endocytosis it cell surrounds a food particle, and the membrane swallows it, creating a vesicle within the cell.

However, what happens to the embedded transmembrane proteins previously in the cell membrane? Do they shut down? Are they degraded? Or do they just not cause a problem that the cell just leaves them be?


texts: Plant respiration produces carbon dioxide, so why are plants regarded as decreasing its atmospheric concentration?

texts: In the absence of sunlight, plants give out the greenhouse gas, carbon dioxide. So why is it said that plants increase the concentration of atmospheric oxygen? Do they not increase the concentration of carbon dioxide and use the oxygen produced in photosynthesis.


texts: How to derive the deactivation time constant in this model of Acetylcholine Receptor state kinetics?

texts:
I came across this simple analytical expression of time constant of deactivation in Elenes et al., 2006. How does one derive this expression

$$\displaystyle\tau_\text{deactivation}\approx\frac{1}{D_+ + 2j_- + \frac{\alpha_2 2k_-}{\beta_2+2k_-}}$$

for the model given below.

   An allosteric reaction mechanism for the muscle AChR. C, O, and D denote the closed, open, and desensitized conformations of the channel, whereas A denotes a molecule of ACh. For simplicity, only one of the (probably several) desensitized conformations is included in the model. Also, the two neurotransmitter binding sites are assumed to be functionally equivalent and independent and, therefore, the two possible monoliganded configurations are considered to be functionally indistinguishable. These simplifications have no consequences on the interpretation of our data. The red arrows indicate the rate constants that, according to Eq. 1, determine the kinetics of the macroscopic current decay upon stepping the concentration of ACh from saturating to zero (i.e., during channel deactivation).

The material is esoteric, but I am hoping someone will be able to answer. The same paper also mentions that deactivation time constant is the reciprocal of
$\frac{\alpha_2 2k_-}{\beta_2+2k_-}$
and references Colquhoun and Hawkes, 1982. This reference will take quite a while to grasp completely.


texts: Effects of Great Pacific Garbage Patch to Phytoplankton?

texts:
I was wondering if the decrease in light received by the area comprised by the Great Pacific Garbage Patch (GPGP) could affect Phytoplankton enough to reduce its potential in that area as a carbon sink.

I mean, it is an area that gets plenty of sunlight, but compared to the overall size of ocean coverage it is not that much and maybe the cover is not intense enough to reduce completely photosynthesis in that area, so maybe the effect is negligible.

I couldn't find any article reviewing this.  If someone can point me to some literature at least.

I found this: https://www.researchgate.net/publication/325022723_Impact_of_microplastics_on_phytoplankton

But I find these results hard to interpret and was hoping more for an ecological studies.

Rephrasing the question for clarity: how much does the GPGP effect C02 capture by effects of disrupting phytoplankton?

PS: Back of envelope calculations:

with a GPGP area of 15e6 Km^2 (source wikipedia)

and a total ocean area of 360e6 Km^2

we have lost 4% of CO2 capture from plankton. But if plankton captures 30-50% of all CO2 emissions, then we lost 2% of all of our carbon capture potential.
But more so, if we assumed that tropical phytoplankton captures more CO2 than from other regions (suppose all of it), then with about 40% of oceans in the tropics we have:

15/(360*0.4) ~ 10% CO2 capturing phytoplankton lost

which would yield 3-5% reduction on our total carbon capture capacity (I am taking this number as a maximum possible impact )

This, to me, seems like a pretty important number, so I must assume that either:
(1) tropical phytoplankton does not contribute majorly to CO2 capture, so its loss would not be impactful
(2) this is very difficult to study and model
(3) some other reason I haven't thought of

In any case, thank you for your attention!


texts: Evolutionary chronology - if any, which species have evolved in the last 100 years

texts: I heared somewhere, I cannot remember where, that there has not been an evolution observed in our lifetime. In life science class, right at the start, we was doing the usual MRSGREN (how to tell if something is a living organism), and the tutor said that you can also tell something is a living organism if it evolves. So I asked if there has been an observed evolution in our lifetime. She said that there had been many but could not recite any off the top of her head, so the next week she handed me a piece of paper with 8 or so websites that aparrently corroborated her claim. I have not got the paper anymore but I recall there been on there the peppered moth or something. So I set out to look for a chronological list of evolution but could not find an authoritative one. I could only find something on wikipedia that indicated that species have been dying out for the past thousand years, but nothing saying that any have evolved.