texts: How does the microbial environment in your gut initiate?

texts:
Clearly, a zygote does not harbor any microbes. As it develops, and the alimentary canal tissue is differentiated, I logically assume that there is still no microbial activity in the fetus's gut. I'm thus also assuming that the commencement of microbial activity in the intestines occurs after birth, but when, and how?

Do newborn babies just happen to ingest only certain e.g., E.coli strains? Is the gut a selective environment in which only certain E.coli strains develop?

Are there any mechanisms to ensure that harmful bacteria do not initially reside in the gut? Is a newborn's digestive tract particularly unstable and ineffective until the proper microbes are established?


texts:
Can anyone pin point, as to where and how, the excess food is stored in fungus (mushroom to be specific).
Like plants store as starch granules, so where does mushroom store?


texts: Because DNA is soluble in water, is it possible to extract PCR product by dissolving excised gel containing the DNA band of desired length in water, mashing the gel piece with a pestle, centrifuging it and then pipetting out the supernatant ?


texts: Species specific White Blood Cells (WBC) composition

texts: In our ongoing immunology undergrad course I learnt that neutrophil primarily fights off bacterial infection and lymphocyte is produced in response to viral infection. I also learnt that neutrophil count in humans is about 70 % in human WBCs while in horse lymphocytes account for 68% of WBC. It is supposed to make humans more immune to bacterial infection and similarly horses better adapted to fight off viral infections. However I cannot find out any relevant material as to what could be the reason that such biased WBC cell component composition has evolved in different species. Please help me find out relevant material on this.


texts: True or False: Dideoxynucleotide sequence analysis Question

texts:
True or false: Dideoxynucleotide sequence analysis is a template-directed method that makes use of chain terminators that stop DNA synthesis because they lack a 2'OH group.
The answer is false.
However I thought it would be true because dideoxynucleotide sequences stop DNA synthesis due to a lack of an OH group on a 2' and 3' group. What have I misunderstood?


texts: How do messenger RNAs regulate each other's expression levels?

texts: I know that researchers learn gene regulatory networks from microarray experiments that measure the mRNA expression levels. However, I do not understand how mRNAs regulate each other's levels. Do they affect the transcription step or the translation step? I know that there are transcription factors which affect the transcription step, but those are not mRNAs but proteins. How does an mRNA (the product before translation) affect another mRNA's expression level? Is this regulation process very similar to the regulation by microRNAs?


texts: What is the purpose of the viscous gel in the Pacinian corpuscle?

texts: I have read that 'when the stimulus (in this case pressure) is constantly applied, the gel repositions itself to prevent the formation of an action potential'. I don't really understand what this means.


texts: Hybrid vs introgression zone in natural populations

texts:
In the book An Introduction to Molecular Ecology, the authors say that

  Introgression is the diffusion of alleles from one population or
  species into another as a result of interbreeding or hybridization
  between them.

And that hybridization is (roughly) the breeding of two distinct species.

I thought that when we were talking about introgression zone and hybrid zone, it was the same thing.

But here is my interpretation:

See the image below. Across an area, you would have 2 populations of 2 species (A-E). They could interbreed in the middle, this would be called the hybrid zone (in C). But the change of allele (or the transfer of allele) between two populations is not only done by hybridization (B vs C). It can be done by a new hybrid breeding with a non hybrid (backcross, in B). Then, B to D would be the introgression zone.

I don't really know what would happen in that case when 2 hybrids breed together for the colours!

So my question is: What is the difference between introgression zone and hybrid zone (is my interpretation correct?)?


texts: Access and decay time of long-term memory

texts:
As for STM (short-term memory), access time is 70 ms and decay time is 200 ms.

Is there any calculated time for LTM (long-term memory) also?

And does LTM really decay with the passage of time?


texts: What causes the yellow and brown spots on our sour cherry tree?

texts:
So at the end of spring (maybe at the beginning of summer) our sour cherry tree started producing these yellowish/brownish spots on its leaves. Can you help me identify the couse of this? What can we do against it? I cannot see any bugs on it, my best guess would be some kind of a fungus, but I am way far from being an expert. Thank you in forward for the answers!
Edit: I am located in Hungary. The brown spots are not bigger than my nails, but the yellow area can cover even the whole leaves. Also, the capillaries visible on the leaves can turn red, as you can see on the pictures. Unfortunately, the exact species of the cherry is unknown to me.


texts: Software to model and analyse protein–ligand interactions

texts:
I am currently trying to model a certain protein (Golgi Mannosidase II) and compare the induced fit of the inhibitor swainsonine. I would like to be able to analyse the distances between bonding interactions and the strengths of bonding regions. I was wondering if there was any type of software that would allow me to analyse this protein and its interactions with swainsonine? I have seen many images like the one below in research papers, but I’m never sure what software the researchers are using to generate these models.

Liberato, M. V. et al. Molecular characterization of a family 5 glycoside hydrolase suggests an induced-fit enzymatic mechanism. Sci. Rep. 6, 23473; doi: 10.1038/srep23473 (2016).


texts: Does tea have its effect if you have a sleep after drinking it?

texts:
If I drink tea, then go to sleep for a while, when I wake up, will the effect of tea still be on me (the refreshing effect)?

Does it depend on the duration of sleep?


texts: How to find Exons in mRNA Computationally

texts:
I'm having trouble finding a method to find exons in the original DNA sequence used to create the mRNA, even given the sequence of the mRNA, as I cannot find a way to reliably identify the beginning and end of introns and exons. Is there an algorithm or method that I can use to do this? What information am I missing to be able to find the beginning and end of exons and introns?

Thanks in advance for answers.


texts: Gap junction proteins, connexins, are known to form intercellular hemichannels, between two adjacent cells. These junctions are maintained cell adhesion proteins (cadherins), yet the turnover of connexins is fairly rapid. As these connexins are being turned over, do the replacement connexins re-form the channel at the same location as previously existing channels, or is the pattern stochastic? Put another way, if we know cells in culture have formed gap junctions, and for any one cell, does it have different connected neighbours with time?


texts: I want to annotate data while analyzing transcritpome data using DESeq2 , usually Biomart R-package (https://www.bioconductor.org/packages/release/bioc/html/biomaRt.html) does the needful , but for non-model organism for which link to Biomart R package is not available seems troublesome, any way to use the custom annotation file( I have one annotation file obtained from Uniprot) or any other alternative to do so?


texts: Can gelatine digestion make blood more thick?

texts: Can gelatine cause blood thickening if digested?


texts:
The explanation given in my textbook is:

  Some members of this diverse group also have an “excavated” feeding
  groove on one side of the cell body. (Campbell Biology)

This still isn't clear, though. What does it mean that this groove is "excavated"? Is it hidden inside the organism and then dug out?? Several websites just say the same thing.


texts: What does 5' and 3' mean in DNA and RNA strands?

texts: What are 5' and 3' in DNA and RNA strands? Please clarify with some images and please use simple English.


texts: Why do cells not spread on soft substrates?

texts:
I recently read a paper discussing how cells (primary mouse embryo fibroblasts) fail to spread and proliferate properly when plated on a soft substrate (i.e. soft PDMS pillars with stiffness k = 2.3 nN$\mu$m$^{-1}$), but spreading and proliferation can be restored with cyclic stretching of cells.

http://www.nature.com/ncomms/2015/150223/ncomms7333/full/ncomms7333.html

My question is if we understand why cells need to be on a hard surface to do normal operations (proliferate and spread)? It doesn't seem to me that a soft surface would be any more difficult for a cell to attach to. I would think that a "slippery" (I'm not sure of a correct biological term for this) surface may have this effect, but I wouldn't expect this from a soft surface.


texts:
From the wikipedia page on stretching:

  Stretching is a form of physical exercise in which a specific muscle or tendon (or muscle group) is deliberately flexed or stretched in order to improve the muscle's felt elasticity and achieve comfortable muscle tone.

How is this improvement of elasticity achieved, at the physiological level?

Searching around on this topic brings a lot of articles about the types of stretches (e.g. again, wikipedia) and what are their benefits and disadvantages.
But how do they differ at the biological level?


texts: stem cells divisions and normal cells division

texts:
I'm a beginner in biology, but I've read that stem cells replace the "worn out" cells or the dead cells. Well, I'm a bit confused - why do they do this?
Aren't there any cells nearby which are the same type as the worn out cells or the dead ones, that can divide and so on?


texts:
I have a male colleague which has a son that does not resemble its father in any degree (apart of being male). The "father" is thin, tan-skinned, brown-eyed and the "son" has blue eyes, blond and already slightly overweight boy. Their faces have no any signs of similarity.

Since, the son gets Y-chromosome from a father, it is interesting to know if the Y-chromosome possesses any phenotypical feature apart of testicular development?

I did not find any Y-gene that influences the phenotype.

So, the second part of the question: Can other 22 parental chromosomes be so "recessive" that a child will have no "any" external signs resembling its biologic father.


texts: Does consistency in minor allele frequency of a SNP across populations imply selection?

texts:
If a particular SNP has very similar MAF value across multiple largely non-overlapping populations, with the assumption of no gene flow between the populations over many generations, would that then suggest that there is a selective pressure that is keeping the MAF stable in these populations?

Are there methods to test that can parse out the drift and selection effects in such cases?

Also, does it matter in this context if the MAF value is high or low - since I believe a low MAF SNP is more likely to disappear than a high MAF one?

Thanks in advance for any insight.


texts: What is this insect? Possible assassin bug? or kissing bug?

texts:
I saw this bug (around 2 cm) in the front of the balcony door inside the room.

I googled and found two same insects- Assassin bug and Kissing bug. Could they hide their eggs inside the room? Should I be worried?
I live in Vienna, Austria
Thanks in advance
Update: I found this bug here https://www.massaudubon.org/learn/nature-wildlife/insects-arachnids/western-conifer-seed-bugs
The bug that I saw looks like a Western Conifer Seed Bugs! Do you agree?


texts: Do we know what the earliest stages of integument like fur or feathers looked like?

texts:
From either fossil evidence or from developmental evidence, are there any models for what the earliest stages of the evolution of fur, feathers or similar structures like pycnofibres would have looked like, and how they would have functioned?
I've been unable to find any good sources on the topic, and was interested in how the ancestors of birds and mammals went from scaly to covered in fur and feathers.


texts: Heterochromatin v Euchromatin. Which is more abundant?

texts:
So I was just reading that whether heterochromatin or euchromatin is more abundant in a particular human cell depends on how active that cell is. But considering that most of the 25,000 or so genes in the human genome are transcriptionally inactive in any given cell, how is it possible for cellular activity to affect the chromatin structure to a degree that significantly alters how a nucleus looks on microscopic images? Since, after all, whether the cell is active or not will only affect little of the chromatin.

And since most of the genome is inactive, shouldn't it be in a heterochromatic form, and thus most of the chromatin in any given cell will be heterochromatin?

(I know this is not true, but I was wondering why)


texts:
Please explain what the term synaptic clearance means. For example, what would dopamine synaptic clearance be? It is important to me in context of dopamine signaling variation due to difference in synaptic clearence level.

Some gene alleles are associated with greater synaptic clearance in dopamine pathways. It used to explain dopamine level variation and throught it some brain areas activity (for example Nucleus Accumbens) difference among people with different genotypes. For more information see for example. Also, reduced synaptic clearence related to greater dopamine signaling levels. So I was interested in this term from prespective of brain activity in areas with dopamine receptors


texts: Is it firmly established, that mutations are sufficient for cancer?

texts:
It is evident for scientists, that all cancer cells have some mutated genes. Say mutations in general.

But this evidence means necessary condition.

But what about sufficient conditions?

Is it possible, that mutations are necessary but insufficient for cancer?

I.e. may be other factors exist, which are probably more important?


texts: Are humans still competing in the same way now that the first life forms did?

texts:
I'm not sure if this is actually a philosophical question, but I was reading a timeline of life on earth and I came to this:

  4500-3500 Ma The earliest life appears, possibly at Alkaline vents
  with the creation of the Last Universal Common Ancestor, possibly
  derived from self-reproducing RNA molecules.[6][7] The replication of
  these organisms requires resources like energy, space, and smaller
  building blocks, which soon become limited, resulting in competition,
  with natural selection favouring those molecules which are more
  efficient at replication. DNA molecules then take over as the main
  replicators and these archaic genomes soon develop inside enclosing
  membranes which provide a stable physical and chemical environment
  conducive to their replication: proto-cells.

..and I thought to myself, are we still essentially doing that as we live our lives?  I think I'm trying to connect the idea of a human "being competitive" with "evolution".. is there any truth to that?


texts:
My biology textbook says that arteries have a small lumen relative to the thickness of their walls. I understand why they need thick walls, to withstand high pressure and stretch etc. But when explaining the reason for the "small" lumen, it says that it is to "maintain the high pressure". I'm not quite sure what this means.

What would happen if the lumen was larger? Wouldn't a small lumen create resistance to blood flow? And what exactly is blood pressure? Also, it says that veins have a "large" lumen. Why is this so? I think my confusion is a lack of understanding of what blood pressure really means. Why does velocity not seem to make a difference?


texts:
I have been trying to identify a mushroom I collected in the nearby forest, and while I think I have it identified, it seems to have a couple of names and I am confused about which grouping is correct.

According to one site, the mushroom is Boletus Chrysenteron :http://www.mycokey.org/result.shtml?genSpec=Species&ID=213&showList=DropDown&random=11837

According to Wikipedia it is Xerocomellus Chrysenteron (picture on right) https://en.wikipedia.org/wiki/Xerocomellus

But the info suggests that this Xerocomellus group is relatively new and belongs to the family Bolataceae.

Are these two different mushrooms (Xerocomellus Chrysenteron and Boletus Chrysenteron)? Or is it that the mushroom is now in a new group?


texts: Is it possible to create DNA of a species that could be any animal

texts:
I was thinking about a fiction world in which all animal (at least vertebrate) could crossbred because they share same number and layout of chromosome but differ in hereditary detail (like human skin color) and/or using epigenetic modifications.

Is it actually possible? And how large of DNA it could be to code all vertebrate form and function?

I'm programmer so I just think DNA as a code. And it seem we could refactor and reuse most of DNA code between tetrapod species (also between arthropod-arthropod species)


texts: Is there any research paper which identifies left and right brained behavior?

texts:
There are many web puzzle to identify, but does it really have any scientific proof?

something like - http://braintest.sommer-sommer.com/en/

any logic behind it?


texts: I'm working on an assignment for my IB biology class and some assistance would be highly appreciated. I've read several articles and I still haven't quite gotten the answer I'm looking for. I have to write a one page summary on whether or not Mitochondrion are alive or not.


texts: Does Remdesivir interfere with human transcription?

texts:
Remdesivir is metabolized into a nucleotide analogue. It is incorporated in the viral genomes causing either termination of transcription or a dysfunctional genome. Thus, the new viral particles produces within infected cells are dysfunctional.

However, how does Remdesivir intefere with human transcription, or does it? I'd imagine that a nucleotide analogue could be incorporated into a human mRNA. Can it?

edit: The mithocondria are discussed below. I would also be interested in usual, i.e. nucleic transcription. Is Remdesivir transported into the nucleus? Does human RNA polymerase accept it?


texts: How can bats hear such high frequencies?

texts:
I attended a talk that glossed over some biology as it was talking about a certain protein. The speaker mentioned humans can hear up to, often less than 20kHz frequencies, whereas bats can hear up to 100kHz. Presumably this is to do with differences in cochlear anatomy.

What about the inner ear of bats is different form ours, and how does this allow them to hear such high frequencies?


texts: Book suggestion on computational molecular evolution

texts:
I'm currently reading Computational Molecular Evolution by Yang. Can you recommend alternative books?

I am finding it to be lacking on conceptual discussion (it's more focussed on the mathematics and statistical intricacies). I'd like to find something which discusses why we do the things, and the strengths and weaknesses of the ideas, which are presented in the Yang book whilst not being overly specialist - more of an introductory text to the field.

Any introduction to phylogenetics books??


texts: Transcription takes place from the 5’ to the 3’ end of the m-RNA. Why?

texts: Only one side of the DNA ladder is copied (the sense side). The sense side starts with a 3’ end. This means the corresponding mRNA will have to assemble starting from the 5’ end. This is my initial thought, but can someone expand on it? Also, is this explained by why replication is performed in the 5' to 3' direction as suggested by this thread: Why is DNA replication  performed in the 5' to 3' direction?


texts: Complementarity Determining Regions (CDRs)

texts:
Complementarity determining regions (CDRs) are part of the variable domains in immunoglobulins (antibodies) and T cell receptors, generated by B-cells and T-cells respectively, where these molecules bind to their specific antigen. (source: WIKI, with a minor change)

Now does this mean that this CDR is the paratope? As it has the same functionality as paratope, to bind to epitope of the antigen. So is CDR a type of paratope?

(I have not studied biology since last 8 years and now I am going through it because I need it for my research. So if someone can describe it in simple language it would be very helpful)


texts: Why do tears fall from our eyes when we ride a bike too fast?

texts:
When we ride a bike too fast why do tears fall from our eyes. What is going on biologically and what may the evolutionary story be behind this?

This quora Q&A gives a few ideas, none of which satisfy my question fully.

This is similar to a response to smoke.

But this is clean air? Why doesn't this happen all the time?

Our eyes always need to be lubricated.

But why the need for excess tears?


texts: Which patterns do I have to avoid when modifying the 3'-UTR?

texts:
I want to change a pre-miRNA sequence (in my case the pre-miRNA is encoding in a 3'UTR of a gene) and then put it in a lentivirus to see if it is still processed.

After modification (permutation of ten regions of ~20 nt) which kind of newly appeared pattern I've to be careful about? I do not want to disturb the gene in which the miRNA is encoded


texts: Are there any animals that get smaller as a normal part of their life cycle?

texts:
It seems that at any given moment in a creatures life, it either grows bigger or has stopped growing.

The only exceptions I know of are extreme events like insects undergoing metamorphosis or evolutionarily irrelevant effects like humans shrinking a bit at old ages due to their spine getting compressed (I consider it irrelevant because for most of human history, people old enough for this effect to be significant enough were either dead or long done with reproduction).

Are there any animals that are known to "grow smaller" over some period of their lives as a purposeful part of their biological functions?


texts: What non invasive methods of estimating Body Time are there?

texts:
I found this article on estimating body time using molecular timetable of 168 genes. researchers looked at gene expressions and plotted them to 24 hour cosines curve with some pretty spectacular results.

Unfortunately the techniques discussed required sampling of liver cells, which may be invasive. Are there non- invasive methods of estimating body time/ biological clock/ circadian rhythm time?

An example of body time: at 8:00 real time, a mouse may exhibit gene expressions more appropriate for 9:30, so the body time of the mouse is 9:30.


texts: What Effect would Cannabinoids have on the Acute Porphyrias?

texts: I should be clear in saying that this question is NOT intended for personal medical advice. Rather what I am looking for is journal articles and/or books that touch on this subject because I think it would be quite an intriguing topic to probe. I am unaware of any interaction between the endocannabinoid system and the formation of haem and porphyrins in general.


texts: Hearing and neurons- do ears have a sampling period?

texts: From what I have read, outer hair cells in the human ear amplify incoming signals and inner hair cells "pick-up" the signals and generate action potential. However, neurons have refractory periods during which they cannot fire again. Does this mean that the human ear has a "sampling period" within which it cannot "pick-up" sounds?


texts: To measure frequencies of eosinophils and neutrophils in airways

texts:
I am reading this paragraph about RS killed-vaccine in Encyclopedia of Virology, Third Edition (2008), vol. 3, pp. 70-77

What is this data called by which you can say that the frequencies of eosinophils and neutrophils increased within airways?

I think sample is first taken from throat and cultivated on some general culture (blood agar).
Then, specimen is looked under microscope.
Similarly done for the sample after vaccine.
Then, visual comparison with identifying visually eosinophils and neutrophils.

Is the conclusion made based on culturing, microscopy and visual sampling by eye?

Mass spectrometry

I am not sure anymore if this technique is useful at all.
Mass spectrometry can give different intensities and masses.
If so, the intensity of the corresponding peaks should be greater after the vaccine.
Can this kind of conclusion be made based on mass spectrometry?

Interesting would be to know the exact spectrum of eosinophils and neutrophils after the vaccine. I think they do not increase proportionally.
The one increases more than the other.


texts: What is a good source for info on disease frequency distribution among age groups?

texts: I need information on the disease frequency distribution among age groups for an Android app I'm building... Hopefully I've come to the right place. Is there a good data source for this? Like a bioinformatics database?


texts:
Can the DNA polymerase in PCR (polymerase chain reaction) recognize both DNA and RNA for use as a template?

I want to know is it possible if my primers bind to contaminant RNA and then any DNA polymerase like Taq DNA polymerase use this strand as the template for elongation?


texts: Do goosebumps always appear in the same spots on the skin?

texts:
Often one gets goosebumps when one is cold. I am curious whether the precise location of the goosebumps on, say, one's leg changes from occurrence to occurrence or not? In case if their precise locations are always identical is there anything particular about those locations that differentiate them from other parts of one's skin?

Thus the question: do goosebumps appear at the same spots on one's body every time or their exact location changes?


texts: Why are riboswitches mostly present in bacteria and not in eukaryotes?

texts:
Riboswitches are a rather elegant way to regulate gene expression without any additional machinery. A small ligand binds to the mRNA and directly influences transcription or translation.

Most of the known riboswitches are found in bacteria, there are few examples of riboswitches in eukaryotes. There are no classical riboswitches in humans as far as I know (there is one example, but triggered by a protein and not a metabolite), it seems that more complex organisms tend to use other methods of gene regulation.

Are there any known reasons for this? What are the drawbacks of regulating gene expression with riboswitches compared to using regulatory proteins? Is there an explanation for the lack of riboswitches in more complex organisms?


texts: Extreme examples of protein translation/use coupling/decoupling?

texts: What are known extreme examples of protein translation/effect coupling/decoupling? For example, examples of proteins that are immediately used at the time the have been translated and vice versa, cases of proteins that are translated but then only used much later in time in/outside the cell?


texts: Results of a complete DNA sequencing - are they 100% reusable?

texts:
Is that correct that a complete DNA sequencing (the whole genome) need only to be done once (per person)?

After that is done, it the complete genome can be stored and once the new genes (and their purposes are confirmed) are discovered, the scientist can simply go back to a previously sequenced data and to find it this particular person has this new gene or not.


texts: My husband had light brown eyes. His father had hazel and his mother, light brown as well. His younger brother however, has blue eyes. Both my children have blue eyes. Is this possible? I thought once the recessive gene was used in my first child, his dominant brown gene would take over?


texts: Is RGB diode lighting okay for the eyes?

texts:
Is a light source giving off light composed of red, green and blue lights harmful to the eyes? Does it lack any important qualities that other artificial light sources, such incandescent lamps or white LEDs may have?

Is it alright to use RGB light panels in a room instead of the usual lighting?


texts:
I am interested in learning about GMO. The topic is so wrapped in controversy, that it's hard to find a good book that introduces the basic concepts involved. I went through various university websites, but couldn't find any lecture notes on the topic. I don't know, is it too broad a topic? Is there even a book called Introduction to GMO? Maybe that's the problem.
I am interested in a book that tells you about how gene manipulation is done. How do biology students get introduced to this concept? I hope the question is not too general.


texts: What are these Bahrain insects living in a colony?

texts:
These insects are in the desert in Bahrain. About 500 in one place both adults and juveniles. Some dung beetle near by. Does anyone know a name?

The adults seem to be protecting the young ?


texts: Corpus luteum during the luteal phase and gonadotropins

texts:
Does the corpus luteum operate independently of the hypothalamic-hypophyseal-ovarian axis? I know that hCG sustains the corpus luteum in the absence of FSH and LH, but in an ovarian cycle where there is no pregnancy, do FSH and LH affect the corpus luteum? It seems to produce a lot of estrogens and progesterone even when FSH and LH levels are low.

(Online I saw that the corpus luteum degenerates because of low FSH and LH levels. Is this true? Why doesn’t the corpus luteum degenerate immediately after the LH surge, then, whereafter FSH and LH levels are so low? If not, then why does the corpus luteum degenerate?)


texts:
An article on bioRxiv, Evaluation of heating and chemical protocols for inactivating SARS-CoV-2, recommends certain treatments to inactivate SARS-Cov-2 for lab work.
The abstract notes: "Although heating protocol consisting of 92°C-15min was more effective rather than 56°C-30min and 60°C-60min to achieve 6-log reduction, it is not amenable for molecular detection on respiratory specimens because of important decrease of detectable RNA copies in the treated sample vs untreated sample."
Do I understand correctly that 56C/30min is broadly as effective as 60C/60min? Given that 56C from previous research seems to be more effective than 22C, I would have expected 60C to require less time to achieve a similar effect to 56C. Especially with 92C/15min being more effective still, though more disruptive.
I'm curious what the explanation may be why effectivity might drop between 56 and 92C. Or why I may be misunderstanding the temperature/time scales. Please keep it simple. Thank you.


texts: How do B and T cells work incorrectly in a person with Systemic Lupus Erythematosus?

texts: Systemic lupus erythematosus is an autoimmune disease in which the body's immune system attacks healthy cells. How exactly do B and T cells attack these cells they mistake for pathogens?


texts:
I was wondering what the actual reason for death by suffocation is. Obviously it is related to oxygen deprivation. But what is the underlying cause of death?

Is it due to insufficient oxygen for aerobic respiration, and the resulting lack of ATP (as anaerobic respiration forms less ATP)?
Or is it because of the build-up of lactic acid, causing enzymes to denature?
Or is it the lowering of the pH of the blood because of a build-up of carbon dioxide which forms carbonic acid and subsequent denaturation of enzymes?


texts: What are good resources for self-learning modern molecular biology concepts?

texts:
My learning of molecular biology ended in the early 90's (and with early 90's era information). While I don't aspire to be a molecular biologist, I do aspire to better understand modern approaches better.

Short of going back to school and taking classes, what are good resources for learning on my own? I'd like to get to the point of being able to understand Nature, Science, Cell, etc. Is this even a feasible goal?


texts: Do primates other than humans have a consistent sleep schedule?

texts:
I'm doing some sleep research and would like to compare a human sleep pattern as recorded by a wrist-based actigraph with a "natural" sleep pattern, such as from apes. In an experiment like that, a human wears an activity monitor on a non-dominant arm over multiple days. The monitor analyzes activity pattern and can detect when the user is asleep versus active.

Can someone suggest a research article or a website that did a sleep study of primates (monkeys/apes) either in captivity or natural habitat over multiple days?

I'm particularly interested in how consistent their bedtimes are - do primates go to sleep in the evening whenever they feel like, or do they stick to a more consistent sleep schedule?


texts: Can viruses survive Super saturated salt solution?

texts:
As we know there is less evidence of biological activity in Dead Sea ( Lake full of salt water).

Also, our blood cells do not survive in too much salt water as they shrink and die.

So I was thinking that about if viruses survive a super saturated salt water.

And if they survive then which thing is making them survive and giving them the tolerance capacity?

And if they get killed then how they get killed?


texts:
I thought that according to cladistics, only monophyletic groups were valid as species or any other taxa. But extinct species, like say H Erectus must be paraphyletic, as the common ancestor of H Erectus is also the common ancestor of modern man. So if species are frequently paraphyletic, how can cladistics be tenable?

Edit. Also, I'm new to this forum. The people responding here, I'm assuming are actually biologists with a specific knowledge of cladistics, right? I'm a post-grad (philosophy of biology rather than biology per se) so I'm not really looking for links which explain what cladistics is, and certainly not wikipedia. I can access most journals if there is a paper on this subject. I can't find anyone in our dept who can give me a steer on this. I realise thhis is a slightly unorthodox research method, but I'm at a bit of a dead end here!


texts: Chromosome position mismatch for SNPs in dna tests

texts:
TL;DR: why is the position reported by DNA testing companies for an SNP on a particular chromosome different than the one in dbSNP/SNPedia databases?

I'm analyzing the raw DNA exports for the same person from 2 different companies.

There is, as expected, a small number of discrepancies on the genotype reported.

Strangely, there is also a (smaller) number of discrepancies on the chromosome and position reported for the same SNP (about 0.02% of the rs-ids that are common to both exports).

Trying to find out who is right, I looked at SNPedia and dbSNP. To my surprise, while SNPedia and dbSNP (logically) agree on the positions, they never seem to match the positions reported in the raw DNA exports.

While the two companies that I used agree on the position in the vast majority of SNPs, they are apparently always different from dbSNP. In 75% of the 101 differences between the two companies, the position number only differs by 1.

I'm surprised by this and I feel that I'm missing some underlying piece of information.

What can explain these differences?

Does the "position" in the DNA exports from 23andme and MyHeritage represent some other biological property than the position reported by dbSNP/SNPedia? Or is there a conversion formula? Or is the information from the exports unreliable?


texts:
I've been reading around Wikipedia recently trying to learn more about various biomechanisms. I’m intrigued by ribosomes — with how small they are, they’re basically chemical machines from what I can tell. I’ve got the general idea of what they do, which is nicely illustrated in the super common GIF below:

My question is how this happens, on a molecular/chemical scale. Even in the GIF, the way the mRNA is being so mechanically fed through the ribosome at the exact-right times seems so deliberate, and I can’t imagine a chemical process that does this so well. It seems like we know the exact protein by protein structure of a few types of ribosome; as such, I naively assume we can work out exactly why and how it does each thing it does. I’m sure it's not a simple question — if it's not really answerable in a stack exchange question, then I guess my question becomes where should I read to learn this.


texts: Explanation of why more Ca2+ ions causes longer root length in plants

texts:
This is for an experiment to test for mineral ion availabity in plants.
So if there is more Calcium ions in the soil, there would be an increase in the length of the root of the plant that is being tested on. Why would that be the case? Calcium ions make up Calcium Pectate in the middle lamella, and causes the cell wall to become more rigid and firmer. But why would it cause the root length to increase?


texts: How long can a naked human survive on Mars?

texts:
How long can a naked human survive at the surface of the Mars planet?

For instance, let's say a worker's base takes fire while he sleeps, the building is totally ablaze and he can do nothing but run to the emergency building 200 meters away without any respiratory equipment, pressure suit, UV protections or anything.

Maybe a human could survive for a rather long time, and apnea time is the real limiting factor?

Climate:

Temperature: 27 °C to −50 °C (base is at a rather warm location, on Equator)
Pressure: 0.006 bar (Earth: 1 bar)


texts: Why is an initiator tRNA required, distinct from the methionine tRNA used in elongation?

texts:
I'm confused by why there is a need for different tRNA-methionine complexes for translational initiation and elongation.

This paper mentions that

  It is important that each type of methionyl tRNA be restricted to its separate function, as competition for tRNA by the initiation and elongation machinery could lead to serious problems for the cell

I don't understand what these problems may be.


texts:
Generally in biology books, it is written that the cell membrane is selectively permeable and that it has a protective function, as in here
It says that the cell membrane protects the cell from its surroundings. However the selective permeability is only for the hydrophilic substances, and not for any foreign antigen which may be dangerous for a cell.
So how does this count as protective?
Also for hydrophilic substances, carrier proteins are present, ready to take the ionic substances inside the cell.
Hence my only question here is how is the cell membrane protective?


texts: Why can bacteria resist topical antibiotics, but not compounds like Benzoyl Peroxide?

texts:
I excerpt from p 2 of 4, but p 4 of 4 reviews the entire article by Debra Jaliman, MD on Apr 17 2014.

Usually, topical antibiotics aren't recommended alone as an acne treatment, as they can increase the risk for antibiotic resistance in skin bacteria. However, using benzoyl peroxide with a topical antibiotic may reduce the chances of developing antibiotic resistance.
[Source:] Substances that kill acne bacteria by inflammation, such as benzoyl peroxide, oil of cloves, and chlorhexidine gluconate. Bacteria don’t develop resistance to these treatments, but they don’t kill as many bacteria, either.

If topical antibiotics can cause antibiotic resistance, why can't compounds like benzyl peroxide? I ask in general about other bactericide, not just benzyl peroxide.


texts: How likely is to develop an infection from a single virion entering a single cell?

texts:
Is there any research (including mathematical or computational modelling) regarding how likely it is to infect an organism starting from a single virion entering a single cell?

I am interested in any virus and any multicellular organism (including immunocompromised).


texts:
How does this value actually get calculated?
Logarithms are usually written as
log(base 10) of x
So what is the 'P' equivalent of 'base 10'? I know it stands for octanol/water, but what does that actually mean in a computational context?

I've found many explanations of LogP online, but they usually just say the same thing, which is what LogP is used for. How does one actually calculate it?

Sorry if this is a ridiculously simple question. Bridging the gap between chemistry and math is not my strong suit.


texts: Will sperm cells exhibit chemotaxis towards sucrose?

texts:
I was wondering if sperm cells will exhibit chemotaxis towards sucrose? One of my friends told me that sperm cells die in presence of salts. So I guess sperms will move away from salt. Can someone give me any reference related to this area.

UPDATE (Answer for why sucrose?):

So I should have made things more clear. I was thinking to do an experiment by taking some sperm cells and its effects on sugar and salt and then to see it under a foldscope microscope. Since I am not a biologist, I wanted some guidance. The common available substances which came to my mind was sugar and salt.


texts:
Why ravens play with small plastic details and other garbage?

Could you explain how this behavior was formed by evolution for birds-scavengers?


texts: How is the sequenced genome of a person useful to him in practice, now?

texts: Currently it is possible and not so expensive for a person to have his genome. This is useful in general for understanding how life works. But, in practice, how is this useful for the specific person at this point in time?


texts: Why don't warts caused by HPV spread to the whole body?

texts:
My son had a plantar wart on his foot, which (as I understand it) is caused by a virus which only infects skin cells. Once in the skin cell the virus replicates, but when attacked by the immune system prompts the growth of a hard, thick layer of skin (callus). Warts are caused by a HPV.

Given the wart has infected a skin cell, and skin cells are next to each other in a great big sheet covering the entire human body, why is it that we don't become completely covered in wart?  I assume that it's not the immune system keeping the wart at bay, because the original wart isn't defeated and we can get other spot infections elsewhere.


texts: Why can't this be 1st meiotic division non-disjunction as well?

texts:
The child has gotten 2 "sick" chromosomes from his dad and 1 healthy from his mom, leaving it with trisomy 13.
I can see how this can happen in the second meiotic division of the father but I can ALSO see how this can happen in the FIRST meiotic division by non-disjunction.
Let me illustrate both ways which I see it and you can tell me where I go wrong as my book only illustrates that is the second division:

The black is the healthy chromosome and the red is the "sick" one. As you can see, we should end up with a double sick chromosome in both cases??


texts: How long do zebra fishes remain transparent?

texts:
As larva, zebra fishes are transparent, at least up to 5-6 days. I wonder what would be the upper limit of the transparent period. This is of relevance considering purposes for imaging.

The question primarily relates to normal zebra fish, and not especially to transgenic breeds.


texts:
In the last few weeks, Pfizer/BionTech, Moderna and AstraZeneca have each released preliminary estimates of the efficacy of their SARS-COV-2 vaccines.
But what do their respective efficacy percentages actually mean? Is the Pfizer/BioNTech vaccine 95% effective in any person? Or is the success of provoking the desired immune response limited to 95% of the population?
Put very simply: is it 100% effective in 95% of the population, or 95% effective in 100% of the population?


texts: Can frequent ultrasound diagnostics be harmful?

texts: Are there any short or long term effects apparent in tissues if a zone (or the whole) of human body is scanned with ultrasonic waves often?


texts: Neuroscience and learning of a single neuron

texts:
Can you teach an alphabet to a neuron?

If yes, how?

How does a neuron 'learn' new information, do all individuals learns similarly ?


texts: Are there any DNA sequences shared by all/most Viruses?

texts:
Is there any one DNA sequence shared by all or most viruses?

I highly doubt there is mainly because of how different all of them are, but it's still worth a try.

Thanks


texts: Can the dietary fibres as chemical compounds be regarded as polymers?

texts: At the level of molecular structure, can the dietary fibres be regarded as polymers?


texts:
Does anyone know some scientific rigorous way to look at a slice of meat. I am not asking what kind of meat it is or which part of the animal it came from. I wonder what is the different lining on the meat, what is that huge white spot in the middle and what do the cells of that red part look like and what they are called.

If someone can provide a reference on that it would be great.


texts: What is the difference between "cistron" and "gene"?

texts:
I'm asking after reading the cognate wikipedia.en article on "cistron". I am still not sure about the difference between the two terms.

To me it seems valid to picture a "cistron" as the genome wide set of a specific gene's alleles ?

Thus if all copies of a gene bear recessive mutations all generating the same phenotypic trait (not necessarily the same mutation) no complementation is observed in a cis-trans test?


texts:
I found this guy in my driveway this morning. I live in Northern Florida, near Jacksonville.

I initially thought that it was a baby snake (note the black on brown lengthwise stripes), but it moves very slowly and methodically, like a slug, perhaps. Never saw a slug so long and skinny.
He's about 3.5 inches (90mm) long, and can hold his head up high to look around, raising up almost a third of his total body length.

Maybe some kind of worm?

The "hammerhead" style head is what is making me scratch mine.


texts: How is it determined in a zygote state of foetus, that which side is mouth and which side is for anus?

texts: After the fertilization when the zygote  is in the growing state to a foetus, the main canal is introduced first, from mouth to anus. But my question is when the canal is created first how does it determine which side is for mouth and which side is for anus?


texts: Why do we only initially feel the bending of a hair?

texts:
In my neurobiology class, my professor prompted us to take the tip of our pencil and fold or push down a single strand of hair on our arm or leg in the opposite direction that it grows in. He then commented on how we are able to detect the initial stimulus, but how after a while we no longer feel the hair being bent.

My question is thus, why does this occur? Why would we suddenly no longer be able to feel the stimulus of the hair being forced back?


texts: Does adding antibiotic after 5-10 mins of innoculation affect the protein yield or growth?

texts: I've asked a lab colleague the same question. She said, it would loosen the bacterial cells in the LB medium and plasmids would come out. Is that true? and why?


texts: Does cell culturing contribute to dangerous antibiotic resistance to the same degree as livestock?

texts:
According to the CDC, antibiotic resistance is one of the biggest public health challenges of our time. The largest incubator for antibiotic resistance is the factory farming of animals where livestock are administered large antibiotic doses often and kept in infection-prone conditions.
Another area where antibiotic use is common is in cell culturing for biological research and engineering. To what degree is this use of antibiotics contribute to the public health challenge today, and moving forward as the biotechnology sector grows?
I am curious both about the impact for yeast cell culturing, and also for the culturing of meats as a future food source. I wonder how the problem differs from the antibiotic resistance problem in the livestock industry, and how this might affect the outlook of a future filled with synthetic biologic products and lab-grown meat.
I see two differences off the bat between livestock farming and cell culturing:

animals have much more powerful immune systems than cultures
culture contamination can be much more readily monitored and responded to by operators


texts:
How many ATP molecules are generated from oxidation of FADH2 formed during complete oxidation of 10 molecules of maltose?

40
60
80
20

My method-

As maltose is a disaccharide ( made up of two glucose molecules )and for one glucose molecule , 2 FADH2 are formed after complete oxidation.
Then for one maltose molecule 4 FADH2 will be formed (since maltose has 2 glucose molecules).
Such 10 molecules of maltose will give 40-FADH2.
1-FADH2 produces 2ATP during oxidative phosphorylation ,so total ATP formed =80


texts: NCBI blast for exact match of short sequence

texts:
I'm trying to Blast for exact matches to the sequence: 'ATTGNNNNGCAAACCA' in the human transcriptome using NCBI Blast on its 'refseq_rna' database. However, when I do a basic query I get "No significant similarity found."
Note the N's in the middle of the sequence, if I get rid of those N's, yielding the sequence 'AGCGGATTGCAAAGCAAACCA', I get a match in the 3' UTR of the human MeCP2 gene (which is correct). I don't understand why adding the N's here make it not work.
I looked at the help section and I believe this may be due to shorter sequences being less "statistically significant". Statistical significance of output is completely irrelevant to me, so I set 'Expect Value' to 100000000000000. However, I still get the same result.
I also tried to modify the HTML of the page to allow me to submit a word size of 4 to the form. This went through, but I still got "No significant similarity found".
Could someone help me out with this? I feel like searching for a short sequence shouldn't be this hard.


texts: Left-handedness and Right-handedness - Are they genetic?

texts:
I have a biology book that states that whether a person will be left-handed or right-handed is determined by the genetic constitutional makeup.

Is this true? As far as I knew, these traits depend on how a person is trained as a child: every child has a tendency to use the left hand first when he starts to write, but if the parents teach him, then it will change to the right hand.

What is the truth?


texts: Is there a realistic "family tree" model for the human population?

texts:
I would like to do some gene inheritance simulations, and I was wondering if there is an accepted model for what mating looks like in the general human population? I am not necessarily looking for the exact graph of any population.

For example, my current model has generations 1, 2, ..., n, n+1, ... where each individual in generation i is the product of a mating between two individuals in generation i-1. This is obviously over simplistic, and I was wondering if there are better models out there?


texts:
What species is making this sound?

You can hear it from the opening samples of this song: Earthgarden by Nada (2003).

I wish to study the frequency distribution of the bird call.


texts: Do non-human animals suffer from insomnia?

texts:
And how do we know whether they do or not?

§

If sleep is a physiological need, it seems weird that we become unable to fulfill on demand even in the absence of any obvious physical issues. We would all probably would like to be able to fall asleep on demand on a long flight and we all know this can be hard even when we are tired.

Thus, my question is whether this is a mostly human dysfunction or a common animal property.


texts: What mammal or creature dropped this? (Warning: Gross Pictures)

texts:
I'm at a loss to explain what creature dropped or created this. This giant pile showed up virtually overnight.  If someone could point me in the right direction, I'd greatly appreciate it.

The geographical area is Sparks, Nevada.


texts: How close to Earth's core can organisms live?

texts:
We don't to know much about organisms living deep below the Earth's crust. Recently a team led by S. Giovanni discovered some microbes 300 m below the ocean floor. The microbes were found to be a completley new and exotic species and apparently they feed off hydrocarbons like methane and benzene. Scientists speculate that life may exist in our Solar System far below the surface of some planets or moons. This raises some questions:

What is the theoretical minimum distance from Earth's core where life can still exist. Please explain how you came up with this number. For example, there are temperature-imposed limits on many biochemical processes.
Is there the potential to discover some truly alien life forms in the Earth's mantle (by this I mean, life which is not carbon based, or life which gets its energy in ways we have not seen before, or non DNA-based life, or something along these lines)?
What is the greatest distance below the Earth's crust that life has been discovered? I believe it is the 300 m I cited above, but I am not 100% sure.


texts: Are there any animals that are both poisonous and venomous?

texts:
From my layman understanding, animals that inject venom into the bloodstream by biting or poking are venomous. And ones that harm you when you eat them are poisonous.

Are there any animals (or plants) that fit both descriptions?

I'm guessing eating a venomous rattlesnake will give you an upset stomach but not cause enough damage to be classified as poisonous. And I'm pretty sure poisonous tree frogs don't bite into their prey and inject them with anything.


texts: Modern views on the correspondence of moles

texts:
In his Memoirs, Casanova wrote:

In the midst of the dimple which added such a charm to her chin Esther had a little dark mole, garnished with three or four extremely fine hairs. These moles, which we call in Italian ‘neo, nei’, and which are usually an improvement to the prettiest face, when they occur on the face, the neck, the arms, or the hands, are duplicated on the corresponding parts of the body. I concluded, therefore, that Esther had a mole like that on her chin in a certain place which a virtuous girl does not shew [...]
I then explained to her the theory of the correspondence of moles on the various parts of the human body, and to convince her I ended by saying that her governess who had a large mark on her right cheek ought to have one very like it on her left thigh.

Does contemporary biology/medicine support this law? Are there publications on it?


texts: Calculation of final magnification when using a CCD camera

texts:
I'm trying to empirically calculate the approx final magnification (mag) of digital images rendered through our confocal microscope. Using a micrometer and the microscopy equipment I have, the following is known:

Objective mag = 63x

Ocular mag =10x

Diameter of field of view when viewing specimen through occular = 320µm

Diameter of field of view when live viewing specimen on the screen = 100µm

What is the final mag of the rendered image on the screen?

This is not a homework question. The manufacturers specification for the degree of magnification that the camera and confocal  (and obviously there is some) provide is unknown.


texts: How to reduce/eliminate cell clumping in suspension CHO cells, without using an anti clumping agent?

texts: what is the best way to eliminate clumping suspension cells used for transfection. Anti clumping agents interfere transfection and hence can't be used. Though maintaining the cell density low helps, but doesn't help in the long run.


texts: Are there known downsides to removing UV mutation hotspots to prevent some skin cancers (Genetic sunblock)?

texts:
Khavari et al. recently demonstrated that a significant fraction of  one of the major forms of skin cancer (cutaneous squamous cell carcinomas) are associated with a mutated KNSTRN gene (a protein associated with the kinetochore). They identify a specific region of the gene as being a hotspot for UV induced mutation and suggest that these mutations may be an early event in the development of this type of skin cancer.(1)

Abstract from their nature paper (paywalled):

  Here we report the discovery of recurrent mutations concentrated at an ultraviolet signature hotspot in KNSTRN, which encodes a kinetochore protein, in 19% of cutaneous squamous cell carcinomas (SCCs). Cancer-associated KNSTRN mutations, most notably those encoding p.Ser24Phe, disrupt chromatid cohesion in normal cells, occur in SCC precursors, correlate with increased aneuploidy in primary tumors and enhance tumorigenesis in vivo. These findings suggest a role for KNSTRN mutagenesis in SCC development.(2)

My question:
Scientists could theoretically alter the nucleotide sequence of the KNSTRN gene to remove the mutation hotspot, potentially lowering the incidence of this type of skin cancer. But are there any downsides to doing so? Are there any cases where a UV mutatable hotspot has shown to have some useful function in a cell or organism?

Thanks!

http://www.sciencedaily.com/releases/2014/09/140907181722.htm
http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.3091.html


texts: At what stage of meiosis does "first meiotic arrest of oogenesis" occur?

texts: An exam question asked what stage of meiosis corresponds with "first meiotic arrest of oogenesis". I can't work out the answer from the wiki page - can anyone explain which step this refers to?


texts:
I'm reading the paper "THE PROBLEM OF THE INTERRELATION OF CO-ORDINATION AND LOCALIZATION", which is written by N. Bernstein.
The paper said
"The degree of tension of a muscle is a function, in the first place, of
its innervational (tetanic and tonic) condition E, and, in the second place,
of its length at a given instant and of the velocity with which this length
changes over time."
I don't know why the tension of a muscle is the function of those values.
If that is just assumption, why the assumption can be established?
Thanks!


texts: If a "parasite" is growing on a dead part of the host or on a completely dead host, does it still count as a parasite?

texts:
What I mean is the case where the parasite does not contribute to the death of the host (tissue). Instead, the parasite may start growing after the host (tissue) is already dead.
I came up with this question when I was following the link in this answer and read the PDF about a fungus on a fungus on a fungus on a tree. In the PDF, the author first says that the Hypomyces was growing on the dead bracket mushroom, and then says again that Rhinotrichella globulifera was in turn growing on dead portions of the Hypomyces.
I'm not a mushroom expert and the author also does not mention whether the parasites caused the death of their respective hosts.
So suppose the parasites only started growing after the death of the host, do they really still count as parasites? My understanding is that a parasite should seek a host that is not dead and try to leech nutrients without killing the host too quickly (at least until the parasite is ready for the next stage of its lifecycle and no longer needs the host).


texts: Why should we use the NA12878 dataset for benchmarking?

texts:
As far as I understand, the human genome sample called NA12878 provides high confidence variants for a human sample. It is being used as a benchmark for many genomic research projects.

Q: Why exactly the NA12878 is such a popular benchmark dataset? Just because we have a set of high confidence variants? But we can also get some high confidence variants from the 1000 Genome project. Does that have something to do with the sequencing technology? Anything to do with the sample itself? Why do we want to benchmark our experiments with NA12878?


texts: Why does capsaicin irritate mammals and also kill fungi? Are the two related?

texts:
From this article I heard about a study (search "Tewksbury") which concluded that chilies make capsaicin to discourage mammals from eating their seeds, since grinding by mammals' molars render the seeds unable to germinate. Birds, on the other hand, don't break open the seeds and spread the plants far and wide.

But, they also reference a different theory: capsaicin evolved to defend against a certain kind of fungi that infected pepper plants.

My question is: why does the same chemical do these two things? It seems like quite a coincidence, unless capsaicin has some general destructive properties. But Wikipedia's explanation talks about how capsaicin artificially stimulates a certain receptor in our mouths -- which sounds totally unrelated to fungi.


texts: Substrates of cytochemical reactions in this immunostaining

texts:
Expression of extracellular protein Laminin 9 alpha-4 chain in human skeletal muscle.
Indirect immunostaining with HRP immunostain marker. Ob.x40.

I have unsuccessfully searched NCBI -database, JSTOR and other major Biology databases for an answer. This suggests to me that I do not understand what is going on.

1. What are the substrates of above cytochemical reactions for the given immunostaining above?

I need to give a simpler question where I apparently know the reaction exactly, since it is possible that people cannot answer the above question.

Mitochondria in Hep-2 cell line cells. Cytochemical test for mitochondria specific enzyme NAHD dehydrogenase. Ob.x40.

2. What is the substrate of the cytochemical reaction?

My answer:

The reaction of NADH dehydrogenase is:

  NADH + H+ + CoQ → NAD+ + CoQH2

Substrate: CoQ


texts: Are the sympathetic and parasympathetic nervous systems exact opposites?

texts:
Suppose mechanism existed that could block function of the PNS. Would this just mean then the sympathetic nervous system would become overly active?

Do the sympathetic and parasympathetic systems act as opposing forces?


texts: Plasmid in the nucleus and gene expression

texts:
If we insert a plasmid into a human nucleus that contains exact copy of gene and all relevant promoters to produce some human protein,  will the cell create functional protein from that plasmid only when the cell needs it?

I am not talking about inserting DNA to some chromosome. Inserting separate plasmid to the nucleus (transient transfection).


texts: Can we dilute PureExpress Cell Free Mix to increase number of reactions?

texts:
Since the PureExpress Cell Free mix is so expensive, I was wondering if it might be possible to just dilute the mix to increase the number of reactions we need to use.
From this image I found:

It seems like by just adding more 3PGA, amino acids we should be able to get more reactions out of a diluted solution. From my understanding, this would mean that 3PGA and the amino acids are the only consumables here. Would diluting just change the amount time it takes for the reaction to occur or is there something else that I'm missing here.


texts: How are the two ATPs (properly 1.5 though) formed from oxidation of 1 FADH2?

texts:
Each ATP Synthase has three sites for binding three sets of ADP and Pi, so when the H+ pass through the a and c subunits are they (3 ATPs) not produced for FADH2 substrate?

Besides is the respiratory chain linked to the phosphorylation process apart from the trasfer of H+ ? How does the cell know which substrate has been oxidised and how much ATP is to be produced?


texts: Can sexual reproduction create new genetic information?

texts:
Is there a small chance that in sexual reproduction a new allele forms in the off-spring that was not present in either of the parents, or are the alleles in the offspring always from at least one of the parents?

Is new genetic information ever created during sexual reproduction, or only through mutations during an organisms life time?


texts: 5,6-dihydrouracil and 5,6-dihydroxyuracil - how they arise in DNA?

texts: 5,6-dihydrouracil can be formed from cytosine after exposure of DNA to ionizing radiation under anoxic conditions [Ref]. What are other ways by which 5,6-dihydrouracil is formed in DNA? What about 5,6-dihydroxyuracil?


texts: Why don't the minus ends of microtubules shrink?

texts: Is this because $\alpha$-tubulin is always in the GTP state? Or is it because $\gamma$-TuRC stabilizes the minus end?


texts: Does breathing air containing 3% carbon dioxide gives you a headache?

texts:
As far as I know, breathing air containing relatively high levels of CO2 may get you a headache.

I also know that CO2 level in the fruit bodies of peppers can reach levels as high as 3% at certain stages in development (Blasiak, 2006). So clearly it is possible in a natural setting to achieve these high level of CO2, at least in a micro-environment like around the locules of pepper seeds developing in its fruit.

So I was wondering, if we would have to breath air containing 3% CO2, would get a headache if we breath it in?


texts: Help me understand how the thyroid secretes

texts:
Please have a look at this close up light microscopic image of a thyroid gland:

So I'm guessing the cubic epithelial cells surrounding this big red pulp are the secreting cells...? If so, is the red pulp a blood vessel that they are secreting into?

Am I misunderstanding?


texts: Why not use Cu(OH)2 as a dye for protein electrophoresis?

texts: As I know, $Cu(OH)_2$ $+$ Protein $\rightarrow$ Purple. So why not use $Cu(OH)_2$ as dye in protein electrophoresis?


texts: You and me are different at DNA level. My eye color gene is different from yours. So, my DNA is different from yours. How can a scientist identify a certain gene in a chromosome (and its function) if chromosomes are different? How can we talk about "the" human DNA when nobody share the same (except twins)? Please, this is a practical question about how scientists identify genes, not a philosophic one (a question that bother me every time I read about discoveries in genetic)


texts: How much heat for how long to Kill RHDV?

texts:
Rabbit hemorrhagic disease is caused by the Virus RHDV.  There are two verisions V1 & V2.

It is extremely devastating to both pet and wild rabbits.  With fatality rates reports of 75%+.

It is currently devastating rabbit populations in the US. There are a number of vaccines but non-are approved for use in the US.

I have been reading up about it and found this claim in a few places.

  RHDV is also reported to survive exposure to pH 3.0, heat of 50°C (122°F) for an hour Source

.

  It survives heat of 122F for one hour. source & source

My question is: How much heat for how long will kill RHDV?


texts: Simple Mendelian sex-linked chromosome fruit fly question

texts:
From my molecular biology textbook:

  When red-eyed flies (dominant) were mated with white-eyed flies (recessive), most, but not all, of the F1 progeny were red eyed. Furthermore, when the red-eyed males of the F1 generation were mated with their red-eyed sisters, they produced about one-quarter white-eyed males, but no white-eyed females. In other words, the eye color phenotype was sex-linked.

First, wouldn't recombination scramble the eye color alleles among the sex chromosomes?

Secondly, even without recombination, the F1 generation will be heterozygous and all F1 flies will have white and red alleles. Some F1 males will have a white X and some F1 females will have a white X, in which case it should be possibly to have an F2 white fly.

Can someone explain this?


texts:
Why is DNA called deoxyribonucleic acid and not something else? I get the nucleic acid part (because that's what DNA is made of) but what about the deoxyribo- part, especially the ribo- part. Maybe because DNA doesn't have oxygen, hence the "deoxy-"?

(Also, please tell me what is wrong with my question or whether there was a duplicate I didn't find so I can fix this question or delete it.)


texts: How many, and how severe, are known single gene polymorphisms for obesity?

texts:
A fairly recent meta-analysis of studies examining the association between adult obesity and polymorphisms of the FTO gene (Peng et al., 2011). The paper looked at 59 studies and concluded that, "FTO may represent a low-penetrance susceptible gene for obesity risk", although the association was weaker (or non-existent) for some ethnic groups.

Are other polymorphic genes which are currently known to be more strongly associated with obesity risk than the FTO gene?


texts: Can someone identify this Lepidoptera larva?

texts: That's from Brazilian Amazon, more specifically a small mountain (300 m high) called "Morro dos Seis Lagos" (six lakes hill), at São Gabriel da Cachoeira municipality, Amazonas state, located at 0.283 North, 66.685 West.


texts: What is the precise mechanism by which exercise reduces chance of cancer?

texts:
Sources like this: http://www.cancerresearchuk.org/about-cancer/causes-of-cancer/physical-activity-and-cancer/how-physical-activity-prevents-cancer point out that we can reduce our risk of some cancers by exercising.

But it seems to just be hypothetical, like "scientists think insulin can turn on signals that tell cells to multiply", and

"This can lead to the cells multiplying much more frequently than usual, to replace dead and damaged cells, increasing the chances of mistakes that could lead to cancer"

But human metabolism significantly increases during and after exercise, implying high rate of cellular division! Therefore, these 'hypotheses' seem questionable in their attempt at saying, "cells don't divide as much". I believe that these may be contributing factors, but I don't believe they're the main cause of most cancers in general. I am deeply skeptical that muscle inflammation requires less cell division than colon inflammation.

I have a hypothesis that exercise simply reduces cancer in the following manner: increase cellular movement, which increases the probability of the following:

1) t-cells tag foreign pathogens
2) white blood-cells capture foreign pathogens
3) damaged cells are repaired/found/killed faster

Statistically, increasing the entropy of a system would allow the individual components to cover a larger area in a shorter amount of time. Since the number of pathogens introduced into the system remains relatively constant while the interal system speeds up, it's like running a high-pressure jet stream of water and soap through pipes to clean them out. The soap (t-cells) and pressure (contractions of heart/blood vessels) together help clean the system effectively.

I'm having trouble finding evidence/support for this hypothesis, so if someone could point out the flaws in my hypothesis or point me to some sources to find out more, I'd be deeply appreciative.


texts: Insect identification request - Is this a bed bug?

texts:
I live in Spain and today I found several of these in my son's jacket. I am afraid they are bed bugs nymphs because last year we had a bedbug epidemic in some neighborhood houses.

The insect in the photo is about 1mm and has green spots in his body. Maybe they are just aphids that have been brought from the park.


texts: Quantitative Comparisons of Phylogenetic trees

texts: I am working on a broad phylogenomic analysis of proteins involved in one particular cellular process.  I have constructed a phylogenetic tree for each protein.  I am now working on comparing those trees in order to extract categories (i. e., allele a of protein a occurs most frequently with allele b of protein b, etc.).  I have attempted to construct a super tree using clann, but the tree is extremely difficult to interpret.  I would therefore like to carryout a quantitative comparison (and subsequent categorisation) of each each tree, but it is unclear to me how to even begin this analysis.  Is there a standardised method for comparison of phylogenetic trees?


texts: How do rare mosquito borne diseases get transmitted if they are so rare?

texts:
I recently read a somewhat alarmist notice by the state board of health in NH who claimed that some man had tested positive for Jamestown Canyon virus, a rare disease even in its natural environment of Colorado. Supposedly the man has not travelled out of state.

So, I am wondering how it is possible for such a virus to be transmitted. My understanding is that a mosquito only bites twice then it breeds, so basically what has to happen is the first bite has to be on an infected human (or animal) and then the second bite on the victim. So, if this guy got Jamestown Canyon virus, then he must have been in mosquito range of some other infected creature of which we have no knowledge.

Now, unless there is some type of animal that is endemically infected with Jamestown Canyon virus which is transferable to humans, it would seem unlikely to me that there would be any source from which the man could have gotten the virus.

So, I am wondering what kind of plausible scenario would have made this disease transmission possible, assuming it really occurred?


texts: Can you consider a human as alive, or is it the cells on the body that are alive?

texts:
Sorry if this question seems strange, but in the recent time I have been interested in the question of what life is and how you can define life.

My question:
How long can individual cells live on a human body from the point the human dies? When a human dies, legally he is dead, but how is the medical explaination? Can a human be partly dead, that the heart and brain has stopped, but the cells on the body are still alive?

When you talk about a human life, is it one life or could you consider each cell on the body as a living piece and the whole human body itself including the consciousness is just a container for the cells?


texts: Significance of prostaglandins in semen?

texts:
I am trying to figure out how prostaglandins in the semen relate to the female reproductive tract.
More specifically,
How does prostaglandins in semen help the female reproductive tract increase the chance for fertilization?


texts: Selection on linked loci in a diploid population

texts:
Let’s consider two linked loci $A$ and $B$ that are both bi-allelic. In consequence, we have four different possible haplotypes $A_1B_1$, $A_1B_2$, $A_2B_1$, $A_2B_2$, which frequencies are $X_1$, $X_2$, $X_3$, $X_4$ respectively. Let the linkage disequilibrium $D$ be defined as:

$$D=X_1X_4 - X_2X_3$$

The change in haplotype frequencies through time is given by:

$$\delta X_1 = \frac{X_1(w_1 - \bar w) - Drw_{14}}{\bar w}$$

$$\delta X_2 = \frac{X_2(w_2 - \bar w) - Drw_{14}}{\bar w}$$

$$\delta X_3 = \frac{X_3(w_3 - \bar w) - Drw_{14}}{\bar w}$$

$$\delta X_4 = \frac{X_4(w_4 - \bar w) - Drw_{14}}{\bar w}$$

, where

$r$ is the recombination rate between the loci $A$ and $B$
$\bar w$ is the mean fitness (sum of the fitnesses of each haplotype weighted by their relative frequencies)
$w_{14}$ is the fitness of the (diploid) individual that has the 1st and the 4th haplotypes
$w_i = X_1w_{i1} + X_2w_{i2} + X_3w_{i3} + X_4w_{i4}$

The change in allele frequency of locus $A$ is $x$ and $1-x$. The change of allele frequency of locus $B$ is $y$ and $1-y$. Those changes are given by the addition of haplotypes frequencies:

$$\delta x = \delta X_1 + \delta X_2$$

and

$$\delta y = \delta X_1 + \delta X_3$$

Question

I don’t fully understand these formulae! Could you please help me making sense of them. Especially of the presence of the expression $-Drw_{14}$.

source


texts:
This is a two-part question:

What is the point of fruit if not to be eaten? It’s my understanding that organisms will adapt to survive and thrive. I understand that being eaten can spread seeds, but this just seems like too much of a risky tactic to rely on.
Following on from part one: If being eaten is the best way to spread seed, why do some plants avoid this (such as by being poisonous or thorny)?


texts: Why does pleural effusion usually occurs in the right hemithorax in acute heart failure? Could someone explain the mechanism? Thank you.


texts: What kind of spider is this from Nova Scotia, Canada?

texts: What kind of spider is this? It was found in Nova Scotia, Canada and is about the size of a quarter.


texts: Are specialized cells considered to have life?

texts:
A common definition of life, including the one in Biology SE Life requires physical entitites to have the capability of being able to reproduce.

A process defining organisms that grow and adapt to stimuli while
maintaining a state of organization and energy production and being
capable of reproduction.

Under this definition one could think that a specialized cell like a bone cell or a skin cell doesnt have life. But also, a common definition of cell, including the one here in Biology SE says a cell is

the smallest unit of life.

So, my question is, are specialized cells which dont reproduce supposed to have life? This question came up to me thinking of other living organisms which have tissues which seems to be inert and survive hundreds or thousands of years (ie, wood, bones, etc.)


texts: After we separate the two DNA strands, what makes one of the two strands combine with the labelled mRNA strand instead of the old complementary strand?


texts:
I was reading about the sharks strong sense of smell ( Shark senses - @EnhancedLearning.com ) and wondered if any research has been done into what they don't like the smell of?

Is there any material that they don't like being near and would stay away from?


texts: How does residual chlorine in tap water work?

texts:
As I understand it, residual chlorine levels in tap water are below 1mg/l in the UK. Most chlorine based cleaning products suggest at least 1% solution to be effective (quite a long way off 0.5mg/l by my maths).

Given that chlorine has a very slight disadvantage to health (albeit a tiny one), if 0.5mg/l is not enough to kill harmful bacteria, why is it there at all? If it is enough to kill bacteria, how does it do it when cleaning products require what seems to be several thousand times greater concentrations to do the same job?


texts: Function of the 'double' leaf on a pomelo tree

texts:
What is the function of the 'double leaf' (I'm unsure what the technical name is...) on a pomelo tree leaf?
Furthermore, what evolutionary 'problem' is this structure solving?
See image with arrows that indicate the two parts to the leaf.


texts: Is the size of the genome across species roughly the same?

texts:
Chromosome number differs across species.

Is the amount of DNA comparable between organisms, just being split into smaller chunks in those species with more chromosomes, or do species have different genome sizes? If so, does the genome size correlate roughly with the complexity of the species?


texts: What does uniprot consider "unambiguous" evidence for the subcellular domain of a protein?

texts:
Uniprot has annotation for subcellular location of protein domains. This topological domain information of proteins is under the TOPO_DOM flag.

In most cases the subcellular location is assigned by rigorous sequence analysis both for the experimentally verified and predicted subcellular locations. Sometimes more reliable information is available...

  ... when the experimental technique used allows the unambiguous
  assignment of the transmembrane boundary to a particular position
  (X-ray crystallography, etc.), the ‘Sequence analysis’ qualifier is
  not added in the topological domain annotation. In this case, the
  positions of the topological domains can be propagated ‘By
  similarity’.

What evidence is available that constitutes "unambiguous assignment" so that the by similarity qualifier can be used?


texts:
I have carried out a native PAGE with 4 reaction mixtures. To each I had added an equal volume of EDTA (1 µl/1mM) to sequester any divalent ions and an equal volume of calmodulin (5 µl/0.5 mg/ml). I added 2 µl of calcium (2 mM), magnesium (2 mM) and manganese (2 mM) ions respectively to three reaction mixtures and had a control that was made up to an equal volume with Tris-HCl. All reaction mixtures were made up to 10 µl with Tris-HCl. Here I ran into a problem with the waterbaths and the reactions couldn't be incubated at 37 degrees Celsius.

After I added the loading buffer to each, I added the 4 reaction mixtures to the polyacrylamide gel and electrophoresed for 45 minutes at 150 V. After this I placed the gel in Coomassie Blue stain for 20 minutes.

After the destaining process, I reviewed the gel to find that the calmodulin in the 4 lanes had migrated the same distance. I had expected the EDTA control to have migrated the furthest on the gel, with Ca2+ and Mn2+ migrating similar distances due to their similar ionic radii; making it a good substitute for the binding to the calmodulin. I was unsure of how far the Mg2+ would travel as I thought it would have a lower affinity to the calmodulin due to its binding to the N-terminus rather than the C-terminus. However, I was wondering if this was negligible in the absence of Ca2+, although now I can't be sure due to the results of the gel.

I was wondering what errors in the experimental design or process could have resulted in this? And if the experiment was run correctly, what results would be expected?

The first image is the result I was expecting. The second is the results from my gel electrophoresis.


texts: How is the side-polarity of the myosin filament in myofibril maintained?

texts: If myosin molecules are the properly oriented relative to their position in the the myosin filaments, the sarcomere is not functional. But how is the orientation of the myosin molecules determined? Why is there a symmetry in the arrangement of myosin molecules in the myosin filament? And are there any diseases associated with the improper arrangement of myosin molecules?


texts: How much time would it take to complete the transcription of an average-sized human gene?


texts:
How do you define Sexual Selection (SS)?

(One might want to subdivide SS into intra- and inter- SS to answer)

Is SS clearly different from Natural Selection (NS)?
Is SS nested within NS or are NS and SS two different and (anti- or not) parallel processes?
Is the evolutionary processes due to sexual conflict are SS processes?

  Sexual conflict arises when the reproductive interests of males and females are not aligned, generating sex-specific selection on shared traits such as mating rate (from this article)

  (One may want to subdivise sexual conflict into intralocus and interloci conlict to answer)

  Are the evolutionary processes of sexually antagonist genes SS processes?

  Sexually antagonist genes are those genes where one allele is favored in females while another allele is favored in males (my own definition)

Can SS be accurately defined or is there a continuum of kinds or processes from complete SS processes to complete NS processes?

Stated differently, is SS defined as the color orange (it is a continum) or like a square and a rtiangle (no continuum)
(I talk here about kinds of processes, not about the relative importance of SS and NS in explaining the evolutionary dynamic of a trait or a locus)

If you define SS based on some other concepts that might be subject to various definition, please define this other concept. For example, if one says "SS occurs on a trait whenever this trait undergoes directional selection due to sexual competition", he will necessarily need to define "sexual competition" as well.

Below is a list of scenarios where you can answer by yes or no whether SS is involved in the evolution of some feature. In all of these scenarios, we'll consider cases where the males have to find a mate…

The males need good ears to find the females before other males. Is SS involved in the adaptation of ears abilities?
The males need good flying abilities (supposing we talk about flying animals) to have access to females before another male. Is SS  involved in the adaptation to good flying abilities?
The males need good flying abilities  to have access to females although there is not much between male competition because the vast majority of females won't never be fertilized. Is SS is involved in the adaptation to good flying abilities?
The males need good flying abilities to be able to fly a long time without spending to much energy otherwise they will die before finding a female. Is SS is involved in the adaptation to good flying abilities?
The males need good flying abilities to be able to fly a long time without spending to much energy otherwise they will die before finding a female. There are quite a few females but there the competition is so rough to find a female that is still unmated Is SS is involved in the adaptation to good flying abilities?
The males need good camouflage because when they fly to find a mate they may get eaten by a predator and die before reproducing. Is SS is involved in the adaptation to good flying abilities?
The males need good camouflage because when they fly to find a mate they may get eaten by a predator and die before reproducing. Here the difference is that the predators are attracted to the spot if they can sense many males. So the presence of the other males influence the probability of finding a mate of a given male. Is SS is involved in the adaptation to good flying abilities?


texts: Specificity in MAPK/ERK pathway and PC12 Cells

texts:
Background

PC12 Cell stimulation leads to distinct outcomes upon stimulation with either EGF or NGF (epidermal and nerve growth factors). The outputs are transmitted through the MAPK/ERK signaling pathway; stimulation with EGF causes transient activation of the ERK, via a negative feedback loop, leading to cell proliferation whereas stimulation with NGF leads to sustained activation of ERK, via a positive feedback loop, leading to differentiation.

Question

How does the signaling pathway know which kind of feedback loop to initiate at the ERK level from upstream stimulation by EGF or NGF?

Helpful Image to explain question

To reiterate: I want to figure out how EGF binding at the membrane level triggers negative feedback downstream, and NGF binding triggers positive feedback?

A link to the image is (http://www.nature.com/nrm/journal/v12/n2/fig_tab/nrm3048_F4.html)


texts: What are the ecological effects of moderately high and prolonged concentrations of nitrogen deposition on an ecosystem?

texts: There are many sources of nitrogen which eventually get deposited out of the atmosphere and onto the land/surface.  Typically higher levels of nitrogen compounds are emitted near urban and roadway locations, raising the levels of nitrogen deposited on the nearby landscape.  What are the ecological effects of moderately high (at least double background) and prolonged concentrations (10+ years) of nitrogen deposition on an ecosystem?  Please be specific about which type of ecosystem your comments are intended.


texts: Heart Rate being normal when under treatment for the bends

texts:
When you surface from diving too quickly; you get "bends" - these are caused by gas bubbles forming in your lungs (especially nitrogen). This causes breathing problems if not treated since the bubbles are essentially blocking oxygen transport.

For treatment, you have to be in a hyperbaric chamber for several hours.

Why is it you don't get nitrogen and carbon dioxide bubbles in your bloodstream while being treated? I would think that in the machine the nitrogen, carbon dioxide and water concentrations would rise causing you to start having signs of low oxygen like loss of brain function.

As I stated previously, nitrogen bubbles block oxygen transport and thus carbon dioxide transport. Since there is nowhere else to go, it goes into the bloodstream where oxygenated blood is supposed to be. This is detected by the chemoreceptors in your arteries; this then tells the heart to beat faster in attempts to rid the body of CO2. Once again; however, this doesn't happen because now there are more nitrogen bubbles from breathing in more nitrogen and water. This leads to a progressively higher heart rate (Ventricular Tachycardia - V-tach) which is dangerous as it can lead to MI (Myocardial Infarction) symptoms - like chest pain. Ventricular tachycardia that lasts a maximum of a few minutes can then lead to V-fib (Ventricular Fibrillation) which, if not treated with epinephrine or defibrillation on time, will lead to asystole and death.

Summary:

When someone has the bends and is being treated in a hyperbaric chamber; how do they not end up having an acute MI (due to accumulation of nitrogen gas in the bloodstream)?


texts: What is the contribution of viruses to the evolution of mankind?

texts:
I'm interested in horizontal gene transfer in bacteria, viruses, and organisms such as Bdelloid Rotifers. I've just read in Carl Zimmer's 'A Planet of Viruses' the following passage:

  As a host cell manufactures new viruses, it sometimes accidentally adds some of its own genes to them. The new viruses carry the genes of their hosts as they swim through the ocean, and they insert them, along with their own, into the genomes of their new hosts. By one estimate, viruses transfer a trillion trillion genes between host genomes in the ocean every year.

It's interesting to consider the scale of DNA-swapping that has occurred given the frequency by which it happens and the evolutionary timescale.

Are there any examples of genes in the human genome that we know were deposited by viruses that would have given an evolving human a physical/mental advantage? Where did they come from? What benefit did they provide?

I'm interested in genetic additions from non-human-ancestor species, rather than the transfer of genes that occurred as mutations from other humans.


texts:
Laughing gas (N2O), well, makes people laugh.

How does just a gas make us do that, there has to be some hormones at work...

So, I wanted to know how this works?  What is the mechanism?


texts: What is the name of this beautiful white trees?

texts: I found this beautiful white trees in an unknown video.


texts: How do fully dioecious plants determine sex?

texts: I know that a minority of plants are fully dioecious, with adult plants producing either only male or only female flowers. When is this sexual differentiation determined? Is the seed of such a plant already male or female? Is it a simple genetic difference?


texts: Why do organisms excrete nitrogenous wastes?

texts:
Organisms excrete nitrogenous wastes in the form of urea, uric acid or ammonia. But isn’t that a bit of a waste? There is a shortage of biologically available nitrogen in the ecosystem, and plants convert nitrogen in ammonia and nitrates into amino acids. Why do organisms then deaminate these amino acids and then excrete them?

It seems to me that it would make much more sense to store the nitrogen for further use. I understand that ammonia is toxic, but surely it could be stored in some specialized structure.


texts: If DNA methylation inactivates genes, does DNA demethylation activate them?

texts:
DNA demethylation can be passive or active. The passive process takes place in the absence of methylation of newly synthesized DNA strands by DNMT1 during several replication rounds – for example, upon 5-azacytidine treatment [23]. These pharmaceutical demethylating agents act via inhibition of DNMT1 and favoring its degradation by proteosomes [24]. This approach is currently used in cancer to demethylate tumor suppressor genes [25].

If we’re demethylating a tumour suppressor gene for cancer curing doesn’t this mean that we’re activating it (to stop the tumours)? I can’t seem to understand the function of DNA demethylation. I came across it when reading about genomic imprinting and haven’t been able to wrap my head around it. Please help.


texts:
How does the body heal a skin wound without bleeding?
I had a wound in which thick layer of skin was gone and which was too painful to touch. I could see the wound secreting clear liquid rather than forming a scab like in a blood wound. What is this yellowish thick liquid being secreted and does it form new skin?


texts: Is urban beekeeeping harmful or are there good practices to follow?

texts:
I have found several newspaper articles on how good could be urban beekeeping both for the bees and for agriculture.
Today I read this one: Urban beekeeping is harming wild bees saying that urban beekeeping is harming wild pollinators. I did not find a direct link to the paper, but it is probably referring to Conserving honey bees does not help wildlife. Unfortunately I only have access to the summary of the paper.

Are there good practices that could be followed to practice urban beekeeping without harming wild life (for example avoid placing hives close to a forest...) or is it harmful in any case?


texts: Is the discovery of dominant and recessive genes the only reason Mendel matters?

texts:
We've known that offspring inherit various traits from their parents since (at least) Aristotle. In The Elements of Plant Hybridization, Gregor Mendel treats that fact as common knowledge. Clearly, we don't credit Mendel with discovering it. Accordingly, it seems to me that Mendel's only notable discovery was the discovery of the existence of dominant and recessive genes. However, that discovery doesn't seem to justify the title 'founder of modern genetics', which Wikipedia, and other sources, use to refer to him.

Why is Mendel the big deal that he is?


texts: Why do animal cells lack a contractile vacuole?

texts: I was asked why animal cells do not have contractile vacuoles. Other than the lack of need, I don't know what else to say.


texts: How to interpret this PubChem record of L-Alanine

texts:
Using the PUG service from NCBI, I am retrieving 3d structure data for a molecule.

Raw data here.

I am trying to understand this record, specifically for the purpose of rendering in a 3D coordinate system using threejs.

Could anyone please assist in understanding this information.
Due to the large size of the json response and as I am using javascript, I have constructed some Typescript types that describe the shape of the data to assist the discussion. I have specific questions, which are stated below.

//// Root Object
interface JSON_Response {
    PC_Compounds: PC_Compound[];
}

//// Compound Object
// must stand for PubChem Compound
interface PC_Compound {
    id: ID;
    atoms: {
        aid: number[];
        element: number[];
    };
    bonds: {
        aid1: number[];
        aid2: number[];
        order: number[];
    };
    stereo: Stereo[];
    coords: Coords[];
    props: Data[];
    count: Count;
}

//////// Sub-types described below

Atoms

The atoms object has two arrays; 'aid' and 'element'.In the above JSON response, these arrays are both of length 13. The data for L-Alanine shows it has 13 atoms. I am correct in saying that the numbers in the 'element' array are corresponding to Atomic Numbers? And these atomic numbers are assigned to ids from the corresponding indexes in the 'id' array?

Bonds

What are aid1, aid2, and order? These arrays are 12 entries each so each must represent 1 bond between two atoms. But what do the number values correspond to? How should they be interpretted?

Coords

In the coordinates object,

interface Coords {
    type: number[];
    aid: number[];
    conformers: [
        {
        x: number[];
        y: number[];
        z: number[];
        data: Data[];
        }
    ];
    data: Data[];
}

The x, y, & z arrays are of length 13. Am I correct in saying that these represent the x, y, and z coordinates of atoms in the corresponding index of the above elements array?

Data

Data Object seems to be part of a esoteric system for attaching arbitrary data to the object. If anyone has any pointer on this it would be greatly appreciated.

interface Data {
    urn: {
        label: string;
        name: string;
        datatype: number;
        release: string;
        version?: string;
        software?: string;
        source?: string;
        parameters?: string;
    };
    value: {
        sval?: string;
        fval?: number;
        slist?: string[];
        fvec?: number[];
        ivec?: number[];
    };
}

stereo

seems to describe planes of rotation

//// Compound sub-types
interface Stereo {
    tetrahedral: {
        center: number;
        above: number;
        top: number;
        bottom: number;
        below: number;
        parity: number;
        type: number;
    };
}

interface ID {
    id: {
        cid: number;
    };
}

miscellaneous chemical information

interface Count {
    heavy_atom: number;
    atom_chiral: number;
    atom_chiral_def: number;
    atom_chiral_undef: number;
    bond_chiral: number;
    bond_chiral_def: number;
    bond_chiral_undef: number;
    isotope_atom: number;
    covalent_unit: number;
    tautomers: number;
}

In addition, if anyone has any techniques or advice on how to extract meaning from the response data from PubChem, if they could please post below it could come in handy for me or some other person working on this.


texts: Does the brain consume more energy when a person is stressed or anxious

texts:
When a person is anxious or stressed or suffering from chronic depression, it is observed that the person is usually tired.
Is there there a connection between fatigue and racing thoughts/obsessions.
Also I want to know what damage can anxiety do to brain and body over time.


texts: How to determine the relationship of competition or cooperation?

texts:
I am currently studying the interaction of Twitter memes (two or many), such as competition and cooperation. Is there any model or method in biology that can identify the types of the relationship, such as competition or cooperation?

I have heard the Lotka–Volterra equations, but when I begin to dig deep, I found that it is still not suitable.


texts:
So I know that Hemoglobin is made of 2 alpha and 2 beta subunits. The alpha consists of 2 genes on chromosome 16, and the beta of 1 gene on chromosome 11.
So why does Hemoglobin only have 4 alleles? Why is it not 6? In my way of thinking each alpha subunit consists of 2 genes, so 4 total. And each beta subunit consists of 1 gene, so 2 total. Together that makes 6. Confused! Thanks in advance


texts: What is the actual size of a nucleotide?

texts: I found in this website that the dimension of a nucleotide is 0.34 nm. Is there any experimental paper confirming this statement?


texts: Cross-integration of puma subspecies populations

texts:
A major concern of conservationists  in south Florida is the population of native Pumas, the Florida Panther.

Until recently, it was thought that the Pumas were a genetically distinct subspecies, but some genetic studies have shown that they may not be, and so their subspecies status is disputed.

If the population of Pumas in Florida is genetically distinct from other populations in North America, is there any precedent for using a distinct subspecies to bolster populations of an endangered subspecies?

If the population of Pumas in Florida is not genetically distinct from other populations in North America, would there be any behavioral issues (hunting, etc.) in animals brought from other biomes to south Florida, either as adults or offspring of transplanted adults?