texts: How can action potentials be generated through thoughts?

texts:
I think I understand how a signal is transferred from neuron to neuron (from  How do the brain and nerves create electrical pulses?).

My question, however, is not about the standard textbook material on neuronal transduction. Instead, I am wondering how an electrical impulse starts in the first place in the brain. In other words, how can an action potential be generated de novo from a conscious thought? I am wondering primarily about a signal like a movement of an appendage or something similar.

So in short, my question is:

How is the 'first' action potential generated in the cortex when one consciously/voluntarily decides of moving a limb (or comparable action)?


texts: What insect is this? Is this harmful in any way. This picture was taken in Bangladesh.


texts: How to use DRAQ5 and MitoTracker CMXros dyes to stain turtle erythrocytes?

texts: I am working on turtle species and want to use DRAQ5 and MitoTracker CMXRos to stain turtle nucleated erythrocytes. Can anyone suggest me a protocol to carry this stain out? Would the two stains complement each other?


texts:
I'm taking introduction to genetics and I'm trying to understand the following question: Lets say there is a male cat with blue ears, a single gene mutation called BLU.
We try to obtain pure bred blue-eared cats, mating the above cat we recieve:
*Males with a different colored ears
*Females with blue mosaic ears.

Now I'm trying to understand which is more likely. BLU being silenced by Xist or having non autonomous transposon on the BLU gene while only females have autonomous genes.

Thank you in advance!


texts:
We're learning about osmoregulation in AP Biology and the terms Tonicity and Osmolarity are really confusing me. I watched this video on Khanacademy to try to understand what the difference is, and from my understanding Tonicity refers to strictly two solutions (ex: you can't take a cup with water and salt in it and claim it's hyper, hypo, or iso- tonic because there's nothing to compare it to), whereas Osmolarity refers to the composition of the single solution itself.

But then my Campbell's biology textbook completely confuses me. It has the following picture and text:

  ...osmosis, a special case of diffusion, is the movement of water across a selectively permeable membrane. It occurs whenever two solutions separated by the membrane differ in osmotic pressure, or osmolarity (total solute concentration expressed as molarity, that is, moles of solute per liter of solution).....If two solutions separated by a selectively permeable membrane have the same osmolarity, they are said to be isoosmatic. Water molecules continually cross the membrane, but under these conditions they do so at equal rates in both directions....

And then as if to clarify, they claim that tonicity refers to "solutions of known solute concentrations"...but how does this differ from osmolarity?


texts: Serological assays measuring antibody response

texts: Given that an appropriate immune response to a bacteria may be thwarted in an individual, including not producing all of the antibodies which are known to occur in people who have been infected, or producing insufficient amounts of antibodies specific to a bacteria --- Are all serological tests using antibodies as a basis for detection of a systemic infection inherently flawed? In this instance, I'm assuming appropriate application of a test and competent laboratory methodology. But, equally important, what criteria can routinely be used to consider the efficacy of a particular antibody test, across the board.


texts: Why do some animals such as some Goats, Ibex, Orangutan etc, have long well-shaped beard like men?


texts: Does level of bats activity differs from day to day?

texts:
Say we measure bats activity as number of passes through given area. Can it differ significantly depending from day to day or it stays on average roughly the same? I am wondering whether the following might have an effect:

Weather conditions (wind or rain). I do not mean here heavy conditions (strong wind or rain), those understandably will affect bats eagerness to fly
Moon cycle
Mating
For insect-easting bats: the prey not being active every night

I would welcome some good reading on the subject.

My question stems from the following problem. Say I have one detector and want to measure activity in three locations. If I rotate it between them, will I get unbiased result?


texts:
I'm a newbie in biology and medicine. I understand that Henrietta Lacks provided the cells that formed the HeLa cell line with which much research has been done. Henrietta Lacks died of cancer. If we assume that she did not have cancer, every cell in her body could divide for an infinite period of time, and she never sustained any trauma ever, would Henrietta Lacks have been immortal?

Thanks,
mj


texts:
I found the below quotation in (Peyressatre, 2015)

  CDK3   1 simple coding mutation/missense mutations (S106N)   glioma
  [135]

The author has cited a database but not a paper. I want to find the paper that talks about the above mentioned type of mutation in CDK3


texts: Do body lotions enter into bloodstream of people? And how do they do it?

texts:
I found this

very disturbing: bombastic tabloid-style writing in capital and the content is doubtful. If it was correct or close "does it really take something like 26 seconds for a body lotion to enter into bloodstream?", you select a lotion with very high level of fat -- now your heart will pump  blood with a very high-level of fat, possible source for heart failure. If you have a dry skin and you put 40%-fat lotion to your skin, it makes it more flexible. I am very-very skeptical whether any fat gets into your bloodstream. I am new to things such as blood lipids (blood fats) and mechanisms how the body lotions really penetrate into the skin. How? And which factors determine the time and does any get actually into bloodstream and after which kind of processes by the body? Is this just a hoax?


texts: Negative value on linear gene expression in microarrays

texts:
I am starting to use microarrays and maybe this is a dumb question:

Using Illumina microarrays, linear gene expression can be negative? Or maybe some artefacts have been introduced?

And, in this case, how to correct them? With scaling (adding the absolute value of the minimum negative value) or flooring (converting negative values to zeros)?

Thanks


texts:
From Hrdy and Burkart (2020):

At birth, both chimpanzee and human newborns seek out eyes, are capable of mutual gazing, and caught just right, may imitate someone else’s outstretched tongue or other facial expressions. Both species exhibit reflexive ‘fairy smiles’, soon to be replaced by more open-eyed ‘social smiles’ in response to someone else.


texts:
I am not sure if this is the right place to ask this question, so please let me know in case it is not. My question is just out of curiosity.

What is the reason for curved human foot profile?

First a bit of clarification in layman terms. When looking at a human foot sideways on the inside, you see an arch along the foot length, however there is no such arch when looking from the other side (imagine a footprint and how it has a curve on the inside and is flat on other side).

I looked on Google to find the answer. Pardon my lack in knowledge of biology vernacular/terminologies. Reading through wiki article on Arches of the foot, they do describe the two arches - longitudinal arch and transverse arch. In the laymen explanation I gave earlier, if I understand the anatomy right, the transverse arch is what leads to the footprint shaped that way. As I understand, they explain how the arches are responsible for the stiffness of the foot, akin to how arches of a building help support more weight will lower deflection compared to other configurations. Also the space under the dome enable the elastic soft tissue to spread and provide enough contact surface for the body weight to be effectively distributed. On transverse arch, they say it creates a half dome and the two foot together form the complete dome. However, structurally, they will not fulfill the same role as a full dome, far from it in my humble opinion. Can someone explain the structural benefit of the half dome of the transverse arch?


texts:
Neurons form complicated networks in brains, but their connections can't be random (at least not entirely). Brains function similarly among all members of individual species, and that functionality is largely dependent on neuron organization. Furthermore, various brain regions have predictable functions, and there are even parts of the brain where specific cells carry out specialized functions (place cells are an interesting example).

Great! We know neurons can organize into very complex networks, but how? They need to find each other, somehow.

The best I can guess is that either:

Neurons find other target neurons with specific chemical signals.
Neurons don't "find" each other, exactly, but grow in predetermined shapes from from set locations. In this case, the connections would simply be due to neurons bumping into each other as they grow in their predetermined paths.
Or both.

In the first case, there would be a mechanism for searching each other out. In the second, there would be a mechanism for staying in one spot (and growing from there). What are the names of said mechanisms? How do I find out more about them?


texts: Does drinking alcohol having UTI may help to kill the bacteria?

texts:
It's well known that ethyl alcohol kills bacteria. And amount of alcohol in urine may be detected by EtG tests (as long as 3-4 days after intake).

Does drinking alcohol in reasonable amount by healthy individual (non alcoholic) having UTI helps to kill bacteria in the urinary tract (in order to get rid of them quicker)?


texts: Do lunar rhythms have really impact on plant growth?

texts:
It is commonly known that lunar rhythms have influence on plant growth, and there are even lunar calendars to know when planting, pruning, transplanting, harvesting, etc.

I know that the lunar cycles affect the tidal patterns, and this consequently can affect the life of sea organisms like reef corals, fishes, etc., but I am very skeptical that this can affect the growth dynamics or plant physiology.
 I would like to know how it works from a scientific perspective, E.g. the temperature and precipitation are the main limiting factors on plant growth, but I'm curious if the moon light or its magnetic field can also be a limiting factor on plant growth.

Then my question is simple, the lunar rhythms really influence the growth of plants, if so, how?


texts: In what circumstances does a mammalian egg copy its DNA?

texts:
In the 2nd episode of the new Cosmos series, the host Neil deGrasse Tyson shows how the white-furred bear could have evolved (reasonable scientific speculation, of course).

If you haven't seen that episode, here's the link. Great show, by the way.

So, it shows the bears eggs, and then goes on to show how there can happen an error in the DNA copying, that leads to the brown pigment production malfunction. Here's an excerpt from the subtitles text:

- great bears roamed the frozen wastes of Ireland.
- This might look like an ordinary bear,
- but something extraordinary is happening inside her.
- Something that will give rise to a new species.
- In order to see it, we'll need to descend down to a much smaller scale, to     the cellular level, so that we can explore the bear's reproductive system.
..
- Those are some of her eggs.
- To see what's going on in one of them,
- we'll have to get even smaller.
- We'll have to shrink down to the molecular level.
..
- When a living cell divides in two,
- each one takes away with it a complete copy of the DNA.
- A specialized protein proofreads to make sure
- that only the right letters are accepted
- so that the DNA is accurately copied.
- But nobody's perfect.
- Occasionally, a proofreading error slips through,
- making a small, random change in the genetic instructions.
- A mutation has occurred in the bear's egg cell.
- A random event as tiny as this one can have consequences on a far grander scale.
- That mutation altered the gene that controls fur color.
- It will affect the production of dark pigment in the fur
- of the bear's offspring.

From my (not professional but kind of passionate amateur) knowledge of biology, I I was under impression that all of the mammalian eggs are present at birth. But the story depicted in the show involves the (erroneous) DNA copying. I see dissonance there, and I'd like to solve it.


texts:
Why is it that cytokine responsiveness is less in progenitor cells than their ancestors(stem cells)?

What will be the benefit of such reduction in responsiveness?


texts: Diffusion coefficients of glucose in mammal tissues?

texts:
Where can I find estimates/experimental measurements of the diffusion coefficient of glucose in mammal tissues? Specefically I mean the inter-cellular space. I'm not looking for a specific tissue, so some examples of values for some tissues, or a generic estimate, is enough for me.

And the same for lactate, although I presume it will be very similar.


texts:
There was a trail of what are commonly known as sugar ants (small, brown, hyperactive) in my kitchen. Three of them walked onto an ice tray placed in their path.

They only walked a short distance on the ice before being immobilized by cold. I put the tray in the freezer beside a very shallow dish of water. When the water in the dish had frozen (about a half hour later) I removed the tray/ants and let them passively drop onto a warm dry surface. After 2-3 minutes they revived, walked in circles a few times, then headed off to forage (they were released outdoors).

There is anecdotal evidence of ants' tolerance of cold but I was a little surprised by this. Do we know the extent of their tolerance of cold?

I guess it would vary with size and conditions. But an obvious question is whether, having survived freezing at (let's say) 22F, they could survive lower temperatures and/or longer periods of cold if properly handled? There may be cell structures that are sensitive to freezing because they break or change shape but it's already amazing to me that ordinary freezing does not distort water-bound structures in a lethal way.

Thanks for any insight.


texts: Techniques for detecting phosphorylation sites in proteins?

texts:
I would like to know how phosphorylated sites in proteins are detected in practice. I read some papers where the authors were talking about mass spectrometry techniques.

But my question is that why can't X-ray crystallography or NMR techniques capture phosphorylated sites?

(Note : My background is electronics engineering, so I am not an expert in this area.)


texts: Why is the species-diversity of deadly parasites greatest in the tropics?

texts:
There are so many parasites living in tropical regions of Africa, South America, or Asia, but very few in Europe or North America.

Is this due to climate, or are there other reasons?

Many of the tropical diseases and parasites are transmitted by insects, such as flies and mosquitoes. Well there are flies and mosquitoes in Europe as well.

There might be malaria-transmitting mosquitoes in the very south of Europe, and there is encephalitis transmitted by ticks. But that's it. Why don't the hundreds of different parasitic species from Africa spread to Europe ?


texts: difference between trisomy and partial trisomy

texts: Trisomy is having 3 chromosomes but then what is partial trisomy ?. I was reading about Patau syndrome and it is called trisomy 13 ( because instead of usual 2 chromosomes,it has 3 chromosomes). it was also wriiten that 20% cases are PARTIAL TRISOMIC...what is the meaning of partial trisomic?


texts: Ways to cause membrane damage to microalgae and yeast?

texts:
I am researching a way to monitor the membrane damage of cells. To do that I fist have to have reference points, namely, cells with damaged membranes.

I am working with Dunalliela, Hematococcus (both microalgae), and common yeast. I have been using mostly ethanol to damage the membranes so far.

What other ways are there to cause the most possible damage to microalgae (or yeast) membranes?. The idea is not total cell obliteration, but rather membrane damage (death is expected).


texts: Should the infraspecific epithet agree in gender with the genus name?

texts:
Let's take the following plant name

  Gymnocalycium mihanovichii

So we were to designate the yellow form of the plant, would it be

  Gymnocalycium mihanovichii f. aurea

because forma is feminine or

  Gymnocalycium mihanovichii f. aureum

because Gymnocalycium is neuter?

Hope the question is on-topic


texts: Is there a command line molecular cloning tool?

texts:
There are many softwares such as SnapGene, Geneious, Vector NTI, ApE, Gentle and others for assistance with cloning. Their key functions are:

Making maps of plasmids
Annotating plasmids with common features
Finding restriction sites
Mapping Sanger sequencing reads
Showing sequence, reverse complement of the sequence, translations in different frames
Designing primers for specific applications (such as Gibson cloning)

Is there a tool that does functions such as these, but runs from a command line?

Note: My intent is not so much to get recommendations for what to use, but to get an idea of what software is currently available. Obviously there exist many CLI tools which can be made to serve also these purposes, up to and including general purpose text editors like vi.

I'm interested in what effort has already been made to produce CLI software specifically intended for cloning (by which I mean the functions described above).


texts:
I'm doing an experiment how fast fruits ripen and decay

I'm wondering how to measure the ripeness of a fruit(banana, mango, tomato, kiwi etc.) so that I will get a quantitative results.

I have looked at using penetrometer to see how squishy it is. Is there any other ways to do it?

If not, I'm thinking of getting qualitative results. Is there any tips of making good qualitative results?

thanks

Sorry, I am not sure if this falls into Biology category


texts: Is 100% accuracy in DNA sequencing possible?

texts: I would like to obtain a complete genome of a canine (with mitochondrial DNA too) at 100% accuracy. Is it even possible with the current technology? The source I have is potential degraded, i.e. dried saliva, dried blood, whisker root, fur roots, etc...


texts:
Cortisol is released under stressful condition. It is known to have anti-inflammatory role. In fact it is used as potent anti-inflammatory drug also.

Though stressful conditions are unwanted and unfavorable, the body's response to such conditions by releasing cortisol, seems to be beneficial only.

If so, why cortisol is considered as undesirable and dangerous?


texts:
Does the brain always think of an appropriate response when reacting to a stimulus?

For example, when seeing things, does the brain have to think of an appropriate response to the eyes?


texts:
Q: Do species which have a closer common ancestor to humans tend to be more intelligent?

Our closest living relative, the chimpanzee, seems to be regarded as intelligent:

  Chimpanzees make tools and use them to acquire foods and for social displays; they have sophisticated hunting strategies requiring cooperation, influence and rank; they are status conscious, manipulative and capable of deception; they can learn to use symbols and understand aspects of human language including some relational syntax, concepts of number and numerical sequence; and they are capable of spontaneous planning for a future state or event.

Does this hold in general?  And, if so, how strong is the correlation?


texts: Are Sharks able to detect electromagnetic waves using their Electroreception ability?

texts:
I will include some publications and links that may help. I could not concluded an answer with my limited knowledge on the subject.

Shark Passive electroreception sensitive to low frequency (below 50 Hz).

Peer-reviewed Publications (Elasmobranch Research Laboratory).


texts:
I am learning about aneuploidy and non-disjunction and just wanted some clarification with regards to terminology. In particular, do the terms monosimony and trisimony refer only to INDIVIDUALS (i.e. a non-disjuction event during meisosi would produce some gametes with an extra chromosome and some lacking a chromosome, however we do not refer to the gametes as having/being monosimotic (?)/monosimony; we only talk about the zygotes and individuals formed from fertilisation involving these faulty gametes as having monosimony/trisimony etc)

Or do we refer to gametes as having monosimony or trisomny also?


texts: Do You Need Vitamin B12 To Utilize Folate

texts:
Just wondering if Vitamin B12 is necessary for the body to utitlize folate. My husband is on Methotrexate for rheumatoid arthritis, a medicine which is known to destroy folate. The doctors therefore prescribe high dose folic acid. He also, however, has a geographic tongue which is supposedly due to B12 defiency. If he is deficient in B12, and yet if B12 is necessary for folate absorption, the extra folic acid is presumably doing no good. Whether the two vitamins are essential co-factors is interesting to know because I've just read that folic acid deficiency gives people a 69% higher risk of heart disease. And he's just had a massive heart attack.

I can't seem to find the answer on standard search engines, would be grateful to know whether B12 is needed to utilize folate. Many thanks.


texts:
Thermophiles, heat-loving organisms, have been a popular topic of research for decades due in large part to the utility of their enzymes in various chemical reactions (Taq Pol single-enzymedly made PCR practical). One of the signatures of thermophiles is that their proteins resist heat denaturation up to much higher temperatures than their mesophilic (middle-loving) homologs.

Is there a corresponding group of extremophiles whose proteins resist cold denaturation down to much lower temperature than their mesophilic homologs? If so, could someone please point me towards a few good literature reviews on the topic? Or at least give me the proper name for this group of cold-loving extremophiles?


texts: Would my hands sweat this much if I wasn't wearing gloves?

texts: I've wondered about this for a long time, and hopefully someone here has a reasonable answer. I'm a cell and molecular biologist, and much of my time at the bench is spent wearing (usually nitrile) gloves. I've noticed that if I wear them for longer than 10 or 15 minutes they start accumulating sweat. However, my hands aren't clammy or damp when I'm not wearing gloves, so my question is whether my hands are always sweating at approximately the same rate, and the impermeable barrier of the gloves just traps the moisture, or does the enclosed environment inside the gloves promote sweating? My hands don't seem particularly hot when I have the gloves on, and the gloves themselves are pretty thin, although they do have some insulating properties, as I can handle items taken from a -80°C more easily gloved than bare-handed. What causes this diaphoresis?


texts:
The tardigrade is often mentioned as one of the most "alien" lifeforms on Earth. This video speaks for itself:

 (from this article)

I have long wanted to see a tardigrade with my own eyes. I have a small microscope. How do I obtain a tardigrade? I know they inhabit mosses and lichen, but is there a concrete procedure an amateur can follow that will reliably net at least one specimen?


texts:
This is the first time I do a centrifuge experiment with my own centrifuge machine, it's just simple made by a rotor that can rotate the tube at high speed. As I know a centrifuge machine can be using for separate biology samples like bacteria, cells, molecules ... But I need some advice to understanding more how to working with it.

As the suggestion from Alan Boyd, I'm planning to separate Lactobacillus from diluted yogurt. How do I know where the bacteria will be located in the tube after centrifugation (is it usually in bottom ?) and how do I  calculate the RPM that is suitable ? And any other interesting diy experiment to do with it ?


texts:
This question has probably been asked a few times but I get the concept I just dont know how to apply it for this paticular experiment

I aim to use cherry tomatoes and determine its glutamate content after drying for varying amounts of time.
This would involve putting the tomatoes into the centrifuge to extract its juice.
Due to this, I am 'preparing' the tomatoes in vivo (I think need clarification) but I am observing the Glutamate content outside of the organism (ex vivo)

I dont know how I should be classifying this experiment (between in vivo and ex vivo)

Help will be greatly appreciated !!!
Thank you!!


texts: Is evolution of gametangia in land plants and charophyceae convergent?

texts: Is the presence of gametangia in both land plants and charophyceae a result of convergent evolution or are they of the same origin (and have been lost in other types of algea)?


texts: Why proteinase K doesn't degrade itself?

texts:
Can anyone tell me why proteinase K doesn't degrade itself?

If possible please provide me the source.


texts: Can Oxaloacetate cross the outer mitochondrial membrane?

texts:
I am aware of the Malate–Aspartate Shuttle, but something is not clear to me and different sources seem to contradict each other. Some show oxaloacetate (OAA) being reduced to malate in the mitochondrial inter-membrane space (IMS), whereas others show the reduction happening in the cytosol.

Where does the OAA → malate reduction happen? i.e., can OAA cross the outer mitochondrial membrane (from the cytosol into the IMS) so that it can be reduced in the IMS, or must it be reduced in the cytosol before crossing either of the two mitochondrial membranes?


texts: I know that one is a female chicken and the other is male chicken. Are the chickens laying eggs considered the same species as those that we use for poultry meat? Or, are they different sub-species, analogous to how there are multiple breeds of dogs?


texts: Lactobacillales vs LAB (Lactic acid bacteria)

texts:
As far as I understand bacteria of order Lactobacillales are all LAB (Lactic acid bacteria). So often "Lactobacillales" and "LAB" are used interchangeably.

But I also thought that this is not the whole truth, because there are LAB which are not of order Lactobacillales.

Can anyone elaborate on this topic and is there a paper/review explaining the consensus on this topic?


texts: A Brain Implant improves memory--but how?

texts:
https://www.nytimes.com/2018/02/06/health/brain-implant-memory.html

A new therapy could improve memory by "sending electrical pulses to aid the brain when it is struggling to store new information." I'm trying to figure out how this works physically, in terms of how it actually helps the brain. I would imagine that it has something to do with the neurons getting past the threshold for firing a signal with more ease, but is this because the threshold is suddenly lower because of the presence of the current, or what?

Could anyone provide me with an explanation of the science behind this in lay terms?

Many many thanks


texts: How long do viruses, such as Zika, stay in the body?

texts:
Can a virus stay in your body (after recovery) in a concentration that is sufficient to infect someone?

Is it known how long the Zika virus persists in the body?


texts:
Multiple myeloma, commonly referred to as myeloma, is a cancer of the plasma cells found in the bone marrow.(source)

Is there any significance in calling myeloma as "MULTIPLE" myeloma?


texts: Is it wrong to consider an allosteric inhibitor a non-competitive inhibitor?

texts: Supose Caspase-1 is allosterically inhibited. Since the inhibitor is not binding in the active site but instead in the allosteric binding site, can I conclude it is a non-competitive inhibitor?


texts: Doubt related to nerve impulse transmission

texts:
Naturally, the extracellular fluid has more sodium ions and the axoplasm has more potassium ions. Since there are more potassium leakage channels than sodium leakage channels on axoplasm, it is more permeable to potassium ions moving out into the extracellular fluid.

Is it correct to assume, due to this huge outflux of potassium ions into the extracellular fluid, there are more potassium ions than sodium ions in the extracellular fluid now?


texts: At what minimum distance the direction at which eyes point becomes parallel?

texts:
This is very similar, but different than this question about focus, let me explain why it's not a duplicate at all.. That other question is about the distance of EACH individual eye FOCUS, this one is about VERGENCE, focus plays no role in this question, here what matters is the angle formed between the direction each eyes points. When objects are close to our noses, eyes get cross-eyed. As objects get further away, the eyes get more parallel, so called wall-eyed. There must a distance just become totally parallel, I deduce this by analogy to what happens to the focus, for which the distance is 6 m as this answer says. What is the corresponding distance for vergence?
I couldn't find the answer in the relevant wikipedia article on vergence.


texts: What is the longest-lasting protein in a human body?

texts:
Protein life times are, on average, not particularly long, on a human life timescale.
I was wondering, how old is the oldest protein in a human body? Just to clarify, I mean in terms of seconds/minutes/days passed from the moment that given protein was translated. I am not sure is the same thing as asking which human protein has the longest half-life, as I think there might be "tricks" the cell uses to elongate a given protein's half-life under specific conditions.

I am pretty sure there are several ways in which a cell can preserve its proteins from degradation/denaturation if it wanted to but to what extent? I accept that a given protein post-translationally modified still is the same protein, even if cut, added to a complex, etc. etc.

And also, as correlated questions: does the answer depend on the age of the given human (starting from birth and accepting as valid proteins translated during pregnancy or even donated by the mother)? What is the oldest protein in a baby's body and what is in a elderly's body? How does the oldest protein lifetime does in comparison with the oldest nucleic acid/cell/molecule/whatever in our body?


texts: Pancretic Acinar Cell - ATP, calcium concentration data

texts:
I need to find a decent source of data for concentration of ATP and calcium in the pancreatic acinar cell.

So far all I can find is ATP or calcium 'levels' based on fluorescence , which are not accompanied by a value of concentration in moles/molar.

Is it possible to find this information in a specific book or website, to avoid trawling though vast amounts of literature?


texts: Difference between autonomic and paratonic movements in plants

texts: I can't understand the difference be because both involvery the main cause that is an external stimuli, so how do they differ(


texts: How to estimate mRNA counts from Relative Promoter Units (RPU) or RNAP per second (PoPS) in E. coli?

texts:
I need a rough estimate on how to translate RPU or Polymerases Per Second (PoPS) to mRNA count (or even better protein count) in E. coli.

I understand that any number we come up with will be a very rough estimate of it, but for now, I need a placeholder value to do some modeling on genetic circuits in E. coli until a more verifiable number comes about.


texts:
I have a BAM file and a BED file for my own chromosome. I would like to get coverage per base and ideally construct a histogram of coverage across each gene.

The motivation is to visualise the coverage across each gene. If my experiment is good, I should expect uniform coverage. It's also important to compare the coverage near the boundary of the genes.

A R (bioconductor) solution is ideal, because I can directly visualise.

How to do it?


texts: What's the mechanism for being mentally tired?

texts:
I notice that after long tests, or long periods of critical thinking, my body and mind feel noticeably tired. Why does this happen? Are the neurons in my head not firing as quickly, or is there just a perceived lack of mental concentration?

What exactly is the mechanism that makes my brain feel worn out, or at least gives me the perception of my brain being worn out?


texts: Is there a name for the evolutionary loss of vestigial structures?

texts:
Consider a biological structure which no longer benefits an organism, such as the eyes of an organism whose population now lives in total darkness.  I can think of three reasons why such a structure might disappear:

0) Random changes to the structure over time wouldn't be corrected by selection favoring the functional version of the structure, leading to a wider variation where most versions of the structure no longer effectively function.

1) The resources the structure demands could be better spent on structures which are actually being used; e.g. human eyes require a lot of blood that could be used elsewhere.

2) Perhaps the existence of a very complex structure leads to biological problems which would no longer be an issue if the structure were not present; e.g. human breasts plus breast hormones frequently leads to cancer.

Are these three examples reasonable means by which a feature would disappear?  Are there any other possible reasons?

Is there a general name for the phenomenon of evolutionary removal of vestigial features due to those features no longer being useful to a population?


texts: Is one single antibody binding its antigen enough to elicit an immune response?

texts: IVIG (intravenous immunoglobulin) is derived from plasma of more than 1000 donors. I wonder if in this preparation is one antibody present that recognize its antigen after infusion - if this is enough to elicit an immune response? Thanks


texts: How does frame-shift mutation not absolutely ruin the organism?

texts:
I'm a bit curious as to how frame-shift mutation works. If you shift one amino acid towards another. How does this not affect the entire chromosome? Wouldn't this mean that the organism would be absolutely "scrambled" as it would essentially be "missing" a whole chromosome...Or having a chromosome that did all kinds of wrong things at least?

Thanks.


texts: So if i were to use a sous vidè water bath and a frog and slowley raised the temperature say 1 to 2 degrees a day would they survive harsh boiling water through thermoregulation


texts:
I have a quick question: Are triglycerides essentially what we call "fats"?
I've tried reading up on it but there seems to be some conflicting information.
Thank you.


texts:
Statement: Protein X consists of 20 amino acids.

Question 1: Is it necessary to write "Functional" Protein X or is it already implied, that it is functional?

Question 2: Referring to question #1 - Does "Active," "Functional", "Native", "Mature," and "Stable" all serve as the same as synonym?

Question 3: How would I refer to the 16th, 17th, 18th, 19th amino acids?

Option 1: AA-16 through AA 19
Option 2: (Subscript) A16A17A18A19
Option 3: The 16th through 19th amino acids ...


texts: How do schistosomes find and attach to human skin?

texts:
Schistosomes are parasitic flatworms that have a snail intermediate host and a human definitive host.

After developing in the snail, they (cercariae stage) escape into the water and can attach to the skin of a human. Then, it will penetrate the skin and migrate into areas of the human's body.

I have been unable to find any information on the mechanisms related to attachment to the human host's skin. More specifically, my questions are:

Do they attach to whatever they can find, and can only develop into the next stage if they (by chance) attach to the right host?
If they selectively attach to human host skin, how do they detect the skin? What makes the skin distinguishable to them?

Here is a great picture of the life cycle of these parasites, for reference.


texts: Which cells are responsible for the extracellular matrix remodeling?

texts:
I am studying a case of tendinopathies induced by an alteration of how the extracellular matrix is being remodeled.

From my understanding there has to be a careful balance of MMP (metallproteinases) and TIMP enzymes to maintain tendon homeostasis.

Which cells produce these enzymes?


texts: What would happen if a person had the right side of their body totally removed (including the brain)?

texts:
What would happen (in reality or theoretically) if the entire right side of a human's body was removed?

Could they live (aside from all the probable infections and such)?

I would guess that humans can live without part of the liver or brain.

The left brain controls the right side of the body.

What do you think (or know) will happen?

Thank you very much in advance!


texts: What is the relation between "classes" (stem cell, proliferative and differentiating) and the types (Ad, Ap, B) of the spermatogonium?

texts:
Describing the question in the title further,
The section, Systems Toxicologic Pathology,
Dianne M. Creasy, Robert E. Chapin, in Haschek and Rousseaux's Handbook of Toxicologic Pathology (Third Edition), 2013), mentions that

There are three classes of spermatogonia: stem cell spermatogonia, proliferative spermatogonia, and differentiating spermatogonia.

In common literature, there are following three subtypes, namely mentioned in the below Wikipedia article:

There are three subtypes of spermatogonia in humans:
Type A (dark) cells, with dark nuclei. These cells are reserve spermatogonial stem cells which do not >usually undergo active mitosis.
Type A (pale) cells, with pale nuclei. These are the spermatogonial stem cells that undergo active mitosis. These cells divide to produce Type B cells.
Type B cells, which undergo growth and become primary spermatocytes.
Source: Wikipedia - Spermatogonium
Also mentioned in Wikipedia - Spermatogenesis : Stages subsection (refer first row of the table)

I am unable to find anything relevant about the "classes" anywhere else (and I do not have full access to the mentioned textbook).
Although I don't have full access to this book, here is the preview to the subsection in the text in ScienceDirect. (You may find in page to locate the above line)
Additional Note : AL is a newly discovered subtype of spermatogonium. So it's Ad, Ab, B and AL now.


texts: Are there any intersections between the biochemical pathways of uracil biosynthesis (or metabolism) and methionine degradation in eukaryotes?

texts: Is there any way in which uracil biosynthesis or metabolism could help cell in degradation of toxic levels of methionine?


texts: Which of the cell types commonly found in mammals has the greatest number of mitochondria?

texts:
This is basically a fun question, inspired by this answer on scifi.se. So, which cell type will have the greatest number of mitochondria? Obviously, I am talking about wild type, healthy individuals and am looking for a rule of thumb. I realize that the number can change under different conditions/ between different individuals.

Off the top of my head, I would say that it's sperm cells given the strenuous exercise they need to perform and their MT-packed axonemes but perhaps there are better contenders?

I am primarily interested in human cell types but answers dealing with other mammals are welcome.


texts:
The three common genotypes at the hemoglobin locus have very different phenotypes: SS individuals suffer from severe anemia, AS individuals have a relatively mild form of anemia but are resistant to malaria, and AA individuals have no anemia but are susceptible to malaria. The frequency of the S allele among the gametes produced by the first generation of a central African population is 0.2.

(a) Assuming that mating occurs at random, what are the frequencies of the three genotypes among zygotes produced by this population?

I know that this is 0.2 for the S allele (q in the hardy weinberg equation)
and 0.8 for the A allele (p in the hardy weinberg equation).

So for the frequencies I got
AA = 0.64
AS = 0.32
SS = 0.04

(b) In this area, no SS individuals survive to adulthood, 70% of the AA individuals survive, and all of the AS individuals survive. What is the frequency of each of the three genotypes among the second generation of adults?

I don't know how to do this! I don't understand what to do! I tried multiplying

0.64 by 0.7 (because only 70% survive), but I know that is wrong answer. I know you have to divide 0.64 x 0.7 by the total that survived, but I don't understand why you have to do that. You didn't have to divide for part a, why do you have to divide for part b?

Also for some reason the frequency of the AS is not 0.32 for the answer. I don't understand why! Please Please help me.

(c) What is the frequency of the S allele among gametes produced by these adults?
I dont know this either!

PLEASE EXPLAIN ALL OF THIS TO ME IN CLEAR STEPS! THANK YOU SO MUCH.


texts: Where would Saccharomyces cerevisiae be found in highest concentrations in environment?

texts:
I have bakers asthma specifically to 'Sc' yeast, and know to avoid bakeries, breweries, etc...

I have figured out to not disturb rotting leaf piles, and fermenting bark mulch. Where else?

What percentage higher are concentrations in say Florida, as opposed to New York state?


texts: Why does replication require primers while transcription does not?

texts: In transcription, there is no need for any primer. I guess the basic mechanism of DNA polymerase & RNA polymerase is the same. So why does replication have the need for a primer?


texts: Neural correlates of the function of the cardiovascular system?

texts:
Are there any known neural correlates of the function of the cardiovascular system? I'm looking for research results that use standard brain imaging techniques (e.g. electroencephalography, magnetoencephalography, or functional magnetic resonance imaging), and compare the brain signals to respiratory and/or electrocardiographic signals.

Actually, ECG is frequently seen in EEG and MEG recordings. It is considered as an artefact, and typically removed in an early phase. Only the QRS complex is usually visible (or the R wave). If the ECG was recorded from the chest/limbs, proper signals would be gained. It would be interesting to compare the heart rate variability etc. to brain signals but has this for example been already done?

I don't have much background to respiratory signals, so I'm particularly interested about that.


texts:
A lot of these popped up recently in our backyard (St. Louis, Missouri, United States).  They are all grouped into these clusters and there were probably 5 of these big clusters.

Anyone know what type of mushrooms they are?


texts: What is epitope annotted protein??  The book from which I got this term is : http://www.springer.com/biomed/immunology/book/978-1-4939-1114-1


texts: Effect of the same caloric intake of different macronutrients on body weight

texts:
To gain weight, caloric intake > caloric expenditure.
To lose weight, caloric intake < caloric expenditure.
But what is the effect of the type of macronutrient ?
That is to say :

does the same caloric intake of carbohydrate, protein, lipid have the same effect on body weight ?
Does X amount of carbohydrate caloric intake > caloric expenditure or X amount of protein caloric intake > caloric expenditure or X amount of lipid caloric intake > caloric expenditure lead to weight gain ?
Does X amount of carbohydrate caloric intake < caloric expenditure or X amount of protein caloric intake < caloric expenditure or X amount of lipid caloric intake < caloric expenditure lead to weight loss ?


texts: Why calf thymus DNA is widely used instead any other body part?

texts:
Calf-thymus DNA is widely used as DNA sample. Such as testing anti-dsDNA antibody activity, nuclease activity etc, as well as certain books include calf-thymus-DNA in various examples (such as the book Molecular biology by Weaver (ed-5) mentions in a table on % (G+C), that %(G+C) of calf-thymus DNA is 40)

Now; my question is; why a peculiar organ like thymus is selected (and not liver or kidney etc); and not any organ from adult cows (which are more available at any meat shop)? whereas all the otherly-situations should contain the same DNA-sequence? Isn't it a bit weird?

Is it more easy to extract the DNA from a calves' thymus gland?

I've searched web, but nothing helpful I found.


texts:
I know that it decreases the amount of leucotrienes in blood.
I saw a patient with high IgE altough under Montelukast medication.
This suggests me that Montelukast does not affect the immunoglobulins, but somehow restrict the allergic reaction indirectly.

What is the effect of Montelukast on the amount of IgE in blood?


texts: When in Ampicillin degraded (gone) in liquid TB-media? Concerns about selectivity

texts:
Question: Specifically regarding Ampicillin; When growing cells in TB (terrific broth) for protein expression - when should I expect the ampicillin to be gone due to degradation by b-lactamases? (and how much Ampicillin do people add in addition to standard 100 ug/ml)

Background: I have heard rumours that all Ampicillin (100 ug/mL) is degraded within few hours (2-3) due to the enormous amount of b-lactamases secreted by the bacteria.I have also heard that some are not concerned about this, because 2-3 hours is anyway enough for the culture to outcompete anything else that will grow after the ampicillin is gone. On the other hand, some people are also writing that they add more ampicillin every 2-3 hours to maintain selectivity; however, I dont really see the point in maintaining selectivity as long as I have plenty of protein I will anyway lyse the cells and not use them for anything else.

My growth conditions: Grow at 37 degrees till OD600=1 (takes around 3h), then induce with IPTG and grow at 25 degrees for 18h, 200 rpm the entire time.

End comment: I know you can generally change to the more expensive carbenicillin which is degraded slower, but i'm more interested in knowing "how bad" Ampicillin really is for my general knowledge (and I will anyway keep on using it). Also: Any general thoughts or references to literature on this topic, specifically for Ampicillin is appreciated.


texts:
I read about the molecular biology of cancer, and I have a mess on my head and a lot of questions.. .

My primary question is-

The damage of the cancer cells is in the dna sequence or in the gene expression(microRNAs)? or even something else?

Thanks:)


texts: Can RNA be extracted from tissue suspended in formalin?

texts:
There are two tumor samples floating in a 10% formaldehyde solution (i.e formalin). Is there a protocol for RNA extraction under these circumstances? I am concerned that using the protocol for Formalin Fixed Paraffin Embedded (FFPE) tissue will damage the RNA, since there is no paraffin for the xylene to remove.

If I were to use the FFPE protocol without xylene, should I homogenize the tissue before removing the formalin, or after?


texts: Do any birds have established "poke a predator's eyes out" behavior?

texts:
Is there a pattern/tactics of behavior in any birds species that consists of attacking a predator's eyes with its beak?

I'm looking for established tactics, not 1 or 2 anecdotal examples.


texts: How can I render a protein non-functional to avoid problem during expression?

texts:
We're expressing a protein in a model organism for crystallization, however it seems the protein has some toxic effect on the cells.

Is there something we can do to make it non-functional during expression so it won't affect production, in such a way that we can restore function later (ex. after purification) in a simple way?

I know there are other approaches available but I'd like some inputs on this one alone.


texts:
I was told that cortisol has to be measured at 9am or 4pm, because those where its peak level. But I wonder if changes on sleep patters affect the cortisol cycle.
I mean, if I usually go to sleep around 11pm, but certain day I go to sleep at 4am.

My cortisol cycle would vary according to my change in sleeping?

Probably the same question can be done using other hormones as example.


texts: I'm curious how much damage is potentially inflicted by shear stress by pipetting. I know that syringes used for stem cell injection can cause a lot of damage. However, to what extent does this happen with P20 and P200 pipette tips? Understandably the shear modulus of bacterial cells is significantly different from that of cancer cells, which will be different from that of stem cells.


texts:
Question:

Given that with genetic engineering we can customize organisms as bio-weapons. Which species have the most worrying potential to be weaponized for mass destruction?

Background:

  Biological warfare — is the use of biological toxins or infectious agents such as bacteria, viruses, and
  fungi with intent to kill or incapacitate humans, animals or plants as
  an act of war.

Examples:

  E.G. bio-weapon species: Anthrax fungus -  was first tested as a biological warfare agent by Unit 731 of
  the Japanese Kwantung Army in Manchuria during the 1930s; some of this
  testing involved intentional infection of prisoners of war, thousands
  of whom died. Anthrax, designated at the time as Agent N, was also
  investigated by the Allies in the 1940s.

  E.G. bio-weapon vector: Anopheles labranchiae (malarial mosquito) - According to Prof Frank Snowden, a history professor at Yale
  University whose book The Conquest of Malaria in Italy draws on
  American archives and the diaries of Italian soldiers, the scheme was
  orchestrated in the autumn of 1943 by Erich Martini, a medical
  entomologist, Nazi Party member and friend of the SS commander
  Heinrich Himmler.


texts: Why is the gene regulation in eukaryotic cells needs multiple level of control than in prokaryotic cells?

texts:
That "eukaryotic cells are more complex" and "compartmentalized" are used to justify the need of more level of control of gene expression. I get the basic idea but can't convince myself why complexity or compartmentalization leads to more complex control (i.e. multiple levels) of gene regulation!

In control theory, we often use multiple level of control to minimize the variance (there are few other benefits as well from design perspective); probably that is what eukaryotic cell would also do. Moreover, simple combinatorics suggest that two level of control with $n_1$ and $n_2$ molecules involved at each level respectively would give me $n_1n_2$ possibilities of output which is higher than $n_1 + n_2$ distinct output I might get if I were to use these molecules with 1 level of control/regulation.

I was wondering if such simple reasoning are correct and can be used in the context of evolution? Are there other reasons as well?


texts: Can a gene-expression or epigenetic 'user-history' be found in the body?

texts:
(EDITED - a lot of what I am saying is implicit and simplified. I'm not looking to recreate the numerous textbooks and scientific papers on how DNA works).

As far as I can understand it, an organisms basic building blocks (proteins) are made up of DNA, Genes, and Chromosomes. The most basic form of this is DNA, made up of molecules in double helix strands. DNA carries all the instructions for the body in a simple 'database' or 'blueprint' form. Genes are chunks, or sequences, of the DNA telling the body 'what to do'(1) by reading the 'DNA database' in a myriad of unique coding sequences. Genes naturally(2) switch on and off throughout an organisms lifespan allowing amongst other things for an organism to grow from young to old. DNA is essentially(3) stored in Chromosomes.

External and environmental factors can influence the expression of genes, and the information stored in the DNA (4) - the study of which is Epigenetics. These Epigenetic factors can change over time, switching genes on and off. (5)

Does the body store a history of these expressions? Do the chromosomes (or some other part) of an older organism store a 'user-history' of which genes where previously activated when the organism was younger? eg, can you tell which genes where active when a person was 12, from the cells of an 80 year old?

Apologies, I do not have a background in Biology. (6)

EDIT NOTES

(1) what to do, how to do it, when to do it. not necessarily all life supporting instructions but also the minute-to-minute, day-to-day processes etc.

(2) naturally. there is no black and white in nature, only shades of grey.

(3) essentially. not exactly and not in all cases but mostly.

(4) As in, factors influence the expression of genes (which in turn are made up of DNA information). I am not suggesting that external factors can influence the 'DNA database' itself but rather just how they are 'read', sequenced and expressed as genes.

(5) again, naturally. no sharp on/offs but variations of concentrations.

(6) I may not have used the correct terminology.


texts: Is it humane to kill fish by immersing them in very cold water or ice slurry?

texts:
I'm doing some research and advocacy for the humane treatment of wild-caught fish. Humane standards are more common on fish farms than at sea, so I am trying to identify some reasonable standards for what might be considered humane and also feasible for companies to carry out. One possible method of slaughter is killing fish through cold water exposure. Below is an exact quote from a representative at a commercial fishing company (which I won't name since I don't have the person's permission to share this quote yet). I would like to know if what the person describes might be considered humane. It's unclear to me whether these fish are actually dying of hypothermia, or if it's 'cold shock' or 'live-freezing.' I'm not even sure whether these three things are distinct phenomena, or different names for the same process.

"In regards to our fish, they are all dispatched in a method to reduce waste and limit stresses to the fish during it’s transition.  A fish left flopping on the deck ruins it’s meat and stresses the fish out enough to change the flavor of the meat.  We move the fish from the ocean directly into sub-freezing temperatures.  In the case of tuna, that means a refrigerated seawater tank, with the salmon it’s a slurry of seawater and ice.  Sardines are scooped out of the ocean in large nets and deposited into tanks of refrigerated seawater.   The cause of death is hypothermia and has been shown to have a calming effect on the fish for the brief seconds before they pass."


texts: When writing about past research should I use the species name they employed or the modern version?

texts:
I am currently writing a literature review in which I am talking about the old research on the subject. When this research was carried out the species I'm talking about were classed under a different genus (specifically, it used to be called Vibrio fetus and is now called Campylobacter fetus). What is the correct approach for choosing when to use the older name and when to use the newer name? I see three options, although there may be more:

Always use the modern name.
Use the name used by the authors when discussing their work.
Largely use the modern name but make reference to the fact a different name was employed where it is appropriate to do so.

I'm tending towards option 3, but it's sometimes a bit unwieldy. Is there an accepted convention I should be following?


texts: What is the role of lamellar bodies in lung cells?

texts:
Lamellar bodies have been found to be secreted in lung cells many of their associated proteins have been identified. What is the current consensus or research on the function that these lamellar bodies play in lung?

(Sourced answers, please)


texts: Why does UV radiation from the Sun cause skin cancer?

texts:
What is the specific mechanism makes non-ionizing UVA and UVB radiation carcinogenic? Can lower energy light, like visible light, be carcinogenic because of this mechanism, or is there some kind of threshold within spectrum at which electromagnetic radiation does not induce cancer in humans?

Ionizing radiation can be mutagenic, which can cause cancer. However, this only applies to high-energy electromagnetic radiation with photon energies exceeding about 5 eV, or about 248 nm. (The FCC defines this threshold even higher at 10 eV, or about 124 nm!) These photon energies correspond to UVC, which is blocked thoroughly by the atmosphere, meaning Sunlight does not appreciably contribute to the ionizing radiation we receive on Earth. Therefore, the mechanism with which solar UV radiation induces cancer must be different from higher energy electromagnetic radiation, right?


texts: What causes the cardiac ventricular pressure change during the isovolumetric part of the cardiac cycle ?

texts: Why does the cardiac ventricular pressure change during isovolumetric contraction and relaxation. The volume ( both valves are closed)  is constant, Does Boyle's Law not apply?  P1V1= P2V2 at constant temperature.


texts: Adding the Propionyl-CoA Pathway to E.coli

texts:
So I'm trying to simulate the production of 3-Hydroxypropionic Acid with E.coli via the Propionyl-CoA Pathway.
However I'm not really sure how the production in the pathway goes.
I got the following picture:

If I understand it correctly the pathway goes:
Acetyl-Coa--> Propionate --> Propionyl-CoA --> .... --> 3-HP
When adding these reactions in Cobra are the stoichiometric coefficients always just 1?

Source of the figure:
Luo H, Zhou D, Liu X, Nie Z, Quiroga- Sánchez DL, Chang Y (2016) Production of 3- Hydroxypropionic Acid via the Propionyl-CoA Pathway Using Recombinant Escherichia coli Strains. PLoS ONE 11(5): e0156286. doi:10.1371/journal. pone.0156286


texts: Phenoptosis, behavior evolved for good of species?

texts:
I was reading this and felt like the argument is being made that organisms die for the good of species. Isn't this nonsense?

This especially bugged me:

  "'Age-induced, soft, or slow phenoptosis'" is the slow deterioration and death of an organism due to accumulated stresses over long periods of time. In short, it has been proposed that aging, heart disease, cancer, and other age related ailments are means of phenoptosis. "'Death caused by aging clears the population of ancestors and frees space for progeny carrying new useful traits.'"

Per the selfish nature of genes, it might be okay if it was only your offspring you are dying for, but even that only when you know you can't reproduce further. And the above argument says that old age death is exactly that.


texts: Why is Electrical Cardioversion contraindicated in AF and Digitalis Poisoning?

texts:
I am thinking why electrical cardioversion is contraindicated in atrial fibrillation with digitalis toxicity/poisoning.

Cardiac digitalis is also called digoxin and cardiac glycoside.
It is antiarrhythmic agent against supraventricular arrhythmias.
It is contraindicated in Atrial Fibrillation with digitalis toxicity.
The Pubmed's article about the topic is a stub without describing its Pharmacology.

Digitalis toxicity is a complication of digitalis therapy, here used for atrial fibrillation.
This may be due to kidney failure when the medication accumulates in the body.
Its treatment is activated charcoal and gastric lavage.
However, assume that these methods do not help in treatment or that we in acute digitalis toxicity.

I think the reason why we cannot recently do electrical cardioversion in digitalis poisoning is the high probability of repolarizing incidences so the likelihood to stimulate heart at the right moment is very small.
This is because digitalis poisoning is associated with cardiac disturbances: ventricular tachycardia, ventricular fibrillation, SA block and AV block.
Without knowing more precisely about the complication, I think the electrical cardioversion has high risk of failure.

Why is electrical cardioversion contraindicated in Digitalis Poisoning of AF treatment?


texts: Can ants distinguish individual ants in the colony?

texts: I am aware that ants have the ability to distinguish which female is the queen and which ones aren't. However, can ants also uniquely distinguish other individual ants in the colony? Is the differentiation between the classes only (worker-ant, queen, non-queen) or is it within the classes as well like hey its bob?


texts: What fraction of sites are expected to be polymorphic?

texts:
Question

Consider a very long (eventually infinite) DNA sequence of neutral sites. Consider a panmictic population of constant size $N$ with a per site mutation rate of $\mu$ where all individuals have the exact same fitness.

What is the fraction of sites that we'd expect to be polymorphic in the population (SNPs)?

Motivation behind this question

I am asking this question to verify the results of simulations I run. For example, I run a simulation with $x$ ($x$ will be varying below) neutral sites, with a per-site mutation rate $\mu = 10^{-9}$ and a population size of $N=100$. I run the simulations for 10,000 generations. There is no recombination. When the number of sites:

$x=10^3$ I get 0 SNP
$x=10^4$ I get 1 SNP
$x=10^5$ I get 3 SNPs
$x=10^6$ I get 25 SNPs
$x=10^7$ I get 238 SNPs

Is there a bug in my model or is it what we'd expect given the parameters?

In the human genome, 1 out of 300 sites are polymorphic (SNPs) (ref.). This is a frequency of SNPs that is 100 times greater than what I observe in my simulations. Note however, that the assumption of neutrality and out demographic assumptions would not perfectly hold and this result could pretty far off neutral expectation. My goal is not to reproduce something that look like the human genome but only to reproduce the neutral expectations for the moment.


texts: What is the focus distance of a 3D screen?

texts:
I've thought long and hard about wheter this is the appropriate section for this question, because I guess it's kind of an interdisciplinary subject.

My understanding of stereopsis (please, correct me if I'm wrong), basically depends of the way we cross our eyes when we attempt to see objects at different distances.
The more "our eyes are crossed", the greater the difference between the images we receive in each eye, which it's more effective to look at closer objects. In order for an object to be in focus, it needs to be at the point where the vision of the eyes intersect (including "at infinity" for very far away objects).

Now, with this mindset, how would such a gadget as Oculus VR work?
It consists of two separate screens (one for each eye) attached directly on an helmet-like device strapped to the user's head. It is capable of convincing 3D representations and has similar features which make it of close interest for gaming and similar applications.

So, my question is: in order to deliver such an illusion of depth, do the users' eyes need to be focused at the screen's distance, or at the represented objects' distance?

Sorry for the long question :P

Thanks in advance!


texts: Why does the funnel-mantle locking apparatus exist, and how / why does it work?

texts:
I was looking up argonauts, and found this article. As someone who builds things for a living, I was intrigued, but could find no information on how it actually functions in order to help the cephalopod.

Since locomotion is mentioned, I'm assuming that the creature cannot locomote efficiently (or at all) unless this locking apparatus in engaged?

Reference images of some kind (even if scribbled) would really help to explain geometry  / motion.


texts: why does blood when oxidized over time become bluish green?

texts:
Oxygenated blood is bright red and deoxygenated blood is dark red or brown.

If you take oxygenated blood and leave it in the air it will turn dark red, then brown, then finally a bluish green from exposure to atmospheric oxygen.

Why does it oxidize this far to get a copper oxide color to it after it has passed the phase where it is the same color as iron oxide? Why doesn't it stay at the iron oxide color?


texts: This looks like a mushroom is it eatable?

texts: This looks like mushroom it's white and there are insects feeding on it....it seems to be growing on a cascabela thevetia


texts:
The skull was found on a beach on the Sechelt inlet on Canada's pacific coast. A marine environment.

What species is this skull from?


texts: Do Angiotensin II Receptor Blockers (ARBs) or other factors control the level of ACE2 expression? [coronavirus receptor]

texts:
Because ACE2 is used by SARS-NCoV-2 to enter the cell, I am curious what factors determine its expression.  Interestingly, myocardial infarction increases ACE2 expression in the heart in an animal model ( https://www.ncbi.nlm.nih.gov/pubmed/15671045 ).  The paper found no significant effect from ramipril, an ACE inhibitor, but I don't think I can assume ARBs would work the same way.  (I am suspicious they might increase it based on the increase in the product Ang(1-7) level - https://www.nature.com/articles/hr200974 )  Note that soluble sACE2 can bind cells that did not produce it, by an RGD independent association with integrin beta 1.

Anything that influences the amount of ACE2 on cell surfaces is a useful answer.


texts: Creating Sperm via cell culture adaptation

texts:
I am wondering if it is theoretically possible to create "artificial sperm" via cell culture adaptation. That is at very high level, can you replace the genes of one sperm cell with those of another sperm cell and still have a functioning cell?

An area of application would be male infertility due to "weak sperm". Here you would take a "strong swimmers" from a donor, replace the genes with those from infertile male, and used the cultured adaption in fertilization.


texts: Plant determination: Lilium monadelphum versus L. szovitsianum

texts:
Lilium monadelphum, L. szovitsianum and L. armenicum belong to group of yellow flowering Lilium species and they are both often cultivated.

These species come from Caucasus area, so the first two are both described in the Flora of SSSR (4th volume). However, I find the dichotonic key description incomplete, and, based on the key, I am not able to clearly distinguish these species. Lilium armenicum is described by some authors as a variety of L. szovitsianum or as a subspecies of L. monadelphum.

What are your experiences with determination of these species?


texts: I am not understanding how water passes through root hair cells

texts: Why do people say that water moves into the cell because the water concentration of the cell sap is low ? the cell sap is surrounded by a membrane so if any water moves into the cell it must be because the concentration of water in the cytoplasm is lower than the surroundings. I am thinking that water from the cytoplasm moves into the cell sap solution and as a result , the concentration of water in the cytoplasm decreases so water moves in from the surroundings.


texts: Taxonomy problems on algae: Is Cryptophyta a Phylum or a Class rank?

texts:
I  am currently interested in algae taxonomy (I am not an expert in the field).

I retrieved the taxonomy of my sequences with their NCBI access number via the taxonkit software (https://bioinf.shenwei.me/taxonkit/usage/).

I noticed that I get Cryptophyta at the Class rank level.

For me -phyta actually corresponds more to the phylum rank.

I checked on NCBI site and is actually tidy in Class rank ( https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=3027&lvl=3&lin=f&keep=1&srchmode=1&unlock) but for example on the algaebase database (http://www.algaebase.org/browse/taxonomy/detail/?taxonid=Xafa8c1d30aa53593), Cryptophyta is classified as Phylum.

Can you tell me why Cryptophyta is rank at the Class level on NCBI and not to the Phylum level ?

Conversely, I retrieve taxonomy with, for example, Phaeophyceae ranked at Phylum level (https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=2870&lvl=3&lin=f&keep=1&srchmode= 1 & unlock) while it is normally a Class on algaebase (http://www.algaebase.org/browse/taxonomy/detail/?taxonid=L8055ac0a94735f3e).

Do you have ideas being considered? I am very interested !

Thank you very much in advance for your answers.

Best regards


texts: Does the term 'protein expression' refer to the production of proteins only or also their regulation?

texts:
I am learning about molecular biology and I have come across the term 'protein expression' in a research paper. I have searched the definition of this term online and on the Thermo Fisher Scientific website it states that "Protein expression refers to the way in which proteins are synthesized, modified and regulated in living organisms". However, on the National Cancer Institute website it states that protein expression "Refers to the production of proteins by cells".
I was wondering, between these two definitions, which one is more correct? Can protein expression also be used to refer to how proteins are regulated (e.g. can you use the term protein expression when discussing how one protein regulates the activity of another)? Any insights are appreciated.


texts: How does new species come into existence?

texts: The only reason for the creation of new species that I found from the internet is geographical isolation. Are there any more reasons?


texts: During acid reflux and vomiting, is the burning sensation from pepsin or acid?

texts: When one's stomach contents enter one's esophagus, a burning sensation usually ensues. Is this from the enzyme pepsin breaking apart your cells or just from the acid?


texts: what chromatin factors are the most potent supressors of meiotic crossover?

texts: I think linker histone H1 is probably involved, but the literature is scant.  What else prevents crossovers from becoming hyper-frequent during meiosis?


texts: Our muscles give us the ability to move our arms but....?

texts:
I have a strange question, but let me tell you something first.

If you think of this carefully, then you realize something, please try this right now:

Contract your muscles only so that your arms move without you doing it. You can't.
The way it happens is that you move your arm (or you do something or whatever you call it), then your muscles contract.
If our muscles weren't there, then we wouldn't be able to move our arms.

We don't contract our muscles, we move our arms, then our muscles contract automatically. So the muscles contract themselves, but what gives us the ability to make our arms move after deciding when we want to move our arm?

We can't contract our muscles so that our arm moves, we make that movement, then our muscles contract, but you can't even feel it because it's so light.
This is hard to explain.

So what gives us the ability to make our arms move, but not the muscles? I'm telling you, some people won't even understand, but this is real.

Thank you.


texts: Why are children more active than adults?

texts:
I have observed that children are usually more active than adults. For example, in the morning they get up and start playing, they have their lunch and get up and start running, while as adults they are relatively lazy.
Why is this so or is it that my observations are somehow errenous?
Thank you.


texts: What happens in a brain of a person suffering with apathy?

texts:
According to this article

  Apathy is a profound loss of motivation not attributed to decreased
  level of consciousness, cognitive impairment, or emotional distress.
  Apathy refers to a set of behavioral, emotional, and cognitive
  features such reduced interest and participation of activities of
  daily life. Another prime characteristic is lack of initiative or an
  absence of responsiveness to stimuli as demonstrated by a lack of self
  initiated action.

Could you describe what happens in a brain (on the level
of neuroreceptors) of a person suffering with a lack of
motivation (or apathy)? And how does it look in the healthy
brain?


texts: Why do neurons die so fast without oxygen and nutrients?

texts:
Some human tissue can survive without oxygen a couple of minutes, even hours.

Why are the neurons are so "weak" and depends so much on oxygen and other nutrients and cannot live without them for more than a few seconds or 1 or 2 minutes?

Are they missing some parts of their cells which can store nutrients for worse times in favor of their function or what is the case?


texts: Is it possible to dock multiple ligands with the target?

texts: Is it possible to dock multiple ligands with a target? If so, what is the suitable software used for? -- Is it possible to fix specific docking region for the target (or) automatic?


texts: Article or answer to whether "blood volume pressure" and "electrodermal activity" have any correlation to stress and or feelings overall

texts:
As the title suggests, I would like some help finding if there is any correlation between between blood volume pressure and electrodermal activity?

The paper I'm writing is about measuring stress and engagement levels of the subject by comparing the levels of electrodermal activity and blood volume pressure during media consuming. This can be anything from music, movies, tvshows etc.

But the papers im looking for can be about the correlation only. Not by measuring the same type of things as I do.

If you know any good articles, I don't really care much about the publication date.

I have full access to ieee articles through university.

Thanks.


texts: What word/expression is used to describe a band's share in the stained portion of the electrophoretic lane?

texts:
I was translating the following sentence from Russian, and realized I was not sure how to put it right:

  The study shows that the electropherograms of the studied samples of DRUG NAME obtained in reducing conditions contain two clearly delineated bands with a mean total coverage of 99%, while the minor bands have a coverage of 1%.

The intended meaning is: of the whole stained area of the lane, the two principal bands cover 99%, while the minor bands only contribute an insignificant amount: 1%.

The original Russian word is содержание (content), but this is ambiguous, because we are really describing the contribution of the bands.

I'm not sure what word/expression to use. Is this "coverage" traditionally measured as the area, or as the length, of the band relative to the total area/length of the lane? How is it usually described?


texts: Is severe but short-term pain worse than moderate but prolonged pain for the body?

texts:
I'm wondering about the effects of different durations and intensities of pain on the body. So the two can be compared, let's say that the cause of pain is the same in both cases, but in one the duration is shorter although the pain is more severe, and vice versa. Also, by effects, I mean biological but also psychological (which is probably more interesting), but the latter might be out of the scope of this site, so forgive me if it is.

For the sake of a (rather grim) example, if someone is exposed to a painful stimulus such as a mid-voltage shock for a long duration, and if someone else is exposed to a much higher voltage shock for a much shorter duration of time, which would produce worse effects on the body's normal functioning? (Somewhat morbidly, I should say to assume that they both live and do not die on the spot.) Since the answer very well might depend on the type of harmful stimulus, I'll give another example of a burn. If one is repeatedly subjected to a first-degree burn for a while and another is subjected to a third-degree burn only once, which is worse?

Upon pondering the question, it seems that the psychological effects would be more interesting since they should be roughly the same regardless of the type of stimulus, but biologically the effects obviously differ.

Thank you for your time, and any responses or thoughts on this would be greatly appreciated.

Edit: Obviously most experiments to test this would be subjective and unethical, especially in the case of psychological effects, so just an opinion from someone more knowledgeable in biology is more than fine.


texts: Taking cold shower / drinking cold water after / during training

texts:
(I am a new-comer in biology SE so sorry if violated any rules)
Effect of cold showers after intense training
I have read the answer to this question, but it seems there are discussions on the validity there so I am still confused. For me,
Benefits: increase heat loss by conduction on the skin surface, prevent heatstroke.
Disadvantages: thermoreceptors in the skin detect a drop in skin temperature, sending nerve impulses to the hypothalamus. Then the heat gain center is activated and causes vasoconstriction, reducing blood flow just under the skin hence reduce heat loss (&dangerous for patients with heart disease like the answer says). This also reduces sweat production by sweat glands.
Won't this 'chain' of physiological actions reduce heat loss (which is needed after exercise), hence trapping more heat inside the body instead of cooling in the long run? Or am I wrong when deducing the disadvantages?


texts: Is it Theoretically Possible to Create a Male clone from the donor Cell of a Female?

texts: I understand that Dolly the Sheep was created without the presence of a sperm cell. Instead, nucleus DNA from somatic cells of adult sheep were used. Since Dolly was female, i am assuming that the nucleus DNA used came from a female sheep. So, i want to know if the sex of the resulting clone is determined by the sex of the donor animal. Also, in light of the science behind sex determination in clones, would it be theoretically possible to create a male clone where a single woman contributes both the egg and somatic cells used in the cloning process?


texts: Why is glycerol kinase absent from adipocytes but present in the liver?

texts: Why don't adipocytes have the enzyme, glycerol kinase? Wouldn’t it be more efficient for them to utilise glycerol present to synthesize triglycerides than to get it from the liver? So what is the advantage of its absence?


texts: Found this gorgeous bush at Port Orleans resort in Walt Disney World, but none of the employees knew what it was. Can anyone identify it for me?


texts: In a monochromatic spectrum, is the human eye equally able to distinguish between lighter colors just as it is in distinguishing between darker colors? I mean is there really a linear relationship between the Lightness property in the HSL color model and the perceived brightness?


texts: Can I use commercial DNA loading dye for my RNA samples without degrading them?

texts: I was wondering if I have to use special RNA loading dye or can I run RNA samples with regular loading dye that is used for DNA?


texts:
This days I read some debates on evolution. That made me more interested to read something reliable on topic - I mean books.

I'm christian - although I think it doesn't matter on that topic - and I would like to read a book that presents all weaknesses and strengths (as much as possible) of evolution. I want that not to be presented as a debate on creationism, but to be a book on evolution theory explanation and presentation.

I also would appreciate if you know to give some details about the author that wrote the recommended book. I mean if he/she is atheist or a christian or a skeptic.


texts: When measuring your blood pressure in your arm, when you hear the sound to measure the systolic, is that sound NOT the heartbeat?


texts: I accidentally spun down the cells after heat shock treatment before adding the media into the tubes while doing transformation? will the transformation work?


texts: Found in blood sample - what is it? Hopefully not a nemotode-

texts: After examining someone's blood - through microscope - I found these. There were some more that were not photographed. Could someone please inform me on what these are? Maybe abiotic material on the slide? Hoping that they are not Microfilariae. #3 threw me in a loop.


texts: Number and function of voltage-independent ion channels

texts:
Googling for "voltage-independent" ion channels neurons doesn't give a good overview over the topic (and yields only approx. 50,000 hits, compared to 500,000 hits when searching for "voltage-dependent" ion channels neurons).

What I want to learn:

How many voltage-independent ion channels are there in the brain (or in specific parts of the brain, e.g. cortex) compared to voltage-dependent ion channels? (Rough estimate, order of magnitude: a tenth, a percent, ...?)
Which functional role do they play (compared to voltage-dependent channels which are mainly (?) concerned with the propagation of action potentials along the axon)?

Are there other (and possibly more concise) references than the one I found:
ROLES OF THE ION CHANNEL NALCN IN NEURONAL EXCITABILITY CONTROL (which states, that NALCN is "widely expressed in the nervous system")?

(I guess voltage-independent channels could support the mechanisms of Rall's model which doesn't pressume voltage-dependent ion channels but only modifiable membrane resistances, possibly realized by voltage-independent ion channels, right?)

Addendum: I made a bad mistake not pointing out, that I meant ion channels that are neither voltage- nor ligand-gated but just influence the membrane resistance passively. (Ligand-gated ion channels are of course examples of voltage-independent ion channels, but not the ones I wanted to ask for.) Are the voltage-independent ion channels I wanted to ask for possibly just what is called leak channels?


texts: Why it is so difficult to treat leukemia?

texts: I want to ask what is the reason that T315I type CML leukemia is currently untreatable. I have read quite a few papers in this subject. Why the current genetic oriented engineering drugs failed to stop the leukemia stem cell's expansion but can only slow the secondary leukemia stem cell's expansion? I found it to be utterly hopeless for a patient to be in such a position, as chemical therapy does not work well and radiation therapy can only target specific area. There are experimental drugs in the developmental stage but from what I know they are mostly unreliable.


texts:
I am looking for references to papers containing the time intervals spent in different phases of the cell cycle (ej., G0, G1, S, G2, M for eukaryotes) for different cells. In particular, I am interested in E. coli and CHO (Chinese Hamster Ovary cells), but any reference to studies of this kind for any typical cell will be useful.

I'll accept an answer containing a representative sample of references to the literature on this subject. Preferably recent papers (since 2010).

If you can provide the times spent in each phase but don't have references at hand, that will also be useful.


texts:
I'm reading over the ENCODE Nature papers, and one of the papers referred to is "Global mapping of protein-DNA interactions in vivo by digital" by Hesselberth et al[1].

Genomic footprinting is a massively parallel variant of DNAse I hypersensitivity screening, which I feel I have a good handle on, but I don't understand this paragraph from the beginning of the results (the troublesome part is in bold):

  To visualize regulatory protein occupancy across the genome of Saccharomyces cerevisiae, we coupled DNase I digestion of yeast nuclei with massively parallel DNA sequencing to create a dense whole-genome map of DNA template accessibility at nucleotide-level. We analyzed a single well-studied environmental condition, yeast a cells treated with the pheromone α-factor, which synchronizes cells in the G1 phase of the cell cycle. We isolated yeast nuclei and treated them with a DNase I concentration sufficient to release short (<300 bp) DNA fragments while maintaining the bulk of the sample in high molecular weight species (Supplementary Fig.1). These small fragments derive from two DNase I “hits” in close proximity, and therefore their isolation minimizes contamination by single fragment ends derived from random shearing. Because each end of the released DNase I ‘double-hit’ fragments represents an in vivo DNase I cleavage site, the sequence and hence genomic location of these sites can be readily determined by sequencing (Supplementary methods).

There's a reference to another paper by Sabo et al.[2] about genome-scale DNase assays using microarrays in that paragraph that I'm reading, but if someone understands the biology well, I'd really appreciate an answer.

Hesselberth JR, Chen X, Zhang Z, Sabo PJ, Sandstrom R, Reynolds AP, Thurman RE, Neph S, Kuehn MS, Noble WS, Fields S, Stamatoyannopoulos JA. 2009. Global mapping of protein-DNA interactions in vivo by digital genomic footprinting. Nature Methods 6(4): 283–289, doi:10.1038/nmeth.1313.
Sabo PJ, Kuehn MS, Thurman R, Johnson BE, Johnson EM, Cao H, Yu M, Rosenzweig E, Goldy J, Haydock A, Weaver M, Shafer A, Lee K, Neri F, Humbert R, Singer MA, Richmond TA, Dorschner MO, McArthur M, Hawrylycz M, Green RD, Navas PA, Noble WS, Stamatoyannopoulos JA. 2006. Genome-scale mapping of DNase I sensitivity in vivo using tiling DNA microarrays. Nature Methods 3: 511-518, doi:10.1038/nmeth890.


texts: Why there is a very high drop in pressure from arteries to arterioles?

texts:
Laplace law explains why the pressure is the same in aorta and arteries (100).
I am thinking why there is so big drop in pressure when going from arteries to arterioles (40-60).

Why there is a great drop in pressure from arteries to arterioles?


texts: How can both strands of DNA code for proteins with similar functions?

texts:
It's not clear from the question but for example:

AAAAAAA

TTTTTTT

The top strand would create a different protein than the bottom, and with the huge amount of nucleotide in a gene, I think it's very unlikely that the same region on both gene could create proteins that are similar to each other, even though they're alleles of the same gene. This would also affect codominance/incomplete dominance, since I'm assuming that only one of the strand would create a functional protein.


texts: What's the difference in roles of GATA-2 and BMI-1 in guiding Hematopietic cells?

texts:
I've discovered that hematopoietic cells become lineage-positive (Lin+) and go down the path of becoming lymphoblasts and myeloblasts, and that both BMI-1 and GATA-2 are transcription factors that play a role in that.

What is the specific difference in the role of BMI-1 and GATA-2 in guiding a hematopoietic cell down either of those lineages?


texts: How do you interpret this microbiology/ bacteriology research figure?

texts: This is a figure from a research article that I am to do a senior presentation for. It is showing  bacterial replication of an enteric bacteria population. The researchers hypothesize that the number of regions near the replication origin will be the highest point (peak) on the graph and the terminus region will be the lowest point because there are least copies of this region in a dividing species. The determine that the ratio of the peak to the trough will reflect the growth rate of the species. That all being said, I don't understand their use of color. The peak has several different colors that do not seem to match any of the examples on the right. Wondering if anyone can help me decipher this? Thanks!


texts: What information does the nociceptor relay to the brain about stimuli below threshold?

texts:
A. The duration of the stimulation

B. The location of the stimulation

C. The membrane potential at the site of stimulation

D. None of the above

I think the answer is B, because when the nociceptor is stimulated it relays information to the brain regarding location. Is this also true about stimuli below threshold?


texts:
Sister chromatids

  $A)$ Cross over during prophase I of meiosis

  $B)$ separate during the first mitotic division

  $C)$ are produced during $S$ phase between cell divisions

  $D)$ cross over during prophase II of meiosis

  $E)$ are also called homologous chromosomes

My thoughts:

  $A$ is incorrect because it's nonsister chromatids that cross over
  $B$ is incorrect because they separate during the second mitotic division
  Don't know about choice $C$
  $D$ is incorrect because there is no crossing over during Meiosis II
  $E$ is incorrect because well...it's just not true

So is the answer $C$?


texts: How many humans have been in my lineage? Is it almost the same for every human currently living?

texts:
If I were to count my father, my grandfather, my great-grandfather, and so on up till, say chimps, or the most common ancestor, or whatever that suits the more accurate answer, how many humans would there have been in my direct lineage?

And would it be almost the same for every human being currently living?


texts: Is there a PSI-BLAST for nucleotide sequences?

texts:
I understand that one can translate a nucleotide sequence and run PSI-BLAST on the protein (proteins if you take the 6 reading frames), but I'm looking for distant homology for bacterial small RNAs (typically 50-200 nucleotides long and noncoding).

If there is no such resource, what are the main obstacles to this implementation?


texts:
Quoting from : Scientific American July 1975 The Manipulation of genes by Stanley Cohen :

  Restriction endonucleases (and modification methylases) are widespread
  in microorganisms; genes for making them were found on viral
  chromosomes and extrachromosomal plasmid DNA as well as on many
  bacterial chromosomes.

Why would the genes for making RE be found on viral chromosomes ? Also, could you give some examples where they are found on plasmids ?


texts: Why boys who inherit more genes of their mother are not born as girls and girls who inherit more genes of their father not born as boys?

texts: If boys as well as girls inherit the genes of the father as well as mother, does it imply that boys inherit more genes from the father to be boys and the girls inherit more genes from the mother to be girls? Or there is some thing else to it that settles the sex of the children? Since girls may inherit more genes of father and less genes of the mother question arises what decides that they are not born as boys or the other way around why the boys who inherit more genes of their mother are not born as girls?


texts:
It's known the human eye takes 24 images per second. But does this refresh?
For example after sleeping.

Or will it always be the same interval?

I talk about when the eye takes the images. So it are 24 images in the second, but this second is not defined. It can start at 09:00:00.00 or 09:00:00.50. Will this change after taking a sleep?

Hope it is clear what I'm talking about.


texts: What is the functional significance of the difference in cardiolipin/cholesterol ratio in different membranes?

texts: I have read somewhere that the plasma membrane has little cardiolipin but excess cholesterol whereas the inner mitochondrial membrane is rich in cardiolipin and has little cholesterol.I just wanted to know why there is this difference.


texts: Do snail shells increase the number of rounds with age?

texts: Do snail shells increase the number of rounds with snail age?


texts:
I am not a biology expert but I have done some homework on understanding alleles, chromosomes, dna in the human genome. Still baffled by a question though:

As I understand it at a particular locus for e.g. if a human has a A on one chromosome and a G on another that individual is considered Heterozygous at that locus because of the difference in the nucleotides (A/G in this case).

However, my question is. What about an individual that has an A on the 3' -> 5' strand (and hence a complement T on the 5'-> 3' strand) on one chromosome but T on the 3'-> 5' (and its complement on the other strand) on the other chromosome. Is this individual considered heterozygos or homozygous?

Basically my question boils down to does the "directionality" of the A-T pairing matter on both chromosomes?

I was thinking it should as only one strand can code for genes which the other doesn't so it should matter whether the A is on the (3'-5') or on the other strand..

Any advice would be great!


texts: Mechanistically, how does calcium chloride aid in bacterial transformation?

texts: I am looking to get more information about the mechanism of the $CaCl_2$ in the bacterial transformation. I read online about the topic but I didn't found any reverent information on the topic, I don't have access to most of the scientific publications. However, I found this website. According to this website, there is a lot of theory about the mechanism of calcium chloride in the bacterial transformation. Would it be possible to get a short scientific referenced explanation about the topic and I can or cannot be related to heat shocks?


texts: Ligase Chain Reaction: Determining the annealing temperature for gene synthesis

texts: Using the tool Gene2Oligo I have a set of DNA oligonucleotides to synthesize a gene using ligase chain reaction (LCR).  The average melting temperature is 72 degrees Celsius.  I am going to use a the thermostable Taq ligase enzyme for the LCR reaction but I am unsure of the annealing temperature to use.  Should I use the standard recommendation as in PCR of 5 degrees less than the melting temperature or should I use another tool?  Taq ligase has a cutoff in activity at 65C so that is the highest I can use.


texts: Would preserving your Eyes from Light keep them healhty?

texts:
I read about why eyesight diminishes with age.
I am aware of the fact that there are different causes that can affect the quality of image received by our eyes and that being vague would not lead to a clear answer, but I will try to make it as clear as possible.

I am wondering if worsening of the ciliary muscle is affected by how much light the eye receives or at least how much we use it.

There might be other areas affected by high light intake. Because the title of the question might not be clear enough: I basically mean the following:

Is our eyesight determined to worsen with age or does it depend on how the eyes are "used"?


texts: Dissection techniques for fruits and seeds

texts:
I'm doing some amateur botany, and I was keying some plants in the Brassicaceae (Cruciferae) family, which requires detailed information about the seeds of the plant. My question is, in a seed, how can one identify features such as:

Cotyledon(s)
Radicle
Endosperm (when present)
Accumbency/incumbency of the cotyledons with respect to the radicle (in dicots)

It also seems like the key parts of the seed will be within the seed coat; it's not always obvious how to remove this seed coat, or what methods exist. Are there resources for this sort of thing?
As a more concrete example, I've identified this Cardamine hirsuta from my backyard, but I'd like to verify some features of the seeds. Unfortunately, the seeds are very tiny, as this microscope photo of the silique shows, and the features are non-distinct.
Flora of North America provides these details for the Cardamine genus:

Seeds uniseriate, flattened, usually not winged, rarely margined or winged, oblong, ovoid, or globose; seed coat (smooth, minutely reticulate, colliculate, or rugose) mucilaginous or not when wetted; cotyledons accumbent, rarely incumbent

How can I figure out from dissection whether the cotyledons are accumbent  or not? At least, that's the sort of question I'd like to be able to answer.


texts: What is the context in which a species gets the name "elegans"

texts:
Quite a lot of Latin binomials from different genera contain the same species name. For example, there are a number that reflect the physical properties of the species (Tables have the latin name, a translation, and the number of European species according to the European Nature Information System).

nigr[a|o|um]    black        545
minim[us|a]     small        325
alb[us|um|a]    white        264
maxim[us|a]     big          166

and some which reflect the way in which they become apparent to us humans

vulgar[is|e]    common       691
sativa          cultivated   70
domesticus      domesticated 19

as well as reduplication for particularly salient/familiar species (e.g. Gallus gallus, Mephitis mephitis)

So, I'm wondering why there are so many elegans (471 European species on the database). It's particularly widespread, but meaning "elegant" or "refined", it's a rather nondescript name to give. Maybe someone might describe a species like this if they were really running thin on defining characteristics, but if this is the reason, why would the name occur so often?

So I'm fairly sure I'm missing something important about how species get named. What is/was the reason for naming so many species "elegans"? Does it have perhaps have something to do with type species?


texts: Why is hydrogen sulphide being generated on Caribbean beaches?

texts: Once again, there has been a massive influx of Sargassum weed in the Caribbean. It is coming ashore on Atlantic facing beaches and forming piles up to 3m deep. As it dries and decays, hydrogen sulphide is being emitted. Why?


texts: Picking up Plasmid DNA using Nanodrop, but not using Electrophoresis

texts:
I am currently trying to see if 2 bacteria contains plasmids or not. I had used promega plasmid extraction kit on the bacteria. I ran a gel electrophoresis (.8% gel) with the extract product, however its not showing the presents of any DNA. I also ran the product through Nanodrop (2000) and these where the concentrations I got:

1 : 6.5 ng/ul & 260/280 = 1.56
 2 : 49.4 ng/ul & 260/280: 1.96

Based on experience, I want to say #1 contains no plasmids, however #2 may have a small concentration of plasmids. Please give me your opinion on what to conclude. Also, if there is another test I can try to do to confirm plasmid presents or not, please let me know.


texts: How does stimulus reach neural threshold?

texts:
I understand that when the stimulus into a neuron is greater than the threshold it triggers the action potential. Do all the contributing stimulus have to occur at the same time, or can they occur over time?

If neurons A and B connect to C, and C needs both A & B to activate to reach the threshold; can A fire first, then B - or do they both need to fire simultaneously?

If they can contribute towards the threshold over time then is there a decay that eventually returns the neuron to resting potential?