texts: V vs S plot looks like hyperbolic but 1/V vs 1/S plot is not linear at all. Looks like some kind of exponential growth. What can be the reason?


texts: How do myosins cause myofibrils to be shortened?

texts: I know that it is the binding and tilting of myosins on actins that cause the sarcomere to be shortened. But I am a little bit confused about the details. The structure of a sarcomere is made of alternative bands of actin and myosin filaments. So when the actin is pulled shortened by the myosin filaments on both sides of it, wouldn't it experience forces in different directions? If so, why can the sarcomere be shortened rather than being torn up? I am a little confused about how exactly the movement of myosins cause the muscle to contract.


texts: Splicing and “the dominance of RNA-world”

texts:
This is a paragraph from my textbook.

  The significance of such complexities is now beginning to be
  understood. The split-gene arrangements represent probably an ancient
  feature of the genome. The presence of introns is reminiscent of antiquity,
  and the process of splicing represents the dominance of RNA-world. In
  recent times, the understanding of RNA and RNA-dependent processes
  in the living system have assumed more importance.

NCERT XII (pg. 111)

I am unable to understand the above sentence in bold. Can anybody explain. Thanks


texts:
There are lots of visual maps of the brain as a whole, especially the cortex, that show the distribution of "features" over a two-dimensional map, e.g. the Brodman areas (their morphology and their functions), or the cortical homunculi.

What I would like to literally see - on a quite different level of resolution - are density distributions of some "items" over the membrane of some prototypical neurons, especially:

excitatory synapses
inhibitory synapses (mainly on the soma?)
vesicles (not in, but near the membrane)
receptors (not only at and near synapses?)
the different ion channels
electrical synapses
sodium–potassium pumps

So my question is for instructive graphical displays of such distributions, may it be in an article, on a website, or in a book.

(I assume that none of the items above is distributed evenly. But maybe some are on a specific type of neuron?)


texts: Does bioluminescence communcation occur on macroscopic level?

texts: Some bacteria are known to communicate using bioluminescence (quorum sensing). Do we observe the same phenomena in any macroscopic species?


texts:
Will a T7 tag still work if it is placed next to a start codon? Meaning, will it still work with a Met attached to it in the amino acid sequence?

Thank you!


texts: Are there viruses that show definite enzymatic activity?

texts: Perhaps due to outer coat protein individually or collectively.


texts: Does AMP/ATP ratio affect lifespan in vertebrates?

texts:
The reference below says that a higher AMP/ATP ratio is associated with lower lifespan in C. elegans.

Is this finding also generalizable to vertebrates as well?

Reference:
Apfeld, J., O’Connor, G., McDonagh, T., DiStefano, P. S. & Curtis, R. The AMP-activated
protein kinase AAK-2 links energy levels and insulin-like signals to lifespan in C. elegans.
Genes Dev. 18, 3004–3009 (2004). PMCID: PMC535911.


texts: Is it possible to have different genes in different parts of our body?

texts:
I want to understand genetic mutation specially in the context of multicellular organisms like humans.
I studied biology only till high school and I can’t fully understand wikipedia pages on this subject.

I know that genetic material is in chromosomes inside the nucleus of a cell. When that cell multiplies, the chromosomes too generates a copy of themselves and both child cells get one set of the chromosomes.

I would like to know:

Does genetic mutation mean an error in chromosome generation at fission stage or will it occur later in the life of the cell?
Multicellular organisms begin their life from a single cell (zygote). Under normal circumstances, every cell that grows from this single cell should have the same genetic material. Can genetic mutation eventually result in us having different genetic material in cells of different parts of our body? For example, when only a part of our body gets exposed to radiation.
If answer to question 2 is yes, which genetic material will control the behaviour of the cells? Let’s say, for example, that the genetic material of cells in our stomach favour high growth rate of hair but the cells in the scalp themselves do not have that particular gene. What will be the result?


texts: Cellulose - why is it fibrous and not granular?

texts:
I was reading a book where it said that the 1 - 4 Glycosidic bond of the Beta Glucose meant that cellulose is fibrous and not granular.

First, what does it mean to be granular and why is not granular unlike Amylose?

Thanks, Dave.


texts:
I have seen the answer to this question which says that T cells do not express MHC II proteins which would make sense.
However, my textbook "The immune system" by Peter Parham disagrees. It says that T cells do gain MHC II receptors after activation.

*Activated T cells express MHC class II molecules, whereas resting T cells do not.

I cannot see why this is needed. MHC II molecules are for CD4 cells (helper T cells).
If the T cell presenting the antigen was a CD4 cell, then that seems useless, because this cell was already the one that could recognise this particular antigen - so why show it to others? The chance that another T cell that could recognise it too would be incredibly small no?
I guess I can see the merit of a CD8 T killer cell to show the antigen, as it could alert other CD4 T cells to come assist (although cytokines seem like a better method...)
So what is the purpose of T cells, in particular CD4, of showing MHC II proteins?


texts:
It seems that many flavor and food preferences can be explained in the context of regulating feeding behavior. Generally, organisms tend to enjoy those foods which are optimal for them to feed on and provide the best nutrition. There are well-known exceptions to this, such as:

Artificial chemicals (eg. the supposedly sweet-tasting but deadly polyethylene glycol) which are very rare in nature, thus there was no opportunity for an appropriate taste perception to evolve
Nutrients which are desirable in moderation but dangerous in excess (eg. sugar), but have only become readily available recently thanks to technology (thus once again moderated consumption has not had opportunity to evolve)

But humans in particular also seem to enjoy consuming a large variety of foods that one would expect to be unpalatable or mildly harmful. For instance various peppers, spices, hot sauces, wasabi, mustard and so forth, don't appear to provide much of a nutritional benefit. Indeed their chief property of interest, the spicy flavor, is a defense mechanism: The plant attempts to make itself unpalatable or toxic to deter predation. Why is it then that this very defense mechanism has ironically become prized as a food ingredient by humans, to such an extent that wars have been fought over access to spices? And why is it that humans do not consider (for instance) pure, fresh, raw meat to be more delicious than meat with seasoning or condiments?

There has been a similar question (see comments) on here but that has also not attracted a good answer. I think this exemplifies the enduring interest in the subject and as such I'd like to keep this question open to stimulate a better response from more recent visitors.


texts: How having sickle cell trait would provide resistance to malarial parasites?

texts: It's mentioned in my textbook that subjects with sickle cell trait develop resistance to malaria. I've read a few research papers predisposing involvement of macrophages and papers asserting involvement of the heme oxygenase system rendering me confused; so what actually causes this resistance. And is this resistance also present in the subjects with sickle cell anemia? Also some African tribes are generally mutated to provide malaria resistance. See this https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3499995/


texts: Why isolated, recombinant plasmid DNA without any restriction is often detected in agarose gel electrophoresis as three DNA bands?

texts: I don't understand why three bands are found without any restriction digest. Please answer me as soon as possible.


texts: By what mechanism do cephalopods regrow limbs?

texts:
As far as I can tell, there are two types of limb regeneration: epimorphosis and morphallaxis. Epimorphosis is used by animals such as amphibians and various phyla of worms, while morphallaxis is used by hydras.
I have been trying to find out which of these mechanisms is used by cephalopods, and no reliable source paints a clear picture one way or the other. Can anyone here help?


texts: It looks like a simple problem, affecting almost half of the population at the post-pubertal age and of any gender and ethnicity [wikipedia]. What is so complex about finding a cure? Also, if you know some of the most effective treatments, they're welcome.


texts: How does geography affect morphological features of the human body

texts:
I've seen many times how a person born in one place, goes to another country for a long time, and then they start looking more like the people there, but I never found out how it works.
This report claims that second generation Japanese, born in the US are taller and heavier than those living in their native lands (there had been no intermingling of races).

To what extent do the genetic/environmental factors control human morphology ?
What factors apart from the diet can bring about such morphological differences ?


texts: Is a Linker sequence mandatory in primers for PCR Cloning?

texts: I have designed the primers for PCR cloning, but i was not getting any colonies after the ligation. One of our colleagues said, that the restriction digestion might not be working as there is no linker sequence before/after the restriction site in the primer. What measures should I take to be successful in the cloning?


texts: Vaccination and population dynamics of an epidemic

texts:
I'm trying to figure out how should a vaccination model be built to correlate with population density, and I'm having problems to understand meanings of the results I receive when I apply theory on specific data I'm provided with.

Theory(i):

The initial phase of an outburst of a disease can be described by an exponential growth
model. The relevant equation is:

$(1)\frac{dI}{dt}=\beta n(1-q)I-\mu I$ where:

$n$ = the population density. Let us measure it in units of $km^{-2}$.

$I$ = the density of already infected individuals in the population; measured in the
same units as $n$.

$q$ = the fraction of the population that is immune to the disease, either naturally of
due to vaccination. Consequently, $1-q$ is the fraction of the population that is
susceptible, i.e., at risk of getting infected. $q$ is a pure number between $0$ and $1$,
and has no units.

$\beta$ = is the transmission rate of the disease. It measures how easily and quickly
the disease can be transmitted from an infected individual to an non-infected
susceptible individual. $\beta$ includes within it both the rate at which encounter
between infected and non-infected individuals occur, and the probability that
such an encounter would result in actual transmission of the disease. $\beta$ has
dimensions of $\frac{1}{time\times density^{2}}$, so let us measure it in units of $week^{-1}km^{4}$.

$\mu$ = the rate at which infected individuals are eliminated from the group of
infected individual, either because they recover, or because they die. $\frac{1}{\mu}$ is the average duration of the infection, i.e., the average time that an individual remains
infected before it either recovers or dies. Let us measure $\mu$ in units of $week^{-1}$.

This equation derives from the differential equation $(2) \frac{dN}{dt}=rN$ where $r$ is called instantaneous rate of increase. It is easy to see that $I$ from equation $(1)$ is equivalent to $N$ from equation $(2)$ and therefore, $r$ for equation $(1)$ will be $(3) r=\beta n(1-q)-\mu$. When we look at equation $(3)$, we see two factors:

$\beta n(1-q)$ - A positive factor(ii)
$\mu$ - A negative factor

Minding the above, when $r=0$, there is no increase in population(iii). From this, we can compute $q_{0}$ which is the minimum fraction of vaccinated/immune individuals in the population that is required in order to prevent the disease from spreading. From equation $(3)$ we can figure out that $q_{0}=1-\frac{\mu}{\beta n}$. Just as $q$, $q_{0}$ is a pure number between $0$ and $1$.

Welcome to the desert of the real (my question):

Suppose we compare two countries with the following data:

Israel: $n=347km^{-2}$, $\beta=0.0015week^{-1}km^{4}$, $\mu=0.25week^{-1}$
Finland: $n=16km^{-2}$, $\beta=0.0015week^{-1}km^{4}$, $\mu=0.25week^{-1}$

When we look for $q_{0}$ for Israel we see that $q_{0}(Israel)=1-\frac{0.25}{0.0015\times347}=0.52=52$% while for Finland we see that $q_{0}(Finland)=1-\frac{0.25}{0.0015\times16}=-9.42=-942$%. Assuming that we've got correct data in the first place, $q_{0}$ is a negative pure numbers which is not between $0$ and $1$.

Do such, and similar results make any sense at all? Especially when they are not between the defined boundaries of the variable.
If they do make sense, what does it mean getting a negative results? How should it affect my vaccination policy?

Footnotes:

(i) Taken from my Populations Ecology lecture slides

(ii) Positive when looking at it from the epidemic point of view

(iii) Of infected individuals


texts: How is consciousness linked to the brain?

texts:
Could the brain be working without consciousness? Does the brain interact with consciousness? Alternately, is it that consciousness can't really control the brain, and you only have the impression that you make the decisions, but your brain does.

If the answer to the last question is yes, it is impossible to know if someone else has a consciousness? Even if he doesn't, he'll say he does, because the brain thinks he does.

We can't be made only from matter. If we would, we'd be a mix of chemicals interacting with each other. What makes us be aware of our feelings, what we think, and our 5 senses?

When and how is consciousnesses created?


texts: What do you call a virus when it's cured?

texts:
When a cure has been found for a virus, can it be called such anymore?

Virus implies it's something you've contracted that you just have to live with until (hopefully) your body can overwhelm and destroy it.

But say someone found a cure for the Common Cold tomorrow, would we still call it the cold virus or would it just be known as the "cold infection" or something to that effect?

Is "Virus" just a nomenclature we've adopted for a bug that has no cure, or is it used to describe a certain type of organism?


texts:
I'm interested in modelling host-pathogen interactions using mathematics. I know there are good resources in Pubmed but seems I'm looking for a book or introductory reviews.

My background in maths is limited, knowing the basics about calculus and algebra, and more recently some machine learning.

The paper inspiring this question is this one:

Front Microbiol. 2015; 6: 235.
A review on computational systems biology of pathogen–host interactionsA review on computational systems biology of pathogen–host interactions


texts:
I know it's a very open question. It's for a paper.
So as a reference I'm looking maybe for the average density of insulin receptors per cell of a human tissue. I want to compare it to the density of MC1R (around 1000 per cell) and it says that's a low amount.


texts: Natural selection and the Galapagos Islands

texts: Woodpeckers found on the South American mainland are able to peck insects from the bark of trees. Would the woodpecker finch have been able to survive if woodpeckers had found their way to the Galapagos Islands where this finch is found?


texts: Why is the GenBank entry for the genomes of RNA viruses like coronavirus written as DNA?

texts:
The reference genome in GenBank of the sars coronavirus from Wuhan is written in the following format:

attaaaggtttataccttcc

(The first 20 nucleotides)

Considering that coronaviruses are RNA viruses, the bases of which are adenine, cytosine, guanine and uracil, I was surprised to see the t symbol in the sequence, which stands for thymine, found in DNA, not in RNA. Additionally, no u symbols are present in the sequence.

So, what's going on here? Where did Thymine come from, why no Uracil?


texts:
I live in Switzerland and have noticed these small bugs appear in my bedroom, either slowly crawling on the parquet flooring, lazily buzzing around or dead on my windowsill (as pictured):

I'm not sure if these bugs are currently appearing more often – or if I just notice them more because of the fact that I'm spending a lot of time in my bedroom due to Corona lockdown.
The only hint I've got is a friend saying that they live in wooden floors. No idea if that's correct.
Thanks for any help or hints!


texts: Identification of a mysterious lifeform, what is this?

texts: For the third time in a row, I found a mysterious life-form inside my house. I live in the Netherlands in the Eindhoven region, in a city called Oss near a forest area. Before I set it free outside, I put it in a jar to make a few pictures for identification purposes. What is this creature?


texts:
I'm in Southern Germany and just captured this animal crawling along my wall at considerable speed, apparently hiding from the light. It looks like a entipede from afar (about two dozen legs), and closer inspection reveals it has long legs, a clearly visible head, two long feelers, and striped hind legs. It's about 3-4 cm (1.5in) in length if I recall correctly. Below are the best-quality photos I managed to take before setting it free outside.
I'm as ignorant about arthropods as I am averse to them, and I'd very much like to know if this one is harmful or not, and whether to expect more of those around the house.


texts: Would Ants and Termites be considered r or K strategists?

texts: My initial assumption is that most swarm species would fall under r strategists due to their prodigious number of offspring, but it also occurred to me that since worker types are non-propagating we would only consider the queen/drones which would be K. So which viewpoint is correct?


texts: Is this basic gene diagram correctly labeled?

texts:
I keep seeing this gene diagram, and I am not sure how to interpret it. I don't know what this diagram is called or where it was first depicted, but in the second picture, I have labeled it with what I think are the correct regions.

Unlabeled

Labeled

If the labels are correct, does this mean that an open reading frame (and consequently, the CDS) does not have to begin at exon 1?
If the labels are not correct, could you make some suggestions on how to fix the mistakes or point me towards some resource for interpreting this diagram?


texts: Can we change the direction of a neurological signal?

texts: My question is can we change the direction of a neurological signal? When a neurological signal is generated it goes to the brain. Along the way it passes synapses. Can we make it change it's pathway to go through another neurone instead of the neurone it was going to ?


texts: Can multiple antibodies bind the same antigen?

texts: Given the size difference between small molecule antigens and antibodies is it ever possible for multiple antibodies to bind to the same antigen if they recognize different domains on that antigen? When the antigen is a protein rather than a small molecule is it more likely that multiple antibodies can bind?


texts: How do gene locations change during crossing over events?

texts:
Suppose you have two variants from the same species, which have slightly different chromosomes I's to each other. Genes may be in slightly different positions on the chromosome, and the lengths of the chromosomes might be somewhat different. Suppose these are crossed to produce offspring. If a crossing over event occurs in the offspring during meiosis, what happens to the positions of the genes?
A concrete example of what I'm asking is the following. Suppose that in the above scenario, the first chromatid is 1Mb long and the second is 1.05Mb long. "Gene A" occurs between 6kb-8kb on the first chromatid and 10kb-12kb on the second. If the crossing over occurs and replaces the first 9kb on the first chromatid, what happens to gene A there? Does it cease to exist? Or does the crossing-over process somehow know to grab DNA from above 12kb from the second chromatid?


texts: Effect of paracetamol or any antipyretic tablets

texts: We all consume a paracetamol or any antipyretic tablet when we have cold or flu. And these tablets just reduce the body temperature. So my question is, when we have an infection and due to that infection we get fever, so unknowingly if we consume antipyretic tablets it will reduce the body temperature, so that means during that condition reduction of body temperature is harmful for our body as the infectious agent can make copies of it, as the body temperature is decreasing.


texts: How do fungi react to being grown in a tissue culture?

texts: I know how plant cells and animal cells react to being cultured and grown this way, but what about mushrooms? Would they respond like plants, and result in embryos growing off the mass? Or does the mass just grow indefinitely as in animals? Has anyone done this? How do they react when grown this way?


texts: Heteromaternal Superfecundation - Any known cases?

texts:
Superfecundation in mammals (fertilization of two or more ova from the same cycle by sperm from separate acts of sexual intercourse) -- Is possible in nature from different fathers (Heteropaternal) as after the first zygote is formed, a second act of intercourse within a certain time span has the potential (of another ovum is present) to form a second zygote.

Has there been any cases where a naturally pregnant mammal was implanted (IVF) with a second zygote from a different set of parents?  Heteromaternal/paternal Superfecundation?


texts: Are the two strands of the double helix collectively called the DNA molecule, or is each individual strand the DNA molecule?


texts: "structural and regulatory elements of genes"

texts:
Can anyone please explain a little about these two elements of genes? My main problem is with "which ‘switch on’ instructions".

  genes have structural elements (which code for a particular protein) and regulatory elements (which ‘switch on’ instructions)


texts: What can I see with a microscope at what magnifications?

texts:
I'm 26 and where I grew up the schools were complete crap so I've never really used a microscope much or learned much about them. And I want to learn some science and look at some microscopic things, like organisms in water, how tiny  bugs or dirt looks up close, blood cells, and whatever else there will be to discover.

So my questions are about magnification  and what I will be able to see at various magnifications. How much magnification would I need to get a detailed look at tiny insects like a gnat or tiny aphid? Or to see microscopic organisms in water, or our blood cells, or the fibres in my microfiber glasses cleaner. And If i was looking at stuff like blood cells, or food, would i be able to see anything like viruses or diseases? (And as an extra question, any good books for self learning about microscopic organisms like that?)  I was looking on amazon and found 500x max up to 2500x max, and would like to be able to see living microscopic organisms if possible.


texts: Is it possible to amplify every single piece of DNA through PCR?

texts: Is there a way to perform non-specific PCR amplification for the purpose of amplifying every piece of DNA present?


texts: I need to identify the genus of this colony just by its morphology, can somebody help me?

texts:
it was grown on TSA
it's a mesophilic bacteria.

(it was contaminated by E. coli, so ignore the clearer and smoother colonies).


texts: Reverse evolution to gain back lost traits

texts:
Many animals return to shapes similar to their ancestors like mammals and reptiles growing fins and fish tails or animals losing limbs they just grew and so on.

But I notice that once an animal loses a feature it doesn't actually grow back... they con only mimic it, no reptile or mammal has fins but only limbs that look like fins... and no aquatic mammal or reptile seems to regrow back their lost legs or arms.

No animal seems to regrew its ancestral gills even though they live 100% of their lives inside deep waters.

If some organs can be so useful to have back, with evolutionary pressure at maximum, why don't they ever return?

What blocks animals from re-evolving something they lost?


texts:
I notice that when I buy basil it is fresh and green in the store, but when I take it home it wilts and turns black within 24 hours.

Why does it do this?


texts:
when i look at a white wall i see little colored dots moving in circles filling my whole visual view, just like the static on a tv but then in color.
I thought everybody had this but recently i discovered it is not normal ?

furthermore i see something which looks like tiny cells, just like you look under a microscope and bright white dots which are moving from the top of my view to the bottom. it is always present but some days more than others.

when it i see it more it is sometime together with a high pitched noise for a few seconds or a weird in my head like you have a beer or 2.

I cannot remember a time in which I did not have this (now 24 years).

I would like to know why the brain produces this noise ? it is not helping me to "survive" so why does it do this ? and what parts of he brain are involved in this ?


texts: Bird identification: song two low, two high, five short

texts:
This morning I heard a bird that had a song which was two low notes, two high notes, and five quick notes in succession. Location is New England.

Is there any way, short of asking an expert, that I can find out what a bird is from a description of its song or call?

Update - Bird Song Uploaded

I have been able to host a sound clip on Vocaroo:

Unknown bird, Massachusetts, forested suburban environment


texts: Is there a way to examine amount of red/white muscle fibers without biopsy?

texts:
I want to conduct some research on red and white muscle fibers, why do some people tire during certain movements while others do not. Obviously I can't get a biopsy on the subjects so I wanted to hear if anyone here maybe had a suggestion to a reliable method to test for amount of red vs. white muscle fibers?

Maybe some strength measurements, endurance tests etc. I'm looking for something that is documented to work.


texts: While human body as a whole will find a increase in temperature by 2 C fatal, what about individual cells? If temperature of a cell or tissue is maintained at higher temperature via external mechanism , say a sophisticated heating rod, how much temperature rise it can take before dieing? Say, endothelial cells lining blood vessels. Or,any other cell.


texts:
What are the main differences between lab-grown tissues and natural tissues from living animals?

Using a biologist's classic "structure (anatomy) and function (physiology)" idea, I thought about the followings:

Structure:

It might be difficult to recreate the composition of different tissues / cells in living things precisely with artificial methods. This may lead to bad results when the tissue is used for tests of medicines and cosmetics.

Function:

Cells might not function and produce as expected (or is harder to make them function) in artificial compositions, as cells need strictly regulated environments to function correctly.

Also, I think using artificial tissues for drug tests helps researchers to avoid ethical issues which may arise if they use living animals instead. I think the cost is generally higher to make artificial tissues than to gather test animals; however I am not sure if this applies to every case - maybe some tissues are relatively cheap to grow in labs.

What are some other differences? The answer can be about the advantages and the disadvantages of making / using lab-grown tissues and using living animals as well.


texts: How does excessive acute inflammation damage tissue (eg, in sepsis or cytokine release syndrome)?

texts:
While inflammation is necessary to recruit immune cells to sites of infection in order to clear the etiological agent of disease, excessive inflammation has often been implicated in many of the poor outcomes associated with systemic infection, specifically end-stage organ failure (eg, in sepsis).

However, what is not clear to me is what the effector mechanisms of excessive inflammation are which mediate the tissue damage necessary to cause the organ damage. It's very clear to me that excessive signaling through neutrophils can, through positive feedback loops, create a large amount of systematically circulating inflammatory cytokines. But what's less clear to me is what the link is between extremely high levels of cytokines and the ultimate tissue damage associated with excessive inflammation. Presumably, it cannot be due to the direct effector functions of humoral responses or cell-based responses, as both antibodies as well as TCRs are exquisitely specific to foreign antigens. One common explanation is excessive fluid accumulation in tissue due to enhanced vascular permeability - a classic feature of the inflammatory cascade and necessary to allow leukocytes to enter the tissue space. But are there other effector mechanisms by which excessively high pro-inflammatory cytokine levels cause tissue damage?

In short then, while I understanding the pathogen --> inflammatory cytokine secretion stage, what I don't understand well is the inflammatory cytokine secretion --> ?? --> organ damage.

Sources:

https://en.wikipedia.org/wiki/Sepsis
https://en.wikipedia.org/wiki/Cytokine_release_syndrome


texts: Where can I find large datasets of protein-interaction networks?

texts:
Where do I find large datasets of protein interaction networks for cancer or alzheimer diseases?  So far, I found String but it is does not have enough proteins for my purposes. Are there such databases with more entries?
I'm still open to any proposition of the disease to choose from .
the most important part is the volume of data .
And how can I get the annotation of each protein  of the extracted network from Uniprot ?


texts: What is an apomorphy? What is a plesiomorphy? Can someone confirm these definitions?

texts:
I want to know the correct definitions for the terms apomorphy and plesiomorphy. Unfortunately, there seems to be a variety of ways to define these terms depending on the language one uses. Thus, it has been hard to determine the correct definitions. I have settled on definitions that seem correct to me and also have examples. I would like confirmation from someone if I am understanding the definitions correctly.

Apomorphy -- any character state or trait novel to a species and its descendants. An apomorphy occurs when a taxon is selected to have a particular trait. Example: within the class reptilia, the suborder serpentes (snakes) has an apomorphy because its members have no legs.
Plesiomorphy -- an evolutionary trait or character state that is homologous within a particular taxon but is not unique to members of that group and therefore cannot be used as a diagnostic character for the group. Example: within the class reptilia, legs are a plesiomorphy for its members.

My Question:

Are these definitions and examples accurate?


texts: Why protons flow back to the matrix through ATP synthase?

texts:
I am reading oxidative phosphorylation and I can't understand why the protons that are pumped out must go again into the matrix and finally produce ATP.
Suppose initially that the inside (Matrix-M) and outside of the membrane (Intermembrane space-IMS) are neutral (for sake of simplicity). The exergonicity of the redox reactions powers the proton pumping. As the pumping goes on an electrochemical gradient arises because of the concentration gradient the pumping produces and due to the electrical gradient which is produced due to the unequal distribution of protons.
After the equilibrium of the redox reaction an electrochemical gradient has established. I can't understand why the protons have to flow back into the matrix. The redox reaction equilibrium means that the ratio $\ce{H_{M}}/\ce{H_{IMS}}$ has a specific value. Do they flow back because of the electrochemical gradient? I was thinking that the flow back is coupled to the pumping, is that correct? I  mean we have the equilibrium: $$\ce{H_{M}} \rightleftharpoons \ce{H_{IMS}}$$
and by pumping we increase $\ce{H_{IMS}}$ so protons must flow back according to Le Chatelier principle. If that is the case then what is the purpose of ATP synthase? Why the protons must flow back through ATP synthase and not from any other region? Are respiratory chain and ATP synthase seperated and the only way for protons to flow back is throught ATP synthase?
I have read Biochemistry textbooks and still can't understand the importance of the so called proton motive force.


texts:
Description: About 5-6 in long

Time: March,2019 (summer)

Location: (Alutila Cave) Khagrachari, Bangladesh


texts: The meaning of the $\alpha$ helix and $\beta$ sheets in proteins

texts: I asked this question to my Biology teacher and he, in collaboration with a Chemistry teacher, couldn't find the answer. My question is the following: "What does the $\alpha$ and $\beta$ represent in the secondary structure of a protein? I do reference to the $\alpha$ helix and $\beta$ sheets in proteins." I had a similar question with the glucose and we concluded that it was related to the Chemistry, the $\alpha$ or $\beta$, was related with the functional groups bonded to the carbon.


texts: Zoology - Help identify the kind of spider

texts:
Yesterday, I bought a banana tree (Musa Basjoo) from a local supermarket.
Today, I noticed a hive of small spiders on the tree.
I do not know where they came from, so I am curious to identify these small creatures.
I am living in Flossenbürg, Bavaria, Germany.

Can someone help me identify the kind of spiders that are depicted on the photos?

A picture of the tree, it is still in front of my house door, planted in a pot:

A near shot of the spiders that are "dwelling" on the tree:


texts:
In a mitochondria, it makes ATP by using energy from NADH and FADH2 electron to pump H+ into the inter-membrane space then use the ATP synthase to bring the H+ back into the matrix while using the proton motive force to create ATP.

My question here is, why does mitochondria do this, I mean, in terms of energy I think it is a waste of energy. For example using energy to put water on the top, then generating energy by making to water come down should make some unneeded energy loss.


texts: maximum # of generations possible in a population of cannibalistic rats

texts: Assume a sufficiently large population of rats (to allow genetic variation and facilitate inbreeding) in a place with abundant water, sunlight, shelter but no food. For how many generations can this population persist solely by cannibalizing?


texts: Crispr/CAS9 genome editing is actually processed at which phase of Cell cycle?

texts:
all,

Is it only happens in certain phases, like S, G1,...or it can happen any time....or maybe, it has some perferences.

Put it in another word, does it going to processe edit if the cell is not growing ?

Thanks for any helps or comments.

Best

Bill Zhang


texts: Membrane conductance in phase 1 of the cardiac action potential

texts: Correct me if I am wrong, but in phase 1 of the cardiac action potential (for ventricle cells) there is flow of potassium ions due to the opening of transdent potassium channels. To me this would correspond to an (sudden) increase in the conductance of the membrane to the potassium ions, $g_K$, however looking at graphs on the internet  do not seem to indicate such a change in conductance. Please can someone explain why such a change does not occur (sources would be helpful).


texts: What is the darkest color human bowel movement can become?

texts: I assume a healthy human, with usual nutrition, without using any drugs or supplements.


texts:
I need help with this practice question.

I'm assuming that would a epsitatic recessive question since the parents are true breeding and then the ratio would be 9.3.4. But I am not so sure.

Any help would be greatly appreciated thanks!


texts: Triangulation number of the SARS CoV-19 virus

texts:
Is the triangulation number of the SARS CoV-19 virus capsid, in the sense of the Caspar-Klug theory, known?   In case the Caspar-Klug theory does not apply to it, is it known what is its tiling, in the sense of the viral tiling theory of Twarock (and coauthors)?
I am a mathematician, trying to learn the geometric and group-theoretic aspects of virus structures.


texts: How many rounds of TCA Cycle would a complete oxidation of a triacyl(15-Carbon fatty acid)-glycerol, give?

texts: This was a trickier question on a previous test, and I'm still not sure why, but the answer was "at least four". I answered "more than 22" and got it marked wrong. I assume that each fatty acid chain would break down into 1 propionyl CoA and 6 Acetyl CoA, but I'm not completely sure how many rounds this would give us. Can anyone help me out here? Thanks!


texts:
Why is the LD50 of botulinum toxin when injected intravenously or intramuscularly 1.3ng/kg but when inhaled it becomes 10ng/kg? Is it something to do with the absorption of the toxin in the lungs which is the explanation?
Any help would be appreciated.


texts: What properties (if any) do AT rich regions of DNA have?

texts:
I was looking up the fluorescent stain DAPI and seeing that it

binds strongly to A-T rich regions in DNA.

That made me wonder what is special about AT-rich regions.


texts:
Diseases can be classified as :endemic ,or pandemic,...etc.
 An endemic disease is an infectious disease which is generally or constantly found among people in a particular area.
Disease conditions are :

acute: rapid onset , severe symptoms and brief duration.
chronic:gradual onset and long duration

Can an endemic disease be acute? Or is it always chronic ??


texts: Alzheimer's datasets highlighting role of individual genes

texts:
A question to the folks who studies Alzheimer's disease here.
My colleagues and I have developed a new program that predicts the master regulators based on transcriptomic changes (yes, another one). We have applied it to Alzheimer's disease RNAseq datasets and we have identified several potential master regulators. We are planning on doing experiments to validate these hits; however, prior to experiments we would like to do additional computational validations of our predicted hits so that we can prioritize which ones to test first. I have been googling a lot and I found surprisingly few datasets on Alzheimer's disease that I could use for validations: specifically, I found clinical association data and GWAS hits. Any suggestions? What is your favorite Alzheimer's dataset and/or what dataset do you think is suitable for me? Ideally I would want to find something like RNAseq of cell lines with individual gene knock downs, but I don't think data like this exists for Alzheimer's.
Thank you!


texts:
This is potentially more or less a question about optics, but I've never been truly satisfied with any explanation that I've been given about Myopia. In fact, I almost can't even believe it. There are a million different versions of this diagram:

I understand that images of things could appear blurry when those things are focused in front of the retina, but then what discriminates between near and far things? Shouldn't everything be blurry? What exactly is different about this image when the thing being viewed is in close proximity to the eye?


texts:
I made some research however there seems to be a conflict with this animal's translation to my language and the original. So I couldn't find it. Do you mind helping me out ?

https://static.59saniye.com/videos/2018/04/21/20180421080742-6014_720.mp4

Some resources say pufferfish or Porcupinefish. Are these the same thing ?


texts: Can heterotrophs use anabolism to obtain energy?

texts:
With that question I mean: directly.

Please bear with me, as I don't know much about Biology or Chemistry (those are my main difficulties while studying).

I know that energy that biological beings use can be stocked in molecular bindings so that they can have it available later, when needed.

But in that process, if anabolic, it is not obtaining energy, but 'spending', stocking some energy in chemical bindings, so that it, through catabolism, can be liberated and used.

Wouldn't heterotrophs, then, obtain energy exclusively through catabolism?


texts: Is it okay to scale the RNA-Seq counts after log-transformation?

texts: On an RNA-Seq dataset, I want to apply a clustering algorithm which requires zero-mean uni-variance gene expression levels. I am wondering whether it makes sense to use "scale" function in R after taking logarithm of the counts. For microarray data, I was actually using the scale function which (as far as I know) makes sense; but this is the first time I am using RNA-Seq. I heard about "voom" normalization (in "limma" library on CRAN), but I don't really want to use that since I am not really familiar with the details.


texts:
Is there a type of blood cell that can reach all other body cells? By "reach", I mean to "touch" the surface of the target cell.

If we look at the red blood cell for example, that moves in blood vessels, there are cells close by - after the wall of blood vessel - that get oxygen by diffusion and not by direct contact, as far as I know.


texts: How is Hypertonic Urine Produced in a Mammalian Kidney?

texts:
I know that the ascending loop of Henle is impermeable to water and ions, and, by end of the ascending limb, the osmolarity of the tubular fluid is very low due to the active transport of ions out (e.g, sodium, potassium, chloride).

However, what if the person had to produce hypertonic urine due to dehydration or some other circumstance? Would the increase in osmolarity be done through a decrease in removal of ions in the descending limb, or has the distal tubule and collecting ducts got something to do with it?


texts: Is this silverfish? My apartment very dry

texts:
Can anyone please confirm whether insect below is a silverfish?  It looks a bit like the picture at our federal government pest control page.  It also moves with a wiggling motion, as described  at the Wikipedia Silverfish page.

I sprayed it with alcohol, and it seems to be dead.  I've seen this type of insect about once per month.  I don't know why they gravitate to my apartment, as the dehumidifier it set to maximum (35% relative humidity).

Sorry for the quality of the photo, but my iPhone SE does not have adjustable focus that I'm aware of. I can only tell the phone where the feature of interest lies within the picture.


texts:
As per few references, fastest G protein coupled reaction known is Drosophila melanogaster phototransduction which produces quantum bumps with average latency of 45 ms (and peak response around 200 ms). Another reaction is chemotaxis which is also in that order. I was wondering are there any known examples which are as fast as these responses?

P.S: Many ion channels are GPCR which triggers very fast but most of them takes long time (in order of seconds) to give peak ion concentration

P.S.S: By fastest I mean, minimum time required to give peak response after activation of receptor(s).

Update:

In abstract case, Let's say you got signal from outside at time t = 0. Now this will leads to reaction cascade which will take time 't1'. Assume output of this is opening of channel which will increase concentration of ion X. Now X will reach it's peak concentration at time t = t1 + t2. So I am looking for such reaction cascades with minimum time 't' (t1+t2).


texts: Why isn't there a standard unit of promoter strength?

texts:
Sometimes in synthetic biology, we need to know rates of transcription of one promoter in relation to others (particularly inducible vs constitutive) in order to perform tasks like balancing transcription products and ensuring an excess of one product over another. As far as I know, there is no standard method of characterizing promoter strengths in relation to one another. However, a logical unit for transcription rate made (by organism or in vitro) could look something like:

Promoter Strength = number of transcript made / (concentration of RNA polymerase) (length of transcript) (unit of time).

Why hasn't this been done yet? What other factors could contribute to rate of expression in a particular organism? Is there another system for comparing promoter strengths?

Note: a similar system could be used for strength of repression.


texts: Wouldn't a non-poisonous variety of a mutant plant be at selective advantage?

texts:
I don't know much of evolutionary biology, but when someone asked, this seemed very much plausible to me.

Say there's a mutant plant, that produces much lesser toxin than its usual counterparts (same species). Then, wouldn't this plant be at a selective advantage over the others, since the predators (here, herbivores) wouldn't consume it assuming it to be poisonous. But sowly, as these mutants increase in number, the herbivores too realize and start feasting on them. Again selecting out ones with more toxin. Ultimately reaching some kind of equilibrium (?)

Is this phenomenon(?) called something? Is it similar to the selection that occurs in the  sickle cell trait? Are there real examples with plants with toxins showing this?


texts: Is there a standard way of measuring culture nutrient levels in real time?

texts:
I am working on optimizing growth rates for a culture, and one thing I'm trying to monitor is nutrient consumption rates to pinpoint any bottlenecks, i.e. the culture goes through all the calcium in a few hours and then stops growing.

Short of manually taking samples every few minutes and running individual tests for wide arrays of nutrients (minerals, amino acids, nitrogen compounds, etc.), is there a standard way of monitoring nutrient levels automatically in real-time? This is a personal research project, so unfortunately I don't have access to industrial bioreactors and the like.


texts: Can a species populated solely by males be saved from extinction?

texts: How, if possible, can a species be saved from extinction if the only surviving population are males that cannot reproduce with each other?


texts: Do any non-human species have packed abs?

texts: The classic "six-pack abs" in humans is due to tendons stretched across the abdominal muscles and low body fat. Do any other animals have a similar arrangement of tendons that could result in visible "n-pack abs" for a sufficiently low body fat individual?


texts: use of antibiotics in selection of good plasmids

texts: I have not understood the role of antibiotic medium in filtering the bacteria containing the recombinant plasmids with the ones having normal plasmids. Since all the plasmids of a certain bacterial species have a antibiotic resistance gene regardless if its recombinant or not , shouldnt there be no effect of the antibiotic on the colony?


texts: In plasmid-based transient transfection of mesenchymal stem cells, do I have to select for transfected cells and verify GOI expression via a reporter?

texts:
I am transiently transfecting mesenchymal stem cells with a mammalian plasmid-based expression vector that does not contain any mammalian selection marker and also the gene of interest will be cloned into the plasmid without co-expression of any reporter fusion gene.
I would like to know if selection or expression testing is good practice and mainstream in plasmid-based transient transfection of mammalian cells.
As you know, in bacterial transformation selection against non-transformed bacterial cells is mandatory so that transformed bacterial cells could be enriched for. I wonder whether this is also mandatory in plasmid-based transient transfection of mammalian cells. If not, then  would not non-transfected cells outgrow transfected ones and affect downstream cell-based functional assays? Also, do I have to measure transfection efficiency beforehand? Also, how long can a mammalian cell retain a plasmid without a mammalian selection marker? Thank you.


texts: What does "Origin" mean in NCBI GenBank?

texts:
I'm having trouble determining what exactly is meant by the term "Origin" in this case. It is just before a 70 bp sequence that the page claims is a plasmid, but does not specify it to be what I assume is incomplete, seeing as I don't think there is such a thing as a 70 bp plasmid (correct me if I'm wrong). So do they mean the origin of replication to the plasmid?

Here is the page in question: https://www.ncbi.nlm.nih.gov/nuccore/M30888.1?report=genbank


texts: I was learning about brain waves, i.e. gamma, alpha, beta, etc., and was wondering what would happen if you mixed them together - e.g. I listened to Gamma waves and Delta waves at the same time. Would I get some sort of brain damage or is the brain able to handle that?


texts: Sucrose inhibit onion root mitosis? Why?

texts:
I am doing an experiment about onion root growing.

I had put an onion in different solutions of $C_{11} H_{22} O_1$ in H2O —with the root touching the water—: 0,1M; 0,2M; 0,3M; 0,4M; 0,5M.

The measurements tell me that the presence of $C_{11} H_{22} O_1$ in the solution inhibites the growing of the root.

Why happen this? The Sucrose affects root's mitosis? How?

Thank you!


texts: Could a sperm be altered to contain a female's genetics?

texts:
While discussing with a friend a while back on the likelihood a futanari (a woman with both fully developed and functioning sets of genitalia) existing in real life, we got into a discussion of whether a child could carry the genetics over from 2 months.

Currently (to my knowledge), for a female same-sex couple to conceive a child and for both women to be involved, one would donate an egg, the other actually gives birth, and the sperm is donated by a third party. However, this means that the child will carry over the genetics of one women in the couple and the unknown male.

I am wondering if there is a way for sperm to contain the genetic information so that way both women in a same-sex relationship could be genetically related to the child.


texts:
From wikipedia:
Biomagnetism is the phenomenon of magnetic fields produced by living organisms.

The present scientific definition took form in the 1970s, when an increasing number of researchers began to measure the magnetic fields produced by the human body. The first valid measurement was actually made in 1963,[1] but the field began to expand only after a low-noise technique was developed in 1970.[2] Today the community of biomagnetic researchers does not have a formal organization, but international conferences are held every two years, with about 600 attendees. Most conference activity centers around the MEG (magnetoencephalogram), the measurement of the magnetic field of the brain.

Do viruses produce such a field?


texts: This white/yellowish bugs are crawling over my walls under cracks and below my wardrobe. I am not sure if they are bed bugs or some other bugs, there are very small in size thus I zoomed very much on the photograph, I hope someone would be able to assist me on identifying the bug.!


texts: Intuitive explanation for Kin- and Group- selection

texts:
It is known from theoretician in the field of kin selection that kin selection (inclusive fitness theory) and group selection are actually two sides of the same coin. In other words, these two concepts are actually only one single process.

Questions

Is group selection equivalent to kin selection for any evolutionary game or exclusively for the prisoner's dilemna?
Can you please provide an intuitive explanation of why kin- and group-selection are the same thing?


texts:
I am not a biologist, but I am fascinated by evolution.

I was watching the news this morning and, as so often is the case, there was a news story about a corrupt politician who was accepting bribes.

This started me thinking about how greed can become such a strong factor in one's life that it cancels out empathy for your fellow human beings.

So I was wondering--is greed an evolved trait?  Maybe some result of an evolutionary pressure to hoard food for example?


texts: What are the units of Phylogenetic Independent Contrasts (PICs)

texts: PICs are a popular phylogenetic comparative method and I was wondering what units the actual contrasts are in. I want to say they are unitless but I am not entirely sure.


texts: What is the mass of carbon dioxide absorbed by an oak tree in one year?

texts: I want to understand the environmental impact of oak trees due to absorption carbon dioxide. So my question is, what is the mass of carbon dioxide absorbed by an oak tree in one year?


texts: Is it true that pigeons became less afraid of humans in recent years?

texts:
My grandfather had told me when I was a kid that at his time the pigeons would not approach humans closer than about 15 meters. At the time he said it the pigeons were approaching us not closer than approximately 1.5-2 meters. And now I often have to make efforts so not to step on a pigeon who hinders my movement along a street.

This is in Europe.


texts: Is territoriality only the domain of the male of a species?

texts:
Is territoriality (recognizing a geographic location, and challenging another member of the same species and gender) only in the domain of the male of a species? Are there any species out there where the female of the species identifies, defines, and protects her territory? What about any species where territoriality is gender neutral (tic humans excluded!)?

I thought of bees, but that is a community affair - even if it is a matriarchial society.


texts:
In non linear model of a neuron there was a mention about bias (Bₖ) which was the summation of the synaptic weights.

I want to understand what synaptic bias is and their application/use in neuronal modelling.


texts: What nutrients are best suited for growing E.Coli

texts: I am looking to grow E.Coli (In a nutrient agar dish) to be used in an E.Coli lawn and was wondering what specific nutrients should be used to ensure the E.Coli grows optimally? Any answers or links to relative resources are greatly appreciated!


texts: How to get taxonomic specific ids for kingdom, phylum, class, order, family, genus and species from taxid?

texts:
I have a list of taxids that looks like this:

1204725
2162
1300163
420247

I am looking to get a file with taxonomic ids in order from the taxids above:

kingdom_id      phylum_id       class_id        order_id        family_id       genus_id        species_id

I am using the package "ete3". I use the tool ete-ncbiquery that tells you the lineage from the ids above. (I run it from my linux laptop with the command below)

ete3 ncbiquery --search 1204725 2162 13000163 420247 --info

The result looks like this:

# Taxid Sci.Name    Rank    Named Lineage   Taxid Lineage
2162    Methanobacterium formicicum species root,cellular organisms,Archaea,Euryarchaeota,Methanobacteria,Methanobacteriales,Methanobacteriaceae,Methanobacterium,Methanobacterium formicicum   1,131567,2157,28890,183925,2158,2159,2160,2162
1204725 Methanobacterium formicicum DSM 3637    no rank root,cellular organisms,Archaea,Euryarchaeota,Methanobacteria,Methanobacteriales,Methanobacteriaceae,Methanobacterium,Methanobacterium formicicum,Methanobacterium formicicum DSM 3637  1,131567,2157,28890,183925,2158,2159,2160,2162,1204725
420247  Methanobrevibacter smithii ATCC 35061   no rank root,cellular organisms,Archaea,Euryarchaeota,Methanobacteria,Methanobacteriales,Methanobacteriaceae,Methanobrevibacter,Methanobrevibacter smithii,Methanobrevibacter smithii ATCC 350611,131567,2157,28890,183925,2158,2159,2172,2173,420247

I have no idea which items (IDS) correspond to what I am looking for (if any)


texts:
I 've an essay about wheat sprout extract, there's a graph about protein content in first 4 day of wheat sprout. so under the graph there's this text

  Phosporylation by endogenous kinases of the macromolecules contained
  in 1 g of the aqueous wheat sprouts extract. Results are expressed as
  cpm/mg of protein±SEM at 4 different days of germination. 0 are
  unsprouted seeds

so my problem is to know how many mg (milligrams?) is content for 1 g of protein
in few words I need how many mg of protein is content in 1g of products, a conversion from cpm/mg to mg ... is possible?

cpm = counts per minute


texts: Correlation between menstrual period and lunar revolution

texts: Is it just a coincidence that the the length of the entire menstrual cycle from one flow to the other lasts almost exactly as one lunar month?


texts: Why is FAD, rather than NAD+, reduced in the succinate dehydrogenase reaction of the Tricarboxylic Acid Cycle?

texts: FADH2 is produced in the conversion of Succinate to Fumarate in the tricarboxylic acid cycle. Why is this so? Why not NADH?


texts: With the oil form of THC being stronger then ever. What would happen if one was to take a stomach full of THC oil?


texts: Resources for the study of the environment of Laramidia in the Late Cretaceous

texts:
I'm looking for resources (book, web, article, etc.) to learn in detail about the environment of Laramidia in the late Cretaceous, including flora, fauna, landscape, and climate. My goal is to get a picture of what it would be like to step out of a time machine into the North American West during the Maastrichian not long before the mass extinction event that ended the dinosaurs, and hopefully get an idea of how that environment varied by region. So far I've only been able to turn up a few brief articles, and some dense scientific reports (which I read the relevant parts of, but as a layman working without the benefit and context of professional knowledge have been of limited use).

I'm aware this question has some crossover with Earth sciences. But as it might fit pretty well on either site, and I've seen you folks answer more paleontology questions, I'd be grateful if you'd entertain it here.

How can I effectively research the environment of Late Cretaceous Laramidia? (Information directly about Laramidia is also very welcome, if secondary.)


texts: What kind of bug is this? I found it on my Cleome plant in Atlanta Georgia

texts: This bug was on my cleome plant in Atlanta Georgia


texts: Is the genetic term "polycistronic" still used in modern biology?

texts: Is the term "cistronic", meaning an ORF on a mRNA, still commonly used in modern genetics? I´ve seen "polycistronic" being applied to prokaryotic mRNA in old textbooks, but I´ve rarely stumbled upon this in recent papers, except for research focusing on plasmid engineering.


texts:
My wife noticed this on her trousers immediately after coming home - probably acquired after brushing past a bush. It's about one inch long, and does not move much - but when poked it will flex and appear to try to roll.

It looks for all the world like a stick - but I've googled "stick insect", and this doesn't seem to have enough (or the right kind of) legs.

We live in England, in a suburban setting. We both work in offices and don't have a lot of contact with nature.

Could it be a thorn moth larva?

Apologies for the quality of the photo; I can try to take a better one if it would help to get another angle.


texts: What advantage does an enzyme serve over catalysis by the addition of heat energy?

texts: I understand that an enzyme lowers the activation energy, allowing the reaction to run faster, however I am not sure, how it may be favorable during the addition of heat energy. Wouldn't that lower the activity of the enzyme since the enzyme is sensitive to heat?


texts: Can sugar be absorbed orally within seconds?

texts:
Whenever I feel a little light headed or tired, it helps to eat something sweet.
Specifically, simply chewing or sucking on a sweet seems to aleviate the symptoms within a matter of seconds and then the sugar seems to kick in. So I was wondering whether it is just a psychological effect, or whether sugars are absorbed in our mouth and reach the brain (or wherever the sugars exert their effects?) within seconds. Or is perhaps the taste of sugar sufficient to signal the body that it can safely release some extra energy as resupply is imminent?


texts:
We all know that bats hang upside down to sleep. I was watching some sleep for a while, and they don't move much while asleep.

If I fall asleep sitting in a chair my lower legs will swell. Lymph fluids in people are mostly moved by muscles in the limbs of the body.

It would seem like a sleeping bats lymph fluids would gather at or near the head, chest and lungs.

How do bats manage lymph fluids?


texts: How does blood reach skin cells and other closely packed cells?

texts:
When I see diagrams of cellular structures such as the layers of the skin, these diagrams show the cells as being closely packed together. For example here is a typical such diagram:

So, it shows the capillaries of the vascular system going only to the bottom of the many layers of tightly packed cells. So, I assume that all the cells need oxygen, so they all need to be in contact with the blood cells that bear oxygen, so how does this happen? Obviously each individual cell can't have its own personal capillary. If blood were to be released just loosely around the cells that would not work either because the blood would have no way to get back. All the blood has to be in vessels of some kind so it can circulate. But these vessels are not shown as reaching the upper skin cells in any way, so how are those cells getting oxygen?


texts: How is nicotinic acetylcholine receptor recognized as self-antigen during lymphocyte maturation?

texts: Lymphocytes (B-cells in the bone marrow and T-cells in the thymus) undergo apoptosis if their receptors (produced by recombination of immunoglobulin gene fragments) recognize self-antigens during the maturation period. In myasthenia gravis, the body produces antibodies that bind to antigen on the nicotinic acetylcholine receptor. During maturation, do these antigen on this receptor have to be expressed in the bone marrow and thymus, or, how does the body learn that it is a self-antigen?


texts: What do we know about "continence" in animals?

texts:
What do we know about continence in animals? In particular, what do we know about the development of continence in animals?

By "continence", I'm referring specifically to whether or not a wild animal, free from human influences, appears to exhibit discrimination in when and where it relieves itself, and to what extent. For example, rats are allegedly incontinent, at least by this definition. (The article would seem to imply they are physically unable to control themselves, but other sources state that rodents can learn continence, which would imply that they normally just don't bother, which is what I want to know about.) Conversely, cats can be quite fastidious, and kittens are reportedly "unable" to void themselves without their mother's assistance. In fiction, we have an example of a species which is said to uncontrollably void when they eat.

Based on what we know from studying real animals, is it plausible that an animal would be unable to control its voiding out of a habit of not trying to do so (I'm ignoring physical problems, here), or is the cited source, if you'll excuse the highly apropos expression, full of sh--? If it is plausible, what types of animals, generally speaking, would exhibit this, and to what extent? Also, how does this change from birth to maturity?

Ultimately, what I am looking for is a set of guidelines that would allow me to predict an animal's voiding habits and the extent to which the animal is able to control the same given the animal's age/maturity and other general information (e.g. dietary tendencies). I am not worried about outliers, unless the answer is that it is not possible to make a prediction with any reasonably accuracy, in which case I would still like to know what range of variation I might expect.

Edit: I'm increasingly suspect of the cited source on rats. If that's bunk, I would still like to know; are there any examples of animals (perhaps excluding humans, because that can turn into quite the argument) who, at any life stage, do not exhibit continence and/or exhibit feline-like "hyper-continence" (i.e. inability, or at least instinctive disinclination, to void on their own) absent physiological abnormalities? (Alternatively, am I also wrong about cats?)


texts:
I first thought that action potentials of His-bundle i.e. Purkinje fibers are Cardiac.
However, I started to think that this is not enough.
I think now that they are neuronal and cardiac.
My conjecture. They have first short-acting neuronal part and then long-acting cardiac part.

Are Purkinje Action Potentials Neuronal and Cardiac?


texts: What's the difference between physical (direct) and functional (indirect) protein interaction?

texts:
I read that the Protein-Protein interactions one can consider are generally of two types, namely physical and functional, but I cannot get the difference between the two.

I was just thinking that if two proteins are linked in a Protein-Protein interaction network like the ones stored in STRING database, then they are experimentally observed or somehow predicted to physically interact through binding sites to explicitly perform a function, e.g. signal transduction. But as I am reading different sources making the separation between the two kinds of interactions I got a little bit puzzled.

Can you please help me?


texts: What's the purpose of segregating a virus from the blood and growing it in the lab?

texts: I heard that the scientist in Australia found a way to segregate the 2019 NovCoronovirus from the blood. Does this mean they are one step closer to the cure? Why is virus segregation crucial in finding a cure for a viral infection?


texts: Can a single axon propagate multiple simultaneous action potentials?

texts:
I have not been able to locate any research that indicates whether a single axon of a neuron or nerve cell can conduct multiple simultaneous (i.e. spatially separate) action potentials. I am aware that in many neurons refractory periods would preclude this possibility, however in some cases delays along axons are large enough.

Is this the case? Can you point me to any citations supporting your answer?


texts: How do liver and lung metastases cause death?

texts:
Metastasis to the liver and lungs are the main causes of death in colorectal cancer.(1)
I understand that colorectal cancer may have metastases. But how do these metastases cause death?

Reference

(1) A. Bolocan, D. Ion, D.N. Ciocan, D.N Paduraru. Chirurgia (2012) 107:555-563. Introduction.


texts:
According to genome.gov, All the cells in a person's body have the same DNA.

I understand that the main reason parents and children have different genomes is because of random mixing of 2 genomes, but that there are also very small differences caused by random mutations.

If all of a person's cells have identical genomes, then does that mean that random mutations only occur in gametes?

I also understand that if sunlight hits my arm, it can cause random mutations.

So do all cells in a person's body really have the same DNA?


texts: phosphorylation of Glyceraldehyde 3-phosphate

texts:
This question is related to something that happens when 3-phosphoglyceraldehyde is converted to 1,3-bisphosphoglycerate during glycolysis.

As I understand it, 3-phosphoglyceraldehyde is deprotonated by NAD+ and phosphorylated by a Pi group, which results in NADH + H. The extra H apparently comes from the Pi group (which I believe is called orthophosphate [1]).

Now, where does the Pi come from? is it just sitting in the cytosol?, does all Pi have a hydrogen? can someone clarify what an orthophosphate is, I never heard of that term.


texts: What do the negative and positive signs mean in the rotation angles of DNA helices?

texts: Does it mean clockwise and anticlockwise?


texts: How does heart beat faster while doing a strenuous task?

texts:
I know that when we do tasks which require extra physical effort (like running etc.), our heart beats faster.

I also know that the reason behind this is that these jobs require more energy than usual and, hence, require more oxygen for breaking down food. And, since, oxygen is transported throughout body by blood (by forming compound with Haemoglobin (present in RBCs), called Oxyhaemoglobin), the heart needs to beat faster to pump more blood.

However, I am not aware of how does the heart automatically start beating faster.

Is there any involvement of the Nervous System?
Does the heart have some sort of special mechanism that activates when the body performs a strenuous job?


texts: How are Thyroid Stimulating Ab destroying thyroid tissues?

texts:
I was reading about Graves' disease, which is an autoimmune disorder. I read a few books, including Endocrinology by Hadley and Levine, and websites where they mentioned that the antibody named TSAb (Thyroid stimulating Antibody) binds to TSH receptors and stimulates synthesis and release of thyroid hormones from thyroid gland. This results in the symptoms of Exopthalmic goiter or Graves' disease.

My question is how are these antibodies actually attacking the healthy tissues (which I presume is the tissue of thyroid gland)?

I've so far found no website explaining this part of the autoimmune disorder. I'd appreciate any information or references in this regard.


texts: What would EEG recordings reveal if their resolution was better?

texts:
1. Temporal resolution

Of course, we would see higher frequencies. But would these be informative? Aren't the frequencies measured today near the border to noise?

2. Spatial resolution

I guess LFP measurement goes in this direction (closer to the sources of the signals being measured). But what would we learn by that? Finding small-scale regions (below Brodman area size) which behave phase-locked/synchronously?

3. fMRI

The same questions could be asked with respect to fMRI. But I guess, as long as temporal resolution is as poor as it is today (and which cannot be much better), we don't have to ask for spatial resolution, or do we?


texts: Why would worker bias sex-ratio toward workers?

texts:
This question prompts for explanation on a topic, an interpretation of this topic is given. A simplified question statement is also given at the end for those who do not wish to read.

Topic
In the Self Gene by Richard Dawkins, it was suggested that genes are the fundamental units of evolution.

In one of the chapters of this book, animals such as the ants are discussed. These animals are specified to have the following properties:

They live in colonies consisting of sterile workers and reproductive queens.
Worker ants possess half of the genes from its queen and half its genes from the king, which is not living in the colony because it died after fertilizing the queen.
The queen produces male "drones"--potential kings for future colonies. Drones are genetically identical to the queen.

The following interaction is suggested: worker ants, being less related to the drones than they are to each other, will manipulate the colony to increase the number of workers and reduce the number of drones present. They may do this by eating some drones before they hatch.

The reason why the workers do this is explained and interpreted as such:
The workers wish to produce more individuals that are more closely related to themselves; other workers are more closely related to a worker than a drone is to that worker; therefore, the worker prefers another worker over a drone.

Question
The Selfish Gene suggest that genes are the fundamental units of evolution, therefore a successful gene must be able to displace its alleles by being better at propagating itself.

Suppose gene-A incentivizes workers' drone-eating behavior, this gene in the short term and within one colony can produce a larger number of its own copy, but all of these copies are inside sterile workers, none of which can propagate gene-A.

When the colony containing gene-A spawns drones and potential queens, there are two cases to consider:

Gene-A is present in drones: If this is true, then by incentivizing the occasional drone-killing by the workers, gene-A has reduced the number of gene-A carrying drones, this is deleterious to gene-A. When workers of the new colony is born, gene-A reduces the number of possibly non-gene-A-carrier drones and decreases the fertility of the new colony in general.
Gene-A is present in female offspring: gene-A decreases the fertility of new queen, making her produce less gene-A carrying drones, this is again deleterious.

So far, gene-A has proven to be often deleterious to itself by restricting the number of reproductive individuals that may carry it. In terms of competition, gene-A may harm its alleles when the queen carries the allele and the king carries gene-A, but this will stop being beneficial when the number of gene-A and the number of its Alleles reach a 1:1 ratio, since after that point, the probability of harm is equal for both.

So, why is the drone-killing behavior still exhibited in animals such as ants?

Simplified question
Worker ants sometimes kill male ants in its colony because they are less related to the worker ants than the latter is to each other. Since worker ants can't reproduce, why do they bother about the number of close relatives who also cannot reproduce?


texts: Biochemistry of production of a yogurt counterpart from coconut milk

texts:
About yogurt:
The biochemistry of changing animal milk to yogurt is well known.
Recapitulating:
After some preperatory steps the milk is inoculated with bacteria that consume lactose, producing lactic acid.
(Quoting from wikipedia: "Lactobacillus delbrueckii subsp. bulgaricus is commonly used alongside Streptococcus thermophilus as a starter for making yogurt.")
Additionally recapitulating:
Once the milk has been turned into yogurt there are no additional preservative steps, which means the bacteria that made the yogurt are still present in the finished yogurt. That is: to make more yogurt you prepare milk and then add some plain yogurt as a starter.

Specific to my question:
Nowadays various milk alternatives are produced in quantity, such as soy bean milk, almond milk, oat meal milk, and so on.
In the wake of that development there is production of the counterparts of derivatives of milk, specifically: yogurts.
I'm curious: what kind of bacteria are used to make a yogurt counterpart of say, coconut milk?
Then again, maybe (I could not find information about that) production of coconut yogurt doesn't involve a bacteria culture at all. It could be that in the production of a yogurt counterpart out of coconut milk a thickening agent is added (such as modified starch), and that, say, a bit of citric acid is added to acidify. All for the purpose of emulating the texture and taste of animal milk yogurt.
But then: in my attempts to find information I read claims that for making home-made dairy-free yogurt you can actually use the same starter as is used for animal milk yogurt. That suggests that the bacteria in yogurt starter culture are actually pretty omnivorous; not dependent on presence of lactose for their metabolism.

The question:
how analogous is production of coconut milk yogurt to production of animal milk yogurt? Or any other counterpart yogurt for that matter.
Is it with Lactobacillus delbrueckii alongside Streptococcus thermophilus, or is it adding a thickening agent and a bit of acification?

(I understand of course why manufacturers of yogurt alternatives do not write on the packaging how their yogurt alternative is made: the majority of prospective buyers wouldn't understand it, and they may even be spooked.)


texts: What do lower case nucleotides mean in this gene sequence?

texts:
The following table (image linked below) shows promoter sequences recognized by different sigma factors. The sequence given for, e.g. sigma B is "GTTTaa"; why are the "a"s lowercase?

(from "A sigma factor toolbox for orthogonal gene expression in Escherichia coli", Bervoets et. al. 2018)


texts: Why do spiders make their web near the ceiling and near a light source?

texts:
Why do spiders make their webs near the ceiling and near light sources ?
Is their an advantage for spiders in doing that? For example do they catch more insects when their web is near a light source because prey insects are drawn to it, hence giving those spiders with a well-lit web a better chance of survival?


texts: Why are worms, centipedes and snakes long?

texts: Some animals have mostly distinct, non-repeating body parts, each performing a particular function. However, some kinds of animals, such as worms, centipedes and snakes, have a long body that appears to be longitudinally uniform in most of its length. What is the evolutionary sense to that? For instance, what advantage does having a hundred of limbs convey to a centipede, while a spider is happy with a tenfold less?


texts: Small yellow bug with black head and three black stripes on the back

texts: Can anyone help me to find the name of this small yellow bug with black head and three black stripes on the back. It was found in Jura, France:


texts: How to measure the biomass of hydroponic plants in netpot/rockwool DWC system?

texts:
I'm doing an experiment with 4 kale plants, each in their own small deep water culture (DWC) system. Each plant was transplanted in rockwool with netpots and clay pebbles. But I need to periodically and accurately measure the biomass of each plant. The roots have grown through the rockwool and netpots and I don't want to rip out the roots.

Is there an easy way to do this?


texts: Making sense out of the visual representation of transcription

texts:
Most people are familiar with the following diagram. Some genomic DNA with a promoter region, exons and introns. This is transcribed into RNA that is then translated into a polypeptide.

When we look closer at the strand that is being transcribed we can distinguish between the two as the sense and anti-sense strands.

So the transcription factors and RNA polymerase bind and begins transcribing mRNA in the 5' to 3' direction and thus reading the anti-sense strand in the 3' to 5' direction and have the same sequence as the sense DNA strand, substituting U for T in the mRNA.

My question would be, shouldn't the exons be numbered in the reverse order as shown in the first picture I provided. So instead of Promoter -> Exon1 -> Intron -> Exon 2, should it be, Promoter -> Exon N -> Intron -> Exon N-1?

Also, in bioinformatic sites are the gene sequences listed in the sense or anti-sense strand? I have noticed in some bioinformatic tools, to determine what polypeptide will result from a DNA sequence, one must input the sense strand in 5'to 3' orientation and not the anti-sense strand.


texts:
A small green lizard (20 cm in size). It was found in the direct neighboorhood of a house, in a small village in the Hungarian hills south of the Balaton lake. It was found in the middle of the day.

Our first guess would be Lacerta viridis. Is this correct?


texts: Confluency or confluence, which term is correct to describe the % area covered by cells?

texts: I noticed that both of them are used in many scientific papers. Are these two terms, or can they be used interchangeably?


texts: Why are some bodily fluids more of an infection risk than others?

texts:
Whilst on a recent refresher course it was highlighted that when considering risk of exposure to infection from bodily fluids we should be aware of two distinct risk levels:

High Risk:

Blood
Semen
Vaginal Secretions
Diarrhea

Low Risk:

Saliva
Vomit
Urine
CSF (Cerebrospinal fluid)

Why is it that some bodily fluids are a greater infection risk than others?  Is it related to the fluids themselves or the species of pathogen that are located within them?


texts: Is this formula describing the loss of unfixed genes from a population accurate?

texts:
In the 1954 science fiction novel Search the Sky by Frederick Pohl and Cyril M. Kornbluth, a formula is featured that "quantitatively describes the loss of unfixed genes from a population".

$$L_T=L_0 e^{-T/2N}$$

  "A final word. There has been much loose talk among the troops about the slogan of the Joneses, which goes $L_T=L_0 e^{-T/2N}$. Some uninformed people actually believe it is an invocation which gives the Joneses supernatural power and invulnerability. It is not. It is merely an ancient and well-known formula in genetics which quantitatively describes the loss of unfixed genes from a population. By mouthing this formula, the Joneses are simply expressing in a compact way their ruthless determination that all genes except theirs shall disappear from the planet and the Joneses alone survive. In the formula $L_T$ means the number of genes after the lapse of $T$ years, $L_0$ means the original number of genes, $e$ means the base of the natural system of logarithms and $N$ means number of generations."

Is this formula indeed an accurate description?

Or was it made up by the authors? I find it suspicious that it contains two different measures of time, years and number of generations, while they seem related to me.

An earlier version of this question omitted the minus sign in the equation. I noticed it when finding it again on Google Books.


texts: Where are the statistics for vaccine side effects?

texts:
My son told me that that during a discussion at school someone mentioned statistics about side effects of vaccines (I assume that the discussion was about standard vaccines in France). The numbers were completely off (1/100 "illness", 1/100 "death" - again, these numbers do not make sense).

I wanted to provide him facts to rationalize (quantify) the discussion but it is now an hour I am searching on French, Canadian and US official sites (as well as WHO) and I cannot find any statistics on side effects (from mild to mortal).

I understand that "side effects" and "vaccines" are general concepts but I want to start with anything to just show the error. Let's say that "side effect" is anything from "reasonably impacting" (so not an arm which hurts for 48 hours) to death, and "vaccines" is anything from the typical set a child will get.

Is there a place where such statistics are available?

Please note that I am not talking here about "vaccines cause autism" (there is plenty of information about that) or "vaccines are not useful" (plenty of comparative studies as well). I also understand that vaccination is a pro-vs-cons decision, I have a hard time finding the "cons" in the form of numbers.


texts: Is there a formula for determining the % of ligand bound to a given receptor in a mixture with multiple ligands and receptors?

texts:
When a ligand and receptor interact with a given kd, one can easily determine % of ligand bound to the receptor when the kd, total concentration of ligand, and total concentration of receptor are known. When there is a mixture of multiple ligands and receptors where each ligand and each receptor can interact with eachother, this is not so simple. For example, lets say you have the following set of information:

$$K_{11} = \frac{[R_1][L_1]}{[R_1L_1]}$$

$$K_{12} = \frac{[R_1][L_2]}{[R_1L_2]}$$

$$K_{21} = \frac{[R_2][L_1]}{[R_2L_1]}$$

$$K_{22} = \frac{[R_2][L_2]}{[R_2L_2]}$$

along with the $K_d$'s ($K_{ij}$) and the total concentrations of $R_1$, $R_2$, $L_1$, and $L_2$. I have not managed to find any publications where this has been demonstrated but I would be surprised if it hasn't been figured out by someone.


texts: Understanding a Chromosomal formula in a karytope analysis

texts:
I am reading a medical reporting results of a karyotype analysis. On it it is written:

Chromosomal formula
46,XX,del(7)(q11q36)[12]/46,XX[13]

I understand that 46 is the number of chromosomes, XX refers to the pair of sexual chromosomes, del(7)(q11q36) means a deletion on the long arm of chromosome 7 spanning the bands 11 to 36.
What do [12] and [13] mean?


texts: Does the Michaelis-Menten equation take in account the non-enzyme formation of products?

texts:
I only recently learned about the Michaelis-Menten equation, since I am not studying biology or anything related. Let's write the equation as
$$\frac{d[P]}{dt} = V_{max} \cdot \frac{[S]}{K + [S]}$$
If I'm not mistaken, this equation describes the rate at which products are formed ($\frac{d[P]}{dt}$) as a function of substrate concentration $[S]$ in steady-state. In a translation of Michaelis' paper I read that $V_{max}$ can be written as $k [E]$, where $k$ is a constant and $[E]$ is the total enzyme concentration.

Mathematically one would say that when the total enzyme concentration is zero ($[E] = 0$), the rate at which the product is formed should equal zero. If I recall correctly, in several reactions products are formed without enzymes (Enzymes only enhance the reaction rate?). Is the Michaelis-Menten equation specifically used for situations where $[E]>0$? If so, how does it account for very low enzyme concentrations where product formation from non-enzyme reactions cannot be neglected?


texts: Why do we encode information in DNA in binary and not in base 4?

texts:
I recently read an article about Harvard scientists encoding 700Tb of data in DNA strands. But they encoded the information in base 2, so T and G was a 1 and C and A was a 0. But why binary? Why didn't they just use base 4? It would be much more efficient!

EDIT: here the link


texts: Dry Bulb Temperature VS Dew Point, which one is most relevant to insects?

texts: I study insects that are leaving freely on my campus. The campus weather station has two different measures of temperature, the Dry Bulb Temperature and the Dew Point Temperature. Which one is the most relevant when studying insects? Are they very different? In other words, can you state the main differences between the two that are relevant when studying insect biology.


texts: Where do I find the CO2 clearance rate for various plants?

texts:
I'm trying to get enough plants to bring my office from ~1k ppm of CO2 to ~300ppm of CO2. (If I can't get below the ambient 450ppm, that's fine too.) It'd be nice to know before I start buying plants if I can expect to reach that target without, say, having to turn a conference room into a greenhouse.

But I can't easily find a table that lists the rate at which various kinds of plants remove CO2 from the local atmosphere. I'm aware of the NASA Clean Air Study, which looked like it was mostly focused on other pollutants, and Kamal Meattle's conclusion that it takes 4 Areca Palms per person. But I want to know where that number of Areca Palms came from. Or, more importantly, be able to calculate it for other plant varieties. (He might have been optimizing for something different than I would want to.)

So where can I find this information?


texts: It was scared because my cat was playing with it. I saw it tonight (22 October) in Slobozia, Romania. I never saw something like it. The back is white with no points or marks or lines.


texts: General anaesthesia and brain cell damage

texts: Do we lose brain cells when we undergo prolonged surgery under general anaesthesia?


texts: GWAS: matched-pairs and logistic regression

texts:
Logistic regression is a common analysis tool used for GWAS when your response variable of interested is qualitative. It comes as one of the standard tools in most GWAS packages (e.g. PLINK).

Most logistic regression models for GWAS would be setup as:

$\log{\frac{P(Y=1)}{1-P(Y=1)}} = \beta_0 + \beta_1*X$

Where $X$ is number of copies of the minor allele for a particular SNP of interest and $Y$ is disease stuatus. However, suppose that my case-control data is matched (In my case matched by age, BMI, reported ethnicity, and distance to procurement site). I don't think standard logistic regression (as I have outlined above) is valid. What does everybody do? I don't see options for this in packages like PLINK.

I also posted this question on (http://www.biostars.org/p/81394/) before I realized they were no longer part of stackexchange.


texts: SARS-CoV - relative size of the spike protein

texts: I was given the task of determining the percentage of the S-protein of the SARS-CoV relative to the total of its proteins from the attached image. However, I have been given no explanation of the image, and with a physics background, I simply do not understand it. Can someone please explain to me how it would be possible to solve the task from the given image (i.e., explain the image).


texts: If aging is caused by "DNA Damage" why is the process of aging generally similar between people?

texts:
When I hear the phrase "DNA Damage" I imagine completely random changes in the DNA of a person's cells. If this is the case, then it seems like every person would age differently depending on what happens to their DNA. But that is not what we see. In general people age in very similar, predicable ways almost as though it was programmed into the system.
Is it just that most random DNA changes result in cell death and that most of aging is just having fewer healthy cells in any given tissue?


texts: Determining whether X chromosome from sperm or egg

texts: Is there any way of determining which X chromosome a female inherited from her father and which from her mom ?


texts:
According to Wikipedia,

"Palmitic acid is the most common saturated fatty acid found in animals, plants and microorganisms. It is also the first fatty acid produced during fatty acid synthesis and is the precursor to longer fatty acids. As a consequence, palmitic acid is a major body component of animals. In humans, one analysis found it to make up 21–30% (molar) of human depot fat, and it is a major, but highly variable, lipid component of human breast milk."
(https://en.wikipedia.org/wiki/Palmitic_acid)

Yet, specifically palmitic acid is also said to be "harmful" (that it increases LDL levels and puts people at risk for heart disease), per the World Health Organization (http://www.freezepage.com/1348239076FHWAJDADVT).

So, I am skeptical --- possibly most ubiquitous saturated fatty acid in nature and a central component of our fatty acid metabolism, is somehow "more" dangerous/unhealthy compared to other saturated (or unsaturated) fatty acids? I'd suspect the opposite should be true -- it seems to me it should be the saturated fatty acid we should be most capable of handling well!


texts: How to choose an assay for detecting virulence factors?

texts:
When looking for a protein of interest, an ELISA is being administered. I read this article about the different types of ELISAs and the advantages/disadvantages.

However, I am conflicted about whether a sandwich ELISA or a direct ELISA would be best detecting a protein virulence factor in a serum sample. The thought behind the sandwich was the antigen would not need to be purified before measuring.

Any advice as to choosing an ELISA for the detection of a specific virulence protein?


texts:
Are humans capable of both anaerobic respiration, and lactic acid fermentation?

And if so, when do they do each?

I understand that the difference between respiration and fermentation is that respiration takes place in the electron transport chain. I understand that aerobic respiration uses oxygen in the electron transport chain, and anaerobic respiration uses some other molecule in the electron transport chain instead of oxygen, like nitrate. Whereas fermentation doesn't use the electron transport chain at all.

I know humans have an anaerobic metabolic process that produces lactic acid, but I'm not clear whether it's respiration or fermentation, or whether it could be either, in which case when it is which?

added
some further discussion w roland at  the chat link / https://pastebin.com/raw/mkxckeqA / http://archive.is/CwCRL   and on this q at chat link here / https://pastebin.com/raw/9sV38LnQ / http://archive.is/HJVVe     and example of conflicting definitions available https://pastebin.com/raw/3EKGmEb6 / http://archive.is/9sAlY


texts:
I watched a youtube video explaining how mosquitoes detect our blood vessels through "chemicals that our blood vessels exude naturally"

I was wondering if it's true that our blood vessels exude any chemicals, and which chemicals are they.

[Link to the video in case anyone is interested https://youtu.be/rD8SmacBUcU]


texts: The evolution equations under different year classes of a age-structured model?

texts:
This sounds a bit complicated but I want to grab more feelings on age-structured problems. Less than 2 days to the exam so I appreciate any help.
So suppose we only get 3 year classes in a school at first. No one can repeat. If you are kicked out of school you must restart from year class $1$. No transfer-in students. Exactly $N$ freshman each year. The portion of being promoted from year class $i − 1$ to year class $i$ is given by $s_i$ (which we can again assume it's constant). Then suddenly at one year $Y$, the school changes its scheme. Only at that year the school take in $N$ year $0$ and year $1$ students respectively. Since year $Y + 1$, the school only take in $N$ year $0$ students each year.
What I want to know the most is how we should decide (1) the steady state no. of the students in year classes $1$ to $3$ before year $Y$, (2) the steady state no. of the students in year classes $0$ to $3$ since year $Y$, and (3) the school years needed to achieve the steady state since year $Y$.

I tried putting forward the Leslie matrix of the old scheme: $$\begin{bmatrix} 1 & 0 & 0 \\ s_1 & 0 & 0 \\ 0 & s_2 & 0 \end{bmatrix}$$ and found the eigenvalues would be $1$ and $0$ (with multiplicity of $2$). $\lambda = 1$ gives $$u_{1, n} + u_{2, n} + u_{3, n} = u_{1, n}(1 + s_1 + s_1 s_2).$$ Am I on the right track? Should I just plug in $u_{1, n} = N$ and then claim the steady state no. to be $N(1 + s_1 + s_1 s_2)$? Or do I need to sort of prove that?

If my thought process is correct, the Leslie matrix of the new scheme becomes $$\begin{bmatrix} 1 & 0 & 0 & 0 \\ s_0 & 0 & 0 & 0 \\ 0 & s_1 & 0 & 0 \\ 0 & 0 & s_2 & 0 \end{bmatrix}$$ Right? Then its eigenvalues are again $1$ and $0$ (multiplicity $3$), and then $\lambda = 1$ gives (let me denote the intake proportion $s_{-1} = 1$) $$u_{0, n} + u_{1, n} + u_{2, n} + u_{3, n} = u_{1, n}(1 + s_0 + s_0 s_1 + s_0 s_1 s_2) = u_{1, n}\left(\sum_{i=-1}^{2} \prod_{j = -1}^i s_j\right).$$ Did I make any mistakes so far?

I can sort of write out the year class size since year $Y$ explicitly. It should take 3 school years to achieve the steady state again right? Any less tedious and/or more persuasive ways to show the same result?

Thanks in advance.


texts: Are there any side-effects from a mosquitoes extinction?

texts: Suppose that we have the ability to make mosquitoes extinct, what would be the likely effects (on disease and ecosystems for example) of such extinction? Essentially, what roles in nature do mosquitoes perform?


texts:
I can see the chain of spreading disease: Humans usually get rabies from domestic animals, those usually get it from wild animals, wild animals in their turn get from the other wild animals and here I'm stuck. Well, so where do wild animals get it from initially?

I know that rabies is a virus and it needs warm-blooded animals to live out. Also according to Wikipedia once an animal is effected it lasts, let's say, no longer than for 2 weeks.

In other words, does it mean that there is a constant population of rabid animals that exists in order to pass this virus from one animal to another every 2 week on the average?


texts: How does the light-independent stage of photosynthesis get H+ ions?

texts:
From what I understand from my grade 11 biology:
During the light-dependent stage of photosynthesis, water molecules split, producing hydrogen and oxygen atoms. The oxygen atoms are basically “waste products” — used by mitochondria for respiration after being inhaled. These H+ ions are then taken by a hydrogen carrier (i.e. NADP+) to form NADPH (which is necessary for the light-independent stage). Where do these H+ ions suddenly just come from?
From what I’ve understood so far, the H+ ions are now “in” the NADPH.
I’m confused as to how in the light-independent stage, the carbon dioxide (CO2 molecules) can combine with the H+ ions to form glucose. I thought that these H+ ions had already got “converted” to form NADPH? Or is it something like only some of the H+ ions are necessary for NADP+ to form NADPH?


texts: Can cell division be stopped during prophase?

texts:
There are three known checkpoints which ensure proper division of the cell.

  These are: the G1 checkpoint, also known as the restriction or start checkpoint or (Major Checkpoint); the G2/M checkpoint; and the metaphase checkpoint, also known as the spindle checkpoint.

I wanted to know that is there any way cell division can be stopped during prophase(once it has started).


texts: How did palaeontologists discover the age of the Tyrannosaurus rex named Sue?

texts: I'm trying to understand how they discovered or speculated the age of Sue the Tyrannosaurus rex to be about 28–29 years old. How do they know exactly the age of Sue? Could it be wrong? Could it be possible that she is older then they thought — maybe 35 years old?


texts: Effective population size of a metapopulation structured on a grid

texts:
Scenario

Consider a rectangular metapopulation consisting of $x \cdot y$ demes, where $x$ is the number of deme horizontally and $y$ is the number of demes vertically. The population size per deme is $N$ and the migration rate between any two adjacent demes is $m$.

Assumptions

I welcome any kind of assumptions for the purpose of this post.

Question

Can you help me to calculate an expectation of the effective population size $Ne$ of the whole metapopulation?