texts:
I was wondering how a scientist in a lab may know which type of animal model to use. I have been looking at the effect of a protein on a disease. And have thought about the ways that’s i know this has been done in other research-
- deletion of gene which encodes for protein
- insert GFP by Gene for protein leaving gene intact
- or insert gfp by gene for protein deleting the gene
However I cannot seem to understand how a scientist decides to choose a certain model?


texts: Prevent biofilm formation on moist surfaces

texts: I have an indoor fountain with lots of water. What are the most common microorganisms in this kind of moist environment, and what are the standard way to prevent biofilm formation by them? I thought of copper and/or salt as general cheap disinfectants so far.


texts: How much energy is in a human brain's electromagnetic activity?

texts:
Lately there has been an increased interest on worldbuilding.se about a realistic depiction of fictional creatures who would feed off thoughts and dreams, with some answers proposing feeding off the electromagnetic emissions of the brain.

As a first guess I would think the energy in those emissions is very small. However, has there been any study to give an approximate amount? Most information a quick search provides stems from sensationalist articles which don't look too trustworthy.

The brain does use up almost 20% of the whole body's energy balance, but I would guess most of it is turned into heat.

If one could extract useful work out of the electromagnetic field generated by an average human brain with 100% efficiency, without any physical intrusion (so, the energy potentially available outside of our head), how much would it approximately be? An order of magnitude approximation would be enough.


texts:
How do molecules signal pre synaptic neurons to activate? and also is it more the structure or the elements in the molecule that allows it to activate the neuron also how do molecules bind to receptors and same as last time what is more important to do so the elements in the molecule or the actual structure? please answer I cannot find the answer anywhere else expert answers are appreciated!

-Gus


texts: Is it trivial to assume a version of Hamilton's rule that applies for numerous generations?

texts:
Is it trivial to assume that a version of Hamilton's rule that applies to numerous generations is:

C > rB

C = lineage fitness lost by an actor,

B = lineage fitness gained from the act, and

r = relatedness between actor and those that gained lineage fitness?

Or does this rely upon a particular derivation of Hamilton's rule?  If so, does anyone know of a citation in which this derivation is made?

Thank you very much.


texts: How do cellular waste products enter arterial blood?

texts:
I recently learned that blood in renal arteries contains waste materials, which is filtered via nephrons in the kidneys.

My question is, how are these waste materials getting into the arterial blood? I believe arterial blood is pure and devoid of waste (since all the waste from cells and tissues must enter veins).


texts: Has research indicated how much koinophillia preferences are learned vs insinctual

texts:
I'm curious about rather the definition of 'normal', as it affects  koinophillia & mate choice, is something instinctual or learned.  To clarify I'm not asking if koinophillia itself is instinctual (I take that for granted), but instead the definition of what constitutes 'normal' vs 'abnormal' for a species which drives instinctual attraction via koinophillia.

Basically, does the definition of normal get affected by those around an individual as they grow and/or select a mate?  Can a trait that would be considered abnormal for a species be considered accepted or attractive if it is common amongst a small subset that the individual spent time in?  For instance, has any study be done in which an animal grew up among a large number of 'abnormal' phenotype animals to see rather the would later be drawn to mates that look like the peers they were raised around or the more normal appearance for their species?

In fact I'm particularly interested in the case of humans.  Does anyone know if koinophillia and attraction is affected by the environment one is raised in?  For example if someone was born in an isolated island where their populations physical features were rather unique and there was limited genetic variation/gene flow from outsiders but was raised in a family/community of people on the other side of the world with very different physical traits has a study been done to indicate rather they are more likely to be attracted to individuals from their home island, individuals that look like the community the were raised in, or no strong indication either way?


texts: Why are Mendelian mutations considered rare?

texts:
I was reading the Wikipedia articles about genome-wide association studies (GWAS) and whole exome sequencing.

As I understand, GWAS is used to identify most common SNPs that are proved to be associated with a disease/disorder. On the other hand there is an article about whole exome sequencing method where it said that it is more sensitive to identify Mendelian mutations in contrast with the SNP genotyping methods used in GWAS.

As the graph shows below, there is a distinction between Mendelian mutations and common mutations. What exactly does Mendelian mutation mean (why do we call it Mendelian)? What makes a Mendelian mutation so rare but effective in contrast with common mutations? Aren't common mutations inherited with the same rules as Mendelian ones?


texts:
GrandParents                  -- 1
                            |
                            |
                -------------------------
                |S                      |D          -- 2
            ---------                ----------
            |S(A)   |D               |S(A)    |S(A) -- 3
            |S      |D                              -- 4

S = Son
D = Daughter
(A) = Affected with a degenerative disease.

The question is how to identify the type of inheritance of the disease - whether
X-based, Autosomal dominant or recessive. Which sex of fourth generation are likely to have the disease? Does it depend on the disease?


texts:
I have few questions about the firing rate of retinal ganglion cells.

1) How to explain the baseline firing rate if either the entire receptive field is stimulated or there is no light stimulus at all? That behaviour means that the intensity of light does not have any effect if the entire receptive field receives the same stimulus. I don’t understand how horizontal cells let that possible.

2) When the on-center is stimulated, the firing rate is maximized at the beginning and it diminishes with time to reach the baseline rate. Why does the firing rate decrease? What is responsible for that?

3) Is it possible to have a simple mathematical model of the process with an artificial neural network?


texts: I know they are non directional movement responses, but like tropic responses, does their movement involve growth?


texts:
DNA response elements are DNA sequences that are could be found upstream, downstream of genes that regulate gene expression at the transcriptional level.

One type -Enhancers- bind specific transcription factors called activators, this binding leads to the bending of DNA, bringing the otherwise distal enhancer near the promoter region of the gene, leading to induced transcription.

My question is:

  How and by what mechanism do enhancers induce and increase transcription rates? i.e how does the interaction between the activators and the transcription complex, increase transcription rates?


texts: What is the most stable globular protein?

texts:
What is the most thermodynamically stable globular protein?

I am looking for a small (ideally less than 50kDa) soluble globular protein motif which folds easily/reliably and is known to be extremely stable and resistant to unfolding once folded.  Also very resistant to proteolysis and degradation.

Any ideas?


texts: Are Richard Lynn's estimates of African IQ inherently innacurate on the basis that most Africans aren't mentally retarded?

texts:
I've been looking at Richard Lynn's studies on average African IQ, and he seems to estimate really low IQs in the 60s range (e.g. http://www.sciencedirect.com/science/article/pii/S0160289609001275?via%3Dihub).

However, is this inherently wrong, as somebody who would score that low in a Western country would no doubt be mentally retarded (and this isn't the case for most African people)?


texts:
Is scratching (aka the scratching reflex) thought to be inherited from a single vertebrate ancestor or is it something that evolved several times e.g. in birds, mammals etc., i.e. is it a case of convergent evolution?

I suppose this question may be somewhat subjective (what level of scratching is homologous) but since more recently the neurochemical basis for it has become more clear namely that

  a molecule known as neuropeptide natriuretic polypeptide b (Nppb) that is released by nerve cells far from the actual itch site triggers an electrochemical cascade that ultimately tells the brain it’s time to get scratching.

perhaps one can ask (the same evolution question) about the signaling cascade for itch-scratch.


texts: How does DNA from sperm fuse with DNA in egg?

texts:
I see this statement all the time "half of our DNA (23 chromosomes) are from mom and 23 are from dad". Fine, but which chromosomes in our nucleus are from each parent? When I think of nucleus (before interphase), I imagine a total of 23 unique chromosomes and 23 copies of them. In the first cell after reproduction (zygote), does chromosome 1 from mom align with chromosome 1 from dad? When zygote divides (after S phase) do you now have 4 copies of the same cell? Since choromosome 1 from mom and dad is the same.
What role does crossing over play in all of this.
I have done lots of reading but nothing is helping me connect the dots.


texts: How does hemoglobin-free blood transport oxygen?

texts:
Snails... We have some kind of huge garden snails appearing lately (read since the last 10 years or so). Try as one might, it's impossible to avoid them when driving. These snails do not appear to have red blood - I doubt they have blood at all. Wikipedia tells me blood's red colour is due to haemoglobin - which serves to transport oxygen.

How do snails (and any other animals that do not have red coloured blood) get oxygen? Or, do such animals need no oxygen at all?


texts: How do firing patterns arise from the activity of many ion channels?

texts:
In his answer to another question, Bryan Krause says:

  Ion channels don't exhibit any firing patterns: neurons exhibit
  firing patterns that depend on all the channels present [...].

I understand it this way: The observable and measureable firing pattern1 of the neuron (created at the trigger zone) is the linear superposition of tiny "firing patterns2" of all the (voltage-gated) ion channels at the trigger zone, which in turn depend on the probabilities of opening and closing which are the same for all ion channels of the same type and obey some Hodgkin–Huxley-like law. These probabilities correspond directly to the shape of firing pattern1.

The rhythm with which each single sodium channel opens and closes ("firing pattern2") doesn't have to mimick firing pattern1 exactly, only roughly and probabilistically: the open-close-ticks must occur near to the spikes of  firing pattern1, but not exactly and not at every spike. And some complete outliers are allowed. The rest is superposition.

Seeing things this way, indiviudual ion channels do exhibit "firing patterns2", but these may look quite different than firing pattern1 (although not completely).

  Is this kind of reasoning correct?

If so: Can the following conclusion be drawn: The time scale of a firing pattern1 depends on the number of ion channels at the trigger zone? This might be seen when looking at the rise time of a single action potential: If there is only one sodium channel, rise time will be larger, if there are many, it will be smaller. Is this correlation strictly linear?


texts:
Imagining that we're now in 1983 (when HIV was discovered), there were no modern machines at that time to sequence massive genome extracted from blood. There was a strange disease and no one know what caused it, it's a virus or a bacteria or something else... So how did scientists find out HIV at that time?

-- Update: I just think that they extracted RNA from blood of those patients who have the same symptoms and using electrophoresis to find out if there was a large ARN fragment exists to indicate that they was infected by a virus, is that true?


texts: Ratio of oxygen produced / consumed by plants

texts:
Related questions:

How long can a plant generate oxygen from its own carbon dioxide, produced during nighttime?

Are plants actual oxygen factories?

But the actual question I'm interested in is:

What is the ratio of oxygen produced during the day vs. consumed at night.

Even ballpark numbers are sufficient, as this came up in a conversation about a Mars colony game where a tree produced 2 units of oxygen during the day and consumed 1 at night (with the game-night being half the length of a game-day because...reasons). Colonists would then need about 1 to 1.5 oxygen per full day/night cycle.

My friend and I were like "this ratio does not sound right" and haven't been able to find any any decent numbers to back up our opinion...or refute it.

Obviously the chemical reactions involved are mirrors of each other, and the output depends on the amount of light, and so forth...But wouldn't trees just be...less active at night in order to conserve energy, while more active during the day?


texts: How does RNA transcription determine which half of the DNA to use?

texts: I feel that I might have a complete misunderstanding here. If DNA has two strands, how does the machinery of RNA transcription determine which one to transcribe?


texts: Why do eukaryotic organisms have introns in their DNA?

texts: We touched on introns and exons in my bio class, but unfortunately we didn't really talk about why Eukaryotes have introns. It would seem they would have to have some purpose since prokaryotes do not have them and they evolved first chronologically, but I could easily be wrong. Did the junk sections of DNA just evolve there by some sort of randomness or necessity as opposed to an actual evolutionary advantage? Why hasn't evolution stopped us from having introns since they seem to be a 'waste' of time and DNA? Why do prokaryotes not have introns?


texts: Unmyelinated long axons in the sympathetic nervous system

texts:
I was recently looking over some textbook material (pdf) which claimed post-ganglionic fibers of the sympathetic nervous system are unmyelinated.  This was surprising to me, since I had previously thought that long distance transmission of an action potential required myelin (I can even remember being told that myelin was essential for large life forms, because the nerves otherwise could not have controlled distant body parts).

First, is the textbook correct?  Second, assuming it is true that post-ganglionic fibers are not myelinated, is there some advantage to this arrangement?  At the very least, I would think it would be far more energetic to send a signal in a unmyelinated axon.


texts: Is it possible to produce a tangible mass of DNA/RNA using a PCR reaction?

texts:
A Polymerase Chain Reaction (PCR) is a method of amplification which enables one to produce many copies of a certain DNA/RNA strand for many applications (as described in the link above).

I have never seen the actual process and the resulting PCR solution, but according to Wikipedia, the volume of the solution is of the micro- to milliliter magnitude.

I was wondering: if this process were allowed to continue on and on, while supplying all necessary nucleotides and other materials, to the magnitude of, say, liters - could we end up with a tangible mass of DNA/RNA? In other words, will we be able to extract from the solution a solid mass of DNA/RNA that is visible to the naked eye? If yes, can we predict the physical characteristics of such mass?


texts: When it is said that “electrical impulses sent from the brain” how is this charge flow produced?


texts: Does it make sense to express membrane transporters as concentration?

texts:
Let's assume a situation where a molecule, S, is transported out of the cell by membrane transporter T. For simplicity we do not consider any other synthesis or production processes. Furthermore, we assume Michaelis-Menten (but another enzyme mechanism would lead to the same question, I think).

Mass balance concentration:
$\frac{d  [S]}{dt} = - [T] \; kcat \; \frac{[S]}{[S] + Km} $

Mass balance amount (moles):
$\frac{d  S}{dt} = - T \; kcat \; \frac{[S]}{[S] + Km} $

In both mass-balances the square brackets [.] indicate concentration.

In order for the units to match, the first mass balance equation expresses the transporter term as concentration (i.e. $\frac{T}{Volume_{cell}}$). Does that make sense? After all, these transporters are stuck in the membrane and not 'floating around' in the cell like the S molecules. Expressing T as concentration assumes that the transporter molecules are equally distributed across the volume, which is not the case. Does this not lead to an overestimation of the reaction rate?

Or did I make a mistake somewhere?


texts: Are males taller than females in humans?

texts: Is there any scientific evidence that in humans males are taller than females? And if so, what is the reason that they are taller (please include genes or hormones that accounts for human growth and how they are affected in males and females)?


texts: What is the normal duration of human sexual intercourse?

texts:
Wikipedia is saying:

  Men's typical ejaculatory latency is approximately 4–8 minutes

How the researchers measured this? How did they know if the test subjects weren't suffering from premature ejaculation?

And is this measured from the start of erection or from the start of penetration?


texts: How do dopamine agonists like amphetamine/methylphenidate affect acetylcholine signalling?

texts: Do they increase it, or is the effect mostly neutral?


texts:
Given the following:

bruises are caused by minor trauma which breaks blood vessels beneath the skin, causing bleeding
the mechanism by which bleeding stops is clotting
blood clots inside the body have an unfortunate tendency to get into the bloodstream and cause blockages, leading to severe problems such as strokes or heart attacks

why is it that people don't die from bruises?  What mechanism does the human body have to keep this from happening?


texts: Do trees in a forest generally grow in a lattice formation?

texts:
The closest arrangement of trees in which they are at least a certain distance away from each other is a triangular lattice, much like a honeycomb. I wonder if you tend to see this sort of arrangement of trees in the wild?

I guess this would actually not be beneficial to the trees since it would mean they would all be lined up in certain directions which might not be good for sunlight etc.

I wonder if there is much research on the pattern of distribution of trees in a forest?


texts:
I know that H2O2 is a chemical with high oxidative potential. It can deliver nascent oxygen which can destroy bacteria.

I understand that open wounds have cells that are dividing at a fast rate to effect healing. Is it good to add a substance that can cause damage to cell membrane and possibly cause mutation in the DNA of these fast growing tissues?

Can H2O2 be safely used to sterilize wounds?


texts: Can one use a hemocytometer on a compound upright microscope?

texts:
I'm posting this as a follow-up on What to look for when buying a light microscope?. The answerer states that you would need to use a an inverted microscope to count cell in the hemocytometer(counting chamber).

I've read, partly, a book on lab diagnostics tests and it was not written that there. Moreover, they mentioned things about microscopes featuring a compound upright microscope both in words and picture.


texts: Can I ask tip for tissue measuring(especially for RNA preparation)?

texts:
I extracted RNA at mouse liver and human blood, but degradation occurs. I think, at mouse liver, too hard to measuring 50mg liver(I am newbie for animal tissue preparation) so spend several minutes. liver is soft but very small, and too hard to keep the weight. (human blood spend time for defreeze, but It degraded, too.)

for example, I want to weight 20mg mouse liver,
1. cut liver by scissors about 10mg after set zero point of scales with ep-tube.
2. cut liver almost 10mg, but it's exceed weight 2~3mg, so I have to cut it 2~3mg.
3. this scale is too small... so I spend for keep the weight for 20mg, like this: 10->23->19->19.3->19.8->21->19.8->20.

I want to ask for advice about how it faster animal tissue measuring and preparation. When preparation genomic DNA, is it OK so DNA is stable than RNA. but, when extract RNA, keep the weight fast and incubate sample at ice for prevent RNA degradation.


texts: I really need some help with a plant identification

texts: I am trying to identify this flower. It was spotted in an Australian Botanic Gardens. I have been advised that the plant was approx 1.8m high and the flowers approx 2cm wide. Any help greatly appreciated.


texts: How is Saccharomyces cerevisiae grown on acetate and ammonium able to produce TCA intermediates?

texts:
I am working with a metabolic model of Saccharomyces cerevisiae and I am studying its growth on acetate and ammonia. I am performing Flux Balance Analysis to compute the growth rate and then I am exploring the flux distribution over all metabolic reactions.

The flux distribution shows that acetate is uptaken and transported to the mitochondria, where it produces Ac-CoA, which enters the TCA cycle. But also some acetate remains in the cytosol and produces Ac-CoA, which is used to synthesize fatty acids and to enter the glyoxylate cycle.

My question is the following: if acetate is the only carbon source supplied and ammonia is the nitrogen source, how can initially Ac-CoA enter the TCA or the glyoxylate cycles? In both cases oxalacetate is needed, which cannot be produced directly from Ac-CoA from other alternative pathways.

My only guess is that TCA cycle intermediates are being produced somehow and keep the cycle running, but as the nitrogen source is not even an aminoacid, I do not understand where this whole thing starts.

Thank you very much for your help!


texts:
This question may seem illogical to some, but I seriously have this doubt. I searched google for some proofs but they were extremely complex and I couldn't understand anything.

I was just wondering whether we really have recessive allele or not? Is it like there are only dominant allele present, and when dominant allele isn't present we consider it recessive.

Is it like there is a place reserved for dominant allele and if that place is empty it turns out to be recessive.

Although this thought is vague but then if you take this example, it probably would make sense:
Let's say there are two allele : T and t for tall and short respectively. Now, because TT, Tt, tT are tall, they all lead to the formation of specific hormone due to the presence of dominant allele. But the plant with genotype tt is short, hence the "extra" hormone for "excessive" tallness is missing in tt plant because the dominant gene isn't present. Can we say that that place for two allele (dominant allele) is actually empty in the plant with genotype tt?


texts: Evolution- Variations, adaptations and selective advantages

texts:
I am trying to understand Variations, adaptations and selective advantages  and how they are all related.
Feel free to add or correct me if I'm wrong- Variations are structural, functional, or physiological differences between individual's within a species that result from mutations.  If the variation provides a selective advantage (genetic advantage) the organism's chances of survival in terms of both survival in a changing environment and reproduction increases. The variation is then considered an adaptation. So basically adaptations are variations which provide a genetic advantage and give some organisms within a species a better chance of survival than those without the adaptations. This survival advantage allows those organisms to reproduce and pass on their adaptation more frequently than those who do not possess these adaptations.


texts: What is the fastest way to build an alanine scanning library?

texts: For interfacial studies, I would like to build an alanine scanning library for one of my proteins examining 20 sites. I will ultimately express the gene using E.coli cell-free protein synthesis. I already have the template gene which was originally built using PCR assembly. Now, what's the best way to build a scanning library?


texts:
Overview

Researchers have been studying a temperate grassland ecosystem with the view to understand it's current status with regard to carbon inputs and outputs and to identify whether the grassland is currently a sink or source of carbon.

The aim of this self-study is to become more familiar with different energy fluxes within the terrestrial carbon ecosystems.

The idea is to calculate energy fluxes in various scenarios, and I am feeling a little confused about the scientific theory of gross primary productivity (GPP), net primary productivity (NPP), net ecosystem production (NEP), net ecosystem exchange (NEE), RT = Total respiration, RA = animal respiration, and RS = soil respiration,

If anyone can help, I would be deeply appreciative.

The relationship between production fluxes and other fluxes summarised by these key equations:

NPP = GPP - (plant respiration)
NEE = NPP - (heterotrophic respiration)
NEP = NEE - (carbon losses from leaching, disturbance, and other inputs, and outputs)

Table of flux values

Questions:

What does the difference between GPP - NPP represent? In other words, what is GPP-NPP equal to (see table for values)? Is the value of 800 equal to respiration?

GPP - NPP = R

1400 - 600 = 800

I understand that GPP is the overall rate of biomass production by producers at the rate at which solar energy is captured as carbohydrate molecules during photosynthesis and NPP (energy captured per unit error per unit time). Producers such as plants use this energy respiration and growth.

I also understand NPP is the rate of energy lost to metabolism or maintenance or the energy stored as biomass by plants or primary producers in the ecosystem.

I am making the assumption that this value of 800 is associated with the respiration of plants; although, I am still confused with what this value represents. From my way of thinking, the difference between GPP-NPP equals the extent of CO2 lost from plant respiration within the ecosystem. Since the value of GPP (1400) is larger than the value for NPP (600), more energy has been used during the intake of carbon during photosynthesis rather than plants using glucose or the energy stored in the system to photosynthesise for the emission of CO2.

Therefore, this value represents the amount of CO2 that is lost from plant respiration or from metabolic activity.

Am I on the right track? Do I have the right ideas about energy fluxes?

Diagram


texts: Is there a difference between "Alpha Helix" and "Alpha subunit"?

texts: In my biochemistry textbook the terms alpha helix and alpha subunit are both used. Are these two terms synonymous? For instance, hemoglobin has an alpha and beta subunit, are these the same thing as alpha helix and beta pleated sheet?


texts: Can these "Promega Wizard genomic DNA Purification kit" be used for samples not stated directly?

texts:
I am not sure if this is a duplicate of my previous question, it is somewhat related, so sorry if I misunderstood.

The question is, can i use the above kit for samples like hair, fingernails, etc?

Here are the guides:
https://www.promega.com/~/media/files/resources/protcards/wizard%20genomic%20dna%20purification%20kit%20quick%20protocol.pdf

and the extended guide:
https://www.promega.com/~/media/files/resources/protocols/technical%20manuals/0/wizard%20genomic%20dna%20purification%20kit%20protocol.pdf

It says that for the animal tissue:

Animal Tissue (Mouse Liver and Brain), so I figure it wont apply given that these cells might have higher percentage of DNA that hair(roots/shaft) could have, or fingernails.


texts: Why insects are so small compared to mammals?

texts: I was wondering what biological limitations make the dimension of the insects small compared to the dimension of the mammals. I know in other eras insect were bigger!


texts: Why are sugars in whole fruits not digested the same way sugars in juice are?

texts:
In this paper of the WHO, it is claimed that we should limit our consumption of free sugars:

  WHO recommends a reduced intake of free sugars throughout the
  lifecourse. [...]  Free sugars include monosaccharides and
  disaccharides added to foods and beverages by the manufacturer, cook
  or consumer, and sugars naturally present in honey, syrups, fruit
  juices and fruit juice concentrates.

At first, I was wondering if the sugars in a fruit can be different from sugars in a juice. According to the answer to my question here, the sugar molecules are exactly the same in both (in the case of a 100% pure juice).

So, why this recommendation? Why doesn't our body digest sugars from fresh fruit the same way as sugars from juice? To make it simple, my question only concerns 100% pure juice with no added sugars.

I tried to find an answer and, according to the answers of this question, because our body is slow to digest sugars from a fruit, it assimilates it better. Is it right? And, if it is the case, if we eat fiber and starch with our fruit juice, it should be the same as a fresh fruit, right?


texts: Do mosquitoes allow for DNA transfer between unrelated species?

texts:
A mosquito can bite individuals of different species and eventually allow for some blood of one species to enter into the bloodstream of another species which I suppose may eventually cause DNA transfer, that is horizontal gene transfer

Do mosquitoes increase horizontal gene transfer among the species they parasitise? If yes, is it considerable or negligible?


texts:
What is the number of ATP molecules formed during the photosynthetic processes which consume 8 molecules of $\text{H}_2\text{O}$ due to noncyclic electron transport and subsequent photophosphorylation?

Assume that quinone cycle facilitates the transfer 4H+ to the lumen of thylakoid membrane for every two electrons passing through electron transport system and one ATP is formed for every 3H+ moving down the proton gradient by the mediation of F0F1-ATPase

MY ATTEMPT: In the lumen, due to hydrolysis 16 H+ are formed. Due to quinone cycle 32 H+ are taken from stroma and transferred to the lumen and NADP+ takes 48 H+ so in stroma there is deficiency of 80 and there are only 48 H+ in the lumen. If I assume that if there were initially hundred H+ on both sides then after non cyclic transport inside the lumen there are 148 H+ and in stroma there are 20 H+ so to have equilibrium then there should be 84 H+ on both side so total 64 H+ should travel then I am getting 64/3 ATP which is wrong. Where I am going wrong?

Screenshot of question paper


texts: I found this insect in Pune/India. Its body size was less than 1 cm. It was near light source. I suspected it to be Juvenile Thread-legged Bug, but i am not sure. Is my suspicion right or is it some other insect?


texts: What is the difference between optokinetic and vestibular nystagmus?

texts:
Optokinetic nystagmus is for stabilising the pictures we see when we are observing moving objects for example if we are rotating on an office chair. If we wear a mask while rotating however, the optokinetic nystagmus will not occur since we don't see. But I read that vestibular nystagmus will occur even if we are wearing a mask.
What is vestibular nystagmus exatly and how does it differ from optokinetic nystagmus?


texts: Why do the humans become sleepy after meals?

texts:
I don't know about all the mankind, but I know enough people, who becomes sleepy after their meals. Also, I'm not sure, what kind of food do they consume, but I personally get sleepy almost from any food: sweet, fat, spicy, salty, liquid, tasty, not tasty, etc.

Is this phenomenon well known? And, if yes, how does it occur?


texts:
I recently encountered a (probable) deathstalker scorpion in the Negev desert in Israel:

However, when trying to identify this species I found that in many/most photos of the yellow scorpion the final segment before the stinger was dark or even black (see the wiki link for examples) i.e., not yellow, as shown in the photo.
Is a black/dark pre-stinger segment an indication of some sort (perhaps venom?), or is it an indication of a separate species, or other? Clarification on this matter is most welcome.

Update - I contacted an Israeli PhD from Haifa University who wrote the following:
"...looks like Andrtoctonus amareuxi (also referred in the past as Andrtoctonus amareuxi hebraeus, Israeli fat-tailed scorpion (קטלן עברי)
the genus common name is fat-tailed scorpion... The color of the last segment of the abdomen before the stinger is not a very good sign alone for species identification, as it is variable in the population and also found in at least 2 other genera/species (in the genus Buthus and in some species of the genus Compsobuthus). Anyway for sure it is not the deathstalker which is easily identified by a marking on the prosoma, behind the central eyes, that looks like a lyre  and the ridges on the abdomen..."


texts: Very introductory online source of information in evolutionary biology

texts:
We receive quite a lot of questions from layman in evolutionary biology in this site that are sometimes difficult to answer just because there is way too much to say. Why don't human keep evolving? is a perfect example. I often want to give some pieces of information and link to a good source of information for them to get introductory knowledge in evolutionary biology.

Obviously nobody that ask a question on a Stack website want to read an answer of the kind You should read that book!. It is often not really pleasant to read a book, it takes time and the OP that get this answer will likely just forget about their question.

What are the best online resources that offer a very introductory understanding in evolutionary biology?

Either a written course of videos such as Khan Academy videos would do (I haven't watched the evolutionary biology section of Khan Academy though and can't really judge of how good it is).


texts: Reason for conversion of glucose to fructose in glycolysis

texts:
In glycolysis, glucose is converted to glucose 6-phosphate so it can not diffuse out of the membrane. Then it is converted to fructose 6-phosphate.

Why is this? Perhaps it makes it less stable so it is easier to break down into pyruvate?

That is just a guess, is anyone able to provide more information about this?


texts: Dorsal vs Posterior and Ventral vs Anterior

texts:
From prior reading, I thought that Dorsal is the same as Posterior and Ventral is the same as Anterior. However, when I checked in google images for these anatomical terms for a horse (just to strengthen my concept), i found that Dorsal is not the same as Posterior and Ventral is not the same as Anterior.

How is this possible? I have checked many websites but all state that Dorsal is the same as Posterior and Ventral is the same as Anterior. Am I going wrong somewhere?


texts: Book on yeast reproduction, evolution and on the use of yeast as model organism

texts:
I am looking for a good book in:

Yeast reproduction

mating types
Recombination
mating type determination mechanism

Yeast evolution
Yeast as model organism and its use in experimental biology

It should include common technics used to work with yeast. For example: We can add a plasmid in order to fool yeast and let them think they have another mating type than the actually have.

Note: I am mostly interested in Saccharomyces cerevisiae of course.


texts: In animals, birds, reptiles and fish, is a male sometimes unnecessary for a female to have/extend a male

texts:
Apparently in the human (animal realm) there are females that are female in body but their DNA is (XY) male, apparently 7500 in U.S., but apparently not able to have children ( http://abcnews.go.com/Health/MedicalMysteries/story?id=5465752&page=1)

I understand species like female hammerhead sharks can make clones with no male necessary for their female offspring (clones).  However, can a female make/extend a male, without receiving male fertilization?

If you also happen to know about the insect or plant kingdom please comment there as well.


texts: Neurones and putting on clothes (Pacinian Corpuscle)

texts:
If I put on clothes, a gentle pressure is applied to the Pacinian corpuscles in the skin, causing Na+ ion channels to open and an action potential to be initiated - hence I feel the clothes on my skin.

However, I was reading that after prolonged time, the action potentials are no longer generated unless there is another change in pressure as the clothes again move over the surface over the skin.

I'm confused why. The reason I am given is that the Na+ ion channels remain open so a resting potential cannot be established, but I can't see how this contributes to the effect.

Can someone explain why?


texts: Evolutionary history: did any organs start out as autonomous organisms?

texts: I've read that the cell nucleus was once an autonomous organism that was "enslaved" by the larger cell at the time of the Eukaryotic Revolution. Are there any organs in the human body that we know of that started out as autonomous organisms (of course they would be unrecognizable in their current form)?


texts: How do absorbance readings indicate diauxic growth of bacteria?

texts:
How is growth rate an indicator of carbohydrate use? How do absorbance readings from a spectrophotometer show growth of bacteria if the absorbance readings are taken several times over the course of a day [and plotted on a graph]? If the second absorbance reading of a sample with bacteria and particular substrate is lower than its initial absorbance reading is there less bacteria present or more? Do the presence of substrates affect the absorbance reading in other words do carbohydrates have any turbidity?

context if needed - experiment determines if a species tested in the presence of a carbohydrate and combination of carbohydrates is able to use each as its sole carbon& energy source and if any are used preferentially to others


texts: Pathogenesis of chronic venous congestion in skin?

texts:
I think CVC cannot lead to heart failure primarily.
So let's think its pathogenesis in skin now only.

I think the pathogenesis is like this

dilation of veins and capillaries due to impaired venous drainage
reduced outflow of blood from a tissue
passive process
$\to$ local increase in blood volumes
$\to$ local increase in venous pressure
pathological
$\to$ shortage of oxygen and built-up metabolic waste
$\to$ structural changes in microvasculature
$\to$ increased venous permeability % hallmark of acute inflammation
$\to$ increased size of venous caliber
$\to$ emigration of leucocytes
$\to$ accumulation at site of injury
activation of acute inflammation
$\to$ protein into extravascular space
$\to$ increased viscosity of blood
$\to$ deoxygenated blood blood stasis
$\to$ congested tissue
$\to$ leucocytes move to endothelial wall (selectins)
$\to$ roll
$\to$ adhere (integrin to stop)
$\to$ migrate
$\to$ dysky reddish-bluish skin (cyanotic)
$\to$ healing via fibrosis
$\to$ scar
Causes: venous thrombosis; venous compression; heart failure;

I am not sure about the role of leucocytes exactly in this process.
I am not sure if they play a big role in the formation of cyanotic skin.
I think the outcome is mostly because of increased vascular permeability and its deoxygenated blood in extracellular space.

What is the right pathogenesis of chronic venous congestion in skin?


texts: Australian Tree Identification - maybe pine?

texts:
Can you help identify this species?

(Link to imgur album with all images)

It was growing next to the Yarra River (maybe 10 meters from the bank) in Melbourne. At first I thought it was a type of pine however this page says Australian pines at not actually true pines. It does look much like some of the images of Australian Pine Casuarina equisetifolia

However the Wikipedia page for Casuarina equisetifolia says there are 2 subspecies, equisetifolia and incana. Equisetifolia is only found in Southeast Asia & northern Australia so that rules that one out. Incana is found on the east coast of Australia (eastern Queensland, New South Wales) - could it also be found as far down south as Melbourne?

I've also compared it against all the pines on this site as it specifically shows Australian species.

From there I thought it looks a bit like a Port Jackson Cypress Pine Callitris rhomboidea but the needles look longer and narrower.

I think it also looks a little like a Narrow Leaved Wattle Acacia linearifolia if you ignore the yellow flowers.

I'm carving a spoon out of some of it's wood so would like to know for sure what species it actually is. Any help greatly appreciated.

UPDATE:

I went back to the tree to get some more photos but the whole tree had fallen in the river!

I did get a branch off it however to get a close up of the nodes / internodes but I could not find any seeds or cones.

FINAL UPDATE:

I've tried to get a close up of the apical portion (the top bit right?). My twig sample has started to dry up a bit so this is the best I could get.

ONE MORE UPDATE

Due to my last pictures being rather fuzzy I got out the DSLR and the tripod. These photos are very high res and around 8mb each so may take a while to load...


texts: Can a living organism run on electricity?

texts:
Each time I'm too lazy too cook I think it'd be cool to be able to just plug myselt into an outlet. Yet I know it is not possible - I need amino acids and a lot of other stuff that electricity can't replace.

Can some simple organism live on electricity alone or is it just fundamentally impossible?


texts: Will you stop sweating if you exercise in a cold enough room?

texts:
It's common knowledge that you will sweat from being in a very warm room. And you will also sweat from exercise, presumably because it raises your body temperature.

But if you exercise in a cold enough room, which magically adjusts its temperature to counteract your body temperature, will you then not sweat at all? And is it therefore possible to exercise without sweating... And not even have to take a shower afterwards?


texts: Why do huskies have markings above their eyes

texts: [1.         Dogs in Antarctica pulling sleds


texts: Have there been any efforts to release opossums as a biological control against ticks?

texts:
There's plenty of examples of people recognizing opossums as a great ally in controlling tick populations (here's one example). However, I can't find any examples of opossums being intentionally released or supported in areas specifically to control ticks.

Have there been any efforts documented that deliberately increase opossum populations to reduce tick infestations? If no, are there specific reasons why this has not been done? For the latter, there are of course examples of biological control gone wrong (e.g. cane toads released in Australia), but that doesn't seem to deter all biological pest controls (e.g. nematodes to control fungus gnats).


texts: Interlocus Contest Evolution means suicide?

texts:
I was reading Matt Ridley's "Genome" book. I am trying to understand the Interlocus Contest Evolution in his X-Y chapter. I do not understand why the X and Y chromosome would want to kill each other. Wouldn't that cause the death of the species (actually, have any species died that way?).

Can someone shed light on the issue?


texts:
I have heard that this is an effective replacement for patients who have a dysfunctional larynx, partly due to cancer.

I am curious to know the inner working of this device and why such a robotic voice comes out?
What is the basic principle of this device. Does it simply captures vibrations and converts it to sound? Just like how a mic does?

Thank you.


texts: Trying to determine Heart Condition? ECG show no P Wave

texts: A young woman was at the gym doing great her normal workout. She would spend 45 minutes on the elliptical and then 15 minutes doing weight training. This was the regular routine for her as she did this almost everyday. One day her normal routine turned upside-down. As she finished her elliptical workout and was making her way to the weight machines, she experienced a rapid heart beat. This washould nothing alarming at first because she had experienced this rapid heart beat before. When it happened previously the rapid heartbeat lasted only 10 or 20 seconds. However, this time was different. She experienced the rapid heart beat, but this time the heart beat did not slow down after 20 seconds. The rapid heart beat continued and she began to feel shortness of bread, some pressure I her chest, as well as feeling light-headed. Scared for what might be happening in general she went home called her husband. Frantically she tried to explain how she was feeling and how scared she was. They went to the E.R during her sTay in the ER her heart rate was constantly monitored. For five hours her heart rate remained between 130 and 150 bpm. After 5 hours her heart rate spontaneously returned to a normal rhythm. She was kept overnight In the ER and attending cardiologist prescribed low-dose beta-blockers She was given a number of different test and the results were: -blood pressure normal - hematocrit normal -cholesterol normal She is 34 mother of two. She is of adequate weight and BMI for her age and height. She has regular wellness checkups every year and has never had high cholesterol or hypertension.


texts:
I usually would search for myself, but I need to be super sure about the identification because I need to know if I need to get an exterminator in here or not. (I think it might be a giant house spider, but don't let me influence your analysis.)

So I live in the northern part of Ireland (About 40 minutes from Derry Northern Ireland over in County Donegal) and I went to my bathroom to a VERY fun surprise this morning. It was this wonderful spider in my bathroom. For reference, the lip of the glasses it is depicted in are 8 - 8.5 cm in diameter.

The missing leg was not my fault either, I was very gentle with the spider and released it outside post photo-shoot. (Warning: these are macro shots of the said spider)

More high resolution photos available on my Flickr (SolarLunix).


texts: Autosomal Recessive Trait when skipping one generation

texts:
I learned recently that given a pedigree it is possible to tell whether a disease is autosomal recessive by observing if the trait skips a generation. If the disease does skip a generation, then the disease is autosomal recessive. But the converse is false. That is a disease that is autosomal recessive does not necessarily mean the disease skips a generation.

Does someone know of a proof of this fact?


texts: Identify this unusually-shaped, orange-colored fruit that grows in pairs?

texts:
The photos below were taken on the island of Penghu in the Taiwan straight in October. This was in a public place and the small tree (about 3 meters tall, trunk perhaps 8 to 10 cm diameter) had probably been planted, so we can't presume it to be indigenous.

Each fruit was about 6 or 7 cm long, the skin was bright orange and seemed a bit waxy. The shape was a little bit like a banana-shaped American football in that it was divided into four quadrants. They attach to a stem in pairs and extend horizontally (sideways) rather than hang down.

Question: What could this gravity defying fruit-bearing tree be?

The first image is cropped, zoomed and sharpened in order to highlight textures.


texts: how do macrophages  have the capacity to digest pathogen in opsonization but not in the            first time when the pathogen is new  and they play the role of antigen presenting cells(APCs) first they digest polypeptide of antigen and then let the plasma cells first secrete an antibody and after that they can destroy antigens?


texts: What does common viruses found in the body weigh?

texts:
On NPR public radio news it was said that if the bacteria that is natural that assist in body function or just present in your body was put it into a ball it would weigh more or less 7 ounces (approximately 200 grams). I tried to find the exact quote but am still looking for it and will revise when I find it.

Can viruses assist in body function as in extending life in any way?

Can a body be 100% free of viruses of not how much would the total virus weigh if put in a ball?


texts:
I was walking down the beach today (Wollongong Australia, near Sydney) and saw this Jellyfish washed up on the beach.

Then I saw another.

I wanted to work out what type it was but didn't know where to start.  I'm looking for a process to determine the category of Jellyfish this is.

I've had a look at this chart:

which tells me it is probably a Catastylus Mosaicus (Blubber fish).

I've also looked at this chart:

which tells me it is probably a Rhizostoma Octopus - Barrel or Root Mouth JellyFish (name only - still a jellyfish).

The biggest identifying characteristic seems to be the eight legs. (Clearly a jelly fish - but still a very confusing trait).

My question is: What are the identifying characteristics of a Jellyfish?


texts: What does microglia process length tell us?

texts: I'm reading a study investigating traumatic brain injury and alcohol consumption and the researchers measured microglia process length as an indicator of brain damage. I was wondering what that would indicate and how does it an imply brain damage?


texts: How can one calculate "probability of possessing a ‘perfect’ profile" from "typical optimal genotype frequencies"?

texts:
Can anyone please explain how the "Probability of possessing a ‘perfect’ profile" was calculated from "typical frequency of optimal genotype" in Table 1 in this paper?

Paper link here


texts: In a complete SA block when there's block of impulse from SA node to Atrial syncitium, The ventricles start pumping at AV nodal rhythm but how do the atria then contract?


texts: How are neuromodulator receptors distributed?

texts:
Irrespective of where, when and how neuromodulators are released, eventually they are detected by some receptors in the membrane of a target neuron (typically G protein–coupled receptors)

Neurotransmitter receptors are typically distributed on the dendrite and the soma of a neuron (and only occasionally on the axon):

at excitatory synapses (more distal)
at inhibibitory synapses (more proximal)

Does this rule of thumb also hold for neuromodulator receptors:

excitatory → more distal
inhibitory → more proximal

And are they clustered (like ligand-gated ion channels at synapses)?


texts: this simulation, you sampled the gene pool without replaceing beads in the beakerafter you drew each one. Thus, f(A) and f(a) in the gene pool changed slightly after each bead was drawn. For example, if you begin with 50 light and 50 dark beads, the probability of drawing a dark bead the first time is 50/100 = 0.5. THe beaker would then contain 49 dark beads and 50 light beads, so the probability of drawing a second dark bead becomes 49/99 = 0.495. Does this make your simulation slightly less realistic? In small natural populations, does one mating change the gene pool available for the next mating, or not? What biological factors must be considered in answering this question?


texts:
Prokayotes, which replicate primarily using binary fission, don't get much genetic diversity. For this reason, they take in any genetic material they encounter, in a gambit to help them better adapt to their environment.

However, Eukaryotes, most plant or animal cells that contain a nuclei, have great diversity from crossing over during meiosis, not to mention genetic materials from two parents.

Due to other means of genetic diversity, it seems that eukaryotic cells wouldn't need to take in foreign DNA as prokaryotes do. But sometimes life has redundancy, so:

Do eukaryotes assimilate DNA that is floating in the extracellular membrane?


texts:
This site says:

  In cell biology, microsomes are vesicle-like artifacts re-formed from pieces of the endoplasmic reticulum (ER) when eukaryotic cells are broken-up in the laboratory; microsomes are not present in healthy, living cells.

Whereas this other site says:

  Microsome is another name for the smooth endoplasmic reticulum (ER).

Are they both correct? Which one is correct?


texts: How verified experimentally is the Marginal Value Theorem for viruses?

texts:
Reading some Stanford notes on R0, they get to MVT and optimal virulence:

  Consider a directly-transmitted infection from which there is no recovery (e.g., Herpes Simplex). The population experiences a baseline mortality rate, µ, and a disease-induced mortality δ. [Then the SI model]

  ds/dt = −βsi − µs
  di/dt = βsi − (µ + δ)i,

  Figure 4: Marginal value theorem for optimal virulence. The ESS [evolutionarily stable strategy] virulence occurs where a line
  rooted at the origin is tangent to the curve that relates β to δ. Two curves are depicted. The
  first curve shows a pathogen in which transmissibility increases relatively rapidly with mortality.
  Point A indicates the optimal balance between β(x) and δ(x) under this case, and the optimal
  virulence is indicated x∗
  . For the second curve, relative transmission is less efficient. Therefore,
  the tangent line from the origin to the curve hits further out (B) along the mortality axis and
  the optimal virulence is higher (x∗∗).

Wikipedia has a page on MVT but it doesn't discuss viruses/virulence at all (although it has some criticism of MVT from other angles/domains). So, how verified experimentally is MVT for viruses?


texts: What is the effect of self envenomation on reptiles?

texts:
If a venomous lizard bites its own tongue will it die?
I've searched the whole internet and I am unable to find a reliable answer on self envenomation.


texts: Do E. coli produce both cellulose and curli?

texts:
I read a paper that describes a specific stain for cellulose and curli (simultaneously) in Salmonella. I think this should work for E. coli but I'm not sure if all strains produce it. If they do, are the tertiary structures similar to those from salmonella?

Real-time optotracing of curli and cellulose in live Salmonella biofilms using luminescent oligothiophenes


texts: Trees growing around objects vs pushing them away. Where is the threshold?

texts:
If a tree grows against a taut wire then the tree will grow around it, eventually enveloping the entire wire. This often scars the tree, and if the wire is thick enough, it will interrupt nutrient flow and cause more significant damage.

But if the tree grows against a larger obstacle, such as a wide board, the tree displaces the obstacle as it grows.

As a real-life example of this, I have a large pine tree on my property next to an old wooden building. The tree, as it grew, pushed hard enough against the building's eaves to bend a 2x4 piece of lumber five inches out of the way. When that 2x4 finally met the rest of the building, the tree could no longer move the board and started growing around it.

Where is this threshold? I assume it can be described as a simple pressure (force over area), and that it is dependent on the specific type of tree. Is this tabulated somewhere?

Specifically, I wish to hang a 40lb (18kg) weight, permanently, from a branch of an ~80ft (~25m) lodgepole pine. I intend to use some sort of wider material in between the cord and the branch. It would be great if I could simply run the cord through a larger-diameter pipe and position this pipe over the top of the branch. But if this wouldn't be sufficient then I'll use boards (or similar) to distribute the weight. I won't be constricting the entire circumference of the branch.

I know that mounting a bolt into the tree would be better, but that isn't an option for me in this case.

I don't want to do this: (!)

image source


texts: What is the effect of garlic on intestinal flora?

texts: Now that we can compare whole microbiomes, has there been investigations on the effect of garlic (or diallyl disulfide, its main ingredient) on intestinal flora? From the proven antimicrobial activity, it should work like antibiotics. But does it leave "good bacteria" counts untouched?


texts: Did the eugenics program in Nazi Germany have a measurable effect?

texts:
Did the killing or sterilisation of people considered as living a "life unworthy of life" in Nazi Germany have any measurable effect on the "average health" of Germany? Is there any statistical evidence that the rate of (a specific) mental or physical illness is lower in Germany compared to other countries that were not affected by the Nazis  (I guess you would need to have data on the rate of that illness from before the eugenics program as well)?

P.S. Please note, I'm neither interested in discussing the ethics of eugenics, nor in condoning what has happened in its name under the Nazis. I just want to know what the result on average health (if there is such a thing) was.


texts: If I graft two trees together while young, will they grow as one plant?

texts: If I were to graft two apple saplings together --  by bending the tops toward each other and lashing them together --  will the plants grow as one and benefit from one another, or will they be fighting each other for root space and light? If they would grow with each other, then I could theoretically grow a line of closely spaced fruit trees to any length, and they would be strengthened by each other in bad conditions.


texts: What's the exact species of this African Giant Snail?

texts:
We've got an African Giant Snail a few years ago but failed to identify the exact species so far. When we got it, it's been about 20 % smaller than now, so it's probably not been an adult snail, but we don't know the exact age.
We only got this single snail, so there's no way to check for the eggs.
Here's a picture (small version, about 400 KiB) and a link to a bigger version. If you need more detailed pictures of certain parts, please let me know.

Bigger version: https://imgur.com/a/O9Bm2Tf (about 2.2 MiB)
This picture shows that the apex is about 12 centimeters (4.7") in length, while the foot is about 14 centimeters (5.5").


texts: Why are males more likely than females to have autism spectrum disorder?

texts:
The male to female ratio in autism spectrum disorder is around 4:1. However it seems ASD is not a simple X-linked disorder.

Then how is it possible males are more susceptible than females, if the causal genes are located in autosomes?


texts: What plastic eating organisms are there to help with plastic in landfills problem?

texts:
I see some popular science articles on the plastic eating bacteria and fungi appearing on the web since 2009. Most of the articles praise discoveries, because such organisms promise to break down plastics which were previously thought to be indestructible. However, from the articles it is hard to understand the total number/names of promising organisms that can biodegrade plastic.

Additionally, it's hard to gather from the dated articles if these plastic eating organisms have passed safety testing - for example that they don't break down plastic into something volatile and toxic.

My question is - which organisms as of 2013 are seriously considered for solving the plastic in landfills problem?


texts:
What is meant by "a codon codes for an amino acid"? Does it mean in order to build that amino acid you must combine those three nucleotides?

Does it mean anything more than provides the instructions for manufacturing that amino acid.


texts:
I've heard that part of cognitive processing is information passing between left and right cerebral hemispheres.

  This is what happens in the Cerebral Cortex which is divided into two hemispheres,
  left brain and right brain connected by a thick layer of nerve fibers called the corpus callosum. These nerve fibers allow messages to pass between the left and right brain
  hemispheres

My question is When a thought 'crosses your mind', does it literally cross between left and right cerebral hemispheres?

Assumptions:

I'm making a big leap from 'electronic impulses of neurons' to 'thoughts'.


texts: Why does excess dopamine activity in the pleasure centers results in less pleasure in schizophrenics?

texts:
According to the dopamine hypothesis of schizophrenia, there is an excess of dopamine in the mesolimbic pathway (nucleus accumbens), and this contributes to the positive symptoms of schizophrenia.

I am not sure what the cause of anhedonia (reduced interest), one of the negative symptom of schizophrenia. If nucleus accumbens plays a role in the reward system and there is an excess of dopamine, isn't it the case that there should be an increase in interest, that is, no anhedonia?


texts:
a quick question. I am looking for complete personal genomic data of human individuals. The only requirement for the genomic data is that it contains the complete set of SNPs of a human individual. So far I found only one, a hispanic female.

Are there any similar personal genomic data available on the web?
Any database I can access with a collection of SNPs per individual?


texts: Could be misleading using some terms to describe certain phenomena?

texts:
I am implementing a series of comparative analyses related to Low Complexity Regions in some organisms. Given that these regions show a wide range of length (measured in amino acids) and different characteristics, writing my report I would like to use "mosaicism" to describe this interspersion. Given that the term mosaicism is used to describe when someone have two or more genetically different cells inside his or her organism, I am in doubt if using this word could be misleading or, given that the term per-se indicates a set of gussets that compose a picture, to consider it somewhat elegant given that is clear enough what I am talking about.
Obliged


texts: Why are my assay absorbance values very low?

texts:
I am culturing SH-SY5Y cells in 96-well plates at a seeding density of $1.2 \times 10^5$ cells/mL. I differentiate the cells with retinoic acid for 6 days before giving them treatments. The cells look okay under microscope after the treatment. However, every time I read the plates, I get absorbance values of less than 0.2 (including my control).

I have tried increasing the volume of MTT reagent (5mg/mL), increasing the incubation time, but in vain.

Increasing the cell density indeed increase the absorbance, but the outcome seems illogical. A seeding density of $2 \times 10^6$ cells/mL gives absorbance values of 0.4+ (less than 0.5).

I am pipetting the mtt reagent and media out one-well-by-one-well using a micropipette. Assuming no pipetting errors and loss of cells, what are the possible causes of getting these low absorbance values?


texts: How does an isotonic environment affect fish?

texts: Fish receive oxygen needed from water that passes through their gills. If fish were isotonic to their watery environment, what problems would this pose to them?


texts: Difference in variance of Cys in protein sequences

texts:
Suppose I have got two sets of proteins (amino acid sequences). In one set, I find that the variance in the percentage concentration of the Cys is way more (65.34) than the variance of Cys in the other group (0.456). Does it mean anything? Does this have any sort of biological implication?

The concentration has been calculated by dividing the total number of Cys found by the size of the protein sequence.


texts: When running gels what is the difference between constant volts or constant amps?

texts:
In general, you want to be consistent with running your gels either at constant volts or constant amps. However, it is very clear that during the progression of both PAGE and agarose gels, the free parameter changes due to the change in resistance of the gel.

While there are safety reasons why you run one vs. the other, I'm curious how these difference affect the migration of your gel.


texts: Why is there no herd immunity against common cold coronaviruses?

texts:
In discussions of herd immunity against SARS-CoV-2 the underlying assumption usually appears to be that the virus basically stops spreading once a sufficient percentage of the population has overcome an infection.
My understanding is that this approach does not work for the seasonal flu, for instance, because the flu virus mutates too quickly. Since coronaviruses do not mutate so quickly, herd immunity "can work" for them.
Question: Given how long common cold coronaviruses have been spreading in the human population, why does there not appear to be herd immunity against the common cold coronaviruses? To what extend can we expect herd immunity to SARS-CoV-2 if there is no herd immunity against common cold coronaviruses?


texts: Sequencing inaccurate at the primer site

texts:
The times I have sent a sample to sequence, both the forward and the reverse primer sites, show high inaccuracy while the rest of the gene is correctly sequenced. Because of this, the sequences of my in silico construct and the sequenced sample do not align in this section; but they do align at the rest of the gene almost 100%.

Is there a reason for this? Is this simply a sequencing artifact or is should I trust the sequenced sample and assume that the primer sites have mutated?


texts: Tests for object size discrimination in mammals?

texts: Are there common testing protocols for establishing whether an animal (mammals especially) can distinguish the size of objects? In particular, are there procedures or is there good literature on ways to determine whether a given species can recognizes a given object as enlarged in specific settings, ideally in ways that can allow comparison across species (e.g., species A sees an object as enlarged while species B does not).


texts:
Food chains generally consists of three or four steps. There are some food chains containing five steps. What are the examples of food chains containing more than five steps and what is the longest known and longest possible food chain?
Edit: Ignoring the decomposes and detritivores, what is theoretically the longest-possible single unidirectional acyclical food chain?


texts:
There seems to be general agreement that theoretical Hopfield networks (consisting of artifical neurons, namely McCulloch-Pitts neurons) are biologically rather implausible, among other reasons because of their (rather strictly) symmetric synaptic weights. On the other side, some authors claim that there are neural assemblies in the brain that qualitatively behave like Hopfield networks, i.e.

they are strongly interconnected
they synaptically store a limited number of (activity) patterns
which they reach as attractors when fed with noisy or incomplete input patterns
they "learn" (mainly) by the Hebb rule

The system of hippocampal CA3 neurons is suggested to be one such assembly.

My questions:

Is there an agreement among experts that hippocampal CA3 neurons really behave similar to a Hopfield network?
Which other assemblies (possibly nuclei?) are believed to behave similar to a Hopfield network, too? (Some examples would be welcome.)


texts: Heterochromatin binding sites position information

texts: I am working on a project and I'm trying to find data on the position of genes and heterochromatin binding sites such as HP1 in Drosophila melanogaster. Is this information available for the DGRP lines? Would I be able to measure the distance between a gene and its nearest binding site from such data?


texts: Metapopulation structure - book recommendations

texts:
What book would you recommend me to study:

the dynamics of metapopulations,
the structure of metapopulations,
the evolution in structured metapopulations?

I am not looking for an introduction but for a book that offers good and extensive mathematical formulations.


texts: Is there an animal venom to which humans are naturally resistant?

texts:
Some species, no matter how poisonous or venomous, have natural predators that can withstand the poison/venom. Does human also have something similar?
This question came to me after I spent an hour observing my pet black widow and looking up related materials online. I realize that some species of wasps can neutralize the poison of the black widow naturally. Hence, I wonder if humans have something similar.


texts: How much can you learn about species variation from a skeleton?

texts: I just read about the discovery of the 1.8-million-year-old human skull in Georgia, and how it suggests that early humans were all one species instead of distinct ones. Would an archaeologist unearthing dog bones a million years from now know that a Great Dane and a Chihuahua are the same species?


texts: What is the name of this bush with red fruits?

texts: I have seen this on Corsica (Island of France):


texts: Cannot see images beyond a certain magnification with a microscope

texts:
Using a new microscope with my son, we cannot see images beyond a certain magnification:

Eyepiece: 25x - Objective lens: 4x   --> OK
Eyepiece: 25x - Objective lens: 10x  --> OK
Eyepiece: 25x - Objective lens: 40x  --> not focused
Eyepiece: 25x - Objective lens: 100x --> not focused

In the last two cases, we try moving the stage along all its range, without getting anything.

Same issue using a 10x eyepiece.

On the 100x objective lens "OIL" is written; does it mean the observation needs to be done through oil instead of air? Or just that oil is used inside the objective?

We did not prepare the leaf; we just put a small piece of it between two slides.

Are we doing anything wrong?

Observing a leaf at 250x, we can see tiny round structures (I think barely bigger than what can be possibly seen by our eye): are those the cells?


texts: What processes are responsible for focusing on an image only seen by one of the eyes?

texts:
When a person is spying from around a corner with only one eye, it's rather easy to ignore the other eye's image, since it's probably much darker, because one usually spies around a corner standing close to a wall.

But if both eyes get equally bright visual input, it takes some effort to try and stay focused on just one of them. What processes in human body allow such action?


texts:
Most organic structures built from hydrogen, oxygen, nitrogen and carbon. They are represent 1-,2-,3-,4- bond relations (chemical valence) which allow to build variety of chain structures.

Are there exist some replacements for these elements to create complex structures that theoretically can create life (self-reproduced or be a part of cell as organelle)?

UPDATE

Is there a common chemical model for life in the universe?
Arsenic-eating microbe may redefine chemistry of life
A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus
https://en.wikipedia.org/wiki/DNA#Alternate_DNA_structures
https://en.wikipedia.org/wiki/Arsenic_DNA


texts: Do tRNAs that recognize multiple codons have any preference for one over another?

texts: What are the effects of the different binding strength/affinity between the synonymous codons corresponding to a single tRNA ?


texts: How do signalling molecules find their receptors at large distances?

texts:
I have been baffled with this question approx. for a dozen of years for now.
There is a default "lock & key" mechanism of action assumed for the interaction between a signalling molecule and its receptor, but while applying a bit of combinatorics and biophysics to it I find the following inconsistencies.

Suppose a long-lasting neuropeptide is circulating in a CSF or blood macrocirculation. Or suppose a norepinephrine or other neurohormones are released by hypothalamic and pituitary cells into the macrocirculation for sympathetic or parasympathetic signalling. Accroding to the logic of "lock & key" mechanism, in order for a "key" signalling molecule to activate its "lock" receptor an active site of this molecule - the molecule partition which directly reacts with the receptor as it is generally not the whole molecule which reacts with the receptor - should come in direct contact with the relevant active site of its in-membrane receptor. So by such combinatorial logic, if there are thousands of receptors on outer membranes of cells in CSF or vessel endotelium along the way of which this "key"-molecule is travelling, this molecule should try to "lock into" every such potential "lock" receptor in order to "check" if this is the right "lock". In other words, while travelling across long distances such "key" signalling molecules should not just float in CSF or blood vessels as is generally depicted, but slide across all outer cell membranes in CSF or across vascular endotelium in blood or lymph circulation in order to "check" every potential "lock" receptor for finding their relevant receptors for eventual activation. It is definitely not the case, but it the result of applying combinatorial "lock&key" logic.

Somehow it seems (for myself, at least) that it is just assumed that a "key" molecule released at distances which are millions> of times larger than the molecule size should just "lock" for granted into its appropiate receptors throughout the organism. But suppose a "key" molecule travels in CSF or interstitial fluid in the vicinity of its appropriate membrane "lock" receptor, but with the molecule's reaction (active) site pointed away from its receptor or at an angle. Should the "key" molecule not then react with its "lock" receptor?? Is there a minimum effective reaction distance established between a "key" molecule and its "lock" receptor in order to effectively activate the receptor?

The latter argument holds true also for small distance 20-40 nm synapses with molecules released in it whose size would be minimum 1000 times smaller than the synapse size. Should a neurotransmitter molecule not react with its receptor in a synapse if the molecule's active site would be pointed 180 degrees away from the receptor's active site?


texts:
In this article, the author says:

  Evolution isn’t “leading up” to anything, it just drunkenly limps along using the same set of tricks in slightly different orders.

On other occasions, however, the term "evolution" is often deployed as a process that develops gradually, typically from a simple to a more complex form, or from not adapted to more specialized and "fit".

These contrasting interpretations of evolution make me wonder how I should interpret "to evolve" and "evolution" in the context of processes involved in speciation?


texts:
Let's say I have a DNA sequence with the following structure:

$$ 5' - N_n - S_1 - N_{1000} - S_2 - N_{1000} - S_3 - N_n - 3' $$

Here, the $N$s represent stretches of arbitrary sequence of the indicated length. $S_1$, $S_2$ and $S_3$ are all unique sequences 20 bp in length.

I design a forward primer PF that anneals to the positive strand at $S_1$. I design two reverse primers PR1 and PR2 that anneal to the negative strand at $S_2$ and $S_3$ respectively. Their annealing temperatures are reasonably close.

Clearly, PF and PR1 together will produce a 1040 bp PCR product, and PF with PR2 will produce a 2060 bp product.

Now let's say I add 0.2 μM PF (standard concentration), 0.1 μM PR1 and 0.1 μM PR2 all in the same reaction. I then run a PCR, with extension time sufficient for the 2 kb product.

I can see the following possible outcomes:

I get a 50/50 mix of 1 kb and 2 kb products.
PR1 competes aggressively and I get hardly any 2 kb product and a lot of 1 kb product.
After a few cycles, the 1 kb product that has accumulated serves as an efficient forward primer for PR2, and I end up getting mostly 2 kb product and little 1 kb product.

Which one will happen? If it depends, what are the major factors on which it depends? Primer concentrations, extension time, annealing temperature, dNTP amount, number of cycles?

This question is basically a very simplified multiplex PCR. While much has been written about practical applications of multiplex PCR, I am hoping that answers will help me understand the considerations that go into deducing optimal multiplex PCR conditions without doing any empirical calibration. This isn't to circumvent the calibration, but to understand the process conceptually.


texts: How do you determine if donated, stored blood is viable?

texts:
Think about stored donated blood; What should we check before transfusing it to a patient, to see if blood is still viable?
What methods to use?
What components should it have in what levels, to be counted as viable?
Detailed version of the question, including some background:
Since I'm a software engineer I'm not aware which kind of topics should I search to find answers that I need. Of course I have tried to find publications and books related directly to this topic. But I could not find any. What I need at the moment is some material to do "some reading/research". And of course, if possible (which I don't know if there are too many possible answers or not) direct answers would be extremely helpful.
Of course I have done some research on indirectly related topics. For example; I have read papers about results of blood storage on blood quality etc. But these papers just analyze the effects, while it is not clear for me if these analyzed materials represents viability of blood.
For more detail, things those analyzed in few papers that I have read are;

CBC: The CBC consisted of 10 parameters: white blood cell (WBC) count, red blood cell (RBC) count, hemoglobin (HGB), hematocrit (HCT), mean cell volume (MCV), mean corpuscular hemoglobin (MCH), mean corpuscular hemoglobin concentration (MCHC), red cell distribution width (RDW), platelet (PLT) count, and mean platelet volume (MPV).
Differantial: consisted of relative percentages (%) and absolute numbers (#) of neutrophils, lymphocytes, monocytes, eosinophils, and basophils.
Reticulocyte: The reticulocyte enumeration consisted of relative percentage (retic %) and absolute number of reticulocytes (retic #), and immature reticulocyte fraction(IRF).
The NRBC: enumeration consisted of NRBC per 100 WBC (NRBC %) and absolute number of NRBC.
Others: Factors V, VII, VIII, X, and XI, protein S (PS), a2-antiplasmin (AP), and fibrinogen; and the activated partial thromboplastin (APTT) and prothrombin (PT) times. Factors VIII and factor IX.

Still, I'm reading about each of these. What I'm in need is someone help and say; like:

"You are totally lost, these are not related to your case"
"You should check this paper which is related to your case"
"This, this and this ones in your list are what you are looking for. Focus on them."

Thanks


texts: Could Cyanobacteria farms help dilute pollutants in the atmosphere

texts:
If I understand correctly, roughly ~2.8 billion years ago cyanobacteria started pumping large amounts of oxygen into the atmosphere.

Using modern industrial processes could this be emulated by making cyanobacteria farms to help slow down the climate problem?

I also read somewhere that someone was able to genetically (or through other means) turn off the ability of a specific bacteria to reproduce causing it to produce a byproduct much more efficiently. Could this also help these "farms"?

Alternatively could we genetically strip the bacteria of all other functions other than procreating and photosynthesis? Making this bacteria live in a "bubble" would mean it wouldn't need a lot of defense mechanisms. This could make a single purpose bacteria that would be super efficient at doing this single task.


texts:
I live in Canada and tap water is drinkable, as a matter of fact, the government puts a little bit of flouride in the tap water so it cleans your teeth.

My wife and mom always tells me not to drink the tap water when it's warm/hot.

Is there something in the water that's bad for the body or is this a myth? (bacterias in warm/hot water vs cold)

Added info: The water is heated in the water heater which is in the basement of my house. It is a new water heater, only a year old. My house is built 7 years ago, which for a house it's not old. I don't know about the pipes though


texts: Textbook for quantitative biochemistry with thermodynamics, as an alternative to Voet, Voet & Pratt (Fundamentals of Biochemistry)?

texts:
I'm looking for a great textbook on biochemistry that covers core topics: relevant aspects of thermodynamics, reaction kinetics, metabolism (e.g. krebs cycle, respiration, etc.). Ideally it would also be quantitative in its approach and use mathematical models where relevant.

The classic textbook is Voet & Voet & Pratt (Fundamentals of Biochemistry) and I think that's a horribly written textbook. It uses concepts before actually defining them (and when it does define them the definitions are obtuse and have no conceptual motivation). Is there an alternative to this? Any recommendations?


texts: Difference vector target and genomic target

texts:
In Pfu turbo DNA Polymerase AD information sheet (and possibly in many other) different amplification targets are divided in Genomic DNA targets, Vector DNA targets and cDNAs.
What is the difference between the first two?


texts: Why do women have less synapses / neurons / brain mass than men despite having the same average IQ?

texts:
I don't mean to cause offence or suggest than men and women shouldn't be of the same intelligence — that's not something I'm here to dispute. What I want to understand is how this is possible given the vastly lower average synaptic / neurone count and weight in the average female vs male brain, in terms of both the overall brain and the neocortex.
Are there some systems that the female brain employs to compensate for a lower number of neurons, and if so is it dependent to the hormone estrogen or is it something inherent to the female brain? Is it just the case that the male brain has vast redundancies, if so why does brain weight correlate with IQ if it is redundant? Or perhaps it's the discrepancies in synapse count do not extend to areas that are most closely linked with higher order thinking. This is the explanation that I am leaning to, and if someone could explain which areas these are and link to a study that shows that the male vs female average in these areas are the same, then that would be greatly appreciated (I'm not looking for areas that are the same size adjusted for total body weight, I'm looking for areas with the absolute same number of synapses/neurones).
Studies:
Female brains on average lighter than male brains: https://pubmed.ncbi.nlm.nih.gov/8072950/
Female brains on average have lower neocortical neurone count than male brains:
https://pubmed.ncbi.nlm.nih.gov/9215725/#:~:text=The%20average%20numbers%20of%20neocortical,brains%2C%20a%2016%25%20difference.&text=Sex%20and%20age%20were%20the,no%20influence%20on%20neuron%20number.
Female brains have on average a lower cortical synaptic density: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2567215/
Context:
I am transgender (and taking estrogen) and have read that taking estrogen can move brain volume and weight closer to average "female proportions" to quote the study, and that this does not appear to negatively affect cognition. So, this is a question that is hugely important to me and does not come from a place of mal-intent.


texts: Can one switch the DNA present in a sperm cell?

texts: Can a donated sperm cell be stripped of its original owners DNA and be replaced with DNA of another person to make a biological child of a man who has low production in sperm?


texts: What makes a bacterium move away from a neutrophil cell?

texts: In this video we see a bacterium seemingly moving away from the neutrophil that is chasing it. What mechanism makes it "want" to avoid the neutrophil? It doesn't seem to mind being around other cells of the same organism. Why does it react differently to a neutrophil?


texts: Does the speed of electrical impulses through neurones decrease with age?

texts:
From what I read on the NatGeo app, it stated that the speed of the electrical impulses that are sent by a neurone will be approximately 332 kilometers per hour.

Will the speed of this electrical impulse decreases over the years as we age?


texts: Why does liver wrap around inferior vena cava?

texts:
As shown in the image, the liver wraps around inferior vena cava, which takes blood from liver via hepatic veins. Is there an advantage of having the inferior vena cava closer to the liver rather than abdominal aorta? I am guessing it has to do with lower blood pressure in the veins, but I want to check.

It could also be evolutionary thing that has no reason for such structure, but that wrapping around structure seems to have a purpose.


texts:
In terms of phyla, mollusca, annelida and arthropoda are schizocoelic, whereas echinodermata and chordata are enterocoelic.

I know that their difference lies in the formation of the coelom but how exactly is enterocoely more advanced than schizocoely?


texts: Does RNA-LPX expression of antigen by DC induce only T-cell with that antigen specificity?

texts:
There was a recent publication concerning use of IV administered RNA-lipoplexes with an adjusted electrical charge to encourage dendritic cells (DC) to pick up the RNA package encoding viral or mutant neo-antigens, for example, a sequence of melanoma tumor cell coded to RNA. The paper is at Systemic RNA delivery to dendritic cells

After reading that abstract and related papers (see Dendritic Cells Pulsed with RNA are Potent Antigen-presenting Cells In Vitro and In Vivo By David Boczkowski et al I came away with the concept that the RNA segment of encoded tumor protein was taken up by a DC and the DC translated that to a protein (antigen) that it presented with MHC of the appropriate class (class I I believe in these tests) to a naive T-cell, which would subsequently amplify and pursue and kill tumor cells with that antigen (by becoming CTL cytotoxic T cell leukocytes).

A quick look at my immunology text from NIH tells me that this mechanism (DC's bringing antigen to naive T-cells in lymphatic tissue) ensures "that rare antigen-specific T cells will encounter their specific antigen on an antigen-presenting cell surface."

My question is does this mean that the so-called "mutant neo-antigen" of a particular tumor in an individual must still find a T-cell receptive to that sequence (epitope) at least in part (say fractionally)? I guess I'm wondering whether there might be the case where a particularly diabolical tumor presented such novel sequences that no existing T-cell rare or otherwise could be receptive to a fraction of its sequence (even when a customized RNA delivery of a selected portion of the sequence was delivered via DC to the T-cell).


texts: Any books/publications about what life was like before antibiotics?

texts: Just wondering. We've been discussing antibiotic resistant bacteria a bit in lecture, and how we're slowly sinking into a pre-antibiotic era again.


texts: What is the difference between Single Nucleotide Polymorphism (SNP), Mutation and Structural Variation(SV)?

texts:
This is a question which plagues many people and today I was wondering it myself while writing a grant. Indeed, I've seen many people use the terms interchangeably, but they are all very different from each other.

So What is the difference between SNPs, Mutations and Structural Variations?


texts: Inheritance simulator not working properly

texts:
I created a python program to simulate inheritance (a simplified version of it) to better understand how it works. A person is represented by a class that contains a chromosome property, a method for reproducing with another person, a method for generating gametes (through recombination), and a method for calculating how similar a person is to another person (by comparing the chromosomes).
The problem with my program is that cousins are not as similar to each other as they are supposed to be. My program says that 2 cousins about 75% similar when they should be 12.5% similar. I don't understand why this is. I think it could be down to 2 things

My similarity function is wrong.
The way I am representing a chromosome is wrong.

Here is the code:
    import random

    CHROMOSONE_LENGTH = 1000
    NCHROMOSONES = 22

    class Person:
        def __init__(self, chromosones = None):
            self.chromosones = chromosones
            if  chromosones is None:
                self.chromosones = []
                for i in range(NCHROMOSONES):
                    self.chromosones.append ((self.get_random_dna(),self.get_random_dna()))

        def get_random_dna(self):
            #return [random.random() for x in range(CHROMOSONE_LENGTH)]
            return [random.choice(["0","1"]) for x in range(CHROMOSONE_LENGTH)]

        def get_gamete_meiosis(self):
            gamete = []
            for i in range(len(self.chromosones)):
                gamete.append([])
                for a,b in zip(self.chromosones[i][0],self.chromosones[i][1]):
                    gamete[i].append(random.choice([a,b]))
            return gamete

        def reproduce(self,mate):
            chromosones = []
            my_gamete = self.get_gamete_meiosis()
            mate_gamete = mate.get_gamete_meiosis()
            for i in range(NCHROMOSONES):
                chromosones.append((my_gamete[i],mate_gamete[i]))
            return Person(chromosones)

        def get_similarity(self,other):
            sim = 0
            for s,o in zip(self.chromosones,other.chromosones):
                for a,b,c,d in zip(s[0],s[1],o[0],o[1]):
                    if a == c or a == d:
                        sim += 0.5
                    if b == c or b == d:
                       sim += 0.5

            return sim/(CHROMOSONE_LENGTH*NCHROMOSONES)

    grandmother = Person()
    grandfather = Person()
    child1 = grandfather.reproduce(grandmother)
    child2 = grandfather.reproduce(grandmother)
    grandchild1 = child1.reproduce(Person())
    grandchild2 = child2.reproduce(Person())
    # Should be 12.5%
    print(grandchild1.get_similarity(grandchild2))

A chromosome is represented by an array of 2-tuples. Each tuple represents a chromosome pair. The number of pairs is set by the NCHROMOSONES variable. There are 22 pairs in the above code.
The actual genetic data is represented by an array of 0s and 1s. The number of 0s and 1s in a chromosome is set by the CHROMOSONE_LENGTH variable.
The similarity function takes two people and compares them at each position of each chromosome. If the two people have the same number at a given position, then it adds 0.5 to the sim variable. It then averages this across all positions. The reason I add 0.5 is because two people can either be 0%, 50% or 100% identical at a given position on a chromosome. 0% occurs when neither pair is identical, 50% occurs when 1 pair identical, and 100% occurs when both pairs are identical.
I noticed that as I use more symbols than just 0 and 1 to represent genetic data, the similarity actually approaches 12.5%. But I don't understand why this should be.
So my basic questions are:

Is my way of calculating the similarity correct.
Why can't I use just 0 and 1 to represent genetic data?


texts:
I know that my blood type is AB. I wanted to know if I am cis-AB since cis-AB seems to have a different approach in blood transfusion.

Is there a lab test that can verify is a person is under cis-AB blood group phenotype?


texts: The Trp operon has 2 methods to check for presence of tryptophan, one indicating the absence of free Trp and the other the absence of charged Trp tRNA. If both methods showed absence of Trp there is tryptophan synthesis. However, the synthesis of tryptophan involves 5 enzymes to be synthesized, and usually we find all the amino acids in a protein such as an enzyme. Therefore, there is high probability that Trp is found in these 5 enzymes. Where does that Trp come from if there is neither free tryptophan nor charged tRNA for Trp?


texts: Can RNases/DNases survive in strong acid/base solutions of around 10M?

texts:
This might be a very stupid question, but I am worried about RNase/DNase contamination of my samples. Since I use 37% HCl and 10M NaOH to pH almost all my buffers, this is a potential source.

I have read however, that both NaOH and HCl should hydrolyze the peptide bonds in amino acids at high concentrations. For HCl, however, I have read that a heating step is required to facilitate the protein hydrolysis, so am a bit confused. Perhaps someone with a better background in chemistry could help?

Thanks a lot!


texts: Rigorous definition of the kinship coefficient and proof of a recursion thereof

texts:
I am reading Section 5.2, Kinship and Inbreeding Coefficients, of Kenneth Lange, Mathematical and Statistical Methods for Genetic Analysis. There the kinship coefficient $\Phi_{i,j}$ is defined for two relatives $i$ and $j$ as the probability that a gene selected randomly from $i$ and a gene selected randomly from the same autosomal locus of j are identical by descent. Then the book states that suppose $k$ and $l$ are the parents of $i$,
$$\Phi_{i,j}=\frac12(\Phi_{k,j}+\Phi_{l,j}) \tag1$$
with some exceptions.

Equation (1) seems intuitive. Yet it is slippery for a proof especially considering the exceptions. The root cause is that the definition of $\Phi_{i,j}$ is vague albeit seemingly plausible. I am seeking a mathematically rigorous definition of $\Phi_{i,j}$ and a proof for Equation (1) together with the condition under which it applies.


texts:
To study DNA-protein interaction, I want to do a DNA retardation test by mixing the protein with DNA and afterwarts loading it on an agarose gel to see if the DNA migrates slower. I've found some articles where they do this and they state that they mix the DNA with protein in an 1:8 charge ratio, but I can't really figure out how to interpret this

Could anyone tell me how to calculate a DNA:protein charge ratio? If 1:8 is stated, how should I interpret this?


texts: Why does vision go blurry after microscope use, and how to prevent it?

texts:
After using a binocular microscope recently for about 20 minutes, my vision went blurry and for an hour or so it was much harder to read small text. This occurs to a (far) lesser extent whenever I use it for a shorter time.

Why does this occur?
Which is the optimal microscope light intensity so this does not happen?
What other variables should I beware of?


texts: What happens to intrinsic factor exactly at the terminal ileum, where B12 is absorbed?

texts:
IF is very important for IF-dependent B12 absorption in the terminal ileum, the mechanism by which most of dietary B12 is absorbed. The B12-IF complex bind to IF receptors on enterocytes, but does the complex in its entirety get absorbed, or does B12 alone get absorbed and the IF is left outside?

The latter mechanism I came across in source 1 (see below), which stated the following:

  IF-B12 complex binds to specific receptors. Following this, the vitamin B12 is absorbed into the cytosol of the enterocyte by endocytosis, leaving behind the IF at the brush border.

However, several other books and articles (like 2-4) rather vaguely state that the IF-B12 complex is absorbed into the enterocyte. I've found two articles that discuss the existence of these two viewpoints, (5 and 6), but they are kind of old (from 1965 and 1989 respectively) and I don't know if the "mystery's been solved" as it were.

Sources:

Concise Textbook of Human Physiology (this specific page)
The Mechanism of Absorption of Vitamin B12 (cobalamin) in the GI Tract
Marks' Essential Medical Biochemistry (this specific page)
Textbook of Pharmacology (this page)
Intrinsic Factor
Vitamin B12 absorption and malabsorption


texts: What is wrong with this analogy: Individuals are to alleles what governments are to individuals

texts:
I'm an amateur when it comes to genetics, I'm hoping to learn something from the corrections. I am taking epigenetics into account (kind of); all 3 entities are susceptible to external physical influences.

Kind regards,

Frank


texts: Pangenesis and Lamarck's theory of inheritance of acquired characteristics

texts: I've read that Darwin had split ways with Lamarck's evolutionary ideas. Yet his theory of pangenesis seems to support Lamarck's theory of inheritance of acquired characteristics. What am I missing?


texts: Can an electrocardiogram be recorded with a single electrode?

texts: Is it possible to do an electrocardiogram with one electrode? Or is it neccesary to have multiple electrodes? I do not understand much about EKG, so I am sorry if this question sounds naive.


texts:
Both names are widely used, with what appears to me as a slight prevalence of “epinephrine” in scientific literature and an overwhelming prevalence of “adrenaline” in popular media.

Are there any well-documented and/or well-motivated guidelines for the usage of these terms?


texts: When reading a Wikipedia article to do with chickens, I have come across the term "clutch", but I was not able to entirely figure out what this word means. I was wondering whether the term clutch can be used to refer to any set of eggs by birds, reptiles, and amphibians, or whether a clutch must consist of a set eggs all by the same bird, reptile, or amphibian. In general, if a typical clutch by a well fed chicken amounts to a dozen of eggs, that seems like a lot of eggs for a chicken to hold within its body prior to laying them, hence my question about clarification and about what number would actually fit (I have seen as high as fifteen). It is this simply the number of eggs expected to live concurrently in a typical nest where more than one chicken would breed?


texts: How does Australia fit into 'New World' / 'Old World' dichotomy?

texts:
How are places such as Australia and New Zealand classified when differentiating geographic areas based on 'New World' and 'Old World?'

My understanding is:

New World = North America + South America (+ Central America)
Old World = Europe + Asia + Africa

This is biologically relevant via biogeography:

Ex: neotropical vs. paleotropical (comparable to New and Old World Tropics)

I've seen online sources group Australia / New Zealand in both New and Old World (or in neither). So what's the right answer?

Reputably cited answers only please!