texts: What is the meaning of 'primary' and 'secondary' sympatric speciation in this paper?

texts:
Sympatric Speciation in the Genomic Era. Both terms are used throughout the paper.
I'm not able to make sense of these terms in the contexts used.
I've also heard the terms 'primary' and 'secondary' gene flow elsewhere on the same topic - are they related?
From the abstract:

However,  I  argue  that  genomic  studies  based  on contemporary  populations  may  never  be  able  to  provide  unequivocal  evidence  of  true primary sympatric speciation, and there is a need to incorporate palaeogenomic studies in  to  this  field. This  inability  to  robustly  distinguish  cases  of  primary  and  secondary divergence-with-gene-flow may be inconsequential, as both are useful for understanding the  role  of  large  effect  barrier  loci  in  the  progression  from  localised  genic  isolation  to genome-wide reproductive isolation. I argue that they can be of equivalent interest due to  shared  underlying  mechanisms  driving  divergence  and  potentially  leaving  similar coalescent patterns.

From the introduction:

Lastly,  I  consider  whether  primary  and  secondary  sympatric speciation represent a mechanistic dichotomy, I suggest that primary and secondary contact can leave a similar genomic signature, when speciation is driven by tightly clustered or  large effect loci. Arguably, the advent of affordable population genomic studies should place less focus on whether study systems result from primary or secondary contact and instead focus on the mechanistic aspects of the genomic architecture and making progress in identifying the conditions and processes under which natural and sexual selection can drive speciation, without extrinsic barriers to gene flow.


texts: Why hasn't there been a serious effort to develop an anti-inflammatory that blocks the responsible genes?

texts:
After numerous years of reading about how to disable inflammation and related treatments, it appears that the common existing approaches are fundamentally wrong.

The most popular over-the-counter treatments target cyclooxegenase (COX) - see:
https://en.wikipedia.org/wiki/Paracetamol#Mechanism_of_action
https://en.wikipedia.org/wiki/Aspirin#Mechanism_of_action
https://en.wikipedia.org/wiki/Ibuprofen#Mechanism_of_action

COX inhibitors have been known to have a wide range of side effects (with even more recently reported, I forget what specifically). They are generally weak and only decrease rather than eliminate inflammation completely at the recommended dose.

The common prescription approach is largely topical steroid creams such as hydrocortisone - another crude and bad approach due to increased risk of infection among other side effects

The most recent and promising novel approach appears to be peptide chains that manipulate the immune system:
https://en.wikipedia.org/wiki/Immune-selective_anti-inflammatory_derivative

The main question: Why hasn't there been visible progress on a gene-blocking approach? There are all sorts of ways to block them - find all the proteins and other products that promote or cause inflammation, then consider all sorts of options to stop them. Options including blocking transcription, blocking translation, stopping the protein/product from exiting its cell, blocking its receptor, blocking intermediates.

Future "last resort" treatment for chronic debilitating inflammatory diseases could include "nonsense mutation" gene edits that permanently disable inflammation in specific cell types.

The end result would be a new generation of anti-inflammatory treatment guaranteed to block known mechanisms of inflammation at the source, instead of the largely ineffective and side-effect ridden standard approaches.

The cost might be prohibitive with today's technology although it would almost certainly become feasible with biochemical 3D printing.


texts: What is the minimum sample size to get reliable results in haplotype and nucleotide estimations?

texts:
Different software have different methods for estimating diversity and each method will have assumptions about the quantity of
data required to produce a reliable result. I am estimating the haplotype and nucleotide diversity by DnaSP6 program of Sanger sequences. I would like what is the minimum sample size requires to get reliable results.

Thanks in advance.


texts: Pee Shiver: Any reliable research about this phenomenon?

texts:
I came across 2 webpages about the science of pee shiver.

Link 1
Link 2

I wonder if there any reliable scientific research about this phenomenon. The 2 webpages I have hyperlinked attribute this to ANS(Automatic Nervous System) or sudden decrease of temperature in exposed body part while peeing.

But these 2 are just hypotheses, not proved reseach. Is there any?


texts: Why do mountain gorilla eat just 1.7% fruit, while lowland gorillas eat 25%?

texts:
Eastern lowland gorillas have more diverse diets, which vary
seasonally. Leaves and pith are commonly eaten, but fruits can make up
as much as 25% of their diets. https://en.wikipedia.org/wiki/Gorilla#Food_and_foraging

The mountain gorilla is primarily a herbivore; the majority of its
diet is composed of the leaves, shoots and stems (85.8%) of 142 plant
species. It also feeds on bark (6.9%), roots (3.3%), flowers (2.3%),
and fruit (1.7%) https://en.wikipedia.org/wiki/Mountain_gorilla#Habitat_and_ecology


texts: How much Cardiomyocyte Move in Relation to its Neurons?

texts:
I am trying to estimate how much cardiomyocyte and its things (mitochondria) move in relation to neurons

Movement of neurons (1)
Movement of cardiomyocytes
Movement of cardiomyocytes' mitochondrias (2)
...
Movement of stem cells - I think we can ignore this one

Motivation: some imaging projects have focused on the neurons etc ECG/... because they move relatively little in comparison to cardiomyocytes and their organelles; my interest is in the electromuscular view and I would like to understand how the movement of cardiomyocytes and their mitochondrias could be adjusted/calibrated in the time-frequency (t-f) data (spectrogram/...) of cardiomyocytes

Pseudocode

Simplistic view about including the effect of cytoarchitecture of organelles on the dynamics/movements based on statistics and probabilistic approaches

function getMitochondriaDynamics2D(signal2D, edges, Cytoarchitecture):
signal2D=$1;
edgesN=size($2,2);
organelles=[neurons, cardiomyocyte_minus_mitochondia, mitochondria, ...]; % given
organelles.cytoarchitecture = $3; % probabilistic values in Statistics
organelles.dynamics = zeros(1,edgesN-1); % preallocation

% Limit dynamics by cytoarchitectural restrictions
for organelle in organelles
    % include here systemic effects on organelles but Ignored here
    % etc Age, Smoking, ...

    % Let's loop local changes
    for edge in organelles.dynamics
        organelle.dynamics(edge) = organelle.dynamics(edge) .* ...
            organelle.cytoarchitecture(edge);
    end
end

return signal2D .*organelle(mitochondria).dynamics;

end

%% TODO here
function analysisMitochondriaDynamics2D(dynamics2D)
    ...
end

To find those probabilistic values

Embryology but I am weak here
databases and/or publications - which?

Biochemistry

I do not understand how much this should be considered here, but it could help to get any model

Atrial cardiomyocyte calcium signalling
mobility of the delayed-rectifer K+ channel Kv2.1 (3)

Useful keywoards

cardiomyocyte adult mobility

Hypothesis and Math/Physics/Bio

Hypothetical View of t-f data (2D) in cardiomyocytes: regular points separated by steady-gel-like areas - - seems to artifact of the movement

Physics about characterizing such areas:

... [ which mathematical methods ] ...

Sources

There are much studies in Embryology about cardiomyocytes and their movement, but I cannot understand their relation in the topic

Piquereau, Mitochondrial dynamics in the adult cardiomyocytes: which roles for a highly specialized cell?, 2013
How to measure Na/K channel activation at the membrane level?
Localization and mobility of the delayed-rectifer K+ channel Kv2.1 in adult cardiomyocytes.
Mitochondrial dynamics in the adult cardiomyocytes: which roles for a highly specialized cell?
PubMed with cardiomyocyte+"patch clamp", about measuring plated cells which are from hearts freshly minced in collagenase / EDTA. See PMIDs 27364017, 27076034, 26142302, 26241168, 26378152, ... [NickSandor]

Useful keywords

adult cardiomyocyte
possibly: Atrial cardiomyocyte calcium signalling
Mitochondrial dynamics
cytoarchitecture restrictions dynamics


texts: Do humans squint more readily at green light?

texts:
I know that humans won't squint their eyes even if exposed to dangerous levels of ultraviolet or infrared light because our eyes simply don't have the capability to detect it. Neither do the irises constrict.

Since the human eye is most sensitive to green light, does this mean that we will squint and/or constrict our irises more readily for green light? Perhaps even when the intensity is safe for our eyes? (Albeit close to dangerous levels)


texts: Why does botulinum toxin seem to be more dangerous to humans than to other mammals?

texts:
Various mammals seem to get away with eating parts of carcasses that we would prefer to not even touch, and that we assume will make us sick.
Because of that, I assume botulinum toxin is more dangerous to humans than many animals.

Is that right so far - can they handle more of some toxins compared to us?
Or are they better in avoiding harmful substances based on more suited olfactory sense?
Or are we just more afraid?

Assuming the differences exist - what is the cause for it?
Are there plausible explanations in terms of evolutionary pressure?


texts: If human proteins are synthesized from only 20 different amino acids, then how can there be such variety of proteins in human cells?

texts: I know that human proteins are synthesized using only 20 different amino acids. However, how can there be thousands of different proteins in human cells, if we only use 20 amino acids to make them?


texts: What is the name of this plant which is located in Hyderabad city of Telangana State,India?

texts: I found this plant in Hyderabad city of Telangana State,India.Many people of Hyderabad city have planted this flowering plant.I don't know the name of this plant.If it's flower treated as a circle,the flower has diameter of nearly 6cm length.Can any one tell me what is the name of this plant?


texts: Green feather-like formations in tap water - what is it? (with pictures)

texts:
These things recently appeared in my tap water Copenhagen Denmark, this summer 2013. They are very small, and have a feather like structure. I've called the water supply, and they thought that it was some tracer put in there by humans to trace if the warm water supply leaks into the tap water. But I could not show them the pictures.

What are they? Are they dangerous?

For size comparison: the green stuff is located on the top right of a piece of A4 paper.


texts: Why do simulations of dichromatic color vision portray medium wavelengths as yellow rather than green?

texts:
Please take the time to read & answer this at your own convenient pace.

Is this even the right way to put this?

Do you think this post better belongs in the Physics or Philosophy forums?

This must be part of the old philosophical question of whether you see the same colors as I do.

This is a simple question really, but the description may get a bit technical if your not familiar with the basics. If you find this complicated to read then I can write it more basically if you desire.

It’s important to bear in mind that we shouldn’t equate or compare other animals’ senses & perceptions with our own, such as ‘modified’, ‘enhanced’, ‘dehanced’, ‘reduced’ or ‘increased’ human senses.
We can form educated estimations about how the perception of other animals is through study of their nervous systems, brain & sense organ anatomies & behavioral tests, but have little way of proving how they actually experience things.
The same applies to other humans, only that we have more ways of proving how other humans actually experience things because we have language, but even that’s still very subjective.
It’s a basic fact that unlike shape, dimension & location, sensations are not matter & energy itself, but our brain & mind’s representation of them. For example, how do we know for sure whether other animals even perceive gradients of light as shades of black & white? It could turn out to be something totally different, even uncomparable or unimaginable for us.
This is common sense when mentioned, but many people forget or aren’t aware of this basic fact to keep in mind.

Nevertheless, what I’m wondering is whether the short-medium wavelength dichromats of most mammals & some humans & New World Monkeys, which have two kinds of opsins sensitive to short & medium visible EM wavelengths in constrast to having the extra opsin sensitive to long visible EM wavelength for most humans & anthropoid primates, actually see green or yellow as their primary color representating the middle EM wavelength?

Simulations of dichromatic color vision usually portray them as seeing the primary colors blue & yellow, with the rest being combinations of those primary colors & shades of black, grey & white.
In fact I’ve never come across a dichromatic simulation using green to portray the perception of the middle wavelength color for them.
Its always yellow.
Could it be because we’re not exactly sure whether short-medium dichromats actually see either green or yellow as their primary color for middle wavelength peak, if they even do see those colors for that matter?

However, yellow is not a primary color. It may be in art & design, but it’s not in biology & physics.
Yellow is the extreme end of red & green, & a mixture of red & green.
In biology & physics, red, green & blue are the primary colors.

So what I’m wondering is why do simulations of dichromatic color vision portray the perception of the medium visible EM wavelengths in gradients of yellow rather than green, the actual primary color for middle visible EM wavelength, & how can we know or give the best answer to what color dichromats see as their perception of middle wavelength of Visible EM?

So which color is it? Yellow or green?
& is it the same for all short-medium wavelength dichromats?

How would we know? If we can’t, then what is the best evidence & way to give the best educated guess?

Like why is the dichromatic simulation of the frog & parrots below using yellow & blue to represent their primary colors? Wouldn’t using blue & green be more honest to biology & physics? Isn’t yellow not a primary color but the extreme end of & mixture of both red & green?


texts: What is this giant mosquito-like insect?

texts:
I found this bug in my kitchen in this morning, in a suburb of Houston Texas, about 30 miles Northwest of downtown. It was on the wall, and when I went in for a closer look, it quickly flew away - up towards the light, then crash landed behind the refrigerator where I hit it with bug spray.
It looks sort of like a mosquito, but much much larger.
Everything I find online about "giant mosquitoes" points to the Crane fly or "mosquito hawk" - which I've seen plenty of (very common here). I'm no expert, but this doesn't look like a cranefly.
I also read that giant mosquitoes are known to hatch after hurricanes, and there was just a huge one <200 miles from me. But those accounts speak of smaller insects (albeit, still very large for a mosquito).
For example, this article about "gallinippers" in North Carolina, speaks of mosquitoes only the size of a penny.
I did not think to put a coin in the shot for reference, but based on the size of the paper towel underneath it, it must be at least the size of a quarter.
Is this even related to a mosquito? What could it be?


texts:
I was doing this question that asked: "How many centromeres does a typical chromosome have?"

I thought one and the answer was:"One, except for holocentric chromosomes."

So then what are "holocentric chromosomes"?

I assume they would be chromosomes with more than one centromere, but then why do they need more than one centromere? And where can I get some more information on them? I tried googling but did not find much info on this.


texts: Do I have to chew for digestion to kick in?

texts: Liquid nutrient-rich products (such as Soylent) are consumed without chewing. But if I have to chew to initiate digestion, are those nutrients really "processed"?


texts: How do different tissue culture matrices affect background in fluorescent microscopy?

texts:
In response to my previous question, I've been reading up a little bit on poly-D-lysine, Collagen I, Collagen IV, laminin, and other tissue culture coatings that promote cell adhesion. I've always assumed that anything other than standard TC-treated plastic or glass would significantly increase background, but perhaps my views on background fluorescence are a little outdated. Does anybody have experience with these in a fluorescent microscopy/high-throughput screening environment?

Specifically in my case, I'm looking at endocytosis and trafficking of a labeled protein into the lysosome. I'm labeling the protein with the pH-dependent dye pHrodoTM from Molecular Probes, which supposedly has very little fluorescence at neutral pH, but becomes very bright as the pH drops when endocytic vesicles become lysosomes. This theoretically means that a final wash step is not needed, but with a matrix coating on the plates I'm worried about background.

So, what is the current thinking as far as background fluorescence of the various TC matrices is concerned? Does the background come from the matrix itself, or by the fluorescent dye becoming adsorbed to it? Is it wavelength-dependent? Fortunately I may not be stuck with my poorly-adhering cells, and I may not need supplemental matrix at all in the end, but I still want a better understanding of how it works.


texts: Why does V. cholerae produce a human specific choleragen?

texts: V. cholerae secrete choleragen to grow and escape human intestines, however choleragen does not work on other mammals, why so? Why didn't it evolve a general mammal affecting choleragen? This question is a continuation of the last comment on the only answer for my previous question, How does Vibrio cholerae benefit from infecting its host? Kindly refer to the answer and comments in that question as well.


texts: What is the smallest known organism with a skeleton?

texts: See question title. After doing some looking around on my own I haven't found much so I figured I'd ask some experts.


texts: Different Mutations Leading to Same Allele?

texts: Can different mutations lead to the same allele? In my genetics books, I always see alleles referenced as, eg. Aa where A = dominant and a = recessive, but are these strictly binary phenotypes? Since there are an infinite number of mutations that could theoretically take place, wouldn't there be an infinite number of alleles? Eg (not an actual biological phenomenon but just as an example) A1C on chomosome 3 leads to allele a1, A1T leads to allele a2, etc.


texts: What species of flying insect is this? Resembles a fly with the wings of a dragonfly

texts:
Locus: Vienna, Austria

Local Time : 12:24 today, 6th of January

Size: length approximately a large thumb. Width much smaller (pic).

Behaviour: possibly attracted by honey in my medicine, along with flies.


texts: Why do we urinate more often in winter compaired to summer?

texts: I have been thinking of this question for a long time, but I do not seem to find an answer yet. Is there a hormonal change in our body during winter due to which we have to run to toilet often?


texts: Is there a hypernym for enzymes that "cut" other molecules?

texts:
I have searched on Google for a hypernym/umbrella term that encompasses all enzymes whose function is to cut other molecules, but I have yet to find such a term. The term I am looking for would encompass enzymes groups such as proteases, nucleases, and lipases.

Is there such a term in molecular biology?


texts: What is the intracellular chloride concentration in rat T-cells or thymocytes

texts: I'm modeling acid-base in T-cells as based on Grinstein J Gen Physiol 1984; 83: 341-369. I have an estimate of strong ion difference (SID), and Grinstein gives Na and K, but for SID to be true at 33 mM with K 147 mM and Na perhaps 20 mM Cl should be  (K + Na) - SID = 134 mM which is hard to believe but I could find no data on the subject.


texts:
It is known that when the human organism is supplied with certain hormones and/or drugs that serve a certain function for a sufficiently long amount of time, he reduces, and may eventually entirely stop, production of those hormones. It is one of the reasons stopping drug abuse by going cold turkey is so hard, because the happiness hormones produced normally in the brain before, are now produced at a reduced quantity now and their neural receptors are atrophied too, so that their effect is even further decreased.

My question then is this: Could we reverse this? Create drugs with catecholamines or some other such hormone so we bombard a patient negative emotions so incredibly potent for an amount of time that after we stop injecting him with the drug, he's chronically euphoric? Maybe a way to kickstart the life of a suicidal person with depression, have them live at least a year or two in that blissful state of withdrawal symptoms to have them want to keep living, knowing it is at the very least possible to feel that way


texts: What happened to pertussis incidence in the US between 1955 and 1974 and why?

texts:
The Wall Street Journal ran a great collection of infographics in 2015 superimposing the dates on which vaccination was introduced for various childhood diseases on their incidence:
http://graphics.wsj.com/infectious-diseases-and-vaccines/

For the most part, it's a fantastically clear story and a useful resource when explaining how effective vaccines are to skeptics. However, what's going on with pertussis?

The note below the heatmap mentions that vaccination was introduced in 1914. A bit of digging online suggests one factor could be the introduction of the (more effective) combined diphtheria-pertussis-tetanus (DTP/DPT) vaccine in 1949 - is this the whole story? Did the original vaccine have any effect? Did anything like coverage, availability, pricing and/or legal requirements for vaccination improve significantly at the same time as the new vaccine was introduced?

And why did the CDC stop collecting data on pertussis cases from 1955-1974 during a period when you'd have expected them to be keen to track the effectiveness of the vaccination programme?

(I realise that the CDC data gathering question might seem like a separate issue, but (a) it's necessary to understand this figure, and (b) the point of lumping these together is because I have a strong suspicion that antivaxxers will point at that gap and come up with a conspiracy theory, and I'd like to be able to point to a full explanation of the data behind this figure in one place. So, to be useful for explaining this figure to sceptics, they need to be answered together.)


texts: How to distinguish between a genetic bottleneck and directional selection?

texts:
Genetic bottlenecks and directional selection should have relatively similar genetic signals: reduced heterozygosity and greater genetic divergence (Fst?) in contemporary populations compared to the past

How would one be able to distinguish between these two evolutionary forces if their signals are so similar?


texts: Transposons, Viruses and RNA interference

texts:
My textbook says that in RNAi, a complementary double stranded RNA sequence attaches to an mRNA and silences it using a protein machinery. I Googled and read about this so now I know what siRNA and RISC and microRNA are. But the next thing my book says is

  “the source of these complementary double stranded RNA
  sequence [obviously my textbook means siRNA] may be viruses and
  transposable elements.”

What does this mean? Do transposons make siRNA? I thought transposons were non-coding except when they travel via the retrotransposon mechanism.

Do viruses that infect eukaryotic cells donate their own RNA genetic material for the cell to use in RNAi? But I thought RNAi was a cellular defence against viruses, how can viruses help give the dsRNA that’s supposed to fight the viruses? A number of sites online simply state that siRNA is exogenous is origin; do they mean that it comes from viruses?

I would greatly appreciate it if someone could take the time to answer each of my questions one by one or even recommend a site that answers them all.


texts: Relationship between leaf structure and Photosynthesis rate

texts:
We can see numerous leaf structures in plant kingdom. As the leaves are designed for photosynthesis, their structure must be a factor for any optimization in photosynthesis or chlorophyll distribution.

This link describes many leaf structures but I cannot find what I am looking for in anywhere.

I think taxonomy of plants deals with the flower structure but is their any relationship among plant species that we can describe with leaf structure ?
Do the leaf structure is optimized for maximum photosynthesis rate if so then why these different structures ?
Any other advantage for these diverse leaf structures ?


texts:
The fruit has form of a cube or icosaheder. It is green but quickly becomes black. The meat of ripe fruit is easily separated from the seed, is sweet and tastes as dried plum. The seed has strange icosahedrical form, like two pyramids connected.

The fruit is seen on Mediterranean coast of Israel.


texts: How are at home fermentations without starter cultures controlled?

texts: When making fermented food at home, particularly those that are made without the addition of a starter culture, how does one ensure that the correct types of bacteria are carrying out the fermentation? Is this generally due to the properties of the food that is fermented?


texts: Improving DNA quality and yield from stool samples

texts: I prepared genomic DNA from pig stools but the concentration was very low — about 3~4 ng/µl, when I measured it using nanodrop. The A260/A280 and A260/A230 values also did not come out very well (0.4~0.5 and 1.0, respectively). I also tried filtering the DNA two times but it didn't improve the quality. Does anyone have experience with DNA extraction from stool samples and suggest me how I can improve the quality and yield?


texts: Why do we use different micropipette tips for different volumes?

texts: Isn’t it easier to use a 1000 µl micropipette tip for all volumes? I don’t understand why there are different tips for smaller volumes. Does it affect the accuracy of the pipette for very small (<5µl) samples?


texts: Simple question. It forms a pseudopod, and then flows in to it. But how does it move its material to form a pseudopod? And even so, if it is floating in water, what is it pushing against so that part of it holds still and part can move forward? It would be like trying to move while wearing ice skates by pushing your arms forward in the air: no net force is transferred.


texts: agglutination test using blood of the donor and the recipient

texts:
we were told that agglutination occurs when the matching antibody react with its antigen on the RBC surface (as antibody B with antigen B)....
Also when blood transfusion, Donors plasma with antibodies is diluted , so when o-donor gives blood to  B-recipient , B antibodies ( of the donor) is diluted
........
My question is in lab cross-matching test  when we put recipient's plasma(o with b antibodies for example) on the donor's RBCs (B with b antigens)..... is there agglutination, If so, how would we know the right group then?....if not ,Why not?
if the whole thing is misunderstood ,i wish to be told how it's done.


texts: Transcription rate expressed in microarray per hour

texts:
This article gives measurement of transcription rate  and the unit they're using is microarray per hour.

For example, at 27°C the average expression of their genes is 236.1 microarray per hour (page 4). What does this unit mean? Given that each DNA spot in a microarray contain 1 picomole of DNA (wiki), does it mean that the gene is transcribed into 1 picomole of RNA (or of nucleotides?) per hour? Or does it mean that 236.1 RNA are created every hours?


texts: What does the "*" in haplogroup I2A1* mean?

texts: I have been told that the "asterisk" in the Haplogroup 12A1* means it doesn't move down stream? What exactly does that mean in layman's terms?


texts: When was it understood that a male haemophilia sufferer can't pass it on to his sons?

texts:
Haemophilia A and B are both X-chromosome mutations, so a sufferer necessarily inherits the disease from his mother. She won't have serious symptoms unless both of her X chromosomes have the mutation, which is very rare. Since sons of a sufferer necessarily inherit his Y chromosome, they can't inherit the disease from him.

I'm trying to find out when it was understood that sons of a sufferer could not inherit the disease from their fathers. The relationship between chromosomes and heredity was clearly demonstrated in 1915. The idea that females were usually carriers and sufferers usually male had been understood since 1813. The XY sex-determination system was discovered in 1905.

However, it is not clear to me when this would all have been put together and become part of normal biology and medical courses. I think the crucial points are:

There are sex-linked genetic conditions.
Haemophilia is one of them, and is an X-chromosome recessive condition.
Men are XY, women are XX.

Can anyone help with when all of that became normal knowledge for doctors and biologists?

Titles and authors of biology textbooks from the 1920s to 1945 would help, since I'm quite prepared to seek out old books, if I know what to hunt for.


texts: Mechanism by which $lacI^{d}$ is a dominant mutation, impairing the function of normal copies of the Lac Repressor

texts:
Jacob-Monod model for the lac Operon was based on experiments using two strands of bacteria which constitutively expressed $\beta$-gal: $I^{c}$(mutation in the gene lacI , which encodes the repressor) and $O^{c}$(mutation in the operator, the site where the repressor binds).

$I^{c}$ mutants are usually recessive: the Lac Repressor cannot bind to the operator, however, if a wild-copy of the gene is present in a merodiploid, the inducible pattern of expression is restored, because the Lac Repressor acts in trans (that is, it will inhibit expression of both operons when lactose is not present).

However, I've read that there's a strain ($lacI^{d}$) which is dominant, so the expression is constitutive even in the presence of the normal repressor. According to the article linked, abnormal subunits may mix with normal subunits, resulting in a disfunctional tetramer, even if a wild type lacI is also present.
In terms of protein structure, why some mutations may have this effect and be dominant while other mutations do not interfere with normal copies of the protein and are recessive?


texts: What does the human body use oxygen for besides the final electron acceptor in the electron transport chain?

texts:
My biology teachers never explained why animals need to breathe oxygen, just that we organisms die if we don't get oxygen for too long. Maybe one of them happened to mention that its used to make ATP. Now in my AP Biology class we finally learned the specifics of how oxygen is used in the electron transport chain due to its high electronegativity. But I assume this probably isn't the only reason we need oxygen.

What other purposes does the oxygen we take in through respiration serve? Does oxygen deprivation result in death just due to the halting of ATP production, or is there some other reason as well? What percentage of the oxygen we take in through respiration is expelled later through the breath as carbon dioxide?


texts: What is the advantage of circular genomes for bacteria and linear genomes for other organisms?

texts: Bacterial are a great group of organisms. They have circular genomes and never went toward linear genomes while other organisms show the opposite strategy and don't have circular genomes (disregarding their cytoplasmic genome). Why they have followed these different strategies?


texts: Why is stimulation of nerve tissue with a negative pulse called "cathodic" stimulation?

texts:
By definition, the cathode is defined as the terminal through which current exits a polarized device. But in the context of neuromodulation, such as spinal cord stimulation, deep brain stimulation, the "cathodic" pulse refers to a negative current pulse that elicits action potentials. A negative current is by definition a current flow that enters the electrode.

Can anyone explain where this terminology comes from and help me resolve this apparent contradiction? It's driven me mad for the past years.


texts: Is it possible to elicit transient gene silencing by using virus induced gene silencing (VIGS) in plants?

texts:
I am looking for a molecular tech' which could result in transient gene silencing in plants. The objective is to not make transgenic plant, but to use these tech' to silence a gene of interest for a short time. From my limited knowledge, I found that virus induced gene silencing (VIGS) may be an option, I wonder how easy and how long such silencing last? Is there any alternative method?

I don't have any candidate gene to be silenced at this moment, but the tissue will be flower. so it would be nice if the protocol works for flower.

Thank you in advance


texts: How does trees know to balance themselves so that they never fall down

texts:
Well i was flying kites today I saw a tree and its branches were spread around in random directions... I would like to know that how do these trees know to nourish their branches in some direction so as it doesn't fall off due to gravity. I know it can get its strength from the roots inside the soil so that it does not fall. But if this strength were not enough the tree may fall due to weight of its own branches. Can this happen??

I am new to this site I don't know much about the rules here. Feel free to edit if I have done any mistakes(especially about tags)


texts:
The gluconeogenesis pathway seems quite pointless to me. I don't understand why an organism would want to spend energy to create a molecule that can then be metabolized again for less energy? The pathway seems only to serve as a complete waste of energy?

Can someone explain why we have gluconeogenesis and when it is used?


texts:
Does anyone know if it is possible to sort micro-beads, ideally magnetic, using FACS and if so what diameters can be sorted. I was thinking of using fluorescent beads that might help facilitate this but I have no previous experience with FACS.
Ultimately I want to separate beads into separate wells that can be used for PCR templates.
It would be helpful if anyone knows any studies that have used similar methods.
Cheers!


texts: I found this grasshopper (although I'm not sure if it was really one) near a lake in Bangalore, back in mid April. This is the only picture i could get and since it's so well camouflaged I would like to point out that it's right in the middle. It had those very conspicuous green bands on either half of the dorsal side with longitudinal white pinstripes. It was around 10 cms in length. Can i get an ID please?


texts: Could an organism evolve to adaptively evolve?

texts: Besides chance mutations sticking around because of their utility towards survival and procreation, could an organism evolve the ability to aid this process by mutating more frequently in beneficial directions in response to the environment (e.g. based on some form of past higher order evolutionary experience)?


texts: Why do we have bacteria in our alimentary canal?

texts:
Our alimentary canal contains lots of bacteria. Most of these are found in the small intestine and large intestine.

Can you a give a few reasons why is it a good thing to have bacteria in our digestive system.

Thank you.


texts: How do biologists infect cells with viruses within a lab setting?

texts: I'm writing an experimental proposal as my final paper for my single molecule biophysics class. Part of the procedure I wrote involves intentionally infecting a culture of HeLa cells with SARS-CoV-2 in order to perform a series of tests on it. Are there any readings or articles that you guys can point me to which detail how biologists intentionally infect cells with viruses within a lab setting?


texts: Number of elongating RNA polymerases on a gene

texts:
I'm interested in knowing how many Pol II molecules are simultaneously transcribing any given gene. There are RNA pol II ChIP-seq (phospho-S5) data for different cells but these come from pooled cell samples. So the different peaks on any given gene would be the average of the cell population. Single cell ChIP-seq data would help but I can't find any.

The other way to check this is to calculate transcription rates of different genes, normalize with copy number and divide by the elongation rate of the polymerase on that gene. However, elongation rate is not unique for all genes.

Is there any resource – paper or raw data, which would help me find the answer to the question?


texts: Are amino acids of viruses L or D enantiomers?

texts: I read a note saying that the amino acids of viruses are D enantiomers but I can't understand how that's possible since their human host can't even recognize that type.


texts: Are microbial antigens selected against?

texts: Antigens provoke a response from the host immune system. Could selective pressures result in microbes losing their antigens? Has this been observed? Or are antigens typically so important that they are constrained from losing them?


texts: Have there been any successful studies showing that it is possible to increase IQ?

texts:
I am curious if there have been any leading studies that show improvement in general IQ. For example, an adult with an IQ of 130 reaching an IQ of 140, over many different IQ tests and then averaged, after some sort of practice (perhaps playing video games, reading books, taking lots of IQ tests, or doing memory exercises).

It would be interesting to know. If you can, please reference sources with your answer, so that I may look at the studies myself.


texts: I am wondering for someone to discuss the phenomena that newborn babies (humans) are able to submerge underwater up until a few months where that ability is lost again? What is the explanation for this?


texts: How are minerals formed by biological processes?

texts: News to me is that about 4500 of the 4900 minerals on Earth have been created by life. What are some examples of such processes? Are some minerals formed inside the human body?


texts: Is Near-infrared focused light safe for your eyes?

texts:
I found a new product, but I'm afraid it's not safe. Can you help me understand what the safety limits are when it comes to near-infrared light focused on your eyes is?

I'm assuming the wavelength of the light is important, but probably more important is the amount of focus. (For instance, visible light isn't very dangerous unless it's focused in a laser).

Product: http://theeyetribe.com/

Here is their quote about safety on the FAQ:

  Yes, The Eye Tribe Tracker complies with the essential health and
  safety requirements set by the FCC and CE directives. The Eye Tribe
  Tracker is using near-infrared illumination, it conforms with the EN
  62471 standard and we have obtained an EU declaration of conformity.
  Our hardware has been tested and approved by a certified lab according
  to said standard, and is therefore safe to use.

Related question:
Is it safe to look at infrared LEDs?


texts: Can neutrophils kill bacteria inside other cells?

texts:
Are neutrophils able to get inside epithelial cells in order to kill bacteria. Therefore, even if a bacteria gets inside the epithelial cells can the neutrophils get inside the epithelium to kill the bacteria?

Also when the bacteria get into blood stream can neutrophils kill the bacteria?

I am not from a biology background. So, a simple explanation will be helpful


texts:
I am working with an Arabidopsis mutant with an F-box protein knocked out. It has been shown that F-box proteins targets must first be phosphorylated (Skowrya et al., 1997). I have heard of phosphorylation sites, but I can't find out whether every protein has them. Can any protein be phosphorylated?

Skowyra, D., Craig, K.L., Tyers, M., Elledge, S.J. & Harper, J.W. (1997) F-Box Proteins Are Receptors that Recruit Phosphorylated Substrates to the SCF Ubiquitin-Ligase Complex. Cell. 91 (2), 209–219.


texts:
The univariate breeders equation is defined as,

$\ R = h^2 s$

where $\ R $ is the response, $\ h^2 $ is the heritability (additive genetic variation), $\ s $ is the selection differential. The multivariate equation is similar to this in principle but includes a multiple trait variance-covariance matrix and multiple selection differentials.

Essentially the breeders equation tells us how strong the response to selection will be as a result of the additive genetic variance within a trait (and between traits in the multivariate) and the selection applied to that variation ($\ s = cov (w,x) $ = the covariance between fitness ($w$) and the trait $x$).

For example, in trait $x$, $s$ = 0.8 and $h^2$ = 0.5 the value of the response for $x$ is $R$ = 0.4. Compared to another trait, $y$, where $s$ = 0.8 and $h^2$ = 0.1 and thus $R$ = 0.08.

My question is, if we look at a trait in a population, measure it's population mean and define $h^2$ and $s$ values, can we then predict the change in the population? IE. can we predict (with the values of $s,  h^2$  and the population mean) what the mean population mean trait will be in the next generation directly from the result of the breeders equation? Does the value of $R$ give us anything of use?

Following from the example above, I examine a trait (wing length in chickens) and find the mean to be 24 cm. I select birds to start my next generation in a way that causes $s$ = 0.8. The additive genetic variance for the wing length is quite high, $h^2$ = 0.5. The predicted response is $R$ = 0.8 x 0.5 = 0.4. What does this tell me about the next generation?


texts: What fills the space between the alveoli in the lungs?

texts:
Do the lungs just consist of a large tree of alveoli, covered by the pleura, like this picture:

Or are they found "inside" the sac that is the lungs? If it's the later, what fills the space in-between the alveoli and forms the walls of the lung?


texts:
So I was wondering if it is possible to get white bioluminescence. Actually, I have heard dinoflagellates that produce blue light when there is some disturbance in the water. So I was wondering how to make this blue as white. If it works inside a flask, that is also fine because it should officially work.
So there are a few certain species of dinoflagellates that produce blue light when there is a disturbance in the oceans they live in. It is something like this:

Now, they regularly live in calm seas, and when there are small disturbances like waves or a person walking through them, they start glowing. This is one of the most stunning examples of bioluminescence.
I was planning to make use of these dinoflagellates. I was planning to put them in a black box, with a glass pane at the bottom. In the black box, there would be a tiny and slow motor to simulate the disturbances. Now, my only question is how to make these dinoflagellates glow white instead of blue. Are there any certain species of dinoflagellates that glow white that I am not aware of, or do I have to add any certain chemicals to the water to make them glow white (Please give a chemical that won't hurt the dinoflagellates), or is there any certain food to make them glow white, or should I add any changes to the glass pane to make the blue light look like white light?
BTW here is an image of the model I am talking about:

It's not perfect but is just a base model. Thanks in advance. If you need any other information, please comment.


texts: What is the minimum air pressure the human body can tolerate if oxygen supply is not an issue?

texts:
Disregarding hypoxia, what is the minimum air pressure that the human body can tolerate?

(i.e. at what air pressure would the blood start to boil, or skin start to burst, or whatever else might happen that would kill you but isn't related to oxygen?)


texts: Why is there a seeming dichotomy between mobility and photosynthesis?

texts:
At least among more complex organisms, I cannot think of any examples of highly mobile species (like animals) that also incorporate photosynthesis. Perhaps there are examples that I'm unaware of, but even so it seems to be exceedingly rare.

Is there some good reason for this, or is it a mere chance of evolution?

I could speculate, perhaps, in that photosynthesis just doesn't provide enough energy for the relatively high metabolism of mobile species; but even then, there seems there should be a "sweet spot" where some level of mobility would still be "worth it" for a photosynthesizing species, rather than the strict dichotomy that seems to be observable, so I naïvely find that explanation somewhat dissatisfactory. There just seems to be little reason for animals to not practice photosynthesis, if only to be able to eat less than they need to without it.


texts: Can we estimate effective population size from DNA sequence data (CR or cytB sequence)?

texts: I have DNA sequence data (control region) of two population of a species. Can anybody suggest me any software to calculate effective population size? Is it possible and meaningful?


texts: Can intracellular protein initiate strong immune response?

texts:
Some autoantibodies escape immune tolerance and can cause autoimmune disease. In order to cause harm to the tissues by these autoantibodies, do the antigen need to be extracellular or membrane bound, so that they are exposed to the immune system?

What happens if the target protein of the autoantibody is intracellular? Does the cellular localization of the target antigen plays any role?


texts: What biological constraints are there on how large a spider can grow?

texts: Spiders fascinate me, but what intrigues me the most is just how big some spiders can get, which leads me to my question. What biological constraints (if any) would limit how large a spider could grow, given ample food and no predators?


texts: What is meant by "alien" probe in a microarray?

texts:
In my lab we did a microarray to analyze differential gene expression in S. cerevisiae treated with UV irradiation. We are now analyzing the results and one of the up-regulated genes is labeled "Alien4_60." I believe this is some kind of control, but I am having trouble understanding what it is.

I would think that a probe labeled "alien" in a microarray would be some kind of negative control. The probe-list (excel file) says "Control stringency: 60% identity to oligo Alien4" as the description for this probe. What does this mean?

..As you can imagine, searches for "Alien4" only brings up sci-fi movies!

p.s. perhaps someone with enough rep could tag this question with more meaningful tags.


texts: What do we call this adjustable platform used to ensure that something is positioned strictly level in a lab?

texts:
This is an adjustable platform. Such a platform is used, for example, to make sure that a gel electrophoresis cassette is level relative to the earth. A passage in a procedure description which I'm translating says that the gel caster (the two glass plates between which we will pour the solution) should be put on top of this platform, after which the platform is adjusted "using a level". The text describes a vertical SDS-PAGE procedure.

I wonder what such benchtop lab platforms are called. In my Russian text it is called "заливочный столик" (pouring table, casting table).


texts:
One usually reads that the functional role of the myelin sheath is being a good insulator, accelerating the speed of action potential propagation along the myelinated axon.

I tried to understand this and came up with these possibilities:

The immediate reason why action potential propagation along myelinated axons is "faster than normal" is a relative lack of leak channels in the membrane. I.e. it is the membrane of the neuron (not the myelin sheath itself) that is a "better insulator than normal". Why there are no leak channels underneath the myelin sheath would be another question. But the myelin sheath would probably be one of the reasons. Thus, it would be an insulator only "indirectly".
Or there are leak channels, but there's no place to go for the ions out of the neuron (no extracellular fluid to diffuse to)?In this case, it would be the myelin sheath that is the "immediate" insulator. But the leak channels would be useless. (So why to maintain them?)

So my question is:

  Are there significantly less leak channels underneath the myelin sheath than normal,
  or not?


texts:
What is the equivalent connective tissue in plants?

Connective tissue in animals are mostly made up of collagen.

What about in plants?


texts: What is the Genetic Cause of Homosexuality?

texts:
So, I'm just wondering about this because I read the following in my Biology textbook about fruit fly genes:

  "Normal male and female flies express distinct forms of the fru gene. When females are genetically manipulated to express the male form of fru, they court other females, performing the role normally played by the male..."

Out of curiosity, have any studies been conducted to see what causes homosexuality? Is there a similar gene in humans that, if randomly altered, causes attraction to same-sex individuals?

EDIT: a similar post exists, but nobody provided an answer related to the poster's question.


texts: Why does bicep activate during dead hang?

texts:
Hanging from a bar causes my bicep to feel much harder than when simply holding my arm straight above my head relaxed, without a bar.
This was slightly surprising to me: I used to assume that since the arms are straight during a dead hang, the biceps don't have to do work.
Are they under static contraction just to hang from a bar? Is it an effect of having to grip the bar, or would I observe the same tension in my bicep from being suspended at the wrists?
Why does this happen?


texts: Does protein kinase A accelerate glycolysis or slow it down?

texts:
In liver cells, the activity of PFK-1 is regulated by the PFK-2/FBP-2 complex, whose activity is in turn controlled by glucagon and insulin.

Glucagon activates protein kinase A.  Then protein kinase A phosphorylates the PFK-2/FBP-2 complex, so that the PFK-2/FBP-2 complex will make fructose-6P from fructose-2,6-bisP.  Since fructose-2,6-bisP activates PFK-1 (in liver cells), without it the process of glycolysis will slow down.

However I read from my notes that protein kinase A is dependent on cAMP (so that when the energy level is low, the increase in cAMP will cause protein kinase A to increase in activity).  It seems that protein kinase A should help increase glycolysis, so why does activating it by glucagon cause glycolysis to slow down instead?


texts: What does the evidence suggest about how Neanderthals became extinct?

texts:
According to "Neanderthals: Facts About Our Extinct Human Relatives" (Szalay, 2013), Neanderthals dominated Europe during the last Ice Age, but may have died out before the arrival of Homo Sapiens (according to research detailed in "Radiocarbon dating casts doubt on the late chronology of the Middle to Upper Palaeolithic transition in southern Iberia" (Wood et al. 2012).

There are a number of theories floating around in the literature - everything from inability to adapt to climate change  to dietary deficiencies.

What does the latest research suggest as the cause of the Neanderthal extinction?

(refereed papers would be appreciated)


texts:
When I wash my running shoes by my hands,
I leave them near the window to dry them quickly.

Although they got sunlight in daytime and well dried after I came back from work, I could feel bad smell from them.

The smell was worse than when it was not washed for long time.

So I guess that the water increases the number of bad bacteria on shoes.

My conclusion is that water should be used to wash dirty things out only for a short time and
it should be dried as soon as possible.

Although our body is alive and can resist against bad bacteria on our skin which get nutrition from water, it seems that water should be used for a short time.

Am I right? Please advise on my thinking.
Thanks.


texts: How do I calculate the change in allele frequency in a haploid population under selection?

texts:
From this book

For simplicity, let us consider a haploid organism and assume that the frequencies of alleles $A_1$ and $A_2$ are given by $x$ and $y=1-x$, respectively. We also assume that the fitnesses of $A_1$ and $A_2$ are $w_1 = 1$ and $w_2 = 1-s$, respectively. In this case the mean fitness $\bar w$ is given by $x + (1-x)(1-s)= 1-sy$, and the allele frequency change per generation becomes
$$\Delta x =  \frac{dx}{dt} = \frac{sxy}{1-sy}$$

If I would have to find what $\frac{dx}{dt}$ equals I would use the Wright-Fisher equation and find that:
$$\frac{dx}{dt} = \frac{w_1 \cdot x}{\bar w} = \frac{x}{1-sy}$$
, which is obviously not the same result as what the author found...
What am I missing? How did the author find out this result $\frac{dx}{dt} = \frac{sxy}{1-sy}$?


texts: Is there a link between autoimmune diseases and X-chromosome inactivation?

texts:
I was reading about the necessity of niche formations to adequate development of blood progenitors and this idea reminded me of the patchy inactivation of the X chromosome which followed that maybe, if some of these pathways passed through X coded proteins, this might make women have different niches, that could account for the seemingly greater occurrence of auto-immune diseases in women.

Is there any sense to this idea? Was this ever researched?


texts: Calculation of Respiration Fluxes in Terrestrial Ecosystems Based on Total Respiration (RT)

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.

Investigation:

The aim of this investigation is to calculate different respiration components within an ecosystem with the energy fluxes within a terrestrial ecosystem consisting of:

Energy Fluxes

GPP = Gross primary productivity
NPP = Net primary productivity
NEP = Net ecosystem production
NEE = Net ecosystem exchange
RT = Total respiration
RA = animal respiration
RS = soil respiration
RM = microbial respiration

Query

I have answered the questions below to the best of my ability but with much confusion (see calculations below).

Am I on the right track? Am I calculating these respiration components correctly?

If anyone is able to help here, your advice and input would be deeply appreciated.

Many thanks!

Table 1: Flux values for temperature grassland

Respiration Components to be Calculated: My answers to the questions

1. Researchers measured the total ecosystem respiration (table 1;
    figure 1) as RT = 1300 g/Cm-2/yr-1. What is included in this total
    respiration?

Rs and Ra are not to be included in this calculation because they are part of the heterotrophic respiration system and they cannot be added to plant respiration.

The respiration components incorporated into RT =1300 g/Cm-2/yr-1 is Rp = 800 g/Cm-2/yr-1 (plant respiration), leaving 500 g/Cm-2/yr-1 to
be designated to roots, shoots, and microbial respiration.

2. The researchers measured soil respiration as  Rs = 900 g/Cm-2/yr-1 and estimat3e animal respiration above ground as RA = 50 g/Cm-2/yr-1. Calculate the respiration values for plant shoots (R,p-s), plant roots (R,p-r), and microbial activity (R,m).

Calculations for respiration components (Table 1; Figure 1)

Fig 1: Visual reprsentation of respiration fluxes


texts: Are there any structures in mammals that are used only by males?

texts: There are examples of structures which only serve a purpose in females, but it seems like the opposite could also be true. Are there any structures which exist in both mammalian sexes and only serve a purpose in males?


texts: I am planning to insert a 45 bp sequence in a vector. After restricting my insert to create compatible sticky ends, I am finding no way to clean it up. Is there any way for cleaning this fragment after restriction or should I proceed without clean-up?


texts: How is the Force of Contraction Applied to the Tendons by the Muscle's Individual Fibers?

texts:
Image and question have been updated for clarity!

The image above is a side view of a semi-transparent skeletal muscle. The dark red lines represent individual fibers, the blue lines represent tendons. The pink area also consists of muscle fibers, but it is made transparent for the purpose of the demonstration. Please assume the fibers are properly encased in fascicles and fascia. Tendons connect the muscle to the bones. The bones can move towards the center of the image if pulled. The arrows show the flow of force during contraction along each fiber.

The muscle has grown large enough that the outer fibers protrude around the tendon (where they connect). During contraction, do the protruding outer fibers help pull the tendon towards the center of the muscle like the internal fibers in the middle of the muscle do? If so, how is the force controlled and directed to accomplish this?

It seems there exists athletes with this type of anatomy (such as very large bodybuilders) but the bio-mechanics of this type of anatomy completely confuse me. It would seem the flow of force of the outer fibers would pull the tendon away, unless the force is somehow redirected. Thank you so much for your insight on this!!!


texts: Is it possible nowadays to artificially create an organism just by inserting organism's DNA into an artificial environment?

texts: Let's say we have a DNA of a bacteria and we want to recreate the bacteria just from this DNA. Is it possible nowadays to get this DNA and insert it into some artificial solution so that from this DNA a bacteria coulb be grown?


texts: Circulating factors affecting human health/longevity

texts:
Circulating factors present in young mice have been shown to promote rejuvenation of aged mice, suggesting that tissues have inherent capabilities to regenerate, and circulating factors may be promoting/inhibiting this [1].

Specifically; supplementation of GDF11 (growth and differentiation factor 11) can reverse some effects of ageing (muscle tissue rejuvenates, and some degree of cognitive improvements) [2]; conversely circulating CCL11 impairs neurogenesis in aged mice and causes cognitive impairment [3]. GDF11 decreases with age, CCL11 increases with age.

(Image from Bitto et al 2014, [1])

These factors (well, GDF11 at least) are not as highly expressed in humans as in mice [4], so the specific mechanisms may differ.

What other circulating factors been shown to affect health or longevity? Particularly in humans, but other mouse (or 'higher' organisms, e.g. primates) experiments would be interesting too.

Bitto, A., and Kaeberlein, M., “Rejuvenation: it’s in our blood.,” Cell Metab., vol. 20, no. 1, pp. 2–4, Jul. 2014.
Sinha, M., et al, “Restoring systemic GDF11 levels reverses age-related dysfunction in mouse skeletal muscle.,” Science, vol. 344, no. 6184, pp. 649–52, May 2014.
Villeda, S., et al, “The ageing systemic milieu negatively regulates neurogenesis and cognitive function.,” Nature, vol. 477, no. 7362, pp. 90–4, Sep. 2011.
Souza, T., et al, “Proteomic identification and functional validation of activins and bone morphogenetic protein 11 as candidate novel muscle mass regulators.,” Mol. Endocrinol., vol. 22, no. 12, pp. 2689–702, Dec. 2008.


texts: Does a gene code for protein molecules or a DNA codes for protein molecules?

texts:
To my understanding, a gene consists of a unique sequence of nucleotides that codes for a polypeptide or an RNA molecule. In my textbook, it is stated that DNA codes for protein molecules.
So I thought, a gene only code for 1 protein molecule or 1 RNA molecule
However, DNA can code for a number of protein molecules or RNA molecules, as a gene is a stretch of DNA.
Is my understanding correct?


texts: why nucleosome spacing is longer in heterochromatin than euchromatin

texts:
Heterochromatin is defined as tightly packed form of DNA. But some experiments show that the average spacing of nucleosomes associated with H3K9me3 and H3K27me3, both heterochromatin marks, are longer than those with euchromatin marks. why packed DNA has longer spacing?

e.g in article :Genome-Wide Nucleosome Positioning Is Orchestrated by Genomic Regions Associated with DNase I Hypersensitivity in Rice. it says:"The average spacing of nucleosomes associated with H3K4me1 and H3K27ac, both euchromatin marks, are 178 bp and 179 bp, respectively. In contrast, the average spacing of nucleosomes associated with H3K9me3 and H3K27me3, both heterochromatin marks, are 205 bp"


texts: What are the buoyancy control mechanisms of Chambered nautilus?

texts: I'm currently working on an underwater robot and was hoping to use the principle used by the nautilus for buoyancy control. So how do the Chambered nautilus control its buoyancy?


texts: Why would a flower evolve such that a particular pollinator cannot pollinate it?

texts:
I went on an interpretive trail today and came across a wild flower sign. It said that some flower species evolved such that they can not be pollinated by humming birds as they are shaped such that only an insect proboscis could get into it. Why would a flower evolve in such a way? Wouldn't it be advantageous to take any pollinator?

An interpreter in the visitor center suggested it might be that the flower wants to save it's limited pollen for pollinators most likely to visit other families of its species. I'm not completely sure I buy this, as a pollinator willing to visit one flower of a species is likely to visit another flower of the same species. That said, I think he might have been on to something. Alternatively, this link made me think perhaps certain pollinators might damage the flower and it would want to discourage them.

This question goes beyond a flower co-evolving such that a particular organism could specialize in pollinating it; I'm curious why a flower would specifically evolve such that it could not be pollinated by a particular organism.


texts: Why do the host cells containing iC3b fragment not undergo phagocytosis?

texts:
As far as I understand, in complement system C3b gets deposited on pathogen surface but it can also be deposited on host cells. Host cells have some negative regulatory system such as membrane cofactor of proteolysis MCP, decay associating factor DAF etc which either removes C3b or cleave it using factor I to iC3b which can not form a C3 convertase or C5 convertase so no production of membrane attack complex on host cells.

However, phagocytes contain complement receptors CR2, CR3 etc that specifically recognise iC3b and engulfs the cells bearing it. While it is very useful for pathogens bearing iC3b (In those cases where pathogens contain sialic acid residue which attracts factor I and prevents forming MAC on those pathogens) wouldn't it be very dangerous for host cells?

So if there is receptors against iC3b on phagocytes then what is the point of host cells converting C3b into iC3b, they get killed one way or another anyway


texts:
I always wear gloves when I'm doing cell culture. Moreover, I always spray my gloves with ethanol to disinfect, so that I don't contaminate everything.

However, I recently heard the argument that EtOH could impair the integrity of the glove, making it an unsuitible barrier between your hand and the culture. According to this argument, the best idea is to not wear gloves during cell culture, but instead thoroughly spray your hands with EtOH to ensure decontamination.

I don't believe it, but I'm wondering if anyone else has heard a similar argument and if there is any truth to the claim.


texts: Online phylogenetic tree of human lineages

texts:
I am looking for a source of information about the diversity of human lineages and their relationships.

With a quick google search it is easy to find this type of tree

A perfect online resource would...

Contain a lot of lineages going to the most detailed lineages
Contain links to wikipedia or other source of information that could help someone to:

identify a group
have an overview of their culture

Contain visualization of their current (or past) geographic range.
Contain visualization of migration patterns
As mtDNA and Y chromosome may typically show different story, it'd be great if the resource would differentiate these and highlights specific cases where the two tree differ.

Can you recommend some online resources?

A review paper with nice graphs would also be welcome.

Related:

The post The best free and most up to date phylogenetic tree on the internet? recommend resources for visualizing the tree of life.
This webite offers a pretty amazing tree of religions.


texts: Does Doxylamine have any Influence on the Monoaminergic System?

texts: Does doxylamine have any affects on the monoaminergic system? Specifically I am interested in adrenergic or serotonergic activity but additional information on its dopaminergic activity won't hurt either.


texts: Do nucleosomes ever completely unwrap during transcription?

texts: In eukaryotic transcription will the nucleosomes ever completely unwind the DNA and the histone complex disassemble? If an operon is more 160 base pairs it seems it must.


texts: How are limits determined for systotic and diastotic blood pressure?

texts: I know that the upper limits for systotic/diastotic blood pressure are 120/80. What is the mathematics behind these numbers? I am curious because I did not find information regarding how the numbers are arrived at. I am not sure if the numbers are based on statistical study or is there a scientific basis for the same.


texts: Proteins in water vs proteins in crystal

texts:
I am not very familiar with the experimental procedure of x-ray crystallography except that it involves the very delicate matter of producing crystal that contain proteins and then diffracting rays through it to get a pattern that tells us about the shape of the protein.

I am curious though when you crystallize a protein that usually stays in the cellular fluid, does it go through any conformational or size changes. For instance isn't there some pressure applied by the water that would potentially result in protein being smaller then what it might be under less pressure. Or what about hydrophobic\philic effects that play an important role in protein folding. Of course once the protein is folded it is bonded through interactions stronger than hydrophobicity so it is not that delicate. But still a complete change of surrounding environment should count as a big change, should it not? So are there any theoretical or experimental explanations as to whether the protein changes size and\or shape during crystallization? References to both experimental and theoretical work are very welcome. Although I guess experimental evidence would make more sense in this matter since usually potentials are optimized to account for the crystal structure to be the minimum of the energy so it I can't see how theoretical works could potentially help to understand this issue. I guess one way would be to take a native protein structure determined by X-ray and run it through AB initio  molecular mechanics where potentials do not depend on parameters obtained from the native states of proteins on PDB database. I don`t know how theoretically sound that would be though.


texts: Hybrid, Japanese or European larch please?


texts: Modern human beings, especially women, cut their armpit hair. It seems to me the armpit hair is trivial/useless. Shortly speaking, what is the armpit hair for?


texts:
Could a potato stay alive and power a clock while growing in the ground?

I know how a potato clock works as a electrochemical cell  and involves chemistry, but I am only interested in a growing plants ability to grow and recover lost compounds, water or otherwise during this process while in the ground.

Side question:
How much power could come from one potato?

Source is in the picture.


texts:
Cross-posted from StackOverflow

This is an odd one. I'm not sure it's the right place to ask, but maybe there are some sound / dog experts who can chime in? (no pun intended)

We use two sounds on our website to indicate success and failure on a quiz. Those are very simple and short sounds.

Somehow one of our customers reported that her dog was whimpering and really upset with both of those sounds. He's normally fine with lots of other sounds that dogs are typically unhappy with including loud sounds, hoovers etc. She even said it happens when she uses headphones!

Other than muting, or replacing those sounds (and upsetting other dogs?), is there anything we can do to clean the sound or detect what specifically makes them upset this or other dogs?


texts: Smallest, specific RNA-binding protein - w/ sequence?

texts: I'm looking to synthetically fuse an RNA-binding protein onto another protein, inside a viral vector which has a size-limit. I've considered some options, but I'm wondering what StackExchange will say. What is the smallest protein known that binds to a specific sequence of RNA, and what is that sequence?


texts:
I haven't been able to find anything that tells me how much ATP is needed for DNA replication, transcription, and translation in humans, just papers that mention ATP used in those processes.

I need to know how much ATP is needed for these processes because once my cell from scratch is alive I feed each cell 50 nanograms of glucose which yields 5 trillion ATP. If I use these numbers plus the numbers for other metabolic processes I get roughly the amount of ATP needed per cell before mitosis. If I know this then I will know if I need to feed my cells more glucose or if 50 nanograms is enough.

So how much ATP is needed for DNA replication, transcription, and translation? I want it in terms of per nucleotide and per amino acid so that I can multiply that by the amount of DNA total, amount of DNA in any given gene, and amount of amino acids in any given protein.


texts: Why is there a difference in the orientation of my imagined body vs. my physical body?

texts:
My Personal Experience

When I visualise a specific aspect of my body, the inner mental image does not seem to be aligned with my actual physical form in space.

What I mean by this is:

Say I identify a pain in my right ankle, and in my imagination I conjure a mental picture of my ankle to help me pinpoint the exact location of the pain ...

... in my mind, the orientation of my body in the mental picture seems to be slightly forward of my actual physical body, and slightly turned or rotated towards the right.

This is a two part question:

Firstly:

Do other people share this experience ?

Secondly

Is there any accepted explanation for the effect ?

My best guess is that it could be related to the lateralization of eye movements accompanying brain activity during different cognitive tasks.

http://www.nlpu.com/Articles/artic14.htm

  In 1977 Robert Dilts conducted a study, at the Langley Porter
  Neuropsychiatric Institute in San Francisco, attempting to correlate
  eye movements to particular cognitive and neurophysiological
  processes. Dilts used electrodes to track both the eye movements and
  brain wave characteristics of subjects who were asked questions
  related to using the various senses of sight, hearing and feeling for
  tasks involving both memory ("right brain" processing) and mental
  construction ("left brain" processing). Subjects were asked a series
  of questions in eight groupings. Each grouping of questions appealed
  to a particular type of cognitive processing_visual, auditory,
  kinesthetic, and emotional (visceral feelings). Each was also geared
  to either memory (non-dominant hemisphere processing) or construction
  (dominant hemisphere processing). Dilts' recordings tended to confirm
  other tests which showed that lateralization of eye movements
  accompanied brain activity during different cognitive tasks. This
  pattern also seemed to hold for tasks requiring different senses.
  Looking upwards and the right can indicate imaginative construction of
  a picture.

(snip)

  Eyes Up and Right: Dominant hemisphere visualization - i.e.,
  constructed imagery and visual fantasy (Vc).

So my interpretation of my experience in terms of the above would be:

When I imaginatively reconstruct my body as a mental image, my inner gaze is upwards and to the right.

the upwards would explain why I visualise my feet slightly forward of my physical body
the to the right would explain why I visualise my feet rotated slightly clockwise with respect to my physical body

Does anyone have any views that would confirm this ?


texts: Bug identification: how to identify this bug?

texts:
I found this cast/shed skin from molting in my house:

The house is in the countryside by the beach in Portugal with a temperate and humid climate and mostly pine trees and eucalyptus. Humidity is 84% and temperature around 21ºC indoors. The size is 1-2 cm.

From bugguide.net it looks like a beetle. I also tried InsectIdentification.org but it's limited to US, Canada, and Mexico.

Can anyone identify the cast skin? And does such bug identification require an expert or can an amateur use some resources to do it?


texts: What does x in "Miscanthus × giganteus" name stand for?

texts: I came across a species name that contains "x" in its name, namely Miscanthus × giganteus. What does this symbol stand for and is it commonly used in taxonomic nomenclature?


texts: Genes and proteins with a significantly inbalanced composition

texts:
According to Wikipedia, the median size of a protein-coding gene is 26,288 bp which makes it possible (from statistical considerations) that the nucleotides C, G, A, T appear in roughly equal amounts in one strand. But maybe this is wrong so I want to ask:

  Are there and which specific protein-coding genes have a significant inbalance
  of amounts of C, G, A, T in one strand?

Related to this is the question if there are larger proteins (containing up to 27,000 amino acids as the titins do) with a significant inbalance of amounts of the 20 different amino acids?

Might it be the case that from an inbalance of the gene an inbalance of the protein may follow?


texts: Why do individuals vary in the number of SNPs for a given gene ( e.g. FOXO3A )?

texts:
Individual #1, sequenced by 23andMe and then inputed into Promethease for SNP data has the following SNP output:

1) rs1935949(C;T)
2) rs2802292(G;T)
3) rs13217795(C;T)
4) rs13220810(C;T)
5) rs2764264(C;T)
6) rs9400239(C;T)
7) rs2153960(C;T)
8) rs2802288(A;G)

Thus individual #1 has eight reported SNPs.

Individual 2 also is sequenced by 23andMe and then inputed into Promethease for SNP data has the following SNP output:

1) rs2802292(T;T)
2) rs2764264(T;T)

Therefore individual #1 has eight reported SNPs for the FOXO3A gene and individual #2 has only two reported SNPs.

Since SNPs represent single nucleotide polymorphisms in the sequence, why does individual #2 only have two SNPs recorded rather than all eight?


texts: Are there more descriptive ways of naming genes and gene interactions?

texts:
I couldn't help but notice just how non-descriptive the gene names that modern genetics is using. Currently I'm reading "The new science of Evo Devo" by Sean B. Carroll and here are some examples of gene names used:

Fzrb
Krox 20
Hoxa2, Hoxb4
ZPA
FGF8
sonic hedgehog

While these names identify genes uniquely, they do very little to express what and where the gene does, or how it is related to other genes (While FGF8 may be related to FGF7, it's relationship to XYZ10 is not obvious).

I get the need to uniquely identify genes , and the book is an example of just how hard it is to presently write about a lot of genes at once. The author creates a picture of what's going on, but the gene names get in the way. Even in cases where a gene has a semi-descriptive name, like "eyeless", the reader has to remember that it's actually the gene responsible for eye formation.

Are there are any efforts underway to systematize or name genes for a given organism in an expressive manner?

As a programmer, I write code for a living, and having descriptive names makes it easier to look at someone else's code, read about code and even discuss it with novices. For example:

initializeDataModel
createViewHierarchy
userDidSelectLayerAtIndex

Modern programming tools make using descriptive names easier, because of autocomplete - typing in the first few letters of a programming structure completes the rest. Even google has a list of autocomplete suggestions.

We are all familiar with the Internet, where biology.stackexchange.com/questionname resolves into a specific page. Stackexchange is the site we are visiting, and Biology is a subset of that site. There are other biology websites, but biology.stackexchange.com uniquely identifies this site. The use of "biology" in the address gives readers a general idea of what the site is about and relates it to other biology sites. Our web browsers resolve the address into a proper string of bytes and get the right page. What if we name genes like like

com.drosophila.eyeformation
com.chicken.limb.structure.ZPA
com.human.development.geometry/XYZ10

,and whatever technology we use would actually resolve that descriptive name into a gene or a series of gene interactions?


texts: How does a fungus protect itself from digestion by other fungi?

texts:
If a fungus releases its digestive enzymes outside its body, how does it protect itself from digestion? How do fungi growing nearby protect themselves?

I have tried searching this on google but couldn't get an answer.


texts: Does the minimum spanning tree tell us anything useful about evolutionary ancestry?

texts:
Question migrated from bioinformatics stackexchange due to lack of interest.

I'm new to bioinformatics and have been reading through a bioinformatics book, and it seems calculating a phylogenetic tree is quite a complicated process.

I'm wondering if generating the minimum spanning tree (MST) from a similarity matrix would provide a decent approximation to the actual phylogenetic tree, i.e. provide some information on the evolutionary ancestry of a collection of organisms?  My thinking is that animals diverging from ancient ancestors will always be farther away than animals that diverged recently, so the MST will at least show me what animals are genetically related and which are genetically distant.

I realize this is not quite the same thing as a phylogenetic tree, but it seems to give me some of the same information provided by a phylogenetic tree, namely which animals are closely genetically related and which are distant relatives.

For reference, I'm measuring similarity based on the normalized compression distance (NCD) metric.  The metric is defined in "Clustering by Compression" by Cilibrasi and Vitanyi.

Here is an example MST using the dataset from the referenced paper.  Some parts make sense from my rudimentary knowledge of biology, like the clustering of primates.  Other parts are new to me, and I'm not sure if the relationships are just an accidental feature of the metric, MST, or if real.  For instance, cows are more related to whales instead of horses according to the MST, cats and dogs appear to have evolved from seals or visa versa, and pigs are related to a wide variety of animals: ranging from bats to rabbits to whales.

Note, the 'randgen' nodes are randomly generated DNA sequences that I added to the dataset as a sanity check.  As expected, they are off on a branch by themselves instead of mixed into the population of real animal DNA sequences.  The reason why they are clustered is because I repeat each DNA sequence 40 times to amplify the signal, and repeated short random subsequences become compressible.  The random DNA sequences are probably clustered because they tend to share random subsequences, while the mammal DNA sequences are orderly and have fewer random subsequences.

Here is the repo to reproduce the tree.
https://github.com/yters/ncd


texts: Is 'disorientation event' a common term among biologists?

texts:
On the South Carolina Department of Natural Resources web page about the marine turtle conservation program it says, "When a hatchling sea turtle is attracted away from the ocean towards a direct or indirect source of light, biologists describe this as a disorientation event."

Does something like the disorientation event describing the sea turtle behavior also occur in other species?


texts:
Are there any studies or general information on the composition of human feces?

I'd specifically like to know the percentage of carbohydrates and amino acids relative to the amount that was ingested in diets of various types and amounts.

Any additional facts are also welcome.


texts: In https://doi.org/10.1016/j.neuron.2018.07.033, Pan et al. use the designation TMC1^delta/delta to describe a mouse strain lacking a functional TMC1 gene.  What if any is the different between the delta/delta superscript and a -/- superscript in this context?


texts: Does cell phone radiation promote longevity?

texts:
This preprint presents results from a 2-year National Toxicology Program study on the effects of cell-phone radiation in rats. On page 8 of the PDF, survival results are presented. The presentation of the results is complicated by the fact that some treatment groups experienced significantly different effects when compared to the control group, while in other groups the effect was small but not significant. However, the gist is that rats treated with phone radiation lived longer, and that the effect is stronger in male rats.

I was confused by the fact that this result is presented in the "Results" section on page 8, while the seemingly less significant finding - that treated rats had higher rates of cancer or tumors - was presented in the "Summary" section on page 4. Obviously the study was funded to address concerns we have about observed relationships between cell-phone use and cancer, but when an effect on longevity was discovered, shouldn't this have become the primary result?

The plots on page 11 (Figure 3) and 12 (Figure 4) show some more interesting relationships between the survival of the various groups. Figure 4A shows the high-dose (6W/kg) CDMA male group overtaking the control males only towards the end of the study. With the GSM males (Figure 3A), as well as the low-dose CDMA males, the control group does worse almost from the beginning.

I'm curious to know why more people haven't commented on this result in news outlets. My opinion is that controlled experiments in animals aren't perfect, but they're much better than cheap "longitudinal" studies in humans. As far as I can tell, this is the best evidence we have to date, and it says that cell phone radiation promotes longevity. So why aren't we being required to sleep with phones next to our heads?


texts: What are these structures inside a cut open Allamanda blanchetti?

texts:
As suggested by @tyersome in my previous question on the same topic which I posted yesterday, I have cut open few flowers of Allamanda blanchetti
in order to observe if any reproductive structures could be found.
I took 2 buds in different stages of opening as well,if they had some kind of bud pollination. But it seems there is no difference in the bud and bloomed flower.

then I found these  yellow long stiff hairs all stuck together, with some transparent secretion on them,no pollen. I think that these hairs cluster together to form this small star shape projection inside the flower we usually see when it is in bloom.

and this small green bulb like thing with a thread like extension to attach it to the base of the pedicel.
and then on further extending the incision this small swollen part almost like a ovary. But on its transverse section I didn't observe any ovules or placenta inside.

I don't have microscope or other high resolution equipment, I tried looking at it with a magnifying glass but no new details appeared.
So what are these structures? Do they enable sexual reproduction for the plant? Links to related reliable websites are also welcome.


texts:
I am currently stuck on working out how to answer this question:

"A random mutation causes the enzyme ATP synthase to change shape so that it can no longer function. Describe the impact this would have upon respiration and the overall production of ATP."

My question is: How does changing the shape of ATP synthase specifically prevent the enzyme from working any longer?


texts: How do brains find the peak/valley point on a curve?

texts:
It costs O(n) time if we find the max/min value in a number sequence with the length n. However, if we convert this sequence into a curve and find the peak/valley point with our eyes, it will use much less time.
How do brains complete this computation? I guess the visual nerve process it in divide-and-merge, like breaking down the curve into small segments and comparing them in parallel. If this is correct, what is the size of the smallest segments?


texts: Are axons of neurosecretory cells in neurohypophysis myelinated?

texts:
According to the pictures that I found in textbooks and Google here these neurons are not myelinated.
I just wanted to be sure. They are not myelinated, are they?


texts: Are epigenetic modifications the most stable mechanisms for cell differentiation?

texts:
Wondering what the general take is on what are the molecular mechanisms that are mostly responsible for cell type differentiation stability; ie, for a cell's identity to actually become 'locked in' and progressively less susceptible to extracellular cues (for example, in heterotopic transplantation experiments such as Sue McConnell's).

I'm pretty convinced it really comes down to DNA methylation / chromatin remodelling / histone modifications in order to reach those truly stable, self-perpetuating, differentiated cell identities, but haven't been able to find a paper or review that actually discusses this. Your suggestions and opinions are welcome.

Also posted on reddit/labrats

Edit: I suppose another way to ask this is: Are Waddington's stable "attractor cell states" most likely or most easily explained by epigenetic modifications such as DNA methylation?


texts:
This source states that there are Barr bodies in 0-4% of males.

Why isn't it complete 0%? why some males loose their only X chromosome? How does then their body compensates for those genes which are inactivated?


texts: Which species of bee or wasp are in this photo?

texts:
Please tell me what do you think :)
The photo is from Santander, Colombia. I didn’t take any closeups photos , but these were little bees, like 5 x 1 mm. The tube didn’t seem man-made, it was indoors and the owner of the house said that they are stingless, since no one has been stung.


texts: What does cell-to-cell variability means?

texts:
I'm reading an article where they claim that transcriptional bursting could play a role in cell-to-cell variability.

  Cell-to-cell variability plays a critical role in cellular responses and decision-making in a population, and transcriptional bursting has been broadly studied by experimental and theoretical approaches as the potential source of cell-to-cell variability.

I was looking for a definition of Cell-to-cell variability and I found only the one of Single-cell variability

  In cell biology, single-cell variability occurs when individual cells in an otherwise similar population differ in shape, size, position in the cell cycle, or molecular-level characteristics. Such differences can be detected using modern single-cell analysis techniques. Investigation of variability within a population of cells contributes to the understanding of developmental and pathological processes.


texts: Is there such substances that body can only send to storage (as fat)?

texts:
I watched video with statement that there are such part of substance in potato chips which body can't use ("empty calories"), that they surely will be stored as fat.

It was here on 12:23:
https://www.youtube.com/watch?v=-jCd6vIF8Co

Is she talking nonsense ?


texts: Spread of a benign virus in a population over time

texts:
This is a somewhat difficult (for me) population dynamics question and I wonder if someone with experience in this area could suggest a reasonable approach?

My simplifying assumptions: As a gross oversimplification, let p(k) be the world's population at generation k, and assume a smooth exponential curve that models p(k) from $k=0$ at 10,0000 B.C.E to generation $k=600$ in 2000 C.E. A generation is 20 years, and in acc. with this Wiki there are about 4 million individuals at $k=0$ and 6070 million at $k=600.$
(Of course the exponential model is bad, as world population growth appears to have been sluggish before recorded history.)

Now assume a benign virus infects 120 individuals in $k=0.$ It benignly infects all individuals who have at least one infected parent. Perhaps unimportantly, it also continues to infect 30 new individuals per million in each generation (because its found in the soil), but would not infect those already exposed.

Call infected individuals II and non-infected NI. They are indistinguishable without clinical tests--which are not done, since the virus is harmless. Since II individuals are almost certain to mate with NI individuals, in earlier generations, the number of II will grow very quickly. For a time the growth rate of II will exceed that of p(k). At some point it will be unlikely that an II individual will encounter an NI mate, however a few NI persons will still pair with NI mates--for a while.

My question is, after 600 generations, what is a reasonable estimate of the percentage of II in the population? Is is possible that there would be any NI individuals left? Or would we have some sort of dynamic equilibrium between II and NI in which (I think) the former would strongly dominate?

FWIW, the population growth model is $p(k)=4e^{0.012 k}$ with $p(k)$ in millions.


texts:
I have a question about osmosis that goes a bit deeper than most basic textbooks so I cannot find the answer.Here's the problem:

Imagine an animal cell, say a red blood cell, in a slightly hypotonic solution.
The water starts to flow in osmotically.
The concentration of solute in the cell decreases.
The cell slowly starts to swell but does not burst.

The question is:
Does this water entering increases the pressure on the membrane (similar to turgor in plant cells only less, because the cell can increase in volume - comparable to elastic energy that must be overcome when blowing a baloon...) and does this cause osmosis to stop BEFORE the concentrations come to equilibrum (meaning that cytoplasm still has a bit more solute concentration than outside of cell) or do the concentrations perfectly match?

Thanx in advance.


texts: Viruses affecting transmission capability of mosquitoes

texts:
I've read about bacteria affecting the transmission capability of mosquitoes. For example:

Wolbachia suppresses dengue transmission
When mosquitoes were given antibiotics that decreased their gut microbiota diversity, they became more susceptible to malaria infection

Have there been any studies to show that the presence of certain viruses/viral diversity (rather than bacteria) has an effect on the tranmission of other viruses/pathogens?


texts: How close genetically is the most human-like chimpanzee to the most chimp-like human?

texts:
I understand that:

Chimpanzees are the closest species to humans genetically. Only 1%-6% of their genes are different.
Within any species there is genetic diversity, i.e. no two individuals have the same exact DNA sequence.
This variability applies to humans and chimps.
Thus, there exists a pair consisting of a human and a chimp that will have the smallest number of different (edit: genes) DNA base-pairs within the two populations. One can say that the pair forms an "inter-species genetic gap".

Question: What is the smallest estimated inter-species genetic gap between humans and chimpanzees?

Edit: I changed the last point to base-pairs instead of genes. Most of the comments seem to suggest the population genetic variabilities are much, much smaller than the genetic distance between the populations. Visually, that looks something like this:

Is this a fairly accurate picture of the human-chimp genetic distance?


texts: What does it mean by adding PAN before the AMPK. I am trying to do a western blot assay on AMPK and I am confused by PAN-AMPK, AMPK. does it mean pancreases? Is pan-ampk the total ampk?


texts: Is saturation of olfactory cells able to create a feeling of another odour when it stops?

texts:
I'm looking for at least one scientific study about how odours could impact human olfactory system and create some phenomenon that could be loosely compared to retina remanence.

As an example, with standard eyes, when you look at a cyan area for a long time and then look at a white paper, the paper looks yellow for a while (see some fun experiments here). This seems to be called an afterimage.

In the type of study I'm looking for, if it exists, the olfactory cells would be involved instead of the retina.

Being exposed to a strong odour for some time would make the subject smell an other odour (a complementary odour?) when the strong odour disappear even if nothing casts this new "complementary" odour to the nose. We could call this an "afterodour" or a "complementary ordour".


texts: Is there any format for official Physiological/Medicine answers?

texts:
Assume you have an exam which has 5 extensive questions and 60 minutes.
You do not have time to cover most if you write everything in essay format.
If you start to write essays, you do not really have time to cover all mechanisms and so on.

I just heard that one student did the exam with by list format, for instance

  sitting -> venous return down & skeletal muscles not working correctly -> trombus.

and then describing relevant mechanisms similarly and combining the their roles shortly.

Another morphology of H. pylori

  Curved (spiral shape), Gram-negative, 2-4 micrometer long, coccoid forms in older cultures,

Is there any official standard or unofficial accepted way how to answer questions in Physiology/Medicine?


texts: Why are the hormones dopamine, adrenaline, noradrenaline and serotonin so ubiquitous across the animal kingdom?

texts: As far as I know there is no reason for the makeup of a given hormone to be universal as it merely serves as a carrier from one part of the brain to another. So why are the above hormones seen across the entirety of the animal kingdom, and used in more or less the same way?


texts: How is Glycophorin A and straphylococcal related to Escherichia coli and what does readily purified mean in this context?

texts:
I am reviewing the paper "Glycophorin A Dimerization Is Driven by Specific Interactions between Transmembrane Alpha-Helices."  There is a statement in the abstract which I don't understand:

"The transmembrane alpha-helical domain of interest is fused to the C-terminus of staphylococcal nuclease.  The resulting chimera can be expressed at high levels in Escherichia coli and is readily purified."

As I understand it, this describes that an alpha-helix within Glycophorin A is fused to straphylococcal nuclease?  Then, how does Escherichia coli come into the discussion and what is meant by being readily purified?


texts: Do similar adaptations result in similiar genetic code?

texts:
Sometimes organisms within the same species evolve similar adaptations to similar living conditions without interbreeding.

Let's say we have two human populations which need to adapt to a colder climate, albeit one lives on the Northern hemisphere whilst the other one on the Southern hemisphere. Both populations develop hairy skin. Would the gene encoding the hairiness of the skin look similarly in both populations? Would this gene be at the same locus at the same chromosome in both populations?


texts: Basic understanding of cell cycle (mitosis) phase

texts:
Update

This is for a diploid cell (2n).

At G1, cell growth before the DNA is duplicated.

At S, DNA replicated. Chromosomes doubled!

At G2, cell growth

Then Mitosis; Prophase, Metaphase, Anaphase, Telophase, Cytokinesis

Could anyone explain if the chart is correct or incorrect?


texts: What is this purple flower? Picture taken from a garden in India.


texts: What is protein folding and how is it relevant to disease?

texts:
I am trying to understand what is protein folding and how it could help cure some diseases.

When reading articles about it, it looks like the goal is to find perfect folds for proteins because some diseases are due to proteins that don't fold correctly. I don't understand why do we need to find them in the first place?  Don't correctly folded proteins already exist in the body of people who aren't affected by those diseases? Why do we need to manually find those structures instead of simply "reading" the structure of the correctly folded proteins in the body of non affected people?
In the end, is the goal to find the best structure or to find the folding proecess ? Or both ?

Thank you!


texts: Why we do not use RNAi to control ebola?

texts: As you know using RNAi we are able to prevent gene expression. so why we do not use it to stop viral genes expression?


texts: Continuous (yeast) culture system satisfying multiple criteria

texts:
There are multiple ways yeast cells can be grown in liquid cultures.

Batch cultures are easy to prepare but cell density, medium composition and physiology change over time
Chemostats allow to maintain cells in physiological steady-state, but growth rate is limited by nutrient availability
With a turbidostat, cell density is kept constant and cells can grow at their maximal rate, with excess of nutrients, but medium composition changes over time
Cells in a microfluidics chamber can attain maximal growth rate with constant conditions, but with extremely low numbers.

I cannot think of a way to get (a) maximal growth rate, (b) constant medium composition, (c) constant cell density and (d) a decent culture volume (>50 mL). Am I missing something?