texts: Statistical Analysis for Blood Sugar Measurements

texts:
I've conducted a lab aimed towards finding the impact of soluble fiber intake on the change in blood sugar levels. Following an 8 hour fast, I had test subjects consume a fixed amount of carbohydrates, with a varying amount of soluble fiber, and measured their blood sugar in 20 minute intervals. This was done for two hours each test, generally until blood sugar levels dropped to normal.

5 test subjects were used for the test, each with individual blood sugar responses - for instance, each had consistently different fasting blood sugar levels before food consumption, each had consistently different blood sugar peaks, and so on. Each test subject was tested 4 times, once with no soluble fiber, and 3 more with varying amounts of soluble fiber. The raw data I am now left with is simply a collection of scatter plot graphs displaying rises in blood sugar from normal condition, a peak, and a subsequent drop to normal condition.

I can visibly see from my graphs that more soluble fiber made blood sugar peaks smaller and longer to reach. Data did not always follow this trend, due to some source of error, but a relationship is nevertheless evident. I hope to make a conclusion from this data. What method of statistical analysis could I use to conclude a relationship from these scatter plots? I would like the method to take into account different individual responses, as well as the few data sets that did not confirm a relationship.

I appreciate your help!


texts:
Note: I thought the Biology stack exchange would suit this question better than the Fitness stack exchange. Please let me know in the comments if this is not suitable here.

I am interested in tracking my resting heart rate as it decreases with aerobic training.

At the moment I take it immediately after I have woken up before I get up out of bed.

What is the correct medical procedure(s) for taking a resting heart rate?

I'm aware a standardized procedure is important but what about:

Body position: Should I be sitting or lying down?
Heart rate: Should I take the lowest value or an average HR?
What duration should I take it for?
How relaxed should I be?

In an academic situation how would one reliably take resting a heart rate?

Please include answers that can be referenced to scientific or medical literature.


texts: How broad are the conclusions that one can make from a heterologous expression experiment?

texts: I am studying whether a neural protein regulates the activity of the protein GSK3. I am using heterologous expression systems where I am overexpressing the neural protein in CHO cells (via transfection) to see if it affects the levels of GSK3 in transfected cells vs controls. I am interested in seeing whether the neural protein regulates the activity of GSK3, and I have found that the levels of GSK3 are higher in the transfected cells vs control. But as I am using CHO cells as a model system, how broad are the conclusions that I can draw from this experiment? For example, will I be able to generalise what I found to neurons, or hypothesise that the same thing that I observed in this experiment occurs in neurons? Any insights are appreciated.


texts: Is better healthcare a bane to the long-term survival of the human race?

texts:
The theory of natural selection has it that individuals with better genes tend to survive and reproduce, passing their genes to their offspring. This gradual process results in a population more adapted at survival. However, due to the advancement in medical science, humans with poorer genes tend to survive and reproduce just as well.

For example, in the past, many people, excluding those with natural immunity due to some genetic mutations, would have succumbed to illnesses such as malaria and typhoid. But with better hygiene and medical treatment, these patients tend to survive.

Now, imagine a future where all illnesses including cancer can be treated. How would it impact the survival of the human race? Would we become more and more vulnerable such that our survival hinges heavily on medical technology, analogous to how an astronaut's survival is dependent on his spacesuit?


texts: Which are the best programs to analyze circular RNA?

texts: Hello I'm just started with bioinformatics and I would like to know which programs are best for the task of finding circRNA (circular RNA) in sequences of tissues and different cellular types. I have heard about circRNA finder, find circ, CIRCexplorer, CIRI, and MapSplice which all are different programs to find circRNA, but I really don't know which one is the most used and easy to use, and which one is most accurate for finding circRNA.


texts: What Effect Does the Endocannabinoid System have on Monoaminergic Neurotransmission?

texts: I know that Δ9-tetrahydrocannabinol and other cannabinoids increase dopaminergic neurotransmission in the nucleus accumbens and that this is what results in the euphoria experienced by cannabis users. Other than this I do not know what effect cannabinoids have on monoaminergic neurotransmission. I would assume that it increases monoaminergic neurotransmission seeing how rimonabant $-$ a selective CB1 inverse agonist $-$ leads to depression and anxiety which according to the monoamine hypothesis can likely be linked to changes in the activity of monoaminergic pathways in the brain.


texts: What is the mechanism by which myelination reduces the capacitance of the axon membrane?

texts:
There are two mechanisms that have been proposed to me.

1) Layering of Schwann cell membrane with conducting fluid between the layers is analogous to several capacitors in series. Since capacitance in series add by the reciprocal rule (as resistors do in parallel), this reduces the total capacitance.

2) The myelin increases the distance between the 'plates' of the capacitor. For parallel plate capacitors $ C = \epsilon A/d$ where d = distance between the plates. Thus increasing the distance reduces the capacitance.

Which of these explanations best applies to myelin, or is it in fact a mixture of both?


texts: What is the oldest example of DNA identified?

texts: What is the oldest sample of genetic material (presumably DNA) identified? What are the prospects of pushing back much further into the geologic record?


texts:
I live in central Massachusetts, and have begun seeing robins, as we generally do in early March. The temperature is well below normal, though, and three feet of snow are covering the still-frozen ground from which they usually feed. We were expecting them to arrive late, when conditions would seem more conducive to survival.

What triggers their migration process?


texts: Infer type of nucleic acid based on number of nucleosides

texts:
Let's say we analysed a nucleic acid and found out that it had 20% adenosine, 25% guanosine, 40% thymidine and 15% cytidine. We know that A always pairs with T and G with C.

So, based on these numbers, could we infer that the nucleic acid must've been single-stranded? Or could it be that it was a double-stranded DNA, but just not perfectly matched? Is it even possible for DNA to not perfectly match? Say like a zipper that is shifted?


texts: I am doing a research project on the peroxisomes, and in it I referenced the enzyme catalase, which breaks down hydrogen peroxide into water and oxygen. However, the assignment asks me to specify the production location of all enzymes, and I cannot find any useful information about where the enzyme is created. I think it is created in the peroxisome itself, but am not so sure of that. Where is catalase produced?


texts: What is the name of this plant with orange fruit clusters in india?

texts:
Location: South India.

Month: June

Season: Rainy Season.


texts: Why does it take so long for the human brain to develop from an evolutionary point of view?

texts:
I have read that it takes about 25 years for the brain to be fully developed.
  Coincidentally, humans from the Neolithic and Bronze Age had a very short life expectancy, in fact most of their life their brain wasn't fully developed.

My question is:
from an evolutionary point of view, is there a reason why humans spend so much of their life not being fully developed even long after being sexually fully developed?


texts: What are some good examples of open-source articles in which the synergy of two medicines is demonstrated?

texts:
I am doing research on Stochastic Cooperative Game Theory (a subfield in mathematics), which I will henceforth call SCGT for convenience. In this theory, entities can work together to receive a bigger combined payoff than they would otherwise receive if they had not worked together.
In the stochastic version of cooperative game theory, the payoffs are not deterministic, but follow a probability distribution.

It seemed to me I could apply this theory to drug synergy. If there is drug synergy, there is a (high) chance that two medicines combined are better at healing a patient than just multiplying the dosage of either medicine by $2$. With SCGT, I could determine how much each medicine contributes to the healing of the patient, if some information is known about the drug-response curves. This in turn could tell us something about how much the manufacturers of each drug receive to be paid (in theory).

However, I am not quite well-acquainted with the literature on drug synergy. Furthermore, I can't access many articles on the topic without paying a lot (as I'm with the mathematics department at the university, I can't view articles on biology for free).

So my questions are:

  Do you know any open-source articles in which it is shown that two drugs work in synergy according to the Bliss Independence model?

and:

  Do you know any open-source articles in which it is shown that three or more drugs work in synergy according to the Bliss Independence model?

The same questions apply to the Loewe additivity framework.


texts: What causes the elongation of Genome down the evolutionary time line

texts:
Theory of natural evolution says that complex life forms arose from simpler ones e.g. starting from Eubacteria to modern day multicellular eukaryotes. {If we try to reduce these changes happening at molecular level, it should be like, from Eubacteria like E.Coli. (20 kilobasepair genome/DNA strand size ) evolving, over time, to Multicellular Eukaryotes ( 3 Gigabasepair genome size) e.g. (humans and other hominids.)}
Now if we see molecular changes happening inside cells, the molecular changes are within nucleus as extra nuclear changes are largely function of nuclear information (and a smaller extent external stimuli). For biochemical changes to take place inside cell Nuclear information is the major guiding force. But according to Central Dogma elongation of DNA shouldn't have happened as there is no scope for it in either doubling, translation or transcription. But actually it is not so according to evolution. So what allows changes to be imbibed in the DNA that also increases it's length ?


texts: If someone's arm is cut off, how does that affect blood circulation throughout their body?

texts: Essentially what I'm asking is that if someone's arm is amputated, doesn't that cut off a significant part of their blood flow because the blood vessels that normally flowed up to the hand of the amputated arm and back can't anymore?  If it heals, does that mean the body has to grow more vessels to sort of complete the circuit again?  Does the body just compensate by putting more stress on the rest of the body's blood vessels?


texts: A theory about the possible connection between protists and first animalia

texts:
I learnt that organisms within Kingdom Animalia can be either microanimals or (nonmicro)animals.

a microanimal is any Kingdom Animalia organism that in general cannot be seen by a human eye without microscope

I understand that while it is controversial how a first cell was formed (or appeared) in earth, it is broadly accepted that archaebacteria was at one time formed in earth and multiplied and that with time cyanobacteria evolved out of these, multiplied and evolved by themselves (while on the way crating stromatolites) and by that time the first protist was formed and multiplied and evolved into various shapes (morphogensis) of protists.

I also learnt that the difference between a protist to a microanimal, is that the latter does have specialized cells, so that its body isn't seemingly just a cluster of cells in a given shape and can possibly do any other function that a protist can't do besides perhaps surviving by morphogensis (if either one isn't a function by itself).

Due to the similarity in shape and size of protists and microanimals, I ask if there is a theory and if it reflects a consensus, that microanimals were the first Animalia and were indeed evolved out of protists?


texts: How does the stem-loop cause intrinsic transcription termination?

texts:
In this animation, towards the end (about three quarters) the process of transcription termination is shown. It states that the transcribed RNA forms a hairpin loop (or stem-loop), which halts the transcription process.

My question is, why does it halt the transcription process, considering that the RNA polymerase moves in the opposite direction of where the stem loop is created? Does it somehow change the RNA conformation such that no further bases can be added? Interpreting it as a physical obstacle doesn't seem to make any sense here.


texts: Are nutrients absorbed in human esophagus?

texts:
Following this question regarding absorption in human oral cavity (sadly not yet fully answered), I'm curious if any nutrient absorption occurs during the descent of food through the esophagus.

And if so, what requirements must a nutrient meet for that.


texts: Are there any known consequences of the right-handedness of the DNA double helix?

texts:
In this article it is suggested (without evidence) that the right-handedness of DNA may be the cause that "kick[s] off asymmetry in the early embryo [of snails]".

On the one hand we know that symmetry breaking in an organism's development happens at multiple levels, from molecular to larger structural levels (see this). On the other hand we also know that right-handed DNA double helix does have many notably distinct properties from their left-handed cousins (see this). Are there any visible macroscopic asymmetries in some organisms that are known to be ultimately traceable back to DNA's handedness? More generally, what could be some consequences of the right-handedness of DNA double helix?


texts: Where does the proton come in the reduction of NAD?

texts:
In our curriculum biology textbook the reduction of NAD+ is depicted as follows:

NAD+ + 2 H+ → NADH + H+

If this proton in the products was not present in the reactants, then where does it come from? Alternatively, if it does not take part in the reaction, then why is it depicted?


texts: Can I use dATP instead of ATP (vice versa) for in vitro assay?

texts:
For example, polynucleotide synthesis reaction requires dATP which gives H on 3'end and synthesizes polynucleotide. For this reaction can I use ATP because I knew that ddNTPs are used so that ATP cannot be worked but I searched about it and found this,

"The unfavorable thermodynamics of the hypothetical dehydration reaction shown in Figure 4.6 leads us to ask: If polynucleotides cannot be synthesized in vivo by the direct elimination of water, how are they actually made? The answer is that their synthesis involves the energy-rich nucleoside or deoxynucleoside triphosphates. Although the process as it occurs in cells is quite complex, the basic reaction is simple. Instead of the dehydration reaction of Figure 4.6, what happens in living cells is the reaction shown in Figure 4.7. The nucleoside monophosphate being added to the growing chain is presented as a nucleoside triphosphate, like ATP or deoxy ATP (dATP), and pyrophosphate is released in the reaction. We can calculate the free energy change for this reaction by noting that it can be considered the sum of two reactions—hydrolysis of a nucleoside triphosphate and formation of a phosphodiester link by the elimination of water...
The coupled reaction is favorable because the net delta G is negative. The reaction is further favored because the hydrolysis of the pyrophosphate product to orthophosphate, or inorganic phosphate, has a delta G = -19kJ>mol. Thus, the pyrophosphate is readily removed, driving the synthesis reaction even further to the right and yielding an overall Delta G of -25 kJ>mol. Polynucleotide synthesis is an example of a principle we emphasized in Chapter 3—the use of favorable reactions to drive thermodynamically unfavorable ones."[1]

So can nucleotide synthesize can be done with ATP in vitro? If yes, how? Also what kind of ATP required reactions can be replaced with dATP?
REFERENCE:
1)[Christopher K. Mathews, Kensal E. van Holde, Dean R. Appling, Spencer J. Anthony-Cahill - Biochemistry (2012, Pearson)]


texts: How does a cell control the movement of flagella? Both the rotatory movements and sideways movements helps the cell to move. How are these flagellar movements controlled ? It is through the regulation of the proteins flagellin and tubulin? I want to know the mechanism for both prokaryotic and eukaryotic flagella ?


texts: Would a complete lack of heterozygotes in a population indicate the presence of a recessive allele?

texts:
This doesn't instantly make sense to me.

Lets say you have 100 people from a subpopulation who were sequenced and aligned to a reference genome. For certain variants, people were either homozygous for the loss-of-function alternate allele, or homozygous for the reference allele.

This indicates consanguineous practices within the population. However, I'm told that this also indicates that the alternate allele is recessive and that if it were dominant, there would be very few heterozygotes due to selective pressure, and individuals would not reach a breeding age. This doesn't make sense to me. If it were recessive, there would be an excess of heterozygotes, and if it were dominant, there would be very few heterozygotes, but if there are no heterozygotes, that indicates that it's recessive?

I also fail to see how either condition can be determined in this case.


texts: Is it plausible that strict lockdowns made it more likely for the new variant of COVID to have emerged?

texts:
My idea is that strict lockdowns put greater evolutionary pressure on the coronavirus by restricting oppurtunities to be transmitted, meaning that a faster-spreading variant had much less competition.
Is this at all plausible? Was it just as likely for a faster-spreading variant to become the predominant one without lockdowns?


texts: Will a store bought cabbage kill my Pieris brassicaes?

texts:
About 4 days ago I found a large amount of caterpillars (Pieris brassicae) in my radishes, I took them aside for seeing how they grow and I am out of radishes to give them. I bought a cabbage in the supermarket to give them as food but I am concerned it could be GMO anti pests which to my understanding could kill the caterpillars.
I took one of them aside and it is happily eating the cabbage, if this cabbage is designed to resist pests how long would it take for the caterpillar to die since she started eating?

Thank you so much for the info :)


texts: What Biology topics are linked to the Nitrogen Cycle?

texts: What other educational topics are linked to the Nitrogen Cycle? I am a Science teacher, and I need to organise my lessons. Thanks!


texts: Mechanics of going from DNA sequence to metabolic network

texts:
My apologies for possibly a naive question. I'm a statistics type and have been asked to assist with analysis of metabolic pathways (and networks). However, I would like to have at least a layman's understanding of how metabolic pathways/networks relate to DNA sequences. Been doing the Google for a few days and, given the results, it's clear I am not formulating the query correctly since nothing seems to be clicking.

Something that helps me understand the mechanics behind going from a string of T,A,G, and C's to a network of substrates,enzymes, and products.

Thanks in advance for your patience.


texts: Layman definition of genetic polymorphism?

texts:
I am reading an article about Genetic Polymorphism and there are lines in the article about genetic polymophism that I don't quite understand like.

  In this area, there are six different chemotypes that are the expression of a genetically controlled polymorphism in T.vulgaris(24).

Can someone explain genetic polymorphism and morphic distribution in layman terms.

Thanks


texts: How to define drug-resistant or -sensitive cell line when knowing the IC50 values?

texts:
I have got the IC50 data for a drug on different cell lines. How to define if the cell line is sensitive or resistant towards this drug?

Could anyone tell me how to define this?


texts: Are there well studied examples of ERAD-mediated membrane insertion, especially from viruses?

texts:
Membrane insertion of transmembrane proteins typically requires highly hydrophobic alpha helixes at the N-terminus, N-terminal signal peptides, tail anchors, or a combination of the three.

Byun, H., Gou, Y., Zook, A., Lozano, M., & Dudley, J. (n.d). ERAD and how viruses exploit it. Frontiers In Microbiology, 5

These processes occur co-translationally and are mediated by the SEC translocon and associated factors (especially GPI anchor transferases for tail-anchored proteins). However, my undergraduate research is focused on a viral protein which appears to be translated in association with SRP and co-translationally translocated to the ER by the translocon, but is not anchored to the membrane during translocation. This was shown (by others) by purification of the ER-associated fraction of the protein and centrifugation showing the majority pelleted with the dense, soluble fraction. A small fraction pelleted with the low density membrane-associated fraction, and my research further suggests that this membrane-associated fraction is important for its escape from the ER.

The protein I am studying functions in the cytoplasm, not in the ER or in the secretory pathway, and therefore its escape from the ER is essential for its function. The typical ERAD pathway for soluble proteins involves retrotranslocation through the Sec61 translocon channel (the same channel involved in co-translational translocation, but with different associated factors during ERAD), but this would result in unfolding of the protein prior to its retrotranslocation to the cytosol. On the other hand, the ERAD pathway for membrane proteins (the "dislocation pathway") appears to dislocate folded membrane proteins while retaining most or all of their tertiary/quaternary structure (previous citation and below).

Avci, D., & Lemberg, M. K. (2015). Clipping or Extracting: Two Ways to Membrane Protein Degradation. Trends In Cell Biology, (10), 611. doi:10.1016/j.tcb.2015.07.003

Knowing that the protein is not co-translationally inserted into the membrane because only a small fraction is membrane associated, and suspecting that the small membrane-associated fraction is important for its escape from the ER because the dislocation pathway allows folded protein to exit the ER, my question is:

How could the retrotranslocation pathway for soluble proteins be disrupted such that it would (infrequently) result in membrane insertion of this protein at an early step in retrotranslocation-coupled unfolding, such that the folded protein could follow the dislocation pathway into the cytoplasm?

I would appreciate any examples of similar processes in viruses or in eukaryotes, but any speculation on possible mechanisms - based on understanding of ERAD but lacking supporting examples - would also be greatly appreciated.

As this is unpublished research, I can't be too specific about what virus or even what model system I'm working in, but if there is additional information that would help, I'll be happy to provide it - if I can.

One final piece of information that is also relevant is that I suspect the protein's transmembrane or membrane-anchored domain is very close to its C-terminus. Another important question that this raises is whether retrotranslocation exclusively proceeds by feeding the N-terminus of a protein into the Sec61 channel, or if the C-terminus can be fed directly into the channel? If only the N-terminus could be fed into the channel, this would suggest most of the protein would have to be unfolded before the C-terminal domain became associated with the channel and was able to become membrane-associated, which voids the main benefit of the dislocation pathway; maintaining the folded state of the protein.

If somebody can answer only this question regarding the translocon (and provide some relevant reading), I would be incredibly grateful because it would suggest further literature search to help support the mechanism I am proposing.

Thank you!


texts: Can methylisothiazolinone/methylchloroisothiazolinone (MI/MCI) behave as bacteriostatic in low concentrations?

texts:
Wikipedia mentions this as a biocide. It also mentions that low concentrations of certain bacteriocides is bacteriostatic. (I am assuming that biocide and bacteriocide play the same role, here.)

Hence, the question. (The only information I can find about MI is with regards to allergies.)


texts: Who creates first nitrogen compounds in the food supply chain

texts:
As I understand the food supply chain, organic compounds have to be created from a unlimited source (air, water...).

For instance, I figure that plants transform CO2 from air to organic carbon compounds, mainly carbohydrates, which are then the main source for most other life forms.

But I never heard about a plant turning atmospheric N2 to nitrogen compounds.

Where nitrogen compounds come from, and from which source ?


texts:
Can anyone actually tell me how acupuncture works?

There are numerous websites with little actual explanation, but assert that it works. For example the below article:

http://www.health.harvard.edu/blog/acupuncture-is-worth-a-try-for-chronic-pain-201304016042

However I have failed to find any article about how acupuncture works, or the mechanism at play. Can anyone tell me how it works?


texts:
What's the current conclusion about humans being omnivores vs herbivores?

And particularly, how is this relative to time? That is, is possible herbivoreness a "strictly" modern phase in human evolution? Or has it even occured yet?


texts: Why is full cell/high antigen dose pertussis vaccine dangerous for adults?

texts:
I do remember that I have read (or heard) somewhere that as a human is older, the whole cell vaccine (and high antigen dose one) has more and more adverse effects.

As it is consistent with the target age group mentioned in the leaflets attached to the vaccines:

whole-cell DTP vaccine (Instytut Biotechnologii Surowic i Szczepionek BIOMED S.A.) is suitable "for children not older then 3 years",
high antigen doseInfanrix-DTPa (GlaxoSmithKline Biologicals S.A.) "shall not be used for children older than 7 years",
low antigen dose Boostrix (GlaxoSmithKline Biologicals S.A.) is "suitable for a person older than 4 years",

I suspect it is true. Unfortunately I lack a reliable source to both confirm that and read more about the effects. Can anyone provide a reference.

As there is a strain of pertussis "resistant" to acellular vaccine, IMHO it would make much more sense to use whole-cell vaccine for adults too.


texts:
Comments from the question How is the blood volume of a living organism measured without killing it? by @Nico discussed that the time of blood recirculation scales with the size of the organism. I was curious if there were a series of dimensionless numbers that characterize blood flow, blood volume, and time of blood recirculation?

Such dimensionless numbers exists for stride length and drug penetration.

Edit
I like @Nico's comment so much it's going to part of the question. Any description of the circulatory system doesn't necessarily have to be dimensionless. However, I would imagine that one could develop a characteristic time (lets call it Tau) based on blood flow (L/t), cross-sectional area (L^2), and circulation time (t). From that characteristic time Tau, interesting observations and appropriate comparisons about the various ratios and how they vary amongst species.


texts:
Which species of rotifer is this?
If found this in a moss sample.


texts:
It seems like a no-brainer than oxidation, playing the, er, role it does in the universe, would destroy prions just like it destroys everything else.

But when does it do that? I assume this has been studied, since people handle them in laboratories and may need to sterilize their instruments.


texts: What is the advantage of being tired after having a sex?

texts: When we have a sex with partner, we feel so tired that we don't have any power to do anything. Then it would be disadvantage to the animals, of course humans too, for they are exposed to danger. For example, the predator's atack. But you know, we cannot help having a sex. Then what is the advantage of being tired after having a sex?


texts: Correct/complete representation of RTPCR statistics

texts: In papers reporting a relative quantification of gene expression by RTPCR, I often see a bar chart with mean ± standard error or deviation, with the deviation belonging to biological replicates. This ignores all the previous layers of technical replicates. In the regular $2^{\Delta(\Delta Ct)}$ estimation with 3 reactions per primer/template, we have the standard deviation (SD) from each technical replicate, then the SD from normalization, end finally the SD from quantification. If the end results are fold changes, add one more layer to this. I'm not even including normalization with the geometric mean of 3 housekeeping genes (the better method)  How can I  correctly calculate / depict the statistical variations in this case?


texts: Is it incorrect to assume alveoli as spherical and distinct, especially when analysing lung inflation/deflation?

texts:
I have recently read the paper "Laplace’s Law and the Alveolus: A Misconception of Anatomy and a Misapplication of Physics". To summarise it, here is a section from its abstract:

The typical representation of the acinus as a “bunch of grapes”
bears no resemblance to its real anatomy; the alveoli are not independent little
balloons. Because of the prevalence of this misconception, Laplace’s law, as it
applies to spheres, has been invoked as a mechanical model for the forces of
alveolar inflation and as an explanation for the necessity of pulmonary surfactant
in the alveolus. . . . Alveoli do not readily
collapse into one another because they are suspended in a matrix of connective
tissue “cables” and share common, often perforated walls, so there can be no
pressure differential across them. Surfactant has important functions along planar
surfaces of the alveolar wall and in mitigating the forces that tend to close the
small airways. Laplace’s law as it applies to cylinders is an important feature of the
mechanics of airway collapse, but the law as it applies to spheres is not relevant
to the individual alveolus.

This paper made many claims that I want to investigate. I have tried reading other papers to make sense of them and it appears fully understanding the lung is still a difficult problem in physiology.
Please could you help me verify if any of the statements put forwards by the paper and listed below are true:

The lung's acini should not be thought of as "bunches of grapes". They are instead much more polyhedral. The interalveolar septa contain numerous interalveolar pores that, although some may contain fluid, can equalize the pressures in the lung and allow ventilation of alveoli with blocked airways. So it is more accurate to think of the lung alveoli as a foam or sponge.

The application of Laplace's law is then flawed in the traditional analysis of a smaller alveoli connected to a larger alveoli (see the image below for the traditional analysis). The alveoli are not spherical nor can they ever attain unequal pressures due to their interalveolar pores. It is instead the tensile properties of the lung parenchyma that keeps alveoli from collapsing, instead of the variable surface tension generated by surfactant.

These 2 points the author makes seem to be very fundamental, yet overlooked in the usual teaching of lung physiology, which is why I want to verify whether they are true or not. Additionally I have read a paper that states "In a healthy lung macro- and micromechanical properties
are dominated by surface tension at the alveolar air–liquid interface at low lung volumes while at larger lung volumes extracellular matrix components become stress bearing and define lung structure and mechanics (Bachofen et al. 1987; Wilson and Bachofen 1982; Bachofen and Schürch 2001)". This seems to state that surface tension of alveoli is in fact more important than lung parenchyma when considering lung collapse, contrary to the paper above.


texts: Are spiders part of the study of entomology?

texts:
The definition of entomology says it is the science of studying insects.

I know spiders are not insects but does entomology include studying spiders as well?

Otherwise is there any name to the science of studying spiders (class Arachnida)?


texts: Difference between strand-specific and not strand-specific RNA-seq data

texts:
I would like to ask the difference between strand-specific and not strand-specific dataset.

As far as I know, strand-specific data means that we know which strand the transcript is from.

I do not have biological background. Please confirm whether it is correct. If we have a transcript, which is from sense strand, when RNA-seq is producing reads, is that first the cDNA is synthesised. Then this cDNA is used for PCR to amplify the sample? Then the reads generated could be from both strands of the original DNA?

For strand-specific protocols, what is different?

========================================================

Follow up.

Please correct me if I am wrong. There are multiple protocols to produce strand-specific RNA-seq libraries. The basic process is like:

Get the RNA;
Get its cDNA;
Somehow mark the cDNA as sense or antisense when amplifying (PCR?) (here comes the differences between different protocols);
Then REMOVE all antisense (or sense) cDNAs;
Read the reads from clean cDNA library.

The result is that, the reads from this RNA can be used to assemble the sense cDNA. And for not strand-specific libraries, using the reads would be able to assemble both the anti-sense and sense cDNA.

Am i right about this problem? Thanks.


texts: Why is it so hard to find the amount of biotin in food?

texts:
According to the WHO publications biotin is a thing we need. Although its non toxic, so you can't get too much.

However, excluding a few (small) lists that deal exclusively with biotin content there doesn't generally seem to be any information on how much of it given foods contain. For instance this page gives a very impressive summary of a kiwi, but there is no mention of biotin.

If this is something we need, why is it not normally listed?


texts: What is happening with this hummingbird and how can I help him?

texts:
Today I noticed a hummingbird next to my feeder (California) which looks very strange. From my observation it seems that something sticks from its head. This thing is rigid (does not look like a spider web) and bothers the bird (from time to time the bird tries to use a leg to get rid of it).
The bird can fly (slower than other hummingbirds) and it seems like it eats from the feeder (but puts its head deeper into the feeder than other hummingbirds).

What is this? And more importantly how can I help the bird?


texts:
first of all I'm not sure if I should post this here or in the astronomy stack. I think biologist are more likely to answer my question. To make it short:

Why when looking for any sort of life on other planets, we keep looking for similar conditions we call "life friendly", like nice temperature, oxygen level, pressure etc...

Is there some rule in biology that says life can only exists under these conditions? Why nobody supposes that evolution did not have enough time yet on our planet to generate other living mechanisms, and that on other planets even if the conditions are not suitable for us, there might be something well evolved through time there. After all if we can conceive electric robots that can survive to radioactivity and to high pressures and temperatures, why nature shouldn't be able to?


texts: Is there a difference between splice-site mutations, and non-stop mutations

texts:
I'm working on a bioinformatics project where a lot of the biology I've had to learn from scratch. From my current understanding, a non-stop mutation alters a stop codon such that the transcription continues, and a splice site mutation alters the region between introns and exons - where the sequence may include introns, or remove part of the exons from cancer.gov. I'm inferring therefore that these could be the same mutation type.

Is this understanding correct?


texts:
What is the criteria for classifying neurons as small and large?
Is this classification based on gross size or the length of axon?
Do they have any physiological difference?

For instance it is said that Substantia gelatinosa of Rolando contains small neurons .

What is so special about calling those neurons as such?
Aren't they doing the same function of conduction of impulses?

I have googled it but couldn't find any explanation for such naming.


texts: Is it true that newborn babies don't produce tears while crying? Why?

texts:
Well, I was just going through an article on eye, where in fun facts it was mentioned that newly born (for initial 1 to 3 months) babies do not produce tear while crying. Actually, I have found this true.

Now, I am wondering why is it so? Does any one know the reason behind this?


texts: Preferred criteria for new bee colony location

texts:
As a human I want a house with a roof, indoor plumbing, bug free, and make my wife happy.  I don't want to drive too far to work, and it has to be well-suited for offspring.

What are the criteria that define a "good spot" for a new location for honey bees.  I'm sure it involves water, shade, access to nectar, and defensibility, but I don't know any of the details.

Has anyone ever made measures of this? Beekeepers? Apiologists?  What are the things bees think are important, and what values of those do they think are "best"?


texts: How does a decrease in free Ca2+ result in nerve/muscle overexcitability?

texts: I have in my notes that a decrease in free Ca2+ increases membrane permeability to Na+ so that it is brought closer to threshold, but no further details. So how does this work?


texts:
If I understand it correctly, humans can discriminate shades and colours based on their inherent contrast, as in we can see colors because there are different colors. Same for shades and for acoustic phenomens, because to differentiate two sounds they have to differ in some quality of sound: pitch, loudness, duration.

So the question is whether all perception is contrast based. One I would presume not to be contrast based is spatial perception, because it simply is there and always works in a standard manner.


texts: Does modern theory of evolution include modification of physical environment?

texts:
Does any branch of modern evolution theories include aspects of evolving organisms modifying the physical environment?

An example from the evolution of life could be early stage introduction of oxygen and carbon dioxide to the atmosphere from single cell bacterial growth, thereby establishing a basis for growth of more complex organisms.

See also somewhat related question: https://physics.stackexchange.com/questions/22771/does-the-universe-follow-a-general-physical-and-computational-principle-of-evolu


texts: What's a mouth ulcer/canker sore "made of", and why do they develop?

texts:
Mouth ulcers are red/white rings with a crater. They are sore and last for 7-10 days.

What I want to know is what they are 'made of' - i.e., what is the ring filled with, and why is the centre crater so sore? And why do these relatively benign and short-lasting ulcers have to hurt so much when they simply heal in a couple of days


texts:
This textbook states

Proteins determined by a single gene may divide to form different proteins with various physiological actions.

First how do proteins divide? Second if it's just fragmentation then what is this process called? Third since my textbook doesn't explain it could anyone explain with an example of how different parts of original protein( considering that protein has divided by fragmentation) perform different physiological actions?


texts: Public fermentation/cell cultivation database?

texts:
I am wondering if there are any large collections of fermentation or cell cultivation data publicly available.
I am interested in all cell types used within industrial biotech and biopharma, especially the most common ones, e.g. CHO, yeast, e.coli, bacillus, lactis.
I am interested in this from a process understanding point of view. So I am very interested in the conditions throughout (pH, nutrients, dissolved oxygen, media comp, turbidity, etc.) as a time series. If manual (offline) measurements are made, CFU, amount of metabolite produced, etc. they would also be incredibly interesting to have.
I have looked around without luck.
I guess the 'perfect' database probably doesn't exist, but I haven't been able to find anything.
So I would really appreciate help finding any dataset on fermentation data, even if it doesn't have all that I am looking for.

I found this article: Bio-Ferment A Database on Bioreactor and Fermentation from 2011, but I cannot find the actual database.


texts: What percentage of cells in the human body are infected during a non-fatal viral infection?

texts:
I understand that this would be a very rough estimate, but approximately how many cells in the human body are infected during an average non-fatal viral infection before the infection is eliminated by the immune system? It doesn't matter what virus you use as an example, I'm just looking for a general case.

Thank you,

CDB


texts: How fast the human eye can [temporarily] change its color?

texts:
I know that human eye can change its color during lifetime because of disease or medication (similar question on Biology.SE). And I know that it may change depending on the lighting.

But I saw several times as the eyes of man with the bright eyes changed color  (blue/gray/green) without changing environment. Is it possible to temporarily change eye color due to the change of emotional state (as a consequence of the effect of hormones or something else) in just a few of minutes? If so, what are the processes behind this?

Or it just optical/psychological illusion for the observer?


texts: What will happen if we expose the brain to intermittent light?

texts: If a brain is exposed to an intermittent light source, are specific areas going to fire? If yes, which of them? Is there a experimental data about this effect?


texts:
This is a very very basic question. I've looked at methods such as chromosome sequencing and shotgun sequencing. Wikipedia says that:

DNA sequencing is the process of determining the precise order of nucleotides within a DNA molecule

For instance, with methods such as shotgun, we already have the original DNA. If we have access to the original DNA itself, don't we ALREADY know the sequence of nucleotides?

Why exactly do we need to 're-build' the DNA with methods such as shotgun and chromosome walking, when we already have the original DNA available? If we have the original DNA, don't we already have the original sequence of nucleotides?

It makes me think that these techniques for 'DNA sequencing' is sort-of pointless. But, obviously I am misunderstanding something.

Thanks in advance, any simple pointers would be great.


texts: Glycogen vs cellulose-curvature of glycogen molecule?

texts: I was wondering if anyone knows what the degree of curvature is or bond angle between the $\alpha$ glucose molecules in glycogen is. I know that glycogen/amylose/amylopectin have a general curved backbone (as well as branches in glycogen and amylopectin). This is a consequence of the 1,4-glycosidic bond between $\alpha$ glucose molecules. On the other hand cellulose has straight molceules, which is a consequnce of the 1,4-glycosiodic bond between $\beta$ molecules with alternating orientation. However I cannot find anywhere what the degree of this curvature is in glycogen backbone, or the bond angle between molecules in $\alpha$ 1,4-glycosidic bond?


texts: Are the byproducts of mammalian digestion simply depleted versions of the food or liquid consumed?

texts:
When mammals consume food and digest it or drink fluids that are then filtered by their kidneys, are the waste products generated simply depleted versions of what they consumed?

Are there other byproducts of metabolism and filtration contained in that waste that are generated by the body and are not directly a part of the food or liquid that was consumed that are excreted?


texts: Why are red blood cells preferred to study the structure of plasma membrane?

texts: If we wanted to study the structure of a plasma membrane, why are red blood cells a more attractive cell type to work with than other cell types such as liver cells or kidney cells?


texts: Water snake with a yellow criss-cross on a black background?

texts:
I saw a 60 cm long, very skinny (~15 mm diameter), black with yellow diagonal criss-cross patterned snake swimming in a pond this afternoon in northern Taiwan.
It was swimming near the top of the water and I could see it very clearly, but as soon as it noticed me it dropped most of its body to the bottom of this shallow pond and just kept part of its head above water, so the photos are not very clear.
I tried to wait for it to continue but something else disturbed it and it took off.
Is it possible to identify this snake or at least narrow down the options?
First image is cropped from the large image. I have played with contrast, color and sharpness to make the pattern and color look most like what I remember before it dropped its body lower into the murky water.

sketch of pattern as I remember it


texts: What physical force attracts the anti-codon on tRNA to the codon on mRNA during translation? I know that these two bond together, but what actually makes the tRNA move through the cytoplasm to the mRNA on the ribosome?


texts:
For synthesis of one molecule of glucose,six turns of calvin cycle are required.

One molecule of carbon dioxide combines with ribulose bisphosphate (RuBP) to form a stable product of two molecules of phosphoglycerate (PGA). This is called carboxylation. Then 2 molecules of PGA undergoes reduction to form 2 molecules of phosphoglyceraldehyde (PGAL).

My question is whether there 2 molecules of PGAL goes in the regeneration of RuBP or in the synthesis of glucose.


texts: The post-apocalyptic science fiction novel Dark Universe by Daniel F. Galouye has some plants living inside bunkers that use infrared light for photosynthesis. There are speculations that extraterrestrial plants might use the same trick on planets orbiting red dwarfs and that their leaves would be totally black. Would this type of photosynthesis be possible and are there any plants on low-light environments from Earth that might do this already?


texts: ID this insect please. SE Brazil Oct 2017

texts: A number of these large flies were praying on smaller stuff / mid day / in the low altitude rainforest sections of SE Brazilian Rainforest


texts: How to prevent a old promoter region from attaching onto a plasmid instead of a new one during ligation?

texts:
What I am trying to do is take out a existing promoter region in a plasmid, and replace it with a new one. So first I use the appropriate restriction enzymes to get rid of the existing promoter region. Next, I add in the new promotor fragment which has the appropriate sticky ends, and then through ligation, I want to place the new promotor in the plasmid.

Since the old promotor region and new promotor region will have the same 'sticky ends', how do I prevent the old promotor region from getting placed into the plasmid instead of the new one during ligation?


texts: What does it mean for a hormone to be "active"

texts:
In my textbook it is stated that the T3 hormone produced at the thyroid gland is 3-5 times more biologically active than T4.

How is being active defined and how can this effect be measured?


texts: How is cancer associated with host pathogen interaction?

texts:
Does cancer by any chance fall under host pathogen interaction domain? What I mean to ask is that, is there pathogen interaction involved in cancer? I went through this article:
http://en.wikipedia.org/wiki/List_of_human_diseases_associated_with_infectious_pathogens
In the cancer category they have used the phrase "can be cause" by this and this pathogen.. Isn't cancer a disease that occurs due to abnormal growth of cells due to genetic change?


texts: Why does the sweat of children not smell like adults?

texts: My kids sweat plenty in this hot heat, but they don't smell afterward. I on the other hand need all kinds of deodorant. Why doesn't kid sweat smell?


texts: "Oblong to Allantoids" .... Is it valid?

texts:
I read on the text book:

The characteristic of Dinemasporium are: superficial, cupulate to Discoid conidiomata with brown satae, Phialid conidiogenous cells that give rise to hyaline, oblong to Allantoids, and Aseptate conidia with an appendage at each end.

My question:

the phrase "oblong to Allantoids"; Is the word oblong valid for this context? if not, what other word would associate?


texts:
In the United States, anencephaly occurs in about 1 out of every 10,000 births. There are several forms of this condition, wherein the forebrain is absent. The forebrain is host to most of the higher functional areas in the mammalian brain. In the most extreme case of anencephaly, the so called holo-form, only the brain stem remains.

In MacLean's model of the brain, the term brain stem is used interchangeably with the term reptilian brain, to designate the most primitive parts of the central nervous system. Many are taught this model.

  An anencephalic newborn (warning: graphic content)
  ("An anencephalic newborn", wikimedia, author: Almazi, license: public domain, DOR 27/09/2012)

From my layman's perspective I can't help but notice a reptilian likeness of the anencephalic newborn. Whilst it goes without saying that correlation doesn't equal causation, I would like to know what is known so far about the cause of this condition to yield this particular morphology (as seen in the picture)?

Perhaps someone (eventually) has even some evodevo insight to share as well?


texts: How is circadian rhythm of gastric acid secretion regulated?

texts:
Gastric acid secretion shows a circadian rhythm where acid production in the morning is minimal and it reaches a maximum towards the evening.

How is this process regulated?


texts: Individuals of each species all have unique facial structure variations (shape of nose, position of chin etc) from humans to birds and fish etc. We humans don't seem to be reaching mathematical limit of uniqueness easily (maybe till the end of the world) considering huge variation and all possible combinations that define our facial structure/traits. However some animal populations are way more larger than humans and each year they reproduce in large amounts.  Considering their huge populations, is it possible for some species to reach their mathematical limit of having unique facial structure variations therefore start repeating the same facial structures?  For example can individuals of some fish species (sardines, sea breams etc) be already sharing exact same facial structure/geometry as a result of reaching all posible facial structure  variation limit?


texts: Have there been new discoveries concerning the perception of taste for the last 10 years?

texts:
What are the last discoveries concerning the perception of taste for the last 10 years?
We discovered the 5th flavour: umami.
Also the 6th and 7th: oleogustus and starchy.
Anything else?
Maybe in genetics, as we all have genetic predisposition?
Or concerning the creation of the systems in charge of the perception of taste during the embryo-genesis?


texts:
I am working on yeast mutant and I am observing their sporulation efficiency on agar plates. One of my plates got some dark green small fungus patches. I can't grow yeast again and dump this one with fungus because I am counting at a specific time interval to compare and it will take a lot of time to go through the entire process.

What should I do? Should I remove fungus from scalpel? And does this fungus going to affect the yeast growth?


texts: Problems in optimisation with applications to biology?

texts:
I will soon have around 8 weeks to do a research project of my choosing  as I am finishing my undergrad in computer science.
My experience is mostly in optimisation algorithms (mostly combinatorial/discrete optimisation).

I have an interest in applying computer science to biology (mostly human biology).
I would like to ask if anyone knows optimisation problems with applications to biology which would benefit current research.

Although I have read a lot about biology in my free time, I am not too knowledgeable about the current state of the research and so it is a bit hard for me to find a good topic.

Some examples to spark the discussion are string problems in genetics (alignment problems), and community detection in graphs (to find proteins in the same functional group).

Thank you!


texts:
I was asking me something weird, and I thought you might validate or not my theory.

Hypothesis: A brother and a sister have one chance over 78 billions to clone one of their parent if they procreate

Here is my method:

I have 23 chromosomes from my mother, and 23 from my father. My father has 23 * 23 = 529 combinations of chromosomes in his "gametes". If my experience is willing to work, I need to have the exact opposites of my father chromosomes than my sister ones. That means that we can't have any of my father's chromosome in common with my sister. That makes approximately 1/529 * 1/529 = 1/279 841.

Then, if I decide to procreate with my sister, our child needs to have the 46 chromosomes back from my father. So the computation stays the same and I will have 1 chance over 279 841 to make it so.

1/279841 * 1/279841 = 1/7.8*10^10

My question is: Is my theory valid? If not why? If yes, that will make a hell of a story at parties...

Thank you for your scientific answers and have a nice day!


texts: Why are pili more common in Gram negative bacteria than in Gram positive?

texts:
Although pili have been observed in some species of Gram positive bacteria, the preliminary research that I have done indicates that pili are significantly more common in Gram negative bacteria.

Is this an accurate assessment of the current body of scientific knowledge? If so, do we know (or have any leading theories on) why this is the case?


texts: molecular indicators of apoptosis: clarification needed

texts: I understand that DNA fragmentation is a molecular indicator of apoptosis. What distinguishes this as a hallmark of programmed cell death, versus one of necrosis?


texts: Does double stranded RNA (dsRNA) exist in eukaryotic cells?

texts:
I know it sounds like a stupid question. Obviously, tRNAs and rRNAs, for example, form loops and could therefore be considered as dsRNAs... but are they really considered as such?
Are there examples of RNAs, in eukaryotic cells, that could be considered exclusively as dsRNAs, or are dsRNAs considered as unique to certain viruses?
Thanks in advance for your help. I couldn't find a clear answer to that question in my textbooks and on the internet, so I hope you can help.


texts: Can molecular genetics make a boolean variable from a continuous variable?

texts:
In the same kind of idea than this question. Gene expression are regulated through complex interactions. The concentration of enhancers and repressors is an important aspect that dictate the level of expression of a given gene. These concentrations can take different value on a continuous scale.

Imagine a case where fitness is maximized when a given gene produce n proteins per minute if the concentration of a given protein is greater than x. If the concentration of the protein was to be lower than x, then the gene should not be expressed (0 proteins per minute are produced). In such case, it would be great if a bunch of reactants were to be able to simulate a "switch function" that would switch from "NO EXPRESSION" to "EXPRESSION" at x.

It seems to me that such switch function should be very complicated to evolve. I would suspect that all chemical reactions, including the binding of enhancer to promoter region should follow the law of Michaelis-Menten and the Michaelis-Menten function is not at all switch function. So, I have been thinking about cooperative binding. Hill's equation describes a function that is effectively a switch function given that the hill coefficient is high enough. However, seeking a bit in the literature, it's seems that the Hill coefficient never really overpass 3 (or 5 for extreme estimates). A Hill coefficient of within this range gives a logistic function but still looks quite suboptimal compared to what a perfect switch function could do.

Are there switch functions in molecular genetics that could translate a concentration into a TRUE/FALSE signal?
How well do they simulate the perfect switch function?
Are they based on cooperative binding or on some other mechanism?

References for estimate of Hill coefficients:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1435008/pdf/biophysj00200-0109.pdf
http://onlinelibrary.wiley.com/doi/10.1046/j.1537-2995.1983.23283172857.x/abstract
http://www.pnas.org/content/93/19/10078.short
http://www.ncbi.nlm.nih.gov/pubmed/8816754
http://www.fasebj.org/content/11/11/835.short
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2816740/


texts:
According to this

Neural Plate

The neural plate appears in day 18 in humans (very specific).

and according to this

Neural Plate (wiki)

  The progenitor cells that make up the precursors to neural tissues in
  the neural plate are called neuroepithelial cells.

And according to this

Neuroepithelial cells

  Neuroepithelial cells are the stem cells of the central nervous
  system, known as neural stem cells, and generate the intermediate
  progenitor cells known as radial glial cells, that differentiate into
  neurons and glia in the process of neurogenesis

So, if it's known when the cells which are precursors of neurons appear, I suppose it should be known when the first neurons appear, but I can't find information about it.

When do the first neurons appear in humans?


texts: Could eidetic memory be related to glial cells?

texts:
I am a plasma physicist so I apologize in advance for my biology ignorance.
I recall from a neuropsychology class I took in college (used Lezak, Howieson, and Loring, 4th Edition) that there are several types of glial cells, at least one of which acts to prune neurons in your brain.  I am curious if those with an eidetic memory have fewer or different or altered glial cells?  That is, could the pruning done by some glial cells affect long-term memory or brain function but not be operating (or at least in a diminished capacity) in those with an eidetic memory?
I found a somewhat related question but it's not directly tied to this one: Is an Eidetic Memory (or other unusual forms of memory) less susceptible to anterograde amnesia?
References
Lezak, M.D., D.B. Howieson, and D.W. Loring Neuropsychological Assessment, 4th Edition, Oxford University Press, Inc., New York, New York, 2004.


texts:
I am looking into Vitiligo it's an autoimmune disease that results in apoptosis of melanocytes due to misfolded protein accumulation.

It also dramatically increases breast cancer rates (600 times) within one to five years from the first symptoms of Vitiligo. One function of melanocytes is to produce chemokines however I was unable to find any info on which ones.

Which chemokines are being produced by melanocytes?


texts: Do non-functional (‘junk’) protein sequences exist?

texts:
For DNA one can distinguish between

protein-coding DNA sequences, i.e. nucleic acid sequences inside DNA (vs. non-coding sequences)
DNA sequences that do not code for proteins but are transcribed into functional RNA
non-transcribed DNA sequences that have other (e.g. regulatory or structural) functions
non-transcribed and non-functional DNA sequences (‘junk DNA’)

The relative proportions of these seem to depend heavily on the organism and are only roughly known.

  What I wonder is whether there are protein sequences (i.e. amino acid sequences inside a protein) that have no functional purpose.

A non-functional protein sequence might be a sequence that is neither effective to the outside (e.g. as a site for post-translational modification) nor to the inside (e.g. in folding). But even those parts of the protein might contribute structurally by their sheer presence and mass which is important when considering proteins not only as chemical but also as somehow mechanical devices. This might be called its structural purpose.

Assuming that each part of a protein has either a functional or only a structural purpose the question arises what the relative proportions of functional vs. only structural parts are.


texts: What is the biological potential for vision of wavelengths outside the human visual range?

texts: Humans eyes have evolved to perceive light only between approximately 350-700nm, because that form of light is most common to our lifes. Other animals can perceive lights with slightly different fequencies. Can eyes theoretically evolve in a way that they can observe all light as we know it today? If not what would approximately be the maximum amount of frequencies that can be perceived?


texts:
Suppose some scientists built a large vat, sterilised it and filled it with distilled water. Then they start dissolving compounds into the water such as amino acids or what ever they deem conducive to life. They can also control temperature, radiation and other environmental factors.

They periodically capture a sample of the water and examine the results.

Would they be able to inadvertently create self replicating molecules and the precursors to life?

Would this kind of experiment be worth attempting?


texts: What medium is the bacteria used to synthesize B12 sourced from?

texts:
Would that be from water, soil, plants, funguses,...?

I asked the question in Quora but that, at the time of posting in this forum, haven't been very helpful. I also have searched for the information, but I haven't been able to find it. In Vegan Health it says that

  "The vitamin B12 component in B12 supplements and fortified foods is
  made by bacteria and sourced from bacteria cultures; it is not taken
  from animal products"

But I wonder where did those cultures come from. One day someone had to collect the bacteria from somewhere in order to start the cultures.


texts: Why does plucking nose hair cause tears in the eyes?

texts:
It's not a particularly sad or painful thing to pluck a few nose hairs, but it's common for the tear ducts to wet up when doing this.

I would like to know the physiological reason for the correlation, how/why are the tear ducts and nose hairs related in the human body?


texts:
I know that often oxidation processes are mentioned when referring to the color change from yellow to brown in bananas (specifically: those that you get everywhere in supermarkets, with no seeds).

However, I am really interested if there is a specific oxidative pathway that is generally followed in this process, and whether it has been examined.


texts: What placement of plasmid parts makes the most sense?

texts: If you want to express the largest amount of a certain or a few proteins using a plasmid, does it make sense for the antibiotic resistance gene to come after genes for proteins you intend to synthesize?  So that the promoter and RBS/origin of replication would specifically come before the proteins intended to be synthesized and the bacterium would put less resources into its antibiotic resistance?  But would that be canceled out by bacteria not surviving as much as if the antibiotic resistance gene is downstream of the other proteins?  Or is it roughly the same in either order because they're both being synthesized anyway?


texts: How can a blood test give information about rickets?

texts: Can we detect rickets from a blood test? What  evidence pf rickets is in the blood and how is the blood treated to detect rickets?


texts: This specie grows in a dry hilly area in the south of France close to Marseille. I made the picture today. It is quite dominant and grow close to the soil maybe about 50cm.


texts: Twins reproducing with each other ( just hypothetical)

texts:
If 2 twins (look exactly the same and also the genes which control their morphology, behaviour etc. are same and present at the same locus) produce an offspring , will their offspring be exact copy of their parents ?

Sorry . I know its not moral.


texts:
I am interested in pulse frequencies of GnRH (gonadotropin-releasing hormone) in the menstrual cycle (MC) i.e. 28 +/- 7 days.
I would like to study its pulsatile nature i.e. within one MC, not same as cyclic nature within many MCs; but possible cyclic dynamics could be found in one MC too but not focus there.

GnRH releases human chorionic gonadotropin (hCG) which can be monitored by beta hCG but also by (source DynaMed Plus on Chorionic gonadotropin)

serum progesterone, Luteinizing hormone (LH)
estradiol levels
ovarian US 7-14 MCD i.e. in late follicular phase
onset of ovulation at 14 MCD
pelvic exam
cryptorchidism: signs of precocious puberty

Two articles on GnRH monitoring:

Monitoring gonadotropin-releasing hormone administration by measurement of urinary steroid conjugates in the morning urine samples.
some gene studies: Episodic gonadotropin-releasing hormone gene expression revealed by dynamic monitoring of luciferase reporter activity in single, living neurons

Possible cases to study

Amenorrhea: Kallmann syndrome where congenitally deficiency of GnRH but how low?

However, I did not find any publication describing direct/indirect continuous measurement of GnRH.

How can GnRH be measured continuously during the menstrual cycle?


texts: Question about *Cryptosporidium hominis*

texts:
Cryptosporidium muris infects mostly rodents and it is usually found in gastric gladns. Cryptosporidium parvum infects humans and certain animals and it is found in the terminal ileum and colon.

There is also Cryptosporidium hominis that infects only humans. My question is

  where exactly in the human gastrointestinal tract it resides?


texts: Partial pressures of different gas in human blood and how they are calculated?

texts:
In Respiratory Physiology, we use the $P_x{O_2}$ and $P_x{CO_2}$ in blood at different regions of the peripheral circulation. From my Chemistry knowledge I know that $P_x$ of a gas in a solution is the fraction of total pressure caused due to the gas dissolved. But in blood $O_2$ is present mostly as $OxyHb$ and $CO_2$ is also present as $CarbaminoHb$ & $HCO_3^-$. In blood their dissolved state fraction is very low. Now my question is how do we measure the $P_x$ of any gas ($O_2$ or $CO_2$) in blood and what is the logic here? [x means either arterial blood or venous blood]
Here is the data I'm talking about.(https://i.stack.imgur.com/lA1M5.jpg)


texts: GWAS: why is replication in another cohort so crucial?

texts:
Almost all the landmark GWAS (Genome-Wide Association Studies) reviews agree that, for a GWAS finding to be valid, it needs to be replicated in an independent cohort. What exactly is the rationale behind this? Is this criterion still valid even when the objective is looking for genes to do functional studies, instead of a clinical perspective of searching for susceptibility loci? Considering the difficulty in replicating some phenotypical characterizations in a large numbers of subjects, for a biologist this whole thing seems irrelevant.

Consider the following scenario: Suppose I have 5000 phenotyped individuals with a budget to genome-wide genotype them all. The phenotyping requires state-of-the art methodology with immense costs, and the cohort was phenotyped through another grant. What would be the point of dividing my cohort to two as a discovery and replication groups, other than to save money in exchange for stat power. To this, add the subsequent functional studies on the associated loci, what would the point in genotyping a few SNPs in 500 more people be? If one can indeed find that additional cohort, wouldn't it be a better option to combine any available cohorts in a meta-analysis, rather than using them for replication?


texts: How can someone share 50% of their DNA with their parents yet all humans share 99.9%?

texts: I have heard that humans share 99.9% of their DNA with other humans. I have also heard that a child shares 50% of their DNA with their parents. How do I resolve this apparent contradiction? It has been really bothering me.


texts: Is it true that the human brain has not evolved in 100 000 years?

texts: I read that the human brain has not evolved in 100 000 years and that's why there are no genes for intelligence.


texts: Effect of soap on the survival of non-enveloped viruses

texts:
As I understand it, non-enveloped viruses are not annihilated by alcohol or have lipid layers to get soluble in soap micelle.
Does soap remove non-enveloped viruses and does hand wash help in their spread?


texts: How does the adaptive immune system store information?

texts:
I am quite curious about this:

Where and how is knowledge that the adaptive immune system accumulates stored?
What is the "memory size limit" of this storage method if there is any?
Why cant this knowledge be transferred between individuals like we transfer computer antivirus definitions?


texts: How do the three mechanisms of the 1000X improved "new" vancomycin work together?

texts:
The BBC News article Ultra-tough antibiotic to fight superbugs says (in part):

One hard-to-treat infection that has been worrying doctors is vancomycin-resistant enterococci or VRE.
It has been found in hospitals, can cause dangerous wound and bloodstream infections and is considered by the WHO to be one of the drug-resistant bacteria that pose the greatest threat to human health.
Some antibiotics still work against VRE, but the 60-year-old drug vancomycin is now powerless.
The Scripps team set out to see if they could revamp vancomycin to restore its killing ability.
They made some strategic modifications to the molecular structure of the old drug to make it better at attacking bacteria where it hurts - destroying cell walls.
Three changes in particular seem to be important, increasing the strength and durability of the drug.
Lead researcher Dr Dale Boger explained: "We made one change to the molecule vancomycin that overcomes what is the present resistance to vancomycin. And then we added to the molecule, two small changes that built into the molecule, two additional ways in which it can kill bacteria. So the antibiotic has three different, we call them 'mechanisms', by which it kills bacteria. And resistance to such an antibiotic would be very difficult to emerge. So it's a molecule designed specifically to address the emergence of resistance." (emphasis added)

Unfortunately I haven't been able to see the PNAS paper. The link in the BBC article just gives me this:

However the title in PNAS seems to be stated in the Genetic Engineering & Biotechnology News article Vancomycin Modified to Combat Growing Antibiotic Resistance Threat as "Peripheral Modifications of [Ψ[CH2NH]Tpg4]Vancomycin with Added Synergistic Mechanisms of Action Provide Durable and Potent Antibiotics"
It sounds to me that the first change was to keep the original vancomycin's original mode of action but to make it more robust against adaptations in the vancomycin-resistant strain, but I'm not sure if that's correct.
The other two differences sound to me like two new mechanisms that were not there before - it almost sounds like they could just as well be on different molecules administered simultaneously, and that their presence on the vancomycin molecule is primarily for issues of delivery.
Are these two new changes essentially independent modes of actions that could be on separate molecules, or do they need to reside on the same molecule as the primary mechanism?
The article puts the word "mechanism" in quotes. I'm trying to understand if these are independent or work together at the molecular level - in other words do they operate together in such a way that they need to be on the same molecule?


texts: I have heard that the Hydra organism is biologically immortal (later I found that there are more immortal organisms). Now I know that its immortality is related to its telomerase. The thing is that we all have telomerase, but we age and Hydra don't. What are the proteins (especially telomerase) related to aging in humans and Hydra and how do they work differently?


texts: Does reproduction cause aging ? Is aging just a strategy to increase reproductive success in all organisms?

texts:
Background for why I am asking this:

I read a book—modern biological theory and experiments on celibacy— which uses life history theory to imply that reproduction is the reason why organisms grow old. Can this really happen?

The book uses several arguments in support of this argument:

Even if an organism does not age, it would still die from accidents.
Therefore, reproduction becomes a higher priority for the organism than repairing and maintaining its body in order to survive over generations.
Consider two organisms, one that ages and one that does not. Now, if the one that ages can 'tune' its rate of aging so that its life expectancy is more or less the same as that of its non aging peer, it will suffer little loss of lifespan and gain a lot of reproductive success in return, giving it a selective advantage.
The book argues that by aging, organisms reduce the cost of dead bodies. For example, if we don't age, all the people dying would be healthy and robust, implying all the energy gone into maintaining health would be wasted. But if, strategically, we start 'spending' health to gain extra reproductive success, we end up gaining what we would otherwise waste. All the really old people in an aging world like ours become corpses even before dying, implying less loss involved.

So, here is my question:

Is reproduction one of the major causes for ageing? Is ageing a strategy to increase reproductive success, as described in the theory above? Does life history theory imply that a 'well fed' individual will strategically age itself to gain a selective advantage? Is that it? Is that why we age?

Some experiments that favour the above theory:

It has been shown in 'hundreds of dietary restriction experiments' done on animals that a decreased rate of reproduction and of aging go hand in hand.
An increase in the lifespan of eunuchs and castrated animals has been confirmed in many experiments.
It has been observed that if a lactating female lacks calcium, the bones in her body are demineralized to nourish her offspring, implying a higher priority towards the child than her own body, which makes sense because the child would outlive her.
Experiments have confirmed that the cost of ejaculate in male adders and Japanese macaques is non-trivial.

It should be noted that this theory assumes life history theory to be correct, and is therefore supported by all experiments that support life history theory.

After reading disposal soma theory, as suggested by rg255 in the comments, I can see that the theory discussed in this book is disposal soma theory with an extra assertion that the best life strategy of any organism is not to have 0 aging, but to have a species specific rate of aging, in order to reduce waste of resources through dead bodies and increase reproductive success.


texts:
I'm well aware of the Gardening/Horticultural approach of "a weed is any plant that you don't want in its current location".
But I think most people would agree that there's a more useful interpretation of "weed" that relates to its growth.
I would say that weeds are the plants that would be extremely easy to introduce if you wanted to them in a particular place, and extremely hard to remove if you didn't want them.
Common properties that I can think of, of the top of my head, for such plants include:

quickly growing.
quickly reproducing.
self-seeding.
re-growing from roots even if the above-ground plant is removed.
not particularly sensitive to ground conditions.

Question:
Why don't all plants exhibit these behaviours?
It feels relatively "obvious" that the plants that exhibit these behaviours should be able to out-compete plants that don't, since they reproduce faster and are more resilient.
And yet the slightest glance outside demonstrates a wide variety of plants that I think would trivial die if I attempted to attack / damage them.
What gives?


texts: Is there any evolutionary advantage of selection of L-amino acid over D-amino acid?

texts: After listening to a scientific talk, I had this question that why in the natural selection process, are the L-amino acids selected over the D- form. However, we still we produce D-amino acids; specifically in the brain there is a higher concentration of D- amino acids. One possible reason is that they act as neurotransmitters.


texts: Are there disadvantages to using Rhizobium rhizogenes for genetic transformation?

texts:
Rhizobium rhizogenes causes hairy roots, which are transgentic. Are the transgentic roots able to eventually grow normal roots or will they always be hairy in the transgenic organism?

  After integration and expression, in vitro or under natural
  conditions, the hairy root phenotype is observed, which typically
  includes overdevelopment of a root system that is not completely
  geotropic, and altered (wrinkled) leaf morphology, if leaves are
  present.  - Cardarelli M, Mariotti D, Pomponi M, Spanò L, Capone I,
  Costantino P. 1987. "Agrobacterium rhizogenes T-DNA genes capable of
  inducing hairy root phenotype". Molecular and General Genetics
  209(3):475-480.

Is this permanent or temporary?


texts:
For the past two weeks, I have been in a group of 3 studying how different lights affect plant growth. So we growth two chickpeas plants and put one in white light and the other in blue light.

These are the results:

Days    Blue light    White light
           (cm)          (cm)
__________________________________
 1          6.6           8.2
 2          8.5           9.9
 3         11.0          11.6
 6         15.8          16.0
 7         17.2          17.6
 8         18.0          18.2
 9         19.6          18.7

The blue-light plant didn't really branch out a lot whereas the white-light plant branched out a lot.

My question is:

What caused the white light plant to not grow as fast like blue;
Why did the white light plant branch out?

What I read about the second question:

Experiments with blue light resulted in plants that are wider than usual. This can be explained by reference to the fact that more flowering buds (more branches) could form by reason of diminished apical dominance at the growth point.
http://www.canna.com.au/influence_of_colours

I don't understand why the blue lights plant did not branch out a lot like the white light ones?


texts: Winter is getting shorter and warmer. Does this mean deciduous trees can photosynthesise for longer and thus absorb more carbon dioxide?

texts:
As springtime is starting earlier this year, I wondered if that would mean deciduous trees had more time to photosynthesise and, therefore, they could absorb more CO2 or have longer periods to grow, etc.

Also, is there any evidence that colder climate deciduous trees would fare better or worse as conditions change for them?


texts: How does the embryo inside a shelled egg get oxygen?

texts:
If I'm not mistaken a typical animal in the womb will get oxygen via the umbilical cord from the mother. Thus allowing it to "breathe" in a liquid environment. I thought maybe shells are permeable and allow air to come in through the shell, but then I thought of eggs laid in the ground like turtles do.

How do animals in soft/hard shells get their oxygen?


texts: After seeing this video I am curious to know why the free living bacteria produce light. What advantage will they have ? Or is it just an "unintentional" result of one of their pathways ?


texts: What reasons allow for women to outlive men?

texts:
It is a well-known fact that women tend to outlive men.

I often hear people unscientifically stating that men generally generally die younger because of the higher stress encountered in their work lives. I would personally immediately rule this out, as who's to say that that women's (past) home lives just weren't as stressful? Also, shouldn't we see a narrowing of difference in age with the recent gender equality issues? Since the trend in question still occurs in virtually all countries of the world, I think it's safe to assume that the phenomenon is purely physiological.

I am curious as to the most sound scientific theories or known reasons for why women typically outlive men. Finally, I understand that aging in itself is not a process that's completely understood, and thus am not expecting a "complete list" of factors.


texts: What's the difference between evolution fitness and reproductive success?

texts: What's the difference biological fitness and reproductive success in the biological terminology?


texts: Why is the amount of ATP Produced from anaerobic respiration is less than the amount produced from aerobic respiration?


texts: Biphasic T wave caused by digitalis toxicity

texts:
Digitalis is a drug that can be used during coronary insufficiency to
  increase the strength of cardiac muscle contraction. But when
  overdosages of digitalis are given, depolarization duration in one
  part of the ventricles may be increased out of proportion to that of
  other parts. As a result, nonspecific changes, such as T wave
  inversion or biphasic T waves, may occur in one or more of the
  electrocardiographic leads. A biphasic T wave caused by excessive
  administration of digitalis is shown in Figure.

Therefore, changes in the T wave during digitalis administration are often the earliest signs of digitalis toxicity.

I was reading about it in Guyton and Hall Physiology (volume 1, heart , chapter 12) and there was nothing about this that answers my questions.

And my questions are:

Why is T wave more affected by digitalis toxicity?
Why does it cause Biphasic T wave?


texts: How can I isolate live Wolbachia endosymbionts from Drosophila

texts: I am interested to culture Wolbachia bacteria in cell line.


texts: Bug Identification: what type of bug is this small ant-like bug?

texts:
It's not an ant; do you know what it's called? Found some in the building different times.

Edit: Size is 4mm (length) x 1mm (height)


texts: Human leukocytes (re)circulation/migration in homeostatic state

texts:
One can easily find information on the topic of leukocytes trafficking between vessels and peripheral tissues during inflammation.

But what happens during normal states when there is no pathology? Do all the subtypes of granulocytes, monocytes, and lymphocytes leave the blood vessels and enter healthy tissues in the same way they do under pathological (inflammatory) conditions?

References and thoughts are very welcome.

Thank you.


texts: How does 2-mercaptoethanol lead to shift of the band to a higher molecular weight?

texts:
I have a project to isolate a protein with biological properties from a plant. The purified protein forms four bands with similar molecular weight on SDS-PAGE (30–35 kDa) in the presence of 5 % 2-mercaptoethanol, and two bands with lower MW (27–30 kDa) when 2-mercaptoethanol is omitted.

How can these results be explained? What is the easiest and lowest cost method to separate closely related proteins (if that’s what these are, and not just subunits of a single protein)?


texts: How can I perform a 1:1 sequence-structure alignment for a pdb template dimer and homologous dimer sequence?

texts:
I have:
1. A PDB dimer protein structure template of a real solved protein.
2. An unsolved, but highly homologous dimer protein (>90% sequence identity.)

How can I use MODELLER to make a theoretical model of my dimer of unknown structure, using the homologous dimer template?

I know I need a PIR alignment file, probably with a 1:1 sequence-structure alignment.  However, I do not know how to make this file.

Please advise?


texts: Is there any evidence that a virus can modify human evolution

texts:
I was just reading Evolution of lactose tolerance, and in it one line says "But there was a time in human history when our diet and environment conspired to create conditions that mimicked those of a disease epidemic".

Something I've always wondered is rather than natural selection occurring and survival of the fittest and so on, is that a viral epidemic caused a mutation in the survivors, i.e. DNA was inserted from the virus that modified the survivors genome. There is some evidence that a significant percentage of the human genome comes from viruses. Probably a naive question - so is there any evidence that this has occurred? From my lay perspective this is what attempts at genetic engineering use, so it's possible nature already did this?

It's always seemed to me that natural selection and point mutations, and the chance meeting of two people with the same mutation would be too slow and viruses would be a more efficient method to evolve a large population at the same time. Things like punctuated evolution might support this? not really sure.


texts: Calculating Possible Combinations of Bases in a DNA Strand of a Given Length

texts:
In my Biology class we were asked this question:

This DNA strand consists of eight pairs of nitrogenous bases. How many different sequences of eight bases can you make? Explain how you found your answer.

I guessed either 28 or 8!. Apparently, the answer is 8! ÷ 24. I asked my teacher, but she did not know the answer. Does anyone know why this would be?


texts: The causes of sweating aside, i.e. I'm not interested in which and how nerve signals are transmitted to sweat glands. But I would like to read a detailed account on what a sweat gland consists of, what it does when not sweating, but esp. what happens when a sweat nerve signal arrives. Is there a good free review or can you give one?


texts:
Is this some type of moth, it looks dangerous is it?
I have only seen something like this once before.
Thank you for any information you can give me.


texts:
Why does thyroid gland enlarge both in hypothyroidism and hyperthyroidism?
Hypothyroid goitre is due to lack of iodine in diet and hyperthyroid goitre (Exopthalmic goitre, Grave's disease) is due to oversecretion of thyroxine, or Thyroid stimulating Hormone. How does these two apparently opposite effects produce similar physical manifestation of the disorder (symptom) i.e is the enlargement of the thyroid gland?


texts: Why we need a plasmid for r-DNA technology

texts: Recently I was studying Biotechnology. When I went through the texts, I had a doubt: both plasmids and gene of interest are made of DNA stretches and bacteria directly absorb plasmids in a test tube (where reactions take place). Why is the gene of interest not directly put in the test tube instead of recombinant DNA Technology (using Edited plasmids), so that it gets absorbed by bacteria?


texts:
Does one parent transmit more DNA to the offspring than the other one? Or do both parents always transmit the same amount of genetic material to their offspring?

In other words, can a baby be provided with a gene from the mother without an "opposite gene" from the father?


texts: Alternate genetic codes in newly sequenced organisms

texts:
Variations of the standard genetic code are pretty rare, but as the cost of high-throughput genome sequencing continues to drop, there is a greater possibility of discovering additional exceptions. That being said, there is a clear emphasis in genome projects on nucleotide (genome and transcriptome) sequencing, with much less (if any) effort put into proteomics work (correct me if I'm wrong there).

Let's assume we're sequencing the genome of a new organism and we're focusing completely on genome and transcriptome sequencing--no proteomics. Let's also assume this organism has slight variations to the standard genetic code. Would it be possible to annotate this genome (for protein-coding genes) completely incorrectly since the gene prediction software does not take into account these variations, or would it be pretty obvious? What would you expect to see in this case?


texts: Is 1 g/l living biomass for a Biogas fermenter plausible?

texts:
A usual number for a healthy biogas fermenter is $10^9 - 10^{10}/mL$ Bacteria, 10-15% of which would be methanogenic archae. Exceptionally healthy fermenters have more total bacteria and up 25% archae.

The mass of E. coli is given with 670 femtograms. If E. coli is representative for fermenting bacteria that would put us on the order of magnitude of 1 g/L living biomass.

This seems like much to me, though this is just a gut feeling.
As additional information, such a fermenter will have a total solids content of about 10%. A typical loading rate will be 4-5 g VS/d l *, two thirds of which get metabolized to gas. To put it another way: The amount of digested biomass per day would be the same order of magnitude as the living biomass. However, as anaerobic digestion is a multistage process, with at least three steps, each population will have a higher rate of digestion to mass.

Are the numbers basically sound? Is E. coli an exceptional bacterium in terms of mass? Are archae generally as massive as bacteria? What are bacteria counts for other fermentation processes?

(*) g volatile solid per day and liter: for each liter fermenter volume, this many g potentially degradable matter are added per day


texts:
I found this guy growing in my compost, but have no clue, what it could be.

Any expert here who want to take a guess?


texts: Do animals with crypsis know where they should stay to save their lives?

texts: For example, would a green lizard know it need to stay on a leaf, and avoid creeping on ground? Or in general, would animals with crypsis know what color they are and then hide on suitable place? Or they don't planned to do it and just be unlucky if they leave their suitable place and be seen by predators?


texts: Where can I find these frequencies for several species?

texts: Where can I find frequencies of nucleotides in the DNA for several species?


texts: Would a plant need light if the chemicals gained by photosynthesis were given through the roots or as a foliar spray?

texts: If you took the chemicals a plant gains through photosynthesis and put it through the plants' roots or by injection, or used as a foliar application for intake through the stomata, would the plant need light? If not, how would it respond to the treatment?


texts: By what mechanism do our nerves lengthen as people get taller?

texts: How do nerves get longer as kids grow taller?  I searched for an answer but I can only find information on the formation of nerves in embryos.


texts: Pathophysiology of pink frothy sputum in pulmonary edema

texts:
Pulmonary edema is a condition where fluid leaks into the alveolar spaces. This can be due to to hemodynamic causes like left heart failure and pulmonary venous obstruction or microvascular injury or increased capillary permeability.

Clinically we are taught to differentiate between various types of sputum. The sputum in pulmonary edema is characteristically pink and frothy.

It is important to mention here that the fluid that leaks into the alveolar spaces is a transudate and not blood. Hence it is by no means that the pink is due to blood. Otherwise it would be called hemoptysis.

My question is, why is the sputum pink if blood has no role to play?


texts:
For years, I've noticed that the day after a night of poor sleep (4 hours or less), my balance noticeably degrades. For instance, while walking 20 feet to the coffee maker, I might stumble into the fridge. Is this a shared experience among humans, and is there a physiological explanation for it?

I have noticed that other functions of my body degrade as well (e.g., my ability to focus), but I am particularly interested in the change in my ability to balance.


texts: Does any organism use both photosynthesis and respiration?

texts:
Chlorophyll and hemoglobin are very similar molecules, as far as I understand. The important difference being one using an iron atom and the other a magnesium atom. Do any organisms use both to get energy from both oxygen and solar rays? If not, is there any good explanation of why?

And do organisms that use chemosynthesis also use macro molecules similar to chlorophyll and hemoglobin?


texts:
I am working with the bacterium Chlamydia trachomatis.

The main test for this species is the naat test, which is based on amplification. But I would like to know how the bacteria affects the blood composition, and if there is a method of diagnosing it from the blood.


texts: Cell differentiation by non-identical copies

texts:
There are in principle two ways that two cells with the same mother cell can differentiate/specialize/diverge:

Because they are not perfect identical copies (= different internal influencing factors). I explictly don't mean "non-identical on the DNA level", but on the level of other cellular components!
Because they are exposed to different external influencing factors (chemical, mechanical).

Can it be said, which of these two reasons of cell differentiation is the more common, frequent, resp. "important"? Or does it completely depend on the (type of mother) cell and some general circumstances?

If internal factors (= non-identical copies) are an important source of differentiation, I have two (optional) questions:

How does the mother cell manage to cleave into two non-identical copies in a rather fine-tuned and determinstic way? Or is any kind of asymmetry enough?
Which is the first cell (starting with the zygote) that cleaves into two non-indentical cells, different enough to give rise to differentiation? (From this answer I believe to have learned that this might happen already after 1-4 divisions.)


texts: What is the optimum length of abstinence for maximum ejaculation volume in humans?

texts:
There have been papers discussing this, and whether the abstinence period should be 1 week, 2 weeks or other [1, 2]. Some think the time to maximum ejaculation volume is even longer than this.

doi: 10.1530/jrf.0.0570391
PMID: 7114956


texts: I saw a news story a few years ago (I think) about a girl with a poor heart having a device implant that took over only some of the functioning of her heart ( I think they called it a piggy-back device , or something like that). The extraordinary thing is that it not only helped her live but all the heart functions started to improve. It was as if giving part of the heart a chance to 'rest'  allowed the whole heart to improve. If this procedure works could it be applied to other organs? Could a Piggy-Back device be made for the liver taking over only some of its functions for instance?  Could such a thing help the liver functions to 'regenerate'?


texts: Why don't we build up an immunity to sore throat?

texts: We often get sore throats once or twice a year, and it clears in a few days sometimes without any antibiotics. I was wondering why doesn't our body become immune after clearing a sore throat?


texts: What is the total number of rounds of cleavage during mammalian embryonic development?

texts:
That for frog is 12, but what about mammalian embryos?
I cannot find the exact number anywhere.


texts: Which nucleotide as start point for maximum parsimony?

texts:
Background
Maximum parsimony is used to build an evolutionary tree by choosing the "simplest" one. I see a lot of examples about how this should be done. For example:

Question
However it's not clear for me WHICH nucleotide should be used as starting point?
Let's consider the first tree(from the figure above):

Nucleotide G was chosen as starting point resulting in one mutation, however if we choose T we would have two mutations and if we choose A we would have three. So what determines the nucleotide which should be used to start with?


texts: What is the difference between floral primordia and floral buds?

texts: As we know an axillary bud differentiates to form a floral bud, but what is a floral primodium?


texts: This plant was seen by a friend of mine in Virginia. What is it?


texts: Can we use the HIV antibody test to detect HIV in newborns?

texts: Adults and elder children can use HIV rapid test to test HIV infection. Can we use the HIV antibody test to detect HIV in newborns too?


texts: Microarray gene expression matrix format

texts:
After scanning the microarray chip we get RAW data with different formats depending on the type of microarray used. However, these RAW data files can be normalized and processed to generate gene expression data matrix.

I've been trying to figure out what exactly is the result of the processed data and what is the format of that data. As I've seen so far, there's no specific format for processed data. Of course most of them agree that columns represent experiments and rows represent genes, but the additional information at the top, they're usually different but I'm not sure based on what. Can anyone suggest me with the most common used formats? Is there any additional information to that processed data file in case I wanted to apply classification on it?