texts: What does the energy in an energy pyramid represent?

texts:
Suppose the energy at the second trophic level as given in an energy pyramid is 100 kcal per square metre. It could mean either of the two following things:

100 kcal is the energy this primary consumer has stored in its flesh - that is, the energy left over from the amount consumed, after assimilation and respiration. This would be the net productivity of that consumer, or the energy available to the secondary consumer which feeds on this.
100 kcal is the energy this primary consumer consumes. It will utilise a part of this in respiration, lose some amount in assimilation, so that a small amount is left over which is then stored in it as mass, or flesh - which would be its net productivity.

Similarly, the first trophic level, the autotrophs' energy could represent either the total amount of food they make (the GPP), that is, the energy akin to the second case above, or the energy stored in them and available to the next trophic level (the NPP), like in the case 1 above. So which of these is correct - what do we represent as the energy of a trophic level in an energy pyramid? I think it should be the first case, the stored energies, since after all these are what you will measure as the energy of any trophic level - the stored energy at that level.


texts: Is there anyway from which we can measure the viscosity of honey using a refractometer?

texts: Is it possible to use a refractometer to measure the viscosity of honey because as we know, a refractometer is used to measure moisture and therefore water influences the viscosity of honey so is there a way that we can use to measure the viscosity of honey that way or using any other method apart from time since time has a high percentage of uncertainty?


texts: Coefficient of relatedness for a locus on the Z chromosome

texts: So i know that the ZW determination system is the equivalent for XY in birds. Moreover, I know that the coefficient of relatedness between siblings for the X chromosome is 0.5 so im guessing that the coefficient of relatedness between siblings for the Z chromosome is the same ??


texts: Was the recent "conservation hunt" of a black rhino supported by science?

texts:
CNN recently covered a sanctioned black rhino hunt in Namibia by Texan Corey Knowlton, who bid US$350,000 for the license. In the story, he claims that the hunt was actually supporting conservation of the critically endangered species, as they were looking to kill an older, non-reproducing male that was consuming resources and potentially threatening younger, breeding males. The Namibian government has a list of 18 rhinos in the country (out of a total population of about 2,000) that meet the criteria.

  Knowlton is targeting one of four black rhinos at the top of the government list, the ones considered "high priority threats to the herd."

Knowlton eventually caught up to and killed the animal he was targeting, and donated the meat to a local village.

CNN.com later published two opinion pieces, one in support of the hunt by Dr. Mike Knight, the Chairman of the International Union for Conservation of Nature (IUCN) Species Survival Commission's African Rhino Specialist Group (AfRSG) and the South African Development Community Rhino Management Group (SADC RMG), and one opposed to it by Jeffrey Flocken, the North America Regional Director of the International Fund for Animal Welfare (IFAW). Knight cites black rhino-specific data in his piece, arguing that in the case of this particular species, limited hunting is actually beneficial. Flocken instead uses a wider argument, citing hunting of polar bears, elephants, and lions, among other species, and claiming that the idea of "conservation hunting" as a whole is flawed. He does not, however, directly address the situation of black rhinos.

I have evaluated each side's argument, but have not yet formed a solid opinion, which is why I'm asking here. In the specific case of the black rhino, does the science support the notion of limited elimination of older males? Are there studies that show this has led to an increase in other types of conservation efforts? Does the money spent for licenses actually go towards conservation and assistance for locals?

As a second, optional question: Are the arguments posed by Flocken against "conservation hunting" in general supported by independent research? Just thinking logically I can imagine they are, as a lot of what he says makes sense in a broader context, if not necessarily in the case of the black rhino. Is there a scientific case for limited, situation-specific hunting, or should all forms of it be discouraged?

Note: I'm asking this here instead of Skeptics because I'm looking for a scientifically-supported answer. If you think it's better suited there, let me know and I'll move it.


texts: DNA as a digital storage medium; sequences algorithmically avoided for safety reasons (or should be)?

texts:
Safety for the environment is probably implicit here as well, but the focus should be on the people who may come in contact with large amounts of synthetic DNA used to encode information as a data storage medium.

The idea of using DNA as a digital storage medium is not new. Two papers are listed below but there are many others.

Recently the concept has been further highlighted by the news of a "movie" being encoded using CRISPR-Cas. A Harvard University video explains the process:

  In this video, Wyss Institute and Harvard Medical School researchers George Church and Seth Shipman explain how they engineered a new CRISPR system-based technology that enables the chronological recording of digital information, like that representing still and moving images, in living bacteria. Credit: Wyss Institute at Harvard University

  For more information, please visit: https://wyss.harvard.edu/taking-cells...

below: a GIF showing the original data, and the "movie" interpreted from the recording in DNA. From the Los Angeles Times:

  DNA DVR? Scientists have uploaded a short movie of a galloping horse into the DNA of living bacteria and were able to retrieve it with a 90% success rate. (Seth Shipman)

The immediate application in the Harvard Wyss Institute work seems to be (based on my understanding of the video) in-situ data logging, where information relevant to an experiment is recorded in the DNA of cells involved in the experiment. So the use of a moving image is a way to bring home the key point of "chronological recording of digital information".

Other uses involve the DNA itself, stored outside of living cells, as simply a mass storage medium.

QUESTION: I'm wondering if there are sequences that are likely to become algorithmically avoided as standard practice for safety reasons (or should be) when using DNA as a digital storage medium. The DNA may be handled by IT personnel rather than trained biologists, or shipped, or otherwise not be treated with the same diligence to safety that synthetic DNA is handled by researchers today.

Some other discussions of DNA as a storage medium:

Next-Generation Digital Information Storage in DNA, Church, Gao, Kosari, 2012. doi:10.1126/science.1226355

Towards practical, high-capacity, low-maintenance information storage in synthesized DNA, Goldman et al. 2013. doi:10.1038/nature11875

For further background on the temporally encoded data work, see the excellent answers to the question What does it mean to “write an image and GIF into the DNA of bacteria”?

edit: I'll quote a comment here just to make sure that the word safety isn't misinterpreted as data integrity or the safety of the bacteria:

  When speaking of safety issues related to the handling of biological or biomolecular samples, it's the safety of people that we worry about. Safety rules, safety procedures, safety courses, safety glasses, these are for the safety of the human, not the safety of the sample.


texts: What is the sedimentation coefficient of Mycoplasma?

texts:
I have attempted to find the sedimentation coefficient of a number of bacterial species, namely E. coli and a number of Mycoplasma species, but they seemed to be rather elusive in the literature.

If such values cannot be easily found, is there a reason sedimentation coefficients of whole cells are not widely reported, but sedimentation coefficients of proteins are? Mentions of "70S ribosome" and "26S proteasome" are common, but I have never seen any mention of "kilosvedberg" or "megasvedberg" appearing in the literature, and I presume the sedimentation rate of whole cells would fall somewhere in this region.


texts: What is the role of Cl-, H+ and Malic Acid in stomatal opening and closing?

texts: I understand that K+ influx brings in water making the guard cell turgid. This opens stomata. What is the role of other molecules/ions in this?


texts:
From what I know, the main function of red blood cells (RBCs) is hemoglobin transport. So, why do we need cells packed with hemoglobin: why can't it travel freely in the bloodstream?

My own thoughts were:

1) Having hemoglobin packed into cells means it can be released where it's most needed. For example, when we are exercising, our muscles need more oxygen, so more erythrocytes release their oxygen in the muscle tissue.

2) The diameter of a capillary is much bigger than a single protein molecule's diameter, but comparable to a cell's diameter. So, when cells are traveling through a capillary, all of them are close to its walls. However, when free molecules are traveling through it, some of them are close to the walls, while the others are in the "middle". I figured, those in the "middle" can't exchange oxygen with the surrounding tissues. So, red blood cells make gas exchange more effective.

Do you think any of this makes sense? Why in reality do RBCs exist?

Any insight or book recommendations would be very appreciated:)


texts: When do 3 germ layers form in embryo? And why is there only one mature egg formed?

texts: During the process of pregnancy, when do the 3 germ layers form in embryo? Is it after formation of gastrula? Also, during oogenesis, why does only one mature egg form? Why don't use polar body egg instead? During oogenesis, is there a crossing over occurring? If yes, at which stage?


texts: How reversible is DAT upregulation from long-term ADHD medication use?

texts:
A mechanism for ADHD stimulant medication tolerance has now been found. See http://neurosciencenews.com/adhd-medication-patient-brains-adapt-dat/.

Here's the thing though: what exactly is the "signal" that the body uses to interpret whether or not it needs to upregulate the amount of DAT (dopamine transporter) that exist? Is it a dopamine-based signal  that somehow then gets carried to a transcription factor that gets carried to the nucleus for additional transcription?


texts: Brain evolution in the age of the caesarian

texts:
I have just been reading an account of the evolution of human intelligence in Matthew Syed’s recent book on diversity, called “Rebel Minds”.

He is not the originator of this idea, but he suggests that the limiting factor in the growth of the human brain beyond it’s already prodigious size is the size of the female birth canal, so that, above a certain size it had killed the mother and itself at birth.

I am not a biologist.  But I wondered whether there is any evidence of increase in brain size in the past (say) 50 years as more gravidae give birth by C-section?  Is such a change possible or probable as this procedure becomes more common?  Or are there other limiting factors, such as the weight that can be carried by the spine?


texts:
Has there ever been a published experiment to take a viral "census" of a human subject's blood?

By a "census", I mean to identify every active virus in the subject's blood with some probability.

So, for example, we can imagine taking different samples of blood, diluting them, then taking the dilution and using it to innoculate a lawn of hemocytes. Presumably, different viruses would make different plaques, so they could be separated, isolated and identified. By doing different combinations of dilutions, one could I suppose make a table or curve that would show the probability of detection of a given virus based on its concentration in the blood. Thus, at the end of the experiment the researcher could state, "I have isolated all the viruses in the subject's blood having a concentration above X with a probability of Y." Obviously, this would require hundreds of samples and thousands of innoculations to achieve an accurate census.

Has anyone published a study like this?


texts: Why is plasma glucose concentration not double that of whole blood?

texts:
It is known that the concentration of plasma glucose is 12% higher than that of whole blood. But since 45-50% of whole blood is red blood cells, shouldn't the plasma glucose be almost double — since it's just the hematocrit that is missing from the denominator.

Obviously something is wrong with this line of reasoning, since it does not meet the observations. Why so? Does whole blood glucose also measure intra-cellular glucose? Is that the reason for the lesser than expected increase?


texts: Basis of enzyme nomenclature — pyruvate dehydrogenase

texts: In the formation of AcetylCoA from pyruvate, why is the enzyme called “pyruvate dehydrogenase (complex)” when it involves the decarboxylation of pyruvate or the replacement of a carbonyl group by coenzyme A?


texts: Kinases that are ATP-sensitive at physiological conditions?

texts:
Phosphorylation is an ATP-dependent process performed by kinases. At physiological conditions it is generally assumed that ATP concentration is high enough so that ATP is not a limiting factor. Therefore the phosphorylation rate is independent of ATP concentration variations. At least this is the case in the examples I came across.

Are there known counterexample? A kinase that is sensitive to ATP concentration at physiological conditions?


texts: Is this a soldier beetle? Bug identification

texts:
I'm curious to find out what kind of bug this is. Reverse Google image search suggested a type of soldier beetle, but I am not convinced.

The photo is taken in summer, in England

Thanks!


texts:
In massage school we are being taught hydrotherapy -- applying cold and heat to specific areas.

It says that when applying cold, first the body goes through vasoconstriction, and then later vasodialation. That makes sense -- preserve heat through the former, but if the cold is applied for too long the body still has to keep the cells alive, thus the latter.

What doesn't make sense is this passage, in relation to applying heat:

  Law of Action and Reaction: Initially blood will rise to the
  surface, applied for too long the blood will recede to the interior
  causing inner congestion to be greater than before

Is that true?


texts: Calcium for Humans: Supplements vs Fortified Sources

texts:
I'm trying to be vegan, and purely natural foods lack sufficient calcium for the Recommended Daily Intake. Links 2 to 4 (but not 1) assert a correlation between calcium supplements and disease.

  [1. WebMD :] "Keep in mind that there's really not that much difference between getting calcium in a supplement and calcium in food."
  "Calcium-fortified foods -- such as cereals, some juices, and soy milk -- are excellent sources of the mineral, experts tell WebMD."

  [2. health.harvard.edu :] An 8-ounce portion of off-the-shelf orange juice contains about 300 mg of calcium. The calcium in fortified soy milk also compares favorably to whole milk.
  Breakfast cereals (which are also fortified) contain substantial amounts of calcium, especially when combined with low-fat milk.
  A portion of oatmeal on its own contains just 100 mg of calcium. “But if you cut up some dried figs and add it to a bowl of oatmeal with milk, you easily get about half of what you need without having any supplements,” Dr. Hauser says.

  [3. NY Times Blog :] All the researchers agree that, given the widespread use of supplemental calcium, better studies are needed to clarify possible risks and benefits, and to whom they may apply.

  Until such information is available, consumers seeking to preserve their bones would be wise to rely primarily on dietary sources of the mineral and to pursue regular weight-bearing or strength-building exercises, or both. Walking, running, weight lifting and working out on resistance machines is unquestionably effective and safe for most adults, if done properly.

  [4. NY Times :]  The institute’s expert committee, which included bone specialists, concluded that most people don’t need supplements of these critical nutrients and warned of serious health risks from the high doses some now take — including kidney stones and heart disease linked to calcium supplements, and the very falls and fractures that vitamin D is meant to protect against.

5. How and why would the calcium carbonate from calcium supplements be asserted as worse than that in the fortified foods?

6. Isn't solid calcium carbonate (e.g. in supplements) chemically the same as aqueous calcium carbonate (e.g. in fortified drinks)?

7. Are calcium supplements really worse than fortified foods with calcium?


texts:
This will sound as a super stupid question, but I just read in the Molecular biology of the gene book (7th edition, Watson, Baker, Bell and al.) that one mistake occurs in 10 million nucleotides added during the replication of DNA.

However, I read in the Campbell's biology book (11th edition) that it is one mistake in 10 billion nucleotides added.

I tried to google it and kept finding these two numbers... probably because people use the same books as I do as sources. So, my question is the following: which book is right about DNA replication precision?

Thanks for your help and sorry if my question isn't very interesting.


texts: What volume of elution buffer for plasmid-containing filter paper?

texts:
I am attempting to elute a 9kb plasmid from a square of filter paper sent to me to be transformed into DH5a E. coli (photo below). Each filter paper square has been spotted with 1ug of plasmid DNA.

I have two questions:

AddGene's protocol states to elute the DNA using 30ul of TE (I'm using H20 as that's all I have atm). Using a similarly sized piece of filter paper to test, I added it + 30ul of h20 to a 1.5ml tube with a quick 4k spin down and have observed that the 30ul is completely absorbed by the paper as shown in the photo. How should I resolve this? Add an additional 30ul? I also tried to use a pipette tip to shove the paper down and squeeze out the water but you can see it didn't work.

What volume should I use for transformation knowing that the filter paper contains 1ug and I need to use additional elution volume? Most protocols I've read call for 1-5ul of DNA and AddGene calls for 2ul assuming 30ul elution volume.

Thank you.


texts: How to derive Hill equation (one specific part)

texts:
There is just one specific step in the derivation of the Hill equation for haemoglobin which I can't understand.

Step from: $Y = \frac{(p\ce{O2})^n}{K_d + (p\ce{O2})^n}$
To: $Y = \frac{(p\ce{O2})^n}{(K_d)^n + (p\ce{O2})^n}$

I don't understand where $(K_d)^n$ comes from. (I can go from this second equation to the Y/(1-Y) equation afterwards).

How I derived my equation is the following.

$\ce{Hb.(O2)_n <=> Hb + nO2}$

Hence the dissociation constant $K_d$ should be:

$K_d = \frac{[\ce{Hb}][\ce{O2}]^n}{[\ce{Hb.(O2)_n}]}$

And Y, which is the fractional $\ce{O2}$ saturation would be:

$Y = \frac{[\ce{Hb.(O2)_n}]}{[\ce{Hb.(O2)_n}] + [\ce{Hb}]}$

If you multiply the top and bottom by $K_d$, the following is obtained:

$Y = \frac{(p\ce{O2})^n}{K_d + (p\ce{O2})^n}$

This is where I became stuck. What am I doing wrong?

Thank you very much for your answer.


texts:
I've found a few of these bugs hanging out on my desk. There aren't many. Maybe 5-10 at any given time. Are they a type of springtail? I couldn't find an image in searching that made me say, "That's it!"

Any help is appreciated!

Thanks!


texts: Was there originally a non-ribosomal way of synthesizing proteins?

texts: Proteins are synthesized on ribosomes from mRNA copies of regions of the DNA. But ribosomes themselves are made up of proteins (and RNA). So how could the first ribosomes have arisen? Was there previously some other way of making proteins other than by ribosomes and mRNA?


texts:
I'm having little trouble studying general relativity or quantum field theory, but remembering all the amino acids and being able to think about them is something that's completely, utterly and absolutely, defeated me...

How do I think about the amino acids, without any memorization, and be able to 'derive' all the names, all the categories they fit into, and their important properties? Memorizing some crazy mnemonic is of no help when it says nothing about the amino acids, I can't memorize it without meaning that explains a lot of things. I ultimately just want to be able to read Albert's Molecular Cell Biology and appreciate it, but I can't without conquering this little issue!

On a side note regarding memorization tricks: is there a mnemonic scheme for the amino acids analogous to the thermodynamical Zhao square, (which gives all the info you need about basic thermo by drawing lines and squares)?

Any help is greatly appreciated, thank you.


texts: Difference between modules in KEGG Module

texts: The KEGG module M00115 includes a set of reactions while M00542 does not have any; it just shows the list of enzymes. Is the reaction set for M00542 still unknown?


texts: Could humans theoretically see infrared better than regular light?

texts:
I have noticed that in infrared film, people's eyes reflect that light within their eyes much like nocturnal animals (and many other animals for that matter) do with regular light. I know that this is in order to maximize their night vision capabilities by reflecting more light onto the retina.

My question is this: If a human had the nerves in our eyes to process infrared light, would someone with these 'special' eyes be able to see better than someone with 'regular' eyes? What would they see? What about in low-light conditions?

...Infra-red illumination of the eye produces the 'bright pupil' effect

Source: http://www.museumsandtheweb.com/mw2003/papers/milekic/milekic.html

(most of the way down the page)


texts: Has a restriction enzyme ever been tagged?

texts:
As part of an experiment that I am preparing, it would seem necessary for me to tag a restriction enzyme (HaeIII to be exact) with GFP. I began researching its domains to determine whether to tag the GFP to the N- or C-Terminus, but I was unable to find any previous studies where this restriction enzyme was tagged. As I got asking around, it would seem that no one has ever tagged any restriction enzyme at all.

It appears that this is only the case with restriction enzymes, because I very quickly found several articles where the HaeIII methyltransferase was tagged with GFP.

So, does anyone here know if a restriction enzyme has ever been tagged before? Is there something that I am overlooking that would inhibit the tagging of a restriction enzyme?

Thank you.


texts: Should we induce fever to assist healing?

texts:
I am currently reading "The Fundamentals of Anatomy Physiology" 10th edition, and have found it an incredibly interesting book. I have just been reading about the lymphatic system, and the various Leukocytes and their roles. When it mentioned fever as an immune response, I was familiar with the concept: Bacteria and viruses operate very nicely at our usual body temperature, but not so well at around 39 degrees Celsius.

What I wasn't aware of was "For each 1 degree Celsius rise in body temperature, metabolic rate increases by 10 percent. Cells can move faster, and enzymatic reactions take place quicker." (Quoted from page 828 of that book).

Now that seems like a massive benefit (though I believe you could only really push 1 or 2 degrees before you start getting into dangerous territory), but I notice that fever is not present in all illnesses. Inflammation seems to induce fever through the wounded area, which makes sense.

So now for my question: Could it be beneficial to artificially induce fever in a person who has an illness if they are not already experiencing fever? I believe a few things would need to be considered (more than likely a lot more than I can think to list):

Increased metabolic activity would surely need a higher energy intake would it not?
Are there cells that are actually going to suffer from the temperature increase?
I'm assuming this would actually be a rather poor technique to deal with cancer as from my currently limited knowledge, it is simply a cell that is producing abnormal proteins. If this is the case, the metabolic increase would likely apply to these abnormal cells, resulting in faster proliferation. Are there other such cells/infections that will benefit from temperature increase?

Finally, what are possible downsides of long term fever if energy intake is sufficient to maintain an increased metabolic rate at these higher temperatures?


texts: Can a pyruvate reaction to acetyl coA be called as acetylation in any way?

texts:
Can the oxidation of pyruvate to acetyl coa be called as acetylation in some ways?
Please include credible sources in the answer.


texts: What adaptations does the human body have to handle frequent and sustained changes in orientation?

texts:
Most animals are horizontal with the ground.  When they lie down, they get closer to the ground, but their orientation does not change.

Humans, on the other hand, stand up straight and tall, perpendicular with the ground.  And when we lie down, we make a complete 90° turn.  So we spent 2/3 of our day at one orientation, and 1/3 of our day at the exactly orthogonal orientation.

It's difficult to think of many other animals that change their orientation so completely on a regular basis, or spend much time in different orientations.  (Sure, prairie dogs, bears, lemurs, and apes stand upright now and then, and I've seen pictures of whales sleeping vertically, but it's never for long, sustained periods.  Giraffes seem so tall and vertical, but it's all neck and legs — the organs of their body are always horizontal with the ground, and this orientation is maintained when they lie down.  Birds, maybe?)

For humans, regular changes in orientation must surely cause biological stresses, and therefore there must be some biological adaptations to those stresses.

Even non-biologists are aware of plenty of orientation-related malfunctions:
— middle-aged people start to get acid reflux and indigestion when they lie horizontally
— elderly people with certain heart conditions and arrhythmias cannot lie horizontally
— some people are affected by changes in blood pressure when they lie down or stand up
— some people have dizziness or balance issues when lying down or standing up
— knees and feet start to have problems from a lifetime of bearing all the weight

What specific adaptations does the human body have to handle these daily changes in orientation?


texts: Book recommendation on experimental mycology

texts: I am looking for any book that elaborates experimental methods to study multiple  aspects of experimental study about fungi including culturing, induction of sporulation and other reproductive structure, fungal hormones/signaling molecules, biochemical characterisation, biosafety while working with fungi, fungal chromosome and DNA isolation, etc.


texts: How does a TOPflash/FOPflash assay work to detect beta-catenin protein expression?

texts: I am reading an article (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3596711/) wherein a TOPflash/FOPflash assay is used to detect beta-catenin protein levels in a COS-7 cell line. I can't find a good explanation in the article, or in any other article, as to how this assay works. I understand the cells are transfected with TOPflash/FOPflash reporter plasmids, but that's about it. Any insight or redirection would be much appreciated.


texts:
A living fossil is a living species (or clade) that
  appears to be similar to another species otherwise known only from fossils,
  typically with no close living relatives.

A living fossil is considered as a successful organism, which has made its way through many  major extinction events. Also, the morphology of living fossils resemble some species of organisms which we know only through their fossil remains.

What is the reason for a particular type of species to become a living fossil; is the engineering of this particular species extraordinary, in that it can survive any selection process encountered thus far?
Is there not enough selection pressure exerted on this species in order to force it to change morphologically?
Have these organisms modified themselves, so that currently their morphology seems to be similar to a fossil organism?


texts: How long will a typical bacterial strain keep in a -80°C freezer?

texts:
I know that a -80°C freezer is the recommended means of long-term cell-line storage, and that cells will typically not last long in a -20°C freezer.  But how long will a typical bacterial strain (e.g., E. coli DH5-alpha) actually stay good in a -80?
Searching around via Google, I'm finding a wide range of answers, anywhere from only 3 months to indefinitely, so I'd like to try to get a better grounded way of estimating longevity.


texts: Mapping a mutation to known SNP, 3' UTR, miR

texts:
I've parsed out a very large TCGA cancer ssm (single mutation file) file to give me the essential information.

The ssm is in the following format:

['Gene name', 'Ensembl Gene ID', 'Chromosome', 'Chromosome start', 'Cancer Type']
['NTRK1', 'ENSG00000198400', '1','156849827', 'Prostate Adenocarcinoma (TCGA, US)']

From there I would like to grab each mutation and :

Map the chromosomal position to a known SNP (rs something output).
See if this snp is found in a 3'UTR
See if this snp is found in a miRNA
Missense or sense mutation
Any relevant genbank etc.. ids

I'd like to do this Python (I think BioPython is suited for this) for downstream applications.


texts:
I've learned programming through great book recommendations; many from the Stack Exchange series of sites. I'm hoping to take this approach in order to gain a fundamental understanding of how fluorescence microscopy and sub-diffraction limit imaging tools work.

What books or reviews do you recommend that offer both a conceptual explanation of imaging biological specimens and practical advice? I'd settle for either one if you find the author to be effective.


texts: In plants why are potassium and nitrate ions absorbed faster than any others?

texts:
Quoting my A-level biology textbook:

  $\ce{K^+,  NO3^-}$ are absorbed by plants faster than any other ions. Whereas, $\ce{Ca^2+, SO4^2-}$ are absorbed with the slowest speed.

What is the reason?

My reasoning: I first though the size of ions would matter in this case. Obviously, $\ce{K^+}$ is smaller than $\ce{Ca^2+}$,  then it 'seemed to me' that smaller ions would be absorbed faster. The same reasoning can be applied to $\ce{NO3^-,  SO4^2-}$. But, there are smaller ions than $\ce{K^+}$ which are absorbed slower eg. $\ce{Na+}$. So, obviously size only does not matter here. There are other factors.


texts:
What does a typical, perfectly healthy vaccinium corymbosum (highbush blueberry) leaf look like?

Colour (darkness of green, redness)
Waxiness
Veins

I'm guessing that soil ph, nutrients, and other factors play a part. Vacciniums seem to have very specific needs, and as far as I know, assessing the leaves is one of the best ways to determine plant health.


texts:
Description

200 years ago, the human lifespan was roughly 35 to 40 years long. And it has doubled in length since then.

Question

Will the human lifespan continue to expand in length?


texts: Can canines communicate with each other using gaze direction?

texts:
After researching why humans have white scleras when most primates have dark scleras, I stumbled upon the cooperative eye hypothesis. It proposed that white scleras may have evolved on behalf that it is an effective form of communication in that it makes the iris stand out and enables another to clearly see where the eye is looking so as to read expressions.

I noticed that dogs, which also have white scleras, use eye direction periodically for expression. Does the cooperative eye hypothesis apply to canines as well? If not, then for what reason might dogs utilize eye movement as they seem to do? Might such a thing be learned behavior?


texts: Are there single-celled organisms that have evolved from multi-cellular ones?

texts:
I'm reading this paper about transmissible cancer cells in clams (Metzger et al. 2015) and I was wondering if there are any single-cellular organisms that are around today that are suspected as having descended from a multicellular organism

My question is different from this question as I'm not asking about cancer specifically but rather single-celled organisms evolving from multicellular organisms in general.


texts: Could two women have a child through artificial insemination/genetic engineering?

texts:
This is something I just thought of while looking up stuff about matriarchies.

I recall a comic series I heard of once, I think it was called 'Y, the last man'. In that story, all males (besides the main character, and one monkey he keeps as a pet) were wiped out by a plague or something, leaving the world's population entirely female. They of course start focusing on developing cloning technology to avoid the extinction of the human race.

But thinking about it, would it really be necessary for them to develope such a technology? Afterall, females can already incubate offspring, they just can't impregnate each other. But could it possible to extract the DNA from a woman's egg, and put it in another egg?

Note that I know nothing about artificial insemination or genetic engineering, so I don't know if that would work (I've only heard of people putting one animal's entire genome into an egg, not from two individuals). So I'd like a more expert opinion. Could you actually do that? Or the mechanism for mixing the DNA of two individuals more complicated than that?


texts: Why does a worm's skin need to be wet for oxygen to diffuse across it?

texts: Pages I've read about worms' respiratory systems says that the skin needs to be wet (covered in mucus) or oxygen won't diffuse across the skin. Why? If there is more oxygen outside the worm's skin than inside, what prevents it from diffusing across the skin, even if the skin is dried out?


texts: NMR spectroscopy detection methods for proteins

texts:
I've stumbled upon a table comparing the sensitivities of different detection methods in NMR spectroscopy: "Direct", "DEPT" and "Inverse", where "Inverse" seems to be the most sensitive.

What exactly are those different methods are and how do they differ?


texts: Is there nutrient absorption in the large intestine of hindgut fermenters?

texts: In hindgut fermenters, plants are digested in the caecum by microbes. I want to know whether hindgut fermenters can absorb the nutrients obtained from the digestion in the large intestine because the absorption of digested materials is not the main function of the large intestine in other animals. I know some hindgut fermenters reingest the materials created in the caecum, but I think not all hindgut fermenters perform this behavior. I want to know the main site of absorption after the caecum.


texts: Question about cell signaling pathways (RTK, Jak-Stat, SMAD, etc)

texts:
I am in an embryology course right now and we've just started covering cell-cell communication in development. We were talking about the roles of the various cadherins and their discoveries but we got to cell signaling pathways and in reading my textbook I'm finding myself confused by these pathways-- some of those that are mentioned include Notch, Wnt, FGF, TGF-beta, RTK, Jak-Stat, SMAD, integrins, PTHrP, Hedgehog, Discoidin domain receptors 1&2, and the unfolded protein response (UPR).

I know the RTK pathway and I know the SMAD pathway, but the others just seem to be specific ligands that are using these pathways -- is this correct?


texts: Would a transparent iris serve its purpose?

texts:
The function of the iris is to regulate the aperture of the pupil. How does the iris obstruct light? Is it due to the pigment present in it? Or is it just due to the sheer presence of it?

I am doing a project where I need to maintain a constant light intensity for albino rats. I was suggested to administer a mydriatic topically but when their iris is transparent, does dilating their pupil make sense?

How is it in human albinos? Does pupil dilation and constriction make a difference in them?


texts:
In a nature documentary I watched a while ago, there was a scene where a flock of flamingos slept in a lake that froze overnight. Each morning they just had to wait until the lake defrosted sufficiently to release them so they could get on with their day.

How do they not get tissue damage etc doing this?


texts: For each movement performed by both the gluteus minimus and medius, what percentage of the movement do the gluteus minimus and medius account for?

texts:
From what I read on Wikipedia, all functions of the gluteus minimus are mirrored by the gluteus medius. Additionally, the gluteus medius is larger than the gluteus minimus (see comparative images here), which leads me to believe that the gluteus medius is stronger than the gluteus minimus. I wonder to what extent it is stronger.

For each movement performed by both the gluteus minimus and the gluteus medius, what percentage of the movement do the gluteus minimus and the gluteus medius account for, respectively? (e.g., 80% of the strength stemmed from the gluteus medius, and 20% of the strength stemmed from the gluteus medius)


texts: Why is a urea solution hypotonic relative to RBC?

texts:
If I place a RBC in 0.5M urea we see haemolysis.

My textbook says that "the solution is hypotonic. Urea enters the RBC down it's concentration gradient. Water follows the movement of urea by osmosis. This influx of water causes lysis".

I am very confused by this, for a number of reasons.

I thought tonicity only applies to non-penetrating solutes (i.e. a solution is hypertonic relative to a cell if the solution has a greater concentration of non-penetrating solutes then the intracellular fluid). If urea can penetrate the membrane, then why is the solution hypotonic? As a penetrating solute isn't it not factored into tonicity.
If urea is a penetrating solute, then won't it just come to an equilibrium across the cell membrane, and hence there will be no net osmosis since the concentration inside the cell will the same as that outside the cell.

I feel like I have a conceptual failing here, but the more I google the more confused I get.


texts: Sodium concentration during action potential generation

texts:
At the peak of the graph, is the concentration of Na+ outside the cell more than inside? That must be to overcome the electrical force in the opposite direction.

When is the concentration of Na+ greatest inside the cell? At the peak assuming the Na+ channel close immediately at it then it is also greatest at 3. If there is still passage of Na+ then 3 is the maximum. Is this true or false?

One last question: is the inside of membrane actually negative, or only negative relative to the outside? In a galvanic cell for example, a given rod isn't actually negative, but it is negative relative to another.


texts: Is there an association between environmental and mutational robustness?

texts:
The robustness of a genotype is the ability of this genotype to resist (always produce the same phenotype) to various parameters such as mutations and environment. The ability of a genotype to resist to mutations is called mutational robustness while the ability of a genotype to resist to varying environmental variables is called environmental robustness.

Is there a correlation between environmental and mutational robustness?

In other words the above question is: is there a among-species/populations/genotype correlation between mutational robustness and environmental robustness? i.e., Knowing that species $A$ has high mutational robustness, is species $A$ more or less likely than a randomly picked species $B$ to have a high environmental robustness? Or are the concepts of environmental and mutational robustness completely different and involve completely different genes and genetic architecture? Both theoretical and empirical studies that offer insights to this question are welcome.


texts:
For example, some leopards have a mutation which causes black fur. So Black fur and normal fur colour (orange-white) are both alternate forms of the same gene, right? So does that mean that mutations cause alleles?

Thanks


texts:
Our lab uses old Gilson Pipetman pipettes. I've been using some for making mRNA by in vitro transcription and started running into RNAse issues. I'm trying to clean everything up, including the pipettes. I'm not sure these old pipettes can be autoclaved, at least not in one piece, I think I can take them apart and autoclave the parts that might touch the solutions. Is there some way to wash the pipettes out effectively and remove any RNAses?

I use boxes of RNAse free barrier tips, do all my work on new pieces of aluminum foil, use commercial RNAse free water, gloves, labcoat, facemask, etc. However yields from the in vitro transcription kit have been reduced, and yields from the tailing kit are even worse, sometimes losing 90% of the RNA. There's only so much I can do, our building is old and full of dust and the damn pipes above my work bench leak ( all the pipes leak, had 2 major pipe bursts in the last 6 months ).

I'll probably have to get new kits. Just have to prove to my advisor that the kits are contaminated.


texts: law of laplace and pressure developed in arteries

texts:
in arterioles the pressure depends on
the impedance of the vessel(elasticity and youngs modulus)
cardiac output
pre arteriolar resistance
what i want to ask is will the pressure also depend on law of laplace
for eg.
if a there is peripheral vasodilation( the muscles of the artery wall are relaxed) so the tension is less
the radius is high
and hence using the equation( pressure=2*tension/r)
the pressure in the arteriole is low
is this arguememt valid??


texts: These are called mushrooms I believe, had been growing on my door for a few weeks. It's monsoon here. Last night I took a picture of it and it looked like this . Today when I woke up it became like this: . All this within 12 hours. I'm pretty sure nobody touched the fungus so I'm inclined to believe this was spontaneous.


texts: Is lysergic acid diethylamide (LSD) metabolized in the body?

texts: Is LSD broken down into other compounds by enzymes or hormones? If so, at what point and where in the body does this happen? I researched several papers appearing in a google search, but unfortunately I did not understand most of it.


texts: Why doesn't submersion in water kill fungi?

texts: I have read that fungi cannot live without air. Does a couple of minutes in a swimming pool full of chlorinated water kill them as it would a mammal? I've never heard this suggested. Will they survive by enjoying trapped air? Or by "holding their breath" for a long time?


texts: Do any plants grow leaves beneath the ground?

texts:
We have a pretty common California weed in our yard. When we dig in the ground, we often find small ones there, with green leaves!  It's as if they form green leaves before they come to the surface. While that seems counterintuitive, there's no purpose in having green beneath the soil, it doesn't seem impossible.

We had our yard redone 6 months ago. It's possible that some mature plants were buried- but would they stay green for six months?  Or perhaps they expect to be close to the surface, so after creating a couple inches of roots, they form green leaves, even though they're buried deep enough that they're not at the surface yet.

Is this a known phenomenon?  How common is it for plants to be able to make green leaves before coming to the surface?

Thanks much...


texts: What species is this beetle (trichius family)

texts:
I took this picture in Jura region (Northern Switzerland, alt: ~700m) of that beetle (July 2018). It was taking food from a flower of a Morus nigra.

It seems to be part of the trichius genus but I want to report the exact species.

In Switzerland we have mainly:

Trichius fasciatus
Trichius rosaceus
Trichius sexualis

I think by the color of the hairs it would be a Trichius fasciatus.

Can someone confirm the species and what field marks I can use to make the distinction between those three species?


texts:
I have two questions concerning self-exciting neurons in the brain.

Have directly self-exciting neurons been oberved, i.e. neurons with an axon terminal building a synapse with one of its own dendrites.
Does self-excitation work?

I guess that self-excitation can only work when the following time constants fit to each other:

refactory period of the neuron's membrane voltage (approx 1 milliseconds)
run time of the signal along the axon
refactory period of the synapse (approx 5-6 milliseconds)

I tried to estimate a typical run time by taking a not untypical axon length of 1cm = 0.01m and dividing it by a typical nerve propagation speed of 10 m/sec, getting 0.001 sec = 1 millisecond. Direct self-excitation would not work because the synapse would not be ready when the self-exciting signal arrives.

The other way around: Only when the run time is longer than the two refactory periods direct self-excitation might work.

Once again: Are there known examples of direct self-excitation in the human brain or nervous system?


texts:
I'm working on a project where I am taking DNA sequences and translating the codons into musical notes. I have some good ideas of how to do this, I'm just not sure what sequences to work with. My case study and a lot of my initial research showed that anything larger than a protein is too much to work with for now.

So my question. Where can I find protein DNA sequences in some standard format. I've looked at NCBI but I have no idea what I'm looking at or if I'm downloading the right stuff. Is there a link that I can go to that will have a listing of a bunch of difference protein sequences that I can download?


texts: How do colds and flu not infinitely recur?

texts: I'm in my third week of university, and a large number of people I know, including myself, still have "fresher's flu", which is probably just a cold and a cough. My lectures are constantly punctuated by the sound of violent coughing. What I don't understand is: how do colds ever go away, given these conditions? Surely by the time you've gotten rid of your cold you've passed it onto someone sitting near you in a lecture, who could then spread it back to you directly or indirectly later? Why don't we have an infinite recursion of colds, coughs and other minor infections throughout the year?


texts: To what extent are lifestyle factors taken into account in medical testing?

texts:
A glance at any official health bodies advice will show that we are entreated to eat more healthily, take more exercise and reduce stress. Presumably, there is some reasonable evidence that these factors play a relatively significant role in disease formation and response (otherwise, one would presume they would not be within the remit of such organisations).

In what little opportunity I've had to read primary research on medical testing, however (I'm a statistician, not a biologist), I've not come across any attempt at stratification for these factors.

If one is, say, testing the response to a new medicine, presuming these factors will promote recovery in your test subjects, then the apparent efficacy of the medicine might be affected by the distribution of these "lifestyle" factors within your test and control groups.

Similarly, on the other side of the coin, if you are testing the response to a new health threat by epidemiological study, a quoted Odds Ratio of 1.2 might be quite radically different for individuals of different general health, yet (in the studies I've read) there seems to be simply a presumption that the control group and the test group will have a similar spread of lifestyles.

It certainly seems to be a relevant factor in some cases as individuals with a history of smoking are almost always controlled for in such epidemiological studies (especially related to lung conditions), but I have never come across similar treatment of individuals in high stress jobs, eating fewer than 5 fruit and veg per day, taking less than three hours exercise a week etc.

For large effects, these factors would probably be insignificant, but where the effect is small (say a slightly efficacious new treatment, or a low risk environmental contaminant), failure to take account of these factors could theoretically lead to the conclusion that the drug is a slight improvement on what we have, or the threat requires some moderate mitigation, when if fact the drug is virtually ineffective in people who are otherwise unhealthy, or the threat is actually zero to a healthy individual, which would be really important conclusions for public health.

My limited interaction with epidemiological studies was quite a few years ago now, so my question is, have things moved on to start controlling for these factors now we have a better idea of their impact, and more significantly, if they have, have any studies from the past been revised in the light of such controls? Also, does anyone know of any accessible studies on the impact of these factors on epidemiology in general?

To clarify in the light of the close reason. The question is a single one which can be simply answered by anyone involved in epidemiology or researching pathology. Do modern epidemiological studies of disease causal factors control for lifestyle factors, such as diet, obesity, exercise and stress? The answer I'm looking for would come from someone who is either involved in epidemiological research or reads a significant number of epidemiology papers and the would at it's simplest be " Yes, they do" or "No they don't". I'm not sure how much less broad it can get.


texts: How does fluorouracil inhibit pyrimidine synthesis?

texts: I was reading in my pharmacology textbook about fluorouracil, and my book mentioned that fluorouracil is an antimetabolite whose function is to inhibit pyrimidine synthesis. However, I was curious to know how exactly does fluorouracil accomplish this. Is this drug involved in a specific mechanism that enables it to prevent pyrimidine synthesis? If so, how?


texts: How are the dominance and additive effects reflected in the mean and variance of the offsprings of two individuals with known phenotype?

texts:
If I estimated the genetic additive σ2A, genetic dominance σ2D and environmental effect σ2E of a trait in a population, what will be the predicted value of the offsprings of two individuals with known phenotypes?

My understanding: given that the two individuals are not close siblings, and that the mean of the two parents is μparents, the offspring will have a mean of:

μoffspring = μparents + μparents x σ2D

and the variance will be the environmental variance,  σ2E

How the additive effect  σ2A plays a role in a single mating ? (assuming thousands of offsprings (like in some plants) )?


texts: What's the difference between Phage DNA and Recombinant DNA

texts:
Genetic engineering:
In my textbook the following sentences describe the two, but to me they seem the same:

The new combination of bases in the DNA (vector DNA + DNA fragment)
is called recombinant DNA.
With bacteriophage vector, the bacteriophage will infect the bacteria by injecting its DNA into it. The Phage DNA (with the
desired gene in it) then integrate into the bacterial DNA.

Without going too much into it. What is the difference between Phage DNA and recombinant DNA?


texts: Living in Brasília, central Brazil; currently experiencing rainy warm/hot days.


texts: What new information does PheWAS add beyond GWAS?

texts: I am trying to understand Phenome-Wide Association Study (PheWAS). If I understand correctly, PheWAS appears to be just the reverse of GWAS (finding gene-trait associations using traits instead of SNPs). So what new information is added by running a PheWAS study compared to just running multiple GWASes? If you have single variant association results between a certain SNP and 10 traits in a GWAS, for example, is that the same thing as doing a PheWAS for those 10 traits?


texts: Does Goryaev's chamber have the same grid layout as the conventional counting chamber used in the West?

texts:
I'm translating a Russian biotec text where some cell counting operations are mentioned. The piece of equipment the authors mention in this context is "Goryaev's chamber" (камера Горяева):

  We discarded the supernatant, washed the cells with DPBS twice (suspended and centrifuged them for 10 min at 200 g), then diluted with 10 ml of ADCC assay medium and assessed the concentration and viability of the cells in a Goryaev's chamber.

Is a Goryaev's chamber any different in terms of its counting grid layout from the conventional hemocytometer chamber described in Wikipedia?

I would like to translate the phrase simply as "using a cell counting chamber" or "using a hemocytometer". The Multitran dictionary does offer these words as possible translations, but it occurred to me that Goryaev's chamber might differ somewhat.


texts: What information do bipolar cells encode?

texts:
Short version: I don't see what information on-centre bipolar cells are actually capturing.

Longer:

Actually, the question could be extended to on-centre retinal cells as well, but I'll focus on bipolar cells for now.

On-centre cells will fire when a spot of light hits the centre of their receptive fields and doesn't touch their surround, off-centres are the reverse (light in the centre is inhibitory, surround is excitatory).

Here's an over-simplified illustration that I made, red is hyperpolarized (excited), blue is hypopolarized (inhibited). Let's pretend that horizontal cell effects have already happened, and ignoring overlapping receptive fields for simplicity.

So my question is, if off-centre cells would be useful to highlight contrasts like edges (as I understand it, though eventually edges get detected further down in the complex cells), what are on-centre bipolar cells used for?

From my perspective it looks like they'd be good for single points in light which are small enough to hit the small number of rods that encompass the centre of a receptive field but not hit the surround. But when would this ever be the case? The centre of a receptive field would be incredibly tiny given the large number of rods in say the fovea (though, granted, maybe on-centre cells become more important in the periphery?).

One source:
http://thebrain.mcgill.ca/flash/a/a_02/a_02_cl/a_02_cl_vis/a_02_cl_vis.html


texts: Can forensic DNA analysis be used to generate a visual approximation of a suspect?

texts: In light of the current US supreme court case, I'm curious if enough information can be teased out of a DNA sample to get a "reasonable" approximation of the suspect (never mind the legality). I realize the term reasonable is subjective, so characteristics, such as skin color, hair color/texture, approx height, eye color, freckles, etc. I came across this article a few years ago, but the company that made the test went bust in 2009. It could detect race (how accurately?). I seem to recall reading an article a few years ago stating that "soon" we'd be able to get an approximation of appearance from a DNA sample that was better than a sketch artist could provide, though I can't recall now where I read it.


texts: Why does HIV belong to a group of retroviruses called lentiviruses?

texts:
HIV is an enveloped retrovirus. Each virus particle contains two copies of an RNA genome. The virus also has a number of enzymes: reverse transcriptase, integrase and viral protease. But, once I also find that HIV also belongs to lentiviruses.
I am not very familiar with the relationship between retrovirus and lentiviruses. And does here have somebody know why HIV is a kind of lentivirus?


texts: By what mechanism is NADP+ converted to NADPH in Photosystem I?

texts:
Here is my current understanding:

$\mathrm{NADP^{+}}$ takes 2 electrons from Ferredoxin at the end of the electron transport chain to generate $\mathrm{NADP^{-}}$.  An $\mathrm{H^{+}}$ ion in the stroma binds through the extra electron, generating $\mathrm{NADPH}$.  All of this is facilitated by Ferredoxin-$\mathrm{NADP^{+}}$ reductase.

Sources: https://en.wikipedia.org/wiki/Ferredoxin%E2%80%94NADP(%2B)_reductase

http://www.bio.davidson.edu/Courses/Bio111/NADPH.html


texts:
Crows are surprisingly clever with tool making/use and even understanding displacement water over sand! Clearly there's some relatively high level cognitive processes going on up in those avian brains.

When I stumbled across a video of what appears to be a bird grieving over its mate (shown in clip below), I wondered how far animal emotion and psychology goes.

Is that bird in the video grieving? (and shaking because of stress?)
What species of bird is this?


texts: Genetic linkage greater than 50 centimorgans

texts:
Classically, the linkage between two loci can be measured in centimorgans (cM), which represents the percent chance that these two loci will recombine an odd number of times (generating a recombinant genotype).

Due to independent assortment, markers on different chromosomes are expected to recombine 50% of the time. As I understand, if one conducts a classic experiment and counts various progeny, then deduces the apparent linkage, values of 50 cM or more are interpreted as "impossible to determine whether on separate chromosomes or just recombines very often". See (source), with grammar corrected:

  The final point that we need to make regards the maximum distance that we can measure. Because of the way in which the calculations are performed, we can never have more (than) 50% recombinant gametes. Therefore the (maximum) distance that two genes can be apart and still measure that distance is just less (than) 50 cM. If two genes are greater than 50 cM apart, then we can not determine if they reside on the same chromosome or are on different chromosomes.

Wikipedia gives an analytical solution and also remarks that (d is physical distance):

  The probability of recombination is approximately d/100 for small values of d and approaches 50% as d goes to infinity.

However, what happens if the linkage is greater than 50 cM? It seems like classical experiments aside, such a situation is possible in reality.

For instance, yeast chromosome IV is 1530 kb long, and averages 0.31 cM/kbp. Let's take two genes on Chr.IV:

DNF2 is at about +631 kb.
TOM1 is at about +1370 kb.

The physical distance between these is about 734 kb. According to the cM/kbp value, the centimorgan distance is $734\text{ kb} \cdot 0.31\text{ cM}/\text{kb} = 228 \text{ cM}$ . How to interpret this 228?

If I mate a haploid yeast which is DNF2 TOM1 with another which is dnf2 tom1 (lowercase indicating minor allele rather than deletion), then sporulate them, what is the chance of getting spores with DNF2 tom1 or dnf2 TOM1 genotypes?

I realize that the cM/kbp value is only a simplification and that in practice linkage is a more complex phenomenon. Nevertheless, it seems plausible that several crossover events can happen on Chr.IV since it is so big. This includes the possibility of 1, 3, 5 and more crossovers which would create a hybrid (assuming they all happen between these two loci), as well as the possibility of 2, 4, etc crossovers which would create a non-hybrid spore (at least as far as our chosen markers are concerned).


texts: Oligonucleotide purification with desalting

texts: I have ordered 36bp oligonucleotides that anneal to each other and create sticky ends to be cloned in a vector afterwards. I have tried cloning many times with different methods and I failed. Now I started to think that my oligos are actually shorter than 36 nt since desalting is not an effective method and most of my oligos do not create complete sticky ends when they anneal to each other. I believe I have also found support for this. So, how much is it possible that most of my oligos are actually shorter than 36 nt ? Is this a good troubleshooting or 36 nt oligos not being purified with more efficient method should not really create a problem?


texts:
Question: Do marsupials ever die in childbirth?

Obviously the notion of there being a linear ordering of "least advanced" to "most advanced" life forms isn't correct. Still, often marsupials are depicted as relic or archaic creatures with an inferior reproductive strategy, since besides possums they are restricted to Australia and New Guinea.

However, compared to some placental mammals, like the spotted hyena and humans, the marsupial method of always giving birth to very small young, who can finish developing outside of the mother's body, seems to be more sensible.

If there haven't been enough field observations of marsupials, then of course this is an unanswerable question, but I was wondering if anyone knew anything about papers or other materials which discuss the advantages of the marsupial reproductive strategy.


texts: Does coloring affect the perception of depth?

texts:
I have a question about the mechanics of human vision which may be as much of a physics question as it is a biology/physiology question. I noticed that if I try to imagine a clear blue daytime sky contrasted with a clear night sky and ask myself which of the two appears closer, my intuition says the daytime sky appears closer. My next thought was, given that a night sky is mostly black, visually the only difference between the two skies is their color. So why is that I want to "blue" is closer than "black"? And if the difference in color is truly what produces the difference in perceived depth, can similar effects be noticed with other color pairs at more familiar distance scales?

But then again, there are a couple of alternative explanations that seem more plausible to me on second thought. A black night sky could just as easily be called a dark sky, and the difference in perceived depth is really more a matter of shading. Then I remembered a night sky has stars of course, and it might be that my mind just wants to place the stars at normal "sky depth", forcing the black backdrop to appear even further away.

(Another related question I've been somewhat curious about: what precisely is the perceived "distance to the sky" as far as our intuitions are concerned?)


texts: How does the presynaptic terminal stay at the postsynaptic neuron?

texts:
I wondered about this because the two neurons never actually touch. The synaptic cleft is very small, but if there is no connection the neurons might easily separate...
[in chemical synapses]


texts: Escaping resource limitations during tumor evolution

texts:
In their discussion of the importance of r- and K-selection on tumors, Aktipis et al. (2013; figure 3) provide the following illustration of a hypothetical cancer growth curve:

In it, you can see alternations between selection for proliferation and selection for survival as the populations breaks through one carrying capacity after another. Of interest to me, is the overall shape of the growth curve as several sigmoids -- with each corresponding to a different serial resource limitation. However, this growth curve is a cartoon and not a measurement of some empirical system. Are there examples of such growth curves in the empirical literature on cancer?

An ideal case would be in a well studied animal model (or humans), with a corresponding analysis of which resource limitation was overcome at each step. With at least two, but preferably more, resource limitations in series. However, I will also be satisfied with answers from cell lines grown in vitro, since growth curves are usually easier to measure there.

Aktipis, C. A., Boddy, A. M., Gatenby, R. A., Brown, J. S., & Maley, C. C. (2013). Life history trade-offs in cancer evolution. Nature Reviews Cancer, 13(12): 883-892.


texts: How much time is required between repeated exposures to sun to prevent sunburn

texts:
After being in the sun, how much 'rest' is required before you can expose yourself again?

e.g. from Wikipedia:

  Sunburn can occur in less than 15 minutes

So if you were in a place where sunburn would occur after 15 minutes and you stayed in the sun for 10 minutes you shouldn't get sunburn.

How long would you then have to stay out of the sun before you could go into the sun again for 10 minutes without getting sunburn?

I'm pretty sure that 1 minute wouldn't be enough, but 24 hours would be fine, is there any logic as to where between those two figures it actually is?


texts:
When chasing away wasps or bees there is a danger of them stinging us in self-defense.
Can a similar danger arise when chasing away a mosquito which is otherwise not hungry? I understand that mosquitoes bite to feed (by sucking blood), but do they use their bites in self-defense against large targets, like humans? Mosquito bites can be somewhat painful or at least uncomfortable, and can carry dangerous diseases, making them theoretically viable as a self-defense weapon.


texts: About the plight of Elephants and efforts to conserve them?

texts:
Poachers are only after the ivory horns right? I read this story from the New York Times ( I think) of saving a Rhinocerous by some Park Rangers and a Vet. ( forgive spelling) ; they tranquilized the Rhino and took its horn off so it wouldn't be killed. I know Rhinos need their horns so maybe a hard plastic 'prosthesis' could be put in its place. Maybe the 'prosthesis' could be colored yellow or have some markings on it so any poacher would know it's fake. Of course this could all be done for the elephant too.

Could this be a feasible way to save Elephants or Rhinos??


texts: Species identification please - Bug is a plague for Italian Stone Pines (Pinus Pinea)

texts: They hangout on the top of Pinus pinea and spray a sticky substance all over the place. Size is about 2mm (head and abdomen) may be 4mm including antennae and legs. Could you please help me identify it and understand some of its habits and biology? I took the photos in a coastal town in Southern Spain. Thanks!!


texts: Can an enzyme be activated without allosteric inhibition or activation?

texts: Are there ways by which an enzyme may be activated or inhibited by non substrate molecules other than allosteric activation or inhibition?


texts: Is there a data base, tool or method I can use to find out which of my genes code for cytokine receptors?

texts:
I have a list of over 600 differentially expressed genes from my single cell RNA seq data analyses. I want to proceed to find out which of my genes code for cytokine receptors so that I can show on a heat map how their expression varies across clusters. Can any one give me a hint on which tool or method I can use to find out which of my genes code for cytokine receptors?

Thanks in advance.


texts: H is the set of all possible Diplotypes that are consistent with genotype data

texts:
I am new to Biology.SX. I have a statistics background, and have almost zero knowledge in genetics. I am trying to understand some things related to genetics in a certain paper of biostatistics.

Haplotype data were simulated using the haplotype patterns and frequencies (shown below) for 5-SNPs along a dabetes susceptibility region on chromosome 22, reported in FUSION study.

I know that haplotypes can be represented as binary sequences. I wonder why all the possible $2^5$ are not present here. (?)
The paper also says that

Let $G=(g_1,\ldots,g_M)$ denote the unphased genotype data for the $M$ loci. $\mathcal{H}_G$ denote the set of all possible diplotypes that are consistent with the genotype data $G$.

If a subject carries at most one copy of the causal haplotype '01100', it belongs to dominant genetic model, if it carries two copies of this haplotype, it belongs to recessive model.

The set $\mathcal{H}_G$ is not clear to me. While computing the likelihood, I need to know $\mathcal{H}_G$. Any help or suggestions?


texts:
I am new biology student which is on molecular biology subject on university. I would like to know something about genetic related to neurobiology, and certainly molecular psychiatry/psychology, perhaps evolution psychology. But i dont know where to start.

Can anybody give me type to literature/articles for beginners?


texts: Why do plants not have fat cells, and store their reserves in vacuoles instead?

texts: Why don't plants have fat cells, but instead store reserves in vacuoles. And vice versa, why do humans feature fat cells instead of depositing storage molecules in vacuoles?


texts: Why do hummingbirds build nests with live ferns instead of dead materials?

texts:
Hummingbirds prefer to build their nests with spore-bearing ferns, and mosses. This is helpful for the reproduction of the ferns, which are then better able to spread their seeds. But how is this beneficial for hummingbirds? Building in this manner is more difficult and energy-consuming.

Do live ferns make for better building materials? Is there a scent that these ferns are giving off to attract the hummingbirds? What kinds of research exist on this question?

References:

Carl Zimmer's National Geographic article, "A Living Nest?" (Feb 4, 2014) http://phenomena.nationalgeographic.com/2014/02/04/a-living-nest/

Question by Twitter-user Jessica: @LadyJaya


texts: how do they identify different protein chains?

texts: Can someone please explain how different protein chains occur exactly? I'm not talking about the side chain, but the protein chain which is typically labelled as A,B,C etc in the PDB. I'm curious as to how they are first found and what causes them? As far as I understand, the protein backbone could be in any of several conformations and each conformation has a label? Is that correct?


texts: Non-Salticidae with °oo° Eye Arrangements

texts:
Since childhood, I've always thought of the °oo° pattern of four frontmost eyes as iconic for spiders (note: the pattern does not account for any additional eyes or lack thereof further to the sides or back; also, title font seems to make the °'s relatively smaller than the main text's font does - this was not intentional). And yet taking a look at a couple of eye-based family identification tables, it seems that the above pattern is the go-to sign of a jumping spider.

Is this pattern unique to salticidae, or are there other groups of spiders with the four foremost eyes matching such a pattern (either four equal-sized eyes, or the secondary ones slightly smaller)? If the latter, what groups sport a similar look?


texts:
I know that the cells of mammals at least stop dividing when they are old, and then die a programmed cell death. Then other cells have to replace them.

But in a bacterial colony, each cell replicates for itself. Obviously, if a division of a bacterial cell of generation N were to produce two new cells of generation N+1, and all bacteria died of old age at generation M, there would be no bacteria left around.

So how is it regulated in bacteria? Are their divisions simply unlimited? Does a cell never die and just divide forever?


texts: If a gene is missing from an operon that structures a protein, then would that protein not be made properly?

texts:
From my understanding, operon is a series of genes that are regulated by a single promotor. In many cases genes in an operon form subunits of a protein.

I obtained a genome in my study and looked for genes that constitutes part of a metabolic pathway, and ended up finding that one of the genes in an operon was missing.

Does that imply the protein made from those genes in the operon will not be made properly or other genes will compensate for the loss?


texts:
Which of the following demonstrates the pattern of development in Greylag Geese? {Please give specific answers, which among the following gives the best available demonstration?, If needed, have a look at the Paragraph (Image Embedded)}

(A) Geese reared by humans cannot be taught to respond to its own species.

(B) The hatching at an advanced stage is critical for imprinting.

(C) The capacity to recognize an adult of its own species is necessarily inherited.

(D) Rearing by humans does not alter the object of the behavioral routine.

Option A: “Geese reared by humans cannot be taught to respond to its own species” is correct.
This is inferred from the 4th paragraph 2nd line: “When young geese are reared wholly by human beings it is towards humans that the young geese direct their behavioural routines”. This line clearly states that geese wholly reared by humans respond only towards humans. Also from the 2nd Paragraph 3rd line It is clear.
Option B: “The hatching at an advanced stage is critical for imprinting” is false.
Hatching at an advanced Stage is not shown by Greylag Geese, it is shown by Godwits. (3rd Paragraph, 1st & 2nd Line: The young of Godwits hatch at an advanced stage of development and soon after hatching can recognize the adult bird.) (So the fact is not conclusive from Behavioural Pattern of Greylag Geese) Imprinting can be shown by Greylag Geese, which do not have a prolonged period of hatching, and imprinting totally depends on whatever creature happens to be present at the right moment in their development.
Options C: “The capacity to recognise an adult of its own species is necessarily inherited” is false. According to the 2nd Paragraph, 2nd line: The capacities to recognise the right stimulus are not always inherited.
Option D: “Rearing by Humans does not alter the object of the behavioural routine.” is false, as shown in 4th Paragraph 2nd & 3rd line: When young geese are reared wholly by human beings it is towards humans that the young geese direct their behavioural routines.
Hence, answer should be A.

So Am I correct?


texts: Can I get 1% of my one of my great great grandparents genes?

texts: I basically took a 23andme test and found out genetically I was 1% African. The weird part though is that family records shows that my father's mother's grandmother was African, making me 1/16 African. Shouldn't it be closer to 6%?


texts: Thymine does not present in RNA but DNA containing thymine why


texts: Red and yellow insect found in kitchen in Conrad, Montana (USA)

texts: Beetle found in our kitchen in Conrad, Montana (USA) on 3/13/19:


texts: Will meat rot in alcohol below freezing?

texts: I understand that freezing slows decay but I'm wondering what will happen if meat is kept in below freezing temperatures while submerged in a liquid that has a lower freezing rate, like alchohol?


texts: Is coral photosynthesis dependant on the wavelength or frequency of light?

texts:
When buying a light fixture for a marine fish tank, it is often sold with some technical data reguarding the spectral output of the light, with a peak in the blue region of visible light, somewhere around 430 to 460nm in air.

As light enters the water with a refractive index of approximately 1.33, the peak wavelength will reduce, but the frequency of light will remain constant. So, for example, a monochromatic light with wavelength 460nm in air would have a wavelength in water of about 345nm, but the frequency is the same. Physics so far, so here comes the biology question....chlorophyll a and b have peak responses between 400-500nm light, so is it the wavelength of light in water that is important to photosynthesis, or is it actually the frequency(therefore the photon energy) that is what counts?

If we were to discover a purely theoretical new plant that grew equally well in air or water, and discovered that photosynthesis only occurred at 650nm wavelength light in air, and not at all to any other wavelength. Then we place this plant in water indoors in the dark and shine a monochromatic 650nm light source at if from air, into the water,  would photosynthesis still take place because the photon energy is the same in water or air (e = hf). Or would we need to shine a monochromatic light source of approx 865nm in air, which would reduce to 650nm in water (865/1.33)? I suspect the answer is that photsynthesis is dependent on the photon energy not wavelength, but I am far from sure about this!


texts: Is diabetes mellitus a sex-linked disease?

texts:
There are two types of diabetes mellitus.

a. Type 1 diabetes mellitus
b. Type 2 diabetes melliuts

Is either of them a sex linked disease? Can either one be inherited? My book says, "this disease is transmitted as a recessive genetic characteristic." What does this mean?


texts: Well saw this on a fish group on facebook. Noone can give a decent answer so I came to you guys hoping you can help us? The one who posted lives in the Philippines and he said he caught it in the river that is somewhat connected to sea.


texts: Binucleate cells of transitional epithelium (bladder)?

texts:
Working through Histology slides of the transitional epithelium (urothelium) of the urinary bladder, I noticed that the dome-shaped cells at the top of the transitional epithelium are frequently binucleate.
In doing research, I found that the top cells of the transitional epithelium are 'often binucleate and usually polyploid'

  Why is this?
  What purpose does this serve?
  Is the binucleate feature consistent enough across slides to be used as a common identifying feature to recognise transitional epithelium from the urinary tract? Is the absence/over-abundance of binucleate cells characteristic of certain diseases?

I also see prominent granules (of glycogen, I presume?) in these cells.

  Is this glycogen? & What purpose does this serve?

Also, I'm having difficulties recognising transitional epithelium in slides. Does anyone have any tips to share on how to easily recognise transitional epithelium as such (common features to look out for, etc.), especially in distinction to pseudo-stratified epithelium, which often looks similar?


texts:
In physical therapy and occasionally in sports coaching, there's often a precise description of the mechanics of what happens during the movement (which muscles are engaged, which joint moves where etc). I couldn't find any information on where that knowledge comes from - observation and "probing" for engagement alone would not be enough as some muscles are tiny and/or hidden under bigger ones. So, how was the theory developed?

Example: how do we know these are the muscled that perform external rotation (at the shoulder, for instance) ? https://en.m.wikipedia.org/wiki/List_of_external_rotators_of_the_human_body What tells us every single one is necessary? What tells us another one isn't involved?

(please let me know if this is better suited for a different StackExchange)


texts: Do people with congenital analgesia feel cold?

texts:
There are a few diseases that cause an insensitivity to pain. This question asks about the relationship between the cold and pain, which got me thinking:

Is shivering a response driven by the sensation of cold, or a response to the pain associated caused by the cold? This is easy to work out by considering people that do not experience pain.

The key here is if people with congenital analgesia (AKA CIPA, CIP) shiver then we may assume that it is the sensation of the cold, not the pain and the cold, that causes the shivering.

Do CIPA patients shiver in the cold?
Does this mean that the shivering is caused by sensation pathways or
pain pathways?

Disclaimer: I am not an anatomist and do not claim to have a working knowledge of the nervous system. Please point out any and all obvious errors in this question that might explain why this wouldn't be the case in the comments or as an answer if its a big error.


texts: The genome size of human is 3.000.000.000 bp and for Arabidopsis it is 255.000.000 bp. I know these numbers because their genomes have been published. Which methods are used by scientists to estimate the genome size before they sequence that genome?


texts: Question about vitamin b6 product and cycling

texts: Can the b6-product of a vitamin b6 reaction such as transaminase be recycled back to active vitamin b6 in man, and if so by means of what reaction?


texts: What is the difference between a protein and a factor?

texts:
In terms of nomenclature/semantics, why are some proteins named proteins, and some named factors?

I've been revising on eukaryotic DNA, and I've come across some proteins that seem to serve roughly the same function, but are named differently. For example,

Replication activator protein
Replication licensing factors
Replication protein A
Replication factor C
Transcriptional factor
Eukaryotic translation initiation factor


texts:
In Werner Herzog's 2010 documentary Happy People: A Year in the Taiga, a dog is reported to run 150 km from the Taiga back to the owner's village, without any stop and seemingly at full speed as it is running next to a snowmobile.

I am skeptical of this. I cannot find any reports of dogs running a distance even close to this. This article on super-distance dogs does not mention any distances over 40 miles (64 km), which is still less than half the distance, and together with the owner running, so at much lower speed.

Can a dog really run 150 km at full speed?


texts: If I enter a room with certain odor, I can sense the odor. However, if I stay there for some time I cannot sense it anymore. A new entrant to the room can still smell it or I have to leave the room for some time and upon returning I can sense it again. Does our nose detect only if there is change in odor?


texts: The amplification on vector transgenic microorganisms and the subsequent purification does not seem that complicated. Also, what are the processes that biotechnological industries follow, in detail, on their production?


texts: How detailed a construction of the family tree of known human fossils do we have?

texts: For the sake of this question, by "human" I mean Hominina. The best I could find is this, which isn't very detailed. Of the dozens of paleospecies we'd seek to link up, do we have a more detailed tree attempt? Of course, it would be provisional and approximate, and the details would be somewhat debated; but I'm trying to gauge how fuzzy it is with our current knowledge.


texts: Is there a difference between a consensus PCR and a pan PCR?

texts:
I know that a multiplex PCR uses multiple sets of primers in one reaction to amplify multiple targets.

But what is a PCR called that uses generic primers to amplify multiple targets? Is this a consensus PCR? Or a pan PCR? Or do those two terms refer to the same thing?

What about a PCR that uses degenerate primers?

Thank you for your help.


texts: If all animals were to die, would all plants die too?

texts: Humans and many other animals are able to breathe because plants produce more oxygen than they need. I was thinking if all animals died all of a sudden, then wouldn't plants die too. Eventually they would produce too much oxygen and wouldn't have enough carbon dioxide to go through photosynthesis.


texts: Why do nearby cells have similar meiosis periods?

texts: A few days ago, I conducted an experiment to observe the meiosis of rye ears. During the experiment, I observed that cells in similar locations have similar meiosis period. Can anybody tell me why does this happen? Does the checkpoint of a single cell affects the checkpoint of nearby cells?


texts: Is human mtDNA unique in its single origin?

texts: Other than Humans, is there another primate who has a traceable “original Eve mtDNA”?


texts:
I have heard that birds have exceptional eyesight. How far does this mean they can see? What's the resolution like? Are we talking about just vague shapes or something like, at 100 feet, seeing individual hairs on a dog's fur coat?

I've also read that, in general,  primates are the only mammals that have color vision. I know birds are not mammals. Is it common for birds to have color vision as well, like primates?


texts: Earth's history: The Great Oxidation Event and the 'Boring Billion'

texts:
From what I understand the 'Great Oxidation Event' occurred around 2.4 billion - 2.3 billion years ago, when cyanobacteria flooded Earth’s atmosphere with oxygen.

The 'boring billion' period was around 1.8 billion years ago, during which it is thought not a lot changed on planet Earth. Low oxygen levels were thought to be 1-40% of modern oxygen levels during this time.

Why did the atmosphere go from 'flooded with oxygen' to 1-40% of modern oxygen levels. Was it because during the Mesoproterozoic era, the rate
of burial of decaying organic carbon matter under marine sediments
flatlined?


texts:
I am looking for a good explanatory book concerning Neurobiology. I am interested on how the brain works but prior to this I believe that I have to start learning things about the biology of neurons. So I searched on the net and found a book called "From Neuron to Brain" from John G. Nicholls et. al.

Actually there are so many books out there and because I have never worked on that subject, all these results are confusing me.

So i would like someone's opinion who has dealt with this subject to help me choose a book for beginners.

Thank you.


texts: When birds fly in V-formation, how is it decided which bird gets to be the 'lead bird'?

texts:
I've read on Wikipedia and in other sources that the lead position alternates due to flight fatigue, but does it alternate between a small cabal of of leadership birds, or does (almost) every bird get to sometimes go first?

Is the process different across different species?


texts: How do chromosome pairs get "paired up" for protein synthesis?

texts:
If my understanding is correct, during interphase a normal human cell will have 46 chromosomes scattered about in the cell nucleus. These chromosomes can be thought of as pairs: there are two copies of "chromosome 1", one from mom and one from dad. Same goes for chromosome 2, chromosome 3, ... chromosome 22. Although we think of these as coming in pairs, are they actually attached or paired up in some way?

At some point, protein synthesis will take place via transcription. What I'm having trouble understanding is how and when the above pairing takes place. Does transcription occur independently for each of the 46 chromosomes? I don't think this is the case, because in my head I imagine that we will only get one set of proteins from the pair of each chromosome. Also, I'm unclear as to how dominant/recessive genes can come into play unless protein synthesis occurs as a function of both pairs of chromosomes.

I hope this is clear enough. Thanks.


texts: What is the real meaning of the statement "*ontogeny recapitulates phylogeny*"?

texts: I tried searching in this site but couldn't find an appropriate answer to the title question: what is the real meaning of the statement "ontogeny recapitulates phylogeny"?


texts: Is life in a supercritical fluid possible?

texts:
Someone claimed that the dinosaurs could only live because back then athmospheric density was around 650 kg/m³, providing some buyoncy, this claim is checked on Skeptics SE. The claim itself is beside the point now. A simple calculation shows us that an atmsphere with this density would be supercritical in underwise normal conditions, the pressure would be increased by a factor of roughly 520. See my answer to the skeptics question for a bit more explanation. I would say that a supercritical air atmosphere rules out life for several reasons:

The high effusity of the fluid may mean that cell membranes don't work
Proteins fold differently under high pressure, requiring specific adaptions
If the partial pressure of oxygen is increased proportionally, the atmosphere is highly toxic
If the partial pressure of oxygen remains at current levels, it is a trace gas and reactions relying on oxygen may run into kinetic problems (There may be a sweet spot between the last two issues)

Anyway, those are just my hunches, I never heard of experiments about life in supercritical fluids and I'm no biologist so my hunches may be totally wrong. My question is: Can we rule out life in supercritical fluids; if not can we rule out air breathing, multi cellular animal life?
Or has any life been shown to thrive in a supercritical fluid?

To stress again, the part with buoyant dinosaurs was given for background (and amusement), I'm only asking here to check my hunch that suprecriticality rules out life.


texts: Why is a gene for a fluorescent protein used rather than one for an enzyme that produces fluorescent molecule?

texts:
Green fluorescent protein (GFP) is a small protein that emits bright green fluorescence in blue light. It was first isolated from the jellyfish.

The gene coding for GFP can be expressed in bacteria, and so it is often used as a marker to show successful uptake of a gene by the bacterium.

What is the advantage of using the gene for GFP to produce easily detectable fluorescence, rather than using a gene for an enzyme that produces a fluorescent substance?

Ps. The original question I got was to explain about the disadvantage, which is that GFP may not fluoresce very brightly and so may be difficult to detect.

Thank you for your help.


texts: How do you find probabilites of carrying an X linked recessive disease in a blank pedigree given only one phenotype?

texts:
In the above pedigree, the black square indicates the male
affected with Hemophilia which is a X-linked recessive trait. What is the
probability that the proposed child, which is a male (indicated as ?), will carry the disease?

I started off by trying to figure out the probability that the sister has an X chromosome carrying the disease, which I got as 10/16 (Since the mother must be XcXc or XcX and the father either XY or XcY; possible genotypes are XcX, XcX, XcXc, XcXc, XcX, XX, XcXc, XXc)

I then repeated the procedure for each generation and got the final answer as 9/16. However, the correct answer is 1/8. How do you obtain this? Are my assumptions flawed?

Source: https://biolympiads.com/wp-content/uploads/2016/08/inbo2009-Q.pdf


texts: Predict if a given protein can pass through the intestine

texts:
Assume that i have a 3d-protein structure in a PDB file on a computer.
Is there any bioinformatic method to predict if that protein can pass through the intestine or not?


texts: Acute cytotoxic T lymphocyte killing capacity

texts:
how many cells can a CTL eliminate sequentially?
Cytotoxic T lymphocytes (CTLs) are a subset of the adaptive immune system which can target cells for apoptotic elimination. This elimination begins with identification leading to a transfer of the CTLs cytotoxic concoction (perforin and CT granules) into the target cell and subsequently inducing apoptosis. A natural acute limit to this elimination seems obvious as the CTL does not have an infinite supply of apoptosis inducing ammunition. However, after a CTL becomes activated it begins to produce and store these constituents in the cytoplasm - resulting in multiple cytotoxic (CT) granules being stored in the cytoplasm as is visible under a microscope. Even, the activation of these cells cytotoxic capabilities can be indicated by the presence of the cytotoxic granules.
I would like to assume that the CTL has had 'enough time' to build a fully stocked store house of CT granules, and will not add to this store house during its sequential elimination. If this question is incapable of being answered due to this assumption outright then I would think it is ok to ignore it.
Generally speaking, this question pertains to acute in situ T lymphocyte exhaustion. Discussion of general T lymphocyte exhaustion may have value, but also may be unneeded.


texts: ECG detection using minimal number of electrodes

texts:
Disclaimer: Hello, I'm someone from an electrical engineering background, so this question may sound dumb.

I wish to make a wearable ECG monitoring device for arrhythmia detection. Since the device is to be wearable, it has to be small and should not obstruct normal behavior (kind of like those ECG patch monitors).

My question is, which lead should I monitor for arrhythmia detection. I read that I do not need all 12 leads for this purpose. The leads should preferably involve electrodes close as possible to reduce area of contact with the body.


texts:
Today I found out that the gene for being Left-handed is dominant while Right-handed is recessive. I personally am left handed and so is my father. My mothers father is also left handed and I was wondering whether or not I am homozygous or heterozygous for the left handed gene. Is there any way to determine this without getting genetic testing or by actually having kids? Thanks.
Source: My science teacher


texts:
Cell lines are often immortalised by artificial expression of proteins which specifically cause the knockout of important cancer suppression genes or the activation of proto-oncogenes.

  Cellular immortality happens upon impairment of cell-cycle checkpoint
  pathways (p53/p16/pRb), reactivation or up-regulation of telomerase
  enzyme, or upregulation of some oncogenes or oncoproteins leading to a
  higher rate of cell division.

However, this would appear to fall under the purview of Biosafety Level 3 since the protein expression vectors are capable of causing cancer in the researcher when they infect the researcher. Cancer can certainly be considered a serious or lethal disease, and aerosolisation of the vectors, while rare, is not impossible (for example during a spill).

According to the biosafety definitions of Columbia University,

  Agents: serious or lethal diseases transmissible via aerosols, e.g.,
  M. tuberculosis, SARS.  Recombinant DNA activities using genetic
  material from BSL-3 organisms or such organisms as host cells.

Why then, does the CDC classify cell line work, including work with viral production cells, as a BSL-2 activity requiring only BSL-2 containment levels, when the act of immortalising the cells would involve working with viral agents that can cause cancer?

  Cells immortalized with  viral agents such as SV-40, EBV adenovirus or
  HPV, as  well as cells carrying viral genomic material also present
  potential hazards to  laboratory workers. Tumorigenic human cells also
  are potential hazards as a  result of self-inoculation.[...]

  Human and other primate cells should be handled using  BSL-2
  practices and containment. All work should be performed in a BSC,  and
  all  material decontaminated by autoclaving or  disinfection before
  discarding. BSL-2  recommendations for personnel protective equipment
  such as  laboratory  coats, gloves  and eye protection should be
  rigorously followed.

Are the transformation cells (eg the 293T viral cells containing the transformant viruses) considered Level 3 biosafety risk, and if not, why not?


texts:
I notice on dbSNP rs6352 has an ancestral allele of G - http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=rs6352

The hapmap in humans for this allele is very rare, the homozygous version practically not existing at all http://hapmap.ncbi.nlm.nih.gov/cgi-perl/snp_details_phase3?name=rs6352&source=hapmap3r3_B36&tmpl=snp_details_phase3

My understanding has been that the ancestral allele refers to the common gene that an ancestor in all humans once shared. Now, I thought the ancestral allele was usually the most frequent in a population, but I can see this was most likely a wrong assumption.

Was it a wrong assumption, or was this example above just a rare exception? Is deviation from ancestral alleles nearly worthless as a metric to investigate possible mutated alleles that may be leading to disease? I realize the proper answer may be too long, but just a brief summary would be appreciated.

Many thanks.


texts: What is the female equivalent of the morning erection that some men experience?

texts:
There was question about what causes "morning wood." It was answered that the erection in the morning is caused by decline of norepinephrine during REM sleep. Which in part allows to prevent uncontrolled urination.

My question is: How does the decline in norepinephrine affect women? They obviously don't get erection.


texts: Why I don't feel pain when I press the skin on my knee and elbow?

texts: Does the muscle on our knee and elbow have some speciality ? Why are we unable to feel any sort of pain when I pinch it ? I also did it with my Mom and Dad and result was same .


texts: How do people measure how many calories or proteins/fats/сarbohydrates are in some food?

texts: How is the composition (in fats, proteins or carbohydrates) of a certain food estimated and how is the amount of calories provided by the food calculated?


texts: Are the destruction of Olfactory Receptor Neurons (ORNs) permanent?

texts:
I lost the ability to smell a particular smell due to an exposure to solvents years ago.  It has never fully come back.  I had always assumed that simply meant I had permanently destroyed my ORNs for that smell.  However, I have recently read that ORNs are replaced every 60 days.

Is it possible to lose all ORNs for a smell and have them never come back?  I'd love to know whether my long term loss of smell is due to something cognative, or whether it is a complete lack of inputs from the nose.


texts:
I was chatting with my friend, and we both found that there's a relation between putting eggs and ears; we count animals and we found that if an animal is oviparous (birds, snakes, etc.), then it does not have ears. We really did our best but we did not find anyone!!

So, Is there any scientific reason laying behind this difference, I'm a little bit curious? Thanks!


texts: Can the RNA in the HIV virus make viral enzymes without entering the nucleus?

texts:
If the provirus was not formed yet, can the virus make viral enzymes?

(I know that it already has some, but supposing it doesn't)


texts: What's the Mechanism of Paradoxical Excitatory Effects with Sedating Antihistamines?

texts: I've been reading the British National Formulary 65 (BNF-65) and it mentioned that in some, especially at higher dosages, sedating (first-generation) antihistamines, can produce paradoxical excitatory (or stimulating) effects and so I felt like asking the age-old question, "Why?" because as I hope is obvious by my questions I am fascinated by drug action and I felt there was no better place to ask this question than here on biology stackexchange.


texts: Why is propanoic acid often added to the diet of C. elegans?

texts:
And what are its effects on C. elegans?

The paper is  Burnett C, Valentini S, Cabreiro F, Goss M, Somogyvári M, Piper MD, Hoddinott M, Sutphin GL, Leko V, McElwee JJ, et al.. 2011. Absence of effects of Sir2 overexpression on lifespan in C. elegans and Drosophila. Nature 477: 482–5.