texts:
As the most recent "ice age" (the Pleistocene) came to a close, changing climatic conditions obviously changed the playing field, driving some species to extinction. But humans were spreading around the world and increasing in numbers and hunting prowess at the same time. There's little question that our ancestors exterminated Madagascar's elephant birds, New Zealand's moas and quite likely Steller's sea cow.

But what about such familiar Ice Age giants as the woolly mammoth and giant ground sloth(s)? We know that they were hunted by humans, but did they die out from overhunting or from environmental changes?

This was the subject of much debate back in the 1980s or so, but I haven't done much research on it in recent years. I'd just like to know if there have been any significant recent discoveries or theories that shed more light on this question.

Obviously, we can't account for every species. Some suffered natural extinctions, while others were exterminated by humans. Still others may have been on their way out when humans along and finished them off.

But I'd like to get a general grasp of what happened. It seems that giant ground sloths would have been easily exterminated by human hunters, just as the smaller ground sloths of the Caribbean islands disappeared after the islands were settled by humans. The pony-sized mammoths that inhabited various islands off the coast of California and Europe also seem like good candidates for human extermination.


texts:
I am trying to use the DAVID tool to do some gene analysis. I have some probe set intensities for some cancer cell lines. I found this link in the DAVID tool http://david.abcc.ncifcrf.gov/tools.jsp. I am a bit confused with the terminology introduced here. It says gene list for the probe sets why is it so? I mean in the example you can see the probe sets like

1007_s_at
1053_at
117_at
121_at
1255_g_at
1294_at
1316_at
1320_at
1405_i_at
1431_at
1438_at
1487_at
1494_f_at
1598_g_at

Buy why are they called gene list not probe sets. Why?


texts: How does gene editing in one cell affect other cells?

texts:
I have read about gene editing and I have some questions concerning this technology:

With gene editing, are we correcting the genes in all the cells or a single cell?
If the gene editing is done for only one cell, then how (or can) it affect other genes in other cells?


texts: human body in an environment where temperature is above body temperature

texts:
What would happen if humans were to live in an environment where the temperature is above the body temperature?

Does the human body have a mechanism to cool the body?

When the surrounding temperature is below the body temperature, the body has a mechanism to heat up. When the surrounding temperature is above the body temperature, the body would require some mechanism to cool down since there will be a net heat transfer into the body.


texts: Can we directly stimulate M cones in retina with current technology?

texts:
I wonder if we could try to see imaginary "supergreen" color by directly stimulating M cones. For this I suppose we'd need:

Non-destructively scan specific human's retina to locate exact positions of M cone cells.
Prepare a high-resolution image (on a retina-like display I guess), which would have light spots in some locations and dark in others, so that when the human we inspected looks at particular point of the image, these light spots were focused exactly on M cones.
Track the eye movements and adjust the image so that S and L cones avoided significant exposure to prevent misperception.

Is anything of this hard to implement with current technology, given typical human retina properties (M cones density, their apparent color etc.)?

If this is totally possible, has such an experiment already been performed?


texts: Why does Cyan appear bluish rather than greenish, when the phototopic eye sensitivity is highest in green (and Cyan contains blue and green equally)?

texts:
Cyan contains blue and green equally.
Phototopic eye sensitivity is highest in green.
Why, then, does Cyan appear bluish to most of us, rather than greenish?


texts: How do microbes develop resistance to anitmicrobial peptides?

texts:
I would like to better understand how bacteria use the "strategy" of alternations to lipid A and membrane proteins in order to resist antimicrobial peptides of the immune system?

It is my understanding that the by altering its lipid A, the bacterium makes its membrane less hydrophobic, increasing hydrophilicity, resulting in an increased amount of fluidity for the outer membrane.

This should then inhibit the hydrophobic portion of antimicrobial peptide embedding into the lipid membrane of bacteria.

Is this accurate? Is there anything I am missing about these alterations than confer resistance?


texts: What vegetation would thrive in the Martian atmosphere?

texts:
Most plants require carbon dioxide for their photosynthesis, which Mars has in overabundance.

Would atmosphere composition (let's ignore temperatures for the purpose of this question) of Mars allow vegetation to grow?


texts: How do the homologous chromosomes pair up and position themselves along the center of the cell?

texts: I am not sure... Most textbooks just state "they line up" but I don't know how... Something to do with the cytoskeleton or microtubules? Thanks for any help


texts:
Researchers have proposed the application of CRISPR/Cas9 and gene drive to genetically alter wild mosquito populations such that they don't transmit malaria. The government of New Zealand has announced a program to eliminate several invasive mammals from that island, also using gene drive (among other things).

Could we use this technology to completely eradicate from the world all species of mosquito that prey on humans? Also, could we accurately predict the extent of the resulting ecological disruption so we could decide if it was worth it?


texts: Can P. falciparum and other malaria parasites be cultured and genetically engineered?

texts: I'm not a parasitologist, and I was wondering about the current state of malaria research. For instance, is it possible to culture P. falciparum? Are there techniques for genetic manipulation, editing or transfection (analogous to in vitro cell culture) ? Are there any major limitations to studying these parasites in culture?


texts: What are "anchor regions" in the human genome?

texts:
I've been reading this paper entitled "A high-resolution map of the three-dimensional chromatin interactome in human cells", about interactome in 3D chromatin.

  We next applied the above algorithm to the 518,032 anchor regions in
  the human genome, with each containing one or a few HindIII
  restriction fragments (fragments shorter than 2 kilobases (kb) are
  merged) (Fig. 2a), and uncovered a total of 1,116,312 chromatin
  interactions with a false discovery rate (FDR) of 0.1

Simple questions: what are these anchor regions in the human genome?

How could I group them into types/categories?

Thanks


texts:
Anal glands in all kinds of animals play a range of diverse functions - providing fat for preening feathers or waterproofing fur, generating distinct scent, even repelling predators.

None of the resources I found about human anal glands ever mention their function. There's info or infections, location, treatment of problems related to them, but never a word about a role they might serve - if any. Are they vestigial organs without any role or do they have some evolutionary purpose?


texts:
What I am looking for
I'm considering to eventually start my teaching sessions with short emotional, awe-inspiring or exciting videos that are somehow related to evolutionary biology incl. diversity of life, history of evolution on earth, specific evolutionary processes (sexual conflict, evolution of ageing, evolution of mutation rate, speciation rate, ...), diversity in mating systems, major transitions, etc...
3-minute long movies would be perfect. 15 minutes would be too long. The videos should be easily accessible for Bachelor students having little background in evolutionary biology.
Examples
Asap Science video about the evolutionary history of life would be a good fit.
The beginning of We are all related by vsauce would be a good fit.
This video from SciShow is typically too long
This video on the evolution of human face would do but I am not quite sure how exact it is and it feels a little weird that the end product is a white male!
It'd be great if not all suggestions were about recent human history or about dinosaurs :)
Do you have any suggestions?


texts:
Today, about 10 to 20 percent of known pregnancy end in miscarriage. Pregnancy is a biological process that has been very well studied by medicine. As a result, modern medicine helps a lot to prevent miscarriages and to prevent death of pregnant women.

What was the percentage of pregnancy ending in miscarriage before modern medicine? Typically, what was the percentage pregnancy ending in miscarriage in early Homo sapiens, during the paleolithic age?


texts: Why does renal artery stenosis lead to activation of Renin-Angiotensin system?

texts:
To my current understanding, stenosis or narrowing of the arteries would mean higher blood pressure, similar to atherosclerosis. So the Renin system should be suppressed to counter the high blood pressure. But..

I have read in a textbook that renal artery stenosis means lower blood flow in the kidney due to the narrowing of the artery. Thus the Renin system is activated to increase blood pressure.

So why does narrowing of the renal artery cause a decrease in blood pressure, and not increase?


texts:
Many instances of this worm-like creature were found in a water system for a mountain cabin in the Sierra Nevada mountains of the US, in late June / early July.  The water system collects water from an enclosed spring.  Can you help identify this creature?

Clues:

The worms have two "points" on their heads.
They can stretch out and be long and thin, or when poked (or are resting) they contract into a small blob.
Here is a picture of a single worm with markings shown.

Here is a picture of a few worms, somewhat contracted.

Here is a movie of them moving, in natural light.
Here is a movie of them moving, with backlight.
Here are pictures of their undersides and their internal structures.

Whenever I pull some out of the water and put them into a tupperware with the same water, they only survive for around 24 hours, after which they seem to disintegrate.  Here is a picture of about 20 of the worms after about 24 hours, the bulk of them have halfway-decomposed and form a heap in the upper right.  After another day it'll just look like debris in the water, you wouldn't even recognize that there were worms in it.  There is a piece of bacon in there because some suggested putting it there to test if they were leeches, but this disintegration happens repeatably and regardless of the bacon; please ignore the bacon.

Someone suggested that they are trematodes, but there are no snails, frogs, or other creatures in the storage and collection sections of the water system;  we have looked very closely.  There may be something within a 30-foot section of pipe, but we doubt it.

Can you help us identify this creature?  Even just possible families of creatures or general categories would be helpful for us.


texts:
Can anyone tell what of kind of insect is in this image ? They have been showing up in my room for the past month; never happened before that. The room is generally hot during daytime.

Thanks


texts: How could I identify whether given RNA-seq data is paired end or single end

texts:
I need to have a RNA-Seq dataset and therefore, I've visited the following site NCBI-geo C. Elegans

In the Supplemantary file part, I clicked the SRP/SRP051/SRP051702  ftp and downloaded sra file. Then I need to convert it to fastq file format. For this purpose I've heard that there is a sra-toolkit and within it there is  fastq-dump exacutable. However in order to use it, first of all I have to figure out whether my sra file contains paired-end or single-end read data. So my question is that how could I know the type of reads in the dataset (in the first link) ?

Without any information, I used --split_files flag of fastq-dump exacutable and it generated two 14 Gb  (both of them  are exactly 14.346.367.840 bytes) files and their name are  SRR1741330_1.fastq and SRR1741330_2.fastq Does it mean my dataset is paired end ?

As an another question (different but related with part 1). In the SRR1741330_1.fastq file, at some lines, sequences contains different characters such as CCCFFFFFGFHHHGJJJJI#1?FEIGGI... Before looking into these files, I have thought that these sequence lines should only contain the letters of A,G,T and C . What are these F,H,J,I,#,? etc..

My questions might be trivial and unmeaningful but since I'm a totally new person in this area, I could not understand them.

EDIT

New question

I wonder one more thing, since its related with previous part of my question I asked it here instead of creating new question. After I generate fastq file with dump_fastq executable, all the sequences are length of 50. Does it because of parameters of the dump_fastq executable or its related with original sra file? In other words, could I increase this length?


texts: What exactly is neuroplasticity, and can it be demonstrated with a simple experiment?

texts:
As far as I know, neuroplasticity is about restoring brain functions by moving some functions to other still functional. Neuroplasticity is more prominent in children than in adults.

What are other examples of neuroplasticity that are unrelated to pathologies? Can it be demonstrated by a simple experiment outside the laboratory? Are learning, or simply the getting used to new things examples of neuroplasticity?

For example, after wearing red-cyan goggles, I see a color mismatch for some time after I take off the goggles. Is it related to neuroplasticity or some other thing?


texts:
I think the answer is no, but I am not 100% sure.

If it was yes, then the dendrite of the nerve cell should each time receive a stimulus causing Na+ channels to open, when the contraction happen.
Also, then it would mean that outside events could alter the function of hearth, which would be dangerous.

The heart has a special excitatory system and a contractile system - Sinoatrial node and Pacemaker cells, which control the action potentials in different portions of the heart.
So heart and primarily myocardium i.e. cardiac muscle can depolarise without any external influence with a slow, positive increase in voltage across the cell's membrane.

Do nerve cells cause action potential in cardiac muscle?


texts: Quantify Protein Denaturation with Change in Solubility

texts:
I plan to run a lab which compares the impacts of ethanol and methanol, in varying concentrations, on the denaturation of whey protein.

Change in water solubility is a good indicator of the degree of denaturation in a protein, but online research doesn't seem to be showing any exceedingly simple method of quantifying a change in solubility. Can protein precipitation be used to measure solubility? If so, I have access to a centrifuge, ammonium sulfate and just about any other chemical compound. Are there any better methods, altogether?

Is change in solubility the only factor which may reflect denaturation?
Thank you


texts:
How much can you improve performance by selective breeding? I am curious of all kinds of performance, physical as well as cognitive, but I guess the latter is harder to answer so to make the question very concrete and measurable: how much have racing horses' and dogs' performance increased the last 100 years or so? They should be good examples of what happens over many generations of selective breeding aimed at improving one specific characteristic (running fast), no? And it should be easy to measure the progress: what was the world record on 1000 m (or something like that) for horses/dogs 1920 and what is it today?

Can these numbers be translated to humans?

Are the progress among horse/dog performance slowing down or increasing?

Any arguments for why/why not cognitive ability would progress in a similar fashion if selective breeding was used and aimed at that instead of physical ability?


texts: Butterfly identification: Dorset England, July.

texts: Can you please identify this butterfly. It was seen in Dorset England 9th July. I think it is a female Silver Studded Blue.


texts:
I'm trying to source a procedure for a transplanting tissue in regenerating polyps. Would anyone happen to know where I can find a method of adhering to donor to host tissue?

Thanks


texts: Why do humans alone have the capability to have religious/spiritual experiences?

texts:
What is it in our brain that makes having such experiences possible? I assume other species don't have these. Sure there are instances in the natural world where you can see individuals of the species gather around the dead one. Sometime even the alpha male in the group allows the kin/relatives of the dead individual to approach it (for whatever reason).

The kind of thing I don't see in the wild-life kingdom is an individual becoming "enlightened" or the likes.

Sure our cerebrum is highly developed and all. But "what" is it in our brain that makes it capable for humans to have such experiences?

I've read articles saying we have identified such regions in the brain. Just want to know what these structures are. Did such research establish that such structures also exist in other species too?


texts: Are there mainstream views on the mandrill's coloration's being so unique?

texts:
According to the Wikipedia article:

  Mandrills are noted as being exceptionally colourful for mammalian
  standards. Charles Darwin wrote in The Descent of Man that "no other
  member in the whole class of mammals is coloured in so extraordinary a
  manner as the adult male mandrill's".

So I know that in many species sexual dimorphism can act as a feature which is selected by sexual selection, I'm not surprised because there are other examples. But the male mandrill seems exceptional, especially according to what I've read, among mammals. Seems very curious to me, especially its face.

I was wondering if there are mainstream explanations for why the mandrill in particular should have such striking colours maybe more than any other mammals.


texts:
You need a solution containing 1000 buccal cells/mL. You count that you have 125 buccal cells in 50uL, from a total solution of 8 mL. How much of your stock solution should you take to make the 1000 cells/mL mixture? How much solvent if you would like a total volume of 5mL?

I don't even know how to approach this!!!
Help??


texts: How can you design a drug to modify apoptosis to treat a disease such as cancer? Im in highschool so can someone please explain in simple terms. Thankyou.


texts: What is the instructional language of DNA?

texts:
DNA carries most of the genetic instructions used in the development, functioning and reproduction of all known living organisms and many viruses (Wikipedia).

Is it already know how ATCG's sequences create theses instructions? Or equivalently, what is the instructional language of DNA? My interest in this question is to know if we already understand how ATCG's sequences can create, for example, human epidermis with an excess of a determined mineral or change cell's shape for more fundamental geometrical ones (triangles, rectangles, diamonds, etc.).

Please, forgive me for this foolish question: I'm not a biologist.


texts: If our DNA determines certain patterns within the human body such as hair color and eye color, if scientists were able to "turn off" such as the gene for eye color after the pattern was established, what would happen?


texts: What is the actual storage form of energy in muscles? ATP or Glycogen?

texts: I was asked this question in my latest exam. I think the answer is Glycogen because ATP doesn't store energy for a long time so it isn't the ACTUAL storage of energy. Some classmates argue that in muscles there are other substances, not only glycogen, that are used to produce ATP. In the process of contraction ATP is required so, they say, the question needs the answer to be ATP. Could someone please clarify this discrepancy?


texts: Why telomere shortening slowing down cancer?

texts:
I am reading Alternative Lengthening of Telomeres in Mammalian Cells, about how telomeres linked to human cancers.

  Due to the end-replication problem,5,6 the ends of linear chromosomes
  shorten with each round of DNA replication.7 In human somatic cells,
  the progressive telomere shortening that occurs with continued
  proliferation eventually results in the triggering of a replicative
  checkpoint. Telomere shortening and the structural changes that it
  presumably causes, leads to a DNA-damage checkpoint response at the
  telomere and induction of a permanent p53- and Rb-dependent growth
  arrest (i.e., replicative senescence).8-10 Because this limits the
  proliferative capacity of somatic cells, including those that have
  accumulated oncogenic mutations, telomere shortening and replicative
  senescence are a potent tumor suppressor mechanism.

The paragraph states a shorter telomere is a potential suppressor to cancers. Why is that? Why exactly a somatic cell proliferate slower with a shorter telomere DNA sequence?

Conversely, why a longer minority leads to human cancers?


texts:
What is the speed of replication of SC2? Any information, including in vitro data would be appreciated.
I would be interested to know the length of SC2 eclipse period, latent period and something like burst size.
Alternatively, per day CT values of qtPCR of COVID+ subjects would be also helpful.


texts:
I have seen corn described as a seed, a grain and a fruit.
What are the kernels or a corncob considered to be? A grain, a seed or a fruit?


texts: Is it possible to do chip-seq on a specfic region?

texts: Is it possible to do Chip-Seq on specific region of the genome. The idea is to enrich before the sequencing step to have more sensitivity.


texts: Is there a period after you have had a cold when you cannot get a cold again?

texts: I always assumed colds ran on a 'no tagbacks' principle: once it's out of your system, it takes a while before you can get a cold again. Is there any truth to this, or can rhinoviruses hit you at any time?


texts: What is the circulation that allows for nutrient absorption and excrete of metabolic wastes in humans?

texts:
Pulmonary veins carry oxygenated blood from lungs to heart, while pulmonary arteries carry deoxygenated/CO2 rich blood from heart to lungs. On the other hand, systemic arteries carry oxygen-rich blood from the heart to other parts of the body and likewise systemic veins carry CO2-rich blood from all the parts of body back to the heart and lungs. This makes sense to me, since oxygen and CO2 are used and generated in metabolic processes, respectively, and need to be transported to and from the lungs/systemic tissues continuously.

However, what I do not quite understand is what blood vessel carry absorbed nutrients from the intestine to other parts of body? Also, what blood vessels carry other metabolic wastes from the peripheral cells to the kidney for excretion?

Any reference/link to basic working of blood circulation would be helpful.


texts: How to find the amino acid in the DNA protein

texts:
3' A T A G T A C C G C A T G T A C G G G C G A G A C A T T C G A G C A T T C A T 5'

This a Template DNA.

How to find the number of amino acids amino acids in the protein encoded by the above gene?

The answer is $7$.

My Try:

First I converted the above DNA to RNA and got

   5' U A U C A U G G C G U A C A U G C C C G C U C U G U A A G C U C G U A A G U A 3'

Then I found the start codon which is A U G

5' U A U C |A U G| G C G U A C A U G C C C G C U C U G U A A G C U C G U A A G U A 3'

From here I am not understanding how to proceed.

Can anyone please explain how to solve this?


texts: Are the human placenta chorionic villi and villous tree the synonyms?

texts: Are the human placental chorionic villi and the villous tree the synonyms? Or, if not, can I say that these tissues would have practically the same gene expression profile in an RNA microarray experiment?


texts:
It seems like a lot of foot (anti-odor or antifungal) powders are often based off of cornstarch (i.e., as the primary filler).

But wouldn't cornstarch (which, in some places, is also a common food additive) just feed the undesired microorganisms anyway? Or, perhaps, is its dessicating effect so powerful so as to nullify whatever nutritional value it might provide anyway?


texts: Does the red blood cell in frogs undergo amitosis?

texts:
It is a notion particularly popular among Chinese high school Biology textbooks, that the red blood cells in frogs can undergo amitosis (not mitosis), a claim which I have not been able to find reference. A search on Pubmed led me to this article, which states:

  The nucleus of the frog erythrocyte is not a regular ellipsoid; ... a single nuclear invagination located at one end of the long axis is frequently seen in the phase microscope.

However I have also been unable to find more recent researches on the nature of this observation, and whether it is related to amitosis. Can you help me find some?


texts: Examples of species whose extinct common ancestor is well documented?

texts:
If we follow the ascendence line of two closely related species we can build a
"Theoretical" common ancestor, whose characteristics were inherited with few differences by the offspring.
         _______ species 1
Ancestor/
        \_______ species 2

Are there examples of extinct ancestors that we can be almost 100% sure they correspond to the ascendant of the two distinct species?
Are these examples well documented with fossils and the inherited traits well understood?


texts: Unwanted E. coli product in plasmid product

texts: Using a TOPO XL Cloning kit, our lab took some amplified human DNA, inserted it into the vector, and attempted to clone it in E. coli. However, upon sequencing the purified plasmid product, the sequence we got back was E. coli rather the human we had amplified. The primers sat down in the plasmid as intended, just the sequence between the primers appears to be from E. coli (as implied by BLASTing it against a human, getting no results, and then blasting it against E. coli and getting a hit).


texts: Identifying structures from anterior end of dissected prawn

texts:
Note: This image might be disturbing.

I want to know what the red and the black structures (directly posterior to the red structure) are. I guess it's the heart.


texts: Why is a nicotinamide-tryptophan combination used to treat affective episodes in a few older clinical trials?

texts: At least one of the journal articles that reported on such clinical trials allured to the nicotinamide-tryptophan pathway that I assume must be related to the metabolism of tryptophan into serotonin since at least one of these journal articles placed some emphasis on the serotonin hypothesis of depression.


texts: Black insect with antennas and large abdomen

texts:
I found this insect crawling outside near my house, and I have never seen anything quite like it!

It was found in the summer in Denmark.

Length is approx 4 cm (1.5 inc) with the antennae.

What species is this insect from and what is the insect called? Is it rare? What caused it to have such a large abdomen?


texts: Is it possible to cultivate cheek epithelial cells in a non-CO2 incubator?

texts: CO2 is important for maintaining constant pH in cell culture. Unfortunately, I do not have access to such incubator and buying a new one is expensive. I found a cheap incubator online, but it doesn't support CO2. I'd like to ask if I can cultivate cheek epithelial cells in such incubator and if it won't negatively affect my cell culture. Another option is building a small CO2 generator inside the incubator. I made some calculations - I know how much CO2 I need to generate, how many grams and mL of solutions I need, moreover the build-up pressure is so small, it should not negatively affect the incubator.


texts:
To me, the phenomenon of polymorphism in cnidarians is particularly troubling. I gather that it essentially refers to existence of various different forms or  kinds of individuals, i.e. zooids and polyps in one species. But when we refer to the cnidarian Physalia, as an animal, aren't we actually referring to a colony of individuals? Physalia consists of several "entities" including gastrozooids, dactylozooids, and the float, and since each of these is a distinct "organism", therefore is what we refer to by saying Physalia is actually a colony of phenotypically distinct forms of the same species?

Therefore, can "animals" like Physalia or Gorgonia or Pennatula be thought of actually as "colony-beings" which always contain several individuals in group?


texts: Antibody production in secondary immune response

texts:
Can IgG antibodies be produced in the secondary immune response without the help of T cells?

Is the affinity of antibody for antigens higher during secondary immune response?


texts: What is this very tiny (3mm) centipede-like insect?

texts:
My kid found this little guy in his bedroom. It’s about 2-3mm long. Lots of legs, and white rings around its abdomen.

Any idea what it is?

Edit: Location in San Jose, CA.


texts: How to convert skin temperature to core temperature?

texts:
As opposed to regular invasive thermometers, there are non-invasive IR thermometers to measure the temperature. For example Thermofocus.

I read in many sources that these IR thermometers only measure the temperature of the object's surface. However, Thermofocus seems to measure the patient's core temperature*.

My question is how to convert someone's skin temperature to their core temperature (Thermofocus does it so I understand that it's possible). I need to use an IR thermometer to measure a patient's skin temperature (say forehead) and predict their core temperature.

*core temperature: I hope this is the correct phrase... I mean the inner temperature as measured with a regular invasive thermometer.


texts: Why do Centipedes always have an odd number of pairs of legs?

texts: Furthermore, centipedes are within the Myriapoda, a subphylum of arthropods which also contains millipedes. Do millipedes also have an odd number pair of legs?


texts: How does the peptidoglycan layer of a bacterial cell wall help prevent osmotic lysis?

texts:
I recently read that penicillin works by damaging the peptidoglycan layers of a bacterial cell wall causing osmotic lysis, which is when the bacteria cell bursts due to osmotic pressure.

I just would like to know how peptidoglycan prevents this. Thanks for any responses!


texts: Can someone please help with this question? Here is my working (just in case it is not clear: 1/300*1/30*1/2) but is this actually correct or do I need to multiply by 0.5 once again? I appreciate any help!


texts: Why didn't a concept like "pointers" in Computer Science evolve in the genome?

texts:
I see that the genome contains large regions of repeating sequences called interspersed or dispersed elements. The long dispersed elements (LINES) such as LINE-1, can reach up to 6-8 kb in length.

I'm wondering, given the amount of repetition that takes place in these regions, wouldn't a system where a pointer (such as in computer programming) existed  be more efficient? For example, instead of including a LINE, include a unique 5 base pair sequence acting as a pointer to that LINE. A separate chromosome (containing one copy of each LINE) would then be read at the correct position once the pointer was read.

Do you think that given enough time in evolution, such a system would be more sustainable? Sort of like using a proper functional language instead of Assembler in computer programming, where f(x) can be defined once, and accessed via pointers, instead of being repeated many times?


texts: If you didn't have an utricule or saccule would you still know if you are accelerating and going up or down?

texts:
In the vestibular system the utricule and saccule makes you that you know whether you are going up or down (saccule) or backwards/forwards (urticule).

But imagine you don't have them anymore or they are damaged, would you still be able to know if you are accelerating or in an elevator? I thought it still would be possible because you would feel the pressure in you back when accelerating or on your feet when going up. But is it true that you still know what is going on by registrating the pressures in you body, or is it not possible any more? If it is still possible what would the surplus value of the urticule and saccule?


texts: Why does closing one eye in bright light allow me to open the other?

texts: I often find it physically painful to open my eyes past a squint after stepping out into the full summer sun. However, if I close one eye entirely, I can keep the other open without pain. This seems odd. Naively, one would assume the pain results from too much light entering the eye and doing some sort of damage to the interior, but if this were true, closing one eye would have no effect on the other. Does the fact that it does imply the discomfort is actually related to (e.g.) the sum-total of information reaching the optic chiasma?


texts: What makes a rotator cuff tear symptomatic in humans?

texts:
The majority of   rotator cuff tears  is asymptomatic {1}. What makes a rotator cuff tear symptomatic or asymptomatic in humans?

References:

{1} Minagawa, Hiroshi, Nobuyuki Yamamoto, Hidekazu Abe, Masashi Fukuda, Nobutoshi Seki, Kazuma Kikuchi, Hiroaki Kijima, and Eiji Itoi. "Prevalence of symptomatic and asymptomatic rotator cuff tears in the general population: from mass-screening in one village." Journal of orthopaedics 10, no. 1 (2013): 8-12. https://scholar.google.com/scholar?cluster=6848408356619886538&hl=en&as_sdt=0,22 ; https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3768248/

  In conclusion, our survey of 664 residents in one village demonstrated that the prevalence of rotator cuff tear was 22.1% in the general population, which increased with age. Asymptomatic tear was twice as common as symptomatic tear.

  […]

  In this study, “asymptomatic” was defined as having neither pain nor
  any other symptoms related to the shoulder when the survey was
  conducted including the past history of shoulder pain, whereas
  “symptomatic” was defined as having pain or any other symptoms related
  to the shoulder when the survey was conducted.

  Caption: Prevalence of symptomatic and asymptomatic tears.
  Asymptomatic tear accounted for 50% of all tears in the 50s. However,
  in the 60s and over, the percentage of asymptomatic tear was
  significantly greater than that of symptomatic tear.


texts: Is the birds' decision to fly away congenital or learned behaviour?

texts:
I see two possibilities how could the birds know what to do every fall:

The birds' migrations are driven entirely by the vertical memetics and today it is just a custom transferred from parents to offsprings.
There is a gene that causes birds to decide to fly to the warmer areas every fall, activated when it is appropriate time

Which of these hypothesis is closer to the truth?


texts:
I learned that, as the spike in a neuron occurs, the calcium-ion concentration increases due to opening of the voltage-gated calcium channels.
Due to location of these channels, I wonder whether the calcium concentration only increases at the tip of an axon, or throughout the cell.


texts: Why Do Ruminants Require A Multi-Compartment Stomach To Digest Food?

texts:
Cows, camels, sheep, goats, etc being ruminants must chew their food repeatedly by regurgitating their food from their first stomach compartment and chewing their 'cud'. This then finer chewed material makes its way to the various stomach compartments to be digested.

These animals are eating plant material, the same plant material animals such as elephants, horses and hippos eat as well. However, these animals only have one stomach compartment.

Why does one need a multi-compartment stomach and one does not if they are all eating the same/similar food?


texts:
Let's assume I am wearing a labcoat for two reasons:

Prevent the various bacteria, proteins, skin cells and substances on my clothes and my skin from contaminating my experiments.
Prevent various dangerous things from the experiment getting on me, and ruining my clothes or endangering my health (eg. toxic chemicals, pathogenic bacteria, ecotropic virus, etc)

A labcoat is an imperfect, but valuable barrier against such hazards. Perhaps a droplet of some Nasty Substance™ ends up flying towards my arm, but instead of getting on my exposed skin, hits my labcoat.

However, what happens when I take off my labcoat? My gloves, which have just been in contact with lots of Nasty Substance™, go through the sleeves of the coat, possibly smearing the substance all over the inside of the fabric. When I put on the coat again the next day, now my skin is in contact with these smears.

I could remove my gloves before taking off the labcoat, to avoid this smearing. But this time, I have to touch the labcoat with my bare hands as I remove it. Remember the Nasty Substance™ that was stopped when it splattered on the outside of the fabric instead of my skin? What if I know end up touching that?

I know that for truly dangerous conditions, there is specialized equipment and detailed procedure. Even at BSL2+, traditionally disposable labcoats are required, rendering the issue somewhat irrelevant. So let's assume the highest level below that, BSL2, as the context for answers.

In short, what is the correct way of putting on and taking off gloves and non-disposable labcoat when working in BSL2 conditions?


texts:
Mammalian cell/tissue cultures sometimes require flasks coated with proteins. My uneducated guess is that these proteins mimic the ECM, perhaps the basal lamina, so finicky contact-dependent cells can attach to it.

For instance, I have a BEAS-2B tracheal culture which requires a coating of albumin, fibronectin and type I collagen. This is applied by incubating an empty plastic dish or flask with a solution of these proteins overnight. I give this as an example of what a "coat" constitutes. You answer should be general enough to apply to at least the most common coat types, or if it depends on the coat, you should explain how.

Likewise, there is some variation in how the trypsinization occurs. To have a starting point, let's say I am trypsinizing according to typical ATCC recommendations: 5 minutes with 0.25% Trypsin-0.53 mM EDTA, then inactivate with equal volume medium. I haven't worked with a cell that can withstand this noticeably (but then I haven't worked with any exotic cells).

My question: When I trypsinize the cells to passage, what happens to the coat?

Since trypsin is a protease that cleaves even the attachment of cells to plastic, I am guessing that it will also destroy the coat. After the trypsin and cells are removed, the flask will have a tiny fraction of the protein coat that it had before, and will not support cells that require a coat any longer.

Am I correct in thus deducing that coated flasks cannot be reused after trypsinization? Are any of the alternative detachment reagents an exception to this?


texts: Is this flying bug swarm termites? Found in New York city, approx 7mm

texts:
Just saw a giant swarm of these fly out in between pavers and a door sill from a small crack in the ground here in New York City.  There seemed to be hundreds of them swarming out very quickly.  They are about ant-sized.  Are they termites?
Here are photos:


texts: Why do chickens continuously lay unfertilized eggs?

texts:
As per subject: why do chickens continuously lay eggs even if they are not fertilized?

Is this sort of behaviour found in other species of birds (or other egg-laying animals), or only in chickens? Is it natural, or domestic chickens have been specifically bred for it?

If it's natural, what kind of sense does it make to divert energies and nutrients to continuous lay unfertilized eggs which have no purpose other than being possibly eaten by someone else? How could such a wasteful reproductive behaviour have evolved? Even if it has been specifically selected for in breeding, it still seems to make very little sense in the first place.


texts: I have a set of microRNA ages with corresponding labels suggesting which clade they first emerged from. For instance, for hsa-mir-1, let's say, it would have an age of Eutheria. I have several peaks in the distributions of my age. One idea I had was to check to see if these peaks correspond to periods of intense specialization. For instance, the Eutheria clade saw a vast diversification of species relative to other clades. I'd like to determine this from a more computational perspective rather than Googling each clade.


texts: Can anyone tell what kind of berry/currant this is?

texts: I found this currant-like plant in Helsinki, Finland. It seems very similar to red currant but it has hairs on its fruits, and the fruits are pear-shaped. Can anyone please identify this plant? Many thanks!


texts: Can Galactose be synthesized with photosynthesis?

texts: I know that galactose can be found in sugar beets and some gums so I thought plants could synthesize galactose but in my book the answer to the question "Which of these can be synthesized with photosynthesis in plants" was only fructose and glucose. Is that correct?


texts: Was the Okazaki fragment experiment ever replicated?

texts:
Prof said that the experiment "proving" the existence of Okazaki fragments was never replicated.

Is this true? I tried looking on Google Scholar and I cannot find any experiments talking specifically about the existence of such fragments. Wikipedia also doesn't list any other researchers "finding" Okazaki fragments.


texts: Can one use dialysis tubing several times?

texts: I would like to know, if one can use dialysis tubes multiple times. Or is there a risk of plugging the pores? I use the tubes for dialysis of a solution that contains a precipitated enzyme (183 kDa) and ammonium sulfate (132 Da). Thanks!


texts: How is propagation of action potentials terminated once the "message" has been sent/received?

texts:
I'm thinking about neurons in the brain that are used for "thinking". As I read about action potentials, I see that an Axon is connected to a Dendrite of a neighboring cell and that there are neurotransmitters involved in the signal propagation from cell to cell.

I'm interested in learning how action potential propagation gets terminated. Let's say a message from the brain region A to brain region B has been delivered through action potentials.

How does the region B know not to "route" the action potential further down the chain of neurons?
How does the region A know that the message has been sent, to stop sending more messages?


texts: Does X-inactivation lead to expression of sex-linked recessive disorders in half of carrier females' cells?

texts: If one of the two X chromosomes in female mammals is randomly inactivated (i.e. becomes a Barr body) in each cell, shouldn't half of all cells in a female who is a carrier for an X-linked recessive disorder (say, Duchenne muscular dystrophy) express the disorder?


texts: What animal makes these spherical sand clusters?

texts:
I encountered these structures on a beach in Hong Kong (the Ham Tin Wan beach in Sai Kung country park). There were many of these structures and I have photographed two of them in detail and attached a larger image which shows the extent to which these were spread on the beach.

It seems these were made by an animal of some sort. All these sand deposits were organised around a single hole in the ground which presumably is the animal's home or hide out. And all such structures had a clear "walking" path which was almost a straight line. These paths had no sand deposits in them.

Am I right in assuming that these structures were made by an animal? If so, then which animal makes them? And what is the purpose of the round(ish) deposits of sand around the main hole? Are they an obstacle for predators?

Image 1: A structure in detail

Image 2: Another structure in detail

Image 3: Overview of structures


texts: Is the SHC014 chimeric coronavirus "eerily similar" to Covid-19 in anything but a journalistic sense?

texts:
Gulf News writes:

In the virology community, their project is known as "chimeric coronavirus", eerily similar to COVID-19. This chimera is created in a petridish, reportedly with the "surface spike protein (S protein) of a coronavirus found in horseshoe bats, called SHC014, and the backbone of a SARS virus that could be grown in mice".
Here's the scary bit: In the lab (we don't know which one), this new coronavirus was found so potent it could infect and replicate in human airway cells naturally. It also infected mice lung cells. It's one of the experiments which prompted Prof Simon Wain-Hobson, a virologist at the Pasteur Institute in Paris, to warn that such research is "misleading" and "irrational", stating thus: “The consequence of any accident would be anywhere from a handful of infections to a catastrophic pandemic.”

Is this SHC014 chimeric coronavirus "eerily similar to COVID-19" in a scientific (not just journalistic) sense? Have any scientific publications drawn a parallel between the two viruses?
(I know that SARS-CoV-2 is most closely similar to RaTG13 at whole genome level and at RBD level [most likely] to Pangolin-CoV. I'm asking what if any scientific relevance does SHC014 have to Covid-19.)


texts: I'm trying to identify a tree i saw in Taormina, Sicily, Italy. Can anyone help?

texts: What is the identity of this tree? These pictures were taken in Taormina, Sicily.


texts:
While reading a 19th century text of new species description, I'm confused by some Latin phrases.

The case here is:

  Corp. long. 8 poll., caud. 9 poll.

I guess 'corp.' and 'long.' are abbreviations of some Latin terms, and the whole meaning of the combination of these two words is probably "body length". But I still can't figure out what "caud." and "poll." (the number seems like is in inch though) are stand for.

The species described is a rodent species. Full text could be found here (p.185).


texts: In a documentary on fitness I saw it was stated that women can't get big like men because of their low concentration of testosterone. If it is true that women have testosterone, where is it made? Why do some women, especially later in life, develop facial hair (though obviously not as much as men)? Do men also have "female" hormones in their body?


texts: Are we "more evolved" than present-day bacteria?

texts: The common ancestor of humans and modern bacteria was most likely a prehistoric bacterium. Does this mean that humans are "more evolved" than today's bacteria?


texts: At What Rate Do Ions Leak Out of a Plasma Membrane Segment That Has No Ion Channels?

texts:
In reading about the purpose of myelin during action potential propagation, I came across a point of confusion.

From what I understand, one of the primary "benefits" of myelin is that it aids in increasing the transverse resistance of an axon...which, biologically, is equivalent to stating that it minimizes the extent to which ions move out of or into the cytoplasm of the axon.

However, I feel as though I have always been taught that "the plasma membrane is impermeable to charged particles" and am therefore confused as to what additional benefit is conferred on the axon by the myelin.

Consider the following two cases:

Case A) The action potential starts at the axon initial segment. The subsequent segment is myelinated. The action potential, through passive diffusion, makes its way down the myelinated section until it reaches the 1st node of ranvier, where the action potential is subsequently regenerated.

Case B) The action potential starts at the axon initial segment. The subsequent segment is unmyelinated but contains no ion channels (or pumps). The action potential, through passive diffusion, makes its way down this unmyelinated section that has no ion channels (the same distance as in Case A) until it reaches a dense collection of voltage gated sodium channels.

In case B, will the action potential be regenerated? Or has the passive diffusion event suffered from too much "leakage"? If so, is it really true that:

(the plasma membrane + myelin) transverse resistance >> (the plasma membrane) transverse resistance alone


texts: Can we achieve complete photosynthesis on a petri dish? Barriers and potential

texts:
If we were to place bacteriorhodopsin and ATP synthase in an acidified solution (for H+ ions) filled with phospholipids, ADP and inorganic phosphate, hopefully the bacteriorhodopsin and ATP synthase will be embedded in the same micelle. Then when exposed to sunlight, the bacteriorhodopsin will start to operate, creating an electrochemical gradient which will power the ATP synthase, synthesising ATP.
Can we create achieve complete photosynthesis on a petri dish? What are the technological barriers against such an invention? Even if such a small working model were to exist, why can't it be scaled up?

What if we could add in the Kelvin cycle and other photosystems to create a fully functional 'chloroplast'? It seems biotech researchers have been trying this since the 1960s, however, why have scientists not been able to create a fully functioning photosynthetic organ *now*?

(see edits)

Several motivations for this:

Does away the need of sugar cane farms and provide us with the most efficient
means of harvesting sugar, literally we do not have to produce a lot
of waste when processing tons of sugar cane just to obtain a little sugar, while the rest (cellulose) mostly goes to waste.
Production of biofuels since the sugars produced is the precursor of lipids, in response to climate risks

Remark: I am not looking for a synthetic system that operates by inorganic means but a system that consists of enzymes and membranous structures, very much like that in plants.

Edit:
As per the comments listed below, here are some fixes, specifically the illuminating comment by @David. I must apologise for the inaccuracies of the original question.
https://www.jstor.org/stable/57795?seq=1
Biochemists did not strive to recreate the whole system from scratch (by making a handful, if not hundreds of protein embed on a phospholipid membrane as implied by my original question), but tried to achieve complete photosynthesis of isolated chloroplasts, which is similar enough to the question proposed if not identical.
https://www.jbc.org/content/235/3/832.full.pdf
According to the paper above, there are some techniques that use chloroplasts extracts, which contain many key components of the photosynthetic cycle, and also a better chloroplast isolation method which tries to preserves the enzymes needed. It alleges that carbon assimilation occurs, even though the end product is 3-phosphoglycerate after carboxylation.
I will further update this question after I read more, but as of the time being, these immediate fixes are done to fix some damning issues as raised.


texts: What do we mean by MHC molecule diversity? Does each human have a variety of MHC molecule isoforms?

texts:
I'm going to try and explain what I think I know

From what I understand, MHC/HLA molecules present peptides to T cells. To be able to present peptides from a wide variety of pathogens, they need to have diversity in their peptide binding domains.
My lecture handout tell me that MHC diversity comes due to polygeny and polymorphism.
Polygeny refers to there being 3/6 (handout says 3, textbook says 6) MHC class I loci leading to 3/6 class I isotypes, and 3/5 MHC class II loci leading to 3/5 class II isotypes.
Polymorphism refers to multiple alleles of each gene, meaning a variety of allotypes produced from each gene.
These processes lead to the generation of a wide variety of isoforms of MHC proteins in the human population.
The textbook also states that there is no rearrangement or structural change of the genes encoding the MHC proteins.

So I get that in the population, there is huge diversity of MHC molecules. But in each human, since there is no rearrangement of genes as in the case of antibodies to generate antibody diversity, is there therefore only one type of MHC protein being encoded? So by MHC diversity, we are not referring to diversity in each human, rather in the entire population? And if so, how do our MHC molecules become capable of binding to any antigen from any pathogen?

Please could someone clarify for me if I've misunderstood something, and also if my above explanation is factually correct, with the appropriate use of terminology?


texts: What would happen if you combined the world's deadliest diseases & viruses?

texts: What would happen if you took the deadliest diseases/viruses in the world and combined them in a single medium (a solution of water or a test subject)? Would the strongest virus defeat the rest or would a  new deadly virus be created?


texts:
I found this little jumpy cocoon thingie clinking approximately once every 4-5 seconds inside a metal lid. It's been jumping inside there for about a day since I first found it like that. It has a tiny flat mark on one of its sides which suggests that's how it initially stuck itself to something, and then got unstuck. What is this thing?

Here's a short web vid of it: https://giant.gfycat.com/IcyHarmfulCentipede.webm

And here's a static pic:

Update:

It stopped jumping around after about 1.5 days since I found it, and we decided to carefully cut it open with a paper knife. Inside was a white grub with a tiny orange dot on one of its ends, all foldy like a bendy part of a cocktail straw. It was still at first, but we sprayed it with water and put it on a leaf. It started moving around slowly, and looked like it was soaking up water. When we checked up on it later, it had disappeared and probably crawled away somewhere. Unfortunately, I didn't take any pictures of that, so it could have been anything.


texts: How to estimate oxygen consumption of an average human during different activities?

texts:
I've tried to find some resource on the internet but had little luck. I'm looking to see if there's any data on average oxygen consumption of average to well trained humans during different activities.
Specifically how much more oxygen does a human consume when panicked/under pressure in comparison to other activities such as cooking, climbing etc. Even better would be if I had a formula where I could plug in weight, height, gender and receive a percentage of how much more O2 is consumed under stress/panic vs. normal functioning. Any information would be much appreciated, please include sources where possible.
NOTE: With "panicked" I mean in the state of fearing for ones safety and being in a life threatening situation with the associated hyperventilation etc.


texts: Significance of the resequencing of the chimpanzee genome

texts:
Introductory remark: I am not a biologist, but a somewhat knowledgeable layperson.

I have been told that sequencing of chimpanzee DNA until recently has been done almost exclusively using human DNA as a “template” to help piece together short DNA sequences. The similarity that emerges to human DNA could then perhaps be somewhat misleading, as the structure of human DNA affects the end result obtained for chimpanzees.

However, recently (2018) a new study was performed in which the assembled DNA fragments from various apes were assembled completely separately from human DNA, giving a better estimate of the similarities and differences between the DNA of humans, chimpanzees and other apes (Kronenberg et al. Science vol 360 issue 6393, eaar6343).

What new information has emerged and to what extent does it alter previous results?


texts:
According to Wikipedia...

  About 55% of blood is blood plasma, a fluid that is the blood's liquid
  medium, which by itself is straw-yellow in color. The blood plasma
  volume totals of 2.7–3.0 liters (2.8–3.2 quarts) in an average human.
  It is essentially an aqueous solution containing 92% water, 8% blood
  plasma proteins, and trace amounts of other materials.

Does this mean it would be possible to boil water from blood for consumption? For example, in The Walking Dead, Rick and the gang are dehydrated and without water. When a pack of wild dogs confronts them, they kill them and cook them for consumption. Could they have collected the blood, boiled it, and used some sort of contraption to catch the clean, vaporized water?


texts: Can threat to survival increase mutation rates in germline cells?

texts:
Can stress that is related to a threat of survival of a population of animals or plants in some environment, like due to hunger, thirst, fear from predators, etc..; results in an increase in average mutation rate in germline cells of individuals of that population, thereby increasing the likelihood of producing heritable trait(s) that might be beneficial to that population in combating those adverse survival conditions in that environment?

In bacteria this is known as "Stress Induced Mutagensis"

Is there something comparable to that in animals and plants?


texts: Why does the heart use lipids (and not glucose)?

texts: Fetal hearts use glucose as their primary metabolic substrate.  Adult hearts use free fatty acids, which are less efficient (require more $O_2$ to synthesize the same amount of ATP); however, during cardiac failure, the heart can switch to glucose utilization.  Why doesn't it just use glucose all the time?


texts:
People who lack the sense of hearing, vision and speaking are called Deaf, Blind and Mute.
But what is the person called if he/she lacks the sense of smell? Is there any case like that?


texts: Does evolution select against genetic diversity?

texts: Only the best genotype in a species will win. So it sounds like evolution selects against genetic diversity.


texts: Can birds raise younglings that are not their own?

texts:
For example, if a scientist were to move a chickadee or pigeon egg from one nest to another, would the new bird (second mother) in the new nest incubate or raise the youngling? Or would the new mother reject the egg since it lacks its imprints (like scent for example)?

In other words, can birds differentiate between their offspring and foreign offspring?


texts: Does the human ear adapt to noise levels?

texts:
I have noticed lately that if I go to sleep, when I have my radio running, it is on lowest volume, I still consider it kind of loud.
In the morning, when being on the edge of waking up, I hear the birds, and the tennis balls already being batted on the court nearby, but I do not hear my radio. If I wait a few more minutes, I start to hear the radio, with no changes in the sound levels outside.

I know that the human eye adapts to the light levels (aperture, what cells used), but is there something similar for sound sensitivity?
Note, the radio is on that occasion running all night long, with always the same sound level.


texts: Is hydroxyproline an amino acid? (Classification question)

texts:
So I know that hydroxyproline is created from proline via hydroxylation as a post-translational modification. I also know that proline is considered an amino acid. However, once you hydroxylize it, you have made a covalent modification to the original amino acid. Can hydroxyproline be correctly considered an amino acid? Or is it simply an amino acid derivative and NOT an amino acid?

Or, a more general question - how much can you change an amino acid and still call it an amino acid?


texts: In the lysogenic cycle, does the provirus split from the cell's main genetic material for replication?

texts:
In a diagram of the lysogenic cycle sent by my instructor in a video, it shows the provirus splitting from the cell's main DNA when the dormancy period ends and the viral DNA is "activated". Is this how it happens, or was he just trying to illustrate the activation?

I guess a better way of phrasing this would be, is the viral DNA replicated as part of the cell's normal DNA, or is it replicated separately?

Thanks!

evamvid


texts: Is lumen space of a thylakoid completely separate from the intermembrane chloroplast space?

texts: The question I have is whether thylakoids form actually completely independent "vacuoles" (i.e. independent membrane enclosed spaces) or whether the lumen space is connected to the intermembrane space of the chloroplast. I have this question because electron photographs that show slices can be sometimes misleading and connected structures may appear to look independent on photographs of slices.


texts: Do different emotions produce different tears?

texts: Do tears of joy, laugh, grieve, and others contain different things or are they all the same?


texts: Is there any possibility of interspecies sexual reproduction in animals like hybridizing plants?

texts: Inter-species sexuals are happening naturally. My questions is, whether it may lead a creation of new species? This question arises, because of the appearance of Pillayar in hinduism. Please clarify, whether it is possible to create a new species with the appearance of "Vinayagar" that is human body with elephant face.


texts: i have a fasta file of yeast orfs (from the SGD database) and i need to find out(predicted) secondary structure/classification for all of them (so ~6K queries and doing this by hand on numerous available websites is not an option). is CATH database a place that can give me this info? (so far i struggle to recover anything that can help me from the website but perhaps i am missing something), if not what's the best way/software to go about it? surely, these predictions have been done before and there is a databse somewhere -- yeast is too much of an important organism, with a lot of information about its genome.


texts: Displaying nucleotide at a single position from RNA-seq reads in a BAM file

texts:
How do I display a single nucleotide position from reads in a BAM file? I have been looking at variation using samtools mpileup, but I want to actually just display the nucleotide at the position I am interested in. This seems like you should be able to do it but I can't figure out how.

To be clear I have a BAM file of a bunch of reads. I'm looking to do something like samtools magic reads.bam chr3:10000 where I get back something like:

T T T T T T T T T T T T T T T T T T T A A A A A A A A A A A A A.

I just want to sanity check the output of bcftools by actually looking at the base calls.


texts:
I live in Michigan.  I just saw a bee that I think I've seen before, but only this time was I so struck by its uniqueness and - for lack of a better word - scariness.

I'll describe it.  It was maybe an inch and a half long.  Maybe bigger, maybe smaller (I'll admit that I was hurrying to get away from it).  It looked like a queen bee, but longer and slightly thinner.  However it had wings that were very profoundly orangish-red.  Like burnt orange maybe.

I haven't been able to find any matching pictures online.  It is theoretically possible that it was covered in pollen, and I am incorrect about what I think I saw, but assuming it wasn't (as I do believe this isn't the first time I've seen this guy or one of his friends), does anyone have any clues as to what this could be?

EDIT:  PHOTOS

After considerable patience. I was able to capture some photos of this guy.  One of these photos is post-processed a little to emphasize the color.

A couple things about these photos.

They were extremely difficult to take because the bee never stops moving.  I don't know if this behavior is useful for identification, but he is always in the same place (in front of one house), and he flys back and forth between a small crack in the sidewalk (a nest?), and between 5 and 10 feet away.  He moves like a dragonfly (that's the best way I can think to describe it), and he doesn't stop - he'll seem like he is going to land, and then flies off.  This morning was an exception.
These photos do not fully capture the depth and vividness of the redness of his wings, nor do they adequately convey just how large he is.


texts: Can we really 'discover' 85% of mammalian viruses?

texts:
This virology [blog] discusses estimates of the number of mammalian viruses and the costs of 'discovering' 85% of them.

My question is whether this is not a forlorn hope. The ".632 rule" in statistics says roughly that as we approach n random samples from a large population of size n we will see only about 62.3 per cent of the population. After a point we would begin to see the same viruses again and again. This argument is probably stronger with respect to marine viruses, as they may be even more numerous and sampling at depths could be difficult.

I wonder if someone with experience sampling small organisms from large populations or familiarity with the literature has an idea about the plausibility of seeing 85% of a large population, such as mammalian viruses, by sampling?

If the samples are really random (in some sense) and the population is large, a few computer simulations reveal the power of this rule of thumb.

Edit in response to comment/question:

Like any such estimate, the blog's estimate of 3.6 million is a guess. I am not reproducing the calculation here because it's just speculation.

Having said that, if 3.6 million were correct, we would have to draw about 6.8 million samples to find 85% of the existing viruses, 8.2 million to find 90%, and so on. As the blog notes, the PCR approach detects viruses similar to those we know, so the sampling is worse than random. If we look at the difficulty of finding/using a method that has a reasonable chance of capturing any of the extant viruses, the number 3.6 million looks very big.


texts: Are serotonin levels in humans affected by light?

texts:
I'm reading this Wikipedia article on light therapy  and noticed a peculiar statement:

  The production of the hormone melatonin, a sleep regulator, is
  inhibited by light and permitted by darkness as registered by
  photosensitive ganglion cells in the retina. To some degree, the
  reverse is true for serotonin, which has been linked to mood
  disorders.

If I read this correctly, when melatonin is suppressed, serotonin is released? This makes some sense. I'm interested if there is any scientific backing to serotonin being affected by light levels.


texts: What is the formula to calculate $R_0$ (basic reproduction number)?

texts:
What is the mathematical formula for $R_0$ and what does each variable represent?

I have tried searching this to no avail.


texts: What if cellular growth and repair is 'forced' to occur repeatedly in a region where it wouldn't normally happen , if the biological area was 'healthier'. Could this more aggressive cellular growth and repair cause any apoptosis mechanisms to shut down permanently?


texts: Can endometriosis be considered a form of cancer?

texts:
In endometriosis the lesions form their own vasculature and compromise organs, arteries, and nerves. It can spread and embed throughout the body. It's difficult to treat as the adhesions resulting from repeated surgeries can cause the same symptoms as the lesions. Treatment often leaves patients with the original level of disability after the 2 year mark.

My question is, for these reasons could one treat and research endometriosis as if it were a form of cancer?

Could the immune system be utilized in treatment as the lesions induce high levels of certain cytokines?

Why or why not?


texts:
Could somebody explain in simplest terms the difference between inverse agonist and neutral antagonist?

Which one is more well natural and less likely to cause pathways to rebound?

Does neutral mean less effect such that stepping from an inverse agonist to neutral is the best idea to avoid withdrawal?

Edit: I am trying to determine how quickly the pathways rebound when stopped during withdrawal.  I would assume this might vary between inverse agonist and neutral antagonist.  I am not asking about actual withdrawal symptoms.


texts: Describing the location of the thalamic adhesion in simple English

texts:
I'm trying to describe the location of the thalamic adhesion as part of a personal project. I can't reference pictures, and I need to be as precise as possible without using convenient anatomical terms (e.g., dorsal, superior, etc.).
I have to use plain and simple English, with a consideration for people who speak English as a second language. My approach is to describe its location relative to more prominent and easily recognized body parts (e.g., bones and organs on the face or side of the head).
In every English construction I've tried, I first start by describing it as being located in the middle of the head. Then I describe its location in reference to common body parts on the transverse and coronal planes.
Most X-ray pictures I've found are only somewhat helpful to me here, because they're a sagittal cutaway of the head but they don't include the ear. Based on the X-rays, I'm confident that it's located at about the same level as the eyebrow ridge on the transverse plane.
The big problem I keep running into here, is that almost every drawing and rendering I find on the internet seems to put the thalamus in different locations on the coronal plane. This makes it pretty hard for me to find a precise coronal location for the thalamic adhesion.
In some of them it seems to be where the tragus of the ear meets the mandible. Some of them draw it further forward, more towards the mandible. In other illustrations it's drawn further back, almost directly above the helix of the ear.
I'm not a physician and I can't remember how many years ago it was that I took an anatomy and physiology class. So my question is, where is the thalamic adhesion actually located in the human body on the coronal plane? Is it in line with the tragus, or the ear canal, or some part of the mandible, or does it vary from person to person?

Here are two possible translations of the above into simple English constructions:

The "thalamic adhesion" is in the middle of the head, as high as the eyebrow ridge, and as far back as the ear canal
The "thalamic adhesion" is in the middle of the head, as high as the eyebrow ridge, and as far back as the temple

Secondary question: could anyone with a more expert knowledge of human anatomy suggest better constructions?


texts: What is meant by "genes involved in the stress response"?

texts: I would like to know about the term stress response. For example "some genes of a species under study is involved in stress response". What does that mean? I got this as a part of my assignment question.


texts:
I am actually a computational biologist, pardon me if my question description is a bit off-note, my curiosity is driving me on

A bit of background and context:
In bacteria, a regulatory protein termed CsrA binds certain structures in the UTR regions of genes and prevents their translation. These structures are short hairpin-like and all have AGGA nucleotides in the exposed part. There are sRNAs that isolate the protein from its targets, a common feature of these sRNAs is that they have several repetitive hairpins that more or less display AGGA nucleotides in the exposed part. So basically, the sRNAs mimic the structures on the targets of the proteins and that makes them potent competitors for protein binding against the genes actually targeted by the protein. By relying on this mimickry the sRNAs bind CsrA, isolate it from its targets and remove its suppression on gene translation.

My question: Are there any other examples that illustrate similar mechanisms of analogy/mimickry of sRNAs to bind protein?

What I tried
I've skimmed through a lot of literature to identify other similar systems in bacteria where sRNAs have conserved repetitive structures but to no avail. I hope someone with deeper experience directs me to such examples in any living organism, preferably bacteria but I am open to suggestion.
I found CRISPRs but these are  DNA based, I have come across few other cis-acting sRNAs which target mRNAs and aren't protein-binding. So could it be the case that sRNA mimickers aren't very pervasive in bacteria after all ?!


texts: Determine the chances of blood group type and rhesus factor of unknown parent?

texts:
First of all, I'm not a biologist so my jargon might not exactly be common on this site. I'm a programmer and as a hobby project I try to make an algorithm that does two things:

Determine the possible blood group and rhesus factor of a child based on the blood groups and rhesus factors of both parents.
Determine the possible blood group and rhesus factor of an "unknown parent" based on the blood group and rhesus factors of the child and the known parent.

I found two great examples online, the "Child Blood Type Calculator" and the "Parent Blood Type Calculator" calculator on endmemo.com.

The first calculator shows some percentages of the chances. But the second calculator does only show a static answer when it comes to the blood group type and rhesus factor. According to the calculator that indicates that the rhesus factor of the "unknown parent" can only be negative when both the child and the known parent have a negative rhesus factor too.

In case the known parent and child have both RH+ the calculator shows that the unknown parent must have had RH+ as well. But isn't the statistical chance  6.25% that the unknown parent still have had RH- instead?

Secondly, how can I calculate the likelihood/chance that the unknown parent has a certain rhesus factor or blood group type? Now the calculator shows 'A/B/O' and 'RH+' when the child has 'O+' and the known parent has 'O+' but what are the chances the unknown parent has A, B or O or RH- anyway?

Side-note: I'm not related to endmemo.com.


texts: What is the role of a chemotroph in an ecosystem?

texts:
Chemotrophs are bacteria that synthesize ATP based on favorable REDOX reactions. This solves the problem as to how they can survive. But what exactly is their function in an ecosystem? For example, can they provide nutrients for algae?
I want to know if we can cultivate chemotrophic bacteria to provide nutrients for plants. This way, we could grow them in a place like Mars where the soil is made of a lot of inorganic material. I was especially interested in algae because some species can provide a lot of nutrients humans need.


texts:
I found them under reefs in Fiji. The hand-like structures moved slowly. I was not sure if it was an animal or plant. I was not even sure if they were several individuals or it was a whole.
The part that was not hidden by the stone was about 50cm length. I did not touch them, since I was not sure if it was dangerous.


texts: How can a brainless Cnidarian hunt and defend itself?

texts:
Cnidaria, such as jelly fish and sea anemones are radial symmetric en feature a simple body plan. One notable aspect is the lack of a brain. Hence, there is no central guiding structure, no mind or will if you like. Nonetheless, they are known to be predatory (such as the sea anemones), and are quite effective in defending themselves as well (such as stinging jelly fish). How does a diffuse nervous system allow Cnidaria to feed and defend themselves?

Sea anemone devouring a crab:


texts:
Chromosome 1 is the designation for the largest human chromosome. Humans have two copies of chromosome 1, as they do with all of the autosomes, which are the non-sex chromosomes. Chromosome 1 spans about 249 million nucleotide base pairs, which are the basic units of information for DNA. It represents about 8% of the total DNA in human cells.

Why is Chromosome 1 called Chromosome 1? Is being the largest human chromosome the only reason?


texts: What is the biological basis for tiredness after eating?

texts:
I can sometimes feel quite drowsy after some "meals" (e.g. a cold cut & cheese sandwich with juice on the side) and less drowsy (or maybe less often) after others (such as a salad).

This drowsiness sometimes affects my work at the office, so I wanted to ask these questions:

What biological factors lead to the body getting tired after eating?
Are there any strategies that can be used to minimize this effect?


texts: TCGA data, and bioinformatics design questions for SNP/ mirna analysis

texts:
It's my first time posting to this forum but was looking for some help on the data aspects of this project.

My tools of choice would be in python/R .

Goal: I'm looking to create a disease specific profile of just SNPs and SNPs in miRNAs and miRNA target sites.

PART 1: TCGA
My first step is using TCGA data which lists a ton of harmful mutations in a LOH .txt format. I'd like to be able to map those mutations to SNPs or genes or miRNAs  (whatever entities they belong to). The TCGA datasheet is here.
Example data is here. for breast cancer. I guess I can use this miRNA and mRNA data as well.

Questions here:

How to decipher the LOH data to figure out if it's meaningful and where it maps?
Which Tools to use for mapping and what formats for final data ? Fasta ?

miRNA/Targets and SNPs
Next up is getting cancer specific miRNAs and mRNAs and mapping SNPs to them?
I'm assuming using dbSNP or Sanger miRNA databases to get miRNA/targets and seed sequences.

I'm a bit lost as how to combine all these pieces of information, what formats to use for output (linked to individual pieces) and which tools if any to use to gather all this data using python. This tool is useful tool mirdsnp.


texts: What are the benefits of elucidating the crystal structure of a protein?

texts:
I have spent months as a student working on trying to form a tricky protein crystal. But I have never actually had explained to me why the structure will be useful. Once elucidated, what can we potentially learn from the structure in terms of biological significance?

Are there examples of drugs, or treatments that have only been made possible because of a known crystal structure?

Generally speaking, why do people spend all the money on synchrotrons, laboratories, robots and so on, for a crystal structure?


texts: How do S and L cone cells sense colors like deep blue and red beyond their peak?

texts:
So I found this diagram of retinal cone cells:

It looks like the S, M, and L cones peak at blue, chartreuse and orange, respectively. If so, how do we see colors past 575 nm and before 445 nm? If the cones really respond to purple, green, and red, (as I previously thought) why do they peak at colors closer to green, as shown in the image?


texts: What causes humans to be physically weak compared to animals like gorillas?

texts:
Animals like gorillas seem to have a physical fitness and muscle mass that don't depend as strongly on how much exercise they get, compared to humans. E.g. gorillas living in the wild sleep and rest a lot. While they do get quite a bit of exercise (a lot more than the average human), they are not going to exert themselves much more than is necessary. So, they push themselves a lot less than people who exercise very hard. Yet the average gorilla would easily outperform even a well trained human being in bodyweight exercises.

So, there seems to be something fundamentally different about maintaining physical fitness in humans compared to gorillas.


texts:
What is the distribution/probability density function (PDF) of impacts on fitness of new mutations?

I very welcome any partial answer that does not give the whole PDF but just some information about the expected value or the variance of this distribution. Information of the kind: "If we consider only beneficial mutations, then the PDF is $P(X=x) = f(x)$" are also welcome.

When I say mutations, one might have want to reduce the concept of mutations only to indels and point mutations.

Of course the answer will depend on the species under consideration and from population to population but I welcome any answer that could give some insights. Eventually, some information according to what is generally assumed to be the PDF of effects on fitness of new mutations might be useful.

Here is a related question

Here is an article that assumes an exponential distribution of effects on fitness of beneficial mutations.


texts: what is the meaning of the genotype values in each snp

texts:
I understand that snp is a single base variation. For example, if person 1 has the sequence in DNA , AAGCCTA the second has AAGCTTA, then the allels are
C,T.

My question is what is the meaning of 0,1,2 genotypes under each snp id (rs#) , and how it is related to the snp ?


texts: Genetic analysis of one sibling relevant to other

texts:
My sister, my only sibling and I have literally no physical traits in common. Whatever trait I inherited from one parent she inherited from the other. We're thinking of using one of those genome analysis services to learn information about our mysterious geographical ancestral origins.

We're wondering if, despite our differences in appearance, if only one of us submitted our genome for analysis, the geographic origin results would still be accurate for the other. Because our parents may both have diverse lineages, the answer might not be so cut and dried.

Understand, please, that we are not so much looking to find out the general "where" of our origins as we are to have each of us know what our individual genetic heritage is.


texts: Can anybody identify this flower for me?

texts: One single flower on small 2 year old tree with alternate leaf arrangement


texts:
I see many products, particularly hand soap and cleaning products, that claim to kill 99.9% or more of bacteria.

This makes me wonder, if the chemicals are potent enough to break down bacterial cell membranes, can they also break down human cells? If not, why not?


texts: Finding steady state concentration given half life and production rate

texts:
Intracellular molecule B is normally synthesized at a constant rate of 1000 molecules/second. The lifetime B = 200 s.

How do I find the concentration of molecule B when it is at a steady state?

I Tried:

For molecule B. P is concentration of molecule B.

2^-(dt/200) * P + 1000 * dt = P

"2^-(dt/200)" is the half life formula. I multiply it by P to give me current concentration of molecule B. Then I add 1000 * dt to give me the amount of molecule B being produced at an exact moment. Rearranging the variables:

P = (1000 * dt) / (1-2^(-dt/200))

Now I limit dt --> 0 to give me P:

lim t->0 (1000 * dt) / (1-2^(-dt/200)) =

l'hopital's rule: lim t->0 1000/ (0.005 * ln2 * 2^(-dt/200))

Plugging in dt = 0, what I get is a steady state concentration of molecule B = 200000 / ln(2).

However, the correct steady state concentration for molecule B is just 200000.

Suggestions?


texts: Are there anyother method under research for curing rabies?

texts: Why is rabies incurable after onset of symptoms? Although we administer HRIG (lyssa virus antibody) to the patient, why doesn't it work after onset of symptoms? And are there any other successful treatments for rabies like that of Milwaukee protocol which are under research? I also want to know how successful  is Milwaukee protocol so far?


texts: Can the dead be brought back to life by viruses?

texts:
Zombies have been a part of popular culture for decades. The living dead rising up to take over the world is a terrifying concept, worthy of Hollywood blockbusters and television hits. Some of those zombie fiction stories are based on infection by viruses or other organisms.

Is it possible to bring dead tissues back to life by virus infection?


texts: Why does doing more physical labour reduce the prevalence of disorders like OCD?

texts:
This just an observation without any study backing it. But people who do more physical labour as opposed to sitting at the couch really do have less rates of OCD.
Why this association of physical work with OCD's?

By OCD, I mean Obsessive Compulsive Disorder.

Here's a study backing up the exercise and its positive effects on reduction of OCD,
https://www.ncbi.nlm.nih.gov/m/pubmed/17568300/


texts: Are there differences in DNA between humans of today and humans from 2000 years ago?

texts:
Are there any significant differences in our genome compared to the genes of our ancestors from 1000-2000 years ago?

And if there are significant differences, do they result in significant differences in phenotypic traits?


texts: what are some examples of how evolution's limitations prevented species from climbing to the absolute highest peak on the fitness scale?

texts: In this answer, the author argued that plants are green instead of red or any other color because of some  limitations of the evolutionary process. what are other examples in which the physical and functional characteristics of an organism were a direct result of limitations of evolution?


texts: Why are parents of contrasting genotypes involved for a reciprocal cross?

texts: In a reciprocal cross, we try to determine whether a trait is sex-linked Or not... One thing I couldn't understand was that, why are parents of contrasting genotypes involved? Does that mean that at one time, female parent has the particular trait we are that interested in and at the other time, the male parent has that particular trait?(please correct me if I am wrong) and if that's so.... Then, why is that? I mean what is the purpose of doing that?


texts: Can I use grayscale images when working with ImageJ?

texts:
I am using ImageJ to analyze Western Blots. I have scanned films in as grayscale images because this is how we did it in my old lab. People in my current lab are not satisfied with that explanation and think I should consider using color images. I've been searching for protocols but they all seem to address how to use the program once you have some films scanned.

Can anyone help me figure out what considerations go into choosing how I scan my films?


texts: How far is stem cell research from being to generate a new organ?

texts:
How far are we from being able to use stem cell research to generate a sperm, a heart, a liver, and a kidney?

In stem cell research, my understanding is that you must start off with some cell to initiate the process. Can this be any cell, or must it be an embryonic cell made out of a sperm and an egg?


texts:
Urban parks in North America teem with sizable cockroaches at night. However, in the daytime they are nowhere to be seen. Where do they go?

I know that they tend to avoid light, but how do they go about finding a hiding spot? Do they just throw themselves into any superficial crack and stay still? Do they travel a substantial distance into storm drains, water pipes, tunnels and hollow walls until they are well out of reach of larger animals? Do they have a nest that they return to every night or do they just use whatever hiding spot is nearby?

And specifically for small urban parks, flowerbeds and lawns - do they dig tunnels in the soil? Do they nest in the trees? Or do they simply leave the park and hide in nearby buildings, sewers, and similar human-built structures?

I ask because while it is obvious they must hide somewhere, I have never actually "gotten the drop on" a sleeping or hiding cockroach in a park - or elsewhere - I've only encountered roaches that were scurrying out and about. Some nocturnal insects can be found by for instance flipping over wet rocks or digging up some soil, but cockroaches despite being large and numerous are nowhere to be seen. Are they just really, really good at hiding?


texts: Calculating pairwise Fst from allele frequencies

texts:
I am trying to refresh my memory on population genetics for a project, and I'm having some trouble.

Assume I have genetic data on 3 populations with 5 individuals in each of a given species, with the following number of genotypes:

      0101 0102 0202 0103 0203 0303 0204
Pop1   2    3    0    0    0    0    0
Pop2   1    1    1    1    0    1    0
Pop3   1    0    3    0    0    0    1

I have named alleles 01-03. So 0101 is a homozygote individual for allele 01, 0102 is a hetorozygote individual etc.

Is it possible to do this, from the following formulae:

If I input the information above into Genepop to calculate pairwise Fst using the following dataset:

Test Genepop
TestLocus
pop
Pop1, 0101
Pop1, 0101
Pop1, 0102
Pop1, 0102
Pop1, 0102
pop
Pop2, 0102
Pop2, 0103
Pop2, 0303
Pop2, 0101
Pop2, 0202
pop
Pop3, 0101
Pop3, 0202
Pop3, 0202
Pop3, 0202
Pop3, 0204

it produces the following result:

Pop    1       2
2    0.0278
3    0.2308   0.0669

However, how can this result be reproduced and calculated by hand?


texts: More extreme phenotypes when parents are from diverged populations

texts:
In quantitative traits we have many loci affecting a trait. If we took a bunch of parents where all mothers and fathers were of a certain value at the upper end of a trait range, and then looked at the offspring would we expect offspring from pairs of parents from more divergent populations to be even more extreme variance in their traits?

For example: if we look at 2 men from East Africa, both 190 cm tall. They each have children with women who are 180 cm, one of whom is from East Africa and the other from Canada. We could assume that the Canadian woman is probably more unrelated to her male than the East African woman. I would therefore expect that it is quite likely that the East Africans in the example are tall because of "tall-alleles" in many of the same loci, whereas there is a greater probability that the Canadian female is tall thanks to mutations at different loci. Therefore would it be reasonable to expect greater variation in the offspring of the Canadian woman?

Is there any evidence of this phenomenon?

Note: Ignore environmental and gene * environment interaction variance, just go with a simple additive model, and assume populations have had some barriers to migration for some time


texts: At what point does muscle mass overcome muscle strength to affect speed?

texts: I'm trying to think in terms of "how fast" someone can do something, like swing a bat or push a crate. Someone might have a lot of muscle mass, but that also increases how much mass an arm has to move which also increases the torque. Is there anything referable in biology that has found at least some estimate of where these two factors trade off?


texts: How is the eye damaged by computer screens?

texts:
Eyes are damaged by persistent use of computer screens. On giving it some thought, it felt quite magical that your eyes are damaged simply by looking at something. I googled where there were articles about blue light and stuff and having felt dissatisfied come to the wiser community here for help.

The question is pretty plain, how does the simple action of looking at a computer screen cause damage to the eye? Is it due to focussing the eye continuously at something close-by?

Is the damage caused to the retina, or the cornea or some other part and in what form? Does the light reshape the lens or something?

Edit: I got glasses of power +1 for both eyes about 3 years ago and 4 years ago, my exposure to computer screens increased to about 6 hours a day. Before that, it was hardly an hour or two a week. The ophthalmologist I consulted also credited it to increased exposure to computer screen.

Hope the questions are clear.


texts: Biological meaning of taking zero as coefficient of the Laplacian in mathematical models of cell motility

texts:
Several mathematical models from theretical biology deal with various forms of cell motility (for example, cancer growth) or evolution of populations.

The equations that make up such models usually contain (among others) a Fickian diffusion term of the form $$- \delta \Delta u(t,x),$$ where $u$ is the cell (or population) density.

To fix some ideas, consider the following examples.

A chemotaxis model:

$$\partial_t u(t,x) = \delta \Delta u(t,x) -  \nabla \cdot(uK\star u),$$
where $K \star u = \int_\Omega K(x,y)u(t,y)dy$, for a certain kernel $K$.

A model arising in population dynamics:

$$\partial_t u(t,x) = \delta\Delta u(t,x) + u(t,x) \left(\lambda - a\int_\Omega u(t,y) dy\right).$$

  Biologically, what is the meaning of a situation where $\delta = 0$ (that is, where there is not Fickian diffusion governed by the Laplacian term)?
  Is there any interest in studying such situations?
  Can you point out some references on this topic?


texts: Synthetic life creation - status of attempts

texts:
First I apologize for my incorrect English and for lack of modern knowledge regarding the subject (I studied biology a long time ago).

I'm interested to find out:

if there were successful attempts of life creation from conditions that we suppose were dominant on early Earth
if there were not, are such attempts still being conducted?

To clarify, by "life creation" I mean the accidental creation of entire organism in conditions of organic compounds, water, electricity, radiation etc. being present (Abiogenesis).

If this is already answered here, I'm sorry for asking, I have researched this, this, this and this question with no luck.


texts: Is the cranial nerve blood supply encapsulated by the blood brain barrier?

texts:
I understand the origin of cranial nerves are within the blood brain barrier. I'm assuming as they extend distally there's a point at which their vasculature is not encapsulated by the blood brain barrier. Is this true? Any idea where the blood brain barrier stops?

Thank you.


texts: What plant is this, seen at the Allan Gardens?

texts:
I tried a couple of apps on my phone, but I could not identify this flower and plant species.  These are at the
Allen Gardens Conservatory, at the beginning of Spring in Toronto.


texts: Is the receptor of SARS-CoV-like viruses in bats still unknown?

texts:
A fairly detailed 2012 review (Whittaker et al.) on the Mechanisms of Coronavirus Cell Entry Mediated by the Viral Spike Protein noted that

  SARS-CoV-like viruses have been isolated in bats. In this case, entry does not occur via ACE2 and their receptor(s) is/are unknown; however, replacement of the amino acid sequence found between residues 323 and 505 with the corresponding sequence of the SARS-CoV RBD is sufficient to allow human ACE2 receptor usage [46].

Is the actual (bat) receptor that allows SARS-CoV-like viruses to replicate in bats still unknown?


texts: What does "fit" mean in "survival of the fittest"?


texts: Does the composition of a meal play a big, or small, role in food's thermogenic effect on the body?

texts:
Reading in: "Diet and Health: Implications for Reducing Chronic Disease Risk /  Calories: Total Macronutrient Intake, Energy Expenditure, and Net Energy Stores" [NCBI Resources]:

  "The thermogenic effect of a meal usually amounts to approximately 10% of the caloric value of the ingested food, and is higher for carbohydrates and protein than for fats".

Does that mean that the thermogenic effect of a meal fluctuates between 9% and 11%, depending on it's composition? If so, the thermogenic impact on the body by a meal's composition would be quite small in comparison with the impact of a meal's calorie content. Or, does food's composition play a bigger role than that? Looking for information from reputable sources.

Calories: Total Macronutrient Intake, Energy Expenditure, and Net Energy Stores


texts: What is the name of this plant or shrub?

texts:
I just found a plant in India.

Here is its leaf.

I tried looking it up on flowers of India & wikipedia, but both databases are too
much to read manually.

Physical description:

Each Stem has 6 leaves on it, Leaves are opposite & Elliptic shape, Entire margin & Pinnate veins on it.

I am thinking it is shrub, not a tree.


texts: Pedigree Probability, Autosomal Recessive Trait

texts:
So, I thought I understood how to calculate the probability for a pedigree, until I came across this answer in my textbook. The question is: what is the probability the offspring of IV1 x IV2 will show the recessive trait? Assume individuals outside the family are not carriers of r unless there is evidence.
White = Dominant phenotype, Black = recessive phenotype.
What I did is:
III3 = 1/1 Rr, III4 = 1/2 Rr, IV1 = (1/2*1/1*2/3=1/3)
III7=1/2 Rr, III8= 1/2 Rr, IV=(1/2*1/2*2/3=1/6)
IV1 x IV2 = 1/3*1/6*1/4 = 1/72.
The answer in the book is 2/35. Can somebody please explain where I went wrong?


texts: It was in the bathroom, 2cm in lenght (or so). It has two small antenas on the head. I live on Balkan peninsula, inland.


texts: How do fish tolerate pH changes in water?

texts:
I want to know how aquatic animals behave as a natural indicator of the acidity in lakes and rivers.

How do they tolerate these pH change?


texts: What is the effect of flash pasteurisation on Maillard reactions or production of AGEs in milk?

texts:
Does flash UHTP homogenision and pasteurisation change significantly the extent of maillard reaction in milk compared with traditional batch pasteurisation? If this is significant does this effect the nutritional value of the milk?

Initial research; i have found via my wikisearch  http://www.food-info.net/uk/colour/maillard.htm and on pub med an abstract: J Nutr Sci Vitaminol (Tokyo). 1990;36 Suppl 1:S57-69.Influence of processing on protein quality.
Mauron J.
Source University of Fribourg, Switzerland.  i dont have full access to pubmed papers.

background to question.I have developed a sensitivity or intolerance to UHT and typical homogenised and pasteurised milk in the supermarket and any products with milk solids. I can consume non homogenised batch pasteurised milk from the specialty organic store, thus the curious chemist in me was alert. Either my body doesn't produce sufficient of the necessary enzymes ,ruled out by the latter scenario,  or the composition of the milk has changed in modern high throughput pasteurisation.

In Flash pasturisation we have P.T and V all being varied to increase proximity and likelyhood of collisions of reactants as well as temporary emulsification.

There is another term AGE see http://agefoundation.com


texts: I need some help identifying this plant please. It is summer flowering in the UK. Its height is approximately 30cm, flowers approximately 2cm across.


texts: Which predator raises its tail to signal no threat?

texts:
A guy in a bar once told me that there is some animal which raises its tail when at a watering area in order to signal to the other animals that it's not going to attack. He told me this as an argument to justify humans eating other animals.

Is this true that some animals do this? If so which ones? Links to video evidence would be extra appreciated.

Cheers,
Steve


texts: How does Oedipus complex fit in the evolutionary theory?

texts: This is somthing that really makes me curious. How is posible that trough a  evolution process the best posible candidate is the one that falls in love whith his progenitor?