texts: How large might a paper wasp nest become?

texts:
About two weeks ago I noticed a new wasp nest in my back yard. I generally leave them as long as they aren't interfering with anything, but this nest has suddenly grown quite large and they are swarming when I mow the lawn. From the nest appearance, I was afraid these were bald-faced hornets, but up close they look more like yellowjackets, I'm uncertain of the species. This is as close as I dared to get with the camera.

I am willing to live and let live until October (when the nest is vacated), but I have two concerns that may change my mind:

How large might this nest become?
If I leave them this summer, are they likely to return to the same place next year?


texts: Understanding transplant rejection - how does the cellular, adaptive, response get underway

texts:
This lay person is trying to get his head around the basic mechanisms of tissue rejection.

A lot of articles talk about T-cells being involve but I'm having difficulty following this. Human tissue is essentially similar between individuals. As I understand it the only cellular membrane protein that is (almost) unique is the major histocompatibility complex (MHC) that is expressed on all nucleated cells.

This means that killer T-cells can't recognise transplant tissue cells because of the MHC mismatch. The only cells that can identify non-self human tissue are the humoral innate immune natural killer cells (NKC) and they do this because they are built to kill anything unless it displays self MHC.

OK so NKC spew out the remains of alien tissue cells, but these residues are surely very similar to any other self cells' internals? How do I move from this view to one that involves the adaptive immune system which requires presentation of cellular fragments to lymphocytes?


texts: I am confused about the term DNA-binding domain. Does it mean that there are some parts of the DNA that tend to coil up? Does it happen because some proteins tend to stick around that area? Also it is my understanding that with some proteins DNA (say for bacteria like E. coli) tends to coil up. Do we know what is the approximately the size of these coils? What is a ‘motif’ in this context.


texts: Using exogenous genes to reduce the set of essential amino acids?

texts:
Various organisms have sets of essential amino acids that they cannot synthesize themselves, but rather that they must obtain from food. Humans have 9 of these amino acids. However, obviously certain organisms like plants contain the necessary genes to synthesize all of their amino acids. Also, the set of amino acids for various organisms differs. For example, arginine is essential in dogs but not in humans.

Have there been any attempts at taking cells from an animal or other organism with essential amino acids and providing them with the necessary genes to synthesize that amino acid, thereby reducing the cell's set of essential amino acids?

I am not asking this specifically referring to human cells, nor do I have any particular motivation for asking this other than curiosity.


texts: What happens in your brain when you receive information which causes you to bristle?

texts:
I'm talking about moments when you watch a film and you bristle, or when you listen to music, etc.

What kind of neurotransmitter flow changes?


texts: Concentration dependent cellular processes

texts:
Are there any famous biological processes that depend strongly on a chemical concentration reaching a particular value, like some sort of switch?

E.g. if concentration of chemical x reaches concentration y at cell location z (membrane, organelle etc) then a particular biological process will occur?

Thanks


texts: What is the relative power of GWAS studies in different species?

texts: I would like to know of any publication studying the relative power of GWAS studies in different species. For example, I've seen reports that say genotyping and GWAS in dog breeds is much more powerful than in humans due to the extent of linkage disequilibrium and other population genetics considerations. Some claims say that many GWAS studies in dogs are 10-20x more powerful than many GWAS studies in humans. I have also heard from pigeons (pigeon-omics) to be a similar case. I would like to know if there are other comparisons for other species and the relative power of discovery for GWAS studies compared to human. For example, are there any numbers for yeast, Drosophila sp., C.elegans, zebrafish and then also for plants like maize, rice, etc.?


texts: What is the name of this berry producing tree?

texts:
I live in Middle Tennessee (USA) and came across this tree while I was hiking through the woods. I'm curious as to what type of tree this is and if the berries have any uses or are poisonous.

The tree is rather short, and I was unable to see any more distinctive features given that the tree was surrounded by other brush. I can supply a better picture in a day or two if necessary.


texts: Why does K+ going out of the cell cause hyperpolarization?

texts:
I'm really  confused by how the terms Hyperpolarization and Depolarization are used in Cell biology and hope somebody can enlighten me hopefully.
Here's what they mean for me so far:

Depolarization means the inner and outer side of the cell membrane become less polarized (so the Nernst potential tends to 0 due to log(1) being 0)

Hyperpolarization that the inner and outer side become more polarized (so the Nernst potential increases).

Assuming I'm not completely wrong until here.
Let me give some examples, so maybe you can see better where the problem lies:

We have a model cell so (K+ internal is 140 mmol/l, K+ external is 4.5 mmol/l) and the external side is increased to 8 mmol/l , then a DEPOLARIZATION occurs because

roughly : $-60 \cdot \log(140/4.5) = -90 mV < -60 \cdot \log(140/8) = -74 mV$ ; or in other words, "energy" was used so a depolarization occurred (so far this seems correct with the solutions I can find to this example)

\
\

Now comes the second example (famous depolarization of a cell with the graph and the peak and repolarization):

Na+ enters the cell : the concentrations im gonna use for this example are inside:$12 mmol/l$ and outside $140 mmol/l$

so before the Na enters we have: $-60 \log(12/140)= 60 mV$

if Na+ enters the Cell, a depolarization should occur (because the difference inside and outside is decreased)

this seems fine with the graph...

the part of the graph which goes over 0 (also called "overshoot"), is it not technically a hyperpolarisation+depolarization?
repolarization: this occurs by K+ ions leaving the cell, but that doesn't make sense according to the Nernst equation?

The concentration inside before the cells leaving is 140, outside 4.5 ; if K+ leave the cell, its simply going to depolarize more... So why does repolarization occur and not depolarization?

It's commonly stated that Hyperpolarization is caused by K+ LEAVING the cell (for example with ion channels) , how does this make sense if the inner concentration is higher than the outer? If anything, this again should lead to depolarization
Same thing with K+ entering the cell, isn't that supposed to cause a hyperpolarization as well?

I appreciate any kind of insight into this matter, since it seems that I'm completely wrong.


texts: Does Cholestyramine (CSM) raise Tyramine levels?

texts:
This is a layman's question.

Will ingesting Cholestyramine (CSM, the resin, in powdered form to be specific) raise tyramine levels?

I am asking because Cholestyramine clearly has "tyramine" in its name, so i don't understand the chemistry behind all this and/or how this interacts with the body.

Thank you.


texts: Low-cost simple water testing for faecal contamination

texts:
I live in Indonesia and there are lots of sewage pipes discharging directly from homes/restaurants/etc directly into the river. It's also common to wash clothes and so on, so there is likely detergent in there as well.
Some water courses that people bathe in seem to be more s**t than water, if you see what I mean, in that it starts off in the river, then diverts into various smaller canals which often end up with trash, diapers, and so on.
I'm wondering what I could do to test/measure this in simple & low-cost fashion, so that I could test in different places and on different dates, and possibly to include quantative values such as 'how much dirtier' the river is when there are many people bathing in it, or when it is dry season, or whatever.
I think I don't need to test for every pathogen so it might be sufficient to just test for E coli? [I think S. aureus is also common, as skin boils tend to occur after bathing in dirty water.]


texts: Feeling warm and cool breezes - how does it work?

texts:
As you travel with your hand sticking out of a car the sensation you have is one of cooling: even though molecules are transferring energy to your hand, you interpret it as being colder. Now, at a certain speed your hand would actually melt down, and I'm assuming you'd be feeling warmth by the time that happened.

I'm wondering how this works: how can your body sense warmth and cold from a phenomenon that, physically speaking, is just about molecular collisions?


texts: What is the molecular mechanism of odorant transduction signaling pathway?

texts:
I have read a few papers on the topic of odorant signaling pathway. The following papers are listed as examples. However, I found that there is not a clear pathway representation of the odorant signaling pathway, through which the involved genes and regulations should be known. Is there any paper I have missed?

Menzel, R. and P. Benjamin (2013). Invertebrate learning and memory,
Academic Press.
Leal WS: Odorant reception in insects: roles of
receptors, binding proteins, and degrading enzymes. Annu Rev Entomol
2013, 58:373-391.
Kaupp, U. B. (2010). "Olfactory signalling in
vertebrates and insects: differences and commonalities." Nat Rev
Neurosci 11(3): 188-200.
Vosshall, L. B. and R. F. Stocker (2007).
"Molecular architecture of smell and taste in Drosophila." Annu Rev
Neurosci 30: 505-533.


texts: How does the nucleophilic attack in DNA replication occur?

texts:
Hi there,

I am confused about how the nucleophilic attack occurs in DNA replication.I watched this video from a biology professor (https://www.youtube.com/watch?v=y4hKibS2fAo)

I watched this video which stated that during DNA replication, the hydroxl group forms a covalent bond with the phosphate and the two phosphorus groups are a leaving group.

I understand the basics of these kinds of reactions, but this one just seems confusing. I can see that the oxygen which was part of the hydroxl group forms a covalent bond with phosphorus. But what happens to the hydrogen? And why does the the double bond and position of the HO change position from the first picture to the second picture?

There are also some pictures which show water being produced. But the video states that the hydroxl group is forming a bond with the phosphate group. How does that work?

Thanks a lot


texts: In a systematic viewpoint, bistability refers to the existence of two stable equilibriums for a biological system. But, I don't understand the difference between bistability and bimodality. In both cases, the system should have two different behaviors, so I guess bistability is a specific case of bimodality, in which either of the system's behaviors might not be stable. Is this a valid distinction between these terms?


texts:
Plant grafting is a process whereby a piece of one plant is inserted into another and results in a change of the original plant. For example, grafting a piece of a lemon tree into a bitter orange tree will cause that tree to produce lemons instead of oranges for the rest of its life.

How does this work? I mean, at the genetic level. I guess the grafted plant is now a chimera of some sort but if so

How does the grafted DNA affect the host cells?
Are all of the host's cells affected?
If we were to sequence the grafted tree which genome would we find?
Is it perhaps that the host DNA is not affected at all and the effects come via a change in expression levels? If that is the case I would assume grafting will only work between very closely related species. Is that so?

Basically I know very little about plant genetics and physiology. I remember from my undergraduate days that plant genetics are just plain weird. Most, if not all, have various levels of polyploidy. Is that relevant?


texts:
Is is possible to cure AIDS patients by using white blood cells of blood cancer, by fooling HIV to attack a false target?

Is it possible to wrap HIV in a physical boundary, such that it has no interaction out side the wrapper, so the functionality of the cell will not be affected by HIV?. Since all cells in out body are replaced within three years, after 3 years, the HIV affected victim will have fresh HIV free cells.


texts: Quantification of concentration from chromatogram paper

texts:
In an experiment, I recently isolated and purified calf thymus DNA, hydrolyzed it with perchloric acid, and then applied the hydrolyzate to a Whatman paper in a polar solvent and let it run overnight.

I must now determine a way to quantify the concentration of each base, now separated based on polarity on the chromatogram. This cannot be the following method: Cutting the paper containing the base and putting it into an acid-containing flask, then measuring the absorbance, followed by Beer-Lambert's Law calculation for the concentration.

I would appreciate any ideas.


texts: Why is EcoRI supplied with a unique buffer when it is allegedly 100% active in universal buffers?

texts:
Thermo packages a unique buffer with EcoRI:

  50 mM Tris-HCl (pH 7.5)
  10 mM MgCl2
  100 mM NaCl
  0.02% Triton X-100
  0.1 mg/mL BSA

However, they also list their EcoRI enzyme as 100% active in Buffer O with no indicated star activity:

  50 mM Tris-HCl (pH 7.5 at 37°C)
  10 mM MgCl2
  100 mM NaCl
  0.1 mg/ml BSA

The same is true of 2X Tango:

  66 mM Tris-acetate (pH 7.9 at 37°C)
  20 mM magnesium acetate
  132 mM potassium acetate
  0.2 mg/ml BSA

Is there a reason one would preferably use the unique buffer over a universal one? Given that buffer compatibility is a major selling point for restriction enzymes, why would they continue to supply a unique buffer?


texts: tools to reconstruct the transcriptional regulatory circuits?

texts: What are commonly used tools to reconstruct the transcriptional regulatory circuits that govern diverse cellular responses and what input data sets do they accept?


texts: Why does autosomal trisomy have more adverse effects than sex choromosome monosomy or trisomy?

texts: Autosomal trisomy syndromes are usually lethal but sex chromosome number related abnormalities do not lead to that much fatality. why?


texts: Ejaculation without orgasm: is this possible to do it at will without external stimulation?

texts:
I know that ejaculation without orgasm is possible for human males with external stimulations, e.g. prostate massage.

My question is, can a human male perform full ejaculation without reaching orgasm without such external stimulation, i.e. with "ordinary" masturbation? Is this technically possible for the body?


texts: 16S sequencing: pooled or individual samples?

texts:
I am planning to run 16S sequencing on a set of individuals to explore microbial diversity. The question I am facing is: should I sequence them individually or I pool them (for example 5 individuals = 1 sample)?
I was just thinking on advantages and disadvantages of both methods:

1) individual. I can get the diversity of each individual, in that way I know the proportion of individuals which have a particular species of bacteria. The cost are higher since I need more samples with respect to the pooled way, but the reads/sample needed should be lower (since this number increases with the microbial diversity).

2) pooled. I have only a general proportion of diversity in the pool (I can't assess how many individuals have a peculiar becterium). The cost are lower due to small amount of samples, but reads/sample should be higher due to more than one individual pooled (?).

Can someone help me? Are my assumptions right or I am missing something?


texts: Will a person with two copies of the same set of chromosomes be normal?

texts:
Would a (theoretical) woman (because she must have two X's), that both sets of
her chromosomes were 100% identical, be "normal"?

Would she be healthy, or would she have genetic problems as a result of that?

Would all her egg cells contain the same copy, identical to all others in her
body?

Thanks very much for any answers!


texts: too low extention time for Taq polymerase PCR

texts:
I am currently working on my masters degree and have recieved the following question:

  "you want to amplify by PCR a gene 1kb long. The Taq Polymerase you have in the lab is able to synthesize 1kb/minute. You make a mistake in programming the PCR machine and set the extension time to 30 seconds instead of 1 minute. what will happen? what do you expect to see on a gel?"

The answer I came up with was that there would be insufficient time for complete replication of the target and therefore only incomplete copies would be made. These strands would show up in a band below 1 kb because the are shorter.
This answer however, was incorrect. I browsed the web but could not find any clear answers on what would happen. anyone knows what happens?


texts: What is the difference between the cellular affix -cyte and -blast?

texts:
The affix -blast means an immature cell, and -cyte indicates any cell. So how do we define if a cell is mature (-cyte) or immature (-blast)? How does this apply to odontoblasts and ameloblasts? Why are they not simply called odontocytes and amelocytes, respectively?

What are the criteria for using the affix -cyte versus -blast?


texts: glycogenesis, glycogenolysis and weight gain or loss

texts:
I am under the impression (from dietary websites) that when excess serum glucose is stored as glycogen, body weight is increased and the reverse: when glycogen is converted to serum glucose, body weight is reduced.

I also understand that the glycosidic bond formation in glycogenesis is a condensation reaction, releasing water, whereas the rupturing of these bonds in glycogenolysis is a hydrolysis reaction absorbing water.

Please help me here: how does the body gain weight by releasing water and lose weight by absorbing water. What am I not understanding?


texts: We know that some halophiles are heterotrophic, but in those highly saline environment what do these organisms eat as there might be very little chance of survival of any other organism?


texts: Looks like a roach to me, but dont know for sure or what kind. Measures about 2cm large. Location: central Mexico


texts:
It seems like most fruits that we consume undergo some sort of ripening process either before or after they are picked from the vine, tree, etc. I understand that sugars are released during the ripening process and this is why ripe fruits are sweeter and more palatable than non-ripe fruits.

Why, though, do fruits have to undergo this process of ripening?

Wouldn't it be simpler to just grow and already be "ripe"? Does the ripening process confer some sort of advantage to the plant?


texts:
I was reading this paper:

https://www.ncbi.nlm.nih.gov/pubmed/26119455

and became confused after this sentence:

"The  ICM-derived mouse embryonic  stem  (ES)  cells and epiblast-derived
human  embryonic  stem  cells have  the  full  potential  to
differentiate  to  ectoderm, mesoderm,  endoderm, and trophoblast."

As far as I know, the trophoblast is originated from morula cells that are totipotent, and ICM cells are pluripotent...

Moreover, are ESCs derived from the ICM of the blastocyst? Because if yes, does it mean that they can also become primitive endoderm and give rise to some extraembryonic tissues? Because as I know only epiblast (primitive ectoderm) gives rise to 3 germ layers... does it mean that ESC are derived from epiblast only or not?

Thanks


texts: I am trying to optimize annealing temperature for some primer pairs. I have tried optimization using cDNA, genomic DNA, Taq polymerase, phusion polymerase etc., but every time I am either getting non-specific amplification, a band of larger size than expected or no amplification. Every time I am getting a primer-dimer. Can anybody help me optimize the annealing temperature?


texts: How can a powernap boost memeroy and cheerfulness?

texts:
Background

  A power nap is a short sleep which terminates before the occurrence of
  deep sleep or slow-wave sleep (SWS), intended to quickly revitalize
  the subject. (wiki)

The results of powernapping are described in An ultra short episode of sleep is sufficient to promote declarative memory performance

  In the first experiment we assessed free recall of a list of 30 words
  after a 60 min retention interval that was either filled with daytime
  napping or waking activity. Memory performance was significantly
  enhanced after napping as opposed to waking but was not correlated
  with time spent in slow wave sleep or total sleep time within the
  napping condition. The second experiment was designed to clarify the
  role of total sleep time and therefore included an additional third
  group, which was allowed to nap for no longer than 6 min on average.
  In comparing word recall after conditions of no napping (waking),
  short napping, and long napping, we found superior recall for both nap
  conditions in contrast to waking as well as for long naps in contrast
  to short naps. These results demonstrate that even an ultra short
  period of sleep is sufficient to enhance memory processing

Question
I'm wondering how it's possible that such a short napping period can boost cheerfulness and memory (thus in a biological sense).


texts: How different is breathing in wildfire smoke in urban areas compared to sitting by a campfire for a night?

texts: The air quality in the Bay Area is currently the worst in the world, due to the devastating Butte County wildfires. I understand smoke inhalation can cause inflammation and respiratory issues, especially with chronic exposure, but I'm wondering in actuality, how different is the exposure to wildfire smoke in urban areas (AQI 100-300) over the course of a few days, compared to sitting by a campfire for a night?


texts: Who were the first authors to talk about local adaptation?

texts:
I was curious to read about what Darwin had to say about the existance of locally adapted subpopulations. I discovered to my surprise that the expressions and terms "local adaptation", "spatial heterogeneity" (or just "heterogeneity" even) and "environment" are completely absent from On the origin of Species. The expression "local conditions" was found 12 times but I could not find a place where he would suggest subpopulation of the same species could be locally adapted to their environmental conditions.

Who were the first authors to talk about subpopulations being locally adapted to their environmental conditions? Who were the first authors to understand the role that migration plays in reducing local adaptation?


texts: Do eye muscles relax when you close your eyes?

texts: I wonder whether the eyes muscle relax when you close them. Common knowledge told us the eyes muscle get tense when you stare at nearby object. If you close your eyes, you eye lids have 0 distance with you eyes. Would the eyes muscle relax in this case?


texts: What organism most efficiently converts a given quantity of mass into heat?

texts:
Question I am trying to answer:

In the popular film The Matrix, heat given off by humans is harvested as an energy source. I wondered, if this were possible, would humans be a good organism to choose? Would any other organism be better?

Question I want to ask:

Many warm-blooded organisms produce heat by metabolism. Do different organisms produce different levels of heat for the same mass of input (food)? Is there any organism that directs energy flux into heat production more than any other organism?


texts:
It seems like most mammals, e.g. dogs, have long snouts. My pet dog's snout would seem to me like an evolutionary disadvantage, since her canine teeth are way out at the end of her jaw, which acts as a force-reducing lever. I suppose the lever does increase the jaws' range of motion and possibly allow the jaw to snap shut more quickly. For an herbivore such as a horse, I don't see any advantage to the long snout. It doesn't need to snap its jaws shut rapidly, and it doesn't need to wrap its mouth around anything very large.

Is there a mechanical reason for the long snout, or is the evolutionary advantage due to some other factor such making the nose have enough surface area to give a sensitive sense of smell?


texts: Do I need primers if ordering from a DNA synthesis provider

texts: Do I need to design / synthesize primers for PCR if I am ordering from a DNA synthesis company and they are providing free cloning into my preferred vector backbone? Any good reason to order primers as well?


texts: How do viroids and virusoids cause infection to a specific host ? How could they indentify the host without protein?

texts: We know, the capsule provides specific  pathogenecity for the virus right ? Then ,  how do viroids and virusoids cause infection to a specific host ? How could they indentify the host without protein ? Seems like they could infect any possible living being ? Please make it clear


texts: Meaning of ‘NC number’ associated with a gene?‘

texts: Genes in listings etc. often have a number of the type NC_000012.12 associated with them. How should this be interpreted?


texts: What is happening in each iteration of PSI-BLAST?

texts:
I understand that the first BLAST yields almost the same results as blastp. The second time the iterated blast generates different results as it uses different matrix based on our first result.

But I don't understand how exactly the second matrix is generated.


texts:
My textbook( biochemistry by Satyanarayana, 4th edition pg.no:166) says:

  The polysaccharides get hydrated during heating which is essential for their efficient digestion.

(I think there is a typo , heating should be replaced with eating)

How does water add into polysaccharides? Am I right if I say it is by hydrogen bonding? It also says  that efficiency increases, is it so because the substance is now more diffused so that enzymes act on an effectively larger surface area(making colloidal solution)? Or if the added(hydrated) water plays some role in interaction between enzyme and polysaccharide?


texts: qPCR: do both primers have to contain a GC-clamp in order to be effective?

texts:
I'm developing software which, among other things, designs primers pairs (forward and reverse) for qPCR. In my research on various properties, I read about GC-clamps and I understand the basics of it I think. There is still something unclear to me.

Do both primers in a pair need to have a GC-clamp in order for it to be effective? Or does one GC-clamp in, let's say the forward primer, just increases specificity, and both primers containing a clam increasing it even more?


texts: Mechanism behind negative conductance of ion channels

texts:
I am struggling to understand negative conductance shown on I-V curves on ion channels. Mechanistically, negative conductance means that inward (or outward) current increases when voltage across membrane decreases. I-V curves of such a channel have both positive and negative slopes. How it is achieved by ion-channels?

For example, this is in addition to the example posted in the answer by aandreev.


texts:
Why are the knuckles of an eagles toes "ridged"?

(I found these pictures to explain.  One was from PBS and the other is one I found on Pinterest):

I circled the parts of the toes/feet I meant in red (from PBS):


texts: Book request: biology of sensation and perception

texts:
I’m interested in learning about the biological and chemical basis of human sensation and perception (on both a microscopic and macroscopic level). This includes

The mechanisms underlying our “five senses,” i.e. the eye, inner ear, tongue, nose, and nervous system, and how (chemically/physically) they are triggered
How our brain makes inferences from the raw sensory data we receive, e.g. using our depth perception to infer distance from a two-dimensional projection onto each of our eyes
Comparison with other species of animals
Experimental results relating to the three points above
An evolutionary perspective hypothesizing about why these sense-detecting organs were important for human survival

There is plenty of information about these ideas scattered throughout Wikipedia, but I was wondering if anyone knows of a single book (or perhaps another online resource) that covers most/all of the points above in an accessible and interesting way.

Any suggestions?


texts: Are $DCX^{-}PSA-NCAM^{+}$ neurons the result of adult neurogenesis in human being?

texts:
A recent study by Sorrells et al. (2018) has stirred a debate whether human being really do have adult neurogenesis in hippocampus or not.

In a following paper- Adult hippocampal neurogenesis: a coming-of-age story, HG Kuhn, T Toda, FH Gage have criticized the original study by stating that

  while Sorrells et al. did count $DCX^{+}PSA-NCAM^{+}$ cells as
  adult-born neurons; they did not count $DCX^{-}PSA-NCAM^{+}$ as the
  same, claiming that the latter exhibited more mature morphological
  features based on their criteria. However, the developmental time
  course of adult-born neurons in the human dentate gyrus has not been
  clearly characterized, and neurons in higher mammals take at least six
  months to fully mature (Kohler et al., 2011).

My Question is- are the $DCX^{-}PSA-NCAM^{+}$ neurons really the result of adult neurogenesis, as claimed in the second paper? Or are Sorrells et al. correct in calling only those neurons adult born that respond to both the markers (DCX,PSA-NCAM).


texts: Do prey animals fail to see incoming pythons/snakes?

texts:
I understand that pythons are considered ambush predators, and I was under the impression that they tend to employ the sit-and-wait strategy: quietly staying in a coiled position near a trail frequented by prey animals, and striking when a prey passes by. However, this is in contrast to the stalk-and-strike strategy I encountered in every video I could find of snakes hunting prey in the wild.

In this video compilation of pythons hunting prey (warning: it's graphic), in every instance shown, the snake can be seen closely approaching the prey, the prey appearing to not notice the snake, and striking when the snake's head is within a few cm/inches of the prey animal.

This seeming appearing-to-not-notice-a-large-snake-nearby behavior can be seen in different animal species:

Pigs: Here
Mice/rats: Here, here, here, here, here, and here
Rabbit: Here
Bird: Here
Possum: Here

Similarly, the-fail-to-notice can be seen another video and here too.

Question: Is the stalk-and-strike strategy the more common hunting strategy that snakes tend to employ? Do the prey really fail to notice a looming large snake? Or do they "play pretend to not see it" as a some sort of adaptive strategy?

My sample of videos could also be biased, but it seems that the sit-and-strike strategy would be more easier to film and thus should be more easy to find in popular video sharing sites. No?


texts: How do I create a probe for in situ hybridization?

texts:
I tried to make the probe several times but it failed again and again. It usually turns out that the probe after hydrolysis is very very short (maybe around 50nt). I did not check the RNA before hydrolysis except last time. However, I saw a band (though very weak) last time, but it still produce very very short probe after hydrolysis.I use Sp6 polymerase to synthesize RNA, and the original length of the DNA is 1.5kb. My expected length after hydrolysis is 500nt.

I'm guessing maybe it's the phenol contamination of the phenol:chloroform extraction step because my 260/280 value is low (around 1.6-1.7), and my 260/230 is also low, which is like 1.6-1.8. Also the peak is not at 260, it's almost at 270.


texts: Are there known functions of AST, ALT, and amylase in the blood?

texts:
A number of enzymes can be measured in the blood or plasma that aid in the diagnosis of certain diseases. For example, patients with particular liver diseases may have elevated aspartate aminotransferase (AST) and/or alanine aminotransferase (ALT) levels in the blood. These enzymes are normally involved in biochemical reactions of metabolism that interconvert amino acids with other metabolic intermediates - that is, biochemical reactions that are common within the liver cell. Also, patients with pancreatitis frequently have elevated amylase and lipase levels, which are digestive enzymes normally secreted into the gastrointestinal tract. During pancreatitis these enzymes are released into the blood, rising and falling with the resolution of pancreatic damage/inflammation.

Pathologically, the tissues that are damaged in these diseases (liver and pancreas, respectively) are the source of the elevated enzymes. In healthy individuals, however, these same enzymes are still found in low concentrations in the circulating blood. What is the source of these enzymes that are found in low circulating concentrations? Is it still those same tissues (e.g. AST/ALT from the liver)? Is this secondary to "normal turnover" of cells within those tissues? Or, alternatively, are these enzymes secreted into the blood to serve a particular function?

For example... There is a freely available manuscript by Arnold and Rutter published in the Journal of Biological Chemistry (1963) that discusses experimental evidence for active amylase secretion from the liver during an isolated liver perfusion experiment. Amylase continues to be secreted, even in the absence of other enzymes that would otherwise indicate liver damage (suggesting that the amylase is intentionally being secreted for some unknown purpose). This is an paper from almost 60 years ago - do we know what some of these enzymes like AST/ALT and amylase do in the plasma? Or are those functions still unknown?


texts: Does apheresis damage any components of blood? If not, why not?

texts:
Blood donation involving apheresis is becoming increasingly common. It looks like the process involves centrifuging blood at very high speeds* before removing the desired fraction and returning the rest to the donor. Is there good reason to believe that the centrifuging process is harmless to all the various cells, proteins, lipids, and other substances in whole blood? Or is it possible that some blood constituents are damaged or altered?

* I don't know if the speeds are particularly high compared to other biomedical processes, but they're drastically outside the conditions in which biological products evolved to function, hence my question.


texts: What is the weight of a single human sperm (spermatozoon) compared to a single human egg

texts: While the difference in dimension is well covered, I have been unable to find the mass measurements of each.


texts:
An often heard theory is that newborns and babies resemble the father more than the mother, a theory apparently ignited by a Nature paper by Christenfeld and Hill (1995). Figure 1 shows one of the tests images. His subjects had to guess which picture was the real dad and which was the real mom. It turned out that tested subjects were indeed significantly better at guessing dads than moms.

Test stimulus of Christenfeld and Hill (1995). Which one is dad: a, b, or c?

It is suggested that paternal matching of a baby promotes identification of the father with his offspring. In turn, self-identification in his kin would prevent the father from doing harm and stimulate protective paternal behavior. This then is hypothesized to increase survival rates of his offspring and et voila, a trait is born (pardon the pun) that makes baby paternal look-alikes fitter than those that don't. This hypothesis seems to have become part of parenting folklore.

However, a Scientific American paper by Matson (2011) contests this view and puts forward several primary research studies showing no preferred resemblance between mother or father, or even predominantly maternal features in babies.

Is the resemblance between father and baby fact or fiction?

References
- Christenfeld & Hill. Nature (1995); 378: 669
- Matson, Sci Am (2011) online article

Credits for this question go to @KoustavPal for his comment in Y-chromosome and phenotype


texts:
I was watching a documentary (don't remember the name or the URL to the documentary) but they stated that the brain is layered and that each new layer is placed on top of the last. So the most primitive part of the brain that sends a signal to move the fingers actually has no way of moving just one, but in fact sends a message to just open and close the hand. That message is then passed on to a newer part of the brain that then filters it into individual finger movements.

I would like to know if this is true and how is the newer layer of the brain able to take an open-close message and identify what finger to move.

This sounds like a strange way for the brain to work; as I'm typing this message out at 86wpm, how is my brain doing such a complex task of moving all my fingers from an open-close message?


texts:
I'm curios to know how many times neurons send signals in one second when the brain is highly active (Highly active meaning during difficult problem solving, or any task that might bring the brain to it's higher volume of activity).

When the mind is highly active, roughly how many neurons become excited in one second? The question might also be posed as: "How many action potentials might "occur" in the brain over the course of one second during any form of complex mental process?"

Answers accurate to whatever accuracy we're currently capable of would suit my interests.


texts: What do you call the non-Wild Type allele?

texts: Can I have a list of suggestions, such as the mutated allele, other allele, etc. ? Are there any blatantly missing ones on my short list?


texts:
Are there any studies that point out that we could have a device in the future  or drug that could give us endless amount of pleasure by stimulating or blocking processes in the brain or nerve system?

Drugs and alcohol end up saturating receptors in the brain. Is it known inside out how this mechanism of rewards / saturation / abstinence work in the brain and how it relates to consciousness?

It is well known that you cannot have the same amount of pleasure by repeating the same action over and over again but is it truly known how that works? Would it be possible to reset the receptors in the brain to accomplish this?


texts: Using proportion or a diversity index when dealing with just two strains

texts:
I'm looking at diversity maintenance in an experimental system consisting of just two strains. I have count data. I can calculate their proportions and I can use that data in my statistical models, or I can calculate Shannon or Simpson diversity, and use that data.

My question is: When dealing with just two strains, is it really necessary to use a calculated diversity index, or will proportions do just fine?

The benefit of using proportions is that it's a more accessible metric - not requiring any (albeit fairly basic) knowledge of diversity indices and how they alter the data.

Having calculated Shannon, Simpson, and proportions, and run all three through my models, it makes no difference which I use - the data are quite emphatic. My slightly educated instinct is, in this case, to use the most simple metric, but I'm looking for some opinions on the case.


texts: Why are male gametes and female gametes not equally sized

texts: Why is it that male gametes are smaller and produced in larger quantities than female gametes that are large and lesser in number. Why aren't the gametes equally sized, or their sizes the other way around. Is there an evolutionary advantage to this, or is it just how things evolved and would it not have mattered if the sizes and quantities were reversed?


texts: Are there diseases for which a placebo treatment is state of the art?

texts:
I was reading about the placebo effect, and I wondered if there exists or ever existed a disease with the following properties:

There are no known treatments for the disease that perform better than a placebo.
The placebo has a positive effect on patient outcomes.

If there is a disease like this, what do doctors do? Do they give out prescriptions for sugar pills because the pills will do better than nothing?


texts: Can you build muscles from watching point of view videos of people weightlifting?

texts:
According to this, "new research has found that viewing other people exercise actually increases your heart rate and other physiological measures, just as if you were working out yourself".

This got me thinking, can muscles be developed to be stronger and bigger from simply watching videos of people weightlifting from the point of view of the weightlifter?


texts: Evolution of hunting behavior of parasitoid wasps

texts:
Wasps in the genus Pepsis lay their eggs in a specific region on a species of tarantula and their larvae eat the tarantula organs in a specific sequence to keep it alive as long as possible.

How could this process have evolved, considering that a mistake at any stage results in death?

This is the description of the egg laying behaviour:

Upon finding a tarantula, the wasp locks its mandibles onto a foreleg and brings its stinger into position so as to paralyze it.

During this process, the tarantula tries unsuccessfully to dislodge the wasp, but the wasp ultimately locates the right part of the tarantula in which to insert its stinger.

Upon inserting it, the wasp injects a venom that paralyzes the tarantula. Note that the tarantula is ten times the weight of the wasp, so the wasp takes very big risk in trying to attack such a tarantula.

The wasp then drags the tarantula into a hole that it has already dug. It pulls the tarantula down into the  hole, attaches its egg to a specific part of the tarantula's body and then covers up the hole so that predators won't find it.

When the egg hatches, the larva eats the organs of the tarantula in a specific sequence so as to keep the tarantula alive for several weeks. Eating in the wrong sequence results in the death of the tarantula, and its subsequent putrefaction, which means the death of the wasp larva.

When the larva successfully eats in the right sequence, it is able to obtain enough nourishment to prepare for metamorphosis, ultimately resulting in a full-grown wasp, which then exits the hole and becomes a predatory wasp.

These wasps are solitary, which means there are no conspecifics to teach the new wasp how to do all this.
Thus, the entire behavioral program described above must be encoded in the wasp's genome.

The description above is based on:

Punzo, F. (2005). Experience affects hunting behavior of the wasp, Pepsis mildei Stål (Hymenoptera: Pompilidae). Entomologica Americana, 113(3), 222-229.

Petrunkevitch, A. (1952). The spider and the wasp. Scientific American, 187(2), 20-23.


texts: Is there any mechanical digestion that occurs once food/chyme enters the small intestine?

texts: Does mechanical digestion occur in small intestines and, if so, how does it occur? I found some sources that say digestion happens mechanically and chemically in the small bowel, and others that say it only happens chemically? Also, does chemical digestion only occur with acids (e.g. HCl) instead of enzymes, or does it occur with enzymes?


texts: closed circulatory system and blood supply to the heart endocardium

texts: Human has closed circulatory system. in this type of circulation of blood, the vessels are not directly contacted with the cells and feed the cells by extracellular fluid. Now, how does the blood flow to the endocardial layer(the endothelial cells) of the heart that doesn't have extracellular fluid? I read somewhere that "the blood in the heart itself can feed them", but how much is this sentence true while we're saying that the extracellular fluid is going- between the blood and cells? :/


texts: What is the genomic position of HLA-B*1502 variation?

texts: I've searched the position and SNP ID of HLA-B*1502 variation. However, I couldn't find that where this variant exactly located on genome or HLA-B gene.


texts: How did the introduction of artificial light changed the life cycle of a plant?

texts:
Plants in urbanized areas are constantly exposed to artificial light after sunset. In their natural habitat there is a more distinct day and night cycle.

Since light is an important factor in a plant life cycle, I wonder if the introduction of the artificial light forces any changes in the life cycle of plants in urbanized areas?


texts: What changes would allow cutting mRNA-based vaccine safety testing to 18 Months

texts:
I see a lot of skepticism among my fellow citizens following an interview that Bill Gates gave the BBC on the topic of Corona vaccines. The Gates foundation is funding several study ventures on Corona vaccines, conventional vaccines as well as experimental mRNA vaccines. In the interview he said:

  "We'll need to fund the ten most promising constructs because we don't know in advance which on will prove to be safe and effective [...] so we gonna have to take something that usually takes five or six years and get it done in 18 months (6:09)
  [...]
  There is an approach called RNA Vaccine [...]
  that looks quite promising but we can't count on that, so we'll back 4 or 5 of that and 4 or 5 using a conventional approach, which unfortunately, the schedule on that would probably not so quick. (6:45)

There are people on the internet that criticize that Gates would want to trade security for speed in getting the vaccine out and cite this comparison (18 months instead of five years) to make a point how unsafe that would be. I interpret the interview insofar that Gates believes that the new technology itself would provide for some speed gains (longer time needed with conventional approaches). Similarly, this review (Section "Good manufacturing practice production") mentions that mRNA vaccines are easier to produce than their conventional counterparts, for example because life viruses and toxic inactivation chemicals are not involved in the process and thus do not need to be removed reliably.

However, I lack the knowledge to judge how big the speed gains due to the mRNA platform could be. Also, the same review as above mentions in the section "Safety" that there are more problems in clinical trials than there were in preclinical ones, so there still seems to be considerable need for basic research left. Similarly, I do not know how long the phase of vaccine clinical trials normally is and how much it could be reduced by logistics without loss of information. Finally I don't know what studies could be left out for an emergency approval of the vaccine to cut the approval time if the benefit would outweigh the risk.

I would be grateful if you could help me on the questions in bold.


texts: Why is my white hair turning black/dark brown?

texts: The only change I have made is I started taking a multivitamin daily (centrum silver, men over 50) about a month ago....Now I see black hairs in my beard and on my head.  I was prematurely gray (started at age 20) and have been completely gray/white for the last 20 or so years. Just curious...


texts:
The mushrooms are gilled with a light-brown cap. The stem is widened to the base.

What species is it? Is it considered edible?

They are found in mixed forest in Moscow, Russia. They grow in the ground quite separated from each other.


texts: Which species were first described by Charles Darwin?

texts: There are many plants and animals named for the naturalist Charles Darwin, such as Darwin's Frog (Rhinoderma darwinii), but which were named by him? I'm finding it difficult to find such a list.


texts: Difference between "transcriptional activity" and "RNA expression"

texts:
I am working with a network object where the nodes are different events in molecular biology.

Specifically;
Catalytic activity of X,
RNA expression of X,
GTP-bound activity of X,
Kinase activity of X,
Oxidoreductase activity of X,
Phosphatase axtivity of X,
Transcriptional activity of X,
Phosphorylation at residue Y.

What is the difference between RNA expression and Transcriptional activity? And which is the one that an Affymetrix microarray is measuring?
eg.;
transcriptional activity of KLF2, transcriptional activity of ATF2 RNA expression of HSPA1A RNA, and expression of CYP1B1


texts: What happens if nerve impulses go the wrong way?

texts:
So in nerve impulses, I get that the refractory period is important because it stops the action potentials going the wrong way along the axon. I have two questions:

What would the impact be of the action potential going the wrong way along the axon?
Are there any diseases that maybe cause the refractory period to be shortened so that the action potential goes the wrong way?

Thanks for any help!


texts: Why did mammals evolve to have two testes?

texts: What makes mammals tend to evolve to have two testes?


texts: Why the genome is divided into several chromosomes and not just a single big chromosome?

texts:
In many eukaryote species, there are several chromosomes. In humans, for example, there are 23 pairs of chromosomes.

Why are there several chromosomes and not just a join of all chromosomes into a single big chromosome?


texts: What is 'exhausted buffer' in gel electrophoresis?

texts:
For gel electrophoresis of DNA, we use TAE or TBE.
TAE buffer is cheaper than TBE but it has low buffering capacity; it exhausts faster than TBE buffer and there is a need to change the buffer during gel electrophoresis when electrophoresis longer.

but what is 'exhaused' in gel electrophoresis?


texts: What is the distribution of the expected number of lineages in a birth-death tree after time T?

texts:
I've been looking at The reconstructed evolutionary process by Nee et al. 1994 and they provide a number of equations dealing with the birth-death process, specifically the "reconstructed" birth-death process where you only have information about lineages that currently exist today.

I am interested in this equation for the likelihood of observing N lineages after time T:

What I want is the distribution of the expected number of lineages N after time T given per-lineage birth and death rates lambda and mu. I've looked around and haven't found anything providing such an equation.


texts: Do the eyes play any role in producing the visual experiences you have during dreaming?

texts: Sometimes, you remember a vivid picture of a dream that you saw. What is the role of your eye in this experience? Please provide me with the answer that is as simple as possible since I am in Class 10(Grade 10).


texts: Amount of reverse transcriptase in µg or mM for qRT-PCR

texts: I am trying to calculate a titration amount for a molecule which I would like to use in my PCR samples. Different molecules have different densities so I would like to calculate the appropriate density of the titrated molecule. How many micrograms or microMolars of reverse transcriptase are used in qRT_PCR kits?


texts: Is Covid-19 likely to mutate into a deadlier form?

texts: When the Spanish influenza hit in 1918, it struck in two waves. The first wave was typical for a flu virus, targetting mainly elderly people, but the second wave was far deadlier and killed far more young people. How likely is it for something similar to happen with the current coronavirus? Also, wikipedia states that people who contracted the virus during the first wave were immune to it in the second wave. I thought when a virus mutates it usually avoids detection, hence why we need to usually get an up to date flu vaccine annually. Why was this not the case for the spanish influenza?


texts:
I realize this is a bit of a long shot, but sometime this year I was reading a paper about experiments that I believe were performed in Drosophila (may have been planaria) where breeding was delayed until late adulthood through separation of the sexes. After a number of generations there was significant lifespan increase.

Anybody come across this that can point me to it?


texts: Would intravenous insulin + glucose significantly accelerate glycogen synthesis?

texts:
Would an intravenous injection of insulin + glucose result in significantly quicker replenishment of exhausted glycogen stores than an injection of glucose alone?

This is a strictly theoretical question and I'm aware of serious dangers of intravenous insulin (Diabetes Spectrum). It is to help with writing a story in which a quick recovery from exhaustion is needed.

After heavy exercise, during which the glycogen stores are depleted, the glycogen can be replenished fully in about a day by consuming high-carbohydrate meals (PubMed).

According to one study, intravenous glucose stimulates glycogen synthesis, but there is no timing mentioned.

Would adding insulin into glucose injection further accelerate glycogen synthesis and for how much? Is there any minimal time needed for glycogen synthesis regardless of the amount of glucose and insulin available?

The added insulin would probably inhibit the natural secretion of insulin from the pancreas, so does intravenous insulin injection even make sense?


texts: Why has the term "natural history" been used to denote the study of nature, and more recently, of life?

texts:
The term "natural history" is a translation of the Latin phrase historia naturalis meaning "the story of nature". Nowadays denoting the study of life, it originally also covered astronomy.

Why has there been the notion of "story" here, even in studies that by themselves have taken the form of the classification of collections using a principally synchronic approach that has paid little attention either to changes that organisms experience during their lifetimes or to evolution?


texts:
I came across a few sources that refer to glycocylation. Is this the same as glycosylation?

See for instance page 237, or the abstract in this paper.

"glycocylation" - 1210 search results on google
"glycosylation" - 5.98m search results on google


texts: Introductory literature for synthetic / systems biology

texts:
I am a computer engineer (MSc in Computer Engineering) who's looking to switch into the field of synthetic / systems biology. I have a comprehensive layman's understanding of evolution, genetics, transcription, etc, but my academic studies have been in the areas informatics, computer science, computer engineering and mathematics.

Does anyone have a good recommendation for standard literature in the field, to get me up to speed?


texts: Why are fearful stimuli more powerful at night?

texts:
For example, horror movies appear to be scarier when viewed at night than during broad day light.

Does light have any role in this phenomenon?

Are there changes in hormones at night versus during the day that makes fear stronger?


texts: Using catalase-test to determine if Staphylo- or Streptococcus

texts:
If the microscope clearly shows bacteria of cocci morphology but it is difficult to determine if they are Staphylo- or Streptococcus, are catalase tests a good way to differentiate between the two since Staphylococcus are positive and Streptococcus are negative? Are there any traps/exceptions?

Thanks!


texts: Is the frequency at which a species mutate affected by natural selection?

texts:
As per natural selection, is it safe to assume that some species will have it genetically encoded so that they produce a certain 'perfect' rate of mutation so that they can adapt to an environment that changes quickly?

Another way to put this; does every type of organisms have  roughly the same amount of mutations each time they reproduce (relative to the size of their DNA)? If so, is/can/could this be governed by natural selection?


texts:
Does the peripheral nervous system have a system of routers that decide where a message is meant to go based on some kind of address, or does a signal from the brain follow a single, unbroken chain of neurons that starts at the brain and ends at one destination?

For example, let's say my brain wants to send a message to my left pinky, telling it to contract. In the first model, a series of action potentials travel down my spinal cord, reaching a node in my chest. The action potentials encode the "contract" command as well as an address. The node in my chest reads the address, and routes the signal down my left arm. It reaches my left hand, where another node reads the address and sends the signal to my left pinky, where the signal reaches the appropriate muscle, telling it to contract.

In the second model, every single muscle in my body has a particular chain of neurons that runs in parallel to my brain. If my brain wants to send that signal, it doesn't have to specify an address, it just sends the "contract" command down the path that says "Leads directly to left pinky and nowhere else".

If the second model is true, does that mean that the large, visible structures that we call "nerves", such as the vagus nerve, are actually bundles of point-to-point connections?

Anywhere I can find more information about this would be awesome. I'm a comp sci/biochem double major, and really love reading about the body as an information system.


texts: Is returning cholesterol to the liver really performed by HDL?

texts:
Various answers in biology SE, including two quite upvoted ones (1, 2) claim that (in humans) returning cholesterol to the liver is done by HDL.

If I understand correctly, Wikipedia's Reverse cholesterol transport page also says this is done by HDL.

However, this blog post (by Peter Attia) says:

  Historically this process of returning cholesterol to the liver was
  thought to be performed only by HDL’s and has been termed reverse
  cholesterol transport, or RCT [...]

  This RCT concept is outdated as we now know LDL’s actually perform the
  majority of RCT. While the HDL particle is a crucial part of the
  immensely complex RCT pathway, a not-so-well-known fact is that apoB
  lipoproteins (i.e., LDL’s and their brethren) carry most of the
  cholesterol back to the liver.  In other words, the “bad” lipoprotein,
  LDL, does more of the cleaning up (i.e., taking cholesterol back to
  the liver) than the “good” lipoprotein, HDL!

Which is right?


texts: How does the structure of the pancreatic acinar cell relates to its function?

texts:
So the pancreatic acinar cell synthesizes, stores and secretes digestive enzyme precursors called zymogens e.g. pepsinogen.

The structure of the acinar cell shows that there is an apical and basal side. The basal half of the cell is almost entirely filled with rough endoplasmic reticulum which can be shown with pyronin stain showing up pink due to the rRNA of ribosomes. The nucleus is also on the basal side which explains why rER is there too, since the nuclear envelop is connected with the ER membrane. Zymogen granules are on the apical region. Any thoughts as to why there is this polarity in cell?


texts: Are all/most/any membranes comprised of lipids from the smooth ER?

texts: I'm attending an introductory high school course to cell biology. Based on my understanding, lipids – the building blocks of membranes – are formed in the smooth ER. Are all/most/any membranes comprised of lipids that are formed in the smooth ER? If not, where do the lipids of membranes come from?


texts: How does someone with red-green colorblindness see yellow on a monitor/television?

texts: I recently watched the video This Is Not Yellow explaining how red, green, and blue pixels can be used to create images of all other colors. Since yellow is created with red and green pixels, how is a person with red-green colorblindness (me, for instance) able to perceive yellow on a monitor?


texts: What is the name of this plant (see pic)?

texts: This plant was found growing in Colombia.


texts: Is this a valid principle of curing HIV?

texts:
I have a set of questions actually, it will be very helpful if you answer them in order.

Where does the HIV virus hide (during incubation period)? Let answer be X cell.
Is X cell in the bloodstream?
What parts of the HIV are constant for all its version? (I suspect it's Reverse Transcription Protein, Glycoprotein 120 and 41) Let answer be Y.
Is there a chemical that can destroy Y?
Is Y present in the normal Human body?
If Answer to question 2 is yes and that to question 5 is no can we inject the said drug into the bloodstream so that it can wipe out the virus?


texts: is left brachiochephalic vein and left pulmonary artery is same?

texts: I am reading about ligamentum arteriosum which connects the left pulmonary artery and descending aorta. But I am seeing that if any figure shows left brachiochephalic vein it does not show left pulmonary artery (and vice versa). Are they both the same?


texts: Do Penicillin based antibiotics affect birth control?

texts:
I wasn't sure whether to ask this question on Biology or Chemistry Stack Exchange, since it is really biochemisty, but this is something that's been puzzling me.

Most pharmacists (all that I've encountered) tell you that antibiotics decrease the effectiveness of birth control. There are side-effect warnings on all Penicillin based antibiotics that say they decrease the effectiveness of birth control, and advise you to use a back-up method when taking antibiotics.

However, most health organization websites (Planned Parenthood, Mayo Clinic, NHS) explicitly state that ONLY two antibiotics have been shown to sometimes decrease the effectiveness of birth control-- Rifampicin and Rifabutin.

NHS Website: http://www.nhs.uk/conditions/contraception-guide/pages/antibiotics-contraception.aspx

Yet websites of Pharmacies like Walgreens or CVS say that to a lesser extent Penicillin based antibiotics can decrease birth control effectiveness, or in general remain vague about antibiotics affecting birth control :

http://www.walgreens.com/topic/faq/questionandanswer.jsp?questionTierId=600006&faqId=600022

So--do Penicillin based antibiotics affect birth control?


texts:
Hello I'm not sure if this is the proper place for this question. If not, I am happy to move it.

I'm trying to find a source of data on different crops, is there some governmental database that houses this kind of data? After looking for a couple hours on google and reading a few different articles, I have not really found what I was looking for.

For example, consider the crops maize, wheat, sorghum and sugarcane. I could be looking at the different kinds of carbohydrates an their proportions in these crops, or I could be wanting to know the amount of water needed to produce some yield, what kind of soil each crop likes as well as how different hybrids and mutants have different needs or qualities.


texts: How to build a phylogenetic tree without an outgroup?

texts: I have whole genome aligned sequences of four beetle populations of same species. I wish to construct a phylogenetic tree with the four. However, I am unable to find a suitable outgroup of the species, so I cannot use an outgroup to root the tree. Is there a particular method that one can use to construct a tree without an outgroup? I found that the MEGA software does this well. What is the theory and understanding of constructing a tree without an outgroup? what are the implications of constructing a tree without an outgroup? Ar the distances between trees measured relative to one another?


texts:
What are the plasmids composed of? Are they composed of genomic or non-genomic DNA?

I guess the answer is "genomic DNA" but I'm not sure.


texts: Y285 Yeast Strain: Where to obtain from?

texts:
Often I see yeast strains mentioned like Y285 or Y301 etc. in papers. Is this some sort of universal notation? (Link to poster: https://ddd.uab.cat/pub/tfg/2014/119349/TFG_narcisferrerledo.pdf)

How does one go about locating such a strain to try in an experiment; are there repositories where you can get a strain from?

e.g. I tried searching the strains databases at Yeastgenome.org & DBVPG but these names ("Y285") don't produce any hits. Is there another canonical name I should be using to search them by?

http://wiki.yeastgenome.org/index.php/Strains

http://www.dbvpg.unipg.it/index.php/en/database

I even tried searching in the "National Collection of Yeast Cultures" but no luck. Any tips?

https://catalogue.ncyc.co.uk/catalogsearch/result/?q=Y285

Edit:

Found this related thread on SE-Biology that gives links to other useful Repositories.

Sources for common laboratory Saccharomyces strains?

Am I just searching with the wrong name? Is it common to refer to Y285 by some other name?


texts:
Reading from Oshima et al. (2016):

  We identified 3,868 noncoding mutations including 394 located <5 Kb downstream, 1,762 intergenic, 1,621 intronic, 81 <5 Kb upstream, 7 UTR 3′, 2 UTR 5′, and 1 intragenic variants.

How upstream, downstream and intragenic variants are defined? Shouldn't intragenic variants be classified within intronic variants, and upstream/downstream within intergenic variants?

Edit: By adding the different numbers it seems they are mutual exclusive. While upstream/downstream variants can be defined as intergenic variants that lie close to genes, I haven't found a definition to tell the intragenic variants from the intronic ones.

Edit 2: The only explanation I could think of for intragenic variant is that it is located in a coding region which is not transcribed due to alternative splicing. Can it be possible?

Oshima, Koichi, et al. "Mutational landscape, clonal evolution patterns, and role of RAS mutations in relapsed acute lymphoblastic leukemia." Proceedings of the National Academy of Sciences (2016): 201608420.


texts: Why do patients with type 2 diabetes not show the body wasting seen in type 1 diabetics?

texts:
Type 1 diabetes results from the destruction of the cells in the pancreas that produce insulin, while type 2 diabetes is characterized by so-called "insulin resistance", presumably a reduced responsiveness of the body's tissues to the effect of insulin.  More succinctly, in type 1 diabetes, insulin is not produced at all, while in type 2 diabetes, insulin is produced, but it is ineffective.

Based on this description, one would expect that type 1 and type 2 diabetes would look similar, with maybe type 2 diabetes being a milder form of the condition.  This is not the case, however.  The diseases are markedly different, at least when it comes to their effect on body weight.

Type 1 diabetes results in wasting:

The images show a type 1 diabetes patient before and after insulin treatment.

In contrast, type 2 diabetes is associated with obesity, exactly the opposite scenario.

If the body does not respond to insulin in type 2 diabetes, why don't those afflicted waste away, in the way that (untreated) type 1 diabetes patients do?


texts: How can I propagate a community of anaerobic bacteria sampled from mud in a bog?

texts: I'm doing research on anaerobic bacteria. In the fall I took mud samples from a bog and have been working with them but I didn't take enough. Now winter has rolled around (Im in Canada) and all the bogs are frozen over. I need more material to work with — is it possible to make a mud mixture myself and carry over the bacteria?  If so could anyone help me out with the mixture ratios? Is contamination a concern here (I would assume not)? And how long would the propagation take?


texts: Is it possible for a human and another ape species to reproduce?

texts: Is it possible for a human and another species to reproduce?


texts: Explanation of the terms "downstream signaling" and "upstream signaling"

texts: In molecular biology, what's the meaning of the terms "downstream signaling" and "upstream signaling"? What's the difference between them?


texts:
Is it possible to tell or rule out (potentially a priori) whether any given substance or compound is likely and how likely to cause allergies with high confidence, without the need to conduct experiments, e.g. by looking at its properties, e.g. solubility, molecular structure or reactivity?

From what I've heard is that generally speaking, things that we come in contact with in early years tend to be less likely to cause problems later on, but still, there seem to be differences even with food and substances that do not quite appear to be exotic, e.g. peanuts.

This question is related to these, though I'd consider it more generic.

Meat and mushroom allergies, why are they so rare?
What is the smallest molecule that can present as an antigen to the immune system in the context of allergies?


texts: How would substances that have anti bacterial characteristics interact with yeast?

texts:
This question has its origins at home brewers where the question was asked how would substances with anti bacterial qualities interact with yeast a fungus?

No one at home brewers was really sure so I thought I would ask here.

LINK


texts: What are the molecular mechanisms behind tachyphylaxis (downregulation of receptors in response to an agonist?)

texts:
Anyone know of a good source which explains this?  Or is this still an open question?  This wikipedia article describes some molecular biology behind morphine tolerance, but it sounds like its newer research, and isn't fully understood. http://en.wikipedia.org/wiki/Drug_tolerance

I would have thought that something like this would be very well understood.


texts: Bird identification by sound; midwestern US

texts:
This one's been bugging me for a couple of years. Location is southwest Michigan.

Here are a couple of song samples (I couldn't separate it from the Titmouse... they're pretty chatty these days):

Unidentified Bird 1
Unidentified Bird 2

Closest I can come up with is an Eastern Towhee, but the trill doesn't seem quite right. All the samples I've been able to find have it pretty constant in pitch and tempo, but this one gets a little higher and slower as it goes on.

This is a rural area. Our property is about half grass/prairie, half wooded. The sounds seem to come from a line of tall evergreens at the front of our property (an otherwise more open area), but I have yet to actually find the bird, so I can't be sure. A creek runs behind our house in a wooded area, about 400 feet from where the sounds appear to be emanating. These clips were taken about an hour after sunrise.

Can anyone identify this bird?


texts: What determines the length to which hair grows?

texts: Correct me if i am wrong, if we cut 2mm from eyebrow hair, it will grow 2mm and then stop growing, or if we cut 5mm, then it will grow only 5mm. My question is, does hair know how long to grow ?


texts: Identification of Unknown Insects found in landfill (spider like)

texts:
Could someone help me to identify the following spider-like insects? They are very small, so I used a macro lens to capture them. I have tried to capture them as clearly as possible.

They are about 2-3mm long with a black hairy head/belly.

They were collected from a closed section of Tseung Kwan O Landfill and Clear Water Bay Country Park of Hong Kong. This area is revegetated so the ecology is much like an area which contains many kind of trees.


texts: Why ml scale blood retrieval is required to run a blood test?

texts: Substances found in blood are present at microscopic scale and tend to be invisible to the unaided eye. Why is a whole vial of blood (at ml scale) is required to assess the presence and concentration of substances, given that the modern equipments and testing is becoming more and more sensitive and efficient?


texts: How do susceptible organisms prevent parasites from overcoming resistance?

texts:
Bt corn is genetically modified to kill borers, but "regulations require farmers to plant conventional varieties as well, which is intended to stop the borers becoming resistant."
-Source

How do susceptible organisms prevent parasites from overcoming host resistance?


texts: Why some muscles have more tendons than others?

texts: Very interesting examples to me are Trapezius or Latissimus - they both have places with more tendons than muscles. Taking into account that now they contract weaker and slower with all these tendons, what are the profits?


texts: Can anyone tell me what type of fish this is?

texts: Notice the reflective patterns on its underside.  I think it must be a deep water fish.  It was found washed up on the ocean sand in Myrtle Beach, South Carolina (USA) after a hurricane.


texts: Is "computational biology" different from "bioinformatics"?

texts: Are "computational biology" and "bioinformatics" simply different terms for the same thing or is there a real difference?


texts: What makes teeth feel sticky after drinking Coca-Cola?

texts:
I asked some of my friends and we all agree that teeth feel funny after drinking Coca-Cola. Other similar soft drinks also cause this effect, but this one most noticeably. It's like teeth become sticky and moving them against each other (by moving jaw) creates rubbery feeling.

What ingredient in this soft drink makes teeth like that?


texts: Why do some women have menstruation-like spotting throughout their pregnancy?

texts: An interesting question that was asked during a lecture about human reproduction: what is the biological mechanism behind some pregnant women getting monthly spotting that they mistake for a regular period? I've found articles and research papers about bleeding during zygote implantation, ectopic pregnancies and problems with the placement of the placenta, but nothing regarding menses-like bleeding during otherwise unproblematic pregnancies.


texts: Why is Glycerol 3-phosphate named in such way? Shouldn't it be named as Glycerol 1-phosphate by proper IUPAC- nomenclature?


texts: Is it possible for two people to repopulate earth?

texts:
Today I was wondering this question whether it is possible for two people to repopulate Earth.

What if everyone else disappeared, except for two people (man & woman)? Can they repopulate? In that case, what are the odds against and in favour of that ever happening?


texts:
I found this insect case in my garden in the south of Melbourne (Australia), under some dried leaves from a tree that I'd cut down.

It is 8 cm long, which is pretty big for an insect! The photo is of the underside. I don't recognise it. What species is it?


texts: How only one follicle develops into graffian follicle?

texts: I've studied that one out of many follicle develops into mature or graffian follicle. The fact which confuses me is that, since all follicles are in same ovary, close to each other with equal supply of nutrients. What causes the other follicles to give up the race? Why our body cannot develop mature follicle from a single one?


texts: Why are human titin and mice titin considered the same protein?

texts:
I have a book that says:

  In humans titin is a chain of 34,350 amino acids, but in mice it is even longer with 35,213 amino acids.

If two polypeptides had different amino acid sequence lengths, how can they be considered the same protein? Or is it because they share in common one or more amino acid sequences - which, if a polypeptide contains, biologists consider it a particular type of protein - that they are both considered the same protein?


texts:
If Rh- mother has Rh+ baby, the mother can become sensitized during first pregnancy and then if subsequent fetuses are also Rh+, there can be eryhtroblastosis foetalis.

I read that if mother is O- and baby is any +ve blood group other than O+ , then mother will not become sensitized during first pregnancy because a and b antibodies present in her blood will attack the antigen present on the fetus RBC and there will be no time for the mother to synthesize antibodies against Rh.

My Question : Can't the same logic be applied to all other blood groups? For example : A- mother and B+ baby.


texts: Is there a more updated version of the book "Genome?"

texts: I read the book Genome by Matt Ridley for my AP biology course. I found it fascinating, although it seems another book must have been written on the topic since 1999. Anything you can recommend?


texts: Why cooked food considered nutritious if proteins decompose at much lower temperatures?

texts: Food is cooked/baked at temperatures that are significantly higher than what's considered normal for proteins/amino acids (40°C). Why is it, then, that such food is still considered nutritious after cooking? (meat, cheesecake, lentils, quinoa, mushrooms, etc.)


texts: Why only water in liquid form is essential to live?

texts:
My question is:-
Only liquid water supports almost every living organism's metabolism, neither the vapour nor the condensed form of water does so. What is the chemical & the biological reason behind this fact?


texts: What happens when you mix catalase found in yeast with a small, medium, and large amount of isopropyl alcohol and hydrogen peroxide?

texts: I conducted an experiment trying to see what isopropyl alcohol does to the catalase found in yeast's catalytic activity. I can not make sense of the results which showed that a 1:10 ratio and 1:1 ratio of isopropyl alcohol amount to catalase had little to no effect on catalase's activity but a 1:2 ratio significantly decreased its activity. Could someone please explain this?


texts: Is hunting animals, crafting and attacking/defending from enemies intellectually equivalent to learning quantum physics?

texts:
Our brains were shaped after natural selection. Which means that, as long as we were being affected by it, our brains were changing, evolving.

Once we stepped out of nature and stopped being targets of natural selection, our brains (structurally speaking) stopped changing.

Civilizations rose, humanities and science developed, and you know the rest of the story.

But the brains that we used to create all that is the same brain that was shaped by natural selection. A brain that was concerned with animal hunting, food gathering, fighting with enemies, relating socially and so forth. It is curious to notice that we used that same brain to develop algebra, geometry, physics, astronomy, arts, and so on.

So, would it be correct to say that all those activities from our ancestors living in nature (gathering, hunting, fighting) are INTELLECTUALLY equivalent to quantum physics, i.e.? Because our brain capacity is limited to what happened to it during natural selection (while we were living in nature), so would it be safe to assume that whatever complex thing we can think of (such as quantum physics) is actually as hard as those activities our ancestors performed in nature?

This may be a very stupid question, but I couldn't find fallacies or wrong assumptions in my thought, but my conclusion seems to be a bit... unexpected? Please, correct me if I'm wrong, I'd really like to know the answer to this.


texts: What "algorithm" are carnivorous larvae using when foraging?

texts:
What algorithms are carnivorous larvae (lady bugs like Adalia bipunctata, Coccinella septempunctata, common green lacewing (Chrysoperla carnea) or hoverfly (Syrphus)) using as they are foraging for aphids?
Is it just random walk or something more efficient?


texts: Which method would more accurately help to identify the unknown concentration of a protein sample between the A280 and the Bradford methods?

texts: I quantified my protein using the standard Bradford method and the A280 methods and obtained values that were far off from the theoretical value of the protein of interest, and therefore was wondering if one method is better to use than the other.


texts: How does membrane potential vary between intraceullar membranes and the cellular membrane?

texts:
Question
Does each type of membrane have a different membrane potential? I'm especially interested in answers that can cite academic papers that have attempted to measure membrane potentials.
Discussion
I've asked about the composition of membranes before , and although I recieved some information, I didn't get all the information I was after. This isn't a problem with our community but rather with the field at large: the popular thinking is membranes are membranes are membranes (mostly due to the difficulties in studying membrane biophysics experimentally).
This is how wikipedia defines membrane potential:

Membrane potential (also transmembrane potential or membrane voltage)
is the difference in electric potential between the interior and the
exterior of a biological cell. - Wikipedia

This isn't strictly true. Intracellular membranes also have membrane potentials as one can imagine, and there is some unverified information regarding compartmental pH values. This is why I am interested to find out if there have been studies attempting to quantify this across the cell membrane, and across different subcellular membranes.


texts: Why there are no plants that offer salt fruits as opposed to sweet fruits?

texts:
Why there are no plants that produce salt fruits?

Is it because other animals do not like salt to the same degree of humans?


texts: Why are dogs so selective about choosing a spot to defecate?

texts:
Anybody who walks a dog knows that dogs are normally selective about choosing a spot to defecate. They sniff around for a long time, while I just want to be on my way.

I understand about marking territory with urine. Is it the same with feces?


texts: Is there a relationship between efficiency of cellular metabolism and warm-blooded-ness?

texts:
My BIO 101 book states that when human cells convert glucose to ATP, the process is only approx 35% efficient, and much of the potential energy is lost as heat.  However, that heat is useful to us in maintaining our overall body temperature.

Cold-blooded animals (reptiles, for example) are not as effective at maintaining their own body temperature.  Does that imply that their cellular metabolism (conversion of glucose to ATP) is more efficient than humans, and thus doesn't produce as much heat?

Or is cold-blooded- / warm-blooded-ness completely unrelated to heat released during cellular metabolism?


texts:
I am trying to plant some trees which are usually native to colder climates into Subtropical climate, is there any possibility that if i plant these 20 trees saplings in winters they will grow to be a tree, due to some random genetic mutation, given all nutrients all provided to it?

Tree in Question is Deodar


texts: Warburg effect in lung carcinoma, the logic?

texts:
Outside of 'purposefully' removing mitochondria to diffuse cytochrome C's apoptotic threat, I would assume that lung carcinomas, and their proximity to high oxygen levels, would have the lowest rate of cells entering the Warburg effect. Would this be a correct assumption?

Thanks


texts: Do we consume DNA and proteins of other organisms?

texts:
When we eat raw meat, e.g. chicken or fish, we are actually consuming the DNA, proteins etc. which are present in their cells.

Wouldn't this affect our cell functions as this DNA might enter our cells?
It is known that we get energy by eating them. Is it glucose or ATP or some other form of energy that is produced from them?


texts: I have several photos of a plant I believe to be in the genus Astragalus. I would like to determine the particular species in my area, the foot hills of San Diego County. Do I need a microscope to determine species, or can it be determined from the naked eye? How exactly should I proceed?


texts:
While sleeping in a Tajik homestay these guys have been feasting on my blood and left (they didn't bother to hang around in my skin). The bite marks are pretty nasty, this one is 5 days old. Locals say they come out of the ceiling, that it is normal and we shouldn't worry. Are they right? (https://i.stack.imgur.com/slA9L.jpg)
Bite mark (https://i.stack.imgur.com/Mx33E.jpg)


texts: What can myelination tell you about the evolution of sensory receptors?

texts:
I am reading Avi Chaudhuri's Fundamentals of Sensory Perception and wondering if the information given about the somatosensory system could tell us anything about the way it evolved.

It seems (at least naively) reasonable to assume that nerves became larger and more myelinated as time went on. The types of somatosensory nerve fibre are (in order from least to most myelinated):

C < A-delta < A-beta < A-alpha

This gives an ordering on receptors of:

warm receptors < cold receptors < nociceptors < tactile mechanoreceptors < proprioceptors

My question is then: was this the order in which these receptors evolved? If not, can myelination still give us useful information about the evolutionary history of the nervous system?

P.S. Meta question: is this question better suited for the Bio or Cog Sci stack exchange? I asked it here since it seemed to be more about evolution than neurons.


texts: Is there any situation where bloodletting should be paired with transfusion?

texts:
Clearly, bloodletting only has benefits in a couple of rare instances —— for example promoting blood flow into reattached tissues1. But could it (or, should it) realistically be used along with transfusion for any purpose? Why or why not? (Based on Bradbury's Fahrenheit 451, where it mentions a blood transfusion/removal device)

1: Bennett-Marsden, M., & Ng, A. (2014). Hirudotherapy: a guide to using leeches to drain blood from tissue. Clinical pharmacist, 6.


texts: How detachment/separation works in biology?

texts:
It might be a strange question, but I'm interested in the mechanics of separation/detachment during asexual reproduction, for example when an organism reproduces by budding (I don't mean cellular budding like baker's yeast). When the newly formed body is fully matured it detaches itself from the parent / original body.

It might not be caused by a specific tissue, as animals with not so differentiated bodies are (also) capable of such, but I could easily be wrong. Is this (the detachment) triggered by changes in the cell membrane? I can't really think of other explanations.


texts:
I have found this 8mm spider in my home, North London. I've been told it may be a false widow but wanted a second opinion.

Note: The silvery parts in the picture are actually brownish in colour


texts: Is it possible to use a biologically active Telemorease Elongation Reverse Transcriptase (TERT) in the place of the Reverse Transcriptase (RT) for quantitative Reverse Transcriptase pcr (qRT-pcr)? Yes I do know that it would seemingly have no advantages. What kind of reverse transcriptase is used in qRT-pcr is there a standard like taq dna pol is used for qpcr?


texts:
When performing a standard curve for some new primers to test for fold change, is it necessary to run the standard curve? I mean, in case your experiment has several genotypes for the same ecotype background, with correspondent control and treatments, must I run the standard curves for all this scenarios, or rather may I pick, just to say a random genotype of treated ones, see that it R=0.99 is or higher and efficiency 2?
It is in order to not to waste material.


texts: Cheapest way to measure S. aureus and Rhinoviruses density at home

texts:
I would like to measure the surface density of Staphylococcus bacteria and Rhinoviruses (only those two, to be specific) within my home.  What's the cheapest way?

The textbook procedure is to:

rub a clean wet cotton swab on the surface in a controlled way
dip the swab into a clean agar (or some living media to detect viruses?) dish
incubate the dish
"look for genetic patterns from special enzyme reactions".

Is it possible to do the last step at home?  Or, is there some easier way if I only care about Staphylococcus bacteria or Rhinoviruses?


texts: Ingestion of cellulose digesting prokaryotes?

texts: If humans digest cellulose digesting prokaryotes,  can  we start digesting cellulose like cows?


texts: How do cells slowly degrade 5,5'-dibromo-4,4'-dichloro-indigo?

texts:
5,5'-dibromo-4,4'-dichloro-indigo is the product of X-gal cleavage, often used as a reporter with B-galactosidase. I've made the (unreferenced) observation that it seems as though the blue product slowly degrades over periods of time within the cell, allowing for cells to lose their blue coloration.

What mechanisms can explain the degradation of 5,5'-dibromo-4,4'-dichloro-indigo within cells?


texts: Can experiments in ELISA kits be monitored via both fluorometry and photometry?

texts: In my bioanalytics course slides, the professor has written at one point that in a heterogenous immunoassay such as ELISA, we use fluorimetry to measure concentration of an analyte. In another slide it is mentioned that we use photometry to measure UV-vis absorption. I am confused... is it one or the other, or can we use both methods depending on whether the marker enzyme on the antibody is given a fluorescent or chromogenic substrate?


texts: Is there anyone discovered new drugs by actively create mutations in drug-producing organism?

texts:
Recently I was reading about drug discovery.

As far as I know, there are currently 2 sources of creating new compounds by:

Screening from natural sources.
Synthesizing by add/remove/replace-ing the functional groups of a known compound using chemical processes.

On the other hand, molecular pharming is the process of producing drugs by integrating the drug-encoding genes into bacterial (typically E. coli) genome.

I came up with the idea that if we create mutations in these drug-producing colonies, by UV light for example, eventually by chance we can obtain some new compounds once the mutations occur in the drug-encoding region or related genes.

I want to search in the previous studies for those who has come up with this idea already, I tried with several keywords and there's no luck.

I would want to ask is this idea practically possible? How high is the chance of having new compounds compare to screening natural sources and chemical systhesis? And if someone has already done this study, can you please provide me some references on this matter?


texts: Can Coronaviridae mutate into something as dangerous as Flioviridae?

texts: Can coronaviruses mutate to an extent to get as dangerous as fliovirusues such as Marburg viruses, Ravn or Ebola Zaire?


texts: How do prions transmit their conformation to other proteins?

texts:
I was reading about prions and many sources say something to this effect:

"Prions may propagate by transmitting their misfolded protein state: When a prion enters a healthy organism, it induces existing, properly folded proteins to convert into the misfolded prion form. In this way, the prion acts as a template to guide the misfolding of more proteins into prion form." (Wikipedia)

How can/does a prion cause another protein to change its shape to match the prion's?


texts: Functional Difference between the Distal Promoter and Enhancer Region

texts:
According to the Wikipedia article on eukaryotic promoter regions, the distal promoter is:

  Anything further upstream (but not an enhancer or other regulatory region whose influence is positional/orientation independent)

What is the difference between the regulatory region and the distal promoter? Does the distal promoter region have a greater effect on the rate of transcription?
If so, is the determination for what has a big enough effect to be a distal promoter subjective?


texts: How do you consider an organism to be a new species? Can a new parthenogenetic organism be considered as a new species?


texts: How can viruses have an incubation period of only 3 days?

texts:
Cold viruses seem to typically have incubation periods of 3 days, but from a mechanical point of view, I wonder how this is possible?

For example, if we read this viral assay protocol document: https://www.virapur.com/protocols/Virus%20Plaque%20Assay%20Protocol.pdf we can see that when a viral plaque is grown, then the plaque becomes visible in "5-7 days". So, since viruses have reproductive cycle of 6 hours, then that would be about 24 generations. Presumably each generation can only infect cells immediately adjacent to the infected cells since viruses cannot move on their own. So, the virus spreads in rings emanating outwards from the initial innoculation site.

If the visible plaque is 4mm in diameter, then we presume each generation is growing by 4mm/24 = 0.17mm which in itself is kind of suprising because a cell is only about 0.005mm in diameter, so the virions would seem to be simultaneously spreading by 0.17/0.005 = 34 layers of cells per generation. It is hard to see how they could do that without moving in some way. Maybe diffusion of some kind is occurring?

In any case, from geometrical standpoint I don't understand how a viral plaque in the wild could spread fast enough in only 3 days given what we see in the lab.


texts: How can I measure the curvature of bird's beak on the field?

texts:
I'm wondering if there is a standard tool to measure the bird's beak curvature.

It seems that a spherometer wouldn't work because the beaks that I'm measuring are not circular but more parabolic.

I guess something like this:

I feel that this can be a problem if your birds have different beak length.

What do you think?


texts: What is name of the red eyed rabbit or hare, found in Himalayan region?

texts:
Is it Rabbit or Hare?

The eyes are red in colour.

These animals are habitat of Himalaya.

The pictures are taken in Dowhill Park, Kurseong, West Bengal, India.


texts: Is there a biological basis for different accents?

texts:
How did accents first develop? Was it climate dependent? or was it a social behavioural issue?

Is there any biological reason for the development of accents?


texts: Found on my deck. We live next to a lake. Don’t know if a bird dropped it?  Not sure whether to save it?  Has scalloped front legs and a point from the end of what I think are wings. Antennae, mouthparts. Back legs either deformed or partly missing because can’t propel forward, just rolling side to side   I put it in a pen to keep it safe for now.


texts:
A hallmark of apoptotic DNA fragmentation is the digestion of DNA into individual nucleosomes. In addition, in the following experiment that tried to isolate the components of the nucleosome, the micrococcal nuclease only cleaved the linker DNA and not the nucleosomal DNA.

I've tried searching the internet but I couldn't find a clear answer to my question. Is nucleosomal DNA ever degraded? Are there nucleases that degrade it, and if there are, are they common? If nucleosomal DNA is not degraded, what protects it? The histone proteins?


texts: How does the splicing enzyme recognize where to splice the introns?

texts: When the DNA from the nucleus is transcribed to an mRNA, the mRNA is spliced by an enzyme before it goes outside through the nuclear pore. What is the name of this enzyme and how does it recognize where to splice the DNA so only the introns remain inside? Would it not need an instruction set itself to recognize exactly where to cut so the sequence does not change?


texts: regarding evolution of ears and sense organs

texts: How could we(or any other organism) have developed ears through evolution when before having ears we did not know that sound waves existed or there was anything such as hearing? How did the first hearing organ develop? The same can be asked for the other sense organs as well.


texts: Calculating sample concentration factor (opposite of dilution)

texts:
I am starting up an algae project, and I am getting a bit confused about some details in calculating density. For example, I take a sample of 250 mL, and concentrate it down to 25 mL with a sand filtration apparatus (factor of 10). I am using a gridded sedgwick-rafter chamber to enumerate the density of algal cells on a cells/mL basis using this formula from Standard Methods 10200F: cells/mL = [(# organisms counted)* (1000 cu. mm.)/ (field area)(field depth)(# fields counted)].

Once I calculate cells/mL, should I DIVIDE that result by my concentration factor (10)? My instinct is to multiply, but wouldn't that be appropriate only if I diluted the sample?


texts: Is there mismatch in injures or death numbers for carnivores that hunt during day time and night time?

texts: Is there significant mismatch in injures or death numbers for hunters (when hunter was killed or injured by its prey), between day time and night time hunts (carnivores that hunt during the day time and night time)?


texts: How do cell repair mechanism ratios change as they age?

texts:
I have seen that embryonic stem cells are shown to use homologous repair for double strand breaks rather then non-homologous end joining (NHEJ). [1]

I am wondering if something also happens to a cell's usage of certain repair mechanisms after diversifying.

For instance, is there any evidence that two cells in the same lineage but of different ages (one from a person who is 20, another from someone who is 80) use different ratios of repair mechanisms? Has there been any research on this or is there any indirect data that could support such an idea?


texts: In course of evolution did some exons become intronic  sequences or will introns in some species acts as exons in other species.


texts:
Location: southern India

Time: noon
Approx. Size:
Length: around 2 feet;
Size: extremely small, like a straw.
Diameter: less than 1 cm.
Was very fast in climbing aisle of mud bed/uphill like 90 degree accent.


texts:
I've been preparing wet slides for my kids to look at from pond water. I have a mason jar of pond water. What can I do to keep the microbes in the jar alive going forward so that we can look at it any time we want without having to go back to get more pond water.

I remember we did something like this in 7th grade biology, it seems like we put in sugar, or oatmeal, or something. I can't quite remember that though, it's been over 30 years. Thanks!

Thanks for the comments. The pond water I get keeps for a couple of days easily. I can always get more at the pond.

If I want amoebas, I go near dark and get them at the bottom of the pond. If I just want paramecia and other critters, I grab some scum and fill the rest of the jar up with water.

The paramecia water I give moderate sunlight. The amoeba sample I keep in the dark. And I just pitch it after a few days. No Legionella for my family, please and thank you.


texts: Why do birds that walk on the ground walk so "bumpy"? Most other animals walk quite smooth, doesn't matter if they are mammals, reptiles or insects or walk on two, four or more legs. Birds seem to be an exception and there is no difference between flying or non-flying birds.