texts: Increasing/decreasing signal intensity in Western blotting

texts: So I was in class and my professor was explaining western blotting. It seems as though there's more than one way to increase or decrease the signal intensity. He presented us the challenge to discover different ways this can happen. As hard as I look all I can find on the internet or even in google scholar is just certain chemicals like 'signal enhancer' and that's it, nothing remotely specific. Legitimately I do not propose this as actual homework, in fact it's just a curiosity I have. Therefore I ask the scientific community what, if any, are conditions that one could increase or decrease the signal intensity in western blotting? I understand what western blotting is, anyone can find this on wikipedia, but conditions that could increase or decrease signal intensity?


texts: Common english name for tissues which are separated from the blood by blood-tissue barriers

texts: Which general term is used to denote such organs/tissues as: brain, testis, thymus etc., which are separated from the blood by blood-tissue barriers?


texts: Why can't I read everything in my field of view?

texts: When I look at a piece of text, I can see all the text on the paper, no matter where I look, because my field of view covers it all. However, if I stare at a specific word, I cannot read the text a few lines above the position I am staring at, even though I can clearly see there is text there. I don't think it has anything to do with the text being out of focus, since I observe this phenomenon no matter what distance the paper is from me. What are the specific causes of this?


texts: Why do I drop my pen in a drowsy lecture?

texts:
I know that there is loss of muscle tone during REM sleep. Is this loss in muscle tone the reason I generally drop my pen in a sleepy lecture? But we were taught that sleep has 4 stages and REM sleep occurs after the 4 stages, ~90mins(?) post sleep. So technically, it should be that I'd be dropping my pen after 90mins of sleep. Though this is not the case. The pen drops generally when I'm at verge of sleeping.

I realise that there also is muscle atonia during other stages of sleep but, there is this famous story of Salvador Dali and the way he slept. He had a key in his hand and kept a tin plate beneath, as soon as he reached REm (dream) sleep, the key would fall and he'd wake up to draw stuff that he saw in his dream.

Why did Dali's key drop at REM sleep but my pen, way before that?


texts: Why is the Trendelenburg position used when placing and removing Central Venous Line catheters in the sub-clavian vein?

texts:
The title says it all. Why is it that patients are placed in the trendelenburg position when a catheter is inserted in the sub clavian vein? What would happen if the patient wasn't placed in the trendelenburg position when placing the catheter?
Thanks in advance for the help.


texts: Why do muscle spindles send impulses at a constant rate when the muscle is at rest?

texts:
According to my book, the sensory neuron around the muscle spindle is sending impulses at a constant rate, while the entire muscle itself is relaxated (at rest).

So when the muscle stretches the impulse frequency gets higher, right?

According to the book, the reason why this 'constant rate frequency at rest' is happening is because otherwise the muscle spindle wouldn't been able to know the difference between a relaxed and contracted muscle.

I don't understand this reasoning, could anyone explain?


texts: General transcription factors vs. DNA Binding transcription factors

texts:
I know that DNA binding transcription factors are trans-acting, but what about general transcription factors?
Are they cis or trans acting?


texts: What does the root "phyllum" mean used botanical binomial nomenclature

texts:
I often encounter the root "phyllum" in binomial names in botany, but I've had trouble finding an actual definition for this root in any Latin dictionary outside of its taxonomic meaning. From context it seems to mean "leaf":

Acer macrophyllum - Bigleaf Maple
Tsuga heterophylla - A Hemlock with distinct two-ranked needles

But the Latin for leaf should be folium. Is there any real rhyme or reason to this? I don't know if this is a question better directed towards the Latin stackexchange, but I thought a botanist might have some insight on the subject.


texts:
I have diagram of oxidative decarboxylation of pyruvate pathway. The pathway is between glycolisis and Krebs cycle.

How to read this diagram?

This excerpt from Harper's Illustrated Biochemistry, 30E, page 173.


texts: What is the difference between cell, membrane and animal based assay?

texts:
I am reading a review about MRP1, discussing it's ability to extrude different compounds from cell interior. When describing the different experiments conducted to observe the MRP1's reaction to different modulators, the writers refer to cell based, membrane based an animal based assays.
What is the difference between these three assays? What would be the purpose of choosing each of them for a specific test?
Thanks alot,
Yaron.


texts: Why is the Mongolian Horse superior in stamina?

texts:
I've heard a lot about the Mongolian Horse over the years, especially that it has more stamina than the Arabian Horse. It's a little smaller/lighter than an Arabian.

Apparently the Mongol Horse can outlast an Arabian, despite having a lower top speed, due to stamina. NOTE: I could not find a good source for this, especially when talking about medieval times. It's very hard to find a true apples-to-apples comparison, because of things like a heavy Knight vs a lightly-armored Mongol, and back then Arabian horses were a little different anyway.
The Mongolian Horse can subsist on grass alone, whereas the Arabian Horse needs a lot of oats if its gonna do heavy hauling or riding.
The Mongolian Horse doesn't need horseshoes, since for some reason the hoof doesn't wear down much over its lifetime.

Source 1, Source 2

I would like to know, what biological differences can explain this? Do they have a different kind of muscle? Is their heart or lungs significantly different? Bones?

And the granddaddy point: What percentage difference exists between the DNA of a Mongolian Horse versus an Arabian Horse? For reference, the difference between a human and a chimp is about 1.2% .


texts: It there any experimental approach to determine the electronic structure of a given aminoacid inside a protein?

texts: It there any experimental method to determine the electronic structure of a given amino acid inside a protein?


texts: Couple months ago noticed something was literally, for lack of a better term, eating paint off of lead pipes.  And I noticed joints in copper pipe seemed to be "leaking" flux. Now all the water in my house causes lips and tongue to feel as if they have cold sores or anesthesised.  taste could be rusty.


texts:
Does the process of photosynthesis occur in insectivorous plants?
Can you please give me a clear answer and explain to me how?
and also can you describe the environment in which they grow ?
Thank you


texts: What does it mean to have a Y-DNA Haplogroup "R-M512"?

texts:
I did a DNA test to learn about my origins, but the results are highly technical.

I see I have a Y-DNA Haplogroup R-M512 and a mutation (zero marker in DYS448). I Googled these terms and came across a bunch of technical papers, but I don't have the expertise in Genetics to make much sense of them.

I wonder if one of you can shed light on this?


texts: More proteins from diet when common cold and flu?

texts:
My coach says that I need to eat 1.2 - 1.5 grams of proteins per kilogram when I have a common cold and flu.
I normally eat one gram of proteins per kilogram, while double it when doing my exercise training.

He explained that the reason why you need to get more good proteins when you are sick is that the body is building antibodies by the adaptive immune system and later for innate immunity.

I think he can be right based only on my own experiences getting better from common cold with low protein diet - it just takes a lot of time, while under high protein diet, you get better faster.
I also think his explanation makes complete sense to me, since antibodies and antigens are proteins.

Why do you need more proteins when you are sick?


texts: In short, if I were to whack someone over the head, what factors play a role in whether the victim survives? Force? Pressure? Location? Something else?


texts: Has Colony Collapse Disorder (or its equivalent) been noted in other species?

texts: Colony Collapse Disorder is a well studied phenomenon relating to the decline of bee populations - has this disorder, or its equivalent, been observed in other colony-based species?


texts:
I am wondering if there is an organization, a document or a research that standardize all the rhythms? Such as describing how long should the ECG be flatline to be considered as asystole? The rhythm I am focusing on is:

Asystole
Missed beat
Tachycardia
Bradycardia
PAC
PVC
Bigeminy
Trigeminy
Atrial Fibrillation


texts: Can we apply NGS (next generation sequencing) on DNA extracted from formalin fixed paraffin embedded tissues (FFPE)?

texts: I'm working on the microbiome and I can only use tissues which are fixed with formalin and embedded in paraffin. Is it possible to apply NGS (next generation sequencing) on FFPE (formalin fixed paraffin embedded) tissues? I'm particularly concerned about contamination that could affect the results.


texts: Are there other examples besides wasps' polydnaviruses in which a parasitic species introduces an immunosuppressant virus in the parasite's host?

texts:
An interesting form of mutualism:

  Parasitoid wasps serve as hosts for the virus, and Lepidoptera serve as hosts for these wasps. The female wasp injects one or more eggs into its host along with a quantity of virus. The virus and wasp are in a mutualistic symbiotic relationship: expression of viral genes prevents the wasp's host's immune system from killing the wasp's injected egg [...]

I'm guessing suppressing the immune system of the host is done by other parasitic species in various ways, but are there any other examples in which a virus is "used" for this purpose?


texts: Topography of motor deficit and spasticity in UMNS

texts:
As a medical student, I have been told that upper motor neurone syndrome is a cause of motor deficit and spasticity. The motor deficit is said to be affecting predominantly the extensor apparatus at the upper limbs and the flexor apparatus at the lower limbs. To the contrary, spasticity is flexural at the upper limbs and extensive at the lower limbs.
Can someone explain me why the motor deficit and spasticity affect differently the upper and lower limbs ? I have found no useful reference dealing with the subject. Many thanks in advance.


texts: Do some colors trigger more neural activity in human brain?

texts:
On this webpage I found this:

  The study found that “globs” in the brains of monkeys reacted differently to colored
  stimuli, and reacted based on color. The brain was most triggered by specific colors
  (red, then green, then blue) and colors with the most saturation. What this tells us is
  that these colors immediately impact a user and draw attention.

Question: Do humans show similar increased neural activity to some colors?

Then I found a perception curve in this webpage

While this curve tells that yellow and green are seen before other hues while red and violet are difficult to perceive; I am not sure if yellow and green elicit more neural activity in the brain.

Anything to say on this matter?


texts: Most eukaryotes posses a certain amount of junk DNA in their cell nuclei. What is (are) the origin(s) of this junk DNA, And is it realy junk (superfluous)?


texts: Disproportion in cranial nerve innervation?

texts:
The cranial nerve innervation is highly disproportionate, as far as humans are concerned.  I am not sure of the advantage of being innervated by cranial nerve versus being innervated by a normal spinal nerve branches, if any.

If there is any advantage to be innervated by cranial nerves, why is there such a largely disproportionate distribution of these cranial nerves?

  Only the Vagus nerve (X) innervates parts other than the head of the
  animal. While there are 3 motor nerves just for the 6 eyeball muscles
  and the ciliary muscles (III,IV,VI), there is only one mixed nerve
  (X) innervating heart, gastro-intestinal tract and the respiratory
  apparatus and all smooth muscles therein. While there are three nerves
  for gustatory receptors, (VII,IX,X), one for retina (II), cochlea
  and vestibule (VIII) and the olfactory receptors (I) each, the
  entire plethora of intero-receptors in thoracic and abdominal viscera,
  aortic arch, external auditory meatus, tympanic membrane etc are
  carried by a single nerve (X). I am not sure if the disproportion is limited to the disproportionate area of innervation or even to the density of innervation in the target tissue.

Below are a few possible explanations that I came across while surfing the net, all without any strong arguments.

Is it because of the fineness of the senses in the head, i.e. the skin receptors in facial skin being higher than in the general body, providing a finer resolution of tactile reception? The special senses (vision, hearing, smelling and tasting) are also very fine in their resolution and might require more concentrated innervation and direct interpretation by the brain. But then the fingers and feet also have a high density of skin receptors, and the tactile sense can also be very fine (owing to several different kind of receptors) requiring dense innervation? Certain body movements (especially of hand) are very fine and detailed, requiring a very dense and co-ordinated motor neuron framework.
Is it because the cranial nerves, owing to some developmental restraint or functional trade-off, can only innervate areas close to its place of origin effectively? This might explain why 11 pairs of nerves innervate only the head region and only 1 pair innervates the remaining body. I have no idea about the validity and the reason of this claim.
Could it just be a random evolutionary outcome, there being absolutely no benefit of cranial innervation leading to random drift in the innervation patterns?


texts:
Major North American cities are full of large cockroaches. Given their numbers and relatively short lifespan, there must be staggering quantities of cockroaches dying in a city every day. However, I never seem to encounter their carcasses in cities.

I notice a fair number of dead roaches indoors, which actually surprises me since you would think that there is more thorough cleaning and pest control indoors vs. city streets. The number of dead roaches I see indoors seems about consistent with the number of live ones.

However, outdoors I see a lot of live roaches, and hardly any dead ones. Most carcasses I notice are mechanically damaged and near heavy traffic areas, so most likely stepped on by someone who was walking by. But what about roaches dying of natural causes (or disease/poison)? Are there animals that scavenge the carcasses very efficiently (ants? birds?)? Do the roaches like to run away and die in isolation? Do they just not die naturally very often, and usually get hunted by a predator?

Note that I am asking specifically about city cockroaches, in mostly concrete areas.


texts: Does ATP hydrolysis reaction have a high or low activation energy?

texts:
I was recently studying about ATP and how it functions as an energy carrier to all biological processes; however, I came across a confusing and paradoxical statement from two sources:
(at 7:36)
and
(the free response question in the bottom of the page)

Basically, in the video, it says that ATP hydrolysis has a high activation energy which is why all of the ATP isn't randomly used by the cell processes.

And in the free response question, the answer is that ATP hydrolysis has a low activation energy and low free energy making it a spontaneous reaction.

A follow up question is: How then does the ATP of the cell used in a selective way to certain processes only?

Thanks for your help.


texts: effect of background selection on promoter regions compared to distant enhancers?

texts:
Has anyone looked at the effect of background selection on the levels of conservation of promoter regions compared to distant enhancers? Do promoter regions have a higher conservation due to background selection from nearby genes compared to more distant enhancer regions?

My attempts to google for this only gave me a 2004 Drosophila paper on a few genes survey:

http://mbe.oxfordjournals.org/content/21/2/374.full

I am wondering if this has been looked at before or if there are any other relevant bits of genetics one should consider first.

EDIT: a bit more of explanation into the hypothesis below, and a reference that could be useful:

Let's start supposing a region near a coding gene that can gain regulatory potential via a new point mutation or small translocation. This new regulatory potential needs to be positively selected after it appears, or it will gradually accumulate more mutations and disappear. But if the region is close enough to the coding gene, recombination rate between the region and the nearby gene body will be low, proportional to their distance. If the gene body is assumed under selective constraint, there will be a hitchhiking effect of the nearby regulatory region by the gene nearby. The background levels of mutation on the regulatory region are then going to be lower (lower background mutation) than in a region that is not near a gene under strong selective constraint. So one way of explaining why close promoter/enhancer regions are more conserved than distant enhancer regions would simply be due to linkage.

A second part of the hypothesis would be about the presence or absence of recombination hotspots in upstream regions of a coding region: if nearby promoter/enhancers are kept via linkage to the closest gene, unbiased measures of cross-over (e.g. PRDM9 experiments in mouse testis) should indicate if there is an increased linkage of functional genomic blocks, like enhancer/promoter/gene blocks (Hi-C, 4C, 3C data), whereas if recombination doesn't play a role, regulatory blocks wouldn't necessarily be kept in the same haplotype block.


texts:
In the following photos can be seen a thread-like (almost like longkou vermicelli) things. At first I was convinced that it was cyanobacteria, however a classmate said it look more like a little worm, and other person said it look like it was probably nothing (nor prokaryote nor worm). I can't find a way to settle what it is, how can I know?

Zoom 40x

This is from another sample

EDIT:
Could the first one be lyngbya? I found this website and the second to last picture kind of looks like what it is in my picture:

And also could my second picture depict nostoc bacteria?


texts: Join a linear plasmid just using a primer (without ligase enzyme)

texts:
Can I use just a primer and PCR to join the cutted plasmid like this ? without using any further enzyme like ligase.

After the linear dsDNA plasmid annealed into 2 ssDNA, primer will bind to middle. And Taq Polymerase will bind to the 3' and start extend the DNA to join the plasmid. So I don't need a ligase enzyme, is that possible?

Edit: I think the plasmid will be nicked at 2 position with this method but will this plasmid still work in e.coli cell?


texts: What are embryophytes? And how are they characterized?

texts:
What does it mean when it's said that plants are embryophytes?
What are the specific characteristics that help determine that?


texts: One of the best "smoking gun" pieces of evidence of humans' close relation to chimpanzees, gorillas and orangutans is that human chromosome 2 is a fusion of two primate chromosomes, with a double telomere in the middle and a centromere on each side. This fusion, which occurred some time after our MRCA with chimpanzees, was an accident with no evolutionary importance, but it happens to provide extra support for our common ancestry with other African apes. In theory, such fusions could be so commonplace that they can be used to infer much of the family tree of life on their own. I'm sure they're nowhere near that common, but this got me thinking: are there any other examples of species with chromosome fusions (or splittings?) that betray their closest relatives?


texts:
In a hospital I can see a long queue of pregnant women waiting for their turn for ultrasound.  Is it safe to go through the ultrasound during pregnancy, especially during last few weeks?
Is ultrasound really required?  What if it is not done? How does ultrasound affect baby?


texts: Is there a measure of human genetic variation, where human genetic variation can differ more than 1%?

texts:
According to this

Neardenthal genetics

  The proportion of Neanderthal-inherited genetic material is about 1 to
  4 percent[12] [later refined to 1.5 to 2.1 percent[11]] and is found
  in all non-African populations

And according to this

Interbreeding between archaic and modern humans

  Neanderthal-derived ancestry is absent from most modern populations in
  sub-Saharan Africa

Now, human genetic variation is usually said to be between 0,1% to 0,5%

Genetics

  While the genetic difference between individual humans today is
  minuscule – about 0.1%, on average

Why are the genomes of humans 99,5% the same

  Human's DNA sequence is said to be roughly 99.5% equal

But here,

Human genetic variation

There are at least 6 different ways to measure human genetic variation and

  human-to-human genetic variation is estimated to be at least 0.5%

Does this last affirmation and the first two articles tell us that the difference in human genetic variation, according to some measures of variation, it's actually more than 1% ? (larger than some ways to measure our genetical differences with other animals like chimps for example that are usually mentioned to highlight our similatiries) Or are there things missinterpreted in all this?


texts: Are there ways to speed up the growth of plants?

texts:
I'm interested in what humans can do to speed up the rate of growth in a plant. I'm interested in both the context of home gardening and large-scale, institution-backed projects.

Obviously, optimal growing conditions are one factor that can be modified. I imagine that there are also genetic mutations that can be done (possibly even at home!). Botany is not my field so what I'm looking for here is are the basics and some good resources for further reading.


texts:
Please help identify this insect - genus, species and anything interesting about it. (Species of beetle?)

Old link - please vote to un-delete it https://biology.stackexchange.com/questions/64042/can-you-identify-these-insects?


texts: When some electrons of the electron beam pass through the specimen, what exactly happens after that in order to produce the black white image? What I understand is that electrons transmitted collide with a film and make that part of it black on the image, and those that don't collide make their part white. But why is it said that electrons that pass readily make the area brighter or more electron lucent and vice versa for scattered electrons?


texts:
This image was taken in Patagonia, near the Torres Del Paine National Park.
What type of biome this is? There are trees and other vegetation, but they seem mostly dried. I think this is either a semi-arid region or some type of transition zone to a forest, but I'm looking for a more concrete answer.


texts:
I've often wondered how squirrels -- specifically, eastern grey squirrels (Sciurus carolinensis) make their nests. Specifically, I've been curious about how they "weave" everything together to make these so called "dreys" stay together (and stay in the tree).

According to this site:

  [squirrel nests are] constructed from various twigs, leaves, moss and other material. To start, twigs are loosely woven together to make up the floor of the nest. Next, squirrels create more stability by packing damp leaves and moss on top of the twig platform to reinforce the structure. Then a spherical frame is woven around the base, which creates the outer shell. The final touches include stuffing in leaves, moss, twigs and sometimes even paper to build up the outer shell of the new home.

I've tried finding a video (preferably time-lapse) of a squirrel nest being built to better understand/appreciate this animal home. However, I've thus far been unable to find such a video on the internet.

Does anybody have such footage or know where I can find some?

Ideally, close-up and even internal shots would be included.
Additional notes about tree-branch drey construction would be appreciated, too!


texts: Why do genes with closely related functions often reside on different chromosomes?

texts:
Why do genes with closely related products are so often positioned on different chromosomes?

To illustrate what I mean, here is an example from immunology:

the invariant region of MHC is on chromosome 5
the variant region of MHC is on chromosome 6
β2-microglobulin is on chromosome 15

These three gene products associate into a single protein-complex to present antigens. Why are these genes situated on different chromosomes? Wouldn't it make more sense to keep them associated into a localized region onto a single chromosome so that their transcription can be jointly regulated?

It is just an example; I get the impression that many multiprotein complexes are formed with products from different chromosomes.


texts: How can one create images like those in the PDB ‘Molecule of the month’?

texts:
I am impressed by the illustrations for the Protein Data Bank ‘Molecule of the month’, e.g. the gorgeous image of DNA Helicase below. Does anyone know how they were made or how one might create something similar?

(source: rcsb.org)


texts: How likely is it that Earth has millions of different species?

texts: I know that the probability of life existing on a habitable planet is pretty slim. But, how likely is it that it hapenned millions of times in the same planet? Or was it only a few species that evolved into millions of other different species over time?


texts: When is wing growth in the bat complete and how soon can bats fly after wing growth is complete?

texts:
I was reading this paper by Cretekos et al (2008), in which they state that wing development in the bat is not complete until after birth - the wing continues to elongate postnatally.  This would suggest that bats are unable to fly immediately after birth, and a brief web search confirms this.

However, I would like to know:

When is wing growth (by which I simply mean outward growth or extension) complete?
When are bats able to fly?  (Are there other developmental processes that take place after wing extension that delay this process?)


texts: Why do ladybugs have a different number of points on their backs

texts:
Everytime I see a ladybug I ask myself this question.
Why does every ladybug have a different amount of points on its back? Is it because of its age? Or because of its genes? Is it inheritable?


texts: Can we knock out Caspase-9 *and* avoid breast cancer phenotype in our mouse model?

texts:
I am trying to design a wet lab experiment with no wet lab experience to name.

Right now, in my dream land, it would be excellent if it were possible to create a Caspase-9 knockout mouse (damage to the Caspase-9 gene is associated with the development of breast cancer), and somehow be able to control the development of the breast cancer phenotype, so I can create a Caspase-9 KO control as well as a non Caspase-9 control group. In total, I would love to have the following control groups:

1. Normal mouse - normal Caspase9 gene, no breast cancer phenotype
2. Caspase9 KO mouse - no breast cancer phenotype
3. Caspase9 KO mouse - breast cancer phenotype

Can anyone help me answer whether or not group 2 above is possible? Can you direct me to any papers, any experiments, where this has been done before, or has been tried below and failed?

Here is a paper that talks about the association of Caspase-9 with breast cancer development: http://breast-cancer-research.com/content/pdf/s13058-014-0443-5.pdf. Caspase-9 is a type 2 member of the Caspase protein family. When I talk of the "Caspase-9 gene", I'm talking about the DNA which codes for these cellular apoptosis susceptibility 9 (Caspase-9) proteins. This isn't my area of expertise, but this is what I currently understand.


texts: Identify vegetable with stalks coming out of it

texts: I know nothing more about this vegetable than the fact that it is safely edible, which a local vegetable vendor in South India told me. It's green (white inside) and has a strong smell resembling that of cabbage. It has these stalks coming out of folds in the outer skin, as well as a few leaves. STP identify.


texts: Did the Great Oxygenation Event also cause a mass extinction?

texts:
It's usually assumed that the Great Oxidation Event around 2.3 billion years ago caused a great extinction of anaerobic life on earth. However, I was reading Nick Lane's book, The Vital Question, and he writes the following:

The 'oxygen holocaust', which supposedly wiped out most anaerobic
cells, can't be traced at all; there is no evidence from either
phylogenetics or geochemistry that such an extinction ever took place.
On the contrary, anaerobes prospered.

Is there really no evidence of such a mass extinction?


texts: I am looking for someone to identify this bug:


texts: What are the effects on hearing of in ear headphones?

texts:
I have been told many times by my teachers and grandparents that using in ear headphones will ruin my hearing, but I was unsure of these claims. So of course I turned to stack exchange to help me.

So really I'd like to know the effect on hearing from frequent earphone use (particularly as I listen to quite a lot of loud rock music)?

Thanks.


texts: Every time I get ill (cold, flu etc) I take a couple of these wonderful tablets for up to 4 times a day and I, eventually, get better.  What exactly is paracetamol?  Why is it so effective and is it really not harmful as my doctor would have me believe?


texts: How are germ cells not reduced in number?

texts:
If germ cells produce haploid daughter cells by meiosis and are thereby "consumed" (where there was a germ cell there are then 4 daughter cells), where do the germ cells come from?  I asked my biology teacher if they undergo mitosis prior to meiosis, but she said they don't and proceeded to give an unclear answer.  Is this true?  If so, are they regenerated from somatic cells elsewhere in the body?

My question basically is - if the germ cells of, say, the testes are dividing by meiosis to produce sperm, where are the germ cells coming from so that the testes don't shrink and ultimately disappear as they're converted completely into sperm?


texts:
Why is it said that bacteria have no membrane-bound organelles, when they often have one or more flagella?

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3386205/  "Cilia and flagella .. are membrane-bounded organelles with unique membrane,"

Also, there is a biological motor (I don't know whether it's considered part of a flagellum or considered to be outside the flagellum, driving it?), but the motor surely has parts, e.g. a flagellum motor -like some mechanical motors, has a part, a "stator".  And surely these parts have membranes.

I understand there's one bacterium discovered, that does have a membrane-bound organelle mentioned here "There is at least one species of bacteria that has a clearly membrane-bound structure inside it called an acidocalcisome (I think that's how it's spelled). This organelle was.. discovered.. this is obviously a minor (albeit important for that bacterium) exception to the rule...that prokaryotes lack membrane-bound organelles."

Note- Alcamo's Fundamentals of Microbiology: Body Systems p124  this link from google books mentions other cases of membrane-bound organelles in bacteria including a discover as early as 1994. here

But putting aside the bacteria that have been discovered to contain membrane-bound organelles and going back to before those discoveries.. The texts that describe bacteria as having a flagellum, say that they don't have membrane-bound organelles. Why is this?

I suppose an answer might be that when people say that a bacterium contains no membrane-bound organelles, they mean except for any flagellum that it has.  They're referring to the main body of the bacterium, like one might refer to the torso of a human.


texts: What is the meaning of a 1,4 bond between sugars?

texts: I don't know how to express my question. I want to know what are bonds like 1.4 bond between molecules. I've read somewhere like the amylase enzyme can break 1.4 bond. I want to know what are these bonds and what are their benefits and where  can I find more info about them?


texts:
In 1918 through 1920, an Influenza pandemic colloquially named the "Spanish Flu", ravaged the world. It infected about half a billion people, and killed as many as 50 million people. But my question is - how did the 1918 flu virus disappear in 1920?

One can hardly believe that after infecting half a billion people, the virus was contained in any sense of the word. Why didn't the more than one billion uninfected people get infected? Why didn't we see some small epidemics continue to circulate the globe infecting the yet-uninfected as well as newly born people for many years - potentially until today?


texts: When muscles contract is the process similar to how non-newtonian fluids react?

texts:
I'm trying to understand how muscles contraction/tension works but getting loss in on the cellular level. From my understanding, when muscle tissue need to contract, the cells are flooded with calcium? Does that mean they get filled up with calcium? If so, are the cells hollow or does the calcium replace the fluid that was originally there? Or does the calcium cause the reaction in the cell for it to firm up?

I'm asking because there's an alien character who's quite thin but is also very strong and I was wondering about the science of that. I know them being alien means that their biology wouldn't necessarily follow earth rules but they could also share similar traits.


texts: Identifying a mushroom. (Pyrenees near Gavarnie, France)

texts: Can anyone help me identify this mushroom? (a still frame from video taken in the Pyrenees near Gavarnie in France). Also is it edible or poisonous?


texts:
This question got me thinking about amino acids and the ambiguity in the genetic code. With 4 nucleotides in RNA and 3 per codon, there are 64 codons. However, these 64 codons only code for 20 amino acids (or 22 if you include selenocysteine and pyrrolysine), so many of the amino acids are coded by multiple codons.

Is there any hypothesis as to why there are only 22 amino acids and not 64? Is it possible that there were 64 (or at least more than 22) at an earlier time?


texts: Are there any solitary species of ant or termite?

texts:
The social insects consist of the ants, the bees, and the termites, which live in colonies rather than living solitary.

But I've heard that there are some species of bee which are solitary and don't live in colonies.

Are there also any species anywhere of either ants or termites which are solitary?


texts:
I found a cultivar of banana that I haven't seen before (and that was significantly different from the standard Cavendish cultivar) in a market in Hong Kong today, due to the language barrier (Mandarin Chinese vs Cantonese), I was unable to ask the store owner about the name of the banana.

This is a picture of the banana, pictured next to a pack of standard AA batteries, as well as the peeled banana and a transverse section of the banana.

Can anyone identify the specific cultivar of this banana?


texts: Range of dry matter yield per kg CO2 of different plant species

texts:
The photosynthetic equation tells us that for every sugar molecule produced 6 molecules of carbon dioxide are used.

I'm interested in how much organic matter is produced by a certain quantity of CO2. Obviously there are differences between plant species so I'm basically looking for a list of plant (categories), which tells how much CO2 does produce how much dry matter.


texts: How can prokaryotes repair double strand breaks by homologous recombination if they're haploids?

texts: Title says it all, I must be going crazy.


texts: Why do Phobia exist if they aren't advantageous?

texts:
A phobia is usually the irrational fear of something, and the individual experiencing it is often unable to justify whether there is such detestation of something which might not even be threatening.

I am aware that there are:

Agoraphobia
Social Phobia
Specific Phobias such as Arachnophobia (fear of spiders) or Ophidiophobia (fear of snakes)

My question is, why do some people have e.g. Arachnophobia but not something closely related such as Entomophobia (fear of insects)?
And why do phobias even exist at all? To me they don't seem to serve a purpose (protection), and do not seem to be of advantageous existence.
Furthermore, I am curious to why exactly a phobia exists – and in some cases manages to be  passed on from the parent to the offspring.

DISCLAIMER:

I am aware of there being several psychological processes involved in this such as events that occurred in early years, or if there is a relative with anxiety, the risk of you suffering of a phobia is significantly larger. I also heard there is a high incidence of people developing phobias after traumatic brain injuries.

However, I am interested in the biological aspect of a phobia, and that why if it isn't advantageous to us, why does it exist?


texts: I have googled this out but no where found a satisfactory answer. The definition of transpiration states that it is the evaporative loss of water from the aerial surfaces of the plant but I am really unsure as to whether flowers transpire or not.


texts: Why does getting soap in your eyes cause redness and irritation?

texts: I am wondering why do eyes become red after getting soap in them. What is the cause behind it?


texts:
They may be responsible for why the leaves are drying out.
Location is in West Europe.
Their size may be 0.5 cm to 1 cm


texts: Why are certain baby (water)fowl yellow?

texts:
Why are e.g. ducklings, goslings, turkey and chicken chicks (partly) yellow?

What is the chemistry background to this? What compounds from the egg cause this to happen?

What is the evolutionary background to this? How could it help the bird to survive?

While domestication has led to selection of all-white adult birds and thus more common all-yellow babies, why does an all-yellow baby become an all-white adult, in terms of biochemistry?


texts:
I am having some trouble understanding how salt water, a simple solution, could so effectively remove the pains of a sore throat.

I do believe that the answer is closely related to hypo/hyper-tonic solutions, but why is this so, and how does this work?


texts: Can anyone identify this tall vine that has volunteered in our back yard?

texts: What is this 5-foot tall vine in Kentucky? It volunteered in our back yard.


texts: psbA-trnH intergeneteic spacer inversion

texts:
What kind of software tool would you recommend as best suited to detect psbA-trnH inverisons?
I have 1x coverage Sanger .fasta files and >2000 sequences, with 1 sequence per species.
Most tools I have found are only suitable for next generation seuqncing data or inversions that are larger than 50 bp.

Here is an example:

(dotted line)


texts: How closely related will your descendants be to you?

texts:
I wonder how similar my DNA will be to that of my great-grand-children. If a new person enters my family tree every new generation, he/she will bring in half of his/her DNA, therefore decreasing the amount of DNA that each new generation shares with me. I assume, then, that after several generations, my descendants are going to be no more closely related (genetically) to me than to random people on the streets?

I also once heard that even though the share of my genes will be descreasing, the mutations unique to me will stay. Is that true, and, if so, how is that possible?

And what about all-males descendants? For example, if I have a son and he has XY, then if there always will be a son down the line then will the Y chromosome stay the same through each generation? More specifically, will it still be the Y chromosome from me?


texts: What is the difference between embryology and developmental biology?

texts: The question is quite explanatory in it self, I used to think that both are same but then find somewhere that embryology is a part of developmental biology, can somebody please elucidate?


texts:
Can anyone help me identify these anole species? All photos taken on St. Thomas, USVI, in close proximity to one another.

(click to zoom in)

Each photo is a different individual, but the overall similarity makes me think they are likely the same species, although I could easily be wrong about that (the third one especially looks different from the others). They are dull brown overall with fairly subtle patterning, a light line that runs down their spine, bordered by a darker stripe on either side, and a broad band between the eyes. My best guess is that they are either Brown Anoles (A. sagrei) or Crested Anoles (A. cristatellus). Searching images online, there are some images identified for each species that are quite similar to these, but based just on comparison with those images, I really could go either way. Is there a definitive criteria to help narrow down the species?


texts: Is DEET (as in the mosquito repellent), a substituted phenethylamine?

texts: Am I correct to say that N,N-diethyl-meta-toluamide (DEET) is a part of the phenethylamine class? It's structure meets the requirements to be a phenythylamine, however, I was not able to find anywhere on the internet that it is part of the phenethylamine class.


texts:
It moves like a worm pretty much. I found it in a pretty big pond with brackish water. The water temperature was around 10 celsius.

Here's a video of it moving


texts: Does someone know of a website that keeps track of a species population?

texts: I am planning on doing some math on population growth, but I need a reliable source of data on population growth of some species over time. Does anyone know of a resource (website/publications/public repository) that has such information?


texts: During DNA foot-printing, what is the purpose of radioactively labeling only one end of the DNA fragment?

texts: I read that during DNA foot-printing analysis, DNA is radioactively labeled on one end before being cleaved by DNase 1. I understand that it is labeled so in order to locate the fragment on a gel, but I don't understand why it is only labeled on one end? If the DNase cleaves it in two, wouldn't the other end be un-labeled and untraceable? Therefore kind of defeating the purpose of labeling it at all?


texts:
I was reading about the different types of RNA polymerases, and I am confused as to how a cell determines which type of RNA it is transcribing.

According to this nature article:

  RNA pol I transcribes ribosomal RNAs (rRNAs), RNA pol II transcribes RNAs that will become messenger RNAs (mRNAs) and also small regulatory RNAs, and RNA pol III transcribes small RNAs such as transfer RNAs (tRNAs)

The system as to how the different types of RNA polymerase are selected makes sense to me, the core promoter's sequence determines the affinity of the polymerase to itself.

But, how does RNA polymerase II determine if the transcript is a regulatory RNA or a messenger RNA? Can someone explain that process to me or point me to where I would find it?

Another question: When RNA polymerases I and III transcribe their RNA, what prevents the cell from processing them the same way as mRNA and sending it off to a ribosome with a poly-a tail?


texts: Is there a comprehensive database of fossils (with images) online?

texts:
Not sure if this is the best stackexchange to ask...

I have not been able to find a decent database of fossils on the web, does one exist?

Here are some of the links I have found through Wikipedia and Google:

http://www.paleoportal.org/index.php?globalnav=doing_paleo&sectionnav=more_submissions&state_id=0&submission_type_id=27&type_id=5
http://www.morphobank.org/index.php/Projects/Index
http://research.amnh.org/paleontology/
http://en.wikipedia.org/wiki/List_of_fossil_sites
http://www.fossilsites.com/STATES/AB.HTM
http://inyo.coffeecup.com/site/ammonoids/ammonoids.html
http://www.historicalclimatology.com/
http://geonames.usgs.gov/pls/gnispublic/f?p=gnispq:3:4473291015495555::NO::P3_FID:354414
http://www.scotese.com/earth.htm
http://www.trilobites.info/biostratigraphy.htm
http://burgess-shale.rom.on.ca/en/
http://www.fossilmuseum.net/FossilGalleries.htm
http://www.kumip.ku.edu/cambrianlife/Utah-Online-Fossil-Exhibits&Collections.html
http://www.ucmp.berkeley.edu/collections/catalogs.html
http://peabody.yale.edu/collections/search-collections?vp
http://books.google.com/books?id=Ezm1OA_s6isC&printsec=frontcover&dq=hartwig+primate&cd=1&hl=en#v=onepage&q&f=false

What are the best places to get fossil data and images of the fossils? Or are museums and textbooks the only alternative?


texts:
I am writing a step by step guide for doing a western blot for a class.  It is intended for any  one with basic Biology lab skills.  I am hoping people will review my draft and give feedback on how to improve it.  Be as critical as you like about any aspect of it, I need it to be clear and concise as well as accurate.  Any tips appreciated.

https://docs.google.com/document/d/1Lpprwn4s127cb0D5TQezpurbjdF9hqJZQC0H7PIovE0/edit?usp=sharing


texts:
I am not sure if this is the good place: I am wondering what sort of insect is in this picture. It is approximately 10 millimeters long and 15 wide with the wings.

I have found one of them each day for one week, in my flat, near the coast of France. Tonight I found three of them at the same time. I am wondering if they are dangerous/damaging....
Thanks in advance for any help


texts: How extensive was interbreeding among human species?

texts:
I have read this article about non-Africans interbreeding with Neanderthals, Neanderthals interbreeding with Denisovans, and Asians interbreeding with Denisovans as well.

Now, I'm wondering what that even entailed.

Were populations of these species cohabitating a piece of land and completely mixing up? Would the humans of that time and place be 50/50?

Or would that just be a single act of interbreeding where an adventurous person had children with another species and those children became a part of the sapiens population?

Do the genetics suggest how much interbreeding happened or can they only say that some interbreeding happened?

Bonus, unrelated question. Does natural selection in any way suggest that mixed species offspring was better adapted to the environment and thus spread so far or can it just be a random event with little effect one way or the other that just spread regardless.


texts: I work at a start up company in a vivarium. My boss would like me to start working with MC38 Cells. I bought all of the equipment (recommended by a colleague) and should be ready for the cells. Could anyone recommend a good place to learn how to do this fast? He has surprised me and already ordered the cells. I do have some knowledge on the subject ( from bachelors degree in Biology), but it is not enough. I need somewhere that can teach me even the little steps. I have tried looking at scientific papers, but they typically skip over much of the steps that are common knowledge (to most).


texts: In my DNA sequence for one sampling site there're W's; Y's; R's and K's?

texts: I also just experienced the same thing with my DNA sequences, there are w's, Y', R', s' and k'. This is the very first time I've seen this. I am used to N but not these ones. Please kindly assist with knowing what might have caused these. Thanks in advance.


texts: I live in Phoenix, Arizona, USA. Can you please identify this spider for me. Is it dangerous?


texts: is it possible to completely reconstruct a family tree by DNA comparison alone?

texts:
Having DNA samples of all or almost all members of a population of, say, a few hundred or thousand individuals, is it possible to draw the entire family tree of those individuals? (Let's not assume monogamy or any other facilitation).

This may be a sum of two different questions:

does comparison of two DNA samples give any information other than topographical distance between individuals? In other words, is it possible to tell two sisters from a mother and a daughter by DNA alone?
(more a mathematical question than a biological one, maybe) having the relative topographical distance of all members of a group, can their full graph be drawn?


texts:
I saw this plant when I was on my trip to the Ukraine.

I wonder if those berries are edible.


texts: Do Acyl Carrier Proteins and Conenzyme A have similar reactivity?

texts: In terms of the reactions they undergo are they roughly equivalent groups?


texts: Are there any techniques for manufacturing exosomes in the lab?

texts:
I'm interested in the idea of using exosomes as an alternative transfection agent / delivery mechanism for gene editing applications (CRISPR/cas9, etc).

Information on the matter is sparse.. Does anyone know of any practical techniques for manufacturing exosomes in the lab?


texts:
The definition of an organism Wikipedia gives is

  An organism is any contiguous living system.

I understand that these are not organisms according to this definition:

A bird and a tree it's perching on are living and contiguous, but they don't form a system.
All humans are living and form a system, but they are not contiguous.

But some things are unclear to me. My veins and my skin are contiguous and living. Do they form a system? I think so, at least according to what I read about systems in Wikipedia. They are definitely interconnected; they have behavior; and I believe they have structure, though I'm not really sure what structure is. Perhaps if we carefully define what we want "structure" to mean, we can save the definition from allowing (skin + veins) to be an organism?

Is (mother + her unborn child) an organism? I think it definitely is according to the definition. Is the unborn child an organism?

Is an apple that's just fallen off a tree an organism? Was it an organism before it fell?

Is (human + their microbiome) an organism? Is a human without the microbiome an organism?

I think the part of the definition that the least clear to me is the word "system", and in the definition of the word "system", it's the word "structure".


texts: Is it a limitation of the eyes, or the brain, that we can't see a moving bullet?

texts: Are the photoreceptors in our eyes not fast enough to register the fast moving bullet, or is the brain not powerful enough to make sense of something happening that fast?


texts:
I'm reading this paper, and I'm already lost in terms of what they mean by GPCR signaling is spatially encoded.

  The trafficking of G protein coupled‐receptors (GPCRs) is one of the
  most exciting areas in cell biology because of recent advances
  demonstrating that GPCR signaling is spatially encoded.
   …
  …
  Some GPCRs appear to regulate their own endocytic rate through
  modulation of clathrin‐coated pit (CCP) maturation.12-14 This
  regulation, which can differ between ligands acting at the same GPCR,
  is an additional method by which GPCR signaling can be spatially
  encoded.

How can signaling be spatially encoded?


texts:
Is there any published data which shows the number of Drosophila melanogaster fruit flies eclosing (hatching out of the pupae) against time since egg oviposition? I'm thinking there should be something like a "cumulative flies eclosed" plot showing the cumulative number of flies emerging per time interval after the eggs were oviposited (something like this dummy figure).

I expected to find this in the Ashburner et al Drosophila book but there was nothing. I am trying to see how much variance there is around the mean for an experiment design. It may be helpful to know (though I am not necessarily after specifics to this set up) we keep our flies at 25 degrees, 12:12 light dark cycle, 60% humidty on a yeast and sugar based food source. The flies are an African lab adapted population (Dahomey ca ~1970's?) and eggs in the experiment would be kept at low density so resource competition is not an issue.


texts: static versus dynamic equilibrium when bending over

texts:
When a person stoops/bends over, is the equilibrium functioning static equilibrium or dynamic equilibrium? I am not sure, because on the one hand the person is not moving (static), however, his/her head is moving (dynamic).

Thank you!


texts:
I have a black mulberry (Morus sp.) in my garden (or 2 actually). According to the information I could find it is a deciduous tree. The trees in my garden do indeed lose their leaves. However, as most native trees start to color yellow/brown/red in september and have lost all leaves by now, the mulberry doesn't. It remains green until the frost kicks in and only then drops its (still green) leaves. It almost looks like it doesn't want to drop its leaves, but is forced to so so. This can be seen at the picture below. Hence my question:
Is mulberry also deciduous in warm winters such as the mediterranean? And is it normal that leaves are still green when dropped?


texts: Does all cells in individual has same mitochondrial DNA?

texts:
I read that genetic code is universal except for mitochondrial DNA.

However, I want to clarify (generally speaking, regarding humans especially):

does all mitochondria in the same cell have almost the same mitochondrial  DNA?
does all cells in a single individual have almost the same mitochondrial  DNA overall?
does all the siblings in one family have almost the same mitochondrial DNA overall?

Thanks :)


texts: Will a mother praying mantis stay with the egg sack?

texts:
We caught a pregnant praying mantis (without knowing it was pregnant). It made an egg sack on the underside of a cardboard bridge in its container.

It is in Pasadena, California. It kind of looks like the one in this link, except that it is paler green color (kind of tan brown/green). In the past I have seen some with red eyes, but I think this one had eyes that were black. I'm not sure if the eye color changes in the light, though.

Not knowing how to care for babies, we left the container outside in the shade with an open lid (so that the mother can climb out any time she wants, and so can the babies when they hatch). The mother climbed out immediately but remained on the outside wall of the container (near the egg sack) for hours.  However, the mother is no longer there.  Is it normal for a mother to abandon the egg sack?  Can we expect the mother to return?


texts: Is it possible to get a XYY genotype by the first meiotic non-disjunction?

texts: I have read that the cause of XYY-Syndrome is a non-disjuction in the secondary non-disjunction in the meiosis. I was woundering if it is possible to get the XYY-Syndrom by the first meiotic non-disjunction? I would assume yes, since you would get XX and YY Gametes.


texts: What is the function of human Trypsin Inhibitor if trypsin is secreted in the inactive form of Trypsinogen?

texts:
I was reading about pancreatic digestive enzymes in a Textbook of Medical Physiology and I came across Trypsin Inhibitor. The text stated that:

It is important that the proteolytic enzymes of the pancreatic juice not become activated until after they have been secreted into the
intestine because the trypsin and the other enzymes would digest the
pancreas itself....  ....substance called trypsin inhibitor. This
substance is formed in the cytoplasm of the glandular cells, and it
prevents activation of trypsin both inside the secretory cells and in
the acini and ducts of the pancreas.

It also states that:

When first synthesized in the pancreatic cells, the proteolytic
digestive enzymes are in the inactive forms trypsinogen,
chymotrypsinogen, and procarboxypolypeptidase, which are all inactive
enzymatically. They become activated only after they are secreted into
the intestinal tract.

My question is, why is Trypsin Inhibitor secreted if trypsin is already secreted as trypsinogen which can only be activated in the intestine?


texts:
Lysosomes are irregularly shaped membrane bound organelles containing 50 different types of enzymes.

But how are they formed? How are they produced??


texts: Excretion of small kangaroos while in the pouch

texts: How is the excretion of small kangaroos done when they are in the pouch of their mother, fastened onto her teat? My question is what happens with the products; do they accumulate in the pouch?


texts: Trying to identify a plant with pain-killing properties from northern Vietnam

texts:
My mother-in-law uses this plant to alleviate her pain caused by a severe case of spondylitis. This is a plant used in traditional medicine in her village near Hanoi, Vietnam. She doesn't know the name of the plant, even in Vietnamese. I'm interested in identifying this plant mainly to find out its exact pharmacological properties (if any) and possible side-effects.
This is a climbing plant that can easily become as tall as a big tree. It is present year-round in this region.
To use it she just cuts it longitudinally and let it dry in the sun before boiling it and drinking the resulting decoction.
Here is a picture that she took of the plant in the wild. This is the one with the heart-shaped leaves.

And here is another picture where she removed the leaves from the plant.


texts: Is there a good analogy that illustrates the difference between early DNA sequencing techniques and shotgun sequencing?

texts:
My first university biology classes begin in September. In preparation, but increasingly out of curiosity, I've been studying some basic biology. Saying that to say, I know as much about DNA replication as the Khan Academy videos teach.

Presently, I'm reading about the two efforts to sequence the genome. From what I've read, Collins' project used "polymerase catalysis and nucleotide labeling"; whereas, Venter's project used "shotgun sequencing". I didn't know enough to understand the article I read on "shotgun sequencing" and couldn't find one that described the other technique.

I suspect that, in order to comprehend a concise description of the two techniques, I'd need to learn more than I could learn from an answer to this question. That said, it'd still be nice to have a very rough idea of what each process involves and how they differ from each other. A crude analogy to something concrete would be great.


texts:
So I need to learn how to find the sequence of a gene, polyphenoloxidase. Please do not do this for me. Tell me how to approach the problem.

I have found : https://www.ncbi.nlm.nih.gov/gene and searched for polyphenoloxidase and get a list of results.

Here is one PPO page:
https://www.ncbi.nlm.nih.gov/gene/107923401
There is a FASTA sequence there under " NC_030099.1 Reference ASM98774v1 Primary Assembly" but I am not sure if PPO gene is there.


texts: What's the difference (functionally speaking) between yeast centromeric plasmids and artificial chromosomes?

texts:
Historically, yeast artificial chromosomes (YACs) have been used for genome sequencing projects in the late 1990's. Nowadays, most researchers seem to use centromeric plasmids for expressing transgenes in yeast.
From what I understand, the only structural difference between a YAC and a centromeric plasmids is that a YAC is linear, with telomeric sequences at the ends, instead of being circular. In both cases, the replication is initiated and regulated by CEN/ARS sequences, and the DNA is maintained by a selection cassette (e.g. auxotrophic marker).
Based on this, what is the point of using a YAC? It seems that YACs are basically centromeric plasmids requiring 1) additional sequences 2) an extra linearization step before cell transformation. In other words, I cannot think of any advantage to using a YAC outside of projects focused on telomere biology. I assume there must be an advantage though, otherwise in the early days of the human genome project back in the 1990's researchers would have used standard centromeric plasmids instead.
Is there any functional difference relevant to the expression of transgenes between a YAC and a centromeric plasmid? For instance, in terms of copy number, sequence stability, ease of transformation etc.?


texts: Where are -HCl supplements absorbed in the human digestive system?

texts:
I see that quite a lot of drugs and dietary supplements sold in the USA have -HCl(hydrochloride) added to their name. For example pyridoxine hydrochloride for Vitamin B6.  I'm interested in knowing where in the digestive system -HCl compounds are absorbed? Is it in the stomach?

It would also help if I get a rough idea of how long it takes for -HCl supplements to be absorbed. Is it an hour or more?

Thank you for your input!


texts: Identify arthropod with many legs in Mumbai

texts:
Can someone please identify this ~5 cm long arthropod? I've been finding one of these every 2-3 days inside my apartment ever since rainy season started here in Mumbai (June).
The bulb portion is its head. The arthropod is capable of climbing walls.
Thanks.

Video of the worm (shot while brooming the floor. Hence the dirt)
https://imgur.com/a/0FZv3eQ
By the way, I've seen it 6 times in the last 2-3 weeks. Except once when I saw it on the bathroom floor, all other instances were during night time. So perhaps this is some sort of a nocturnal creature?


texts: Why do we get bored of certain food items after repeatedly eating them?

texts: Why do many people not like certain food items after eating them for long? They seem tasty first, and after eating many times, it feels like we get bored.


texts: Is ovum + ovum fertilization possible for human?

texts:
In humans is it possible to fertilize a ovum with another ovum from the same female subject?

I already found some works in which the ovum is fertilized by a somatic cell (see e.g.  this ), but I am looking for fertilization specifically by another ovum.

Around a year ago I found in the internet a Japanese (ongoing) study on this, but cannot locate it any more.

I would greatly appreciate any help.


texts: Why Insect bites are itchy rather than pain?

texts: i don't understand if some thing bites or hurt we feel pain, but its differ for insect bites, why so?


texts: What do chimpz/bonobos/orangutangs/gorillas feed their babies with?

texts: I just read this question and it made me curious about what a more original baby diet would look like. So, at what age do our closest relatives in the animal kingdom start giving their offspring more solid food, in addition to milk, and how do they prepare it?


texts: What is so difficult about mushroom cultivation?

texts: I am just wondering why it is so cheap and easy to cultivate this type of mushroom: Agaricus bisporus, however a typical forest mushroom such as Boletus edulis  has to be harvested. What makes one mushroom species much more difficult to cultivate compared to another?


texts:
During the time when the passenger pigeon was hunted down to only captives in the zoo, how could the zoo not maintain a small population and keep the species alive? Why did the population slowly die out? I thought a bird can successfully raise multiple young, given the near perfect conditions in captivity in which the people there are trying to keep them alive?

Just a question I ramdomly thought of, so answers would be appreciated!
Edit: this is not a duplicate. Birds can have multiple young. That will increase the population success rate.


texts: Secondary structure and function in mRNA and single-stranded virus RNA

texts:
Although some mRNAs and the RNA of single-stranded RNA viruses do have some secondary structure, this is much less than in rRNA, tRNA etc.

Why is this so? What prevents their folding to the extent of the RNAs mentioned?

And surely mRNA cannot have very much secondary structure. It enters the ribosome in a linear fashion, so if it bound to itself, wouldn’t that stop translation?


texts: Calculating sequence divergence score for a protein from identity or similarity score?

texts:
I have % identity and % similarity scores for ~50K protein alignments, that I fetched from Ensembl Compara database. The issue is that I wanted to have divergence scores instead. So in order to calculate divergence scores, I first looked for the conventional method to calculate divergence score from protein alignments. But turns out, most of the methods/tools calculate % identity and % similarity scores instead of divergence scores.
(1) So I wonder what is the conventional method to calculate divergence scores from protein alignments.
(2) Could I simply calculate % sequence divergence as 100 - % identity or 100- % similarity score? If that's ok, should I prefer 100 - % identity or 100- % similarity?
Any suggestions from experts are welcome.
Update: As suggested in a comment below, I should mention that the average % identity score is more than 70. I hope this information would be helpful.


texts: Whole Genome Sequencing and Chromosome Counts

texts:
In general, do standard whole genome sequencing techniques rely more on known chromosome counts, independently arrive at chromosome counts, and/or not directly address issues such as base number, aneuploidy, and polyploidy?

For example would have normal whole genome sequencing techniques detected that humans have 46 rather than 48 chromosomes?

Maybe a better way to put this question would be as follows:

Given the whole genome sequence for humans and a belief that chimpanzee had 46 chromosomes would whole genome sequencing of the chimpanzee most likely say

1) Here are the sequences for those 46 and by the way there was material left over.

2) Here is the best representation of all the chimpanzee's DNA mapped onto 46 chromosomes.

3) Here are the sequences for those 46 and chimpanzee's appear to have 48 chromosomes.


texts: Is there a fundamental reason that plants cannot fix their own nitrogen?

texts:
Plants must have nitrogen to grow. According to the answer to this question, there are no plants that can fix their own nitrogen (without the help of bacteria).

Plants get their nitrogen in the form of nitrates (NO3-) or ammonia (NH4+). Nitrates and ammonia get into the soil through

lightning (causing N2 and O2 to combine to form NO which then reacts with atmospheric water and is brought to earth by rain)
nitrogen-fixing bacteria associated with leguminous plants
fixed nitrogen from dead plants/animals (ammonification), urine, etc.
ammonifying and other bacteria

The answer also states that it seems to be possible to engineer plants to be able to fix nitrogen.

So one could think plants could have evolved to be able to fix nitrogen, but did not.  Maybe it just did not happen based on it's probability to happen.
Is there any other explanation?

Maybe the ability to fix nitrogen would have a harmful effect on plants? Or fixation requires a complex set of related mutations? Are there enough areas with soil depleted of nitrates to exert a selection pressure for nitrogen-fixing plants?


texts:
When puting a real time PCR, parameter CT, which means threshold cycle, is used. What does it mean really? according to wikipedia "The number of cycles at which the fluorescence exceeds the threshold is called the threshold cycle (Ct)"
could anyone put it in conext?


texts: List of amino acid frequency of different foods?

texts:
I'm trying to write a little application calculating the biological value of protein content of different meals using the amino acid frequency of different foods.

The idea is that the user can choose amount and type of different ingredients and finally obtains the biological value index for the meal.

For this calculation I'd need a list of amino acid frequencies of the different foods.

Any idea how I could obtain this?

My first idea was to just use the DNA of the different plants to extrapolate the proteins synthesized and then obtain the amino acid frequency from there but I know that genome and proteome is not correlating.

Any ideas / thoughts?


texts: How are lipid-coated mRNA-based vaccines transported into cells for expression?

texts:
In CNN's video Scientist says Coronavirus vaccine could be ready by 2021 after about 00:25 'Robin Shattock, the Head of Mucosal Infection and Immunity at Imperial College London' says:

We were able to access the sequence that was published by Chinese scientists and made globally available, which was a tremendous thing to do. And we went from that sequence to identifying part of the sequence that encodes for the surface proteins of the virus. And we’re using that sequence to manufacture our vaccine.
We’re using a particular approach where we make a synthetic vaccine based on RNA, so essentially it’s essentially genetic code, we package that in essentially a lipid droplet, and use that to inject in a muscle; it expresses that protein, and the body recognizes that as foreign and it makes protective antibodies.

I'm assuming that the RNA mentioned is mRNA, and so once it reaches the cytoplasm of the vaccine recipients muscle cells it will be expressed and somehow returned to the cells' membrane where it will be recognized as foreign by passing lymphocytes.
Questions:

Is this basically correct as far as it goes?
If so, what causes the lipid droplet to fuse with muscle (or other) cells in the first place?


texts: The following guys (about an inch long) were seen in the Willamette Valley of Oregon in summer.  When one would fly by a resting one, they'd get into a high-speed little "dogfight".  What genus might they be (or species, if you know).  Are they in the "skipper" group of butterflies?


texts: Basic text/notes on DNA structure (for non-biologists)

texts:
I am a mathematics grad student researching knot theory, and I've recently discovered that there is a connection between knot theory and DNA structure (if I understand correctly, when DNA strands repackage, they do it in a way similar to what is known as Skein relations in knot theory, therefore tools from knot theory can be applied to DNA research).

The problem is that I have almost no background in biology, therefore it is difficult for me to understand how exactly DNA repackages and what happens on the molecular level.

Could anyone suggest some basic (and preferably not too long) text which gives an introduction to the structure of DNA? I have some basic background in organic chemistry, and I am not really looking to understand the topic thoroughly, just to visualize what's going on so I could see the analogy to the mathematical theory.

Thanks in advance!


texts: Can a virophage potentially be used to cure a viral disease?

texts:
Wikipedia states "Virophages are satellite viruses that inhibit or impair the reproduction of the auxiliary virus."

Is it theoretically possible for a virophage that doesn't hurt the human body to attach itself to a more serious virus like the AIDS virus for example and be used to wipe out the virus, or at least inhibit it's reproduction?  I'm completely ignorant of the virophage relationship, so feel free to inform me as needed.


texts: Do toxin producing strains of E. coli constantly produce toxin or only under certain conditions?

texts:
Background

E. coli is prevalent everywhere but only some strains produce toxins harmful to humans, such as E. coli O157:H7.

Questions

1) Would anyone know if these strains are always producing this toxin or is it only under certain conditions?

2) Is it the toxin itself that makes people sick and not the presence of the bacteria?


texts: Do any predatorial animals attempt to appear smaller?

texts:
There are many animals that have behaviors or characteristics to make themselves appear larger than they are as a defense mechanism, such as butterflies have large eye patterns on their wings.

Are there any animals that do the opposite? That attempt to appear smaller in order to lure their prey closer?

I'm more interested in physical characteristics but behavior that does this, also counts.


texts: Which is more important for protein expression mRNA structure or codon optimization?

texts:
The field seems extremely divided on the debate. On one hand, artificial experiments have suggested that synonymous mutations don't correlate with gene expression but rather, the mRNA 5' structure is the most important 1. On the other hand, genome wide analysis suggests that tRNA biases are better associated with high expression 2. What other works balance out this discussion?

Coding-sequence determinants of gene expression in Escherichia coli
Translation efficiency is determined by both codon bias and folding energy
An evolutionarily conserved mechanism for controlling the efficiency of protein translation


texts: 120-year-old gene regulation problem independently solved by a computer. How?

texts:
My Background:

I'm a mathematics graduate student with a physics background.  I have a very little biology knowledge and a little knowledge of machine learning and statistics.

Topic:

I recently found out about the following computational biology breakthrough: A computer managed to independently develop an explanatory theory for a 120 year old problem in biology. It is detailed in the popular media here and here and in great detail in this paper.

Questions:

I lack domain expertise but I'm very curious as to how this was possible and why it happened now. For example:

Were these methods novel (from a machine learning perspective), or does the novelty lie in using old tools/techniques and adapting them to a
workable problem?
Mathematically speaking, what kind of models were produced by the computer? Are these standard in this field of genetics/biology? Is this area particularly mathematically tractable?
What about this particular biological problem made it amenable to this machine learning approach?
What other kinds of low hanging fruit (in biology or science in general) could we expect to see tackled with these techniques?


texts: Can you be infected by two coronaviruses at once?

texts: E.g. could you be infected by COVID-19 as well as a different strand of coronaviruses (e.g. those that circulate in the population every flu season)?


texts: What is this insect with scary antennae?

texts: I encountered with this insect on the wet floor in Sri Lanka. Is it dangerous?


texts:
My father undergone surgery 10 years ago to get 3 bypasses close to the heart. Surgeons did a very long cut on his leg to get the material to make the bypasses they would later put on his chest.
What I understood at that time, is that they took three sections of the popliteal artery to obtain the material to make those bypasses, and that they fixed the cuts again to restore such artery. The reason why that artery was chosen is because it is very elastic and surgeons can extract a section and stick it together again.
My father is convinced they removed the whole popliteal artery from that leg and chopped it down to make the material they would use for the bypasses.
I am trying to find information about this procedure to find out who is wrong. The problem is that we both are completely illiterate in medical stuff, so we are lost in the mist. What I found is that the popliteal artery is important and blockage could be problematic.


texts: What light intensity starts melatonin release in humans?

texts:
I'm interested in whether any studies have determined the intensity of light at eye level that starts melatonin release in humans.

I know that:

melatonin release is suppressed by blue light with peak suppression
occurring at 420-480nanometer range.
This light is registered by Melanopsin, a photopigment in the
eye.
Melanopsin signals the Suprachiasmatic Nucleus, the master clock of the human body.
The suprachiasmatic nucleus makes a decision to suppress melatonin
release in response to blue light observed.

What I need to know is how much light is "enough" to trigger the suppression by the mechanism described above. I've seen a mention of as little as 200 lumens of white light, but do not have any reference to verify that. Additionally, the figure of 200 lumens was given for a typical smartphone screen, not necessarily translating to 200 lumens at eye level.

I'm aware of this experiment involving rats, where the light intensity at eye level was quantified. I'm looking for a similar measurement in humans.

Here's my original question on the subject, but I've learned quite a lot since then to refine the question

I appreciate your input!


texts: Misunderstanding about nucleotide biosynthesis

texts:
Some months ago, I asked what was a phosphoester bond, because I didn't really understand the following picture and explanations provided in the "Molecular biology of the gene" from Watson, Baker, Bell and al. (7th edition).

The explanation is the following:

We can think of how the base is joined to 2'-deoxyribose by imagining the removal of a molecule of water between the hydroxyl on the 1' carbon of the sugar and the base to form a glycosidic bond (Fig. 4-2). The sugar and base alone are called a nucleoside. Likewise, we can imagine linking the phosphate to 2'-deoxyribose by removing a water molecule from between the phosphate and the hydroxyl on the 5' carbon to make a 5' phosphomonoester. Adding a phosphate (or more than one phosphate) to a nucleoside creates a nucleotide.
Thus, by making a glycosidic bond between the base and the sugar, and by making a phosphoester bond between the sugar and the phosphoric acid, we have created a nucleotide.

What I didn't understand months ago was, to resume, "why is the bond between the phosphate group and the 2'-deoxyribose called a phosphoester bond since the phosphoester bond (which is, by definition, a P-O bond) already exists before the bonding between the phosphate group and the sugar?"
While this question is still bothering me (I was not entirely satisfied with the answers I got back then, because the synthesis of a single strand of DNA is something which is probably different from the synthesis of nucleotides themselves), the question I'm asking myself right now is: "why do general biology books always talk about condensation reactions, while this article and this book do not mention it in the biosynthesis pathways of nucleotides?"
What I mean is: it seems like the biosynthesis of nucleotides is far more complicated than just being two condensation reactions. Furthermore, when I look at the 10th step of this picture (which comes from the article I mentioned above), I see a condensation reaction at the end of the pathway, but it does not occur where the book from Watson and al. suggests it should:

So, after months of wondering and researchs about all this, my final question about this is, as mentioned above:
Why do biology books always mention condensation reactions while, apparently, it doesn't have a lot to do with the manner in which the nucleotides are synthesized?


texts:
I found this insect in Pune/India. It looked like a fly, and it was running over a leaf.
Size is about 2mm-3mm. Is it juvenile of some fly species or is it not even a fly?


texts: I read that there are labs that can produces the spikes of the coronavirus. I wonder can they also synthesize ACE2 receptors or parts of them? If yes, can they be used as drugs?


texts: I am doing an experiment in which I plate for example 3x10^5 cells, and every day I have to count the cells growing. I find the number and a convert it in x10^5. In my graphs I have to use the cell concentration. I am not sure which units are used for cell concentration. Is it ml, μl or anything else?


texts: Understanding recombination scoring in family pedigrees

texts:
I am having some problems understanding recombination, and I am not sure what element I am missing here. This figure is an example from my text book. The pedigree belongs to a family with an autosomal dominant disease, typed for a marker with alleles A1-A6.

So, all meioses are phase-known, meaning we know which combination of alleles was inherited from each parent. Apparently this leads us to be able to unambiguously score III1-III5 as non-recombinant (N) and III6 as recombinant (R).

This is were I get lost, I don't understand how it is possible to unambiguously score each individual as N or R. Also, if the disease is dominant, how is it possible that III6 is affected, as both alleles originate from the both unaffected I1 and II2?

EDIT: Blue colour in the pedigree means the person is affected by disease, white symbolizes unaffected individuals. I believe the red stars symbolizes that the person carries the disease gene. That would mean blue corresponds to not carrying the disease gene. If this is the case The red colour of III2 is a fault in the figure.


texts: What attracts cells to: pathogens, professional antigen-presenting cells, and cells with an antigen on its MHC-1 protein?

texts:
I have a few questions in regards to attraction/stimulation in the immune system.

What attracts leukocytes and antibodies to pathogens in the first place?
What attracts CD4+ cells to professional antigen-presenting cells (APC)?
What attracts CD8+ cells to cells with an antigen on a MHC-1 protein?
What attracts macrophages to pathogens that have been tagged with antibodies?

Is it just a case of everything bumping into each other and if cells (and antibodies??) bump into chemokines and/or cytokines they will be stimulated (and not attracted) to stay around that area moving to an area of a greater concentration of chemokines and/or cytokines?

That said point 1 can occur without chemokines and/or cytokines (in the case of antibodies, they could be taken/administered by the person).  While in case of point 3, (I may be wrong here) but chemokines and/or cytokines may not be present in the case of MHC-1?


texts: Are any arthropods poisonous to the touch?

texts: I'm particularly interested in whether any insects are poisonous to the touch.  Note that toxic-bristled caterpillars are actually venomous, since in all species I'm familiar with, the bristles puncture the skin.  If there are any arthropods poisonous to the touch, I'm also curious as to what the most dangerous one is, but that may be beyond the bounds of this site.


texts: Has the human body the greatest total length of nerves of all animals?

texts: I've read that a human body contains about 150,000-180,000 km (Pakkenberg et al., 1997; 2003) of nerve wiring in the whole body. But does this length increase with the size of the animal? For example, an elephant is much bigger than a human and perhaps even his brain is bigger but is an elephant also the animal with the longest nerve cells in total?


texts: Valid comparison of gene expression between several genes in several cell lines

texts:
We have gene expression data (Affimetrix mRNA gene expression results) for several cell lines, over a set of genes.  Our goal would be to be able to compare relative gene expression for genes over the different cell lines.

The method we have thought of so far involves calculating some sort of gene-based average (the expression of a particular gene over all the lines) and normalizing our expression data, grouped per gene, based on that.  However, we are not sure that this is a valid method for obtaining relative expression data from our data set, especially so that we can compare the data from several lines.

Does this seem like a valid strategy?  How is this normalization commonly done?  Should we do something differently to get a better comparison?

Thanks so much!


texts:
Low-frequency sounds are more penetrating, damaging. Hearing damage caused by blasts typically occurs at frequencies around 2 - 8 kHz, while age-related hearing loss starts at the high frequencies. The frequency range for noise-induced damage is biased upward, because the low-frequency conductive structures damage first.
https://www.entandaudiologynews.com/features/ent-features/post/effects-of-blast-and-acoustic-trauma-assessment-of-hearing-status-on-war-veterans
Why does hearing loss occur at high frequency first? It should occur at low frequency, because that is the more damaging sound. The distribution of hearing loss is totally incompatible with the noise exposure explanation. It could be due to growth factors, i.e., the high frequency parts die first because more distal.


texts:
To what extent do brains (e.g. of humans) contain recurrent  connections?

I am studying artificial neuronal networks and frequently encountered the statement, that recurrent neural networks are closer to biological neuronal networks than for example feed forward networks. But I didn't find information on the question if feed forward or recurrent architectures dominate the brain architecture.


texts: What is the difference between a bacterial artificial chromosome (BAC) and a plasmid?

texts: Is it just that a BAC is generally larger and artificially constructed? Or are there any other differences?


texts: To what extent is eating and nutrition important in recovery from minor illness like viral fever?

texts:
I'm guessing it is important,  but just to be a little more precise,

What would be the maximum amount of calories above which it is just a waste (or even harmful)
How much does the metabolism raise during the illness?
More carbs or more proteins? (or less?)


texts: HIV has a very high mutation rate due to its inability to correct errors in DNA replication and it is very adaptable to its environment. Hence I wonder whether is it possible for it to mutate such that it becomes an airborne virus and what mutations was needed for it to occur. After all other viruses such as influenza have done so before. Furthermore from the virus point of view, doing so will allow it to be more successful evolutionary speaking since that would allow the virus to infect more people and hence reproduce itself more quickly. And what will be the consequence if it happens?


texts: Do blurry images cause eye strain? At what point is an image so blurry the eye stops trying to focus it?

texts:
I'm a user experience designer concerned about a new trend of blurring screens when showing a lightbox/dialog box over top (see below).

From what I know, blurry images cause the brain to work hard unnecessarily as the eye tries to focus an image. If my team really wants to blur images, perhaps I can give them guidance on how blurry the image needs to be.

Here's an example of a page loading, using the blurry effect:

Other than the dialog box in the foreground, you can see that the rest of the words are blurry but are just clear enough to make out, which makes me fear the eye is trying to focus them.

Whereas something like Apple's iPhone blurs the app icons in the background of its Search feature so much that it looks like a pretty image when you search, and it seems the eye wouldn't focus on that background:

So my questions are,

Does trying to focus a blurry image cause eye strain, cognitive load or any sort of discomfort?
At what point does the eye stop trying to focus and just accept the blur as an abstract image, something that can't be focused, at which time it might relax?  Or is that point subjective and, hence, cannot be measured or put into words?


texts: What is the best method to check for differential gene expression in large dataset? I want to identify aging differentially expressed genes

texts: My data is RNAseq data and I want to know which all genes (which I am looking for) are differentially expressed with age. I have tried the Kruskal-Wallis test and fold change methods. Do you have any better suggestions?


texts: Would there be more amino acid residues in the extracellular or intercellular space?

texts: I am working on a bioinformatics project with HMMs and want to write some initiation probabilities for the location of amino acid residues. I know for different transmembrane proteins there will be different cases, but, in general, which regions of the protein would correspond to more AA residues: intracellular or extracellular? Or is there no general pattern?


texts: Genetics - Is this hybridization possible?

texts:
Suppose you hybridize two plants - One has a red flower and a long stalk, the other has a pink flower and a short stalk. This resulted in these 4 type of plants, with ratio 1:1:1:1

Long stalk red flower
Long stalk pink flower
Medium stalk red flower
Medium stalk pink flower

What possible genotype could the parents have that would result this way?


texts: Fruit identification - What is this green long fruit?

texts:
I found this fruit in the South of France, but I have no Idea what it is. It's a green, hard fruit. I tried to cut it to see the inside (on the following pictures).
It fell from a big tree, but I don't remember much information about it.

Thanks in advance!


texts: What kind of spider is this? And is it dangerous? (photo)

texts: I found this spider hanging from a web off the side of my house (in Buffalo, NY). It's probably 3-4in total length. Any thoughts on what kind of spider this is? And if it's dangerous?


texts: How can rapid growth cancer get nutrients in vivo?

texts: When I was little, before I get into biological studying, I read a news talking about cancer would be totally cured after decades. I still remember that researchers had a theory to claim if they could limit the blood vessel generation near to tumor, then the rapidly growing cancer cell couldn't get enough nutrients and would kill them. However, this theory seems not to work well. Cancer cells or tumor still have another way to get enough nutrients to live, or at least, maintain themselves to survive and endanger the host. So, my question is how can rapid growth cancer get nutrients without blood vessels in vivo?


texts:
Under anaerobic conditions E. coli has two options to generate ATP: fermentation (substrate-level phosphorylation), and respiration (proton gradient, chemisomotic phosphorylation). Which is favored? What determines the choice? If availability of enzymes required for anaerobic respiration is decisive, what regulates them under anaerobic conditions?

I looked into the web but did not find the answer.


texts: How predictably will RNA polymerase not transcribe repetitive sequences?

texts:
I am working on an (expensive) synthetic construct, which happens to have many "repetitive" sequences within it that are integral to its function. Primarily, the two sequences that are worrying me are:

A long polyA (about 15 nucleotides).
A consecutive sequence of two nucleotides: GGGUUUGGUUGU, etc.

I've heard from many some of the transcription horrors they've been through because of similar sequences with similar nucleotides. However, some advise that transcribing it shouldn't be a problem.

How predictably can RNA polymerase transcribe these sorts of sequences in E.coli?


texts:
A population of 600 birds faced a problem of biological magnification resulting in a large number of deaths reducing their population to 350. But 230 births also took place and 21 birds immigrated into the population while 13 birds migrated out. How many deaths took place in the population? What is the growth rate of this small population?

So I guess we need to use the
PGR = (BIRTHS + IMMIGRATION) - (DEATH + EMIGRATION) / INITIAL POPULATION x 100%

So.. I keep getting -2% as my answer, but apparently the correct answer is -41.7%

Thanks!


texts: Are male and female brains physically different from birth?

texts:
Male and female brains are wired differently according to this article:

  Maps of neural circuitry showed that on average women's brains were highly connected across the left and right hemispheres, in contrast to men's brains, where the connections were typically stronger between the front and back regions.

But since learning in the brain is associated with changes of connection
strengths between neurons, this could be or not the result of learning.
What about physical differences from birth? Are there differences in size, regions, chemical composition, etc. from birth?


texts: Do animals' facial expressions have similar meanings to humans'?

texts:
In the following pictures, the dog seems to be smiling to the camera. People staring at these picture also tend to feel comfortable and relaxed, presumably because they think it's very happy playing with the swing.

However, my question is, is the dog really happy, or we are just (incorrectly) interpreting the dog's facial expression according to our experience used to read humans' facial expression?


texts: What does "f.a." stand for in the name of the "Wickerhamomyces menglaensis f.a." yeast species mentioned in this article https://ijs.microbiologyresearch.org/content/journal/ijsem/10.1099/ijsem.0.003350 ?


texts: Can supplements affect DNA? (Could 10,000% Methylcobalamin affect MTHFR genotype)

texts:
Originally titled "Could B12 supplementation affect dna test results for B12 need?" - B12 just seems like a good example question to frame the more general question of "Can supplements affect DNA?"

I recently got a DNA test done from DNAFit and found out I do not have a raised need for B12 - however - I've been supplementing with about 10,000% B12 (as methylcobalamin) for quite some time now. Been taking 10,000% every day for 5 months and like 1,000+% B12 for another 5.5 months before the increased dosage. I actually am quite dependent on my supplements, and think it's quite possible that my DNA has adapted to them, if DNA does such things. (Just looking briefly, it appears there is some disagreement as to whether DNA can change due to supplementation: google.com/search?q=CAN+SUPPLEMENTS+CHANGE+DNA )

So there's the root of the question - can supplements affect DNA - more specifically - could B12 supplementation affect the result of my MTHFR genotype (which is CC, just FTR)


texts: Why does my room suddenly look 'reddish'? My eyes seem to adapt to color

texts:
To get the context of this question clear, I would like you to walk through some parts of my house.

We'll start with one of my rooms as it appears normally -

As evident, this part of my house has a creamish tinge to it, also the balcony door is open which further gives this room a yellow tint. Nothing special. I'll call it "area Y" (for yellow)*. Let's move on.

Here we arrive in another part of my house which has greenish/blue shades acting as a sunlight blocker. This gives this entire place a greenish/blue tint as shown. (Ref. "area G")

So, now let's visit the area Y again. I am always surprised with what my eyes now see. This. {1}

You see, the same room, same lightning, yet the room now looks much more reddish than before! That's what intrigues me, why does it  happen? Why my eyes suddenly become sensitive to red color?

I am not a biology student but I do know that our eyes have cones which specialize in color perception, and that there are different types of cone cells to perceive different types of colors (If I remember my high school biology correctly).

So, I somewhat get a feeling of what's happening inside my eyes (or the brain perhaps?). I suspect that as I go to area G, my eyes 'adapt' to the dominance of bluish/green light, either by decreasing pigment of blue cones or by increasing pigment of red cones, which makes my eyes more sensitive to the other end of visible light spectrum (red-yellow), causing an 'outburst' of red coloration in area 'Y'. Since pigments need time to degrade, by the time the red color pigment of my cones decreases, its activity is less than normal. It may be increased as the blue pigment's activity is less than normal and I see a reddish tinge for few moments.

This was a pure hypothesis from my part, but it seems correct to me. But why do my eyes even adapt to blue color? Why can't my eyes be  unbiased towards colors?

{1} Obviously I photoshopped the red tint in the image how else could I have replicated my vision? Though it's not the most accurate description of what I see it's still a very close approximation.


texts: Our senses are not as sensitive during sleep compared to wake. There is an arousal threshold during sleep that only when it is overcome will it wake a person up. My question is how is this arousal threshold lowered as sleep progresses? And how it is raised again during the latter stages of sleep?


texts: If the liver can regenerate why can alcohol abuse permanently damage it?

texts:
The liver is a fairly unique organ in that it has the ability to regenerate itself even if parts of it are removed/damaged. It is a well known fact that continual alcohol abuse damages the liver and can lead to many liver problems.

Why is this the case? If alcohol does damage the liver, why can it not simply regenerate it's damaged cells from healthy cells?


texts: Is it possible, at least in theory, for a species to evolve into another species and then evolve back into the first species?


texts: Interpretation of qPCR results for low expression genes

texts:
I am attempting to validate existence of a transcript using 40 cycle qPCR. I designed primers for a unique feature of this transcript, and also designed primers for a sequence in the transcript that is common to several transcripts of this gene, and finally I used GAPDH as a control. I already knew beforehand that this transcript has very low expression.

For the unique region, my ct values for primer 1 were between 31-34.8, and my ct values for primer2 and primer 3 were all consistently 35, and primers 4-6 gave no result at all.

For the region that is common to several transcripts of this gene, the ct values were between 30-34 for one primer, and consistently 35 for another primer.

For GAPDH, ct values were around 22.

Can I use these results to indicate that my transcript exists (or even may exist?) in the samples I tested? Is the fact that the ct values for the region unique to the transcript I am targeting and the region in common between several transcripts are quite close indicative of anything? On the graph from the qPCR, there are distinct rises respectively around 33 and 35 for the unique region amplicon.

EDIT: I was doing a bit more research, and it appeared that this study: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4296690/
also had results that came up "late cp call last five cycles has higher uncertainty" and considered these results positive if they could be replicated in a duplicate - if I were to show this as well, can I use this data in a paper?