texts: Pharmacokinetics: why do certain drugs follow zero-order kinetics?

texts: I understand that alcohol and phenytoin are two examples of drugs that follow zero-order kinetics. Why do these two particular drugs follow zero-order kinetics as opposed to first-order kinetics?


texts: It is possible to store a digestion of cells with lysis buffer several days at -20 degrees and then proceed with the phenol chloroform isoamyl purification?


texts: DNA of Different Species and The Fossil Record of Their Common Ancestor

texts:
Let me please be clear about something. I believe in evolution. The evidence and data are compelling and conclusive which makes it a very well-established theory.

I'm seeking a certain evidence (if it's existent) for evolution.

Assume we have two species (species A and species B) and we have full information of their genomes. I believe, by using their genomes, we can deduce when their most recent common ancestor lived (let's say X years ago).
Are their any instances in which this X number (which was produced mathematically) matched the age of some fossil (say species C) which has similar attributes to species A and species B? Any data about the ancient DNA of species C which may reinforce the evidence? Do we have something for humans and chimps?

I'm seeking a gourp of, arguably, unrelated quantitative data that point remarkably and decisively to common ancestor/evolution.

Thanks.


texts:
I am a CS graduate working in Computational Biology. While the theoretical aspects of both AP/MS (and the various types) and Y2h are quite clear to me, the actual technical aspect of building large-scale PPI networks is not. Is there a machine that can do these experiments? How long would building a network take for say, 2000 proteins? Is there a company that can provide this service?

I would appreciate any help. I have searched a lot but was unable to find an answer for this question.


texts: Is it possible to force Sars-Cov-2 virus to mutate?

texts:
The title may definitely be a stupid question since I have no background in biology. I would like to know if the coronaviruses or any other can be manipulated artificially so that they stop spreading among humans and target other animals, for example cats. I like cats but they can spare one of their lives for humanity.

¿Is it possible?

Furthermore, is it possible to create a surface made of articifial cell membranes which is better than human cells for the viruses to stick? As I understand the viruses have no life, which means they are like machines, they have no aim in "life" other than stick. Am I correct?


texts: Request for an ID of two spider species found in Australia, NT

texts:
These two spiders were found in the Northern Territory in Australia in July (winter time). Both arachnids were shot during the night (I suspect them to be nocturnal), and both were found close to the ground. They do not build webs I think (way too big).

The upper spider is quite big, pretty much hand-sized, and about as big as a bird-eating spider. I think the guy with us told us it was a species of wolf spider (if I recall correctly - I'm unsure). The bottom hairy spider with its nice camouflage is somewhat smaller (if I recall correctly), but still well sized.

I have been searching for their names, but the amount of spider species is overwhelming and Australians tend to focus online resources on the poisonous ones. I'm fairly sure these two are harmless.


texts: Tree Identification - California Bay Area

texts:
I've seen these trees in the Bay Area in Mountain View and Fremont, and have been searching for different pine tree varieties that have wider canopies. Does anyone here know what trees these are, they are very beautiful.

Here is the link to the exact location where I saw them recently:
https://goo.gl/maps/NSfAXZSgzypWXKqj9


texts: How does a new species survive without suffering inbreeding?

texts:
Just what the title states. The thought came from reading When has an organism evolved enough to be called a new species?

I'm probably wrong but I understand new species happen sporadically rather than in whole-sale lot during breeding season. Is the new species capable of breeding with members of its parent species? How does a new species survive inbreeding initially?


texts:
Does the tannin level in plants go down or up after they die? Or does the tannin level stay the same regardless?

As they decay, do they release more tannins or does the production stop?


texts: What portions of the brain have drastic changes in activation when we "sense" someone is there?

texts:
I was watching an old Arnold Schwarzenegger movie ("Commando") where he plays an elite soldier (surprise).  An enemy tries to sneak up on him, and Arnold says that he smelled the other guy approaching.  While this is possible, I find it to be more hyperbole than truth, but what modalities and areas of the brain would he would harness for this detection task?

All of us not being super soldiers, we do occasionally get a feeling when someone has entered a room silently behind us.  Is it audible clues that fall below a certain threshold, is it the sensation of air moving in a the room, some sort of vibrational or proprioceptive sensation, or a combination of all three of these?


texts: What is the rationale behind IgM being the default antibody?

texts:
I know that the$\ C _\mu $ gene appears first in line for class switching and hence the IgM is the default antibody. But what is the rationale for it being so? There must be some advantage (evolutionary?) of having the IgM first in line over the IgG or so on.

The IgM is different from the IgG in being a cluster of five, better agglutination, having more avidity, and more cross reactivity (correct me if any of these is wrong). How do these properties help in containing the infection only for the very first time? Or, why is the IgG is not good for the initial response?


texts: Literature about industrial enzyme application

texts:
Can someone point me out to literature (reviews or better workbooks) describing industrial chemical reactions catalysed by enzymes?

What I'm most interested in are case studies of how the output of a reaction on a big scale is optimized with respect to enzyme activity.

Most of the literature I'm finding is about optimization of cell growth, which is not what I'm looking for.


texts:
I am slightly confused as to what part of the genome codes for non-coding RNAs. Is it the introns? This would make sense to me as to why they are not transcribed as the introns are not transcribed. Or is non-coding RNA actually exons which are simply not transcribed? If so, what are the introns actually for? I cannot seem to find a succinct answer to this. Wikipedia, for example, seems rather vague:

  While introns do not encode protein products, they are integral to gene expression regulation. Some introns themselves encode functional RNAs through further processing after splicing to generate noncoding RNA molecules.[18] Alternative splicing is widely used to generate multiple proteins from a single gene. Furthermore, some introns play essential roles in a wide range of gene expression regulatory functions such as non-sense mediated decay[19] and mRNA export.[20]

In either case, does anyone also have any information as to why the ncRNA is not translated? What is the mechanism that prevents it from being translated? My guess is that, for some ncRNAs, it is a matter of them not being able to leave the nucleus as I understand many ncRNAs deal with post-transcriptional gene silencing, although tRNA and rRNA clearly do leave the nucleus...

I would be very grateful for any help about introns/exons/ncRNAs. Thank you :)


texts: Why do horses recycle their endometrial lining while humans don't?

texts:
How does not recycling the endometrial lining of the uterus benefit humans (and other organisms that menstruate), while recycling it is beneficial to horses (and other organisms that undergo estrus cycle)?

So the question linked by user137 gave me some useful points to work from. Bear with me though, because I learned alot of new jargon just by reading it.

Helps immunity:

"forces loose not only the endometrial lining but sperm-borne pathogens contained therein."
"menstruation delivers immune cells to the uterine cavity, triggered by the mechanical pressure exerted via the shedding of endometrial lining."

Energy efficient:

its simply more energy efficient to shed. saving 6 days worth of food per 4 cycles.
for individuals/species with high fecundability shedding of the lining is less useful
larger uterus = increased likelihood of menstrual shedding (from the answer I learned humans have a larger uterus -- relative to body size -- compared with other mammals who don't shed.)

Miscarriage discardation?:

the comment section also had an interesting reason saying that sloughing off the lining regularly helps get rid of dead embryos.

All of this is very useful and interesting but I'm still confused as to why horses don't shed. I would think horses have low fecundability since their awkward bodies would make it hard to mate. And if shedding the lining is more energy conservant, then why don't horses? I want to know why it is evolutionarily better for horses to fully reabsorb, compared to humans?


texts: Will DNA nanostructures be useful for medical applications?

texts:
There is a lot of work being done on developing small nanomechanical structures and even small nanomechanical actuators built with DNA.  I have heard researchers motivate this research with claims that it could have biomedical applications.  My question is, how likely is this to be true?  In particular, a few potential problems bother me:

(1) What is the risk that the foreign DNA strands used to build nanomechanical devices will be accidentally incorporated into the host genome?  Are there plausible strategies for avoiding this?

(2) Will it be effective in the presence of an immune system?  If the foreign DNA is not incorporated into the host genome, it seems likely to instead be destroyed by the host immune system.  Is there research addressing this issue?


texts:
In most books the size of long-necked sauropod Mamenchisaurus is stated as about 26 meters. Recently, a huge specimen of Mamenchisaurus sinocanadorum was discovered.
However, Gregory S. Paul estimates its size in length of 35 meters and weight of more than 65,000 kg, rivaling Argentinosaurus and Patagotitan, the largest known dinosaurs. However, many doubt these estimates and say they are exaggerated. What are the current and most reliable esimates of the size of Mamenchisaurus sinocanadorum?


texts: I read somewhere (I think it was Bill Bryson's book on the origins of the English language) that of all animals, we are the only ones that can choke on food (having something to do with how our larynx is positioned).  I'm unable to find reference to this fact online, however, and am curious if this is just my having misunderstood something (or Bill having led me astray!).


texts: Leaf-curling type spider southeastern US

texts:
I have a spider in my backyard in Mobile, AL.  It seems to have sewn itself up inside of a living water oak leaf.  I tried googling it but only came up with this Austrailian spider that does a similar thing, but not exactly.  Notably, there is no attendant web, just the folded leaf container.  The leaf has been folded twice into a perfect little tetrahedral home.  Here is a picture... I didn't want to disturb her too much:

What species is this beautiful geometer?


texts: Mitochondria and plastids in eukaryotes evolved through a process of endosymbiosis. How does an event like a eukaryote engulfing a bacteria, become a part of the genome? Some of these primitive eukaryotes could have been more predisposed to more vigorous endocytosis as a result of their DNA, but how could the physical event account for evolution of organelles?


texts: Bootstrapping (symmetry breaking) in evolution

texts:
Many fascinating phenomena in nature show different behaviours on the micro and the macro level. Here I am especially referring to phenomena that are symmetric on the micro and asymmetric on the macro level. Let me give an examples from physics:

  Arrow of time: Physical processes at the micro level are
  completely time-symmetric, if you reversed time, all laws would remain
  the same. Yet on a macro level they are not time-symmetric, we have an
  obvious direction (flow) of time.

It seems to me that we have a similar situation with evolution:

On the micro level it is really only about adaption (and not about improvement): You put some beings into an environment and they adapt, you change this environment and they adapt. No improvement, just blind "back and forth".

Yet looking at the whole tree of life on the macro level we have a different picture, we see all kinds of emergent phenomena:

explosion in diversity
emergence of complex interconnected ecosystems with completely new dynamics of their own
true innovations in functionality (sensors, actuators, information processing etc.)
and finally of course higher order functions like abstract intelligence (and  even qualia)

To make the difference more concrete I will give a gedankenexperiment of two planet simulators. In both cases you accelerate time so that one hour translates into one billion years. Both simulators function differently in a subtle way but you don't know how. You throw some simple sims onto both planets and let the evolution simulation run. You don't switch your computer off and go to bed, the next morning you decelerate time and take a look:

Planet 1: The simple sims quickly adapted to the environment as expected (but they stayed simple because evolution is not about improvement but about adaption).
Planet 2: Some strange looking sims wish you a good morning and want to discuss the technicalities of the Riemann hypothesis with you.

My question
What are the minimal conditions that have to be met to get this kind of bootstrapping (symmetry breaking from micro to macro level) started. And what is going on at the core of this transition from micro to macro.

Edit
My specific point is about the symmetry breaking process in the sense of system dynamics. To give an example of a possible answer it could be something like Parrondo's paradox, a fascinating phenomenon from game theory where you combine two symmetric (losing) processes to get a (winning) asymmetric process. More can be found here: Parrondo's paradox.


texts: What is the function of multiple nuclei in syncytial cells?

texts: What is the function of multiple nuclei in syncytial cells specially in protists with cilia? Is multiple nuclei a special characteristics of only ciliated cells?


texts: Are bananas C3, C4, or CAM plants? I have been researching for some time and cannot find the answer.


texts: What kinds of fish tend to have a rapid death after being caught?

texts:
I am asking this question because I am trying to make my diet less cruelty-oriented, for this reason this question can be related to trolley problem since I am coping with an ethical problem trying to minimize the the core aspect i.e. suffering.

On the contrary I would like to know what kinds of fish suffer the least after being caught. I know that shrimps/prawns die very quickly since they cannot breathe out of the water, for instance here I have read that prawns die after  just a couple of minutes out of water. But for medium/small size fish is different, especially for those which are mass-caught. Not to mention the explosion of bowels caused by rapid pressure variation.


texts: What do we mean when we say that a muscle fiber contracts strongly?

texts: Sounds dumb but anyway, i heard that superfast fibers contract more strongly than fast twitch fibers. And i never thought of muscle contraction as something that has a magnitude (i thought of it as "1 or 0" meaning either contracted or not). So lets say we have two fibers, the same length and thickness, if one contracts more than the other does that simply mean that it becomes shorter ?


texts: Found in a web by a very small, slow moving stream. Douglas-fir forest in Gales Creek area, April 28.


texts: What's causing leopard frog abnormalities?

texts:
In the mid-1990s, large numbers of leopard frogs with abnormalities were discovered in Minnesota, Vermont and other locations. They consisted primarily of frogs with missing or deformed hind legs and toes.

It was later claimed that a national survey concluded that the number of deformed leopard frogs was actually much smaller than at first feared. However, there are local "hotspots" where the problem is worse.

It appears that no precise cause has been pinpointed, but it was believed that a number of factors (e.g., pollution, heavy metals) were contributory causes.

Can anyone offer a good update? Has any progress been made in narrowing the suspects, and is the problem worsening or has it more or less stabilized?


texts:
I have heard from a (usually very knowledgeable) friend before, that a human can only tap his fingers 7 times per second.

I generalized this to "our muscles are limited to 7 hertz"

When my wife heard this she was like "no way, I'm faster" and we recorded a video of her blinking as fast as she could (her eyes hurt afterwards) and over 5 seconds she averaged exactly 7 blinks per second.

I can't find any articles on the subject, but I did find this video of a drummer doing 1208 beats in 60 sec, setting him up at 20.13hz, meaning 10hz each hand. However if you look at his hand, his muscles are not even really tapping, they are just in a vibration (like a spasm), while holding the drumsticks, which than do all the tapping...

Ussain Bolt sprinted 100m in 9.6 seconds, with 41 steps, that's a little over 4 steps per second.

Both these are very impressive. The drummer sticks out for coordinating his 10 taps per second on each hand, alternating with the other hand, while the motion is certainly faster then our eyes can see.

So what's up with the 7 Hz speed limit? Is it a thing, or did the drummer disprove it? Could the 100m world record be beaten by another 25% when we can find a tall guy capable of doing 7 or even 10 steps per second?


texts: Data Bias in protein-protein interactions data

texts:
Databases like STRING have so many predicted as well as experimental interactions data for many organisms.However there is a bias in the data which they have?.

a)The first is gene co-occurrence  which is more like a circular argument.
b)And the second one is that all interactions that are predicted computationally are tested for experimental interactions.This leads to a bias in the interaction data available for organisms in STRING.

How do we overcome this data bias while using STRING interaction data for analysis purpose?

a)Avoiding evidence channels of gene co-occurrence is one way.Is there any other way other than this?
b)How to statistically say that the bias is not governing the data or any way to test statistical significance of the data bias?


texts:
In an amphibian blood entering the right atrium shows higher levels of oxygenation than that in left atrium when :

A.It is hyperactivated

B.it is hibernating

C.it is submerged

D.it is in the terrestrial habitat

I think it should be C.


texts: I am told that there are some species, like fish or rabbits, that if let, will eat their own children. If this is true, how does a species like this exist? Shouldn't the fact that they kill their own lineage make them nonviable?


texts:
If we hold a rose in front of our nose for an hour, we can barely notice the smell after that duration, since the smell receivers ( Or the brain, I'm not an expert ) get used to it, and become sort of deaf.

Now my question is, are we deaf to the smell or taste of water simply because our body is consisted mostly of water and we are deaf to it, or is it because we do not have any receiver for this liquid?

If so, is this shared between all the living organisms?

UPDATE

By water, I mean pure water. Now what we practically have is never 100% pure, but a good place to start is distilled water.

I've come across multiple articles about this, but they lack of evidence and scientific proofs.

These are 3 of them:

Ask Anything: What Does Water Taste Like?
Does ordinary water really have no taste [...]
Water taste in man


texts: Can elephants drink water by directly sucking it up from its nose?

texts: For animals and humans, our noses are connected to the esophagus. When us humans go to the pool and do flips in the water, we often get water stuck in our noses, and drips into our esophaguses. What I am wondering is whether or not elephants can drink water by sucking it up directly up their trunks, instead of putting their trunk in their mouth and spraying water into it.


texts: Highly spherical Radiolaria; does this image accurately depict the organism?

texts:
If I understand correctly, Cenosphaera spp. is a type of Radiolaria, which is a type of zooplankton.  The following is an image of Cenosphaera spp. is from the supplementary material (Figure S2) of the following paper:

  F. Lejzerowicz et al., Ancient DNA complements microfossil record in deep-sea subsurface sediments, Biol. Lett. (9) 2013.

  Question: Does this image accurately depict the organism?

More specifically, in other images of this organism, there are numerous thorns pointing outwards.  Is this thorn-less version a natural variation (or e.g. the result of the process of imaging the organism)?  Also, is it largely a sphere with a hollow inside?

The authors give the following description of the process involved in obtaining these images.

  Eighteen sediment samples were wet washed over 63 μm and 20 μm sieves. The >63 μm residua were dried and picked for radiolaria and foraminifera. From most samples all specimens were picked. Rich samples were divided with a dry microsplitter into fractions, from which at least 100 specimens were picked for each group. Specimens were arranged by taxa on micropaleontological slides. Radiolaria are classified on the generic level, according to the classification utilized by [8]. Foraminifera above the species level are classified according to [9]. In addition, for radiolaria, the 20-63 μm fractions were soaked in peroxide, then washed with tap water and propanol. For each sample, a few drops of suspended material was left on a glass to dry, covered with Durcupan ACM resin and a cover glass. The micropaleontological slides were analyzed under Olympus BX50 light microscope (electronic supplementary material, figures S2 and S3).


texts: How can I create a microcapillary for manipulation of single cells?

texts:
i'm working as a diy bio. I'm finding a way to create a micro glass capillary for picking up single cells. I see this video on youtube and would like to know what is the minimum I/O diameter if I pull a capillary like this.
Can it be 10-50 µm at least ?


texts: Land recultivation? Land revegetation? Land reclamation? Land rehabilitation?

texts:
I'm translating a Russian text about the recultivation (рекультивация) of land formerly used for open-pit mining. The process of 'land recultivation' in Russia involves three general stages:

Preparatory stage: a feasibility study, justification of investment, development of working documentation.
Technological stage: engineering operations that involve large-scale movement of soil, removal of machinery and buildings, etc.
Biological stage: seeding of trees and plants, soil improvement operations, irrigation & drainage work, etc.

It is said that the last two stages can last for "years or even decades".

Which English word should I pick? Recultivation, revegetation, reclamation, or rehabilitation?

Example sentences (I retained the original "recultivation" here):

  All too often a coal mining company implementing a recultivation project in this region limits itself to the use of simplified technological solutions that fail to take into account the need to preserve biodiversity. The range of plants used at the biological stage of recultivation is limited to five tree species, which depletes the genetic resources of the region's ecosystems and exacerbates the existing invasive species problem.

P.S. The authors of the text do no imply that the land should be used for agriculture - to the contrary, their goal is to improve biodiversity.

P.P.S. Here is a newspaper article about this "recultivation" of open-pit mine land in Kuzbass: source (in Russian)

P.P.P.S. I've just discovered that the English-language title of the Russian national standard GOST R 57446-2017 that comes into force on 1 December 2017 translates the term as land reclamation. However, those who translate Russian documents into English are not always correct.


texts:
I already had a question about dealing with mosquitos: Really virulent mosquitos - dealing with them and their bites

But this question is about whether they really do vary in virulence and toxicity. A few people in the other question suggested I am naturally a target and react badly to bites. However:

I haven't in other locations had such big reactions, I get nasty lumps but not swellings several centimetres across
My wife gets even worse reactions, e.g. her whole calf went red and swollen from a single bite - and I currently can't clench my fist because one bite made it swell up!
several other people, including a gardener and a tree surgeon who both deal with such things all the time, have commented they react particularly badly when working in our garden

Interestingly this summer I am reacting differently than this time last year - bigger swellings but less itchy and no weeping wounds. This may be due to the difference between midges and mosquitos.

So - are there a large number of sub-species prevalent in the UK (NE UK specifically) or can a given population become more nasty for some reason?


texts: What is the difference between Crossbreeding, Outbreeding and Outcrossing?

texts:
I only found one book which isn't a textbook  named Storey's Illustrated Guide to 96 Horse Breeds of North America By Judith Dutson (not sure if it is good enough to follow) that defined these terms.

Outbreeding/ outcrossing is deliberately crossing one line of horse within a breed to a very distant or unrelated line. The term is also occasionally used as a synonym for crossbreeding.
Crossbreeding is the deliberate crossing of horses of different breeds.

My understanding:
Outbreeding or Outcrossing is the mating between two individuals of a  breed but different varieties/sub-varieties.
Crossbreeding is the mating between two individuals of different breeds (could be intraspecific or interspecific as well).
Are these definitions correct?


texts: Membrane potential after exposure to glutamate

texts:
Neurons were kept in a physiological solution. During the resting
  phase, the membrane potential in the axoplasm of neurons was negative
  compared to the extracellular space and a potential difference of -70
  mV was observed in this phase. Neurons were then treated in two
  different experiments with either gamma-amino butyric acid (GABA; an
  inhibitory neurotransmitter) or glutamate (an excitatory
  neurotransmitter) and the membrane potentials were recorded. Choose
  the correct statement/s:

  (A) The resting membrane potential of -70 mV would not change with
  either GABA or glutamate treatments.

  (B) The membrane potential would be even more negative than resting
  phase with GABA treatment.

  (C) The membrane potential would be positive when the neuron was
  exposed to glutamate.

  (D) The membrane potential would be more negative than resting
  potential after glutamate treatment.

I feel, since, glutamate is excitatory, so resting potential should decrease when exposed to glutamate and increase when exposed to GABA. So (A)&(D) automatically gets eliminated and (B) is correct answer. I am confused at (C)


texts: Ligand-binding assays: IC50, EC50 and Kd

texts:
I am reviewing several MHC-peptide binding affinity predictors trained on  IEDB data. Quantitative records for MHC class I allotypes come from a lot of different assays and, by extension, have different measurement types. Here are the most common measurement type descriptions (I haven't altered them in any way):

dissociation constant KD (~IC50)
dissociation constant KD (~EC50)
half maximal inhibitory concentration (IC50)
dissociation constant KD
half maximal effective concentration (EC50)

All of the predictors I've reviewed so far consider these measurement types interchangeable, which I find extremely odd. While IC50 and EC50 can indeed be similar under certain experimental circumstances, I find it hard to believe that any one of these can be approximately equal to Kd (this site already has a post on this matter). I've contacted several authors and database curators, and all of them have assured me that these values can indeed be considered more-or-less interchangeable, but I can't find any references to support these claims.


texts: How do cellphones calculate heart rate ? I understand that the cameras there try to count undulation in blood flow, but is the method of calculation same as that of professional SpO2 monitors ?


texts: I have wifi on at my home almost all the time. I learned that the frequency of visible light is around several hundreds of THz, while the frequency of wifi is only several GHz, which is only 1:100,000. But I'm not sure how the amplitude of wifi wave compares to the amplitude of the visible light? Are the frequency and the amplitude the only concerns when we talk about the radiation? Can someone educate me to quantify the effect wifi radiation could have in our life?


texts: Calcium carbonate minerals in marine organisms shells

texts: Calcium carbonate minerals exist in seawater in two main phases: calcite and aragonite. While calcite is the most stable phase, it is aragonite that precipitates first in seawater because of the high magnesium content of the oceans today. But for a similar environment, e.g., tropical shallow water, some organisms have a calcitic shell while some other have an aragonitic one. How can organisms choose which phase composes their shell?


texts: What is the mechanism of cytokine release syndrome in CAR T cells?

texts: CAR T cell administration results in cytokine release syndrome (CRS). But what is the mechanism that induces the CRS in CART therapy? Also, what factors correlate with CRS severity? CAR structure? Or tumor burden?


texts: My dad found it so I don't have a lot of good information, but it was probably about 2.5 inches, somewhat west of Portland, and was found on a sidewalk. I don't know the area so I can't say what habitats are there that it might have come from.


texts: Calcium concentration in activated dendritic spines?

texts: What are the typical calcium levels reached in single postsynaptic spines following activation of NMDA receptors by an EPSP or backpropagating spike? Everyone seems to refer to that one Neuron paper (Sabatini et al. 2002) which reports experimental estimates of around 1 uM following single synaptic stimulation in CA1 neuron spines. However, most computational papers on LTP (even biophysically detailed models) work with much lower values for Ca2+ transients that do not seem to have concrete experimental support. I am trying to put together a realistic model for hippocampal spine calcium signaling, and would really appreciate it if anyone can point out other relevant experimental papers that provide estimates for spine calcium transients.


texts: Modeling yeast biochemical pathway using enzyme kinetics

texts:
I need enzyme concentration and metabolites concentration values to en-corporate these values in my model and do some simulation.

I searched through some database

yeast metabolome database http://www.ymdb.ca/
brenda and other enzyme databases for enzmye conc
and also did some literature search

but couldn't find much of data

where possibly i can get these data ??
is there any other way to do simulation without data.


texts: Textbook/lab manual for mammalian cell culture

texts:
For general techniques involving molecular biology, I know of Sambrook and Maniatis Molecular Cloning which covers many of the standard cloning techniques.

However, mammalian cell culture has many significant differences from bacterial cell culture, some of which include the many different variants of cell culture media as well as the relatively complex systems which cannot be provided using standardised media such as LB or TB in E. coli culture.

Are there any similar textbooks/lab manuals for cell culture? Alternatively, good review papers covering the different kinds of media used in mammalian cell culture and their relative benefits would also be a good answer to this question.


texts: Why doesn't the avocado turn brown when it is kept with its seed?

texts:
Why doesn't the avocado turn brown when its kept with its seed?
What does the seed release that slows down the oxidation process?


texts: Is rabies virus infectious outside host?

texts: Can rabies virus remain infectious on environment i.e on soil, grasses, leaves and water?


texts: As we know that the preferred source of energy for our body (source) are carbohydrates but heart muscle is an exception and need some explanation for this exception, that why the preferred source of energy for  or cardiac muscle are FATS?


texts: How are muscle fibre size and oxygen consumption related?

texts: Does anyone know of a paper which correlates the muscle fibre size to oxygen consumption in mammals? I am trying to find a correlation between muscle fibre type, size and (absolute and specific) oxygen consumption.


texts: How to determine if the amount of manganese chloride will change neural resting potential

texts: If I am treating an organism in MnCl2 dissolved in water, how do I determine if the amount of Cl (in MnCl2) will change the neural resting potential Oor if it will influence motoneurons?


texts: Is anything known about the speed with which viruses spread geographically in R. affinis (or at least bats in general)?

texts:
RaTG13, which is the closest known relative of SARS-CoV-2 at full genome level, was sampled (just) in a R. affinis (bat) specimen in Yunnan Province... which is about 1,500 km away from Hubei, the epicenter of the first Covid-19 cluster.

So, what if anything is known about the speed with which viruses spread geographically among bats, particularly R. affinis? Basically, do we have any idea how long it would take a virus to "travel" in (R. affinis) bat populations 1,500 km?

A paper still in draft estimates that the most recent common ancestor of SARS-CoV-2 and RaTG13 "lived" around 2009.

  the inferred the time to the most recent common ancestor in the recombinant region of the clade leading to RaTG13 and SARS-CoV-2 is no later than 2009 (2003-2013, 95% HPD limit).

I'm trying to figure out if this time frame is compatible in some sense with the speed with which viruses are known to spread in bat populations.


texts:
Whenever we see something delicious, rapid salivation starts in our mouth. Also, it doesn't happen for all other food, which we eat regularly.

So, Is there any particular use of "rapid salivation"? and why doesn't it happen for everyday foods?


texts: Could something akin to Cyanobacteria evolve on earth today or are all available niches taken for different kind of life to come to be?

texts: The most basic form of my question would have to be: could new life form from molecules as happened with the first life on earth, here on earth? If not why not?


texts: How do people who have lost both of their legs produce red blood cells?

texts: As far as I know, just leg bones produce red blood cells. So, how people who lost their both legs produce red blood cells?


texts: Does overfishing in one ocean hurt fishstock in another?

texts:
If there's overfishing in the Atlantic or North Sea - will this affect fish stocks in the Indian ocean? Are there papers on this?

The question I'm trying to answer is whether overfishing by developed countries has an impact on developing countries fishstocks?

I could see two different scenarios:

-fishstocks are connected globally and if you overfish in one ocean biomass from other oceans will 'flow in'
- the oceans ecosystems are more or less 'disconnected' and somewhat independent of each other

I would appreciate citations if there are any.


texts: How can they know that they found "all the PERVs"? (porcine endogenous retroviruses)

texts:
The New York Times article Gene Editing Spurs Hope for Transplanting Pig Organs Into Human links to the recent Science publication Inactivation of porcine endogenous retrovirus in pigs using CRISPR-Cas9
 Niu et al. Science  10 Aug 2017: eaan4187, DOI: 10.1126/science.aan4187.

The highlighted section of the abstract says "...we inactivated all the PERVs in a porcine primary cell line..." where a PERV is a porcine endogenous retrovirus, an RNA virus which carries its own reverse transcriptase molecule and converts to DNA before incorporating into the host's genome.

Question: Do they mean to say all currently known PERVs or is there some way to be absolutely sure that every PERV in the pig's genome is known. In other words, could they have missed one? Could there be an as-yet unidentified PERV? I don't really want to ask about the possibility of an entirely new and unknown class of retroviruses; rather I'm trying to understand how all PERVs as currently defined can be identified in a pig cell line.

The reason that this is important is that the motivation here is to generate pig organs for transplantation into humans. The concern is that the pig genome may contain retroviruses that could then infect the human host, and the further possibility that it could be passed infectiously to others. As pig to human infectious disease is always a concern, starting with a "clean" pig genome is of particular epidemiological importance.

The first sentence of the NYTimes article:

  In a striking advance that helps open the door to organ transplants from animals, researchers have created gene-edited piglets cleansed of viruses that might cause disease in humans. (emphasis added)

Abstract of Niu et al. 2017:

  Xenotransplantation is a promising strategy to alleviate the shortage of organs for human transplantation. In addition to the concern on pig-to-human immunological compatibility, the risk of cross-species transmission of porcine endogenous retroviruses (PERVs) has impeded the clinical application of this approach. Earlier, we demonstrated the feasibility of inactivating PERV activity in an immortalized pig cell line. Here, we confirmed that PERVs infect human cells, and observed the horizontal transfer of PERVs among human cells. Using CRISPR-Cas9, we inactivated all the PERVs in a porcine primary cell line and generated PERV-inactivated pigs via somatic cell nuclear transfer. Our study highlighted the value of PERV inactivation to prevent cross-species viral transmission and demonstrated the successful production of PERV-inactivated animals to address the safety concern in clinical xenotransplantation. (emphasis added)


texts:
After a period of heavy rain, several trees in my garden will put out an impressive burst of new leaves, with an incredible vibrant red colour, almost the colour of port wine. The new leaves will then slowly turn green.

I understand that the leaves turn green once they start producing chloroplasts and chlorophyll, but what is responsible for this initial red colour that is so very vibrant? And what biological role does it play?


texts: Identify round, green, flying insect with spikes in South Carolina (USA)

texts:
The tables have turned -- I need some help IDing an insect:
I've been unable to identify an insect that I came across about 6 years ago in South Carolina (USA).
We were doing a vegetation survey in a northern South Carolina forest when I felt a pinch (or bite) feeling on my hand. When I looked down a seemingly nearly round insect was at the site of the pain but flew away shortly after.
I have no photo of the insect, unfortunately, but I can best describe it as being light green, round (0.5-0.75 cm diameter) and shaped like a deep (i.e., slightly recessed) dinner plate with a ring of soft spikes around the perimeter of the slightly raised edges of its round body. I unfortunately have no recollection of the head or wings.
Here is a rough sketch of what I remember:

The spikes were very reminiscent of the backside of some adult scale insects (such as here) [seen below].

Given it's similarity to some scale insects, I've always assumed it was some species in the Coccoideae superfamily, but I have never been able to find a matching species.
Anyone have any ideas?


texts: Do disaccharidases require a cofactor or coenzyme to function?

texts: I'm doing research on lactose intolerance and am curious if disaccharidases (enzymes that break down disaccharides) require a cofactor or coenzyme to function? Reviews or references would be greatly appreciated.


texts: Why don’t bone marrow donations harm the donor in the long term?

texts:
I have googled about this, and the most I can really find is that donating bone marrow/blood stem cells is not harmful in the long run, but I want to know why and how much is really known about this.
My question “stems” from my maybe cartoonish notion that you have all the stem cells you’ll ever have at the beginning of your life and that their depletion relates strongly to aging.
In my googling, I have read studies that lifespans of older mice can be extended with bone marrow stem cell transplants from younger mice. Based on my cartoon, I guessed that perhaps older mice have some depletion of and/or damage to their own hematopoietic stem cells that reduces overall formed element production, and this is the state that a transplant helps to fix. With this frame of mind, I have a hard time imagining that even a young donor of blood stem cells is not harmed in the long run. Hasn’t their pool of stem cells effectively been aged somewhat by the donation? Or is damage to the population of cells over time by environmental factors much more significant, more the “bottleneck” in cell health than the gradual deterioration caused by repeated division? Is it that donation effectively only forces something on the order of one extra division per cell? I also wonder whether that “bottleneck” could vary depending on the typical longevity of the animal under study.
Regarding my question about what is known—I suppose I’m asking what kinds of principles or studied effects are likely being referenced in laypersons’ articles declaring that donors do not experience long term harm.
I’m sure that I am probably saying some nonsense things because biology is not my field. Any corrections and disentangled conflations would be appreciated!


texts: How are electrons entering the electron transport chain in cellular respiration energised (excited)?

texts:
In photosynthesis, electrons are excited by light energy from the sun (photoactivated).

How do they become excited in human cellular respiration?

I believe it has something to do with NADH and FADH2.


texts: What is the relationship between independent assortment and cross over?

texts:
During meiosis, the independent assortment will be made first and then cross over will be made. I am so confused, what is the difference between this two process? I looked at the diagram on internet.It is said that law of independent assortment is alleles of genes on non homologous chromosomes assort independently during gametes formation, but I don't quite understand that.
So, another way for understanding this topic, independent assortment is tetrads can line up four different ways between homologous separate. Is that right.
Appreciate your help.


texts: Recessive alleles at Hardy-Weinberg equilibrium

texts:
I've run into a question that I disagree with others on but I would like to receive the input of others. The question is:

If a population is at Hardy-Weinberg equilibrium, which of the following can be predicted for the recessive alleles in the population? 1) They will eventually disappear, 2) They will be selected against, 3) They will be maintained at the same frequency, 4) They will be expressed in the heterozygous condition, and 5) They will become dominant.

Some people said that the answer to this question was that the recessive alleles would be selected against, but I interpreted the question as having the answer that the allele frequency of the recessive alleles would not change and instead would be maintained at the same frequency.

My rationale for this was that Hardy-Weinberg equilibrium means there is random mating and basically no radical shifts in allele frequencies from outside sources, such as gene flow, natural selection, etc. I would think that the allele frequency would not change, but I may be incorrect.

Is my methodology correct?


texts: Are enhancers and silencers considered as epigenetic modifications? I am confused as it seems like enhancers and silencers are sequences on the DNA and how they work is through binding with proteins, while epigenetic changes seem to be changes made to the bases for instance adding a methyl group.


texts: Is there a type of mutation that changes the phenotype of an organism, but not the protein sequence?


texts: Are all non-breeding naked mole rats the same sex?

texts:
In many eusocial species, all the non-breeding members are the same sex.  Honeybees are a good example, with only female workers.

Are naked mole rats that do not breed also all either male or female, or are they mixed?


texts: How do stem cells produce 200 billion new blood cells every day? Does 1 stem cell division result in production of just 1 blood cell or many?

texts: It is given on wikipedia that everyday 200 billion new blood cells are produced in the bone marrow. I want to understand how this is achieved. Does one hematopoietic stem cell's single division result in just one blood cell produced, or many so as to meet the demands of trillions of cells? For example, does single myeloid progenitor (refer to the image) produced from one stem cell further divides into several other identical progenitors before further differentiating into specialized cell, so multiple blood cells are created with the involvement of just one stem cell so that work load is shifted from stem cells towards the progenitors? Also, does the fact that RBC lacks nucleus help in producing trillions of them, making the entire process cost effective.


texts: Why are triacylglycerols broken down before being absorbed?

texts:
So when dietary fats are in the small intestine, they are emulsified by bile salts in order for action by lipases to occur.  Lipases degrade the triacylglycerols into monoacylglycerols, diacylglycerols, free fatty acids, and glycerol, and these are taken up by intestinal epithelial cells.  Once taken up, these are reformed into triacylglycerols.
My question: why do these have to be broken down in order to be absorbed, and what is the driving force for reformation of triacylglycerols once absorbed?


texts: What is the difference between a viral strain and a viral isolate?

texts: Both are characterized, their genes are usually described and published, they are kept safe, they could be used as inoculum or to produce vaccine... Would it be correct to say a strain would be somehow a successful isolate ?


texts: What causes people to smell one persistent smell during Covid-19 infection?

texts: Some of the people I know got COVID and they loss the smell. After discussing with them about it, they told me that they only smell one persistent smell, everywhere (like onion). Is this frequent for people with loss of smell ? How this is possible ?


texts: Do four-leaf clovers have some disadvantage in reproduction?

texts: As far as I understand, four-leaf clovers are caused by genetics, so when reproducing, they should produce four-leaved children. I haven't found any disadvantages of four-lead clovers (e.g., infertility or worse survival capabilities), so I wonder why four-leaf clovers are so rare. Do they have any competitive disadvantage that makes them less likely to reproduce?


texts: Why do we need to grow plants to make food?

texts:
Why can't we synthesize the nutrients that we need directly from chemical reactions, from energy and simple inorganic molecules found around us? If it's hard, why not try to copy how plants do it?

I feel like growing plants is very inefficient: it is consuming a lot of energy for intermediate steps that may not be required – growing roots or inedible parts, performing reproduction, consuming soil and space, requiring constant light and irrigation... And huge amounts of energy is invested to slightly compensate for these caveats and increase productivity, while it still looks like an inefficient way of doing synthesis of nutrients and other compounds we need to eat.
Is there a reason that such resources are not directed to building processes to perform such synthesis via other – hopefully more efficient – means than growing plants/animals?

Note that I found a partial answer there, however I was not satisfied by an unexplained "photosynthesis is the only viable way to create material that can yield those nutrients".

Is photosynthesis that hard? If that so, why?

If it's so hard using organic chemistry, why cannot we simply extract/mimic the biological reactions happening in the plants to generate nutrients? (we still don't need to grow whole plants)

If we are not able to do that, what does it means about our current understanding/mastery of chemistry and biology ?


texts:
Our lab manager suspect that something wrong with our lab Bacto agar (Difco). So she decide to throw it to the garbage. I think that it's just a waste to throw that thing.
Can someone think of reason why don't use that agar for molecular cooking in my kitchen?
(My lab manager think that i am totally crazy without give any reason)


texts: In whole animal cloning ( eg. Dolly ) the nucleus is taken from a somatic cell. So isn't shortening of telomeres a problem ?


texts: Do we have the complete metabolic map for humans? Do we know from the genome what enzimes are expressed and what each enzime does?


texts: Why isn't there 1' to 2' direction or something else except 5' to 3' in dna replication?

texts: I hope i would get logical answers. I  request to post it as soon as possible.


texts: Critical pO2 threshold for cell division?

texts:
I'm a physicist asking questions on an aspect of cellular metabolism, so excuse my biological ignorance! Hypoxia is a frequent complication of certain tumour types, and has quite an implication for treatment prognosis - at certain low oxygen levels, metabolic functions become massively reduced or even halted and eventually necrosis sets in.

My question is what kind of partial pressures will cell division typically be halted at? From this review paper, it indicates that below 8-10 mmHg, adequate metabolistic functions cannot be maintained. In this case, the critical parameter being measured is ATP production. However, I've seen quotes for Chinese Hamster Ovary cells of 0.5-1mmHg. In radiotherapy, "hypoxia" as a condition is defined as < 2.5 mmHg but this doesn't tell me much w.r.t cell division or lack thereof.

Does anyone know a ball park figure for the cessation of cell division, in a typical cell line, and where I might find information on this? Thanks!


texts: I'm trying to unserstand Yamanaka's iPS cells paper

texts: Can someone please explain to me what is the beta-geo cassette and why is it used? I understand that it was inserted in the Fbx15 gene, and this gene is present in ES cells, and I believe this cassette is used as a marker of the Fbx15 locus, but why does it have resistance genes (beta-galactosidase and neomycin), what are they resistant for? What is their role? Thanks!


texts: Meaning of red blood cell volume expansion

texts:
In the scientific papers about EPO I read RBC volume (mL) expansion. What is it? The volume of a single cell or the volume expansion (=that is the increase of the number of cells) caused by the EPO?

Thank you in advance.

EDIT: see fig.1 page 3 please http://s000.tinyupload.com/index.php?file_id=08669957844938542361


texts: How to identify the subspecies/breed of a bee

texts:
I have been a beekeeper for a number of years and originally obtained my first colonies from a guy in my neighbourhood. However, when I sell bees to someone else, they typically ask what species of the European/Western honeybee (Apis mellifera) I have/they're buying. Technically, they're after the subspecies or breed (like Italian, Carniolan, Buckfast, ...), but I don't know what to tell them. I just call them local (or locally-adapted) bees.
Is there a way that one can find out the subspecies/breed I currently have? Perhaps through DNA analysis/sequencing or some other kind of scientific analysis? Regardless, is such subspecies identification available/accessible to the hobby beekeeper (should read as being relatively inexpensive)?
Images like the following are circulated to estimate one's breed:

However, traits are hardly a definitive assessment of a breed, especially if you consider how close some of the breeds are listed above. For example, what's the difference in a trait ranked 5 and 6, say.


texts: Is blood donation risky for patients with MGUS?

texts:
Monoclonal gammopathy of unknown significance (MGUS) is often considered a pre-cancerous condition.

Blood donors with MGUS are typically advised to discontinue blood donation as their blood may be risky for blood recipients.

This paradigm has been recently challenged (e.g. La Raia 2015), but also reinforced (e.g. Felldin 2016).

It is also possible that blood donation may be risky for donors with MGUS as well, as it leads to an overall boost and stimulation in hematopoiesis which may indirectly favor prograssion from MGUS to myeloma.

Is it true?


texts: It was found in Malaysia in my school compound.


texts: Does it make sense to classify all humans in a single species?

texts:
For what biological reasons do we consider that all human beings belong to the same species?

A Thai and a Nigerian share a common ancestor that is 140,000 years old (see Gravel et al. 2010 and this post). Would, for example, a mixed Thai - Nigerian baby suffer from any outbreeding depression?


texts: Assay for Beta-galactosidase activity in single cell microscopy

texts: I'd like to be able to measure the activity of $\beta$-galactosidase in living cells with simple optical (maybe fluorescence) microscopy. Ideally I'd like to do a minimum of genetic engineering, and use this assay with strains I already have (that have a WT lactose system), i.e. a fluorescent lactose-mimic would be ideal. Additionally, it would be nice if the lifetime of the fluorescent byproduct of $\beta$-gal activity was short, so I could detect a decrease in $\beta$-gal activity as well as an increase. Does such a fluorescent analog exist? I'm hoping to look at the switch from lactose to glucose utilization under the microscope, so I want lactose-using cells to light up and glucose-using cells to be dark, or vice versa. It does not have to be fully quantitative--a qualitative sense is fine.


texts: Which are the best apps and websites for insect identification?

texts:
My kids keep asking me to identify some insects they found, and I am often caught off guard, as I have very little matter knowledge.

I have found the Insect Orders app quite useful, but still quite challenging.

Is there anything else, in terms of apps or websites, which is better for insect identification?


texts: Does the Miller-Urey experiment explain the origin of life?

texts:
According to the Miller-Urey experiment, the early earth atmosphere could have supported the formation of amino acids - and the experiment is hailed as being important in the explanation for the origin of life. However, I do not understand how life could have started from amino acids (or proteins) which do not self replicate. Certain types of RNA do self-replicate, and it is plausible how life could have evolved from there.
Does it matter if amino acids came before RNA if they did? Is it correct to assume that in the RNA world, life somehow learnt how to use amino acids?


texts: Can DNA be transferred from one person to another

texts: kissing, handshaking, blood transmission, sexual intercourse etc,through  which of these DNA can be transferred to another person ?


texts: Meaning of "Antibody is 50% w/w pure of interfering proteins"

texts:
From Google Patents, "Preparing antibodies from cho cell cultures for conjugation":

  An isolated antibody or ADC is typically at least 50% w/w pure of interfering proteins and other contaminants arising from its production or purification but does not exclude the possibility that the monoclonal antibody is combined with an excess of pharmaceutical acceptable carrier(s) or other vehicle intended to facilitate its use. Sometimes monoclonal antibodies or ADCs are at least 60%, 70%, 80%, 90%, 95 or 99% w/w pure of interfering proteins and contaminants from production or purification.

Does it mean that even after purification the antibody solution may have an amount of impurities totaling to up to 50% of the antibody itself, in terms of weight? That the total weight of impurities may reach 50% of the antibody weight?

Maybe "an isolated antibody" is an antibody just after it has been produced? But the mention of "purification" confuses me. Why then such a high impurity content?


texts: Why do insects avoid being on their back?

texts: I have noticed that when insects are placed on their backs, they tend to turn themselves over quickly or else appear to be in distress. Is there a physiologic, anatomic, or adaptive reason why supine positioning might be unfavorable in insects?


texts: Are descriptive statistics sometimes more useful than tests of significance?

texts:
How does the biology community currently feel with regards to publishing descriptive and effect size statistics rather than significance stats?  Almost every journal article I read in the cell biology field almost always reports things like P values and stats tests to report statistical significance, but should effect sizes be more important to a biologist?  Do we even care if something is statistically significant if the effect size is negligible?  Rather than crunch for significance, could one get away with showing things like confidence intervals, eta^2, Cohen's d, and r values instead over P values?  P values tell you the odds that if you assume the null hypothesis is true, then the observation you're making are only 5%(assuming of course P<0.05).  However, this can lead to the logical fallacy as noted by Aristotle--theory A predicts that changing X will cause Y.  An experimenter thus performs experiments to manipulate X and sees changes in Y, therefore he/she concludes theory A is supported, which is however completely wrong.  Theories B, C, D, E....... could all also predict that X changes Y and may even be better at it.  Even if you conclude that your findings "support" theory A, it's still weak because you haven't ruled out all of the other possibilities.

So in order to avoid statistical significance relative to null hypothesis that has all sorts of pitfalls, can one just use descriptive and effect size statistics just as effectively, if not more so?


texts: Can DNA sequencing of food provide quantitatively the fraction of protein from chicken vs soy?

texts:
There is some news about a report from Canada's CBC about fast-food chicken items containing as much as 50% soy protein, based on DNA testing. I won't do the report the service of linking to it directly, but you can search for the news "What's in your chicken sandwich? DNA test shows Subway sandwiches could contain just 50% chicken."

Isn't quantifying ratios of various DNA sequences fairly difficult, requiring rigorous sample preparation? Could results vary dramatically by varying cooking times, and the independent processing of the animal protein and the vegetable protein? Is there an reason to expect isolated DNA ratios to be a good indicator of protein ratios?

I'm also curious, is there a better way to at least try to do this study - perhaps search for key sequences of amino acids within the proteins to at least try to distinguish animal from vegetable proteins quantitatively?

edit: Here is a newer, more reliable, independent news item not written by the agency who paid for the testing.

The NPR news article DNA Tests Find Subway Chicken Only 50 Percent Meat, Canadian News Program Reports says:

  The tests were conducted by a DNA researcher at Trent University's Wildlife Forensic DNA Laboratory, for a CBC Marketplace episode dedicated to testing fast-food chicken dishes, and have not been independently confirmed.

Later in the same article a strong statement by one of the companies refuting the results has also been provided.


texts: How does the Endoplasmic Reticulum scale with Cell Volume in Epithelial Cells?

texts:
I am working on a mathematical model of a biological tissue (drosophila pupal notum; an epithelial tissue) where the tissue is built up from cells all described by the same cellular-model. The tissue is generated using a somewhat random process, and so each cell in the tissue has a different size (volume, surface area, etc.)
The model focuses on the movement of particles both between cells as well as between the cytosol of each cell and internal stores (like the Endoplasmic Reticulum (ER)). In order to use the same parameters across the entire tissue, I need to know the ratios of various volumes and surface areas, such as the ratio of the volume of the cell to the volume of the ER, or the ratio of the volume of the cell to the surface area of the ER.
So my question is, if we have a cell of some volume $V_1$, and we look at another cell with volume $V_2$, what can we say about how the volume of the ER of cell $1$, $V_{\text{ER},1}$, or the surface area of the ER of cell $1$, $A_{\text{ER},1}$, compares to the volume and surface area of the ER of cell $2$, $V_{\text{ER},2}$, and $A_{\text{ER},2}$? For example, would we expect $V/V_\text{ER}$ to remain constant across all cells in the tissue? Or maybe we would expect $V/A_\text{ER}$ to be a constant across cells in the tissue? Or maybe both of these ratios follow some other sort of scaling law?


texts: What is the difference between GFP and rhodopsin?

texts: GFP and Rhodopsin are both fluorescent proteins. What is the main difference between GFP and Rhodopsin in terms of how they work? I know that their excitation and emission wavelengths are different, but in terms of the biological mechanism, how are they different?


texts:
I used Google to try to figure out what kind of mixture honey has with hot water, and I found several Ayurvedic sources claiming that honey in hot water is toxic.

For example:

Honey – NEVER Put It in Hot Water/Teas
5 Reasons You Should NEVER Cook With Honey
Honey: A Must Read For Those Who Eat It Regularly

What I would like to know is how does heating honey make it toxic?

Is there something that happens at the molecular level that changes the chemical properties of honey when it is heated? If so, are these chemicals harmful, as claimed?

Are there any other reasons other than heating that may make honey toxic?


texts: Again, it is a basic question. What is our skin made up of? is it made up of many cells arranged in a systematic way or is it just like any layer say of a book?? what is the difference? where is the living and dead thing coming into picture? is it the fact that skin can self-heal makes it living and in turn made up of cells??


texts: How can plants be grown in hydroponics, and yet not handle too much water in soil?

texts:
It's pretty much common knowledge that plants planted in pots or soil that doesn't have good drainage can't be watered too much, or they'll "drown". Regardless of what actually happens, experience seems to show that it's true that plants planted in soil can't handle too much water in the soil.

Yet on the other hand, in hydroponics, plants can grow and grow very well indeed with their roots entirely submerged in water. Clearly, it's not about "drowning".

So what's the deal? Why do soil-planted plants die when they're watered too heavily?

(I wasn't sure if this is a Biology.SE or Gardening.SE question, but I figured it was biology since I'm looking for a more theoretical answer about what happens to the roots, rather than practical advice.)


texts: Does turbidometeric method count cell number or cell mass?

texts:
Here it says that scattering is inversely proportional to cell number but also says that we can observe greater absorbance as cell number increases.

So does turbidometeric method work on cell mass or number ?


texts:
Can anyone identify this species of spider and whether or not is is venomous?
Location: South Carolina, USA.


texts: Basic Amino Acid Residue Binding Mechanism to DNA

texts: I understand that many protein DNA binding domains bind to DNA via basic residues such as Arginine and Lysine. But what is the mechanism used to bind to DNA and where on the DNA would these residues bind?


texts: How to identify genes in Ralstonia that synthesize PHB and promote granule formation?

texts:
The compound polyhydroxybutyrate (PHB) is of considerable industrial interest as a biodegradable substitute for plastic. PHB is synthesized from glycerol by the bacterium Ralstonia eutropha. PHB accumulates to high levels in proteindelimited inclusion bodies called PHB granules that are thought to protect the compound from degradation. PHB stains with the blue dye polyphorin 3Z27, so Ralstonia colonies on polyphorin plates have a blue color when glycerol is present (and PHB is made), but a white color if glycerol is absent (and PHB is not made).

Since bacterium E. coli is not able to synthesize PHB, but it would be useful to engineer an E. coli that does so. What approaches can I use with E. coli to identify the Ralstonia genes that synthesize PHB and promote granule formation?


texts: Why are sushi proteins called "sushi"? What are the origins of this name?

texts: Does anybody know why complement control proteins (also short consensus repeats) are called "sushi" proteins? Is there any special reason for their name?


texts: How does intron retention make the alternative transcript non-coding?

texts:
I faced with a non-coding transcript that specified as one the isoform of BIN1.

It sounds that this isoform generated as a result of alternative splicing with a intron retained; am I right? However, Ensembl reports that the transcript has 5 exons, could you please let me know more about this event? How does the transcript have 5 exons and all are non-coding?
Also, I'll glad to hear why the organism or cell has retained such a transcripts? they have any function?
Thanks


texts: Relationship between lifespan and reproductive age?

texts:
I remember reading a while ago that there is a "general rule" in biology between an animals lifespan and when they reach reproductive age.

In other words, an organism that reaches sexual maturity after a short amount of time (for example, less than a year) will have a short lifespan (for example, 2-3 years) and an animal that reaches sexual maturity after a long time (elephant, 10-12 years) will have a much longer lifespan (40-60 years in case of elephant).

Is there a special name for this "law" or "rule"? Are there any major papers/theories supporting it that also attempt to propose why (perhaps from an evolutionary perspective) this trend exists?

Some quick supplemental questions:

1.) Is there also a trend between lifespan and animal size?

2.) Is there also a trend between lifespan and base metabolic rate?

3.) Do the two aforementioned "trends" or "rules" have technical names that I could look up as well?


texts: How is a specific fragment isolated for PCR amplification?

texts:
For background I am interested in studying engineering applications of a specific protein, which is not commercially available. My end goal is to express the gene for the protein in bacterial cells, most likely E. Coli, if that is a feasible procedure. I am mostly familiar the process of forming recombinant DNA, and though our lab does not specialize in Biology, we will be working with another lab in our Biomedical department which can provide necessary equipment and some advise.

The last time I did a lab where we expressed a new gene in E. Coli cells was a biotechnology class in high school, though much of the set up was done for us. I recall that our first step was amplifying the desired DNA fragment through PCR, but what I don't know is how the fragment was initially isolated. I know the primers help by essentially setting the start and end positions for the DNA cloning, but if you were to use an entire chromosome that contains the desired gene, it would seem likely that there would be many possible sites that the primers could attach besides the desired region. So if the DNA sequence for the protein I want is already known, how would I get a fragment that contains the gene I want?

Additionally, how difficult will this process be? Since the end goal is actually to study the protein, I do not want this step to turn into a full thesis on its own. For some specific proteins, the process seems well documented and can be done using relatively common materials and by following simple instructions, but how much should I expect the procedure to diverge for attempting this with gene that has not been specifically done before?


texts: Does pouring water on your skin affect the evaporation process and heat loss?

texts: Recently I've been playing football in the sun pretty hot temperatures. During the water breaks I tend to pour a lot of water over my head to cool me down, now this has an instant effect on cooling me down but in the long run would this have any affect on my body temperature? We know that the body cools itself by using heat to evaporate sweat on skin, would drenching  my head and face in cool water affect this process or not?


texts:
The first time I saw these was in an old cooler full of water by my shed, there were 3 of them about 2 weeks ago. Now tonight I found one crawling up my door. Can anyone offer some insight? I have dogs and I'm horrified that it may be some kind of parasitic worm that they can contract.
This was observed in northwestern Pennsylvania, US. Rainy, cool fall weather currently, as it's the end of October. They're about 2 inches long. Very thin, blackish red in color and extra wiggly.


texts: How to automate this custom gene expression microarray chip?

texts:
I have 16 gene sequences that I am interested in their detection in clinical samples. I already measured their RNA levels by using RT-qPCR technique and their benefit has already been proven to help in diagnosis of clinical cases. Now I want to take this gene expression profiling into another level of automation. The first thing came to my mind is the microrray chips. I don't have much experience in micrarrary, I want to have a custom chip containing these 16 genes in question. These are 13 target human genes and 3 reference genes (housekeeping genes) for normalization.

Question
- is it possible to have this custom chip?
- How can I get such a custom microarray chip?
- What is needed to automate this process at a production level?


texts: Is it fact or myth that our heart stops beating for moments when we sneeze? If it is fact, what drives the heart to start beating again?


texts: I am in the process of making biochar, this means producing charcoal with pyrolysis. I want to use it for agricultural purposes, so I need to activate it with microorganisms to produce inoculated biochar. My question is: would the micro-organisms within die if the inoculated biochar dries out?


texts: What happens to the enzymes produced by the digestive system?

texts: Our digestive system produces a lot of enzymes and they help to catabolize the food, and after completing their work are they excreted out or as they are also made up of proteins are they catabolized and assimilated back?


texts:
I heard this fact that you can use some [hypertriade] for vibrio cholera diagnosis which has compontents

sucrose (yellow)
mannose (yellow)
arabinose (do not ferment; stay dark pink)

I did not find this hypertriade agar on Google.
It reminds me of Egg Yolk Agar, but I think cannot be it because of the arabinose.
Otherwise, it seems to be similar.

What are the best detection medias for cholera?


texts:
Currently either PET-Fluorophore or FRET is used as output of the molecular/DNA-based logic gate. Likewise, in a logic gate, lets say YES GATE, you provide an input to the logic gate and in return you got fluorescence. Please help me understand what other transfer method can be used as the output. I want to develop a complex system i.e. connect multiple logic gates with each other which, definitely, cannot happen if molecular logic gate would return output such as fluorescence, can any other method be used?
Thanks in advance


texts: I know ringworm is caused by a fungus on the skin, nails or scalp but what causes the rash to form as a ring instead of like a normal spread out rash?


texts: Grafting vegetables onto fruit-bearing trees

texts:
There are multi-fruit trees with as many as 40 different fruit, but would it be possible to graft a vegetable onto a tree?

Or maybe something in between, like grafting onto an apple tree a fruits in the botanical sense, but one of those often eaten as savory food, similar to vegetables: tomato, squash, avocado?


texts: What mechanisms tell temperate trees when to drop leaves?

texts:
I've been looking around and cannot find a definite answer on what it is that tells trees to change their metabolism and drop leaves. I see that such activity is called Deciduous.

What interests me are the specific mechanisms by which a tree knows that it's time to drop leaves. Is it photoperiod shortening (day duration?) Is it temperature changing metabolism? Is it build up of some toxic compound?

Thank you for your input!


texts:
Lentivectors are widely used in molecular biology, most commonly to transduce in a stable way a desired gene. These vector system takes advantage from the ability of viruses to introduce their own genome in the host cell. Thus the lentivectors are transfected to a producer cell line (typically HEK) and there viruses are produced with the desired insert. Eventually this viruses will be harvested and the desired cell lines transduced.

For bio-safety reasons, this system is engineered in a way that that the risk posed by the "virus system" is reduced. Thus the viruses produced by this system are incapable of replication, meaning with this that, as far as I understood, the viruses that are formed are then unable to form more in the second host as the genes in charge are not recruited. Yet, apparently the plasmids used can recombine and pose a possibility to create a replicating capable virus. Yet as far as I found in the literature this has never been detected and stands as a theoretical possibility.

My first question, in actual numbers, what is the probability that such event would take place (the number of recombinations in the specific locations). In the case that this would happen, the lentivector system would be potentially dangerous, as this system is based in HIV most of the times. Additionally, this vectors use not the endogenous HIV envelope protein but rather VSV/G from vesicular stomatitis virus, in order to increase the tropism and stability.

Additionally, even though HIV derived, most of the HIV genes are taken away from the lentivectors, yet in my opinion the most important ones are there. Second question, taking into consideration all of this, this theoretical "created" virus would be able to eventually cause AIDS or other whatever adverse effect? it is noteworthy that now is able to infect almost all human cells due to the VSV protein, then is it correct to think that the disease would be much worse, and much more contagious than the original HIV? note that even the stability is increased.

Yet, I can additionally think that this recombinant new virus may be indeed destroyed by the immune system, despite the increased tropism, due to the fact that vesicular stomatitis virus does not cause pathologies in humans, and possibly this protein works as an antigen and can induce an enough immune response.

Last, would theoretical recombinant virus be detected by a standard HIV test?

To simplify things, I am referring to third generation lentivectors


texts: pI and pH relationship in context of ion exchange protein purification

texts: I am confused about relationship between isoelectric point and pH in context of ion exchange protein purification. Why we cannot use this method for protein with pI below 7? Thank you very much for any tips.


texts: Why bananas accumulate a radioactive isotope of potassium (K40)?

texts: A quick google search reveals many pages that intend to calm consumers down and assure them that quantities of radioactive potassium in bananas (K40 isotope) is not sufficient to be concerned about, e.g. http://www.raw-food-health.net/Natural-Radiation.html. I am not worried that bananas may be harmful, but I wonder if bananas are actually enriched in K40 relative potassium in soil? Maybe bananas are not enriched, and so every potassium-rich food is equally radioactive... but if specifically bananas are particularly enriched in K40, then what is the mechanism of this process?


texts:
Is it a myth that modern whales have been found with hind legs sticking out of their sides and full formed tibias, fibias, and toe bones? I keep finding assertions, but no citations. For example, the wikipedia page has no citation for it.

http://en.wikipedia.org/wiki/Whales#Appendages


texts: Do all polygenic traits involve epistasis?

texts:
Consider the following statement

  All polygenic traits involve epistasis.

I think its true because polygenic traits involve several genes interacting together to result in a certain phenotype and if one of these genes is altered, the resulting phenotype is different.


texts: Why do redheads tend to sunburn more easily?

texts:
Reading Marion Roach's book on redheads she mentions visiting Rees lab where he shines UV light on her skin. Apparently this is an ongoing experiment of his regarding the propensity of redheads to sunburn more easily, but the book doesn't adequately explain why.

Why do redheads sunburn more easily?


texts:
I am doing a rtPCR to detect the watermelon mosaic virus (WMV). My set of primers are:

WMV primer forward: 5'-TNGARAATTTGGATGYAGG-3'
WMV primer reverse: 5'-CTGCGGTGGACCCATACC -3'

both of which at the concentration of 10 microMolar.

The first step of my rtPCR reaction was looking for a positive control.

I did the rtPCR against to a field sample (In the NGS results showed a positive against to WMV) and two greenhouse samples (the first one of my greenhouse samples was inoculated with WMV and the second one it was not).

These samples were extracted with good concentrations and integrity.
After that, I did the rtPCR with rt enzyme (from Affinity company).
Following the next steps:

I added 2000 ng of my RNA samples (in different tubes; one of them to one greenhouse sample, another tube for the remaining green house sample and the latest tube with the field sample) with Reverse primer (2 ul) and H2O (until get 12.5 ul).

1.2. I incubated them 65ºC 5' and 25ºc 10'.

2.1.  I added the next volumens for 1 sample: 2ul of my buffer, 2ul of my DTT, 2ul of my DnTps, 0.5 ul RNAsa block and 1 ul of Rt enzyme.

2.2. I vortex them and I incubated them 1 hour 50ºC and 10' 70ºC.

3.1. The PCR reaction was performed with the takara polymerase enzyme.
I added the next volumen per one tube: 2.5 ul of takara buffer, 0.5 ul forward primer, 0.5 ul and primer reverse, 0.5 ul DNTPS, 0.25 ul of taq polymerase and 15.75 ul of watter. All these volume 20 ul I added 5 microlites of my rt samples (2.2 point). I did this process with my remaining two samples.

3.2. Finally I incubated them 98ºC 5', then 35 cicles of 98ºC 30'', 56ºC 30'' and 72ºC 1'. out of the 35 cicles the temperature goes to 72ºC 10'.

I run the gel and I got primer dimmer. What I am doing wrong? All help will be very useful.

Note: These protocol was following by a labmate who got good results with the same field sample. Now I am following the protocol that was written in his notebook.


texts: How do the first and second law of thermodynamics adhere to breakdown of glucose?

texts:
I know the first law is energy can only be converted from one form to the other, therefore in the breakdown of glucose 40% potential energy is converted to ATP and 60% is converted to thermal and unusable.

Does the second law adhere to the breakdown of glucose? Isn't it just the same as the first?


texts: Why do doctors still advise HIV+ couples to wear a condom during sex?

texts: HIV infected people already have HIV, but why do doctors still advise condom use for HIV+ couples?


texts: Poisonous plants, animals, mushrooms: is this always a kind of defense?

texts: I wonder whether developing deadly toxins in the organism's body is always or usually a defensive strategy rather than a by-product.


texts: If I built a concrete pool, would it ever contain fish?

texts:
Imagine that I built a concrete-walled pool the size of a football field and filled it with fresh water - obtained from another lake but free of bacteria, plantlife, eggs, etc.

Would it ever, over time, become a life-filled "lake" - with fish, amphibians, algae, plants and other water-dwellers?

If yes, how?

What would the chain of events look like?  I'm assume plant-life would get there first but how would it develop an established eco-system?

Please re-tag as appropriate as I am new to this SE site.


texts:
When inbreeding depression occurs, a genetically unrelated individual is mated with the animal to introduce genetic variability and remove homozygosity. In this case either outbreeding or crossbreeding may be carried out. Is there any preference for either technique over the other?
Out-breeding here refers to mating between two individuals in the same breed, but no recent common ancestors.
Cross-breeding refers to mating between two individuals of different breeds entirely.


texts:
What are the benefits of CLARITY over this technique that was published more than a year earlier?

Of course the second technique needs a fancier microscope that is likely more expensive and requires more technical ability. But CLARITY requires an objective with a very long working distance. I'm no expert in optics, but I'm pretty sure this results in a significant decrease in numerical aperture and therefore resolution.

It seems as though the other method is simply better than CLARITY, and that a lab serious about doing whole brain imaging could afford to invest in a setup similar to the one described. Yet this technique received none of hype that was bestowed on CLARITY. Am I missing something?


texts: Can diploidy evolve in absence of sexual reproduction?

texts:
Theoretical question

Can diploidy (or polyploidy) evolve from a haploid lineage in the absence of sexual reproduction ?
For what theoretical reason? How can such evolution take place?

Empirical evidence

Beside theoretical answers I'd like to also ask for empirical examples:

Are there any examples of diploid (or polyploid) species that reproduce exclusively asexually, and for which sexual reproduction never occurred in the evolutionary lineage of this species?

Or in other words,

Does diploidy (or polyploidy) exist in lineages that has never underwent sexual reproduction?

Is my assumption correct?

I am assuming that in eukaryotes haploidy appeared before diploidy. Is this assumption correct?

By sexual reproduction I mean that the genome of the offspring is a combination (with or without recombination/crossover) of two parent individuals. I don't mean reproduction with sexes (or with mating types). I welcome the discussion of self-fertilization if needed.


texts: At the present time it looks as if there is no other life in the Universe other than here on Earth . If this is true then why didn't it occur anywhere else ? Is it possible for something to happen only once ? Hundreds of Billions of  other Planets have formed so whatever happened here why wouldn't it have happened again elsewhere ? It is very , very strange indeed .


texts:
Warning: I have almost no knowledge of biology past the high school level.

Viruses generally have three components: the DNA, the virus protein coat, and an outer membrane "decorated" with these surface marker glycoproteins. I am thinking that a virus would want to infect as many hosts as possible, so that it would reproduce as much as possible, why would a virus just infect one group of organisms.

What evolutionary advantage do viruses have in host specificity?


texts: Why are Birds and Reptiles with abundant yolk sac polyspermic?

texts:
I was given an explanation that birds and reptiles are polyspermic because they have an abundant yolk sac. But how does it explain the thing?

Chicken as an adult is not using in my opinion yolk as an energy source.
Yolk is used during embryogenesis as the primary energy source with blastula and gastrula -stages and during organogenesis, since the embryo needs proteins and energy somewhere.

How does abundant yolk sac make birds and reptiles polyspermic?


texts: What kind melanin do fair or light skinned black or mixed people have, eumelanin of pheomelanin?

texts: I am doing a study on melanin and conductivity but I cannot find the answer to this question anywhere. Do light complected black or biracial people have eumelanin or pheomelanin? or both?


texts: Is it feasible to eradicate a virus without vaccines?

texts: Although a vaccine for hepatitis C virus (HCV) remains elusive, new direct-acting antiviral (DAA) drugs can cure HCV effectively and conveniently. The latest DAA, Epclusa, can cure 95-99% of chronic hepatitis C regardless of genotype (e.g. see here). So if DAA drugs become universally available, will HCV be the first virus eradicated solely by drugs?


texts: We're working on an algorithm for processing images of cells, similar to but much more basic than Cell Profiler, and we are looking for a large database of cell images to test our software. Can anyone point us in the right direction? We found the Cell Image Library immediately, but it seems almost empty.


texts: I am a 5th grader learning about the plant transport mechanics and I learnt that the xylem is made up of dead cells.So if water travels up the xylem and water travels only 1 way, is it like how water travel up a tissue paper?


texts: What insect is this? I saw it in my house in Kolkata on 2 April 2018, at 8:00 p.m

texts: I saw this insect in my house in Kolkata (India) on 2 April, 2018 after a storm at around 8:00 p.m.  I would like to know what insect it is.  Thanks in advance.


texts: Can different bacteria strains of same species have different genomic sizes?

texts: Can two different strains of a single species have different genomic sizes? I am not asking about plasmid. Can they have different sizes of actual chromosome?


texts: At what age do babies begin to synthesize their own antibodies?

texts: When babies are first born, they receive their antibodies from their mother (I assume because they do not yet have the capacity to synthesize their own).  So my question is, at what age do babies begin synthesizing their own antibodies?


texts: How does exercising/starved muscle import glucose (released by liver)?

texts: Adrenaline releases glucose from the liver during sport or if starved. This glucose goes to the blood through GLUT2 transporter. But how does it get transported into the muscle cells? GLUT4 is the glucose transporter into muscles, but it is activated (translocation to plasma membrane) by insulin, but when exercising/starved, there is no insulin. So is the glucose transported through some other transporter?


texts: How do I calculate amount of nutrients retained/excreted in fish?

texts:
In preparation for my exam in fisheries and aquaculture, I looked through last years exam (with an answer sheet) and stumbled upon this multiple-choice question that I can't figure out how to solve.
The question is:
1000 kg fish is produced with an FCR of 0.9 on a diet with 42% protein. ADC for protein is 0.9. The amount of N retained in the fish, excreted in dissolved form, and excreted in solid form is
The possible answers:
27.2 kg retained N, 39.3 kg dissolved N, and 7.4 kg solid N.
27.2 kg retained N, 33.3 kg dissolved N, and 6.7 kg solid N.
27.2 kg retained N, 27.2 kg dissolved N, and 6.1 kg solid N. (correct)
27.2 kg retained N, 22.4 kg dissolved N, and 5.8 kg solid N.
27.2 kg retained N, 45.5 kg dissolved N, and 8.1 kg solid N.
So I know what the answer is, but not how to calculate it.
Thanks in advance.


texts: What happens when you tag a protease with its own degradation tag?

texts:
I've been learning about the ClipXP, ClipAP, and Lon proteases. They are proteases from the AAA+ family, which seek out proteins tagged with certain peptide sequences, unfold them, and chop them up.

But what happens when you tag a protease with its own degradation tag? For example, what if you took DNA encoding mf-Lon and added its ssrA tag to the end, and then expressed this sequence in bacteria?

Would this result in any interesting dynamics? Will the protease start trying to degrade itself like an Ouroboros? Will it get stuck trying to do so? Will we observe any interesting dynamics when we incorporate this into a gene circuit?


texts: How did fig tree take root in trunk of palm tree?

texts:
Please see pictures below.

I never saw anything like this.  Do the roots of the  fig tree penetrate the trunk of the palm tree?  Is there a symbiotic relationship between the two?


texts: I read in an article that ESTs are partial or sub-sequences of cDNA. What are ESTs exactly? Which part of cDNA is cut in order to make ESTs? Why are they so instrumental in genomic research?


texts: Anyone know what these are? I found them in our local park today attached to a wooden earth-retaining wall.I was thinking some kind of insect nest/egg sac (spider?) They're about the size of a medium egg (hen's egg!)


texts: Do human populations differ in core body temperature?

texts:
Human body temperature is a very complex and tightly regulated system. Hypothermia or fever of only 1-2K (i.e. changes of about 5%) already cause major symptoms and changes of 3-4K (i.e. about 10%) are life threatening. Many humans live under relatively cold outside temperature conditions and maintaining an inside 36-37 degree C in these conditions is very energy consuming (most probably a reason why the body temperature in the periphery is several degrees lower), indicating very strong evolutionary constraints on not changing the core temperature too much (I remember a professor in biology classes in university saying that most fungi have a growth minimum around 37 degree C). However, other mammals have higher or lower body temperatures than humans which suggests that the 36-37 degree C of humans are not a universal gold standard (in mammals).

Probably, for a long time in hominin evolution maintaining the core body temperature was not extremely energy consuming due to tropical conditions. This could have changed during the out-of-Africa migration some 100-60 thousand years ago. Of course this is somewhat difficult assess because early modern humans started to wear protective clothing. In fact, wearing clothes is a most probably adaptive trait to save energy while maintaining core body temperature. Still, it is unclear to me whether physiological adaptations took place as well. Furthermore, there is considerable variation between individuals and also within individuals, the latter in response to environmental conditions and/or behaviour (e.g. exercise), which in principle allows natural selection to change the trait and also shows that slight shifts in body temperature are not harmful individuals.

My question is: Are there significant differences in core body temperature between human populations? Please note that my questions is not why the (average?) human core body temperature has this particular value or why it is different from other mammals or birds.

There is a somewhat related question (also on Skeptics.SE) about lower core body temperature in Japanese people. As far as I know, this difference is rather a measurement thing than a real biological difference, so my question remains unanswered.


texts: How many transcription factors are there?

texts:
In molecular biology and genetics, a transcription factor is a protein that binds to specific DNA sequences, thereby controlling the flow (or transcription) of genetic information from DNA to messenger RNA.

My question is simply how many transcription factors are there in the genomes of:

Humans
Anopheles gambiae (or it's close taxonomic relatives)
Less prioritized: any other species


texts: At what stage is the nervous system developed enough to interpret neuronal signals as 'pain'?

texts:
According to this article in Live Science, one of the reasons the fetus can't feel pain until 19 weeks is because the nervous system isn't fully developed.

But according to this article, the heart starts beating at day 16.

And according to this article, the nervous system controls the rate beating of the heart.

Then my question is, **how can it be assured that the nervous system isn't developed until 19 weeks, when the nervous system controls the heart beating rate since day 16?


texts: Are B Cells unique to an individual's immune system?

texts:
I was wondering how the body "remembers" viruses after having once overcome them, and while reading this article on the immune system (page 14, Vaccinations), I read:

  There are many diseases that, if you catch them once, you will never catch again. Measles is a good example, as is chicken pox. What happens with these diseases is that they make it into your body and start reproducing. The immune system gears up to eliminate them. In your body you already have B cells that can recognize the virus and produce antibodies for it. However, there are only a few of these cells for each antibody. Once a particular disease is recognized by these few specific B cells, the B cells turn into plasma cells, clone themselves and start pumping out antibodies. This process takes time, but the disease runs it course and is eventually eliminated. However, while it is being eliminated, other B cells for the disease clone themselves but do not generate antibodies. This second set of B cells remains in your body for years, so if the disease reappears your body is able to eliminate it immediately before it can do anything to you.

Which made me wonder, instead of vaccinating people with weakened forms of the disease, getting their B cells to activate as described, what would be wrong with growing large colonies of B cells for a given virus and injecting them into someone who has never had the disease so that one can go straight to the last sentence of that paragraph, having many of those B cells in place before the virus is ever experienced?


texts: What does the 34/70 in Saccharomyces pastorianus Weihenstephan 34/70 stand for?

texts:
I've searched everywhere.
No Wikipedia page.
No information on NCBI.
I searched all occurrences of 34/70 in some primary research articles!
The best I've found is this brewery forum where someone asked the same question.

And the user rockfish42  answered:

  No idea why they use that number, but it's the catalog number at
  Weihenstephan's hefebank.


texts:
This is a hypothetical question

What would happen if the DNA of a prokaryote was replaced with the one of a prokaryote of another species, would the cell structures change and adapt to the new DNA and would the cell survive?

(Would the result be similar if we did the same with two eukaryotic zygotes of different species?)


texts: I use RNase AWAY in the lab. I would like to know how dangerous this chemical is for health. For example, when I remove my gloves my hands smell because of the RNAse AWAY


texts: What happens to the language processing brain part if no language is ever learned?

texts:
Language is processed in the human brain in multiple regions.
Some of them seem to be used exclusively or mainly for language processing,
other regions are distributed overlapping with other functions.

If a feral child is never exposed to any language, and therefore never
learns one: What happens to the language related parts of the brain,
like the ones exclusively used for language?

The language processing is not the central point - so feel free to use analogous examples of brain regions that are unused based on exceptional circumstances. Blindness from birth on comes to mind. Also, no need to base examples on homo sapiens.


texts: What is the family of this insect caught by my Drosera?

texts:
I am currently trying to find out what type of flies are flying around in my home. If they are fruit flies, fungus gnats or something else.

Currently my Droseraa caught one of them and I am currious what species it is.

It is a small fly, like fruits flies and fungus gnats. As seen in the third photo the length is about 1,5 to 2mm (The distance between each line is 1mm).

The location is Stockholm in Sweden (in my apartment).

Could you help me identifying it?


texts: Does a mRNA molecule bond to itself? I heard that only tRNAs have hydrogen bonds that let them have second structures, but after searching the web i found multiple answers. If yes, does anybody have a credible reference for that?(books, articles etc.)


texts: Do biological facts determine when a human fetus is considered alive and human?

texts:
I often hear or read this statement:

  "It's not a human, it's a fetus."

In other words, some think a fetus is non-human until a certain point.

And another similar statement:

  "The fetus isn't alive until 26 weeks of gestation."

So some think the fetus is not actually "alive" until a certain point.

What does biology have to say about these two statements?

I encounter these statements often in discussions about abortion, but that issue, and other similar philosophical issues, are outside this question. I'm wondering strictly from a scientific/biological standpoint: are these statements true?

Is the fetus in a human mother non-human until a certain point?

Does the fetus not classify as "alive" until a certain point?

The people I encountered truly believed these statements (3 of the 4 in mind also claimed science was on their side), so it's not as if the question has no merit. I assumed that in the realm of science and biology, there must be a convincing and sure answer.