texts: Have traditional categories such as phylum, class, genus, been dispensed with in modern taxonomy?

texts: Looking through the one zoom and EOL projects I see no reference to such categories.


texts:
Cross-posting, as I'm not at all sure which StackExchange this belongs in. Very happy to move / delete where I've chosen poorly, and a better SE can be recommended.

Question:

Can anyone advise on how long clothes moths eggs can last unhatched, and how long the larvae would then be able to survive without any natural fibre food.

I'm currently trying to deal with a clothes moth infestation, and your site has been invaluable.
Are you able to advise how long the larvae can survive without any available food?

We've removed the carpet and soft-furnishings from a room, and thoroughly hoovered, but there are nooks and crannys (especially around the skirting boards), which I suspect still have eggs in. I've thoroughly removed any fibres left from the carpet, so my plan is to leave the room for 10 days to ensure any remaining live eggs have hatched into larvae (which then have nothing to eat, and then ... X? ... days to ensure that those larvae have all died.

Are you able to advise what X should be?

We're under the impression that the larvae can ONLY eat natural fibres, so they can't eat, e.g. artificial foam underlay or cardboard boxes & books. Even if those are the only things around them, they can't consume those and will thus starve.


texts: Let's say you're a 23-year-old man who impregnates a woman. Will your genes be the same if you were to impregnate another woman at age 35? Will your genes in those 12 years have changed/mutated/become smarter?


texts: What causes people to feel sleepy due to recycled air?

texts:
I notice this the most in cars, when I set the air con to recycling air (instead of pulling in fresh air). After a while, I start to feel sleepy, and the sleepiness passes almost as soon as I open a window or change the air con setting to bring in fresh air.

I notice it also in shopping centers, or long bus rides, where there is inadequate fresh air. I know a lot of people who get sleepy from this, but also some people who just notice the air smelling 'stuffy' - but there's no particular smell, just 'stuffy'.

What causes recycled 'stuffy' air to smell stuffy? Is the sleepiness to do with increased Co2 / decreased O2 due to people breathing? Then is the 'stuffy' smell just the smell of CO2?

Any ideas how big of a change in concentrations we're talking about? Wikipedia says concentration of O2 in air is 20.95%. So are we talking about a drop by less than 1%, or a drop by a few %, etc.?

Is this 'stuffy air' bad for you? e.g. hypothetically if I have trouble sleeping, could I seal my bedroom (as sealed as an ordinary passenger car is), install an air con, and have it start recycling air when it's bedtime. Would this be bad for me long term?


texts: What is methamphetamine's transport carrier across the BBB?

texts: Which carrier protein allows methamphetamine to cross the blood brain barrier? I would assume it's SLC22 and possibly SCAMP1


texts: Ideal lab glassware cleaner for molecular biologist

texts:
I'm using Alconox powder detergent to clean my laboratory glassware, the powder is a pain to store near the sink and to use. Would like to make a   concentrated liquid to use in its stead.

I have tried a few things, obviously just water and mixing, even up to overnight. It really doesn't go into solution very well, even at seemingly low concentrations. Ive got it up to about 20% w/v but I've tried heat, glycerin, adjusting pH to ~8.8, adding EDTA. I have not added these things in any scientific way, just kind of pouring glycerol or EDTA in.

Wondering if anyone in here has experience with detergents like this , or has done something like this before. Thanks in advance!


texts: Difference between NCBI's /genomes and /1000genomes

texts:
Wondering what the difference is in the data hosted here:

ftp://ftp-trace.ncbi.nih.gov/1000genomes
ftp://ftp.ncbi.nih.gov/genomes/

Also (sidenote), would be interested to note what the difference between ftp-trace and just ftp is. But there is probably over 1TB of data in /genomes, and I assume something of "a thousand genomes" is in /1000genomes, but I'm not sure what data exactly. Would like to know what is i thse two folders, and where the 1000genomes data is exactly. It looks like /1000genomes/ftp/data/ has "sequence data", but I'm not sure how that compares to the /genomes list of species names (and I'm also not sure what "sequence data" entails exactly).


texts: My family and I have almost never seen a wild male turkey though we have seen countless female turkeys. Is the male to female sex ratio of turkeys at birth extremely low? If not, what happens to the male turkeys?


texts: Do marine deep sea life forms exhibit circadian rhythms? If so, what entrains them?

texts:
I've been reading a lot about circadian rhythms, when suddenly this question popped into my head: do circadian rhythms exist for deep sea organisms (3000 ft / 1000 meters+)?

For land mammals, the entrainment of circadian rhythms is done through exposure to light (retina or other photosensitive elements), but in the deep ocean there is no light. How are circadian rhythms maintained there - what acts as an entrainment signal? Is it the moon, currents, etc.?


texts: What is the biological basis of "energy" that extraverted humans draw from social engagements and introverts expend?

texts:
This question is related to this question about introverts becoming exhausted after extended social events on cognitive sciences stack exchange.

As I read more on the topic of human extraversion-introversion, I keep seeing the mention of "energy" which extraverts draw from social engagements and introverts expend in such engagements.

When energy is drained, the state can be called "exhaustion", depletion, being drained
When enough energy is accumulated, the state can be called "elation", being energized

The idea makes sense, and I see many diverse writers use it, but nobody defines what this energy is in a biological sense.

What is the biological mechanism behind "energy" spent/gained in social interactions - what is it in brain terms? I'm looking for an answer like: Dopamine in X part of the brain? Mirror neuron activation? Amygdala overreacting?

I found a quote from this article on introversion, although it does not seem to have any sources listed

  Research has shown that the mind of an introvert works differently
  than the mind of an extrovert. Introverts have more pronounced
  activity in the parts of the brain that deal with long term memory,
  planning, complex thinking and organizing. Our introverted mind is
  always turning and running and because of this, we need very little
  outside stimulation. The extrovert's brain has more pronounced
  activity in the areas associated with sensing and processing
  information from the outside. That's why extroverts seek outside
  stimulation

What are the scientific names of the brain regions described in the quote above?


texts: The total numbers of mutations on different branches of gene tree are independent or not?

texts:
I was reading Tajima's 1989 paper on his test for neutrality.

Tajima, Fumio. "Statistical method for testing the neutral mutation hypothesis by DNA polymorphism." Genetics 123.3 (1989): 585-595.

Here is the question:
Suppose we have three sequences labelled $C,D,E$, and their genealogy follows $\{\{CD\}E\}$  (i.e. $C$ and $D$ coalesce first before they coalesce with $E$). Let $B$ be the most recent common ancestor of $C$ and $D$.

Now, let the random variable $k_{ij}$ be the number of nucleotide differences between sequence $i$ and sequence $j$, then Tajima shows that $k_{BC}$ and $k_{BD}$ have a non zero covariance.

But aren't mutations in the branch $BC$ independent from mutations in the branch $BD$? I was thinking that the total numbers of mutations in the brand $BC$ and $BD$ are two independent identically distributed variables, so $k_{BC}$ and $k_{BD}$ are independent, then why they have a non-zero covariance?

============Update=============

Now I have some basic ideas, but haven't worked out the full answer.

Tajima's definition of $k_{ij}$ is neither independent of the sample size, nor for a fixed coalescent time. (See his 1983 paper: Tajima, Fumio. "Evolutionary relationship of DNA sequences in finite populations." Genetics 105.2 (1983): 437-460.)

For example, in a sample size of 3, if you pick 2 individuals, and condition on that the two coalesce first, their coalescent time will follow:
\begin{align*}
\mathbb{P}(t=T)=p(T)=\frac{3}{2N}e^{-\frac{3}{2N}T}
\end{align*}
Now conditioning on a fixed coalescent time $t$, the number of mutations under the infinite sites model in each branch either from $B$ to $C$ or from $B$ to $D$ will follow a poisson distribution with parameter $\mu t$, where $\mu$ is the mutation rate per sequence per generation. Let this poisson random variable be $\xi_t$ in branch $BC$ and $\eta_t$ in branch $BD$. Then
\begin{align*}
k_{BC}=\sum_{t=0}^{\infty}\xi_tp(t)\\
k_{BD}=\sum_{t=0}^{\infty}\eta_tp(t)
\end{align*}
If we only consider the partial sum of the above series,
\begin{align*}
k_{BC}^{(n)}=\sum_{t=0}^{n}\xi_tp(t)\\
k_{BD}^{(m)}=\sum_{t=0}^{n}\eta_tp(t)
\end{align*}
then $k_{BC}^{(n)}$ and $k_{BD}^{(n)}$ clearly have a zero covariance, because $\xi_t$ and $\eta_t$ are independent poisson variables, hence
\begin{align*}
\mathbb{E}(k_{BC}^{(n)}k_{BD}^{(n)})&=\mathbb{E}(\sum_{t=0}^{n}\xi_tp(t)\sum_{t=0}^{n}\eta_tp(t))=\sum_{i=0}^{n}\sum_{j=0}^np(i)p(j)\mathbb{E}(\xi_i\eta_j)=\sum_{i=0}^{n}\sum_{j=0}^np(i)p(j)\mathbb{E}\xi_i\mathbb{E}\eta_j\\
&=\mathbb{E}k_{BC}^{(n)}\mathbb{E}k_{BD}^{(n)},
\end{align*}
so their covariance is zero.

But as $n\to+\infty$, how $k_{BC}^{(n)}k_{BD}^{(n)}$ converges to $k_{BC}k_{BD}$ is questionable. It will not uniformly converge to $k_{BC}k_{BD}$ because otherwise we can first computing the expectation then take the limit, which gives us a zero covariance. Tajima didn't explicitly show us how he computed the covariance by summing together three infinite series (Line 7, Pg. 448, 1983's paper). I tried directly working on that series but failed in the last sum. His result is correct, though, I hope someone can give some hint on why there is inherent correlation between these seemingly independent random variables.

=======Update: a simple explanation has been posted==============


texts: Do plant and animal bacterial pathogen differ too much?

texts:
I will be involved in a plant disease produced by a bacterial pathogen, Acidovorax citrulli. I've previously worked with animal pathogens such as Haemophilus parasuis. Are there any big differences among them?

H. parasuis and A. citrulli are 2 and 4 MB genome size. What are these 2 MB extra genome size for?


texts: Mutation-drift equilibrium and among loci variance in heterozygosity

texts:
At mutation-drift balance, the increased heterozygosity brought by new mutations is exactly equal to the loss of heterozygosity due to genetic drift. At equilibrium, the expected heterozygosity for a given locus is:

$$\hat h = \frac{4Nu}{1+4Nu}$$

The expected heterozygosity is only the first moment of the whole distribution of locus specific heterozygosity. What is the (among loci) variance in heterozygosity?


texts: Difference between medicinal caffeine and regular caffeine

texts: There are some OTC paracetamol tablets, some with caffeine. Is this caffeine the same as the regular caffeine (found in a coffee)? Does it perform better than it in any way?


texts:
Describe what might happen if there were no mechanisms for modulating the level of acetyl CoA.

I am not sure what is meant by "modulating the level of acetyl CoA", or what mechanisms contribute to this. Presumably the citric acid cycle would be affected in some way because acetyl CoA enters it, but I'm not sure what exactly would happen.


texts:
I'm just wondering how the placebo effect works on people. If a patient is given fake drugs , how does that make him better? So what if they feel more "assured", how would that help the body immunity (t cells, phagocytes, etc) fight the infection better? How does phycological emotions affect the physical aspects of our immunity? Also I've read an interesting article online showing us that placebo effect works even when you know you are given fake drugs? This really complicates my understanding. How would such a approach even work?
http://www.health.harvard.edu/blog/placebo-can-work-even-know-placebo-201607079926


texts:
Genetics aside, what are the biochemical reasons for the different colours of human irises?

Also, related, how does eye colour change, particularly in childhood?  (example:  my eyes used to be blue, but are now greenish-hazel).


texts: Is it possible to synthesize chiral version of an organism (incompatible with our pathogens)?

texts:
In theory, it should be possible to synthesize chiral (mirror image) version of some organism: with all molecules replaced with their enantiomers, e.g. L-sugars in place of our D-sugars.

Direct application of such chiral life could be production of enantiomers of proteins in e.g. chiral E. Coli, what might be useful for example as new drugs.

However, the most interesting is that such chiral life would be incompatible with our pathogens, for example allowing to design really sterile ecosystems for harsh environments like Mars. Finally, such chiral human would be immune to most of our diseases.

Nice article: http://wikibin.org/articles/chiral-life-concept.html

The question is if it is technologically possible to synthesize e.g. a chiral version of E. Coli?

Update: Wikipedia https://en.wikipedia.org/wiki/Chiral_life_concept


texts: Has anyone confirmed Darwin's theory that nectar began as something "injurious" to sap?

texts:
In "Origin of Species", Darwin says (I have added bold for emphasis):

  Certain plants excrete sweet juice, apparently for the sake of
  eliminating something injurious from the sap: this is effected, for
  instance, by glands at the base of the stipules in some Leguminosae,
  and at the backs of the leaves of the common laurel. This juice,
  though small in quantity, is greedily sought by insects; but their
  visits do not in any way benefit the plant. Now, let us suppose that
  the juice or nectar was excreted from the inside of the flowers of a
  certain number of plants of any species. Insects in seeking the nectar
  would get dusted with pollen, and would often transport it from one
  flower to another. The flowers of two distinct individuals of the same
  species would thus get crossed; and the act of crossing, as can be
  fully proved, gives rise to vigorous seedlings, which consequently
  would have the best chance of flourishing and surviving.

My first question is, has anyone done any experiments or chemical analysis or any other kind of science to show that nectar does in fact contain something "injurious" to the sap (or to the plant in general)?

More importantly, has anyone tried to "prove" Darwin's theory of the evolution of nectar in flowers?

I understand that Darwin seems to provide some hints by mentioning the

  Leguminosae, and at the backs of the leaves of the common laurel.

as examples of a plant removing toxic substances from somewhere other than a flower, but I'm wondering if someone has "proved" that nectar in flowers started as a toxic substance the plant needed to remove.

Additionally, I'd be interested in how plants that haven't developed nectar/flowers deal with this waste (other than the common laurel and Leguminosae).  For example, does the plant just store the waste in a vacuole until it dies (please pardon my bad biology if "vacuole" isn't the correct organelle -- I'm not a biologist)?


texts: Can a crowded mitochondrial membrane limit O2 uptake?

texts:
The mitochondrial inner membrane is crowded with proteins (electron transport chain complexes, ATPases, etc.). As the proteins are packed more and more densely in this membrane, the diffusion of any molecule through the membrane should decrease, since there are less "gaps" for it to go through. I have no idea if this effect is insignificant for the entry of O2 into the mitochondria.

So my question is: Can O2 entry into the mitochondria become limited due to the high density of proteins in the mitochondrial inner membrane?


texts: Where can I find resources of the biological processes occurring after death of a mammal at various temperatures?

texts:
Using google I usually end with results in cell death. I found some layman articles, but that does not help.
My main interest is the brain part.


texts: What is the structure of heterochromatin?

texts:
A short article about euchromatin and heterochromatin mentions that the structure of heterochromatin usually depicted in images "has never been visualized in vivo, and its existence is questionable". Obviously, heterochromatin exists, since you can see it on photomicrographs, but what about its structure?
Is it true that the structure is not confirmed? Are there any other candidate structures?


texts: What is this insect I found in northern Europe?

texts:
Found this one in my bed in Northern Europe.

Around 6 mm long (5 mm body + 1 mm nozzle). Seems to have 6 legs. The back looks a bit like black-brown camouflage, the legs are red-brown, the nozzle is black.

Could this be some kind of bed bug?


texts: Do animals get "unhealthily" fat in the wild?

texts:
Looking at a picture of a seriously fat cat, apparently directly nurtured by humans, popping up in a language learning app, I started wondering:

do animals "in the wild" (this might be ambiguous, but you can discuss it in your answer) get obese? If so: which animals and how fat? Under what conditions do they get fat?

To be more specific (following the advice of user theforestecologist):

Do they become unhealthily obese (i.e. so fat that it negatively impacts their survival)?


texts: Question about the Derivation of the cable equation for neurites

texts:
I read in Wikipedia how the cable equation was derived (here) and had a specific problem regarding one of its equation:
At the start of the derivation it states that we first need to pretend that the membrane is perfectly sealed (Rm=∞) and that the capacitance of the membrane equal zero. Then we can say that the change in voltage over distance depends only on the resistance of the axoplasm, by the equation:
 and from that, the current equal:
But later when they derive the last equation, , they set  as in the equation above, which seems to me incorrect, since the resistance of the membrane also affect  . What did I get wrong?
Thanks!


texts: Relationship between genetic diversity within and between species

texts:
Here is a quote from Wagner (2008)

  A second line of evidence [against neutralism] comes from the relationship between the mean number of polymorphic differences between alleles within a species, $\pi$, and the number of fixed differences between genes in two species, $d$. For neutral mutations, a positive association between $\pi$ and $d$ should exist, because the neutral theory predicts that both quantities are linearly proportional to the rate at which neutral mutations arise. Recent genome-scale data shows instead that this association is in fact negative.

What do "the mean number of polymorphic differences between alleles within a species" and "the number of fixed differences between genes in two species" have to do with each other?  Why should there be any relationship at all?  And by "two species", are they talking about Eastern Yellowback Whooping Finches versus Western Yellowback Whooping Finches, or any arbitrary two species, like E. Coli versus Muskrats?

I found this related question, but it doesn't say anything about different species.


texts: Blood as newtonian flow and Poiseuille law

texts:
For a prep exam:

A healtly pacient has a carotid with the following characteristics:

intern ratio: = 2.8 mm,
2 = 89 ,
1 = 90 ,
 blood = 3.5 cp,
=10.0 cm.

Using the following equations calculate:

$$V(r)=\frac{P_1 - P_2}{4 \mu L}R^2 [1-(\frac{r}{R})^2]$$
$$V_{max}= V(r=0)$$
$$\overline{V} = \frac{Q}{A}=\frac{1}{2}V_{max}$$
$$Q=\frac{\pi(P_1 - P_2)}{8 \mu L}R^4$$

where P_1 and P_2 are the mean pressure to in and out the vase, R is ve vase radius, L is the length of the vase segment and $\mu$ is the viscosity of the fluid.

A healthy patient has a carotid withe the following characteristics: intern radius R = 2.8 mm, $P_2$ = 89 mmHg, $P_1$ = 90 mmHg, $\mu_{blood}$=3.5cp, L = 10cm.

Using the previous equations calculate:

a) Mean velocity on the carotid artery Rta: 0.372 m/s
b) Maximum velocity Rta: 0.744 m/s
c) caudal on the carotid artery Rta: $9.16x10^{-6} m^{-6}$

I have tried to solve this problem but when i try to replace changing the units to the adecuate I have not the correct answer


texts: How much does sleeping correlate with daily activity?

texts:
I'm a very lazy person. I spend most of my time in a chair, at a computer; I eat more than three meals a day. I don't do any sport, at all.

What I want to know is: why do I need to sleep 8-12 hours daily since I don't waste myself physically during the day?!

Wouldn't 3-5 hours be more reasonable? With an increase to 7-10 if I were a bodybuilder or a construction worker.. something that would actually deplete my body of energy?


texts: DNA Sequencing - Sanger termination method: What effects will more ddNTPs in solution have on the resolution on agarose gel via electrophoresis?

texts:
Say instead of a small amount of ddNTPs, you add a significant percent of ddNTPs to dNTPs. I was thinking this would reduce the resolution for larger fragments due to more ddNTPs terminating elongation earlier on.

I am doing a project on Sanger Sequencing and was wondering this, thank you. (Any suggestions would be appreciated)


texts: How can we smell odor direction if we breathe through one nostril at a time?

texts:
It's known that humans breathe mostly through one nostril at a time. How can we then perceive the direction the smell is coming from? Some articles claim similarity between olfactory and auditory directional perception:

  The direction of a sound source can be determined binaurally by using
  the time difference and the loudness difference of the sound waves
  arriving at the two ears. Similarly, the direction of an olfactory
  source can be determined by using the time difference and the
  difference in sensation magnitude of the olfactory stimuli between the
  two nostrils as the air surrounding the odorous object is inhaled.
  Time differences of the order of 0.1 msec can be recognized—a value
  similar to that found in hearing.

However, that explanation runs afoul of breathing mostly through only one nostril at a time because at least the difference in sensation magnitude of the olfactory stimuli should depend heavily on which nostril is 85% shut and which one is wide open.


texts:
I am trying to extract RNA from mice ears and for some reason I don't have RNA when I perform the electrophoresis. I directly cut the ears and I put it in a tube with a bead and trizol. then I place it on ice and I use a mash machine for tissue lysis for 8 minutes and 4 ºC. After that, I perform RNA isolation according with a protocol using chloroform, isopropanol and ethanol.

I think the problem could be the extraction. Do you have any suggestions?

Thanks.


texts: How large is the variability in human bone thickness, and is "big boned" a real thing or not?

texts:
My girlfriend is arguing that there are "big boned" people, I read some articles that there is no such thing but she still didn't believe in me because she saw some articles too that big boned people exist. Am I missing something and is my girlfriend correct?

I know that some tall people or some people living in Europe or US have of course bigger bones that in some Asian countries because some Asians are really small. However, this is not how most people understand "big boned".

How large is the variability in human bone thickness in persons of the same height? Could this variation mean that a person might appear overweight, when they in reality are only having relatively thick bones (large diameter), so that the expression "big boned" might have some truth to it?

UPDATED

I'm asking about the most people perceive about the "big boned" thingy. Most people (like my girlfriend) sometimes touch chubby people and when they feel like it's not fat, they say "ohh, you're not fat, you're just 'BIG BONED'". I'm asking if there is a real health/scientific basis for that. Personally, I don't believe that 'big boned' is a real thing. However, it's hard to find information about this on the web.


texts: Neuronal membrane resting potential for large cells

texts:
I'm reading Medical Physiology by Boron and Boulpaep (a really terrific book). In the chapter Electrophysiology of the Cell Membrane, section Membrane Potential Is Generated by Ion Gradients, Not Directly by Ion Pumps, the text reads:

  It may seem that the inside negative Vm originates from the continuous pumping of positive charges out of the cell by the electrogenic Na-K pump. The resting potential of large cells -- whose surface-to-volume ratio is so large that ion gradients run down slowly -- is maintained for a long time even when metabolic poisons block ATP-dependent energy metabolism. This finding implies that an ATP-dependent pump is not the immediate energy source underlying the membrane potential.

I totally get the main takeaway, that Vm results from the net accumulation of ion gradients, rather than the immediate consequences of the ion pumps. But I'm unclear on the phrase large cells -- whose surface-to-volume is so large that ion gradients run down slowly.

Presumably a cell with a large surface-to-volume ratio, like a long thin neuron, would have many ion channels which leak constitutively. So I'd expect the net ion conductance to be high, and gradients would run down quickly. But that contradicts the book's run down slowly point, so I'm confused.

Does passive diffusion play a role here? A long, thin cell would have slow passive ion diffusion, so is that why Vm would run down slowly?

Am I overthinking this?

What is the authors' point here?


texts: Material(s) That Tissue Can Grow Into And/Or Not Be Rejected?

texts:
I once watched a special on Dr. Roger Leir, a doctor made famous for removing supposed ET implants. Whether they were as such or not isn't important for this question. What is important is that he documented the removal of several devices that were at least partially made of material that tissue would somewhat grow into so that the body wouldn't reject it.

The question is: what, if any, such materials exist? Of course what the body won't reject and what it will grow into are two different things. I'm interested in both. It would also be helpful to know where people tend to discuss this and what companies are working on it. This is a question of biology and material science.

When I think of materials that won't be rejected, the only thing that comes to mind are materials made out of tissues themselves (like cat guts). Of course, we have things like pacemakers and all manner of implants but I don't know to what degree the body accepts them. Keep in mind that devices wouldn't have to be made entirely of such materials, just the outer shells of them.


texts: During bridge amplification of DNA sequences, why aren't sequences amplified in both orientations?

texts:
During bridge amplification, when sequences attached to adapters on the surface form "bridges" and are replicated, it seems like sequences with either end attached to the surface will be created.
For instance, in this link in figure 7, there are sequences facing both ways on the plate. In step 8, all the sequences are oriented in the same direction (pink end attached to the surface)
How are does this occur? How are the other sequences removed?


texts: A bit west of Portland. It doesn't look native to me, and we didn't plant it. This is the first year it flowered, so I decided to see if I can get it identified. If it matters, the flowers are aromatic.


texts: What is the mechanism of transgene integration (from expression vector to the host genome)?

texts:
How does a transgene (in vector) integrate to the host genome? (e.g. in glass bead method, neither biolistic nor agrobacterium).

I already cut some parts (NdeI-PciI) of the vector (pUC18) and wondering if it affects the integration procedure. Is there any recombination-like procedure same as gateway?


texts: How do ribosomes contribute to their own synthesis?

texts: In other words, what products synthesized by ribosomes are actual parts of ribosomes (if any)?   How are they involved in their own synthesis otherwise? What is the cycle/chain of products starting with the proteins synthesized by ribosomes and actually ending with the synthesis of a ribosome?


texts:
What kind of bug is this?

Size: About the size of a pencil tip

When was it found: spring time

Where was it found: In northeastern USA, inside the bathroom of our house


texts: Why do the feet of the Gecko Lizard not stick to Teflon surfaces?

texts:
I have noticed that lizards feet can stick to walls but not to Teflon surfaces?

Why is that?


texts: What exactly is tinnitus? What is it's cause, and why do some people hear it and others don't?


texts: Barring Antibody-dependent enhancement (ADE), how else can vaccines enhance the infection?

texts:
The link to the 2007 article below was broken for me. I Googled and read it on NCBI.

  Decades ago, vaccines developed against another coronavirus, feline infectious peritonitis virus, increased cats’ risk of developing the disease caused by the virus (T. Takano et al. J. Vet. Med. Sci. 81, 911–915; 2019). Similar phenomena have been seen in animal studies for other viruses, including the coronavirus that causes SARS (Y. W. Kam et al. Vaccine 25, 729–740; 2007).

At p 737 on the right column, the authors "could exclude this mechanism of enhancement as
sera from triSpike vaccinated mice did neutralize, rather
than enhance, virus infection on VeroE6 cells." So I similarly exclude ADE for this question. But in the last para. they wrote

  Interestingly, we observed the
  enhancement phenotype only in human B cell lines but not in
  mouse macrophages despite the presence of FcγRII. Reasons
  for this are unclear, but the respective role of activating and
  inhibiting human FcγRII which have identical extracellular

p. 738

  but heterologous intracellular domains and signaling capacities
  might play a role [63].


texts:
I’ve been told that the unfertilized egg contains cytoplasmic determinants (e.g. proteins, transcription factors, mRNAs) that are divided unevenly during the early stages of cell division in an embryo. Thus, each embryonic cell has a different cytoplasmic composition with a different set of transcription activators, allowing the expression of only certain genes.

By this token, it seems to me that this uneven partitioning of cytoplasmic determinants occurs in the very first division of the zygote. Thus, the first blastomeres are already no longer totipotent. Is that correct?


texts:
This question below turned to be completely faulty. I don't have to do anything with DNase data for GRCh38.
I asked it because of the file count difference between hg38 and hg37, which I thought to be too big.
For hg38 there're 95 files *Peak.txt.gz. For hg37 there're 236 *narrowPeak.gz, but after merging pairs PkRep1 & PkRep2 (probably FASTQ(SE/PE) reps) we get only 123 files. Finally, this difference (123 & 95) no longer seems to be big and we have even cleaner situation without PkRep1 & PkRep2.

One again: there's no problem with DNase data for GRCh38 assembly and only my question was misleading. I'd like to apologise for the confusion I introduced.

I'm interesed in transciptional activity, thus I'm willing to use DNase hypersensitivity sites to detect regions where transcription factors are allowed to bind.
In previous genome assembly GRCh37 / hg19 I used to use narrow peaks files from these two sources (University of Washington and Duke University, respectively) (files with suffixes .narrowPeak.gz):

http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/

With the most contemporary assembly GRCh38 there're also some annotations attached (files with trailing Peak.txt.gz):
http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/

And here four complementary question arise:

Consider only datasets, which come from University of Washington.
For GRCh38 / hg19 I counted 236 narrow peak files, whereas for newer
GRCh38 there're only 95 files. How to explain this differene? Do the datasets represent exactly the same coverage, but with much lower granularity / precision (datasets that come for several tissue lines are merged into fewer files)?
With GRCg37 / hg19 we have both narrow peaks as well as broad peaks,
whereas GRCh38 comes with only one type of of file *Peak.txt.gz.
Does it mean that with the newest version we have only narrow peaks? Are the broad peaks hidden somewhere else?
With GRCh37 / hg19 we have two separate sources of DNase data: UofW and Duke. For GRCh38, it seems that only UofW datasets are availabe. Is any other source of DNase data available, maybe stored separately (Duke or other lab)?
Let's suppose that you're in my place and you would like to determine cis-regulatory areas. What type of data can be used to do so? Mabey DNase datasets but from other source or even completly different type of data (NOT DNase)?

Thank you in advance for your answer.


texts: Have there been any experimentally-verified systems of microRNAs targeting a gene set (e.g., in cancer, perhaps)?


texts: Accuracy of genome size estimation by flow cytometry

texts: I'm working on a genome project and using an in silico k-mer analysis to estimate the size of our genome based on the available Illumina reads. The k-mer based estimate is consistent across a wide range of k values, but is substantially lower than the previous estimate based on flow cytometry (described in Experimental procedures of this paper). How accurate are estimations of genome size based on flow cytometry?


texts: How to predict Protein-Protein Interactions from a pair of gene symbols?

texts:
I have a list of pairs of gene symbols who interact (putatively) and would like to assign each pair a score (and record other details) based on the predicted Protein-Protein Interaction (PPI). The existing PPI webservers I've looked at (ClusPro and HADDOCK) require that I use PDB ID's as input. Unfortunately, PDB ID's don't always exist for the gene symbols I'd like to compare. I believe I need either:

a way to generate PDB files myself (perhaps with a folding program?) and then connect/upload them to a PPI webserver.

or

a way to find the most similar sequence that does have a PDB ID and upload it to a PPI webserver.

Am I understanding my problem correctly? Are there resources that can help with 1 or 2?


texts: What are the potential dangers (if any) facing the twin girls recently born in China with their CCR5 gene modified?

texts:
According to this Nature news article, a Chinese researcher claims to have made the world's first genome-edited baby using the popular CRISPR–Cas9 genome-editing tool. A gene called CCR5 was modified before the embryo was implanted into the mother. The CCR5 gene is known to produce a protein that is utilized by the HIV to enter human immune cells, and the genome editing performed is expected to make the babies HIV-resistant despite their father being HIV positive.

As a Chinese, I am deeply concerned with the ethical consequences and scientific impacts of this highly controversial experiment. However, to form an opinion for myself, I believe that I first need to know the potential dangers, either expected or speculated, that the twin babies might face in their life. Unfortunately I am not familiar enough with molecular biology to be able to know and judge these myself, and the reports in the media seem very vague on this issue.

So please let me ask: What are the potential dangers (if any) facing the twin girls, and how sure are we now about these dangers, their consequences, and possible countermeasures?


texts: Need help to determine % difference between DNA-strand from two different haplotypes. Known nucleotide diversity and more

texts:
Backround:
229 DNA sequences
493 bp in length
Haplotype diversity: 0.9956
Average  number  of  nucleotide  differences: 12.50544
Polymorphic sites: 145
Nucleotide diversity: 0.02426

Is it possible to determine how many percent difference there is, on average, between DNA-strands from the different haplotypes?

The answer may be quite obvious, but this is new to me.


texts: What effect does ambient temperature have on the cardiovascular system?

texts:
I am sorry if this is not appropriate for this site, but I think it fits so I am asking it here:

I went for a run yesterday, and it was about -8⁰C.  I was wearing a couple pairs of shorts, a t-shirt and a long sleeved shirt, which is not that much, so I went with the idea that I would warm up a lot while running.  After running for a while, I found that I was tired and out of breath much earlier on then I would normally be.  It raised the question:

  How does decreasing the ambient temperature affect the cardiovascular system?

There were two things I could think of that might directly affect it.  (1) The fact that my body's metabolism has to work to heat itself, and this takes energy.  However I am not sure how much of a role this plays since running warms you up anyway.  (2) The air being so cold, and entering the lungs, I imagine my body has to work much harder in some way to deal with it.  What exactly happens here, and how is the process different from breathing at 25⁰C?

Also, how much faster would we expect a runner to be able to finish a 10km run when it is 25⁰C outside versus -5⁰C outside?


texts: Do diurnal birds of prey recognize each other by their appearance?

texts:
Just what the title states.

I recognize people around me by their facial appearance to begin with, then by their little idiosyncracies; this applies perhaps to most other humans too. We rely pretty heavily on vision - perhaps because we are a primarily diurnal species gifted with the ability to distinguish colour. But then, so are birds of prey e.g. eagle, kite ...

Do diurnal birds of prey identify each other by their appearance?


texts:
I have a follow-up question about an in-lecture question (this is not a homework question). As you can see I have already answered the question and the question is closed to further submissions.

In any case, this is my reasoning.

The male has the genotype Gg and BB. Fur color is incompletely dominant so to have black fur this implies the male has the genotype BB not Bb (which would likely be gray).

The female has genotype Gg and Bb because as the question states, the female is doubly heterozygotic.

The two have a FEMALE offspring - this is critical. This means that the male "donates" a copy of his X chromosome to the offspring. Now if the question had asked about a male offspring, then that would mean the male had donated a copy of his Y chromosome instead, and the male would have no "say" in the male progeny's eye color.

So the probability of green eyes between a cross of Gg with Gg is 3/4.

The probability of black fur between a cross of BB and Bb is 1/2 given that there is incomplete dominance.

So the probability of both events occurring simultaneously is 3/4 * 1/2 = 3/8 = 0.375.

Is this correct? Or should I account for the "female" offspring part and half the answer?


texts: Can white eggs be considered as non-vegetarian?

texts:
I am basically a vegetarian and I find it very difficult to get an actual biological answer for this question on search engine.

There are couple of links which discuss these argument but can not be acclaimed as a proof as being Egg either a veg or non-veg food item. Below are couple of links which I found depicted this in authors perception:

Egg Non-Veg (a proof)
Egg is veg
Types of vegetarian
If it is veg why products are marked with red dots

Is there any biological proof to consider White Eggs either as vegetarian or non-vegetarian?


texts: what are the factors that can be used to compute the probability of getting the coronavirus?

texts: Our team and I work on a project for the Lauzhack 2020 and to achieve this work, we need to determine some factors that can tell us what is the probability of contracting the coronavirus.  Is there any one who know what are the determining factor to compute the probability of catching the virus ? (for example some research paper about it). For example, we know that if we are old, and if we are in contact regularly with people, we are most likely to catch the disease. We would like to have some basic knowledge about the transmission of the virus. We would need data about the probability of being infected as a function of the time we had been in contact with someone who have the disease. Any help would be appreciated !


texts: Can wood frogs who have frozen and thawed remember their past lives?

texts:
Wood frogs (Rana sylvaticus) can survive being frozen for up to 7 months at temperatures as low as -16 °C. Their breathing stops, their heart stops and all signs of life disappear. (Source)

I have looked for research that shows that when these frogs thaw in spring, they retain memories from before they became frozen, but I haven't found any. Can anyone give me any insights?

Note: This research shows how butterflies can remember experiences they had as caterpillars, before their metamorphosis. Perhaps something similar can be done or has been done with wood frogs?


texts: Why doesn't infection with Clostridium Tetani immunize you?

texts:
What Immunity to COVID-19 Really Means - Scientific American

  It is less clear what those antibody tests mean for real life, however, because immunity functions on a continuum. With some pathogens, such as the varicella-zoster virus (which causes chicken pox), infection confers near-universal, long-lasting resistance. Natural infection with Clostridium tetani, the bacterium that causes tetanus, on the other hand, offers no protection—and even people getting vaccinated for it require regular booster shots. On the extreme end of this spectrum, individuals infected with HIV often have large amounts of antibodies that do nothing to prevent or clear the disease.

Clostridium Tetani - StatPearls - NCBI Bookshelf

  It should be noted that infection with C. tetani does not provide immunity, and thus, all patients with the diagnosis of tetanus should receive immunization immediately with three doses of tetanus and diphtheria toxoid.


texts:
So I was reading up on articles to do a project about cloning but there were no places in the article where It states the tool used to take the gene out of the nucleus and insert it into plasmids ? can anyone accurately tell me what the tool is. I don't mean the process but the actual names of the tools like CRISPR etc.

As a reference The article was the wiki https://en.wikipedia.org/wiki/Molecular_cloning


texts: Relationship between immunologic response to specific gluten epitopes and clinical antibody testing

texts:
Celiac disease is understood to be an immune response to certain proteins which occur in a group of cereals; most commonly they are glutens (wheat), secalins (rye) and hordeins (barley). A clinical test for celiac examines serum levels of two specific antibodies: Deamidated Gliadin peptide Ab IgG and Tissue Transglutaminase Ab IgA.

Is it possible to test positive for the above antibodies while being sensitive (raise an immune response) only to hordeins?

There are two components to this question:

Can a person be sensitive to hordeins while being unaffected by either wheat gluten or rye (secalins)?
Would the above test produce a positive result given only hordein-specific antibodies? In other words, is the test specific to wheat gluten antibodies or will antibodies to any gluten epitope produce a positive result?

The reason behind this question in a short case history:

Mature adult subject experienced mild/intermittent IBS symptoms, onset vaguely extending back several years. Diet notably included regular/daily consumption of wheat/rye products as well as intermittent (2-3/week) beer (barley).
Recent clinical screening for celiac (serum levels of Deamidated Gliadin peptide Ab IgG and Tissue Transglutaminase Ab IgA) performed to investigate cause of suspected osteoporosis; both antibody levels assessed as positive.
Symptoms apparently abated within about one week following an initial dietary change successfully removing only barley gluten (beer), while regular consumption of wheat/rye continued.

Observations suggest a specific response only to barley, and raises the question about specificity of the clinical antibody test.


texts: What hydrolyses aspirin within the digestive tract and blood stream?

texts:
I have had some further thoughts after my previous question regarding the buccal delivery of medication.  The active compound in aspirin (acetylsalicylic acid or systematically 2-Acetoxybenzoic acid)  is salicylic acid (2-hydroxybenzoic acid).

I understand that the hydrolysis reaction occurs as follows within the stomach - therefore in the body it is an acid hydrolysis:

N.B. The H2O is not shown in the diagram.

However having done this experimentally I know that in the lab to ensure a decent yield of salicylic acid I had to reflux the solution for several hours.  Yet the onset of action of aspirin tablets is much faster than this.  To me this suggests some enzymatic activity, but I have no idea which enzyme this is likely to be.

To follow on directly from my previous question, if the aspirin is absorbed directly into the bloodstream bypassing the stomach then what causes the hydrolysis in the blood stream and is it the same factor that increases the rate of hydrolysis in the stomach if the medication were to be taken orally?


texts: Do both TSG and Proto-oncogenes have to suffer mutations to cause cancer?

texts:
I'm having a conceptual nightmare trying to understand when a group of cells may become cancerous and the more resources I consult the more confused I seem to get.

In order for a cell to become cancerous, does it have to mutate to knock out tumour suppressor genes and have a proto-oncogene become an oncogene?

I'm  currently working on the basis that that is the case, or at least that a mutated TSG on its own will not cause uncontrolled division.  However wikipedia seems to suggest that an oncogene alone can cause uncontrolled division with a functional TSG in place.

It could be a flaw in the idea I have that tumour suppressor genes only trigger apoptosis once a cell has started to divide rapidly, are they actually carrying it out to a regular schedule independent of oncogene presence?


texts: Are neurodegenerative diseases such as dementia inevitable?

texts: For the sake of this question, let's imagine a person who lives to 200, would it be at all possible for them not to get dementia? Is it an inevitable disease as we get older or can it be avoided?


texts: How is a stem-cell induced to assimilate a knock-in DNA construct?

texts:
While looking at (daylight) color perception I came across a paper by Jeremy Nathans (et al., Proc. Nat. Acad. Sci., vol. 100 no. 20, 2003, full text here) in which he describes the creation of a mouse with genetically modified vision.

My threshold question is just about the mechanics of the process, which he characterizes as "site-directed mutagenesis." My understanding (a guess, really) is that embryonic stem cells are induced to assimilate homologous human DNA sequences and these cells are injected into mouse blastocysts.

In outline I understand the idea of the DNA construct but wonder physically how the stem cell initially acquires the knock-in construct.

Thanks for any enlightenment.

Edit: I see that there are several ways to do this and that the paper's "Materials and Methods" section focuses on the molecular genetic details. Maybe we can't get the information from the four corners of the document? If so I'd still be interested in whatever process seems likely given the sort of mouse they made. Thanks.


texts: Mechanism by which water flows through xylem

texts:
I was doing a Cambridge iGCSE past paper when I came across the question:

  Describe the mechanism by which water flows through the xylem

I thought the correct answer would revolve around the xylem being composed of dead cells, thus allowing water to use capillary action to flow upwards, but it wasn't.

Instead, the mark scheme referred only to transpiration causing tension and so forth, not even mentioning capillary action.

Is capillary action not a valid answer? And if not, why not?

Thanks


texts: How to select genes before log2 ratio on a RNASeq gene expression matrix, based on signal median

texts:
I want to transform a TCGA mRNA expression matrix (in linear data format) to log2-ratios and then run a feature (gene) selection, selecting the 1000 most variant genes (genes with higher standard deviation across samples). The workflow is the following:

Select "good" genes before log2 ratio (genes each with median signal at least t in p% of samples);
On selected genes, run log2 ratio, dividing each gene by its median signal and then log2-transforming the result matrix;
Select the 1000 most variant genes along all samples.

How do I select t and p?


texts:
It’s simple deductive logic to follow that for a species to survive it must provide it’s offspring with the best possible conditions to ensure it’s survival – either that or to reproduce in such quantity that it ensures survival. The obvious application of this for women is sharing parental investment with the best possible mate her own genetics allow her to attract and who can provide long term security for her and any potential offspring.

  Thus women are biologically, psychologically and sociologically the filters of their own reproduction, where as men’s reproductive methodology is to scatter as much of his genetic material as humanly possible to the widest available quantity of sexually available females. He of course has his own criteria for mating selection and determining the best genetic pairing for his reproduction. This is evidenced in our own hormonal biology; men possess between 12 and 17 times the amount of testosterone (the primary hormone in sexual arousal) women do and women produce substantially more estrogen (instrumental in sexual caution) and oxytocin (fostering feelings of security and nurturing) than men.

From a biological point of view, is the bold sentence correct? And is the quantity of hormonal differences the only explanation of this?

Link to article: http://therationalmale.com/2011/08/23/schedules-of-mating/


texts: Does anyone know what this living creature is?

texts:
There are two different things I am trying to identify. I live in Lexington, Kentucky. The first one I started seeing was a small white larvae looking worm thing. They would very in size but never bigger than a few centimeters long and very thin.  I started seeing these around my house about two months ago.  I had not seen them before.  It seemed like they showed up all of a sudden.  They were in the floor and on the furniture.  I never would see them move. When I would try and pick them up or investigate, at the slightest touch they would turn to liquid almost like water, clear.  Just disappear.  The other form I am seeing is a bit bigger I don't know if they are both the same species just in various stages or if they are 2 separate species.  The second ones I seen were almost an off white with rings vertically around its body. With hair all over them.  Some were hairier than others and they were not all the exact same color.  It seemed to me that they used their hair as a weapon or defense not sure how that was intended.  They started showing up on my hanging cloths in my closet as well.  Shortly after we started noticing small holes in our cloths.  I call them creatures since I am not sure what they are.  They then started burrowing into us. I never seen the darker one with hair burrow but for sure the small white larvae looking one.  But only me.  Not my kids or husband.  The doctors can't tell me what they are.  The darker one in the picture came out of my leg.  When I got it out it was still alive.  They seem to prefer my nose and sinus's.  I spent hundred on exterminator and have not seen anymore.  The pest control company said they had never seen them before.  The one picture of the white larva is one that I had to download.  I accidently lost all of my pictures on a phone before they were downloaded to my computer.  That picture is identical to what I have found.  I may have more pictures.  I will go thru all of them in the morning and try to add some here.

Hairy:

White in colour:


texts: Gene flow analysis with a single mitochondrial marker

texts:
I am currently studying a mud snail genus called Ecrobia. Several species of this genus occur in both the Mediterranean and Black seas. Therefore, I would like to investigate whether there is:

Intraspecifc gene flow between the Mediterranean and Black sea populations
Interspecific gene flow between the Ecrobia spp. occurring in the same water body

Therefore, I have a couple of questions:

Is it possible to perform a gene flow analysis with a single mitochondrial marker (COI)? If so, which program could I use to run the analysis?
Ideally, how many individuals per population are required? If I don’t have enough individuals, is there a rigorous way of clustering populations?


texts: What is the purpose of ultrahydrophobicity in lotus flower leaves?

texts: I read about the lotus effect on wikipedia, but I haven't found an explanation as to why droplets collecting dirt on the surface of a leaf is helpful to the flower's survival.


texts: Which culture media is suitable for cheek epithelial cells?

texts: A month ago, I tried isolating cheek cells from saliva and the experiment was a success, however, I was wondering if it is possible to cultivate these cells in vitro. I'd say it's possible, but I wasn't able to find any publications about this topic online, even on PubMed (I found one, but it was outdated and the part with used media wasn't clear). Is it possible to use just DMEM media and if so, how long will the cells survive in the media, or are there any other alternatives?


texts: Multiplication to formalize Microbiological Processes

texts:
I am not from the field, but have a question regarding modeling in biology:

I know that some processes can be modeled with the mathematical multiplication operation, and wondered if anyone could give me an example (or examples).
Especially with regards to axonal growth and the chemical (de-)stabilization taking place which involve microtubuli and actin, I was wondering if these processes again could be formalized mathematically as multiplication of (several) variables.

I have looked through the internet but did not find anything so far,
any help is appreciated


texts: Why are pilots under the illusion of gaining altitude without doing so?

texts:
We had a lecture about the balancing systems of the body (mainly the otolith organ / semilunar canals) in which a case was described where a pilot crashed into a ship. He was supposed to keep his altitude and had not been looking at his instruments, but was guiding the plane by feeling.

However, he was under the illusion that the plane was gaining altitude when it wasn't and so steered it downwards, dropping and eventually crashing into a ship which happened to be at that particular spot that moment.

Since the otolith organs detect de- and acceleration in all directions (that just comes from how the mechanism works), if the pilot was flying at steady altitude, why would they signal that he is rising?

(Will add an article later if I find one.)


texts:
While reading this - Surviving under water in air bubble - this question came to me:

How long can an adult person survive on breathing in only exhales of another adult person? Can this be even calculated by not relying on rough approximations or there are too many variables?

In order CPR (mouth to mouth breathing part) to be effective, logic says that exhaled "air" is not poisonous to bring a fatal blow, but for how long?


texts: Just a simple, quick question: how are the mRNA and the template strand of the DNA structured during transcription? I've seen models and videos of them when they're both flat/straight (is that just for simplicity?) and others where they're spiralling around each other. Could someone just briefly shed some light on my situation please?


texts: Why can't we breed watermelons without any remaining seeds in the flesh?

texts:
Watermelon is just starting to come in season in the northeastern U.S., and having a seedless watermelon is convenient.  The only downside is, the "seedless" almost always still have the immature, sterile white seeds in them.

What is the mechanism for breeding these watermelons so that only these white seeds remain?  What is the genotype that results?  Could the genetics be modified so that there are virtually no seeds (short of any minor aberrations) left in the flesh of the fruit?


texts: Can people be bred for tameness in a similar way to Russian foxes?

texts: Russian foxes were selectively bred for tameness. Can a similar process happen to humans, under the right conditions — say, extreme political pressure to obey ?


texts: How well understood are the long-term effects of nuclear radiation?

texts:
Sometimes, when people are concerned about radiation, it is not because it is precisely quantified how dangerous it is, but because we don't know how dangerous it is.

How well understood are the long-term effects of nuclear radiation, for example on cancer? (As opposed to short-term effects such as acute radiation sickness, which is easy to quantify)

I assume this can be researched from an epidemiological approach (Wikipedia mentions an epidemiological study on the atomic bombing of Hiroshima and Nagasaki, for example), and also from an experimental approach.

Also, is the effects of radiation easy to understand, or difficult? My assumption is that something physical, like radioactivity, would be easier to understand than the effects of more complicated things, like complicated organic chemicals or obesity.


texts: When cancer is detectable, how many sub-clones are there at that stage?

texts:
I have read somewhere that cancer is detectable when the number of cells reaches $10^7 - 10^9$, which probably varies according to the specific tumor. At this early stage, what is the expected number of subclones of the tumor? Any references would be super appreciated!
p/s: To answer this, I tried running a simple code for a birth-death process, but my laptop freezes at $10^7$ cells. :(


texts:
I remember hearing a saying that goes like "men think of sex every 7 minutes (or seconds?)". I take this saying to mean that men have sex related thoughts more often than women.
I'm interested if these thoughts are related to hormone expression within the male body. particularly, I'm interested in the very few seconds before a sexual thought emerges - one moment a man is thinking about daily stuff, next moment his thinking has sexual content. What is responsible for this shift in thinking?
I've read that oxytocin is responsible for men feeling romantic attachment to a partner, but is there a hormone that initiates sexual thoughts or fantasy? For example, would a burst of testosterone increase the likelihood of a man thinking of sex?


texts:
Related to the question What causes the colors we see in eyes?, I am wondering why human eyes are restricted in colour. Most common eye colours are blue, green and brown. Why not yellow, orange, purple, red and so on?

I am guessing this is related to the function of the iris and that other colours do not have the same effect on light absorbing or something like that.


texts:
I have a problem in my reasoning on the fatty acid synthesis in the human body.
In the synthesis process you have this homodimer.

So the synthesis starts with the transfer of a acetyl group from acetyl-CoA to the sulfhydrylgroup of the condensing enzyme (CE) with help of the acetyltransferase enzyme (AT) and this on 1 of the 2 monomers.

At the same time a malonyl group from malonyl-CoA is transfered to the sulfhydryl terminus of phosphopantotheine from the ACP, and this on the other monomer and with help of the malonyltransferase (MT) enzyme.

AND HERE THE PROBLEM STARTS

The acetyl residue will be condensing with the malonylACP and at the same time there will be a decarboxylation (CO2 goes off) and CE goes off from acetyl. At the end acetoacetyl-ACP is formed. So if I got it right; the acetyl residue is being 'cut off' from the CE from the first monomere and binds to the malonylACP on the other monomere. Right?

And after that the acetoacetyl-ACP will be swept back to the other monomer (to the reduction part), is this also right?

Then the reduction-dehydration-reduction steps are happening and at the end of the road you will get butyryl-ACP which will cut off from the ACP and migrate on the same monomer to the cysteine residue at the condensing enzyme (CE) (= translocation).

And after that you can start a new condensation-reduction-translocation cycle and go on until you end up at palmitoyl-ACP.

So the actual question is; is my reasoning right about how the product is going from one monomer to the other several times?
In my book it's a pretty messy explanation and so I want to be sure I'm right.

I hope somebody can help me out =)

Greetings


texts: Why do 60S & 40S ribosomal subunits make an 80S ribosome (not 100S)?

texts: Why do 60S & 40S subunits make an 80S (not 100S) ribosome and, similarly, 50S & 30S make 70S? 60+40 is not equal to 80, nor is 50+30 equal to 70, so why are the subunits of the 80S and 70S ribosomes named so weirdly? I couldn't come up with any other mathematical explanation.


texts: How much gas is exchanged in one human breath?

texts:
When we breathe, our lungs absorb a portion of the oxygen in the air, and replace it with some amount of carbon dioxide and water vapor.  Typically, how much $O_2$ (in grams, milliliters, or moles for instance) is absorbed and how much $CO_2$ and $H_2O$ are released in one breath of a healthy adult?

Of course, the exact amounts will vary from person to person and based on how deeply the person is breathing, lung health, etc.  I'm just looking for a ballpark figure.


texts: What is the glide angle of a herring gull?

texts: I went on a wild goose chase looking for that information on the internet and couldn't find it. I think it would be useful to know the answer. It tells us how streamlined their bodies are. I believe that in an fluid with zero viscosity and infinite bulk modulus, a tear drop shape would encounter absolutely zero resistance. However, the real world isn't in such an ideal situation like that. I believe that in general, the evolutionary stable strategy of any species has the population size stabalized by starvation and all the individuals are finding food at just barely a high enough rate to survive. So then natural selection would select to minimize energy consumption.


texts: Why some viruses can spread with aerosol droplets, but others some cannot

texts:
Why can some viruses spread with droplet like influenza virus, but some can not like HIV?

Is it due to their physical shape or the protein of their wrapper? Is there any formalized logic decide this before test the virus in lab?

Thanks in advance!


texts: How would the brain represent represent elapsed time?

texts:
When we are waiting for an elevator, we know that the elevator will not open right away. There is a delay of 2 or 3 seconds. How does the brain (likely cerebellum) represent the running time of 2 or 3 seconds vs 10 seconds?

What would the neural code representing elapsed time look like? A mouse can be presented with a stimulus after 2 or 3 seconds and 10 seconds. It "learns" to recognize the difference between the two elapsed times, and it is partly experience-dependent (a prior of history). But how?


texts: How does the sticky ends of foreign gene bind with its counterpart in the plasmid DNA if positions are not matching?

texts:
Consider  a foreign gene with recognition sequence as GAATTC  for EcoR1. Now suppose that it is being cut at two palindromic sequence  to form sticky ends.

Here the sticky ends are formed such that its position is parallel to each other around the axis of DNA.

The plasmid DNA has a recognition sequence and is  being cut at a  site and as obvious would be  cut with the sticky  ends as  counterparts. If we join the foreign DNA to this vector DNA the problem of combining the DNA arises. How will we cope with this problem  or if I am going wrong can someone tell me where?


texts: Why there is such low diversity of higher plants in sea?

texts:
I think it could be because of mycorrhiza or maybe because of the problem with flowering and seeds.
But really, I don't know.

edit:
by higher plants I meant Embryophytes


texts:
Animal -> bacterial gene transfer seems easier than bacteria -> animal (rotifers are an interesting exception); there are bacteria live in close contact to us but our germ-line cells are protected. Given enough time, even free-living bacteria would start to pick up some of our genes (once the introns were lost).

Is this true? If so, do we see animal/plant genes gradually spreading into single cell organisms as time goes on (although "seeing" this would be difficult)? Is this effect "significant" for evolution in microbes?


texts: When designing primers how important is the GC clamp?

texts:
I'm designing a set of primers and reading about the principles of primer design one of which is:

  GC Clamp: The presence of G or C bases within the last five bases from
  the 3' end of primers (GC clamp) helps promote specific binding at the
  3' end due to the stronger bonding of G and C bases. More than 3 G's
  or C's should be avoided in the last 5 bases at the 3' end of the
  primer.

From here.

My question is how essential is it to have a GC clamp?


texts: complete DNA transfer across different organism zygotes

texts:
Consider we have a monkey zygote (i.e. single cell just fused) and a tiger zygote. If we extract the nucleus of monkey zygote and place it into tiger zygote where nucleus of tiger zygote is already removed. Is there any chance of zygote to survive and finally turn into a monkey offspring ? I tried Google for any such experiment ever conducted but seems like biology is googol to Google, no close result at all.

For more clarity it can even be considered all chromosomes transferred  instead of nucleus.

As far as I think this could be possible as all 20 amino heads must be present in zygotes of both the mammals and thus synthesizing protein should not be a problem. However I can't say anything about their respective immune system response.

This question came to my mind considering Darwin hypothesis/theory(interpret as you wish) of evolution, where even if some mutation changes the DNA sequence how much chances are there for a completely new organism if cells don't support growth natively.


texts: Is there a way for a 19th century scientist to prove that the octopus doesn't revive?

texts:
Say a sophiscated scientist in the 19th century noted that applying soy sauce on a dead octopus leads to movement of the legs, as a result of the voltage differences resulting from the salt in the soy sauce. (For example, see this video)

Is there a way for that scientist to prove, using only the methodologies available at that time, that the decapitated octopus doesn't regain the functions that a octopus brain normally has, for even a few seconds, when the soy sauce is applied?


texts: The current taxonomy has family names like Canidae and Felidae. But Felidae has sub families like Felinae and Pantherinae. Roaring cats and non-roaring cats. My question is based on the fact that we can have common words for these families based in Latin: Felines, Canines, Pantherines. Can every family in the taxonomy be represented by this latter form? Is Pantherine a valid name? Is was created by dropping the a from the subfamily but caninine was created by dropping the da from the main family and replacing with in.


texts: Why do I get such a strong background in a detection of DIG-labeled DNA (Southern Blot)?

texts:
I have done a Southern Blot Analysis of DNAmt transferred to nylon membranes. The DNA was firstly loaded on a 2% agarose gel. An immunoassay was done to detect the bands using Anti-Digoxigenin antibody with Alkaline Phosphatase which catalyzes a colouring reaction with NBT and BCIP.

The results has a very strong background as you can see in the following pic:

I am not sure about what can be the reason of that background. I have read that thick agarose gels produce strong backgrounds, but I never experienced that before. If somebody has experience on this or alternative explanations, I would thank him/her to share them with me.


texts: Won't natural selection miss the overall minimum of a function?

texts:
Suppose we have a population of about 1000 with an environment that does not change a lot (e.g. the atmosphere is more or less the same) and we leave this population to evolve. From what I understand some genes will be lost because they won't be suited enough to continue in the next generation. Also the generations can only reproduce within their generation (e.g. a male can only have reproduce with people from his generation).

My question is: won't some genes, combined with others have a better chance to make the individual "better" but they for example make it less fit right now. Or will the mutation of the genes actually promise that eventually we will hit that minimum of the function.

I want to point out that I'm a computer scientist and my biology is awful. I'm looking at this from evolutionary algorithms point of view in particular genetic algorithms.


texts: What is the modern state of the theory of evolution?

texts:
When I studied biology at my medical school, we used to learn topics around a century old: the famous Darwin's voyage on "Beagle" to the Galapagos Islands, the classical triad of his Theory of Evolution, etc.
At the same time we were told that there is no evidence found in nature for many of these statements of his evolutional theory. For example, people studied wildlife around Chernobyl and found that no new species emerged due to much higher mutation rate as a consequence of radiation. On the contrary, there were no significant differences between the species living under elevated radiation level and those living in "normal" conditions.
Do these facts somehow influence our understanding of the theory of evolution? Are there any breakthrough findings which happened in the last 20 years that prove or disprove it?


texts: Does the new virus tree of life change their position between living and non-living things?

texts: Viruses still do not fit the criteria of living or it's simplest form (the living cell), why would some say that the new virus tree of life makes it more closer to life? Aren't mitochondria in a point of view closer to life than viruses?


texts:
I'm preparing for an Olympiad and while I was going through some of the old papers I found a question. I googled it but a lot of people have different answers to it. Please help.

A student treats some onion root tips with colchicine that is responsible for arresting cell division at the metaphase stage (by dissolving spindle fibres) and further prepared a slide of the root tip staining with acetoorcein (stains chromatin) and observed under high power of compound microscope. He is well aware of the cell cycle given alongside.

Question: Which of the following is not true about his observation?
a) Most cells are in Interphase
b) Most cells are in the metaphase
c) No cells are in anaphase or telophase
d) Chromosomes could be observed better than a slide prepared without colchicine
treatment.

According to me the answer should be (c) because if colchicine arrests cell division at metaphase, anaphase and telephase being the subsequent processes would not happen. But a lot of people are saying it should be (a) or (d). I'm stumped, any help would be appreciated.


texts: What selective factors drove the evolution of lactose in lactation?

texts:
As far as I can determine, lactose, and the monosaccharide galactose have few biological uses outside of mammalian lactation.  It not only required enzymes for its production, but enzymes in offspring for its digestion, suggesting that it serves some specific purpose.  Yet intuitively, it seems like it would have been significantly easier to just concentrate glucose from the blood or generate a disaccharide readily found in the diet like sucrose, for which digestive enzymes already existed.

What drove the evolution of lactose in mammalian lactation?


texts: where i can download reference MSU7 rice genome?

texts:
I am working with RNA Seq data analysis. I have to download MSU7 rice genome. somehow i downloaded from

"http://rice.plantbiology.msu.edu/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/pseudomolecules/version_7.0/all.dir/ "

. But i am not able to find Annotation (.gtf) file and reference genome (.fa) file . so how can i find and how can i download..help me


texts: Mechanism by which hypokalemia reduces insulin secretion

texts:
Is there any known mechanism by which hypokalemia reduces insulin secretion?

This video explains a mechanism, but its inherently wrong because ATP dependent K+ channels will allow movement of K+ from inside of cell to outside.


texts: Why don't protons diffuse out of the mitochondria during chemiosmosis?

texts: If the outer membrane of the mitochondria is very permeable, how do mitochondria maintain a proton gradient by pumping protons into the intermembrane space? Wouldn't they just diffuse into the cytosol?


texts: What is the composition of a standard diluent buffer in a leptin ELISA kit?

texts: I am trying to find the composition of the diluent buffer used for the dilution of a human leptin stock to be used in an ELISA assay. The manufacturer of the kit (https://www.thermofisher.com/elisa/product/Leptin-Human-ELISA-Kit/KAC2281) only indicates that the buffer contains 8mM of sodium azide, but I cannot find the precise composition of the buffer anywhere on the internet.


texts: Are there animals which can see movements better than shapes or colors?

texts:
I remember that in Michael Crichton's novel Jurassic Park, Tyrannosaurus Rex was supposed to have movement based vision. (Of course, that is a novel and not a scientific text.)

I have also noticed while feeding chickens, that they behave differently when they see me adding the food for them into the container as opposed to leaving it there for them when they cannot see me. (But this can be explained easily by different reasons, for example they are used to human as a source of their food, so they naturally go close to them.)

So my question is:

Are there some kinds of animals who have primarily movement based vision? If yes, which animals are examples for this?

The Michael Crichton's novel has been widely discussed online, I found for example this and several answers at Yahoo Answers. Frogs and reptiles are mentioned there.


texts: In plant cells, is water stored only in the vacuole?

texts: In the turgor of plant cells, is water stored only in the vacuole or can it be stored in the cytoplasm and the other cellular organs too?


texts: I had an interesting discussion today in which the question arose how insects survive in the winter. Since they need a high enough external temperature to be active, this seems a bit difficult in the winter. With frost they should completely freeze and I don't think they will survive this. Do they rely on eggs laid in the fall (which have to survive freezing temperatures as well) or do they employ other techniques for that?


texts: What is a protective epitope? An epitope is basically a part of antigen. So does it mean that when the epitope combines with an antibody, it helps in the functioning of the antibody instead of going against it?


texts: Why is polyploidy lethal for some organisms while for others is not?

texts:
Polyploidy is the multiplication of number of chromosomal sets from 2n to 3n (triploidy), 4n (tetraploidy) and so on. It is quite common in plants, for example many crops like wheat or Brassica forms. It seems to be rarer in animals but still it is present among some amphibian species like Xenopus.

As I know in mammals polyploidy is lethal (I don't mean tissue - limited polyploidy). I understand that triploidy is harmful due to stronger influence of maternal or paternal epigenetic traits that cause abnormal development of placenta, but why there is no tetraploid mammals?


texts: Why male gametes doesn't go through antipodal cells in chalazogamy

texts: Male gametes in double fertilisation enter the embryo sac through synergid cells even in chalazogamy i.e. when polen tube enters the ovule through chalazal end. Regarding the fact that compatibility reaction has already taken place (i.e. they are the right gametes) after pollination then why male gametes doesn't enter through antipodal cells? Is it just because of filiform apparatus that affiliates the entry of male gametes through only synergid cells or is there something else as a reason?


texts: Why don't mammals have more than 4 limbs?

texts: Arthropods have 6 or more limbs and arthropods with 6 limbs appear to move faster than arthropods with 8 limbs so I wonder whether this might have something to do with fast and efficient locomotion. But, this is just a guess. I wonder what the official explanation is, if it exists.


texts: What are the most well-understood vocal animal languages?

texts:
Just as the Bee dance, for a "language", I mean that there are vocal pattens, or "grammar".

In the nature, there are many intelligent animals like human beings.

Bird songs, whale songs, dogs?

In fact, bird vocalization includes both bird calls and bird songs. There are Parrots, hummingbirds and songbirds,...

I wish to know the most well-understood vocal animal languages. Which species?


texts:
As I sit here after eating too much chocolate, I wonder:

What are the biological mechanisms behind eating too much candy candy causing nausea in a healthy individual?  Is it a spike in blood sugar, or does the stomach run out of a particular chemical, or is it a pH shift?

Is it the same reason that greasy meals can cause nausea?

From an evolutionary perspective, candy causing nausea seems counter-intuitive since candy is easy calories.  Then again, candy and concentrated carbs are modern inventions...


texts:
Do any animals other than humans undergo menopause?

Also, is there any difference between animals in captivity and animals in the wild as regards menopause? For example, even if menopause has been observed in a captive member of a particular ape species, do individuals of that species typically live long enough in the wild to also undergo menopause?

I guess here's what I'm really getting at: is menopause a common thing in the animal kingdom, or is it only a common thing in humans?


texts: Growth mediums required for human cell cultures

texts: So i would like to try a culture some of my keratinocytes just to see if i can do it. Ive read about a few different types of growth medium such as DMEM and RPMI but i am not sure about when to use which medium. So I am asking how do i detrimine which growth medium i need to use to culture human cells


texts: What are these shrimp-like insects in my cat's water bowl that appear overnight

texts:
Our family has 2 cats and a dog.  We keep food and water bowls outside for them.  We clean and refill the water bowls every day.  Almost every morning, the water bowl is teeming with small aquatic insects of some kind, which look and act like little shrimp.  I would guess them to be 5 to 8 mm in length, on average.

What are these, and where are they coming from?  They appear to be aquatic, since they survive and swim in the water for hours -- but how do they get there?

We live in central Florida, USA.


texts: Many of the compounds of sulfur have a strong odor.  Hydrogen sulfide from rotten eggs, the mercaptans of a skunk, the odor compounds in onions and garlic, the bitter taste of brassicas (cabbage, Brussels sprouts, collard greens, and similar plants) are all sulfur compounds.  What is it about sulfur that makes this so common?


texts: If you have water on you, does it *actually* cool or down, or do you just *feel* cold?

texts: I'm sure many people have noticed after getting out of a shower or out of a swimming pool that moving air makes them feel colder. It seems like one way to beat the summer heat is with water and also moving air. But, does having water on your body actually cool you off more with moving air, or is that simply what it feels like because water cools differently than air?


texts:
Muscles of the spine help to support it against gravity. For example, the multifidi interweave throughout the vertebrae and, as I understand, sort of reinforce the spine. So let's suppose muscles help to make the spine more stiff and rigid and this somehow helps it fight gravity.

What portion of support comes from the muscles? Would a spine by itself be able to support itself? In other words, to what extent is our ability to support our spine to remain upright due to muscles and how exactly do they help keep the spine erect in this capacity?


texts:
i have designed primers for HLA locus DPA1(exon 2 region) based on Real-Time PCR (qPCR) Primer Design guidelines. primer will start from intron regions to cover full exonic region.

F-CAGCAACAGAGAATGTCAGC

R-CCCTGAAGCAGCAATTGATG

to check for amplification of only a single region  i have used in silico PCR UCSC but it shows multiple region from chr6.

pls kindly help me with solving this.

thanks


texts: How does motor nerve innervation determine type of muscle fibre?

texts:
Muscle fibres are of two types - type I and type II. They differ from each other in various properties. Even the underlying biochemical processes are different to suit their function (slow vs fast)

In a normal muscle, on certain stains like ATPase and SDH, to differentiate between the types of fibres, a checkerboard pattern is seen. But in reinnervation following long standing denervation, there is a loss of the checkerboard pattern and fibre type grouping is seen.

This happens because, the the denervated fibres are reinnervated by other ones, which can change their type.

The question is, how can neural innervation lead to biochemical changes in muscle type?


texts: How can hyperplasia occur in non-fetal hypokinesis?

texts:
I have read that the hypoplasia can occur in fetal hypertrophic cardiomyocytes.
However, I am interested if this can be theoretically be possible in non-fetal cardiomyocytes which are hypokinetic. I think there must be some growth factors to allow this to happen. Other proposals

lysozyme, sepsis and cardiac adrenergic neural response / NO / G protein 1
shear-wave, vortex and refolding of proteins [2 Yuan et al.]

Sources

1 Lysozyme, a mediator of sepsis, impairs the cardiac neural adrenergic response by nonendothelial release of NO and inhibitory G protein signaling.
2 Yuan. Shear-Stress-Mediated Refolding of Proteins from Aggregates and Inclusion Bodies.

How can hyperplasia be regulated in non-fetal hypokinesis?


texts: Spider identification assistance Phoenix

texts:
Anyone know what kind of spider this is? They seem to be in the walls of my house...

LocationL Phoenix, AZ, USA


texts: Is the central axon of pseudounipolar neurons in dorsal root ganglia typically myelinated

texts:
As I understand, sensory nerve cells in the dorsal root ganglion are pseudounipolar neurons, with a sole protrusion from the soma branching into a central axon (or functional axon) and peripheral axon (or functional dendrite). Depending on the kind of nerve fiber, the peripheral axon may be myelinated to various degrees, and even not myelinated at all.

Now in an online lexicon (which is in German, unfortunately: http://flexikon.doccheck.com/de/Pseudounipolare_Nervenzelle), it is asserted, that while the peripheral axons (signalling from the periphery to the dorsal root) are usually myelinated, the central axon (signalling from the dorsal root to the posterior horn of the spinal cord) is usually NOT myelinated. The claim is unsourced. In spite of thorough research on the internet, I have not been able to find any notion whatsoever on the central axon being myelinated or not. So my question:

Is there any evidence that in dorsal root pseudounipolar neurons central axons are typically unmyelinated even when the peripheral axon is? Evidence on human neurons is preferred, but evidence on other species is welcome as well.


texts: Purifying a linear plasmid after restriction digest?

texts:
I expressed a yeast vector in E.coli and purified about 13µg of it. I then linearized it using a restriction enzyme, and attempted to gel purify it. I attempted this twice. The gel showed a clear bright band at the right spot, but after gel purification I end up with only 0.7µg of linear plasmid. I doubt I made the same mistake twice. What is the best way to purify a linear plasmid after digest?

Edit:

The plasmid is about 3.5 kb. I incubate an overnight culture of E. coli, miniprep the following morning, elute into water. I end up with 13µg of DNA in 200µl of H2O. I add the PmeI (10µl) and the CutSmart buffer (23µl) from NEB, incubate overnight. The following day, I run the 230µl through a 1% gel and get a single band around 3.5 kb. I excise the band, and perform a gel purification using the Biobasic kit, add denaturant (probably guanidine hydrochloride), wait for 10 minutes for the gel to dissolve, run through column, wash 2X with wash buffer with ethanol added, elute in water.

Thanks,
Max


texts:
If I'm not mistaken only RNA viruses insert themselves into the host genome. As an example of DNA viruses, herpes viruses for example do not insert themselves in the host genome.

Can CRISPR cut DNA that isn't in a chromossome, like a DNA virus?


texts: what are hyperbranched amplicons in DNA sequencing?

texts:
I am reading an article about single-cell sequencing:
http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.2720.html

And came across the concept of "hyperbranched amplicons". I googled for it but don't get much luck. The best I could find is it mentioned in another single-cell sequencing method here:

http://en.wikipedia.org/wiki/Multiple_displacement_amplification

Can someone give me a definition for it?


texts:
I'm new in biology. could you please let me know if the following 2 assumptions are correct

A nerve cell in the CNS along with its loop back neurons (Collaterals) is a memory unit. It will trigger per given spikes pattern (example – from the PNS). The said pattern should be “close enough” to enable the memory unit to resonate.

A memory unit is a cyclic sub-graph with its “root neuron”. An inhibitory neuron eliminates multi resonance of the memory unit.


texts: What does genetically tractable strain mean?

texts:
I want to study the properties of Pyrococcus Furiosus in surving to gamma irradiation by exploiting the analysis of DNA sequencing data as a bioinformatics study. Before learning how to analyse this kind of data, I wanted to have a look at some work that was already done. I found this interesting article: Genome Sequencing of a Genetically Tractable Pyrococcus furiosus Strain Reveals a Highly Dynamic Genome.
I think that it could be a good starting point. However, it is not easy to understand the whole article for me and I suspect
that the source of this difficulty is mainly due to the fact that I do not know what "Genetically Tractable Pyrococcus Furiosus Strain" means.
Searching in Google I found this article: Systematic evasion of the restriction-modification
barrier in bacteria, that explains:

Bacteria that are recalcitrant to genetic manipulation using modern
in vitro techniques are termed genetically intractable. Genetic intractability is a fundamental barrier to progress that hinders basic, synthetic, and translational microbiology research and development beyond a few model organisms. The most common underlying causes of genetic intractability are restriction modification (RM) systems, ubiquitous defense mechanisms against xenogeneic DNA that hinder the use of genetic approaches in the vast majority of bacteria and exhibit strain-level variation. Here, we describe a systematic approach to overcome RM systems.

Then it tells also that:

A strain that is not amenable to alterations of its genome or to the introduction of new genetic information during genetic engineering is termed genetically intractable.

Therefore, from this short explanations, I have an idea of what genetically intractable means. But, I still wonder why in the first article that I mentioned, the scientists should have been interested in sequencing such a genome (genetically tractable) and in comparing it with the one that was firstly sequenced (the so called reference strain) ? Moreover, what does genetically tractable mean?
Indeed, in the case of the first article, the following description is reported:

The best characterized of the Pyrococcus species is P. furiosus, the first to be isolated (19) and the first to have its genome sequenced (49). This organism has been studied by numerous “-omics”-based approaches, including transcriptomics by tiling (59) and DNA microarrays (14, 35, 51, 54, 57), comparative genomics (8, 33, 60), proteomics (32, 42), metallomics (11), and structural genomics (25). In many ways, it has become one of the model hyperthermophiles, a status recently sustained by the development of a genetic system for the organism (37). This was based on isolation of a variant in a lab strain population, designated COM1, which was highly efficient in taking up and recombining exogenous DNA in both circular and linear forms. The COM1 strain was obtained by targeted gene disruption of the pyrF. locus (PF1114) using a plasmid designed for double-crossover recombination (37).

Then what they do is:

The genome sequence of COM1 has now been determined, and comparison with the published sequence of the P. furiosus reference strain (49) (NC_003413) revealed a surprisingly large number of changes.

Thus, I do not understand (both in the case of this article and also in general case) what genetically tractable means (the description given by the article is not sufficient for me to understand) and why are we interested in doing the alignment between the reference genome sequence and the genome of genetically tractable strain ?
Sorry if my question could be trivial but my biological backgrounds are really poor. I reported the extracts of the articles because they give me an idea of the answer but, to be honest, I do not have fully understood them. Therefore, if you can explain me also those extracts, it would be great. Thank you in advance.


texts: Can a gene be split between different genomic locations several kb appart?

texts:
Can you have exons and introns of the same gene separated by hundred of kb in a genome? If so, how is the full mRNA assembled in such distance?

I'm working on plant mitochondria and I've seen an annoted gene that is cut between very distinct part of the genome.


texts: What is the evolutionary relationship between heme, chlorophyll and other tetrapyrroles?

texts:
As a non-biologist, I have searched the Internet and found dozens of papers discussing the similarity between the structures of heme and chlorophyll molecules, but I could not find any discussion of their evolutionary relationship.

To be more specific, I would like to know whether the use of tetrapyrrole in the blood and in photosynthesis can be traced to the earliest organisms in which tetrapyrrole had some function, and then the molecule evolved to be capable of the different functions it currently performs in animals and plants.


texts: How can homosexuality evolve despite natural selection?

texts: I would imagine that the answer to this question would be population control, especially since even if one sibling is homosexual this does not necessarily mean that the other siblings will be too.


texts: Calcium levels and nerve hyperexcitation

texts:
Why does lower blood calcium levels (or lower calcium levels in ECF) cause nervous hyperexcitaton? Why does it cause over stimulation of nerves and muscles and spasmic contractions of muscles?
This is why undersecretion of parathormone causes parathyroid tetany.
I am aware of the role of calcium in opening the synaptic vesicles for transmission of impulses and the role of calcium in muscle contraction but fail to understand how that might hep me understand the overexcitation of nerves and spasmic contraction of muscles. It actually seems that higher calcium in ECF might cause over stimulation and spasms of muscles due to sustained contraction.


texts:
A number of countries are using test kits for detecting new cases of nCoV (2019-Coronavirus) and apparently China is running low.

What exactly is in a nCoV "Test Kit" — How does it work?

(Surely they also differ, so in which way do they differ?)


texts: Glucose 6-phosphate dehydrogenase: reaction mechanism

texts:
I have searched the internet for the reaction mechanism of G6PD but couldn't find it, so I am asking whether anyone here knows its mechanism and whether they could recommend some sources that give detailed info about enzyme mechanisms generally.

I would be grateful for this because it seems difficult to find enzyme mechanisms on the internet.


texts: the range of interleukin 2 and 12 that can be used to activate nk-92 cells

texts:
I am one of the biotech students. I want to know the dynamic ranges of interleukin 2 and 12 that i can use to activate the NK-92 Cells.
    thank you


texts: Why is cartilage replaced by bones in a vertebrate adult?

texts: Why is cartilage present in a vertebrate embryo replaced by bones in an vertebrate adult even though cartilage can also provide me the structural framework like as in Chondrichthyes and they seem to do well with it as Sharks are members of Chondrichthyes which are some of the most fearsome creatures of the world.


texts: Why do many cells together survive better than one cell alone?

texts:
I know that one cell with no ECM is subject to anoikis. That's why in general one cell alone not in its environment is dying.

But are there advantages for a cell to live close to other cells even of the same type (for many types it looks obvious) ? If yes what are they and could you give a reference if it is possible please ?

I don't mean only what evolutionary advantages do cells together have over one cell (which is more simple, and there is a wikipedia about it), but I'm more interested if one wants to culture cells that you find generally in tissues, why is it better to take many of them (because it is better, right ?) ?

To be clearer, my point is that I want to understand the mechanisms of what happens when cells (of the same type) are in community and to understand given those mechanisms the advantages a cell has when it is with other cells rather than alone.

Thanks !


texts: Does $-//-$ sign between trpR and P indicate separation of the trpR gene from the operon? Or could the sign mean that the trpR gene may be present adjacent or far away from the operon, both the possibilities?


texts: Are there any organisms that perform photosynthesis-like processes with thermal energy alone?

texts: The closest I can find are thermophiles, but it seems they use the chemicals present in the hot environment for energy, not the heat itself.


texts: Why does atheroma contain thromplastin/tissue factor?

texts:
From my understanding, when the endothelial lining of arteries is damaged, atheroma is formed at the site of the damaged area. If the atheromas is ruptured, thromboplastin contained in atheroma is released into blood stream thus thrombus is formed after atheroma gets ruptured - this phenomenon is known as atherothrombosis. As a result, atheroma is characterised by its thrombogenic activity.

My question is, how come atheroma contains thromboplastin thus when it is damaged, thrombosis occurs? What was the source of this thromboplastin? Was it in the bloodstream? If thromboplastin was always present in the blood in which it entered into the atheroma during the formation of atheroma, why don't thrombosis occurs at the start when endothelial lining of the artery is damaged (without the need for an atheroma to rupture)?

I've read a couple papers and watched some videos on this topic. I've put one of my research below for reference to back up 'my understanding'.

  Rupture of the fibrous cap will typically release all the semiliquid
  material from the central portion of the atheroma. Because this
  material contains thromboplastin, it will trigger blood clotting, and
  a thrombus will develop at the site of intimal ulceration.


texts: What tests can be performed to test the purity and quality of the raw peptide HCG (Human Chorionic Gonadotropin)

texts:
What tests could be run to test the purity and type of HCG?

We are looking to purchase HCG from China but the purity and quality varies between labs, we are able to receive samples of the raw peptide and can use a contracted lab to perform tests but due to my academic background I have no clue which tests to request to determine the purity and type of the raw powder. The following is what we should be receiving from the labs in China.

Product Description
CAS Number: 9002-61-3
pI = 2.951
Extinction Coefficient: EmM = 3.88 (278nm)2
Synonym: Choriogonin, hCG
The molecular weight is approximately 37.9 kDa (with
approximately 31% carbohydrate by weight). The
theoretical molecular weight is 37.9 kDa based on the
native form, which contains 2 subunits. The α subunit
has a molecular weight of 14.9 kDa of which
approximately 10.2 kDa is for the polypeptide and
approximately 4.7 kDa for the carbohydrate. The
β subunit has a molecular weight of 23 kDa of which
approximately 16.0 kDa is for the polypeptide and
approximately 7.0 kDa is for the carbohydrate.3,

To answer Mad Scientists Question, the peptide is "supposed" to be CGA (1081) for use on humans. This is why it is so important for us to find a test that can define the qualities of the raw peptide.