texts:
I'm confused about the terminology and directions described in processing DNA to proteins in this paragraph.

  RNA polymerase reads a DNA template in the 3’ to 5’ direction to
  synthesize RNA in the 5’ to 3’ direction. Transcription can occur in
  either direction, but not in either direction from a single promoter.
  RNA polymerase can only transcribe in one direction (5’ to 3’) with
  respect to reading one strand of the template DNA in the opposite
  direction (3’ to 5’). In general, each promoter recruits RNA
  polymerase to a particular site and indicates in which the direction
  RNA polymerase will move along the DNA. As RNA polymerase is moving,
  there will be only a single strand that can be used as a template to
  allow 5' to 3' synthesis of a transcript.

Sentence 1:

What's the difference between reading and synthesizing RNA?

Sentence 2:

What's the difference between synthesizing and transcribing?

Sentence 3:

Didn't this just contradict sentence 2?

Sentence 4:

If RNA polymerase is recruited at a site to and directed to "move along" the DNA, what is it doing when it "moves along" (reading? synthesizing? transcribing? wtf?).

Sentence 5:

My understanding is this is the "transcribed strand", not the "coding strand" of DNA, correct?

Question:

I don't understand this paragraph and the more I read it, the more confused I get. Could someone please clarify (preferable with visuals)?


texts: Are tumor-associated antigens unique to cancerous cells?

texts:
Are tumor-associated antigens found only on the membrane of cancerous cells or just over-expressed on the membrane of carcinogenic cells?

In other words, are these antigens also found on healthy cells?


texts: Do ovaries produce estrogen before menarche?

texts:
It is traditionally taught that estrogen is produced by the granulosa cells of the follicle. But before menarche, where does the estrogen come from? Is it from the thin layer of granulosa cells lining the primordial follicles?
The adrenal zona reticularis produces androgens physiologically. Are they converted to estrogen? If yes, by whom? If not by the ovary, would the levels of estrogens be same in prepubertal boys and girls?

More importantly, are there estrogens in a girl before menarche? If yes wouldn't they cause endometrial changes?


texts: Preserved alpha complementation over evolutionary time?

texts:
Has the result of alpha-complementation ever happened via mutation through evolutionary time, and been preserved in modern day organisms?

In other words, has a functional gene product ever been split or terminated by mutation, exhibit alpha-complementation, and has since been preserved as a quaternary protein? This could be found out by comparison of proteins in closely-related species, but don't know of any specific examples. Has such a thing ever happened?


texts:
I was reading this article : Perspiration
The first question which came to my mind after reading the composition of sweat was whether it contains any information about the DNA or not?

I haven't had much interaction with biology since 12th grade (2010), so kindly answer in layman's terms and detail as well.


texts: Is there such a thing as transcranial magnetic inhibition? inhibit regions of the brain?

texts:
is there such a thing as transcranial magnetic inhibition?
There is an instrument capable of inhibiting regions of the brain as does transcranial magnetic stimulation, but in reverse?
By inhibiting, I mean that the neuron loses its action potential, as do benzodiazepines or alcohol.


texts: Are microtubules in centrioles helical, like they are when in isolation?

texts:
Microtubules tend to be of a helical structure, do microtubules in centrioles also have a helical structure?

The centriole is composed of nine circularly arranged triplet microtubules, one complete microtubule (the A-tubule) onto which two additional partial microtubules are assembled (the B- and the C-tubules, respectively. )

What are the structures of A, B and C respectively, are they helical?


texts: Is the EC50 of an activating protein for an enzyme a good indicator for the binding affinity Kd?

texts:
We work with a membrane protein system where measuring the affinity between the enzyme and the upstream activating protein has been difficult, and when measured in detergent solution, it is almost 100 fold lesser (ie ~100nM) whereas the EC50 in an enzymatic assay using vesicles in ~1-2nM. Would it be reasonable to say that the "real" affinity is ~1nM than 100s of nM based on the biochemical assay?

Alternately, is there a documented system where a huge discrepancy exists between measurements from direct binding and biochemical assays?


texts: Why do the most structurally well-characterized bacterial RNA polymerases belong to thermophiles?

texts:
From Lewin's Genes (11th edition, page 515):

  The only bacterial RNA polymerases for which high-resolution crystal structures have been solved, however, are from two thermophilic bacterial species, Thermus aquaticus and Thermus thermophilus.

Is this just a matter of economy? I mean, as X-ray crystallography is exceedingly expensive and complex, did scientists consider enough to resolve the RNA polymerase structure of one species and deduce those belonging to the rest by homology-based folding prediction?

Or is it because thermophilic proteins are inherently more stable and thus easier to crystalize?


texts: XXY (Klinefelter's) & Trisomy 21 & X-inactivation

texts: I read that X-inactivation doesn't tend to happen in males, but then when someone is XXY, they are a male because of the Y. However these individuals tend to live. So does that mean that X-inactivation happens in males or else these individuals would die?


texts: Why aren't all infections immune-system resistant?

texts:
It's been less than a century since the widespread use of antibotics started, and already we're seeing bacteria that have evolved immunities to the antibotics we use.

On the other hand, we've been using immune systems to to fight bacteria for millions of years, and bacteria evolve much faster than humans do.  Why have bacteria not evolved immunities that let them completely overwhelm our immune systems and kill us all?


texts:
What I mean to say regards facial and androgenic hairs.  There are many theories as to why some people have both kinds of hairs, while others have one or the same and others still have neither.  The best and most popular guess is that those hairs were secondary sexual organs, meaning that they just make the boys more attractive to the girls.

It's a well-known fact that hair provides insulation, and in the last ice age, Europe was dominated by a hominid built specifically to deal with the cold.  I am talking about, of course, the Neandertal.  Is there any evidence that the Neandertals, as a means of adaptations against the cold, were equipped with body hair?  If not, then would it be safe to speculate on such?


texts: What is the relationship between complexity and organization in biology?

texts: Is there any relationship between what we can call complexity and what we can call organization in biology? And if there is, what is it? Can we define these terms independently of each other or would the definition of one of them always inescapably include the other and vice versa? If the second is the case, what can such a relationship tell (or, at least suggest) us about life?


texts: Does DNA Ligase look for complementarity in sticky ends?

texts: Can DNA ligase seal two non-complementary sticky ends if the reaction is incubated at the optimum conditions ? I do almost 100% double digestion in the lab. However, during ligation, when I do a control without the insert, I still get many circularized vector and they cause massive false positives during transformation. Can ligase sealing two non-complementary sticky ends be a possible reason behind this ?


texts:
Short:
Thinking in particular of a Royal Python (US: Ball Python) such as some people keep as exotic companion animals, what sorts of "emotions" or "feelings" are they capable of?

Long: http://simonsnakesite.tripod.com/snakebasics.html says that

  scientific studies show that snakes just don't have the cerebral capacity for [emotions like joy, anger, and affection] but do have "primitive" feelings like aggression, fear, and pleasure

Based on the parts of the human brain where we develop emotions, and on the more primitive brain in a snake, this makes sense, but beyond being able to tell whether it's feeling the primitives such as "fear" or "safety", what "emotions" or "feelings" can we realistically ascribe to a snake?


texts: Which are mobile and immobile elements in plants?

texts:
I am confused with this element or nutrient classification in the plants, since some authors set elements like $\ce{S}$ and $\ce{Ni}$ as mobile and other as immobile elements (Citation 1, 2, 3, 4, 5). Then, I would like to know if there is a fixed and official classification.

I found a classification only for those elements:

Mobile: $\ce{N}$, $\ce{Mg}$, $\ce{P}$, $\ce{S}$, $\ce{K}$, $\ce{Ni}$

Immobile: $\ce{B}$, $\ce{Ca}$, $\ce{Mn}$, $\ce{Fe}$, $\ce{Co}$, $\ce{Cu}$, $\ce{Zn}$.

And what about the rest of elements like $\ce{Sr}$, $\ce{Mo}$, $\ce{Ba}$, $\ce{Pb}$, etc?


texts: Do single crossovers occur in circular polynucleotides?

texts:
Single crossovers in circular pieces of DNA do not seem to be a big topic, because if they happened, they would lead to a kind of combined chromosome with two inner strands and one large outer strand. (A bit like an 8)

 ________
|  ____  |
| |    | |
| |____| |
|  ____  |
| |    | |
| |____| |
|________|

But do these single crossovers actually not occur, for example because the crossover machinery is physically not able to do it, or do we just not observe them because they will inevitably lead to cell death and/or the chromosome somehow breaking?


texts: Variance of Stochastic Growth Rate for Average Population Size Over Time

texts:
I'm interested in calculating the variance of the stochastic growth rate for the average population size over time,
$$\ln \beta = \lim_{t\to\infty}\dfrac{1}{t}\ln V[N(t)]$$
which shows that the variance of $N(t)$ grows at a rate $\beta$.  The equation to compute this is given in the book "Matrix Population Models" by Hal Caswell.  The variance can be calculated as,
$$\beta = \lambda_1^{(\bf{B}_2)}$$
where $\lambda_1$ is the dominant eigenvalue,
$$
\begin{align*}
\bf{B_2} &= \bf{F_2}[\bf{P}\otimes(\bf{I}\otimes\bf{I})]\mathrm{,} \\[1em]
\bf{F}_2 &= \mathrm{diag}({\bf A_1 \otimes A_1, \ldots, A_k \otimes A_k})\mathrm{,}
\end{align*}
$$
$\bf A$ are the population projection matrices of dimension $s$ from $k$ independent environments, $\bf P$ is the column-stochastic transition matrix of dimension $k$, and $\bf I$ is the identity matrix of dimension $s$.  I tried doing this in R using the goldenheather (Hudsonia) example from the Caswell book that can be loaded into R as follows,

library(popbio); library(Matrix); data(hudsonia)

I ended up with a value for $\beta$ of 0.9366351.  This cannot be right, the variance is way too high.  I must be doing it wrong, or perhaps there is a mistake in one of the equations (very, very likely the former).

Here's my code (if it helps),

s = NROW(hudsonia[[1]])
k = length(hudsonia)
P = Matrix(1 / k, k, k)
I = Diagonal(s, 1)
F2 = bdiag(lapply(hudsonia, function(i) kronecker(i, i)))
I2 = kronecker(I, I)
P2 = kronecker(P, I2)
B2 = F2 %*% P2
lambda(B2)


texts: How do you define a male-biased gene and a female-biased gene as they are found in the abstract of this article.


texts: Is sugar absorbed into the bloodstream through the walls of the mouth?

texts: If you let a piece of candy melt in your mouth, but did not swallow it, would the sugar be absorbed through the walls of your mouth?


texts: The double bonds in naturally occurring fatty acids present in our body are in cis configuration while the enzymes for beta oxidation can act on trans double bond. Then what will be the significance of cis double bond in naturally occurring fatty acids? Why the naturally occurring fatty acids don't have double bond in trans configuration?


texts:
Which of the following shows the correct changes in thermodynamic properties for a chemical reaction in which amino acids are linked to form a protein?
A) +ΔH, +ΔS, +ΔG
B) +ΔH, -ΔS, -ΔG
C) +ΔH, -ΔS, +ΔG
D) -ΔH, -ΔS, +ΔG
E) -ΔH, +ΔS, +ΔG
Answer:  C

I know that dehydration is endergonic (+ΔG).
I have two questions:

Why is entropy decreasing? In the beginning of the reaction, we have two amino acids. By dehydration, we have at the end two molecules: the two amino acids together and the H2O molecule. The same number of particles before and after.

Why is enthalpy change positive? You made a bond between the two amino acids. That is exothermic.


texts: Why do humans transport glucose but not sucrose like plants?

texts:
The reason why plants transport sucrose rather than glucose is due to the fact that it is more efficient and that nearby cells would not take up all the glucose too quickly.

Hence the plant convert glucose to sucrose before transporting them throughout the plant.

However, why is that humans and other animals all transport glucose in their bloodstreams? Why is it that they do not convert glucose to sucrose before transporting them since, as mentioned above, it would be more efficient?


texts:
When our instructor asked us about the speed of action potentials in cells, I told him that action potentials and two-wheelers travels at similar speeds. He thought that this is an 'interesting' way of looking at it.

Needless to say after the class I tried to figure out the minimum, average and maximum speed of action potentials in neurons. Wiki helped but its not authoritative. Some place it says that the fastest is 110 m/s and other place it is 120 m/s. While slowest one varies between 7 m/s (in Rana frog) to 0.5 m/s (Nociceptors) on Wiki. The average speed would be hard to calculate.

I am looking for any references where slowest and fasted action potentials are described. They would be interesting cases to write a note for classromm.


texts: Why is thoracic breathing dominant in women while abdominal breathing is dominant in men?

texts:
In human males, lateral movement of thorax constitutes 25% of breathing while abdominal movement accounts for 75% of breathing. It is exactly the opposite in the case of women.
I got this piece of information Trueman's Elementary Biology.


texts: Are original x-ray diffraction data available

texts: Is it customary for investigators to publish the original x-ray diffraction data used in macromolecular structural determination? If not, why not; and if so, is there an online database where these data may be downloaded?


texts: What is a T7 tag and can if be used to purify synthesized proteins? Is it charge based like a His tag?


texts: Easy derivation of Kimura's approximation for the probability of fixation of a mutation

texts:
Kimura's approximation for the probability of fixation of a mutation under selection finds recurrent use in population genetics models till date. I am trying to understand the mathematical basis of this equation but none of the textbooks or online resources that I have checked, provide an easy derivation of this approximation but rather simply cite Kimura's 1962 paper.

$$P_\text{fix} \approx \frac{1-e^{-4Nsp} }{1-e^{-4Ns}} \qquad (1)$$

So, I was reading the original paper but the provided derivation doesn't appear clear to me.

Details

Kimura starts with definition of probability of change in allele frequency as:

$$u(p,t+\delta t) = \int f(p+\delta p; \delta t)\ u(p+\delta p,t)\ d(\delta p) \qquad (2)$$

where (quoted exactly)

$u(p,t)$ is the probability that an allele will be fixed in a time interval $t$ given that it's initial frequency is $p$.
$f(p+\delta p; \delta t)$ is the probability density of the change from $p$ to $p+\delta p$

Then he uses Taylor series approximation to obtain an equation of this form:

$$\frac{\partial u(p,t)}{\partial t}= \frac{V}{2}\frac{\partial ^2u}{\partial p^2}+M\frac{\partial u}{\partial p} \qquad (3)$$

He defines $M$ and $V$ as mean and variance of change of $p$ per generation. These are formally defined as:

$$M=\lim_{\delta t \to 0} \frac{1}{\delta t}\int (\delta p).\ f(p+\delta p; \delta t).\ d(\delta p)$$

$$V=\lim_{\delta t \to 0} \frac{1}{\delta t}\int (\delta p)^2.\ f(p+\delta p; \delta t).\ d(\delta p)$$

($V$ actually should be just the second moment as per the mathematical definition and not variance)

Then he solves equation 3 at steady state with boundary conditions $u(0,t)=0$ and $u(1,t)=1$ to obtain this:

$$u(p)=\frac{\displaystyle\int_0 ^p G(x) dx}{\displaystyle\int_0 ^1 G(x) dx} \qquad (4)$$

where:

$$G(x)=\exp\left(-\int \frac{2M}{V}dx\right)$$

I understood the derivation till this point.

Then he just puts:

$$M=sx(1-x)$$
$$V=x(1-x)/2N$$

and obtains equation 1.

In short

Is there an easy derivation for equation 1?
If not, can someone explain me how M and V were approximated as above?


texts: Why does the protection afforded by some vaccines last longer than for others?

texts:
After reading an answer to the question of How Do White Blood Cells Learn? Or Do They?, I came to wonder something. Specifically,

  The effect of this is that every new B and T cell that your bone marrow makes will recognize a unique, random protein sequence, and you will have billions of these cells floating around in your blood circulation at any given time. These cells however will only float around in circulation for a short period of time before dying and being replaced by other cells with new random sequence receptors.

Assumption: What I gather from this (and the remainder of the answer) is that basically, a vaccine "teaches" the existing white blood cells in your body; eventually, these cells will  be purged, so you will no longer be immune.

However, many vaccines seem to only be once-in-a-lifetime, or at least require a vaccine only once per decade (or less).

Some examples would be the Varicella vaccine, which can last up to 20 years, the Tetanus vaccine, which recommends a booster every 10 years, and the HPV vaccine, which lasts 5-6 years. Durations also vary with Hepatitis, Influenza, Polio, and numerous other common vaccines.

I would assume that, regardless of what a cell has "learned," it is purged with the same likelihood as any other cell; yet, it seems that some "learned" defenses can be retained longer than others. In essence, my question is: Why do some vaccines take longer to "wear off" than others?

(Note: This question is not a duplicate of Why do I need a flu shot every year, while many other vaccinations last years or even a lifetime?; I understand that some pathogens can mutate, so immune cells are of no use against mutated strains since they were not vaccinated against the mutation.)


texts: Does acuity of a re-mapped region of cortex depend on the need of the animal to resolve between two closely related stimuli?

texts:
From my informal research so far, I've learned that cortical magnification is evident in at least the visual cortex and the somatosensory cortex.
My question is the following:
If there were a hypothetical experiment to be done where the one area of the cortex, say the visual cortex, were to be re-mapped to a different sensory modality like touch, would the acuity or "resolving power" of the re-mapped region depend on the extent to which the animal needed to distinguish between closely related touch stimuli? In other words, has anyone tried an experiment that results in a re-mapped and magnified cortical portion in one go?


texts:
As is advised with most fish you should avoid sudden changes in water temperature (for example by introducing new water that hasn't been left to come to room temperature). I have, however, never understood why that is the case, in particular given that most fish are cold blooded so there is no issue with needing to "ramp up" the metabolism when in cold water.

Say a particular species of fish can survive in water between 20°C and 30°C what causes a fish that was previously in 30°C water to die when suddenly plunged into 20°C water? I understand this effect is called "shock" but I'm looking for the biological reason for it.

To be clear I'm not looking for "chemical x is released and that leads to the fish dying,  I'm looking for why these chemicals are released at all. So to give an example if my question had of been "why does adrenaline shock kill" I'd be looking for "adrenaline release is usually a good thing, it's released in response to a fright and prepares the body for a fight or flight response. However this heightend preparedness can cause additional strain on the body which can cause death in some cases"


texts: How long can E. coli stocks be stored at -20°C?

texts:
I'm volunteering for a biohacker lab - biocurious in Sunnyvale.  The have a pretty good set of equipment - gel boxes, incubators, but they don't have a -80°C freezer yet.

I'd like to set up some glycerol stab stocks of some E. coli strains, but i'm told even untransformed (i.e. no plasmid) bacteria will get funny after a while at -20°C.  It would also be good to hear how long you can keep a plasmid transformed strain at -20°C.

Can anyone be specific about what happens and how long it takes when you store them at -20°C for long periods of time?

I have done a little reading for competent cells and I guess they stay active for about 4 days without a -80°C freezer.


texts: I found the Hill muscle model, which helps relate the force a muscle can generate to its change in length over time (its "contraction velocity").  Is there a similar model to get an idea of the energy consumed during a contraction as a function of the force generated?


texts: Describing trait evolution across a very small phylogenetic tree

texts:
I am very new to phylogenetic comparative methods but I want to explore the evolutionary patterns of a number of quantitative traits I have across a small sample (5) of closely related species (between .45mya and 4.3mya divergence). I am confident in the structure of the tree, but I only have phenotypic data for a small sample of the tree. I want to measure how correlated the evolution of the traits are across this small phylogeny and test the traits to neutral evolutionary models.

Should I even attempt this?  I know that there will be limits for what I can infer about evolution of these traits, but I’m not sure where to start in terms of identifying the specific weakness. I know it will depend closely on my trait measurements, some traits display notable divergence and others do not change much across the phylogeny.

Are there any approaches that would be useful for describing the evolutionary patterns for this small sample?  What references would be useful for convincing me to hold off until I have a larger phylogenetic sample?
Thanks in advance for any advice!


texts: I know that RBCs use glycolysis of glucose to lactate to produce most of their energy, but, if they are just carrier cells, where do they use the energy?


texts: What comes out of this bump in this vegetable?

texts:
I live in Denmark, Europe and I have in my garden this gigantic vegetable.

It has a big bump on the top and i was wondering about what comes out of it?


texts: We found this on a beach in the Bay of Lannion, Brittany, France. What is it? About 6 cm long.


texts:
WebMD writes:

  Skin tags are small, soft pieces of skin that stick out on a thin stem. They most often appear on the neck, armpits, upper trunk, and body folds. The cause of skin tags is not known.

Do we really know nothing about why they appear? Is there research that suggest hypotheses of the causes of skin tags?
It seems to me a pretty well established phenomena for it to be without good research.


texts: Does this equation have a typo? (Systems Biology, singular value decomposition)

texts:
I'm reading a systems biology paper, and I'm suspecting there's a typo in an equation, but I want to make sure.

The article is "Systemic metabolic reactions are obtained by singular value decomposition of genome-scale stoichiometric matrices." (Famili & Palsson 2003, http://www.ncbi.nlm.nih.gov/pubmed/12900206 / http://www.sciencedirect.com/science/article/pii/S0022519303001462). In equation 5, I wonder if the final subscript u_kr shouldn't be u_km, as the vector u_k^T is a column vector in the matrix U, which has dimensions m x m. Of course, some elements in u_k might be zero, in which case there would be less than m products in the sum, but I see no reason why there would be maximally r non-zero elements either (where r is the rank of the matrix S which has been decomposed). I worked out a simple example on paper where r < m and still got vectors with m non-zero elements. Can someone give me a second opinion on this?

Edit: Here are the main equations.
A model of a metabolic reaction network is described by a stoichiometric matrix S of dimensions m x n and rank r. For the metabolites in the model, changes in metabolite concentrations is equal to S multiplied with the vector of reaction rates, v:

${\frac{{dx}}{{dt}} = Sv}$

The singular value decomposition of S is given by

$S = U\sum {V^T}$

Multiplying on the left side with $U^T$ (The transpose of U) we get:

${U^T}\frac{{dx}}{{dt}} = \sum {V^T}v$

After matrix multiplication, we have for each row in $U^T$ and $V^T$, where $\sigma_k$ is the k'th singular value

$\frac{{d(u_k^Tx)}}{{dt}} = {\sigma _k}(v_k^Tv){\text{   k   =  1}},...,{\text{r}}$

And finally, equation 5:

${\text{u}}_k^T \cdot x{\text{  =  }}{{\text{u}}_{k1}}{x_1} + {u_{k2}}{x_2} + ... + {u_{kr}}{x_m}{\text{   (5)}}$


texts: How was Restriction Site of EcoRI sequenced?

texts:
The sequence of restriction site of EcoRI - GAATTC was identified in the early 1970s, before Sanger Sequencing was invented.(1977)

How was the restriction site of EcoRI sequenced ?


texts: RNA interference and the former Petunias experiment >

texts:
I'm having problems trying to understand how RNA interference works.

From what I understood, in simple terms there is this  dsRNA which is fragmented into siRNA by the enzyme called Dicer, and those siRNA make the RISC complex active, which leads to the degradation of mRNA which are complementary to one of the strands of the original dsRNA.

Said this (which I don't even know if it is correct), how this relates to the petunias experiment? From what I understood the researchers put into the petunias an enzyme that coded for the pigment and not strands of dsRNA which then would have created the inhibition...

What am I missing?

PS. I don't have technical knowledge about Technologies so excuse me in case I said wrong things.

Thanks in advance everyone.


texts: How increased potassium intake increases sodium excretion?

texts: "K+ antagonises the biological effects of Na+". I have been reading the same many times without any explanation. How actually (mechanism) K+ helps excretion of Na+?, their interactions? And eventually lowers blood pressure?


texts: What is the most effective way to eliminate silverfish (g. Thysanura) from walls and floorboards?

texts:
I've had our home fumigated, but the silverfish seem to return unaffected.

Are their eggs unaffected?

What's the best way to eliminate them from your home?


texts: Are there any thermogenic plants which are suitable as houseplants?

texts:
I have been wanting to supplement my heating system with some plants that produce heat! I have become aware that there are around 14 species which generate significant amounts of heat for example the eastern skunk cabbage.
However I have also read that many species which are thermogenic release odours such as the smell of rotting flesh. I would rather avoid plants which will make my house smell like this!
Are there any plants which produce heat which would be suitable for storing in my house?


texts: What effect do oligosaccharides, like those found in legumes, have on the composition of intestinal flora in humans and if so how so?

texts: I know that intestinal flora metabolising oligosaccharides, like those found in legumes, is the cause for the well known fact that legumes cause flatulence, but does an oligosaccharide-rich intestine change the composition (i.e. which specific bacteria make it up) of intestinal flora in humans?


texts:
I am looking for a good book about Clinical Microbiology, particularly good in Bacteriology and Bacteria Diagnosis (medium, plates, type of colonies...). With good photos. What are the bests in your opinion?

Thank you.


texts: Does sex-chromosomes exist in all the cells in a human body?

texts: Each cell of a human body contains 46 chromosomes. So every cell must contain a pair of sex-chromosome. Is it true? Then a cell of a male and a cell of a female are always different and never be the same?


texts: How well does the event-driven DVS sensor approximate the rods of the retina?

texts:
There is a neuromorphic vision sensor that is generating some interesting research these days that is called the Dynamic Vision Sensor. One of the claims of this sensor is good approximation of the conventional retina. However, there's no detail on the website in what way this is true or to what degree this is true.

It does not detect colour, so obviously it isn't an accurate approximation of the cones found in the retina. Additionally, the function of the cornea is fulfilled by the lens of the camera, so this input isn't totally approximated. Consequently, the only significant component that remains to be evaluated is the rods of the retina?

What are the similarities and differences between a retina and the DVS sensor?

First, let me save you some reading by explaining how the DVS sensor is different from a typical camera. Instead of synchronously sending frames with data about every pixel, the DVS is event driven. That means, when a light intensity change occurs, an event is fired with the address of that change, a time-stamp and whether the pixel observed an increase or a decrease.

Do rods also encode changes in light intensity in the same manner? If not, what is the difference?


texts: Why do we need deep sequencing? Why cannot the sequencing technologies read all the nucleotides correctly at the first read? Sorry since this question is too trivial, I don't have a biological background at all, and I have just started doing research in CompBio. Thanks.


texts: Auxotrophic complementation test with yeast

texts: If auxotrophic strains grow on minimal media do they complement each other or not?  Also, is complementation the same thing as complementing each other?


texts: Why are fatty acids consisting of even number of carbons predominant?

texts:
Most of the fatty acids in animal biology consist of even number of carbons in its parent chain. What property of such fatty acids cause the biological systems to prefer them over the odd counterparts? What's so bad about fatty acids containing odd number of carbon atoms in their parent chain?

Why are fatty acids consisting of even number carbons in their parent chain predominant?


texts: How is adrenaline (also known as "epinephrine") a ligand?

texts: I keep reading that adrenaline is a ligand, however, from what I understand a ligand is a molecule or ion which donates a pair of electrons to a central transition metal ion in a complex. If this is the correct definition of a "ligand", then how can adrenaline be a ligand?


texts:
I'm confused with this explanation in my book:
2-aminopurine is incorporated into DNA in place of adenine but can pair with cytosine, so an AT pair becomes a CG pair.

This sentence seems odd to me. It says that adenine is replaced with 2-aminopurine, but can pair with cytosine. And the AT pair turns to CG pair. Does it mean that 2-aminopurine substitute adenine, and then it works like cytosine to bind with guanine?? Because 'AT pair becomes CG'. But it says 'but can pair with cytosine', which one is going to bind with cytosine??

I've Googled on this but couldn't reach to a clear explanation about this. Can someone please explain to me how this analog works or rephrase the sentence in my book? Thank you.

The book that I'm referring is Microbiology: an introduction 10th ed. By tortora, funke and case. Page 229.


texts:
When two parents (regardless of species) reproduce in sexual reproduction each offspring is generally a random combination of genetic traits from each parent. Their developed traits then depend on the expression of each of their genes per established genetic combinatory science. All well and good.

Now my question - when does the actual randomization of genes for a given offspring happen? Does it happen when the individual sperm and egg cells are formed, or does it happen when they combine?

So does every one of a female's eggs have the same genetics, and every one of a male's sperm have the same genetics, and when the two combine it is randomized to form the zygote?

Or is each egg unique and each sperm unique, and already "pre-randomized", and the combination to form the zygote is then a straight-forward addition?

Or is it some variation or combination of those two options? Maybe the answer actually even differs across species, or across plants vs animals, or fish vs mammals, or something?


texts: After the primer is removed from the leading strand, how does DNA polymerase I add dNTPs without a 3'-OH?

texts:
I have a question about replication in prokaryotes. I learned in school that:

DNA polymerase needs 3'-OH to add a dNTP.
The chromosomes of prokaryotes are usually circular.
The primer in the leading strand (of course the primers in the lagging strand too) is removed by the 5'→3' exonuclease activity of DNA polymerase I.

It makes sense that on the lagging strand the primers are removed and then replaced by new dNTPs using the 3'-OH of the previous Okazaki fragment. However, for the primer on the leading strand, there is no Okazaki fragment upstream and thus no 3'OH that DNA polymerase can use for polymerisation.

How is the primer replaced by new dNTPs on leading strand?


texts: I only know dogs and humans sneeze... so do other mammals sneeze as well? Is it possibly an evolutionarily-determined immunological trigger?


texts: What type of fish is this and why is it so big?

texts:
This is a screenshot from a youtube video that you can watch here:

https://www.youtube.com/watch?v=zcdJNPYkIE0


texts: What is the difference between neurotransmitters acting as neurotransmitters and hormones?

texts:
My main confusion is what differentiates the action of a transmitter substance as a neurotransmitter and as a hormone. For example, when norepinephrine is being talked about as transmitter substance that modulates brain responsiveness and information processing, it's a neurotransmitter. But when norepinephrine is involved in the functions of the autonomic nervous system (ANS), does it work as a hormone or a neurotransmitter?

Quoting from Physiology of Behavior, by N. Carlson, 2013 edition:

  "Neurons in the central nervous system contain a1- and a2-adrenergic
  receptors and b1- and b2-adrenergic receptors. All four kinds of
  receptors are also found in various organs of the body besides the
  brain and are responsible for the effects of epinephrine and
  norepinephrine when they act as hormones outside the central nervous
  system."

So does that mean that whenever norepinephrine works outside the CNS, it works as a hormone?


texts: How are haplotype blocks different from genes?

texts:
According to Cardon et al. 2003, a haplotype block is

  A discrete chromosome region of high linkage disequilibrium and low
  haplotype diversity. It is expected that all pairs of polymorphisms
  within a block will be in strong linkage disequilibrium, whereas other
  pairs will show much weaker association. Blocks are hypothesized to be
  regions of low recombination flanked by recombination hotspots.

It seems obvious that the parts of the genome that compose genes will have a somewhat similar behavior.

So what are the differences between haplotype blocks and genes? Are genes a kind of haplotype block?

Cardon, L. R., and G. R. Abecasis. 2003. Using haplotype blocks to map human complex trait loci. Trends in Genetics 19:135–140.


texts: Mechanical cause of loss of consciousness

texts:
Consciousness is an electrical and chemical interaction in the brain, caused by neurons firing and chemical interactions. How does a mechanical "force" cause this to stop working?

i.e. How does a mechanical action (such as a punch to the head) cause this electrical/chemical system to stop working (leading to unconsciousness)?


texts: Since plants shed their leaves and don't perform photosynthesis during winters, where does oxygen come from?


texts: Centriole genes Knock-out Experiment in Common experimental animals?

texts: Anyone know of any experiments that have knocked out the genes for producing centrioles in a worm, mouse, fish, fly or whatever animal? Are the genes for centrioles even identified? It has been shown that centrosomes form with out centrioles so I'm curious how lack of centrioles would effect the system of an animal as a whole.


texts: What is the metagenome like for other classes of animals?

texts:
Lately there's been a lot of discussion around the many non-human cells essential to a healthy human body — called the microbiome, or metagenome.  Much of this is in the gut microbiome.  See this question, for example.

The Human Microbiome Project at NIH emphasizes we are just beginning to measure the specifics of this for the human case.

I assume this is similarly true for all mammal species, and I don't know how much farther.  Fish have a fairly different body plan than mammals, including a fairly different gut. And coelenterates have an even more different body plan in many ways, again including the gut.

Does a typical fish depend on as large a microbiome as a human?  Is there much known about that?  What about jellyfish?


texts: What are the problems in using an ssDNA or an mRNA for expression instead of using a plasmid?

texts:
Let's say you want to do a gene cloning experiment. You have an empty expression vector (mRNA or DNA) and are looking to clone some gene X into it. Why is it you can only buy X already inside a vector (which is in turn often inside a bacterial carrier)?

What is the problem with handling pure mRNA nucleotides of gene X? Or even sscDNA?


texts:
I can't remember if I saw it in a cartoon, a documentary, or both, but the notion is that the clients of cleaner fish wait in line to be cleaned. "Clients" means the fish (or other aquatic animals) who are cleaned by cleaner fish.

I tried to find a study whose sole purpose is to confirm that client fish wait their turn to be cleaned by cleaner fish, but I only found articles that seem to refer to this while studying other cleaner fish behaviour.

Statements I came across that support the notion:

Most photographs of fish in coral reef are at cleaner stations because the fish are waiting there which allows photographers time to photograph.
Cleaner fish "have a positive impact on local reef fish diversity", which could imply many different fish come and may not attack each other to benefit from the cleaner fish. This one's more of a stretch.
"Others wait no longer than 30 seconds before searching for cleaners elsewhere." The source is German, so I can't go deeper.

Do fish wait in line to be cleaned by cleaner fish?

Side question: Is this an example of reciprocal altruism?


texts:
In rho-dependent termination in prokaryotes, how does RNA polymerase “know” that it has reached the end of a gene and that it has to stop so that the rho-factor can bind mRNA’s rut site? Is there a termination sequence on the template DNA that “signals” the end of a gene?

And consequently, how does the rho-factor “know” when to bind to mRNA?... how does rho-factor recognize that the RNA polymerase has stopped so it can start its ATPase activity to dissociate the transcription complex from DNA and release the mRNA?


texts: Book recommendation: Modern Synthetic theory

texts:
I'm a zoology minor. I wish to study modern synthetic theory (evolution) is there a good book available online for reading?
The book should cover a basic idea about what the elements of modern synthetic theory are and briefly what are the conclusions of the theory.

Feel free to suggest edits.


texts: Choice of Molecular markers to carry out molecular phylogenetics

texts: For evolutionary analysis of different individuals within a population, the preferable molecular markers are non-coding regions of mitochondrial DNA. My question is that why they are used what is the logic behind that and why specifically mitochondrial non-coding region is taken for evolutionary analysis between them?


texts:
Beginner question here:

The definition of decussation I see is the crossing through the midline of a bunch of neurons.  But I was wondering if there was a little more to it than this, because I'm given the impression in readings that this is a somewhat difficult task to perform developmentally, like the body might have to take extra effort to regulate the crossing so that the neurons do not interfere.  So when nerves from both eyes cross, for example, do they pass AROUND each other or do the bundles of nerves all weave through each other?

Thanks in advance.


texts:
I live in Denmark, Europe and I found this insect wandering around in my garden the other day. It's some kind of beetle, but I don't know what kind it is or the species. The beetle could also fly and had red wings beneath its armor.

Help would be much appreciated. Thank you.


texts: Can anyone identify this dragonfly spotted outside of Boston, MA?

texts: Can somebody identify this dragonfly please? It was seen about 15 miles west of Boston.


texts: ATP Hydrolysis to AMP in the Urea Cycle. What is the Free Energy Change?

texts: How is the hydrolysis of ATP into AMP and PPi in making arginosuccinate equivalent to the hydrolysis of 2 ATP?


texts: What is the difference between eugenics and evolution by natural selection?

texts: So with the working definition of Eugenics: "the aim to improve the human gene pool". What are key features that distinguish Eugenics from evolution by natural selection?  I mean, besides that natural selection occurs naturally.


texts:
Used for instance in this article

  The role of genital mycoplasmas as pathogens - - are
  generally neglected by diagnostic laboratories in the United Kingdom,
  possibly due to the lack of a suitable commercially-available culture
  medium. We have evaluated the bioMerieux Mycoplasma-Lyo system using
  qualitative and quantitative studies and have found it to have
  suitable qualities and practical advantages for detection of
  Ureaplasma urealyticum and Mycoplasma hominis.

What is Mycoplasma Lyo medium?

I think it is some sort of anaerobic solid medium for all other mycoplasmas except M. pneumoniae (strict aerobe).


texts:
If I have some synthetic DNA sequence (<=20 bp long), is there a way for me to reliably insert this sequence next to some n-bp motif?  I'd like for this to be possible in humans.  If so, are there any restrictions on the size of n?

I have explored the use of CRISPR/Cas9 for this end, but it is limited in the sense that the gRNA target sequence must be adjacent to a PAM sequence.  Attempts have been made to solve this problem (http://www.nature.com/nature/journal/v523/n7561/full/nature14592.html#affil-auth), but they fall short of full generality for n.  Are there any better approaches?


texts: Do Asian giant hornets (Vespa mandarinia) prey on other nests of Asian giant hornets?

texts: Asian giant hornets are known to attack nests of other bees and wasps, but should they encounter another nest of their own, would they attack it?


texts: Oral allergy syndrom, continuation of continuous consumption of allergen

texts:
Wikipedia states on its page that

  In addition, patients are advised to avoid the triggering foods, particularly nuts.

And same thing goes for webmd.com

  The basic rule: If a food makes you uncomfortable, don’t eat it.

So two very related questions flow from this:

Does continuous consumption cause such an allergic reaction to become stronger?
And if that is the case, by what mechanisms does that happen?


texts: During what phase is the cell polyploid? Why is it polyploid at this point--what has happened to create this state and why is it important to the process?


texts: Homology modelling of protein with two identical subunits in its quaternary structure

texts:
I am using homology modelling to assign the 3D structure of Torpedo acetylcholine receptor (Unwin 2004, 2bg9 in RCSB) to human muscle nAChR. The problem is, both Torpedo receptor, and human receptor have subunit structure A-B-D-A-E: so a same subunit (A) occurs in the model twice. This seems to cause problems for homology modelling software, as it tends to align the second 'A' sequence over the first 'A' sequence, creating a hole in the pentamer, and not filling it up. Any ideas on how to make sure the modelling software acknowledges the quaternary structure? Below please find a link to a file generated using pdb.gz structure data from Unwin model + a set of corresponding FASTA sequences, and attached picture shows the problem (revealed when alignment is set as shown in the picture, by clicking on the same 'boxes' as in the image). Long story short, I need to get the A subunit to complete the alignment in a different spot than it is automatically placed in, as it occurs in the whole structure twice.

https://swissmodel.expasy.org/interactive/JJ5mQf/models/


texts: What is the function of the kidney in terms of osmoregulation and excretion

texts:
Also include the role that ADH plays
I am fully aware that ADH has a role in osmoregulation  but does it also play a role in exretion?


texts: Why do myelinated axons conduct impulses faster?

texts: How does the myelination help in better conduction? I would prefer answers that are not too technical please.


texts: Does DHA increase the effects of clarithromycin?

texts:
I've read on this publication that every drug that induces CYP3A can reduce the effectiveness of clarithromycin. Clarithromycin inhibits CYP3A.

But it does not say anything about the opposite situation: does a low concentration of CYP3A increase the effect of clarithromycin?

This research shows how DHA can inhibit CYP3A.

Now the final question is: does a high concentration of DHA increase the effect of clarithromycin?


texts: Why are stem cell therapies more preferred (theoretically) over current measures?

texts:
i understand that when stem cells are used to treat injuries using induced pluripotent stem cells (IPS), they can prevent the risk of having any tissue rejection and thus, there isn't a need for use of immunosuppressant drugs.

However, based on the researches using animal models thus far, I note that surgeries are still the main mode of delivery of such stem cell-regenerated organs/organoids. Meaning, to transplant a part of a organ or a tissue into the animal model, a surgery still needs to be done - how is this different from current measures?

Specifically, how are stem cells going to aid or further research into areas such as curing heart or lung diseases and I wonder how are these methods going to be better than current ones.


texts: Difference between ‘tagging’ and ‘conjugating’ a fluorochrome to an antibody?

texts:
The Wikipedia entry on fluorescence repeatedly states that “a fluorochrome must be tagged or conjugated to the antibody”.

How is tagged or conjugated different? Is this a mistake or are these indeed different concepts?


texts: Do some animals have a tolerance to the negative effects of inbreeding?

texts: Are some animals more or less tolerant to inbreeding? By tolerant I mean do they have a genetic mechanism that allows them to inbreed and corrects for issues introduced through this? When I started searching for this I quickly ran into theories on how inbreeding is avoided but did not find information on whether some animals have genetic mechanisms that make them less likely to get negative effects from inbreeding.


texts: Salvaging a plasmid from a cell culture stored at the incorrect temperature

texts:
I have E. coli with transformed plasmid on agar in a vial.  It has been stored at -20 degree C without glycerol stock for 18 hours.

This is a continuation of: Survival of E. coli on agar plate at -20 degree C without glycerol stock

I have transfered this vial from -20 degrees to 4 degrees after 18 hours when I determined that I had made a mistake. Since this is a very important vial and I don't have another one, what should I do in this stage?

What is the procedure for saving the plasmid if I am unable to save the whole cell?


texts: When a parent amoeba undergoes binary fission, two amoeba are obtained. Are those two amoebas, both daughter, or 1 parent and 1 daughter?


texts:
Generally plant tissues:

meristems tissue: meristems cells, apilal meristems, lateral meristems
Non meristem tissue: dermal tissue, vascular tissue, ground tissue

my question:

What is the difference between intials cells  and meristems cells? Are intials cells the same as meristems cells?


texts: Are there examples of encryption in nature?

texts:
There are examples of mathematics in nature such as Fibonacci number, fractals, etc.  Are there examples of encrypted information?

What I am looking for is a pattern that seems random on the surface, but once you put it through a "decryption" process, it is actually something else.  Not patterns that seem random because they are complex.

One example that comes close is DNA.  But I see DNA as a form of encoding, not encryption.


texts:
Are there multiple distinct genetic lineages of asexual species that are closely enough related to not be considered distinct or does any genetic change result in a new species?

I would assume there's tolerance for variety as much genetic material has either no phenotypical expression, or a very subtle one. It's also consistent with my understanding of differential antibiotic resistance. Normally I'd expect a large degree of acceptable differences as long as there could be reproduction that makes viable offspring, but that's obviously not applicable here.


texts: I am trying to find homologs for some proteins and I am wondering if it is better to find it by comparing the proteins or the coding genes or either is fine.


texts:
In the article "A Topological Paradigm for Hippocampal Spatial Map
Formation Using Persistent Homology" by Y. Dabaghian, F. Mémoli, L. Frank, G. Carlsson I read some sentences with huge confusion concerning the use of the termss firing and spiking. Do they mean the same thing? It seems to me that when they say a place cell is firing or a place cell is spiking they refer to exactly the same thing. The confusion comes from using both words in the same sentence as in the following sample sentences from the article (emphasis mine):

  Indeed, a rat’s path through a small space can later be re-traced with a high degree of accuracy by recording hippocampal spiking activity during its explorations and then
  analyzing the location, size, and firing rates of a mere 40–50
  place fields [...]

  To understand what algorithms the brain might use to decode
  hippocampal place cell firing, then, we should rely solely on the
  information provided by place cell spiking activity [...]

  It is, in fact, generally assumed that neurons downstream of the hippocampus interpret place cell spiking patterns based on co-firing [...]

  It should thus be possible to trace the emergence of topological information as more and more spikes are fired [...]

  There are biophysical variables (firing rates, spike amplitude, etc.) [...]


texts:
I read this in a paper

  Keller and Ross describe their greenbeard gene as an ‘outlaw’.
  Admittedly, the comment is only made in passing, but are they correct?
  In this context an outlaw is usually defined as a gene whose action
  favours itself, but opposes the reproductive interests of the
  individual organism. Where there are outlaws, natural selection at
  different loci is pulling the organism in different directions.
  Theoretically speaking, green-beard genes...

Yes: http://www.sciencedirect.com/science/article/pii/S0140175083901562

Basically loving your children is outlaw because it makes you sacrifice resources for your children. However, if your interest is defined as maximizing the number of children, then it's just your stuff working properly. Outlaw genes will be something that makes you die for a cause or stuff like that I suppose.


texts:
I found this young Eurasian Magpie in my garden:

He is just standing there, not doing anything. I believe he fell from a tree and can't fly yet and is just waiting for the feeding from his parents until he can fly, but I wonder if that’s true and if I should do anything to help.

There’s another young one on a branch of a nearby tree, also:


texts: Is molecular oxygen (O₂) consumed in any process (in humans) other than acting as an electron acceptor for the ETC?

texts:
I know that molecular oxygen (O2) serves as the electron acceptor in Complex IV of the electron transport chain, which maintains the proton gradient that produces ATP for, as far as I know, every cell in the human body.

Is this the only reason we need molecular oxygen for life, or are there other vital functions (i.e. necessary for life) that molecular oxygen serves within the human body?

Edit

For clarification, there are probably well over a million oxygen-containing compounds, from water all the way up to the largest proteins, which perform repeatable roles in basically every system of the body. But in cases where oxygen is exhausted, specifically consumed requiring a continuous supply of new oxygen, what roles does oxygen serve with the exception of serving as electron acceptor in Complex IV of the electron transport chain?


texts: Does "mind" has any physical reality in biology? Or is it just an assumptive concept?

texts: Biologically,  Brain controls our thinking,  ideas,  decisions everything along with controlling each body parts. My question is,  is there anything real as "mind "?  If it's controlled by brain then how does brain controls the mind?


texts: Insect Identification (even the family name would do)

texts:
I found this insect in Bhopal,Madhya Pradesh,India could you please help me identify it??
I think it is some kind of beetle. Approximately 2-3 cm in size.


texts:
I have a quick question regarding Vitamin A deficiency.

The photoreceptor molecules in both rods and cones have the same general structure which is retinal which is bound to a protein called opsin and depending on the photoreceptor opsin changes but the retinal is always the same. And it is the retinal that makes the opsin light sensitive and so it is highly important.

My question is, why is it that when researching the symptoms of vitamin A deficiency one of the most common ones is night blindness. I understand that if not enough retinal is formed not enough rhodopsin is formed and so the patient would suffer from night blindness but wouldn't it also mean that the patient wouldn't be able to produce enough of the other photoreceptors as well and so doesn't only suffer from night blindness but from complete blindness?


texts:
A common way to define species can be found on Wikipedia:

  A species is often defined as the largest group of organisms in which any two individuals of the appropriate sexes or mating types can produce fertile offspring

This got me thinking. Imagine the case where we have three "groups": A, B and C, where A and B cannot produce fertile offspring together (different species) but C can produce fertile offspring with both A and B.

Have this ever been observed? And how would you classify C?


texts: Movement of the Thoracic Cage During Movements of the Thoracic Spine

texts:
Just for a bit of context: I am trying to create a 3D digital model of the human skeleton as the first step towards computer generated muscle simulation, and as such I want the skeleton to be as anatomically and biomechanically correct as possible. However, I am currently struggling with the movement of the ribcage. I am quite capable in the 3D side of things, but without any medical background I've essentially had to learn everything about the skeleton so far from the ground up.

Whilst there is plenty of information on the internet about the movement of the ribs and sternum during inspiration and expiration, I haven't been able to find any detailed descriptions/diagrams/animations of how the various movements of the thoracic spine (lateral flexion, sagittal flexion and extension, and axial rotation) influence the positioning of the ribs, including in scientific papers (however I can't see that this topic hasn't come up before?).

The only thing I've found for this are three diagrams from this website http://body-disease.com/movements-in-the-thoracic-region/ (bottom right hand corner in each case):

Whilst these diagrams are definitely helpful in showing the general movements and shape, they don't really have the detail that I am looking for: for example the movement of the sternum isn't specified or the exact movements of the ribs and costal cartilage. These diagrams are a good starting point but I can't really work with them - as really I need to understand the four movements of each rib (torsion, calliper, bucket handle and pump handle) where they connect to the thoracic spine in order to create an accurate 3D model.

I would most like an accurate diagram or (even better) an animation of the spine movements with a complete rib cage; however X-ray images, sketches or anything that might provide more information would be useful. Descriptions are also great but as I'm not very experienced with anatomy I may not be able to glean as much information from text as I would from images. Essentially I am not trying to understand the concept of how the rib cage changes, but the specifics of this complex movement.

I know this might be quite a specialist topic (especially given the lack of online information) however I thought I would ask anyway in case anyone knew. Thanks for any information you can give me!

(Also let me know if I've made an error - this is my first forum question)

Edit: after some more digging I've found this image (from http://www.orthotech.ethz.ch/research/musculoskeletal-biomechanics/sarcopenia--implications-of-age-related-muscle-loss-for-spinal-p.html) showing thoracic flexion and extension, which may help in understanding the sorts of thing I'm after. the issue with this image is the fact that the movement of the sternum and costal cartilage is still very unclear:


texts:
What causes the elephants' ear to rip like this?

Is it a natural process as they get old, or it's injuries, like consequence of fighting with other elephants?


texts: Would current-day human-initiated panspermia be effective?

texts:
With current technology, we are able to easily send a probe to the Alpha Centauri star system at a speed of about 20 km/s (velocity of voyager probe), which means it would take about 65000 years to get there.

In light of this, suppose we sent a probe capable of delivering 100g of biological material to an Earth-like planet in α-Centauri.

  Are there organisms that:

  1) Could survive the journey, perhaps frozen or in a dormant state;

  2) Would have a fair probability of surviving in the barren oceans (or land if preferred);

  3) Eventually have a change of evolving to more complex lifeforms?

If possible, give a rough estimate of how likely you think that would be -- would we need to send 10 probes for a good chance, or billions of probes?

The lifeless environment seems to necessitate either photosynthesis or chemosynthesis to survive. But what about the necessary food (organic matter)? Would any of those restriction make it virtually impossible to achieve long term life with current goals?


texts: Which enzyme catalyzes transcription and which translation?

texts:
My attempt:

Transcription - RNA polymerase
Translation - aminoacyl tRNA synthetase

I know that the ribosome almost runs translation, but I don't think ribosomes are enzymes, which is why I went with aminoacyl tRNA synthetase.  Is this right?


texts: Elements that make action potential to conduct quicker?

texts:
The texts, online materials describe the velocity of conduction of action potential depends on axon's length and cross sectional area e.g. short length and large diameter decreases the resistance. Myelin sheath increases the speed of conductivity as well.

Can someone explain why chemical synapses allow quicker conduction than regular arrangement of sodium fast channels along the axon? Can regular arrangement of Na channels help in propagation of AP (I guess it's referring to the nodes of Ranvier)? What's the difference between fast sodium channel and a 'normal' sodium channel?

The question is: Of the following, which allows action potentials to conduct quicker?
1. Chemical synapses
2. Regular arrangement of sodium fast channels along the axon
3. Small axon diameter
4. Depolarisation suppression through the majority of the axon's length

I picked 2, but the answer is 1. I want to know the reason behind me being wrong and that being correct. 1 doesn't make sense at all to me. Come to think of it, I see that 4 could be the most relevant.


texts: Why can't complex multicellular organisms reproduce by regeneration?

texts:
My textbook says that regeneration isn't  possible in complex multicellular organisms.

But why? Why can't specialized cells be present in the bodies of complex multi cellular organisms which can proliferate and ultimately make a whole new organism, when (for example) cut in two?


texts:
About four times in my life I have experienced the feeling of my eyelid fluttering for a few minutes by itself, and then it stops.

I have talked to other people who have had the same experience so I presume there is no pathology.

Could someone please explain the physiology behind these random eye twiching experiences that I and many others have had?


texts: Are peanut proteins similar to chicken meat proteins?

texts:
I'm studying amino acids content in vegetable food. I was looking at peanut protein and noticed its similarity with chicken meat, as you can see in the table below (quantities are measured in grams). Third column is first column minus second column. Green amino acids are the essential ones.

The biggest difference (-1.11) happens for Lysine, but Lysine quantity (0.901) is still bigger than the lowest one, which is Tryptophan (0.2445). So in this case, is Tryptophan the limiting factor in protein synthesis? (Tryptophan amount is < than any other amount).

The table below lists the optimal profile of the essential amino acids (first column). Second column is obtained by dividing the values in table 1, first column, by 25.3055 and multiplying by 1000.

Notice that Lysine is the only one amino acid less than the reference (36<51).

So the questions are:

1) Have peanut proteins a limiting factor (if yes what is and why?) or can be considered a complete protein?

2) If the answer to 1) is "yes it has a limiting factor" what vegetable foods rich in lysine can be eaten with peanut in order to obtain all the amino acids? And how to calculate the ratio of peanut and the complementary foods to eat in order to get the proper profile of the essential amino acids?

Source for first table (first and second columns) https://ndb.nal.usda.gov

Source for second table (first column) http://nutritiondata.self.com/help/analysis-help

I'm not sure if biology is the correct site to post this question, so if you know a better one let me know, thanks.


texts: What are the genus and species name of different breeds of dog?

texts: Can you refer me to a good source containing the genus and species name of different breeds of dogs?


texts:
I'm new here and I would like to know if ants can see, I mean with their eyes not with antennas: I was walking around and found an ant specy,  they were reacting when I moved my fingers towards them, as if they were seeing.

I would also to know  do they have a "brain" and what I'm the most fascinated by is how do they find their way?

PS: English is not my local language that's why my vocabulary is limited. Please feel free to correct any mistakes and or improve my words. Thanks


texts: What are the enzymes with the lowest concentrations in a cell?

texts: Or are there any enzymes which are only translated one time per cell?


texts: Is there any strong factor against human edible plants being widespread and easy to gather?

texts:
While many habitats have plants, fruits, nuts and berries available for consumption by humans walking by, most places (if any?) seem to require significantly more effort than simply picking our food from trees and bushes in order to survive.

Borrowing @BryanKrause's words in a comment below:

"Why don't you find enough things like broccoli, green peppers, almonds, and wheat to support a human population when you are walking in the woods/natural fields?"


texts: Endophytic Xylariaceae: diversity and taxonomy inferred from rDNA sequence analyses

texts:
"Thailand is considered as one of the areas containing a high percentage of unknown taxa of Xylariaceae (Rogers 2000).  In Thailand, several studies on endophytic fungi have been documented, namely, from several bamboos (Luyong et al. 2000), banana (Musa acuminata) (Photita et al. 2001), monkeypod/rain tree (Samanea saman) (Chareprasert et al. 2006), and several xylariaceous endophytes were also reported from those plants."

Review quoted from Izumi okane, Prasert Srikitikulchai, Kyoko Toyama, Thomas Laessoe etc. Full Paper; Study of endophytic Xylariaceae in Thailand: diversity and taxonomy inferred from rDNA sequence analyses with saprobes forming fruit bodies in the field.

Have any of you known the similar cases (the high percentage of Xylariaceae) in the USA, France, or UK, proved by reference(s)?


texts: Is it technically possible to make someone see something when their eyes are closed?

texts:
I'm writing a little article and need any information about how human vision works and latest
technologies and discoveries around. Actually its not a professional article. Its for a group of my friends.

In fact I'm looking for any possible way to make someone ACTUALLY see when their eyes are closed. I don't know maybe convince some of brain cells that a real pulse is coming from eyes, but in reality its coming from a computer; or something like that.

I call it a virtual vision, myself.

Do you guys know if there's any professional article, discoveries or technologies available about this topic?
I'm very very interested in this topic by the way.


texts: It is common practice after surface staining cells for flow cytometry analysis to wash the antibody out of solution before analyzing a sample. I have tried analysis with and without washing the antibody out and notice no significant difference by flow. So is there a reason people do this step that maybe I'm just not noticing?


texts:
It's my understanding that fevers are an immune system response to infection. Like the body's cells can take more heat than most viruses or bacteria.

So if that's the case then can you even get a fever if you have a non-functioning immune system due to AIDS?


texts: How to clone and sequence a gene transcript of unknown sequence?

texts:
How might I go about amplifying a gene transcript (mRNA) from animal tissue of which little is known about the genome? In some applications, I have used reverse transcriptase PCR to amplify all mRNA transcripts from cultured cells, but this required that I knew the sequence to PCR amplify.

How do I go about this without knowledge of the gene or transcipt?


texts: Why so fewer birds in the yard come late summer and early autumn?

texts:
We've enjoyed watching birds in our yard this past summer. We're in a suburb, fairly forested, inland northeastern USA hardiness zone 5. As we scaled up the amount of diversity and net primary production around the house, and added a bird feeder, we notice an uptick in various kinds of wildlife. However, we're surprised to see a stark decline in the amount of birds starting around late summer/early autumn.

What could cause the sudden decline in birds in late summer? Is there a migratory trend starting up around this time; it seems early to me for birds to be flying south?

The birds in question include a family of cardinals, occasional blue jay, downy and hairy woodpeckers mid-summer (some are still around), many various sparrows, yellow finches, chickadees, et al.

We continue to fill the bird feeder as usual. We haven't changed anything about our yard routine. We have a rescued feral cat which goes outside and hunts despite our efforts to stop it, and it has killed many mice and a few chipmunks mid-summer, so perhaps the birds have become wary of him and the dead bodies of small mammals left in forested edges around the yard.


texts: What is the human ear's temporal resolution?

texts:
What is the smallest sound duration that the human can hear? In other words, what is the lower duration limit for a sound to be translated into electrical signals by the ear?

Suppose the human ear can discern or distinguish between 18 kHz and 20 kHz sounds, this would mean that, if a single wave could  be processed at 20 KHz, the sound duration would be 1 / (20KHz) = 0.00005 second, which would be next to incredible (and probably impossible).

I am particularly interested in the lower duration limit as depending on frequency.

I am expecting something like this (I am not sure)

 Freq   Duration needed to be aware of the sound
 20KHz  0.05S (50 mS)
 10KHz  0.04S (40 mS)
  5KHz  0.03S (30 mS)
2.5KHZ  0.02S (20 mS)


texts: Evolution theory - roses spikes - being more bulgy doesn't give you advantage

texts:
I've seen spike, huge spike. And I thought that development of such spikes could be contrary to the evolution theory.

Being „little more” spiky doesn’t give you any advantage... So those individuals having one won't have smaller mortality rate than those with smooth stem.
Even more, the individuals with bulgy (more spiky) waste resources their ruggedness and have more things to feed, which should mean that they would have higher mortality rate.

So I can see no way to develop spikes on the stems of roses according to the evolution theory which embrace "small improvement". Spike is only efficient (to deter aggressor) when it's very sharp, it's either sharp or it isn't - there is little in between.

Could anybody tell me that this is bullshit (and why it is bullshit), and that I should us believe in Darwin competence?;)


texts: Mechanism of Tear Gas (chloropicrin/Trichloro methane)

texts: Tear gas (CCl3NO2) makes people cry, and crying doesn't seem to be a simple procedure. There has to be a triggering process somewhere. Can someone explain its mechanism / how it works?


texts: Is there a family equivalent to "congener"?

texts:
Is there an equivalent word to "congener" but for species in the same family (family in the sense of the taxonomic rank)?

"confamer"? "confamiler"???

I know I can just say "species X and other taxa in the same family" but I thought a nice one-worder would be better if anybody uses such a word.


texts: Does the light color spectrum and frequency matter for photosynthesis?

texts: Do plants grow differently when given sun light, wolfram lamp, fluorescent light, LED light, infrared, ultraviolet, x-ray, unfocused laser and stroboscope?


texts: Hybrid seed production requires a male sterile parent. Why?

texts:
Hybridization is the process of crossing two plant species or varieties. In this case, two varieties of plants. In plant breeding, crossing is a very useful technique to improve the features of the offspring. For example, if a maize corn variety has lost yield over the years, it can be crossed to a variety with a higher yield and the offspring will also have a higher yield.
In order to cross these two varieties, the male needs to be sterile. Why is that? I don't understand how the process works and I cannot find the reason anywhere. The answer should be pretty basic, and I think I am missing something that everybody assumes I should know.


texts:
My state (Tripura) originally had a mostly mongoloid-feature-possessing population (ethnic group: Tripuri). Recently a large number of non-mongoloid people (ethnic group: Bengali) have migrated to Tripura.
Assuming that reproductive barriers are not present between these two subpopulations in future, are epicanthic folds likely to be a prominent feature of the new hybridized population?

I've found some non-scientific discussions here and here.

In this newspaper article, an anthropologist is cited as saying the following:

  Poirier attributes the fold to pleiotropic genes--single genes that control more than one characteristic or function--but he has no explanation for its origin


texts: Arabidopsis thaliana RCSB active site gene mutant

texts:
I'm looking for an Arabidopsis thaliana gene listed in RCSB with a clear mode of function and active site. In addition it needs to have an obvious phenotype when knocked out like severely retarded growth, lethal or near lethal. The gene also has to be exclusive to plants so RNA polymerase wouldn't work.
I found this paper in plant physiology but I'm having trouble finding those genes with an obvious active site.
Thank you very much


texts:
I have found these tiny ant-sized black bugs on the floor that are a little hard to kill; I have to hit them with so much force otherwise they stick to the back of my sandals alive! or i have o squeeze them hard between the Kleenex.
Can anyone identify these please so i know how to get rid of them.
I live in Asia, Iran by the way, thanks.


texts:
Why ATP synthase EC number is 7(Translocase)?
My textbook says it's a hydrolase but when i checked its EC number it was changed to 7.
And also ATPase(adensointriphosphatase) page that was previously classified as hydrolase is deleted in qmul.ac.uk


texts: How long does it take a leech to attach?

texts:
How long does it take a hematophagous leech to attach?

Specifically, how dangerous is drinking water which might be infested with leeches?

Presumably, once the leach enters the stomach, it will be quickly dissolved, so the only danger is that it might attach in the mouth or esophagus. Can this actually happen?

(should I ask this elsewhere?)


texts:
After searching online for peptide mapping to my understanding it can be treated as the fingerprint of the protein. It is obtained at the end of several chemical processes and it helps to understand the protein being analyzed.

Does this method operate in "sequence space" then? If so, what exactly is the relation of the two?


texts: Research from the early molecular genetics era that supported protein as the primary carrier of genetic information?

texts:
I can't seem to find anything on my own. Surely there were experiments performed (possibly using bacteriophages) that managed to come to this conclusion?

Specifically I'm interested in anything pre-Hershey/Chase.


texts: Which is better against genetic mutations? Asexual or Sexual Reproduction?

texts: In terms of genetics, which type of reproduction is better against adverse mutations? I understand a bit of Muller's Ratchet—in which asexual organisms accumulate a number of deleterious mutations in their genomes. However, doesn't the crossover process and corresponding genetic diversity in sexual-reproducing organisms make them more susceptible to these mutations?


texts: Does the biosphere have infinite resources and are they infinitely renewable?

texts:
Does biomass represent all of the resources of the biosphere and therefore it would be theoretically infinitely renewable (as long as we have the sun) since all the biomass is part of the carbon cycle?

Also, should I consider resources like gold to be part of the biosphere and therefore all the resources would not be infinite nor infinitely renewable?


texts:
I live in east Tennessee. I went outside today (May 27.2017) and saw all these tiny insects all over my truck.

They are yellowish in color and have 6 legs, one solid body (including head). They move pretty quickly (like a chigger)

What are they?


texts:
Articles commonly state examples of carbon sinks are plants, soils, and oceans (e.g., link). My understanding is that carbon sinks must directly take up carbon from the atmosphere. Therefore, other organisms such as herbivores and carnivores are not considered carbon sinks (I understand their roles as carbon sources) although they store much carbon. Is this interpretation true?

If so, what is the main mechanism that soils (independent of plants) directly absorb carbon from the atmosphere? It looks as if most articles simply say that soils contain much carbon from plant organic matters, which is a carbon store rather than a carbon sink.


texts: Can men with Klinefelter syndrome produce chromosomally normal sperm?

texts:
Individuals with Klinefelter syndrome are XXY. Even though sperm counts are low some individuals can generate enough to be used in IVF and have offspring.

Does this mean that when sperm are formed, the process works correctly to separate all 3 of them and only sperm with a single sex chromosome are formed?

(Excluding same genetic issues happening again of course)


texts: How to find ion/water channel related genes

texts: We now have a collection of transcripts at hand. We would like to investigate some particular ones, which are ion/water channel related. How to perform this? Could anybody point out how to find the annotated genes those are ion/water channel related? If there are some places particularly for fish, that would be perfect. Thanks.


texts:
We all know that females have an inactivated X chromosome (Most of its genes are inactivated).
Consider a female who is a heterozygous carrier of an X linked abnormality,
If the inactivated X was that carrying the normal gene, shouldn't the abnormality be expressed in this female? Why is it not expressed even though the other X is inactivated?


texts: Cheap enzyme assay for a high school lab

texts:
At the moment, I'm designing an experiment for a high school lab with no financial resources. I need to assess the impact of a variety of factors on a specific enzyme's reaction with its respective substrate and determine the rate of reaction. Normally this would require some combination of an assay kit and a plate reader. Though cheaper versions of the former are within my budget, the latter is not.

What are the cheapest ways you can think of to:

1) Get access to enzymes and the substrate;

2) Make them react in a controlled manner;

and 3) Assess the rate of reaction from the resultant substance?


texts: How medical studies induce cancer in lab animals?

texts: To test the effectiveness of drugs, they are typically tested on animals. How cancer is induced in lab animals to test the effectiveness of cancer drugs?


texts: What is this long, thin and segmented insect I found in my house in India?

texts:
Found this inside my house, along the wall, there were few going somewhere few distance from each other.

I suspect it is a centipede but didn't found similar images on Google. What is this?

Location: Mysore City, India.

Size(only which I saw): the one in the image is about half centimeter, and the smallest one was less than 1/4th of a centimeter.

Color: the one in the image is kind of brownish I guess and the smallest one's are nearly white (pigmentless?)

We assumed this thing is kind of larva of cockroach or big white ant. Is this fully grown insect or still it is a baby? These were behaving like ants do.


texts: How many ommatidia does a honeybee have?

texts: European honeybees (Apis mellifera) have compound eyes made of tiny facets called ommatidia. The number of ommatidia is usually known in most model insects, but I cannot find reference for the European honeybees, despite bees being highly studied. How many ommatidia does a European honeybee have on average?


texts: How did mosquitoes expand their habitations to a place they never lived before?

texts: So, in the region I live, we have some sort of like a "mosquito zone", spanning for thousands of Kilometres, this is the place where you will normally find lots of mosquitoes, and this has been so for years and years. But last year, we were surprised to see that the mosquitoes have "invaded"a village which has never experienced them even once. The village though, is at the border with what I call "mosquito zone" but never has these insects "visited" this village. So I became curious to know, what has happened so that the mosquitoes said "now let's invade this village and live there"? I can't see anything suspicious that has changed. Do we have any explanations?


texts: Can gut flora affect what we can eat and what we cannot?

texts:
Back many years ago, I've read a mushroom guidebook, which I don't have anymore. I was unable to find the name of a particular mushroom. The book comprises listing of edible and poisonous mushroom species. One particular mushroom was said to be "poisonous to some people". the effect is not allergy-based, but rather straightforward poisoning. What drew my attention was the phrase:

  If you haven't tasted it before, do so in small doses first. Each family member has to do it regardless of how other family members responded, because the condition is not genetic

This has lead me to think, that if condition is not genetic, then it may depend on which gut flora you have. Gut flora is very helpful in digesting many substances in our food, and possibly even toxins. This has lead me to ask the question Can a human be inoculated with gut flora from another animal and thus be able to eat food otherwise poisonous to humans?

Supporting evidence:

I have read that pronghorns can browse on sagebrush, a herb that is poisonous to ordinary cattle. The toxins kill the cattle's gut flora, that is supposed to aid in their digestion. It is not, however toxic to the pronghorn's gut flora, which can digest the toxins.
Changing your diet abruptly may result in embarrassing stomach upsets. These upsets are transient, however. This may reflect a change in the ratio of bacterial species which reflects optimal adaptation.

Putting that theory to the test:

Attempting to inoculate Pronghorn's gut flora to cattle -- Will the cattle be able to feed on sagebrush?
Diversity of gut flora in humans: One may expect some difference in gut flora between that of city dwellers, such as in Europe, and that of tribes in the rain forests of the Amazon and Africa. Can a city dweller in Europe eat anything the forest dweller may eat? Does he/she need some bacteria inoculation to adapt to certain foods?

Limitations

Not all poisoning cases may be avoided by introducing gut flora that is supposed to digest the toxins. Failures to avoid poisoning may include:

Poisons that are absorbed by the body and the animal eating the plant or mushroom is not affected by it. Floral gut from the animal will not avoid that type of poisoning in a human eating the plant/mushroom.
Poisons that are digested by the animal's own digestive enzymes.
Environmental incompatibility: The introduced bacteria must be compatible to the type of food the host feeds on, as well as the chemical environment of the guts. For humans, this limits us to gut flora extracted from animals with diet similar to ours (Not counting processed food and cooked food). Ruminants and predators are out, Omnivores are in.
Poisons that an animal avoids by excreting it rather than absorbing it, and the bacteria does nothing in digesting it.
Host compatibility: The introduced gut flora must do its job in the guts, and not turn against its host. In turn, the host's immune system must "leave it alone".

DISCLAIMER -- a somewhat-related breakthrough research is underway at the Weizmann Institute of sciences. Conditions such as diabetes, Krohn's disease, obesity, resistance to infections, behavioral and psychiatric tendencies among others were once considered issues on their own, and unrelated to gut flora diversity (or lack of). This research shows otherwise. The research even includes a custom diet which is unlike common diets. Rather than counting calories, your diet is tailored to suit the type of gut flora you have. You may assume that some bacteria may secrete toxins which cause organ damage, such as kidney, liver or pancreatic failure. The healthy gut flora may keep those harmful bacteria in check. On the other hand, it is possible gut flora may digest some of these toxins before they are absorbed by the body.


texts: Can Dpn1 digest hybrid PCR product with only one methylated strand?

texts:
In Site directed mutagenesis using PCR, after a cycle we obtain a hybrid molecule with one parental strand and other newly synthesized unmethylated strand. This is followed by Dpn1 digestion. Does this digestion just cut the parental strand leaving behind single strand of newly synthesized product?
Does this means that Dpn1 can use ds methylated DNA( both strands methylated) as well as ds hybrid DNA (with one methylated strand and other unmethylated strand) as substrate?


texts: Gene terminology - is one gene a concrete, single physical sequence?

texts:
Suppose you have two identical copies of the same, coding nucleotide sequence (e.g. two copies of BCL2 - a random gene I found on Wikipedia).

Could you say that these are two genes (i.e. the name "gene" refers to a specific, physical sequence, and where there are two of them, you have two genes, even if identical)? Or just two molecules of one gene (in the same way that when you have two molecules of carbon dioxide, you can't say that they are two carbon dioxides)?


texts: I don't wash my hands and never get sick. Any theories?

texts:
I have only been sick a few times in my life(I'm 21 and probably 3-4 times) and even when I am sick I don't feel that bad and I am over it within a day or two. My family has always given me slack for never washing my hands but I see no point unless they physically look dirty. Unlike me though my family gets sick around the same amount as other people(a couple times a year).

I have this theory that since my body is always exposed to germs and other bacteria that it is stronger and able to fight off most colds before they ever happen. This theory obviously contradicts popular opinion and what doctors recommend but I have always felt fine not washing.

What do you guys think?


texts: Advantages and disadvantages of sporulation compared with competence in bacteria?

texts: Why do bacteria have both of these mechanisms to deal with the same environmental stress: nutrient deprivation? In a culture exposed to this condition, often both competent cells and sporulated cells are found.


texts: I always feel more afraid in the dark than in light conditions. Is this a common phenomenon in all the people? Does it have biological underpinnings?


texts: Plant growing very rapidly near my house

texts:
please see attached photos of a plant, that is growing rapidly near my house. All my friends failed to classify this plant. Can any botanist/biologist help to discover the species of this plant?
Thank you in advance!


texts: How do neurons receive the ions needed for creating electrical pulses?

texts: I really wonder how ions are transported into the brain and the neurons for creating electrical potentials - how do ions get from our digestive system to the neurons? Or are the ions just freely released into the brain like hormones? Or are they transmitted during neural signalling somehow (via neurotransmitters maybe)?


texts: What is the primary energy source for sprouting plants?

texts:
To what extent are young plants powered by the potential energy stored in the seeds and when does solar energy take over? Are there other energy sources involved?

I was observing sprouts in a germinator [is this a word?], pushing up the lid after being left alone over three-four days. As this is a considerable amount of work (for such young plants) I wondered how long the plant can access the original energy stored in the bean/seed and how it compares to the amount of energy it can get. As you can see in the picture, the sprouts have only access to water and some sunlight.

I suspect the potential energy it draws somehow decreases monotonically (perhaps linearly, quadratically, exponentially?) over time, while the solar energy pics up.

Is this mental model correct?
I'd appreciate an answer that a non-expert can understand.

I think these were radish sprouts, but my question is more general.


texts: Specified effect of trans cranial electric stimulation on neurotransmitters

texts: Can a specific voltage from a trans cranial stimulation activate specific neurotransmitter receptors or channels? By specific, it means receptors dedicated to specific neurotransmitters such as acetylcholine, dopamine, etc.


texts: Why don't phospholipid bilayers dissolve?

texts:
I just started learning about the structure and composition of cell's membrane and there is something that I fail to understand.

The membrane is composed of a phospholipid bilayer. The phospholipid has a polar, hydrophilic head and a nonpolar, hydrophobic tail. My question: Why doesn't the hydrophilic head dissolve in the extracellular fluid outside the cell? I suppose that the extracellular fluid is watery, so how come that the water-loving head doesn't interact with the water from the extracellular fluid?


texts:
I have heard about existence of full brain connectome data of some worms or fishes. I have heard about GEVI - genetically engineered voltage indicators - that allow to see voltage data at subcellular level. My question is: are there available the mentioned data in processed form (approriate for simulation, mathematical analysis, modelling) and, possibly, are there available some analysis and modelling of them? I am searching materials for neural code that is used in brains and those data and analysis would be very helpful for me.

I am aware of enormous body of coarse resolution MRI imaging data. But my question specifically targets connectome/neuron/subneuron level full data and their analysis.


texts: How to predict the effect of a non coding SNP variant on the expressed protein?

texts:
I am writing a paper for non coding SNPs on patients with metastatic breast cancer. Having used a specific gene panel (NGS) of approximately 60 genes, I'm currently running out of ideas on what to write in the discussion section.

I am looking for suggestions based on somewhat efficient methods like a bioinformatics approach or specific textbooks revolving around RNA biology/biochemistry, in order to predict the outcome of non-coding SNP variants.

Some details:

The majority of the variants are intronic (~2300/3300), so I will mostly focus on splicing.
There are two commonly repeated SNPs in 3'-UTRs in over half of the patients, involving KRAS and CDKN2A.


texts: Do proteins contain phosphorous? If its true then how alfred hershey and martha chase used the statement that proteins do not contain phosphorous?

texts: I hv heard about phosphorus that it is a constituent of certain protein, although we know that no amino acids have phosphorus... and if its true then how Alfred hershey and Martha chase experiment got acclaimed whose base of the experiment was that "protein doesn't have phosphorus"??


texts: How do plants maintain air spaces in leaves?

texts:
As we know, there are air spaces in the mesophyll layer which allows carbon dioxide to diffuse in and oxygen to diffuse out, but cell membranes are partially permeable and allow water to diffuse to regions with lower concentration. Yet these air spaces still manage to not get flooded by liquid water.
How does this happen?


texts:
As far as I know, Fishing has been one of the important occupation since early ages, and infinite number of fishes have already been captured.

As the time passes, they must've developed some sort of knowledge about the fish-nets, and should've figured out a way to escape from them. But, still now, we are able to capture them at the same rate(I guess)

So, Are they developing any sort of hereditary memory to escape from us?

P.S. I'm not sure whether this is the right SE to ask.


texts: Effect of UV radiation on retinoid (vitamin A) receptors in the skin

texts:
The retinoid receptors in the skin (face) can be disabled by UVA sun radiation as these study states : https://www.sciencedaily.com/releases/1999/03/990331063314.htm

In this article it says the same : http://www.abc.net.au/news/science/2015-11-18/how-uv-light-damages-our-skin/6856742

  " UVA activates receptors that produce the enemy of firm skin: matrix metalloproteinases. These enzymes have one job and they do it beautifully: breaking down collagen. And it doesn’t take much UV at all to get this going, so even without sunburn any parts of your skin that are exposed to the sun will age.

As if the collagen attack wasn't insult enough, UV radiation also interferes with the production of Vitamin A receptors on our skin cells.

Vitamin A is critical for cell growth in our skin, but without functioning receptors for the vitamin to activate, our skin ends up thinning, and that’s something no amount of carrots can fix.

Question is: do these receptors actually work again after sun exposure is stopped? Or any topical/oral treatment with vitamin a will be useless for skin regeneration?

Thank you


texts:
I was talking to my science teacher about the body specifically the red bone marrow.

She said that blood is created in the red bone marrow. Does that mean that if you were to cut a fresh bone open it would bleed?


texts: What are the interactions between mtDNA and nucelus' DNA?

texts:
In an exam situation I have been presented with the following question by the teacher:

  What are the interactions between the mitochondrial DNA and the cell's nuclear DNA?

To my knowledge there is no such interaction. At the best you could say that the nuclear genome provides the mitochondria with some proteins and vice versa the mitochondria may participate in intrinsic apoptosis by releasing cytochrome C. Unfortunately this answer was not accepted by the teacher and I was not given an explanation. My question is wheter there is an actual interaction I've never heard of or if maybe the poorly worded question was alluding to something else.


texts:
I found a a few of these guys on my composter, so they could have easily been eating bugs or decaying organics (or both):

To me it looks like a stink bug with oversized legs, not like the ones I'm used to seeing. His body measures just under 3cm, and I haven't pulled on his legs to get a measurement (I haven't pulled on it at all).  The legs seem to be at least 1.5 times the body length as do the antenna.  The body is grayish brown and the antenna and parts of the leg seem reddish brown.

I'm a microbiologist, so things big enough to see in a jar are not really my specialty.  That said, here's info that I've been trying to use ID it:

Wingless Normal compound forelimbs (don't seem to have any kind of   prey modification)

Segments filiform antenna (I think)

2 Tarsomeres (I think)

In the middle of South East US

Have had (unusually) heavy rains

Underside of the limbs and antenna seem red, but to seems gray

I've never seen it before! (and I usually notice such things).

Update: Despite my 4 year old putting other bugs and some leaves in with it, the bug died.  I took the opportunity to get some much better photos, and low and behold when I started manipulating it I was able to pull out a substantial rostrum that I missed!  These guys are good at hiding those.  So going back to assassin bugs, can anyone id which assassin bug it is?

More photos: [I would add more but I think this should be plenty]

I at least think it's quite a pretty specimen (to betray my mammalian aversion to bugs).


texts:
In some proteins (such as 4ZXB, 6CE9 which are respectively apo and halo forms of insulin receptors), I see ligands such as FUC (ALPHA-L-FUCOSE) and NAG(N-Acetylglucosamine). No matter which paper I checked I see no explanation for these ligands and therefore I assume they have to do with the experimental procedure but I do not quite understand what is their role. Do they stabilize a particular state of the protein? Note that the proteins above are determined by different methods the first one X-ray crystallography and the second by electron microscopy. I have no technical knowledge about the neither method so any input or link to a paper that actually explains them would be appreciated.

Thanks


texts: Name of dsRNA (or dsDNA) where all strands are identical

texts:
What is the name of dsRNA (or DNA) where all component strands are identical (i.e. where the complex consists of multiple copies of the same ssRNA)?

Example: 2 identical ssRNAs forming a dsRNA

C C G C G G C G G
| | | | . | | | |
G G C G G C G C C

Furthermore, is there a different name for it depending on the degree of complementarity (full Watson-Crick complementarity vs. full complementarity with non-Watson-Crick basepairs vs. lower complementarity due to bulges etc)?

My thoughts

You probably wouldn't say "RNA homo n-mer" (for the example above "homo dimer/2-mer") since I assume that would be referring to a 2-nucleotide long ssRNA?

Can you use the terms dimer, trimer, tetramer, 5-mer, 6-mer etc in multiple ways; (a) referring to the binding of nucleotides to each other to form a polymer/n-mer of nucleotides i.e. polyribonucleic acid, and (b) to whole ssRNA or dsRNA binding to each other to form a "dimer"?

You also probably wouldn't refer to it as a "homo duplex" since that refers to  something related to chromosomal crossover.


texts: What can you tell about a person, having only their whole genome as information?

texts: Well, the question is in the title, no explanation need.


texts: Have any genetically altered organisms actually become abundant in a natural environment?

texts: Most of the things that come up in Google and Google Scholar for this question have a mostly/completely speculative tone, or at best use models instead of measurements. This report describes some actual measurements in pollen transfer to neighboring fields from GM fields, though they all seem to have been one-off measurements at some unknown time after the GM plants appeared, rather than investigations on if the genes are becoming more common over time, which might imply the ability to become unavoidably common in some environments or even a weed/pest/parasite. This doesn't seem like an obvious problem to me, because the traits associated with those genes are always meant for the context of being farmed or raised by humans and therefore probably wouldn't contribute more to fitness in wild populations relative to the wild alternatives of those genes, but a few counterexamples would smash that belief to bits.