texts: Games with non-uniform interaction rates

texts:
Background:
Many models in evolutionary game theory assume uniform interaction rates. For instance, consider the $2\times 2$ game:
\begin{array}{l c c}
    & A & B \\
    A & a & b \\
    B & c & d
\end{array}
The fitness of the strategy $A$ is $xa + yb$, where $x$ and $y$ are the frequencies of the strategies $A$ and $B$, respectively.

Taylor and Nowak "Evolutionary game dynamics with non-uniform interaction rates" (link to the paper) rewrite the fitness function to allow for non-uniform interaction. In particular, the fitness of the strategy $A$ and $B$ become:
\begin{equation}
f_{A} = \frac{ar_{1}x + br_{2}y}{r_{1}x + r_{2}y}; \quad f_{B} = \frac{cr_{2}x + dr_{3}y}{r_{2}x + r_{3}y}
\end{equation}
According to this model, ``[a]nalogous to a chemical reaction, an $A$ player interacts with another $A$ player with reaction rate $r_{1}$, an $A$ player and a $B$ player interact with reaction rate $r_{2}$, and a $B$ player interacts with another $B$ player with reaction rate $r_{3}$." (p.244).

Question: What would be an intuitive interpretation of $f_A$ and $f_B$ (as defined by Taylor and Nowak)?

Further comments: When $r_1 = r_2$ and $r_2 = r_3$, we have the situation with uniform interaction. But I am not sure how to interpret the above fitness function for when $r_1 \neq r_2$ (and $r_2 \neq r_3$). I thought of interpreting $r_1$ and $r_2$ as the conditional probabilities $P(A\mid A)$  and $P(A\mid B)$. However, if I'm right about this, $f_A$ would have to be  $r_1 a + r_2 b$ instead. For this reason, I am under the impression that the $r$s should not be conditional probabilities. But if the $r$s are not conditional probabilities, what are they exactly?


texts:
How is the breakdown of lactose regulated at the gene level?

This is my answer: Without lactose in the cell, the repressor protein binds to the operator and prevents the read through of RNA polymerase into the three structural genes. When there is lactose in the cell, lactose binds to the repressor. This causes a structural change in the repressor and it loses its affinity for the operator. Thus, RNA polymerase can then bind to the promoter and transcribe the structural genes.

But I'm not sure if this is right...


texts: Can someone tell me what kind of reptile is this?

texts: It was found in El Paso Texas. It was very scared and weak when I found it. But I bought it a small aquarium and some food to make sure it’s ok before I let it go. It’s tail is broken off. It have blue and yellow dots on top of it and I think it’s a male. Can someone tell me about this lizard?


texts: Where to obtain metabolic pathway datasets

texts: I've been looking through the files available at www.reactome.org along with some others but I only find images/pdfs of metabolic pathway diagrams. Where is the actual data these pathways are drawn from? I imagine there should be some kind of directed graph representation. I'm limited to freely available datasets, so unfortunately I'm not able to check out those such as KEGG.


texts: Can someone identify this tree in Playa Del Carmen, Quintana Roo, Mexico?

texts: I just noticed this tree in Playa del Carmen in Yucatan. It was swarming with bats, the bat seem to be eating either the fruit or the flowers of the tree. Any idea what it is?


texts:
I understand that they are generally "vented", but why such a poor fit? For the batch I bought, the lid and container don't even recognizably go together (like 1/2" difference in diameter). The wind from a box fan could blow the lid off. Even "non-vented" designs appear to have no positive connection between the dish and lid.

Then it looks like the people that do need a positive connection or a seal have to go through a lot of work with tape or wax to seal them.

Seems like a petri dish lid that has a snap, thread, bayonet, or even just friction fit, would be superior. The manufacturing cost differences would be negligible. What am I missing? Thanks!


texts: What is the difference between tissue engineering and 3D bioprinting?

texts: 3D bioprinting is the modified version of the tissue engineering but when we want to describe the both terms, what are the basic criteria or points to make difference between these?


texts:
I saw a very tiny black bug crawling over my computer screen the other day. Having recently acquired a "fingertip microscope" for smartphone, I started investigating.
On a white paper it seemed like a small black dot. I think its in the 0.3 - 0.8 millimeter range.
It would have been fairly unnoticeable if it weren't for it to crawl over my screen.
What could it be? I was thinking about dust mites, but they say it should appear as white. So I'm not entirely sure.
I live in Western Europe.
Note: don't look at the scale. It is wrong.


texts: What prevents mRNAs that are localized to a specific part of the cell from being translated before they reach their destination?

texts:
One of the methods of mRNA localization, for example, is random diffusion of mRNAs where the mRNA binding proteins are localized to a certain part of the cell. However, I was taught that the ribosome can translate mRNAs before they've even finished being exported from the nucleus. So what stops localized mRNAs from being translated all over the cell before they reach their designated location?

I was thinking maybe they're bound by hnRNPs that inhibit their translation, which dissociate when they're bound by localized mRNA binding proteins, but I could be wrong.

Or is it that they are translated all over the cell, but the concentration at their locale is just way higher in their locale?


texts: What controls the southern range of willows?

texts:
Many willows (Salix spp.) grow in northern states but do not grow in southern states, for example Salix viminalis.

What mechanisms control the southern range of temperate hardwoods such as willow? Is it disease? Temperature sensitivity of respiration? Water use efficiency?


texts: What material is permeable for plant roots, but "impermeable" for fungi & bacteria?

texts:
I'm designing an experiment where the roots of the plant will grow in a sterile environment while the shoot will grow in a non-sterile grow room. For this reason the environments of the shoot and the root should have some form of physical separation.
Is there any material that allows roots to grow through it but will stop fungi and bacteria?


texts: What is the X-chromosome responsible for?

texts: I understand that the X-chromosome is responsible for certain disorders, like red-green colorblindness; but besides disorders, what do the genes on the X-chromosome determine?


texts: Does medication make the body dependent?

texts:
First of, I know of course that certain medication can cause an addiction if incorrectly used. But as far as I understand it, drugs prone to cause addiction have some agent in it, that makes them addictive.

What I am interested in is a bit different though: If a drug "helps your body" do something your body can not or only insufficiently do alone, does it get dependent on this drug, even if the drug does not have addictive substances in it?

Or in other words: Can the human body unlearn something because of the fact that medication helped it do it for some time?

Edit: To make the question a little more clear, I can give the following example: I recently received medication containing Etilefrine, which contracts my blood vessels and thus prevents me from fainting in certain situations. If I take this medication regularly for a year and the suddenly stop it, could it be possible, that my blood vessels "forgot" how to contract on their own?


texts: Can someone tell me the species of this lizard?

texts:
It's a green lizard with a silver tail, and it has pretty, bluish eyes. I saw it today, July 26th, trying to get some shade on a hot, sunny day (32 degrees) at around 18:00 in Austin, TX USA. It's been hot and dry here the past few weeks, but it rained a lot a few months back.

Austin has a humid subtropical climate. The city is characterized by hot summers and mild winter days and usually cool to cold winter nights. The geo coordinates are 30.4 (lat), -97.7 (long).

Oh, it was able to jump a good meter.

Thank you.


texts: Modern research or study on patterns in nerve signals

texts:
I am trying to find any recent study on pattern recognition in nerve signals. It does not really matter the part of the body where the research is focused on. It can be anything from studying activity of one group of nerves to signals coming from an entire limb.

I was only able to find old (1996) research, which could be much more complete with the modern advancements in computing and manufacturing of micro-instruments. Here is an example of an old paper.

P.S. I am generally looking for information on how nerve signals differ within multiple subjects of same specie. For example, how would nerve response to a stimuli differ for two mice from same offspring and how will they differ from it's parents.


texts: Are people genetically predisposed to being interested in specific fields/ideas? How does specialization occur?

texts:
I'm not sure if I formulated my question well, but I'm curious about a couple statements made by Steven Pinker and and James Heckman.

In this interview: http://www.youtube.com/watch?v=KJ9Ad6s8g7I&t=7m51s Steven Pinker says

  "there'd be a wide variety of families I could have grown up with and
  had the same kinds of interests"

and in this interview with James Heckman, he says:

  But anyway, Smith says people are basically born the same and at age 8 one can't really see much difference among them. But then starting at age 8, 9, 10, they pursue different fields, they specialize and they diverge. In his mind, the butcher and the lawyer and the journalist and the professor and the mechanic, all are basically the same person at age 8.
  This is wrong. IQ is basically formed by age 8, and there are huge differences in IQ among people. Smith was right that people specialize after 8, but they started specializing before 8.

Can anyone explain Heckman's statement that people "start specializing before 8"?

What do we know about genetic influence on interests? (Is this the right stackexchange to ask this on?)


texts:
I would like to know in deep how exactly is the wood fossilisation process. I am fascinated how after millions of years the fossil wood preserves its microscopic characteristics. Look at this cross section where you can see clearly differences in the cellular tissues as parenchyma, vessels, and rays.

I know that in the fossilisation process the wood was replaced by mineral particles, but I don't understand how the organic material went outside to stay only the minerals.


texts: How do bile salts affect lipase activity?

texts:
BACKGROUND: It is well known that bile salts are needed for emulsification of fats. It is then said that this increases the surface area for activity of pancreatic lipase, implying that bile salts make pancreatic lipase more effective. But it is also said that pancreatic lipase do need a colipase to overcome the inhibitory effect from bile salts.

QUESTION: So what does bile salts actually do? Do they increase or decrease lipase activity? How does colipase overcome it?

MY ATTEMPT: After some research , I found that bile salts above critical micelle concentration have inhibitory effect, but could not still comprehend how does the colipase makes lipase more efficient. Also if greater concentration is inhibitory then why does our body just secrete it in sufficient amounts? Isn't it be more efficient than to make a whole protein(colipase)?


texts: Long term liquid food diet by blending/grinding all quality foods one would normaly eat, not any weight loss or prepared drinks

texts:
I want to know what are the effects of not using your teeth to grind foods but preparing it before eating with blending and grinding them into a liquid.

Here I am not talking about any weight loss or fitness industry prepared drinks. I mean the ordinary raw and cooked foods like meat, vegetables, cereals, and fruits that one would normally eat in classic meals.

Would this decrease of work done by teeth and digestion system have positive or negative health effects?


texts: Pet 28a plasmid is obtained from which type of bacterial strain

texts:
I want to ask some question which is very confusing
Pet28a is a vector.I want to know which strain of bacteria have pet28a plasmid?
E.coli DH5 alpha strain have pet28a plasmid?
Please help me ....Please answer this question


texts: Insect ID, found in shower, northeast USA

texts: I want to know if this is the kind of critter that will lay eggs in the drain and then have larvae emerge from there. We had that a few years ago and it was nasty...


texts: Do two compatible tRNA codons bond together?

texts: Can two tRNA with complementary anti-codons link together?  For instance UUU with AAA. If not, why not?


texts: Can retroviral delivery systems "overwrite" genes?

texts:
As the question states, what are the limits of retroviral genetic delivery systems?

Are they limited to adding additional gene sequences to a cell, or can they actually overwrite specified segments of DNA?

Or, more aptly described, can they remove one segment of DNA, and insert a new segment (whether the same or different length) in the spot where the old segment used to be?


texts: Why are clementines easier to peel than oranges?

texts:
In my experience, clementines have been significantly easier to peel by hand than and orange.  The skin of the orange seems to cling to the rest of the orange much more so than the skin of the clementine does.

What causes this?  Wikipedia (Clementine) merely mentions that they are easy to peel, but leaves it there. What is different between the way the skins are attached?


texts: Why does the PR form of phytochrome exist?

texts: I know how it gets converted because PR is more stable and when there is neither red or far red light PFR naturally converts to PR. But what is the point of it? If PFR is the biologically active one why didn't evolution just make one pigment, PFR. At night neither is active so PR again has no point, in the morning PR gets converted to PFR. So why do we need a PR?


texts: I am interested in dryland ecosystems, and I am trying to find material on what determines the time at which plants in dryland ecosystems, either shrubs or grasses, grow and shoot? Is it only related to water availability? Is temperature also a factor?


texts: What happens to a human body once a sugary snack is consumed?

texts:
I'm looking to understand the effects of sugary snacks and/or drinks on a human body. I'm particularly interested in the timing of the ingestion versus various hormonal levels that may be circadian in nature. Is the release of insulin circadian in nature?

Scenario 1:
A person eats 50 grams of trail mix- raisins, sugared pineapple, sugared mango.
What happens in the next couple hours?
Which hormones get released and for how long?
Does the timing of ingestion produce different effects (ex: consumed at 11AM vs 3PM vs 8 PM?) on the body?

Scenario 2:
A person eats 100 grams of trail mix and drinks a can of sugary nectar (48 grams of sugar dissolved in water).
Will this cause the sugar "crash"?
Is there some grams per kilogram of weight guideline on how much refined sugar or corn syrup a human body can handle at once?

Thank you for your response or any keywords that may help me search for this information!


texts: What does "chlorophyll photosynthesis peak" mean in relation to photon wavelength?

texts:
When reading about how green / leafy plants work,
I saw that they have chlorophyll A & B, which allow the plant to use the energy from light by capturing and transforming.

When reading about Chlorophyll, I saw some charts showing "peak points" for each type for light wavelengths. Apparently, each chlorophyll type has both peak points.

Since from further reading I learn that plants can use all the light in the visible spectrum for photosynthesis, I'm wondering (my questions >>):

What do "peak points" of wavelength correspond to / stand for?
How does light peaking in red spectrum (say around 630nm) differ to (or affect plants) compared to light in red spectrum peaking at 680nm (which I gather is Chlorophyll A peak-ish)?
When same amount of radiant flux is projected to leaves on different wavelengths, one far from a chlorophyll peak the other near, which one gives more energy to plant and why?


texts:
I have a set of gene expression data downloaded from http://www.ncbi.nlm.nih.gov/geo. I have two sets of data, one is the raw probe intensity data set in the form of CEL files. Another is processed txt file.

Here is a link for example
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE7904

I don't know what kind of processing is done to generate the processed data from the raw CEL files. For example in the above link, I have processed data like

SOFT formatted family file(s)
MINiML formatted family file(s)
Series Matrix File(s)

I don't know what sort of processing is done to generate those files. Any suggestions? I can read the raw CEL files in matlab but what sort of preprocessing am I supposed to do?

I also want to map these probe its to gene ids and get the corresponding gene. How can I accomplish this? I know matlab. But I am bit confused about the terminology and all. Any suggestions?


texts:
From Genetics by Ursula Goodenough

  E.coli harboring an F element are endowed with a number of phenotypic
  traits :

  1.They are sensitive to infection by ssRNA phages and certain ssDNA phages.

  2.They resist the growth of female specific phages as T3 and T7.

What is the molecular mechanism behind this sensitivity and resistance ?


texts: Is there any completely Computation Drug ever launched in market?

texts:
I am working in bioinformatics(part of it in Drug Designing) for years, still if I have no idea about it. As it is too hard to prove (Pass all Clinical trials) and get FDA Approvals.

So, My question is there a drug available in market, which is actually designed computationally?


texts: I know Ginkgo is a gymnosperm, but I was wondering whether Ginkgo is also technically a conifer. I did a Google search, and found several confident authoritative-sounding answers. Unfortunately, those answers were divided between "is" and "is not". So which is it? Is a Ginkgo a conifer?


texts: Are there organisms which have compartments of different body temperature?

texts:
I was wondering if there are organisms which have compartments(inside the body) with different body temperatures. To clarify are there organisms which have tissue/organs which are surrounded by something (other cells, tissues) which have an other temperature.I'm not talking about fluctuation in body temperature, such as in ectotherm organisms. I have never heard about something like this and nor I could find information or articles about this (the reason why this question doesn't provide much background research). However I'm still wondering if there are organisms like this (or at least come close to this)?

Ps. please edit this question or comment if you can provide more background information regarding this topic


texts: How to Diagnose this hepatitis A, B and C case?

texts:
Male patient who is working in the hospital and may be infected with contaminated blood had hepatitis
with genome IA 5 years ago. His hepatitis A at that time was confirmed with the rise of anti.HAV IgM and
later with anti-HAV IgG type antibodies. His wife is known to have antibodies against C hepatitits. The
patient had icteric illness in about three weeks ago. Which are the best indicators in
diagnosing his hepatitis?

Right answer is: Detection of HBsAg and anti-HCV antibodies.

I think this is because

to check if he has hepatitis B by HBsAg
to check if he has HepC by the antibody

Serum antigen of HB tells us about the levels of IgM and IgG.
If vaccinated, then IgG should be positive, I think?
What does HBsAg tell you?

Why do we need to detect anti-HCV?
If they are found, what does it mean?
I think that then it means if found that he does not have hepatitis C then.


texts:
In Uncompetitive inhibitors , the Km decrease .
With uncompetitive inhibitors , the affinity of the enzyme for the substrate (E+S) increases .

I've searched up on the net and it says that the substrate has now been taken up to form E-S and E-S-I , therefore consuming more substrate than the original inhibitor-free equilibrium .

E + S -> ES (equilibrium position shifts to the right)

I've read up on all these and more doubts form in me .

Why is substrate needed to form ESI ?

I understood what it meant by equilibrium position will shift to the right . It is harder to form E + P as more substrate will form ESI.

Thanks !


texts: Impaired circadian rhythm is associated with cancer. Light pollution affects the circadian rhythm and the circadian rhythm affects the metabolism. But what is the (molecular) connection between impaired circadian rhythm altered metabolism and cancer?


texts: What kind of mushroom is this? Found in SF

texts: We found this on a trail in San Francisco. Could someone please tell me what kind of mushroom this is?


texts: What are the predators of Glaucus atlanticus?

texts: I'm researching the Glaucus atlanticus, also known as the blue glaucus, among various other names, but after reading quite a few articles and searching on the Internet as many different ways as I can think of, I can't find any of its predators, or any indication it has no natural predators. Everything I've read is just silent on the issue. Does anyone know what, if any, predators this has? Thanks!


texts: Aerosolised particle released during autoclaving

texts: During autoclave heat-up, the inside chamber's air is released in order to be displaced by steam. Because of that, many modern autoclaves are equipped with filters at the release outlet. The aerosolisation is understandable when working with potentially dangerous bacteria and viruses. However, are mammalian cells (used, for instance, in gene editing cell cultures) capable of aerosolisation as they are significantly larger in size compared to bacteria? If so, is the frequency of mammalian cells aerosolisation higher or lower than in bacteria?


texts: Can fructose take multiple forms ? Which of these structures of fructose is correct?

texts:
When I look up the structure of fructose I get various different structures
Which of them is correct ?
Are these all just isomers of fructose ?


texts: Virus-to-virus gene transfer via "sequences integrated into a common host organism"

texts:
From "Risks from GMOs due to Horizontal Gene Transfer", by Paul Keese:

  In addition to direct HGT between organisms as depicted in Figure 1, forms of indirect HGT have been observed, which involve an additional intermediary organism in gene transfer from a host organism to the final recipient organism. The most notable are virus mediated gene transfer (transduction) between bacteria (Weinbauer, 2004), retrotransfer of a plasmid to a second bacterium, acquiring host genes and returning to the original bacterium (Ronchel et al., 2000), the spread of donor genetic material between several different bacteria coexisting in complex communities or biofilms (Molin and Tolker-Nielsen, 2003; van Elsas et al., 2003; Wuertz et al., 2004); or from virus to virus via sequences integrated into a common host organism.

Does it mean that a viral gene or other DNA sequence gets integrated into the host's genome and then some other virus (that chanced to be in the same organism) manages to obtain this sequence and package it into its own DNA?

Keese's article has no reference for this statement, and perfunctory googling brought nothing to clear the matter for me.


texts: Why are there two abrupt changes in the genome sequencing price curve?

texts:
In the price curve of the genome, from NIH:

NIH explained the abrupt drop at 2008 thusly:

  beginning in January 2008... the sequencing centers transitioned from Sanger-based (dideoxy chain termination sequencing) to 'second generation' (or 'next-generation') DNA sequencing technologies.

The NIH did not give any details as to why there was a similarly precipitous drop in 2015, or why there was such a saddening (for me!) plateau after that. Please explain them to me?


texts: Why does glomerular filtration result in a filtrate with the same osmolality as plasma?

texts: Unlike the plasma, the ultrafiltrate has no proteins which are prevented from filtering out. Shouldn't the loss of these proteins result in a loss of oncotic pressure and thus a different overall osmolality?


texts: Why does the human brain not overfit when training at some task?

texts:
One of the problems that occur during (artificial) neural network training is called overfitting. The error on the training set is driven to a very small value, but when new data is presented to the network the error is large. The network has memorized the training examples, but it has not learned to generalize to new situations.

The human brain does not overfit when training at some task, but becomes better and better instead. Why? Or conversely, why do artificial neural networks overfit when are trained too much, in contrast with the human brain?


texts: Is this necrotizing skin infection caused by Staphylococcus aureus?

texts:
A 5-year-old boy returns from summer camp with several minor cuts and abrasions on legs. He has fever
and extensive cellulitis, subcutaneous tissue and muscles are involved. Necrotic tissues were surgically
reomoved and broad spectrum antibiotics were used. Which of the following microorganisms usually
causes necrotizing fasciitis?

a. bacillus cereus
b. clostridium tetani
c. A-group streptococci
d. Micrococcus sp.
e. Staphylococcus aureus

It is so severe that I started think that Staphylococcus aureus is possible.
My previous answer was A-group streptococci, but I disagree with it now.

What is causing the case?


texts: How Does the Body Know a Finger is Fully developed?

texts:
When a baby is being developed inside the womb,

1) how does the baby's body know a finger, or any other part of the body, has been fully developed?

2) following question, how does it "stop" the development of that part? What kind of signals are being communicated here?

3) I have hairy arms. The length of the hair is almost the same length if i don't cut it. If it breaks, it grows back almost the same length. How does the body know the current length and how to stop when it reaches the "target length"? Is it the same "procedure" as the development of parts inside the womb?


texts: What difference does it make in the organism's physiology/metabolism whether oxygen binds reversibly or not?

texts:
A follow-up to How does hemoglobin-free blood transport oxygen?

I'm unsure about the use of physiology/metabolism in the title there. The question in mind is whether this reversible binding makes an organism slower, or faster; perhaps more capable of surviving in rarefied atmosphere.

EDIT:
I apologize that my comment made it appear this question is only about the Icefish; it is not. There are still other species (for instance, molluscs, and arachnids) which acquire oxygen by means other than haemoglobin.


texts: Is telomere length a reliable measure of health/lifespan?

texts: Several companies are commercializing tests for telomere length such as this one here. I understand the basic mechanism for why telomeres shorten during DNA replication, but how good is the evidence that telomere length is a reliable indicator of healthspan/lifespan?


texts: How hard it is to determine a 3d structure of a protein?

texts:
I seeing tens of thousands of PDB files on the internet. I really want to determine a 3D structure of my protein of interest. I've heard that 3D structure determination is a complex, expensive, and specialized procedure that can take months or years and is hard to perform routinely or even purchase commercially.

Could you please explain why and how hard it is? What are the requirements and how big of a budget is typically needed to perform this kind of experiment?


texts: Coalescent Theory - Probability for $k$ alleles that of one coalescence event occured $t+1$ generations ago

texts:
From this textbook
Under the wright-Fisher model of genetic drift and under the assumption that all alleles are neutral, the probability that $k$ alleles had $k$ distinct parent alleles the previous generation is
$$Pr(k) = \prod_{i=1}^{k-1}1-\frac{i}{2N} ≈ 1-\frac{{k \choose 2}}{2N} $$
The chance of two alleles not coalescing for $t$ generations is $\left(1-\frac{1}{2N}\right)^t$ , and the chance that they coalesce in the next generation is $\frac{1}{2N}$. Therefore, the probability that 2 alleles had a common ancestor t+1 generations ago is
$$\frac{1}{2N}\left(  1-\frac{1}{2N} \right)^t ≈ \frac{1}{2N}e^{\frac{-t}{2N}}$$
I understand up to this point!
The probability that the $k$ alleles do not coalesce for $t$ generations, and then one pair coalesce to give $k-1$ alleles at $t+1$ generations ago is as follows:
$$Pr(k)^t \left[ 1-Pr(k) \right] ≈ \frac{{k \choose 2}}{2N}exp\left[ -\frac{{k \choose 2}}{2N}t \right] $$
Can you help me to understand this last part? (both the left and right part of the equation)


texts: How do you identify this particular snake shedding?

texts:
Aloha,

Snakes are illegal in the State of Hawaii, with the exception of the Hawaiian Blind Snake (Brahminy Blind Snake (Ramphotyhlops braminus)). I've read through a plethora of articles to no avail. It also doesn't help that snakes are virtually non-existent in the Hawaiian Islands.

I would like to identify this particular shedding, however, it has proven to be just as difficult as I predicted. Could anyone identify the species of this shedding?

Mahalo


texts: What is this bug found in a garden in Utah?

texts:
Apologies for the poor quality of the photo.

I found this bug in a garden in Utah.  The body was flattish, with teal markings (lighter than it looks in the photo) with an interesting pattern of three dots along the back, and a pink cone projecting down to the rear.  It was about the size of my smallest fingernail.

From the searching I've done, the shape and the light "rim" on the outside of the shell look like a June Bug or a Stink Bug, but this one was not as green and the markings seem a lot more pronounced.

Is it a pest to be concerned about?


texts: Is the number of nucleoli in a nucleus fixed?

texts:
A nucleus can have multiple nucleoli. But are there any constraints on the number of nucleoli in a nucleus?

Can cells of individuals of different species have a different number of nucleoli?
Can cells of different individuals of the same species have a different number of nucleoli?
Can cells of different types have a different number of nucleoli?
Can different cells of the same type have a different number of nucleoli?

I've found snippets of information implying the number of nucleoli is fixed per species, but none authoritative enough to stoke my doubts.


texts: How can computer predictions of protein folding be verified computationally?

texts:
Currently, there is a lot of research focused on solving the folding patterns of proteins using computers (Folding@Home, https://fold.it/portal/, etc.).

The question that I have is: How do you know when you get it right?  Is there some way of verifying, in silico, that you have found a legitimate/correct structure for a protein?


texts: Can I force evolution in a group of cells by removing all the smaller cells?

texts:
I actually have algae growing in water in a container. I was thinking if it was possible to filter the water so that all the small cells will be filtered out and only the bigger ones will remain to reproduce cells that tend to be bigger.
Is that possible?
What type of filter should I use?


texts: Task-dependent "reversed" handedness: why use left hand for some tasks? How is it controlled by the brain?

texts:
I am right-handed. Which means that when I hammer down a nail, I hold the nail in my left hand, with which I can hold it straight and at a controlled position.

This is true in situations where the task of holding something in place is  simultaneous with a more complex task, such has hammering, done with the right hand. But I note that even when there is no other task, I personally use my left hand to hold in place, e.g., a  bottle that I am filling up in a stream of water.

To generalize a little, it seems to me that while I use my right hand for precise motion or applying a force, I'll use my left hand to maintain a position against forces.

Is this behaviour something documented? Does one develop specific brain control to implement this controlled-position tasks?


texts: Is there any biological reason that professional swimming is dominated by white people?

texts:
I suppose that the question should be turned around to "Why is it extremely rare to see black people competing in professional swimming?" because it is the absence of this phenotype while watching the Olympics that caused me to ask this question.

So,

why are there very few black people competing at world class level swimming?

While I'm here I may as well ask the question:

Why are black people faster sprinters than white people when it comes to world class level?

And of course I want biological reasons.


texts: Will I hyperventilate if I breath twice as fast at an altitude with half as much oxygen as I am used to? If not twice as fast, should I breath any amount faster on average than usual when at high altitudes?


texts:
Principle of genetics mentions

  The fact that introns accumulate new mutations much more rapidly than exons indicates that many of the specific nucleotide-pair sequences of introns,excluding the ends, are not very important.

Though 'are not very important' is not true as introns do have a number of functions (both discovered and undiscovered).

But why is DNA polymerase less efficient at replicating introns? Is it known?


texts: What is the simplest organism that was observed to learn: change its behavior permanently in response to some event/stimuli in a way that this change persists even if the event does not happen again?


texts: Having a lot of trouble identifying this insect


texts: Help me please! I have to get rid of these!


texts:
A few weeks ago I encountered a peacock while driving to a friend's house in Central KY, USA. I don't believe I've ever seen a peacock in KY, and when attempting to ID [just through Google searches], I could only find restaurants & musical artists that contain "peacock" in their name.

Can someone help me ID this bird? And, are peacocks wild in KY? Have they always been, and are just rare? Aside from species ID, any insights about this bird and its prevalence within KY would be most appreciated.


texts:
I'm reading a paper and the authors mention a "protein pulldown" assay.

I've never done this before, and googling doesn't bring up much. Could I get a rundown of the basic theory behind it?

Also does % coverage have anything to do with this assay?


texts: What is the closest possible analogue to human cells?

texts:
For an experiment, I need a specific number of cells. I will grow these cells in an incubator, and then measure the number of cells which have decayed due to the induced radiation. I am using a standard cell counting chamber (Hemocytometer) to count the number of cells.

The research question is to find the best armour for radiation; low-level really.

I was wondering which cell is the closest substitute to a standard human cell. People are telling me about yeast, but doesn't that grow from budding?

Any help and/or suggestion is appreciated.


texts: Virucides - Herbal and otherwise, for HHV6 type virus or any inner-cell virus

texts: Does anyone know where I can find a reliable list of virucides (not anti-virus) that can be used by humans? This virucide must be able to affect viruses that are already inside the cells. St John's Wort is considered a virucide along with it's other properties, for example.


texts: Where can I find the length of each anopheles chromosome? I've obtained data in which the length of each 2L chromosome for several anopheles is 39101648. I'm looking for an article that gives the length of 2L so I know my output is correct.


texts: I looked up online to find which type of carbohydrate is found in egg white, but the only information I found is the quantity of sugar. I would like to know the exact name of the carbohydrate found in the egg white in order to draw the sugar molecule.


texts: Does low gravity exposure to early stages of human fetus have potential to unloc unused genetic information from earlier stages of evolution?

texts:
The title seems quite self explanatory but let me elaborate.

New mutations do take a very long time and many generations to occure in the genetic code. But our genetic code already holds all the information gathered trough evolution process...even information that are older than mammals.

In case of start of pregnency in zero g or gravity of Mars (0,38 g)... there are many replications from the single cell egg to fetus couple month old...

Can gravity in this case has potentional to "open new variant" of genetic information gathered in our cells? Does diferent gravity has impact on metabolic processes on cellual level?


texts: Can DNA & RNA be considered as nature's programming language?

texts:
The final frontier of Biological Sciences could be considered understanding the effects of variation in the DNA (and RNA).

If after fertilization the DNA of the zygote could be genetically engineered to prevent complications occurring later in the life of that human being, it could become the ultimate medicine.

Also, we know that (in humans) only 2% of the genome encodes genes that are translated into proteins; is the rest required for function?

Can DNA & RNA be considered the ultimate blueprint of all living organisms?


texts:
So during research, my professor mentioned a type of stem cell, a name that was like 5-6 words long, that can be used to treat diabetes by creating an "artificial organ". That hypothetical organ would then be used to create insulin or treat diabetes using other methods.

However I can not remember that name for my life...

This community may not be able to assist me much, as I am aware of the many types of stem cells. This is all the information I have access to, and I cannot contact my professor until the weekend, so it would be great if I could get some prior knowledge about these stem cells; I just need to know the name.....

Thanks in advance.


texts: Why doesn't recombination occur in male Drosophila?

texts:
"Males do not show meiotic recombination, facilitating genetic studies."

For a while I have known that this phenomenon occurs, this quote comes from the Wikipedia page on Drosophila melanogaster, and I frequently use this feature of Drosophila in constructing hemiclones for my own research in quantitative genetics.

But, until now, I have never asked why doesn't recombination happen? Why would this feature evolve?

Further, why is the absence of recombination sex-limited to males, why do females have recombination?


texts: Number of genes required to sustain life

texts:
Are there estimates of the minimum number of genes required to sustain life?

In what I mean by life here, I don't include viruses.


texts: How do mothers handle acid from embryo bone mineralization?

texts:
This is a relatively trivial question, but, I have not seen it discussed much. It could be one factor in the "acidosis of pregnancy" (JAMA, 1929). Are the compensatory mechanisms measurable, by dietary phosphate requirements increase by 3 mmol (40% more than adult average of 7.4 mmol) or something similar?
A human fetus  acquires 30 gram of calcium during pregnancy (Kovacs, 2014). The molecular weight of calcium is 40 gram per mole, 30 gram is 30/40 = 0.75 moles. Bone mineralization releases hydrogen ions since bone mineral requires hydroxide ions (Bonucci, 1992). Calcium and hydroxide ions have a 5:1 ratio in bone mineral, bone mineralization during embryogenesis releases 0.75/5 = 0.15 moles of hydrogen ions, 150 mmol.
80% of this H+ is generated during the third trimester of gestation (Kovacs, 2014), with up to 1.5 mmol per day (300 mg calcium/day, see Kovacs, 2014) between weeks 35 and 38. When 1.5 mmol H+ is distrubuted on an average 70 kg body, with 60% water, 70 kg * 60% = 42 kg = 42 L of water, the molarity is 1.5 mmol/42 L = 0.035 mmol/L. This is equal to -log10(0.035 mmol) = pH 4.45.
References
THE ACIDOSIS OF PREGNANCY. (1929). Journal of the American Medical Association, 92(25), 2104. https://doi.org/10.1001/jama.1929.02700510034014
Kovacs, C. S. (2014). Bone Development and Mineral Homeostasis in the Fetus and Neonate: Roles of the Calciotropic and Phosphotropic Hormones. Physiological Reviews, 94(4), 1143–1218. https://doi.org/10.1152/physrev.00014.2014
Bonucci, E. (1992). V. Regulation of hydroxyapatite formation. In Calcification in Biological Systems (p. 134). Boca Raton: CRC Press.


texts: What is the chemical makeup of mealworm frass?

texts:
We have been raising mealworms for some time and while mealworm frass has proven very useful as a plant fertilizer, I started wondering about other potential uses of this leftover waste.

Can someone please explain what kind of compounds make up the frass from mealworms as percentages of overall makeup?

In particular I would like to understand how mealworm waste compares to other commonly used animal wastes used as fertilizer.

Bonus points if you can suggest other applications (than just fertilizer) for mealworm frass!


texts: Are there any pictures of an actual trigger point looks like? All I am able to find online are animations.


texts: What does it mean for there to be no correlation between phylogenetic independent contrast?

texts:
I am testing the correlation between two physiological parameters in plants using the pic function in R. I am a bit stuck on the interpretation of the phylogenetic independent contrast (PIC). Without considering the PIC, I got a significant correlation, but there is no correlation between the PIC. What does the absence of correlation between the PIC mean:

the correlation without PIC is the effect of phylogeny

OR,

There is no phylogenetic effect on the correlation.

Thank you


texts: How do precordial leads measure electrical changes in the heart?

texts: In precordial leads the electrodes from limbs are connected to a common point via resistors. What is the potential at the common point?


texts: Europe: big fly with black/yellow striped body: I'm guessing a horse fly?

texts:
This one made a summer night visit to the room and tried to escape by banging against the ceiling. What is it? I found nothing which corresponds, though "horse fly" might be a close match.

Location: Central Europe, Luxembourg
Locality: Where the suburb morphs into the not-yet-conquered countryside
Time: Late August, Nighttime
Weather: Quite warm (~27°C). Dry.

Here is an MP4 of the beast: https://i.imgur.com/F5yqMQ8.mp4

It is about 2 cm (0.8 inch) large. Relatively plump, keels over and likes to clean itself a lot.

Large head, large eyes, a bit hairy, two black stripes

Once it falls on its back it wallows a bit, there is clearly a probabilistic algorithm to get itself out of the predicament:


texts: Please help me identify this caterpillar species (Sabah, Malaysia)

texts: I kinda having trouble searching the internet to find this caterpillar name. Does anybody know what kind of species they are?


texts: Don't the radioactive labeled molecules of dNTPs or DNA harm themselves or their surroundings?

texts:
I'm reading some papers for the first generation sequencing methods and some earlier than them, like Ray's Wu first time DNA sequencing from a λ phage virus cohesive 5' ends. Ray Wu, like Maxam-Gilbert and Sanger, used 32P / 3H to label either dNTPs or DNA molecules.

But what happens if you add such radioactive materials inside a test tube with DNA and other molecules like DNA Pol I? For example,  32P emits electrons at 1.709 MeV. Couldn't these high energy electrons harm the DNA or Pol I molecules (bonding destruction), that are present nearby at the time of reaction?


texts: Does music enhance neural activity/cognitive or cerebral function, or is it just mania?

texts:
I always find myself drew upon curiosity whilst studying, to whether certain types of music are or are not, effecting me in a sense of cognitive ability.

Take a fantastic piece such as, Mozart's, Symphony No. 40 in G minor, K. 550, for example. Whenever i'm listening to it, at the same time as studying, I feel more fluid... and somewhat enthusiastic. Is there a reason for this?

So to conclude, does music of specific  genre's (i.e. Classical) or, music in general, have any impact on cognitive performance? In particular, cognitive performance, in regards to Mathematics.


texts:
Technology has evolved so much as to clone animals. But, what about human cloning?
Is it really possible to create humans in lab? Or is it that technology has not advanced to that level..?

Why cant it be attempted..?


texts: Is there a chemical that can be used to subdue ants only temporarily without permanent harm?

texts:
I would like to know as I want to contribute to a biodiversity project that wants to create a database with ant feature measurements. I'm not sure if I like the idea of killing ants however (even though it's just a single ant with limited ability to suffer, I know) so I'm looking for a way to immobilize ants long enough to take some detailed measurements but without having to kill them or harm them permanently.

Related question: how could I clean the ant so that it's not marked with the chemical used in the perception of other ants?

I know that for the database they may require keeping the specimen (and therefore killing it) in the name of science so that it can be checked by others but I'm more concerned with the question whether in principle these measurements could be taken without permanently harming the ant and how this could be done in practice.

Thank you for your help!


texts:
I have read that general soap can kill bacteria by opening holes in the bacterial membrane.

http://questions.sci-toys.com/node/90

However, I found some articles as well saying that it cannot.

http://goaskalice.columbia.edu/answered-questions/does-soap-kill-germs

There seems split answers among experts,
so I would like to know which one is correct.

Could anyone advise me?

Thanks.


texts: This is a question that has always bothered me. A quick internet search yields "metabolic processes" as the reason for how marine mammals obtain water, but what are those processes and why don't land mammals have them? In other words, what are the specific differences between marine and non-marine mammals in how they stay hydrated?


texts: Insect identification: Fly with eye strip

texts:
Location details:
Country - India,

State - Tamil Nadu,

District- Chennai.

Found this fly in my backyard keen to know its exact name. Thanks for the help


texts: Where are the gastralia (stomach ribs) attached?

texts: Crocodiles and some dinosaurs have a second set of ribs between the sternum and pelvis called gastralia. Where are the gastralia attached to the rest of the skeleton?


texts: Fluorescent protein tags and colocalisation

texts: We want study if 2 proteins A and B are co-located, for that we use 2 FTP(Fluorescent tag proteins) for each protein?and after the expirement these 2 FTP are co-located. Does that mean necessarily protein A and B are co-located?


texts: Why do fat people and thin people get hungry at the same time?

texts: Say a fat person and a thin person take breakfast at the same time. Around lunchtime, they'll both be hungry. Why? After all, the fat person theoretically has lots of body fat the body can consume instead, so the fat person does not have to feel hungry.


texts: External "lungs" that process your blood the same as your real lungs do - would that stop your need for breathing?

texts:
So say your blood goes with a tube out of your body. In an external device all the chemical/biological magic would happen and it would be fed back to your body.
Of course this doesn't exist (yet), but if this would be possible - would it mean you automatically stop your need for breathing?
Is "gasping for air" linked to the amount of oxygen in your blood? Or is there something else going on?
Just a random (theoretical) shower thought. The idea that you wouldn't feel the need to breath feels weird to me.


texts: Fe in bacteria light-harvesting system Reaction Center

texts: Is the Fe in the reaction center of bacteria light-harvesting system bounded or free atom?


texts:
I am looking for a cell line (preferably hematopoietic) that has an inactivating DNMT3a mutation. I have checked the Cancer Cell Line Encyclopedia but of all the hematopoietic cell lines I know I can't find any with a DNMT3a mutation.

It would be great if somebody knows of a cell line with a DNMT3a mutation, but it would also be helpful if somebody knows of a database that I could use to find this information in the future. Thanks.


texts:
I have been cracking my fingers for 2-3 years and on the first year I was told that I'm going to get arthritis because of it.

I've been researching this since the first year and I've never gotten an answer. Most people say either Yes, No or I don't know.

Arthritis is mainly cause by bones rubbing together and cracking fingers is just air sockets poping.

I've asked my biology teacher and he said that he's not sure. He then explained to me that the cracking sound from people cracking their fingers is just air sockets poping.

So can finger cracking cause arthritus?


texts: Significance of lipids in biological membranes...?

texts: Membranes are specifically designed by lipids to maintain internal hydrophilic environment in narrow range.There are hydrophobic amino acids among naturally occurring 20 amino acids and as well as there are also number of water insoluble polysaccharides like cellulose. These hydrophobic and water insoluble materials can also be used to build membranes but why not? Why lipids are only choice?


texts: Batch convert miRNA names to Accession IDs?

texts:
Does anyone know of tools to convert lists of miR names to their miRBase Accession IDs? I know they exist, but my search keeps pulling up gene ID converters.

EDIT: both @rg255 and @shigeta have provided solutions to the underlying issue, but I am curious to know if something exists for miRNAs that is similar to a site like this.

EDIT 2: miRNA names are of the form 'hsa-let-7a' and Accession IDs are of the form 'MI0000060'


texts:
I want to know how thoughts are biologicaly generated. I know that electrical impulses can trigger formed memories in the brain but what I want to know is how the electrical impulse is generated in the first place. I don't have a background in biology or neurology but I think it's probably one of the three options:

Impulses are generated randomly at parts where there are stronger connections.
We have loops in our neural network, electrical impulses stay and go around the brain to trigger memories and thoughts.
We are deterministic and only react to impulses from the outside.

Any reading suggestions about this topic are also highly appreciated. I want to understand the human brain a little more to compare it to artifical neural networks.


texts: Consequence of Plants as Incomplete Protein Source

texts:
Some years ago, in a 1000~ level biology course we learned that the DNA essentially encodes formulas for creating proteins from amino acids. While the human body can synthesize many many amino acids, some we are unable to synthesize and we dub these as essential amino acids because we must obtain them from our diet. However, surely something must be capable of synthesizing the amino acids, otherwise they would not make it up the food chain to us, which opens the door to the possibility that animals may have varying capabilities in regards to amino acid synthesis. Presumably, this is why cats have to obtain a high protein diet, as they have high need for protein but a poor ability to synthesize them?

Moreover, in doing basic research into nutrition to plan a regular workout schedule there is some need to distinguish protein sources as not all protein sources are considered to be complete proteins because they do not provide all amino acids, or otherwise do not provide them in the right balance.  Particularly, many fruits and vegetables tend to be poor sources of protein.

For plants which are incomplete protein sources, they would seem to lack the ability to synthesize some amino acids. They also would not be able to obtain these through diet, as they're plants. Consequently, does this mean that some plants may not encode for a specific amino acid throughout their entire DNA?


texts: Whole genome amino acid composition tool?

texts:
I'm interested in a statistical tool to get bacterial codon usage at genomic level. Ideally, the tool should be flexible to analyse hundreds of bacterial genomes.

I've looked in MeSH terms database but I'm a bit lost when I search for "Genetic Code" and Software.

I'm looking for an output like this one:


texts: Why does an electric shock contract the muscle?

texts: From what I understand, the electrical impulse in our nerve cells is not made of electrons, but of ions that move from different environments with different concentrations, which is totally not related to the electricity we use, which is made of electrons. The electricity we use makes our muscles contract, why? Does it have to do with the fact, that when we put electrodes with electricity in an electrolyte, ions move?


texts: Would there be any particular reason to choose strawberries for this DNA extraction tutorial?

texts:
The NileRed video What is DNA and what does it taste like? | Edible Chem shows the extraction of a surprisingly large amount of DNA from some strawberries. At 02:22 the narrator says:

  What I think is really cool, is that it’s actually possible to isolate DNA from pretty much any living thing. For this video though, I’ve decided to get it from strawberries, because it’s one of the easiest sources.

I'm wondering if DNA is inherently easier to extract from strawberries than other fruits, vegetables, or other foods in general, or if for some reason there is more DNA (or DNA plus other molecules bound to it) it in strawberries than other foods to begin with.


texts: Is the cell cycle applicable to meiosis as well, or just mitosis?

texts:
All the diagrams I can find, show the cell cycle as having G1 phase (growth 1), S phase (DNA replication), G2 (growth 2) before the Mitotic phase (mitosis + cytokinesis).
Is there an equivalent "cell cycle" for meiosis, since the chromosomes in parent cell in meiosis also having "double" the genetic material prior to cell division (presumably from DNA replication too)?
Is it simply the same cell cycle as mitosis but with a Meiotic phase instead of Mitotic?
If so, would appreciate if anyone had a diagram :) Thanks!


texts: Peptides neither produced by the ribosome or the non-ribosomal peptide synthase complexes

texts:
I read in Wikipedia:

  While there exist a wide range of peptides that are not synthesized by
  ribosomes, the term nonribosomal peptide typically refers to a very
  specific set of these as discussed in this article.

I was wondering what peptides are being referred to. I can only think of synthetically produced peptides. I can not find any source for other peptides not produced either by the ribosome or by the non-ribosomal peptide synthases described.


texts: What are the allowed evolution operators (on protein encoding sequences)?

texts:
What are the evolution operators, meaning allowed actions on the DNA sequence that encodes a protein.

I assume all evolution of genes is a result of duplication errors. So an answer could look somewhat like this: duplication of gene into two identical ones, omitting of nucleotide, addition of nucleotide and so on.

And some followup questions:

Does this mean that originally there were very few genes and they were very short?
If so - how few? How short?


texts: Measuring the protein content using UV Vis

texts: The experiment is to determine the protein content of the solution. I followed the procedure of the Bradford assay but the reagent needed is unavailable and so we use an alternative by using cold pure ethanol. Since ethanol precipitates the protein can I still determine the protein content of my sample using UV Vis at 260nm absorbance? or the protein content can be measured by its precipitate using a different method?


texts:
I was reading my chemistry textbook, when in the chapter on 'solutions', i came across a problem, which calculated the amount of oxygen that can be dissolved in 1cc of water at STP. Then they commented, "this amount is just perfect for aquatic and marine life. Had this been lesser, life in the oceans might not exist at all.' This raised the following question in my mind:

1)aquatic species of flora and fauna evolved over time to adapt to this concentration of dissolved oxygen, and their biological processes were also fine tuned based on the environmental conditions.

2)It really was fate that the dissolved quantity was just enough to support marine life, as the textbook said.

Which of the two is the actual scenario? My personal pick happened to be 1), but I have no proof of it. Can someone explain?


texts:
I found this insect inside of my shoe. It is approximately 1cm in length and less than half a centimetre wide. It was found in the Netherlands, in the province Gelderland.

Close shot

Distant shot

Upside down

What kind of insect is that?

Edit:

As @fileunderwater suggested: the question is "close" but not identical.
I think that the suggested duplicate will only provide an identification of the family of the insect, but nothing more precise and specific. Therefore, the answers for the 2 questions vary.


texts: In the explanation of the sulfur cycle, it is often said that sulfur moves from the atmosphere to the ground by acid rain in the form of sulfuric acid. Can plants directly use sulfuric acid to assimilate sulfur?


texts: Can DNA base pairs go through each other?

texts:
Consider the simplified version of the motion one DNA base pair held together by a hydrogen bond:

Use u and v to denote the displacements of the bases from their equilibrium position along the direction of the hydrogen bond that connects them,
Define y = u-v to measure the stretching distance between the bases in a pair of bases.
So, y = 0. u=v. No stretching. When y > 0. Stretching. When y < 0. Compression. u

I would like to say, that physically, it is not possible for u to go through v or vice versa. Meaning that the stretching distance measured by y has a lower bound. In other words and my question, does it make physical sense for two base pairs to go through each other?


texts: Is there a negative correlation between the mRNA produced by the cell and the time of extraction?

texts: I am doing some data analysis about gene expression time series. When I plot mRNA produced by P. Furiosus cells irradiated by gamma radiation against the time of extraction, it seems that there is a negative correlation between them. Is it a good result from a biological point of view ?


texts: Why do some people actually experience measureable effects when given a placebo(fake drugs) versus the actual drug?  Is is the power of suggestion, belief, or something else?


texts: How do the lungs act as a sieve to trap blood clots?

texts: Does anyone know? I'm curious to find out  as my human anatomy and physiology book doesn't go into much detail on how the lungs function as such


texts: What happens to the cut-out introns from a pre-mRNA?

texts: Once the spliceosome has cut out the introns from a pre-mRNA they are said to be degraded. What does that mean and is that happening in the cytosol? Can the nucleotides be used for something else within the cell?


texts:
Whenever I see a squirrel in the woods, it is always the big bushy tail flipping around that gets my attention first.  A pray animal with a big bushy flag calling attention to it's self seems to be counter survival, a big flag waving here I am, come eat me.

*Image from Wikisource

Video link, of tail twitching

Why do squirrels have twitchy bushy tails?

Edit to Clarify
Squirrels do not have a high reproduction rate, there are multiple difference between species but most seem to average about half a dozen young per year.. While a pair of rabbits can (though unlikely) create 1300 offspring in a year Wild rabbit and squirrels have similar coloring and predators.  There are of course multiple differences between rabbits and squirrels.  Given the difference in reproduction and a big wavy flag that says come eat me.  It seems that if there is a rabbit and a squirrel sitting on the forest floor eating breakfast, the one waving the flag is most likely to be seen and eaten.


texts: Can cancer grow forever if supplied with unlimited resources?

texts: If somehow a human could give a tumor unlimited resources, would the cancer grow forever?  It seems like it would until it gets so large that it physically affects vital organs.  Is what would likely happen?


texts:
Disclaimer: I know nearly nothing about biology.
I was wondering how did the migratory behaviour of birds evolve. Assuming that evolution/natural selection works slowly and gradually (at least most of the time) I don't understand how some birds decide to fly thousands of kilometers once a year and then fly back.
How does a bird species start it's migrational behaviour? The first generation flies close by, then the next a bit further and so on up until the migration distance is thousands of kilometers? Or do they randomly fly in small groups until they find nice land (abundant sunlight and food) and only the small group which find the nicest land reproduces succesfully?
If evolution works gradually and migration distance increases also gradually, how did, for example, the artic tern evolve to migrate from pole to pole? In the gradual increase of distance, some generation of artic tern must have migrated to a tropical latitude and be unable to survive there. Obviously this must be very wrong.
Can someone explain the evolutive mechanism behind migrations?
Thanks!


texts: Insect identification request. Long anteni. Grasshopper legs

texts: Found in solo cup used to catch drips from toilet valve. East coast of U.S.


texts: What does ensemble-based model of enzyme mean?

texts:
I am reading Pan et al. (2000), a paper about dihydrofolate reductase (DHFR).  They claim using a ensemble-based model of DHFR.

What is a ensemble-based model?


texts: Differences in the action of Scopolamine and Atropine

texts:
Both Scopolamine and Atropine are muscarinic antagonists, having essentially the same action: blocking parasympathetic nerve receptors.

The action on the brain by muscarinic antagonists is presumed to be caused by dilation of blood vessels, thus we might expect the effect on the brain by the two compounds to be similar.

However, in actuality the action of the two compounds on the brain is somewhat different. Scopolamine begins causing strong psychotropic effects even in very small doses before it has any effects on the skeletal nervous system. Conversely, atropine begins having effects on the muscular system long before it begins having psychotropic effects and in fact, potentially toxic doses of atropine have to be administered before significant psychotropic effects begin manifesting.

If the apparent biochemical action of the two compounds is similar, why do we see this difference in the effects between the two with regards to the brain?


texts:
I know that a centrosme is composed of two perpendicular centrioles, but the following sentences of Wikipedia confuse me:

Interestingly, centrioles are not required for the progression of mitosis.
Many cells can completely undergo interphase without centrioles.
Unlike centrioles, centrosomes are required for survival of the organism.

If centrosomes are essential then does this doesn't imply that centrioles too are necessary since centrosome is made of two centrioles, if not then what is it made of?


texts: What are the teeth of the viperfish composed of?

texts: One of the viperfish's (genus Chauliodus) most unique traits is the transparent, needle-like teeth. Some other abyssopelagic fish (e.g. certain angler fish) have similar teeth. I'm curious as to what these teeth are actually made of. They clearly aren't made of bone, and from what I can tell from various fish skeletons, they decay fairly quickly with the rest of the fish.


texts: Why is the enteral route seem by far the most common way to administer a drug to the body?


texts:
What, physically, does the body do to measure it? I assume it's measured by how how turgid or plasmolysed certain 'sample cells' are, or water concentration in the blood,

What is the way they use to measure it?
What do the receptor cells that do the measuring actually do that is variable with water concentration, etc.


texts: What is meant by `individuals do not evolve, populations do`?

texts: My university professor stated that "individuals do not evolve, populations do". But aren't populations made up of individuals? That's like saying when a compound changes in stability, none of the elements' properties change. If someone could clear this up, that would be great.


texts: Many species of fish have 2 or 4 fins combined into pairs. But is there a fish with 3 (or even more) paired fins? Or has it ever existed in the past?


texts: Binding of Multivalent Antibody to mutiple epitopes?

texts: A multivalent antibody molecule such as Immunoglobulin M Immunoglobulin A etc bind to more than one antigens or epitopes but I am confused about that wheather these multivalent antibodies bind to identical epitopes or can bind to different epitopes? means if one molecule of Immunoglobulin M being pentameric can bind to 10 epitopes at a time the 10 epitopes that it binds Will be identical or can be different..? Confused about that..       2. And also another Question I want to ask that as Immunoglobulin G,Immunoglobulin D and Immunoglobulin E are monomers but all of them have 2 antigen binding sites so we consider them as Mutivalent antibodies or not and if we cnsider them as multivalent antibodies then what are the Examples of monovalent antibody that Specifically only bind to One antigen molecule or epitope? Because as far as i Have studied Antibody or Immunoglobulin molecule hae specific "Y" structure that contains 2 binding sites. Similarly in this case also want answer that these momomeric ImmunoglobulinsG,D,E each binds to 2 identical antigens or epitopes or can bind to two different epitopes. Means that if Immunoglobulin G is binding to two epitopes these epitopes will be identical or can be different...??? :/


texts:
I was in Cobija in northern Bolivia, and these spiders were hanging around a lamp post. There were over 100 of them.
The picture is not a good one, but I can describe them:

They were black with light blue stripes on their body, and the legs were black and yellow. They formed a big X with their legs.

Anyone know what spiders these are?


texts: Why have humans evolved much more quickly than other animals?

texts:
Humans have, in a relatively short amount of time, evolved from apes on the African plains to upright brainiacs with nukes, computers, and space travel.

Meanwhile, a lion is still a lion and a beetle is still a beetle.

Is there a specific reason for this?  Do we have a particular part of brain that no other animal has?


texts: Is oxytocin (or other peptide hormones) produced from a gene through translation, or is it made some other way?


texts: Can I make an population genetic analysis from incomplete protein?

texts: I have an dataset of fasta sequences. This proteins are not complete (My sequences have 700 nucleotides,while complete sequences have 1725 nucleotides)I would like to know if i can make an population genetic analysis from it(like TAJIMA-D test) and similars.


texts:
Self-preservation, or preservation anyway, probably happens throughout the animal kingdom, and perhaps through the plant kingdom as well (some plants/trees, apparently, produce chemicals to repel bugs).

Where does self-preservation stem from? Is it only about a biochemical imbalance?


texts: Structure separating the left atrium from the ascending aorta?

texts:
With reference to the (adult) anatomy of the human heart:

The left atrium (LA) and the proximal part of the ascending aorta (Ao) abut one another, as shown nicely in this image [1].  Is there a name for the wall(s) separating the LA and Ao?  And is this a single structure (i.e. septum), or is there a sinus?

[1] http://www.radiologyassistant.nl/data/bin/w440/a5097978b829cd_3-chamber.jpg


texts: Designing primers with restriction sites

texts:
I want to design a forward and reverse primer that include overhangs with restriction sites, with the dna used for restriction enzyme cloning.

If I want to send my dna to a synthesis company should I include the attached overhang with the restriction sites to the dna? Does it matter if the primers have the overhang of the dna within their sequence ?

From the sequence right at the end what bp sequence would be recommended I use for my primers if I want approx. 20-25bp for the primer?

See below for cDNA sequence:

Nde1 cut site: 5' ... CA|TATG ... '3'

Xho1 cut site: 3'...GAGCT|C...5'

cDNA with overhangs that have restriction sites, Ndel1 (5'->3') and Xho1 (3'->5')

5' catatg - ATGGGTTCAAACACTTCCAAAGTGGGTGCTGGTGCAGAAAAACAACAAGTCTATACTCCG
CTAACACAGATCGATTTTTCACAGTCTTTGGTTTCTCAATTGGATTCATCGAAGGAATCA
GACTATGTCACCAAGCAAAATGCAGAAAAGTTCATTGAGAAGAAGGTTTCACAAAGGCTA
TCTAACCTAGAAGTTGAAACGTTAAAGAAGTTTGAAGATACTTTGAACAATTCACTATTA
TCAGACGACGACAAGGATGCCGTTGATGGAATATCATCAAGTTCATTGAATAATCAAATC
GAGTCGTTGAACAAGAAACTAACATTATTTGATCAATTAGAGTTACAAAAGTTGGAGAAA
TATGGGGGTGCCAAAGGTAAATCTGATAAAAAAACCGACAACGGCAGCATTTCTATAAAG
GCAAAATTGACTGAGTGTCTTTTGGCCAATAAGGGCAAGCCATTGAATTGTTACGAAGAG
ATGGAAGAATTCAAGAAGCTCGTTATGGGTTGA - gagctc 3'


texts: Why proximal muscle weakness is seen earlier than distal muscle weakness in Dermatomyositis?

texts:
It is said that in dermatomyositis(DM) , proximal muscle weakness is seen earlier than distal muscle weakness. It is also said that , DM is due to damage to small blood vessels contributing to muscle injury.( from Robbin's textbook of pathology pg.no: 1238-1239, 10e)

Shouldn't the distal group of muscles being smaller show weakness earlier? Why inclusion body myositis does not follow the pattern as in DM?


texts: Is it possible to perfuse chemicals into brain after removal from body?

texts: I've read studies where fixatives (eg glutaraldehyde) have been perfused into the brain while it is still inside the skull. I would have thought that this could also be done after the brain is removed, provided all the veins/arteries are connected to a perfusion machine. Is this possible, and are there any major obstacles?


texts: How to batch convert gene names to protein IDs in Uniprot?

texts:
I have a list of >1000 "ordered locus names" from the STRING database (also called gene numbers, ORF numbers, or CDS numbers by uniprot). They're in the form of 'b0014', 'b0015', etc. I'd like to convert them all to Uniprot protein IDs.

I know how to do it in a non-batch way, since searching Uniprot for 'b0014' returns what (I think) is a protein ID. However I'd like a batch solution since there are so many IDs that need converting.


texts: Significant presence/absence of plant species

texts:
I have approximately 300 cluster of 200 different plant species and a presence absence matrix of all species versus clusters (since some species don't have clusters so they are checked if they are present or absent in other clusters). Now I want to find out if there is significant presences or absences of this plants in their clusters. At the same time I need to know which clusters have this significant presences. I want to know that if there is spesific software can do this or do I have to write code?

edit: it is not clear what i mean with significant presence and absence as i understand. by significant presence i mean "species being in the same clusters all the time. not one of them being in another cluster without the other." by significant absence i mean that "if leys say Y species never tooks place in clusters of which X species exist."


texts: ExAC Browser: What does a "dubious variant annotation" mean?

texts:
I am studying a protein in the ExAC browser. However it is flagged with a "LoF flag". What exactly counts as a "dubious" variant in ExAC.

I couldn't find any further information neither at the variant's page nor in the FAQs.

Link to ExAC browser.

Link to variant site (This is a bad example, because there is a multi-allelic warning, but this is the variant shown in the picture)

Further links to variants with LC LoF flag:

14-45636336-C-T

14-45636346-C-CTA


texts: Is it easier to burn a calorie of fat or a calorie of a carbohydrate?

texts: Say someone eats 100 calories of chocolate vs. 100 calories of carrots. Something tells me that eating the chocolate will lead to you generating more fat. Will it? Is it harder to burn the calories that you consumed from the chocolate?


texts: How to convert FASTQ file format into GTF file format?

texts:
I have a plenty of FASTQ files (FASTQ is a standard for storing the output of high-throughput sequencing instruments such as the Illumina Genome Analyzer) and need to convert them to GTF format (gtf - file format used to hold information about gene structure which significant feature is that it is validatable: given a sequence and a GTF file, one can check that the format is correct. This significantly reduces problems with the interchange of data between groups).

I assume that (if those formats are popular files' standards) there must exist some software that easily converts information from FASTQ files to GTF file.
Did anyone hear about any such (is possible open-source) software? I am familiar with R statistical package and SAS and can learn Python on a fly.

Thanks for any help.


texts: I live in KwaZulu-Natal, South Africa, and the only indoor bugs I've experienced issues with are fleas, as I have two cats (and a big garden). This morning, however, I put on a fleece top that had been lying around somewhere, got a lift to the store, and returned to suddenly feel a crawling sensation. I lifted up my shirt to find these tiny bugs crawling all over my upper body. I did some Googling, went upstairs and carefully observed my bedding and bed, however, the only evidence I found was a few newborn fleas / flea larvae (which I intend to deal with today). I should also mention that a flock of wild Egyptian Geese have been raising five goslings in my yard, and they get very close to me when I'm walking outside at times. My house is also not carpeted, it has oregon pine floors throughout. I tried to take a photo of the critters, however, they're very tiny and move very quickly, so it was difficult to get a clear shot. Any advice would be greatly appreciated.


texts: How can mammalian red blood cells live without a nucleus?

texts: Even though they have a shorter lifespan than other varieties of cells, I would think that 120 days without a nucleus is still quite a long time.


texts: What is meant by 'genes overlapping inherited structural variants'?

texts:
I am reading a journal paper about genes that are related to autism, and I have come across the following statement:

To assess commonality of biological function among rare risk alleles,
we compared functional knowledge of genes overlapping inherited
structural variants in idiopathic ASD subjects relative to healthy
controls

I am not sure what is meant by 'genes overlapping inherited structural variants'. I searched the definition for structural variants and according to Wikipedia, structural variation refers to the variation in structure of an organism's chromosome, such as deletions, duplications, copy-number variants, insertions, inversions and translocations.
However I am not sure what is meant by genes overlapping the inherited structural variants. Does this mean for structural variants that are common between ASD subjects, there are some common genes that are found in these regions (the inherited structural variants)? Any insights are appreciated.


texts:
A reciprocal translocation is denoted for example: t(4;12)(q32;q24) indicating that q32 on chromosome 4 being swapped with q24 on chromosome 12 if I understand this correctly.

My question is: How do I know whether this is a balanced or an unbalanced translocation?


texts: Design arbitrary degenerate primers (with non-binding criteria)

texts:
I would like to design a number of arbitrary degenerate primers (primers with variable bases, e.g. NGATWGCTSATNGC) for a TAIL-PCR.

I would like to be able to specify the following parameters for the design function:

Annealing temperature (ideally 44°C)
Degeneracy (how many variations of the AD primer there are (ideally 128 or 256)
Binding frequency on (mouse) genome (ideally 1/3000) - though this may be contingent on the degeneracy, and vice-versa.
Non-binding area (of course I would not like any variation of the primer to bind to the known-sequence area in between my specific primers and the unknown area which I want to sequence)

Any ideas of any tools that can help me with the above steps? For Primer design I have used eprimer3 thus far (with invariably satisfactory results) - but it seems to not support the concept of arbitrary degenerate primers.

Ideally, if I had a function which could sort out the first of the above criteria, I could use Biopython and BLAST to script the rest myself. Though the binding frequency would take hours if not a day or two, for BLAST to determine it. It would greatly help if anybody already wrote something more elaborate for this.


texts: Harvest honey without damaging brood cells

texts:
I want to make a homemade beehive, I want to know how to differentiate honey cells and brood cells, therefore, I'd like to know how can I organize the beehive so bees will create honey and brood cells separately. By this way, I would be able to harvest the honey without killing the larvaes :)

Ancillary issues : Do bees need cells to sleep in ? Can I populate a homemade beehive with several bees caught from my garden ?

Thank you for your attention :)


texts: Why are many unable to defecate and urinate simultaneously?

texts: Many people (including myself) do not defecate and urinate simultaneously, but rather in succession.  Only after one is completed, the other commences.  I have noticed this in myself, but the internet suggests this is neither unique nor universal: for example, see quora, reddit, grasscity.  I don't seem to find any references explaining why people would be unable to do both at the same time.


texts: How much energy does human body fat contain?

texts:
I have been reading the Wikipedia article about food energy, but as I'm not a biologist, I don't really understand it properly, so I came here to ask you guys.

My question is: If a human body needs X kcal of energy and it's taking it from the stored fat, how much fat (weight/kg) does it need to burn?

I know that 1 gram of fat represents 9 kcal of energy, but according to the food energy article, the efficiency of getting that energy isn't 100%, so the formula might be a lot more difficult.

I'm not sure what is the real efficiency value here. The article mentions more values, ranging from 18% to 40%.

P.S.: If this belongs to Chemistry.stack, please, tell me or move it there.


texts:
I have a question regarding the following image:

In my book, it states that this is a dorsal view which shows the formation of the neural tube. However, isn't this a caudal view of a transverse section? A dorsal and ventral view wouldn't apply to a transverse section right?


texts:
Why can the immune system kill its host?

It is always better to just take up the insect poison, or peanut protein etc. instead to kill the host by preventing the breathing.

Is it just a modern symptom or did humans always have to fear death from anaphylaxis after an insect sting?


texts: Is there a biological basis to physical attraction?

texts:
Is there something encoded within us that makes us attracted to, e.g., someone

taller or shorter
with blonde or brunette hair
with green or blue eyes?

Or, is this phenomenon completely based on our social/cultural environment?


texts: How does Line Integrate work on a laser scanning confocal microscope?

texts:
Most microscope software provides options for line average or line integrate as a function that helps the signal to noise ratio when taking an image. The math behind line average seems straight forward, but not so much for line integrate.

Line average takes X number of scans per pixel and averages the scans into a final pixel intensity. The same principal of multiple scans for a single pixel is taken for line integrate, but the math involved in the integration of the intensity is not clear to me. I assume it involves summing pixel intensity and operating on that somehow, but it simultaneously is able to reduce noise in the system so I am not sure what else it is doing.


texts: Why do mutations in Drosophila dsx (double sex) affect both males and females?

texts:
Reason: Loss-of-function mutation of dsx gene in female embryo leads to production of a nonfunctional protein that fails to repress male specific gene expression. So somatic characters of both the sexs persist forming an intersex.
...This is all that I have figured out.

But what is the reason of appearance of intersex characters in male drosophila? Is it due to gain-of-funnction mutation.


texts: How to preserve tissue DNA without using formalin?

texts:
Except using formalin to preserve human corpse for autopsy. I heard from the news that technique damages the DNA in the organs

Question:
Suppose corpse will be investigated next by another juridical unit
Do we have any other techniques which are better than this?
For example like freezing in the fridge. Because police office needs all above questions to complete his case.


texts:
The article about "rapture sequencing" found
here says:

  "This protocol also recovers more unique (nonclonal) RAD fragments, which improves both standard RAD and Rapture analysis. Rapture then uses an in-solution capture of chosen RAD tags to target sequencing reads to desired loci. Rapture combines the benefits of both RAD and sequence capture, i.e., very inexpensive and rapid library preparation for many individuals as well as high specificity in the number and location of genomic loci analyzed."

My question is regarding the second sentence. What does it mean to combine in-solution capture of chosen RAD tags to target sequencing reads to desired loci? How do the RAD tags target sequencing reads, if that is what is being said here? How does this relate to combining the benefits of both reduced representation sequencing techniques, or am I missing the crux of the paper?


texts: ProteomeCommons.org seems to once have been a resource for raw proteomics data. Thought, the website now offers gardening tools. It seems to be hacked. Does anyone know whether the data is still available somewhere?


texts: How do viruses or bacteria survive outside the body long enough to spread?

texts: Say I cough on my table, then someone else touches it and picks up something I've got... how is it that these things can live outside the body, how long can they manage it, and how long is generally 'safe' to consider something no longer carrying these germs?


texts: Why are particulate matter toxic to humans?

texts:
There are many studies on fine particles (PM2.5) and their fully negative effect on human health. There doesn't seem to have any positive aspect of inhaling particles, except very particular ones, but most often people smoke, and release all sort of unwanted and toxic PM2.5, same goes with for fuel combustion.

At a huge dose, we die within minutes, like in a gas chamber, at small dose below this hazardous health risk level, is it still dangerous to us? If yes, why aren't we equipped to fight them, I guess this smoke concentration and pollution level is very recent on human evolution scale, but at the lowest layer of life, bacteria may develop to break and eat toxic particles, does it happen it our blood? Is it hard to explain to a non-biologist like me?


texts: What is the difference between Ostracodermi and Placodermi

texts:
I looked the word origin and found Placodermi is PLATE SKINNED while Ostracodermi is Shell Skinned.
Can someone please explain the difference between being Plate skinned and Shell skinned?


texts: Why does influenza sometimes cause GI symptoms?

texts: I'm speaking strictly of influenza, not gastroenteritis which is sometimes mistakenly called "stomach flu." I just read this article on the mechanism through which rotavirus causes diarrhea and vomiting. Since the flu is a respiratory disease, through what mechanism does it sometimes cause diarrhea and vomiting? Does it also release proteins that activate the enteric nervous system in the gut? Is it caused by inflammation from cytokines being washed down the throat in mucus? Or is it the result of a secondary infection resulting from the decreased immune system?


texts: What is the difference between non-coding and intergenic regions?

texts:
The initial question was about understanding what is in the downstream of a gene in a eukaryotic organism. I understand that this region is located 3' of a gene, and therefore I would expect to find non-coding regions, but is there a difference between non-coding regions and an intergenic region?
A small background of what I am doing: I am studying the effect of retrotransposons in S. cerevisiae populations, and I already identified the potential impacts of these retrotransposons and these were the consequences:
Upstream gene variant   49
Downstream gene variant 42
Intergenic variant  4
Transcript ablation 3
Coding sequence variant 1
Feature elongation  1
3' UTR variant  1

So is it clever to say that downstream of a gene there are non-coding genes?


texts:
Even though knowing the number of neurons in a functional unit or with the same function is not of main importance, it may be interesting to know their orders of magnitude, especially in the human brain. For example:

|------------------|------------------|
| cerebellum       | 100,000,000,000  |
| cortex           |  20,000,000,000  |
| telencephalon    |  10,000,000,000  |
| brainstem        |   1,000,000,000  |
| sensory neurons  |                  |
|          haptic  |     500,000,000  |
|          visual  |     100,000,000  |
|        auditory  |           2,000  |
| limbic system    |                  |
|         amygdala |      10,000,000  |
|------------------|------------------|

Surely, for many parts of brain you will find a reference where the number of its neurons is estimated (e.g. for the amygdala) - when you search hard enough. I also found The Human Brain in Numbers where some numbers are given. But I am looking for a reference where many of these numbers are given in a systematic way, ideally in a table like the one above. Is there any?


texts: Can salt-water frogs survive in normal water (A well)?

texts:
I don't know much about frogs, but there seem to be salt water frogs.

1) Are there such things as salt water frogs?

2) Are there frogs that live in the sea? (in reference to Vivekananda's quote)

3) Can salt water frogs survive in well water or fresh water?

  Well, one day another frog that lived in the sea came and fell into the well. - Vivekananda


texts:
Is there interphase between meiosis I and meiosis II?
After 2 haploid cells are formed in meiosis I, do the cells go through a period of interphase (G1, S, G2) or do they go directly to meiosis II?


texts: DNA extraction from oil-containing seeds

texts: Which protocol of DNA extraction from plant oil-containing seeds take fast and good result in purity that can use in RT-PCR(Real Time polymerase chain reaction)?


texts: Enzyme Inhibition by alpha-2 macroglobulin

texts:
Alpha-2 macroglobulin is a plasma protein which acts as an anti-protease. It does so by a "bait mechanism" - the protease cleaves the bait domain, following which a conformational change causes binding of alpha2-macroglobulin with the protease, and consequent irreversible inhibition of the protease.

This seems to be very similar to "suicide inhibition" or "mechanism based inhibition" - when an enzyme catalyses a substrate analog's conversion to an active inhibitor, which subsequently binds strongly to the enzyme to inactivate it.

Is alpha2-macroglobulin's inhibition of proteases a case of suicide inhibition then? If it is, why is not more commonly described as that (I have not come across any description of alpha2-macroglobulin as a suicide inhibitor)?


texts: Why do human eyes glow red on a photo and dog's eyes green?

texts:
Previous Research

I know that cameras sometimes come with an anti "red eye" functionality that involves two flashes, presumably the second flash coincides with the shutter opening.

Question

Why do camera flashes sometimes lead to photos of humans with red eyes? And why do dog's eyes appear green?

Related

The reason for the green dog's eyes has been answered quite shortly under the question "why-do-dogs-eyes-glow-green-on-a-photo", but that question does not answer my specific question: Why do humans have red eyes on flashed photos and why are dog's eyes  green?


texts: To what extent can bacteria actually see?

texts: I found some popular articles (e.g. nbcnews and iflscience) that bacteria can "see," but I highly doubt it's in the same way as people do just from looking at the limitations in the vision of small animals like insects. So what exactly are bacteria capable of "seeing" or what are the limitations of their vision?


texts: Why are fifth order Markov Models, the ones most often used for gene prediction?

texts:
As far as we know that smallest polypeptide chain length is 60 amino acids - so if we found an Open Reading Frame (ORF) of about 60 codons without the interruption of stop codon we can consider it to be a possible coding region or gene.

The fifth order Markov Model uses hexameric frequency to predict coding regions, however this doesn't seem very specific.

Why wouldn't we use higher order Markov Models with higher frequencies and more specificity? Wouldn't increasing the order of Markov models prevent false positive results?


texts:
I wish to transfect yeast and want to control my efficiency. So I thought to use pEGFP-N1 as control. The EGFP is driven by a CMV promoter. Can yeast read CMV promoters.
Thanks
Hermann


texts:
A microbiologist has discovered what she thinks are two new types of algae. The first cell
(Organism 1) appears cubic and is approximately 1.5 μm long, 1.5 μm wide and 1.5 μm deep.

The second (Organism 2) is rectangular and 2 μm wide by 5 μm long by 2μm deep.

a.  What is the surface area/volume ratio of each organism?

b.  Which organism will find it more difficult to interact with surrounding environment (receive nutrients, excrete metabolites etc.)?

c.  How will this organism cope with the reduced capacity to interact with environment?

In respects to question A.

V of Rectangular organism= (V = L x W x D)

Surface Area= (L x W)

Im assuming these simple rules still apply to organisms concerning minuscule measurements.

Im assuming for question B., that the molecule with the smaller dimensions will have the most difficult time interacting with its environment, due to the fact that it has a smaller perimeter with less channels & ports.
I am completely lost for problem C.

Any insight Would be awesome. Thanks all !


texts: Brown spider in New Hampshire White Mountains area found in sheltered areas around house

texts: Found this light brown spider in sheltered locations outside my home in Franconia, New Hampshire.  Should I be concerned about its presence and the dozens of others?


texts: A question about how the brain determines the source of a sound

texts: If a person's eardrum vibrates, let's say, 440 times per second for 1 second, how does the brain know its because 1 sound source vibrated 440 times, as opposed to 440 sources vibrating once, one after the other, or 2 objects vibrating 220 times per second, but out of sync with each other, or any other combination? Thanks.


texts:
I went to the doctor today with my girlfriend, and the doctor said that she had a virus but doesn't know which one and she should let the infection heal with some rest.

The fact that the doctor didn't know what type of virus she has bothers me.

Do physicians/biologists not know all the different types of viruses out there? Is it not possible to identify all of them?


texts: Any relevant knowledge/studies about voluntary goose bumps

texts:
I'm not entirely sure how normal this is, but since I was a child, I've been able to produce myself voluntarily a "chill" sensation that seems to start on my head and traverse the rest of my body, being least intense in the feet. Looking around the internet and forums, looks like other people but not everybody also describe this ability. However, unlike other people's reports, I don't see "goose bumps" on my skin, at least there aren't any visibly; it's just the sensation.

Does anybody know if there are any relevant studies or knowledge out there about "voluntary goose bumps"? Is there even a proper name for that?


texts: Can a human cell live indefinetely in a controlled environment?

texts:
How long can a human cell live in a controlled environment, given all necessary nutrients, temperatures, mechanisms for waste removal, and other requirements are provided for? Put differently:

Can a human cell live on indefinitely?
What's the longest known lifespan recorded for a human cell in a controlled environment?


texts: What further research can the result of gene variation detection be used for

texts: We do a research on a particular cancer (for e.g. breast cancer). Now, we have a result for the gene variation detection (VCF file). What next steps do we need to do? We don't have a clear picture about this. Can you give us some directions or few papers as an example? (of course it is a huge number but just mention a few). Thanks!


texts: Why some plants can be propagated from a leaf cutting but some can not?

texts:
I understand the process of leaf-cutting propagation as following:

1) with the help of auxin from the leaf, callus is forming on the wound and then roots are forming from callus,

2) with the help of cytokinin from roots, shoots are forming.

Is it wrong or too simplified or do I miss something? Why some plants can do this and some can not?


texts: Toothache is a useful signal to us as we can visit the dentist who can try to fix any problems with our teeth. But what is the natural biological role of toothache? Does toothache make animals take action that helps them to deal with their dental problem?


texts:
I found this monster on my lawn in New Hampshire USA, with a pileus that measures about 8.5 inches across. My mother has threatened to eat it unless I can demonstrate that it's poisonous, so any help identifying it would be greatly appreciated. I should mention that the mushroom is a slightly richer more brown than the fluorescent lighting suggests.

My best guess so far is an armillaria of sorts.

Cheers!


texts:
Is the molecule nitric oxide responsible for healing blood vessels?
How does nitric oxide heal the blood vessels?

I watched a documentary about the healing effects of nitric oxide. In the video I saw a cardiologist show an X-ray picture of one of his damaged heart blood vessels, and then another X-ray picture showing the same heart blood vessel completely healed. He claimed it was due to a radical change in his diet of consuming lots of nitrogen rich vegetables which the body in turn converted to nitric oxide. Is this possible?

Sources :

The original source was the youtube video Forks Over Knifes, however it was recently taken down. I have provide the following links which provide a little bit of information :

http://www.happyhealthylonglife.com/happy_healthy_long_life/2010/06/esselstyn-session.html

http://www.happyhealthylonglife.com/happy_healthy_long_life/2010/12/no.html

Dr. Caldwell Esselstyn was the one who made the statement about heart health and nitric oxide, also showing the xray pictures of one of his colleague cardiologists in the documentary.


texts: Vegetation Monitoring - Why permanent plots

texts:
Why do most vegetation monitoring programs rely on permanent plots?

Take the context of a single ecological restoration site, for example.  Let's say the variable of interest is cover by plant species, and monitoring is conducted throughout several seasons to track the relative/total cover of multiple species.

If plots are randomly sampled within homogeneous vegetation assemblages, why not just establish new plots each sampling period, rather than locating and re-sampling the same plots over and over again?

If the goal of sampling the is to represent characteristics of the population (i.e. the homogeneous area of vegetation), then why do researchers always sample permanent monitoring plots again and again rather than using a new set of randomly selected plots each time?


texts: response elements in transcription regulation

texts:
I'm studying eukaryotic gene regulation and I want to know whether there are some instances where transcription factors don't need to bind to response elements to initiate transcription. RNA polymerase can directly bind to the DNA.
I can't find any evidence for this. Does anyone know of a case that exhibits this?


texts: What is the state-of-the-art algorithm for multiple sequence alignment?

texts:
Which algorithm or algorithms are considered the standard or state-of-the-art for multiple sequence alignment?

How big is the need for better algorithms? How many sequences need to be alignment in a typical test? I am trying to understand how important problem this is in bioinformatics.


texts: Is there any evidence showing that copy number variation changes over time? I'm wanting to model interactions in expression level as a dynamic bayesian network, but an assumption my approach will need to make is that it is static.


texts: List of species recently found of economic value

texts: Is there a website or organization cataloging lists of biological species to have been recently found of great economic value? For example, a plant that wasn't of economic relevance a while ago but has been found recently to be important, due to advances in breeding varieties and more crops being planted. The same for species that were already important but have turned to be even more important in the last few years.