texts: Exact definition of 'convergent' and 'divergence' in cell signalling?

texts:
From what I understand, we refer to 'signal convergence' as being when two different ligands/stimuli lead to the same (at least in part) responses inside a single cell. This may or may not be due to activation of the same pathway, so for example we can refer to the response of a muscle cell to adrenaline and to stimulation by the nervous system via acetylcholine as convergent because they both lead to the release of calcium. We can also refer to the activation of the phosphoinositide pathway by both activation of beta phospholipase C via a heterotrimeric Gq protein, and activation of gamma phospholipase c via the tyrosine kinase pathway, as signal convergence.

So it seems to me that 'convergence' is defined on the level of the cell with it being, in a nutshell, different stimuli resulting in the same effect regardless of at which point in some internal signalling pathway the two responses 'converge' (at least in part).

Now with divergence I am getting slightly more stuck, and I have not seen a single, clearly stated, definition. Firstly, does divergence refer only to the level of the cell, or also for the whole organism? In particular, I am thinking of cases where a single ligand has different responses in different cells, such as adrenaline leading to increased contraction in muscle cells and glycogen breakdown in the liver (I know this isn't the best example because adrenaline technically leads to glycogen breakdown in both cell types).

Perhaps instead divergence is only referred to on the level of the cell, as with convergence? So for example generally tyrosine kinase stimulation activates several different proteins, which trigger different responses: ras, gamma phospholipase C etc. Even the phospholipase C pathway produces DAG and IP3, which have different responses. But then it seems to me like practically all pathways are divergent if this is the case, because generally pathways lead to several responses inside the cell. So with the case of phospholipase C which cleases PIP2 to DAG and IP3, the DAG can regulate metabolism and transcription etc via protein kinase C and the IP3 leads to calcium ion release that causes muscle contraction. Would this be referred to as divergence?

I would greatly appreciate if someone could just state what exactly convergence and (especially) divergence refer to. I am relatively new to cellular and molecular biology.


texts: What is the reason behind more severe proteinuria in nephrotic syndrome than in nephritic syndrome?

texts: Why is there less protein loss via urine in case of nephritic syndrome than in case of nephrotic syndrome?


texts: Why is Thermus aquaticus and Taq Pol stable?

texts:
What is the molecular basis of the stability of the bacterium Thermus aquaticus and the enzyme Taq Pol it produces ?

I have tried googling this but did not get a good answer.


texts: Pitch shift in hearing after wisdom teeth removal

texts: Yesterday I had my wisdom teeth removed. This morning, when I heard our phone ringing, it sounded a little lower-pitched than usual (I have perfect pitch). Sure enough, when I opened FL Studio (music-making software) and loaded up one of my projects, I had to adjust the master pitch up by about 20 cents for it to sound "in-tune". What could cause this shift in pitch perception?


texts: How does it make sense to speak of heritability of qualitative traits?

texts:
As far as I understand, heritability is defined as "proportion of variation of a phenotypical trait due to genetic variation between individuals in a population".

I see the concept is being applied on quantitative that can be measured with numbers, can be compared (i.e., $\mathrm{A}$ is taller than $\mathrm{B}$ by $x$ units of height) and varies continuously to form a distribution (e.g IQ forms a Gaussian distribution).

heritability in the narrow sense ($h^2$) has a mathematical definition. For a given quantitative trait $x$ of a population that forms a distribution with certain average and certain variance $V_P$ then $$h^2 = \dfrac{V_G}{V_P}$$ where $V_G$ is the variance in population due to variance in genetics and $V_P=V_G +V_E$ where $V_E$ is variance in population due to enviromental variation (I ignored other terms in the definition of $V_P$).

IQ has mean of 100 with $h^2=0.8$. So for a person whose IQ is 105 (5 points above average), genetic contribution contributed to this $0.8*5=4$ points difference and the remaining 1 point difference is environment.

I also see how the concept can be applied on qualitative traits (by this I mean traits that don't satisfy the properties of quantitative traits) even in the absence of well-defined notion of variance $V_P$ because the trait doesn't form a distribution. For example in a population of flowers that can only be red or blue.This red/blue trait does not have a well-defined $V_P$. We can still meaningfully say that this trait has $h^2=1$ since any variation in the color (red vs blue) is due to genetic variation. We can also speak meaningfully and say a certain qualitative trait has $h^2=0$ meaning any variation in the trait is due to different environments.

On the other hand, I think qualitative traits can have either $h^2=0$ or $1$ but no value in between, since $V_P$ is not well-defined (and hence $V_G$ and $V_E$ as well are not well-defined) for them.

Consider sexual orientation for example. Based on some twin studies it was estimated that homosexuality has $h^2=0.5$. But what does that mean really? how does homosexuality vary to form a variance? A person is either homosexual or not(heterosexual, bisexual or asexual).

My question is how to apply this $h^2=0.5$ value of homosexuality in the same way I applied it above on IQ?

More generally how to meaningfully be able to interpret heritiability of other qualitative traits (mental disorders for example like schizphrenia with $h^2=0.8$) that has has no well-defined $V_P$ and whose $h^2$ value is not $1$ or $0$ but rather lies between them?


texts: What is the mechanism behind the association of a sensation with a stimulus?

texts:
I'll explain the question with an example.
Consider Gustation: glucose tastes sweet, bitter gourd tastes bitter and salt tastes salty. Now, sweet obviously feels good but suppose there is an alien species whose biochemistry is different from us,  they don't use glucose as a fuel. Now glucose maybe toxic to them so they experience a bad taste whenever they ingest glucose. In this case, the sensation is different!

Another Example would be Photoreception. How is it decided that light having wavelength of 700–635 nm would be considered red and not blue? I know that your answer would be "This is because light of this wavelength stimulates the red cone and not the blue one." Then my question would be why stimulating the red cone gives us the sensation of red colour and not of blue colour?

Similarly, Why does air of temperature higher than our body gives us a sensation of "Hot" and not of "Cold"?

I know that having different sensations for different stimuli affects our reproductive fitness. Those which can detect changes in the environment are more likely to survive than those which don't. Those which developed "sweet sensation" for glucose can gain more energy than those who don't. But it doesn't explain the relationship between the experience of a stimulus and the stimulus.

It seems like our own body has invented experience and sensation and these phenomena don't have any physical significance.


texts: Why is urea not converted to ammonia in the body?

texts:
After the liver processes metabolites to produce urea and other by-products, these travel in the blood to the heart, then they are oxygenated, and some travel through the renal artery to the kidneys.

Urea in water can decompose into ammonia which is toxic, as mentioned in a textbook page no 170 (6), under production of ammonia.

Reactant and product are at equilibrium. Also a gaseous product, CO2, is present which could potentially escape during oxygenation of blood. Hence, according to Le Chatelier's principle, an equilibrium shift towards  the product is possible

NH2CONH2 + 2H2O → (NH4)2CO3 ⇌ 2NH3 + H2O + CO2

The chance of urea decomposing into ammonia is high while travelling in the blood (i.e taking long route) and in the bladder, but it still does not happen. Why not?


texts: What species is this interestingly colored brown moth

texts:
This fella fluttered into a kitchen at night, maybe from the vegetation in the yard, and I got lucky to trap it in a transparent plastic bag for a while (with enough room to move, which it started doing at about the same pace it had been flying before but sometimes sitting still) so I got a couple of close-up pictures.
I think the coloring and some other features are too far off the familiar plodia interpunctella to be the same species, also a number of other features seem different in appearance and behavior. (Wings not folded straight back and much wider, doesn't like sitting still on wall for extended period of time.)
Length is about 12-13 mm (wings included and folded). It also sat down wings spread out very wide where I first found it (no picture of that posture included).
Location: Southern part of Germany, city landscape with river/lake within half a mile
What species is this and what would it live and feed on (if the adult feeds at all in this species) ?
As it was examined bottom up, I noticed a contracting and expanding movement of the abdominal segments (roughly last 2 images). What is that movement?


texts: Collected in northern West Europe in autumn 2017


texts: What is the evolutionary or biological origin of apathy and indifference. Is it uniquely a human thing?

texts:
I believe that social apathy is one of the main reasons why changes cannot easily be brought about in contemporary society due to the general lack of interest of the public, and this has ties with many mental diseases

But does the act of indifference and apathy actually has an evolutionary advantage and more curiously, do animals known how to demonstrate that in some manner?

A Google search on "evolutionary origins on apathy" returns no relevant hits other than the links to schzophrenia and other related neuropathies

  Are there known studies on apathy and indifference in animals and their evolutionary origins?


texts: Species Identification: Snake, New Mexico

texts: The snake is about one and a half inches in diameter at its widest, a half inch at the head, and about two feet long. I found it in central New Mexico. It's hard to see the head in the pics, but it wasn't triangular or any bigger than the body/neck


texts: What are the application areas of Pattern formation studies specific to biology?

texts: I was reading about reaction-diffusion processes, morphogenesis concept by Alan Turing and works of Murray in describing pattern formation on animals etc. But one question which came to my mind was even if we describe these processes in mathematical and physical contexts, are there any application areas awaiting for the results?


texts: Algae are a source of taurine and mushrooms are a source of vitamin D3. Both also contain high protein. So, it seems possible to feed a cat or other felines without any meat. Are there any concerns to have them live with this kind of diet?


texts: Bioenergetics of bioconversions: is there a surplus of energy?

texts:
By bioconversion, I mean a microbial process during which resting cells are used in order to convert a substrate to a desired product, whithout cell growth. For example, in this paper, they used Lactobacillus reuteri to convert glycerol to 3-hydroxypropionaldehyde, while L. reuteri can't grow on glycerol. Basically, during bioconversions, cells produce energy for their metabolism, but do not grow.

The energy thus yielded by cells is supposed to ensure their energetical maintenance cost. I was wondering what happens to cells if the energy gain is superior to maintenance needs? Is there some kind of homeostatic regulation of the ATP/ADP ratio? If not, what could be the consequences of too much ATP?


texts: If all B cells are present at birth, why should the primary response to an infection take longer than the secondary response?

texts:
When learning about the immune response, my teacher mentioned that all the bodies B cells are present at birth, and there is one to counter every disease. But if this is the case, why should the primary response take a long time?

As far as I know, the primary response involves the non-specific response followed by the specific response, where APCs cause the activation of T cells resulting in clonal selection and expansion of T and B cells. The B cells then differentiate into plasma cells and produce antibodies. It results in the memory cells being produced, which can quickly reengage the specific response the next time the pathogen enters.

Why doesn't the body just make memory cells to begin with? As if it has already encountered every possible pathogen. I presume it is just a lack of specificity in the A level teaching, but I am curious to know what I am missing here.

Thanks,
Jamie


texts: Can Mung Bean Nuclease only digest a ssDNA 5' overhang?

texts:
Can Mung Bean Nuclease only digest a ssDNA 5' overhang, if the double-stranded region of DNA (20bp) is A-T rich at the ends?
Does this enzyme degrade 5' overhang (5bp or 30 bp) with 100% efficiency?


texts: What happens to eyeball when you push your eye muscles harder?

texts:
I have myopia and I read that the rays of light intersect before the retina.
When I can not see clearly I can push somehow my eye muscles and can see a bit clearly. The object gets clear but moves some distance ahead (getting smaller).
My question is: What is in fact happening to the eyeball? Do the eye muscles contract it and make it more round than ellipsoid thus bringing the retina forward  so the light intersects on it?
In fact I have the feeling that the eye ball gets longer (ellipsoid).


texts: To what extent is Ebola airborne? (aerosols)

texts:
Recently, CIDRAP at the University of Minnesota announced that Ebola may be more transmissible through aerosols than previously thought.

I lack the familiarity with the field to critically evaluate this release. They also seem to more interested in making the point that there is a risk of aerosol transmission, not to settle whether it does transmit by air or not.

What is the simple answer? Can Ebola really be transmitted by aerosols?
If so, how come nobody realized this before? Is this a general phenomenon allowing any pathogen to become airborne? I don't see why you couldn't aerosolize a great many pathogenic objects, not just Ebola virus.
How does the number of virions necessary for successful infection compare to what you could get from aerosols?


texts:
The post Solving Hardy Weinberg problems offers an easy explanation of Hardy-Weinberg rule. The current top answer explicitly does not talk about the assumptions of Hardy-Weinberg. A model makes sense only if one is able to tell its domain of definition and therefore it is critical to understand the assumptions underlying Hardy-Weinberg assumptions.

What are the assumptions of Hardy-Weinberg rule?


texts: What is the name of this plant with leaves having two different shades of green?

texts:
I am trying to find the name of this plant. I am attaching the relevant images. Thank you for your help.

Location: Hyderabad, India


texts: Are there animals who do things just for pleasure like humans?

texts:
In a debate my father said that only humans do things that are not directly linked to survival(painting, playing musical instruments, singing etc). He said that this is because we are "special" and not like other animals on the planet.

I said that this is only because we have much more developed brain than other animals. But now I'm also interested in one question.

Are there animals who do similar things(not exactly same, of course) not for mating/survival but just because they like it?


texts: Rosette formation: in which order are leafs created

texts:
From the picture below, it seems that new leaves are formed something like this (if you imagine the plant as a regular, 12 hour clock):

new leaf at 12 o'clock, then at 7 o'clock, then at 2 o'clock, then at 9 o'clock, and so on.

I imagine it could be some things as simple as 'always add 190 degrees'. Are the exact rules for this documented somewhere for various plants?


texts:
The word seems to be of German origin.
I have it here

  Saccus lymphaticus inguinalis,
  Saccus lymphaticus jugularis,
  Saccus lymphaticus posterior,
  Saccus lymphaticus retroperitonaealis.

I would like to use the word "sinus" instead.
However, Google search does not give good results for it.

What is the meaning of the word "saccus" here?


texts: I'm studying microbiology and I see these words - epizootic and enzootic, often but there are no clear explanations for them online. Can someone help please?


texts: Non-fatal / low-harm measurement of Drosophila traits

texts:
I am trying to generate some candidate traits to measure in a fitness assay of wildtype outbred (lab population) flies. The key trait I will measure is lifespan.

I am looking for some additional traits which can be measured from the same flies as those in the lifespan assay without harming or killing the fly in the process. For example, I could measure wings using a technique devised by the Houle Lab called WingMachine. I think I could also do some other measures with the same equipment, leg length etc.

The traits should also be present in both sexes (can be monomorphic or dimorphic) and quick to measure; I'm aiming for 200-250 measures/collections/images a day. Traits that can be measured properly in a fly which has died of old age would also work. Traits can be morphological, behavioral etc..

What other traits can be done like this?


texts: Why are trichomes important for both the roots and shoots of plants?

texts:
In what ways are trichomes vital to the plant?

Why have them on the plant shoots as well?


texts: What is this grainy surface on my two-week-old sourdough starter?

texts:
I'm baking bread at home as a hobby, using sourdough. After skipping one baking day, I haven't used my sourdough starter for two weeks. When opening the jar in which I keep it, I saw the surface had taken on this unusual look. When viewed from the side through the glass, the contents looked normal below the surface.

The sourdough starter consists of whole rye flour at 100% hydration (flour:water = 1:1). I had removed it from the ripe sourdough on the last baking day and have since kept it in the refrigerator with a lid (only loosely screwed on) for 13 days.

Normally I'm using it already after keeping it for 7 days, and I'm used to the surface turning light gray and dry (but smooth and soft) after that time, which didn't ever seem to be a problem. Now the color of the surface was identical, but it has become grainy, like tiny worms.

I have removed and discarded the top layer (3 mm). It was soft (unlike dried out, crusty, dough) and smelled a bit like fresh yeast. Below that, the contents smelled normal, like very ripe sourdough.

The jar is about 6 cm in diameter and was filled to about 2 cm (→ volume of the starter ≈ 60 ml).

What are we looking at here? Could it be actual yeast cells (or other microorganisms normally found in sourdough)?
Is it harmful?

After 13 days (click for full-resolution version)

Reference pictures

After only 2 days, the starter looks like this:

(click for full-resolution versions)


texts:
I did some tests to a bacteria colony and I observed the following:

First of all let's start from the shape and after that we move on to the chemical tests that I did to them:

Form: Circular
Colour: Yellow-to-white (something like pale yellow)
Margin: Entire
Elevation: Flat

Chemical results:

Gram: Negative
Catalase: Positive
Oxidase: Positive

After some research to the databases, I figured out that it might be:

If it belongs to the family of Pseudomonas:

Chryseomonas luteola OR Pseudomonas luteola group Ve-1 with a chance of 48.21%
Flavimonas oryzihabitans group Ve-2 with a chance of 48.21%
Xanthomonas maltophilia OR Pseudomonas-like spp, with a extremely low possibility of 1.34%.

So, my question has 3 parts:

Can someone please tell me if my hypothesis is right?
And if it is possible which bacteria from the above is the correct?
If you manage to find the correct type of bacteria can someone tell me the ideal enviroment to study them better? (agar plates, temperature, time needed, etc.) Thank you for all the efforts made!

Important notice: I have used a blood agar plate with a concentration of 5–10%. It contains as far I know, mammalian blood maybe from sheep or horse. I forgot to check the temperature, but I don't think that it is very important.


texts:
What purpose does the wax coating on blueberries serve? Is it some sort of protective layer?

A search on the web reveals that it is called "bloom". But the source is not a credible, scientific source. And it doesn't explain in detail what the coating does.


texts: Optical and digital magnifying enough to see red blood cells?

texts: I am buying a microscope with 150x optical zoom and an overall of 800x zoom (5x digital zoom). Somewhere here I read that a 400x zoom will be required to see the red blood cells. Will the digital zoom do the trick as well or I need to look for an alternative?


texts: Can hunting of large specimens of a species make the size and weight of the species tend to be smaller?

texts:
Siberian tigers in the wild don't grow as much as they used to be in past (in the 1900s).
Their average weight was measured 176 kg in 2005 study. But it was also said that those tigers observed in study were sick and in conflict to humans.
I think their smaller size is because of low prey density because at that time, hunting of animals that come as tigers' prey was high.
Could it also be because all the large specimens were shot?


texts: Do humans sneeze or cough in their sleep?

texts:
As far as I know, I've never seen anyone sneeze or cough while they're sleeping. Google wasn't very helpful either; a lot of contradicting claims.

So the questions remains: do humans sneeze or cough in their sleep? (a few other things I've never seen with sleeping people are yawning and vomiting) If they don't, why?


texts: Modularity score comparison between different algorithms in network analysis

texts:
I used different algorithms for splitting my large gene network into different sub-networks using Cytoscape. I compared the modularity scores and decided that the algorithm with the best modularity score will be used for clustering the network.

My colleague came up with the argument that modularity scores can only be compared for different number of clusters being created by the same algorithm.

So, my question is if modularity scores can be used to compare between different algorithms or only in the case of the same algorithm producing different number of clusters.


texts:
If tardigrades are so resilient and nearly immortal, why are they so rare when looking at samples of a pond or lake, where tardigrades should thrive?
I've met people who've been studying protozoa and metazoa in nature all their life and have only seen tardigrades once or twice!


texts: How does Vibrio cholerae benefit from infecting its host?

texts: As far as I know, V. cholerae secretes a toxin called choleragen into the intestinal lumen which affects the intestinal epithelial cells causing release of Na+ and Cl- ions into the lumen and reducing the lumen's water potential which causes water to flow into the intestinal lumen resulting in diarrhea. How does this benefit V. cholera in any way?


texts: Does myopia tend to decrease the risk for later hyperopia?

texts: It seems like being nearsighted for much of your life due to elongated eyes would make it easier in general to focus on near objects rather than far since the lens would not have to change much. Since in old age we lose the ability to focus close images due to a hardening of the lens over time, wouldn't having eyes shaped more for near images be helpful in maintaining the ability to see close up, and thus nearsighted, or myopic people, would be less likely to develop farsightedness, or hyperopia, with age? It seems then that nearsightedness is more of an adaptation that occurs at a young age, so that these people can work up close for longer periods of time both in the the short term(studying) and long term(age). I'd love to hear if any research has been done on this subject, and any other input you have.


texts: How many molecules NADH are produced in the Krebs Cycle?

texts:
I don't know which source i'm going to follow.

Some say its 3 molecules NADH per cycle → 2 cycles × (3 NADH) = 6 NADH

Some say its 4 molecules NADH per cycle instead?


texts:
For a few weeks now I keep seeing these small bugs in my flat. I first noticed them in my bed when I was reading with the light on and had the window open during the current warm spell. Today I had several of them in the kitchen, some in the cupboard with the spices. One was in the open carton with salt.
I tried photographing them alive, but they crawled out of the frame faster than my mobile phone camera could focus, so I killed one of them. Unfortunately my mobile phone camera isn't too good at this narrow range, so the image is a bit blurry:

They are pretty small. The scale is in millimeters. I live in Germany.


texts: Do the antibodies in a patient suffering from Hashimoto's, attack the thyroid hormones or the thyroid gland (or both?)?

texts: If oral thyroid hormone supplement is administered, is the attack stopped or does it just create an excess of thyroid hormones so that even after a lot of it is destroyed by the antibodies, there is still enough for normal bodily functions?


texts: Meaning of “gene expression heterogeneity” of embryonic stem cells

texts:
What does it mean if a gene has a heterogeneous expression? Does it describe the differences of patterns of expression of that particular gene in a population of cells that are identical? The papers I have found did not really elaborate on what it meant, and I do not know where else to find the definition.
In particular, I want to understand heterogeneity in the context of stem cells. In the paper by Angarica and Sol, 2016, it reads:

“Experimental studies at the single-cell level have revealed that embryonic stem cells (ESCs), and more generally pluripotent stem cells (PSCs), exhibit significant gene expression heterogeneity.”

“Single-cell studies have allowed gene clustering, depending on the levels of heterogeneity in the gene expression landscape in PSCs.”

Does it have more to do with the variation of its expression in the population?

“In mouse ESCs genes exist that are uniformly expressed in most cells and exhibiting a unimodal distribution (Oct4, Rest, Tcf3, Sal4); other genes exhibit bimodal expression and are expressed in some populations but not in others (Nanog, Rex1, Tet1, Esrrb), and yet another group of genes display sporadic expression (Neurod1, Klf4, Otx2, Pax6) and are undetected in most cells but highly expressed in some speciﬁc subpopulations.”

Reference:

Angarica and Sol, 2016, Modeling heterogeneity in the pluripotent state: A promising strategy for improving the efficiency and fidelity of stem cell differentiation.


texts:
Recently, I was taking a walk down by a riverbank and saw this spider:
Here's all the info I think would be useful

Where? Missoula Montana, United States of America. Specifically, Greenough Park, on the riverbank (as mentioned earlier)
When? today, May 28, 2019
Behavior? They were hard to approach and scuttled away fairly speedily whenever I approached.
Population? They were everywhere, everywhere I looked they seemed to be there, occasionally, I found them in pairs, but never in groups of three.
Additional Info: they were passive until approached, moving rarely if observed from a distance, but when they did move it seemed that their movements were somewhat sporadic, with quick bursts of speed and then stopping and resuming (if they found that necessary)


texts: Can anyone help me identify this insect?

texts: I'm trying to identify the insect below that I found in Edmonton, Alberta, Canada. Any help would be appreciated.


texts: How did viruses learn to utilize the workings of a cell?

texts:
This is my first post here, so excuse me for its simplicity.

Viruses can infiltrate a cell, overtake it and multiply. It has projecting fibers whose ends are shaped as kind of a "key" to a mobile sentry on the cells membrane so it can be permitted access into the cell. When it enters the endosome of a cell, a protein pump blows an acidic gas onto the virus to break it down, thinking it's a special nutrient. But the virus expects this of course, and when the protecting fibers break off (and so too the body of the virus) proteins are released that rips apart the skin of the endosome so the virus can escape.

These are just two of many things the virus does to compromise a cell. Its entire existence is for the sole purpose for infecting a cell, and it seems to know how to do that perfectly. How did the virus evolve to know how to do things like this?


texts: Colorful Large Wasp (?) on Milkweed Arizona USA

texts: Observed this very colorful insect on Asclepias subulata (Desert Milkweed) in Phoenix Arizona. About 8 am, temperature about 90F, sunny, late-September.  When flying it seemed to have a narrow waist like a wasp.  About 5 cm long, appears rusty-red in flight (not surprisingly given its size).  As the pictures show, it was enjoying a bit of nectar from the flowers. Would love to know its name so I can greet it properly next time!


texts: Replicator equation for mixed strategies?

texts:
The the replicator equation is usually defined for pure strategies. More specifically, the replicator eqn for $n$ strategies is given by:
\begin{equation}
  \dot x_{i} = x_{i} \left( \sum_{j=1}^{n} a_{ij}x_{j} - \phi \right)
  \qquad i = 1, \ldots, n
\end{equation}
where $x_i$ is the frequency of the strategy $i$, $A=[a_{ij}]$ is the payoff matrix, and $\phi$ is the average fitness of the population. Basically, what the replicator equation is saying is that the per capita rate of increase of the strategy $i$ (i.e., $\dot x_i/ x_i$) is the difference between the fitness of $i$ (i.e., $\sum_{j=1}^{n} a_{ij}x_{j}$) and the average fitness $\phi$ of the whole population.

Question: Does anyone know of a formulation of the replicator eqn for mixed strategies?


texts: To what extent do gonads affect differences in gendered behaviour?

texts: I'm not sure whether this question makes sense, but someone said that they result in gender differentiation on an organisational level in the brain. I'm wondering how important these changes are, in terms of magnitude of average differences in neural structure between males and females?


texts:
My bougainvillea plant hardly flowers and only at the tips. It has one very long vertically growing stem(if I may call it so).

Is this an example of apical dominance.
If so how is it to be corrected?
Do I have to cut the long step?


texts:
Here's my theory:

If you consume x calories each day with y amount of caloric expenditure each day you gain zero weight, regardless of x and y being out of balance.
If you then mechanically remove a large percentage of body fat (surgically), the fat should not come back.

Is this a true theory or not? It seems to me that if the body is stable at the current consumption of x and expenditure of y then the removal of excess weight/fat should not affect anything.
Anyone have thoughts on this? Is my thinking flawed? Why? Even if x and y were equal why might the fat come back if there is no net gain when the fat exists?


texts: Why is exclusive breastfeeding recommended for 6 months only?

texts:
The WHO recommends exclusive breastfeeding for the first 6 months of a child's life.

  Review of evidence has shown that, on a population basis, exclusive breastfeeding for 6 months is the optimal way of feeding infants. Thereafter infants should receive complementary foods with continued breastfeeding up to 2 years of age or beyond.

Their website mentions "review of evidence", but what is that evidence? Why 6 months and not 4 or 5 or 7 or 8 or 9 or anything like that?

Can anyone give which review is WHO talking about?


texts: Are there any open phylogenetic projects that don't require coding to make a contribution

texts: I am stay at home learner, not pursuing education formal education and currently doing a part time job. I've however completed masters in biotechnology and I'm studying to pursue PhD in molecular evolution eventually. I'm interested in knowing if there are any online open projects in phylogenetics and computational molecular evolution where I can contribute. Leave the projects involving coding. So are there such open projects that don't require coding? An example of contribution I can think of right now is submitting new phylogenetic trees. Please help, I can't find any information online.


texts: If a protein is heterologously expressed in E. coli under the T7 promoter, what fraction of the total protein concentration in the cell is the heterologously expressed protein? What could be its concentration at most? Does it strongly depend on the size of the protein or are there certain size thresholds for low/high expression?


texts: Comparing gene expression levels between control and disease at different time points

texts:
I have a data set with expression levels of a list of genes, measured in replicate at two different time points between two groups; a control group and a disease group.

I want to identify the changes in expression between the two groups, however I'm having some trouble on formulating how best to do this. For example, if I have $[C_0]$ and $[C_1]$ as the control group measured at $t=0$ and $t=1$ respectively, and $[D_0]$ and $[D_1]$ as the disease group, I had tried to do:

$$\frac{([D_1] - [D_0]) - ([C_1] - [C_0])}{[C_1] - [C_0]}$$

I feel like a fold change would be appropriate, however it doesn't seem to make any sense logically for the genes where $[C_0] = [C_1]$ or $[D_0] = [D_1]$.

Could anyone suggest an appropriate ratio or measurement? This is straightforward enough when it's simply comparing between C and D, (e.g. you just find $\frac{D}{C}$), however I'm not sure how to treat the different time points.


texts: Punnet Square for Genotype Probabilities

texts:
I'm a computational physicist by trade, and today I was working with a student that is coding a simulation that requires the interactions of different genotypes to determine which phenotype will be expressed. This student drew a Punnent Square like so:

$
\begin{equation}
\begin{matrix}
& O & Y \\
\_ &\_ & \_ \\
Y& |YO& YY \\B &|BO & BY
\end{matrix}
\end{equation}
$

and then stated that each genotype should have a 25% probability of being expressed. I remember learning this as well in highschool bio, but since finishing my Bachelor's in Physics (with some focus on complex adaptive systems/chaos theory) I am a bit skeptical that biology really obeys the probabilities of the Punnet Square. Are there examples in biology where the probabilities of the Punnet Square are clearly broken?


texts: What is allelic effect sizes and direction?

texts:
In a paper, Berkley, C. A., and C. Lexer. 2008. Admixture as the basis for genetic mapping. Trends in Ecology & Evolution 23:686–694, the definition of Genetic architecture is given. It says:

  Genetic architecture: the number and genomic location of loci that
  contribute to variation in a trait, as well as the allelic effect
  sizes and direction, the genotypic effects (additivity and dominance)
  and the extent of epistatic interactions among loci.

What is the allelic effect sizes and direction?

I found that allelic effect sizes is the same thing as penetrance. But the direction?


texts: How big is the change in proteins due to alternative splicing?

texts:
How different can the proteins be that are coded from the same DNA-sequence but undergoe alternative splicing?

What I am trying to wrap my head around is why we are so fixated with the DNA-sequences and what they are coding for, if the outcome can differ a lot due to alternative splicing.


texts:
If I cook some food, I get apparently several energetic advantages:

thermal : the temperature of the food is closer or superior to the temperature of my body or internal organs, so I do not have to produce energy to warm it.
chemical : the transformations of the organic compounds during cooking operations may store energy in a potential form: more energy will be released by the digestive process from these compounds than from the raw ones.
mechanical : the food may become easier to chew, absorb, conduct in the digestive tract, leading to less muscular force used.
The cooking procedure may involve water immersion, and the water may penetrate the food and improve all three energetic aspects outline above.

(I may have forgotten a few things)

But what are the respective scale of these advantages, compared to the Joule intake of the raw food ?

Focusing on meat, for instance, is there an optimal cooking duration/temperature and eating temperature for human eaters, independently of personal tastes, for say, beef or chicken meat ?


texts:
I found this plant in Rajasthan, India.
This sample is 4-5 cm long.
This is an ornamental plant. It was a potted plant.
I put my fingertip in the photo to give an idea of size of the specimen.
I can't figure out which plant this part belongs to.
Please give the species name if you can.
I would be very thankful to anyone out there who will help me.


texts: Typical firing patterns of neurons in the default mode network in resting state

texts:
Inspired by the Wikipedia article on the default mode network where I read:

  Hans Berger, the inventor of the electroencephalogram, was the first
  to propose the idea that the brain is constantly busy. In a series of
  papers published in 1929 he showed that the electrical oscillations
  detected by his device do not cease even when the subject is at rest.

I came up with the following question:

  Are there data available for typical firing patterns of single neurons
  (of a given type, in a given region or functional unit) in the
  default mode network in resting state  over some significant
  period of time, say a minute?

By "typical firing pattern" I mean:

the overall number of spikes (per minute)
the number of isolated spikes
the number and duration of tonic bursts
the number and duration of other firing patterns as proposed e.g. by Eugene Izhikevich
and the mean distances between them

Or are such data not available, maybe because they are too hard to gather or cannot be summarized in a sensible way.

I ask just to get an idea, and because I would like to know if - for example - the maximal, mean, or median number of spikes per minute has an order of magnitude of 10, 100, 1,000 or 10,000 - or even more?


texts: Why can't a corn cob have 13 rows of seeds?

texts:
Every time before eating a corn, I count its lines. I would always find 12 or 14 rows of seeds, but never 13.

Is there any biological/scientific reason behind this?


texts: How does cerebrospinal fluid circulate in the central nervous system?

texts:
Cerebrospinal fluid (CSF) is produced in the choroid plexus of the lateral ventricles and in the 4th ventricle of the brain.  CSF then circulates through the ventricles of the brain and the subarachnoid space of the meninges.  CSF is returned to the venous system via the arachnoid granulations connecting the subrachnoid space with the superior sagittal sinus at the superior portion of the neurocranium.

What circulates the CSF such that it can return to the venous system against gravity?
In other words, why does CSF not all just pool in the caudal cistern?


texts:
1.When I autoclave media should I close the cap tightly or slightly?

I put all tools in plastic bag when I autoclave, should I close slightly the plastic and when it finish I close tightly the plastic? The air steam need to go inside the bag?
I read some document told me autoclave 21 minute, but in my lab everyone operate 35 to 40 minute, What you think?
Thank for your help.


texts:
EcoR I ........ 5'-GAATCC-3'
  BamH I ....... 5'-GGATCC-3'
  Hind III........ 5'-AAGCTT-3'

  The enzyme BamHI recognizes a palindromic sequence and leaves one strand longer than the other. A piece of DNA is cleaved by BahM I. What does the end of the DNA look like?

  A. ...GATCC-3'
       ...C-5'

  B. ...C-3'
       ...GATCC-5'

  C. ...G-3'
  ...C-5'

  D. ...G-3'
  ...CCTAG-5'

  E. ...CTAGG-3'
  ...GATCC-5'"

I understood that one strand should be longer than the other, that's why I eliminated the "C" and "E" answer choices.

Then, I thought the answer choice is the "A" one. The first strand is similar to that in the data in the task, while the second is palindromic to it.

But this answer choice is incorrect. Then, I chose the "B" one. I thought: if we are given the sequence 5'-GGATCC-3', then the sequence 3'-GGATCC-5' is palindromic to it. (In this case, we have different letters near each number. That probably means they are vise versa versions of one another.)

It turned out the correct answer choice is the "D" one. I found such an explanation:

  The end of the DNA cleaved by BamH I is complementary to the
  recognition site sequence shown in the table. One strand must also be
  longer than the other. The sequence CCTAG-5' is complementary to
  GATCC-3'.

But I can't understand this explanation... Please tell me what I do wrong..


texts: Researchers have found mosquitoes cannot fly in dense fog because fog particles adhere to its halteres and stop them working. Is it possible to disrupt mosquitoes flight by mimicking fog particles?


texts: Any ideas? This was taken in July on the beach of Bandon, OR, in the USA.


texts: 3 flaws of genes from the perspective of a programmer

texts:
Having a double helix structure seems like a waste of space. In programming you would have a single array and just before mitosis you would double the single helix.
Having an exact copy of a cromatid. As long as a cromatit exists, there is always a possibility of errors, for example if something attacks the chromosome. So why isn't the cromatid just before mitosis, just like in 1? Then you are 100% certain, you have an exact copy. Again, a waste of space, but additionally vulnerability now.
Having 2 nucleobase (adenine, thymine, guanine, cytosine) seems like it makes more room for errors. Why aren't there just two of them? They are complementary anyways, so adenine for example can only be on the opposite side of thymine. Is it so that splitting is easier? In programming, if you only have to deal with a boolean value, you would always take it over having to deal with 4 values.

So, what does nature do different than a computer and why does it behave so differently?


texts: What is the benefit for cells having the ATP production regulated in mitochondria compared to being from the nucleus?

texts:
Mitochondria have their own DNA and appear to be loosely connected to the nucleus and it role.

Why are the functions of mitochondria not in the nucleus? Why doesn't the nucleus control the mitochondria's functions as it controls regulation for other chemical reactions?
Are there evolutionary/competitive benefits for this separation?


texts: Do local field potentials (LFP) create waves on the surfaces of nerve cells?

texts:
Are waves created by the LFP on the surfaces of neurons cell bodies? Since the cells have a resting potential, do these waves create harmonic oscillation of the membranes at particular frequencies?

Are there studies available that look at electrical potential waves on the cell surfaces? I think that membranes should be sensitive to the LFP since they maintain a charge.


texts: If life began at sea, why organisms are less salty than the sea?

texts:
We may take it for granted that a fish, a seaweed, or clams are not too salty to eat, although the sea around them is salty. I know about the existence of a mechanism which prevents their body from becoming as salty as the sea itself, but this raises an important evolutionary question.

As life evolved from single-celled organisms, those organisms started as very simple cells with the bare essential metabolic functions. Possibly their DNA had no nucleus, and obviously they could not (yet) balance the salts within their body. In theory, this would say that their metabolism should have evolved to function is a salty environment. Yet, we see that this is not the case of modern organisms.

Which of the following scenarios describe the evolution of marine creatures with no excess salts in their body?

1- Metabolism may have started in a salty environment, cells have later "discovered" that less salt makes metabolism more efficient, and therefore the energy expended to clear-out the salts is worth the effort.

2- The time it took for salts to accumulate in the seas allowed marine creatures to adjust to a gradual increase in salinity.

3- Fresh water bodies (Rivers and lakes) are better suited for life to evolve. Eventually, some of the rivers will pour into the sea with all their content, including any living thing facing the challenges of salty sea water. This article mentions "ponds", but larger bodies of water are a better means of transporting those organisms to the sea.

What do we know about the timeline of changes in oceans salinity vs. timeline of evolution? Do we have fossil records that show the salinity content of the organisms?


texts: Why are semi log graphs used in drug Dose response curves?

texts: Why are Dose response curves, as well as most biological graphs shown in semi log graphs and not normal graphs? What is the advantage of semi log graphs over regular graphs? I still haven't gotten an intuitive sense of the answer, can someone explain, maybe with a diagram?


texts: Why doesn't the ambient lighting condition change the perception of colors we see on a monitor?

texts:
Suppose that I take a picture of an object illuminated by an incandescent light bulb and I choose the daylight white balance setting. The picture I then get will display a white object as looking yellow, which is how the object would look had my brain not processed the image according to the ambient lighting conditions.

The question is then why the way the picture looks doesn't change depending on the ambient lighting conditions. If a white piece of paper continues to look white when illuminated by an incandescent light bulb, then why would that same piece of paper displayed on a computer monitor look yellow when I'm viewing it in a room illuminated by incandescent light bulbs?


texts:
Aconitase in the TCA (tricarboxylic acid) cycle isomerizes citric acid to isocitric acid via cis-aconitic acid intermediate. Since overall it functions as an isomerase, why it does not belong to isomerases? Why does it belongs to lyases even though it involves hydrolysis of water in second step? Should not it belong to hydrolases in this way?

So how it can be justified that it is lyase?


texts:
In Neuroscience 3rd ed by Bear et al. on page 607, immediate early genes are described as related to changing synaptic strength, yet have decreased expression during sleep. The explanation given is that "learning and memory formation are largely absent in [sleep]." But that seems somewhat counterintuitive as LTP occurs during sleep.

What is really going on here?


texts: Why doesn't crossing over happen in mitosis?

texts: If there was crossing over in mitosis, then there would various nature of somatic cells. May be that's the logic, but what is the mechanism? Why are there no crossover events during mitosis?


texts:
Why do rodents' teeth continue to grow? Enamel formation and/or root formation continue throughout rodents' lives.

What's the mechanism that causes this?


texts: What would be the conduction speed of A-alpha fibers, were they unmyelinated?

texts:
It's known (Hursh 1939) that myelinated axons exhibit the behavior $v = 6d$, where $v$ is the propagation speed [m/s] and $d$ is the axon diameter [μm].

A related relation for unmyelinated axons is (Malmivuo & Plonsey, eq. 2.1):

$$v = \sqrt{\frac{i_\text{Na max}}{r_i c_m^2 V_\mathrm{th}}}$$

I want to approximate the propagation speed that A-alpha nerve fibers would exhibit, if they were unmyelinated. How could I find values for the constants in the above equation? Is there an easier way to conduct these calculations, or has there already been a study done on this?

For the (myelinated) A-alpha fibers, d = 13-20 μm and v = 80-120 m/s according to Wikipedia.


texts: Why does the cell initially swell, then return to original volume rather than shrink first in a hyperosmotic solution of NaCl and urea?

texts:
When a cell is placed in a hyperosmotic solution of NaCl (0.15M) and urea (0.05M), why does the cell initially swell, then return to original volume rather than initially shrink?

Firstly, my understanding is that since it is a hyperosmotic solution, the cell will originally shrink as water will diffuse and flow out of the cell, and thus shrink, to maintain similar water concentrations, and then since urea is membrane permeable and flows back into the cell, the cell will then return to its original volume.

However, I do not understand why swelling would occur first since the solution is hyperosmotic!


texts:
Overly simplified, macrophages recognise pathogenic patterns and endocytose anything that matches them.

That also works on bacteria, which are quite often very mobile. What if a bacterium was just randomly twitching around when a macrophage recognised it - would it be possible for it to "swim away" (as a reaction to the macrophage or just randomly)? Or do macrophages employ some sort of fixation mechanism to keep anything they recognise close until it is engulfed? Or is engulfment in itself just so quick?


texts: Gibbs free energy and entropy in enzyme catalysis

texts: In enzyme catalysis, the formation of the enzyme-substrate complex causes a reduction in the entropy of the system. If entropy reduces, the gibbs free energy will become less negative. How then is enzyme catalysis favorable? Are there any other factors that off-set this?


texts: How Does The Presence of Livestock on Land Increase Net Methane Production?

texts:
It's a hot topic, and I've just read this article that debunks the claim I'm about to make - But even though I read it, I still don't really understand it. I'm happy to change my opinion if I understand the facts.
Suppose we have a closed system, imagine a pasture in an aquarium. Light goes in, grass grows, dies, decays, is recycled, all that good stuff. I imagine the air going into the aquarium is pretty atmospheric, and the air exiting has been changed depending on the amount of CO2 that is absorbed through photosynthesis, the amount of O2 is absorbed through plant respiration, and the amount of greenhouse gasses produced from decaying plant material in the thatch/soil.
(I think I have that right - my biology education doesn't go past high school level)
Now suppose we add a cow into the mix. If anything, to me, the cow reduces net emissions while it grows because less grass decays, and is instead turned into cow. Once the cow is mature, in this closed system, it's only eating and "processing" the grass that was already part of this natural cycle of growth/decay.
Here's where I think I am possibly going wrong:

Does the cow increase the amount of "decay"? Does eating the grass make it re-grow faster, thus speeding up that natural cycle?
Or, does the cow output different (more harmful) greenhouse gasses than the grass would normally produce through decay?

In short, how does the cow increase emissions? It can only have eaten what has already been grown -  And what has grown is doomed to someday decay and be re-released into the atmosphere anyway. I don't particularly like having contrary opinions, so help me out!


texts:
The majority of living things have some form of symmetry.  Many mammals and fish have bi-symmetry, and anemones, starfish and jellyfish (among others) have radial symmetry.  However, there usually are many small or major differences that make them not perfectly symmetrical.  Is it possible for something to evolve to be 99% perfectly symmetrical, possibly even spherically?

Edit: I'm talking about something big, maybe as large as a cat or dog, not something tiny (ie. cocci bacteria).


texts: Is this a variety of banana slug (Ariolimax columbianus)? (California)

texts: These very dark (dark grey to black) banana slugs are an anomaly. I live on the north coast of California and see many slugs every day. These particular slugs I find only on the west-facing headlands at the ocean. There is no cover from the sun since there are no plants taller than about a foot. Also these particular slugs are never longer than 2-1/2" to 3". Are they a sub species, a variety, or something else? Thanks for taking the time to answer.


texts: Material on the analysis of (micro)array data

texts:
I'm at the moment analyzing cytokine array data. The available material on the statistical analysis of these data is more than unsatisfactory. Since a lot of effort is being made in the analysis of gene microarray and MALDI-TOF proteome data, I seek to apply these methods on my cytokine arrays.

What is a good introductory text on microarray analysis, especially quality control and error estimation?


texts:
In this article the athors used the Standardized Selection Ratio (SSR) in order to infer what is the preferred host (anemone) of anemonefish.

Here is a quotation coming from their methods:

  The “preferred host” of anemonefish was assessed calculating the “Standardized
Selection Ratio (SSR)” (values between 0 and 1) (Manly et al. 1993). Manly’s standardized
selection ratio represents the probability that an individual will use a particular habitat
type, taking into account the different resource availability. For each anemonefish species (i) inhabiting an anemone species (j), SSR was calculated as:

$$SSR = \frac{wi}{\sum{}{wj}} $$

where $wi = \frac{oi}{pj}$

    `Oi` is the relative frequency of the anemonefish species i and `pj` the relative frequency
of the anemone species j. Higher values of SSR indicate a strong preference for the
selected resource. The Log- Likelihood statistic (χ2L) (Manly et al. 1993) was used to
check the significance of the observed distribution under a null hypothesis of a random
host choice.

Here is the book they cite (Manly et al. 1993).

Can you help me understanding basically what they did and how they calculated their SSR and p.values. If $wi = \frac{oi}{pj}$ what does wj equals to?


texts: Has the most recent common ancestor of all living birds lived after dinosaur mass extinction?

texts:
I wonder if one or more phylogenetic threads of dinosaurs survived the mass extinction.

In other words, are all living birds equally related to any given ancient dinosaur, or do some birds relate more to some ancient dinosaurs while other birds are more related to other ancient dinosaurs?


texts: Differentiating between hormones triggered on specific types of happiness?

texts:
Achievement:- Dopamine
Applause:- Seratonin
Discovering something new:-?
Remembering something after a long time/struggle:-?
Nostalgia:-?
Lust ;-Testosterone/Estrogen
Romantic Love:- Dopamine?
Attachment:- Oxytocin or Vasopressin?
Cuddling pets/babies:- Oxytocin or Vasopressin?
Motherhood:- Oxytocin & Vasopressin?
Also, is happiness in all cases equal? I mean that is happiness just differing in magnitude rather than type when comparing different activities? For eg, happiness on discovering something new is the same exact as happiness on kissing your crush, just differing magnitude and triggered by a different hormone?
Like in video games, we have damage versus status effect (losing hitpoints versus getting paralyzed or stunned), is that a better analogy to the various kinds of happiness or is it more like fire damage versus ice damage,


texts: Why is ATP synthase sometimes referred to as ATPase?

texts:
Quite a few times I have seen the term ‘ATPase’ used for what I would consider ATP synthase. For example, my text has:

  “The phosphorylation of ADP to ATP is also catalysed by the enzyme ATPase.”

I don’t understand this. Surely the enzyme that catalyses the synthesis of ATP should be entitled ‘ATP synthase’, so why is ‘ATPase’ used in this case?


texts: What is this (seed/berry)-like object and where is it coming from?

texts:
I've been finding these little green (seed/berry) like objects in my garden for three years now.

This picture shows either a large variant or simply  a later lifecycle stage of development.

At their smallest, they look artificial - kind of like nerds candy - almost too green to be natural.  In the picture above, it is obvious that the item is a berry, but at the smallest sizes, my first thought was that it was fertilizer.  And indeed, I would've continued to think that if not for two things:

We re-mulched our garden two years ago, and didn't fertilize (nor have we ever, but this house is only 3 years old).
When you squeeze even the smallest sized objects, they squirt juice or water.

When the larger berries are crushed, many little seeds come out along with liquid; and it looks almost like a miniature pickled tomato.

There is nothing in my garden that produces any kind of visible berries; and I've never seen one of these attached to a plant.  That is part of what makes them so odd (and part of what made me think they were fertilizer); I always find them mixed (sometimes deeply) in soil or mulch.

If no one knows after a couple days, I'll go take a picture of one of the baby ones to help.  Any thoughts?

Location: Brighton, MI (USA).

Update:. Here are some other shots.  These are both flash shots because it is overcast today.  These are also of the younger variant because I couldn't find any  of the mature berries today.  Hope this helps.


texts: How is AMP "recharged" to become ATP in a cell?

texts:
I understand that after the translation stage of ribosomal protein synthesis, tRNA molecules are floating in the cytoplasm without attached amino acids until they find the correct aminoacyl tRNA synthetase enzyme which revitalizes them.

However, in this process the enzyme takes an ATP molecule and returns an AMP (not ADP) molecule. It's been my understanding that an ATP's energy is normally harnessed via removing a single phosphate group and leaving an ADP molecule. Processes like respiration and photosynthesis deal with the conversion of ATP to ADP and vice versa. I understand that in removing the extra phosphate group to get an AMP more energy is released, but that also means that more energy has to be used to convert the AMP to ATP.

Does the cell convert the AMP to ADP, which will ultimately become ATP in respiration, or does the cell use some retrofitted respiration/metabolism to revitalize the AMP?

I would expect the first option but it would take energy (most likely from an ATP) and I would expect the amount of energy released from an ATP becoming an ADP to be different from the amount of energy released from an ADP becoming an AMP (so an ATP becoming an ADP would take more or less energy than would be required to make an AMP become an ADP, leading to inefficiencies). The other possibility (that I can see) is that the AMP is just used as a nucleotide in DNA and RNA, but I don't think that the numbers add up there. I've looked around but I can't find an answer.

So how do cells convert AMP to ATP? Also I was told that the ATP to ADP conversion is the general power-conversion. Is that not the case, or is this just some rare occurrence when AMPs are involved in power conversions?


texts:
I have asked a question on physics stackexchange, but was redirected here. I copy the entire question word for word. The original is here.

Let's, for example, take a ribosome. It is an enzyme that is in turn just a molecule that must follow the laws of physics.

Correct me if I'm wrong, but it can be looked upon as a molecular machine made up of several pieces. What exactly makes those pieces work together?

Why does the ribosome bind to a strand of RNA? Is it just the shape and electric charge or is it something more? Once the ribosome is bound to a piece of RNA, how does it move?

In a way, I'm looking for the "ghost in the machine". I'm interested in molecules in general, not just ribosomes. What is it that, on a level of single atoms, makes molecules "alive" - move, assemble a protein, etc. ?

PS. I'm having trouble phrasing my question, so if anything is not clear, please leave a comment and I will address it.

Edit 1: This is most definitely a physics question. I'm looking at the scale of several atoms.

Let me give a hypothetical example:

Imagine a strand of carbons. Also imagine that there exists a molecule that can move along this strand. How would it do it? What forces would move it along this strand? Is it electromagnetism? Would gravity be involved to a significant degree? What effect would shape have?

Does this make the question clearer?


texts: Madrid, Noise by the river: Bird or cricket?

texts:
I currently live in Madrid, Spain. In July there was a loud animal near the river, in an out of town area surrounded by grassland, with trees along the river.

It's continued into August, though it has reduced.

It sounds like a cricket in general tone and rhythm, but it is always high in the trees, and sounds too deep to be an insect. It's in the frequency range of a squawking bird, so if it's a cricket it must be huge.

On the other hand, if it was a bird, I should have been able to spot one.

Does anyone have any idea what it is?

The sound is rhythmic, rasping note, with two beats of equal duration but slighly different tone, repeated over and over again without any pause.  The animal that makes it calls continuously for long periods.

EDIT: thanks to AliceD for the comment, I didn't realise we had cicadas in Europe. It could be a cicada, but it's deeper and more consistent / regular in its song than this one:

https://www.youtube.com/watch?v=DSdxm52VwOg


texts: Breeding mosquitoes at lower temperature

texts: It is well known fact that, to slow down the growth of drosophila, they are grown at 18-19 degree Celsius. It helps in maintaining stocks for longer time without frequent change of food. Is it applicable to mosquitoes? especially Aedes aegypti?  can we slow down its growth by growing them at lower temperature?


texts: How exactly are petri dishes used (e.g. in medicine)?

texts:
I know that petri dishes with a growth medium are used to grow micro organisms. I guess this works as follows:

The petri dish has to be kept sterile. To make it easier, I guess one could cool it.
The microorganisms are somehow put on the petri dish.
The petri dish is put in an incubator (e.g. 37 °C if one wants to simulate the human body).
After some time (how long?) one can look at the colonies.

Does one only look at them with the naked eye or is there a way to make more detailed studies?

For example, when I have an illness, can the doctor (for some illnesses) simply use this petri dish / naked eye technique to confirm a hypothesis what kind of illness I have?


texts: What is the difference of pressure a human eyeball cornea (cornea, lens and other elements separating vitreous body from air) can handle? Or asking differently: what the outside pressure should be to "blow up" a healthy man's eyeball?


texts: Differences between Heracleum mantegazzianum and H. sphondylium

texts:
I have heard about the hazards associated with Giant Hogweed and the trouble is when trying to identify it, it is very similar by the looks to normal hogweed.

When fully grown, there is a big difference in height with Giant Hogweed (hence the name Giant Hogweed, but when it is small, how can you tell the difference?

Giant hogweed (Heracleum mantegazzianum)

Image from WikiMedia

Hogweed (Heracleum sphondylium)

Image from WikiMedia


texts:
I live in Belgium, and I've just witnessed a weird looking wasp/fly flying around in my room. Here's a picture:

So, what's this? It's still in my room, just chilling there. It zooms like a wasp, and flies VERY FAST. You can see white vertical stripes on his upper body, and then golden vertical patches. I couldn't get the camera to focus, so it's not really full-hd.

[Edit (better picture)]


texts: How is tolerance to an allergen developed?

texts:
My question is mainly about how allergy shots work.

I did some basic research before posting here, however I could not find an explanation of what occurs at a cellular level.

Is it the persistance of the antigen which somehow induce immune tolerance?


texts: Which wavelength to use to determine algae using a colorimeter?

texts:
I am doing a Biology project involving the measurements of the density of algae (Nannochloropsis) using absorbance colorimetry. What wavelength should I set my colorimeter to?

The issue is that there are two types of chlorophyll, each with a different absorbance optimum, there is spectral scatter to consider, as well as UV absorption when going to low wavelengths. What to do?


texts: What limits the speed of human perception?

texts:
I'm writing a novel in which the main character's perception and thought processes are sped up considerably, in essence slowing down the world around him. To others, it seems like his reactions are far faster than normal. Of course, there's a fantasy explanation for this in the story, but it led me to wonder exactly what limits the speed of human perception and reasoning in the real world.

From what I know, the speed at which we perceive events appears to be a constant. What exactly determines that rate? Is it possible to change it? Is it possible that different people perceive things at different speeds?


texts:
Edit: If somebody (anybody) wants to add an answer so the bounty won't go to waste, please do so! The comments have already introduced me to the Kegg metabolism database, some interesting papers, and an amazing chapter on the biochemistry of cats. Thus, this question has been useful to me (and hopefully, to the community as well).

  There is a question on Skeptics.SE that asks if "cats have a chemical in their brains that resembles LSD." I haven't found any similar claim online, but started wondering:

 1. Do cats produce (natural) compounds that structurally resemble LSD?
 2. Do cats produce (natural) compounds that functionally resemble LSD?

Quickly glancing at the structure of LSD, it contains an indole ring. Hovering over the various indoles here found one substance that occurred in animals and was consumed as a psychedelic drug.

There is a paper that writes:

  N,N-Dimethyltryptamine (DMT) is an indole alkaloid widely found in plants and animals. It is best known for producing brief and intense psychedelic effects when ingested. Increasing evidence suggests that endogenous DMT plays important roles for a number of processes in the periphery and central nervous system, and may act as a neurotransmitter.

The paper also proposed the role of DMT as a neurotransmitter. However, I haven't been able to confirm DMT is naturally produced by cats.

Do cats produce DMT? If so, what is the purpose of DMT in the cat?


texts: Does our brain use up more ATP after smoking cannabis?

texts:
kind of an amateur here.

If the firing of the neurons' signals uses up some ATP, and smoking cannabis makes them fire off more quickly, do our brains use up more ATP to sustain that rapid firing?


texts: Why is the 3'UTR AES of the Pfizer/BioNTech vaccine preceded by a CUC GAG?

texts:
According to the WHO submission and one of the preprints from BioNTech/Pfizer, the 3'UTR of their Covid-19 vaccine's mRNA is the combo of the AES and mtRNR1 sequences, which (in the preprint) BioNTech cites to a paper on library screening of 3'UTRs that achieve high mRNA stability etc.
But as far as as I can tell, BioNTech added a "CUC GAG" between the (doubled) stop codon and the beginning of the AES as it's given in Supplementary Table 3 of the library paper cited, i.e. the actual AES starts with CUG GUA CUG, or more precisely using the global Ψ substitution as given in the WHO submission, the sequence starting with the stop codon(s) is:

ΨGA ΨGA CΨC GAG CΨG GΨA CΨG CAΨ GCA

So, what's the point of the bolded "glue" CUC GAG?


texts: What is this black insect (wasp-like?) South America?

texts: I live in the Pacific coast of South America. Seems to have two wings, like a wasp's. The "tail" is a bit bulky but is only connected to the rest of the body by a thin part. It's black overall. The antennae in the photo are downwards but they just spring normally to the front...


texts: Phylogenical differences with nuclear and mitochondrial DNA

texts:
This is a textbook question, I would like to verify my answers. According to the textbook it is possible to construct a phylogeny using nuclear and mitochondrial DNA and these trees to be different, I should give reasons why this might occur.

Here's two that I think might be valid

(1) Mitochondrial DNA is maternal, while nuclear DNA comes from both parents. It is possible to have a (female) hybrid C between species A and B, and if C cross with an individual with genotype (A), the offspring could show some genes from the species B. I consider this to be a phenomenon of introgression, and genic flux would be in these case shown in the nuclear DNA, but not in the mitochondrial.

(2) Mutations might occur. mtDNA has a higher mutation rate than nucDNA. If the phylogeny is constructed looking at a gene, more recent mutation could should in the mtDNA.

This is what I could think of, I would like to know if they sound acceptable, and if there are more possible reason to find different phylogenies using mtDNA and nucDNA.


texts: What tools can help me determine if a plant homologous protein interacts with an ncRNA in the same way?

texts:
First post here, so bare with me if I violate any etiquette or formatting rules.

Let's say I've got a protein in humans. When it interacts with an ncRNA found in humans, it does something that I'm very interested in.  I see a highly homologous (~85% AA identity) protein in plants, and it's widely conserved.  I'm interested in eliciting the same activity of this protein in plants.  Only problem is that there's no native plant-produced ncRNA to interact with my protein of interest in the same way.  So I had an idea:

What if I introduce a transcript to plants that addresses this problem?  If the plant version of this protein interacts with this (introduced) RNA in the same way it will be really cool.  I'd like to test this hypothesis with some synthesized constructs.  But before I plunk down thousands of dollars on a few constructs, I'd like to explore any predictive or analytical tools to strengthen the case.  I'm aware the odds are against me.

Thanks!


texts:
Is it possible to say that there is a maximum exposure time for the virus so that even an exposure time beyond that - will leave us with the same chances of infection?
If so, is there a way to estimate the interval between the minimum exposure time for infection and the maximum exposure time for infection and what happens inside?


texts:
I need a mammalian promoter that will maintain stable expression through differentiation.

I was originally planning to employ UbC for this specific project, however new information from a different experiment has come to light and now I need a promoter that has both extreme stability and high strength (as you know, UbC is renowned for it's very low expression rates).

Do any of you have suggestions? Perhaps I should look into a hybrid promoter of sorts...

Thank you,

CDB


texts: How can the leakage of mitochondrial protons generate heat?

texts:
I read the following about thermogenin:

  "When thermogenin is
  inserted into the inner mitochondrial membrane, it
  accentuates mitochondrial proton leak and dissipates
  the proton motive force. Since oxidation is no
  longer coupled to phosphorylation, thermogenin is
  said to cause uncoupling. In the presence of thermogenin,
  oxidation and proton pumping continue
  at high rates but with low rates of ATP synthesis. So Thermogenin enhances
  mitochondrial proton leak so there would be heat."

Why does proton pumping without ATP synthesis generate heat?


texts: Shigella's O antigen (PAI synthesised) and passage through host defences

texts:
The O antigen is synthesised by Pathology islands (PAI).
O antigen may be a factor why Shigella survives the passage through host defences.
I am interested in which step of pathogenesis.

There are Bacterial ATPase (actin tail, intracellular movement), M-cell (enter) ...-> extracellular movement.

Where can the O antigen affect in Shigella?


texts: Do any known viruses contain "junk" or parasitic genomic information?

texts: After reading about so-called "mystery proteins" in this excellent summary of the coronavirus genome (and acknowledging that the "mystery" simply reflects our lack of knowledge about a very new virus), I'm curious if any known viruses can contain parasitic genetic information "along for the ride", or if their genomes are selected, generally speaking, to be as informationally efficient as possible, for what is encoded? In other words, does selection pressure allow for these parasites to contain their own parasites, and are there known examples of such, if so?


texts: Is cardiac output the amount of blood pumped by both ventricles in 1 minute or only by the left ventricle in 1 minute?


texts: How do I run each individual record in a multi-fasta file against a database using PSI-Blast?

texts:
I'm new to standalone blast+ and the linux terminal.

I set the bash-profile to load the PATH and BLASTDB for my blast already, but I don't know how to use psi-blast yet.

How can I do the search against db with one query sequence? The file has >400 FASTA sequences. I need to checkout every sequence alone against database. Is it possible to run this job automatic in blast+?  (one run in loop for every seq?)


texts: Why do chromosomes uncoil back to chromatin after cell divisions?

texts: At the telophase of meiotic and mitotic cell divisions, the chromosomes of daughter cells uncoil back to chromatin, but after interphase, it coils up again to form visible chromosomes. Why do this happen? Isn't it simpler and more convenient for the chromosomes of the cells coil up in 1 cell cycle?


texts: Why is mRNA needed in the Protein translation?

texts: The original question was to predict the basic requirements for information storage. Then the discussion moved to why is it necessary to include mRNA in the protein translation process. Why can't there be a similar chemical molecule like tRNA which can directly read from DNA and exclude the mRNA intermediate. Also is the current translation process optimal in the sense that can there be a system which does not need mRNA or a similar intermediate altogether. Or is the presence of an intermediate a necessary requirement.


texts: Pink growth (aka pink slime) in bathtub or shower

texts:
I was wondering if anybody had studied or was knowledgeable about the pink growth that people often find around water fixtures in their homes, especially bath tubs and showers?

My understanding is that this pink growth is actually a bacteria and not a fungus as many assume (source1,source2). Supposedly, the bacteria, Serratia marcescens is airborne and thrives in areas of retained moisture and fatty residue.

My main questions are:

How ubiquitous is this bacteria? What is the bacteria's geographical range of occurrence?

For example, is this species more prevalent in more humid environments?

Are there other species of Serratia that can create similar pink biofilms in tubs? (Are the sources of "pink" separated by geographic location?)

Is S. marcescens even forming a biofilm in these pink stains??

What likely introduces S. marcescens into a bathroom?

I ask, because I've seen this bacteria both present or absent from similarly clean or dirty bathrooms, and thus far have not really seen any consistent patterns in the bacteria's spatial occurrence.

Any other interesting facts or sources on S. marcescens would be great!


texts: Enzyme Assay, absorbance change to concentration change

texts:
I have a few issues with this question.

An enzyme assay is performed and the kinetic data graphed. The y-intercept of a Lineweaver-Burk plot is 0.6 min/ΔA. The substrate being assayed has a molar absorbance coefficient (ε) of 4500 L/mol.cm.
What is the V max of the enzyme in mmol/L.min?

My working:

Vmax = 1 / 0.6min/ΔA = 1.66ΔA/min (the units switch back I believe?)

And then 1.66ΔA/min / 4.5L/mmol.cm to get 0.37 mmol/L.min?


texts: Cancer a method for early Earth Evolution?

texts:
Something I have been wondering for a while is looking at cancer from an evolutionary standpoint.

It's easy to conclude (from observations today) that cancer is something we would rather avoid. However I kept asking myself what would be the purpose of cancer existing in the first place? In my experience of studying biology if a organism or mechanism in nature exists it is because there was a pressure to create it.

It has led me to think that perhaps early on, when cells were just beginning to clump together forming very very primitive organisms, that cancer was a way for a cell to proliferate very quickly and make their particular genomic sequence more common within what would have been organisms made of a lump of cells. Perhaps the different organs we have today exist not just because there was environmental pressure to have a specific organ with a specific function. Perhaps the cells descended from a "cancer" that proliferated faster over other cells in a primitive ancestor of that organism.

The answer that "cancer exists because our bodies make mistakes" doesn't satisfy me when everything else around us evolved and formed due to a multitude of different pressures.

In an effort to make this question less broad my question is basically this:

Is it plausible that cancer is a phenomenon that began to occur relatively early in Earth's evolutionary history as a form of survival for cells in primitive organisms or am I applying evolutionary theory incorrectly?

(I know there is a better word for "pressure" to describe the variables that guide evolution but right now my brain can't come up with anything better).


texts: How to combine gene set enrichment analysis with hierarchical clustering?

texts:
I would like to find out how to combine gene set enrichment analysis with hierarchical clustering. The motivation for this combination is that potentially
too many gene-set symbols for leukemia may pass the p-value significance threshold. We are using an R-package for fast preranked gene set enrichment analysis (GSEA) with the URL, https://github.com/ctlab/fgsea.

Subsequent to the fast gene set enrichment analysis on a ranked list of gene symbols with different expression t-statistics, we specifically need to identify gene-set symbols belonging to a common functional group using the R language hclust function intended for supervised hierarchical clustering with a Euclidean distance between features in a timely manner, for example 15 or fewer minutes.

Quoting from Alan Moses 2017 book, "Statistical Modeling and Machine Learning for Molecular Biology" , "Clustering is meant for exploratory data analysis and therefore doesn't really have a strong framework for hypothesis testing".A new R package ClusterProfiler provides enrichment analysis of gene clusters as reported in this URL,  http://guangchuangyu.github.io/2015/05/use-clusterprofiler-as-an-universal-enrichment-analysis-tool/

The fact that most quality measures found in the literature have been conceived to evaluate non-overlapping clusterings, even when most real-life problems are better modeled using overlapping clustering algorithms is analyzed
in detail in the following paper and University of Texas Ph.D thesis

Academic paper: CICE-BCubed: A New Evaluation Measure for Overlapping Clustering Algorithms. Available from: https://www.researchgate.net/publication/260421976_CICE-BCubed_A_New_Evaluation_Measure_for_Overlapping_Clustering_Algorithms [accessed Apr 16, 2017].

and

https://repositories.lib.utexas.edu/bitstream/handle/2152/ETD-UT-2010-08-2022/KRUMPELMAN-DISSERTATION.pdf?sequence=1&isAllowed=y

As I am a novice to this type of bioinformatics research, please correct any inaccuracies in my problem statement.


texts: Do non-pathogenic organism not have PAMPs? Are there any research paper which proves that a certain microbe is non-pathogenic?

texts:
According to this

  PAMPs are delivered along with additional information that can be
  used by the host to distinguish pathogenic from nonpathogenic
  microbes and thereby guide the ensuing innate immune
  response.

Does this statement mean that non-pathogenic bacteria do not have PAMPs? If yes, then how would the host body differentiate between a pathogenic and a non-pathogenic microbe? Is there any well-known source containing a list of non-pathogenic microbes? Are there any research paper which proves that a certain microbe is non-pathogenic?


texts: Chromatin shearing: what is it and what are the effects of high-sensitivity?

texts:
I am reading a paper  which discusses a complex (MSL-DCC) involved in dosage compensation of the drosophila X-chromosome. Descriptions of the complex's structure and function are given in the papers introduction.

To start with, could someone explain what is chromatin shearing? what is happening during the process?

Secondly, the authors then say:

  "Our data suggest that the complex is particularly sensitive to shear
  forces on transcribed chromatin so that only the direct interactions
  on MSL-3 with nucleosomes are retained" - discussion section (subheading: interaction of the MSL-DCC with target gene bodies)

Could someone explain what is meant by 'particularly sensitive to shear forces'? In comparison to what? And what are the consequences of it being more sensitive?


texts: What is the body density of insects on average?

texts: What is the body density (in $\text{g}/\text{cm}^3$) of insects and is there a list of animals and their value of body density?


texts: How does one confirm the discovery of a new species of plant/animal

texts:
Hearing from the National Geographic and the news about the discoveries of new species of plants/animals, I was wondering how can a person confirm when they have actually discovered a new species of plant or animal?

How can they identify with enough certainty that it is not one of the species that has been previously discovered (out of the umpteen varieties of species)? Is there some kind of official/international database of species for plants/animals they typically look up to to confirm it? Also, how is the process of naming of a new species decided and why does it end up being a Latin name?


texts:
I found it outside in the City of South India in the month of May.

Another view:


texts: Are there any plants that fix their own nitrogen?

texts: I know that most nitrogen is fixed through industrial processes and bacterial symbiotic relationships. However, are there any plants that can fix their own atmospheric nitrogen?


texts: How do I determine this logistic growth model formula?

texts:
The Question

  Two yeast cells were placed into a special container to which food was
  continually added, to keep it at a constant concentration. All other
  factors were set for optimal yeast growth (for example, temperature,
  oxygen, and pH). The population was sampled every hour for 21 hours
  and the results of the estimated population size were recorded in the
  table below.

  Time (hour), Number of yeast cells

  (0, 2) (1, 10) (2, 15) (3, 20) (4, 40) (5, 60) (6,
  100) (7, 190) (8, 260) (9, 350) (10, 450) (11, 530)
  (12, 580) (13, 600) (14, 600) (15, 600) (16, 600) (17,
  600) (18, 600) (19, 600) (20, 600)

  What population growth model does the population appear to follow?
  Write out the mathematical equation it follows.

The Attempt

Looking at the values, I recognize the carrying capacity is reached at hour $13$ with $600$ cells, signifying a logistic growth model. The formula given to me for logistic growth is:

$\frac{dN}{dt} = rN[\frac{(K - N)}{K}]$

From what I have researched:

$dN$ = population size change
$dt$ = time interval
$r$ = (max) growth rate
$N$ = starting population size
$K$ = carrying capacity

So:

$dN = 600 - 2 = 598$?
$dt = 21$ hours
$r = $?
$N = 2$
$K = 600$

Plugging the values in gives me:

$598/21$ = $r2[(600 - 2)/600]$

Update 25/01/19

With some help, I have discovered how to determine the r/rmax value and have the following formula:

$r = (90+100)/2$
$r = 95/hour$

$dN/dt = 95N[(K - N)/K]$

With $N= 2$

$dN/dt=95(2)[(K-2)/K]$

and if $K$ value is carrying capacity, $K = 600$

$dN/dt=95(2)[(600-2)/600]$
$dN/dt=190(598/600)$
$dN/dt=190(0.997)$
$dN/dt=189?$

However, the question asks me to "Write out the mathematical equation it follows." So am I supposed to leave a value unknown?


texts: meaning of abbreviations h and m in Na channels

texts: In a voltage-gated sodium channel, there are two gates, one for activation and one for inactivation. They are also known as h- and m- gate. What are these letters standing for?


texts:
We can easily recall our visual stimulus and auditory stimulus but why can't we recall chemical stimulus like smell and pain?

We can recall a song or picture but we can't exactly recall smell and pain. Why is that so?


texts: Why does affinity of Hemoglobin increases for Oxygen in carbon monoxide poisoning?

texts: I have studied this in almost every physiology book but I just can't understand how carbon monoxide can affect oxygen's affinity to Hemoglobin. I know that there is left shift in oxygen dissociation curve but  why?


texts: Is working with (nitrile) gloves around a bunsen burner safe?

texts:
Recently I have started in a new microbiology lab, and with a new lab come new habits. When I was working with my bacterial (liquid) culture next to the flame (Bunsen burner) wearing nitrile gloves, my colleague warned me to not wear gloves close to the flame. Personally, I never experienced any problems with them and I think that wearing them provides better sterility.

Is it more dangerous to work with gloves close to the Bunsen burner than without?


texts:
Could cancer be in itself a evolutionary process? Maybe in some way could it be a process of variation? Or would this idea be completely without support, if so, why?

I don't mean that each case would lead to evolution, but that within an entire group of organisms, it could lead to case of of individuals developing ways to resist what caused the cancer, maybe in cases of individuals beating the cancer or in cases of successive generations of off spring from individuals with cancer?

Could it be possible that in rare cases it could lead to the development of new organs or specialized cells?


texts: Like squirrel undergoes hibernation during unfavourable periods if we induced the hibernation causing pitutary hormones in the human blood stream, can humans go to hibernation?


texts: How do genes get passed from one hive to another?

texts:
In hive species, like honeybees, how do genes propagate from one hive to another?

If the queen only mates with drones from the same hive, and queens and drones are born to the hive they end up mating in, I'd expect that each hive would end up like its own little species, a tiny gene pool with no outside influence.  But since honeybees haven't broken into myriad local species, there must be some gap in my understanding here.


texts: Resource plant anatomy/lifecycle vocabulary

texts:
I've been curious about a lot of vocabulary words in the world of botany. I've had quite a bit  of trouble finding somewhere online to help me out, but I'm having some trouble finding a resource like that.

Optimally, I'm looking for something with diagrams of anatomy, over the course of time, maybe some photo examples, and some sort of dictionary to accompany. Is there anything like this, online or offline that anyone knows about?


texts: How is the nasal secretion system of local immunity coupled with lymphatic circulation?

texts:
I started a thread about Nasal chronic Inflammation after influenza virus here.
However, I do not understand enough well the structure of the nose to answer the questions there.

I know that the lysed DNA (proteins) of small bronchial tree are circulated on the nasal epithelium.
I am not sure how this happens but my intuition is

first through lymphatic circulation
then on posterior nasalis membrane upward progression on the nasal membrane in the nares.

Picture about the nasal membrane.

Better pictures about the linkage of lymphatic circulation from the small bronchial trees into posterior nasal membrane are wanted.

However, I am not completely sure how this organisation occurs.

How is the nasal secretion system of local immunity (IgA) coupled with the lymphatic circulation around the back of the nose?


texts:
Some people like to say that vitamin D is a hormone.
A simple set of differences between hormones and vitamins is described here.

Vitamin D is not (for the most part) absorbed through food but created by our body when our skin is exposed to the sun, so it does look more like a hormone than a vitamin.

Another difference listed is whether it has catalytic action or not (that I don't know what it means - answers with an explanation would be nice).

So, is vitamin D a hormone? And if so, why is it called vitamin D?


texts: Could be an union/synergy between Math, Computer Science and Marine Biology?

texts: I'm studing for my bachelor's degree in Natural Science and I have to chose the path for my future life. I have to chose the right kind of graduate studies. Since I love computer science, maths and marine biology more in details I love the tropical ecology especially that of the coral reefs and atols in the pacific ocean, the whales (e.g. the humpback whales and their migrations), the computer simulations and mathematical models. Thus, I want to ask you if is there a branch of marine biology that allow me to study and specialize myself in tropical ecology and in math & computer science too, because in my current course we don't have any exams of computer science and only one of maths, and I'm feeling sad for this. The right path coul be the computational biology? Exist in biology, some field called "Computational Marine Biology" or "Computational Marine Tropical Ecology"? One last thing, what about Ecoinformatics?


texts: External tissues, connected to the body?

texts:
Some cancer tumors suppress themselves from spreading. When such tumors are removed by surgery, the metastasis process is accelerated.

Isn't it possible to put such tumors into external device like hemodialysis device and slow metastasis process this way?

Are there any experiments or clinical usages of own body tissues in such a devices? Not for cancer, but probably for some other reasons, in humans and animals?

Some sort of grafting for animals.

Such a tissue can interact with main body by blood and cause some effects.


texts: Why do flagella form a bundle only when they rotate counterclockwise during chemotaxis?

texts:
During Chemotaxis in bacteria with flagella, the flagellar rotation dictates how the cell moves. If the flagella rotate counterclockwise, then they form a bundle at one end of the cell (---O) and propel it forward in a coordinated fashion. However, if the flagella rotate clockwise, then each flagella acts independently to push the cell in many different directions.

My question is, why doesn't clockwise flagellar rotation simply cause the bundle to form on the opposite end of the cell? (O---)


texts: Filter proteins by domain with InterProScan

texts:
I have a bunch of proteins (over 300000) in fasta format, and I want to find the ones that contain a specific domain (using a specific InterPro accession).

I can run InterPro on the proteins and get every domain they have, but with so many proteins, it will take a large amount of time, which I'm short on. I'd like to limit my search to the specific domain I'm looking for, as I assume it will be considerably faster.

Is there a way to do this with InterPro? Browsing the docs doesn't give me any hope. If InterPro isn't capable of that, would it be doable with a single database like Pfam or CDD?


texts:
So for Google Earth Day's quiz I ended up being a "Pangolin." Turns out I had no idea what it was so I looked into it and honestly it reminded me a lot of an Armadillo. So I decided to find out the difference between the two, and I stumbled across this site.

It was all making sense until I got to the "bullet points" at the bottom where I saw this

  Pangolin is a mammal while armadillo is a placental mammal.

And I'm now very confused. I thought placental mammal was just a subset of mammals. And I look up Pangolin's taxonomy and now I'm seeing all kinds of stuff I have no idea how to interpret. Back in my day, it was "Kings Play Cards On Fat Green Stools" for "Kingdom Phylum Class Order Family Genus Species". And now I'm seeing things like clade, infraclass, subcohort, superorder and all kinds of things I just don't get.

So I guess I have many questions, but I'm going to boil it down to "If the Pangolin isn't considered a placental mammal, then what kind of mammal is it, and where does it diverge in taxonomy from the Armadillo?"

Oh, and if someone could point me to a primer on the changes to taxonomy in the last 20 years, that'd be cool too.


texts: I know that white blood cells have lysosomes but what about other body cells? I mean, any other cell such as cells in the respiratory system.


texts: Is it possible that by mutation a human could see infrared or other 'colours'?

texts:
Incoming light reacts with the several types of cone cells in the eye. In humans, there are three types of cones sensitive to three different spectra, resulting in trichromatic color vision. Each individual cone contains pigments composed of opsin apoprotein, which is covalently linked to either 11-cis-hydroretinal or more rarely 11-cis-dehydroretina.

The opsins (photopigments) present in the L and M cones are encoded on the X chromosome.  A very small percentage of women may have an extra type of color receptor because they have different alleles for the gene for the L opsin on each X chromosome. X chromosome inactivation means that only one opsin is expressed in each cone cell, and some women may therefore show a degree of tetrachromatic color vision. Tetrachromacy is also demonstrated among several species of birds, fish, amphibians, reptiles and insects.

Humans cannot see ultraviolet light directly because the lens of the eye blocks most light in the wavelength range of 300–400 nm.

So, besides above mentioned exceptions, is it possible due to mutations or genetic engineering to see UV or infrared. What kind of mutations should be made or are the changes to be made in the opsines to big to create 'alien' eyes?


texts:
I am looking for an ID of this fly at genus or preferably species level.
Location: The Netherlands.
Size: approx. 7-8mm
Habitat: indoors, attic.
Timing: usually appears late winter, early spring


texts: Methods for varying insert size in E. coli clones

texts:
I'm writing my master's thesis proposal, and I need to improve the solution-behavior of some truncated protein domains which have previously shown poor solubility when expressed in E. coli.

To prevent this unwanted aggregation, one experiment I will perform will be to alter the domain boundaries.  I will create gene constructs where each clone will have an A domain of a certain length and domain border (see below).

My question: Is Gateway cloning better than restriction/ligase methods for this?  If i use restriction/ligase methods to construct vectors for transformation, then my choice for domain boundaries will be determined by restriction sites. Howevever, with a system like Gateway cloning, I can define boundary limits to bp resolution by simply desining an appropriate primer.

Is my reasoning here correct? I need to justify my choises for experimental design to researchers, so want to make sure I'm being efficient and logical.


texts:
Deer ran away from tiger or cheetah, but not from giraffe or zebra.
where did deer learn this?

How animals know which is carnivorous and herbivorous?


texts:
I compiled different data sets of invertebrate occurrences across some countries and now I want to ensure that all the taxonomic information is homogenized and correct. To this end, I am looking for a database which allows me to evaluate my date. Basically, the equivalent to what algaebase.org is for algae.

I know about gbif.org but already found some mistakes in there.


texts: Species Identification: Beetle having trunk!

texts:
Today morning I found this beetle in Cynodon dactylon grass. It had this beautiful head bearing a trunk like structure. I'm wondering what beetle it is

Images:

Approximate size: 1.75 cm
Temperature: 29°C
Location: Uttar Pradesh, India


texts: Do plant-plant interactions inhibit growth?

texts:
Plants produce lots of compounds that inhibit (kill or irritate) microorganisms and insects.  They have defenses against plant viruses and infections.

What kinds of compounds or hormones to plants use to regulate the growth of other nearby plants?  I have hear of ethylene, but I would like to hear about more specific compounds that might be known that work against specific species or kinds of plants?


texts: Why can't men produce milk, just like women?

texts:
This might seem a bit weird, but why can only women produce milk? Wouldn't it be more beneficial to our species if all humans could produce it? I can't think of any reason only one gender would need it, unless it would somehow be harmful to men.

I know that men can secrete milk in some cases, but why not in general?


texts:
At some point the neanderthal and modern human lineages diverged. I'm not sure what exactly their most common recent ancestor was (I see some sources suggesting homo heidelbergensis), but in any case I'm interested in the innovative/apomorphic features of neanderthals relative to that MRCA. What new features did they have, and what existing features changed most?

In particular I am not asking how neanderthals differ from modern humans.

This question is partially inspired by popular science pieces (e.g., Human Hands More Primitive than Chimp Hands) discussing human hands, which are essentially basal, vs. chimpanzee hands which are less similar to the common ancestor.


texts: Is viral protein expression important for peptide vaccine?

texts: I would like to know if proteins expressed in higher quantities, such as DNA polymerase, would be better vaccine candidates for a T-cell based vaccine.