text:
What causes a small bump in the arterial pressure plot?

In my book there is a plot of the arterial pressure against time.
From the plot, during heart contraction, there is greater pressure on the artery and during heart relaxation, there is lower amount of pressure on the arteries.
This makes sense because P = F/A, the surface area of the heart is smaller when it is contracted versus when it is relaxed, hence greater pressure.
But why is there a small bump while the pressure is decreasing from systolic pressure to diastolic pressure?

This bump is related to the closure of the aortic valve as a reaction to the retrograde blood flow which in turn gives small change in blood pressure.


text:
Why should or shouldn't we allow the human body to take its natural course?
For example, when you are sick but don't feel thirsty, this could be due to baroreceptor reflex that is attempting to readjust salt and water balancing.
Why shouldn't a patient be left thirsty and let the body to adjust until he or she feels thirsty again?

Are you suggesting that we should throw away modern medicine and go back to natural selection?

I find this very unclear and broad (there are a huge number of processes and responses to consider).

imagine you have diarrhea and eventually will lose a lot of water. Would you like an IV with saline/vitamins or to be left alone?

I am assuming that your question is: "why can a human intervention improve health?". Let me know if I misunderstood your question.
Why can a human intervention improve health?
Let's first avoid going into the details of your example. It is quite obvious that human intervention can often improve health in a way that your body alone cannot. To me, an intuitive way to classify the reasons why human intervention are important to improve health into two categories.

The body does not always react in an adaptive manner.

Example: Anaphylaxis is a serious and sudden allergic reaction that may cause death. An allergic reaction is what is happening when your immune system recognize a chemical as a infectious element while it is not. The reaction of the body is not adaptive and taking medication such as an anti-histaminic can force the body to stop this "stupid" reaction.
Note: There are reasons why the body cannot be always perfect but it is a bit long to make an overview here. There is stochasticity in the developmental processes, there is genetic variation for example due to always occurring deleterious mutations, there is also an arms race between parasites and host. This arm race leads parasites to take advantage of normal host physiological pathways. There are tons of other reasons that relate to the stochasticity and to the physic and physiological constraints of evolutionary processes.

The body sometimes cannot (physical constraint) produce the action that is required to be performed to improve health.

Example:  If you have an important wound, then a human-made compression can by far improve your chance of the survival. The body is not able by itself to simulate this external compression to prevent blood to exit the body through the wound.

You might easily find semantic issues with these categories though such as the question of cancer and its removal for example and some may argue against this categorization.
Dehydration and thirst
Your example would fall into the first category. It is not so uncommon that the body needs water while not causing thirst. Because after 50 years old, the sensation of thirst start to diminished, dehydration without the sensation of thirst is common among old people. Dehydration along with hyperthermia is a relatively important cause of death during hot weather in summer. It is especially true in old people as the sensation of thirst diminishes with age. Dehydration following diarrhea is also a common and important issue in old people sometimes leading to death.

Dehydration/hyperthermia isn't just an issue for elderly people, it can affect anyone.

I meant that it is an issue of particular importance in old people as old people the sensation of thirst decreases with age. Feel free to edit my answer to clarify this point if it is a bit unclear.

I'd also add that many pathogens have evolved to abuse reflexes that would otherwise be beneficial. Coughing for transmission of airborne disease, fungi causing itch...

It is a good point. I felt it quite complicated to add this point without having to make consideration of the other evolutionary processes that may explain why an individual does not always react adaptively. I put all that in some kind of messy text as a "note" under the first category.

source: Stack Exchange

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sort: votes


text:
Do muscles still hold glycogen reserves if there is no carbohydrate input
Afaik skeletal muscles take glucose from the blood to store it localy as glycogen, to be used in the case of intensive exercise.
Does this still happen

if the calorie input is exclusively made up of fats and proteins?
while fasting / starving?

I know that muscles can run on fatty acids and ketone bodies.
And that the liver can create glucose by gluconeogenesis.
But is this "backup"-glucose still used to refill the glycogen stores in the skeletal muscles in those two respective cases? (while resting)
If not, how would the performance of exercises like sprinting, that normally make use of those stores, be affected?

Most of it isn't but a little bit is.
When your body has very little glucose and a lot of fat(Which can be the case if an overweight or obese person goes on a low carb diet) the ketones and fatty acids and glucose produced by the liver are used almost exclusively to keep the body alive although a little is synthesized into glycogen.
Specifically when you don't eat anything gluconeogenesis alone supplies enough for 1 day. Then the fat metabolism accelerates because gluconeogenesis is not enough. This is when you get into a state of ketosis(this can also happen in bodybuilders since increased muscle = increased fat metabolism). This ketosis causes fast weight loss from not just water like a lot of other diets but also from fat. This fat then eventually depletes and it metabolizes protein exclusively(during all this time it does metabolise some protein). However that can't continue forever even if the amino acids get reused over and over again because some are used to produce ATP. Thus you eventually would die from starvation with obese people surviving longer than underweight people.
Anyway as far as exercise assuming that you start off obese, getting your body into a state of ketosis makes your performance even better than on just glucose alone after a while of adjusting to fat metabolism since 1 molecule of palmatic acid(16 carbon fatty acid) produces 106 ATP compared to 32 ATP for 1 glucose molecule so your muscles can go longer without being exhausted. Theoretically someone who is 50 pounds overweight could exercise 24/7 for several days if he/she is in a state of ketosis.
Here is a reference to the low glycogen and increased muscle performance:
http://www.bodybuilding.com/fun/glen12.htm
As to why it is 106 ATP it is because each NADH produces 2.5 ATP and each FADH2 produces 1.5 ATP and because of the activation step using 2 ATP just like how NADH transport from cytoplasm to mitochondria takes 2 ATP, 1 per NADH in glycolysis.

interesting, can you add some references? I'm not convinced you can draw any conclusions about muscle performance from the molar ATP yield of fatty acids vs. glucose, those are two very different substrates ... Also, for the original question, is there some data showing that muscle does not synthesize glycogen when on low carb diets? I imagine low insulin would have this effect, but I'm not aware of a study.

Well I looked at some websites and I was wrong about no glycogen being synthesized when the body is in a state of ketosis but there is a very low level of glycogen that is synthesized because of the low insulin. This low insulin also makes the fat be the primary metabolite since insulin causes there to be more fat in adipose tissue.

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text:
Before Evolution was proposed by Charles Darwin, what were the leading secular theories to explain how life developed?
Outside of evolution, what were the leading scientific schools of thought that Charles Darwin contented with when he published his evolution theory as way of natural selection in 1859?

Hello. I think you'll get the answer to your question on this wiki page. There is probably too much to say in a post. I vote to close because it is too broad. Please let me know if you think the wiki post can't answer your question.

Saltationism maybe?

Darwin stood on the shoulders of giants, most notably Alfred Russel Wallace

@Remi.b I did not know that all theories before Darwinism were listed under the umbrella of evolution. For example the theory of Spontaneous generation, did that ever have any mainstream acceptance within the scientific community?

@GabrielFair absolutely. And it makes total intuitional sense - you take a piece of meat, put it outside, and within a relatively short period of time it has maggots on it. Same thing with hay - cut and dry it in the field, put it on the wagon and bring it back to the barn, and before you know it there are mice in it, which certainly weren't in there before. It feels completely logical. Besides, fresh hay doesn't produce maggots, and rotting meat doesn't produce mice, so the "seeds" of those animals must be within the originating substance.

Of course, not all things behave this way - we know that ducks come from duck eggs, and puppies come from a bitch, and so forth, but when you don't have the knowledge or creativity to set up a completely controlled experiment, it all seems to make a great deal of sense. Remember, the average level of education back then was much lower than today, and most "scientists" (they called themselves natural philosophers) were self-taught.

Most of the evolutionary thoughts presented in the wiki article I linked were build at a time where the word science (and the scientific methodology) didn't even exist, so it is a bit complicated to group those opinions into any category. Lamarckism was clearly an important mode of thinking at the time of Darwin, there are a number of works that kinda anticipated the process of natural selection before Darwin. You can have a look at this history on wiki.

Voted to re-open as it is a valid question with an interesting answer. Broad yes, but philosophical questions such as this one are fundamental to science. Darwin is seen as the founding father of evolution, but some major players pre-dating him set the stage for his appraised evolution theory.

related: How was the resemblance between apes and humans explained in pre-Darwinian biology?

Oh wow, Thanks @fileunderwater, for sharing that.

There were many (more or less) non-theological theories of how life had developed before Darwin, starting at the ancient greeks. Many theories included spontaneous generation but also aspects of modification by descent of existing species (i.e. evolutionary change), but most were not that well developed and complete thought. However, one of the more complete evolutionary theories that pre-dated Darwin was Lamarckism, which claimed that individuals pass on traits that they have acquired during their life time. So the basic idea was that individuals respond and adapt to the environmental conditions they experience, and that these traits are then transferred to their offspring. This is one example of a non-theological theory that pre-dated Darwin, but I cannot really say if it was the leading one. I do know that Lamarck's ideas were relatively ignored during his own lifetime.
Darwin included some aspects of these ideas in his "Origin of Species", but challanged Lamarckism when it came to the main processes of evolution. A weak interpretation of Lamarckism has actually seen a revival after the discovery that epigenetics can be transferred from parents to offspring, see e.g. Heard & Martienssen (2014) and Szyf (2014).

Wow this was really fascinating, I did not know this.

@fileunderwater - shouldn't this question be re-opened? It is a valid question and your answer is great (+1'd fyi)

@AliceD I think the close reason is somewhat valid. You could write a book on this topic. On the other hand, a couple of answers that highlight different theories could probably provide a nice overview for somebody new to evolution.

Autochthonous generation proposed that different species were formed independently and through natural processes, "by chance". Scottish philosopher David Hume believed that if the universe had no beginning, then it became likely that somewhere (e.g. Earth) the unlikely event of particles accidentally arranging into orderly entities (e.g. life) could happen.

Deism was also invoked to explain biology during the Enlightenment. Deists believed in a god, but largely rejected religion and worship. So it was a kind of "secular theism", where intelligent design is inferred, but the identity of the creator is left unexplained. Much before that, some Greek philosophers ascribed to a "demiurge", a god-like being who arose from primordial chaos and then proceeded to order what was around it to create the world.


text:
How to tell if a given gene is a tumor suppressor or oncogene?
This is a problem taken from "Concepts of Genetics", Klug et al, 10e. I'm given the following table about the mutations in the BRCA1 gene:
$$\begin{array}{c|c|c|c|c}
\text{Kindred}&\text{Codon}&\text{Nucleotide}&\text{Coding}&\text{Frequency in}\\
&&\text{change}&\text{effect}&\text{control chromosomes}\\
\hline
1&24&-11\text{ bp}&\text{Frameshift or splice}&0/180\\
2&1313&\text{C}\to\text{T}&\text{gln}\to\text{stop}&0/170\\
3&1756&\text{Extra C}&\text{Frameshift}&0/162\\
4&1775&\text{T}\to\text{G}&\text{met}\to\text{arg}&0/120\\
5&\text{N/A}&?&\text{Loss of transcript}&\text{N/A}\end{array}$$
Footnote: "*N/A indicates not applicable, as the regulatory gene is inferred, and the position has not been identified."
Using this information, how can I decide whether the gene is a tumor suppressor or an oncogene?
I already know that BRCA1 is a tumor suppressor, so put another way, how can I arrive at this conclusion given the data above?

I assume these are all carcinogenic mutations. Because some them are clearly recessive loss-of-function mutations (like loss of transcript), you can conclude that the function of the gene consists of "holding back cancer". When these mutations occur, they can generally be complemented by a healthy allele on the sister chromosome.
Oncogenes on the other hand, require gain-of-function mutations, like translocation to a more active promotor or dominant negative mutations (like a loss-of-function mutation in a protein which forms multimers, which get "polluted" by the mutant and thus can not be complemented by the other allele). In most cases this "increases" their stimulation of cell division and thus cancerous growth.
Loss of transcript of an oncogene would not cause cancer.


text:
Can yeast in a primary fermentation of wine be used as a source of yeast for new fermentation?
So if I were to pitch bread yeast, and get to primary fermentation, which as I understand it, is the point at which regular cellular respiration can no longer continue due to a lack of oxygen , which is needed for the electron transport chain. Therefore the yeast switch to fermentation, which produces my desired product, ethanol.
But as I understand it, at this state the yeast are no longer reproducing and are in a survival mode.
Therefore if I were to cut a 2$L$ bottle of my primary ferment in half, and then add more sugar and water to the now separate 1$L$ bottles, and oxygen (if possible), up to 2$L$, would I be able to have the same amount of ethanol produced/would fermentation even occur?
I feel there would be diminishing returns even if it was possible, since yeast can only reproduce asexually so many times, which happens during stressful times, which this process might induce?

Yes, it is possible to reuse yeast in both beer and wine fermentation - commercial brewers do it all the time for cost savings and batch reproducibility, and although I'm not as familiar with making wine, many sites including this one say it's perfectly fine, as long as the viability of the cells is high enough.
The yeast aren't necessarily in stress-induced survival mode during fermentation, they're just living (and metabolizing) anaerobically. They may no longer be reproducing, or doing it very infrequently, but they'll remain perfectly happy little buggers (that's a technical term) for quite a while. Give them more food (sugar), and they'll keep fermenting. What eventually stops the process with wine is the level of ethanol rising too high for their comfort. If you were to dilute the ethanol out with water, they'd keep going.
Now, I wouldn't recommend doing this indefinitely (some strains may exhibit genomic instability, etc.), but new batches can certainly be produced with existing pitches.


text:
What is this mushroom?
I found a singular mushroom in my back yard,  It is jet black, seems to have gills and looks somewhat like a flower do to it's upturned-ness. Sorry for not having spore colors, but I didn't want to disturb it. I will post a picture soon. I found this mushroom at 4/11/15 and it disappeared the next day. I'm just south of San Antonio.

picture + geographical location + micro-environment are necessary info

Welcome to Biology S.E.! If you need any assistance, please visit The Help Center. Please do edit this by adding a picture as soon as you can. Also, as @AliceD said, it would be very helpful to have the general location and climate the mushroom is growing in.

May be http://www.mushroomdiary.co.uk/2011/11/blackening-waxcap/ . If you are looking for an answer, here is a hint, it's black because it may had a disease called black inking.

@DevashishDas isn't the stem a bit to tall and the cap to small to be a blackening waxcap?

@tox123: Yup. Then maybe be a mushroom with the disease. But something is wrong. you are sure its a mushroom?

@DevashishDas Yes it had gills and looked like it had the texture of a mushroom.

It has gills? Are you sure it's not a fish?

The mushroom suggestive for one of the inki ones of Coprinus family, especially Coprinus comatus. The black color can be very intensive in some stage of their development, since it is a part of the spread mechanism.
"Members of the genus Coprinus have been collectively known as the "inky caps" because of the curious character of autodeliquescence of their gills-- in other words self-digestion to release their basidiospores. Most of these species have gills that are very thin and very close to one another, which does not allow for easy release of the spores. Moreover the elongated shape of mushroom does not allow for the spores to be shot off the basidia and get caught in air currents as in most other mushrooms. Coprinus species "compensate" for this by a sequential maturation of the spores from the bottom of the gill towards the top. After the spores have matured and been released, the gill tissue digests itself and begins to curl up, allowing easy release of the basidiospores above. In other words, the digestion opens up the fruiting body so that spores from further up the gills become exposed to the air and a clear path of spore release. The self-digestion continues until the entire fruiting body has turned to black ink. In the olden days this ink was actually used for writing. The self-digestion is also a way of releasing the spores over a longer period of time, and allowing the release of spores from very closely spaced narrow gills borne inside a longitudinally tall pileus. If any Coprinus species are collected for eating or for scientific study, they must be cooked or dried right away, since the self-digesting enzymes seem to kick into high gear after the mushroom is removed from its substrate. They're pretty easy to find too-- the genus name Coprinus gives you a pretty good idea where to look for these mushrooms-- in dung or very rich organic soil."
examples:
1.

2.

3.


text:
How can the phenotypic effects of a tumor suppressor mutation be silenced?
I've been reading a little about the "two-hit" hypothesis for tumor suppressor genes here, which mentions that some genes exhibiting haploinsufficiency are exceptions to the hypothesis. I've read elsewhere on this site (namely the answer to this question) that suggests haplosufficiency as a means of "silencing" the mutation of the tumor suppressor gene such that the expression of the wild-type allele compensates for the mutant allele.
Are there any other mechanisms that contribute to incomplete penetrance of tumor suppressor mutations?

This is more of a comment

Mutation in tumour suppressor is a recessive trait and there is no active "silencing" of the mutation. If a tumour suppressor is a TF then a mutation in the DNA binding domain can have no effect if there is a complementary mutation in its binding site. This is just a theoretical possibility and I have not heard of any examples as such. I don't think any other mechanisms exist for "silencing" any loss of function mutation.


text:
What governs the distribution of blood vessels?
Whenever someone is sick, doctor places 2 fingers on wrist & observes the heart-beat-rate by feeling pulses of a certain artery.
To me it seems the distribution of blood vessels are pretty standard across all variations of humans (I mean identical blood vessel positioning seen across Caucasians, Africans, etc. members)
So when someone is born with extra finger or joined skull - which rule/gene/algorithm decides the distribution of network-of-blood-vessels in those special parts?
PS: I am definitely / apparently not a biology student, so pardon my ignorance

Is positioning of blood capillaries random or they too are identically positioned among all humans, although we can't see them.

Like most of human growth, the development of blood vessels (angiogenesis) is fractal or procedural in nature; for the same reason that supranumerary digits (extra fingers or toes) generally still have the shape of a finger or toe, they are likely to have similar vasculature. Capillary growth, while also fractal, is much more "random" in nature, and is driven primarily by the fact that ares of tissue which are low on blood supply stimulate the growth of capillaries towards them in a dynamic process - which is why tumours are generally able to maintain blood supply however large they get.

Damn :) all you people are just so smart... Awe inspiring knowledge, honestly.

The growth of blood vessels is called angiogenesis. This process occures during embrional development, tissue repair, and even tumor formation (in fact this is a crucial step for tumors to survive). This Nature review ("Molecular regulation of angiogenesis and lymphangiogenesis")provides great overview of the process, I'll try and briefly summarize things:
In general large arteries grow circumferential  to keep up with increased blood transfer, while capillaries branch to a more complex network in order to be able to supply blood to every cell. The circulation system starts as a

primitive
  and uniform vascular structures, known as primary capil-
  lary plexi,

that later develop into a hiearchical system of arteries, capillaries and veins. Main regulator of the morphogenesis of blood-vessels is the

vascular endothelial growth factor A (VEGFA; also known as vascular
  permeability factor (VPF)).

This needed for the chemotaxis (the movement of an organism in response to a chemical stimulus. from: http://en.wikipedia.org/wiki/Chemotaxis) and differentiation of endothelial precursor cells (EPCs; angioblasts), endothelial cells (ECs) and the assembly of ECs to vascular structures (termed vasculogenesis), as shown in the figure taken from the article I linked. EPCs themselves differentiate from mesodermal cells during early embryo development and aggregate to form blood islands that later form the  vasculogenic formation of honeycomb-shaped primary capillary plexi.

Also it is important to note that :

alternative splicing of VEGFA can generate several variants of the growth factor, including the so-called b isoforms that differ in the last six C-terminal amino-acid residues and have anti-angiogenic properties. The balance between the different VEGFA isoforms can regulate blood-vessel
  growth and patterning.

Also local composition of extracellular matrix (ECM) and the interaction between ECM and cells can affect angiogenesis. For example release of matrix bound VEGF is important in the regulation of the level of available VEGF. Also:

Furthermore, the physical contact between ECs and pericytes is thought to induce a quiescent, non-sprouting phenotype.

Sprouting itself carried out by the selection of some ECs in the capillary wall to lead the growth of the new sprout. See next figure also from the linked article:

Notch receptors and Delta-like 4 (DLL4) ligands play key role in this process. In tip cell(s) DLL4 expression is induced (in response to VEGFA), while the Notch signaling in neighboring cells (activated by the DLL4) represses sprouting (by down regulating VEGFR2 - VEGF receptor 2) . This is important, because otherwise excess sprouting would lead to a dense network of capillaries and blood would just spread out too thin and would be unable to supply the organs with oxygen and nutrients.
In order to tip ECs be able to grow new capillaries they ahve to undergo some changes. Mobility is most likely gained by activated secreted or cell-surface bound proteases, to locally degrade the basal membrane. Interaction with other ECs have to be changed, without completely disrputing cell-cell junctions and the integrity of the vessel-wall. Also the apical-basal (apical side - faces the lumen of the vessel) polarity of the cells have to be reversed in order to be able to grow outwards (from the basal side of the endothelium. In order for the new capillary vessel to grow, the elongation of the new sprout has to be polarized and directional. This is achieved by spatial concentration gradient of ECM bound VEGFA isoforms along with prominent expression of VEGFR2 in the tips of sprouts.
For blood functional blood vessels to be formed the tips must cease growing and exploratory phenotype when they find their target, and string EC-EC junctions need to be formed. Also the generation of the lumen of the newly formed vessel is required.
As you can see forming of new blood vessels is a complex process that is controlled by local signals, yet it is part of a bigger process - the development of the embryo and organs that is regulated by many many genes and processes. Since our general architecture is the same it is logical that or circulatory system is similar. As for the abnormal structure of a body I think perfusion of that extra body part depends on the local environment.
The review linked at the beginning of this post has extra info on arterio-venosus differention and many other things.


text:
Could an action potential produce few or more neurotransmitters based on the stimulus received?
I reckon that if you would be able to widen the AP width, it would produce more neurotransmitters in that larger time interval. Is that correct? Or does the neuron have a standard amount of neurotransmitters it releases in order to pass the signal post-synaptically?
(bonus: could it NOT result in neurotransmitter release, or does the definition of an AP include the release of neurotransmitters?)

Short answer

Widening of the action potential increases neurotransmitter release;
Generally, an action potential results in the release of about one vesicle of  neurotranmitters;
An action potential does not have to lead to neurotransmitter release - the chance being anywhere between 9 - 100%, depending on the synapse under investigation.

Background
Neurotransmitters are released in packets, called neurotransmitter vesicles:

Source: Science blogs
Vesicles are released via a mechanism involving Ca2+. When an action potential reaches the synaptic terminal, voltage-gated Ca2+ channels open, which leads to Ca2+ influx. The increased Ca2+ in the terminal leads to release of vesicles.
A study by Sabatini & Regehr (1997) showed that widening of the presynaptic action potential in rat cerebellar cells resulted in enhanced Ca2+ influx, which in turn greatly enhanced neurotranmitter release.
According to a study in rat hippocampal cells it was shown that, on average, a single action potential releases approximately 0.5% of the vesicle pool from the presynaptic terminal. The presynaptic vesicle pool was estimated to be 100 - 200 vesicles, which hence added up to 0.5 - 1 vesicle released per action potential (Ryan & Smith, 1995).
An earlier study of Rosenmund et al. (1993) confirms these findings in hippocampal neurons, and investigated the variability between different synapses in greater detail. They found that the chance that a single action potential released neurotranmitters was 9 - 54%. They reasoned that larger synaptic terminals, or terminals triggered by long-term potentiation have a higher chance of releasing neurotransmitter. Moreover, such terminals with enhanced release probability may also have a higher chance of releasing multiple vesicles per action potential. They predicted that 54% of release events from such enhanced terminals may release multiple vesicles per action potentials, whereas just 9% of normal terminals may do this.

References
- Rosenmund et al. Science 1993; 262: 754-6
- Ryan & Smith, Neuron 1995; 14: 983-9
- Sabatini & Regehr, J Neurosci 1997; 17: 3425-35

Neurons encode the "largness" of the stimulus in firing frequency. Neurotransmitters are stored in vesicules near the end of the axon. It has been shown that neurotransmitter release follows Poisson-distribution and that usually a single "packet" (quantum) is released - this is known as quantal release. Although the actual number of molecules in a single vesicle vary a bit, and ocasionally multiple vesicles may be emptied, it is accepted that for a single AP a neuron releases a single vesicle.
These two pages can give you more info and details:
http://neuroscience.uth.tmc.edu/s1/chapter04.html
http://neuroscience.uth.tmc.edu/s1/chapter05.html
Also this link provides introductionary info on the topic
A great image from :http://onlinelibrary.wiley.com/doi/10.1113/jphysiol.2006.123224/full

+1 for your answer. In an article (Ryan and Smith) I cited it was said that neuromuscular junctions released relatively small percentages of vesicles. Perhaps an interesting read?

I rather focused on the quantal nature of the release than actual release frequency, because in my opinion that is what the OP is interested in. I do not doubt that neurotransmitters are not necessarily released but when they are released it is done in a quantal manner. Also the graph shows that most of the time no release event occured that corresponds to what you've described.

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text:
Why is there smooth muscle in our bronchioles?
Having muscle tissue in our bronchioles that can constrict seems like a poor choice for tissue. Why would our airway want to ever close up? Wouldn't it be more beneficial for our bronchioles to just remain open?

There are at least two things to consider.
First, ability to limit airflow is a defense mechanism for animal. Imagine getting into area of some sort of toxic evaporation, e.g. CO2 cloud near volcano , then it makes sense to decrease delivery of toxin via lungs to minimum. As I understand, that is what an allergic asthma attack. (Sorry for not providing good enough source of that)
Secondly, you are incorrect in assuming that normal state is "dilated". Dilation of branchioles is sympathetic ("fight-and-fly") response of the nervous system to something like danger, that requires short-term boost in energy production. That is, by default, your airflow is limited. Probably, to limit amount of energy you effectively burn via oxygenation. But most importantly, you leave yourself a reserve in terms of oxygen supply for critical moments.
Some more information you might find here.

Our airways close up to make them more efficient. The respiratory tree from the mouth to the terminal bronchioles can't absorb oxygen, so each time you breath all the air moved into and out of the trachae, bronchi and terminal bronchioles is extra unnecessary work for the muscles. We can make it more efficient by shrinking the size of those tubes down by contracting the smooth muscle.
When you exercise these small tubes won't be large enough to get enough air in and out, so the smooth muscle relaxes to allow more air to move into the lung faster. It's a bit less efficient, but necessary when you need a lot of oxygen.


text:
What's the proton concentration around a DNA helix?
Let's suppose the concentration of a 20-nt DNA strand is $10^{-4}$M and the solution does not contain any salt ions. In a solution with pH 7, $[H^+]=10^{-7}$M, on average each DNA has only 0.001 protons. But the DNA phosphate groups become charged through de-protonation so each DNA should effectively release 20 protons thus we would expect $[H^+]=20\times 10^{-4}$M. How does the system maintain chemical equilibrium while keeping charge neutrality? If $[H^+]=10^{-7}$M because pH=7, where do other protons go?

If you added DNA with a protonated phosphate backbone to a sample of pure water with pH of exactly 7.0, the extra protons on the backbone would be picked up by waters to create a deprotonated backbone and hydronium ion. The charge is still balanced, the backbone becomes negative and the hydronium is positive. The pH would change, becoming more acidic, I don't know how acidic, depends on the amount of DNA and equilibrium constants, and I don't want to do that math right now.

I'd suggest specifying in your question that your system is just water at some sort of default conditions.

 DNA stands for deoxyribonucleic acid. Acid, by definition and mechanism in aqueous environment, is something that donates proton ($H^+$). HCl dissolved in water will donate proton to solution, thus bringing pH down, since $pH=-log_{10}[H^+]$.
DNA, being an acid, donates protons to water and brings pH down a notch. Just like in case with HCl, it has nothing to do with keeping charge neutrality. Water is not a buffer, that is able to tolerate or smooth change in pH. What happens when you add DNA to buffered solution, say phosphate buffer, is completely different story from biochemistry.

Note that DNA also has "bases".. But since they are paired, they may not contribute to basicity.

indeed. Single-stranded DNA will act differently

The nitrogenous bases are Lewis bases (that can donate an electron pair) and are extremely weak, similar to pyridine.

Since DNA is an acid it is reasonable to ask: what is the pKa of the phosphate residues located all along the polynucleotide's sugar-phosphate backbone? Apparently that number is at a pH between 1 and 2 (http://www.bio.brandeis.edu/classes/biochem104/DNA_lecture.pdf). That  means at physiological pH ranges (for example, the pH found inside the nucleus or cytoplasm of a cell, around 7 or so) 100 % of these phosphates would be ionized (unprotonated), and therefore strongly negatively charged.  The counter ions would be any suitable mono- or divalent cations handy. When you purchase intact DNA the fibres are typically the sodium salt--I believe this is similar to the material Wilkins & Franklin used to obtain the images Watson & Crick used to solve the structure.
So strictly speaking, the experimental situation described in the question does not exist. You could never obtain a pure sample of protonated DNA that you could then add to pure water. At the pH the DNA would be protonated the DNA would depurinate leading to strand scission at the abasic sites.  This is the whole principle of soaking your agarose gel in HCl in preparation for a Southern Blot, to fragment the high molecular weight fragments so they will migrate more efficiently out of the gel and onto the blotting membrane.

nice expansion of original problem!


text:
Retrovirus Production
I have been having difficulties with low transduction efficiencies of my retrovirus production. I expand my plasmid of interest (on MiG-GFP plasmid) in DH5α E Coli for ~24 hours, purify with Qiagen midi prep kits, then put on ~90% confluent 293FT cells with either retronectin or polybrene for 24 hours. I then change media and harvest supernatant at 48 and 72 hours of incubation with the 293FT cells. I then expose 3T3 cells to varying volumes of the virus containing 293FT media and am able to transduce about 10% of the 3T3 cells, which is really low. That being said, here and there I am able to get very high transduction efficiencies on the 3T3 cells, but for unknown reasons. I have tried concentrating the virus but transduction efficiencies don't increase all that much. And I have tried growing up the plasmid in Stbl3 cells, which if anything gives me worse virus.
Anything here jump out as being responsible for low transduction efficiencies. Or is there another way somebody does this that works really well?

Have you tried using a transduction agent? I personally suggest effectene if you decide to try your luck there. What titre are you using? How much did you change the titre when you concentrated it?

I also use polybrene as a transduction agent and have used 5-FU to get my cells cycling prior to transduction. But I have not tested effectene, I appreciate the suggestion. And when I concentrated the virus the titre tested on 3T3 when up by about 5-10% with what I would have expected to be a 10X concentration.

Hmm, that titre should definitely have increased the efficiency by quite a bit. I'm not sure what could be restricting that. Well if you want to keep the retroviral vector (of course effectene is only good for free DNA) there are several reliable brands of transduction agents you could try.

In my experience, transduction efficiencies skyrocketed when I applied a spin-infection procedure. A 30 min low speed centrifuge with the virus changed a lot. Here is the TRC protocol for this: http://www.broadinstitute.org/rnai/public/dir/download?dirpath=protocols/production&filename=TRC%20viral%20infection%20200909.pdf

I have tried this. I have even spinfected for 2hr followed by a 3hr 37C incubation and it does make a slight difference, but still doesn't solve the problem.

In this case, using ideal (nontoxic) dose of polybrene and spinfection, I'd look for an optimal stage on the growth curve of your 3T3s. It's been a while since I've worked with that line. But in other cases of transfection, establishing the curve on uniformly spread cells (with polydL coating or so) helped a lot. (I am aware of transfection&transduction differences, yet I find that fast growing helps with the latter as well.

Also, try titering your virus in HEKs or HeLas, just to make sure that your production is not the issue here. Protocol here: http://ow.ly/LFQHe
There are qRT-PCR titering methods as well saving effort; such as this one:http://ow.ly/LFQK2


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What is a complex?
In my text book it says that "Troponin" is a complex of Troponin C, I and T. In this sense, what is the relation between Troponin complex and C, I, T?

http://en.m.wikipedia.org/wiki/Multiprotein_complex

Even a simple "google question" needs to be answered (ref). Also, it is not necessarily easy to go from the word complex that is used everywhere the the biological concept of protein concept. Let's not be too harsh :)

This is a homework question, please elaborate.

How about a question from a robotic engineer who does not know anything about biology but wish to understand how the muscle works so to make better robot arms?

Sounds like a very exciting project! $\ddot \smile$

@Remi.b no, they do not need to be answered. If they are answered, they should be answered correctly, which I agree to, instead of posting a link to LMGTFY. However, I think canadianer's comment is a completely sufficient answer, and after it the question can be closed as homework. I don't think this site should be for explaining every single piece of terminology (especially extremely common terminology) that is come across in a paper or textbook. A very important part of learning is being able to find answers for yourself, and not just asking someone to answer it for you.

@Remi.b - how on earth did you generate that smiley?!

ha ha \ddot \smile gives you $\ddot \smile$

The word complex in your sentence designate a protein complex, also called multiprotein complex.
A protein complex is a group of two or more polypeptide chains that bind together to make up a functional unit. A complex can be made up of similar polypeptide chains or totally different polypeptide chains. Proteasome, Metabolon or hemoglobins are examples.
For more info, have a look at wiki

Are they binded through electrostatic attraction or some sort of chemical compound? How are the "polypeptide chains" connected to each other? i.e. intertwined together

@IllegalImmigrant For all complexes, various intermolecular forces play a part: electrostatic, van der Waals, hydrophobic. For some complexes, the polypeptide chains are connected by disulfide bonds (covalent). Technically this makes the polypeptide chains one molecule, but they are still called complexes because the individual chains are produced and can sometimes act independently.

There is this sentence in the introduction of the wiki link: Proteins in a protein complex are linked by non-covalent protein–protein interactions. Also, there is an assembly category in the wiki link. I would expect that different kinds of forces leads the the binding of different pair of proteins. I don't think there is a general rule for that but I know little about biochemistry.

@canadianer This is pretty mind blowing to think about these tiny little chains in our body is arranged in a way that it binds to other chains in a manner that forms a larger structure called a complex without being pulled apart by trillions of chains, molecules and atoms. Hard to believe that something like this exist but this is the human body after all.

@IllegalImmigrant Yes, biology is the most interesting and generally best science ;) When you step back and think about this stuff, it's amazing.


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How is ATP involved in muscle contraction?
The sliding filament mechanism as explained by my text does not elaborate on how ATP is involved in the cross bridge binding and contraction process. How does muscle contraction utilize ATP?
In my text explains this is the procedure for a contraction:

Ach released by motor neuron cross cleft and binds to motor end
plate
AP generated in response to binding of Ach gated channels and propagates down T tuble
T tuble triggers Ca2+ from sarcoplasmic reticulum
Ca2+ binds onto tropinin on actin filament and removes tropomyosin
This opens up sites for myosin to attach to actin using protein heads
Actin filament is pulled toward the center of sarcomere, causing contraction

I see that the action potential definitely needs ATP in order to be generated, aside from that I am surprised that the actual contraction via cross bridge binding does not seem to need ATP.

It is used in the movement of the actin filament.
https://www.youtube.com/watch?v=H6okUPuyby0

ATP prepares myosin for binding with actin by moving it to a
  higher-energy state and a "cocked" position.
Once the myosin forms a cross-bridge with actin, the Pi disassociates
  and the myosin undergoes the power stroke, reaching a lower energy
  state when the sarcomere shortens.
ATP must bind to myosin to break the cross-bridge and enable the
  myosin to rebind to actin at the next muscle contraction.

The muscle contraction cycle is triggered by calcium ions binding to
  the protein complex troponin, exposing the active-binding sites on the
  actin. As soon as the actin-binding sites are uncovered, the
  high-energy myosin head bridges the gap, forming a cross-bridge. Once
  myosin binds to the actin, the Pi is released, and the myosin
  undergoes a conformational change to a lower energy state. As myosin
  expends the energy, it moves through the "power stroke," pulling the
  actin filament toward the M-line. When the actin is pulled
  approximately 10 nm toward the M-line, the sarcomere shortens and the
  muscle contracts. At the end of the power stroke, the myosin is in a
  low-energy position.
After the power stroke, ADP is released, but the cross-bridge formed
  is still in place. ATP then binds to myosin, moving the myosin to its
  high-energy state, releasing the myosin head from the actin active
  site. ATP can then attach to myosin, which allows the cross-bridge
  cycle to start again; further muscle contraction can occur. Therefore,
  without ATP, muscles would remain in their contracted state, rather
  than their relaxed state.

Summary from: https://www.boundless.com/biology/textbooks/boundless-biology-textbook/the-musculoskeletal-system-38/muscle-contraction-and-locomotion-218/atp-and-muscle-contraction-826-12069/
Also this:
Essentially look up the cross bridge cycle (http://muscle.ucsd.edu/musintro/bridge.shtml)
I would also suggest reading it from the master himself here:
Huxley, A. F. "Muscular contraction." The Journal of physiology 243.1 (1974): 1-43.

It begs the question what the mechanism of bending of the myosin head during the power stroke is . Is there any reference for this?

The two links in the question are dead - can you offer us other ones instead?


text:
Can a person's body produce enough electricity to break a wristwatch?
I know of someone who cannot seem to wear watches without the battery dying or something else about the watch going haywire. this person was told it is because their body is producing too much electricity and that by putting nail polish on the reverse of the watch to block the current the watch would work.
This was tried and it actually worked. My question is, is this a real thing? I couldn't find a legit discussion of this online.

Static electricity (depending on clothes, floor material, air humidity, etc...) seems more plausible.

I would hazard a guess that sweat or something similar would be more likely. (That is a guess, though.)

I'm voting to close this question as off-topic because it is better suited to skeptics SE - I don't view this as a biology question

I do think this has the potential (haha, electricity joke) to be a very interesting question - there's a lot of anecdotal evidence out there about people (a friend of mine included) who cannot wear watches because they are continually dying or otherwise malfunctioning. It would be great if someone could find a study on this.


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Why are people unable to develop lasting immunity against Norovirus?
Infection with many viruses will result in decades-long if not lifetime immunity, for example chicken pox.
Because of the large number of viruses responsible for the common cold, lifelong immunity to the common cold isn't possible; we will still be susceptible to those we haven't encountered before. But we do develop immunity to those we've been exposed to.
Influenza virus mutates quickly enough that there will nearly always be strains which will be new to us. Immunity to HIV is difficult because of the particular cells the virus attacks (as well as mutations).
However, Norovirus, while there are many strains, is particularly problematic because immunity to a strain lasts less than a year, making reinfection with the same strain repeatedly possible.
Is the reason Norovirus infection doesn't confer longer-lasting immunity known?

Your first question! :) interesting read +1, but I'm not able to answer it I'm afraid. And congratz with your moderatorship @Parents!

@AliceD - I was researching this, and thought, "Wait! I know where I can ask!" ')  Also, thanks. It's a great site.

I cannot answer this with anything but a guess, still: Some norovirus immunity seems to be caused by non-functional fucosyltransferase, which is (to keep it short) related to the ABH antigen. (see http://en.wikipedia.org/wiki/Norovirus) If (something similar to) a normal human antigen can confer immunity to norovirus, maybe the "real" norovirus antigen is so close to autoimmunity that our immune system filters a lot of them out.

I am soooo going you have to come back to this when I have time. I'm currently struggling with the scope I want to include (mucosal immunity, IgG vs IgM, HRV serotypes, noro infectious dose...). If I want to dive deep into the biology here would it be better to repost the question there Q/A style, or can juat do it here?

So the direct mechanisms of norovirus immunity aren't well understood - the shortage of straightforward animal models, and the extreme difficulty in culturing the virus make mechanistic studies really rather hard.
A modeling study pegged the duration of immunity at 4.1 to 8.7 years when talking about symptomatic disease, which is much higher than many of the estimate's you've encountered, and isn't actually all that fast. The older estimates were built off human challenge studies, which involved massive doses of norovirus, rather than the normal exposure you'd have. Now that is for a single strain, but immune cross-reactivity for strains isn't well understood. There's also several efforts to develop norovirus vaccines, which suggests some duration of immunity is at least possible. It's also possible that a proportion of the population (~20%) is simply immune due to the absence of the FUT2 gene, which acts as a receptor for the virus in the intestines.
In addition, there's definitely some antigenic drift, where mutations in the primary antigens negate previous immunity to the disease (the same mechanism that causes you to eventually lose immunity to a particular strain of influenza).
This paper is a pretty brief review of all these factors, written by some norovirus experts.

Thank you! I was getting some impressions in my reading last night and touched on some of the topics, for example lack of cell cultures that will grow the virus, something that seems to be getting better) but was getting nowhere fast with "why". Thanks for the link!!

+1 I should point out, that my comment that I want to come back with an answer to this question is not because of a disagreement with anything here. Having worked on a culturing system for norovirus, I just have a lot of opinions on the matter. There are no italics extreme enough to to be apllied to the extreme difficulty in culturing, but I really appreciate that note :)

@AtlLED Nothing bad ever happened by having a subject matter expert provide an answer with more detail :)


text:
What is the insight of Frank Starling law of the heart?
The Frank Starling law appears to be a trivial observation:
stroke volume is directly related to the end diastolic volume
In everyday language, as more blood fills the heart, the heart pumps more blood out.
Can someone point out whether there are some inaccuracies in the above description because I don't understand why every article on FS law requires upward 20 pages. Even youtube video on this topic is 8 minutes long.
What is the big idea here that I am missing?

This is the short answer from wikipedia :) :

As the heart fills with more blood than usual, the force of cardiac
  muscular contractions increases.[2] This is a result of an increase in
  the load experienced by each muscle fiber due to the extra blood load
  entering the heart. The stretching of the muscle fibers augments
  cardiac muscle contraction by increasing the calcium sensitivity of
  the myofibrils, [3] causing a greater number of actin-myosin
  cross-bridges to form within the muscle fibers. The force that any
  single cardiac muscle fiber generates is proportional to the initial
  sarcomere length (known as preload), and the stretch on the individual
  fibers is related to the end-diastolic volume of the left and right
  ventricles.
In the human heart, maximal force is generated with an initial
  sarcomere length of 2.2 micrometers, a length which is rarely exceeded
  in the normal heart. Initial lengths larger or smaller than this
  optimal value will decrease the force the muscle can achieve. For
  larger sarcomere lengths, this is the result of less overlap of the
  thin and thick filaments; for smaller sarcomere lengths, the cause is
  the decreased sensitivity for calcium by the myofilaments.

in one sentence, it is a response to tension.


text:
Microalgae without cell walls?
Most microalgae have rigid cell walls.
Dunaliella Salina is a pretty famous example of an algae with no cell wall, but just a plasma membrane.
Are there any other microalgae without a cell wall?. I have researched but I can only find Dunaliella being mentioned.

Cyanidioschyzon merolae seems to be an example of such algae. Cryptomonad, aka Cryptophyceae also lacks cell wall.
I think, problem you encounter is that most studies are concerned with structure and function of cell walls, as such knowledge can be used in biotech industry. Hence, you will not find answer by looking for "algae without cell wall".
As a suggestion, I would point to this evolutionary study on development of plants: Evolution and Diversity of Plant Cell Walls: From Algae to Flowering Plants. Seems like trying to look through evolutionary trees might give you more examples.


text:
What does it mean for a hormone to be "active"
In my textbook it is stated that the T3 hormone produced at the thyroid gland is 3-5 times more biologically active than T4.
How is being active defined and how can this effect be measured?

This is quite a general question (and bit too broad). Activity of bioactive molecules such as hormones can be defined as how much change do the make to the receipient cells. For eg. let's take two growth hormones A and B. If they are given to some cells at equal concentration but hormone A induces proliferation 5 times more frequently than hormone B, then  A is 5 times more active than B. This is not the best definition / example but I think you can get the point from this.

This question is not broad and pretty well focused. I did a literature search and it is actually hard to find! In all a good question from my point of view +1.

@AliceD - I have to disagree with you on this one. I think we both agree that the effect of a hormone or any biologically active molecule can be measure in several ways, eg gene expression by RT PCR, flurescent riporter gene, riporter gene activity assay etc. and that's just one thing and few examples. This in my view is too broad. But on the other hand I might interpret the question in the wrong way....

If you think about a jackhammer, the better effector is the one that can chip away the most concrete. If the jackhammer had low power or no power (T4), we can safely imagine you'd have lower efficacy than the full-power jackhammer (T3). We can measure the activity of a jackhammer as a function of the work done vs. power provided. In much the same way, we can measure biological activity as a function of concentration vs. catalytic/binding activity. All they're saying is that T3 has more activity at comparable concentrations to T4. Plasmon surface resonance can help measure binding/interactions.

Activity of a hormone represents the efficacy of the hormone in causing the intended effect.
In case of T3 vs T4, though T4 is the majority fraction, T3 is more active, meaning it is much more efficacious in effecting the results.
The concentration of T4 is 30 - 50 times higher than T31. Though T3 is produced by thyroid it is in minority. The majority of T3 is produced by peripheral conversion of T4 into T3.
Thyroid hormones are transported in the blood vessels by albumin, thyroxine binding prealbumin (also called transthyretin). T4 binds more tightly to these transport proteins than T3. In other words T3 constitutes the majority of the free fraction (unbound to carrier/transport proteins). Only the free form of the hormone is metabolically active. So T3 is 3 to 5 times more active than T4.

T3 - triiodothyroxine
T4 - tetraiodothyroxine
1: pg. 312, Essentials of surgery, Sanjay Azad

Biological activity has a range of definitions, but in this case I believe it to mean that the T3 hormone is produced at a rate 3-5x that of T4. This can be measured with fluorescent tags. Typically, fluorescent tagging uses a reactive derivative of a fluorescent molecule, called a fluorophore. The fluorophore selectively binds to a specific region or functional group on the target molecule and can be attached chemically or biologically. Using technologies, such as microscopes, fluorescence can be viewed/imaged; this allows scientists to count, track, and/or monitor molecules over time.

Thanks for answering! Could you back these figures up with a reference or two?

It is unclear what you mean by "produced at rate 3-5x of T4" because 90% of all hormonal output from thyroid is T4, but T4 later get converted to T3 at liver and kidney. Do you mean the net total T3 present in the body at any given time? The sadly text is also unclear what it means by "biologically active", it is as if T3 has little legs and sprints while T4 crawls, not a very helpful image

In my opinion, activeness of a hormone is more about its effect than its production rate. Cortisol and Aldosterone are both adrenal hormones, yet as a mineralocorticid, aldosterone is the active one by great margin (due to intracellular degradation of the glucocorticoids).


text:
from an ageing reproductive stem cell's DNA to baby's "brand new" somatic cells' DNA
On the one hand, somatic cells's DNA age as life goes on, mitosis after mitosis, and that is reflected into reduced telomeres.
On the other hand, during life, reproductive stem cells must age too. However one half of the DNA of some random old reproductive stem cell is eventually transferred through reproduction, and the ageing cycle begins again, with new somatic cells with long telomeres.
What mechanisms can explain reproductive stem cells DNA do not age as somatic cells' DNA ? Or do we know how telomeres are growing back from old reproductive stem cells to gamete during meiosis ? Put another way, how is it possible that we are born with long telomeres ?
I am sorry for the formulation of my question. I think it is understandable but not really well written. However I don't know how to formulate it another way yet. Do not hesitate to reformulate it if you feel like it.
Thanks.

Some cell types have an active telomerase, stem cells are among these cells. Additionally sperm cells/eggs do not divide any further once they are haploid.

I was not aware of the "active telomerase". It seems to me like some great advantage for a cell. Why would some have it and others not ?

One advantage of somatic cells not having active telomerase enzymes is that they die when become too old / damaged / used etc. and new  somatic cells can take their place. These new somatic cells from progenitor cells aka "adult stem cells". This way we can renew our skin, relplace old red blood cells (although they don't even have nucleus) etc.

Then is'nt damage to stem cells' DNA, reproduction event after reproduction event, increasing as well ?

We have to be careful about how much we mix telomere length and aging. Yes diseases that cause artificial telomere shortening accelerate aging, but exercise causes widespread telomere shortening but not accelerated aging. And constitutive telomerase expression does not mean that cells are immortal, for example mice have constitutive telomerase expression in every cell. I believe the more plausible advantage to somatic cells not expressing telomerase is reduced transformative capacity because pre-cancers must first find a way to express telomerase.

I am still a little unclear about your question though, if it is how to we increase telomeres between generations, I guess that is explained, or is it  how we don't age as a population (a great question) due to constant mutations accumulation in germline cells?

Yes ! the second question is exactly what I tried to ask. Should I open a new question, asking "how we don't age as a population, due to constant mutations accumulation in germline cells ?"

Possible duplicate of How are new people created from the DNA of an aged person. i.e. Why are we young?


text:
Heterocyst function in cyanobacteria and its localization
1.What is the function of heterocyst?
2.Where it is present?
A heterocyst I think may be a protecting organ in cells!

Welcome at Biology SE! If this is meant to be a homework question, then please share your effort on the subject. If you need help please take the short tour, or read the guidelines at our help center. If you can please elaborate and put your question into context. Have a nice day!

They help in nitrogen fixing . Ex nostoc of and anabaena

According to wikipedia :

Heterocysts are specialized, pale-yellow,thick-walled cells with disputed function nitrogen-fixing formed during nitrogen starvation by some filamentous cyanobacteria, such as Nostoc punctiforme...

Thus by definition these are not within the cells, but differentiated cells themselves.
This is a good paper that can give you details on nitrogen fixation in the cyanobacterium Anabaena variabilis.
In general: cyanobacteria are photosynthetic prokaryotes, and many of them are capable of fixing nitrogen (that is the ability to use and incorporate nitrogen from the air as N2 gas). The enzyme called nitrogenase is oxygen sensitive thus either temporal or spatial separation of nitrogen fixing must be done to avoid damage to the enzmye from oxygen produced by photosynthesis.

In Anabaena spp., aerobic nitrogen fixation is confined to differentiated cells called heterocysts that form in a semiregular pattern in a filament in response to nitrogen starvation. Fixed nitrogen in the heterocysts is transported to vegetative cells in the filament, while vegetative cells supply carbon and reductant to heterocysts

So as you can see spearate cells work together to supply each other with necessary nutrients. It is important to note that when sufficient fixed nitrogen source is available the number of such specialized formations is low due there is no need for extra nitrogen to be fixed
There are plenty of details on heterocysts and nitrogen fixation in the linked article. Also this paper hold details of regulation of nitrogen fixation and also has a thorough image of the process:

Though perhaps not relevant to the question, and certainly not true about any cyanobacteria that I know of, but just because something is a "cell" or single celled organism, does not mean it can't be contained within other cells.  Mycoplasma, for example, do it all the time.  Admittedly it doesn't normally end well for one group of cells, but it happens. +1

First of all the short and sweet definition of heterocyst are the specialized cells with homogeneous protoplast. Both the ends have thickenings called polar nodules.  Polar nodules are provided with minute pores.  Heterocyst help to fix the atmospheric nitrogen compounds.
In some species of Nostoc like N.commune heterocysts function as resting pores. The protoplasm of the heterocysts become functional and germinate to form a new filament.

Hi Christina. Welcome to [biology.se]. Can you add some references to your answer. You can have a look at the other answer. In general, if you post an answer make sure that you are not exactly repeating the stuff already said in the other answers. You can of course provide a better answer than the previous ones by adding additional supportive references. That is not the case here.


text:
Does hypothalamus regulate posterior pituitary gland?
We have the hypothalamus-anterior pituitary-endocrine axis, but is there a similar chain of command for posterior pituitary gland such that oxycotin and vasopressin are regulated by some tropic hormones?

The difference between secretion of ACTH  and neurohypophysial hormones is that the prior is a two step process, with CRF from hypothalamus stimulating the anterior pituitary. The latter is produced and secreted from the same cell, only in different organs! Magnocellular neurons stretch from the hypothalamus to the posterior pituitary, where they have their neurosecretory endings packed with hormone storing large dense-core vesicles. The same neurons are osmosensitive, regulating their secretion themselves as physiological need arises. Also, they apparently do dendritic secretion as autocrine signalling. Some reading about this: http://www.ncbi.nlm.nih.gov/pubmed/24265070
and
http://www.nature.com/nrn/journal/v7/n2/full/nrn1845.html
Hope it helps.

This is a complete citation from the paper and not well liked here. Please answer the question in your own words and use the reference to back up what you say.

Sorry, error due to being new to the format. Edited appropriately.


text:
What is the difference between "physical interaction" and "genetic interaction"?
I searched sac1 in uniprot to know more about this gene. in interaction I selected this link and there I see that this gene has some "physical interactions" and "genetic interactions". I am wondering that what is the difference between "physical interaction" and "genetic interaction"?

Physical and genetic interactions are described in the help wiki, accessed via the top menu bar on the page you linked to.
Physical interactions refer to experiments where the gene product (protein) has been shown to physically interact with another protein, such as by co-immunoprecipitation, fluorescent staining, yeast two-hybrid system, etc.
Genetic interactions refer to experiments where changes in a certain gene reflect in changes to your gene of interest (or vice-versa) - dosage lethality, dosage rescue, synthetic haploinsufficiency, etc.


text:
Can we knock out Caspase-9 *and* avoid breast cancer phenotype in our mouse model?
I am trying to design a wet lab experiment with no wet lab experience to name.
Right now, in my dream land, it would be excellent if it were possible to create a Caspase-9 knockout mouse (damage to the Caspase-9 gene is associated with the development of breast cancer), and somehow be able to control the development of the breast cancer phenotype, so I can create a Caspase-9 KO control as well as a non Caspase-9 control group. In total, I would love to have the following control groups:
1. Normal mouse - normal Caspase9 gene, no breast cancer phenotype
2. Caspase9 KO mouse - no breast cancer phenotype
3. Caspase9 KO mouse - breast cancer phenotype

Can anyone help me answer whether or not group 2 above is possible? Can you direct me to any papers, any experiments, where this has been done before, or has been tried below and failed?
Here is a paper that talks about the association of Caspase-9 with breast cancer development: http://breast-cancer-research.com/content/pdf/s13058-014-0443-5.pdf. Caspase-9 is a type 2 member of the Caspase protein family. When I talk of the "Caspase-9 gene", I'm talking about the DNA which codes for these cellular apoptosis susceptibility 9 (Caspase-9) proteins. This isn't my area of expertise, but this is what I currently understand.

is there even a thing like Cas9 gene? As I know, cas9-CRISPR system is used to create double-stranded breaks in genome, so it can be used for targeted mutagenesis, including creating knock-outs. Please, provide reference to cas-9 gene and breast cancer association

and there Cas9 is bacterial protein

There seems to be a caspase 9 in mammals which is different from cas9. The question should probably be edited to make this clear.

I think the paper you refer to uses cas to refer to the cas family of proteins, still not the CRISPR/Cas9. Biologists need better names.

Cas9[CRISPR] totally dominates google search these days, yes.

Edited question to clarify issue, feel free to roll back if I actually misunderstood your intent.

Did you look at any papers (such as this)?  Caspase-9 KO mice are there and they suffer from cerebral malformation (abnormal enlargement). The linked paper also says that Caspase-9 mutations are associated with Non Hodgkin Lymphoma and lung cancers. Try doing a google scholar search with right keywords. I think you can find many case 2 situations (do you count neonatal inviability as one of the situations?)

There seems to be no CAS9 in the CAS-CSE1 family

http://www.informatics.jax.org/marker/MGI:1277950 Homozygous targeted mutants die perinatally...

Caspase-9 is a well studied mediator of apoptosis through the intrinsic (mitochondrial) pathway. Global deletion as stated above, is often perinatal lethal, a conditional deletion could feasibly be generated, but the experiment is not likely to be worthwhile, see answer below.

The short answer is that it is likely a bad experiment; being that it would be expensive and is not likely to provide useful new information.
The long answer (i.e. why) is identifying an interesting target gene (e.g. caspase-9 in breast cancer) is only the first step, and considerable study of what is already known is required before planning an experiment (especially an expensive one that requires numerous mice).
Caspase-9 is a critical effector of apoptosis through the mitochondrial pathway. Many different signals such as DNA damage, Endoplasmic reticulum stress, etc induce cells to die through this pathway. This is important both in normal development and in preventing cancer. Homozygous deletion of caspase-9 is lethal, the mice will not live to adulthood. (http://www.ncbi.nlm.nih.gov/books/NBK6153/) A conditional knock-out of caspase-9 in breast cancer cells would be needed, not a global deletion.
Furthermore, the given the known functions of caspase-9 this experiment is not likely to provide interesting new information. This pathway is well characterized and known to play an important role in cancer (Resisting cell death; a hallmark of cancer: http://www.cell.com/abstract/S0092-8674(11)00127-9 ) Loss of caspase-9 activity makes cells resistant to apoptotic signals through the mitochondrial pathway(they won't die when they receive these "suicide" signals). This allows mutant cells to survive when they should otherwise die. Cancer cells can also become resistant to this pathway through other means (such as the up regulation of anti-apoptotic Bcl-2 family members.
Many scientists are already studying how to restore normal function of this pathways in various cancers; what do you hope to learn by breaking it that isn't already known (I'm not saying that there couldn't be a good reason, but if you don't have one, you shouldn't do it.)

+1 for pointing out that the results of this proposed experiment are already known (for knockout, not knockdown)

This seems to be a standard procedure knockout and complementation rescue experiment.
Breed 2 can be produced from Breed 3 (assuming the Caspase 9 gene indeed causes cancer when it is not expressed).
Firstly, knockout Caspase 9 from a wild type, creating Breed 3. Verify that the cancer phenotype is shown and is statistically significant.
Then, transform Breed 3 with an artificial copy of the Caspase 9 gene in an alternative chromosomal location. This breed (Breed 2) will act as a positive control for the gene, and should behave identically to the wild type.
Finally, you can then produce multiple breeds of mice transformed with different versions of the gene (for example serine/threonine mutagenesis to detect the kinase specificity) in order to determine mutations that cause the Caspase 9 protein to become non-functional. Alternatively, the same gene but with a stronger/weaker promoter can be used to determine the dose-dependent effects of the gene.
This paper regarding a circadian clock gene shows the general procedure required to carry out such a complementation rescue experiment.

If you transfom a previously knocked out gene, then it is not a knock out anymore since it has functioning copy of the gene... At least my logic dictates this.

It seems you are confused with some other gene instead of caspase 9, but if KO of some gene causes development of breast cancer, and you want to compare something between none-cancerous and cancerous states, you could take several ways:

See if you could have littermates carrying and not carrying cancer. You could compare them. Sometimes, phenotype do not express 100% among mice through the life spam or at younger age.
Breast cancer is rare in human males, probably in murine males, too; think you could compare what you want to see between males and females.
When you cross KO mice with other strains, occurrence of phenotype could vary. Then you could compare what you want to see between less and more susceptible mice strains.


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What are phenetic analyses used for?
Phenetics (grouping of organisms based on similarity) used to be claimed to be an alternative to cladistics, but now it is widely accepted that phenetic analyses cannot be used to infer evolutionary relationships. However, phenetic methods like neighbor-joining trees are still being developed today.
Are phenetic analyses still valid today for purposes other than determining evolutionary relationships, or are they completely obsolete? Does anyone have an example of a recent paper that uses phenetic analyses in a valid way?

The phenetics reference  in Wikipedia describes several places to look for phenetic analyses.

As usual, a rant from Joe Felsenstein's webpage seems relevant. Specifically, this:
"There is no consensus, even among systematists, as to what the word "cladistics" means."
Everyone seems to have agreed that phenetics--which is to say the blind faith in the results of clustering algorithms such as neighbor-joining etc.--is on its own not very useful, compared to a principled dedication to placing organisms taxonomically into monophyletic groups.
However, the hard-line cladistics point of view (e.g. Willi Hennig society) is that no method of inference other than maximum parsimony (in one of its various flavors) is acceptable, for obscure philosophical reasons that no one cares about. Frankly, for any realistic purpose, cladistically unacceptable methods such as Bayesian inference and likelihood methods perform the best. From cladistics wiki:

Although traditionally such cladograms were generated largely on the basis of morphological characters and originally calculated by hand, genetic sequencing data and computational phylogenetics are now commonly used in phylogenetic analyses, and the parsimony criterion has been abandoned by many phylogeneticists in favor of more "sophisticated" but less parsimonious evolutionary models of character state transformation. Cladists contend that these models are unjustified.

In other words, cladistics is more of a philosophical point of view than a group of methods. There are "soft" versions that everyone pretty much agrees on, namely the principle that monophyletic groups are preferable to paraphyletic groups. But methodologically, it's just a lot easier and more workable to use non-cladistic or even phenetic techniques rather than the (computationally frequently more onerous and not necessarily more accurate) parsimony techniques of cladistics.
For a (fairly) recent apologia specific to neighbor-joining, see here.
In short, given the highly heuristic nature of most science, most workers aren't really paying attention to these debates, and just use the tool that works for the problem they're working on. And in many cases those methods are phenetic, even if cladists claimed a victory of principle.


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Term for a leaf in a family tree
Imagine a family pedigree.
Mathematically it is a graph, which consists of nodes and edges.
Nodes being family members, and edges - their relationships.
In a clinical setting, what is the proper term for the nodes? Would they be called 'leafs'?

So in a pedigree, Standardized Human Pedigree Nomenclature: Update and Assessment of the Recommendations of the National Society of Genetic Counselors notes that these "nodes" in the pedigree are the "individual symbol" denoting individuals. Although, when you read it, you'd read "Male," "Female," "Gender Unspecified," etc. instead of individual symbol.


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Do blood glucose "spikes" contribute to insulin resistance, or is prolonged elevation required?
There's increasing public discussion about the health risks of chronic insulin resistance* (IR). In many cases there's a focus on high glycemic index foods that "spike" your blood sugar, which implies that a rapid increase in blood glucose is by itself sufficient to contribute to IR.
On the other hand, I've heard the claim that if a person is 1) moderately active, 2) not in caloric surplus, and 3) not already insulin resistant, then they will will quickly clear excess blood glucose by replenishing glycogen or through general energy expenditure. This is claimed to have no effect on IR, even though the individual was temporarily exposed to elevated glucose / insulin.
This leads me to two questions:
1) Is it true that high blood glucose is normalized substantially more rapidly in people who have depleted their glycogen, or who have higher energy needs?
2) Does repeated exposure to high levels of blood glucose contribute to IR by itself, or are high and prolonged levels of blood glucose required?
This has public health implications -- If the "spikes" theory is inaccurate, then glycemic index may not be very important to sufficiently active people**, and low glycemic index meals may not be as helpful as expected for people at risk of developing IR if total glucose exposure is high.

*"chronic insulin resistance" would exclude gestational diabetes and the reversible insulin resistance seen on ketogenic diets.
**For this discussion, let's ignore effects of blood sugar swings on hunger, mood, behavior, etc, since my interest is in the specific physiological triggers for IR.

The topic is immensely interesting, but this question is too complex for me to answer. A very nice, concise and informative review is freely accessed here: http://www.ncbi.nlm.nih.gov/pubmed/12081851

Great Question.
The biggest problem is persistent insulin signaling from prolonged excessive high blood glucose over time. The reason being that it is this kind of signaling that results in insulin insensitivity due to down-regulation of the insulin receptors.
Any bolus of carbohydrates > ~ 25grams in a sitting is going to bump up blood sugar at a fast enough rate to warrant the release of insulin to help lower blood sugar levels.  This can be mitigated by an excessive amount of fat along with the carbohydrates, thus slowing down the spike.

Your question: 1) Is it true that high blood glucose is normalized substantially more rapidly in people who have depleted their glycogen, or who have higher energy needs?

So this is a little confounded by several variables.  The thought process is that people that have less glycogen or higher energy needs, don't have insulin insensitivity; thus the same amount of insulin would do a better job of shuttling glucose into cells.  We know that consistent exercise increases insulin sensitivity, as does lack of persistent insulin signaling (such as comes from being in a glycogen depleted state).  So the answer to your question is generally YES for these reasons.

2) Does repeated exposure to high levels of blood glucose contribute to IR by itself, or are high and prolonged levels of blood glucose required?

What we know from epi studies suggests that it isn't insulin spikes.  It is prolonged insulin signaling that causes insulin insensitivity through down-regulation of insulin receptors.
If you are fuel deprived, or only getting what you need from your food, insulin spikes are normal and transient and don't cause this IR.
Persistent insulin signaling causes many many side effects. Insulin is mitogenic,  has downstream pro-inflammatory cascades, and the insulin insensitivity that results is a major player in non-alchololic fatty liver disease.
Some references for these thoughts and further reading:

This one gives evidence of reduced IR activity, not
downreglation
Insulin signaling and NAFLD
Exercise and Insulin Sensitivity

John, I bet this is a great answer, but a reference or two to allow for further research and background reading is preferable. Ping me once done and I'm happy to upvote

@AliceD Thanks for the suggestion.  I'm new here.

No worries +1 :) Referencing is a great habit.


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Green Film Build up in Glass Water Bottle
So I have this Large Water Jug that I fill only water with.
And this is the 2nd time there has been a layer of green film that builds up at the bottom of the bottle. I don't have any way of getting to the bottom to clean this.
I wanted to know.

What does this green film consist of?
What Chemicals or methods can I use to remove the film without having to manually scrub the bottle?

Thanks
ps. not sure if this was the correct place to ask this question.

a) algae b) if it has formed a scummy biofilm, it might have to be harsh treatment to get it off. kerosene?

@shigeta What about more common household items?

please, remove part on cleaning, as it might be considered as requesting advice concerning personal health. We don't want to be responsible for your/your dog's/your child's chemical poisoning

(but I just leaned my water bottle from that using several washes with 70% ethanol followed by wash with bleach solution. Then rinse with tap water x 5, rinse with distilled water x 5, rinse with MilliQ water x 1)

try diluted bleach - or if you go to the grocery/hardware store you should be able to buy a bottle brush for cheap.

Another way to "scrub" things you can't reach is with a handful or more of sand or tiny pebbles. Bleach and sand swirled around vigorously for a few minutes will remove the majority of it, if not all.

What seems to be forming in reusable water bottles and water coolers is a biofilm. Since it is a complicated system, after maturation biofilm might be very hard to remove without scrubbing. There is a nice article about cleaning water coolers, which might give you some information.
If you look closer on the Google Scholar search results, you'll find that quite a bit of research has been conducted in the area of sanitation of water coolers and study of their flora. For example, consider the following paper from 1996: Analysis of the Virulence Characteristics of Bacteria Isolated from Bottled, Water Cooler, and Tap Water.
There is a very nice list (Table 1) of different bacteria isolated from water. But I would like to point your attention to following table from the paper:

Quote from methods section listing tested antibiotics:

The
  natural and first generation antibiotics included:
  penicillin, ampicillin, erythromycin, kanamycin,
  streptomycin, tetracycline, chloramphenicol, and
  sulphonamide. The synthetic and later generation
  antibiotics included: gentamicin, cefoxitin,
  cefoperazone, oxacillin, piperacillin, imipenem,
  ciprofloxacin, and sulphonamideftrimethoprim

The green slime you observe, I think, is a combination of all those bacteria, plus some that were brought after the water was poured into the container. And it seems that all commercial sources that you didn't purify yourself, will have a variety of microorganisms growing. And around 5% of the total bacterial cell mass is resistant to common antibiotics.


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Do ant colonies prioritize survival of particular members above others?
In some (perhaps small) human communities people may starve because they have no income. This could be interpreted as a consequence of them not participating in the community, hence they don't get any income and are left to their fate of starvation. Also, we can imagine that important members of the community are less likely to starve, as they are given priority treatment (e.g. a royal family will less likely starve to death during a given famine).

Do ants in a given colony allow members to starve when they don't serve the colony, even if there is no scarcity of food?
Secondly, do ants follow a chain of importance and are members of least importance allowed to starve first in times of shortage?

@poka.nandor I just made an update, I hope it clarifies a bit more my question.

husker - I edited the question further, please feel free to roll back if it does not reflect the original question any longer. Nice question! +1

The edited verion(s) look much much better.

@AliceD I really like the way you rephrase my question. Let's hope we get an answer! Thanks!

I couldn't find any information about ants starving in times of plenty, most likely since it's difficult to determine whether an ant colony is "letting" certain members starve or whether the ants have just died for whatever reason. To your second question, though, yes! This paper, The Effect of Colony Size and Starvation on Food Flow in the Fire Ant by Howard and Tschinkel, shows the effects of different lengths of starvation on the passing of radioactive food through different sized ant colonies. First, the queen:

Generally, queens received radioactive food earlier in starved colonies than in well-fed ones

Starved foraging ants distributed food more quickly than forager ants who had not been starved:

And interestingly, in large colonies, larger worker ants were more likely to receive food (radioactivity) than smaller ants. Very cool paper.

Nice answer! I gave you thanswer, because you're the first one and because you also support it with a reference to a paper.


text:
Why are pharmacology studies so experimental?
I am a med student, and as far as I see from our pharmacology lectures, pharmacologists work almost completely experimental. Quite typically they take a substance (e.g., from nature), they add, change or remove some chemical groups, and then they test it (either with high throughput screening or on animals), for example to see whether the new drug is active or not. To me, this sounds a bit indirect.
Ideally, we should know exactly what we are targeting, and then custom-make a new drug. For example, if we know which receptor (the 'lock') we wish to activate or inhibit, why do pharmacologists not simply design a fitting key (a plug to block, or a substrate-resembling activator) to the specific lock?

I edited the question in the hopes to improve clarity. Feel free to roll back.

You can be pretty sure that this would be done if it would be that easy. This kind of design is done using computers, but real life looks very often different. So you are stuck to test a lot of substances.

Thank you. What you mean by 'real life looks very often different' is chemical synthesis techniques being shortfall compared to the complex design in computers, so the problem here is chemistry is not enough to do such things, am I right?

Sometimes during drug discovery, you'll just array hundreds of wells of cell culture, hit it with similar compounds featuring slight modifications, and see which compound(s) produced the greatest effect.

Is there an exception of 'sometimes'? Has human-being ever designed and synthesized a drug?

Even if we could design the perfect compound (key) to fit the target (key), you're ignoring all of the other things that have to go right for a drug to work: it has to get to the target; it has to survive the body trying to get rid of it; it has to not harm the patient in some other way; amongst other things.

There are attempts to similar what you mention, using a computer simulation of a protein model and adding fragments of drug molecules and trying to build a ligand that fits. However, this requires a lot of computer power, even more if you make the model more accurate by including motion, interactions with membranes, waters, etc. Then you actually have to make whatever drug you predict works well and test it. If it works in the test tube, you pray it works in animals because the absorption, distribution, metabolism, and excretion are all important and hard to predict.

@user137 Exactly. After several months, I've been able to learn a little bit about chaos theory, and the answer partially lies within there. Even the smallest variable in the system can create a whole another butterfly effect, including the factors you've counted. Seems like the best thing researchers might be able to achieve, is, making the use of this particular situation - most probably by discovering novel attractors.

The First thing is that that you can't study any process until it happens. So even if you know the structure of receptor molecule, you can't always be sure that it is completely safe.
It does seem a bit random in beginning but this is how it works. You can't just derive a medicine or drug and send it for mass production. You never know what are the side effects of the drug. For this reason, the drugs are tested on other animals (usually rats because they are quite in number, having short lifespan and not many oppose experiments on rats ethically.)
If the side effects are severe, then the drug is banned from mass production.
But if such drug is produced,more harm will be done than good. Also you can't give it to humans first. If all tests are successful, then only the drug is tested on humans.
So Screening and Testing are indirect but essential steps for studying the effects of it.

'it does seem a bit random'. Random was the word I was looking for drug discovery process. It's like shooting around with an automatic weapon and checking if enemy is dead or not. It seems that's because of the complexity of system.


text:
Are Sciomyzidae fit to combat snails?
I read that Sciomyzidae are also called snail-killing flies, which immediateley made me think: "I need those"!
Questions:

Are they really fit to control snail over-population in my garden? and
if so where do i get them?

Short answers:
These insects live near water or marsh areas so that's where you can get them from. This is because many species of this group has larvae that are aquatic or semi-aquatic.  According to wikipedia:

The adults drink dew and nectar.

And it is their larvae that either prey on or become parasites of gastropods.
In this article the following is stated:

(...) Sciomyzidae is of interest from practical viewpoints because of their potential as biocontrol agents of aquatic snails carrying diseases (e.g. schistosomiasis and fascioliasis) and terrestrial, pestiferous snails..

So the answer is yes, they might be fit to use as biological pest control, yet they may not be suitable against all species. Details of their life cycle and their biology can be found in the linked article or in this book:
https://books.google.hu/books?id=vqE1AMIj-HUC&pg=PR16&lpg=PR16&dq=Sciomyzidae&source=bl&ots=pCVJJUu2cb&sig=M1F8GhR51VI1Y62htF7eX0kNpfo&hl=hu&sa=X&ei=AF0uVf_tKI3taNLhgIAL&ved=0CFgQ6AEwBzgK#v=onepage&q=Sciomyzidae&f=false

To be honest I did not read the whole book, but the title is quite specific for what you might need.

didn't think you read the whole thing and i won't do that either. But i agree that it sounds very specific to my question.


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What is the mechanism behind plants losing their leaves?
Do plants that lose their leaves (i.e., deciduous plants) do so because of external conditions (e.g., drought, cold), or because of an internal process?
Another way of looking at it: if you take a deciduous plant that loses its leaves during cold winters with long nights (e.g., Canada), and plant it in an environment where it is always warm and sunny (i.e., at the equator), would this plant continue to shed its leaves and re-grow them according to the seasons in Canada, or would it behave as an evergreen instead?

I think lose of leaves depend upon both external condition and internal condition .By internal I mean cell death (Programmed Cell Death ).

I edited the question to improve clarity. Please feel free to roll back. Nice question! +1

The process of a deciduous plant losing its leaves seasonally is known as abscission. It occurs when a layer of cells known as the abscission zone elongate and weaken, causing the leaf to fall off. It is mediated mainly by the hormones auxin and ethylene.
The functional purpose of abscission is to remove leaves when they are no longer producing a net gain of biomass. Leaves decrease in productivity during drought, decreased day length, and when under the effect of herbivory.
In some species (according to the day-length source), "When the daylength exceeds a certain 'critical' duration, growth may be
maintained continuously for at least 18 months under favourable temperature conditions, e.g., in Liriodendron tulipifera, Robinia pseudacacia". So, to answer your final question, some deciduous species (but not all) may indeed retain their leaves if they are grown in favorable conditions. One reason why not all deciduous trees retain their leaves even in favorable conditions is that internal ageing can also induce abscission: "In such species, growth is determined primarily by the endogenous ageing process and is only modified by environmental factors, including daylength"

So, to understand correctly, the plant produces the hormons because the growth is unsustainable. So my next question would be, why not all deciduous retain their leaves in favorable conditions? the answer stems from your answer or I make a new question?

You can edit your post to include your new question and I'll try to answer it

The shedding of leaves has more to do with the condition of the leaf itself. When leaves become inefficient and unable to produce food and
growth regulators, a process of abscission starts.
Abscission a step in the planned senescence process within tree leaves. Senescence is a series of events that allow trees to conserve resources, prepare for a dormant period, and shed inefficient tissues. Senescence is not disruptive and not always caused by climatic factors.
Senescence is a highly ordered and carefully controlled set of steps initiated in preparation for a resting period of a tree (winter).

Are the signalling and detachment mechanisms different in the case of senescence vs. seasonality of the environment?


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Neuronal coordinates of C.elegans
Is there a list of neural coordinates for C.elegans? I need it to build a 3D model.
Update:
What is available at the moment is:

full connectome for example, at openconnectome;
neuron description with images of relative position at wormatlas;
2d position data at dynamic-connectome.

Update 2:
I've created very simple 3d model that consists of three layers (left, right and center) based on neuron labels. This shouldn't be considered as a real biological, but better than nothing. Code and data is on github.

Clarification:
The question is still there, I've provided very basic model and everyone are welcome to use it. But it still would be interesting to get experimental results. I'll keep the question open in case someone could share the data.

Any research done already? Please share or the question may be closed as 'homework' (I removed the "lazy" part in your post, but that is exactly trhe reason why this question may be put on hold :-)

nice piece of work!

Now that you have done some analysis yourself, can you clarify your exact question. You seem to have answered it yourself; if not then add some details.

I've revoked the -1 after these edits.

The Worm Atlas you cited is NOT just a "model." The neuronal cell coordinates were determined from an actual 3-D reconstruction of a worm based on serial thin section electron micrographs.  The serial sections were manually digitized to permit annotation and analysis using computer graphics. The annotation (over a period of years) established the synaptic connectivity, published by John White et al. in 1986 in the Proceedings of the Royal Society of London.


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SDS Laemmli Gel that did not solidify
In my lab class this week my partner and I were making a SDS-PAGE Laemmli Gel. We made the resolving gel solution which was made of 30% Acrylamide, DI water, 1.5 M Tris-HCL pH8.8, and 20% SDS. We mixed the measured amounts into a conical vial. We then added 10% APS and TEMED and mixed carefully. We then immediately pipetted the solution into the casting stand so the gel could solidify. We then pipetted DI water onto the top of the gel so it would not dehydrate. We left some solution in the conical vial so we knew when the solution would be solidified completely. After waiting 45 minutes the gel in the conical vial was solidified but the gel in the casting stand was still liquid. How come the gel did not solidify in the casting stand but solidified in the conical vial?

How long is your polymerization time? How old are APS and TEMED? Why do you use water on top and not an alcohol?

the polymerization time was said to be ~30-45 minutes. The TEMED was provided to the class so I'm not sure how old it was but the APS was made during the lab. Also the teacher suggested to use DI water so the gel would not dehydrate. Would it be the water that could have caused it to not solidify because that's the only thing that was not added to the conical vial which did solidify

You put a liquid on top of the gel because you want to avoid contact with the air. Air catches the free radicals needed for the reaction. Water can mix with your solution and dilute it (depending on the amount of water used and how cautious you pipetted it), thats why I usually use a few hundred microliters of isopropanol.

The polymerisation time appears to be rather long. From personal experience, it rarely takes more than 15 minutes for both the gel in the falcon tube and casting stand to solidify. How much APS and TEMED did you add?

The water shouldn't be an issue if it's layered carefully.

I would guess that the casting glass may have ethanol from cleaning process, or the water you added diluted mix.
Sorry for not entering this as a comment, for I dont have the necessary rep.

We added 150 ul of 10% APS and 15 ul of TEMED. The water was also added a couple drops at a time alternating between each end of the casting stand.

I don't understand, how do you know that the gel mix did not polymerize in between the glass plates? For example, did you attempt to remove the layer of water so that you could pour the stacking gel and discovered that the entire solution remained liquid? The liquid that you layer on top of the freshly poured gel serves two functions. As mentioned by others it excludes air (oxygen) that would inhibit polymerization. It also helps to form a smooth flat surface to pour the stack. 0.1% SDS works nicely too. Best bet: the plates were not clean enough and inhibited polymerization.

This is very strange. I used the variables given here and yet it solidified much faster. Additionally, I remember the one time I added 50µl of TEMED instead by accident and the gel solidified within 30s after vortexing. I agree with @mdperry's conclusion that the glass plates could have been dirty, or that the TEMED was somehow nonfunctional.

Could be a problem of improper mixing too.