text:
Nomenclature for mutations at specific nucleotide positions
I'm sure this is a basic question, but I couldn't find an answer anywhere. Let's say I'm provided with the location of a nucleotide as location as  FGFR3:c.1843-35A>T. What does "1843-35" mean?

As 'c.' stands for 'coding' sequence (instead of 'g.' for 'genomic'), according the HGVS guidelines it denotes the A to T substitution at nucleotide -35 of an intron (in the coding DNA positioned between nucleotides 1842 and 1843).


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FitzHugh–Nagumo system with diffusion
I was studying the FitzHugh-Nagumo model with diffusion and I quite do not understand the meaning of it.
If we consider the system without diffusion,
\begin{equation}\label{FHN}\begin{cases}
\dot{u}=\mu\left( u-\frac{u^3}{3}+v+z \right), \\
\dot{v}=-\frac{1}{\mu}\left( u-a+bv \right),
\end{cases}\end{equation}
where $u=u(t)$ and $v=v(t)$, then it models the control of the electrical potential across a cell membrane. It models the action potential in neurons, for example. But this happens because in the system there is a stimulus current, $z(t)$. The system with diffusion
\begin{equation*}\begin{cases}
\frac{\partial u}{\partial t} = \epsilon D_u \nabla ^2u+\frac{1}{\epsilon}(u-\frac{u^3}{3}+v), \\
\frac{\partial v}{\partial t} = \epsilon^2D_v \nabla ^2v-(u-a+bv),
\end{cases}\end{equation*}
where $u=u(x,y,t)$ and $v=v(x,y,t)$, models exactly the same but just adding diffusion and removing the stimulus current.

How can it model the same biological behaviour if the stimulus current disappears?
Therefore, which is the exact meaning of this sistem (the second one)?

I've implemented numerically this system, and ploting $u$ in terms of $x$ and $y$ in a specific time, I get something similar to the following images:
https://chemoton.files.wordpress.com/2010/07/fitzhugh-nagumo-type-reaction-diffusion-system-i.png
Where the first image corresponds to $t=0$, the second one $t=10$ and the last one $t=100$.

What does this pattern formation mean? I do not know how action potential (which is modelled in this system) is related with these images...
Does this happen because the activated cells activate the ones in the neighbourhood (since diffusion acts)? Or this is wrong because the system only takes into account one single neuron?

Thank you so much!

The FHN equation describes a dynamical system which is only dependent on time using a system of non-linear ordinary differential equations. When you allow diffusion (of the current) then you'll get a partial differential equation with spatial as well as temporal variable. You will get travelling waves along the spatial co-ordinates. Also have a look at the cable equation.

Thanks for your comment. The system with diffusion also models the behaviour of a single neuron, like the system without diffusion? Or it goes a step further and models a group of them?

It is also of a single neuron. Perhaps you can add details to clarify the premise of your question.

Mmmm... But in the output of the numerical implementation of the system with diffusion (the three images in the link) we observe a kind of pattern formation, which seems to represent that activated cells activate the cells near them.  Therefore, many cells should be taken into account, in this model, or not? If it only models the behavior of a single neuron, what represents the "pattern formation" of the images?

Are you talking about the wikipedia article? I am not sure what exactly you are referring to. Can you add the right reference and also include the diagram that you were talking about. AFAIK, the diffusion is within a cell.

I'm talking about the wikipedia article, right. But I've also included a link with the three images I'm referring to. I wanted to know the meaning of these images: Why do we get a pattern formation and which relation this has with the action-potential.
Thank you for your comments!

Why do you get those patterns? That's the steady state property of some of these reaction diffusion systems. You can read Alan Turing's article on the chemical basis of morphogenesis. All these images denote a 2D space. I presume that the diffusion considered for the FHN model would be 1D (action potential travels along one direction). Moreover, FHN model oscillates and the steady state behaviour of FHN+diffusion would be travelling waves. So none of these plots denote the FHN model.

I've implemented a numerical simulation of the system with diffusion and I also get plots like the ones in the link. I plot "u" (coloured) in terms of "x,y" and the output are pattern formation [x is in the x-axis, y in the y-axis and u is represented just with different colours, not in the z-axis].
I don't quite understant these images because of action potential travels in one direction, as you said. Then I don't know how to connect the meaning of the system with the output of implementing it.

You should first understand the model before simulating it. I cannot be sure what you simulated actually. This is getting into a long discussion. Please ask a precise question. As the question stands it is difficult to determine what it is actually about.

I've changed a bit the question. In fact, what I want to know is the exact meaning of the system with diffusion. Thank you!

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text:
Mangroves and desalination of sea water
I am not an expert but I guess that mangroves (or some other plants that thrive in sea water) perform some kind of desalination to extract fresh water from sea water.
Is this true? If yes, What biological mechanisms are used to remove salt from sea water?
I am interested in any research about biological desalination.

This paper might be of interest to you: https://advances.sciencemag.org/content/6/8/eaax5253.
The researchers created a synthetic mangrove that actually performs desalination, using the principles of natural mangroves.
The introduction has a good overview of the main ways mangroves desalinate saline water, namely:

Physical blockage by suberin within cells walls
Selective permeability of cell membranes in root
Negative pressure caused by evaporation that acts as hydraulic pressure to cause take-up of water by roots

All these combine to turn the mangrove into a kind of natural RO (reverse osmosis) machine.

There has been a lot of research in this field which asserts that mangroves desalinate sea water.
Scholander (1968) concludes that this process in mangroves use an ultrafiltration mechanism in the roots of the plant where membranes extract freshwater which is taken up the plant.

 Scholander, P.F., 1968. How mangroves desalinate seawater. Physiologia plantarum, 21(1), pp.251-261.

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text:
Effect of ethanol and detergent on cell membranes problem
I am currently writing my biology report for an experiment I did on how ethanol and detergent affect the cell membrane. For my ethanol experiment, all went as expected. However, for my detergent experiment, the results seemed quite strange. The absorbency rate was higher for the 20% and 40% detergent than it was for the 100%. It seemed as though the results were backwards. I'm really confused.
What might have happened? Was it just an experimental error or is there a reason behind this? Can you also please explain to me what detergent does to a cell membrane exactly?

See https://www.thermofisher.com/in/en/home/life-science/protein-biology/protein-biology-learning-center/protein-biology-resource-library/pierce-protein-methods/detergents-cell-lysis-protein-extraction.html (membrane disruption, protein binding & solubilization). It says only moderate concentration is useful, though I couldn't the reason.

Can you please describe what you actually did? Are we talking about whole cells in a photometer or just a membrane experiment such as black lipid membranes?

Detergent and membranes
Moderate concentrations of non-ionic detergents facilitate lysis of cells. This can be exploited for extracting soluble proteins, often in their native form (ThermoFisher). Detergents affect the membrane at concentrations lower even than those that cause an increase in membrane solubility (Ahyayauch et al., 2010). Two ways this manifests is an alteration of the flip-flop effect (the lipid action caused by flipases) and leakage.
Note that the relationship between detergents and membranes aren't mechanistically well understood, and there aren't yet good general mechanistic rules that explain the relationship between concentration and permeability.
Your experiment

The absorbency rate was higher for the 20% and 40% detergent than it was for the 100%. It seemed as though the results were backwards.

It depends on your specific experiment, but typically the higher concentrations will more readily lyse the cell/make them more permeable. It's hard to say exactly what went wrong here without more information. Unless you were using an exotic detergent, it is quite likely that there was an experimental error and the test should be repeated. Alternatively, the results have been misinterpreted and indeed at lower concentrations, there was no cell lysis, and at 100% there are no cells left intact or something along those lines.


text:
How do T-cells determine which cells they've already inspected?
From what I understand, T-cells are constantly traveling in the body, inspecting cells by looking for antigens. If they're self antigens, then the T-cell doesn't attack, whereas if they're non-self, they attack. My question is how does a T-cell know when it just inspected a cell? Does the T-cell leave something behind on the cell to mark it as checked or does the cell itself present something on its surface to indicate that it has just been checked? If there is no such system, then what prevents the T-cells from being stuck in a loop, and just inspecting the same cell over and over?

As answered on Reddit, where you asked the identical question, it's because there's extensive movement even in the relatively calm environment of the lymph nodes, so that once the T cell disengages from its target the natural movement makes it unlikely to bump into the same cell.  See the references and videos on Reddit.

Here is the Reddit link for anyone who's interested.

I've edited your title and removed anthropomorphic 'know'.

Your question spans two activities of T-cells that are related to each other: migration and activation. T-cells that usually stay in lymphoid organs migrate to non-lymphoid organs with different mechanisms for each T-cell subtype. When migrated to non-lymphoid organ, the T-cells move through the organ looking for infected cells.
Migration
As you can see in the image below, there are many mechanisms for moving T-cells across the endothelial layer.

The main idea for all three mechanisms is that the tethering of the T-cell to the endothelial layer is weak. Because of the weak interaction, the blood flow causes the T-cell to move across the endothelial layer while still being attached to the endothelial layer. This is known as rolling. Other stimuli (usually chemokines) such as CCL21, CCL25, or ICAM 1 are needed to induce T-cell to migrate across the endothelial layer. This is important because these chemokines are expressed where there is inflammation. For example, there is a correlation between CCL25 level in the gut and inflammation in the area.
T-cells express α4β7 integrin or CCR7 that bind T-cell to the endothelial layer. Central memory T-cells and naive T-cells express CCR7 and CD62L and thus reside preferentially within the secondary lymphoid organs. Effector memory T-cells bind to gut endothelium with α4β7 integrin, CCR9, and LFA-1.
CCL21 is expressed by both stromal cells of lymph node paracortex and endothelium of lymphatic vessels to assist migration of activated dendritic cells and naive and central memory T-cells to lymph node respectively. Dendritic cells are professional antigen-presenting cells (APCs) that migrate to lymph node where it can interact with T-cells more efficiently.
T-cell activation
One important concept to take away from T-cell activation is that there needs to be direct contact between MHC complex and T-cell receptor (TCR).
T-cells that have moved into the lymph node interact with dendritic cells, which have high MHC complex concentration on their cell surface. This leads to subsequent activation of the T-cell leading to release of cytokines such as IL-2 leading to proliferation of activated T-cells.
The activated T-cells now are able to freely move across the endothelial layer of non-lymphoid organs to infiltrate and look for infected sites. (Naive T-cells enter endothelial layer of non-lymphoid organs as well but this is chemokine independent nad thus not a reaction to inflammation).
Sources:
Difference between naive T-cells and memory T-cells: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1782715/
Dendritic cell's role in immune response: http://lab.rockefeller.edu/steinman/dendritic_intro/immuneResponse
Memory vs naive T-cell migration:
http://www.nature.com/icb/journal/v86/n3/full/7100132a.html
Dendritic cell and role of CCL21:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3078419/
Naive T-cell non-lymphoid organ infiltration: http://onlinelibrary.wiley.com/doi/10.1002/eji.200535539/full
CCL25 and inflammation relation:
http://www.sciencedirect.com/science/article/pii/S0896841116300014

Please add a citation to your answer (like the process of a T-cell inspecting a cell, there are no such markers ever discovered, etc.)

Sorry, I meant there's no marker that is well known to have that function. Several literature searches yielded no results, so I simply have written "none commonly known".

Its all right. You should just have a back-up claim if someone asks you about the correctness of your answer.

@John It was hard to find in other literatures whether T cell bind to MHC or antigen first. However, that doesn't matter in this case because you cannot have one without the other! MHC and antigen go together. If the cell wasn't antigen presenting cell, it wouldn't have MHC to bind in the first place!

The more effector T cells respond to antigen, the more inhibitory receptors it starts expressing that lead to death of that particular T cell. At that, the longer it takes for the T cell to die, it starts to enter progressively more severe stages of exhaustion. So really the T cells regulate their own persistence (in part). It would be useful to cover this as well.

@CMosychuk I believe the question was about the affinity of T-cell to APCs and duration of binding between the two cells. The concept you mention is interesting, but outside the scope of the question. Which means to not be hypocritical I should take out the "Unrelated" last paragraph.

Down voted, because this answer is wrong.  T cells do bind to APC that don't have non-self antigen, although it's a transient interaction unless the appropriate antigen is present.

Building on @iayork's comment - T cells bind to endothelial APCs (not professional APCs necessarily, just regular endothelial cells) in the blood vessel walls via weak interactions between molecules on the T cell surface and on the APC. This produces a "rolling" phenotype, where the T cells "sample" the surface of the APCs In the absence of pro-inflammatory cytokines or activating chemokines from the surrounding tissue, the weak interactions break under the force of blood flow and the T cell moves on. (...)

(...) If there is inflammation nearby, the cytokines and chemokines will very quickly induce the surface expression of other adhesion molecules, allowing the T cell to come to a stop and begin the extravasation process. This is a good image from the Nature journal Immunology and Cell Biology.

@iayork Thank you for your inputs. I changed the answer to fit your statements. Yes, T-cells bind to endothelial cells lining the blood vessel. Also, please feel free to give input to the answer (the edit answer button).

@MattDMo Thank you for your inputs. I changed the answer to fit your statements. Yes, T-cells bind to endothelial cells lining the blood vessel. Also, please feel free to give input to the answer (the edit answer button).

T-cell does not inspect any cell until the cell shows a piece of the "non-self" antigen on it by the MHC.
The helper T-cell connects with the antigen which is on the cell's surface. The T-cell sorts the cytokines that activate the cytotoxic T-cell to divide and form a colony of cytotoxic cells. The colony of cytotoxic cells then attack the "non-self" antigen expressing cell.

It'd be a lot better if you give some more explanation and a reference too.

I'm confused, although maybe I'm just confusing terminology. Please see here (http://sepa.duq.edu/regmed/immune/SpecifAntigen.html) and here (http://sepa.duq.edu/regmed/immune/SpecifAntigen.html). As this site seems to be saying, T-cells attach(bind) themselves to cells regardless of the antigens on its surface and then after its attached, sees if it has  a matching non-self antigen, which binds it further. Am I reading this incorrectly?

Sorry, the other link is (http://sepa.duq.edu/regmed/immune/SpecifMHC.html).


text:
What is the name of this about 5cm high, grey, Beanie shaped fungus?
I found those below some stone stairs in Germany. The grass gives you an impression of the size (I guess the grass is about 5-7cm tall)

I think this is Coprinellus disseminatus, also known as "Fairy Inkcap". Size (they are pretty small) and also the color fits pretty well. See the image from the Wikipedia:

Some more information can be found here.


text:
Can magnetoreception occur in humans?
Magnetoreception is a sense which allows an animal to detect the Earth’s magnetic field in order to perceive direction, altitude, or location. Magnetoreception is present in bacteria, arthropods, molluscs and members of all major taxonomic groups of vertebrates.

There are several hypotheses that magnetoreception could occur in humans due to cryptochromes, which are a class of blue light-sensitive flavoproteins, because they have been observed to detect magnetic fields in a number of species.

Furthermore, I read somewhere that magnetic bones exist in the human nose, specifically in the ethmoid sinuses. $^1$
Is there more research on those "Magnetic bones", and to what extent is magnetoreception possible in human-beings?
$^1$nature.com/nature/journal/v301/n5895/abs/301078a0.html

What is the dislike about?

Where did you read about "magnatic bones"? Do you have a citation?

@kmm Yes, I do actually – http://www.nature.com/nature/journal/v301/n5895/abs/301078a0.html

Do be aware that most biomagnetism (even those published in Nature) can turn out to be bogus. In this preprint, Markus Meister debunks 3 recent nature papers claiming biomagnetism. Nowhere in the referenced Nature paper do I see an attempt to link the magnetic field range of the ferrous ions and the range needed for the biological function that aids bone growth and repair. It's just an exciting hypothesis as far as I can see.

@James That sounds logical, the idea of magnetoreception in humans would just be too awesome! Thanks for the useful link btw

Almost same question: http://physics.stackexchange.com/questions/266833/why-human-body-is-not-affected-on-magnetic-field

When we talk about 'can something happen', then I don't think the answer would need a reference.
Of course, humans can attain the ability of magnetoreception, but the main question is What good will it do to us? Instead it'd prove to be disadvantageous as:

We already have smartphones, compass for identifying magnetic field, so why will the body prefer to waste energy on something which can be done without wasting energy?
We all know that the earth has its own magnetic field. So whenever you wake up or go for a walk (just do any movement), you'll feel an irritating magnetic sensation. Why would that be useful?

Even if we don't talk about disadvantage, then also magnetoreception wouldn't prove to be much useful in whole human population. Randomly, some guys might get a few genetic mutations which would allow them to feel magnetic field, but that wouldn't be of any use to them.
BUT, to your interest, humans do have magnetoreceptors, in retinas. See this article:

But cryptochrome isn’t unique to birds – it’s an ancient protein with versions in all branches of life. In most cases, these proteins control daily rhythms. Humans, for example, have two cryptochromes – CRY1 and CRY2 – which help to control our body clocks. But Lauren Foley from the University of Massachusetts Medical School has found that CRY2 can double as a magnetic sensor.

or this Wikipedia article:

Humans are not thought to have a magnetic sense, but there is a chemical (a cryptochrome) in the eye which could serve this function.(2)

Source                                                           Source
So, acquiring magnetoreception might be easier than you'd expect, but it doesn't happen even in this condition. Why?, who knows? Maybe because our body rejected magnetoreception as useless. Maybe at some point of time, humans had the ability to feel/see magnetic field, but this feature now seems vestigial.
EDIT: Regarding "magnetic bones", every article that I could read only points to this Nature article you referred to in your question. So it doesn't seem like there has been much research on it, or maybe this article itself is enough to conclude the topic.
References:
1.http://blogs.discovermagazine.com/notrocketscience/2011/06/21/humans-have-a-magnetic-sensor-in-our-eyes-but-can-we-see-magnetic-fields/
2.https://en.wikipedia.org/wiki/Magnetoreception
3.http://www.ks.uiuc.edu/Research/cryptochrome/
4.http://www.microsystem-components.com/html/magnetoreception.html
5.http://www.nature.com/nature/journal/v301/n5895/abs/301078a0.html


text:
What is the name of this plant with small, 5-leaved divided pink blooms?
I found this in a forest in Karlsruhe (Germany).
The blooms are pink and have 5 leaves. Each leave is divided into two parts. It is pink and has a diameter of about 1-2cm.

It looks like a Red Campion, which is native to northern and central Europe.

It would be nice to see a close-up of the calyx (which is usually striped) and the leaves to be sure; it may be a cross between a White and Red Campion.
There are many members of the genus, and many look alike. Your close-up is of a male flower (anthers only). The plants are male or female.

Looks kind of like a species in the genus Silene. Interesting group, I believe some species in this group are dioecious and have sex chromosomes.


text:
Fate of Acetyl CoA in well fed state?
When we have eaten well and take fat rich diet then in this condition Acetyl CoA produced from fatty acid breakdown will be gone to storage in adipose tissue or not? If it will go for storage then why and if not go for storage then what will be reason?

It may not be compulsory to store it. It should be converted into CO2 to yield energy. I don't think a few more ATP in the cell would hurt.

But if cell has enough ATP then what will be fate of Acetyl CoA?

respiration-related processes is not my field of research, so I'd just give a guess that yes, it'd be converted back to fatty acid & then stored. But, I don't think humans have ability to do so, so I'm not sure on this.

This is either a trivial question, to which the answer is "If energy is needed then it will be used to generate ATP (in the liver) through the Krebs TCA cycle, if not it will be used to synthesize triglyceride (in the liver) which will be transported to the adipose tissue for storage. Why? because use or storage are the only options (other than excretion)." If you want biochemical details of the regulation then your question is too broad to be answered here. You need to read an account of fat metabolism in a biochemistry text book.

I don't think your premise is correct. Acetyl-CoA is not produced at all unless needed, because there is a limited pool of Coenzyme A, which limits Acetyl-CoA abundance. If there is an excess of fat, it is not catabolized to acetyl-CoA at all, but simply stored away until needed. Adipose tissue is capable of taking up fatty acids directly and esterifying them into triacylglycerides (fat).

As Roland mentioned in the comments, in the well fed state, not all of the Acyl coA is converted to Acetyl coA. This picture from Harper's Biochemistry, 29th, should come handy.
It is the CPT-1 gateway that regulates the amount of acyl-coA (from FFA) that enters into the mitochondria to form acetyl-coA.
In the Fed state, the CPT gateway is shutdown (regulation by malonyl-CoA) - allowing esterification by sending them back as VLDLs. In the starved state, the gates open, leading to beta oxidation giving acetyl-CoA.
The acetyl coA then can enter the Kreb's cycle to get completely oxidised and give ATP + CO2 (this ATP the liver readily utilises). Or, the acetyl-CoA can be channeled into ketogenesis, where this energy can be used by other tissues (since liver lacks the enzyme thiolase and hence can't metabolise ketone bodies). How the liver distributes the acetyl-coA for ketogenesis/Kreb's cycle is a different story altogether.


text:
Statistical genetics: Allele frequencies that follow a Dirichlet distribution
From Foll and Gagiotti (2008) (software BayeScan). They consider a model where several subpopulation are derived from a unique ancestral population.

We consider a set of $I$ loci and let $K_i$ be the number of alleles at the $i^{th}$ locus. The extent of differentiation at locus $i$ between subpopulation $j$ and the ancestral population is measured by $F^{ij}_{ST}$ and is the result of its demographic history. Let $p_i=\{p_{ik}\}$ denote the allele frequencies of the ancestral population at locus $i$, where $p_{ik}$ is the frequency
  of the allele $k$ at locus $i$ $\left(\sum_k p_{ik} = 1\right)$. We use $\mathbf {p} = \{\mathbf {p_i}\}$ to denote the entire set of allele frequencies of the ancestral population and $\mathbf {\tilde p_{ij}} = \{ \tilde p_{ijk}\}$ to denote the current allele frequencies at locus $i$ for subpopulation $j$. Under these assumptions, the allele frequencies at locus $i$ in subpopulation $j$ follow a Dirichlet distribution with parameters $\theta_{ij}\mathbf {p_i}$,
$$\mathbf {\tilde p_{ij}}  \space \tilde \space\space  \text{Dir}(\theta_{ij} p_{i1}, ..., \theta_{ij}p_{iK_i})$$
, where
$$\theta_{ij} = \frac{1}{F^{ij}_{ST}}-1$$

(I don't have much experience with Dirichlet distributions but I understand its definition and its usefulness in bayesian statistics).
Can you please help me to understand why $\mathbf {\tilde p_{ij}}$ follows this Dirichlet distribution?
Calling the $j^{th}$ parameter of the Dirichlet distribution, $\alpha_j$, I typically don't understand why they "chose" $\alpha_j = \left(\frac{1}{F^{ij}_{ST}}-1\right) p_{ij}$ and not, say just $\alpha_j = F^{ij}_{ST} p_{ij}$ or anything else.

It looks like it is a solution to an integral equation as described in Sewall Wright's Evolution in Mendelian Populations, Section Nonrecurrent Mutation https://www.genetics.org/content/genetics/16/2/97.full.pdf.

Largely an informed guess based on properties of distributions rather than specific knowledge of statistical genetics: a beta distribution is useful for modeling the frequencies of two alleles at one locus. A Dirichelet distribution, which is a multivariate generalization of a beta distribution, would thus be useful for modeling a set of loci.
The flip side is to think of beta as just a special case of Dirichelet: if you only have one locus, beta works. If you have multiple loci, then Dirichelet.

Thanks for your answer. Yes, those are things I know about statistics (+1 anyway as a thanks). I fail to understand why typically $\alpha_j = \left(\frac{1}{F^{ij}{ST}}-1\right) p{ij}$ and not, say just $\alpha_j = F^{ij}{ST} p{ij}$ or anything else. (I will add this precision in my question).


text:
How does a protein reach its substrate within the cell?
After a protein has been synthesized and its the final tertiary/quartenary adopted, how does it reach its substrate within the cell and what causes it to interact with it?
The transcription factors for a particular gene are proteins which are translated from genes on some other portion of the DNA. (That happens in the cytoplasm) But how do the transcription factors know that it has to diffuse into DNA region of the nucleus.

proteins as well as other small molecules like pharmaceuticals and steroid hormones all bind with specificity for particular targets within the cell - this specificity is what makes the protein seem like it wants to seek out its target - I'm sure there are more chemical-minded individuals that can give you a good explanation about binding energy and exergonic reactions, etc - good quesetion

A protein doesn't "know" anything, just like gravity doesn't "know" anything. There are all kinds of proteins as well; there are cell receptors, carrier proteins, cytoplasmic enzymes, structural proteins, etc. Are you specifically asking about enzymes and substrates? Or generally how do proteins "know" what to do?

As a side note, we don't know anything as per the Central Dogma.  The Central Dogma was a model, not a set of observations, not even a hypothesis; it was deliberately named to be provocative, and was overthrown pretty quickly.  It's a mere footnote to history, not an important biological concept. Unfortunately, there seem to be a group of teachers -- mainly in India -- who don't understand this, who force it onto students, and who put it on exams, leading to widespread misunderstanding.

The protein doesn't move towards anything. It just randomly diffuses (bounces around) in the cell until it sticks to something. The particular chemical structure (the shape) of the protein and whatever it hits will determine how tightly they stick together and whether or not a chemical reaction occurs.
A way to imagine this is to think of a jar filled with a lot of glass marbles (water), 1 marble shaped magnet (the protein), and 1 metal marble (the substrate). Put the magnet at the bottom, fill the jar most of the way full with glass marbles, and then put the metal marble on top. Then close the jar and shake it. Eventually, after colliding with a lot of glass marbles, the magnet and the metal marble will collide and stick to each other. That's how it works in cells also. In cells, the speed at which the molecules move is proportional to temperature.
Here's a cool video that shows how proteins with a very specific shape bouncing around randomly can assemble into a complex structure.
To get a sense of just how quickly molecules move in a cell, think of a bacterial cell. An E. coli cell is about 1 micrometer in diameter. In a cell of that size with no sub-cellular compartments, every molecule will collide with every other molecule in the cell about once every second (if we make some assumptions such as no binding to other molecules). So if the cell contains just one unit of a certain enzyme, and just one molecule of its substrate, they will still collide fairly frequently (about once every second).
This rate decreases dramatically as radius of the cell increases. For example a cell with double the diameter (2 micrometers) has a volume eight times larger, so collisions between any two molecules take 8 times ($2^3$) as long to occur (in other words, it takes molecules 8 times longer to "find" each other). This is one reason why there is a kind of upper limit on the size of an individual cell. Bigger organisms are bigger because they have more cells, not because they have larger cells.
The field of biology concerned with how likely it is for a reaction to occur is called enzyme kinetics. A related field, which deals with how frequently molecules collide is called statistical mechanics.

It just randomly diffuses in the cell until it sticks to something. This isn't entirely accurate. The secretory system can deliver proteins to specific parts of the cell and then some are embedded in the membrane whilst others have signal peptides which can be cleaved off, releasing the protein into the local vicinity. Motor proteins are even involved in the final stages of this, making it a particularly directed process. Furthermore, could you provide a reference supporting that as a reason for the upper limit of cell size?

You're right of course. I should have stipulated that this applies best to soluble, cytosolic proteins.
I would argue however, that what you're describing with secretory processes, is just a special case of diffusing around randomly until it sticks to something. In the case of secretory pathways it's just that there's a cascade, where once it interacts (sticks) to the first other protein in the cascade, it forms a complex that interacts differently than any of the two precursor proteins. And so on as the cascade hits different steps. It's just a bunch of molecules randomly bouncing around.

As far as a reference for cell size. I think I heard that in a class or read it in a text book a long time ago. Quickly looking around the Internet, I found a reference that is sort of sufficient (it doesn't account for eukaryotic cells, just bacteria). Here's that.

@SeanJohnson I understand your implications of statistical mechanics to chemical interactions inside the cell in order to reach a binding affinity that is sufficient to keep the molecules together. But as I had mentioned about transcription factors in my question, I am not able to correlate it exactly. The transcription factors' activity is within the nucleus. In that case how would it travel inside through the nuclear membrane? I am unable to understand how would it be a random interaction if it has to specifically penetrate the membrane to reach its target.

So your question is more about how proteins in eukaryotic cells enter various sub-cellular compartments? Or is it more about what distinguishes the outer membranes of different compartments?
Check out the Wikipedia article about "nuclear pores"

@James The collision propensity is proportional to concentration. And concentration decreases with increasing volume if the number of reacting molecules are constant.

Thanks both of you @SeanJohnson. I sort of get what you are trying to say. I will read about your reference for better clarity.

@Synaptic_Pik There are many more factors that affect the activity of transcription factors. There are phenomena like macromolecular crowding and chromatin organization that play a significant role. If that is your specific question then you can ask it separately along with all necessary details.


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What are Codominant vs Dominant Genetic Markers?
When talking about types of genetic markers, the adjective "dominant" and "codominant" are often used. I don't fully understand their definitions and found contradicting definitions.
Foll and Gagiotti (2008)
Typically reading from  Foll and Gagiotti (2008), they list give two examples of markers of each type

Codominant markers

SNP
microsatellite

Dominant markers

RFLP
AFLP

reddit
This reddit post indicates that RFLP are codominant markers (unlike stated in  Foll and Gagiotti (2008)).
wageningenur
On wageningenur.nl (random website I never heard of before), they define dominant and codominant markers based on gene expression suggesting that the terms dominant and codominant used for markers have the same definition than those used for allelic effects on the phenotype (dominance, recessivity, overdominance, etc..).
Questions

What are the definitions of dominant and co-dominant genetic markers?
Can you please offer examples for each type and explain why they fit in one or another category?
Do the terms dominant and codominant have the same definition when used to describe a marker and when used to describe allelic effects on the phenotype (dominance, recessivity, overdominance, etc..)?

So does it make any sense to say that SNPs are codominant while RFLP are dominant (or vice-versa)? Thanks

I don't think that would be right. RFLP is a technique which may in certain circumstances differentiate SNPs as well. It is a low resolution technique. Now SNP is just a physical feature on the DNA: it is not a phenotypic marker; more of a genotype you can say. However SNPs may be in a non-geneic region and affect the phenotype. SNPs create allelic variants (let's also consider any region that affects the phenotype as a part of the allele i.e. include the promoter/enhancer etc). These alleles can be dominant, co-dominant or recessive. It does not make sense to say SNPs are codominant.

I would agree but these terms I used over and over. See a search on Google Scholar with the terms "codominant dominant marker".

From wikipedia

If the genetic pattern of homozygotes can be distinguished from that
  of heterozygotes, then a marker is said to be co-dominant.

This definition seems to be different from the one used to explain allelic effects. For example, as you would know a SNP is basically a feature of the DNA sequence. It is more of a genotype rather than a phenotype. Markers are supposed to be phenotypes (can be a molecular phenotype too for example a marker for stem cells etc). SNPs do create allelic variants but they may or may not contribute to different phenotypes. Consequently, the allelic variants may exhibit dominance or co-dominance with respect to each other. So, going by the definition used in classical genetics, you cannot call SNP as a "dominant"/"co-dominant" marker.
That is a weird usage of the terminology but people have done it so the deed cannot be undone. I would avoid future usage of such misleading terms. Having said that SNP would fit the definition of a "co-dominant marker" if it is observed by DNA sequencing .
Personally, I would consider RFLP a technique and not a marker per se. RFLP can be used to differentiate SNPs but sometimes it may not even resolve different strongly visible phenotypes (its efficacy basically depends on the polymorphism at restriction sites). Heterozygotes however, would have a different band pattern compared to homozygotes. So it should be a "co-dominant" marker.
AFLP, as far as I know is simply PCR amplification of restriction fragments. It would be "co-dominant" for the same reasons. However, just a PCR based screen would not differentiate between homozygotes and heterozygotes and would thus be a "dominant" marker. Now again, these are techniques and not, in a true sense, "markers" whereas SNPs and microsatellites are actual DNA features. So these cannot be even compared. A technique, depending on its resolution, can be "dominant" or "co-dominant" as per these definitions.

For general interest
I would want to reiterate that these definitions, for some reasons mentioned above, are quite flawed and are therefore misleading (they may have been okay at certain point of time but are obsolete now). Please avoid their usage in your papers and reports and if possible point these flaws out, so that they do not propagate.


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When is gene density an important parameter in experiments?
As per wikipedia definition, gene density is defined as:

"In genetics, the gene density of an organism's genome is the ratio of the number of genes per number of base pairs, usually written in terms of a million base pairs, or megabase (Mb). The human genome has a gene density of 12-15 genes/Mb, while the genome of the C. elegans roundworm is estimated to have 200."

But I would like to know in what circumstances one would consider gene density as an important parameter? To be specific in what kind of experiments the model organism's gene density plays key role?

I don't know about experiments, but it might be useful in estimating size of exons & predicting length of mRNA.

Of the top of my head two fields that could make use of gene density arw Bioinformatics and evolutionary studies. Gene density says something about complexity of organism, information storage, etc

"Note that interaction effects among genes also depend on their physical distance." I think that's more of a pragmatic assumption, because we tend to associate regulatory features with their closest downstream TSS, though it's certainly not a hard and fast rule. e.g., in certain organisms like budding yeast, its known that the most transcription factor binding sites are downstream of gene bodies. even in humans, the association is not entirely clear as there are both cis and trans effects especially notable with things like super enhancers and things of that nature. Or consider the following, http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1004461

This is an open-ended question and will be impossible to correctly answer. I am voting "to close as too broad". Note also that the question in the title is not the same as the question in the post.
But I still wanted to give you some information that may help you. Here are just a few examples for which knowing gene density matters.

Background selection is the process by which purifying selection reduces heterozygosity at nearby loci. Knowing the density (and positions) of genes (and other sequences potentially under selection such as regulatory sequences) is essential to understand the variation of background selection throughout the genome. Being able to design maps of variation of background selection throughout the genome is essential to improve our ability to detect local adaptation and positive selection as background selection leaves similar genetic signature.
The evolution of the genome size is in itself of interest to evolutionary biologists. Species having large genomes ave large genomes mainly due to repetitive neutral sequences. As such the question of gene density is essential to understand the evolution of genome size.
The gene density varies throughout the genome (with a variance greater than the mean, that is it does not follow a Poisson distribution). Understanding the evolution of gene density at different regions is of interest to many. Note that interaction effects among genes also depend on their physical distance.


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What are the significances of chromosome mapping?
The few point that I have come across are:
The following are the significances of chromosome mapping:

Chromosome maps help identify the location of gene of interest on a chromosome for genetic studies.
It helps to locate the region of a chromosome surgery.
Maps of the animals chromosome provides methods to study evolution process.

Can somebody add some more points to this answer?

As I understand your question, you ask about genetic mapping which has been demonstrated in the HGP (human genome project).
The human genome project:

enabled humans to find the gene responsible for relatively rare, single-gene inherited disorders such as cystic fibrosis and Duchenne muscular dystrophy
is useful in guiding scientists to the many genes that are believed to play a role in the development of more common disorders such as asthma, heart disease, diabetes, cancer, and psychiatric conditions
allows the production of new drugs based on DNA base sequences of genes or the structure of proteins coded for by these genes
gives the chance to study migration patterns of humans and origins
improved knowledge of the evolutionary relationships between humans and other organisms, which will help to develop better, more accurate classification systems

Sources:

https://www.genome.gov/10000715/genetic-mapping-fact-sheet/
https://www.genome.gov/12011238/an-overview-of-the-human-genome-project/
https://www.genome.gov/10001772/all-about-the--human-genome-project-hgp/

nice answer, but I think that OP asked for chromosome mapping (general), not HGP.

Yes that is correct I asked for chromosome mapping in general, still thank you for your efforts.


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Physical activity in fasted state: Glucose for brain vs muscles
Let's consider this scenario:
You do sports in the morning in a fasted state (i.e. without consuming any calories after waking). Your brain of course needs glucose and your liver probably still has some of it in stock. So it keeps releasing it. Is there a mechanism to prevent the working muscles from consuming the glucose (so that the brain can be supplied longer)? If yes, how does it work?
(Please answer not too technically, so that people outside this area can also understand it.)

In general it is the reciprical action of the hormones of the fed and fasted state — insulin and glucagon — that are responsible for this, together with the differences in hormone-sensitivity of the glucose transporters in muscle and brain. See the accepted answer to this question: During starvation, does the human body do anything to prioritize which organs receive nutrients?.


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What is the name of this green plant with thin leaves?
I've seen this in Scotland between Balmaha and Inversnaid:

A higher resolution is here: https://commons.wikimedia.org/wiki/File:Balmaha-Inversnaid-9.jpg
What is the name of this green plant with very thin leaves?
(I guess it was most of the time about 60cm high, but I don't quite remember)

Some kind of Equisetum? https://en.wikipedia.org/wiki/Equisetum With this picture it is pretty hard to figure it out more detailed.

Could be too-many things. Higher resolution of whole landscape is usually NOT helpful. What  needed, is more close-up. So that it could be observed in a technical way. As well, I could not find any possible-reproductive-structure. You could go through this page Are there any guideline about species-identification questions?. I think it may help where to look for before photograph it.

@AlwaysConfused Thank you for the link. For future questions, I will try to follow these guidelines. However, I have no idea how reproductive structures look like for plants.

To me it looks like many other things such as 1. some tropical angiosperms like Alternanthera philoxeroides (syn. Telanthera philoxeroides ), amaranthaceae; Leucas aspera,Lamiaceae;  [Hygrophila spinosa] syn asteracanthus longifolia (acanthaceae), etc. I think this is a very common growth found in broad groups from bryophyte to grasses and dicots.

Reproductive structures mean inflorescence, flowers , fruits seeds in angiosperm, cones and seeds in gymnosperms, sorus and cones in pteridophytes, capsules in bryophytes, and in case of algae they are oogonium and antheridium. Are they very difficult to recognize? flowers and fruits couldbe very tiny in shape. Btw not much discussion is possible here. You could go through plant morphology chapters in school textbooks(here these topics taught commonly class-5(10yr kids)to  8 (13yrs youths) in life science and nature studies). Though these books may contain some technical mistakes but will help

when I wrote reproductive structure 'means'; I didn't meant 'definition' (because the term 'reproductive structure' means itself). I should write 'example'. However if the language was too-technical for you, I'm sorry don't worry I think its not at all difficult to recognize a flower or inflorescence or such-sort of things emerged on the plant-body.

This is a moss of the genus polytrichum, most likely it is P. commune or P. formosum


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do game animals have poor eyesight?
I have been watching some bow hunting videos on youtube. When hunting with a bow, the hunter needs to get really close to the animal, sometimes less than 10 meters.
It seems to me implicitly, and some hunters even say explicitly, that the animals (deer/elk/moose/buffalo) only see the hunters when they move. As long as the hunter has reasonably camouflaged clothes and is not smelled by the animal, they can stand in plain sight and the animal does notice them.
Do these game animals (deer/elk/moose/buffalo) really have such poor eyesight?
here are some videos as examples:
https://youtu.be/OqGSaGXHXgY?t=654
https://youtu.be/9tx_l9Jco_M?t=213
https://youtu.be/bP38tYhyhW0?t=303
https://youtu.be/xP9L885noEI?t=58

Their eyesight is not poor, it is just adapted to seeing moving predators. It is actually incredibly keen in that respect.

@MattDMo - if deer have acute eyesight, why don't they notice the hunter then (and the even more conspicuous cameraman). Besides, if deer are only capable of seeing moving predators, would not the predators evolve to take advantage of it ?

You are comparing deer to humans, which is a bad idea. Deer (and many other prey animals) evolved this type of eyesight as it protects them from their natural predators. Wolves don't have guns or bows, and so need to move to attack their prey, and deer can detect this type of movement very easily. Humans have not been using projectile weapons for that long, evolutionarily speaking, and deer have not evolved to address this new threat. Camouflage also helps the hunter blend into the surroundings.

These species likely don't see you as a predator, or if they do they don't know if you've seen them yet.
A study indicated that the vision of the White-tailed deer was good;

As expected for a crepuscularly active prey species, the visual system of white-tailed deer is specialized for sensitivity in low-light conditions and detection of predators.

The observation that many prey species only notice movement may relate to behavioural adaptations that increase their chances against natural predator species. Staying still while monitoring your surrounds decreases the chance of the predator seeing you.
I'll quote D'Angelo et al again;

The visual streak of deer in combination with
  their wide-set eyes likely provides them with enhanced ability
  to monitor the horizon and to detect movement with a
  wide field of view while keeping their head stationary.

Visual specialization of an herbivore prey species, the white-tailed deer.
G. J. D’Angelo, A. Glasser, M. Wendt, G. A. Williams, D. A. Osborn, G. R. Gallagher, R. J. Warren, K. V. Miller, M. T. Pardue
Canadian Journal of Zoology, 2008, 86:735-743, 10.1139/Z08-050


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Is it possible to transfer acquired hemophilia with breast milk?
There is a transplacental form of acquired hemophilia: http://www.jpeds.com/article/S0022-3476%2895%2970132-X/abstract
This disease is caused by polyclonal immunoglobulins (IgG1 and IgG4) against the A2 and C2 domains of factor 8. So acquired hemophilia is an autoimmune disease. By the transplacental form the maternal IgG antibodies causing this disease in the newborn. As far as I know IgG antibodies are transferred with breast milk too. Can breast milk cause this disease?

Acquired Hemophilia is an AutoImmune Disease, hence it is possible to transfer it from mother to child through breastfeeding milk. The antibodies subjected to autoimmune disease also passes into the infant or baby from breastmilk in addition to the healthy antibodies. These abnormal antibodies will act as an inhibitor to the enzyme responsible for production of Factor VIII , a blot clotting protein. Less number of factor VIII protein results in increased amount of internal bleeding.

Thanks James! The question was not about explaining what this disease is. Do you have any proof that it can be transferred to the child with breast milk?


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Are all quadrupeds edible?
I wonder if all quadrupeds (or, mammals, at least), are edible?
From what I have collected, even down to fish, everything is edible apart from being sick or infected, and, apart from some glands secreting (deliberately, as far as this term makes sense in evolution) poisonous molecules.
This is (if correct), in stark contrast to plants, where frequently many parts of the plant contains poisons. (It has some logic: plants can't run away or mechanically fight back.)
Q: Are all quadrupeds edible?
An additional bonus on: WHY?

Edible by whom? Lets assume humans.
Yes all quadrpeds are edible though you may not want to eat every part.
For example, the scent glands of a skunk, or the quills of a porcupine are repulsive or impossible to eat. Also, some organs, like the liver of a polar bear, which accumulates vitamin A to toxic (to humans) levels.
It's impossible to say why this is so, since we can't prove why evolution occurs one way or another. What you suggest about mobility is reasonable, but not universal, since the poisonous puffer fish is able to move.

Yes, I had humans in mind, but anyone who has an answer for non-humans (up to other multi-cellular organisms) is welcome. Will wait to see other answers before accepting yours.

What makes polar bears tolerant to high levels of vitamin A?

Polar bear (and probably a seal) liver is toxic due high concentration of Vitamin A.
Hawksbill Sea Turtle is probably toxic as it consumes poisonous sponges and its "body fat absorbs the toxins without making the turtle ill, but their meat is potentially poisonous to humans".
Shrikethrush birds (three species) are toxic as they consume melyridae beatles.
Moreover, there's a plenty of toxic amphibians like toads (bufotoxin called after them) and frogs.

Polar bear meets my question as a living counter example. As for the other species, the poison is not produced but consumed, in other words, those animals are not poisonous of their own. Good enough for a warning!

@GyroGearloose Whether they make it in their body or bring it in from outside they are still toxic. You can't eat them safely.

@GyroGearloose: The platypus synthesises its own venom, but that's only in one gland so I don't know that it makes the animal inedible. Btw I'm not sure that polar bears are synthesising much if any of that vitamin A -- generally speaking omnivores can generate vitamin A from carotenoids, but polar bears aren't eating veggies. They're probably just sequestering vitamin A from their food (seals).


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Why are both glucagon and cortisol released in hypoglycemia?
Cortisol is released in response to prolonged stresses; one situation when cortisol is released is when blood glucose level is low. In this situation cortisol acts on adipose tissue promoting fatty acid mobilization, and also promotes gluconeogenesis by degrading muscle proteins and converting them into pyruvate. Cortisol also stimulates gluconeogenesis by increasing the expression of PEP Carboxykinase the enzyme of gluconeogenensis pathway promoting the TCA Cycle intermediates or Oxaloacetate to convert into Phosphoenolpyruvate and promoting gluconeogenesis to balance the blood glucose level.
These are the same effects produced by glucagon to increase the blood glucose level when it is low.
My question then is what is the need for release of Cortisol? Also, if its release is important to control other pathways I haven't mentioned here, then why does cortisol produce the same effects as glucagon? Why is glucagon alone not enough to maintain blood glucose level?

Since the ability to utilize glucose for energy is necessary for life (look at the effect of hypoglycemia on brain function, for example), it makes sense that the regulation of serum glucose concentration would have a number of pathways, that is, redundancy helps to ensure continued proper function should one of the regulatory mechanisms fail.
Glucagon is considered the main physiological response to hypoglycemia; however, epinephrine, growth hormone, and cortisol - in that order - and very probably other factors yet to be named/elucidated also help to increase plasma glucose when it drops.
This kind of redundancy is very common. Cortisol, epinephrine and growth hormone all have other effects on tissue unrelated to glucose as well.
Glucose Counterregulatory Responses to Hypoglycemia


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Why do pink rain lilies flower only after rains, and not from being watered?
We have pink rain lilies (Zephyranthes carinata) in the garden. In my personal experience, I've found that they always flower, without exception, shortly after rains. However, there are roughly ten totally dry months each year. During this time, even though I water them regularly with well-water, they never flower. I've tried copious amounts of water, and frequent watering, but to no avail. They seem to depend on rain.
The rains here come at different times each year. We just had a totally unexpected rainstorm in May, causing them to flower. We are inland in southern India. It's very hot here, and the climate is quite dry in the periods when it's not raining.
How can this be? What's going on inside the plant, biologically speaking? How can it "know" whether it's getting rain water or well water? I'm looking for a description of the biological processes inside the plant which cause these different responses to rains versus watering.
Also, (minor, secondary point) is there any evolutionary reason why a plant would develop this trait?
I prefer answers that cite their sources for the information.
Edit: A user added some quite relevant personal observations in the form of an answer. I'm adding it here, as the observations are quite relevant to the question.

I live in central India which is marked by a heavy rainy season from mid June to September and almost dry rest of the year. This behavior of rain lilies has been a mystery to all of us for generations.
No matter what season, what temperature, the lily bush will give you
  at least one bloom even if rains for a mere few minutes. Rest of the
  time, any amount of watering does not help. I've seen the plant bloom
  with just a bit of drizzling in summers when temps cross 40 degrees
  celsius.
Whereas, a friend is growing them in a pot in a water lily pond.
  Basically, in shallow water where the rain lilies are just dipping
  their feet in water all the time. So basically, for a large portion of
  the year, the plant is meeting the low temperature, high water criterion.
  It doesn't work. The plants bloom only and only when it showers.
By the way, the behavior is not limited to pink rain lilies. It's the same with yellow and white lilies.

These are seasonal rains? Does any rain cause the plant to flower? Plants do have flowering cycles.

@WYSIWYG The rains can come at any time during the year. It depends on a complex set of conditions in the Indian Ocean and Bay of Bengal. It's pretty random. There are some months when it's more likely to rain, though. Yes, it seems the rain causes the flowering. I've seen it flower every single time after rains, but never without rains, even though I water it a lot with water from a well. It should be noted that rain generally tends to be pretty heavy here when it does come.

Perhaps they bloom just after it rains because many bees come out of their hive at this time, which would allow the flower to reproduce more effectively and thus get the evolutionary advantage. I don't have any information to back this theory up (couldn't find any), and I don't know much about biology. Can somebody confirm or deny this hypothesis?

@DivideByZero We could test this hypothesis by having several plants, and surrounding some of them with insect netting.

@Fiksdal - I don't think that's what DBZ meant. I think what they meant is that perhaps the plant flowers because they are expecting (because of past experiences) more bees to come around, not in response to more bees coming around at a particular time.

@KevinFegan Ah, I see. Interesting.

It looks like sustained or consistent moisture might be (at least part of) the phenological cue for flowering:
The wikipedia article mentions that consistent humidity will induce flowering in at least some species and cites Fernández-Alonso & Groenendijk (2004), which says:

It generally flowers after the rainy periods, but in humid pastures and under cultivation conditions, colonies show staggered flowering during the whole year.

There's a reference in Lange et al. 2013 to Zephyranthes flowering after "watering of at least 10 h[ours]", but I'm not able to find the original citation in the google books preview (which is given at "Nitsch 1965").

Edit: I tracked down Nitsch 1965, who cites 2 sources on the topic. He reports Kerling 1949 as showing that Zephyranthes rosea after a certain period of development goes into dormancy, which is broken when two conditions are met: low temperature and high water, which must be extended over at least 10 hrs. He adds that Holdsworth (1961) presents evidence showing that Zephyranthes citrina and Z. tubispatha are primarily triggered by soil moisture.

Fernández-Alonso, J. L. & J. P. Groenendijk (2004). A new species of Zephyranthes Herb. s. l. (Amaryllidaceae, Hippeastreae), with notes on the genus in Colombia. Rev. Acad. Colomb. Cienc. 28: 177-186
Holdsworth, M. (1961) The flowering of rain flowers. Journal of the West African Science Association 7︰28-36.
Kerling, L.C.P (1949) The gregarious flowering of Zephyranthes rosea Lindl. Annals of the Botanic. Gardens. Buitenzorg 51: 1-41
Nitsch, J. P. (1965). Physiology of flower and fruit development. pp 1537-1647 in Encyclopedia of Plant Physiology Vol XV Part 1, W. Ruhland (ed.)
O. L. Lange, P. S. Nobel, C. B. Osmond, H. Ziegler (2013). Physiological Plant Ecology III: Responses to the Chemical and Biological Environment. Springer.

Thanks for this answer! Does this suggest that it's the mere duration of the watering that's the key here? This would make sense, rains are typically heavy here and last for a long time. Maybe I could test this hypothesis by setting up some sort of automatic sprinkler that watered it constantly for a few days?

@Fiksdal sounds like a great experiment to me! For +1, have a control patch that you don't water / water normally! :)

There's a new answer (which isn't really an answer, but includes very relevant observations). I have added it to OP in case it gets deleted (as not an answer.) After considering this information, I have concluded that we still need to look for different hypotheses here.

It's a nice question, I've tried looking for research papers to no avail. But I will add a few things that I hope will help:

Firstly, tap water's composition is quite different from rain water- two criteria for distinction that  come to mind would be pH and TDS, details follow:

Tap water has a higher TDS (total dissolved solids)than rain water, making it harder(1). Additionally it has a higher pH(2). Rain water has virtually no dissolved solutes in it that affect it's hardness and it's pH is acidic(3)(4). Thus while tap water may have a TDS in the hundreds, rain water has a TDS in the tens- a stark difference.

Have you considered that 'Photoperiodism' may be at play? Having grown up in India, I can attest to the over-cast sky after heavy shower, sometimes for hours. This plant may be a short-day plant i.e. it flowers only when the duration of daylight has fallen below a certain threshold(5).

References:

http://www.water-research.net/index.php/water-treatment/tools/total-dissolved-solids
https://www.watersystemscouncil.org/download/wellcare_information_sheets/potential_groundwater_contaminant_information_sheets/9709284pH_Update_September_2007.pdf
http://www3.epa.gov/acidrain/education/site_students/phscale.html
http://ei.lehigh.edu/envirosci/watershed/wq/wqbackground/tdsbg.html
http://extension.oregonstate.edu/gardening/what-are-short-day-and-long-day-plants

Some of the resources aren't as reliable as I would want them to be, but it's the best I could find. Number 4 has a great run-down of TDS for different water sources.


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Insulin and leptin action on Anorexigenic Neurons in Hypothalamus?
Receptors for Insulin are present on liver, adipose tissue and muscles. In addition, there are Insulin Receptors present in arcuate nucleus of hypothalamus, which influences anorexogenic neurons through IRS2 and PI-3K signaling. They also causes the inhibition of Food intake by increasing the expression of POMC, and cleaving its protein to alpha melanocortio stimulating hormone (αMSH). This is however the same response produced by the release of "LEPTIN" that act on anorexogenic neurons, and stop eating behavior - similarly as insulin by producing (αMSH).
My question is: why insulin goes to brain and produce this effect when their was Leptin available to do the same task? What is the significance of Insulin action here?

This question is identical in nature if not in subject to this one. I'm a bit puzzled. Can the body not have several pathways for achieving a "goal"? Why, to you, should this overlap not exist, since clearly it does, and we seem to be surviving in spite (or because) of it?

receptors for insulin are present in many more tissues than just liver, adipose and muscle... the insulin receptor is expressed in numerous tissues throughout the body (as well as the leptin receptor - it's not just expressed in the CNS or adipose tissue)... different tissues may express the same receptor but the tissue effect can be very different (as well as overlapping with other hormones).


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Variant VCF: AD vs DP?
In my VCF file from GATK, I have the following definitions for AD and DP.
AD - Allelic depths for the ref and alt alleles in the order listed
DP - Approximate read depth (reads with MQ=255 or with bad mates are filtered

I don't understand the definitions, can anybody explain in a less technical way?
From what I can read, AD gives the number of reads spanning the reference and variant allele. But what does DP mean? This doesn't look like the total number of reads spanning a variant, so what is this? How does this different to AD?

DP is the total number of read bases spanning a particular position. If you add up the different AD, you should get a number close to DP, the difference being merely in how the reads are filtered in either set of numbers.


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Coordinates of amino acids in a protein sequence
In PDB format, the coordinates of each of the atoms are available. Are the coordinates for the amino acids available separately? As in say a protein sequence consisting of a chain of amino acids MKL... Where would I get the coordinates of M and K and L separately? Is there any method by which the coordinates of the amino acids can be calculated? I don't want the coordinates of the atoms, I want the absolute coordinate of each of the amino acid in a protein sequence as a whole...

It depends what you want them for. You could take an average of all the atomistic co-ordinates of each residue, you could take the co-ordinates of only the carbon in C-R. It's unclear what you're asking for. Are you asking for a sensible method, an available tool, or are you more broadly wondering what constitutes the center of an amino acid conceptually?

Each atom is annotated in the PDB-file in terms of which aminoacid it belongs to - is this what you are interested in? It might be useful if you would clarify your question, as I think that we are trying to guess at the moment what you actually want to know.

@Gerhard now is the question clear?

Are you saying that you want the 3D-structure of an individual amino acid?  I assume so,  as you have accepted the corresponding answer.

How is this question unclear? To me it's pretty clear that she wants the "pivot point" or "origin" of each individual amino acid on the chain (most likely along with its orientation in space), as if the amino-acid was a single molecule as a whole, not subdivided into particular atoms.

If what you are after are the structural co-ordinates of particular  amino acids crystalized individually (i.e. considered as small molecules independently of any role in proteins), then you should find them along with other small molecules in the Cambridge Structural Database.

Another way of approaching this problem is to focus on the middle carbon atom between the H2N- from one side and -COO from the other side that make peptide bonds with adjacent amino-acids. This middle carbon has the rest of the amino-acid molecule attached to it, and it's definitely on the chain, so you can use that atom's center as the "pivot point" for the entire amino-acid; perhaps even calculate its orientation in space relative to the chain by looking at the bonds connecting this atom with its neighbors. That would be my answer if the question wasn't blocked ;q

It may not make a lot of sense to consider one amino acid as an indicator of the position of the entire amino acid as different amino acids vary a lot in size. For non-sensitive applications such as plotting the protein backbone you may use the alpha Carbon. If side chains are important you can use what is known as the last heavy atom (What is the last heavy atom of an amino acid?).


text:
Why is tRNA called an adaptor molecule?
All I know about adaptor is that it is a device that converts attributes of one electrical device or system to those of an otherwise incompatible device or system.
Thank you.

When you make a statement like "why is tRNA called an adaptor molecule" you imply that it is some kind of a definition, which it is not. I can call tRNA using any of its attributes for example "carrier molecule" or "essential molecule" etc. You can check the meaning of "adaptor" in a biological context and see why it fits for tRNA. IMO, this question has a very narrow scope.

RNA and proteins are not electrical systems, but the idea of translating a signal between incompatible systems can be applied here.
Proteins are made through a process called Translation, where instructions stored in a piece of mRNA are used by the Ribosome to make protein.
tRNAs adapt the mRNA nucleotide sequence into a protein's peptide sequence by acting as an intermediary. A tRNA is charged by attaching an amino acid to one end, it then binds the ribosome mRNA complex at the position defined by a codon. A codon is a sequence of 3 nucleotides that codes for an amino acid.

You could think of the tRNA being like a SD Card to USB adaptor to get information from one device to another.

The term "adaptor" does not solely refer to electrical connections. In fact, any system that can establish a connection between two otherwise incompatible systems is called an "adaptor", as you can tell from the following list:

Electrical adaptor (mechanical incompatbibilty between power sockets/plugs)
AC/DC converter/adaptor (electrical incompatibility between electrical currents)
Pipe coupling adaptor (mechanical incompatibility between different pipe types)
Railway coupling adaptor (mechanical incompatibility between different railway couplings)
Computer periphery adaptor (mechanical and/or electrical incompatibility between different periphery links)

It is just natural that the term "adaptor" has been applied to concepts in biochemistry. You can't connect an amino acid to the RNA template directly. The two incompatible systems are thus RNA and the amino acid. The tRNA solves this problem. It is also not the only case where this term is used in biochemistry. Other examples include the signal transducing adaptor proteins or the vesicular transport adaptor proteins such as adaptin, that establishes a connection between the clathrin molecule and the cargo receptors during vesicle formation:

Francis Crick published the The adaptor hypothesis in a privately circulated article (now available online) “On Protein Synthesis” in 1958. He wrote:

“One would expect, therefore, that whatever went on to the template in a specific way did so by forming hydrogen bonds. It is therefore a natural hypothesis that the amino acid is carried to the template by an ‘adaptor’ molecule, and that the adaptor is the part which actually fits on to the RNA. In its simplest form one would require twenty adaptors, one for each amino acid.”

The word ‘adaptor’ has no intrinsic electrical connotation: the Oxford English Dictionary online gives the first definition and examples for this as:

Adapter (also adaptor)
A device for connecting pieces of equipment that cannot be connected directly.
‘the adapter converts the lens focal length to 5.5 mm’
‘a tube fixed to the cleaner by means of an adapter’

Crick clearly used the word in this sense.
At that time the idea was first mooted (reportedly 1955) it was not known that the adaptor molecule was transfer RNA (tRNA), although I have labelled it as such in the illustration I have prepared for the iPhone generation.

[Textual Explanation for the visually impaired
The illustration shows: 1. Chemical incompatibility: a three-pin electrical socket, labelled ‘mRNA triplet codon’, and the flat connection end of a USB cable, labelled ‘cognate amino acid’; 2. The Adaptor: an adaptor plug (labelled tRNA) with the three pins labelled ‘anticodon loop’, and the USB socket labelled ‘acceptor stem’; 3. Decoding: the USB lead connected to the adaptor plug, which has been inserted into the the three-pin socket.]

Not sure why this question resurfaced, but I thought that the accepted answer did not address the analogy, and the comment fails to acknowledge the historical use of this term. I have not included a diagram of tRNA showing the key features as it is assumed the reader has encountered this already. It is available in numerous pages on line, although best read about in a book.


text:
Storage of energy in muscles vs fat depos
How does the body control, where consumed energy (fat, glucose) is stored? And what is its strategy?
More specific:
1) How does the body control storing glucose in muscles and not as (subcutan) fat? (E.g. exercise lets more GLUT4 translocate in muscle cells; because of this, do muscles in total simply have more transporters to suck in glucose than all fat cells, or is there another mechanism? How does the liver refills its storage)
2) Same question as 1) but regarding FFA and not glucose.
3) What is the overall strategy for energy storing? (Can it be stated as simple as "Fill the liver and muscles until they reach full capacity and then store extra energy as fat?")

Funny, that you think that is "homework" :D
I am a sports enthusiast and would like to have a deeper understanding in the "technical" details...

The  regulation of metabolites and signals in general (glucose (Glc) or FFA in this case) and their selective uptake by cells, depends on the number (from few hundreds to many thousands) of receptors expressed and displayed to the surrounding environment, the type of receptors (what they can bind, and do as a result) and their properties.
The regulation of glucose storage and use in muscle cells is determined largely by the dynamic energy state of the cell, which is can be described (to first approx at least) as the cellular equilibrium between ATP<-->ADP<-->AMP. The key here is to be aware that nothing is happening in isolation and the whole metabolism of the cell is one giant equilibrium. You make a change at one place that will result in proportional changes elsewhere to compensate.
If you start exercising, that is using ATP rapidsly, suddenly AMP spikes, the increase in [AMP] results in the upregulation of key enzymes in Glycolytic and TCA pathways, which causes and increase in ATP producting. How much is made? Whenever possible always just enough enough to meet the demand (assuming cell has resources to supply it and manufacture it).
Absolutely, in the same way, the energy state of the cell, and the availability of Glc in and outside the cell (which it knows, because increase in blood Glc causes insulin to be release, muscle cell can bind to insulin, which results in activation of more GLUT4 to be expressed and expressed) directs how Glc is used, stored as glycogen, converted to FFA etc. When cell energy state is low, or exercising, signaling from muscle cells to liver (via lactate in blood/ Cori cycle) tell liver to release stored Glc into the blood.  l
If Glc in high in blood, insulin released from the pancreas, which tells the liver, to start sucking up Glc from the blood, and the way it does that is a lot better than muscle. Why? because of the binding properties of the different isozyme receptors expressed (same function but slightly different physical properties).
FFA metabolism is a same general concept, but different key enzyme players. The increase in metabolite availability causes or is a signal, which results in the appropriate response to balance level out the steady state dynamic equilibrium.
The strategy is basically, if available in excess and can be stored it's stored until the limit of cell is reached, which is determined by the thermodynamic equilibrium of metabolite inside and outside the cell.
Nelson, D.L.,Cox, M.M.(2013) Lehninger Principles of Biochemistry, 6th Ed.
In response to your comment questions,
In general, like I mentioned, the strategy for coordinated fat uptake holds.
Majority of insulin-stimulated glucose uptake occurs in skeletal muscle, with about 10% of insulin-stimulated glucose uptake occurring in adipose tissue. However When it comes to FFA, these are largely delivered, absorbed and stored (as triglycerides) from bloodstream into adipose tissues. This process is definitely actively controlled and regulated, as you do not want fat globules floating around in your bloodstream. When energy state of the organism as whole is low, adipose tissue can sense and release FFA that can be take up by other cells (muscle, liver) and energy in molecules extracted during FFA catabolism pathways. How exactly adipocytes translate changes in glucose uptake or storage into signals that affect global energy balance is not completely understood it seems.
For a good place for much more detail, check out
Leto D., Saltiel A.R (2012) Muscle and adipose tissue in energy homeostasis, Nature reviews of Molecules Cell Biology, 13, 383-396
http://www.nature.com/nrm/journal/v13/n6/box/nrm3351_BX1.html

Thanks for the answer! What is still unclear to me is: are muscle cells preferred over fat cells for storage and how? Again, is this because of different properties of the isozyme receptors?
Does the mentioned storage strategy also hold for fat cells? I.e. is the fat cell "actively trying" to fill its storage (when the mentioned conditions (equilibrium in/out side) are met)?

I updated my response to hopefully address you questions more specifically


text:
What is the difference between "genetic" and "hereditary"?
What is the difference between the adjectives "genetic" and "hereditary"?

I suppose, that "hereditary" means something that comes from your parents (captain obvious yeah), but "genetic" also means mutations, SNP's etc. that can appear occasionally. But sorry, i should tell you that homework questions are not appreciated.

We usually use the word hereditary when we refer to ones lineage and by genetic we refer to the genes, something that is carried by the genes. Hope it helps.

Genetic information/changes are heritable. Not everything that is inherited is genetic (for example the money that you inherit from your parents or even in biological context, the cellular resources and organelles). I think this is just an issue of semantics and is therefore off-topic.

Semantic is essential to any science and, when used in the scientific literature, it is the role of scientist (and not philosophers) to define them properly. Some authors have made an entire career by clarifying semantics used in some field. I think it is a good question and should not get be closed.

The only downside I can see in this question is that it is a homework question (even if it only remotely look like one) and we would then expect the OP to show its effort at answering the question.

Possible duplicate of Why is a heritability coefficient not an index of "how genetic" something is?

From dictionnary.com

Genetic:
  pertaining or according to genetics
Hereditary:
  passing, or capable of passing, naturally from parent to offspring through the genes:

Note: I selected the pieces of definitions that I found most relevant to the current discussion.
Genetic information can be passed on to offspring. As such, I understand the confusion you may have.
When the adjective "hereditary" does not apply
By its definition the adjective "genetic" can be used in multiple situations where the adjective "hereditary" could not. It is specifically obvious when the term "genetic" is used in the context of a whole population. Indeed, not all genetic patterns are inherited especially when referring to population-wide patterns. Also, the adjective "genetic" focuses on genetics and not necessarily on its characteristic of being inherited.
Example
Consider for example the concept of "Genetic signature of selection". A genetic signature of selection is any pattern in the genetics of a population that can be used to infer past selection invent. These patterns include
 - high population divergence around the specific site
 - loss of heterozygosity (and polymorphism) around the selected site
 - modification of the site-frequency spectrum
 - genetic - environment covariance
Further information
Please note that the concept of heritability might have an unexpected definition for some layman. You might want to read Why is a heritability coefficient not an index of “how genetic” something is?.
When the adjective "genetic" does not apply
There are non-genetic information that can be transmitted from parents to offspring (or even between unrelated individuals).
Examples
Niche construction inheritance or epigenetic (esp. in the broad sense) modifications are examples of non-genetic inheritance.
Further information
You will get more information about non-genetic inheritance (and its role in evolution) in this answer.


text:
How to get rid of mosquitoes in a small lake
I own a small lake. Give or take it is about 50 meters wide and 100 meters long (or 160 feet wide, 320 feet long), with a max depth of around 2 meters / 6.5 feet. One third of the lake is surrounded by forest, the rest is grass / small enclaves of tress. The lake absorbes only rainwater from the surrounding residential area. There is a small outlet towards a much larger lake close by. The lake was recently dredge to remove many years of plantlife that had almost turned it into a swamp.
The lake has a large number of mosquitoes. There is also quite many frogs and a few birds that live near the lake.
What can I do to decrease the amount of mosquitoes in the lake?
For example, can I set up certain nesting boxes that will attract birds or bats that will eat a large number of mosquitoes?
Can I release certain fish that thrive on mosquites?
It is in Scandinavia.
EDIT
The shorelines are sharp and most of the vegatation has recently been removed. The lake was recently completely emptied and about 2 meters (or more) of vegatation and soil was removed. The lake has previously been contaminated which was cleaned away. I guess this means that a very large part of the ecosystem has been removed, a few fish did manage to survive, but not very many.

Salitifing the water will terminate larva before developing into mosquitoes.

What does the shoreline look like? Is it "sharp" or does it merge into wetland areas that are flooded during spring? The latter will most often lead to more mosquites, since they are usually found in stagnant waters.

Maybe you can find help at gardening SE? It's not about plants, but I would guess quite some gardeners have faced this problem before.

If the lake was a lot smaller I could suggest tablets of bacillus thuringiensis that you can actually toss into the water and you let the bacteria control the mosquito larvae. For a lake that large though, this would entail quite a bit of control. You maybe want to try and get small top-feeding fish in there, almost like minnows, that will eat the mosquito larva. Other solutions I can think of are tightly regulated or available only to approved agencies/providers in the US or basically otherwise require special handling, or harm other insects/plants.

Bear in mind most solutions refer to owners of small artificial ponds, and local wildlife authorities normally do mosquito control (again speaking from the USA) in larger bodies.

Gah - I knew someone else would add Bti while I was writing my answer! :(

I recommend getting a Mosquito Laser :-)

The Guppy fish is good at eating the larvae. But you'd have to investigate if its introduction into your ecosystem is OK or forbidden.

Try buying a simple 'propane mosquito catcher'. Easy to purchase and easy to setup and get results fast.

There are a number of environmentally destructive methods that would be effective, including draining the lake, covering the surface with a continuous layer of oil, or adding toxins to the water, but I'm assuming you're looking for a method that will have the minimum possible off-target effect.
Different mosquito species breed in different habitats and are thus susceptible to different control strategies, so good photos of some adults might help, but I'm assuming here that you've correctly identified the lake as the breeding site. If there are any other possible breeding sites in the area please add them to your question.
If the assumptions above are correct then, broadly speaking, your best options are habitat modification or biological control. I'm not going to go into chemical control here since as stated above I assume you want low environmental and financial cost; if this is incorrect let me know.

Habitat modification: regularly removing
plant growth within the lake and trimming vegetation overhanging the edges will limit the ability of mosquito larvae to escape predators and may have some effect. However, the recent management you describe has
probably gone some way towards this (did you
notice whether the mosquito problem got any better after the plants
were removed?)
Biological control: introduce predators or parasites into the environment. Plenty of species eat adult mosquitoes but there aren't really any that primarily feed on them (unless they're the only food source available) and many adult mosquitoes will have laid eggs already - the most effective strategy will be to target the immature population. Larvivorous fish have been shown to be effective in many parts of the world, for example fish in the genus Gambusia ('mosquito fish'). I don't know of any that have been shown to be effective and can thrive as far north as Scandinavia, but if you stock the lake with fish (combined with managing vegetation as above) I'd be surprised if you don't see some improvement.
Biological control, part 2: Use Bti (Bacillus thuringiensis var. israelensis). This is a bacterium that produces toxins which are highly specific to dipterans and don't really affect anything else. You can buy the bacterium in various formulations including sprays, tablets etc. I'm mainly familar with its use for controlling container-breeding mosquitoes, but this paper describes its use in large lakes so should give you some idea of dose required, optimal application method and time to reapplication.

Without knowing more about your budget, available time/manpower etc I can't really help you choose between these but I suspect #3 is your best bet.

My suggestions, based on mosquitoe projects I've heard about in Sweden, would be to:

Thin vegetation along the shores
Remove accumulated detritus
Manage grasslands along the shore, by grazing if possible.

The idea here is to remove the stagnant pools where mosquitoes develop, either coming from rainfall or spring flooding/snowmelt. By removing pools and increasing sun exposture you will probably decrease habitats and larval survival. Continously managing grasslands usually also helps, since it removes excess plant materials and kills mosquitoe larvae by trampling (if grazing is used). To introduce grazing by e.g. sheep (if possible) will probably also have positive conservation effects. Stocking of fish might help, but I suspect that the mosquitoes mainly comes from adjacent waters and edge pools and not the main water body. I doubt that birds and bats can control the mosquito population to any larger extent, but don't have anything specific to back-up this statement.
Also note that actions depend on the types of mosquitoes found in the area. There are both "forest mosquitoes" and "flood mosquitoes" in Sweden, but most perceived problems come from the latter kind, and since you are referring to mosquitoes from the lake/pond I suspect you are dealing with the latter kind. You should try to determine the most common species found there though. Treatment with Vectobac G (Bacillus thuringiensis israelensis) might be an option, but I don't know what kind of retrictions there are on using it privately.
You might be interested in this report from a Swedish county board, since it mentions ways to control mosquitos (in Swedish):
Lundqvist et al. 2013. Förslag till hur myggproblemet vid Nedre Dalälven kan hanteras på lång sikt. Länsstyrelsen Gävleborg ("Suggestions for how to handle the mosquito problem at Lower Dalälven over the long-term" freely translated).

Don't salinate the lake. It'll be a nightmare to maintain.
The 'standard' biocontrol measure is to release 'mosquitofish', but outside their native range they're almost as good at killing native mosquito-eating fish as they are at eating mosquitoes.
Find some native fish(perhaps in the bigger lake?) and stock your pond with them. Small fish are probably better for this purpose. If your pond freezes all the way through in the winter(it almost certainly does not, but it depends where you are in Scandinavia) you'll have to find something else. If it just freezes over lots of fish can handle being under an icecap for a few months.
If you have a local fish and game authority they will probably have advice about stocking your pond, or at least handled that question before.

And please: Do not release any fish and mess up the eco system of the lake.

There are some native fish in Scandinavia, such as the crucian carp (ruda in Swedish), that can survive even in ponds that freeze (nearly) to the bottom in winter. They'll eat pretty much everything, including insect larvae, so they should be at least some help in controlling mosquitoes. Do note that crucian carp tend to outcompete other fish in small ponds, and can be hard to eradicate once present. If your pond already has an existing fish population, think twice before introducing them.

According to http://baliadvertiser.biz/mosquitoes/, more specifically the 3rd paragraph:

The next easiest solution is to add a submersible pump, a waterfall or fountain. Flowing water is pleasant and will also enhance the water quality. If it is possible keep the water flowing at all times. Mosquito larvae can only survive in stagnant water. Newly hatched mosquitoes must rest on the surface for a few minutes to let their wings dry, because of this they will not lay eggs in water that is constantly moving.

Mosquitos don't breed in moving water, because their larvae have to rest on stagnant water for a few minutes so their wings can dry. Flowing water will also improve the water quality by adding extra oxygen.
The trick is that you likely want a way to get rid of the mosquitoes that doesn't require maintenance, which rules out most mechanized methods that you could use to make the water move like wave generators, pumps or bubble generators. In theory, you can just let it run during the breeding season so they can't lay their eggs. The best solution will probably depend on how much effort you're willing to put into it. Maybe you can promote the pond as a nice place to play with remote controlled boats during the spring and early summer?


text:
Multiple start and stop codons in mRNA and pre-mRNA
I have a main question that will lead to further questions depending upon the answer.
In the process of transcription, will there be multiple start and stop codons in one sequence of pre-mRNA?  If there is, do they remain in the mRNA after splicing?  If they do, does that mean one mRNA has the coding sequence for the synthesis of multiple different proteins?
One last question: assuming a single mRNA has the sequence for synthesis of a single protein, is the stop codon always the final sequence before the poly-A tail?
Thanks in advance for your help and sorry for the mini rabbit hole.

I've changed the title to reflect what seems to me the particular essence of the question: the concern with multiple start and stop codons. For this reason it doesn't really appear to be a duplicate.

In reviewing some of my older answers in order to update them, I find this has been marked as a duplicate of a question that, at least in its current form it is certainly not a duplicate of. This question asks "does that mean one mRNA has the coding sequence for the synthesis of multiple different proteins?" The one it is a duplicate of only asks about stop codons. Is there a mechanism for rescinding this sort of incorrect decision?

Whether or not there are multiple start and stop codons depends on what you mean by "start codon" and "stop codon".
The start codon has the sequence "AUG", and the stop codon has the sequence "UAG", "UAA", or "UGA". Both the pre-mRNA and the mature-mRNA can, and usually do, contain multiple instances of all of these sequences. However, only one "AUG" instance serves as the translational start site, and only one instance of the stop codon sequence serves as the translational stop site.
The translational start site is usually the first (5' most) AUG. However, for reasons that are still not entirely understood, in about 5% of genes the first AUG is skipped, and translation starts at one of the other AUG sequences.
The translational stop site is always the first stop codon to occur in-frame with the translational start site in the mature mRNA.
The stop codon is usually not (I'm tempted to say never) the final sequence before the poly-A-tail. The coding sequence (the RNA region that codes for the protein) occurs in the middle. There is a 5' untranslated region (UTR) before the protein coding region, and a 3' UTR after the protein coding region. The UTR sequences vary among genes and can have different functions depending on the sequence.

As this question is a first post it is probably just a basic question about protein synthesis, which @Sean Johnson has answered adequately. However I’m not quite sure. And as I used to work in protein synthesis (but am a rather out of touch now) I decided to look at the recent literature a little to address some more esoteric or obscure questions it raised in my mind. I’ve set out the results below, and divided my answer into mature mRNA (which Sean covered primarily) but have also considered pre-mRNA. If the answer is not very useful to the questioner it may still be of interest to others.
Start and Stop Codons in Mature mRNA
The general picture of initiation and termination of protein biosynthesis in eukaryotes (bacteria and archea are different) has been described by Sean and can be found in standard texts1. In most cases the first AUG from the 5'-end of the mRNA is the one recognized as the ‘start’ signal for protein synthesis by the ribosomal-subunit initiation complex that scans along from the cap, according to the Kozak model2; and any one of the three termination codons encountered in the reading frame is recognized as ‘stop’ and (almost) invariably lead to termination of the polypeptide chain.
START EXCEPTION 1
As mentioned, in some 5% of mRNAs certain aspects of the environment of the first AUG from the 5'-end results in it being ignored by the complex, and the insertion of methionine and start protein synthesis occurs at the second (or perhaps even a subsequent) AUG.2
START EXCEPTION 2
Certain eukaryotic viruses were found to initiate the translation of the mRNAs internally, by a mechanism distinct from the 5'-scanning method. This involves an ‘internal ribosomal entry site’ — IRES. It subsequently transpired that a small subset of host mRNAs posses an IRES and can initiate translation internally. These include some growth factors, transcription factors and translation factors.3 Such (rare) mRNAs can therefore have several AUGs in their 5'-untranslated region.
Although it is possible to envisage an mRNA with several IRESs, and thus encoding several different proteins (analogous to a bacterial polycistronic mRNA), this does not appear to happen. It is striking, for example, that poliovirus RNA has just a single IRES for the start of the synthesis of single a large polyprotein, from which it generates multiple proteins by proteolysis. It would seem that the main purpose of this alternative initiation is to allow protein synthesis to proceed in the absence of a 5'-cap.
STOP EXCEPTION 1
There are some AGU codons that are recognized by a specific tRNA that inserts selenocysteine into the polypeptide chain. Some aspect of the environment of these codons causes them to be ignored by the protein termination system, and the ribosome continues translating, eventually terminating at a subsequent stop codon4.
STOP EXCEPTION 2
It has long been known that certain bacterial and eukaryotic viral mRNAs can increase their genetic repertoire by what is known as ‘read-through’ of ‘leaky’ stop codons. This is a ‘percentage’ effect, rather than all or nothing, and results in a mixture of ‘normal-length’ and extended products. It is now clear that the same phenomenon can occur in some eukaryotic mRNAs: quite frequently in Drosophila5, but also in mammals6.
STOP CODONS & THE 3'-UTR
I’m not clear what the questioner means by “is the stop codon always the final sequence before the poly-A tail?”. If the question is whether there can be additional stop codons in the 3'-UTR between the functional termination codon and the AATAAA polyadenylation signal (purple in Sean’s diagram) the answer is yes. Looking at the sequences of some muscle protein cDNAs done years ago, I found several stop codons in this region in each that I looked at. Of course they are without any function as the ribosome has already departed, but there is no reason for them not to be there on a random basis (and at apparently random positions).
Start and Stop Codons in pre-mRNA
By pre-mRNA I assume is meant the initial RNA transcript before splicing. There is no reason why an intron that is spliced out so that it does not appear in the final mRNA should not contain start or stop codons, which if not removed would have altered the reading frame. Many do.
A more interesting situation is where there is alternative splicing to produce different mRNA transcripts that encode different proteins. Pertinent to the question is the situation with start codons where the proteins differ in their N-termini, and stop codons where the proteins differ in their C-termini. The latter are quite common, but the former also occur, particularly were there are alternative forms of a protein, with and without a signal peptide7. In these cases the start or stop codons will be present in both of two exons, one of which is spliced out in each case. Examples of this from a couple of Drosophila genes are illustrated:

In both cases the coding regions are in orange, and the untranslated regions in grey. The thin lines represent the position of introns that have been spliced out. The arrowhead represents the direction of transcription and is at the C-terminal side of the protein. (i) Different N-termini for alternative products of gene vha14-2; (ii) Different C-termini for alternative products of gene vhaSFD.9