text:
Magnetic-activated cell sorting vs. FACS
When sorting cell populations it is possible to use either magnetic-activated cell sorting or fluorescence-activated cell-sorting (FACS). I am wondering when you would choose either technique and what the pro's and con's of each technique are.
As FACS sorts cells one by one, I can imagine magnetic-activated cell sorting is a faster process. So I guess if time is an important factor this could be used to base your decision on. Also by sorting cells one at a time I assume FACS is a lot more precise, and will lead to less 'contamination'.
So, are there other factors at play here that can influence the choice of magnetic-activated cell sorting over FACS, and what are the pro's and con's of these techniques respectively?

Well for one, MACS only works with surface exposed antigens.

@canadianer assuming one would want to use live sorted cells in their subsequent experiment(s), FACS has the same constriction.

@MattDMo Presumably a genetically expressed fluorophore should allow sorting without the need for fixation/permeabilization.

@canadianer true, I hadn't thought of that. I'm an antibody guy, so I usually think in that direction :)

Exactly as canadianer said, GFP sorting is very common.
MACS is much faster, which can also help with viability (especially if the cells are very sensitive) especially when it comes to working with large cell numbers. CliniMACS, for example, is routinely used to isolate CD34+ hematopoietic stem and progenitor cells precisely for those factors (time and viability)

Magnetic-activated cell sorting (PDF download), or MACS, is a procedure developed by Miltenyi Biotec to separate cells from complex mixtures using antibody-coated magnetic nanoparticles. The antibodies are specific for certain cell surface markers, either expressed on your population of interest (positive selection), or expressed on undesired cell types (negative selection). After adding the antibody-coated beads to the cell mixture and incubating, the suspension is added to a special single-use separation column affixed to a magnet, to which the beads stick, while unlabeled cells flow through. If performing a negative selection, the flow-through is your population of interest and the bound beads and cells are discarded. If your cells of interest are bound to the beads (positive selection), the column is washed several times to make sure unbound or weakly-bound cells are washed through, then the column is removed from the magnet and the cell-bead complexes are eluted.
In fluorescence-activated cell sorting or FACS, the initial complex cell mixture is first labeled with one or more cell surface marker-specific antibodies that have been conjugated to fluorescent dyes. Cells can also be analyzed that express one or more recombinant fluorescent proteins in conjunction with a gene of interest, allowing for selection of cells without using antibodies. After incubation and wash steps, red blood cells are lysed, if analyzing whole blood. The reason for RBC lysis is shown below:

Without lysis, the RBCs overwhelm the cytometer, as they make up around 95% of the cells in human whole blood. White blood cells (leukocytes), on the other hand, only make up 0.1-0.2% of cells, and lymphocytes between about 15 to 50% of leukocytes.
The cell mixture is then analyzed on a cell sorter such as a BD FACSAria.

From: https://commons.wikimedia.org/wiki/File:Fluorescence_Assisted_Cell_Sorting_%28FACS%29_B.jpg
The cells pass in single file past one or more laser beams, which excite the dyes and cause them to fluoresce at a certain wavelength. The user can then use gating to select the combination and intensity of colors they are interested in, and when a cell meets the criteria, it is given an electrical charge, and electro magnets direct it into a collection container.

So what are the pros and cons of each technology? MACS separation generally is quicker than FACS staining, and a greater number of cells can be processed at one time (sometimes orders of magnitude more, depending on instrument and protocol). If you are, for example, looking to purify large numbers of CD4+ T cells from whole blood, MACS may be the better choice of the two (although I prefer the RosetteSep system for that particular requirement). MACS doesn't require a rather expensive dedicated instrument, although automatic platforms are available if needed. On the downside, most MACS-qualified beads are mostly only available from Miltenyi, so if they do not have beads with your particular marker of interest available, you will need to do the conjugation yourself, at the expense of time and possibly precious antibody while you optimize conditions. Fluorescent-conjugated antibodies are extremely common, and available from practically innumerable companies, so unless you are working with a self-generated antibody it's much more likely that you'll be able to find one for FACS quite easily. There are MACS beads that contain antibodies directed at certain fluorophores, so you can use flow antibodies for MACS, although optimization is likely still necessary. Finally, MACS separation is only an option for cells that have your marker of interest expressed on the cell surface.
One of the major advantages of FACS is multicolor staining (depending on the instrument you're using). This makes it much more straightforward to purify potentially rare populations that are only differentiated by their combined expression of a number of surface markers, necessitating multiple gating steps. If this were to be accomplished by MACS, you would need to go through multiple rounds of purification, something that could take longer than FACS, and not necessarily be feasible, as a certain number of cells are required for each MACS run. With FACS, these rare populations (which may only be tens or hundreds of cells per million) can be collected just as easily as more common ones. Also, as mentioned above, there are more antibodies available for flow/FACS than for direct MACS. Additionally, FACS allows for sorting of cells expressing GFP and relatives, letting you collect populations based on internal markers.

Thank you, this is a great answer! I have one question about something you wrote in the second paragraph. Why do you have to lyse the RBC when analyzing whole blood?

@Wolgast see my edit above for a detailed explanation. Basically, RBCs make up about 95% of all cells in blood, while white blood cells are only 0.1-0.2%. They just overwhelm the cytometer.

That makes sense! It seems like something I should have thought of myself! Thanks for the extra explanation!


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

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

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

and there Cas9 is bacterial protein

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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What is the molecular mechanism of odorant transduction signaling pathway?
I have read a few papers on the topic of odorant signaling pathway. The following papers are listed as examples. However, I found that there is not a clear pathway representation of the odorant signaling pathway, through which the involved genes and regulations should be known. Is there any paper I have missed?

Menzel, R. and P. Benjamin (2013). Invertebrate learning and memory,
Academic Press.
Leal WS: Odorant reception in insects: roles of
receptors, binding proteins, and degrading enzymes. Annu Rev Entomol
2013, 58:373-391.
Kaupp, U. B. (2010). "Olfactory signalling in
vertebrates and insects: differences and commonalities." Nat Rev
Neurosci 11(3): 188-200.
Vosshall, L. B. and R. F. Stocker (2007).
"Molecular architecture of smell and taste in Drosophila." Annu Rev
Neurosci 30: 505-533.

Information available on this is huge. I will pin point main points. Generally this signalling will involve four components viz. receptors, transduction machinery, perireceptor processes and downstream processing of chemosensory information.
Receptors
First step is to receive signal (here odorant or chemicals). Following figure shows comparison between primary chemoreceptor neurons in vertebrates, insects, and nematodes.

These neurons constantly undergoes birth-maturation-death and process is well studied in many model systems.
Signal transduction
After stimulus is received, it needs to be transfer inside cell for further processing. In this case, generally transduction happens via GPCR signalling. These neurons use two widely used signalling cascades. Following figure shows main components in this signalling ( (a):vertebrate olfactory receptor neurons (b): lobster olfactory receptor neurons),

Perireceptor Processes
These process are important for receptor activation and transduction. They can be any type like mechanical or biochemical.
Downstream processing
There is huge information available at the level of pathway. Following figure represents main components in two model systems.

For finding genes, you have to search in specific part of this process (like this is good example of receptor genes in human).
I would strongly recommend reading chapter 4 of "The Senses - Comprehensive Reference". All above information is taken from this book. Another good open source reference is The Neurobiology of Olfaction, this reference has all things you need for free.

thank you for your comprehensive answer. I will peruse the references.

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Why does a cockroach not die even after decapitation?
Why does a cockroach not die after its head is cut off?

Could you give a citation referring to this fact?

Based on an article here, unlike humans, cockroaches have an open circulatory system. They don't have a huge network of blood vessels like that of humans, or tiny capillaries that you need a lot of pressure to flow blood through. Hence after you cut their heads off, very often their necks would seal off just by clotting.
According to the article cockroaches breathe through spiracles, or little holes in each body segment. Plus, the roach brain does not control this breathing and blood does not carry oxygen throughout the body. Rather, the spiracles pipe air directly to tissues through a set of tubes called tracheae. In addition cockroaches are poikilotherms, or cold-blooded, meaning they need much less food than humans do. Hence cockroaches can survive decapitation.

Although the answers to date are all factual and sufficient to answer the question why cockroaches would live without its head, some answers don't seem to be necessary as explanations.
Summarizing the given answers so far.

Roaches' simple  circulation would still function without its head.
Roaches' decentralized respiratory system can still function without its head.
Roaches are cold-blooded and demand less energy.

However, chickens can live without its head as long as the injury does not significantly damage its brain stem, which controls the animal's vital reflexes such as respirations.

Chickens do have complex network of blood vessels and capillaries.
Chickens don't breathe via spiracles and do have centralized respiration system like us.
Chickens are warm-blooded.

Thus, an animal (such as a cockroach) can live headless if its remaining organs can still control its "vital functions".

"Thus, an animal (such as cockroaches) can live headless if the remaining organs can still control its "vital functions".- until & unless it's internal food resources are depleted...

@souvik bhattacharya However, Mike the Headless Chicken from SYK's link finally died by suffocation. It could eat if fed.

Cockroaches are insects which means their brain is distributed.

The predominant characteristics of the cockroach central nervous
  system (CNS) are its segmented nature and decentralization of control
  processes (Ganihar et al., 1994; Pipa & Delcomyn, 1981)

.
 There is a pair of ganglion on each segment- head, thorax and abdomen. The ganglion on head is controlling the antennae inputs,proboscis,mandibles,eyes etc. When we cut off its head the ability to control all the above described organs fails(although, that doesn't matter because these organs are also decapitated) & it can't eat.. but the ganglion on the thorax is actually responsible for the breathing and digestion of food(with the help of ganglion on the abdomen). So if there is any food in the gut it will be normally digested and cockroach can live days consuming this energy. Also when head is gone there is no need to provide resources for the organs in head. So it can live more days by saving these resources.Plus, it can copulate if it is placed properly and this copulation is controlled by the ganglion on the abdomen.

Hello and welcome to SE Biology! It would be great if you added some references to support your response!

It's part of writing a good answer @souvikbhattacharya, Bez is perfectly right to request this - consult the help pages

@GriffinEvo , I get your point...but what if I already know that the answer provided is correct???

ok..I get it..it's for greater good...

@griffinEvo: :)


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Water soluble molecules
I believe I may have misunderstood water solubility this entire time.
I assumed that water soluble meant that it would literally dissolve in water. It would break down into atoms. A sugar molecule would break its bonds and become something else...
However I must be mistaken because I'm reading about why DNA is spiral shaped and it says that it is to keep the hydrophobic bases inside the spiral to protect them from the water, but keeping the hydrophilic phosphate and sugar molecules on the outside.
I would assume that because these molecules are hydrophilic they would disassociate from each other but this has to be incorrect. What am I misunderstanding about water solubility and what would happen if the bases were exposed to water?

Water solubility only means that a substance is soluble in water. Usually it will not decompose (break into single atoms) in this step, as dissolving is a purely physical process.

So why is phosphate a "water soluble" molecule but yet it stays as "phosphate" in water? It doesn't dissolve in water it stays phosphate?

@BjarniJóhannsson see my answer below for an accessible explanation. If you are having trouble with the English words, you may want to look them up in your native language. You are confusing dissolve with hydrolyze.

You might be thinking of simple ionic compounds like sodium chloride, which when dissolved do separate into their constituent ions (e.g. sodium cation and chloride anion).

This question would be more on-topic at Chemistry.SE, but I'll give you a quick answer. A substance is soluble in water when its solid form (such as a sugar cube) completely dissolves in water to become a sugar solution. The sugar molecules themselves are unaffected, essentially - instead of all being bound to one another in a crystal, they are now floating around in the water, hydrogen-bonded to the water molecules. The proof is in the taste - solid sugar and sugar solutions taste pretty much the same. If the sugar had been broken down into component hydrogen, oxygen, and carbon, it would taste much different!
On the other hand, hydrolysis is what happens when water actually participates in a chemical reaction to break one or more molecular bonds within a certain molecule, breaking it down to two new molecules (or one molecule and an atom, or whatever). While sugar can be hydrolyzed, it requires either very high heat, or the presence of a catalyst such as an enzyme.

And it's more: If you remove the water, the substance will be the same as before. Dissolving is a purely physical process which will not change the molecule. This is only done during chemical reactions.

Except for ionic compounds which do dissociate when dissolved

It's about sugar and DNA. It is fine here at Bio.SE. Well answered too. +1

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text:
First discovery of long-term depression?
LTP was first described by Tim Bliss and Terje Lømo in their paper Long-lasting potentiation of synaptic transmission in the dentate area of the anaesthetized rabbit following stimulation of the perforant path.
When was LTD first described? By whom?

The process of long-term depression (LTD) was first discovered in the cerebellum by Ito et al. in 1982:
Ito M, Kano M. Long-lasting depression of parallel fiber-Purkinje cell transmission induced by conjunctive stimulation of parallel fibers and climbing fibers in the cerebellar cortex. Neurosci Lett. 1982;33(3):253-8
Ito M, Sakurai M and Tongroach P. Climbing fibre induced depression of both mossy fibre responsiveness and glutamate sensitivity of cerebellar Purkinje cells. Journal of Physiology 1982; 324: 113–134.
Check this source.


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How do CpG islands remain unmethylated?
In most of the genome CpG sites are pretty much always methylated, but CpG islands are instead often unmethylated. This has been linked to the fact that they often are associated to transcripted genes.
What are the current theories on the mechanisms involved in this preferential demethylation?

Methylation is increasingly seen as a consequence of gene activity rather than a regulatory mechanism. There are cases where methylation is controlled because of gene regulatory control, especially at the famous H19/Igf2 locus[1]. Here is a generally good recent review[2], note they mention that DNA methylation does not cause transcriptional silencing, and likely methylated promoters are probably more active than unmethylated, they just create silencing RNAs when methylated (resulting in an apparent silencing).  This may help explain some of the story[3], but note how old that paper is, yet generally I'd say few people know of its existance.
The exception seems to be transposable elements[4], but their control is probably also controlled by silencing RNAs.
References:

 Zampieri M, Guastafierro T, Calabrese R, Ciccarone F, Bacalini MG, Reale A, Perilli M, Passananti C, Caiafa P. 2012. ADP-ribose polymers localized on Ctcf-Parp1-Dnmt1 complex prevent methylation of Ctcf target sites. The Biochemical journal 441: 645–52.
 Deaton AM, Bird A. 2011. CpG islands and the regulation of transcription. Genes & development 25: 1010–22.
 Rountree MR, Selker EU. 1997. DNA methylation inhibits elongation but not initiation of transcription in Neurospora crassa. Genes & Development 11: 2383–2395.
 Bourc’his D, Bestor TH. 2004. Meiotic catastrophe and retrotransposon reactivation in male germ cells lacking Dnmt3L. Nature 431: 96–9.

This came out mere hours ago ( http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002422 ). Imprinting of the maternal SNRPN allele (which is unmethylated) requires transcription, again underscoring that methylation is a consequence of transcriptional silencing, rather than causal in gene silencing.


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Is there a hormone combination that makes humans grumpy?
Imagine a typical situation that is likely to give rise to a bad temper within an individual: a person is awoken very early in the morning by a sound of a lawn being mowed next door.
Unlike expected awakening by an alarm clock, such unexpected awakening by a lawn mower is likely to leave the person in a bad temper, feeling grumpy or sulky.
I'm interested if there's a specific hormone or process that makes a person experience the feeling of grumpiness? Is it related to adrenaline and fight or flight instinct?
In other words, can experience of grumpiness be induced under laboratory conditions by using some combination of hormones/drugs?

I don't think morning grumpiness is related to adrenaline or fight/flight. It's more a matter of being irritated by the discomfort of abrupt awakening (at an inappropriate phase of sleep). "Grumpiness" per se is also poorly defined; for anger I am sure adrenaline and (if male) testosterone is often high, but I doubt just these hormones by themselves can induce anger (although they could make someone more prone to fits of anger).

I've seen anecdotal evidence suggesting that "low dopamine" contributes to irritability

This is a hard question to respond to.
Many things might make someone grumpy.  There are also individual temperaments, making grumpy hard to quantify - a Grumpy to one person might barely be a blip on another individual's scale.  Hormones like cortisol reflect stress, and can make people in general irritable, but I doubt any one combination of hormones would always cause grumpiness.
But I thought I'd venture an answer since I did see this paper today:  "Low glucose relates to greater aggression in married couples" doi: 10.1073/pnas.1400619111
Being hungry will do this for lots of people, so maybe a bit of an answer for you. There are lots of different kinds of signals that mediate hunger though, so still a tough call.
Update: here's an additional article that specifically talks about parts of the brain involved in aggression and grumpiness as response to a drop in glucose.


text:
Do neurons secrete multiple neurotransmitters, or just one type?
I know that neurons communicate between each other by filling the junction between dendrites with neurotransmitters.
What interests me is if a single neuron only works with one type of neurotransmitter(ex: serotonin), or if it can secrete/receive all of them (serotonin, dopamine, etc).
If a neuron can secrete all, then can all dendrites secrete and respond to all neurotransmitters, or is it one per dendrite (one branch only works with dopamine, another one with serotonin, etc)?

My knowledge isn't detailed enough for this specifically but as far as I know: each postsynaptic membrane has receptors to one specific neurotransmitter and each terminal only secretes one specific transmitter - which doesn't exclude that other terminals of the same neuron might secrete different transmitters. Once the postsynaptic receptor generates a membrane change from the interaction, it's all just potentials, so a neuron is not limited in number to how many different transmitters it can receive.

I've googled this for a biology class I taught, and the quick answer is that both possibilities happen in different instances.  Some specialized neurons secrete more than one type, even though the ruling concept used to be one neurotransmitter for one neuron.

If you could reference the works in which you read this, it would make for a better answer.

Check this link out, It's a little simplistic but hopefully, will give the info you want so you can search elsewhere.


text:
Is there such thing as "meters per calorie" for living organisms?
I'm interested in learning if there's some way of quantifying the organism's metabolic efficiency associated with movement.
It seems to me that some organisms would be more efficient than others at using energy. For mechanical systems, there are clear metrics of efficiency, for example "miles per gallon" or "liters per 100km". Is there a similar metric that converts calories into how far an organism can go?
Thank you for your input!

This isn't what I'd call metabolic efficiency. Metabolic efficiency would be calories per gram of some standard nutrient(s). When you're converting calories into movement, it's more a matter of mechanical efficiency.

Halsey & White (2012) Comparative energetics of mammalian locomotion: Humans are not different. Journal of Human Evolution 63:718–722

This paper presents a comparison of the metabolic cost of walking and running in humans, Australopithecus and other mammals.  They use a parameter NCOT (net cost of transport), whose units are ml O2 consumed m-1. The inverse of this parameter would be related to your metres per calorie.
The authors quote an NCOT of 12.77 ml O2 m-1 for a walking human. Using a value of 4 kcal g-1 for glucose, I calculate that this NCOT is equivalent to 14.6 m kcal-1.
Here I found an energy consumption value of 5.8 kcal min-1 (for a 73 kg man) walking at 6.4 km h-1, which translates to 18.5 m kcal-1.
Incidentally, according to the authors of the paper:

The predicted net cost of transport (NCOT, ml O2 m−1) of mammals is related to mass (M, kg) according to 0.54M0.70.


text:
What is the relationship between Homocysteine and Norepinephrine metabolic cycles?
I've been researching neuromodulators and have taken a look at the Norepinephrine/Noradrenaline  system.
The diagram of biosynthesis of Norepinephrine is presented in the wikipedia article:
Catecholamines_biosynthesis
The diagram appears to state that Dopamine gets converted to Norepinephrine , which gets converted to Epinephrine, and as a side effect, Homocysteine cycle gets advanced too (or is it involved?).
This article describes the homocysteine biosynthesis
I would like to understand what this means when two biosynthesis cycles are related like that. If I envision two cycles as connected gears, then turning one would turn the other, and if one is malfunctioning, so will the other. Is this a correct analogy?
What are the implications of the Homocysteine and Norepinephrine cycles touching each other? As far as I understand, Epinephrine(Adrenaline) is a stress related hormone, does this mean that stress also results in elevating the levels of Homocysteine ?
Thank you for your clarification!

Norepinephrine is converted to epinephrine by phenylethanolamine N-methyltransferase (PNMT). In mammals PNMT is just one member of a large family of methyltransferases which use S-adenosylmethionine (AdoMet) as a cofactor to provide a methyl group. These methyltransferases are involved in a very diverse set of pathways including the synthesis of nucleic acids and of certain phospholipids, as well as the methylation of DNA and histones.
As you point out, these reactions generate homocysteine via S-adenosylhomocysteine. However, because AdoMet is such a critically important cofactor it is thought that cellular levels are tightly regulated. As part of this regulation, homocysteine is re-methylated to methionine via two different routes requiring either methionine synthase or betaine-homocysteine methyltransferase. Methionine synthase obtains the required methyl group from 5-methyltetrahydrofolate in a vitamin B12 (actually methylcobalamin)-dependent reaction. This latter reaction links the AdoMet-based methyl transfer system to the other part of the cellular one-carbon economy, the folate pool. This is why vitamin B12 deficiency leads to hyperhomocysteinemia.

This Figure is reproduced from Luka et al. (2009) Glycine N-methyltransferase and regulation of S-adenosylmethionine levels. J. Biol. Chem. 284:22507–22511. I show it here just to illustrate the point that there are, in fact, many gears interacting in this system. The minireview is interesting and I recommend it to you.
In conclusion, my answer to your question is that it is unlikely that stress leads to elevated levels of homocysteine as long as all of the relevant regulatory machinery is functioning correctly. If there is a problem with homocysteine recycling then yes, homocysteine levels would rise, but given that there so many AdoMet-dependent methylation reactions it is unclear how big a contribution PNMT would make to the overall homocysteine load.


text:
What modern insects are not (flying OR descended from flying ancestors)?
What modern insects are not flying or descended from flying ancestors?
(I read somewhere that 99% are, so of course I instantly became curious which aren't. xD )
EDIT:  Sorry, I should have been clearer: I meant examples of modern insects with no flying ancestors.

To make sure I understand your question: You want examples of non-flying insects which ancestor was flying. Or in other words your want examples of insect lineages that lost the ability to fly?

Sorry, insects with no flying ancestors. Edited.

Do you ask for examples of non-flying insects which ancestor were flying? In other words do you ask for examples of insect lineages that lost the ability to fly?
The ability to fly arose with the clade called the Pterygota. All species from this monophyletic taxon come from ancestors that had once the ability to fly.
For nonflying species with no flying ancestors, you can navigate back in Tree of Life and look at the other two clades in Insecta: Archaeognatha and Thysanura.
For nonflying species with flying ancestors, you can look within Pterygota on Tree of Life, and you can find many non-flying species in the following clades for example:

Hemiptera (bugs, aphids)
Coleoptera
Siphonaptera
Many Vespoidae (clade contained in the hymenoptera)

EDIT:

Did Flying only evolved once in insects?

Yes it did evolve once only. At the start the ancestor had 3 pairs of wings that are though to have evolved from gills or from the sclerites (competitive hypotheses) of the prothorax. the most anterior pair of wing was lost. The diptera lost a second pair of wings (the posterior ones) that degenerate into halteres (particularly easy to see in crane flies). The insects that perform the most "primitive" fly are the Odonata (dragonflies and damselflies). These insects can move their wings independently which is not the case of other flying insects because the way their wings are attached to the rest of the body has changed.

So flying only evolved once in insects, eh? (That is, all flying insects have a single common ancestor, which was the first flying insect ever.) Interesting!

Wow, this tolweb.org site is awesome, thanks! I see it's only the orders Archaeognatha and Thysanura that have no flying ancestors.

3-winged insects? Cool! Do we have many fossils?

And if we're not sure whether the wings came from "sclerites" or gills, does that mean we don't have any fossils of the presumably gliding ancestor of this first flying insect?

Yes, there are some fossils (especially those coming from a famous fossil site in great britain) and there still exist a 3-winged species that live on trees that use their wings to head their fall toward the trunk when they let themselves fall to avoid predators. This species might hold the ancestral trait of first winged insect species but it is not sure. Unfortunately, I don't remember where I found these information. There are several points that are still unclear in the evolution of flight in insects (such that which organs developped into wings).

Do we know if this gliding "pre-first-flying-insect" ancestor was terrestrial, or if it developed flying even before it left the water...?

Fossil records does not allow to know which organ developped into wings. If I am not mistaken, there was one study who should that given the position of the wings compare to I don't remember which structure, it is likely that wings developped from gills. And one study who showed that the molecular factor causing wing devlpoment is a factor also causing sclretie development suggesting that wings come from sclerite. But I am not sure of what I am stating

Well, that's a good question too! Because the living habitat is only poorly correlated with the phylogeny, it is sometimes hard to really know what was the ancestral stat of a given clade. If you take the example of the most "primitive" flying insect, the Odonata, you'll realize that eggs and larvea live in water. But more "primitive", non-flying insects mostly lived on earth. And the ancestor of all Hexapoda lived on earth. But more recent flying species do not have larvea that live in water.

Now I realize looking on tolweb.org that the phylogeny is actually quite unclear and the info I had in mind might be wrong. I am not an insect specialist and I don't provide any reference. So please consider I might missing some important point or even saying some mistakes.

This all very interesting (really) but I don't understand it getting accepted since it doesn't appear to be an answer to the question from OP - modern insects with no flight in their ancestry.

@AlanBoyd Oh, right, now that you mention it, I answered my own question in the second comment ("it's only the orders Archaeognatha and Thysanura that have no flying ancestor"), but I did that in a single step from the link Remi.b gave me, and my question was stupidly ambiguously phrased at the time, so... yeah.

Silverfish, also known as Lepisma (order Zygentoma), does not fly and does not descend from flying ancestors.
It's close to Archeognatha, which don't fly either nor descend from flying ancestor.


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Can a drug induce specific mechanism of resistance in tumors?
For example, can a drug that targets a given protein induce overexpression of that protein or increase the copy number of the gene coding that protein?
I strongly suspect that antineoplastic resistance happens due to natural selection alone but I was wondering if there are examples that suggest otherwise.

Yes.
There is a lot of literature on cancer evolution and now several countries have genome sequencing programs for "pharmacogenomics", for example Genomics England, specifically to see which cancers are likely to evolve resistance to which drugs.
One small detail is that mutation exists before treatment in a subset of the cancer population —as happens with evolution normally. That mutation is neutral for the fitness of the cancer before, but is advantageous during treatment.

Thanks, the last phrase is especially useful

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/


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Which cultivated plants produce most nectar for pollinators?
Pollinators are important for many crop types (e.g. wikipedia list), but I am wondering how important the crops are to feed the pollinator. Obviously, some of the crop plants provide much more food than others, and the plants that depend on pollinators for their reproduction will be likely to attract the pollinators with pollen, nectar, or both. But I am not sure that I can use the dependance on pollinator as an accurate estmator of the quantity of nectar that is actually available for pollinator.
I can think of the rapeseed as being very rich in nectar, but are there other "nectar rich" flowers ? For instance, what about sunflower, potatoes, peas ,sugar beet, mustard, flax, lucern, clover, maize, wheat...
To sum up, I would like to have a list of the most common European cultivated plants that produce a reasonalble amount of nectar accessible to insect pollinators. (rem : I've asked a similar question about pollen, and maybe the answer is the same, but as far as I understood some plants have more pollen and some plants have more nectar.)

That doesn't answer your question directly but it's worth noticing that – independently of their nutritional value – crops are a problem for pollinators since monoculture is an all-or-nothing regime.  By which I mean : a few weeks when food is plentiful yet totally absent during the rest of the year.  Characteristics of the supply during the all-you-can-eat weeks is only a side topic. Hence the insistance on biodiversity in agricultural settings.

thank you for your remark. I understand that the a large quantity at one date is not enough to sustain a population of pollinators, but I can find data about the flowering period and the landscape diversity. I find it more difficult to find data about pollen/nectar production during the flowering period (if any).

What about trees? in apple producing regions in the US, they have to bring over hundreds of bee hives to pollinate the trees, there was info on it in a program about monocultures.

trees are indeed part of the whole picture, but I've tried not to be too broad. And I already have some info about trees (in monoculture or in diversified hedges

Lacy phacelia or purple tansy (Phacelia tanacetifolia), which can be
planted any time of year due to its short growing season. After
flowering, it is plowed into the ground to enrich the soil with
humus
All types of clovers: excellent nectar plants that plowed after
flowering and enrich the soil with nitrogen, or scythe them and use
as feed for animals
Sunflowers: after flowering, they greatly enhance the structure of
soil and enrich it with hummus
Rapeseed and poppy
Buckwheat: planted it in summer and when it fades, the seeds and
ground into flour

Scroll to page 13 (Appendix II). Here you will find a list of all significant nectar-producing plants in Europe
Scroll to page 21 for average nectar production (mg sugar/day/flower) of important agricultural crop flowers
Melliferous potential of twenty-seven plant families determined from the N data sets recorded in thirty-eight papers ranked by decreasing median values - scroll to page 5 under Table 1)
The google keywords you are looking for are along the lines of: "melliferous potential of agricultural crops in europe" and variants of this

https://www.prairienursery.com/resources-and-guides/plants-and-gardening/planting-for-pollinators.php
This link should answer your doubts concerning such plants. Asking for a list concerning whole Europe feels something a little bit out of reach considering how diverse the environment is there, this link concerns mainly the UK, albeit you have to consider that a wide gamut of species concerns various different territories with similar climate, thus many plants listed there can be found easily elsewhere.

thank you for your answer. This is an interesting link but I am looking for this kind of data in the case of the main (in terms of area coverage) crop plants.


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What are the pros and cons of eating earth (soil)?
I wonder if there are any benefits to eat earth. What I mean by earth is the topsoil that is sometimes on vegetable (I eat organic vegetables and some of them like spinach are full of topsoil).
I found this article (a study about why people, in certain culture, eat earth) but it doesn't clearly answer my question as it's about clay and not topsoil. Topsoil has a highest concentration of organic matter than clay.
I wonder if we can digest the soil nutrient (Phosphorus, Potassium, Calcium, Magnesium, Manganese, Zinc, Copper) just as we would if there were coming from vegetable and fruits.
What are the other pros and cons of eating earth (soil)? (I am aware of the cons about parasite and bacteria but my question is not about these risks. It's about nutritive value of earth.)

The article (a PDF can be found here) suggests that this happens neither for feeding reasons (to get your belly filled, when anything else is available) nor that this is done for supplemental reasons.
They suggest that this happens more for protective reasons. In the abstract they write:

Our results indicate that human geophagy is best explained as
  providing protection from dietary chemicals, parasites, and pathogens,
  whereas animal geophagy may involve both micronutrient acquisition and
  protection.

In the paper they give a few examples for this. First the earth eaten is usually digged up from deeper layers of the ground and sometimes even cooked. Then they bring in the example of people, which eat soil, when they have gastrointestinal problems as a kind of medicine to calm down the problems.
In my opinion there is not much nutritional value in eating soil. Organic compounds can usually not be metabolized (for example we don't have the possibility to break down cellulose). I am not sure, if we can get minerals from clay into our body, since a lot of them is present in soil as unsoluble minerals.

Thanks a lot Chris! You wrote "I am not sure, if we can get minerals from clay into our body, since a lot of them is present in soil as unsoluble minerals." Is it the same for topsoil ? Are its minerals also present as unsoluble minerals ?

In the topsoil probably not (though I haven't found any data on that yet) since a lot of the minerals is set free from organic matter. But it also gets washed away with rain if it is soluble.

A/ stronger immune system. children without soil environments are weaker, and the immune memory doesn't last forever across the decades, so it's good for adults too.
http://www.npr.org/sections/health-shots/2017/07/16/537075018/dirt-is-good-why-kids-need-exposure-to-germs
B/ Stronger bones and nerves and mineral content. We get calcium from milk, according to our culture, which is stupid because, if you have a soft water source or rain, milk is more harmful for adults that water treated with clay/chalk etc. Magnesium is important to nerves and it's one of the biggest mineral defficiencies in people. the main mineral that doesn't dissolve well is Silicon Si (same reason why there wouldnt be silicon based life in a water soluble animal). If you eat chalky clay, your body can dissolve it with the HCL ann digestive acids, and get many times more calcium than from milk. the body contains 1.2 kilos of calcium. crystals with lattice energy dissolve less easily than less structured stones, permeability helps a lot to dissolve stones/sands, so small particles like clays release a lot more minerals in water than rocks and sands do.
C/ better digestion. If you leave a bit of soil microbiota on your potatoes, and make a soup, and let that soup ferment for a few hours, you will have many times more microbiota in your gut that can eat potatos, than if the potatos were totally washed of soil. https://www.thecandidadiet.com/soil-based-organisms/


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Earliest ancestor of humans who could integrate into modern society
Assuming the current model of human evolution to be correct, approximately when did the earliest ancestor of humans live, who was intelligent enough, that if raised from a young enough age, could learn the necessary skills to live in today's society:

learn a modern language
learn to read and write
learn to use most common tools and household items
learn to drive a car, use a telephone, a computer, have an average job.

Interesting question but I doubt it can be answered conclusively, we just don't have the necessary data. Also bear in mind that chimps can do all (or at least most) of the above.

@terdon : of course, it is impossible to give an exact date, but I was asking it in terms of orders of magnitude. (5k years? 50k years? 500k years?) And chimps definitely don't fit, not just because they are not the ancestors of humans, but because they can't learn the above skills. Learning it as a circus trick does not count. You can teach a bear to drive a bicycle, that does not mean it will have the skills to live in and integrate into human society.

That's exactly my point, how can you define what is a "circus trick" and what is not? Short of trying this with a real hominid, I don't see how this question could be answered. You could assume that a certain hominid would have been able to do some of these things but you can't know. Perhaps a better question would be which was the first hominid to show a society whose complexity is comparable to ours.

Some of your bullet points are already challenging for many Homo sapiens sapiens. ;)

Interesting question.
The organism would have to be monogamous, that's for sure, otherwise it would be too competitive and it would be a beast - as chimps are. Chimps couldn't integrate into the modern society.
So, monogamy is the prime prerequisite as it's also prerequisite for intelligence. Bipedalism is another obvious prerequisite, as you need an organism with fine motorics of front limbs - and fingers.
For "modern language" you need high intelligence and the ability of abstract thinking. Same goes for reading and writing.
Humans split from great apes between 8 and 4 million years ago. Problem here is that every new piece of fossil of a human ancestor is classified as a new species, so there's very little we're certain of. I'd say the first organism capable of doing the above things existed around 200.000 years ago. Either homo erectus or, more likely, a Neanderthal.

Well... given than mitochondria eve was around 99–148 thousand years ago https://en.wikipedia.org/wiki/Mitochondrial_Eve The human species is at least that old.
So a human baby from 148 000 years ago likely could learn to do all the things listed.
Could  Neanderthal do all those things... Well Neanderthal are not an ancestor species.. more like a cousin species (separation by 500,000-700,000). And from hyoid bone... appears to be able to speak like modern humans do.
http://www.ibtimes.com/did-neanderthals-speak-60000-year-old-hyoid-bone-virtually-indistinguishable-our-own-1559113
So probably yes.. on mastering modern language.
Reading and writing.. well no idea. But then again there are no examples of humans writing older than 3200BC. And the human species is at least 150 000 year old.
However Neanderthals do have a reduced semicircular canals compared to humans. An almost defining feature of Neanderthals.... so Neanderthal were probably less  graceful in 3d space... so probably no gymnastic and kungfu for neanderthal.
Homo erectus... well they have high larynx.. limiting the sounds the they could make. The position is approximate that of a human 2 year old.
The other things on your list... no answer can be given.


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If a dead snake reflexively attacks itself, why does it not always attack itself?
Recently there has been this video going around of a snake that had been decapitated.  Its body swung around to the decapitated head and the head attacked the body on "reflex".  Now we know that most reflex arcs bypass the brain.  So if it is the case that this strike attack is reflex then how is that suppressed when the snake is alive? Why aren't snakes always reflexively attacking themselves?
Here is the video.
Is this some other phenomenon than reflexive attack?

+1 to Damien, just a few more thoughts.
If you notice it took several whacks of the head to get the bite reflex to trigger. I know that many animals have reflexes that will suppress other reflexes so that fluid motions can be achieved (righting reflexes are examples).
I don't know if anyone has studied the species enough to know this definitely, but I bet that snakes behaviorally/reflexively doge their own tail so that they don't keep hitting themselves in the head.  After the head is severed, higher level restrictions are lost, fight paths are probably lose inhibition, and the reflex to bite anything hitting you in the mouth takes over.  That said it probably had to hit the mouth just right to get this to trigger.
I'm looking for some definitive information on bite reflexes in snakes, and will edit if I find anything relative.  I have experience from studying amphibian reflexes years ago, and I have feeling this general trend will hold true for snakes (but I'm looking for someone who has actually studied it).

Interesting. Yes perhaps there is inhibitory behaviors or reflexes to avoid the snake's tail bumping into its face, thus avoiding the strike.  I am interested if anyone ever studied this, but you are probably right.


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Western blotting questions?
everyone. I've just been introduced to the procedure of Western blotting from my reading, though I'm not entirely sure about some points. I'd appreciate it if someone could help me with this.
What exactly is the function of the blocking buffer?
Why does one need a secondary antibody?
When discussing nitrocellulose membranes, say of a 0.45 5m pore size, what does 5m refer to?

Blocking buffer
Once the proteins in the gel have been transferred to the nitrocellulose membrane it is necessary to coat the rest of the surface of the membrane with an unrelated protein. This is necessary because all proteins will bind non-specifically to the nitrocellulose. Once the membrane has been blocked the only way that antibiody proteins (the probe) will bind to the membrane is via the transferred proteins that they recognise. The usual source of a blocking protein is defatted milk powder, i.e. casein, although some people use (or used to use) bovine serum albumin.
Secondary antibody
In a typical blotting experiment you expose first with a primary antibody directed against the protein of interest, for example this might be an IgG raised in a rabbit. Then in a second step you add a secondary antibody which will bind to the first one - in this case this might be goat ant-rabbit IgG (i.e. anti-rabbit IgG raised in a goat). Why is this done? The secondary antibody is in the form of an antibody-enzyme conjugate, typically with horseradish peoxidase, and the final development of the blot detects the presence of the conjugated enzyme.
Why use a secondary antibody? Two reasons: - firstly, there will sometimes be a degree of amplification if more than one secondary antibody molecule binds each primary antibody molecule; but more important is that it means that it is not necessary to produce an enzyme conjugated form of every primary antibody, which is time-consuming and quite tricky. So in your work you may be studying several different proteins using Westerns, but you will be able to use the same secondary antibody to detect all of them.
Pore size
That should be 0.45 - 0.5 µm. Pore sizes are measured in micrometres.


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Does xylitol kill all kinds of bacteria?
Xylitol is known as a bad bacteria killer in human's mouth.
But I am curious about one thing.
Does xylitol kill all kinds of bacteria regardless of good or bad?
If so, Does xylitol kill bad bacteria more than good ones at least in human's mouth?

Toxic compounds do not differentiate between good or bad.

Xylitol does not kill any bacteria.
Xylitol is a sugar alcohol that bacteria happen to not be able to use as an energy source. In the absence of other sugars, bacterial growth slows. Therefore, its antimicrobial mechanism is bacteriostatic rather than bactericidal.
No antibiotic exists, or will ever exist, that kills or inhibits all kinds of bacteria.
One thing xylitol can kill is a dog – keep xylitol-containing products such as gum well out of their reach.

Your answer is punctual, thanks. It does not kill bacteria directly. But does xylitol make all bad bacteria starving while it doesn't much affect to good bacteria? To understand my question, vice versa, if there's much sugar in human body, which bacteria grow faster, bad bacteria or good bacteria?

In one study, using xylitol-sweetened chewing gum reduced levels of the bad bacteria by 27-75%, while it had no effect on the friendly bacteria. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3434645/


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Deletion of codons at the start of a sequence in preparation for heterogeneous expression. Why?
I am reading a patent where they isolate a gene from cDNA constructed from RNA extracted from plant matter.
The subsequent step (in preparation for heterogeneous expression in E Coli.) puzzles me:

The codon optimization I can understand but this part confuses me "...remove the first 23 codons from the DNA sequence and replace [the start?] by the ATGGCT sequence."
Why would one remove a set of codons at the start of a sequence? How did they decide how many to remove Is there an obvious reason I am missing?  Also what is special about the ATGGCT sequence.
Any ideas why they would do this?
The start of the new sequence (1650 bp) looks like this:
atggctaccg ataatgacag ctctgaaaac cgtcgtatgg gtaattacaa gccgtccatc       60

tggaactacg acttcctgca gtccctggct acccgccaca atatcatgga agagcgccac      120

whereas the original sequence (1710 bp) was this:
atggattctt ccaccgccac cgccatgaga gctccattca ttgatcatac tgatcatgtg       60

aatctcagaa ctgataacga ttcctcagag aatcgaagga tggggaatta taaacccagt      120

Another point I am confused about is that 1710 - 23 x 3 + 6 is 1647. But the new seq. is 1650 bp. What gives?

Obvious reasons would be: a signal peptide, nope, doesn't look like one, annoying restriction sites, nah, not the case either

Proteolytic cleavage and N-end rule

@Ashafix Can you elaborate more on that? How is the N-end rule applicable in this case? If I translate both those sequences the first Amino Acid is Met. So no stabilizing residue seems to have been added.

The easiest answer would be to ask the authors of the patent.
Several other possibilities (see comments) were excluded, such as:

restriction sites which interfere with cloning
signal peptide
proteolytic cleavage

Although it's just a theory, removing part of the N-terminus might improve protein stability and half-life time because the first 30-40 amino acids lack an ordered structure (as judged by submitting the structure to Phyre). Those structures are known to aggregate and influence protein stability.
References:
The use of systematic N- and C-terminal deletions to promote production and structural studies of recombinant proteins.
Sequence composition of disordered regions fine-tunes protein half-life
Production of prone-to-aggregate proteins


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What plastic eating organisms are there to help with plastic in landfills problem?
I see some popular science articles on the plastic eating bacteria and fungi appearing on the web since 2009. Most of the articles praise discoveries, because such organisms promise to break down plastics which were previously thought to be indestructible. However, from the articles it is hard to understand the total number/names of promising organisms that can biodegrade plastic.
Additionally, it's hard to gather from the dated articles if these plastic eating organisms have passed safety testing - for example that they don't break down plastic into something volatile and toxic.
My question is - which organisms as of 2013 are seriously considered for solving the plastic in landfills problem?

Do you have URLs to the articles you found? Adding these to your question would improve its specificity and allow others to answer your question more easily. Your comment that you find it, "...hard to understand the total number/names of promising organisms..." might be a non-issue for another user who might be able to just look at the words and answer your question "off the top of the head" without additional research.

I remember this link - about a high school student who's science fair project was a basic but effective selection experiment.  He cut up plastic and put it in a yeast medium (growth medium for microorganisms) for a few weeks.  It says he tweaked the temperature and other incubation conditions for a few weeks and got a significant degradation of the plastic in the media.  The microorganisms in the media were not characterized.
That article is great because the bloggers compiled a list of similar work.
There are a couple of links that point to styrene degradation by Pseudomonas putida variants.  Pseudomonas putida is a likely candidate from bacteriology - it was first isolated near chemical and petroleum spills - they can degrade petrochemicals and organotoxics, so researchers might tend to start with this bacteria or an isolate of it.
This paper identifies Phanerochaete chrysosporium, a white rot fungus as an organism that can degrade phenolic resins.  White rot fungi are found in wood rot and can degrade lignin which is derived from a poly-phenolic like biosynthesis pathway.  So this is also an interesting lead.  It doesn't always grow to industrial scale - I've known people working on this even in the early 80s.
So it seems despite the fact that plastic never seems to go away, there are organisms in the wild that will chew away at the plastic, and with a little bit of selection work you can pick them out pretty easily.  This survey of the plastic dump in the Pacific gyre found that there were marine microorgs that might be eating plastic there too.  They had a preliminary report:

So far, the DNA sequences obtained by her lab show that almost 25% of the bacteria on one polyethylene surface were vibrios

A survey of the tropical rainforest also found a collection of fungi that can subsist on polyurethane. These included Pestalotiopsis microspora which seems to be have the so far unique property of anaerobic degradation of polyurethane.
Overall it seems that finding organisms in the wild is of ongoing interest.  This may be because biodegradation of plastic tends to be slow, which makes sense because if it were quick there would be no problem with dumping it into the dirt of into the ocean, but it would also rot over time in the back yard or in your boat.  While its possible that more fishing trips may find the perfect plastic eater, its also possible that industrial processes for the bioremediation of plastics may have to wait for some engineered organisms.

I know this is an old question however when it was posted there was not as much information as there is today. I have heard about two insects that have bacteria in their gut that degrade polimers. One of them is Tenebrio molitor which was reported to degrade polyatyrene. The other one is the waxworm, it was reported that waxworm larvae degrade poliethylene. This is really exciting news, currently we are working in Guatemala with a couple of insects that also degrade polymers, but we still have work to do before publishing.


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Can animals like squirrels leave "gifts" or tribute for humans?
I've heard anecdotal reports of squirrels bringing up gifts to a person's house after that person left out food for them. Sounds bizzare and unbelievable, until I actually saw some kind of a nut right on the welcome mat in front of the door. I moved it and saw that it was eaten (shell fragments) a couple days later, telling me that it was actually a good nut.
This makes me ask - is this just a coincidence, or do some animals, like squirrels indeed offer gifts or tribute to humans?
I'm aware that cats frequently bring killed animals to human doorstep:

By leaving a dead animal on the back porch, your cat is acting out its
  natural role as mother and teacher. You, her loving owner, represent
  her surrogate family. And frankly, she knows you would never have been
  able to catch that delicious mouse on your own.

However, for squirrels there's no domesticated relationship, humans are not a part of their family. Why would this behavior take place?

Crows have been known to reciprocate.  You may be interested in the BBC news article "Girl Who Gets Gifts From Birds" http://www.bbc.co.uk/news/magazine-31604026

@PCARR John Marzluff's book Gifts of the Crow looks into this behavior even further from an ethologist's perspective.

@Corvus  Oh cool!  Crows are amazing, I'll check this out.

I am almost sure squirrels are simply not intelligent enough for this

I believe a lot of these behaviours can fall under the umbrella term of reciprocity, or  reciprocal altruism.

In evolutionary biology, reciprocal altruism is a behaviour whereby an
  organism acts in a manner that temporarily reduces its fitness while
  increasing another organism's fitness, with the expectation that the
  other organism will act in a similar manner at a later time (...) The concept is close to the strategy of "tit for tat" used in game theory.

For example, red-winged blackbird males help defend neighbor's nests. There has been some discussion around the reasons for this behaviour, but it has been observed that males reduced the amount of defense given to neighbors when neighbor males also reduced defense for their nests. Since kin selection doesn't seem to be an important factor here, this would support a tit-for-tat strategy (animals help those who previously helped them).
Some primates do this frequently too:

A monkey will present its back to another monkey, who will pick out
  parasites; after a time the roles will be reversed. Such reciprocity
  will pay off, in evolutionary terms, as long as the costs of helping
  are less than the benefits of being helped and as long as animals will
  not gain in the long run by "cheating" – that is to say, by receiving
  favours without returning them.

The example with the crows, mentioned in the comment, can be interpreted under this light too. Those crows seem to give presents expecting something in return (albeit delayed!).
What's interesting though is that altruism, at first sight, would seem to go against reproductive success. Group Selection, however, is something Darwin was already talking about in Origin of the Species.
So, back to squirrels. I didn't find particular research about them in their relationship with humans (will keep looking), but analysing it under reciprocal altruism it could be justified that they give nuts expecting a potential future benefit for them or their group. There's much more to this complex dynamic, but reciprocity is definitely a strong candidate for explaining your kind gift-presenting squirrels.
Some quick references and materials:

The evolution of reciprocal sharing
The Gift, by Marcel Mauss (complete online book) --> From an anthropology point of view, Mauss was the first one to talk about recicprocity as economics. Absolutely recommended read.
Social semantics: altruism, cooperation, mutualism, strong
reciprocity and group selection

Look, I searched your question about the animals that bring to humans some "gifts" and the only thing I found, was only for the cats. So, if you are intrested check this :
Cats are, first and foremost, natural-born hunters, as recent studies of the effects that feral and indoor-outdoor cats have on bird and rodent populations have shown. Cats allegedly kill billions of small animals every year in the United States alone. But that doesn’t make them evil — just extremely well-adapted to a carnivorous lifestyle.
Though they were first domesticated nearly 10,000 years ago, cats retain the keen hunting instincts of their wild ancestors, as well as the simple gut that allows them to digest raw meat.
However, many cats don't eat their prey, and sometimes they don't even kill it. (If you've ever had to chase an injured squirrel out of your kitchen, then you've seen this behavior firsthand.) Spayed female cats are the most likely to bring gory gifts to their owners. But they have their reasons.
In the wild, cat mothers teach their young how to eat their food by bringing home dead or injured prey. Domestic cats are no different. But in this modern age of spayed domestic cats, many female felines have no young to whom they need to pass on their hunting wisdom.
So, if cats love their owners, they bring to him some kinds of "gifts" such as mice and birds.This is a way for the cats to say "thank you" for the care that him gives to them. Also, squerls do not give "gifts". They are simply hiding supplies for the winter near human residents.


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Does a rapid cooling step improve pasteurization of medical equipment?
I learned that pasteurization consists of two steps: first heating and then rapid cooling. The rapid cooling was explained as "it's a thermic shock for the germs, so the ones remaining after the heating step will be definitely killed with this". But on Wikipedia, the rapid cooling is explained as being part of a step that protect food product and it is not mentioned for the medical equipment.
I am actually asking the question to find out the best solution for this situation: let's say I am in some remote undeveloped place and I need to disinfecting a piece of equipment (something akin to a medical equipment, not food). I only have hot water (between about 60°C and 80° C) and cool water (both of them are clean water) in clean containers (I also have soap and have washed the equipment with it before). Will it improve the disinfecting process if I do the rapid cooling step after the heating step or is it unnecessary? If yes what procedure is the best?

Because if you continue with the heat, you'll have (partly) cooked food?

Because the remaining bacteria (pasteurisation is not sterilization) will grow fast when it is warm.

@PolypipeWrangler, if it's to reduce the growth of the remaining bacteria, why isn't this cold phase mentioned for the medical equipment on the wikipedia page? is it an omission or it is really never used for pasteurizing equipment and only for food?

@MagTun because pasteurization is very different then sterilization. medical equipment is sterilized, the goal is to kill ALL bacteria.

@John but the Wikipedia mentions it for some medical equipment. Also what I have to pasteurize is not medical equipment only akin to, it doesn't need to be sterilized, just pasteurized.

@MagTun there is no cooling phase for that equipment, in fact they are heated for a long time.  the intent is to sterilize, it is just  sterilized at a lower temperature than other equipment because high heat or chemical sterilization would damage the equipment.

@John, I get uit now, for medical equipment, the pasteurization is long enough so that it doesn't only remove the parasite but really sterilizes the equipment [killing or deactivating all forms of life].  But what if I can't keeping heating long enough. I am in a remote place with limited means and I can't only keep it at around 60-70°C for 5-10min.  Would a fast cooling steps help the pasteurization by creating a thermic shock for the germs or won't affect in anyway the germs?

They cool it fast to maintain the taste and quality and to avoid the food danger range which is 5 to 60'C, because typical pasteurization is only 99.999% effective. A fast transition through 30-40'C improves the quality a lot compared to keeping the product at 30-40'C ... If you had limited means, you could easily use extra pasteurization at the expense of the taste, and you would achieve 99.99999 percent bacteria reduction, and the slower cool would then let that figure rise by i.e. one order of magnitude.
See the conclusions here:
https://onlinelibrary.wiley.com/doi/full/10.1111/1541-4337.12357
To know which process best suits your equipment and product, check the tables to achieve the reduction and follow similar times:
charts
graphs

Thanks for your answer and sorry for not being more precise, but what I have to pasteurize is not food but a piece of equipment akin to a medical equipment (I have added italic part in parenthesis to make it clearer). Your answer seems nonetheless to apply as the "danger zone" from 5° to 60° would, I guess, still apply for equipment for which we want to remove pathogens. Could you confirm it please? Also I can easily have a fast cooling step. The problem is not here, it's just that I wondered if this step was useful for equipment as it is not mentioned on Wikipedia for the medical equipment.

I'd recommend that you select the pasteurization process and temperature that best suits your equipment. Study the temperature graph images, i'll add references. Some pasteurization processes take 40 minutes to cool. Industries deal with giant vats of 1-2 tonnes, so the cooling can be slow, their studies have established flash pasteurization national protocols and cooling times. see end graph and conclusion https://www.researchgate.net/publication/268799840_Investigation_on_a_Tunnel_Pasteurizer_for_Nocellara_del_Belice_Table_Olives_Obtained_with_the_Castelvetrano_Style_Process

the study is about table olive so it's food. Are you sure this is the  link you wanted to share?

Disinfecting medical equipment is not pasteurisation. Its 2 questions in one. Pasteurisation can use slow cooling. Medical equipments doesnt denature with heat so you sould keep long time close to 100C. At least 80C for 20 minutes is best.

@MagTun - the danger zone is a temp range where bacteria can rapidly multiply given an appropriate food source (e.g. in food). This should not apply to your "medical equipment", you should be able to get it almost entirely without substrate for the bacteria to grow in.

@bob1, thanks for this info, I thought the danger zone was related to the germs characteristics not the food sources, it makes more sense now. But still I wonder, what if I can't keeping heating long enough to remove entirely the bacteria. I am in a remote place with limited means and I can only keep the heat at around 60-70°C for 5-10min. Would a fast cooling steps help the pasteurization by creating a thermic shock for the germs or this fast cooling won't affect  the germs in anyways. Thanks for your help!

@MagTun it doesn't affect the bacteria/yeast/fungi as far as I know. What is your end point here? How clean/sterile does it need to be? Have you looked at chemical cleaning methods instead - formaldehyde (1-4%), phenol (conc??), alcohol (70% 1-5 min) all work well in general with fairly fast times.

@bob, I have limited means as I am in a remote place. So I am trying to find a solution but apparently this won't work this way. Thanks!

Are you in an igloo or a place with no energy?

@DeltaEnfieldWaid, sorry didn't see your comment, yes I am in a place without access to energy


text:
Genotypic distribution of a population with two characteristics and linkage
I am currently doing some research into distributions and probabilities with Mendellian genetics. I came across this problem that I cannot seem to wrap my head around.
Given that the population has two characteristics, they are color and texture. Supposed two dihybrids reproduce (AaBb x AaBb) and if the dominant form of the
color gene is contributed, then the dominant form of the texture gene is three
times as likely to be contributed as the recessive form. If the recessive color gene is contributed then the dominant and recessive genes for texture are equally likely.
From this the geneotypic distribution has to be calculated.
I know the solution is:
[9/64   6/64   1/64   3/16   1/4   1/16   1/16   2/16   1/16]

 AABB   AABb   AAbb   AaBB   AaBb  Aabb   aaBB   aaBb   aabb

When I performed the punnett square I got the distribution of:
 [1/16   2/16   1/16   2/16   4/16   2/16   1/16   2/16   1/16]

 AABB   AABb   AAbb   AaBB   AaBb  Aabb   aaBB   aaBb   aabb

and did not know where to go from there.
My question is how did they incorporate the "times as likely" condition into the solution.

What are these traits exactly ? just colors ?
From the data it seems that homozygosity is not preferred

You are...  done. You fully answered the question; if I were you, I might just put it in ratio format instead of probability, just to be safe.
The three times thing is a bit weird, but I have seen it before. First, let's look at the phenotypic ratio of the progeny: 9:3:3:1 for Dominant Both:Dominant A Recessive B:Recessive A Dominant B: Recessive Both.
Let's find out how many dominant and recessive there are for each trait. For the dominant A trait, you add up the 9 and 3, because they are the only two types of dominant phenotypes, and find that 12 different organisms of the 16 possible are dominant for Trait A, so the probability of getting trait A is 3/4 or 75%. This means that 4 of the 16 orgamisms are recessive for Trait A, so the probability of being recessive for Trait A is 4/16, or 25%. Therefore, the ratio of Dominant Organism probability:Recessive organism probability is 75% to 25%, or 3:1. This means that it is 3 times as likely to get the dominant trait than the recessive trait. Make sense?

Hi, I understand what you are telling me there but what I really wanted to know is how to move from the punnett square distribution I got ( [1/16 ... 1/16] ) to the distribution that was stated in the solution ( [1/64 ... 1/16] ).


text:
How to seek information on the duration of biological entrainment processes in mammals?
This is a question that is a little bit hard to define for me. I'm interested in learning more about times of "attractor/entrainment" processes that may take place in the body/brain of mammals, and particularly humans. I want to get a general idea of how long it takes for a mammal to switch into a new mode of operation, be it behavior or physiological change? Is it days, weeks or more?
For example, a polar circle animals may change the color of their fur in response to photoperiod changes. How quickly does the change get registered and take place? Is it days, weeks or months?
Another example might be a mating season of siberian hamster, where their testes weight changes in response to photoperiod duration. How long does it take for a behavior change like that to fully manifest?
I've read that it takes ~21 days for a human to create a habit or break one. Is there any biological basis for this observation?
I'm not sure how to search for information like that, as it seems to me such things might only be incidentally mentioned in scientific articles. Are there some keywords that may help me improve the search results?
Thank you for any input.

This is still somewhat ambiguous. I think you need to restrict your question to a specific process you are interested in. Learning and switching to a new state can happen on a much shorter time scale (milliseconds to minutes) in the brain.

You can narrow down your question. Just one precise question.. (You are asking 5 questions here )


text:
What biological systems are affected by Vitamin B6 (or B vitamins in general)?
B vitamins and particularly the B6 vitamin appears to the one of the main ingredients in energy drinks.
There has been anecdotal evidence from people interested in dreaming that ingestion of vitamin B6 at night time changes the pattern of dreaming and is likely to produce "lucid" dreams.
From a biological standpoint, what is the effect of the B6 vitamin on the human body and brain? Do other animals require the same vitamin?
Are B vitamins in any way related to the circadian rhythm regulation within some organ systems? Does it speed up metabolism?
I would be grateful for any scholarly papers on the subject or keywords that I may look up myself.
Thank you!

More related to this question but long term exposure/abuse of laughing gas is linked to severe B6 deficiency.

The main effect, of vitamin B6, is neurological, becouse  moderate variations in the intracellular concentration of pyridoxal 5'-phosphate (PLP), the biologically active form of vitamin B6, can have pronounced modulatory effects on steroid-induced gene expression. So you cannot get the effect of stress hormones.
Also neurological damage has been reported on doses from excess of 500 mg/d. Check this papers http://www.ncbi.nlm.nih.gov/pubmed/2661220 and http://www.fasebj.org/content/8/3/343.short


text:
Relationship between toxicity of drugs and negative effects on brain
Are psychoactive drugs with lower lethal doses more neurotoxic (more damaging to the brain)? For example, tetrahydrocannabinol (one of the active components of cannabis) has a much higher lethal dose than benzoylmethylecgonine (cocaine), so could we deduce that cocaine is more damaging to the brain?
Moreover, is a mathematical relationship between neurotoxicity and lethal doses known?

I think this is the wrong way of looking at the question. Neurotoxins are more lethal (have a lower LD50) because less of it is required to kill the organism due to their specific action.

@March Ho I figured it wasn't that simple. My chemistry/biology knowledge is very limited

Short answer
The causes of death after heroin, cocain or cannabis overdose are mainly due to cardiac and respiratory arrest, and not to neurotoxic effects.
Background
The cause of death after a lethal overdose of your mentioned drugs are the following :

Cocaine (lethal dose: 30 mg - 5 g via mucus membrane (EMCDDA)): Cocaine-related deaths are often a result of cardiac arrest followed by an arrest of breathing (NIH). Cardiac effects are mediated via increased sympathetic output and a local anesthetic effect (Schwartz et al., 2010);
THC: (lethal dose: ~1000mg/kg i.v. in primates (Drug library)): No known cases of human fatalities. Toxicity appears as achypnea (rapid breathing), tachycardia (fast heart rate), ataxia, hyperexcitability, and seizures (Fitzgerald et al., 2013), but death seems mostly associated with respiratory arrest and cardiac failure (Drug library);
Heroin: (lethal dose 200 - 2000 mg i.v.(EMCDDA)): overdose often due to respiratory arrest (Anoro et al. 2004) caused by mu-opiate receptor activation in the brainstem (Karch, 2006).

Hence, heroin, THC and cocain are lethal mainly due to peripheral causes (i.e., cardiac and respiratory arrest). Although these effects are mediated, at least partly, through central mechanisms (i.e., occurring in the central nervous system and specifically the brain), the drugs themselves do not cause death because of neurotoxicity.
And a closing comment, with credits to @MarchHo - In general, neurotoxins do not cause death due to neural toxicity per se. Most notably even botulotoxin, being one of the most potent neurotoxins known, causes death due to respiratory failure (CDC).
References
- Anorro et al., Rev Esp Salud Publica (2004); 78(5): 601-8
- Fitzgerald et al., Top Companion Anim Med (2013); 28(1):8-12
- Karch, Drug Abuse Handbook (2006)
- Schwartz et al., Circulation (2010); 122:2558-69

I think that this answer is only partially correct, since almost all (I can't think of one which does not) neurotoxins cause death indirectly via paralysis of nerves or muscles.

@MarchHo - the question is on drugs of abuse.

What I mean is that in general, neurotoxic drugs cannot cause death solely by their neurotoxicity.

@MarchHo - I checked it quickly and you are absolutely right. I'll add a sentence.

Hm, I would say that botulotoxin does indeed cause death because of neurotoxicity; it is simply a peripheral neurotoxin, and since the vagus nerve is paralyzed, death ensues. But if it were not neurotoxic, respiratory arrest would not occur. Things are a bit muddled here. There are lots of neurotoxins; I'd still say their mechanism of action and the cause of death is due to neurotoxicity. I might have to consult a toxicology text. :-/

I would agree with @anongoodnurse. If it is interrupting the normal function of peripheral nerves, then it is a neurotoxic event, usual interfering with ligand receptor binding. That being said, it depends on whether or not you consider pacemaking cardiomyocytes equivalent to neurons, so that disruption of their electrical rhythm would be a neurological event.

@anongoodnurse Ah! I read the title again... It is asking for effects on the brain. Christiaan's answer is placing it in that perspective.


text:
How can a ligand be an integral membrane protein?
My background is in mathematics, and not biology, so please bear with me. I am currently working on a project involving the effects of Epidermal growth factor treatment (EGF) on cell migration. I am reading a review of EGF signaling (Epidermal growth factor receptor targeting in cancer: A review of trends and strategies by Chetan Yewale, et. al.), and it states that "Various ligands can activate EGFR ... These ligands are expressed as integral membrane proteins." This statement makes absolutely no sense to me, and makes me question my understanding of signal transduction. I think of ligands as freely floating molecules that may eventually come into contact with the cell membrane and attach to some receptor. But a ligand expressed as an integral membrane protein? This seems contradictory to my understanding of ligands, which (I thought) are released from the cell in order to signal with cells (be it the same, neighbor, or distant cells). Integral membrane protein ligands would only be useful for autocrine signaling, which I don't think is true of EGF.

Can you please link the review?

Membrane-bound ligands are also used in cell-cell signaling. This is especially (but not exclusively) true in the immune system, where circulating immune cells "scan" other cells for signs of, say, viral infections, which will induce the expression of certain proteins on the infected cell's surface, which are in turn ligands for receptors on the immune cell's surface.

You're thinking of hormones. Ligand is a much broader category of thing that includes everything that can be bound by some biomolecule.

Wow, I must say this is my first ever post to biology stack exchange, and I'm very impressed with the quality (and even quantity of answers!!)
The article I was describing is http://www.sciencedirect.com/science/article/pii/S0142961213009289

These kind of ligands act via juxtacrine signalling because they cannot diffuse. Ephrin is another example.

@WYSIWYG I think you should make that an answer since it seems to address the crux of the question.

@canadianer Actually Poka Nandor has almost said it. I'll either suggest him this point or add this to his answer as an edit.

In biology ligand is a very broad term. Everything is called a ligand that has a receptor for it, regardless whether it is free or membrane-bound. There is very much sense in membrane bound ligands, because many cells in our body are capable of actively moving around (for example T-cells). Cells can use signal transduction by direct cell-to-cell contact - like in activation of T-cells, or cytotoxic T-cell killing. This wiki page covers the basics quite well.
Also, a quite thorough wiki page on ligands.
From the comments under the question by @WYSIWYG:

These kind of ligands act via juxtacrine signalling because they
  cannot diffuse. Ephrin is another example.

I am beginning to see now how a ligand can be a transmembrane protein. I think I am still confused, however, because my understanding is that growth factors (such as EGF or TGF-beta) are secreted by cells during migration, and I always assumed secretion meant the release of a soluble thing that is able to diffuse to other areas of the cell population (maybe I should mention, I'm considering this during an in vitro experiment in a well plate). It doesn't seem to me that a membrane-bound ligand would be useful during migration, as the movement of cells and signal propagation may be opposite.

You can add that these kind of ligands act via juxtacrine signalling because they cannot diffuse. Ephrin and Notch are other examples. Sometimes diffusible signalling may not be. preferred.

Ah, so EGF acts via juxtracrine signaling, and is not some sort of diffusible ligand released by cells? I think this would answer my question if my understanding is correct!

@NaiveHalmos EGF/EGFR do not act via juxtacrine signaling. EGF is soluble, and EGFR is transmembrane. The juxtacrine signaling being referred to by WYSIWYG is the interaction between an immune cell like a T cell and, for example, an activating cell like a dendritic cell.

OK, I'm sorry for continuing this thread far longer than it needed to be, but then was the review I read possibly incorrect about "Various ligands can activate EGFR ... These ligands are expressed as integral membrane proteins." If we consider the main ligand for EGFR to be EGF?

A perfectly reasonable definition of a ligand from Wikipedia:

In biochemistry and pharmacology, a ligand is a substance that forms a complex with a biomolecule to serve a biological purpose.

A ligand can be anything, so long as it binds to a biomolecule. Often, the ligand is a small molecule or peptide, and the thing that it binds to is a protein. On the other hand, both ligand and binding partner can certainly be proteins (or one could be a Mg$^{2+}$ ion and the other an RNA molecule, etc.). Ligand is a very broad term, and is often used in other biochemical areas aside from signaling. For example, the things that an enzyme binds to (substrates, allosteric regulators, etc) can be called its ligands.
Also, the things you describe in your post:

This seems contradictory to my understanding of ligands, which (I thought) are released from the cell in order to signal with cells (be it the same, neighbor, or distant cells).

are hormones, which is a much more specific category of thing than is ligand.
Edit
There seem to be some 'ahem'... doubters as to the broadness of the definition of ligand, so, time for some examples from the literature:
From the biochemistry textbook Berg, 7e (emphasis added):

The final step is affinity chromatography with the use of a ligand specific for the target enzyme.

From the paper Electrostatic steering and ionic tethering in enzyme–ligand binding: Insights from simulations, Wade et al (emphasis added):

To bind at an enzyme’s active site, a ligand must diffuse or be transported to the enzyme’s surface, and, if the binding site is buried, the ligand must diffuse through the protein to reach it.

From the paper Geometries of functional group interactions in enzyme-ligand
complexes: Guides for receptor modelling, Tintelnot et al (emphasis added):

There are many more examples of arginine-carboxyl interactions that appear to have key functional
roles in enzymes, including some in which an arginine-like structure in the ligand interacts
with a carboxyl group from the binding site (i.e., the reverse of that described above).

It is true that the one particular compound that natively binds to an enzyme's active site is often called a substrate, in part to differentiate it from allosteric regulators and other ligands that can also bind to the enzyme. Thus, the set of all of an enzyme's substrates can be thought of as a subset of the enzyme's ligands. Again, ligand is an extremely broad concept that simply refers to something which binds.
Edit 2
Fun fact! The modern word ligand comes from the latin verb ligāre, meaning "to bind". More specifically, ligand derives from the gerundive form of ligāre, ligandus, which translates to something like "(that which is) to be bound".
Not that this has much bearing on how it's used in the modern scientific literature. I just thought it was cool.

Umm as far as I know "the things that an enzyme binds to" are called substrates rather than ligands...

@Nandor Whelp, you're partially right, but mostly you're wrong. An enzyme's substrates are a subset of its ligands. See the edit for more details.

Ligands are not "usually a small molecule." A ligand is something that binds to a receptor. It can be a neurotransmitter, hormone, peptide, protein, bacterial/viral/parasite component, or a higher-order complex made up of multiple species of any of the above. I would suggest completely removing that from your answer, as it's just factually wrong (probably based on the bias of the person that wrote that phrase in WP).

@MattDMo That's legit. I can appreciate your point. If you feel strongly that this is wrong, edit the Wikipedia page and I'll update my quote to match.

OK I now see that ligands can include integral membrane proteins (IMP), however, I thought a hormone has to be secreted by a cell and transported through the circulatory system to another area? If we're working in an in vitro experiment (in a well plate), this clearly cannot happen. So I guess my real question is, if we are considering EGF in a well plate (during a cell migration experiment), is its ligand really an IMP? a soluble factor that diffuses makes much more sense to me, as cell movement and signal propagation may be acting in opposite directions.

@user3521072 First, EGF is not a hormone, it's a protein. Second, there's no rule that says that a hormone "has to be secreted [...] and transported [...] to another area". You can very easily grow cells in a 96-well plate and treat them with insulin or estrogen or whatever hormone you feel like. EGF's receptor is EGFR, which is an IMP, to use your abbreviation. I'm not very clear on why you're thinking that its binding partner (here called a receptor, since EGF is the soluble ligand) should be soluble as well - if it was, how would the target cell receive the signal? (...)

(...) I'm also not sure what you mean by "cell movement and signal propagation may be acting in opposite directions." Cells move one way or another, signaling cascades generally move from receptor to nucleus (to affect gene transcription), or in this case, from receptor to cytoskeleton (to move the cell).

@tel I'm on my phone now, but I'll edit the article as soon as I can tomorrow.

@MattDMo You imply that proteins cannot be hormones but then mention insulin (a protein hormone). See also human growth hormone and follicle stimulating hormone, to name a few.

@MattDMo Actually I believe I misinterpreted your comment. In any event, proteins can be hormones but, as you say, EGF isn't necessarily one.

@canadianer yes, there are several classes of hormones, including peptide-based (insulin, oxytocin, etc.) and protein hormones like human growth hormone. Perhaps my wording was slightly off, I probably should have said "EGF is not a hormone, it's a protein growth factor."

@tel I have corrected the Ligand (biochemistry) wikipedia page to remove the emphasis on small molecules.

@MattDMo I didn't think EGFR was soluble -- I am having a bit of trouble understanding how the EGF ligand can be both soluble and an IMP. But seeing that EGF uses juxtacrine signaling, am I right in thinking that EGF is not soluble, but is an IMP and thus spreads through a population via cell-cell contact? This would clear up my confusion from yesterday. (And you can ignore my statement about cell migration and signal propagation moving in opposite directions -- I was thinking about a very specific, unrelated study)

@MattDMo I changed the quote to match the new one on the Wiki and updated the wording in my answer a little bit to deemphasize small molecules

@NaiveHalmos see my other comment. I think you were getting confused with comments about entirely different things. Just to put it plainly here: EGF is soluble. EGFR is a transmembrane receptor. Plain typical paracrine signaling here, with maybe a bit of autocrine thrown in just for fun in certain cases, like cancer. I don't believe EGF even has a transmembrane domain in its gene sequence, so juxtacrine signaling isn't even possible. Some cytokines and other proteins have both soluble and transmembrane domains, and can be cleaved, so they can signal via both juxtacrine  and paracrine means.

Most ligands are synthesized as the same way as receptors integrated in membrane: synthesized on rough-ER, pulled into the lumen of ER. If proteins synthesized on rough-ER have a hydrophobic amino acid sequence, the hydrophobic region could stay in membrane because inside of membrane is hydrophobic and has affinity to hydrophobic amino acid sequences. Soluble ligands do not have such a region in the sequences, but membrane integrated ligands have it.
As I mentioned above there are ligands integrated on membrane: Fas, TNF, Notch ligand family, etc. As you mention in the question, they are not soluble so that ligand-receptor signaling occurs by cell to cell contact.
You can see various types of membrane integrated ligands from the URLs below.
http://www.nature.com/onc/journal/v27/n38/full/onc2008229a.html
http://www.sanfordburnham.org/talent/Pages/CarlWare.aspx
http://www.sci-online.org/article/view/3946/4855
http://www.bio.davidson.edu/courses/immunology/students/spring2003/swails/fas.html

I don't understand how this answers the question...


text:
Experiment to show that carbon dioxide is needed for photosynthesis
In my school test, the question is as follows:

Will the experiment work satisfactorily?
What alterations can you make to obtain expected result?

What I wrote:

Yes, it will work satisfactorily. Lime water absorbs carbon dioxide and hence there is no carbon dioxide for the leaf and hence photosynthesis does not take place and no starch is prepared. Hence on iodine test, the presence of starch is negative and thus proves that carbon dioxide is required for photosynthesis.
We can put half of the leaf inside the flask and half of it outside. So, the inside part will not show presence of starch and the outside part will show presence of starch.

[Note]: It was marked incorrect by my biology teacher. It got it reviewed by another biology teacher and HE SAID WHAT I WROTE IS CORRECT and the teacher who marked it wrong gave the opinion as follows:

It will not work satisfactorily because lime water does not absorb carbon dioxide. [which to me, seems incorrect as lime water ABSORBS carbon dioxide]
The alteration is that you have to use Potassium Hydroxide instead of lime water. [which to me, seems incorrect too since both lime water and potassium hydroxide absorbs carbon dioxide and then there is no need to use potassium hydroxide when lime water works!]

Now I am confused what is correct and what should I write in my final examination??  Please help. Any help will be appreciated, Thank you.

Not an expert answer but from experience, I’ve seen limewater absorb $\ce{CO_2}$ mostly when $\ce{CO_2}$ is bubbled through the solution. However, in respirometers, KOH is used to absorb any neighboring $\ce{CO_2}$ in the chamber. Analogically thinking, it seems to me that limewater won’t be very efficient in removing $\ce{CO_2}$ from the flask in your experiment. Thus, you are correct in stating limewater absorbs $\ce{CO_2}$, but it might not work “satisfactorily,” making the teacher’s answer correct. For q2, I feel you should combine both your teacher’s and your answers. A control is needed.