text:
What repairs faster when injured: white matter or grey matter?
This was the exact wording of a test question given by my biology teacher and she said that white matter would repair faster, because there is a myelin sheath to protect the cells.
Do you agree with this answer? Could you give me a more detailed, real life (not school, but real neuroscience, real data) explanation?

I disagree with the close votes based on homework - this is not the type of question that close reason is intended for.

Short answer
As @BryanKrause indicates, neither answer really makes sense.
Background
This is basically per the answer of @BryanKrause. Myelin is the stuff that forms the main characteristic component of white matter. White matter being

[the tissue] found in the deeper [in] the brain (subcortical). It contains nerve fibers (axons), which are extensions of nerve cells (neurons). Many of these nerve fibers are surrounded by a type of sheath or covering called myelin. Myelin gives the white matter its color. It also protects the nerve fibers from injury. Also, it improves the speed and transmission of electrical nerve signals

I think what the question aimed to target was your understanding what a myelin sheath is for (and, hence, what it is not intended for). Quoting from (Morell & Quarles, 1999):

What

[A] greatly extended and modified plasma membrane wrapped around the
  nerve axon in a spiral fashion. [It] originates from and are a part of
  the Schwann cells in the peripheral nervous system (PNS) and the
  oligodendroglial cells in the central nervous system (CNS)

What for

Each myelin-generating cell furnishes myelin for only one segment of any given axon. The periodic interruptions where short portions of the axon are left uncovered by myelin are the nodes of Ranvier, and they are critical to the functioning of myelin.

How

In myelinated axons, the excitable axonal membrane is exposed to the extracellular space only at the nodes of Ranvier; this is the location of sodium channels. When the membrane at the node is excited, the local circuit generated cannot flow through the high-resistance sheath and, therefore, flows out through and depolarizes the membrane at the next node, which might be 1 mm or farther away []. The low capacitance of the sheath means that little energy is required to depolarize the remaining membrane between the nodes, which results in local circuit spreading at an increased speed. Active excitation of the axonal membrane jumps from node to node; this form of impulse propagation is called saltatory conduction (Latin saltare, “to jump”). Such movement of the wave of depolarization is much more rapid than in unmyelinated fibers. Furthermore, because only the nodes of Ranvier are excited during conduction in myelinated fibers, Na+ flux into the nerve is much less than in unmyelinated fibers, where the entire membrane is involved.

What not
Although the myelin sheath is formed by a glial cell type, and although glial cells do structurally and metabollically support neurons, I would not say that this means myelinated tissue heals faster. Instead, myelin is more about the functional role of white matter, namely efficient, fast and reliable long-distance transfer of information across distant brain regions.

Reference
- Morell & Quarles. The Myelin Sheath. In: Siegel et al (eds); Basic Neurochemistry. 6th ed. Philadelphia: Lippincott-Raven (1999)

Your biology teacher's question is unfortunately poorly formulated and the justification is even worse, not just biologically but also logically. For the logical error, consider this statement: Knights wearing chain mail heal faster because they are protected by their armor. This makes no sense. Perhaps if you allow that the initial damage is less, but even that makes little sense.
It doesn't really make much sense to talk about healing speed of white matter and grey matter because you are talking about two different things. White matter is mostly axons and their myelin sheets, whereas grey matter consists of cell bodies and neuropil. Grey matter damage implies cellular death. White matter damage implies loss of connectivity. Grey matter damage can also lead to white matter degradation (i.e., the cells that sent projections are now dead). White matter damage can also lead to grey matter degradation due to loss of connectivity.
However, it is true that different types of brain injury could differentially impact white versus gray matter, but going into all the different causes of brain injury is too broad of a topic for a single question at stack exchange.
Furthermore, repair of CNS tissue is just as much about compensation rather than repair per se. Repair processes are important for limiting damage, cleaning out dead tissue, and restoring some types of connectivity, but recovery from a major injury is just as much about brain plasticity and effectively relearning how to function after an insult.

I'd like to upvote here, but w/o references I'm hesitant to do so. I'll spare you the banner though ;-) Thanks for your efforts here, I voted to leave open (too). If you like a question, it can also help to upvote it (I did)

Yeah, I agree with your statement, the test question was definitely not a well formulated question, extremely unclear for everybody.

@AliceD Yeah, I didn't put much effort into my answer but also didn't want to leave it unanswered - although I don't love the question itself I also don't want to leave someone hanging who is currently being instructed by someone uninformed. I'm not sure your answer really gets to the question although it does have good information about the distinction between white and gray matter and you are also probably closer to what the instructor was aiming for.

And a lot of times myelin is lost after injury.


text:
Are sensory mechanoreceptors and mechanical nociceptors the same type of neurons or are they different?
I always supposed the neurons / receptors which transmitted touch and pain were the same, since they react to stimulus which are the same but with different intensity, and they just sent a stronger signal in the case of something that has to be interpreted as pain. Though recently I've read some articles that imply they aren't, even so they don't say it directly. Reading more information I found this,

A nociceptor ("pain receptor") is a sensory neuron that responds to
damaging or potentially damaging stimuli by sending “possible threat”
signals.
Types and functions
Mechanical nociceptors respond to excess pressure or
mechanical deformation.

Nociceptor
Then,

Are sensory receptors neurons?
Receptor cells are specialized neurons

Are sensory receptors neurons?
And finally,

Sensory receptors are primarily classified as chemoreceptors,
thermoreceptors, mechanoreceptors, or photoreceptors.
Mechanoreceptors detect mechanical forces.

Sensory receptors
This doesnt give me a definitive answer, but it tells me both "sensory mechanoreceptors" and "mechanical nocireceptors" are neurons which responds to pressure/ mechanical forces. Are they supposed to be the same types of neurons named differently by different authors, or are they different types of neurons?

Short answer
Nociceptors are different from mechanoreceptors.
Background
Mechanoreceptors in the skin have specialized dendritic regions that facilitate their specific role in sensing different types of mechanical force, e.g., pressure receptors (Merkel’s disks) versus vibration receptors (Pacinian corpuscles and Meissner's corpuscles). See Fig. 1 for schematic representations of these types of receptors (Iheanacho et al). By contrast, pain receptors (or nociceptors) do not have specialized dendritic regions and consist of free nerve endings that respond to harmful mechanical forces (Purves et al., 2001).

Fig. 1. Skin receptors. source: Teach Me Phsyiology
References
- Iheanacho et al., Mechanoreceptors. In: StatPearls. Treasure Island (FL): StatPearls Publishing (2020)
- Purves et al., eds. In: Neuroscience 2nd ed. Sunderland (MA): Sinauer Associates; 2001. Nociceptors

I don't know if this directly answers your questions, but I think some confusion may stem from an underlying misconception of receptor vs receptor cell.
In most contexts (though not this one), 'receptors' do not refer to cells. Receptors are proteins on the cell membrane that transduct some signal/stimulus to the cell. Sometimes a "normal" peripheral neuron will have end processes that contain receptors that pass the signal directly to the neuron. Other times, a special 'receptor cell' is present. These cells are labeled as mechanoreceptors or nociceptors. The difference here is that a "standard" neuron is responsible for signal gating and propagation, whereas a receptor (cell) is primarily responsible for converting an external stimulus into a chemo or electrical signal recognized by "normal" neurons (or other cells).

Edit: As noted by AliceD's answer, different receptors have different proteins and thus have different mechanisms. To add, "nociceptor" and "mechanoreceptor" are categories. There are many different receptors that are nociceptors and many different receptors that are mechanoreceptors. Furthermore, nociceptor is a category of 'function' - it describes that the receptor responds to a pain/damage stimulus. A mechanoreceptor is a category of 'mechanism' - it describes how the receptor works. These categories are not mutually exclusive, and there are indeed nociceptors that are ALSO mechanoreceptors. (E.g. "Joint nociceptors are classified as high threshold mechanoreceptors" (source)) But not all nociceptors are mechanoreceptors and not all mechanoreceptors are nociceptors.

Added. As I understand it, cells that are both nociceptors and mechanoreceptors seem to be classified as one or the other depending on the use/field of research. In cases investigating the mechanisms of nociceptors, it seems they may be distinguishing the two to separate "other" mechanoreceptor from mechanical nociceptors as the mechanisms are indeed different.

"high-threshold mechanoreceptors respond to stimulation of higher intensity, and are a type of nociceptor." From the ever-so-very credible source of lumenlearning.

In any case, after revisiting op's question, I think your answer is more what op is looking for: the two are certainly not the same thing. We're sort of arguing semantics here, as some nociceptors are technically mechanoreceptors by definition, but few people would ever refer to them as both.

so, there are different types of mechanoreceptors, some will detect touch,  others will detect harm, those last ones are also called nociceptors? Or did I get it wrong?

Yes, that is correct.
Normally, people would not refer to them as such though. They would be one or the other. If it detects harm, regardless of mechanism, it will be recognized/addressed as a nociceptor only.

source: Stack Exchange

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

sort: votes


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Can a brain process auditory signals at 18 weeks of human development?
According to When a fetus hear , When a baby can hear in the womb and several other similar articles, a baby starts to hear sounds at week 18. And according to How hearing works. Hearing involves

nerves communicate to the brain. The hearing nerve then sends the
  information to the brain with electrical impulses, where they are
  interpreted as sound.

Does this actually mean a brain is actually processing auditory signals at 18 weeks of human development, or is the brain at 18 weeks only processing sounds by a process that doesn't involve the brain? Perhaps the conclusion might seem obvious for some, but not for me considering the supposed inability of the brain to process several others (or any other?) kind of signals at that stage, such as pain At what stage is the nervous system developed enough to interpret neuronal signals as 'pain'? and being the hearing experience directly connected to pain sometimes.

The ear is innervated at 18 weeks, if I recall. There is some evidence of varying quality looking at the response to acoustic stimulation, but good evidence of demonstrating cortical processing puts it much later... i think third trimester. I'd have to do some digging to find this though. A quick search didn't yield anything.

According to a concise review by Graven & Brown (2008) the development of the auditory system (Fig. 1) in the human is as follows:

15 weeks gestational age*: structural parts of the cochlea and the middle ear are well formed;
20 weeks: middle ear and cochlea are anatomically functional;
Around 25 - 29 weeks: auditory system as a whole becomes functional, as the spiral ganglion cells in the cochlea connect inner hair cells to the brain stem
and temporal lobe of the cortex. In other words, only at this point, the peripheral end organ becomes connected to the central nervous system. At 25 to
26 weeks' gestation, a loud noise in utero will produce detectable changes in autonomic function.
28 - 30 weeks: neural connections to the temporal lobe of the cortex are functional. The development of tonotopic columns in the auditory cortex commences. They are needed to receive, recognize, and react to language, music, and meaningful environmental sounds.

* Gestational age is a measure of the age of a pregnancy which is taken from the beginning of the woman's last menstrual period (LMP), or the corresponding age of the gestation as estimated by a more accurate method if available. Gestational age can be obtained by adding 14 days to the point of fertilization.

Fig. 1. The adult auditory system. source: Graven & Brown, 2007
Reference
- Graven & Brown, Newborn Infant Nurs Rev (2007); 8(4): 187-93

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How are the receptors in the thalamus weakened/shut down during sleep?
During sleep, GABAergic inhibition of the thalamus occurs and along with that, it should "block" our senses. Are the receptors weakened, or completely shut down? If they are weakened, what is the exact process that can hinder their function? If they are completely shut, how can we still have the ability to hear during sleep and wake up as a result?

Sleep research is a big field and the answer to your question can take many forms and fill libraries. Having said that, it is not so much inhibition of the thalamus per se, but a change in firing behavior that results in a decreased relay function of thalamic neurons afaik. Specifically, during stages of sleep, or in phases of reduced consciousness where thalamic relay of sensory inputs to the cortex is blocked, the thalamocortical neurons are entrained in slow oscillatory bursting behavior, resulting in more synchronized, slow-wave EEG (Fig. 1). This intrinsic slow wave, bursting activity in the thalamocortical network effectively reduces the ability for peripheral sensory input to reach the cortex via the thalamocortical fibers. This explains the unresponsiveness of people with slow wave EEG to external stimuli.
Slow-wave EEG is most prominent during deep sleep. By contrast, during active wakefulness these neurons fire more chaotically, very much dependent on their inputs, resulting in the EEG rich in high frequencies. A succinct overview is given here on the site of McGill University. Fig. 1 shows the dependency of thalamocortical neurons and cortical neurons in cats (Fig. 1A) and rodents (Fig. 1B) during different vigilance states. The figure is taken from a rock in sleep and epilepsy research, namely David McCormick.
Because the thalamocortical neurons are so occupied with their rhythmic bursting, phasic input from the thalamus may not be relayed. However, stimuli strong enough to push through / override the oscillatory behavior may still result in cortical activity in the sensory regions.

Fig. 1. Slow wave sleep in cats (A) is associated with slow oscillations and spindle waves (equivalent to the K complex in man). The waking state is characterized by rhythmic activity at  higher (gamma) frequency range. In mice (B), mere inactivity like cessation of walking is associated with an increase in slow rhythmic activity. (C) Schematic of thalamocortical circuitry responsible for the generation of rhythmic activity. The slow oscillation and gamma frequency oscillations are generated within the cortex, as an interaction of excitatory and inhibitory neurons. Spindle waves are generated during sleep in the thalamus as an interaction of thalamic reticular GABAergic neurons and thalamocortical relay cells. source: McCormick et al. (2014)
Reference
- McCormick et al., Curr Opin Neurobiol (2014); 31: 133-40


text:
Help identify this red/black Vietnamese insect
I found this strange insect while on Son Tra, Da Nang in central Vietnam. It was about 4cm long and although it was on the ground, was obviously capable of flying. I've never seen anything like this and would like help identifying it, please. Thanks!

It looks very much like a robber fly. I'm voting to close as a duplicate.

Possible duplicate of What type of insect is this?

The duplication is taxonomic only, not geographic (but a brief search found few images of live robber flies from Vietnam, so going deeper is best considered problematic).

Dasypogon is a genus of robber flies in the family Asilidae.

Kingdom: Animalia
Phylum: Arthropoda
Class: Insecta
Order: Diptera ,
Family: Asilidae
Tribe:Dasypogonini
Genus:Dasypogon.

84 species belong to the genus Dasypogon. Among these, this one is Asilidae Dasypogon diadema.

Thanks for the link. Could you link the site to the picture as well - it looks like the same image btw ? It's best practice to dig up an image form a reputable website to show the positive ID. I took the liberty to clean up your post a bit. Thanks for your contribution. +1

Welcome to Biology.SE! According to several sources this is a European species and not found in Vietnam. In general, you are more likely to get a positive response to your answer if you explain why your identification is correct. Specifically, please [edit] your answer to add discussion of key features that led you to this conclusion and supporting references or at least validated images. Without this your answer is indistinguishable from opinion. ——— You may also wish to take the [tour] and then consult the help pages for additional advice on [Answer] effectively on this site. Thank you!

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How many ommatidia does a honeybee have?
European honeybees (Apis mellifera) have compound eyes made of tiny facets called ommatidia. The number of ommatidia is usually known in most model insects, but I cannot find reference for the European honeybees, despite bees being highly studied. How many ommatidia does a European honeybee have on average?

4700 - 5400, according to Somanathan et al. (2009). They base their reported values on two other papers.
Reference
- Somanathan et al., J Exp Biol (2009); 212: 2448-53

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Is glyphosate carcinogenic?
I'm trying to understand if glyphosate is carcinogenic. The information in internet is very confusing. There are many ecological oriented websites which claim it's carcinogenic which I suppose they could be biased, but also news websites stating that World Health Organization says "it's probably carcinogenic". In the other hand the European Union seems to sustain it's not, and it extended its license of use in a "heated debate". is it known if glyphosate is carcinogenic or not, or just there isn't enough evidence to sustain one thing or the other?

The substance that have to be used in conjunction are very problematic, so many glyphosate-containing formulations are suspect. Glyphosate itself is not under direct suspicion, but the drive for a ban aims for the substance itself nonetheless... Glyphosate and the products containing it are linked, as the only valid(=big) exposure studies naturally come from producs in use. Nobody will douse thousands of people in pure G just to get epidemiology statistics... The problematic additives need (?) to be there because G alone does tend to not stick to plants, threby loosing much of its power.

So, if the experts of the WHO and the EU cannot agree, do you really expect someone on this list to be able to resolve the problem? This is a question and answer site, not a discussion site, so even though the question is important I have voted it off-topic. I suggest you read discussions of the topic from authoratitive sources, such as this recent one in Nature.

@David Actually I do. I've seen completely ridiculous researchs with zero scientific credibility and evidence from Harvard itself, which is supposed to be the most prestigious university or one of the more importants. Also I've been seen completely ridiculous and pseudoscience claims from WHO in other subjects. So I wouldnt be surprised if this issue was treated with little scientific strictness in favor of economic interests by WHO, European Union and any other "prestigious" entity and someone here with facts and real science could point in the right direction

There is a difference between potential and risk. That's why different agencies came to different conclusions.
The IARC (International Agency for Research on Cancer, a body of the WHO) assesses the potential of a compound to cause cancer. They go through the research that point into this direction and if there is any hint that any dose of the compound might cause cancer they have to rate it accordingly. If you go through the IARC report on glyphosate, you find that a lot of the studies they looked into did not actually find a link between glyphosate and cancer in humans. Nevertheless, there are some studies that show that high doses of glyphosate can result in cancer in animals. So, the IARC had to conclude that glyphosate has the potential to cause cancer. They put it into the category 2A (probable carcinogens). In the same category you find red meat, hot beverages and being a hairdresser, because these things have the potential of causing cancer.
Agencies like the FDA, EFSA etc. are assessing the risk of cancer from "normal" glyphosate exposure. While it seems to be possible to get cancer from "too much" glyphosate, we are only exposed to a tiny fraction of that dose. While it's unavoidable that small amounts of glyphosate residues are found in our food, these amounts are most probably not harmful. At least, that's what most research concludes. The dose makes the poison. While eating fresh organic berries does not pose any risk to harm you, they naturally contain small quantities of chemicals that have the potential to harm you at high concentrations. Your body itself makes small amounts of compounds that have the potential to harm you (e.g. Formaldehyde).
That's why the debate is so heated. Environmental activists are taking the cancer potential assessment of the IARC and turn it into a risk for the consumer, which is untrue. If they would work with the same energy against other group 2A carcinogens, we would have to close down barber shops...
So, does glyphosate has the potential to cause cancer? Probably yes.
Does this provide a risk for the consumer/farmer? Probably no.

The research on Glyphosate and cancer is ambiguous however the journal Nature published a paper on January 9, 2017 that found that rats fed ultra-low doses of glyphosate developed non-alcoholic fatty liver disease. The article is: Multiomics reveal non-alcoholic fatty liver disease in rats following chronic exposure to an ultra-low dose of Roundup herbicide

First: This article is not published in Nature, but by the "Nature Publishing Group", it is published in "Scientific Reports". It has another big red warning flag attached to it, as one of the authors is Eric Seralini, who has already been proven to produce bad papers about the connection of Glyphosate and cancer in rats. His credibility in this field among serious researchers has gone below zero and I trust him as far as I can throw my car. Some of these had to be retracted due to bad conclusions and methods and he has followed a clear (political agenda) to which he fitted his experiments.


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Pain perception in animals with nerve nets
Are animals with nerve nets, like sea urchins and jelly fish, theoretically able to feel pain? They have output and input organs which would make them "vulnerable" to feel pain but on the other hand, they don't have brains. I was wondering if they show any signs of "pain" when they are attacked or eaten?
And if they don't show any signs of pain is there the possibility to measure something that could be interpreted as pain?
Edit:
The word pain is here meant in a way, that it responds to an outer force with behavior which one could interpret as an inner-process that shows discomfort. The important parts are here the words "interpret" and "show signs of".
Pain is here thus meant as a behavioural response that could lead to an interpretation of an inner-process


text:
Where could I find biology-specialized transcription services for my conference?
I'm a conference organizer for various conferences in the field of biology. Just recently, I stumbled upon this Nature article: https://www.nature.com/articles/d41586-021-03487-2 and I have difficulties in finding biology-specific expert transcription services for my conferences. The generally well-known transcription service providers do not have people available that are familiar with the ubiquitous scientific terminology used by speakers on my conferences. Where could I find scientific experts that are capable of transcribing terminology-heavy talks across various fields of biology and willing to do so?

I’m voting to close this question because it is not about a problem in biology.

Short answer
To provide accessible conferences for the hearing impaired, automated artificial intelligence (AI) based captioning services are a good and affordable substitute to live captioners these days.
Background
I took the liberty to outsource this question to a giant in the field I work in (Auditory Neuroscience and specifically auditory prosthetics) and they wrote me the following back, and I quote (web links and comments in square brackets added by me):

'We previously used a remote live transcription service that cost
about $5000 [USD] for the [conference] week.  But the AI based automatic transcription
service is now so good we didn’t think there was enough difference in
quality to justify the expense of live captioners.  The institutional
version of Zoom has AI captioning built in – there’s a cc button at
the bottom of the screen, and the captioning built in to youtube is
excellent for prerecorded videos.  We used these two for the recent
[conference].'


text:
Western blotting with multiple antibodies
Normally I wash/detect with one primary/secondary-HRP antibody pair, strip, then wash/detect with the other primary/secondary-HRP pair which works well. However, I recently started working with a HRP-conjugated primary antibody for my protein of interest and wondered if I might add this together with the secondary antibody for my loading control to save the stripping and second washing.
Are there any general guidelines for Western blotting with multiple antibodies at the same time, i.e. changing antibody dilution?
An obvious first step is to make sure the HRP-conjugated primary isn't from the animal recognized by the secondary. I anticipate blotting with mouse HRP-conjugated anti-GFP and a secondary rabbit anti-mouse would not be a very good decision.

Do you mean HRP conjugated secondary? I have not heard of HRP conjugated primary antibodies in the context of Western blotting.

I have a HRP-conjugated primary, yes.

it is generally recommended not to use multiple antibodies at the same time mainly due to cross-reactivity/interference either from your primary or secondary Ab since the primary conjugated can bind to the first primary already bound. Also are you confident you can recognise which signal is coming from which Ab? this can be tricky if you have degradation products or dimerisation of your proteins! I generally use one membrane for 1 Ab and another membrane for another Ab. Although this is time consuming but its the safest!

@Bez using a different membrane kind of defeats the purpose of a loading control, doesn't it? Also, in my case there are definitely no multimers or degradation products and the proteins are quite different in size so there should be no confusion as to what is what.

What you can do depends on your proteins: If both proteins (your target protein and the loading control) are seperated far enough, you can detect both of them in the same step by adding both primary antibodies and both secondary ABs into the buffer at the same time. They will bind only to their specific epitope and you will get nice signals. This is something I have done several time. This avoids the stripping process (which can be tricky sometimes) and you have both signals on the same film. Additionally you save chemicals, film and time.
There is another way with which you can come around the stripping: Do you first primary/secondary antibody combination and then incubate the blot with a buffer containing sodium azide. This inhibits the enzyme irreversibly, you have to make to wash very carefully afterwards. Then you can proceed with the second antibody combination.
If you want work with a marked primary antibody (which is unusual, but will of course work) and your loading control at the same time, I would definitely make sure that the secondary antibody with the HRP is not binding to your marked primary, otherwise the signal might get very strong (from the primary and also from the bound secondary), but I don't think it would cause other problems.


text:
How are light sheet microscopy 3D images and their computed sections built up from stacks of 2D images?
The iBiology Techniques video Microscopy: Dual-View Inverted Selective Plane Illumination (diSPIM) (Hari Shroff) describes light sheet microscopy and the improvement in resolution by introducing dual-view (two cameras) capability.
What's happening is that the object is moving randomly in 3D, and so for each frame, the stacks are used to generate a 3D image, and then it is de-rotated to synthesize a view in a plane fixed to the object, rather than the microscope.
Is there a simple way to understand how these image stacks are processed to obtain a smooth 3D reconstruction that can then be sectioned computationally? Is there some kind of interpolation or modeling of structure at the limit of the depth resolution?
Rather than a complete explanation, which would likely be fairly mathematical and in depth, a simpler explanation plus a reference or link to a more in-depth description might be a better way to help me get on the right track.

According to their website dispim.org they are using registration software like the ImageJ Multiview-Reconstruction Plugin. Judging from the descriptions, this plugin uses the alignment of multiple points in the different angle images (like fluorescent beads that have been introduced to the medium or the cell nuclei) by rigid transformation and then deconvolves the 3D information using the point spread functions.
Knowing your optical system (microscope lenses etc.) you can calculate how the image of a point light source would look like in the image. This can be used to reversely calculate the actual position of your light source from the image and reconstruct an image without the distortions.
From that they get a volumetric image that can be projected into any coordinate system. I recommend watching the videos on the plugin page to get an idea how this works.

Oh this looks really interesting, thank you! I'll have a look now...


text:
Is the chitin in an insect's exoskeleton cross-linked?
This answer to the question How to clean and preserve a cicada's molted exoskeleton (exuvia)? states:

The exuvia is made of cross-liked chitin, and will not decay. You don't need any special preservatives as all. If you need to get the mud off, just rinse it as you said, in soapy water, let it dry, and you are done. Simple.

Wikipedia's Chitin says only:

Chitin is a modified polysaccharide that contains nitrogen; it is synthesized from units of N-acetyl-D-glucosamine (to be precise, 2-(acetylamino)-2-deoxy-D-glucose). These units form covalent β-(1→4)-linkages (like the linkages between glucose units forming cellulose). Therefore, chitin may be described as cellulose with one hydroxyl group on each monomer replaced with an acetyl amine group. This allows for increased hydrogen bonding between adjacent polymers, giving the chitin-polymer matrix increased strength.

I'm not a chemist, but "increased hydrogen bonding between adjacent polymers" doesn't sound the same as cross-linked polymers. So I would like to ask for an answer based on sources other than Wikipedia:
Question: Is the chitin in an insect's exoskeleton cross-linked? If it depends on the type of insect, then the focus should be on "a cicada's molted exoskeleton (exuvia)" as discussed in the linked answer.

I'm not sure I've tagged correctly.

Crossliking implies covalent bonds between adjacent polymer chains. I did a non-exhaustive search and it seems that there is no example of naturally crosslinked chitin. There seems to be a mention of a crosslinked protein, though.

@WYSIWYG that's my understanding as well, thanks!

much like cellulose, chitin strands are bonded to other strands by hydrogen bonds. here is a slide share with a breakdown of the structure.
It is crosslinked in the sense strands are linked to other strands in such a way that most enzymes cannot access it to break it down. this is the same thing that makes wood last untreated. In a strictly chemistry sense it is not a crosslinked polymer (which requires covalent or ionic bonding) but it still has crosslinking. Your hitting a difficulty in jargon.
source.

Thanks for the clear and sourced answer, this clears things up!

I would say that the requirement for "covalent or ionic bonding" as in the Wikipedia article is just usage of an English term that has no intrinsic chemical definition. And the difference between an ionic bond and a hydrogen bond is only a matter of degree. If the hydrogen bonds are specific (which they are) I would say that it is perfectly valid to talk about chitin being "crosslinked by hydrogen bonds". However an article on preserving dead beasties is hardly attempting chemical. I think this question would have been better on SE Chemistry and voted to close on that basis.

In polymer chemistry (and also in biochemistry) crosslinking always refers to covalent bonds (or very short covalently bonded chains) between two polymer chains.


text:
When something "smells moldy" what are we really smelling?
When things smell moldy --  it could be clean clothes left in a heap, a damp basement, old books stored in elevated humidity -- they can smell moldy.
There are distinct smells for each of these.
Are we smelling the mold spores themselves, or are there other molecules released by molds that causes the "moldy smell" we perceive?

The vast majority of the things you smell are odorants, or volatile molecules; not spores. They are light compounds that have high vapor pressure (are airborne), and that interact with your chemoreceptors in your nose (can be smelled). The most-often reported microbial volatile organic compounds in living environments according to this study are as follows:

2-Methyl-1-propanol
3-Methyl-1-butanol
3-Methyl-2-butanol
2-Pentanol
3-Octanol
1-Octen-3-ol
2-Octen-1-ol
3-Methylfuran
2-Hexanone
2-Heptanone
3-Octanone
2-Methylisoborneol
2-Isopropyl-3-methoxy-pyrazine
Geosmin
Dimethyl disulphide

Geosmin is probably the most moldy-smelling and is detected very sensitively by olfactory systems of animals that want to avoid contaminated food. To me it smells muddy, or earthy, like soil after a rain shower. In our lab, about half the people find it a pleasant smell. It can be smelled in wine, it's the earthy taste found in vegetables, it's the smell of dead bacteria, and so on and so on. The term petrichor describes the odor and geosmin is a major contributing odorant for this.

Of course, this is just a shortlist of the major odorants. There exist hundreds if not thousands of other volatiles that are released by microbial life. And very often, the mixtures/proportions of odorants can be useful for the perception of smell; it need not be a single compound that makes things seem moldy.

Okay this is really interesting, I'll get a hold of the paper soon and give it a read. I've  about VOCs in the past in the context of air pollution and air quality, but this is the first time I've heard of MVOCs!

I believe geosmin is from bacteria, not mold, and at least the sources you cite are consistent with that. Therefore, geosmin doesn't really seem to answer the question, unless you can support a suggestion that "moldy smell" is unrelated to mold. Also the hypotheses I have heard about geosmin sensitivity are related to the importance of fresh water in a fairly arid environment, not detection of food contamination, hence the pleasant perception.

Geosmin is abundantly released by moldy fungi. It's microbial, not strictly bacterial in origin. I defer to any and every textbook on the topic, or a quick google search. I also work with it in the context of insect ecology :)

not sure if this is relevant but I just ran across it today by accident mVOC 2.0: a database of microbial volatiles.


text:
Deeper Learning in Physiology?
I am a Pharmacology and Toxicology major at a large state school. I was only required to take physics I and II. (algebra based)
At first I thought that was fine, but I soon began to realize that I can't just memorize like my professor and book asks me too, but I need to go in-depth.
So my question is this, I am looking for a way to learn the "physics and chemistry behind physiology" or deeper that what we are taught?
For example, say we are taught that atherosclerosis can cause aneurysms and that aneurysms can rupture.
But what we aren't taught is that blood flow through a closed vessel is constant, so any dilatation in the mid-length will increase the cross-sectional area and decrease the fluid velocity to maintain flow.
In accordance with Bernoulli's principle, the decrease in velocity is met with an increase in pressure, which increases wall tension. Vessel integrity is already compromised from the three layer degradation. So now you start to see this great positive feedback loop whereby atherosclerosis damages the vessel wall causing it to dilate, which increases the pressure, which causes it to dilate further, which damages the vessel wall further, etc, etc, until the aneurysm finally ruptures. (I did not write this example, but it is an example of how I would like to learn it.  I would like to know how the author of that explanation came to that conclusion or what kind of book would explain in heavy detail.)
The question I am asking how can I learn the "science" behind the physiology?  I'm a type of learner that needs to know the how and why.  Will I need to take more physics classes?
** Sorry if I posted in the wrong section, I am new to stack exchange!

It is very easy, use google + pathophysiology and read some articles in the actual topic. There are a lot of pathophysiology books as well (some of them pretty expensive). Another way to do an online course.
Just a simple search about your example:

It is known that AAAs are characterized by destruction of elastin and
  collagen in the media and adventitia, loss of medial smooth muscle
  cells with thinning of the vessel wall, and transmural infiltration of
  lymphocytes and macrophages. Atherosclerosis is a common underlying
  feature of aneurysms. However, atherosclerosis is not the primary
  driving factor in the development of AAAs. Atherosclerosis is a
  disease that is widespread throughout the vasculature, however
  aneurysms only form in specific locations and only in certain
  individuals. Additionally, atherosclerosis is primarily a disease of
  the intima, while aneurysm formation primarily affects the media and
  adventitia.

2009 - The Pathogenesis of Abdominal Aortic Aneurysms


text:
How are lipid-coated mRNA-based vaccines transported into cells for expression?
In CNN's video Scientist says Coronavirus vaccine could be ready by 2021 after about 00:25 'Robin Shattock, the Head of Mucosal Infection and Immunity at Imperial College London' says:

We were able to access the sequence that was published by Chinese scientists and made globally available, which was a tremendous thing to do. And we went from that sequence to identifying part of the sequence that encodes for the surface proteins of the virus. And we’re using that sequence to manufacture our vaccine.
We’re using a particular approach where we make a synthetic vaccine based on RNA, so essentially it’s essentially genetic code, we package that in essentially a lipid droplet, and use that to inject in a muscle; it expresses that protein, and the body recognizes that as foreign and it makes protective antibodies.

I'm assuming that the RNA mentioned is mRNA, and so once it reaches the cytoplasm of the vaccine recipients muscle cells it will be expressed and somehow returned to the cells' membrane where it will be recognized as foreign by passing lymphocytes.
Questions:

Is this basically correct as far as it goes?
If so, what causes the lipid droplet to fuse with muscle (or other) cells in the first place?

From what I read transfection of DNA vaccines are based either on electroporation or viral vector

@reuns There is a whole world of nonviral transfection reagents that do not depend on electroporation. They typically include cationic polymers, lipids, and peptides.

@user137 It says you'd want a few of the mRNA lipid-PEG coated particles to become endosome in dendritic cells where (after release and translation by ribosome) the protein is taken by the MHC pathway for presentation on cell's surface. Then (because particles provoked an inflammation?) the surface MHC-antigen is processed by the immune system for acquisition of new antibodies. Is it the real-life scenario you are thinking to ? The possibility of replacing the mRNA by a replication competent RNA virus encoding it is briefly mentioned.

@reuns I've just asked Do both DNA and mRNA-based vaccines sometimes require electrical pulses to work?

@user137 ditto.

“Essentially Genetic Code?” No, No, No. A thousand times No. Educate a public that understands the difference between a current and a voltage, and don’t discredit one of the major scientific achievements of the 20th century. Or does he really not know what the genetic code is?

I can't give an authoritative answer on this because my PhD work was based on mRNA delivery using peptides instead of lipids, but many of the concepts are the same. I also don't have time to provide proper citations, but this is probably too much for a comment.
Anyway, mRNA is a very fragile molecule, it can be broken down extremely quickly in the blood by serum nucleases. Therefore we must protect the mRNA by mixing it with some other chemical, in this case a mixture of positively charged lipids. The positively charged lipids are attracted to the negatively charged phosphate backbone of the mRNA, and form a nanoparticle trapping the mRNA inside and hiding it from the nucleases. The lipids are often, but not always, PEGylated, which means that a molecule of polyethylene glycol (PEG) is attached to the lipid. The PEG groups form a layer on the outer surface of the nanoparticle that helps prevent protein binding.
These mRNA lipid nanoparticles are then injected into a patient. This will probably be an intramuscular injection so that the particles are most likely to be taken up by muscle cells. The exact mechanism explaining why lipid nanoparticles are attracted to cells isn't entirely clear, but it's likely a combination of electrostatic attraction between the positively charged nanoparticle and the negatively charged cell membrane and proteins that bind to the nanoparticle and are then recognized by receptors on the cell surface.
After the particle is taken up by a cell it is usually trapped inside a membrane-bound structure called an endosome. As the endosome matures it is acidified, and as the pH drops from about 7 to about 5.5 the nanoparticle is disrupted. The lipids that made up the nanoparticle can merge with the lipids that make up the endosomal membrane, disrupting that membrane and breaking open the endosome, allowing the mRNA to escape into the cytoplasm.
Once in the cytoplasm the mRNA will find a ribosome and produce protein. Just like you said, the protein in this case will be membrane bound and expressed on the outer surface of the cells for eventual immune recognition.


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Which animal dug this 5 cm diameter hole deep into mud and build a large mound around it?
I noticed the large structure below today at the edge of a very small pond in northern Taiwan lowlands. It is June and it has rained a bit the past few days, and this 15 cm mud dome with a 5 cm diameter hole going straight down looked fresh and wet and glistening.
It is hard to tell for sure but it looks like the borough went deep enough to reach the water line of the pond next to it, but I could not tell because it's dark inside and I did not have a flashlight.
The mound is large, perhaps 15 cm tall and wide, which suggests that a lot of material has been removed and the tunnel could be quite deep.
The pond is only about 3 x 5 meters in diameter.
Question: Snake? Crab? Mole? What further information can I collect about it that would help to identify what produced this?
click images for full size view

A crustacean (land crayfish). There are a lot to choose from.
http://web.nchu.edu.tw/~htshih/crab_fw/fw-crabe.htm

Cool link, thank you! I certainly do see land crabs around from time to time. Can you add a little more to your answer though, perhaps a link demonstrating that they do indeed build chimneys or whatever this is? I found this while googling after your answer, perhaps it can help https://www.semanticscholar.org/paper/Burrows-with-Chimneys-of-the-Fiddler-Crab-Uca-and-GUSM%C3%83O-JUNIOR-Machado/5de43358797ebf5a6b5156f36b15b8e28e77f3df

I haven't found a ref for this, just now talked with an old farmer from Taiwan, he says they are shaped  more like crayfish, with a tail.

I'm quite sure this is the right answer, thanks for checking on that!


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What were the challenges to sequencing the last 8% of the human genome that took 20 years to overcome and how was this done? (T2T Consortium)
CNN's March 31, 2022 article Scientists sequence the complete human genome for the first time says:

In 2003, the Human Genome Project made history when it sequenced 92% of the human genome. But for nearly two decades since, scientists have struggled to decipher the remaining 8%. Now, a team of nearly 100 scientists from the Telomere-to-Telomere (T2T) Consortium has unveiled the complete human genome -- the first time it's been sequenced in its entirety, the researchers say.

and

The research, published in the journal Science on Thursday, was previously in preprint, allowing other teams to use the sequence in their own studies.
Until now, it was unclear what these unknown genes coded.
"It turns out that these genes are incredibly important for adaptation," Eichler1 said. "They contain immune response genes that help us to adapt and survive infections and plagues and viruses. They contain genes that are ... very important in terms of predicting drug response."
Eichler also said that some of the recently uncovered genes are even responsible for making human brains larger than those of other primates, providing insight into what makes humans unique.
This remaining 8% of the human genome had stumped scientists for years because of its complexities. For one thing, it contained DNA regions with several repetitions, which made it challenging to string the DNA together in the correct order using previous sequencing methods.
The researchers relied on two DNA sequencing technologies that emerged over the past decade to bring this project to fruition: the Oxford Nanopore DNA sequencing method, which can sequence up to 1 million DNA letters at once but with some mistakes, and the PacBio HiFi DNA sequencing method, which can read 20,000 letters with 99.9% accuracy.

CNN's explanation is helpful as far as it goes, but with Nanopore's error rate of 1% to 3% (1, 2) and the difference between the repeats of some repeated sequences presumably a lot less than that, how was the error-prone Nanopore method combined with the HiFi method to nail the last 8% of the human genome accurately despite the repeated sequence challenges?
Question: What were the challenges to sequencing the last 8% of the human genome that took 20 years to overcome and how was this done? (T2T Consortium)
A premise of the question post is that it was the presence of repetitive sequences that posed the primary challenge, but the CNN article says "...because of its complexities. For one thing, it contained DNA regions with several repetitions..." which suggests there are other important factors as well.
Update: From the March 31, 2022 item in Science Most complete human genome yet reveals previously indecipherable DNA:

In six papers in Science, the Telomere-to-Telomere (T2T) Consortium—named for the chromosomes’ end caps—fills in all but five of the hundreds of remaining problem spots, leaving just 10 million bases and the Y chromosome only roughly known. And today, the T2T consortium announced in a tweet it had deposited a correct sequence assembly of the missing Y.

I think that of the six, the main paper is The complete sequence of a human genome

1Evan Eichler, a Howard Hughes Medical Institute investigator at the University of Washington and the research leader, said Thursday.

may need additional tagging, and the usage guidance for repeatitive-sequence may need some help as well :-)

The researchers did the easy bits first, and left the hard bits for later

@BryanKrause I think the question post as written is squarely on topic but it's those few words that seem to distract users here (but did not in Matter Modeling nor Politics). Each community's sensibilities are different and I'm not always as adept at shifting into the correct gear when moving from site to site. Does this look better?

Yes I think that is better. It may be a duplicate here but I don't have that post off hand.

@BryanKrause I'm having my morning coffee early today, I didn't see one when I did a quick check but I have time to look further now. If I find both the challenges and how they were overcome as described in the six new papers published in Science by the T2T Consortium already in answers here I'll vtc as duplicate myself! In the mean time I'll hunt them down and add links to the question. Thanks for your help!

The ~8% of the sequence that was missing was, as you say, complicated by high repeat content. Repeats make the problem of computational genome assembly hard at the best of times. Long repeat arrays make the same problem impossible unless you have sequencing technologies that have reads at least as long as the arrays in question.
A non-genomics example
Consider a sentence in human language where single words or phrases are heavily repeated. An example from German would be:

Wenn hinter Fliegen Fliegen fliegen, fliegen Fliegen Fliegen nach.

This is a grammatically correct and meaningful sentence that happens to have a "repeat array" of 6 copies of the word fliegen. But it can be confusing when the brain has trouble tracking that much information. Imagine that you only caught the beginning and the end, but otherwise you just know that the word "fliegen" was in there a bunch in that repeat array. How would you figure out what is going on? You just know:

Wenn hinter Fliegen Fliegen....

...Fliegen Fliegen nach.

Your understanding of the sentence is "anchored" in the unique words on either side of the fliegen array. But you have no idea what's going on in the middle there.
How you solve this problem is by paying close attention and remembering the sentence in its entirety. You may not be doing this habitually in casual conversation, but a highly motivated person who knows the language should not have any issues with this.
How this is related to genomics
Genomics technologies got very good at reading DNA a little bit at a time. At the time of the publication of the draft human genome originally in 2001, the predominant method of sequencing had an average read length of ~500 base pairs. A chromosome on the other hand is on the order of 100 million base pairs. This is ok from a genome assembly perspective without repeats. Even with repeats it is asymptotically ok for naive assembly as long as your repeat arrays are shorter than your longest reads. In other words, if your reads can pay attention through the whole repeat array, you can probably assemble the repeat array into the genome.
People got very clever with tools like BACs and YACs to get up to a million or so base pairs, though those tools still suffer from a lot of limitations and are quite labor intensive.
Now, consider that over half of the human genome is repeat. When we got lucky we were able to assemble human genome repeat arrays of around a million base pairs or so, but not in every case. Wherever we failed to assemble through such a repeat array, or where we simply were unlucky for some other reason, there exists a "gap" in the human genome.
In some cases we know what's on either side of the gap (e.g. it is in a chromosome), but not what's in the middle. In 2001 there were over 100,000 gaps with a total length of 80M bp in the human genome. That's a lot of missing stuff. In more recent genome builds it is actually higher (~5%), mostly because we simply ascertained more genome sequence since 2001.
In other cases we don't know what's on the other side of a gap, and these sequences are properly called "contigs"; these are little scraps of sequence that we weren't able to put into a chromosome at all, that we know exist somewhere but can't place properly. (There are some technical quirks here in that there anchored contigs and unanchored contigs, and a whole taxonomy of different flavors of not knowing stuff about sequence, but we don't need to get that down in the weeds!) The current standard build of the human genome, which improved dramatically on the 2001 publication, still has ~400 such contigs.
So there are lots of repeats in the human genome that were very hard to bridge. Up until now, the human genome has had a lot of Wenn hinter fliegen fliegen...??? without being able to read through the whole sentence.
Long read sequencing closes gaps
The T2T consortium is different in that it used "long read sequencing" of two kinds, nanopore ("ONT") and PacBio HiFi.
Nanopore reads are huge. They can get up to 1 million base pairs for very good runs. That's just enormously longer than methods like Sanger (~1000bp max) or current workhorse Illumina (~500bp max). You can read through tons of stuff with reads that long that was simply impossible.
The downside of nanopore is that you have somewhat low confidence in the accuracy of any given base, but on average it is still good enough to computationally take the average of a bunch of reads and get a good idea of what the genome looks like. Nanopore is great at stitching together problematic regions separated by repeat arrays, by just blowing through the whole array by brute force. HiFi is higher confidence but shorter (a mere ~20K bp per read!!) and much higher volume, so it is great for building the chunks to stitch together with nanopore.
Conclusion
The change of the T2T consortium was chiefly a technological change that allowed us to read through repeat arrays. People had previously used a lot of clever algorithms to bootstrap short reads, but they were still fundamentally limited by short reads failing on big repeat arrays. T2T removed that limitation, such that our long reads are now long enough to read through basically everything in the human genome.


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What makes cherry blossoms so delicious? Does this delicious molecule (or molecules) have some function in the blossom? Does saliva activate it?
My friend showed me a news item about a monkey (or macaque) recently (early February) seen in Taiwan eating cherry blossoms. I assumed it must have been eating caterpillars or other insects that eat the blossoms, but a quick search in google found a related video shot in Japan Monkey Eating Cherry Blossoms in Slow Motion.
So a few days ago I tried a few. I pulled off the petals (since the monkey also seemed uninterested in them) and when I first started chewing I tasted nothing but inert vegetable matter.
But then over about 15 to 20 seconds of chewing the little blossom bodies I noticed it first became bitter, then slowly increasing taste of what I describe as "Black Cherry" flavor, but without any sweetness. It continued to get stronger and more delicious, and I did not want to stop!
That day I'd chewed (and eventually swallowed) about a dozen blossoms and felt absolutely wonderful; like I had been treated to a real delicacy.
note: The cherry trees planted and cultiated for their decorative blossoms in the early spring are not the same as the trees that yield commercial cherries. I'm told their fruit is quite sour.
Question: What makes cherry blossoms so delicious? Does this delicious molecule (or molecules) have some function in the blossom? Does saliva activate it?
It's possible that it's stored in structures that take time to break down during chewing, but I got the impression that a chemical reaction was taking place, perhaps a bit like how starch becomes sugar as we continue to chew on bread.

slightly related (and currently unanswered) Why Japanese cherry trees blossom so early in spring?

just asked in Cooking SE: Are cherry blossoms ever used in cooking for their flavor? Is there a preference between ornamental and agricultural varieties?

There actually is a study in the Nature magazine identifying the volatile (in the sense that they easily evaporate, as most aromatic substances do) organic compounds in cherry flower essential oils (basically a liquid cherry flower "extract" in which these volatile organic compounds are enriched by a process similar to distillation) the researchers made from cherry flowers from four different cultivators.
In the study, you find a table.
It contains a list of the volatile organic compounds found, including
how much they found in the essential oil created from the cherry blossoms from each cultivator, respectively.
I copied (one copy-paste suffices) the table into a spreadsheet program (LibreOffice Calc), and then added a column with the average share (probably wrt. weight, see study for details) of the respective volatile organic compound found (averaged over the four oils the scientists made from the blossoms from the four different cultivators), and sorted the table by that column.
The compounds with the largest average share are:

compound
average share [%]
taste

Ethanol
15.8600
it's alcohol

(E)-2-Hexenal
11.4725
like green apples

Benzaldehyde
10.4025
like cherries

Dimethyl sulfide
5.7000
savory

Acetaldehyde
5.4625
tart flavor, like green apples or dry cider

Linalool
4.0625
flowery and citrus like flavor

Followed by compounds with shares of less than 2.8%.
Now the question remains which of these are most important for the cherry blossom taste you observed.
Regarding this, I would like to remark the following:

benzaldehyde and linalool probably play a major role, as you described the taste as black cherry like, and according to this article, benzaldehyde, linalool and eugenol are the most important constituents of the cherry taste (eugenol was not found in the essential oil, and methyleugenol only had a very small share, see the original table).
Ethanol probably only has little effect on the flavor, as it has not that strong of a flavor to begin with, and may even have appeared in the study in such large quantities just because the blossoms were not handled quickly enough and rotted a little, so that possibly, in fresh blossoms, one would find much less ethanol.
Dimethyl sulfide possibly only has little effect on the flavor of fresh blossoms, as it's savory taste doesn't fit the taste you described and the quantity found in the study may similarly actually mostly be the result of the blossoms rotting (as dimethyl sulfide indicates bacterial contamination when brewing).

Explaining the time delay:
Obviously, the compounds are at first contained in the cells of the blossoms (mostly in the vacuoles of the cells). It takes time for the chewing to destroy those cells and for the compounds to leave the destroyed cells and enter your saliva by diffusion, possibly explaining the short time delay.
Safety of eating blossoms:
As you see, those blossoms contain a variety of organic compounds, some of which are actually poisonous in still quite small amounts.
I don't know in what amount, if any, those cherry blossoms you ate are safe to eat, maybe they are totally fine, maybe they are fine in small enough amounts, and maybe those specific cherry blossoms are downright poisonous. This may even depend on details, maybe some cherry blossoms are safe to eat and others aren't (considering that table for example, one of the cherry blossom essential oils tested had 0.54% coumarin, while another had none, and coumarin is poisonous). Please ask someone qualified whether the cherry blossoms you eat are safe.

What a wonderful, thorough, fact-based, well-supported, and informative answer! Also, you emphasize a really important point - don't just eat stuff! A video of a monkey eating one kind of cherry blossom in Japan is not an indication that I should feel safe eating a different kind in a different place. Consider me suitably reminded. :-)

In the linked paper's introduction, this caught my eye: By volatilization, the smell of some flowers not only generates a signal to stimulate the immune response to self-heal but also has an important role in plant resistance to various stresses¹⁸

¹⁸ is Potential applications of glucosyltransferases in terpene glucoside production: impacts on the use of aroma and fragrance who's abstract includes "It is now well established that odorless glycosides represent a significant pool of aroma precursors in plants where they act as preformed but inactivated defense or attractive chemicals." Perhaps that's why it takes circa 15 seconds of chewing before my perceived "black cherry" flavor starts to kick in (which is part of my question)

Possible, but it may also simply be the time it takes to extract the aroma by chewing...

I ate a few more a few days ago and paid careful attention. They start out tasteless after many seconds of chewing but then turn first bitter for several seconds before the deep, satisfying "black cherry" flavor kicks in, so I slightly edited the question to reflect this as I don't think it affects your answer. Also fyi I've just asked in Cooking SE: Are cherry blossoms ever used in cooking for their flavor? Is there a preference between ornamental and agricultural varieties?

As an aside, cherries (Prunus avium) and almonds (Prunus dulcis) belong to the same genus. Stonefruit kernels contain cyanogenic glycosides known to be toxic in large amounts, so some caution is warranted. That faint almond smell is more than sweet. See: https://repositum.tuwien.at/handle/20.500.12708/4851?mode=full


text:
how do we feel electricity on skin even though merkel cells are pressure sensitive only?

Note: Here I am not talking about electric shock (one feels when a lot of electricity passes through), I am talking about smaller sensations one feel directly on the skin.

Note: I am not able to find any correlation graph between feature of electricity that determines the intensity of feeling i.e., voltage, current or frequency. So is there any research paper or anything else around that can shed light on this? This will be very helpful.

I have studied that humans sense touch because of the "Merkel cells" in the skin, and Merkel cells are essentially pressure sensors. I don't think electricity leads to pressure changes, So then how do we feel the sensation of electricity on skin. Is it because electricity directly interface with neurons some how?
If I am not able to explain the question here is a more practical way of thinking about it:
If I touch two electrode close on the skin (or maybe possibly one even though I am not sure one can do the trick) and pass electricity how will skill feel it.

Do you mean static electricity?  (I've never felt anything else that wasn't a shock.)  I'd suspect that the static electric charge on body hair is causing them to move, activating pressure receptors.

Why do you assume electricity isn't passing through your skin just because it doesn't feel like a shock? Electricity doesn't always feel like a shock. For example, when electrodes cause your muscles to twitch.

@jamesqf I am not just talking about static electricity. One practical example that you might have felt could be if you take a 9v battery and touch it on your tongue you will feel sensation that can't be described as shock. Similar things are possible to do on skin at higher voltages.

@DKNguyen ya electricity is definitely passing through skin (and I am not assuming it isn't. But for my particular application I am interested in sensation directly felt on skin.

In the skin, there are 4 types of tactile receptors, dependent on whether it is glabrous or hairy skin;

Meissner's corpuscles
Merkel cells
Ruffini endings
Pacinian corpuscles

Ruffini endings are thought not to be sensitive to electrical stimulation, the other 3, however are. These other 3 can readily be electrically activated and each type can be separately targeted by changing stimulus and placement parameters. Activation is normally due to pressure differences. However, the nerve endings are basically axons, and these can be activated electrically as well Kajimoto et al. (2002).
Some parts of the body have high densities of these tactile receptors, such as the fingertips and the tongue. That's why electrical stimulation has been applied as a means to convey information via the skin. Take for instance the BrainPort device (Fig. 1); this device consists of a camera hooked to a tongue-display unit (TDU). The TDU translates camera pixels into tactile images on the tongue, brought about by 144 electrodes. It is designed to substitute vision for blind people. (Stronks et al., 2016).

Fig. 1. BrainPort device. Source: Nau et al. (2014)
References
- Kajimoto et al., Electronics and Communications in Japan, 85(6) 120-8
- Nau et al., Front Hum Neurosci (2014): fnhum.2014.00291
- Stronks et al., Exp Rev Med Dev (2016); 13(10): 919–31

Thanks for answer I also read your answer to this question https://biology.stackexchange.com/questions/37207/why-can-humans-feel-electricity and it was also helpful. But is there research on correlation between electrical features and sensations on body.


text:
Are there gaps in what our ears can hear?
I know about the hair cells in our Cochlea and it is the movement of the fluid that makes them vibrate. And it is this that activates the transmission of electrical signals to the brain that become sound.
But I've heard that hair cells are each built to detect specific pitches of sound. And if they don't get that particular pitch then they don't transmit.
So as I understand it, we have cells that each respond to one particular pitch and nothing else. Since we have many that each respond to a different pitch, this is what gives us a wide spectrum of hearing.
What I've been wondering is this, if each hair cell responds to one particular pitch, what happens if we try to hear a sound that is in between two hair cells?
Imagine a hair cell that only responds to 1 Hz (and based on my understanding they do) And next to it a cell that responds to a sound at 2 Hz.
What happens if there is a sound that is 1.5 Hz? Can we not hear that sound because it exists in the gap between our hair cells? Or can hair cells cover a wide range so they overlap and cover the gap?
As our ability to hear sound quantised or continuous?
I know that there are sounds so low or high they are beyond our range of hearing but what about within our range of hearing? If someone played a sound that was right in between two hair cells could we not hear it? Is there a finite number of different sounds that we can hear within our hearing range?

Good question. I think clearly the range of the hair cells do overlap, because if I listen to a tone that slowly changes in pitch, such as slowly tuning a guitar or piano string I don't notice gaps where the sound goes away and comes back as I tune the string. Although it would be interesting to know exactly how much they do overlap.

Short answer
No, there are no between-hair cell induced tonotopical gaps in frequency perception.
Background
Young people are able to hear over a frequency range of about 10 octaves, with a frequency resolution of about 0.3% of an octave. So we would have about 2300 resolvable frequencies. This number is dependent on the sound level, as excitation spreads at higher sound levels, but it gives a reasonable starting point to answer your question.
The human cochlea contains on the order of 3,500 inner hair cells. Hence, according to this (highly simplified) calculation, it seems that the number of hair cells is redundant.
In other words, the notion of in-between hair-cell stimulation is stretching the limits of physiological frequency resolution a tad too far.
Reference
- Elliott & Shera, Smart Mater Struct (2012); 21(6):064001
Source
- Cochlea.eu. Cochlea: function

To add to the good answer by @AliceD, take a look at some tuning curves for hair cells, the sound receptors in the cochlea (these happen to be fairly low frequencies and a turtle cochlea, though those details aren't all that important):

Fettiplace, R. (1987). Electrical tuning of hair cells in the inner ear. Trends in Neurosciences, 10(10), 421-425.

The horizontal axis is frequency; the vertical axis is the response of the neurons in voltage. The data are produced by recording responses to a bunch of different pure tones.
What you see is that the cell that is "tuned" to 131 Hz doesn't only respond to 131 Hz, that's just where it responds most. Same for another cell that is tuned "best" to 314 Hz. There would be many cells in between with different best frequencies, and you could take a weighted average of the activity across that population of cells to precisely identify the actual tone.
Generally, the hair cells that actually monitor sounds are some of the most poorly tuned cells in the early auditory system. At higher levels of processing in the auditory brainstem, lateral inhibition improves tuning.

Great answer! And +1 for that ancient graph of Fettiplace ;-)


text:
Why does sympathetic activity constrict pulmonary vessels?
I don't know understand why sympathetic stimulation constricts pulmonary vessels?
I thought that the sympathetic nervous system activated the body for physical activity. Physical activity would need more oxygen supply. Doesn't constriction of pulmonary vessels reduce the gas exchange?

Short answer
The sympathetic nervous system mediates the fight, flight and fright response. It constricts the arteries and arterioles to increase blood pressure, in turn pushing the blood to the muscles and other organs vital for physical activity.
Background
The sympathetic nervous system functions triggers the fight, fright, flight (FFF) response (Fig. 1). It provides the body with a burst of energy so that it can respond to danger (source: Harvard Medical School).
The FFF response is initiated in the hypothalamus by activating the sympathetic nervous system through the adrenal glands. These glands release epinephrine (adrenaline) into the bloodstream. Epi increases heart rate and blood pressure to push blood to the muscles, heart, and other vital organs. The person also starts to breathe more rapidly and the small airways in the lungs open up. This way, the lungs can take in as much oxygen as possible with each breath. Extra oxygen is sent to the brain, increasing alertness (source: Harvard Medical School).
In blood vessels, as you say, sympathetic activation constricts arteries and arterioles (resistance vessels), which increases vascular resistance and decreases distal blood flow. When this occurs throughout the body, the increased vascular resistance causes arterial pressure to increase (Klabunde, 2012). This enhances the distribution of oxygen already present in the blood.  I don't think the pulmonary circulation responds differently than that in the rest of the body. The stress response is meant to support the evasion of acute dangers. But indeed, chronic exposure to adrenaline may eventually lead to impaired oxygen exchange in the lungs (Krishnamoorthy et al., 2012).

Fig. 1. Fight, flight, fright response. source: Freelap USA
References
- Klabunde, Cardiovascular Physiology Concepts, 2nd ed. (2012). Lippincott Williams & Wilkins
- Krishnamoorthy et al., Anesthesiology (2012); 117(10): 745-54

This is a good answer for explaining sympathetic constriction overall but doesn't say much about the specific question regarding pulmonary circulation.

@BryanKrause, true, but I don't think the pulmonary circulation responds differently than that in the rest of the body. I adapted my answer accordingly.

The stimulation of sympathetic system in the lungs causes vasoconstriction of the blood vessels surrounding the lungs and causes dilation of the bronchioles. This increases the ventilation-perfusion ratio, allowing more oxygen to enter the lungs increasing the chances of oxygenated blood. The confusion could be from what happens when blood flow to a part of the lungs is occluded, in the normal systemic circulation, we would expect the blood vessel being occluded to dilate increasing blood flow, however, this is not the case in pulmonary circulation, the blood vessel constricts diverting blood to other areas of the lungs, so the lungs acts in a way to maintain its pressure and reduce shunt.

Neat explanation, good first answer. Just a minor nit-pick, but the post could be improved by adding citations, but I'm upvoting anyhow as it stands as-is. Welcome to Biology, enjoy the site.


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How does natural selection process escape from local optima?
How does natural selection process escape from local optima towards global optimum in a fitness landscape during evolution?

Even getting to a local optimum can be difficult and shouldn't just be assumed. See for example this question or this paper.

From your profile, I see that you have some knowledge in computer science so I will try to use some terms from the field of machine learning!
Natural Selection
Natural Selection (NS) can only lead a population toward local optimum. In other words, NS is like a greedy algorithm. Mutations and genetic drift do not behave like a greedy algorithm.
Genetic drift
Genetic drift may allow to go toward the other direction than the heuristic of NS allowing eventually to reach another attractor. This concept is called shifting balance theory.
Mutations
Mutations can allow all sorts of jump! Mutations Causing large jumps are generally called large-effect mutations (see this section of the wikipedia article for more information).
Fitness landscape changes through time
Also note that the fitness landscape is not stable over time. The fitness landscape depends upon the environment the individuals experience. It would therefore be naive to assume that a specific population had to go through a specific fitness valley in the past just because the valley exists today.
Sexual reproduction and recombination
The fitness landscape analogy depicts the genotype - fitness relationship (some fitness landscape depict the phenotype - fitness relationship but I will ignore them here) for a given individual. One can place all individuals of a population over this landscape and may have some feeling of where the population position over the landscape is. However, this may be misleading.
The fitness landscape is highly multidimensional (one dimension for each amino acid and there are billions of them) and therefore through sexual reproduction and recombination, it is possible that an offspring finds itself in a totally different attractor than the rest of the population. As such, in presence of sexual reproduction and recombination, NS only could lead a jump from one attractor to another one (see Bergman and Feldman 1992). This effect is even more considerable in presence of epistasis.

One question came into mind. You mentioned Mutations separately from Natural selection and Genetic drift. Isn't the outcome of a mutation become visible through either of them? Why has Mutation been mentioned separately?

I am not sure what you mean by "outcome of a mutation" and "visible". When a mutation occurs, it needs no further evolutionary process to exist in the population and can be detected straight ahead.

Is it ok: mutation makes the jump for a single, natural selection and genetic drift follows the mutation for whole local population?

Yes, weirdly phrase, but yes. Note that the whole population will not necessarily (it probably won't actually) move toward this single individual that first had a mutation.

My bad english. :(


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

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


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Ways to cause membrane damage to microalgae and yeast?
I am researching a way to monitor the membrane damage of cells. To do that I fist have to have reference points, namely, cells with damaged membranes.
I am working with Dunalliela, Hematococcus (both microalgae), and common yeast. I have been using mostly ethanol to damage the membranes so far.
What other ways are there to cause the most possible damage to microalgae (or yeast) membranes?. The idea is not total cell obliteration, but rather membrane damage (death is expected).

To get to the membrane of these species you first need to get past a formidable cell wall. The methods listed below are therefore more aimed at making cells permeable but the membranes must sustain some damage in the process.

At our lab we regularly use glass bead transformation for microalgae
transformation. The microabrasion allows DNA to go in so I imagine
the membranes must be damaged somehow.
I've also used hypotonic media (depending on the strain) to swell
cells close to their bursting point. I imagine they become rather
permeable at this point since they let several dyes in that are
otherwise excluded.

Do you just use deionized water as the hypotonic media?. By the way, Dunaliella lacks a cell wall. Thanks for your answer!

I did not know that about Dunalliela, thanks for pointing that out! Yes distilled was always the first thing we tried, it did not work on every alga though. There actually is a paper about this on swelling Dunalliela: http://www.plantphysiol.org/content/93/2/403.full.pdf
The other thing that actually came to mind while writing this thing was digitonin which is often used to solubilize membrane proteins. Other detergents might be worth a look too.


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Do The Traces Genetic Diseases Remain in families?
I know that there are certain diseases that are predominant on genes. But, is there any sort of surety that if parents are suffering from a disorder then their offspring has to suffer from the same. Like my dad is schizophrenic so will I become the victim of the same mental disorder?

just like any genetically affected traits (e.g. height), there is on average greater resemblance between parents and offspring than between two randomly chosen people. If a parent has a genetically controlled disease there is an increased likelihood of it developing in the children but it is by no means a guarantee (even for dominant mendelian traits if mutation occurs). Few things are entirely genetically determined.

In the case of schizophrenia, it has always been evident that there is a genetic factor. However it has not been identified. More recent hypotheses suggest epigenetic mechanisms. Meaning the trait can be inherited, but is very sensitive to short-term environmental changes.

Welcome to Biology.SE. Your question reveals that you probably don't know the concepts of Mendelian segregation/dominance/additivity/pleiotropy and epistasis. You should check out those terms on wikipedia. Also You will probably want to increase your understanding of heritability. Here is an answer that link to 4 other posts that talk about heritability.


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Identify chromosome location from gene nucleotide or amino acid number
I'm sure this is a basic question, but I couldn't find an answer anywhere. Let's say I'm provided with the location of an amino acid or a nucleotide (for example, which lists the location as the ACADM gene, 985A>G (the nucleotide polymorphism) and 304 as the amino acid mutation (from Lys>Glu)). How would I go about now identifying the exact position of this on the chromosome? Eg: Chromosome 1, location 76123456?
Currently the only way I can think is to manually count 304 amino acids, or 985 nucleobases, from the start of the gene where the start location is listed. However this isn't practical. I downloaded some software (IGV & GenomeViewer) and can't see a way I can view the actual amino acid or nucleobase number from the start of the gene.

Have you tried the reference docs ? Eg. For IGV )https://www.broadinstitute.org/igv/Navigate) under searching

Option 1: You can use the SNP database, to see if it has (and it usually is) characterised before: The tutorial is here (http://www.sciencebuddies.org/science-fair-projects/project_ideas/BioMed_Bioinformatics_NCBIGene_SNP.shtml)
Option 2: is to use a go to character function in a few text editors. If you are on windows, You can do it in Notepad++ (https://superuser.com/questions/487507/how-can-i-find-nth-character-in-notepad); if in Linux/mac, you probably know how to do it in vim (https://stackoverflow.com/questions/22862558/go-to-a-specific-offset-in-a-document). If using other text editors in Linux, ask around that community, and they'll tell you how to go about it.
Option 3: One another labour intensive but easy way to do it is to use the tools available online. I personally use NCBI for this, and play around with the region shown. This prevents you from counting. Once you get the local region, select a  few nucleotides  to the left and right, and use that as a search term in your sequence (find text and replace text)

Option 4: And my personal favourite, get the computer to do it for you like this: https://stackoverflow.com/questions/23662748/replace-a-nucleotide-at-a-certain-position-in-a-dna-sequence-file
If you are using IGV, it is said in the documentation here (https://www.broadinstitute.org/igv/Navigate) on how to search for regions and even insert mutations. Were you not able to make this work ?

Some really helpful options there, thanks Rover. I'm going off 23andme data, and it seems it has listed the locations different to the ch38 genotype. Unfortunately it seems the SNP's in the NBI are also missing the 304 variant. Would I be correct in saying no SNP exists for the 304?


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Ancestral Allele and Hapmap
I notice on dbSNP rs6352 has an ancestral allele of G - http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=rs6352
The hapmap in humans for this allele is very rare, the homozygous version practically not existing at all http://hapmap.ncbi.nlm.nih.gov/cgi-perl/snp_details_phase3?name=rs6352&source=hapmap3r3_B36&tmpl=snp_details_phase3
My understanding has been that the ancestral allele refers to the common gene that an ancestor in all humans once shared. Now, I thought the ancestral allele was usually the most frequent in a population, but I can see this was most likely a wrong assumption.
Was it a wrong assumption, or was this example above just a rare exception? Is deviation from ancestral alleles nearly worthless as a metric to investigate possible mutated alleles that may be leading to disease? I realize the proper answer may be too long, but just a brief summary would be appreciated.
Many thanks.

It is kind of confusing.  Here's the sequence, from the ncbi link
GGACATTTAAMGAGGTACGTG
So M is "A or C"
Its a missense mutation, the amino acid called for is either an N or a K.
GGACATTTAAAGAGGTACGTG = K amino acid
GGACATTTAACGAGGTACGTG = N amino acid
GGACATTTAAGGAGGTACGTG = K amino acid
GGACATTTAATGAGGTACGTG = N amino acid
When you blastx it, the top hits are all the K allele, across a few species.
When you blast the DNA, the non-human hits in nr all have a G, not an A or C.  So I guess that's why they are calling that the ancestral allele.  The human hits to nr all have A, so the K amino acid is conserved.

Typically, the ancestral allele is inferred from the allele chimpanzees as our closest relative (and possibly some primates) have. While for most sites humans and chimps have the same allele, there are many cases where the ancestral allele is even completely absent from humans, and where all humans have a different allele from chimpanzees, which we call a substitution.
A substitution in a critical part of a protein can indeed indicate some biological significance, a classical example is the FOXP2 gene, that is related to speech development. In most cases however, substitutions are merely due to genetic drift occurring over millions of years.


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Osmoregulatory Acclimatization in amphibians
If a frog is gradually exposed to increasing concentration of salts can they acclimatise or will they die of exosmosis ?

Can you be more specific? e.g., What kind of frog? How much of an osmotic challenge? What length of time?

@kmm A frog with no special adaptation. This is those kinds of homework question with limited information :)

It will depend on how quickly the salinity is raised and to what level.  Two studies (Karraker 2007, Karraker et al. 2008) looked at the effects of road salt (used to reduce icing on roads in winter) in the spotted salamander, the wood frog (a small frog), and the green frog (a big frog). Their studies showed that survival decreased, especially for larval individuals, as salt concentration increased. Deformities in embryos and larvae increased with salt concentrations$^1$.
Another study (Shpun et al. 1992) showed that a few species of frogs and toads that could tolerate high levels of blood plasma urea concentrations could also tolerate elevated levels of NaCl in their environment (but not all species that had high urea tolerance could tolerate high environmental salt concentrations.)
There would naturally be an upper limit of salt tolerance in amphibians, especially if they are not able to retain or regain water at a rate they are losing it to the high salinity environment.  The studies suggest that higher salinities do decrease survivorship and increase deformities. While they may acclimate to the short term, I would question long term adaptation unless the rate of salinity increase is very gradual.
Footnote

They made their salt solutions based on conductivity, measured as microsiemens. For lab experiments, they made salt solutions that varied from 5 µS (control) to 3000 µS. These translate to 1 mg/L to 945 mg/L Cl$^-$.  In the field, they measured salt concentrations that were more than 3000 µS.

Literature Cited
Karraker, N.E. 2007. Are embryonic and larval green frogs (Rana clamitans) insensitive to road deicing salt? Herpetological Conservation and Biology 2: 35-41.
Karraker, N.E. et al. (2008). Impacts of road deicing salt on the demography of vernal pool-breeding amphibians. Ecological Applications 18: 724-734.


text:
Gel electrophoresis question
Leena is a molecular biology student. She purifies two fragments of DNA, 800 and 300 base pairs long. These were obtained from a plasmid after digesting it with HindIII. Each of these fragments has a single EcoRI recognition site.
Leena wants to join these two fragments to get a 1.1kb gene as shown in Figure 7.1. She suspects that this gene has a unique protein-coding sequence.
She, therefore, mixes the two fragments in the presence of excess DNA ligase in an appropriate buffer and incubates the mixture. She removes an aliquot (a small part of the reaction mixture) after 30 minutes and loads it on an agarose gel to check the results. She is surprised to find many bands along with the expected 1.1kb band  in the gel.

FIG 7.1

Leena is interested in the 1.1kb fragment shown in Figure 7.1. Hence, she elutes the 1.1kb fragment from the gel shown in Figure 7.2 and subjects part of this sample to HindIII digestion. She obtains the expected pattern with two bands, 800 and 300 base pairs long. To confirm its restriction map, she subjects the remaining sample to complete EcoRI digestion. Which pattern of bands would she obtain?

The answer given is this and I understand why this is the answer and other options given in the question(not posted here) are definitely not the answer but I do not understand why there are no 0.4kb fragments, 1.1kb fragments here.

@A. Kennard beat me to it. Here is my answer, assuming complete digestion. The two HindIII fragments can ligate to give four different products as shown below. I have marked one end of each HindIII fragment to help in seeing polarity, and I have left the ligated junction as a gap to help see what is going on. I don't understand the point about the 1 kb band.

Nice graphics! I had a typo in my response, I meant to say that if you assume the digestion is incomplete, in addition to 0.4 kb and 1.1 kb bands, it should be possible by not cutting at one cut site to get an extra 1kb band not present in the complete digestion case.

You are being too smart for this question ;) If you assume that the enzyme is perfect, you've optimized the amount of template, and you leave the reaction for a really long time then there will be complete digestion. If you assume complete digestion, then there won't be any 1.1kb fragments. Furthermore, if you work out all the possible orientations of the 800bp and 300bp that were ligated together (each piece can be in the orientation shown and the opposite orientation) and you force an EcoRI cut at every available EcoRI site, then you won't have any 0.4 kb fragments from imcomplete digestion, either.
In reality, I've never been able to optimize my reaction conditions to get complete digestion of my template, and I always have some residual template around, so it's good your thinking that way for "real-world" preparation.
If you do not assume incomplete digestion, in addition to the 1.1kb and 0.4kb bands missing from this gel, I calculate that there should be a 1kb band as well.

Edit: I goofed up the last paragraph. It should read: "If you do not assume complete digestion, in addition to the 1.1kb and 0.4kb bands missing from the complete digestion gel, I calculate that there should be a 1kb band as well.

I agree with @Alan Boyd. Even I do not understand why 1kb should be there ?

I had a typo. I meant to say "if you do not assume complete digestion." Look at any of the possible restriction products that @Alan Boyd has displayed. If you get 800bp and 200bp products (or 700 and 300, or 900 and 100) with compete digestion, you would get a 1kb product with incomplete digestion. Sorry for the confusion!


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Fibronectin glass surface adsorption
Short summary
I'm having a glass surfaces and I want to adsorb proteins onto them. I have no problem, when I first adsorb fibronectin (human) onto some areas and afterwards any other protein. The second protein will only adsorb onto the remaining "free" areas.
But as soon as I apply fibronectin in the second place, it just adsorbs everywhere. And I want to avoid this.
More detailed Protocol
(direct microcontact printing):

Incubate a pdms-stamp with Protein-Solution #1 for some time and concentration
Dry pdms stamp and press onto coverslip for some time
Remove stamp and put a drop of Protein-Solution #2 for some time and concentration onto the coverslip

I varried already concentrations and times without noticeable success. I also tried adding some BSA to Fibronectin - also without success. All solutions are within PBS.
Further steps I anticipate:

Varying pH around the protein's isolectric point (Fibronectin: around 5.2)
Adding some detergens to fn-solution (e.g. Tween)
Variation of salt-content in fn-protein-buffer

My question
I'm wondering what the exact reason for the stickiness of Fibronectin is and which parameter is the best to vary? Did I miss something? Does Fibronectin stick to the other proteins or rather to "free areas" of the surface?
Please note: surface modification techniques (e.g. using epoxys) are no option.
I'm not sure, whether this topic perhaps suits the chemistry-community better. Feel free to move.

What exactly do you mean by "But as soon as I apply fibronectin in the second place, it just adsorbs everywhere."? Are you applying another protein (which one?) in spots, then flooding the coverslip with fibronectin? Fibronectin, like the related collagen proteins, is extremely "sticky" and will bind to many surfaces, as well as many different types of proteins.

Exactly, that's what I'm doing. I tried various other proteins (e.g. Laminins and Vitronectin). My idea is to modify the conditions when applying Fibronectin (e.g. pH), to make FN less sticky.

What is the exact reason for the stickiness of Fibronectin?

Fibronectin interacts with diverse substrates which reflects its non-specificiy and its interaction with hydrophobic substrates is better suggesting that the adsorption is dependent on hydrophobic interactions.

Does Fibronectin stick to the other proteins or rather to "free areas"
  of the surface?

It can stick to both as you can see from the table. However, its binding to hydrophobic materials like polystyrene and PVC is the most efficient.

which parameter is the best to vary?

Note that there will be a lot of free regions in the substrate. You cannot block all the sites unless you use a high concentration of fibronectin. So the best parameter to vary would be the concentration of fibronectin. You may also use fibronectin-BSA mixtures as their mutual binding is not that great (A stepwise method would be nonetheless better). You can also vary the adsorption time (see the figure below) but that is not as easily controllable as concentration. Since fibronectin does not bind to agar, you can also block some sites on your coverslip using molten agar (or agarose).

Reference:
Klebe, Robert J., Kevin L. Bentley, and Robert C. Schoen. "Adhesive substrates for fibronectin." Journal of cellular physiology 109.3 (1981): 481-488.

Thanks, really nice answer! Thanks also for the reference. So in my experiments (which is actually not exactly micro-contact printing) I varied Protein concentration/Incubation time already a lot. However, this does not yield the wanted result - Fibronectin will just adhere onto the first Protein (Laminins/Vitronectin etc), even tried BSA-blocking. Just out of curiosity: what is telling you, that there are lots of free areas on my substratum after adsorption?

@Vincent Well just an intuitive calculation. If surface area of the substrate is  in the order of mm² and lets say the area occupied by each FN molecule is in the order of nm² (taking the length of FN as diameter of a circle). You can adsorb at least ~10⁶ molecules. So you are coating with a layer of lamins and then FN? Reducing the concentration should work.

Well I reduced the concentration, still FN seems to stick to "laminin"-areas. Sure, I will accept your answer. I'm just waiting one or two more days - perhaps someone had already a similar problem and another hint.