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Doubt related to nerve impulse transmission
Naturally, the extracellular fluid has more sodium ions and the axoplasm has more potassium ions. Since there are more potassium leakage channels than sodium leakage channels on axoplasm, it is more permeable to potassium ions moving out into the extracellular fluid.
Is it correct to assume, due to this huge outflux of potassium ions into the extracellular fluid, there are more potassium ions than sodium ions in the extracellular fluid now?

You can look up any table of the intracellular composition of nerve cells, and actually any other cell, that K+ is always high inside. You should attempt to include some of your prior research and specifically tell us what you don't understand.

The question is different but see if this answer clears it up for you https://biology.stackexchange.com/a/57066/27148 tldr: very very few ions move to change a cells' voltage.

@AliveD I know K+ is always high inside (axoplasm), but the thing I wanted to know is, at that particular region and time, after the leakage channels do their job, is the concentration of K+ in extracellular fluid more than Na+?

Check the answer I linked to.

@BryanKrause Thanks a lot! I got the answer (similar) to what I was looking for.

One friendly correction. The Indian English usage of the word “doubt” to mean “query” or “question” is not standard US or British English. It’s difficult, I know, but you should try not to use it Internationally. It can be misleading as it suggests that you do not believe some person or idea.

@David Okay! I'll take care of that.


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Why is brown fat brown?
I read in Tortora and Derrickson Anatomy and Physiology that :

Another type, called brown adipose tissue obtains its darker color
  from a very rich blood supply , along with numerous pigmented
  mitochondria that participate in aerobic cellular respiration.

From Wikipedia :

...brown adipocytes contain numerous smaller droplets and a much
  higher number of (iron-containing) mitochondria, which make it brown.

The conclusion seems to be that there should be some iron containing pigment in the mitochondria of  BAT which (along with a rich blood supply) gives brown colour to the BAT.
What is the brown pigment present in the mitochondria of BAT ? Is it the uncoupler protein - thermogenin ?

You quote it yourself: The adipocytes contain higher numbers of mitchondria (which contain iron) and this makes the cells look brown. See red blood cells for example. The high iron content makes the color in both cases.

@Chris But what is the iron doing in mitochondria? Cofactor to some enzyme present in excessive amounts ?

There are different functions: Mitochondria store iron, then it is part of enzymes in the form of iron-sulphur complexes and is also important in the heme synthesis. See this paper if you want to got into the details.

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how to change format of ent file into PDB format?
whenever i download files from Protein Data Bank(PDB),they are downloaded in .ent format. How can i convert them into PDB format??

Just rename the file to .pdb - in other words, .ent files are PDB format:

The archival PDB files will be distributed with the reserved conventional names, in the form pdbentry_id.ent, where entry_id is a PDB 4-letter code, e.g. pdb1abc.ent, for PDB format entries; rentry_idsf.ent, e.g. r1abcsf.ent, for X-ray experimental data; entry_id.mr, e.g. 1abc.mr, for NMR experimental/constraints; entry_id.cif, e.g. 1abc.cif, for mmCIF format entries; and entry_id.xml, e.g. 1abc.xml, for canonical XML format entries.

From http://www.wwpdb.org/about/faq

nothing happened..:/ still it's a ENT file

Not sure what you mean, sorry. If you open it in a text editor you should see that it looks the same (I think). I can't seem to access the pdb's ftp server at the moment, sadly.

@HayaDar Open the file fresh in notepad, file > Save As > file types: all files and change the whole thing to filename.pdb

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bacterial cell wall degradation in humans
can human degrade the D-amino acid present in bacterial cell wall, I'm confused about it i have read somewhere that human can do so.If yes than why we need antibiotic to kill bacteria???If it is not so than why??

Humans have at least one enzyme which can break down D-amino acids, the D-amino acid oxidase (DAAO). They are able to break down these amoino acids, interestingly D-serine seems to play a role as a neurotransmitter. For more information have a look at these papers:

Physiological functions of D-amino acid oxidases: from yeast to
humans.
Human D-amino acid oxidase: an update and review.
d-Amino-Acid oxidase and its physiological function

We still need antibiotics, since only a small part of the bacterial cell wall is composed of D-amino acids. The cell wall is made of monomers from N-acetylglucosamine and N-acetylmuramic acid which are crosslinked by small peptides (these are short amino acids chains) to form the peptidoglycane polymer. A part of the amino acids in the crosslinking peptides are D-amino acids. I am not sure if the DAAO is able to attack these peptides in the polymer. Additionally most of the enzyme in the human body is present in liver and kidney, indicating that it breaks down D-amino acids that are transported there by the bloodstream.


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More entropy: Atom or Macromolecule?
A question that appeared on my last exam was :

Which of the following has greater entropy A) An atom B) A
  macromolecule

The question doesn't specify anything else(i.e. type/size of atom or macromolecule). The macromolecules we learned class were proteins, sugars, nucleic acids(DNA/RNA) or lipids. What is the correct answer and why(hypothetical calculation, if possible) ?

I see the close vote is for off-topic.  I think this question is safely in the intersection of chemistry/physics and biology. Entropy is very important in biology and I think this standard question is not off-topic.

This is an exact duplicate of a recent question on chemistry SE, though by different users. Don't know if that's allowed or not. http://chemistry.stackexchange.com/questions/14438/greater-entropy-an-atom-or-macromolecule

The OP should have indicated the question was cross-posted. Otherwise it is allowed. The answer at the other SE points out a weakness of the question but  cross-pollination is good. It looks like I will be making my case on Meta again.

Link to Meta question: (http://meta.biology.stackexchange.com/questions/640/is-a-basic-question-about-entropy-off-topic-here)

@daniel.. i dont think this is on-topic even if it was not cross posted.. this is a very general question and general principles of physical chemistry are applicable everywhere.. this doesn't make it a biological question.. it is not that we cannot answer it.. it is better suited in chemistry se.

@WYSIWYG: While I think "better suited in ___" is not a basis for closing the question is just not very good so I think it should be closed anyway. Thanks.

@daniel.. i see your concern.. But don't you think OP will benefit more from asking this question in a forum that is more dedicated for this kind of questions. I agree that this question is fine. In fact there are posts which I have voted to close after giving an answer; just to avoid further discussions.. Defining the scope of a forum is important. If we wish to participate in this discussion then we can join the more suitable forum and then post our opinions. I would have totally agreed with you a year back :)

To whoever moderators concerned, I see this question is causing question of relevance. You are free to delete it if you wish-the wonderful users on this site has already given me the answer to the question...

Entropy is a measure for the number of states accessible to a system. The more states available, the higher the entropy.  If you think of an atom confined in a volume V, then, without further restrictions, the atom can be anywhere inside that volume, i.e. the number of states will be a function of the volume V. The bigger the volume, the bigger the entropy. Now, if you add another atom to that volume so that the two atoms form a gas, i.e. they do not bind, then these atoms can access states individually. The number of states for the system will be the number of states of atom1 times the number of states of atom2. Thus, in a gas, the number of states, and therefore the entropy, increases with the number of atoms. What happens now, if the two atoms bind together. They now can't access states individually, so the total number of states, and thus the entropy, will be smaller than that for a gas of the same atoms. But the two atoms can still access states similar to the one atom gas, plus they can do new things like rotating around each other. So the number of states of a molecule of two atoms will be bigger than the number of states of just one atom.Thus, if you compare the entropy of a single atom to the entropy of a molecule of N atoms, the entropy of the molecule will be larger.  If you compare the entropy of a gas of N atoms to the entropy of a molecule build from these N atoms, the entropy of the gas will be larger.

Ahh entropy. The bane of many undergraduates. You won't need a lot of mathematical rigor needed to solve for absolute entropies in most biological fields so it's best to think of it abstractly.
Consider the atom. What can it do? Well if you remember from chemistry class, it can bounce around a process we call translate, and the electrons can basically switch spins. For the most part, if you had a single atom alone in the universe, that's all it could do. Move around and have its electrons switch states. It's best to think of these as "states" of the atom.
Let's see, the atom can move in the X direction and be in spin up. It can move in the x and y direction and be spin down...etc. But the point is, there is not a whole lot the single atom all by it's lonesome can do.
On the other hand, if we start adding other atoms to the mix, say across chemical bonds, then they can start to do more. If two atoms are bonded, they can stretch and contract (vibrational states), they can rotate around each other, and they can do everything the atom can do as well.
As you can see, there a lot more "things" or "states" that the two atoms can be defined in at any one time. They can be rotating one direction, vibrating in one way, moving in another... etc etc...even this sentence seems to be getting more chaotic! And that is really all entropy is. Adding up more and more ways for matter to get into all these possible configurations.
So the answer to your question is the macromolecule. It has tons of atoms and bonds. An uncountable number of ways to rotate, translate and vibrate, and be struck with photons, and emit light, and do all kinds of chaotic "stuff" (you can count it actually, it's just really hard).

Being struck by photons and emitting light have nothing to do with entropy in this setting.

sure it does. if you have a bond in molecular orbital theory that has a ton of states that can an excited electron can sit in, they are microstates

Number of microstates, yes. Being struck (or not) by photons, no. Incoming photons may affect the entropy of a system but the entropy is defined in terms of  possible microstates (restrictions on freedom of rotation, etc.). I think the language is confusing.

Ok first off, this is a biology forum and I said to think in abstract. Second off yes it does, because the same photon can be strike an N number of microstates. Oh my god!!! what is with trolls on SE.

As this table shows, the more complex a molecule is (in general) the more entropy it has.
Entropy is an absolute quantity which is zero at $0^o K.$ When an atom or molecule has no way to rotate (is 'frozen') there is only one state in which it can exist. An atom of a gas or a molecule of a diatomic gas at $25^oC$ is also somewhat constrained compared to a complex molecule like sugar at the same temperature and pressure. The carbons and hydrogens in sugar have more possible states in which to exist. So, for example, chlorine gas, $Cl_2 (g),$ has lower entropy than propane, $C_3H_8.$
Trends for $S$ for various atoms and molecules generally reflect the idea that S is determined by molecular mass and restriction of motion.
A typical calculation.
If you want to measure the entropy of a simple molecule you assume the entropy is 0 at $0^o K$ and measure changes in entropy as the molecule is heated. In practice this might mean measuring the decrease in entropy of the surroundings as a substance heats up. By measuring the changes carefully up to a standard temperature (25$^oC)$ you get a number that is characteristic for each substance.
The equation used in chemistry courses is usually given as
$$\Delta S  = \frac{\Delta H}{T}$$
In English, the change in entropy equals the change in heat (per mass or per mole), usually at some phase change, divided by the temperature in degrees Kelvin.
As a simple example, if liquid benzene is converted to vapor at its boiling point $80.1^o C$ and the heat of vaporization for benzene is 394 J/g then for 50 g of liquid benzene ($C_6H_6$) the entropy change is
$$\Delta S = \frac{(50 g)\cdot(394 J/g)}{(80.1+273.15)^oK} = 55.7 J/^oK$$
Chemists have created tables that measure entropy changes for states of various molecules. With the exception of very simple molecules predictions of entropy based on structure are difficult and the tables are empirically derived.


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Vitamins that could help "make us smarter"?
I was at Sprouts health store and saw a lot of vitamins/herbs that claimed to be "Study Aids" etc, so if there is any basis to it, where exactly does it hold truth? And are these supplements safe?

Can you show what effort you have made in answering the question yourself?  If you need help with something to google, try "herbal cognitive enhancers"

Are there vitamins that make us smarter?
Vitamins are micronutrients required in small quantities for normal human metabolism. Extra high (supra-physiological) doses do not generally result in improved performance. Of course, if one is deficient in certain vitamins (e.g. Vit B-1 deficiency causing Wernicke-Korsakoff encephalopathy), taking a vitamin can restore normal function. However, with adequate access to a normal diet, you are unlikely to be deficient. Commonly cited exceptions include:

strict vegans (Vit B12)
alcoholics (thiamine (B1), folate)
cultures highly dependent on maize as a staple (niacin (B3))

In people with a normal diet, taking additional vitamin supplements is usually not helpful.* (An exception may be Vitamin D depending on whom you talk to, but this is unrelated to cognitive performance.)
There have been scattered studies showing some benefit of various plant extracts and other “natural” substances. Studies such as this one about Bacopa monniera do demonstrate benefit. However, many such studies are of limited value due to sponsorship by the makers of supplements and publication in journals with questionable quality of peer review. This meta-analysis reviewing the effects of phosphatidylserine, phosphatidylcholine, citicoline, piracetam, vinpocetine, acetyl-L-carnitine, and antioxidants reached a more guarded conclusion:

for most of the "brain-specific" nutrients we review, some mildly suggestive effects have been found in preliminary controlled studies

Note that most of the substances discussed thus far are not vitamins but rather amino acids, more complex plant extracts, or — in the case of caffeine — a synthetic crystalline xanthine alkaloid. These sorts of things are commonly included in supplements found at health stores. As for vitamins specifically, this large randomized controlled trial found no effect of multivitamin and mineral supplementation on cognitive function.
What component of Cognitive Supplements are active?
The answer is usually caffeine. Caffeine is cheap, widely available, and markedly improves short-term cognitive and physical performance. By modulating adenosine activity in the central nervous system, it improves alertness, prevents impairment in neuro-plasticity associated with sleep deprivation, potentiates synaptic transmission in animal models, and may slow neurodegeneration in certain disease states.
This review article looked at ”enhancement supplements” containing taurine, guaraná, ginseng, glucuronolactone, B-vitamins, and other compounds  as well as caffeine and concluded:

there is an overwhelming lack of evidence to substantiate claims that components of [energy supplement drinks], other than caffeine, contribute to the enhancement of physical or cognitive performance.

To your question,

Are these supplements safe?

You should look at the ingredients. If it is caffeine, the answer is: usually. However, it is not recommended for those with insomnia, anxiety, palpitations, or who are underweight. As for other components of these, you need to read the label and do your research. As mentioned in the footnote, vitamins themselves are not without the possibility of harm at supra-physiological doses. For other components the danger is likely uncertain and under-researched.

*For those interested in the vitriol around this subject, check out this series of editorials that followed the paper linked above. Quoting the first of these:

 In conclusion, β-carotene, vitamin E, and possibly high doses of vitamin A supplements are harmful. Other antioxidants, folic acid and B vitamins, and multivitamin and mineral supplements are ineffective for preventing mortality or morbidity due to major chronic diseases. Although available evidence does not rule out small benefits or harms or large benefits or harms in a small subgroup of the population, we believe that the case is closed— supplementing the diet of well-nourished adults with (most) mineral or vitamin supplements has no clear benefit and might even be harmful. These vitamins should not be used for chronic disease prevention. Enough is enough.


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What creates the feeling of 'excess' blood pressure to an area of the body?
If I hang upside down, and feel blood rushing to my head, what structures are actually responsible for me "feeling" this excess flow of blood? Baroreceptors? Mechanoreceptors? Something else?
Regardless, how does this process actually work? How do I "feel" excess blood pressure to a certain area of my body?

Thanks @WYSIWYG (+1) I appreciate the help but must request that you remove the "possible dupe" label on this question.  If you really read both questions, I am actually asking 2 different things. Here I am asking for root causes of the feeling of pressure to any area of the body. The other question is specifically about ears and what types of structures cause the sensation of pressure. I argue these are 2 separate questions. Thanks again!

Ok removed my vote.

Arterial Baroreceptors felling the pressure.

Arterial blood pressure is normally regulated within a narrow range, with a mean arterial pressure typically ranging from 85 to 100 mmHg in adults. It is important to tightly control this pressure to ensure adequate blood flow to organs throughout the body. This is accomplished by negative feedback systems incorporating pressure sensors (i.e., baroreceptors) that sense the arterial pressure. The most important arterial baroreceptors are located in the carotid sinus (at the bifurcation of external and internal carotids) and in the aortic arch (Figure 1). These receptors respond to stretching of the arterial wall so that if arterial pressure suddenly rises, the walls of these vessels passively expand, which increases the firing frequency of receptor action potentials. If arterial blood pressure suddenly falls, decreased stretch of the arterial walls leads to a decrease in receptor firing.
The carotid sinus baroreceptors are innervated by the sinus nerve of Hering, which is a branch of the glossopharyngeal nerve (IX cranial nerve). The glossopharyngeal nerve synapses in the nucleus tractus solitarius (NTS) located in the medulla of the brainstem. The aortic arch baroreceptors are innervated by the aortic nerve, which then combines with the vagus nerve (X cranial nerve) traveling to the NTS. The NTS modulates the activity of sympathetic and parasympathetic (vagal) neurons in the medulla, which in turn regulate the autonomic control of the heart and blood vessels.

Of these two sites for arterial baroreceptors, the carotid sinus is quantitatively the most important for regulating arterial pressure. The carotid sinus receptors respond to pressures ranging from 60-180 mmHg (Figure 2). Receptors within the aortic arch have a higher threshold pressure and are less sensitive than the carotid sinus receptors. Maximal carotid sinus sensitivity occurs near the normal mean arterial pressure; therefore, very small changes in arterial pressure around this "set point" dramatically alters receptor firing so that autonomic control can be reset in such a way that the arterial pressure remains very near to the set point. This set point changes during exercise, hypertension, and heart failure. The changing set point (response curve shifts to right) explains how arterial pressure can remain elevated during chronic hypertension.
Baroreceptors are sensitive to the rate of pressure change as well as to the steady or mean pressure. Therefore, at a given mean arterial pressure, decreasing the pulse pressure (systolic minus diastolic pressure) decreases the baroreceptor firing rate. This is important during conditions such as hemorrhagic shock in which pulse pressure as well as mean pressure decreases. The combination of reduced mean pressure and reduced pulse pressure amplifies the baroreceptor response.

Although the baroreceptors can respond to either an increase or decrease in systemic arterial pressure, their most important role is responding to sudden reductions in arterial pressure (Figure 3). This can occur, for example, when a person suddenly stands up or following blood loss (hemorrhage). A decrease in arterial pressure (mean, pulse or both) results in decreased baroreceptor firing. Autonomic neurons within the medulla respond by increasing sympathetic outflow and decreasing parasympathetic (vagal) outflow. Under normal physiological conditions, baroreceptor firing exerts a tonic inhibitory influence on sympathetic outflow from the medulla. Therefore, acute hypotension results in a disinhibition of sympathetic activity within the medulla, so that sympathetic activity originating within the rostral ventrolateral medulla increases. These autonomic changes cause vasoconstriction (increased systemic vascular resistance, SVR), tachycardia and positive inotropy. The latter two changes increase cardiac output. Increases in cardiac output and SVR lead to a partial restoration of arterial pressure.
It is important to note that baroreceptors adapt to sustained changes in arterial pressure. For example, if arterial pressure suddenly falls when a person stands, the baroreceptor firing rate will decrease; however, after a period of time, the firing returns to near normal levels as the receptors adapt to the lower pressure. Therefore, the long-term regulation of arterial pressure requires activation of other mechanisms (primarily hormonal and renal) to maintain normal blood pressure.
This information from PhD Richard E. Klabunde lecture, that based on his book Cardiovascular Physiology Concepts (chapter 5, pages 93-123)

+1 for a good detailed answer, but I was just wondering, shouldn't venous baroreceptors also play a part in this, since the veins are more likely to change their internal pressure due to gravity (as compared to arteries?)


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Nerves, Neurons, Axons and Dendrites by Example
Here is a simple diagram of a neuron:

A few (very closely related) questions:

Where are receptors located (for pain, pressure, temperature, etc.): in the axon terminals or the dendrite tree?
Please confirm: for sensory nerves, signals travel from axon terminal to dendrite tree, yes?
According to Wikipedia, axons communicate with each other across synapses, and nerves are chained bundles of axons (basically forming a cable with each other). However, if sensory signals travel from axon to dendrite, then how can axons be chained together? In other words, if axons are a "male" recepticle, and dendrites are a "female" recepticle, then how can you have a chain of all-male recepticles?
Please confirm: a nerve is just the cabling that houses bundles of long, individual strands of neurons, yes?

many questions in one is generally considered sub-standard here - could you edit in to individual questions please.

Receptors are typically not located in a neuron. Instead, receptors generally synapse onto a primary neuron, and specifically on the primary neuron's dendrite;
Within the neuron physiological signals are received in the dendrite and are transmitted uni-directionally via the axon to the axon terminal. Between neurons the signal is transmitted from axon to dendrite via the synapse (see figure).
Although axo-axonal communication exists, it is not the typical way of neural communication (they are regulatory in nature and do not convey information as such). Typically, axons synapse onto another neuron via the dendrite of that second neuron.

The typical connection is the following:

Nerves typically do not contain cell bodies, only the elongated parts of neurons, i.e. the axons. A nerve is a bundle of axons that contain closely related signals from closely related structures in the body.


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Anatomy of nervous system's sensory pathways
When I touch my hand on a hot stove, I feel pain. I'm interested in knowing all the main "endpoints" (components/parts of the body) that are involved in relaying this pain signal. As I understand it so far, they are:

Nerve (thermoreceptor)
Fibers
Spinal cord
Brain stem (medula => pons => midbrain)
???
Somatosensory Cortex

A special sensory nerve in my hand, called a thermoreceptor, receives a thermal input (the hot stove) and fires a pain signal to my spinal cord.
My spinal cord then sends the signal up into the brain stem, where the signal travels through the medula, the pons and the midbrain.
At this point the signal is somehow wired to my somatosensory cortex; the part of the brain that ultimately processes the signal and interprets it as "pain".
Have I identified all the key players here? What connects the midbrain/brainstem to the somatosensory cortex?

The key player you are lacking is the thalamus, which integrates a lot of stimuli, and pre-processes them before sending them to the cortex


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Has anyone attempted to add extra senses to a creature through a BCI/Neural interface?
Basic BCI's (Brain computer interfaces) have been available for quite a while now and allow users to preform rudimentary tasks such as moving prosthetic limbs with force-feedback or moving a mouse on a screen through only neural impulses.
I'm interested if anyone has performed experiments in the direction of adding non-native extra senses to a creature using a neural interface/BCI. For example, feeding a magnetometer's sensor reading or clock data into a BCI and using that to give the person/creature a "sense" of magnetic fields or exact time.

Short answer
Yes
Background
This subject touches upon a related technologie, namely sensory substitution, where a lost sense is replaced by a still functional sense, for instance:

The BrainPort developed by Wicab that lets blind people taste light (Fig. 1) (Stronks et al., 2016).
The, now discontinued, yet still highly popular Optacon device developed by Telesensory Systems that allows blind folks to scan a normal printed book page with a camera and read it back through braille input via this device (Stronks et al 2016).

However, you are specifically asking for devices that add novel sensory information, referred to as sensory augmentation, or sensory enhancement. The technique of sensory substitution can,quite obviously, be easily extended to add novel sensory perceptions, simply by using a sensor capable of sensing stimuli that the human sensory systems cannot, for example magnetism, infrared light and what not, for instance:

Mapping the magnetic North on the human body through auditory or tactile actuators (Schumann & O'Reagan, 2017).
Electrically stimulation of the brain in response to otherwise invisible infrared light (Thomson et al., 2013).

References
- Schumann & O'Reagan, Sci Rep (2017); 7: 42197
- Stronks et al., Brain Res (2015); 1624: 140–52
- Stronks et al.., Exp Rev Med Dev (2016); 13(10): 919–31
- Thomson et al., Nature Communications (2013); 4: 1482

Fig. 1. BrainPort V100 vision substitution device. source: Plaid Zebra

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Are neurotransmitters part of the endocrine system?
I was speaking with a substitute teacher of mine, and we were discussing whether neurotransmitters are part of the endocrine system or not. My class just spent an entire semester on the topic of the endocrine and nervous systems. From my knowledge, they are not part of the same system, because they function very differently and they are not activated by the same triggers. Does anyone have any info on this subject? I am interested what the case is an why.

I think that the "neuroendocrine system" is a better way to think about hormones and their regulation. Without neurotransmitters, the brain could not inform many of  the body's glands that hormones need to be secreted, e.g. the pituitary gland's secretion of TSH, FSH, LH, oxytocin, etc. Separating them is fine for study, but in reality, they often work together.

I think the reason is because neurons don`t deliver their contents into the blood stream.

Short answer
Synaptic signaling can be seen as a type of paracrine signaling, and is hence not an example of an endocrine system.
Background
Khan Academy has a nice accessible overview on this confusing topic:
Paracrine signaling
Signalling between nearby cells that are near one another van occur through the release of chemical messengers that diffuse through the intercellular space. This relatively short-distance communication is called paracrine signaling. Notable paracrine signaling occurs during development, where growth-hormone gradients regulate the differentiation of the various tissues.
Synaptic signaling
A unique type of paracrine signaling occurs between neuronal cells, namely synaptic signaling.
Autocrine signaling
Autocrine signaling refers to cell signaling to itself. Like paracrine signaling, autocrine signaling is important during development, but also in tumor metastasis.
Endocrine signaling
Communication over longer distances often occurs through the circulatory system is called endocrine signaling. Often it occurs through the release of hormones into the bloodstream. Hormones are produced and released by specialized cells and target cells in distant parts of the body. Endocrine glands include the thyroid, hypothalamus, and the pituitary, among others. For example, the pituitary in the brain releases growth hormone that affects growth and other functions throughout the body.
Juxtracrine signaling
Cells can also interact via direct contact. For instance, gap junctions in animals and plasmodesmata in plants allow for a direct communication between cells by forming tiny channels, allowing small compounds and ions to cross the cell's membrane to a neighboring cell. It occurs for instance in the brain.

Neurotransmitters are secreted by the nerve cells and act directly on other nerve cells, muscle cells or glands (like adrenal medulla) via synapses, so they travel "short distance" (nanometers).
Endocrine glands secrete substances (mainly hormones) into the blood by which they travel "long distance" to the target organs.
Neurotransmitters are quick (seconds) and endocrine substances are slow messengers (minutes).
Norepinephrine (noradrenaline) acts both as a neurotransmitter (between the nerve cells) and hormone (secreted from the adrenal medulla into the blood). Several other substances, such as dopamine, can also act both as neurotransmitters and hormones, but they are still a part of two different systems - the quick one that acts via the nerves and the slow one that acts via the blood.
As mentioned in comments, nervous and endocrine system are connected, so one can merge two systems into a larger neuroendocrine system, a part of which is, for example, hypothalamic–pituitary–adrenal axis that enables stress response.

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What is the Baculovirus and how does it help in research?
I was reading up about Biotechnology and the use of insects, and came across an interesting article about Insect Cell culture Techniques that specifically talked about the usage of the Baculovirus. If I understand correctly does this virus help express certain genes when inserted into a cell?
Sorry if I am way off or did not use proper terminology, I am a high school IB Biology student who still has a a lot to learn
Thanks!

Baculoviruses are a a class of viruses which infect only a pretty small number of insects (or their cells in cell culture). To do so, the virus has to infect a cell, take it over to produce the own proteins and DNA to make new virus particles and finally set these new particles free. This is basically what is shown in the image below (from here):

From the proteins encoded by the viral genome, not all are essential, meaning removing them will not do harm to the virus or its function. And this is used in Biotech to produce proteins of choice. One of the non-essential proteins is replaced by the sequence of the protein you want to have produced by the cells. You then take insect cells in cell culture (these are single insect cells which live in a big vessel full of culture medium), infect these cells with the modified virus and eventually harvest the protein from the culture.
The advantage of Baculoviruses is that they only infect the insect cells on which they are specialized so they are a safe way of producing proteins for pharmaceutic applications. If you want to read some more about this, start here.


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How does Pothos grow in only water?
The popular potted plant, Pothos aureus (or Epipremnum aureum) is happy to grow in a jar, with only water, for years. How is this possible when other plants need at least Nitrogen, Phosphorus and Potassium?

Pothos needs those nutrients as well, but they are more tolerant of poor nutrition than most plants, therefore rendering them better houseplants (most people don't fertilize their plants properly). But with no nutrients, the plant will begin to fade. A good hydroculture system includes a nutrient solution, to keep the plant fed, and an aerator, to add oxygen to the root zone.

"Tolerant" is an understatement... the plant is putting on mass for years, without those nutrients at all.  How is this possible?

This is a good question but unfortunately you are making the false assumption that the water has no nutrients in it. Pothos probably is simply very efficient at extracting these nutrients from water.

It is not possible, that a plant grows without any nutrients. Magnesium for example is needed in every chlorophyll, so there is no photosynthesis without magnesium. Another point is that plants can not get nitrogen from the air, so they have to get it from the soil and nitrogen is present in every amino acid, which build the plants proteins. Proteins are essential for every living organism. This are only two points and there are many many others why every plant needs nutrients like nitrogen phophorus, magnesium...
If it seems that Epipremnum aureum does only need water, maybe the plant gets its nutrients from a place you don't expect. Maybe the water is contaminated. Are there leafs falling into the water for example? Another possibility could be that Epipremnum aureum stored a lot of nutrients before it got only water but this won't last for ever.
I read your comment, thats why i think the nutrients have to come from the water. Additionally I found this publication about Calcium Deficiency Symptoms of Epipremnum aureum
I think you know that tap water or rain water isn't pure H2O. We just measured the tap water in Cologne, by ICP-MS. This is no official measurement, and we measured only once but I think its nice to see whats else in tap water.     Unfortunately we couldn't measure nitrogen, because normally the machine is used for plant extracts and there would be to much nitrogen.

Maybe your Epipremnum aureum gets enough nutrients from the water, I don't know if this is possible and how often you change the water.
Your pot could also be a source for nutrients if its not sealed up.
In conclusion the answer is that in general it is not possible, that your plant grows without nutrients. So there is a source which can be only detected by yourself, because you know the exact conditions under which your plant grows. I hope I could give you some hints.

Tap water does contain a significant amount of metal ions in solution, and this applies to all water sources (rainwater, groundwater) with the exception of ultrapure (eg distilled or reverse osmosis water).
For example, the official analysis of the NYC water supply in 2015 shows that there are significant quantities of nitrogen, phosphorus and potassium in the tap water samples taken.

In short, pothos does in fact require minerals to grow, and these minerals are provided by the water.

I owned a commercial soil/plant/water testing laboratory for 28 years, and have written 3 books on Tropical Foliage Plants, including Epipremnum (pothos). There are likely a lot more minerals in your water in that vase than you think there are, enough obviously to keep the plant alive and to some extent growing for years. I find nothing wrong in this  answer. You will find small amounts of nitrates, sulfates, calcium, magnesium, boron and several other plant nutrients in most tap and well waters. My reference is 35 years of analyzing water samples; also refer to the book Groundwater and Wells.


text:
What Causes Shin Splints?
My shin splints are clearly tied to running. Though the pain level doesn't seem to correlate  to my running intensity. So what is it about running that causes shin splints?
My real hope is that if I understand the cause clearly enough I can adjust to fix them.

By shin splints you probably mean the pain on the inner front side of the lower 2/3 parts of the shins? This is called medial tibial stress syndrome (MTSS).
Causes, mechanism, prevention and treatment of shin splints are still poorly understood.
From what I managed to find, custom-made cushion insoles are the only proven prevention that can help in some cases.
What has not been proven to help (I'm not saying it does not help, only it has not been firmly proven):

various types of shoes (supinator/pronator)
taping
stretching/strengthening exercises
various running techniques (pose-tech, chi-running, barefoot...)

Possible causes:

running downhill or on an uneven terrain with heel striking and forefoot slapping
sudden increase in running intensity, mileage or frequency
a way of running with moving the hips (left , right) forward
(my experience): running in a forced, conflicting way, like you feel you should not run and you still go...

Possible mechanism: vibration stress in the shinbone (tibia) and the pulling force of the muscles and tendons attached to it and possible local inflammation of then periosteum.
Do not try to run through the pain. The pain will go away but on the long-term, shin splints may worsen.
Source: Shin Splints (MTSS) (Ehealthstar)


text:
Does Spinning dancer has anything to do with your eyesight
I came across the spinning dancer as part of the brain test to determine left brain vs right brain dominance.

I saw the dancer is turning clockwise. The other people around me saw it turning clockwise for the first time, but soon they got confused and said they saw it turning it in both direction.
I know the tips of how to see it anti clockwise, but no matter what I do I always see it clockwise. I have shown it to a number of people and all of them could see it spinning in both direction after looking at it for longer time.
I am the only person who has never see the dancer turning in both direction.
My question is does this has anything to do with my eyesight? I have very limited(almost blind) eyesight in my left eyes. This is from birth.
Does my visual impairment has anything to do with this or does this mean anything else?

It's very frustrating to me that I can only see her spin one way…

@canadianer Check the answer to see her spin the other way.. We'll just cheat.. No thanks necessary.. :P

Okay actually now my life is complete because she's going the other way. It really helps if you just focus on her lower foot. I actually scrolled the page up so I couldn't see the rest of the image.

When I first saw this it quickly started switching back and forth on me, then for me. However after reading your predicament I too found my perception stuck. Looking at image, I closed my eyes and imagined it spinning the other way. When I opened them what I saw matched my new perception. Hope this helps anyone else.

For a bit of background, this test was devised by Nobuyuki Kayahara and it was originally thought that it shows the dominance of one part of the brain to the other. This was later on discarded as a misconception (reference). It is now widely believed that the clockwise - counter-clockwise rotation is a phenomenon called Bistable perception (Reference 1 and reference 2).

Multistable perceptual phenomena are a form of perceptual phenomena in
  which there are unpredictable sequences of spontaneous subjective
  changes. While usually associated with visual perception, such
  phenomena can be found for auditory and olfactory percepts. Famous
  examples include the Necker cube, structure from motion, monocular
  rivalry and binocular rivalry, but many more visually ambiguous
  patterns are known. Since most of these images lead to an alternation
  between two mutually exclusive perceptual states, they are sometimes
  also referred to as bistable perception(reference 1 and
  reference 2).

No, the fact that you can only see her turn clockwise has not got anything to with your vision (for the record, I have never been able to see the girl go counter- clockwise myself).

Sometimes, a person will stare at an image and it will never reverse.
  Dr. Toppino advises staring at one part of the image, such as the
  foot, and most of the time it will eventually flip. In people who
  can’t see the reversal, it may be that one underlying neural structure
  is more dominant, but once someone finally manages to see the flip, it
  will start to happen more often (reference).

This image would help you watch her rotate counter-clockwise.

Here she is spinning clockwise.

That blew up my mind. Now I can see her rotate in both direction!!! Thanks for the references.


text:
Why do restriction-modification systems work?
Some RM systems (restriction-modification systems) are plasmid-borne and are transferred through bacterial conjugation. As you all know, there are two genes in an RM system, the gene that codes for the restriction enzyme that restricts a certain nucleotide sequence and the other that codes for the methyltransferase that methylate the sequence to protect the cell from its own restriction enzymes. If these genes are both being expressed at the same rate after the bacteria receives this plasmid, how is the bacteria's DNA protected from the restriction enzymes for the first few hours of expression if the methyltransferase have not yet methylated the entire host genome yet?
Thank you,
CDB

About which systems are you talking? CrispR? LoxP?

Is it different from one system to another? My main focus would probably be type II, but beyond that it doesn't really matter, any system you choose to answer for would be fine.

So you're asking about what happens when bacteria are simultaneously transformed with a gene for a restriction enzyme that cuts at unmethylated site X, AND an enzyme that methylates site X?

In essence yes. I'm wondering how the cell protects its own DNA from the restriction enzymes until the methyltransferase methylate the DNA.

I don't really know, but I assume it comes down to how quickly each protein is expressed, how quickly each enzyme catalyzes its reaction, and how well a cell repairs it genome. With a large population of transformed cells, I assume some will be methylated before they are cut, and survive. If methylation can be passed down from generation to generation, those will be selected. But again, I barely know anything about DNA methylation.

You have a good point there. My original assumption for why this happens was that one methyltransferase can methylate almost an unlimited number of sequences, whereas restriction enzymes can only restrict one sequence, I'm actually not sure if this is true though, thus why I asked the question. Thanks for your answer.


text:
What percentage of cells in the human body are infected during a non-fatal viral infection?
I understand that this would be a very rough estimate, but approximately how many cells in the human body are infected during an average non-fatal viral infection before the infection is eliminated by the immune system? It doesn't matter what virus you use as an example, I'm just looking for a general case.
Thank you,
CDB

The following isn't really an adequate answer because (1) HIV dynamics aren't typical virus dynamics and (2) this tells us how many cells are killed, not how many cells are infected. But in case it is useful, there are roughly 2*10^11 CD4 T-cells in an adult and untreated HIV eventually infects and kills the large majority of those.

Actually, that's about the answer I was looking for. Feel free to transfer it to answer form (if you want). Anyone else with information/sources pertaining to this please don't hesitate to post them, I'll take as many cases as I can get. Thanks.

Different viruses infect different cell types. You should narrow this down. Do you mean what percentage of "target" host cells? And it also depends on the viral replication dynamics

Given that Corvus' answer gives a nice and interesting global estimate worthy of an answer, I think the question should not be closed - but an edit is definitely appropriate to narrow it down a bit. -1

I was really just looking for cases/studies, I don't care which virus they use, that's totally up to the answerer. I thought that if I narrowed it down it would just decrease my chances of getting any sort of an answer. I'm still in the beginning stages of setting this project up, so it's highly adaptable. Seeing as I was looking for a broad selection of answers (thus I did not limit the acceptable answers by adding too many details/requirements), I do not believe this questions needs editing.

This is now basically answered at https://biology.stackexchange.com/questions/93782/what-fraction-of-human-cells-gets-infected-during-a-viral-infection.


text:
Electroporation of one-cell embryo?
Would electroporation be successful on a one/two-celled mouse embryo? If it would, what buffer could be used and what percentage of cells would be viable?
Thank you.

The buffers are usually supplied with the electroporation instrument; at least Lonza provides buffers for different types of cells. Single cell electroporation techniques exist, but they have been mostly done on neurons.[1,2]
You can also try microinjection but it requires some practice. This study reports a transfection agent called VisuFect which can be used for zygotes as well.
I am not very sure about the success rate (AFAIK it is not that good) but I think it is anyway risky with organisms which do not produce a lot of embryos.


text:
Where is the aneurysm in this picture?
I'm a curious person, I've never had any medical training, but I wish to know some more about aneurysms. Aneurysms are basically weakened spots in the elastic artery wall. This can eventually result in a blood-filled balloon bulging from the artery wall due to the high blood pressure in these vessels. Aneurysms can rupture and this can lead to brain damage when it occurs in the brain. Aneurysms can be detected by injecting contrast material into the bloodstream and making an X-ray (called an angiogram). Now I was reading a wikipedia article about aneurysms where I saw the following picture of an angiogram where reportedly an aneurysm should be visble:

Now, as I said, I know nothing about biology so I would really appreciate it if someone could download the picture and reupload it with the aneurysm circled.
Is it the really dark spot or the big soft spot to the right? Thanks!

big blob just in the middle of picture

@aandreev Thanks so the black spot is normal?

I edited the question by adding some background info. this way other folks can more easily add answers if they wish.

Your image comes from the wiki page Aneurysm. The figure legend on the wiki page identifies it as:

Angiography of an aneurysm in a cerebral artery

I am not an MD so I chose to first dig up a similar appearing cerebral angiography with the aneurysm identified (dark protruding spot indicated by the arrow):
Source: WestJEM, UC Irvine
Taking into account the normal vasculature as seen on this graph from UC Irvine, and given the similarity between the identified aneurysm in this angiopgraph and your wiki angiograph, I tentatively have identified the red-encircled structure in your original image as an aneurysm:

Thanks! It looks like the one un the center of the wiki picture, as @aandrev said

Yes it does absolutely, but I found 'center' rather ambiguous

Exactly, that's why I asked for some circling or something haha, well, I guess my curiosity is satisfied, thanks!

I don't have enough reputation to comment, apparently, but I can answer that AliceD is correct. I'm a neuroradiologist, so I look at these images for a living.


text:
Are Gram negative bacteria classified as such because of their negative membrane potential?
Does the membrane potential usually quoted for Gram negative bacteria (e.g., E. coli) refer to the potential across both membranes? - If yes, then does the potential fall more over the inner or outer membrane? Are there any studies that estimate/measure the relative fraction for each membrane?
I assume that the measurements of potential are usually carried out by inserting an electrode inside the cell and measuring the difference with the outside, this would make the answer to the first question yes.

There is probably a clue in the context. Generally though potential refers to the intra-extra cellular potential (i.e in this case both membranes). Is there a particular source you can cite that is ambiguous?

This is a good answer to the first part of the question. My motivation for asking is partly that I would like to understand the membrane potential experienced by a trans-membrane protein present only on the inner membrane.
Even a rough educated guess (with reasoned argument) would be helpful. For example: Would the presence more proteins that are driven by membrane potentials being located on only one of the membranes be a good indicator that the the potential would be likely to fall mostly over that membrane?
If no literature exists, is it reasonable to construct an argument in this way?

I suggest you edit this question to ask only about Gram-staining and open a new question that asks about Gram-negative membrane potential.

Short answer
The distinction between Gram positive (Gram+) and negative bacteria (Gram-) has absolutely nothing to do with membrane potentials; it is all about the Gram staining procedure.
Background
The Gram staining was named after the Danish bacteriologist Hans Christian Gram, who originally devised it in 1882 (Gram, 1884). Gram staining is a common technique used to differentiate two large groups of bacteria based on their different cell wall constituents. The Gram stain procedure distinguishes between Gram+ and Gram- groups by coloring these cells violet or red, respectively (Fig. 1).
Gram+ bacteria stain violet due to the presence of a thick layer of peptidoglycan in their cell wall, which retains the crystal violet these cells are stained with. Gram-, on the other hand stain red, which is attributed to a thinner peptidoglycan wall, which does not retain the crystal violet during the decoloring process.
Gram staining procedure
The procedure involves staining the cells with a crystal violet dye. Next, an iodine solution (iodine and potassium iodide) is added to form a complex between the crystal violet and iodine, which is insoluble in water. Then, a decolorizer, such as ethyl alcohol, is added to the sample, which dehydrates the peptidoglycan layer, shrinking and tightening it. The crystal violet-iodine complex is not able to penetrate this tightened peptidoglycan layer, and is thus trapped in the cell in Gram+ bacteria. In Gram- bacteria, however, the thinner peptidoglycan layer does not retain the crystal violet-iodine complex and the color is lost. Lastly, a counterstain, such as the weakly water soluble safranin, is added to the sample, staining it red. Since the safranin is lighter of color than crystal violet, it does not disrupt the purple coloration in Gram+ cells, but it does stain the decolorized Gram- cells red.

Fig. 1. Gram+ bacteria (left) and Gram- on the right. source: Lab Tests Online
Reference
- Gram, Fortschritte der Medizin (1884)

Good answer to the question. However it's a classic XY problem. OP is actually looking for the membrane potential for the periplasmic space to the cytosol.

@James Thanks! Regarding your point, I agree and that's why I upvoted the other answer here.

The following is not an answer to the original question: "Are Gram negative bacteria classified as such because of their negative membrane potential?" but to the questions later in the text.

Usually the membrane potential is given for the inner cytosolic part and the extracellular space, for E. Coli it is around -120 mV; see also this article.
Due to the small size of E. Coli it is very difficult to reliably and accurately measure the membrane potential.
For the periplasm only the Donnan potential is reported, it ranges between 5 and 100 mV, typically around 25 mV.
I don't know about any report measuring the relative contribution but I would guess that the inner part makes up most of the total potential.


text:
Why basement membrane thickens in diabetes mellitus?
Untreated diabetes mellitus may lead to blindness and kidney failure because the basement membrane of small blood vessels in these organs thickens due to increased production of collagen and laminin.
My questions : why are these organs most susceptible ? Why will collagen and laminin production increase in diabetes mellitus ?

The endothelial cells in small blood vessels take in more glucose (as glucose levels in blood are high due to diabetes.) Thus they form surface glycoproteins which causes the basement membrane to become thicker yet less strong. This leads to blood and protein leakage from the blood stream in other tissues in the space between cells. Blood leakage alters cellular blood supply for all cells.
Less blood means less oxygen and less nutrients. As you probably know nervous tissue gets damaged fastest without oxygen thus explaining diabetic neuropathy. Also retina and kidney contain cells that get easily damaged when there is not enough blood.
Probably the worst complication is neuropathy, because the person suffering from it may suffer a heart attack (caused by the accelerated process of atherosclerosis in diabetes) and feel less pain (http://medlineplus.gov).
Collagen and laminin poduction increases as a result of the fibrosis process that takes place when a tissue gets less nutrients than it needs.
Diabetes affects all blood vessels, even the larger ones. See macroangiopaty.
From http://en.wikipedia.org/wiki/Microangiopathy

Plasma glucose can react (non-enzymatically) with the side chains of some amino acids to form Advanced Glycation Endproducts (AGEs).  AGEs are pro-inflammtory and can cause signalling via specific receptors for AGE - the RAGE family.  This, in large part can drive OP's thickening. Do you have a reference for reduced pain in heart attacks ?

@playsdice Could you please elaborate it in the form of an answer ?

@biogirl - comments were to suggest tweaks to this answer.  You should also search 'complications of diabetes'.  Its a fascinating field.

@cornelius could u explain ur first statement ? increase insulin level leads to increase in uptake of glucose in cells. Instead of saying that cells take inglucose EVEN THOUGH insulin level is high u should say that because insulin level is high.

@biogirl insulin has nothing to do with the amount of glucose that endothelial cells take in. They simply take in glucose based on its concentration in blood.


text:
How does Ultra-pasteurized milk compare with pasteurized milk?
I am specifically interested in whether all proteins and nutrients lose their structure permanently because of the very high temperature of ultra-pasteurization.
What is the case for pasteurized milk?

Have you done any research on your own? What have you found?

From the basic web research I did, I found that many proteins are permanently destroyed. However, I would prefer someone with references to a study on this.


text:
Why is high fructose corn syrup unhealthy?
I understand that high fructose corn syrup was found to have detrimental effects on peoples' health. Why is this so?

could you please reference this claim and what makes you think fructose is a contributing factor?

@Bez The OP may not know. I've heard this too, though, that corn syrup is bad for you, and I like the question.

One answer could be: because it's sugar.

High fructose diet cause many bad things: liver and kidney damage (oxidative stress, increased urate levels), insulin resistance (increased triglicerid and free fatty acid levels), atherosclerosis (low NO levels, high urate levels, high salt levels, high LDL/HDL ratio, high blood pressure, etc.), cancer (increased oxidative stress). So you should avoid foods rich in fructose and sucrose except fruits, vegetables and honey, because the polyphenols in them, can counteract with the fructose related problems.

@inf3rno could you provide sources for that please?

@user8669 Read Raoul's answer! Note that some antioxidants in fruits can render fructose harmless.

Besides a lot of propaganda there is not much evidence that high fructose corn syrup (HFCS) is more dangerous than normal sugar. Lets have a look at the sugar in detail:
HFCS is produced from corn and is originally a glucose syrup. Since fructose is obviously much sweeter, the glucose is converted enzymatically into fructose (see here for more details). Before the use in food production additional glucose is added to the syrup so that typical syrups contain 55% fructose and 42% glucose or 42% fructose and 53% glucose (the remaining % are water).
If you look at saccharose (which is our ordinary sugar) then this is a disaccherid which is build from one molecule of glucose and one molecule of fructose. The enzyme sucrase breaks this molecule up into one molecule of fructose and glucose each, so reaching a 50%:50% ratio between the sugars.
As the ratios are more or less the same, it doesn't matter for the human body, where the sugar come from meaning that in this context it is more too much sugar in the food than a problem with HFCS, as also this study suggests:

Straight talk about high-fructose corn syrup: what it is and what it
ain't.

Fructose itself is not without problems as this induces the production of fats in the liver, but again, it doesn't matter for the body, where this fructose comes from:

Fructose induced lipogenesis: from sugar to fat to insulin
resistance.

For further reading I can also recommend this article on Gizmodo:

Is High Fructose Corn Syrup Really Bad for You?

Clearly whoever named this substance "high fructose" corn syrup, while technically correct (regular corn syrup is almost entirely glucose), didn't understand marketing very well :)

Thank you for your answer. I am not sure I understand that it doesn't matter for the body that the ratios are 'more or less the same'. Any slight difference in structure or composition, can play a vital role in the effect on human health. In this case, however, I think that the way the HFCS is made plays a more important role than the percent composition of fructose and glucose in HFCS.

@user8669 The problem are the huge amounts of sugar which are consumed. And here fructose causes indeed problems since the glucose is used by all cells for making energy, while the fructose is used by the liver to produce fat and store energy, which promotes obesity when consumed in large amounts. What can also cause problems were contaminations from the production process, but I found sources saying that this problem is gone with todays production process which relies on the use of enzymes and not caustic soda anymore.

Moreover, fructose uptake is not regulated by insulin. And fructose can bypass a rate limiting regulatory step of glycolysis ( $F$-$1P \rightarrow F$-$1,6 BP$ ).

Just to clarify-- is there a difference between fructose in fruits and isolated fructose (such as the type that is converted enzymatically from glucose)?

Chemically? Not. Both have the same structure. They are not distinguishable.

You say that chemically there are no differences. Does this imply that there are differences in another way?

@user8669 Yes, fruits can contain other materials which counteract the diabetic effects of fructose and slow down the absorption, so they are much safer than sugar or fructose syrup. So it does matter where fructose comes from, but not by comparing fructose syrup and saccharose which both are bad...

Some reference about fruits: http://ajcn.nutrition.org/content/99/2/328.abstract

The following study abstract of "Consumption of high-fructose corn syrup in beverages may play a role in the epidemic of obesity" copied from http://www.ncbi.nlm.nih.gov/pubmed/15051594 seems to address your question.  I added a paragraph break; the second paragraph seems most relevant to me:

Obesity is a major epidemic, but its causes are still unclear. In this
  article, we investigate the relation between the intake of
  high-fructose corn syrup (HFCS) and the development of obesity. We
  analyzed food consumption patterns by using US Department of
  Agriculture food consumption tables from 1967 to 2000. The consumption
  of HFCS increased > 1000% between 1970 and 1990, far exceeding the
  changes in intake of any other food or food group. HFCS now represents
   40% of caloric sweeteners added to foods and beverages and is the sole caloric sweetener in soft drinks in the United States. Our most
  conservative estimate of the consumption of HFCS indicates a daily
  average of 132 kcal for all Americans aged > or = 2 y, and the top 20%
  of consumers of caloric sweeteners ingest 316 kcal from HFCS/d.
  The increased use of HFCS in the United States mirrors the rapid
  increase in obesity. The digestion, absorption, and metabolism of
  fructose differ from those of glucose. Hepatic metabolism of fructose
  favors de novo lipogenesis. In addition, unlike glucose, fructose does
  not stimulate insulin secretion or enhance leptin production. Because
  insulin and leptin act as key afferent signals in the regulation of
  food intake and body weight, this suggests that dietary fructose may
  contribute to increased energy intake and weight gain. Furthermore,
  calorically sweetened beverages may enhance caloric overconsumption.
  Thus, the increase in consumption of HFCS has a temporal relation to
  the epidemic of obesity, and the overconsumption of HFCS in
  calorically sweetened beverages may play a role in the epidemic of
  obesity.

Welcome to biology.stackexchange. If you cite sources, please mark the citations as those and make sure that you not only write answer which contain only of citations (in this case the abstract). Besides that: The paper shows that the problem is fructose in the food, not the HFCS.

It is also interesting to read the comments on this article, which can be found here and here. Especially the second is very clear about the Fructose and HFCS.

I've not read the study but I'm skeptical. During the same period, there was also a huge rise in obesity in the UK but we don't use HFCS.

Ah, but we do use [invert(ed) sugar syrup)[https://en.wikipedia.org/wiki/Invert_sugar_syrup] which is a 50/50 glucose/fructose mixture made by hydrolyzing sugar (typically beet or cane sugar in the UK). On the other hand, invert sugar syrup isn't nearly as widely used in the UK as HFCS is in the US.

Skimming through the article itself the authors seem to pick two trends, conclude their both rising and et volia, a causal relationship - not too strong of an argument. The title's "may" says it all.

@ChrisStronks This is not my answer.

@Chris - I know, the two "here"s are in your comment in this thread, it is not referring to your answer.

@ChrisStronks Ah, now I understand. I will see, if I can repost the second link.

Fructose has a special characteristic that other sugars do not have: its absorption in the human intestine is not regulated, as opposed to glucose, for example.
The important implication is that all the fructose you consume will end inside your organism, either used immediately or stored as fat. Other sugars will only be partly assimilated, or will require more energy to assimilate. If you take the example of glucose again, a glucose molecule requires active transport (meaning consumes ATP, the most basic fuel of your organism) to transit across the intestinal wall. Fructose is absorbed via free transport (i.e. no ATP consumption).
This claim can be verified by opening any human physiology book, and while it is debatable whether fructose itself is deleterious, increasing the sugar amount in an already sugar-saturated environment clearly does not seem a good idea to me.
I (inf3rno) appended the answer with further details:
Sucrose is split by digestive enzymes (sucrase, glycoside hydrolase) in the small intestine into fructose and glucose (1:1 ratio). By the high fructose corn syrup (HFCS hereafter) the fructose - glucose ratio is dependent on the HFCS type according to wikipedia. For example HFCS90 has 90% fructose, while HFCS42 has only 42% fructose (the rest is glucose).
Glucose is mainly transported by SGLT1 (active transport, which involves ATP), while fructose is mainly transported by GLUT5 (passive transport, does not involve ATP) into enterocytes in the intestines. After that the cells transport these sugars with GLUT2 (passive transport, not insulin dependent) into the blood. Fructose and glucose is transported to the liver (hepatocytes) from the blood, with GLUT2.
In the liver fructose is more dangerous than glucose, because it is transformed without any regulation. It uses the same pathways as glucose and mostly fatty acids are created from it, which increase the blood VLDL, LDL, FFA level and cause insulin resistance. The byproducts are urate and free radicals, which cause hyperuricaemia and oxidative stress. Hyperuricaemia cause decreased NO levels (by counteracting with eNOS and reacting with NO directly), which cause increased blood pressure due to vasoconstriction. Hyperuricaemia damages the liver and the kidney too. Too high urate levels enhance LDL oxidation as well, which cause atherosclerosis. The free radicals deplete the antioxidants of the body and probably cause cancer in long term.

High dietary fructose intake: Sweet or bitter life? -
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158875/
A causal role for uric acid in fructose-induced metabolic syndrome -
http://ajprenal.physiology.org/content/290/3/F625
Gut microbial adaptation to dietary consumption of fructose,
artificial sweeteners and sugar alcohols: implications for
host–microbe interactions contributing to obesity -
http://www.drperlmutter.com/wp-content/uploads/2014/04/Payne-et-al-2012-Obesity-reviews.pdf
Early Life Exposure to Fructose and Offspring Phenotype: Implications
for Long Term Metabolic Homeostasis -
http://dx.doi.org/10.1155/2014/203474
Dietary fructose, salt absorption and hypertension in metabolic
syndrome: towards a new paradigm -
http://onlinelibrary.wiley.com/doi/10.1111/j.1748-1716.2010.02167.x/abstract?deniedAccessCustomisedMessage=&userIsAuthenticated=false
Toward a Unifying Hypothesis of Metabolic Syndrome -
http://pediatrics.aappublications.org/content/129/3/557.short
Uric acid transport and disease -
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2877959/

@Chris: So summed up I think this is enough proof that HFCS with higher fructose - glucose ratio, than sucrose have a higher health risk.

It would be great if you added references to your response!

Thank you for your answer. I cannot understand, then, how it is healthy to eat fruits (which contain fructose). hi fructose in fruits absorbed differently by the body than other types of fructose?

@user8669 Where did you get the idea it was so healthy to eat fruits? ;-) No, the fructose in fruits is in no way different, and gets absorbed in the same way. In the wild, it used to be the best sugar-concentrated food around, which is most likely why its absorption is less regulated. However, diabetics for example are required to limit their intake of fruits to avoid hyperglycemia. So its a question of amount, and pure sugar used to be quite rare in the wild.

Yes, but according to your answer it would be better to eat something sweetened with sucrose than to eat naturally sweet fruits which contain fructose. Do I understand you correctly?

No, fruits are good for you and other sugars are ok too. However, fruits are nowadays good for your health because of all their other components (vitamins, etc.), because we already get high sugar loads from elsewhere (bread, etc.). If you were to limit your sugar intake to that of a wild animal, then fructose would become extremely valuable, while it is not so valuable to the civilized human.

In one comment you said "where did you get the idea that it was so healthy to eat fruits" and then you said "fruits are good for you". If I understand you correctly, fruits are good only because they contain vital nutrients, but the fructose that fruits contain is not as healthy as glucose or sucrose.

@user8669 Fructose is just as healthy as others. In a wildlife context sugar is difficult to come by, so fructose would be extremely valuable. Now that we get as much sugar as we want, it is no less nor no more healthy than other sugars. The point is that if you already eat too much sugar of whatever type, eating fructose will add more sugar to your organism than eating  an equal amount of another type, and in that way would become a less healthy option. It's not the fructose itself that is not healthy, but its relation to modern food.

But fructose's is not as regulated by our body as are glucose and sucrose. This does not play a role in the health factor?

@user8669 As I said above, in a wildlife setting this makes it extremely valuable. In a civilized setting, this makes it less healthy. If you want more info, get us into a chat room, 'cause it'll be easier than in commments


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Ultra Pasteurization and Pasteurization
What is the effect of pasteurization and ultra-pasteurization on proteins, enzymes, and nutrients found in milk and other dairy products?

This is an interesting question and it is rather hard to find reliable information. According to a review which also did a meta analysis of all available articles, pasteurization (and also ultra pasteurization) affects the vitamins to some degree.
According to the analysis, vitamin B1, B2, B6, B12, C, E and folate decreased. The author notes however, that with the exception of vitamin B2, where milk is an important dietary source, the other vitamins are not included in very high concentrations. See the first paper for all details.
These findings are supported by another review (see reference 2), which shows some values in table 4:

This study finds proteins and amino acids not affected to a measurable degree, but data on protein behaviour is missing. My guess is that a part of the proteins are denaturated, but not all of them. There is some research which analyzes the effect of thermal treatment on milk in connection with other processes like the yoghurt or cheese production (have a look at reference 3). I haven't found any data on the proteins in milk which is directed to human consumption.
References:

A systematic review and meta-analysis of the effects of
pasteurization on milk vitamins, and evidence for raw milk
consumption and other health-related outcomes.
Which Milk is Fresh?
The Effect of UHT and VAT Thermal Processing Systems on Whey Protein
Denaturation and Gel Strength of yoghurt


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Is the heterotroph hypothesis universally accepted?
I was wondering whether there are hypotheses that take a different approach that is contrary to the heterotroph hypothesis.
The heterotroph hypothesis states that autotrophs evolved from heterotrophs because of the lack of food.
Is this issue still debated by scientists or is the heterotroph universally accepted?

I would say the the topic is still very much under debate. This paper by Ferry and House (2006) briefly review the heterotrophic vs chemoautotrophic hypotheses. They include citations from proponents of each hypothesis. Interestingly, Ferry and House propose an "energy conservation" hypothesis that attempts to merge ideas from the other two hypotheses.  Overall, much work remains to be accomplished in this field before we have a clear understanding of the origins of life.
Literature Cited
Ferry, J.G. and C.H. House. 2006. The stepwise evolution of early life driven by energy conservation. Molecular Biology and Evolution 23: 1286-1292.


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Why was Darwin's Finch argument valid considering Weismann's argument?
According to Darwin, there was only 1 species of Finch bird in Galapagos. Then Darwin argued that due to diet adaptation and natural selection, their beak changes causing new species--which is confirmed by John Gauld at the Geological Society of London.
In contrast, Weismann's and his mouse proofed that environment factor won't effect next generations.
Don't Weismann's argument contradicts Darwin? Ok, say that the Finch bird adapts (and killing the one who don't) with their diet. Their beak changes. But when these Finch bird breeds, their new generation's beak should reset to normal beak again.
The reason I asked this reason is because one article said that our teeth are changing due to overbites using utensils(1). However, not everyone use eating utensils. Indian mostly used finger. Indonesian don't really care whether we use our hand or spoon. If this trend keeps happening in the future, won't human evolve into two species? Homo sapien and Homo spoon (pun intended.)
Or am I mixing Darwin with Lamarck?
(1):http://www.theatlantic.com/health/archive/2013/01/how-forks-gave-us-overbites-and-pots-saved-the-toothless/267252/

Weismann's mouse tail experiment showed that mouse tail length is not inherited, if the change in tail length was caused by mutilations, and there was an absence of selection pressure.
However, Darwin's finches represented a completely different idea of evolution. In this case, the beak size of the finches did in fact change, but this was not due to mutilation. The beak sizes of the finches changed because finches with lower fitness due to their beak sizes were selected against, leading to the beak size changing over time.
If the mice were instead selected for tail length by preventing the long-tailed mice from reproducing, then it is indeed possible that the mice would eventually evolve to have shorter tails, or even absent tails.
Similarly, if the finches had their beak sizes reduced artificially but their fitness preserved (for example, by grinding down their beaks and feeding them soft food that does not require large beaks to break), the finches would not be expected to evolve smaller beaks.
It is not clear which method is the one through which the evolution of the overbite occurred. It could be due to a change in relative fitness, but a case can also be made in which fitness was not a large factor.

You are confusing with Lamark, yes. Ironically enough, some epigenetic information does transfer some adaptations, (see citrus cold adaptations for a well-known example. If they freeze, they go sour and pass that on.) but the Lamark idea is mostly discredited, anymore.
Darwin promoted a very distinct idea: Creatures must pass on traits to their offspring from the set available in them, so the effect of the individual success effects the selection of traits in the population.
The sets of traits that better equip an individual to successfully spawn will tend to eventually outnumber lesser sets, due both to superior survival and more effective breeding. They'll make more children in the first place, and these will be less likely to die.
The result is a shift in availability of traits* towards the successful.(*heritable)
None of that requires any transfer of developed traits beyond any intrinsic ability to adapt or the mentioned epigenetic advantages that pass.
Mammalian milk-transferred immunities are not genetic and very much passed from mother to child from her body's own adaptations. The ability to do that is inherited genetically, but  the information providing the adaptation advantage is not.
A mutation that mucked up that system would not be an advantage, so would usually be selected against.
As to the spoon:
First question is "which definition of species are you using?", which is not a pedantic question. If using the populations not interbreeding option, (among a few others) we're already many different species. If you're specifically thinking about genetic incompatibilities, well, that would require changes related to breeding.
Could that theoretically occur? Sure, but it's gonna need to happen to multiple individuals in a compatible way all at once or it would need to be progressively developed over time, or it can't pass on. That's highly unlikely.


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Western Blot: Fischer ECL substrate 2:1 instead of 1:1?
i recently developed a b-actin-ab-incubated PVDF-WB-Membrane with the Thermo Scientific Pierce ECL Kit. According to the manufacterers orders i mixed Reagent 1 and Reagent 2 1:1. But unfortunately i got kind of "unbalanced" bands (on the right side of the picture). Then someone gave me the tip to try to mix the reagents 2:1. For this substrate i got the result on the left side which actually looks much better.
Has anyone of you had the same experience and can anyone explain to me why this is so?
Is it "legal" to do so, or does it alter somehow the results of my experiment?
Yours,
p1ssn3lk3

I have put some potential reasons for your observations, however it would be great if you expanded your question in terms of the the exact steps you followed.

Yeah you're right, i should add some more details :)!
So it's a beta-actin-antibody which is already coupled with HRP, i didn't use a second antibody. I incubated on a roller board overnight in the fridge. I washed 3 times with TBS-T afterwards and also after the first ECL reaction i washed 3 times (10mins each) with TBS-T.

when you did your second ECL, was it without any new Ab staining?

Thats it.. no new staining..

I think the problem is unequal ECL distribution and if you done immediate ECL second staining without washing the membrane thoroughly and waiting a while before second ECL. There is a chance that when you overlaid your film on the membrane, you didn't get a good contact. what is your exposure time? This can also be a one of results! to make sire of the difference, redo the experiment as I have discussed in the first paragraph of my response. p.s why do you use a single step staining? is that part of your project?

Well usually in an ECL kit, one of the reagents is the substrate and the other one is hydrogen peroxide, which activates the substrate for breakdown using the HRP on your secondary antibody (Ab) so I genuinely doubt what you are seeing is the result of ratio difference. In order to make that conclusion you need to run your samples twice (on two separate membranes) and do a 1:1 and 2:1 ECL and if you observed such a difference then you are on firmer grounds.
I suspect what has happened in the above experiment is that you have done a 1:1 (with 1Ab and 2Ab not distributed equally on the membrane) then after perhaps not a very thorough wash, you have done another 1Ab and 2Ab incubation using the a 2:1 mix. I suspect what has happened is that in your 1:1 the left hand side has not received the Ab mixtures very well and when you did the 2:1 since the right hand still Ab attached to it (if you didn't strip the membrane) so the left hand side was "forced" to get the Abs hence again the Ab mixture and ECL not equally bound. It is obvious since one image is opposite the other so its the Ab incubation step that has gone wrong. Otherwise if you have done the second ECL incubation mixture straight after the first and didn't do a wash step, the same can result if the membrane did not receive the initial ECL mixture equally since you can get a blocking effect by the old ECL mixture and perhaps what has happened is that the H2O2 or the substrate was present in excess in the second incubation step hence amplifying the signal in the sections of the membrane that did not receive the ECL mixture very well in the first place, relative to the rest of the membrane, which still has ECL liquid on it from the last experiment (again if you haven't washed the membrane well as ECL can be active for up to 24 hours in some kits but after a few hours the activity usually reduces but can still be observed)
What you need to do is after ECL, wash the membrane with TBST for a few minutes followed by TBS, leave the membrane in the sun to dry so that the Ab slowly denature (although that doesn't always happen specially with high affinity Abs such as anti-tubulin and actin). After at least 24 hours, strip the membrane from Ab and redo the Ab incubation. The best thing to do is to do all the incubation steps in a sealed bag then make sure the membrane receives the ECL mixture equally and do the visualisation. I would say however since the membrane is unequally "contaminated" with the Abs then the best thing to do is to redo the experimental run and re-run the gel. Its a pain but you need to get to the button of this!

U sun dry your blots? Really?

indeed! it helps reducing the signal from any previous Ab staining which uses the same secondary or even a different 2Ab sometimes, specially for anti-Tubulin!

Interesting stuff, I've always used BME but may try this sometime.

@buzrw after ECL wash with TBST first, then TBS and then just leave it on a filter paper to dry but then you need to go through methanol socking step etc once you need to re-use the membrane. If you found the response helpful would appreciate a vote. If you needed any further detail just leave a comment.

I had a similar problem. In my case, I realized that it is absolutely essential to wash the membrane in TBS without Tween (TBS, not TBST) before you use ECL. If you have any amount of soap (Tween) on your membrane it reacts in some way with ECL and each time you should be getting a different pattern of these stains. Washing the membrane in TBS and then incubating with ECL made a difference for me and fixed the problem.

Pierce (or Thermo Fisher now) recommends washing the blots with a buffer containing Tween. It also doesn'z list Tween as a problem in the trouble-shooting section of the manual. And I haven't seen problems with detergents in my blots with ECL. It was rather a problem of incomplete mixing or distribution.

Try rinsing the blot in TBS or PBS before treating. Shake it try and place on level dry surface. When I pour the a chemo reagent on there I just pour enough so the surface tension keeps the fluid on the paper not allowing it to run off.
Other possibilities I see could be in your transfer. The temp could not be uniform in the buffer


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Is it possible to both extract DNA sequences from plasmids and fuse them using primers for Gibson assembly?
Maybe I'm overcomplicating this, but I'm having some issues with a construct.
So, I have three plasmids containing a total of eight DNA sequences that I need to fuse into one linear sequence. I plan to fuse the sequences using Gibson assembly. However, before I can fuse them, I need to amplify (PCR) them out of their plasmids.
I would like to use as few primers as possible, so my question is this; can I use the Gibson assembly primers to amplify them out of the plasmids and add the overlap sequences separately, then fuse them all together in a separate reaction without primers? Would the overlap sequences already added to each sequence separately be enough to act as primers for assembly? Even better (but I doubt it would work), could I amplify them out of their plasmids and fuse them in the same reaction?
If both these scenarios are unrealistic, I can still just order another round of primers to extract the sequences from their plasmids, but I would like to just use the primers I have if I can.

It's a little unclear what you mean by 'add the overlap sequences seperately' Normal gibson primers look like this:
5'Overlap sequence- Binding region-3'
You can use these to PCR our the fragments without any issue. I've added 5' extensions of 60bp without problems. Gibson assembly normally occurs without any primers as you purify the PCR fragments first. Your reaction will be very inefficient with 8 fragments, gibson really peters off at 6 put you can be lucky sometimes...

@mimat - I am mostly wondering if the plasmids will get in the way of my assembly at all. After a little discussion with some colleagues, I have determined that it will probably be fine as long as I add the overlap sequences first with their amplification primers, then fuse them in a different PCR reaction (in Gibson assembly, I have always just added my sequences and the overlap primers to the same PCR reaction). I forgot to mention in my original question that I will actually be splitting the fusion of all eight sequences into two or four different reactions. Thank you for clarifying.


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Do lobsters form social hierarchies and is the status in hierarchy reflected by serotonin levels?
In his book 12 rules for life Jordan Peterson claims that:

Consider serotonin, the chemical that governs posture and escape in the lobster. Low-
ranking lobsters produce comparatively low levels of serotonin. This is also true of low-
ranking human beings (and those low levels decrease more with each defeat). Low
serotonin means decreased confidence. Low serotonin means more response to stress and
costlier physical preparedness for emergency—as anything whatsoever may happen, at
any time, at the bottom of the dominance hierarchy (and rarely something good). Low
serotonin means less happiness, more pain and anxiety, more illness, and a shorter
lifespan—among humans, just as among crustaceans. Higher spots in the dominance
hierarchy, and the higher serotonin levels typical of those who inhabit them, are
characterized by less illness, misery and death, even when factors such as absolute income
—or number of decaying food scraps—are held constant. The importance of this can
hardly be overstated.

at another passage he claims that:

A lobster with high levels of serotonin and low levels of octopamine is a cocky,
strutting sort of shellfish, much less likely to back down when challenged. This is because
serotonin helps regulate postural flexion. A flexed lobster extends its appendages so that
it can look tall and dangerous, like Clint Eastwood in a spaghetti Western. When a
lobster that has just lost a battle is exposed to serotonin, it will stretch itself out, advance
even on former victors, and fight longer and harder.

For the second passage he cites the following paper
While there are many papers linking position in the social hierarchy in primates and humans I could not find a paper supporting the first passage.
The best I could find to support the first passage is an interview with Bret Weinstein where they mention that Peterson is indeed correct claiming that social hierarchy of lobsters in linked to serotonin levels. Interview with Bret Weinstein
A review paper claims that:

Is the marine environment less conducive to the establishment of dominance hierarchy structures, or does this just underline the lack of detailed behavioral information about most marine invertebrates?

Which suggests that not much is known about the relationship between serotonin levels in lobsters and the position in the social hierarchy.
Peterson basically argues that since the injection of serotonin leads to aggressive behavior in invertebrates, which is dominant trait in the animal kingdom this is proof that serotonin is indicated by the status in the social hierarchy. However It could just as well be that serotonin just leads to aggressive behavior in lobsters without being an indicator of the position in the hierarchy.
Are there any studies which specifically investigate whether the position of lobsters in a hierarchy is reflected in their serotonin levels?

https://pubmed.ncbi.nlm.nih.gov/33772639/

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The paper Peterson cites about serotonin and lobsters explicitly contradicts him in two major ways. First, although serotonin plays a role in aggression across many species, its role is not the same across those species:

The nature of the linkage [between serotonin and aggression], however, is not simple, and it has proven difficult to unravel the role of the amine in the behavior. In vertebrates, lowered levels of 5HT (endogenous or experimentally induced) or changes in amine neuron function that lower the effectiveness of serotonergic neurons generally correlate with increased levels of aggression (19, 20) whereas in invertebrates, the converse is believed to be true (11–13). Genetic alterations of amine neuron function also can change aggressive behavior in animals (21–24) and in people (25–27) although, again, in most cases, it is not clear how the genetic change is linked to the behavior. ... Finally, direct injections of amines like 5HT into animals also cause changes in aggression, but even here the relationships are complex. For example, in ants, injections of 5HT and its precursors lower interspecific aggressiveness toward intruders but raises intraspecies aggression (28, 29).

Clearly, the role of serotonin plays in aggressive behavior is not conserved between lobsters and humans. The most we could say is that serotonin plays some role in regulating aggression, but that role changes between species.
Secondly, the same study observed that although lobsters injected with serotonin will fight for longer, but are not more to start a fight or to win:

Thus 5HT selectively decreased the likelihood that subordinates withdraw from the attacks of their dominant opponents without altering their locomotor activity, the rules of escalation of fights, or the eventual outcome of an encounter.

Peterson is directly contradicting the conclusions of the paper he is citing:

A lobster with high levels of serotonin and low levels of octopamine is a cocky, strutting sort of shellfish, much less likely to back down when challenged.

Either he is a liar or does not understand the paper he is citing, and I can't decide which is worse.
P.S. Here is a video thoroughly dismantling Peterson's entire philosophy. The part about him being incorrect about lobsters at 40:00.

You did not answer the question if there are studies linking the position in the social hierarchy to serotonin levels.

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Adaptability in immune system
I read somewhere that recently some people are trying to use harmless bacteria that live symbiotically in humans to express some portions of antigens of the harmful ones. Some people have raised concern that continuous exposure to the same antigen may lead to adaptibility of immune system to that epitope and render it useless when the germ actually comes.
Can't we use the same procedure for exposing some parts of MHC of the donor to the recipient before transplantation, so that, by the time the real transplant is done it may become adapted ? How much time would it take for this to occur ?
I can already see one drawback : In emergency transplants, this can not be used due to time factor. Can you see any other drawbacks ?

A patient needing an organ transplant, even if it is not an emergency, is usually seriously ill. Triggering a potentially severe immune reaction is not a good idea for them. If you would manage to trigger an adaption in some patient, this does not mean that it will always work. So you need a (error save) method, to check for adaption, because non adapted patients will need immune repression before transplanting the organ.

I don't know how long the adaption process would take, but it will only be possible for transplants from living donors, because it will sure take a lot longer than an organ can be kept alive.

@skymninge I am saying that this can be used complementary to the "traditional" way. If patient gets adapted, then good otherwise go with the conventional way.

@skymninge I like the first point in your comment - triggering an immune response in the already sick patient will be not so good.

Do you have a link to the place you read that?

@Amory I don't have a link but I read that in a book - Good Germs, Bad germs by Jessica Snyder Sachs

No. MHC works differently from any other antigen. MHC is involved in the maturation of T lymphocytes in the thymus. Forming lymphocytes need to recognise the MHC with a certain affinity (lymphocytes with too much affinity for the MHC are destroyed). In all this process there is no intervention of foreign antigens, so the system you propose won't work because the lymphocytes would search the MHC of the graft and they would attach them with abnormal affinity. This would trigger autoimmune response.
What you propose is the main functioning of allergy vaccines. You expose the immune system to low dose of antigen during long time, and that would make the body to not react aggressively to the substance. However, this phenomenon is based in B lymphocytes, which recognaise soluble antigens and little cells (humoral immune system) instead of whole cells (cellular immunity).
In the domains of science fiction, however, it would be technically possible to transfect thymal cells in order to express the MHC of the donor, since it would express both. Actually, this should be theoretically easy (The thymal cells seems to express almost any protein in the body, in order to prevent autoimmunity), but it face the problem of thymal degeneration.

Angel Naranjo Oritz : Just wondering, why are lymphocytes with too much affinity for MHC destroyed ?

Could you explain the first paragraph more elaborately ? I am not able to understand your idea.Thanks !

@biogirl If there is too strong of an affinity for the MHC complex, the lymphocytes may be able to bind outside of the specific MHC:antigen context; in particular it may allow them to react to self-peptides, resulting in autoimmunity.

@Amory I may be wrong but what I understood is - If lymphocytes bind too strongly to new MHC , they may also trigger autoimmunity ?????

Exactly. MHC function is to "show" internal peptides to the immune system. When this peptids are alien, the lymphocyte assumes that the presenting cell is infected by a virus or a bacteria, and try to destroy it. There is a double check that ensures the lymphocyte attach the MHC and also that it can separate. If an alien peptide is present in the system, the second check doesn't trigger, and instead the lymphocyte will induce apoptosis.

@biogirl Yes.  It's a Goldilocks process.  If they don't bind strongly enough to MHC, they're useless and are destroyed.  This is called positive selection, and occurs first.  Next, lymphocytes undergo negative selection, where they are selected for moderate binding, lest they always bind MHC, even in the context of self-antigens.

@MiguelÁngelNaranjoOrtiz Thanks ! I get it now.

"...lest they always bind MCH even in the context of self-antigens" surprises me. You mean any naive T cell that binds self antigen on MHC "too strongly" i.e. "doesn't let go" will be eliminated as non self tolerant. However, there are naive T-cells who bind to specific antigen on self MHC which bind and then "turn away"? Highly interesting, as the latter look like good candidates for mounting response against non self, foreign, transplant MHC presenting their specific antigen. Sorry for wondering about such basics.

"....because the lymphocytes would search the MHC of the graft and they would attach them with abnormal affinity. ..." - No need for antigen to be presented on foreign MHC?