text:
What does x in "Miscanthus × giganteus" name stand for?
I came across a species name that contains "x" in its name, namely Miscanthus × giganteus. What does this symbol stand for and is it commonly used in taxonomic nomenclature?

It means that the plant is a hybrid. Having it in the middle means that it is between species of the same genus, else the × (it's not the letter x but the multiplication symbol ×) would have been in front.
It is very commonly used in taxonomic nomenclature, namely every time you have a hybrid. This means you'll usually see it with plants, as animals very rarely interbreed.
Wikipedia says that your plant is a hybrid from Miscanthus sinensis and Miscanthus sacchariflorus. It is an easy place to look up most hybrids you might encounter.

Well, would be rather hard to eat due high cellulose content, but it is one of the promising spices for 2nd generation biofuels production.

Lemongras is also a tough gras, but still used as a spice, sometimes even eaten, http://cooking.stackexchange.com/questions/53671/should-lemongrass-be-edible-or-just-a-flavoring. I don't know why you'd look at spices when you choose biofuel sources though.

I'm working in research where we develop cellulase activity assays - the cheap, fast and quantitative ways to say what mixtures of enzymes will produce most glucose from lignocellulotic biomass in industrial context. Miscanthus is the sample we got from other research group and I got curious what the symbols in the name means.
In general finding a good energy crops for 2nd generation biofuels is an active and well founded research field [C. Somerville, H. Youngs, C. Taylor, S. C. Davis, S. P. Long, Science 2010, 329, 790–792.] [J. Wang, J. Xi, Y. Wang, Green Chem. 2015]

I think Klara is talking about a species name, not a spice's name.

It is very commonly used in taxonomic nomenclature, namely every time you have a hybrid. I second that, and I think I had better give an example everyone knows about: the beautiful Iris, especially the German one, Iris germanica L.. Dykes' taxonomy is most widely used these days, not seeing the plants as a "wild species" (as Linnaeus partly did) but as hybrids, e. g. Iris × germanica var. florentina' (L.) (Dykes) The × is particularly common with this very kind of flower.

@senderle Oh, thanks for catching it. I realized that there must be some misunderstanding after Klara's second comment, but I just didn't make the association with species

Thanks @senderle for catching the typo, I totally overlooked it and I was quite confused with rumtscho comment.


text:
What determines excrement's caliber?
Often, pieces of feces have a clearly-defined shape and size — both length and width (that is, cross-sectional diameter, or caliber). But that width seems to vary quite a bit, even among pieces of feces from the same person. Why? What determines the width? Why is it wide when it's wide, and why is it narrow when it's narrow?

With the help of Bristol Stool Chart (BSC) and full explanation of conditions related to different stool sizes from this link you could have a full understanding over stool size.

» Type 1: Separate hard lumps, like nuts Typical for acute
  disbacteriosis. These stools lack a normal amorphous quality, because
  bacteria are missing and there is nothing to retain water. The lumps
  are hard and abrasive, the typical diameter ranges from 1 to 2 cm
  (0.4–0.8”), and they're painful to pass, because the lumps are hard
  and scratchy. There is a high likelihood of anorectal bleeding from
  mechanical laceration of the anal canal. Typical for post-antibiotic
  treatments and for people attempting fiber-free (low-carb) diets.
  Flatulence isn't likely, because fermentation of fiber isn't taking
  place.
» Type 2: Sausage-like but lumpy Represents a combination of Type 1
  stools impacted into a single mass and lumped together by fiber
  components and some bacteria. Typical for organic constipation. The
  diameter is 3 to 4 cm (1.2–1.6”). This type is the most destructive by
  far because its size is near or exceeds the maximum opening of the
  anal canal‘s aperture (3.5 cm). It‘s bound to cause extreme straining
  during elimination, and most likely to cause anal canal laceration,
  hemorrhoidal prolapse, or diverticulosis. To attain this form, the
  stools must be in the colon for at least several weeks instead of the
  normal 72 hours. Anorectal pain, hemorrhoidal disease, anal fissures,
  withholding or delaying of defecation, and a history of chronic
  constipation are the most likely causes. Minor flatulence is probable.
  A person experiencing these stools is most likely to suffer from
  irritable bowel syndrome because of continuous pressure of large
  stools on the intestinal walls. The possibility of obstruction of the
  small intestine is high, because the large intestine is filled to
  capacity with stools. Adding supplemental fiber to expel these stools
  is dangerous, because the expanded fiber has no place to go, and may
  cause hernia, obstruction, or perforation of the small and large
  intestine alike.
» Type 3: Like a sausage but with cracks in the surface This form has
  all of the characteristics of Type 2 stools, but the transit time is
  faster, between one and two weeks. Typical for latent constipation.
  The diameter is 2 to 3.5 cm (0.8–1.4”). Irritable bowel syndrome is
  likely. Flatulence is minor, because of disbacteriosis. The fact that
  it hasn't became as enlarged as Type 2 suggests that the defecations
  are regular. Straining is required. All of the adverse effects typical
  for Type 2 stools are likely for type 3, especially the rapid
  deterioration of hemorrhoidal disease.
» Type 4: Like a sausage or snake, smooth and soft This form is normal
  for someone defecating once daily. The diameter is 1 to 2 cm
  (0.4–0.8”). The larger diameter suggests a longer transit time or a
  large amount of dietary fiber in the diet.
» Type 5: Soft blobs with clear-cut edges I consider this form ideal.
  It is typical for a person who has stools twice or three times daily,
  after major meals. The diameter is 1 to 1.5 cm (0.4–0.6”).
» Type 6: Fluffy pieces with ragged edges, a mushy stool This form is
  close to the margins of comfort in several respects. First, it may be
  difficult to control the urge, especially when you don‘t have
  immediate access to a bathroom. Second, it is a rather messy affair to
  manage with toilet paper alone, unless you have access to a flexible
  shower or bidet. Otherwise, I consider it borderline normal. These
  kind of stools may suggest a slightly hyperactive colon (fast
  motility), excess dietary potassium, or sudden dehydration or spike in
  blood pressure related to stress (both cause the rapid release of
  water and potassium from blood plasma into the intestinal cavity). It
  can also indicate a hypersensitive personality prone to stress, too
  many spices, drinking water with a high mineral content, or the use of
  osmotic (mineral salts) laxatives.
» Type 7: Watery, no solid pieces This, of course, is diarrhea, a
  subject outside the scope of this chapter with just one important and
  notable exception—so-called paradoxical diarrhea. It‘s typical for
  people (especially young children and infirm or convalescing adults)
  affected by fecal impaction—a condition that follows or accompanies
  type 1 stools. During paradoxical diarrhea the liquid contents of the
  small intestine (up to 1.5–2 liters/quarts daily) have no place to go
  but down, because the large intestine is stuffed with impacted stools
  throughout its entire length. Some water gets absorbed, the rest
  accumulates in the rectum. The reason this type of diarrhea is called
  paradoxical is not because its nature isn‘t known or understood, but
  because being severely constipated and experiencing diarrhea all at
  once, is, indeed, a paradoxical situation. Unfortunately, it‘s all too
  common.
Interestingly, the interpretations and explanations of the BSF scale
  that accompany the original chart differ from my analysis. To this I
  can only say: thanks for great pictures, but, no thanks for the
  rest...
Excerpted from Fiber Menace, page 117-120; BSF Chart: wikipedia.org

But to make it more clear:
Reasons behind thicker and harder stool:

Lower fiber food
Lower liquid intake
Lower physical activity
Lack or lower amount of bacteria related to retaining water inside rectum and colon
Medication:

Many medications have constipation as a side effect. Some include (but
  are not limited to) opioids also known as narcotics, diuretics,
  antidepressants, antihistamines, antispasmodics, anticonvulsants, and
  aluminum antacids. Certain calcium channel blockers such as nifedipine
  and verapamil can cause severe constipation due to dysfunction of
  motility in the rectosigmoid colon.

Metabolic and muscular

Metabolic and endocrine problems which may lead to constipation
  include: hypercalcemia, hypothyroidism, diabetes mellitus, cystic
  fibrosis, and celiac disease. Constipation is also common in
  individuals with muscular and myotonic dystrophy.

Structural and functional abnormalities
Any physical digestive tract line problem which cause interference of stool movement. Like cancer or some kind of inflammation that could ban the canal

Constipation has a number of structural (mechanical, morphological,
  anatomical) causes, including: spinal cord lesions, Parkinson, colon
  cancer, anal fissures, proctitis, and pelvic floor dysfunction.
Constipation also has functional (neurological) causes, including anismus, descending perineum syndrome, and Hirschsprung's disease. In
  infants, Hirschsprung's disease is the most common medical disorder
  associated with constipation. Anismus occurs in a small minority of
  persons with chronic constipation or obstructed defecation.

Psychological

Voluntary withholding of the stool is a common cause of
  constipation.The choice to withhold can be due to factors such as fear
  of pain, fear of public restrooms, or laziness. When a child holds in
  the stool a combination of encouragement, fluids, fiber, and laxatives
  may be useful to overcome the problem.

Edit:
In the second provided link you could get how cross-sectional diameter changes based on what you eat or how you behave with your body mentally or physically if you are a healthy person.
But as you are interested more on cross-sectional size of stool and reason behind it, consider the fact that colons and rectum are water absorber. The more stool stays there the more thick and dry it gets. So if you ate more fiber you will probably have softer stool and thinner caliber as the result of pressure of the rectum canal. Because some bacteria which are active in the fibers of stool are water absorbers too and the reason behind why doctors insist on eating more probiotic products is to keep these bacteria present and stable and also to get vitamins from their activities. So you could change your caliber only by eating more fiber more water and having more physical activities and also for consistent thick and dry stool (constipation) individual must share the problem with doctor because it could bring more dangerous problems in future or maybe it's a sign of some other serious disease that person's body is already dealing with. Most of the time it's nothing but our diet and hours we are sitting for variety of reasons or maybe focusing on another activitys (work, computer games, disabilities, watching tv and so on and so forth).
https://en.wikipedia.org/wiki/Constipation
https://www.gutsense.org/constipation/normal_stools.html

As this post isn't about cross-sectional diameter, it doesn't seem to answer the question.

I've edited my answer to make it more clear to get your answer about why stool size differs even in one person. If there is still something not understandable, feel free to ask. It helps me too.

source: Stack Exchange

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Are there any organisms with larva more advanced than adult form?
Usually adult organisms are more sophisticated than corresponding larva, i. e. frogs, mosquitoes, fish. Are there species where the opposite is true?

What do you mean by "advanced" and "sophisticated"? These are qualitative.

Difficult to convey. Something sort of this quote from wikipedia about crocodiles: Crocodiles are among the more biologically complex reptiles despite their prehistoric look. Unlike other reptiles, a crocodile has a cerebral cortex, a four-chambered heart,and the functional equivalent of a diaphragm, by incorporating muscles used for aquatic locomotion into respiration (e.g. m. diaphragmaticus);

I guess I'd object to that characterization of crocs. See http://en.wikipedia.org/wiki/Evolution_of_biological_complexity

Maybe, but the characterization is still useful in clarifying the meaning of "advanced".

I mean even if crocs are not as good as wiki describes them, the I would be more than happy had a larva got listed advancements.

To add in some more complexity: There also is the - somewhat disputed - hypothesis, that larva and "adults" actually are two different animal species with one shared genome. ( http://www.pnas.org/content/106/47/19901.full )

First let me agree with the commenters that your question doesn't really make sense.  Nonetheless here's an example that you may find interesting. Arachnocampa are insects that spend almost their entire lives as larva. These larva spin silk trap lines which capture and poison prey. They can only live in windless places (wind will mix up the lines) so to lure insects into caves they glow. By contrast their imago forms are short-lived poor fliers which are unable to eat.

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text:
How to learn DNA Origami
Can you tell me is there any good softwares and tutorials which can be used to learn DNA Origami. I am new to this and want to learn from basics.
Advance thanks for your help
edited: INSILICO

I am assuming you want to do it in silico, right?

you can also do a little origami DNA... http://www.youtube.com/watch?v=0jOapfqVZlo

@nico yes, my current idea is to do it in insilico..but may be in future i will try to do it in invitro also..it will be helpful if any one can explained both procedure

Try this.

cadnano simplifies and enhances the process of designing three-dimensional DNA origami nanostructures. Through its user-friendly 2D and 3D interfaces it accelerates the creation of arbitrary designs. The embedded rules within cadnano paired with the finite element analysis performed by cando, provide relative certainty of the stability of the structures.

I would try to read everything from Shawn Douglas's body of work. cadnano is definitely the best start.

According to Rothemund, the original algorithm in the DNA origami paper is the same and much improved in caDNAno.


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Master Catalog of all Fossils / Literal Fossil Record?
Is there a website or other resource that catalogs all fossils ever found? Basically, is there a literal "Fossil Record"?
Where do scientists gather their results from excavations? Are they just scattered in various peer-reviewed papers in science journals?
I'm imagining something like manuscripts and master texts. You have some researchers who analyze manuscripts to produce the text of that manuscript in electronic form, for instance. Then, other researchers take these various readings and assemble a master text, taking into account the variations and attempting to recover the original work.
By analogy, this would be like when a paleontologist at a dig site submits a paper about his/her findings to a science journal. Is there another group of scientists who look at all of these papers and compile a "master text" of the fossil record?

No main website because it is expensive to make one and involves risks. Those found in internet are mostly useless for research purposes. Those fossil collections are located mostly in their owners. It is a research advantage to have such collections. Similar situation is with iPS cell collections and embryo samples. Iran has the biggest iPS collection, while Japan biggest embryo collection. It depends how you define fossils and in what context to say where are the most significant collections.

Honestly, I think what you would do is contact a institution that you know has an excellent collection of what you want, and ask them for their catalog of their samples.

what kind of fossil records are you looking for? I don't think all of them would be segregated in the same database but there could be separate lists for dinosaurs maybe.

@TheLastWord I thought there would be some kind of master catalog, per species listing the find and the estimated date attached to it... Like a Messier catalog for fossils. I'm just surprised it doesn't seem to exist.

@John Can you go through http://fossilworks.org/ and http://paleobiodb.org/ . Let me know if they suffice. Paleobiodb has a map based view which I found quite interesting.

@TheLastWord Wow... this is really cool. Submit this as an answer and I'll accept it for the bounty.

fossilworks.org and paleobiodb.org are reasonably good databases for fossil records. Paleobiodb has even got a map based view which is really convenient. Thank you.


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What is the optimal frame size for protein secondary structure prediction methods?
The whole question is

What is the optimal frame size for the second and third generation protein secondary structure prediction methods? Justify your answer.

I remember it has something to do with the average length of alpha-helix. More specifically, 3 on both side of a site. So in total the frame length should be 7. But I can't remember the reason behind the argument.
What do you think?

According to what my professor said in class, 2nd and 3rd generation of protein secondary structure reconstruction relies on statistics data of several consecutive residues.  I guess what he meant by "frame size", is how many adjacent residues we should take into account in the algorithm.

By frame size, do you mean sliding window?
I know that if you want to predict a secondary structure of a transmembrane protein, then your window size should be 20 amino acids (this is the average length of 1 transmembrane alpha helix spanning through the membrane).
I found this paper by Chen, Kurgan, and Ruan[1].
It basically says that the window size depends on what kind of pattern you are looking for, but in general, 19 residues should be optimal.
Also, secondary structure predictors rely on many features like hydrophobicity, missing coordinates in X-ray structures, B-factors, motifs, etc.

Chen K, Kurgan L, Ruan J. 2006. Optimization of the Sliding Window Size for Protein Structure Prediction. CIBCB '06: 2006 IEEE Symposium on Computational Intelligence and Bioinformatics and Computational Biology, pp.1-7, 28-29, doi:10.1109/CIBCB.2006.330959.

That's the problem of computational biology - sometimes it's difficult to find what exactly what a term means.  But I think my professor asked for general protein secondary structure predication, not transmemebrane protein.

OK, so 2 responses, each concerning different protein segments of different types/functions/structures, but not an answer really getting to the heart of the question. Because of the homework tag, I am tempted not to reply - this is something the student should accomplish on his/her own. So, I'll give a general answer to start you thinking. Basically, such a value - be it 7 or 20 for TMs or 13 - is determined empirically.

I found that 13 worked best for Neural Nets and SVM performance of secondary structure information when I ran this in R.

Any reason behind it?


text:
"selective pressure" or "selection pressure"?
Editing a manuscript of mine, a co-author changes "selection pressure" to "selective pressure". Are those two terms interchangeable? Or are there subtle differences that I'm not aware of?
The sentence under consideration: "In contrast, gene expression changes during development and tissue formation are under high selection/selective pressure."
FWIW, "selection pressure" is a bit more popular in the literature.

I had a colleague that was against the use of "pressure" altogether - I can't fully remember his argument but it was a long the lines of just saying selection is correct grammatically, and selection is not a type of pressure. I feel he is fighting a losing battle though because its becoming more common. You might get a better justified response on the English language SE.

Selective/selection is being used as an adjective to qualify 'pressure'. My gut feeling is that is better to avoid using a noun (selection) as an adjective, so selective is to be preferred.

From a grammar standpoint I would think that "selection pressure" is a compound noun. But I was looking for a biological answer, if one is more appropriate than the other.

Could you possibly give the sentence it is in?

@GriffinEvo: done

I'd say "subject to strong selection"

Selective sounds better to me, though I cannot think of a reason why. I expect that a reader will get the same meaning from either choice.

As far as online references are concerned, they should be equivalent (as "selective" becomes "making a selection"). The important difference in my understanding is that speaking in terms of biology, "selection" triggers associations with evolutionary terminology, whereas "selective" doesn't. Thus, as far as I am concerned, "selective pressure" could be referring to some machine that has a method of applying pressure to one thing but not another, whereas "selection pressure" immediately makes me think of factors benefitting the proliferation of one thing over another. Hence I would personally prefer "selection pressure".
Given the ambiguity, you probably won't be able to make all readers happy with either of the two. Thus, it might be best just to use a different phrasing as suggested e.g. by rg255 ("subject to selection").

... if you do say "subject to strong selection" does this make me a co-author??? @michaelkuhn ;)

I think second author at least! :P

let me think about it :)


text:
Are there any online resources one can use to access raw clinical trial data without having to contact those involved in the study?
I want to do some statistical analysis and I have a preference for real data so I was wondering if there's somewhere I can get such data for free without a heap of bother in phoning those involved in the studies in question.

Have you seen this question on stats SE: http://stats.stackexchange.com/questions/18833/where-to-find-raw-data-about-clinical-trials ?

More options in a similar question on Open Data SE: http://opendata.stackexchange.com/questions/11/de-identified-patient-data

See these three sites:

ClinicalTrials.gov
NIDA
ClinicalStudyDataRequest

For clinical trials conducted by other agencies (in different countries), you may have to contact those authorities.


text:
Which Enzymes are Responsible for the Biodegradation of Beta-endorphin?
Which enzymes are responsible for the biodegradation of the endogenous opioid peptide, beta-endorphin?

As far as I have been able to find out, there isn't a definitive answer to this question.
β endorphin is a peptide, and it would seem that there are numerous brain peptidase enzymes that are implicated in the hydrolysis of β endorphin and other peptide neurotransmitters. These include aminopeptidase N, membrane-dipeptidase A, angiotensin-converting enzyme and neutral endopeptidase (also called enkephalinase).
For an early (1984) review of this topic see here; there doesn't seem to be a more up-to-date review, but there is quite a bit of literature on the effects of inhibitors of these various enzymes.


text:
What does effect would Sulforaphane have on Kennedy's Disease?
Sulforaphane is a isothiocyanate found in cruciferous vegetables including broccoli and cauliflower. Its 2D structure is as follows:

It's been found to serve as a histone deacetylase 6 (HDAC6) inhibitor and to inhibit androgen receptor expression in prostate cancer cells.1 This caused me to become curious as to whether it would do the same in lower motor neuron cells and thus manage to prevent their polyglutamine-induced death and thus halt the progression of spinobulbar muscular atrophy (SBMA; Kennedy's disease).


text:
Where can I find pdb files for macromolecules like receptors?
I have tried going to the RCSB website and quite frankly it was useless since when I looked up receptors like say the metabotropic glutamate receptor 2 (mGluR2) I got no helpful results.

The RCSB is the primary database for 3D structures of biomacromolecules, if it isn't in there, there is likely no public structure available for that molecule.

As pointed out in the comments, if you look for PDB files and you don't find them in the PDB, there is no solved structure. However, you can look in databases that contain models of proteins. Especially for the receptors the coverage has been increasing in recent years and so you may be lucky.
A good starting place to look for protein information is UniProt, where you find links to the Protein Model Portal and SwissModel. They contain models based on the PDB structure for Metabotropic glutamate receptor 3.


text:
How do I get the current "camera position" in PyMol so I can reuse it in scripts?
I have a few protein models I want to take pictures of with various ligands bound.  It would be nice if I could do it from the same "position", but the only way I can figure out to repeat the same view is with zoom resi. 64, 152, 150 or the like, which isn't framed that well.
How can I manually position the viewport, capture it's parameters, and repeat it in the script?

I have found get_view, e.g.
PyMOL>get_view
### cut below here and paste into script ###
set_view (\
     0.590180993,    0.670941532,    0.448923886,\
    -0.507570565,    0.740831316,   -0.439937204,\
    -0.627747774,    0.031782545,    0.777776182,\
     0.000000000,    0.000000000, -417.497009277,\
     0.741809845,    7.078243256,   16.473480225,\
   329.157806396,  505.836212158,  -20.000000000 )
### cut above here and paste into script ###

but this doesn't work in a .py script, where I need to modify it to cmd.set_view(...), as it complains it wants just (or up to 5) arguments, not 18.  The wiki is vague about it, it just says

PYMOL API
cmd.set_view(string-or-sequence view)

Try to pass the matrix as a String containing 18 floats separated by commas, e.g. like
cmd.set_view ('''
     0.590180993,    0.670941532,    0.448923886,\
    -0.507570565,    0.740831316,   -0.439937204,\
    -0.627747774,    0.031782545,    0.777776182,\
     0.000000000,    0.000000000, -417.497009277,\
     0.741809845,    7.078243256,   16.473480225,\
   329.157806396,  505.836212158,  -20.000000000 ''')

cmd.get_view() seems to return a tuple, so you'll have to convert that to a String if you want to pass the same position to cmd.set_view().
I tried it in Pymol 1.3 on the command line (not in a script though) and it seemed to work.

Ah, I guess if I translated the "command line/interactive form" of the commands into the API version, I should have also kept those parenthesis that get_view returns so they're really nested (so you do pass it a tuple).  Would look like cmd.set_view((1,2,3...))

Note that you might also want to make use of get_viewport and viewport in case you do not only need the same perspective, but also the same paddings to the outer boundary.

I should add that get_view seems to be undocumented at the moment. It works for me with PyMOL 1.5. Looks like this or a related command does not work reliably in all situations. You might also want to read https://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg08419.html


text:
What nutrients can humans absorb in the mouth?
For instance, I realise being able to absorb simple sugars in the mouth is pivotal in the rapid action of oral glucose gel. Thus I was wondering what nutrients in general can be absorbed directly within the mouth, and at what speed?

This could be a fairly long list, though off the top of my head Vitamin C and Glucose would be good places to start for nutrients and drugs GTN and Aspirin.  This Question is also related.

Quite a bit can be absorbed through the mouth. Most commonly, starches are broken down to maltose (two glucose molecules formed by a condensation reaction) and are easily absorbed by the bloodstream.
A lot of other factors balance into this, ie pH, lipid solubility, and molecular weight. Generally, if a substance is easily dissolved in saliva, it can be administered buccally or sublingually because the only remaining step is the diffusion into the subepithelial capillaries. In regards to speed, anything properly absorbed via buccal or sublingual administration goes to work much faster than a standard oral medication, and with a higher availability in the bloodstream. You are taking first pass metabolism and enzyme breakdown in the stomach out of the equation by diffusing the drug directly into the bloodstream.
There is quite a laundry list of medications that can be administered transbucally or sublingually, just a few of these:
Nitroglycerin
Acetylsalicylic acid (aspirin)
Glucose gel (as you mentioned)
Fentanyl (a narcotic painkiller)
buprenorphine (for opioid dependency)
Benzodiazepines (alprazolam, clonazepam)

so you said pH and lipid solubility... if the salivary secretions are alkaline would that mean that alkaline compounds would be deprotonated and more lipophilic, hence better absorbed?

This answer could be improved by including references.

The mouth or the oral cavity is lined by oral mucous membrane. The oral mucous membrane has two parts the epithelium and its supporting connective tissue known as lamina propriya. The charecter of the epithelium and lamina propriya varies to a great extent from the gingiva and hard palate to the floor of the mouth based on functional requirements. However basically the mucous membrane lining the oral cavity is not designed for absorbing nutrients, which was the primary question.
As for the oral glucose gel - read the American Red Cross, Scientific Advisory Council recommendation that the buccal absorption of glucose is limited and not recommended. ARC SAC Advisory

Actually, absorption does take place through the mouth.There is a ptyalin enzyme in the saliva which hydrolyzes carbohydrates of the food.  These contents are then absorbed in the blood through the facial vein.The facial vein opens into subclavian vein,and it opens into the superior vena cava.

I think the main question of the asker is "which" nutrients are absorbed through the mouth, the fact that absorption takes place in mouth is taken as a given fact.

Many vitamins are absorbed in mouth. Even spraying vitamins will help you overcome vitamin deficiency.
Even some drugs can be absorbed directly into mouth.

Source of this info?

Alcohol, a very important source of nutrition in undergrad students, can also be absorbed through the mouth.

www.crohns.net/Miva/education/aboutsprays.shtm

@biogirl that's not really a credible source

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text:
Which Receptors are Involved in the antidepressant effects of SSRIs?
From what I've read the major receptor subtypes involved in the antidepressant effects of SSRIs are:

5-HT1A
5-HT2C
5-HT3
5-HT6

Please cite journal articles to back up your claims, I don't want any piece of information to be unverifiable.

I noticed you've asked a few questions about antidepressants recently--did you know that there's a cogsci stack that you can try too? I'm not saying these questions should be there instead of here, just saying you could ask in both places and see if it's helpful.

No, I didn't know that. Thanks for this suggestion, Alexandria.

You're right, those are all important! There are several good reviews on the mechanism of action antidepressants. I like Molecular Pharmacology, by Nestler, or even Principles of Neural Science, by Kandel. I think a textbook is going to be your best bet, in terms of getting up to speed here, as this is largely an already-researched issue, but here are some good review articles as well:

Bonhomme et al., 1988
Charney et al., 1981
Norbert & Esposito, 1998
Spencer, 2012

If you have a more specific question, let me know!

The question was which receptors are involved in the antidepressant actions of SSRIs, bupropion isn't a SSRI. I was going to say you're a little right up until I saw that you were talking about NDRIs -- by blocking the 5-HT2C receptors or downregulating them they manage to increase the dopamine and norepinephrine concentrations in various regions of the brain thus increase the activity of their respective receptors.

@BrentonHorne: Ah, sorry about that. I started talking about antidepressants and got carried away, I think!

@BrentonHorne: If you're really interested in SSRIs, I highly recommend the Nestler text--it talks about all classes of drugs, but it is one of the best bits of scientific writing I have encountered.

Which one's the Nestler text?

@BrentonHorne: The Molecular Pharmacology one. It's a text book, but totally worth the money, I think! I think it's most recent edition is 2008, but it's definitely a good overview of everything up until that point!

@BrentonHorne: I removed the Bupropion part to my answer, as it didn't pertain to your actual question.


text:
Does Doxylamine have any Influence on the Monoaminergic System?
Does doxylamine have any affects on the monoaminergic system? Specifically I am interested in adrenergic or serotonergic activity but additional information on its dopaminergic activity won't hurt either.


text:
Endocannabinoid Transporters - which ones are Likely to Exist and what is the Evidence for their Respective Existence?
Endocananbinoid = Endogenous Cannabinoid or CB1 and CB2 ligands.
I'm asking which endocannabinoid transporters exist and could the one answering show all the evidence for the existence of the transporters they mention. For instance anandamide is suspected to have a transporter and there is some evidence for its existence, and paracetamol's chief active metabolite, AM404, appears to work by inhibiting the actions of the anandamide transporter.

Could you clarify your question a bit? I'm having a hard time understanding what exactly you are looking for as you provide no context to your question.


text:
What Effect Does the Endocannabinoid System have on Monoaminergic Neurotransmission?
I know that Δ9-tetrahydrocannabinol and other cannabinoids increase dopaminergic neurotransmission in the nucleus accumbens and that this is what results in the euphoria experienced by cannabis users. Other than this I do not know what effect cannabinoids have on monoaminergic neurotransmission. I would assume that it increases monoaminergic neurotransmission seeing how rimonabant $-$ a selective CB1 inverse agonist $-$ leads to depression and anxiety which according to the monoamine hypothesis can likely be linked to changes in the activity of monoaminergic pathways in the brain.


text:
JMol "calculate HBONDS": which atom is the donor/acceptor?
JMol can be used to identify Hydrogen bonds in proteins by the script "calculate HBONDS".  By outputting the state of the network, we can obtain a lisdt of H-bonds.
Here's one line from an example output (PDB ID number 1a1x):
74    540    4096    0.001    -2.507   hbond;

I believe the correct interpretation of the first two numbers is that atom 74 is H-bonded to atom 540.  (I'm not really sure what the other numbers mean.)

Question: How can we determine which atom is the donor and which is the acceptor?

In the above example, atom 74 is a Nitrogen atom and atom 540 is a Carbon atom, so presumably the Nitrogen atom is the donor.  But, how can we tell in general?

I dont know about JMol, but this can be easily done with UCSF Chimera.
I loaded the 1a1x structure.
Then selected: Tools > Structure Analysis > FindHBond
I kept the default values and selected Write information to reply log
Then clicked OK
On the structure the H Bonds will be identified with a coloured line.
To view which is the donor and acceptor go to: Favorites > Reply log
An output of the reply log is below:
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
ASP 12.A N    GLU 25.A OE2  no hydrogen  3.012  N/A
HIS 13.A N    GLU 25.A OE1  no hydrogen  3.338  N/A
HIS 13.A ND1  ASP 12.A OD2  no hydrogen  2.835  N/A
LEU 14.A N    TRP 70.A O    no hydrogen  2.934  N/A
TRP 15.A N    ARG 23.A O    no hydrogen  2.866  N/A
...
120 hydrogen bonds found

As you can see the donor and acceptor has been identified as defined in the header line.
If you wish, the information can also be written to a file by selecteing Write to text file in the FindHBond window.

I also had to do the same using Jmol, and I figured it out how to get a list of all the hbonds.
Step 1: Calculate the hbonds with or without RASMOL method. It's up to you, e.g.,
jmolScriptWait("select not hydrogen; set hbondsRasmol FALSE; calculate HBONDS")

Step 2: Only display the hbonds
jmolScriptWait("display connected(hbond)")

Step 3: Export the bonding info to JavaScript array
jmolGetPropertyAsArray("bondInfo")

You will have an array of objects each will contain the atoms connected by this hbond and the bond length.


text:
What can you tell about a person, having only their whole genome as information?
Well, the question is in the title, no explanation need.

I love the "only" part of the question :)

More every day.

Which level of certainty do you prefer? (If you want 100% certainty, you can tell less than if you were also considering risks and probabilities, and "Insecure knowledge", such as newest and speculative research findings. I hear that most things you could learn about from the genome are not that deterministic at all.)

I've had a little encounter with this question in the past few months so I'm updating here...
The overall answer is 'really a lot about some things, but not as much as you'd like to think about others.'    There is a scientific genome interpretation 'contest' that has been going on for the past few years called CAGI (Critical Assessment of Genome Interpretation).  This is meant to be a cutting edge set of challenges and its worth looking them over.  Last year there was in particular one challenge - answering questions about ten individuals given only a list of traits and their genome sequences.
It was not so easy it turns out - simply looking up variants and cross referencing them to the literature led to poor predictions.  Glaucoma, asthma, migrane, irritable bowel syndrome, color blindness, lupus, lactose intolerance are examples from a list of 40-odd contest questions.  If you register onto the site you can get some of the results or there is a paper reporting the results, only four labs tried the challenge and the accuracies were sometimes not great, topping off with Rachel Karchin's lab with an AUC of 90%.  Even some of the phenotypes you think are easy are not a simple lookup.  Genetics is not as pre-determined as we think.
While we are good at inferring our history and geneology on the other hand.  A reasonable example of this is the 23andme analysis.  They have a lot less information about you than a complete genome sequence, but they do seem to make the most of the 0.0001% of the genome that they do have.
They have a nice lookup of some of the hereditary disease data that is available.  "Increased risk of skin cancer" or for Alzheimers are only chances and its never clear how much your actual lifestyle has impact on 44 outcomes, but its there.
What they also have is your ancestral analysis which is crazy interesting. it shows where your maternal and paternal lineages come from and how strong.  they have a very pretty heatmap of the continents for this.  National Geographic's DB is probably more sophisticated and ancestry.com also does this.  This is pretty cool.
Also included things like curly hair, color of skin eyes and hair.
Like SimaPro says they are described in OMIM.  OMIM stands for 'online mendelian inheritance in man' and all the straightforward directly inheritable traits we know of are listed there.  its worth taking a look. There are not a lot of known single mutation genetically inheritable conditions.
If the genome sequence includes methylation, then some other traits which are epigenetic, not genetic but would also be determined from a genome sequence.  Most famous example of this is MEST which will give an indicator of whether you are a doting parent or not.

The first paragraph is (unintentionally?) misleading since you cannot extrapolate from the 0.00001% and conclude that the genome holds 10000-fold more information than 23andme is using: they are obviously picking their 0.00001% rather carefully. Given that there’s a SNP about every 100 bases, this then is the total increase of information you could gain about a single person – that is, a factor 100 over what 23andme is currently offering, not 10000.

@Konrad Rudolph: no, you would have a factor 100 if genes did not interact between each other, which is not the case. The effect of 2 SNPs at the same time may not be just the sum of those of the single SNP.

@nico True, as far as pieces of information are concerned. But as far as the information content goes, the numbers work out. Note that in information theory the information content is a logarithm of the number of different possible outcomes. Same here.

@Konrad Rudolph: sure, in terms of information content I agree with you.

Well - a lot if you knew what questions to ask...
The most obvious thing is sex: if you can find the x and/or y chromosomes.
Other things like skin color, eye color, etc, or hereditary diseases and all that would involve running the genome through some sort of database which had values for both pheno and genotypes so you could correlate some of those things and find those physical characteristics.
Scientists are discovering these correlations all the time.
You can go to http://www.ncbi.nlm.nih.gov/omim and search for something like eye color and find out more than you need probably.

The first place to look for answer to this is the 1000 Genomes Project. I feel that their efforts in data analysis offer lessons on what one can and cannot learn from such a dataset as posed in the question.
One obvious thing that is easy to overlook is a whole genome sequence will tell you the mid- to large-sized insertions and deletions in that genome. Any of those that are novel, private or extremely rare (take a word of your choosing) can be used to place that individual in a family tree (if other data are available) and to predict certain phenotypes (from the affected genes). This is also true for some SSRs - simple sequence repeats.
Good haplotype analysis from the genome sequence can predict ethnic ancestry - with a fair degree of accuracy. This is especially so as more genomes are sequenced and available for comparison. Haplotypes of the Y chromosome and mitochondrial genome, give paternal and maternal ancestry, respectively.
If the whole genome sequence gives accurate telomere lengths, then a prediction of age of the individual can be gained +/- 10 yrs.
Disease phenotypes or risk of disease is tricky. For monogenic diseases, this is more accurate and that accuracy falls off as the complexity of contribution to variance of the trait increases. At least a hundred loci contribute to risk of type 2 diabetes, but that risk is also age-dependent and so a young person may not have the disease but only be at increased risk. Furthermore, not everyone with elevated risk will acquire the disease and not all at reduced risk will remain disease-free - for that disease.
Lastly, if this analysis included epigenetic measures, such as methylation of the genomic DNA, then one can predict genome changes from environmental exposure such as tobacco smoking or air pollution. In addition, loci with differential methylation and showing a phenotypic consequence, such as elevated obesity status (BMI) or colorectal cancer risk, are beginning to be defined. This is in its infancy, but the data are growing.

Astonishingly, if they are male you can take a pretty good punt at working out their surname and narrowing down exactly who they are. There was a recent paper on doing this with anonymous genome data, discussed in a blog post here if you want a more accessible account.


text:
Creating a cell, not from another cell. Will it be possible?
If some time in the future, we can know exactly what a cell (for example simple prokaryote bacteria) contains, (I mean, exactly which molecules, the shape of them, the density of each, everything), Then can we create a new cell (not from another cell)?
I mean, if we have such technology, then create a soup just like what that cell contains, and a DNA exactly same as that bacteria cell, and then put some of it inside a Cell membrane, will it start living?

This has -at least partly- been done by Craig Venter's group: http://www.sciencemag.org/content/329/5987/52.abstract However, they did not recreate the entire cell, "just" the genome which they reimplanted in a recipient cell. Recreating a whole cell would be much much much much [...] much more complicated.

@nico But will it be possible in the future?

I should check in my crystal sphere... :D Jokes aside, I think 10 years ago Creig Venter's experiment would have raised a lots of eyebrows and would have been said to be impossible. I think we cannot do it right now, but possibly in the future we will have the technology to do it. Synthetic biology is a brand new branch of biological sciences so we should not expect too much too soon! My knowledge on the topic is quite anecdotal however, I will leave the answer to someone more knowledgeable than me!

So, is it believable that some day, we may can create Two primary cells of a human so we can create a complete person?!

Again, we are extremely far away from creating a whole bacterium, a yeast cell already will be WAY more complex, let alone a human cell. Ethics aside, right now we are not even able to clone a human using preexisting cells.

Science advances incredibly fast :D Maybe we can do that in the next 50 years! Can you post your comments as an answer?

There is the more recent work by Szostak on artificial protocells. The IVC world all aims to achieve this to some degree.

@bobthejoe Can you explain some more?

I think it could feasible to assemble complete synthetic cells in future. One of the first successes will probably be a simple bacteria. The synthetic genome is already on the road, so here, I'm pointing to other technologies that can be helpful. Feel free to add/edit/complete.
Inorganic chemistry. Self-replicating inorganic cells can be already obtained from polymer emulsions: optimistically, one may try in future to work with organic macromolecules.
3D printing technology may also evolve to the point that it will be possible to assemble cells by printing microscopic 'ink' molecules with the correct cellular organization. 3D printing works by serially printing one layer on the top of the other: to prevent molecular layers to mix, a technology to serially froze the printed layer will help in obtain a frozen synthetic cell.

Many of the parts of a cell, which perform its basic functions, such as transcription, translation, DNA replication, etc. have been already isolated and successfully recreated in a test tube. So if we obtain a complete list of all the parts we need and know how to make those parts and mix them together, we can make a cell from scratch.
However, this will probably be very time-consuming and costly and will serve no other purpose than showing that it can be done. It is much more time- and cost-efficient to create a genome only, transplant it into an existing cell, and wait for the cell to replicate and synthesize new molecules until it changes in a way that completely fits the new genome.


text:
Databases for gene regulatory network graphs?
What databases are available for gene regulatory network graphs starting from a given gene? For example, starting from p53 gene, where can I find a gene regulatory network image that can be exported or embedded to another website?

For a free resource, try GenMAPP. Commercial products like Ingenuity Pathway Analysis do the same thing with prettier graphics and a curated approach to network-building, but access can be expensive if you're not affiliated with an institution that will foot the bill.

If you can't afford ingenuity, KEGG has branched out into regulatory networks as well.  Here's the link to their version of the pathway.
http://www.genome.jp/kegg/pathway/hsa/hsa04115.html
Its free to use as a reference and for academic research.

How did you get to this page? I want exactly the same thing for other genes but I keep winding up at pages that look like this: http://www.genome.jp/dbget-bin/www_bget?ko:K02583 and don't know where to go

i can click on 'pathway menu' and then use the box to search for my genes and get more diagrams like this one.

I highly recommend you to visit Pathguide to get a sense of how vast is the catalog of Pathway Databases. Looking into the category Pathway Diagrams or in Transcription Factors / Gene Regulatory Networks should help in your task.
I would start by looking at these DataBases:

GeneMania
BioCarta
WikiPathways
Reactome

If you are working with a species other than human, perhaps you'll find a more suitable database in PathGuide.
Good luck!
PS: Sorry New user limitations impede me to post more than two links :/

You can write the links into the comments and someone else can edit your answer.


text:
Confusion related to the DAVID tool
I am trying to use the DAVID tool to do some gene analysis. I have some probe set intensities for some cancer cell lines. I found this link in the DAVID tool http://david.abcc.ncifcrf.gov/tools.jsp. I am a bit confused with the terminology introduced here. It says gene list for the probe sets why is it so? I mean in the example you can see the probe sets like
1007_s_at
1053_at
117_at
121_at
1255_g_at
1294_at
1316_at
1320_at
1405_i_at
1431_at
1438_at
1487_at
1494_f_at
1598_g_at
Buy why are they called gene list not probe sets. Why?

Its a bit confusing, but DAVID uses the term Gene List as a generic term.
Looking at Step 2, you can submit many kinds of lists to DAVID, including actual gene symbols, Ensembl or RefSeq Accessions, etc... actually nearly 30 kinds of terms including 'not sure' which probably looks at your list and tries to guess.
Affymetrix or Illumina probe set IDs are each designed to measure a gene, ideally, though its not precisely a one Probe Set to one Gene relationship.  This is because when the array is designed there may be a partial transcript RNA records which turn out later to be parts of a single gene.  There are also probe sets which may turn out to hybridize to similar sequences in more than one gene.
Its messy, but its also true that often more than one gene symbol will appear for the same gene because of historical naming conventions...


text:
What biochemical molecule viewer allows for changes in amino acids and resulting tertiary structure?
I am familiar with the Jmol, Rasmol and PyMoL softwares, and was recently introduced to BioBlender. However, I am completely unaware if any of these programs (or others) are capable of loading a .pdb and allowing for the change in a particular amino acid, to ultimately visualize the change in tertiary structure caused by that substitution.
Are any programs capable of performing an amino acid substitution on a molecule loaded by .pdb and showing the change in tertiary structure?

Pymol should have that capability... try Gromacs

This may help: http://www.pymolwiki.org/index.php/Mutagenesis

One application that I am aware of that will do this, as well as much else besides, is Swiss-PDB Viewer aka DeepView. If you go to the site and select User Guide in the left hand tabs you will see a subsection called mutations and following that will tell you what the application can do.

Visualising the change induced by an amino acid on the 3D structure is part of an entire field of research call molecular modelling (http://en.wikipedia.org/wiki/Molecular_modelling). There is a huge body of research available on the subject and I am not up-to-date anymore in this field.
What I used to do was simulating the optimal shape of a AA chain (~10) which was part of the bigger molecule. The technique consisted in using a Monte-Carlo procedure to simulate heating the molecule and cooling it down millions of time and checking for the stability of the resulting conformation using . I used Modeller, Procheck and Prosa. That was in 2000.
There is a wikipedia list of molecular mechanics modelling software here (http://en.wikipedia.org/wiki/List_of_software_for_molecular_mechanics_modeling)

If I understand what you're attempting to accomplish, as David said, this is a vigorous area of study in structural biology. I'll start by saying that a single amino acid substitution will often make virtually no difference in a structure, but there are proteins where a couple substitutions will convert an all alpha-helical protein to all beta-sheet, so I'll leave it to you to judge what's worth trying. There are three routes you can take:
First, for small changes, pymol does have a built in force field ("molecular sculpting") and residue mutagenisis.  Chimera has a tool called "minimize structure" that are probably better developed. And VMD has the force field tool kit plugin.
If you expect larger changes, you might go with a full simulation package like NAMD or CHARMM.  They would take significant effort to get running, but they're there.
Finally, you can just go with an empirical structure prediction server. All you do is open your sequence file, make your substituions there, upload it to the server, and wait for them to email you the results.  They'll do sequence alignments to find relevant PDB files and everything. I recommend the Robetta server (running David Baker's Rosetta). http://robetta.bakerlab.org/


text:
What happens in your brain when you receive information which causes you to bristle?
I'm talking about moments when you watch a film and you bristle, or when you listen to music, etc.
What kind of neurotransmitter flow changes?

Do you mean you bristle or get goosebumps?

You mean piloerection?  Adrenaline or cold tightens the muscles, which makes the hair stand on end, to trap heat and make the animal look larger.

yes exactly is it just Adrenaline or there is another flow of neurotransmitters increased or decreased ?

One thing is that we can't control the Goosebumps. It is an involuntary function caused by the Sympathetic Nervous System which is the major part of the Automatic Nervous System. The major function of the SNS is fight to flight response along with maintaining homeostasis in which case it internally will be alert maintaining body status from the background.
Before sending any response to target tissue when there is input to SNS it has to secrete neurotransmitters but before this to the sympatho-adrenal response of the body, as the preganglionic sympathetic fibers that end in the adrenal medulla (but also all other sympathetic fibers) secrete acetylcholine, which activates the great secretion of adrenaline (epinephrine) and to a lesser extent noradrenaline (norepinephrine) from it.
So whenever SNS senses (message flow is bidirectional) any stress it responds it in following action mentioned:

At the synapses within the ganglia, preganglionic neurons release acetylcholine, a neurotransmitter that activates nicotinic acetylcholine receptors on postganglionic neurons. In response to this stimulus postganglionic neurons - with two important exceptions - release norepinephrine, which activates adrenergic receptors on the peripheral target tissues. The activation of target tissue receptors causes the effects associated with the sympathetic system.

Once the receptors receive the information then the response flows to the target tissue via neurons with the help of the neurotransmitters. To explain goosebumps technically:

Properly known as piloerection, horripliation or pilomotor reflex, the bumps we get are stimulated by fear and cold and they are essentially just a temporary change in the skin. These stimulants cause a nerve discharge from the sympathetic nervous system (which is an involuntary portion of nerves we have) and the nerve discharges create muscle contractions called arrrectores pilorum that raise the hair follicles in our skin. It is the elevation of the hair that causes the Goosebumps.  The name Goosebumps actually comes from the fact that plucked goose feathers resemble the human hair follicles.

Goosebumps also occur when we listen to surprise songs, sad songs or some other kind of thrilling music. Researchers have tried to explain it and they call it "Frisson".
Check out this small video which talks about it. It is nice:
http://www.youtube.com/watch?v=-EA2eWZuYDs
Also refer to this website: Goosebumps


text:
Open Mass Spec Database
Wondering if there is an open (freely available) database of Mass Spec Data, particularly for the Substances/Compounds listed in NCBI.
Specifically, I am not sure if NCBI includes the mass spectrometry data / datafiles in their FTP server related to any of their chemicals. So I am just wondering if there is an open database of mass spec datafiles out there somewhere.

It's unclear what you are looking for, there are many substances/compounds listed in NCBI. Could you clarify this so the question can be answered?

The Human metabolome database (HMDB) contains many MS/MS and NMR spectra for human metabolites. You can acquire the spectra from the downloads section. The HMDB includes external identifiers for each compound. This includes the PubChem Compound IDs that are given on the NCBI database. There are 2 265 compounds with LC-MS/MS spectra in the HMDB.
The excellent MS-DIAL software package also comes with extensive positive and negative ion mode LC-MS/MS and GC-MS/MS spectral libraries in flat text format; that's also worth a look.
A lot of the raw spectral data is restricted due to multi party agreements (NIST, chemspider).

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


text:
Where to find all "authorities" for taxonomic names?

https://en.wikipedia.org/wiki/Author_citation_(botany)
https://en.wikipedia.org/wiki/Author_citation_(zoology)

I am using NCBI to get a fairly complete list of organisms and their taxonomic name. Going to look further how to find the common name programmatically. Next is where can I find the author / authority name and date, is that stored in a publicly accessible database anywhere? Where does it get stored in the first place as well, if not a central db?

https://species.wikimedia.org/wiki/Catalog:Taxon_Authorities/A

That's the best I've seen so far.

Admittedly, I haven't had the need to look for it, but I have not been able to find a common list of all authorities, partly because the vast majority of these sorts of things were done a long time ago - dating back to Carl Linnaeus in the 1700's.
You could try the various authorities on naming of organisms. International Committee on Taxonomy of Viruses, International Committee on Systematics of Prokaryotes,  International Association for Plant Taxonomy, and the International Committee on Zoological Nomenclature, but even these might not work.
You may have to dig through some very old literature to find the authorities. I've done so for similar posts in the past looking at finding primary authorites, such as this one, but it is very time-consuming and not easy without a very good local reference library and academic access.


text:
What factors must be taken into account for the maintenance of the immunogenicity of ovalbumin antigen?
What factors must be taken into account for the maintenance of the immunogenicity of ovalbumin antigen?
If the ovalbumin is aggregated, could we inject it for induction of immune reponse?

The preparation of a soluble antigen for injection often includes treatment with an adjuvant which usually creates aggregates of some sort. It is my understanding that particulate antigenic material is preferable because it elicits a better immune response.

Do u know the size of antigens which aggregated by the effect of adjuvant?  If the aggregates' size are around 150 um, do they can activate the immune response? I've read a review article  that suggested that the size of particle (Drug delivery system) should be 1 um for the advantage of to be engulf by phagocytes. It seem like, the antigen aggregate more than 1 um, can not be engulf by the phagocytes ?

Ovalbumin is frequently used in immunology to induce an immune response (see some publications about mice and ovalbumin here.
You usually inject it together with an adjuvans to enhance the reaction. The factors that must be taken into account for its maintainance are the same as for the other antigens, so you should boost this "vaccination" from time to time.


text:
Are descriptive statistics sometimes more useful than tests of significance?
How does the biology community currently feel with regards to publishing descriptive and effect size statistics rather than significance stats?  Almost every journal article I read in the cell biology field almost always reports things like P values and stats tests to report statistical significance, but should effect sizes be more important to a biologist?  Do we even care if something is statistically significant if the effect size is negligible?  Rather than crunch for significance, could one get away with showing things like confidence intervals, eta^2, Cohen's d, and r values instead over P values?  P values tell you the odds that if you assume the null hypothesis is true, then the observation you're making are only 5%(assuming of course P<0.05).  However, this can lead to the logical fallacy as noted by Aristotle--theory A predicts that changing X will cause Y.  An experimenter thus performs experiments to manipulate X and sees changes in Y, therefore he/she concludes theory A is supported, which is however completely wrong.  Theories B, C, D, E....... could all also predict that X changes Y and may even be better at it.  Even if you conclude that your findings "support" theory A, it's still weak because you haven't ruled out all of the other possibilities.
So in order to avoid statistical significance relative to null hypothesis that has all sorts of pitfalls, can one just use descriptive and effect size statistics just as effectively, if not more so?

I wonder how much of this is because biologists have been taught statistical significance and haven't been taught to use effect size. In my introductory stats class in college, we never got beyond linear regression (yes, it was sad, but at least I learned R), and that was more stats than most people knew. I learned about effect size simply because of a well-informed PI whose background was not in biology. I, personally, would favor the use of descriptive and effect size statistics in combination with significance statistics, i.e. these are significantly different, by this much.

Agree with @dd3. You can try and talk about effect size and such, but then when the infamous third reviewer whines about p values you gotta play the game... To be honest most biologists I know (many of whom are very good at biology, nothing to say there) only have a very basic -and often slightly wrong- understanding of statistics. I can tell you I always have a hard time convincing people to use things like generalized mixed models or such. Most people will just say: I'll do a t-test or an ANOVA instead...

@nico: Agreed on all points. I would also agree that I am one of those people...which is why I visit Cross Validated.

On a related note: http://xkcd.com/882/

@GPI For a better answer this should really be on http://stats.stackexchange.com/ - you are asking biologists  when you could be asking statisticians, generally they know more about stats than us biologists! Personally I think each case is different so this question is also a bit difficult to answer, but my approach tends to be: do the stats, report the statistical significance and some descriptive statistics, but discuss the scientific significance - stat & sci significance are not perfectly correlated (p>0.005) ;)

(just because I feel it is better suited to cross validated it does not mean I would close this question - as I said biologists would probably ask this question a lot themselves - but could you place it on cross validated and put the link on here so we can find it?) @GPI

@dd3: well, but that just means that you DO want to understand what is the correct way of applying statistics to biological problems. I do not understand when people want to stay stuck with their t-test because "the rest is too difficult I won't understand it anyway". I am not a statistician either, but if I use a tool I want to know exactly what it gives me and how to use it correctly.

@Alan Boyd: even better http://www.wired.com/wiredscience/2009/09/fmrisalmon/

I'm not a statistician, but I think the comments have got it right.  There is never a reason to omit P values, statistical power or some other measure that you have done something that is not a random outcome.
For the sake of reference lets define the terms you reference:
Eta squared is a ratio of the variances of two sets of measurements
Cohen's d is a measure of the difference between two means.
R value or Pearson Correlation describes the linearity of two numbers, usually one of them being a measurement and the second being an experimental variable.
These numbers as you say are descriptive, but they could be created by throwing coins and writing them up.  With small numbers of measurements, and a large enough range of possibilities, its possible to get terribly large numbers here.
Biology, medicine, social science and economics are really susceptible to this.  You go into the field and measure butterfly wings or do surveys of people's opinions, or try to guess who is going to win the election and its quite expensive to do more measurements.
If you are measuring something hard to determine because accuracy is important such as a close election race or that is really complicated such as which genes convey a susceptibility to type 2 diabetes (a problem which remains unsolved because so many genes play a role) you need large numbers of responses.  Yet each study that comes out gets some answer, but if you want to believe it these numbers should convince no one in most cases.
Microarray data and RNASeq data analysis for instance often suffer from this problem.  The measurements are all statistically significant but each one costs hundreds or even thousands of dollars.  Most experiments do a minimal three measurements to understand the variance in each measurement and then do 2 to 8 actual measurements.  That's not going to so revealing when working with a system with thousands of genes in it. one bad sample with slightly different culture conditions can ruin the experiment.
Our butterfly biologist may measure 100 butterflies and stop when the P values are 0.05 or 0.001 - its a lot of work camping out and setting nets.  The truth is that 5% is a number that can happen at random a lot.  Even a 0.1% error will happen in one in ten such experiments.  In thousands of experiments published that means that 10% of them have a mistake.  Not so great.
It gets worse though - not only significance, but bias needs consideration.  Because biologists and most other scientists don't understand statistics, the assumptions that we use when we calculate a P value are often inappropriate and don't give honest estimates of the chance that this is a random phenomenon.
If good looking result is chosen specifically to show to prove the point or some data are thrown out because they simply don't look good, or if a hypothesis is chosen in a biased way simply to fit an unreliable set of data.
Or the statistical assumptions of the calculation might simply be so inappropriate that to really cite them is an out and out lie. An everyday example of this is to do a BLAST search.  The E-value calculations, if read as a P value would be wrong, even though they are mathematically correct - two strings that show a 10% identity will have a small E value - 10^-8 for instance, but this is only the chance two strings of these lengths will have so many letters in common.  Anyone who plays with BLAST will quickly throw out anything that has less than 30% identity unless they are desperate, even though the E-values are infinitesimal.
John Ioannidis has made this subject his focus and has published widely on this topic.  A good place to start is his commentary "Why Most Published Research Findings Are False".

There is increasing concern that most current published research findings are false. The probability that a research claim is true may depend on study power and bias, the number of other studies on the same question, and, importantly, the ratio of true to no relationships among the relationships probed in each scientific field. In this framework, a research finding is less likely to be true when the studies conducted in a field are smaller; when effect sizes are smaller; when there is a greater number and lesser preselection of tested relationships; where there is greater flexibility in designs, definitions, outcomes, and analytical modes; when there is greater financial and other interest and prejudice; and when more teams are involved in a scientific field in chase of statistical significance. Simulations show that for most study designs and settings, it is more likely for a research claim to be false than true. Moreover, for many current scientific fields, claimed research findings may often be simply accurate measures of the prevailing bias. In this essay, I discuss the implications of these problems for the conduct and interpretation of research.

Very interesting response thank you.  Does anyone in the community use Bayesian statistics rather than classical statistics as well to analyze their data?  My understanding is that a Bayesian analysis will actually tell you the probability that YOUR hypothesis is correct based on data.  Are journals accepting of Bayesian stats?  It seems like a Bayesian analysis would also address the questions of false positives/negatives quite effectively.

There is lots of bioinformatics work with bayesian statistics. Use of Bayes rule by itself is not free us from the need to estimate statistical power of the probabilities used in the analysis though...

Of course reading BLAST e-values as p-values is wrong. e-values give the number of hits of this quality you would expect to find by chance, given the size of the hit and the size of the database (and the composition of the sequences in question, low complexity etc). They do not give the probability of finding such a hit. They are not even similar to p-values and should never be confused.

so you are saying they are never confused?  they are probabilities even though they are not p values. I'm open to other examples that can be used, but couldn't come up with one while writing.


text:
What is meant by single molecule sequencing?
When sequencing papers refer to single molecule sequencing, what is their definition of a "molecule". Are they saying base by base? The entire DNA chain in a chromosome can also be though of as a "molecule". In that case, that's a much larger read. What's the default interpretation?
For instance, is the Illumina sequencing "single molecule" as they fluoresce one base at a time?
Thanks!

For the classic Sanger sequencing you need quite large amounts of DNA to be able to run the sequence reaction. This is a problem when you want to sequence whole genome since the DNA needs to be amplified then, which for some sequences can cause problems, introduce errors or cause bias.
Single molecule sequencing is a huge step forward here, since only one molecule of DNA is used for sequencing. There are different sequencing technologies based on this principle.
The system of pacific biosciences uses a polymerase bound to a small well which binds a singlestranded DNA and begins to make the opposite strand, when nucleotides are present.
See the image below or this video, which explains the technique quite nicely.

Illumina binds singlestranded DNA molecules to the surface of the reaction chamber and starts amplifying them there. The use of fluorescently labelled nucleotide allows to monitor the reaction. This looks like the following (left side of the figure from the review mentioned below):

An illustration from Illumina which is more detailed, can be found here.
Although it is a bit older (and the technology develops fast), this review is a nice introduction: "Sequencing technologies - the next generation."

Nanopores typically use an unlabelled oligo. Your figure is Pac Bio's immobilized DNA polymerase approach that uses the wonderfully named Zero Mode Waveguide to visualize a 20 zeptoliter volume and observe each labelled oligo being incorporated by the polymerase.

Yep, thats right. Have a look at the video, it is about the same method.

But it doesn't use a pore.  Its a well.  My comment was that a 'true' nanopore approach like Oxford Nano doesn't use label.  Both are examples of single molecule analysis.

I'd +1 if you add a sentence about nanopores or other single molecule approaches and answer OP re Illumina.

@Chris: So for some of these methods, they say "1 molecule = 1 count". So say they had a read count of 100 for a gene. What exactly does that mean? There were 100 reads from that gene? 100 reads of bases from that gene? Something else?

@Chris Is this same as what is called - Sequencing by synthesis ?

@biogirl Yes, as far as I know this is one of the other names for it.


text:
Do toxin producing strains of E. coli constantly produce toxin or only under certain conditions?
Background
E. coli is prevalent everywhere but only some strains produce toxins harmful to humans, such as E. coli O157:H7.
Questions
1) Would anyone know if these strains are always producing this toxin or is it only under certain conditions?
2) Is it the toxin itself that makes people sick and not the presence of the bacteria?

1) That depends on the fact, if the protein in the bacterium is regulated somehow or it is constantly expressed. That could be different for different toxins and even for the same toxins in different strains, so there is no  plain answer for all strains and toxins.
2) That, I guess, also depends on the toxin. There are some that are basically toxins, but do not make people sick. Sometimes, the toxin is produced by the bacterium, but never secreted. Sometimes it is secreted, but has no influence on the host. Sometimes the host does react to a toxin. But the human immune system can also react to the bacteria before they start producing toxin (if it is somehow regulated) or before the toxin concentration secreted by the bacteria starts to be harmful.
In the case of E. coli O157:H7, this paper states it produces two different Shigatoxins (that were supposedly causing its pathogeny), but also some other toxins/toxin-like proteins.
I have studied some E.coli genomes previously, some non-pathogenic had several toxin-related genes, some pathogenic had actually none at all (at least none that could be annotated).

Thanks. I'm looking over that paper. In your research did you ever come across some info as to what E.coli uses it's toxin for? I might actually just post that as a separate question..

I was not quite interested in the Shigatoxines, as they did not occur in the specific strain I was mainly interested in. I guess, secreting toxines is basically a fitness factor, as it could kill off competitors for nutrients.


text:
How to obtain bacteria samples?
Would anyone know how to go about obtaining samples of Salmonella or E. coli for purely educational purposes?
Note: I just want to look at the stuff under a microscope.

Shopping questions are off-topic, unfortunately.

As he mentioned below, you probably don't have what you want, but that is not the point.  My point is that this question will not likely be helpful for future visitors because that vendor could go out of business leaving an obsolete answer.

It's regarding a different type of product, but this meta.Biology answer gives a general overview as to why these questions are discouraged.

@Jonsca, I'm actually ok with this type of question. The alternative way to ask how to achieve such things but not exactly from whom, which is a reuseuable question. (ie how to appropriate go about contacting certain people)

As requested I removed the request for a purchasing location and reworded the question.

Can't answer because the question is on hold. If all you wish to do is view cells, you can buy prepared slides here for example. (I have no connection with this company, I have not used their products, and I am sure that other suppliers are available.) Alternatively live yoghurt is a source of safe bacteria if the species aren't important to you. Most rods look very similar.

If you just want to look at stuff under a microscope get a sample of dirt from your garden, dilute it in some water and behold the extreme variety of microscopic critters you will find in there!

@nico I don't understand the fear of the normal man getting his hands on what he could get quite easily if he didn't cook his food long enough...

@Usman Mutawakil: I am just saying it is much easier and cheaper to go into your garden and get some dirt than to order bacteria from a company, which would probably most likely involve quite a bit of bureaucracy on top of it. On top of that, fear or no fear Salmonella should not by law be handled in a normal household.

In a litigious world no supplier will want to take the risk of supplying you, as a private individual, with something that you could claim had made you ill.

@bobthejoe As currently asked (after the edit) I have little problem with it.  "Where to buy" questions are never good SE questions, IMO.

I would be happy to update my answer with good ways to isolate microbes around your house, and prep them on slides, if we can decide if this message is to be kept or not.

@jonsca I think I have modded my answer in such a way as this can be kept.  Feel free to edit if I'm wrong.

@AtlLED: that would DEFINITELY be better IMHO, although it seems the OP is not of that opinion. However, maybe you could write a new question?

If the mods want to close this one, I'd be happy to put it in a Q/A.  As long as this stands, I'm happy for it to stay here.

@Jonsca, shall we start the reopenning process?

@bobthejoe I started another question as suggested. I'm fine with it being closed if this is re-opened.

To be honest, you really shouldn't be buying such things if you're not prepared to handle them properly.  If you work with a proper lab, you will be inindated with vendors trying to sell you these and many others.
But to answer your question, if you are looking to purchase many such items ATCC is an excellent resource.  Not only will you have to meet regulatory requirements, but you will also have to deal with a great many MTA's depending on what you are trying to get.
In response to edit: Salmonella is actually not normally a serious pathogen to a healthy adult.  It is, however, still a human pathogen and should be handled under BSL2 conditions.  So if you have the funds and time to setup a BSL2 lab at your house, by all means go to town.  And I hope you don't live with any children, the elderly, or otherwise immunocompromised individuals.
In response to further edits:
If you just want to look at things under the scope, then I suggest you get started by making your own homemade culture plates.  If you can get your hands on some Lysogeny Broth (LB), agar, and petri dishes then you can make lb plates like a researcher in a real lab (minus an autoclave but you could use a pressure cooker).  These are items the public could get, but might be harder to come by.
I however will assume that you want to make your own plates from common household ingredients (I used to do this a lot as kid, whatever that says about me).
**
Making your own culture dishes:
**
1) The "plates" themselves.

I recommend getting the smallest Tupperware like
containers your can find that are microwave safe, dishwasher safe, and
really make a good seal (water tight at the least).  They really
don't have to be big, and you will make your life easier if you buy a
bunch to match.
They need to be super clean.  After running them through your
dishwasher at home, put them all in a boiling pot of water until you
are ready to pour in your "media." A mid-low simmer will work

Note that you won't probably be able to have perfect sterile technique at your house, but you should try to do what you can.
2) Your "Media" or Broth

I highly recommend using pectin as your gelling agent if you can't
get your hands on some agar.  After that comes plain unflavored
gelatin, but I recommend pectin.  You can get it at almost any
grocery store and my recipe is made assuming that.  You can determine
how much you want to make, just scale up the ratios.  I'm going to
list things as rough volume by volume so you won't need a scale.
i) Make the powder first:

45mL of pectin;
4 bouillon cubes ground as finely as you can (you can get different
types and results depending on if you start with vegetable, beef, or
chicken.  I recommend starting with vegetable.);
125mL of refined white sugar;
Additives (more on this later)

ii) Mix the powder into 500mL of water

Before you mix in the powder, hear the water to 50-75oC (mid low
heat), but not boiling.  Mix the powder in while stirring until
dissolved.

iii) Bring the mixture up to a boil.
Let it boil for about 2 min, stirring all the while.
iv) Cover the pot and let it cool for 4-5 min.
You by no means want it cool down to room temperature, you just want to get it a little below boiling.  If you are at 55oC or bellow it's definitely time move on.
v) Dip/fill your "plates" 1/3 full of media using clean/sterile utensils and seal while hot but not boiling.
You may have noticed this seems an awful lot like canning, and that's because it is.  Again you want to be as clean as possible in this step and of course try not to burn yourself on anything.
vi) Let your media plates set and chill over night in the refrigerator.
You really probably only have to wait a few hours if you are anxious to get going.  You are going to want to store the plates that you are not using in the refrigerator anyway.  Also if you made a bunch of plates, let the cool on a counter before you put them in the fridge so that you don't raise the temp of your fridge too much.
Remember the thing about additives?  You can play around with adding different amounts and different types of salts, vitamins, food, or other items to see how they effect the cultures you get to grow.  All kinds of fun there.  First go round, leave them all out.

Now you have your own home made culture plates!  The above recipe was empirically tested by my childhood, and repeated by my son's.  Not all pectin from the store may be equal, this is with Ball Classic (I have no relation to the company).  I'd love to know people's results in trying it, because I might need to re-think how/what I'm doing to get it to work.
Go around your house swabbing things with sterile swabs (you can get these at a drug store), and then streak them out on plate.  While it will be a little different with a swab and homemade plate, the idea is similar to what is done here.
Leave your plate in a warm wet place, but not in direct sunlight.  Ideal temp is going to be around 37, but you can leave them above and below that and still get things to grow.  On top of our dryer is where I leave.
After a day or so you should have colonies you can streak out on a slide and look under a scope.  You will find all kinds of things this way.  If you want a more formal way to put things on a slide, you can check out dry and wet mounting from a Google search.
You are actually quite likely to run into E.coli if you sample enough "areas" this way.  Obviously don't eat or huff the stuff that ends up growing.  Maybe you can post some fun pictures of this if you try it.

[I would comment above but I don't have the rep yet.]  It is certainly true that ATCC could go out of business, but if I were to reference Coke-a-cola to someone who was asking for a referral to a soda manufacturer, I don't think that would be on list of common concerns.  Instead, pathogens in general, select agents in particular, are by design not easy to get your hands on.  I would be interested if a member of the general public could get a pathogen from ATCC. That would let me know that there are people that need to be made aware of that fact.

Great answer! Did you ever try using food grade agar (a.k.a. agar agar)?

I have, i just found it less avalable and more expensive for what you need.  They may vary on your local market's demand for canning supplies.

I remember from my own childhood microscopy fun, that in Germany, agar agar is found even in the supermarket and it was cheap enough to make my dad buy it without him complaining once. Pectin would be harder to find. Seems to be regionally quite different.

@skymninge  In places where food grade agar is relatively available, it will absolutely work, probably getter.  You just need to get a sugar based gelling agent.  I double checked after writing the second version of this, and really couldn't find agar in our grocery stores.  Pectin is pretty cheap, ether way I don't think it should be expensive.


text:
What makes a gene dominant or recessive
We all carry two copies of each gene (outside of male sex chromosomes).  If the two differ from each other often one is dominant and one recessive.  How does this mechanism work on a molecular level?  What mechanism determines which gene gets expressed?

It is not the gene but the allele of that gene that is dominant or recessive. In addition, we do not contain two copies of each gene. Some genes exist at zero or one copy and others are somewhat to greatly duplicated - and this is considered normal (copy number) variation.

I don't have time for an answer, but someone should definitely mention haploinsufficiency somewhere.http://en.wikipedia.org/wiki/Haploinsufficiency

Related: Evolution of dominance of alleles

On the molecular level, genes most often encode proteins which perform some function for the cell: For example, they could be enzymes and catalyze chemical reactions. They could also have some structural function, such as make up the "muscle" part of your muscle cells... You get the idea.
In the most simple case, the dominant allele encodes a protein that can perform its function. For example, the dominant allele for the CFTR gene encodes a channel that can let chloride into and out of the cells. The recessive allele, on the other hand encodes a protein that cannot do its job correctly (this also called a loss-of-function mutation). So if you inherit a functional copy from one parent and a non-functional copy from the other parent, you will still have one copy of the protein that can do its job. Only if you get a nonfunctional copy from both parents will you have a recessive condition called cystic fybrosis.
On the molecular level a gene can also encode a dominant-negative variant of a protein. In this case the protein cannot do its job and also prevents the functional version of the protein to do its job too.
A third way this could work is by a gain-of-function mutation. In this case, the gene encoding a protein acquires a mutation that gives a new function to the protein. For example, in Huntington's disease, the mutant Huntingtin protein acquires the ability to clump together in large plaques, which are poisonous to some neurons in the brain. Since it takes only one copy of the protein to perform the new function, the gain-of-function allele is a dominant one.
These are only a few examples that deal with simple dominant and recessive inheritance. Most often there are more complex mechanisms of inheritance at play.

Is there an example in which we observe a dominant condition in which  the protein of the mutant allele prevents the functional protein from doing its job?

Generally if one of the genes' biochemical functions becomes knocked out completely, the other copy will fill in for it, making the trait recessive - requiring both copies being knocked out.
An example of such a recessive trait is Albinism - if both copies of the enzyme participating in melanin biosynthesis are ineffective, the result is someone with no pigment.
Dominant genes are often variant genes which convey a new ability (phenotype) and as such the trait can show up with just one copy has this variant.  Phenylthiocarbamide tasting is an example of this dominance.  If both copies of the gene were the variant, the original ability might disappear - making the original trait dominant as well.
There are other sorts of dominance.  If a variant shows up that inhibits a the other copy this can cause dominance by a variant; it can remove or modulate a phenotype (trait) by turning off or turning down the other copy of the gene.  This would be a case of trans-dominance.
I'm sure there are many other variants on these themes others could post.  Dominance and recessivity are relative and broad terms when you see how traits are inherited.

Generally if one of the genes' biochemical functions becomes knocked out completely, the other copy will fill in for it, making the trait recessive - requiring both copies being knocked out.
An example of such a recessive trait is Albinism - if both copies of the enzyme participating in melanin biosynthesis are ineffective, the result is someone with no pigment.
Dominant genes are often variant genes which convey a new ability (phenotype) and as such the trait can show up with just one copy has this variant. Phenylthiocarbamide tasting is an example of this dominance. If both copies of the gene were the variant, the original ability might disappear - making the original trait dominant as well. On the molecular level, genes most often encode proteins which perform some function for the cell: For example, they could be enzymes and catalyze chemical reactions. They could also have some structural function, such as make up the "muscle" part of your muscle cells... You get the idea.
In the most simple case, the dominant allele encodes a protein that can perform its function. For example, the dominant allele for the CFTR gene encodes a channel that can let chloride into and out of the cells. The recessive allele, on the other hand encodes a protein that cannot do its job correctly (this also called a loss-of-function mutation). So if you inherit a functional copy from one parent and a non-functional copy from the other parent, you will still have one copy of the protein that can do its job. Only if you get a nonfunctional copy from both parents will you have a recessive condition called cystic fybrosis.

A trait cannot be dominant/recessive, only alleles can be dominant/recessive. As a sidenote: There is a extra 3 at the beginning of your answer and you down vote is not really justified.


text:
Why do antidepressants have a delayed onset of action?
Why do antidepressants take so long to reach efficacy? I've read of theories about it perhaps being due to the strength of negative feedback via serotonergic and adrenergic autoreceptors during the first few weeks of treatment. What I'm looking for in an answer is the following:

The current theories regarding why currently-in-practise antidepressant regimens have a delayed onset of action.
The evidence for these theories.
How these theories fit in with the monoamine hypothesis or whether it is inconsistent with the monoamine hypothesis and how.
Possible solutions to this problem of delayed responses to antidepressant therapy.

All of this is strictly theoretical, there are no actual people involved here, this is simply a scientific inquiry.

Short answer
The mechanism of action of serotonin-specific reuptake inhibitors, a commonly-prescribed class of antidepressants, is a downregulation of 5HT1A receptors through negative feedback. This downregulation of receptors takes time.
Background
Serotonin-specific reuptake inhibitors (SSRIs) are a class of antidepressants commonly prescribed to treat depression. Their therapeuric effects may need weeks of treatment (Celada, 2004), which can be explained by their action on 5HT1A receptors in the dendritic region of the serotoninergic neurons in the raphe nucleus. By blocking serotonin (5HT) reuptake, negative feedback mechanisms cause the 5HT1A receptors to downregulate. This downregulation of the presynaptic modulatory 5HT1A receptors changes the firing pattern of the serotonergic neuron into a more fluttering mode, so that it releases more 5HT (Duman, 2007). More 5HT makes you feel better. That is how it fits into the monoaminergic hypothesis. To have the 5HT1A receptors respond this way takes time, as it is an adaptive response that downregulates of 5HT1A receptors, i.e., less receptors are present on the cell's membrane.
This is only an expanation of delayed action of SSRIs, a specific subclass of antidepressants. For example, there are newer classes of antidepressants that seem to work faster (5HT4 action) (Duman, 2007).
References
- Celada et al., J Psychiatry Neurosci (2004); 29(4): 252–65
- Duman, Neuron (2007); 55(5): 712-25

All regulatory administration (any reg. admin, FDA, TGA, EMA, MHRA, etc.)-approved antidepressants have a delayed onset of action, although mirtazapine may act slightly faster. So it isn't just the SSRIs. Even antidepressants with no appreciable serotonergic effects (e.g., bupropion) have a delayed onset of action.

Intetesting! I wasn't aware of that. I have made some changes in my answer, as it applies to SSRIs only. Thanks!

Did I start a trend?!? @AliceD

+1 thanks bunches Alice! Interesting that there are delayed and non delayed classes. I was not aware of this. Very cool

@StanShunpike - thanks for your appreciation. I improved the answer too. It's one of my first answers and it needed some additional referencing. Thanks!

@AliceD I have realized how much effort some contributors put in and appreciate it. I also know the feeling of writing an answer and having no one say anything and no acceptance! I'm sure u understand that feeling. I have gotten in the habit of thanking more as a result, where appropriate. :D

There's some clinical evidence for the relevance of 5HT1A autoreceptors, namely that pindolol augmentation accelerates the effects of SSRIs, but it doesn't do much more than that, i.e. ultimately if someone is unresponsive to SSRIs, pindolol augmentation apparently does nothing.

And @BH2017 is correct that even for drugs like bupropion, there's no difference in scores over time from SSRIs... at least in one study which is pretty damn odd, although perhaps there's not enough data.


text:
Are all Autoreceptors Downregulated by their Respective Endogenous Ligands?
I know that the 5-HT1A and $\alpha$2 adrenoreceptors receptors serve as autoreceptors for serotonin (5-HT) and norepinephrine respectively and are down-regulated by repeat exposure to their respective ligands, it's believed that this is likely the cause for the therapeutic delay in the actions of antidepressants that target the serotonergic and noradrenergic systems.  My question is this: "Is this the case for all autoreceptors? Are all autoreceptors down-regulated by the actions of their respective ligands?"

Autoreceptors - are receptors of the presynaptic terminal.
α2 adrenoreceptors receptors are down-regulated due to repeated exposure.

Pharmacodynamic tolerance begins when the cellular response to a substance is reduced with repeated use. A common cause of pharmacodynamic tolerance is high concentrations of a substance constantly binding with the receptor, desensitizing it through constant interaction

This is a common occurrence - not just for autoreceptors but receptors in general.
But for your interest here is one for dopamine autoreceptors (Pay-wall).


text:
Parse PDB using DSR-PDB Library
I'm trying to parse ATOM section of a PDB file. I'm using the dsr-pdb library for this purpose.
I've encountered a problem. This library interprets CD1 atom of ILE residue in the PDB file as AL_CD instead of AL_CD1*. Does it have a particular reason?
It's maybe helpful that within the source code, in Residue_data.cc, there is a mapping between atom lebels:
Atom_fallback_data atom_fallback_data_[]=
      {{Residue::AL_CD1, Residue::AL_CD},
       {Residue::AL_1HA, Residue::AL_HA},
       {Residue::AL_1HB, Residue::AL_HB},
       {Residue::AL_1HD, Residue::AL_HD},
       {Residue::AL_1HE, Residue::AL_HE},
       {Residue::AL_1HZ, Residue::AL_HZ},
       //{Residue::AL_1HH, Residue::AL_HH},
       {Residue::AL_1HD1, Residue::AL_1HD},
       {Residue::AL_2HD1, Residue::AL_2HD},
       {Residue::AL_3HD1, Residue::AL_3HD},
       {Residue::AL_INVALID, Residue::AL_INVALID}};
It means that AL_CD1 is deliberately converted to AL_CD or for example AL_1HA to AL_HA.
Thanks.

In general, in dsr-pdb library, AL_X is the atom label of atom X.

Isoleucine only has one delta carbon, which we can just call CD. But it seems like some PDB files still name it CD1, and hence programs map CD1 to CD in this case. (E.g. see this tutorial where this practice is shown.)