text:
Which concentration of BSA is recommended for dynamic light scattering experiments?
What is the recommended concentration of BSA to be mixed with water so as to prepare a very dilute solution in order to clearly study the intensity-intensity correlation with single scattering ?
I want to plot the intensity vs time correlation curve/graph, and eventually calculate the hydrodynamic radius in each case. I've seen different journals and texts provide varied concentrations ranging from 0.001 g/L to 3 g/L.

Needs more context. What is your goal? What have you tried? What references have you consulted?

You should be able to find these answers in any methodology text or looking through the literature.

I've edited the question a bit, it would help a lot if you could add more detail. It would help if you added more detail about the method (I guess it's DLS?) and equipment you're using, I'm don't know much about this area, so I can't say if the information here is sufficient to answer your question.

Yes i'm using DLS. The objective is to find the hydrodynamic radius of the corresponding protein. I'm doing a project on it and require to know the range of concentration to prepare a dilute solution of the protein with water to visualize single light scattering. Hope that might help.

You can easly calculate the absorbance from Beer's Law
A = εlc
Here you can get the values for Extinction coefficient by sequence at http://web.expasy.org/cgi-bin/protparam/protparam1?P02769@25-607@
So for your example 0.001 g/L  3 g/L with this R code, you can get the absorbance values for each concentration.
> PM <- 66432.9 #g/mol
> c <- seq(0.001,3,0.05) #get values from 0.001 to 3, by 0.05 increment
> V <- 1 #liters
> M = c((c/PM)/V)
> #Lambert Beer Law
> e <- 42925
> l <- 1
> A <- c(e*l*M)
> plot(A ~ c, ylab="A (280nm)", xlab="g/l")
> data.frame("conc"=c, M=M, A=A)
    conc            M            A
1  0.001 1.505278e-08 0.0006461407
2  0.051 7.676919e-07 0.0329531753
3  0.101 1.520331e-06 0.0652602099
4  0.151 2.272970e-06 0.0975672445
5  0.201 3.025609e-06 0.1298742792
6  0.251 3.778248e-06 0.1621813138
7  0.301 4.530888e-06 0.1944883484
8  0.351 5.283527e-06 0.2267953830
9  0.401 6.036166e-06 0.2591024176
10 0.451 6.788805e-06 0.2914094522
11 0.501 7.541444e-06 0.3237164869
12 0.551 8.294083e-06 0.3560235215
13 0.601 9.046722e-06 0.3883305561
14 0.651 9.799361e-06 0.4206375907
15 0.701 1.055200e-05 0.4529446253
16 0.751 1.130464e-05 0.4852516599
17 0.801 1.205728e-05 0.5175586946
18 0.851 1.280992e-05 0.5498657292
19 0.901 1.356256e-05 0.5821727638
20 0.951 1.431520e-05 0.6144797984
21 1.001 1.506784e-05 0.6467868330
22 1.051 1.582047e-05 0.6790938676
23 1.101 1.657311e-05 0.7114009023
24 1.151 1.732575e-05 0.7437079369
25 1.201 1.807839e-05 0.7760149715
26 1.251 1.883103e-05 0.8083220061
27 1.301 1.958367e-05 0.8406290407
28 1.351 2.033631e-05 0.8729360753
29 1.401 2.108895e-05 0.9052431100
30 1.451 2.184159e-05 0.9375501446
31 1.501 2.259423e-05 0.9698571792
32 1.551 2.334687e-05 1.0021642138
33 1.601 2.409950e-05 1.0344712484
34 1.651 2.485214e-05 1.0667782830
35 1.701 2.560478e-05 1.0990853177
36 1.751 2.635742e-05 1.1313923523
37 1.801 2.711006e-05 1.1636993869
38 1.851 2.786270e-05 1.1960064215
39 1.901 2.861534e-05 1.2283134561
40 1.951 2.936798e-05 1.2606204908
41 2.001 3.012062e-05 1.2929275254
42 2.051 3.087326e-05 1.3252345600
43 2.101 3.162590e-05 1.3575415946
44 2.151 3.237854e-05 1.3898486292
45 2.201 3.313117e-05 1.4221556638
46 2.251 3.388381e-05 1.4544626985
47 2.301 3.463645e-05 1.4867697331
48 2.351 3.538909e-05 1.5190767677
49 2.401 3.614173e-05 1.5513838023
50 2.451 3.689437e-05 1.5836908369
51 2.501 3.764701e-05 1.6159978715
52 2.551 3.839965e-05 1.6483049062
53 2.601 3.915229e-05 1.6806119408
54 2.651 3.990493e-05 1.7129189754
55 2.701 4.065757e-05 1.7452260100
56 2.751 4.141020e-05 1.7775330446
57 2.801 4.216284e-05 1.8098400792
58 2.851 4.291548e-05 1.8421471139
59 2.901 4.366812e-05 1.8744541485
60 2.951 4.442076e-05 1.9067611831

And you can get this plot from 0.001 to 3 g/l for albumine

Now you can choose the desired concentration for the absorbance you wanna work with


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Energy use by muscles, actual work done by muscles and more
Lately, I've started exercising in the gym and outside. I've also started to look at the details of food I eat.
Food usually has a label saying the amount of energy is inside it. For example, some chocolate says it has 400 kilocalorie for 100 grams.
I have some questions about that:

Does the label say the amount of total chemical energy exists inside the food, which will be released if burned, or the energy available to the human body after digested, and because digesting requires energy, the food contains actually MORE energy then written?
When I'm riding on a static bike, it has a screen which counts the kcal I burn. It has a thing connected to my arm, measuring my heart beat. After about an hour of riding, it said I used about 700 kcal. Is it the amount of work I did, i.e if there was a battery connected to the bicycle, I'd generate 700 kcal of electricity, OR, the amount of energy my body LOST, because muscle efficiency is far from 100% (so, I lost 700 kcal, but generated only 150 kcal of electricity, for example)
When doing a physical activity, the heart beat and breathing rate increases. Lets say I'm riding a bicycle or running. Whats the ratio between energy consumed by the muscle to energy consumed by the lungs or heart?

Looking at the answers for question one it's hard to think of any other meaningful way to do it other than recording the energy released when burnt, any other measure would hardly be standardised between people.

I speak only for the U.S. regulations: the calorie labels on wrappers refer to the energy released when burned. Sometimes these are inaccurate. Many dieticians recommend calculating the calories based on weights of protein, carbohydrates and fats in the serving: 4 kcal in each gram of protein and carbohydrate and 9 kcal in each gram of fat in your food. Multiply carbs, proteins and fats by the appropriate value and add them up.
The reading on the bike does not take into account your pulse. Just the raw work done turning the pedals. Some very smart bikes do take pulse into account, but the often inaccurate heart monitors lead to inaccurate calculations of total energy.
The heart and diaphragm (muscle primarily responsible for breathing) do use more energy when exercising than when you are sitting still. But that increase is small relative to the increase in the primary muscle sets involved in the exercise. Your resting heart rate is probably around 70 bpm, your exercising heart rate is probably around 160-180 bpm. So it has increased its rate and energy consumption by about 3 times. Your skeletal muscles maintain a basal metabolic rate during inactivity (one purpose of this is your body needs the heat from slightly tensed muscles to thermoregulate itself) - but during exertion, their metabolic rate increases enormously. Exercise increases their energetic demands by whole orders of magnitude.

The actual value of the (energy used by heart) / (energy used by skeletal muscles during exercise) depends on what exercise you do and how efficiently you do it. The change in the ratio between inactivity and activity depends on how much muscle mass you have (more muscle uses more energy during inactivity) and how strenuously you exercise. But the point is that the increased energetic demands by skeletal muscles far outpace the 3x increase in energetic demands by the heart and diaphragm - so the latter accounts for pretty much all total energy consumption at even moderate activity levels.

to be clear one of the major sources of error in calories in food is fiber and other such material that will burn but not be digested. which is why many countries require carbs to show fiber content.

1) It depends on each country and your minister. In Finland, the thing is done so that it says the energy stored in food, which will be released if burned.
2) It is the energy pushed to the bike when the bike does not take into account your pulse. If the bike is smart one, it takes into account your pulse rate, then it tries to estimate the amount of energy released by your body. This is done differently among different manufacturers of those watches.
3) By the way heart is a bunch of muscles, a myogenic muscular organ! So consider instead heart and some part of lungs. Very broad problem otherwise.

source: Stack Exchange

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/

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Is there a gene that starts meiosis 2?
Yesterday I thought about a question and asked it to my friend.  The question was
which gene is completely the same for a male cell that made meiosis 1 recently.
My answer was the gene that starts meiosis 2, but he said he thought that there is no such gene - only a gene to start meiosis and meiosis 1 and 2 are just parts that scientists named.
My question is is there any gene that starts meiosis 2?

all_licenses: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/


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Online course on Plant Taxonomy and Physiology
After following a course in Permaculture, I realised that if I want to get serious about it, I need to be able to distinguish plants. So I am looking for an online Video course on Plant Taxonomy and Physiology. My understanding is that it is a fairly standard course in basic Botany degrees, and since there are more and more school that put their material online it is quite possible that one of them might have placed this online too. Any suggestion?

these are traditionally taught separately, unless the class were to address the relationship between these topics.

What other science courses have you taken? What are your goals? It sounds like a general botany course that touches on these subjects would be a good place to start.

I don't think you're likely to find a good online course in taxonomy - you will be able to find the basics (mentioning mono/dicots and key families). I might make a quick guide as a blog post (but it will have to wait a couple of weeks until I have more time). As for plant physiology, your best best is to read a good text book. I strongly recommend Plant Biology by Smith et al. (2009). Before going into plant physiology you will need a grounding in biology. As David already asked, what's your background?

Thanks for your answers. I have a degree in math, a Master in IT and a PhD in systems biology. Yet none of this was of any use respect to actual recognizing plants. Yes, books can help but I have several books but they never helped much. On this topic (and I stress that on other topics is different) it looks like I absorb more from seeing things than from reading about them.

Well, I wasn't able to find an online video course. The closest I came was this site, which links to courses that put their material online. Most of these are compilations of the lecture notes. There's also this page from the University of British Columbia, that has a nice little overview of the field of plant taxonomy.
In my experience, botany and plant identification are subjects where one really needs to learn by doing. You really need to grab a plant and take a close look at it while noting why its in the group that its in. A great way to get started might be to join a local gardening club or native plant society. The people in those groups can provide their tips for ID-ing plants.
One of the primary skills you'll want to learn is identifying what family a plant is in. Plant families have (mostly) consistent characters, and learning how to spot the most common families in your area will be a big help.

I don't know of video course, but here are two book recommendations:
First, Botany in a Day by Elpel is superb in terms of being an approachable, systematic look at plant identification and basic botanical knowledge.
Second, as I mentioned in this answer, the Botany Coloring Book is a great resource for basic self-education on botany / plant anatomy.


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T7 phage promoter action in mammals
Does anyone know if the T7 phage promoter is efficient in mammalian systems?

Amazingly, yes.
See High level gene expression in mammalian cells by a nuclear T7-phage RNA polymerase. The authors recognize that the T7 RNA polymerase tends to work only in the cytoplasm thus is unable to transcribe genes in the nucleus. To remedy this limitation, the T7 polymerase was fused to a nuclear location signal peptide to localize the polymerase correctly.
Promega sells a T7 expression system for RNAi production.


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Are there dog breeds that are so far apart genetically that they can't produce viable offspring?
Obviously, a very large dog would have difficulties mating with a very small dog and vice versa.

But putting that problem aside (using, say, insemination), considering the large variation of dog breeds, are there any two breeds that are so different genetically that they can't produce viable offspring together?

Isn't that what distinguishes species from breeds/races? Whether they can reproduce with each other?

Wolves can breed with dogs, still they are considered different species.

@Zano: wolf and dogs are the same species (canis lupus), different subspecies (canis lupus familiaris vs canis lupus lupus). Dogs are domesticated wolves.

@nico: Fair enough.

I actually found some sort of reference for this.  Apparently in the case of a beagle and irish setter pairing, they had a lot of difficulty in producing pups, but as breeds have a lot of genetic quirks, this might be due to a genetic accident; this is probably a case of mutual infertility rather than speciation.  There are probably mutations in their genomes which are causing non viability in the pups the way that it does with some human parents who have difficulty having children - an immunological incompatibility or traits which cause most offspring non-viable.
In fact the discussion points out that the species designation does not always mean they cannot produce offspring, but simply do not.  Coyotes and wolves will produce offspring too if they are encouraged to do so, but are competing and antagonistic in the wild and so never do mate in practice.
So the answer is probably no. (the beagle/setter pups did show up, but with a much smaller litter than usual with just 2 pups).

I was looking for something like this. The definition of species was never an issue as far as I was concerned.


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Troubleshooting bioconjugates migration in a SDS-PAGE gel?
We do a lot of bioconjugation chemistry (click chemistry in particular but also NHS and Maleimide chemistries). Our method to valid the conjugation reactions have been to use SDS-PAGE gels followed with densitometry. However one particular challenge with such analyses is that proteins conjugated with non-proteins like DNA or PEG migrate with an inconsistent MW and also in a smear making it hard to isolate the relevant bands. I assume that this has to do with having a poly-disperse radius of gyration. Are there tricks that I can do to get tighter bands?

where would the poly-disperse radius of gyration arise from if the molecules are coated with SDS?

@Ben, my hypothesis: SDS disrupts hydrophobic interactions as a surfactant. However, something like DNA has purely enthalpic interactions and will not undergo denaturation or be evenly coated by SDS. This is the underlying roots of my problems.

The first step in troubleshooting is to run controls - run lanes with your protein input alone, and the conjugate alone (you may need to play with the type/percentage of the gel if the conjugate molecule is much smaller than your target protein - attaching biotin to a 50 kDa protein, for example) to see if the smear shows up. Depending on the type of conjugation you're using, the number of acceptor sites on the substrate, and the time and conditions of the conjugation reaction, you may be adding a highly variable number of conjugate molecules to your substrate. For example, when I first started working with adding fluorophores like Alexa and DyLight dyes to antibodies, the fluor/protein ratio was highly variable from reaction to reaction and between antibodies in the same reaction.
This is most likely what is happening in your case - the number of conjugate molecules being added to each substrate molecule is highly variable. If you haven't already, I'd suggest getting in touch with your conjugation kit vendor's tech support, as they likely encounter this problem all the time. You may need to change the type of conjugation chemistry, get a higher-quality conjugate, or purify the substrate before and/or after the reaction. One of the solutions to my antibody labeling problem I mentioned above was to purify the reaction products through a size-exclusion column. This had the dual effect of separating out the un-reacted antibody and fluorophore, and allowing us to pick different fractions of the conjugated product and decide which were best for our needs.

+1 Thanks! Issues with the suggestions so far. a) we're not conjugating a protein to another protein so standard commassie staining will not stain the conjugate molecule. b) we are the vendor since everything is done inhouse. c) While we can easily separate the reacted molecules from the unreacted, this doesn't answer the problem of quantifying the extent of the reaction.


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Is kissing a natural human activity?
The word natural here is meant in contrast to it being a sociological construct.

Is kissing in all its forms something natural for humans? Is it instinctively erotic? Or is it just a conventional form to show trust and intimicy, i.e. the association besically just comes via a social means?

Because the only other advantage of this mouth to mouth contact I could see is maybe for the immune system.

It's probably one of the arbitrary reward systems for actions beneficial to reproduction. Social contact is advantageous for reproduction, so rewarding it makes sense. Kissing may just have developed because the lips are full of sensory receptors for food-proofing purposes already; so it's not a big effort to use them for additional purposes.

Wikipedia actually has a note on the evolution of kissing.  They point out that there are grooming behaviors such as licking and social behaviors like dogs touching noses in many species even insects.  They note that it is not decided at all whether kissing is learned or from some sort of instinct.  They also mention that its reminiscent of feeding behavior common in birds (and other animals) where food is pushed down the throats of young.  (try thinking about that next time!)
I seem to remember though that there are some culture which do not kiss. with their lips at least. This would favor kissing as a learned behavior, but these cases are very rare and isolated peoples and it might be simply a taboo to talk about kissing with researchers or at all, which is a hazard of that sort of work.  In addition, bonobos, one our our closest primate cousins, do kiss frequently with the lips, as a social and intimate gesture and the parallels with most human cultures are difficult to ignore.

And here I thought my wife was making up the "Eskimo kiss" thing.


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What is the correct model for enzyme-substrate complementarity?
This Wikibook shows both proposed models of enzyme-substrate complementarity, the Lock and Key model and the Induced Fit model. I've always been taught that the Induced Fit model is  the proper one. However, my biochemistry professor mentioned that often times, enzymes behave as lock and key. I also noticed that the Wikibook doesn't mention which model is in fact true.
The Lock and Key Model

The Induced Fit Model

Is there currently one accepted model? Which is it, and why?

IIRC there's no "accepted" one--depending upon the enzyme, it can be either.

This is true of all protein binding as well as the special case of enzyme-substrate interaction:
Various proteins are more dynamic than others: some have only one or two overall conformations and are relatively implastic otherwise. An example would be a receptor tyrosine kinase like Kit (or CD117, or Mast Stem Cell Growth Factor Receptor, whatever you want to call it), which has a very stable structure and binds its substrates in a lock and key manner.
Others, for example p53 (not an enzyme), have much more structural placiticity - even to the point of being mostly disordered when not bound. They tend to be induced fit binders (of other proteins, not catalytic substrates) and often exploit that to bind a broader range of possible targets than lock and key proteins.
The point is, it is a continuum between lock and key <-----> induced fit rather than discrete classes you can sort proteins into.

Thanks for the answer, like mention of continuum. I'll wait to see if there are more answers before I accept though.

Both models are true depending on how you frame the mechanisms of catalysis. As mentioned by @Blues, proteins are highly dynamic. In that manner, a protein will adopt both the unbound active state shown in the induced fit model and the complementary shape shown in the lock and key model.
(apologies since this is the only figure that I could find to explain this concept). Using the above description the induced fit model (E) will change its structure to the ES model. In the lock and key model, the E state will be equivalent to the ES state. According to the below figure, this would imply that the ES state always exists but as it is a few kcals higher in free energy, the state is rarely seen. Thermodynamically, this means that the "lock" always exists but it is an unstable configuration. When the substrate is added to the system, it will stablize the lock and thermodynamically favor an ES state.

Long story short, the induced fit model is a good explanation of how enzymes morph into an active state but depending on how you frame the mechanism, you are always seeing a lock-key model (at least according to my enzymology professor). Unfortunately, the majority of biochemistry textbook continue to teach using the induced fit model since it is a much easier concept to understand given the majority of undergrads; and 1st year graduates' understanding of statistical thermodynamics.
The induced fit model is more appropriately used to understand the mechanisms of substrate specificity. As hinted by your professor, enzymes will perform their function in the lock-key mechanism. This is true for many serine proteases which all do the exact same reaction. However, substrate specificity can be incorporated by unstabilizing the E*S complex which largely has to do with the E state.


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Are the cytosol and extracellular fluids electrically neutral?
I've found several sources that state that overall, the cytosol of a cell is electrically neutral. The extracellular fluid is also purportedly electrically neutral. How can that be when we have membrane potentials?
Also in that regard, how do the ion transporters that set up the membrane potential know when to stop pumping ions to get a certain potential set up?

Membrane potentials are caused by different concentrations of ions on opposite sides of membranes in micro-environments along the membrane. The membrane can be, overall,  electrically and chemically neutral with small areas that have differences in electrochemical gradients.
For cells to produce these potentials they have proteins embedded in the lipid membrane. Ion pumps are the main players in creating potentials and gradients; through active transport (the use of ATP) the protein moves ions from one side to the other. When the concentration of that area of membrane is at one concentration the proteins are held in one conformation (active or inactive) and when the gradient is changed or meets a threshold the protein changes conformation and becomes activated or inactivated. So the actual electrochemical gradient dictates when the proteins are transporting.
There are also other proteins/messengers that are produced which can interact with the transmembrane proteins that keep them in one configuration or another to facilitate the production of an action potential. Once again, when this specific concentration is met the signaling molecule/transporter will become inactivate or activated.
This is just stuff I recall from some classes. Honestly, wikipedia is a fine general knowledge source. And more detailed than my explanation.  http://en.wikipedia.org/wiki/Membrane_potential#Ions_and_the_forces_driving_their_motion

Thanks for your answer! I didn't know about microenvironments and just assumed it meant the whole cell would be at these different voltages. Regarding second question, are you saying that the sodium-potassium pump would be regulated by both sodium and potassium concentrations?

Good response.  If you look at a neuron, you will see that it has a lot of surface area and its easy for a small portion of it to have a strong potential while the rest of the cell would hardly feel the difference.

@GorgeHomless Basically. Proteins are effected by what environment they are in, ie. temp, pH, salt, etc. These factors affect the bonding that makes proteins a certain conformation. So when the concentration is at a specific level, meaning the environment has changed, the bonding and interactions of the amino acid side chains will be altered; the protein will change shape. So, when sodium or potassium or other ions are in high concentration they interact with the protein & enviro, disrupting or enhancing bonds, making the shape change. Hopefully that answers the question and makes sense :)


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Does caffeine increase the speed at which sperm travels?
I'm not even sure if this claim is true, but...
This source states that

Caffeine gives both types of sperm a boost, but the Y-sperm would get a little more of a boost.

This article reinforces the quote. In fact, this "tip" can be seen all over the internet to preferentially conceive a male rather than a female.
My question is how. What is happening at the molecular to increase the overall mobility of sperm? It clearly wouldn't work as a neurotransmitter (as it "normally" works).

I also realize that this question could be formatted for Skeptics.SE. Feel free to edit the question so that it's more suited for this site.

This answer suggests that the "extra boost" could be due to all Y sperm being lighter and therefore perhaps faster than X sperm - regardless of caffeine consumption.

@RoryM I'm familiar with that, as the comments to this answer also suggest: http://biology.stackexchange.com/questions/1062/x-chromosome-weight

I'm more interested in the "boost" itself rather than the differential boost.

Ah it was that question I was trying to find earlier xD

The cell response for caffeine, is at the molecular level of RyR (Ryanodine receptor), and the main effect could be a temporal rise in Ca+2 cytosolic concentration, so it can change the electrical behavior for the whole cell, and then affect their mobility. But the main area for RyR research is at spermatogenesis, there are a lot of papers like this one, for that topic


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Which cells are responsible for the extracellular matrix remodeling?
I am studying a case of tendinopathies induced by an alteration of how the extracellular matrix is being remodeled.
From my understanding there has to be a careful balance of MMP (metallproteinases) and TIMP enzymes to maintain tendon homeostasis.
Which cells produce these enzymes?

Taken from The role of matrix metalloproteinases (MMPs) in the pathophysiology of chronic obstructive pulmonary disease

Metalloelastase (MMP-12) is (as the name suggests) capable of
  degrading elastin, as well as other extra-cellular matrix components.
  It is produced predominantly by infiltrating macrophages and appears
  essential for macrophage migration through extra-cellular matrix

Matrix Metalloproteinases in Cancer Cell Invasion gives a more thorough description of the various MMP and TIMP types

MMPs are mainly produced by nonmalignant stromal cells in malignant
  tumors. Tumor cells also secrete factors, such as extracellular MMP
  inducer (EMMPRIN), which enhance the expression of MMPs by stromal
  fibroblasts (see Toole, in this book). In addition, growth factors and
  cytokines secreted by tumor-infiltrating inflammatory cells as well as
  by tumor or stromal cells modulate MMP expression.

Thanks for your input... I am trying to understand how Fluoroquinolone drugs can degrade tendons. From what I am understand MMP-9 is of my concern:
"Our study provides preliminary evidence that topical application of fluoroquinolone drugs can induce the expression of MMP-1, MMP-2, MMP-8 and MMP-9 in the undebrided corneal epithelium compared to artificial tear eye drops." (http://www.ncbi.nlm.nih.gov/books/NBK6598/)

Here's another one:
http://www.wikigenes.org/e/ref/e/12428247.html
Ciprofloxacin enhances the stimulation of matrix metalloproteinase 3 expression by interleukin-1beta in human tendon-derived cells. A potential mechanism of fluoroquinolone-induced tendinopathy.


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Why do we like salt?
A few friends of mine told me that salt provides zero nutritional value to us, and in fact can harm our bodies. Now, these guys are medical students, and being an engineering student myself, I decided not to argue with them. The rest of this question assumes that this fact is true, so if it's not, you can just go ahead and call me out now...
So here's my understanding of things: we 'like' doing things because of our instincts, which have slowly become refined over millions of years. For example, I 'like' eating foods with fat in it because my instinct compels me to do so. Fat is 'good' for my body, since it provides a lot of energy (obesity problems aside).
So are there certain things, such as eating salt, that are not in fact beneficial in any way, and we only do these things because we were trained to as children? This is the only thing I could come up with, but it's not a very satisfying explanation for a few reasons. First, I think humans have been eating salt for a long time. This would mean that most likely, it is actually our 'instinct' to eat salt. Also, salt is eaten in every culture today, which has the same implication.
So is there some better explanation?

Look into hyponatremia (low Na+) and hypokalemia (low K+) as evidence that the body does in fact need both nutrients.

But does salt help prevent those? And if so, could this be reason enough for us to like eating salt?

Well, the proper balance of salt and water does (though hypertonic saline is not always given to hyponatremic patients), so it was meant more as a counter to your friends' assertion rather than an answer to the question.  I would guess that the cravings do have something to do with maintaining that salt/water balance, but I do not know for sure.

@jonsca Okay thanks for the info, you learn something everyday.

Welcome.  That first comment wasn't meant to be chiding at all, I just think some of the key to what you are looking for might be within those two pathologies.

I didn't interpret it that way at all. And yes, you brought us very near an answer. Now I think the question is whether our bodies' uses of salt is the cause of our craving it.

Speaking as a non-medic, I have seen people use salt in a pinch (pun unintended) on a couple of occasions when others suffered near unconsciousness due to a sudden fall in blood pressure.

Old question, but are you asking about table sale (NaCl) or any salt in general?

@canadianer: Well, I meant table salt. Does the same apply to other salts that we consume?

In developed countries we usually consume enough salt (sodium to be exact) without actually adding table salt to food. Everything can become toxic when consumed in excess - even water - and when we frequently add more salt to foods, we tend to consume sodium in potentially harmful excess. That's what your friends are referring to.
However, salt (sodium) is one of the most essential substances your body needs to stay alive, for several reasons. One of the main purposes of sodium is the upkeep of blood's osmolarity (i.e. concentrations of osmotically active compounds. Higher salt concentration on one side of a permeable membrane attracts water to that side - I'm sure you've heard that before). There are numerous systems in your body to make sure the osmolarity of blood is correct. If they fail and blood becomes hypo or hypertonic, your cells will be sucked dry or pumped full of water and in either case, burst and die.
Look up the renin-angiotensin-aldosterone system for example: when the kidney filters blood, it reabsorbs or lets through water depending on the current blood osmolarity; leading to higher or lower amount of higher or lower concentrated urine. You drink lots, your blood is diluted, it becomes less tonic, kidney registers that and lets water through more, you urinate more. There are many more elements involved there, including blood pressure, nerve signals stimulating thirst or hunger of different kinds, some hormones etc.
As you can see, there's a reason why the basic infusion given in hospitals to replace lost blood quickly isn't just water but normal saline.
Delayed update to pick up some side aspects of your description: 1) There are of course things that humans do which have absolutely no value to them whatsoever. Anything that plays into the feel-good-reward-circuit in our brain can become such an unhelpful habit. Take smoking and drug consumption as examples. 2) About evolutionary relevance: Being a key player in maintaining body function, evolution selected for instictively liking salt. Simultaneously, most people will not like food that is extremely salty - a protective mechanism against excess.

I described "one of the main purposes"; the other main purposes that come to mind are: 1) Upkeep of membrane potential - all cells utilise gradients of Na and K ions to maintain a voltage differential between their interior and the extracellular liquid, enabling various cell-sustaining processes including energy generation. 2) Nerve signalling - neurons utilise Na ions to transduce targeted voltage spikes.

I agree with Armatus, however I feel his answer incomplete.
Sodium (along with chlorine) is the most important ion in the blood if we are talking about osmolarity and water transport. Water wants to move to the high osmolarity places so its transport is mainly controlled by the transport of sodium through selective sodium channels. This is not just about blood osmolarity, e.g. the absorption of water from the guts, the filtration of blood in the kidney, the sweating, etc... all major water transport in the body is mediated by sodium transport. So sodium is essential.
Your friends are right about too much sodium can harm you. Just try out something: eat something salty, and wait a few minutes. You will be thirsty, because sodium concentration increased your blood osmolarity, and so your body released hormones to restore osmolarity, and these hormones make you thirsty. After you drunk water, your blood pressure becomes higher until the kidney get rid of the extra sodium. High blood pressure is bad to your heart. This is just one way too much sodium can harm you...
Your friends probably meant that if you don't have a lot of training and so you don't sweat a lot, you don't need crystalline salt in your food, because your food already contains enough sodium.
It is an interesting question why do we love extra salt despite the fact that our food contains enough of sodium. I don't know the answer of that. It certainly makes foods tastier, but I cannot find or find out anything about why this is evolutionary good. I think it is something similar to narcotics or sugar, it has a (small) hedonic value, despite that it isn't necessary good...

Evolution is still basically a random "pseudo-process" with pruning. Even if a trait were negative, it will only be removed from the population if it is harmful enough in the environment you live in. Most people don't like to drink seawater, and other ready sources of salt were not readily available in our ancestral environment (the same with other mammals, who also tend to crave salt). Historically, you were probably more likely to suffer from a lack of salt, rather than too much salt; which also means that there'd be a benefit to a "craving for salty food".

Look into how long would a human live with no salt in there body. And im not talking about the table salt.

@TheVoid Where should we look into that? Do you have any human experiments? Mice can live at least 3 months with hyponatremia. http://physiolgenomics.physiology.org/content/43/5/265.short

@TheVoid I found something: http://www.acep.org/Clinical---Practice-Management/Hyponatremia-Case-Review/ "Severe hyponatremia may result in cerebral edema, encephalopathy and death. " , "1986 study in which 27% of previously healthy women undergoing elective surgery died after developing acute hyponatremia (averaging 108 mmol/L). " I did not find the study, but I think this must have been relative fast, because they weren't able to treat these patients.

Salt adds flavour to food. That is why.


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Understanding Membrane / Resting Potential from the perspective of ions?

From wikipedia article RESTING potential: "there is no actual measurable charge excess in either side. That occurs because the effect of charge on electrochemical potential is hugely greater than the effect of concentration so an undetectable change in concentration creates a great change on electric potential."

the effect of charge on electrochemical potential significantly larger then the effect of charge on concentration - is this a general statement or true in all cases?
And if charge is more significant then concentration in influencing electrochemical potential why does a small change in concentration greatly effect electropotential? Or does it mean electrochemical potential? Either way how does it make any sense, is it correct or nonsense and what is the exact meaning behind the message?
other questions I have:
1) What is the reason Na+ stays at its location right across the barrier on the extracellular side of the membrane? Diffusion? Electrochemical potential? Electric Charge.. if so because of Attraction or Repulsion?
2) If the answer is the electrochemical gradient/potential, because it is trying to move to a "less" positive potential.. if its located extracellularlly isn't that the "great unknown" where any molecules/cells/protein etc. are able to float by and possibly influence it? What happens if one of these has a "LESS" positive potential then the membrane that Na+ is currently attracted?
3) Why can't Na+ be used for the entire process to establish the same voltage interactions leading from resting to action potential (as long as thier was less concentration intracellularly... if it is about LESS positivity ..Or vice versa for K+?)?
I am preparing for ACSM certification exam, so any help is appreciated.

Ah, what a classic biophysics problem.
One first needs to understand how a membrane gets a potential. The lipid bilayer is a large sea of hydrophobic interactions that essentially prevents any ion from crossing. As a result, Na+ and K+ concentrations remain constant and different on the cytoplasmic side and the extracellular side. However, ions can pass through ion channels like the K+ channel. It is important to understand that in K+ channels, only K+ can pass and these channels are actually selective against Na+ (answer to question 1).
There are two potentials at work here. First is a chemical potential created by the flux of K+ from high K+ to low K+. The second is a counteracting membrane potential created by a charge imbalance. Note, that the swapping of a few ions will a) result in a negligible change in the concentration ie. the chemical potential, b) result in a large change in the membrane potential. At some point, the flux out due to the chemical potential and the flux in due to the membrane potential will be equilvant and the cell will reach a resting potential otherwise known at the Nernst potential or equilibrium potential (technically a steady state).
When a cell depolarizes by closing these channels, the local charge will quickly go back to an equilibrium or a non-charged state.
So why K+ rather than Na+? For typical cells, the extracellular concentration of Na+ is 145 mM and cytoplasmic is 12 mM. For K+, it is 4 mM and 155 mM respectively. Doing the appropriate calculations of the Nerst potential, for Na+ it is +67 mV and for K+ it is -98 mV. Qualitatively we can see that this would result in vastly different things.
Most of this information can be found from Pollard and Earnshaw's Cell Biology

For anyone else interested I found a voluminous, free, online resource with animations and very detailed explanations which addresses the topic here: http://www.st-andrews.ac.uk/~wjh/neurotut/mempot.html

The resting potential is only validly called an equilibrium potential in a system containing only one ion species. Of course, cell environments are composed of several ions so the resting potential is not described by any equilibrium potential, because (as you say) the system is at steady-state rather than equilibrium. A more general term is "reversal potential" which describes the potential at which net current switches sign (e.g., inward to outward). The concept of reversal potential simplifies to a Nernst/equilibrium potential in single ion cases, but also covers multiple ion cases.


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Is there a relationship between efficiency of cellular metabolism and warm-blooded-ness?
My BIO 101 book states that when human cells convert glucose to ATP, the process is only approx 35% efficient, and much of the potential energy is lost as heat.  However, that heat is useful to us in maintaining our overall body temperature.
Cold-blooded animals (reptiles, for example) are not as effective at maintaining their own body temperature.  Does that imply that their cellular metabolism (conversion of glucose to ATP) is more efficient than humans, and thus doesn't produce as much heat?
Or is cold-blooded- / warm-blooded-ness completely unrelated to heat released during cellular metabolism?

As far as I know the difference is not in the efficiency but rather the simple amount of catabolism of nutrients. Cold-blooded animals ingest less but also burn much less and generally expend less as well. I'm not entirely sure about this though. The central metabolic pathways are pretty much the same in most animals.

While heat is lost during glycolysis, a lot more heat can be lost during chemiosmosis.  This is the movement of H+ (protons) across the inner mitochondrial membrane.  The energy potential of having a greater concentration of H+ on one side of the membrane usually powers ATP synthesis through ATP synthase.  In mammals, however, special proteins called uncoupling proteins (UCPs) can make the membrane 'leaky' to H+, so the energy is lost as heat, instead of being used to make ATP.  This is called non-shivering thermogenesis, and usually happens in brown adipose tissue (because fatty acids are used to enable UCP production).
It is not that glycolysis in ectotherms is less efficient (as far as I'm aware), but that ectotherms have different levels of different types of UCPs. Some UCP genes may have their expression altered in response to colder conditions (e.g. UCP2 and 3 may be upregulated) or the genes may not be present at all (e.g. UCP1 is not present in birds and crocodiles).
A better summary of UCPs in reptiles etc. can be found in this abstract:
http://rspb.royalsocietypublishing.org/content/275/1637/979.long


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Effect of single-gene overexpression in the cell's response
Which are the factors that modify the overall gene differential expression by introducing a vector for single-gene overexpression?
If you overexpress a gene for a protein involved in signal transduction (e.g., a kinase, scaffold, or receptor) by vector cell transfection, then you overdrive the cell using this signaling pathway, it's useful to isolate the pathway and study them.
Is there any way to modify the overall gene expression or cell differential expression pattern by gene transfection? I think this would work if you delivered a gene for overexpression in proteins involved for RNA processing (e.g., splicing, ribosomal proteins, etc.), RNA transcription (e.g., TFs) or protein translation.

This sound like all of genetics.

Looks very similar to Metabolic Engineering

Single protein over expression, was the main strategy to get information about protein function. I do my research in signal transduction, and we use this method. but this is the trick question, every member in our lab get in seminars.

Which are the factors that modify the overall gene differential
  expression by introducing a vector for single-gene overexpression

This is a very relevant question and the field of experimental biology needs to revisit the experimental strategies.
One of the explanations that you gave is correct- that the overexpressed protein might override the cellular processes.
Another problem that this practice gives rise to is incorrect inference. We are mostly interested in knowing what a protein does in a cell at general physiological conditions. If the stoichiometry is altered wrong results will definitely pop up.
For example in the case of a repressor/activator with multiple targets: At its general physiological concentration it may not really activate gene-X because of low affinity but in high concentrations it just may, and we end up concluding that gene-x is a target of repressor-1 by an OVEREXPRESSION experiment.
A synthetic biological approach is very good in studying small signaling/transcriptional modules. The entire module can be cloned and expressed in a cell under an inducible/constitutive promoter. This can be implemented in a heterologous cell also. A mathematical model generally helps in making certain predictions.
Other strategies which can be used instead of overexpression:

using sensor constructs harboring a functional or non-functional
target sites instead of overexpressing the upstream protein
downregulation experiments

There are lots of different overexpression vectors (usually they're promoters/regulatory elements upstream of the transfected gene). Here's an example of an overexpression vector (overexpression vector pCAMBIA1300S) that was used to overexpress a transcription factor called NAC in rice, resulting in large phenotypic changes (drought and salt tolerance): http://www.ncgr.ac.cn/articles/2009ZhenXN_NAC.pdf

Can you expand a little bit maybe giving some example of how the modulation of a single gene can subsequently affect many others?


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How quickly do estrogens break down in the environment?
Of all the synthetic hormones we use, estrogens are probably the most common.  They are used for birth control as well as hormone replacement therapy.  This researcher also shows that there is plenty of it in milk because dairy cows are often pregnant while they are being milked.
Estrogen is a sturdy compound, very much like cholesterol.  I was wondering if anyone had any idea how long it would survive in the environment, given that some people are concerned about it interrupting animals life cycles.  How fast does it break down in the wild?

As in, in the air..?

estrogens have negligible concentration in the air. they would tend to be in the ground or in water taken in by plants an animals.

Months to years - although the actual duration in a specific environment depends on the nature of that environment and is tied to oxygen level. Higher oxygen, faster degradation. Less oxygen, the estrogen molecules interconvert among various closely related molecules which hampers both their detection and their degradation.
For more info, please see: Environmental science: The hidden costs of flexible fertility (Nature 485, 441 (24 May 2012))  and this Science Daily article.

Thanks for telling me about doi links and doing it for me in this case.


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Are there any examples of proteins with no or minimal sequence identity, but highly similar structure?
What are they, and do they share a common ancestor? How far back in evolutionary time must we go to find them?
If none are known, what computational tools might be used to search for such examples?

Your current question ("Are there any examples of proteins with no or minimal sequence identity, but high structural homology?") uses the term "homology" in a wrong way: Homology refers to common ancestry. So "homology" is binary (like being pregnant), and there is no such thing as "structural homology" (or "high homology" etc.). A more exact question would be: "Are there proteins with little sequence similarity but a very similar structure (and do they share a common ancestor)?"

My god, you're right. Apologies for the oversight, and question edited accordingly. Thanks!

The answer is that common folds are discovered in sequences which are completely divergent where essentially no alignment can be found by conventional means.
David Eisenberg's group created profiles based on alignments from known structures which were more sensitive to discovering whether a given protein sequence was related to a given structure, solving what he called the 'inverse folding problem'.  More recently HMMs have been used from raw aligned sequences which are even more sensitive to predicting whether a given protein structural family can be found in a query sequence.  PsiBlast also deserves a mention as a method that builds such a profile on the fly.  It can come back with sequences that are so divergent that they are probably not really related (personal experience).
A classic example of this is hexokinase, an enzyme that phosphorylates sugars - which shows up in single cell eukaryotes and all animals.  When the structure of actin was solved, it proved to have the same core fold as hexokinase.  Actin is one of the most venerable proteins known in eurkaryotes, so this is now called the actin fold.  None of the software mentioned above would detect this relationship. (I just verified this with psiblast).
Its probably not true all the time, but it probably happens a lot that sequences with the same protein fold are so different that they cannot be detected by any of these means.  Most genomes that are sequenced have dozens or hundreds of 'novel genes' - 40% of E coli is still uncharacterized.  Either there are novel folds popping up spontaneously over short evolutionary time frames or the possible sequences for many protein folds is quite large.  My expectation is that a novel protein sequence can emerge with the same fold in quite quickly, especially in bacteria.

These are all helpful answers, but I think this one is most complete. Thanks!

This paper published last year, address the answer for your question, about computational methods, they mention 3 principal algorithms for structural alignment
of proteins:

Structural alignment directly at the level of C atoms.
The second class of algorithms first uses the SSEs (Secondary Structure Elements) to carry out an approximate alignment, and then uses the C atoms.
The final class of algorithms uses geometric hashing.

And finally you could find useful this paper for an example of this kind of analysis with structural analyses of metabolic families.
References:

 Venkateswaran JG, Song B, Kahveci T, Jermaine C. TRIAL: a tool for finding distant structural similarities. IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM 8: 819–31.
 Marsden RL, Ranea JAG, Sillero A, Redfern O, Yeats C, Maibaum M, Lee D, Addou S, Reeves GA, Dallman TJ, et al.. 2006. Exploiting protein structure data to explore the evolution of protein function and biological complexity. Philosophical transactions of the Royal Society of London Series B, Biological sciences 361: 425–40.

The group of Andrei Lupas studies this. He argues that the vast majority of folds arose only once, so that proteins that share a fold are homologous, even if their sequences have diverged. See for example this paper: "Evolutionary Relationships of Microbial Aromatic Prenyltransferases" where they show that there are subtle sequence similarities between two protein families of the same fold, arguing for a common ancestor.

An example possibly worth taking a look at is the variable surface glycoprotein of the bloodstream form of Trypanosoma brucei.
Trypanosomes are the causative agent of sleeping sickness, and the entire cell surface is covered by a single glycoprotein called the variable surface glycoprotein, or VSG. (see here for more information)
These parasitic protozoans have the ability to 'fool' the immune response by antigenic variation.  At any one time just a single VSG is expressed on the surface, but (very rarely) a trypanosome may express a different VSG gene product.  Thus if the immune response succeeds in eliminating all trypanosomes expressing VSG-A, but there exists in the population just one parasite which has switched coat, this variant will poliferate as it effectively presents a different antigen to the host's defenses (and a second immune response will result).
There is litte sequence identity between different VSGs but they are homologous (descended from a common ancestor).
The crystal structure of the N-terminal domain of two different VSGs (MITat1.2 and ILTat1.24) have been solved (Blum et al. 1993; Freymann et al., 1993).  Despite the low sequence identity (~16%), the structures are almost identical.
One other very interesting property of all VSGs is that they are covalently anchored to the plasma membrane via a (C-terminus) glycosylphosphatidylinositol anchor (or GPI anchor).
References

Blum, M. L., Down, J. A., Gurnett, A. M., Carrington, M., Turner, M. J., and Wiley, D. C. (1993) Nature 362, 603-609 [pubmed]
Freymann, D., Down, J., Carrington, M., Roditi, I., Turner, M., and Wiley, D. (1990) 2.9 A resolution structure of the N-terminal domain of a variant surface glycoprotein from Trypanosoma brucei.  J. Mol. Biol. 216, 141-160  [Pubmed]

The following reference contains much useful background information, and is free to all.

Chattopadhyay, A, Jones, N.G, Nietlispach,D, Nielsen, P.R., Voorheis, H.P., Mott H.R., Carrington, M. (2005)  Structure of the C-terminal domain from Trypanosoma brucei variant surface glycoprotein MITat1.2. J. Biol. Chem., 280, 7228-7235 [Pubmed] [pdf]


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How distantly related are eusocial insects? Aren't members of a species much more related than 1/4, 1/2, or 3/4?

Possible Duplicate:
How many genes do we share with our mother?

I went to a lecture that talked about the behavior of social insects in terms of their relatedness of genes. For instance, workers were 3/4ths related to each other, so it was in their gene's interest to care for each other instead of having their own, half-related offspring.
However isn't it the case that members of the same species are much more related than 1/2 or 3/4s? I've read that we share anywhere from 95-99% of our genes with chimpanzees. Also I believe I've read (perhaps in Pinker) that we share some 60% of our genes with daffodils.
So when they talk about the relatedness of social insects, and they say it's 1/2 or 2/3 or 1/4, aren't they really talking about the 1% to 5% of genes that are in play in sexual reproduction within the species? In other words, aren't I 97% + 1/2 * 3% related to my sister, assuming human beings share 97% of our genes?

I guess the issue is that related is a generic term that can induce confusion without a proper definition.

In evolutionary genetic comparison, you are talking about members within species. They will share almost all genes, because if they didn't they would belong to a different species.
However, within species there exist different versions of the same genes, called 'alleles'. When we say that you are 0.5 related to each of your parents, we mean that statistically, 50% of your alleles should be those which your father has, and 50% of your alleles are those passed down from your mother.
Eusocial insects have different mechanisms. Bee males are produced without fertilisation, meaning that they only have one copy of each bee gene. When the male produces sperm, it only has this one set, so all sperms end up carrying the same set of alleles.
Females on the other hand have the normal double set, with two different versions of each gene. So if you look at one gene, half of the female's egg should have one version and the other half should have the other version. All females of one hive are produced by the same queen and the one male that she mated with. Remember, the male only has one set, so the versions coming from the male are the same in all female offspring.
This means a female's genes are made up of: 50% from the father (these are the same across all females) and 50% from the mother (where half the females have one version and half have the other version). Statistically, this means that looking at one gene, there is a 75% chance that two bees will have the same version of that gene.

So it's not only the selfish gene, but also the selfish allele?

Yes, evolutionary biologists tend to talk about genes when they mean alleles. (Usually because what they are saying goes for both genes and alleles; the 'relatedness' is an exception to that)

So in biology, there is gene competition between species, and allele competition within species?

That sounds possible to me, but I think that's another question which I'm not very confident about.

The part that is probably specific to this question is that some species of insects divide their population in the reproducing individuals, that are usually diploid and the working individuals, that are sometimes haploids, meaning they only have one copy of their set of chromosomes. This means that the workers have about half the amount of DNA material compared to reproducing individuals, although they share that copy in full with the diploid individuals.
There are variations of this mechanism in different species. Some species keep the copies but epigenetically "shut down" one of the copies. Others shed specific bits of the genome in the somatic cells. Sometimes this loss of DNA is not perfect, so different parts of the genome are lost just by chance.
We humans don't lose any material at all, we just epigenetically "shut down" one of the X chromosomes in XX individuals -- females.


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ChIP-seq vs ChIP-exo
I'm currently investigating ChIP-seq vs. ChIP-exo for finding binding sites.
As far as I can tell, ChIP-exo seems to be better in every way than ChIP-seq... but then again, I'm not strong in this area.
Are there any weaknesses in the ChIP-exo approach?

just as a first pass I'd say the extra ligation and primer addition steps for CHP-exo might resolve fewer hits in a given run, though that might also make your results less noisy as well.

ChIP-exo does seem to be the "ChIP-seq killer." I've seen Dr. Pugh present it a few times, and the audience is pretty much always impressed.
One thing I'd do if I were of the "experimental bent" would be to add random degenerate barcodes in the library prep to control for potential PCR artifacts. I imagine that since the "peaks" in ChIP-exo seem to be quite a bit narrower than ChIP-seq, I reckon it'd harder to use some coverage-in-local-neighborhood to remove such biases (assuming you wanted to do so).
To give you an idea of what I'm thinking of -- it would be somehow similar to what is depicted here.


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What would be the best dredging/trawling tools to collect macrofaunal priapulids?
Title says it all. I've been searching for the best way of collecting macrofaunal priapulids and would like advice on sampling methods and particularly sampling tools. Since large priapulids are usually found in low densities any form of grab-sampler would probably be inefficient and a dredge/trawl would be preferred. Any ideas on what tool(s) would sample at the right depth and filter efficiently?

The Ecology listserve (ECOLOG-L@listserv.umd.edu) would be a good bet to find expert responses to such a question; it would be useful to reference this question if you were to post there.

My first question would be is there any external indication of them such as air holes or anything else that you can assess from the surface?  I would think that if there is, you could use transects and a quadrat.  If you need to dive for them you can obviously make a weighted quadrat by filling pvc pipe with sand and gluing it together.  Then take an area and lay out transects and and randomly choose different lengths along each transect to put the quadrat down and that will give you an estimate of density.  If you actually need to extract them from the mud, I imagine that varies by species and you could make due with a grab sampler of the right size, something on the small end I would imagine.  That way you aren't dredging up tons and tons of mud to sort through.  If they are even rarer than I imagine, you could just lay out transects and swim them until you see something and do away with the quadrat.  Hope this helps.


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Can NSAIDs impact negatively the healing of tendons?
There are a number of articles regarding nonsteroidal anti-inflammatory drugs
 (NSAIDs) having a negative effect on healing conditions like tendonosis and tendinitis. From what I understand the channel through which they reduce inflammation disrupts healing. In general, many of them constrict vessels, thus reducing bloodflow even further to tendons. Are there other reasons, or interactions they can have with  cells that may also disrupt healing?
Are there advantages of using NSAIDs to promote healing?

I would suggest you contact your doctor if you are suffering from tendinitis.
NSAIDs are often used as part of treament for tendinitis, but like all medications they can have side effects. Therefore again if you have concerns about taking NSAIDs contact your doctor.
As for the mechinism of action of NSAIDs they don't constrict vessels but instead reduce the production of inflammatory mediators (prostoglandins) which act to dilate some vessels. These inflammatory mediators also make blood vessels more permeable so that nutrients and cells from the blood can pass through the vessel walls and carry out repairs to damage tissue. The problem however with the bodies inflammatory response is that it can be too severe, so that rather than providing healing it itself can cause damage and pain. For this reason (and many others) NSAIDs may be useful.
But again if you have concerns about taking NSAIDs or any medical condition these please consult your doctor. The internet is not an appropriate place for medical advice, your doctor is.

"But again if you have concerns about taking NSAIDs or any medical condition these please consult your doctor. The internet is not an appropriate place for medical advice, your doctor is." -> the internet is a perfectly fine place for medical advice and can be a great source of information in addition to a 15-minute appointment with a physician.

As far as I know there is no clear scientific evidence on whether and at which stage of a tendon injury one should use NSAID. Here is the conclusion of a systematic review from Cochrane {1}:

There remains limited evidence from which to draw firm conclusions about the benefits or harms of topical or oral NSAIDs in treating lateral elbow pain. Although data from five placebo-controlled trials suggest that topical NSAIDs may be beneficial in improving pain (for up to 4 weeks), non-normal distribution of data and other methodological issues precluded firm conclusions. Some people may expect a mild transient skin rash. Evidence about the benefits of oral NSAIDs has been conflicting, although oral NSAID use may result in gastrointestinal adverse effects in some people. No direct comparisons between oral and topical NSAIDs were available. Some trials demonstrated greater benefit from glucocorticoid injection than from NSAIDs in the short term, but this was not apparent in all studies and was not apparent by 6 months in the only study that included longer-term outcomes.

Some papers argue that the inflammation has a positive action on the tendon repair whereas some other papers claim the contrary. Given the current state of tendon injury research, it's not even clear how much inflammation happens during a tendinopathy {2,3,5}. From {4}:

FYI:

Do nonsteroidal anti-inflammatory drugs (NSAIDs) decrease or increase swelling during the acute phase of a tendon injury?
What is the proper timing for dexamethasone injections to improve the healing of damaged tendons in humans?

References:

{1} Pattanittum P, Turner T, Green S, Buchbinder R. Non-steroidal anti-inflammatory drugs (NSAIDs) for treating lateral elbow pain in adults. Cochrane Database of Systematic Reviews 2013, Issue 5. Art. No.: CD003686. DOI: https://dx.doi.org/10.1002/14651858.CD003686.pub2
{2} Rees, Jonathan D., Matthew Stride, and Alex Scott. "Tendons–time to revisit inflammation." Br J Sports Med 48, no. 21 (2014): 1553-1557. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4215290/ ; https://dx.doi.org/10.1136%2Fbjsports-2012-091957
{3} Khan, Karim M., Jill L. Cook, P. Kannus, Nicola Maffulli, and S. F. Bonar. "Time to abandon the “tendinitis” myth: painful, overuse tendon conditions have a non-inflammatory pathology." (2002): 626-627. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1122566/ ; https://dx.doi.org/10.1136%2Fbmj.324.7338.626
{4} https://youtu.be/z_QJYDgO6yQ?t=1129 "History and future of tendinopathy"
Sports Medicine Congress 2016. Comwell Hotel, Kolding - 04-06 February 2016. Follow the conference at twitter @sportskongres or #sportskongres
{5} Mosca, Michael. "Re-evaluating tendon disease: an emerging role for inflammation and alarmins." Master Thesis, University of Oxford, 2016. https://ora.ox.ac.uk/objects/uuid:360eb093-9a3b-4271-a5b6-31314c7e1bbd ;  (Google Scholar) (mirror)

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


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Why don't teeth glow?
Hydroxyapatite is the main component of tooth enamel. It contains phosphorus in the form of phosphates, pyrophosphates etc. that are found to exhibit the the property of phosphorescence. But why don't the teeth glow in the dark ?

Why is this being downvoted? I think it is a good question. Anyway, if you downvote please give a reason.

I agree with nico. I think this is a good question. It offers another perspective about the subject which I have never thought before.

Just to add a little more on the interface between optics and dentistry:
Whilst teeth do not phosphoresce, they do in fact autofluoresce.
The differential auto fluorescence of healthy tooth and carious tooth has been used for the early diagnosis of caries. (Gugnani N, Pandit IK, Srivastava N, Gupta M, Gugnani S. Light induced fluorescence evaluation: A novel concept for caries diagnosis and excavation. J Conserv Dent 2011;14:418-22 and http://www.opticsinfobase.org/boe/abstract.cfm?uri=boe-2-1-149)
To see teeth glow, or rather, fluoresce, they should be illuminated with short wavelength light, like blue light (wavelength 450 nm) and the teeth will glow green, which will be visible if the the blue light is filtered out.
Also see http://www.inspektor.nl/dental/qlfmain.htm#QLF%99%20Basic%20Principle

I'm gonna test this and vote based on results.

Firstly, phosphorus does not exhibit phosphorescence on its own (don't let words mislead you, they often don't mean what they seem like): See http://en.wikipedia.org/wiki/Phosphorescence#Materials and http://en.wikipedia.org/wiki/Phosphor#Standard_phosphor_types
Even if phosphorus did do so on its own, it would not do so in the body because it is always (almost always?) present as phosphate (PO4-), and this again is most often incorporated in other compounds such as nucleotides.

Teeth are made up of 3 substances.  Enamel, dentin and cementum.  Inside is the pulp.  The best chosen answer is incomplete.  Enamel fluoresces and undergoes phosphorecense but dentin of teeth is three times more phosphorescent than enamel.  Phosphorescence is a specific type of photoluminescence related to fluorescence. Unlike fluorescence, a phosphorescent material does not immediately re-emit the light radiation it absorbs. The slower time scales of the re-emission are associated with "forbidden" energy state transitions in quantum mechanics. As these transitions occur very slowly in certain materials, absorbed radiation may be re-emitted at a lower intensity for up to several hours after the original excitation.  When exposed to light sources containing UV components are turned on teeth, the fluorescence of human teeth gives them the quality of vitality, and they exhibit a fluorescent emission with a peak of 440 nm observed peak light. (bright blue hue)  Because of dentin's atomic composition contains special collagen and mineral matrix phosphorescence allows it to collect light photons slowly to change tooth color.  In this way, natural tooth color can be used as a measure of oral health and health of the brainstem which innervates the dentition.  Dental OCT is now used in this way. Optical coherence tomography (OCT) is based on low-coherence interferometry, typically employing near-infrared light as its source because it deeply penetrates tissues with water. Water is the ideal chromophore for red light. The use of relatively long red wavelength light allows it to penetrate into the scattering medium of teeth and the pulp.  Using light this way, OCT can provide “optical biopsy” without the need for excision and processing of specimens as in conventional biopsy and histopathology. Application of OCT in dentistry has become very popular since 1990.  This is why in my Redox Rx blog I have used pulp testing as a modern redox variable for human health.  It is from the dentinal pulp where light is released from cells and collected into the atomic lattice of dentin to change its frequency and this changes its color we observe.  Tooth color can be used a health metric. So for these reasons the accepted answer is quite incomplete.  We have known about tooth phosphorescence since 1941 as published in pubmed.

http://www.ncbi.nlm.nih.gov/pubmed/17774027


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Color of the Fur coat of Polar bears
Recently I was playing a quiz and a question was asked about the color of the fur coat of a polar bear. To my surprise the answer was black. I thought it was yellowish white or creamy. Why so ?

The fur coats of polar bears are in fact clear tubes - not white fur as is often believed. It is their skin that is black, to absorb the most warmth from the sun (and the clear tubes allow the majority of the light to pass through to the skin).
I recently watched the BBC's Frozen Planet TV series (with David Attenborough), where I heard the above answer. If you haven't already, I recommend watching it.

Also the tubular hairs, like a hollofil padding, are better insulators than solid hairs so they keep more heat in the bear.


text:
Is there a comprehensive database of fossils (with images) online?
Not sure if this is the best stackexchange to ask...
I have not been able to find a decent database of fossils on the web, does one exist?
Here are some of the links I have found through Wikipedia and Google:

http://www.paleoportal.org/index.php?globalnav=doing_paleo&sectionnav=more_submissions&state_id=0&submission_type_id=27&type_id=5
http://www.morphobank.org/index.php/Projects/Index
http://research.amnh.org/paleontology/
http://en.wikipedia.org/wiki/List_of_fossil_sites
http://www.fossilsites.com/STATES/AB.HTM
http://inyo.coffeecup.com/site/ammonoids/ammonoids.html
http://www.historicalclimatology.com/
http://geonames.usgs.gov/pls/gnispublic/f?p=gnispq:3:4473291015495555::NO::P3_FID:354414
http://www.scotese.com/earth.htm
http://www.trilobites.info/biostratigraphy.htm
http://burgess-shale.rom.on.ca/en/
http://www.fossilmuseum.net/FossilGalleries.htm
http://www.kumip.ku.edu/cambrianlife/Utah-Online-Fossil-Exhibits&Collections.html
http://www.ucmp.berkeley.edu/collections/catalogs.html
http://peabody.yale.edu/collections/search-collections?vp
http://books.google.com/books?id=Ezm1OA_s6isC&printsec=frontcover&dq=hartwig+primate&cd=1&hl=en#v=onepage&q&f=false

What are the best places to get fossil data and images of the fossils? Or are museums and textbooks the only alternative?

If you already found some sites that fit the bill, they may be better off posted as an answer. Per the [FAQ#dontask]: avoid asking subjective questions where... your answer is provided along with the question, and you expect more answers: "I use ______ for ______, what do you use?".

What are you looking for that these sites lack?

paleodb.org seems to have a huge database linking fossil records to publications. But it is not clear what you want, nor is it clear why the 16 pages you listed are insufficient. If you clarify that I am sure someone will be more able to help.

there are a few places trying to create a comprehensive list, but most of those are still specialized towards things like vertebrates or pollen. the morphbank in particular want to not only create a list but also include all  relationship studies in a single searchable index.  Adam gives a good reason why these take so much time and effort to create.

http://tolweb.org/ can at least give you names.

note that  publication descriptions of a fossils are required to provide a repository, a location the fossil can found at. this is why a common database has bot been a big issue until recently, a researcher would know where all the relevant material could be found. In paleo many comparisons are still done by traveling to the place and looking at the fossils side by side. I have been to museums were the only database of their specimens was a card catalog.

No. Museums are the traditional repository for fossils, and the process of "digitizing" their collections is slow and labor intensive. Often, the museums only aim to digitize what me might call the "meta-data" associated with the fossil, as was done here:
http://ucmpdb.berkeley.edu/cgi/ucmp_query2?admin=&query_src=ucmp_index&table=ucmp2&spec_id=V8111&one=T
A truly comprehensive database is not feasible in the near future. A single photograph likely would not be sufficient to characterize the fossil -- the interesting components of fossils are often microscopic. For example:
http://www.pnas.org/content/99/14/9117.full.pdf
Even taking a single photograph can be very labor intensive, and fossils can be fragile. Proper photo-documentation would probably require multiple images. More generally, a comprehensive database would probably need to include non-photographic data relating to the fossil -- such as chemical composition of non-visual imaging techniques (X-ray, IR, UV, etc).
For the foreseeable future, "comprehensive" collections will be housed in museums without full digital representation. The only way to know how comprehensive these collections are is to ask the museum curator, who will be aware of the scope and limitations of the collection.


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Why are (some) cats attracted by bleach?
(Sorry if this question is only partly biological)
I have noticed that several cats (including the one that keeps sleeping in my house), are fond of the odor of bleach (eau de Javel) and chlorine.

Among examples, chlorine is used in small quantities in tape water and the cat is fond of licking the faucet in acrobatic positions even if there is mineral freshwater nearby.
I was one day not careful enough using a bleach based gel cleaning product and some of it got on my hand. Even after cleaning my hands, they still had a bleach "perfume" and my cat cling to me and even cleaned my hands with his tongue for minutes.

Why is this so ? Are there other animals known to have this taste ?
Might it be in fact acquired through living with humans ?
Is this potentially detrimental to their physiology ?

Searching for an answer, because our cat does the same thing, she goes crazy for my hands if I've gotten plain Clorox bleach (sodium hypochlorite) on them. I can smell the difference on my hand even after thorough washing, and she licks, gently bites, grabs with her paws, rubs my hand across her mouth/face, etc. Behaviors she does not typically do, but she does each time my hands have been in contact with bleach.

I can't give a definite answer, and there's nothing in the literature about this specifically, but perhaps some relevant information and a suggested behavioural experiment will help.
Background
Firstly, I assume you are talking about sodium hypochlorite (which is usually what people mean by bleach)? If so, there are several compounds your cat could be reacting to. Chlorine is an obvious candidate, which is released as sodium hypochlorite decomposes in solution. Additionally, bleach can react with various organic materials to release a variety of volatile organic compounds (VOCs), which your cat might be able to smell. In addition to also releasing chlorine gas, the same suite of VOCs are released when the chlorine in chlorinated tap water reacts with organic contaminants (Odabasi, 2008). The VOCs include chloroform and carbon tetrachloride.
Next, cats are known to exhibit modified behaviour in response to a variety of compounds. Some are suspected pheromone components of cat urine, such as felinine (Hendriks et al, 1995) and its breakdown products, such as MMB (Miyazaki et. al, 2006).
Some cats also react to externally-produced compounds with a particular response called the 'catnip response', which involves rubbing the face on the ground or other objects, shaking the head, rolling, etc. (Tucker & Tucker, 1988). Not all cats exhibit the response, around 50-50% do, and susceptibility is genetic and heritable. Some sources eliciting the catnip response include:

nepetalactone released from catnip (Nepeta cataria)
actinidine released from valerian (Valeriana officinalis)
essential oil of Actinidia macrosperma (Zhao et al., 2006)
the compounds epinepetalactone, dihydronepetalactone, isodihydronepetalactone, neonepetalactone, iridomyrmecin, boschnialactone, onikulactone, boschniakine, actinidiolide and dihydroactinidiolide (Tucker & Tucker, 1988)

In general all the catnip response elicitors share a two-ring structure, which is not to my knowledge shared by any of the volatiles given off by bleach.
A possible experiment
So, two obvious possibilities (regarding what type of behavioural response is being elicited) are that either:

your cat is interpreting the volatile as a pheremone and therefore as some sort of sexual or territorial signal, or
it is showing the catnip response

As a first experiment, you could check whether your cat (and any others you can get hold of - in an ethical way) respond to bleach and/or to catnip. If the cats do not exhibit the catnip response to catnip, they aren't exhibiting it in response to bleach, and thus some other explanation is more likely.
As a second experiment, you could make a detailed observation of the precise behaviour shown in response to bleach. Compare it to that exhibited when the cats encounter catnip (depending on the outcome of the first experiment) and when they are oestrous (if female) or encounter an oestrous female (if male). You could also compare to the response to the urine of other (male and female, familiar and unfamiliar) cats.
An experiment you shouldn't do
If you wanted to find out which chemical your cat is responding to, you could allow your cat to sniff pure chlorine which hasn't encountered organic contaminants, as well as chloroform, and carbon tetrachloride. However, all three of those compounds are extremely dangerous and could easily kill you or your cat, so please don't.
I general, I would caution against exposing your cat to bleach, because it can induce serious health effects depending on dose and mode of exposure, ranging from asthma to third-degree burns to carcinogenesis. If they are attracted to it, that is a good reason to keep it away from them to prevent them ingesting it, which is more harmful than inhaling the fumes.
I can't comment on whether the behaviour is acquired as result of domestication, but that too could be tested by comparing the reaction of a large sample of wild cats (!).
References

Hendriks, Wouter H., Paul J. Moughan, Michael F. Tarttelin, and Anthony D. Woolhouse. “Felinine: a Urinary Amino Acid of Felidae.” Comparative Biochemistry and Physiology Part B: Biochemistry and Molecular Biology 112, no. 4 (December 1995): 581–588.
Miyazaki, Masao, Tetsuro Yamashita, Yusuke Suzuki, Yoshihiro Saito, Satoshi Soeta, Hideharu Taira, and Akemi Suzuki. “A Major Urinary Protein of the Domestic Cat Regulates the Production of Felinine, a Putative Pheromone Precursor.” Chemistry & Biology 13, no. 10 (October 1, 2006): 1071–1079.
Odabasi, Mustafa. “Halogenated Volatile Organic Compounds from the Use of Chlorine-Bleach-Containing Household Products.” Environ. Sci. Technol. 42, no. 5 (2008): 1445–1451.
Tucker, Arthur, and Sharon Tucker. “Catnip and the Catnip Response.” Economic Botany 42, no. 2 (1988): 214–231.
Zhao, Yun-peng, Xiao-yun Wang, Zhi-can Wang, Yin Lu, Cheng-xin Fu, and Shao-yuan Chen. “Essential Oil of Actinidia Macrosperma, a Catnip Response Kiwi Endemic to China.” Journal of Zhejiang University. Science. B 7, no. 9 (September 2006): 708–712.

Thanks a lot for these references and these suggestions.

In response to your experience proposal, I can already give partial answers:

I have already exposed this cat to various compound known to cause "catnip" behavior in cats such as catnip and valeriane (the first bought, the second naturally occuring in my garden), and he did not, did not show any interest in it whatsoever while another visiting cat did.

(I know we are on biology.SE and not on Pet.SE but) Would a neutered male cat exhibit a change in behavior when crossing the path of a female in oestrus?

I marvel on the international character of scientific research on cats (japanese, american, chinese).

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


text:
What is the functional difference between hemoglobin and ferritin?
I read that both hemoglobin and ferritin are for storing iron in the body. So, what is the difference between them in terms of storing/binding iron?

Why close this now? It is 5 years old and has a good answer.

Hemoglobin is the protein of erythrocytes (red blood cells) which has ferrous ions (Fe2+) bound in its subunits. These are able to keep oxygen bound which enables the cell to transport oxygen through the circulation. It's not really for storage of iron, it's for using it.
Ferritin is the actual storage protein, cells express it to store iron in case of deficiency and also to regulate the amount they have in the cell. According to this, it's mainly expressed in muscle, liver and kidney cells (but I'm not too sure about the details of that study so I might have got that wrong).
Edit: just found this in one of my old lectures; unfortunately it doesn't quote sources: ferritin stores iron in liver and heart. The total iron in the body is ~3.9g, of which 2.5g are in use in hemoglobin, 500mg in stores (an additional 250mg in the liver), 150mg in bone marrow, 300mg in myoglobin and 150mg in other enzymes. The remaining 5mg are bound to transferrin in the plasma.

yah - hemoglobin doesn't really store iron, its using the iron :)

Strange, I always thought that was myoglobin's job in muscle tissue. Anyone know myoglobin and ferritin's function in relation to one another?

According to Wikipedia we don't really know the function of myoglobin yet. Given its high relatedness to hemoglobin though, I highly doubt it serves to store iron.

@LanceLafontaine: myoglobin is essentially the muscle equivalent of haemoglobin, carrying O2 to muscle cells. Iron is used in both myoglobin and haemoglobin as the "attachment site" for O2.


text:
Too few transcripts from transcriptome assembler Oases
I am trying to run Oases for transcriptome assembly. The result is far from expected, so I would like to ask whether I am running it in a right way? Thanks.
Here is my running command:
python scripts/oases_pipeline.py -m 25 -M 29 -o output -d " -strand_specific -shortPaired data/reads.fa" -p " -min_trans_lgth 100 -ins_length 300"

My library is strand-specific and pair-ended with length 67bp. The reads are shuffled as:
>0(left_mate_forwarded)
ACTC...
>1(right_mate_reverse_complemented)
TATA...

I got some transcripts, but are far from the transcripts annotated, also far from the result of Trinity. The longest contig from Oases is ~2500bp (vs. ~10000bp from cufflinks and ~6000bp from Trinity). The N50 value is also low. It only reports 20 contigs those cover full-length of some transcripts from Cufflinks (totally ~4000), while Trinity reports ~650.
The dataset I am using is a subset of S. pombe. Does it matter?
Could somebody help me point out whether something wrong here?

You mentioned that the result is far from expected--in what way? Is it just the number of transcripts, or the lengths of those transcripts?

Also, as stated in the FAQ: Questions on interdisciplinary subjects like bioinformatics are also welcome, as long as they focus on the biological part of the subject. I'm afraid if you can't highlight a significant biological component to you question, it's likely to be closed as off-topic.

Em, I tried to post to BioStar, but nobody answers me...

Here is the mailing list for Oases, http://listserver.ebi.ac.uk/mailman/listinfo/oases-users also there is a thread in SEQanswers http://seqanswers.com/forums/showthread.php?t=3877&highlight=oases some people also have problems to get Oases work.

Unfortunately, if nobody answered on Biostars, the chance of getting an answer here is very slim indeed …


text:
How and why did mouth and nasal cavity evolve separate?
My initial objection is that nose filters air, mouth is for eating but is used for breathing also, plus they both are used to create sounds. What is the cause and reason in this case, why do we need two "holes" and one is not good enough?

Neither the nostrils nor the mouth originally evolved for breathing.  Fish have (two pairs of) nostrils which they use to smell and mouths which they use to eat, but they breathe through their gills.  Some lobe-finned fishes (the ancestors to tetrapods) evolved a connection between the posterior nostrils and the oral cavity called choanae.  A fossil called Kenichthys is a transitional form in this development.  The evolutionary reasons behind this development are not particularly well understood.  (This should not be surprising when discussing something that happened in the Devonian.  It's only recently that the discovery of Kenichthys ended the controversy of whether chonae in tetrapods are homologous to posterior nostrils in fish.)
Basal reptiles have nostrils and mouths and can breathe through both of them, but do not have a separation between the oral and nasal cavities.  The next important development is a secondary palate (which separates the nasal and oral cavities).  This allows animals to continue breathing while swallowing food.  Animals without such a separation must hold their breath while swallowing.  This ability is certainly useful in many situations, and unsurprisingly several solutions to this problem have evolved in different lineages.

I'm not sure if other can do that, but I cannot breath when I start swallowing, there is a break on breathing even via nose. But I can keep chewing food in mouth and breath at the same time with nose. What are the other "several solutions"?

Snakes have an extended trachea "straw" called a glottis, that allows them to breathe while swallowing.  See http://www.youtube.com/watch?v=Pq18vg6vBGA

Adult humans can't breath while swallowing, but infants can. That we can't breath and swallow as adults is related to the facts that we are upright and have throats highly modified for speaking.

Yes, I remember reading, that part of the throat called larynx shifts at some age to get on more proper position for speaking. I could accept this answer, but waiting if there comes other views and especially explanations how this happened in evolutionary terms.

@PHPGAE  Added some more info.

In general, only mammals (animals like humans, dogs, cats, mice and cows) have an epiglottis. Some reptiles have an extra flap of skin that does pretty much the same thing as the epiglottis, but it does not have cartilage in it. This is an example of what scientists call an analogous structure (same job, but made in a different way) instead of a homologous structure (made in the same way – although sometimes it has a different job). ref


text:
Why are we using upper teeth and lower lip on labiodental sounds?
I came to wonder this when studying language (as well as other same theme question posted just few ago). For example the word "fantastic" we use upper teeth and lower lip to produce F sound, instead of using lower teeth and upper lip, which would work as well with a small practice.

I'd imagine I'm not the only one who just said their saying it to see if you're right.  It could be something to do with the bottom teeth being set behind the top ones I suppose, you have to use energy to pull your bottom jaw forward if you're doing it the other way.  Really interesting though xD

It definitely feels like an unusual jaw movement to do it with your lower teeth. The jaw is required to laterally move forward rather than longitudinally move, which is a more common movement in terms of other vocalisations and eating.

@RoryM Yeah, I hope nobody was looking a second ago when I was biting my lip and blowing! :)

lol, yes I found that funny experiment. But again more you do it, more natural it comes plus you may become economical with jaw movement. What is the variation of jaw placement on human skulls? Some have a different shape jaw and more in front than others.

This article might help, and is at least related. http://www.psych.mcgill.ca/labs/mcl/1528.pdf

@LanceLafontaine: Broken link (403).

@Mechanicalsnail, works for me.

@LanceLafontaine: By any chance are you accessing the site from within that university?

Nope. Anyhow, here's a PubMed link which should work.
http://www.ncbi.nlm.nih.gov/pubmed/8035233

The alternative articulation, called dentolabial, is more difficult to articulate, so it is very rarely used in human language. However, it apparently is common enough in disordered speech to be allocated an ExtIPA diacritic.
The reason labiodentals are easier: Humans normally have a slight overbite.

When the jaw and lips are in a "neutral" position, the lower lip is close to or touching the upper teeth, so with a small vertical movement of the jaw (together with tensing the lip) one can articulate a labiodental. Articulating a dentolabial requires moving the jaw a fair distance forward, to go around the upper teeth before reaching the upper lip. As Ben pointed out in the comments, front-back jaw movement is unusual, a less "common movement in terms of other vocalisations and eating".
Furthermore, since labial articulations are directly visible to observers, learners are especially likely to imitate others' exact articulation. Thus even though labiodentals and dentolabials sound similar, everyone in the population of speakers uses the same articulation (rather than having both articulations in free variation).
Perhaps dentolabials would instead be more common if most people were like this:

I wanted to suggest the slight overbite, but had no supporting information. Great answer!


text:
What part of food gives the blood red color?
Roughly, what I know is, when we eat food it goes into our: Stomach > Small Intestine > Large Intestine > Rectum. So, it just moves through a digestive pipe.
What I don't understand is, what part of the food is responsible for blood's color and how does the food that we eat mixes with blood?

The red colour of blood isn't actually to do with food at all.  The primary purpose of the blood is to carry oxygen to all the cells that require it to release energy.  Red Blood Cells are filled with an iron containing pigment called haemoglobin.  When it has oxygen bonded to it, haemoglobin  has a bright red colour - it is this that gives blood its red colour.
In terms of how food enters the bloodstream, it is first broken down into extremely small constituents.  This is done by mechanical action (i.e. chewing and the squeezing movement of your digestive system) and by chemical action through the use of enzymes.  Enzymes are proteins that are secreted by various glands in the mouth (and are therefore contained in saliva), stomach and both intestines.  These chemically break large food molecules down into small products such as glucose (sugar) and amino acids (protein-building blocks) amongst other things.  These then move across the wall of the intestines and into the bloodstream, which are separated by only one cell:

Unfortunately that's the best image I could find.  The intestine is everything outside of the pink layer (which is the wall of the intestine).  The small molecules are able to pass through the pink layer and straight into the blood stream.  The picture shows a fold in the wall of the gut, which increases its surface area so allows more molecules to diffuse across.

Ok, I understand the intestine part. So, the iron in the food is responsible for creating hameoglobin which is bounded with oxygen to form red blood cells? Please feel free to correct me.

@user132314 yep, that's pretty much it :)

Just one slight correction - red cells aren't coated in haemoglobin; the haemoglobin is to be found inside the cells.

In essence, some of your food contains iron (especially red meat). This is taken up by your body and integrated into the haemoglobin protein which red blood cells contain in high amounts.
The iron in haemoglobin can bind oxygen (it does this when it passes through the lungs) which enables the red blood cell to carry it through your blood circulation.
The colour of blood comes from this haemoglobin. When the iron is binding oxygen, it is red. Otherwise, blueish-red. (http://www.ebi.ac.uk/interpro/potm/2005_10/Page1.htm)

Ingested food is digested within the digestive canal. This means that it is broken down into smaller molecules that are then transported into cells lining the digestive canal (by proteins that expend energy to do this). The nutrients are then further transported until they reach blood vessels (or, in the case of lipids, lymphatic vessels, which eventually empty into veins). However, the 'pigment' that gives blood its red color is generally constructed from smaller molecules and atoms within the body, and not directly acquired from food.
Ultimately, the red hue in human blood is due to a protein known as hemoglobin. Each hemoglobin protein is bound to four 'heme' molecules, and each of these are in turn bound to a Fe2+-ion* (a form of iron) and either O2 (oxygen) or CO2 (carbon dioxide). All of these components are required to give hemoglobin (and thus blood) its distinct hue.
The molecules derived from food that are used to build the complete hemoglobin complex are:

Amino acids

Used to synthesize the actual hemoglobin protein. Obtained from dietary protein, as free amino acids, or (in the case of non-essential amino acids) synthesized from other molecules.

Succinate

Used together with glycine (an amino acid) to synthesize heme. Most succinate is derived from lipids (e.g. fatty acids), carbohydrates or amino acids in food.

Iron

Obtained from a variety of dietary sources.

CO2

Mainly produced at the final step of aerobic energy production where mitochondria break down carbohydrates, lipids or amino acids to form water, CO2 and chemical energy.

O2

Almost exclusively obtained from the air via direct absorption in the lungs.
For more information on how proteins such as hemoglobin are synthesized from amino acids, you could see e.g. this video. For more information on metabolic pathways, I suggest having a look at this map. In the latter, you can focus on human metabolic pathways by unchecking "Unicellular organisms & Fungi" and "Higher Plants" in the menu. It should be noted, though, that this only describes metabolic pathways, and does not go into much detail in terms of how these processes actually work.

*Except in the case of methemoglobin, which has bound a Fe3+-ion and cannot bind O2.


text:
Regarding TIMP and MMP enzymes
Are there substances that can promote TIMP enzyme production, or MMP enzyme production or supression in tendons?
Are there medical tests that measure quantities of MMP and TIMP enzymes in tendons?

For your first question
Both enzymes, are components of Epidermal growth factor receptor (EGFR) signalling pathway.
MMP is a matrix metalloproteinase, that triggers EGFR signalling, this can be done by a mechanism called transactivation

So, A signal from G-coupled receptor, or cytokine receptor could activate the cleavage of MMP,  then MMP converts to a ligand for EGFR activation
For example Angiotensin II type 1 receptor (AT1R) and type 2 receptor (AT2R) which are GPCR, there are evidence for crosstalk with EGFR, look for this paper. This could be linked with hypertension or inflamation. Also cancer, could trigger EGFR receptors by NMP's.
And finally tissue inhibitors of metalloproteinases (TIMPs) are the negative regulator of MMP's
This are only an overview of the whole biological process involving MMP, so I think there is no single answer to your question, but you can delimit the topic for a specific disease, and look for papers at google scholar.

Did you mean to make this community wiki?

Yes, because I do not have, the complete answer, and if someone could help to complete that or have more examples, can enhance the reply, I think this is a very interesting field to research. I'm finishing my MSc thesis in signal transduction, for a model like this.