text:
What advantage does an enzyme serve over catalysis by the addition of heat energy?
I understand that an enzyme lowers the activation energy, allowing the reaction to run faster, however I am not sure, how it may be favorable during the addition of heat energy. Wouldn't that lower the activity of the enzyme since the enzyme is sensitive to heat?

Enzymes have two benefits over raising the temperature:
First, reducing the activation energy by reusable enzymes is far more energy-efficient, apart from the fact that the required temperature would vary for different reactions.
Second, enzymes are able to be controlled by allosteric mechanisms, which facilitates metabolic control by feedback loops, feedforward motivs and receptor-mediated processes. In the example of glycolysis this enables the cell to fine-control its supply with energy equivalents (see figure from Wikimedia Commons below). This mechanism may be the most important function of enzymes.

Reference

William C. Plaxton: Principles of Metabolic Control. In Kenneth B. Storey (ed.): Functional Metabolism: Regulation and Adaptation, John Wiley & Sons, Inc. 2004

The enzyme does only one thing: It lowers the activation energy which is necessary for the specific reaction to happen. It does not change the speed of the reaction, nor does it change the rection enthalpy or the quilibrium of the reaction. See the figure for clarification (from here):

Without the enzyme the Ea (activation energy) would be so high, that the reaction would be possible in the cell. Either because this high amount of energy is not available or because the amount of energy would destroy the cell or the reaction. So the lowering of Ea allows this specific reaction to take place.

By reactions there is an energy barrier called activation energy. Your substrate molecules have kinetic energy (they move, rotate, etc...), so when they collide properly, their kinetic energy can be used to overcome the activation energy and so the reaction takes place. According to the Arrhenius equation the reaction rate depends on the temperature, which is evident, because the kinetic energy of your molecules is higher by higher temperature. Enzymes lower the activation energy, because they help the substrates to collide with the proper orientation.
Enzymes are mostly composed of amino acid chains. These chains must have proper folding. Increasing (or decreasing) the temperature can disrupt this folding and make the enzyme useless. This inactivation can be reversible or irreversible depending on the enzyme type, the temperature and other environmental factors e.g. pressure, osmotic pressure, etc...
To answer your question, every enzyme have an optimum working temperature. At this temperature the inactivation is slow enough to be compensated by the increased reaction rate.

figure 1 -  optimum temperature of a single enzyme - ref

figure 2 - optimum temperatures of multiple enzymes - ref


text:
What is a group of tortoises called?
This post at Mental Floss stated that a group of tortoises is called a 'Creep'. I had never heard of that before, and in trying to find the references for the name, I was surprised that I couldn't actually find anything.
Wikipedia showed no results in either of their lists for animal names.

http://en.wikipedia.org/wiki/List_of_animal_names
http://en.wikipedia.org/wiki/List_of_English_terms_of_venery,_by_animal

Neither did the Northern Prairie Wildlife Research Center: http://www.npwrc.usgs.gov/about/faqs/animals/names.htm
The closest I found was that a group of turtles is called a nest or a bale.
Is there an actual source for what a group of tortoises is called?

How big of a group do they say a creep is?

@rhill45 They didn't say anything about the size of the group, just what the (supposed) name is.

@rhill45 I asked this to my new friend at The Tortoise Group, and he replied: I thought that a group was any collection of more than one. So even though there are words for two (pair, brace, duo, couple, etc.) it would still officially qualify as a group!

Isn't it an English Vocabulary question? Should it be migrated to English site? To my view it not looks like a biology question, even not on nomenclature ( identifiers ).

Creep is correct. I sent an email asking this question to The Tortoise Group, which is a non-profit organization whose mission statement is:

Improving the lives of wild and desert tortoises through education.

The Executive Director replied:

It's a bale for turtles and a creep for tortoises. I am sure they could have come up with a better name!

If you have additional questions, there's a wealth of scientific information on their website.

Okay but where does the word come from? The OP isn't asking for someone to validate the claim but explain the origins since it isn't common or listed on many sites. Read the last sentence of the OP it asks for a source not a validation. He has already learned that creep is a word used to define this.

I apologize if I missed the point of the question. I emailed the same source asking specifically for the origin of the name, and will let you know if/when he replies.

Maybe for the etymology part of the question, this related question on a related SE site could help: http://english.stackexchange.com/questions/21336/a-murder-of-crows

I received this from The Tortoise Group: "That's a good question. I think with all those collective nouns, it's difficult to find out exactly when the term was first used, or how or why.  All I know is that it was used because tortoises creep slowly. Sorry I couldn't help with this one!"

What I found was that creep is a collective noun. The professor Peter Trudgill uses the word in a chapter about collective nouns and the example is of tortoises. I don't know what book to tell you to look in though. He is professor of sociolinguistics. From a search on collective nouns for animals, turtles, and reptiles, I only found turtles having the following collective nouns: bale, nest, turn, dole.
My guess is then that Peter Trudgill made up the word and some people have adopted it or it is primarily an English (England) word.

collective noun list two

I believe I found the source. In Geology, a creep is defined as a slow moving mass. By borrowing the word creep from Geology, one can accurately describe a group of tortoises.

Creep

I have worked in various parts of the world in sales of engineering equipment, but have always been involved in animal conservation, especially for turtles and tortoises.
One of my previous employers, now an engineering company was originally purveyor of turtle meat to HM Queen Victoria. They provided the Green Turtle Soup entrée  for Queen Victoria's Coronation Banquet, and for the Royal Family in general up to H.M. Queen Elizabeth II, who also had green turtle soup at her coronation banquet. It was not on ration points. The company had the royal warrant.
I'm afraid the general terms for tortoise and turtle in English come from the meat trade.
A "creep" originated in the Galapagos, where the tortoises were hunted often to extinction, by sailing ships crews, whaling or other, and even HMS Beagle.
Once on board a creep became a bale, also the usual description for sea turtles caught by nets, and stored, like their land cousins in tightly bound nets. There was a number of individuals and weight for a bale. There was a market standard for different species - say 4 Leatherbacks per bale, 6 Green per bale. Green turtles were favoured as they had tasty meat but did not expire quickly.
If the animals were caught by bill hook or harpoon they were put in a 'drag bale', thus injured they would be the first consumed by the crew. Those captured at sea or on land put in nets were "bales" (uninjured) when landed. Galapagos Tortoise may be one per bale.
There were markets all over the world; in London, it was Billingsgate for the meat, and for the shell it was Lower Thames Street. Turtles were delivered live to restaurants. Generally, the voyage and the occasional wash with water had purged them. Shell and meat would then be subdivided with other terminology, depending on the quality of species meat and shell.
Obviously, there are many other terms for chelonian meat and shell in other languages - florid descriptions in China and French/Creole on the East Coast of America for the Diamond Back Terrapin and the alligator and common snapping turtle, for instance.
I obtained this information from an old employee of the former employer's green turtle soup restaurant at a company dinner in London. No, we did not have turtle soup, and I did not kill him. He was a really nice guy and a war hero with the London Scottish Regiment. For the shell business, I know something from another of my employers. We were involved in trading heavy equipment to the former Soviet Union. Our offices were next to the dreadful fur trade warehouses on Lower Thames Street, which was next to the Turtle Shell Exchange (this may not be the correct title of the market).
My point is that our naturalist forbears took collective nouns, in this case, from general parlance. They were generally scientists. Conservationists came later. I think the collective noun was thus applied outside the tortoise/turtle trade to all species by English speakers.

can you add some external references to back up the claims in your answer? we generally like to see references for nearly all information so that other individuals can read more/further on the topic - thanks

http://www.britishcheloniagroup.org.uk/testudo/v2/v2n5darwin

https://www.theguardian.com/books/2004/jul/31/featuresreviews.guardianreview7

source: Stack Exchange

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

sort: votes


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Can anyone identify the worm in this video clip?
My wife came across this youtube clip of a spider and a worm. Can anyone identify at least the phylum?

I think it's a Gordian worm or more accurately known as Spinochordodes tellinii . Good music for a parasitic event like that by the way. Nematomorpha is the phylum.

If your a molecular guy, check out Spinochordodes tellinii and the WNT pathway, pretty cool stuff.

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


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What is a triglyceride?
I'm confused on what a triglyceride is, from what my text book it says its a type of gylercide, then from a website it said

Glycerides can be subdivided into two categories. The first group, the neutral glycerides are nonionic and nonpolar. The second group, the phosphoglycerides contain a polar region, the phosphoryl group.

Which makes triglyceride not a directly under a glyceride but under one of these groups. Then it says

Esterification may occur at one, two or all three positions producing monoglycerides (monoacylglycerols), diglycerides (diacylglycerols), or triglycerides (triacylglycerols). The most prevalent and most important are the triglycerides.

So does that mean that triglyceride can be produced by either of the two groups phosphoglycerides and neutral glycerides. And if that's correct then how are monoglycerides and diglycerides produced.
Source

Welcome to Biology.SE. Perhaps Chemistry.SE may be a good alternative SE to post this question.

@chris or the answer should be brought over here as a CW with a link to the answer on Chem as the original source identifying the author from Chem. Closing the question will just allow people to ask it again since we can't cross exchanges to mark as a duplicate.

Good point. I retract my close vote.

The following answer was giving by Michael D. Dryden from https://chemistry.stackexchange.com/questions/24797/what-is-a-triglyceride/24799#24799
There is some minor argument as far as nomenclature goes for these lipids. Most sources I can find, including IUPAC have glycerides as only including esters of glycerol with fatty acids. Monoglycerides have a single fatty acid ester with two free OH groups, diglycerides have two fatty acid esters, and triglycerides have three. Phosphoglycerides are defined separately as esterified derivatives of phosphatidic acids, so you can think of them like glycerides where for one of the substituents, instead of a fatty acid, some derivative of phosphoric acid is present. However, the way the two terms are defined, they don't encompass any common molecules, i.e. there are no molecules that are both glycerides and phosphoglicerides and neither group is a subset of the other.
So: mono-, di-, and triglycerides are subsets of glycerides while phosphoglycerides are a different group altogether, though structurally similar.

Triglyceride. It has 3 fatty acids, which are non polar (water-fearing). so they are hydrophobic. These 3 fatty acids are connected to a glycerol molecule. This molecule is polar and is hydrophilic (water-loving). The glycerol is attached to the 3 fatty acids via  a dehydration reaction. When they are connected, they loose a water molecule, and form an ester.


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Why are cell lines frozen in vapor phase?
For most of the cell lines I've come across, ATCC recommends storing them in the vapor phase of liquid nitrogen. I'm taking that to mean any place above the level of liquid in the nitrogen storage tank. What is the reason for this? Under what conditions/requirements would one store cells/tissue submerged in liquid?

The storage itself can be done both in the liquid and also in the vapor phase in the liquid nitrogen. Both have their advantages and disadvantages. In my experience there are two main reasons why storage in the vapor phase (although there may be temperature fluctuations when the nitrogen gets low) is recommended.
First, you avoid cross contaminations of your cells lines with mycoplasma (and possible other contaminants) which can get transferred into the liquid nitrogen phase and then into your other cultures. This is not a theoretical danger, but pretty real. See the papers in the reference below.
Then liquid nitrogen will enter your cryotubes (which is also the cause for contaminations). If you use tubes which are not explicitly made for this kind of storage (which is not a problem for the vapor phase storage) then the liquid nitrogen which made it into the tube will expand upon thawing and can cause your tube to explode. This can cause injuries. For more details see here and here.
References:

Risk of contamination of germplasm during cryopreservation and
cryobanking in IVF units.
Microbial contamination of embryos and semen during long term
banking in liquid nitrogen

I don't think there can be any contamination issue with mycoplasma but is possible with viruses.

It can happen. Mycoplasma can survive in liquid nitrogen for very long periods of time and then cause contaminations. Been there, seen that. We had to discard a whole set of cells.

So how do the cellular membranes/viral proteins handle the liquid nitrogen? I assume nitrogen is a non-polar solvent, but would it be enough to disrupt a phospholipid bilayer?

It is indeed non-polar. But it will not disrupt the memnrane layers, as these have polar groups to the outside (the non-polar tails are directed to the inside of the membrane). Otherwise we couldn't store any cells in there. Additionally these cells survive as the other cells frozen in there. As they are more simple than an eukaryotic cell, they are more likely to survive.

Definitely right about the myco problems I've lost almost a thousand samples like this. I wish they made these dewers  able to hold more n2. Chris good answer here.


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What is the genome size of Saffron (Crocus sativus)?
I searched the web but cannot find an answer for my question. Has the genome size of Crocus sativus been determined?

Neither NCBI nor Ensembl have a genome project listed for any crocus species, although individual ethidium bromide stained nuclei have been analyzed by flow cytometry, revealing approximately 11.4 pg of DNA per nucleus (warning, pay wall).
C. sativus is triploid, giving it a C-value of 3.8 pg which works out to a haploid genetic content of about 3.45 Gbp.
(full credit to canadianer for finding the Brandizzi paper)

Here's a paper that actually measures C. sativus: http://link.springer.com/article/10.1007%2FBF00985356 They got around 11.3 pg and 3.45 Gb

3.45 Gb is apparently for the haploid genome, by the way.

Yep, you nailed this question. Why not put it as an actual answer instead of commenting on my, less awesome, answer? I feel like I should actually delete mine now.

Haha well when I first read it the numbers were so close that I thought it was just confirming your estimate. I can post an answer later if I get time, but feel free to edit yours.


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Why do endotherms need more food than ectotherms?
I have a rough idea: endotherms need more food to keep their temperature stable whilst ectotherms use less of their food in respiration.

but that's just me parroting the textbook I don't really understand it.

Could someone help out? Thank you.

That's basically right.

Endotherms also called warm blooded animals have the ability to regulate their body temperature by themselves.

If the endotherms are in a cold place their body increases the metabolism and generates more heat. This will compensate for the cold outside.
In a hot region the body metabolism is tuned down (this is not as efficient as the adaptation to cold region - as the metabolism can't be turned down below a certain limit - this will result in death) a little and heat generation is somewhat reduced. The second and more efficient mechanism is the heat dissipation by sweating and through skin (directly).

Ectotherms on the other hand, do not have efficient temperature regulation systems.

In warm regions when the temperature is high, the ectotherms seek shade and low-temperature areas to prevent over-heating
In cool regions they seek sunlight and expose themselves to the sunlight for warmth. For the same reason, they can also search out and stay near fire pits, campfires etc...

So when we calculate the energy demands, the ectotherms need more energy as they regulate their own metabolisms to match the need.
The increase in need for energy in hot condition maybe due to:

The extra-processes that are regulated like sweating, increased peripheral vasodilation - thereby increasing circulatory rate (increased work for heart)
This thermo-regulation inturn affects other processes and systems like electrolyte and water balance, excretory system, endocrine system, thrist, etc...

During the cold season increased metabolism itself is the main cause for increased need for energy.

At least in cold temperature elevated demand of food fulfils the law of conservation of energy. To raise the body core temperature requires energy, which has to be taken from anywhere. Apart from depots of fat or glycogen the premier source of energy is food. Homeothermy also has advantages, however, since homeothermic animals are able to move, hunt etc. in conditions, where poikilothermic animals are massively restricted by torpor or staying at shady places.

An ectotherm is an [cold-blooded] organism which is dependent on external sources of body heat. They do not need to regularly consume food to warm their bodies. As a result, they can subsist on lower metabolic rates and varying internal temperatures (poikilothermy). However, physical activity is restricted to certain hours (night) and or habitats; ectotherms tend to be rapidly exhausted.
An endotherm is an [warm-blooded] organism which is dependent on the interal generation of heat. To maintain consistent temperatures (homeothermy), they must regularly consume food for metabolism. This also allows for a greater work capacity than ectotherms. Physical activity is not limited to certain hours and or habitats.

Here's a (hopefully) simple answer:
Ectotherms eat, and convert most of the energy in their food into new biomass (i.e. producing more tissue and growing). Between meals their metabolism (all the reactions in all their cells) slows right down so they don't use much energy.
Endotherms eat, and convert most of the energy in their food into generating heat, converting a small amount into new biomass. So they need to consume more, as generating heat all the time takes loads of energy, even when resting between meals!
Hope that helps, along with the previous answers.

Ben - can you add some links to your answer or other references so others who are less familiar follow your answer? It would help strengthen your answer significantly - thanks for your contributions.


text:
How does estrogen influence collagen synthesis?
Through what mechanisms does estrogen interact with collagen synthesis? Especially in the context of elevated estrogen levels and genesis of purpura simplex .

Questions that show no research are generally not well received in this site (they may be closed as homework). Please see here for help. The moderators are strict about effort put into research before asking a question. So please include what you found in your search for the answer in the post to get good answers.

You should look this up yourself, this is basically asking someone to do a very specific piece of reading and interpret it for you... unless you can provide some of the background info and point out points you don't understand or are interesting for discussion.

Is this a homework question?

this is a very vague question - but one that is easily addressable if you go to http://www.ncbi.nlm.nih.gov/pubmed and search for estrogen and collagen. There are numerous effects that aging and estrogens have on collagen synthesis and metabolism.


text:
What is overdiagnosis?
What is overdiagnosis ?
I have searched this Wiki result but didn't understood at all.
Can you please explain the first two line of Wikipedia :

Overdiagnosis is the diagnosis of "disease" that will never cause symptoms or death during a patient's lifetime. Overdiagnosis is a side effect of screening for early forms of disease.

Also

What is over treatment ?
Are overdiagnosis and over treatment same or different ?

@dustin, You can't ping a person if the person is not involved anywhere in the question/comments. You must ping Anne somewhere where she has either answered or commented

There is a good video of a conference dealing with this issue. Take a look if you are interested.

Overdiagnosis and overtreatment are intertwined. There is debate about how to best describe the problem, but narrowly defined, overdiagnosis occurs when increasingly sensitive tests - or changing definitions - identify abnormalities that are minor, non-progressive, or likely to resolve on their own, and that, if left untreated, will not cause symptoms or shorten an individual's life. Having a diagnosis makes well-persons think they're ill (overdiagnosis). If they are then treated for this diagnosis, they are overtreated.
An example involving changing definitions pertains to diabetes. When the official definition of diabetes changed from having a fasting blood sugar (FBS) of "X" or greater to an FBS of "X-y" or greater, 1.6 million new diabetics were instantly diagnosed, some of whom are not likely to develop symptoms and complications and are not likely to benefit from treatment. This is overdiagnosis.
If one goes on to put such a patient (let's say, on the lower end, "X-y+1" on a blood sugar (BS) lowering agent, and they pass out because their BS drops too low, then they are overtreated. If they happened to be driving when they pass out, and get into a fatal accident, they literally die from overtreatment, if it can't be shown that they would have suffered from a marginally elevated FBS. (If it can be shown to be dangerous to have an FBS of X-y+1, then this is a risk of treatment, not overtreatment.)
For an example of increased sensitivity of tests, say a new test is available, a blood test called a "D-dimer", which will reveal with 100% accuracy the presence of a dangerous pulmonary embolism (it's very sensitive). However, it is also known to be positive when there is no pulmonary embolism as well, but it's not known how often (so it's not specific). But it's an exciting new test!
A patient goes into the Emergency room for one of the following: atypical chest pain, dizziness, shortness of breath, leg pain consistent with a blood clot in the calf, or loss of consciousness. In addition to an EKG, chest x-ray (CXR) and a few other tests, a D-dimer is ordered. The EKG, CXR and other tests are negative, but the D-Dimer is positive. The tentative diagnosis is pulmonary embolism (PE).
Because the D-dimer indicates that a dangerous condition may be present, a spiral CAT Scan with contrast is ordered on all those people. Some will have a life-threatening PE (appropriately diagnosed*). A large number will have a negative CAT Scan. (diagnosis excluded) But a significant number will have a very small PE. Because this is relatively new and surprising, and it's not known whether they should be treated (maybe nothing will happen if they don't treat? Maybe this happens in normal people and we just never knew it?), the doctors, who are accustomed to treating all PE's will put the patients on blood thinners. This is overdiagnosis of PE, and treating it is overtreatment, because some treated people will have "bleeds" - a stroke, GI bleeding, other. It is now known that these tiny PE's are often seen in patients who suffer no harm at all from them, therefore in order to stem overdiagnosis (and subsequent overtreatment), the D-dimer test is ordered less frequently.

...[We] are in the midst of an epidemic of diagnosis. Conventional wisdom tells us that finding problems early saves lives because we have the opportunity to fix the problems early. [Conventional wisdom tells us that} There is no risk in finding things early. The truth is that early diagnosis is a double-edged sword; while it has the potential to help some, it has a potential to harm us. Such overdiagnosis leads to overtreatment when these “pseudo-diseases” are conventionally managed and treated as if they were real abnormalities; because these findings have a benign prognosis, treatment can only do harm.

Overdiagnosed: Making People Sick in the Pursuit of Health
Overdiagnosis
Using Evidence to Combat Overdiagnosis and Overtreatment: Evaluating Treatments, Tests, and Disease Definitions in the Time of Too Much

Are all overtreatments due to overdiagnosis? If yes, please mention it explicitly. If no, please make a distinction.

As with most things, it depends on your definition. If you define overtreatment as the result of overdiagnosis, as most do, then yes. If someone treats a medical condition which needs to be treated, but with more medicine than needed to control it, that is considered overaggressive treatment. If you define overaggressive at overtreatment (which confuses the issue which is very much discussed and written about), then you're correct. But in light of the issue, I would avoid that definition.

Thanks for clarifying. But overaggressive treatment is generally not considered overtreatment? Or is the definition not properly set yet (meaning no standard definition?)

Screening is the process of testing the population enmasse to check for the presence of risk factors for a disease or to detect the early form of a disease.

Usually the tests that are used in screening are not highly effective in excluding people who do not have the disease (low negative predictive value). Instead the goal of screening is to identify as many people as possible (high positive predictive value) who may have "the disease" which is being screened.
When screening for early form of disease, people who may never develop the disease in their lifetimes are also detected and they may be treated without the actual need. In such cases the treatment will result in more harm than the disease itself.

Usually after screening, people who are recognised to have the risk factors are subjected to further confirmatory tests which will then exclude the people who do not have the disease.
Overdiagnosis is said to be done when a lot of people who don't have the disease at the present time are treated for the disease just because they have the risk factors for getting the disease or have the early form.
Overtreatment is not the same as overdiagnosis. Overtreatment refers to treating a disease more vigorously than warranted. The main difference is that in overtreatment, the treatment is provided for even correctly diagnosed disease but excessively. This may include unneeded medical procedures, injections etc...
For example getting antibiotics for a common cold (with just running nose) which has lasted for less than one week may be considered overtreatment.
Overdiagnosis may lead to overtreatment. However all overtreatment is not due to overdiagnosis.
Edit:
I have edited the answer thanks to anongoodnurse.

An X-ray is not a treatment. It can't be included with overtreatment, nor is a chest ray alone without findings ever part of overdiagnosis. That would be a negative CXR. Treating a newly diagnosed disease in it's early form may be very beneficial, e.g. with Multiple Sclerosis. That is not overdiagnosis or overtreatment. You've got a few things confused here. I don't know if this is because you over-rely on Wikipedia or not, but I think it may have something to do with it.

I have written nothing about chest xray and overdiagnosis. Are not redundant medical procedures considered overtreatment? Now that you said that unnecessary diagnostic procedures can't be considered overtreatment - what would they be called? (I am genuinely interested in knowing and not asking for the sake of arguement (which seem to set the tone between us in most of our conversations! Lol)) @anongoodnurse

"For example getting a X-ray for a common cold which has lasted for less than one week may be considered overtreatment." I assumed you meant a CXR? What other XRay is commonly obtained for a URI?

Yes, I meant chest x-ray but I did not mean that it was overdiagnosis. I did not mean to say that getting a chest x-ray was overdiagnosis. Just that it is unwarranted in such a case therefore unnecessary medical procedure - which (I thought) was overtreatment @anongoodnurse - This idea was corrected thanks to you. But I am interested in knowing what you call such unnecessary medical procedures


text:
Where do the phosphate units come from when EGF units dimerize?
Upon EGF binding, EGFR units dimerize and cross-phosphorylate. The phosphate groups are transfered to intracellular c-terminal tyrosine rich regions. Where do the phosphate units come from in this cross-reaction? Is it from bound GTP units?

In protein phosphorylation, the phosphate group transferred from the kinase to the substrate comes almost universally from ATP. However, there is evidence of some protein kinases using GTP as their phosphate source, although they are few and far between.

I see, so it's similar to the insulin receptor.

@TMOTTM yes, and just about every other kinase out there, with the exception of CamKII, which I mentioned, and possibly some others. You can pretty safely generalize and say that the phosphate group in protein phosphorylation reactions comes from ATP.

Ok. Except for the GTP used by G-proteins.


text:
What are senescent cells doing in our bodies?
I'm reading a paper that mentioned the elimination of senescent cells delays aging. I'd like to receive more information about it.
The Baker study published in Nature demonstrates that targeted elimination of senescent cells in mice results in remarkable protection from several age-related pathologies, cancer, and makes cancer cells resistant to chemotherapy. I know that senescent cells drive aging, and induce cancer. Can we grow them in cell culture as a kind of stem cells ? How might they contribute to the aging process ?

Welcome to Biology. Could you provide a source for this claim? Also, have you done any research on this topic, such as performing a simple Google search for "senescent cells", reading the Wikipedia page, or clicking on the [senescence] tag in your question and reading some of the linked questions? If not, please do so, then [edit] your question to include what you know so far, and what specifically you still have questions about. Otherwise, this post may be closed as "homework."

@MattDMo Did you actually review this one? I'm asking because it isn't in queue, and I thought it would be.

@L.B. nope, I just saw it appear on the main page

Hi,my question is the senescent cells is kind of aging cells? What are the similarities and differences between them?

Voted to re-open. Although there are some misconceptions here this question is well within the realms of an overview answer of our current knowledge, in my opinion.

Edited the question, prepared a comprehensive answer.

@MattDMo I know that was a strange question on my part... I was just confused! Thanks!

Sorry for not being more specific. I would like to further clarify my question by stating that cells reach senescent state after prolonged cell stress caused by DNA damage.The study published in Aging Cell indicates that senescent cells are seen with increased frequency in premature aging skin and are thought to cause age-related dermal thinning thus, accelerate aging of the skin. I'd like to know are both terms (cell aging and cell senescence) the same? Is a senescent cell an aged cell? If a young cell undergo a stress or damage can be induce senescence? Thank you .

@Microbiologist please include a direct link to the paper you are asking about (PubMed, DOI, etc.) so that we can answer your specific questions. "The Baker study published in Nature" is not very helpful...

Senescent cells are cells that go into permanent cell cycle arrest. Although they may be metabolically active, they are not actively dividing. This may occur when cells in our bodies undergo damage from an extraneous or endogenous source. I understand that its role in cancer and aging is a great topic of study.

this is a rather incomplete answer, and could easily skew a newcomer's viewpoint. Many, if not most of the cells in the body are senescent, and will never divide again. However, they is programmed to do this, it is not as a result of damage.


text:
How to characterise a protein family in a putative genome island?
We have sequenced the genome of 200 bacterial strains belonging to the same species, a swine bacterial pathogen. In a previous work, it was observed that a protein family of adhesins is present in some of these strains. Each strain has multiple copies separated in their genome. Genetic differences have been observed among the DNA sequence in the different strains. Since some mobile genetic elements are present near these genes, it is possible that they are playing a role in the molecular evolution of this protein family.
How could I add additional evidences that this is a putative genomic island?
Some references would be also appreciated.
Thanks
UPDATE: For each strain, I thought about extracting the genomic region were these genes are located, maybe 8 Kb up- and down-stream of the gene. Then, running a miriad of tools to try to predict some of these island-associated elements. However, assuming that these "sequence-based" tools need the entire genome sequence, is it possible that I run them using the whole genome sequence and then focus on certain selected genomic regions?

Check this. You might find tools you are looking for. For second question, you can do cheap trick by just separate your area of interest from your whole genome and then feed that sequence as single genome into tool again.


text:
Why can't there be fructification of mycelium in submerged culture?
I am very new at this. I am wondering why fed batch cultures produce a lot of mycelia but no fruit. I thought the more mycelia you had, the greater chance of it forming a fruit body.
I am refering to this paper http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3768415/ but there are many others with the same methodology. It seems to oppose fruit  body production to submerged cultures.
It seems to be submerged in water and in sugar.
It also seems you can have fruit bodies with a single mating type :
- Coprinus sterquilinus (The Fungi by Sharma)
- A bisporus and V volvacea (Chang Chiu)

Can you provide some more background to your question? What species are you working with, for what purpose, and exactly what do you mean with "submerged culture" (grown in water?)? In general, fungi produce fruit bodies (Sporocarps) after hapliod hyphae of different mating types have fused, and environmental conditions are also important. If your culture only  includes one mating type/batch culture, this could be a reason why you do not see any fruit bodies.

Do you have a reference on what those environmental conditions are ?

Can be all sorts of things, and depends completely on the species. Note that many species produce fruit bodies during a particular time of the year (in seasonal environments), which can give you some clue. Can you back up your last statement (fruit body from a single mating type)?

I think it's a paper by Ohta but let me check

Great. It might occur, but should be an exception from what I know. Sex in fungi is complicated though, and not my area at all.


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Why aren't green eyes more prevalent?
Why aren't green eyes more prevalent, given that the green allele is dominant over the blue one?
My understanding is that human eye colour is determined by two genes:
1) HERC2, with alleles Bx, BB or xx,
2) gey, with alleles GG, Gb or bb,
where

B means brown
x means not brown (this is less confusing than using b for blue here, because having no B allele in HERC2 doesn't necessarily give someone blue eyes; their eyes will be either blue or green depending on the gey gene)
G means green
b means blue.

Capital letters stand for alleles that are dominant; lower case, ones that are recessive.
So the 'algorithm' goes:

1) look at HERC2; if it's anything other than xx, you've got BROWN eyes
2) if HERC2 is xx, look at gey; if it's anything other than bb, you've got GREEN eyes
3) still here? then you've got BLUE eyes

My question is this: why is it that green eyes are so rare if the green allele is dominant over the blue one? When a blue-eyed person and a green-eyed person interbreed, their offspring will either be equally likely to have green eyes as blue (if the green-eyed parent is Gb) or always have green (if that parent is GG).
But many more people have blue eyes than green eyes, despite blue being recessive to green.
The obvious answer is that people with blue eyes (xx bb) and people with green eyes (other xx-ers) have tended to avoid breeding with each other to a large extent. Is any other explanation in the ring? Perhaps the greens are catching up?

The gene which is important for the eye color is actually OCA2. In HERC2 is a regulatory region located which regulates the OCA2 expression. And there is a polymorphism which affects this.

Thanks @Chris. Will the question I'm trying to ask be more accurate if I (or you) amend HERC2 to OCA2? (That said, if HERC2 regulates the OCA2 expression, then HERC2 must be important for eye colour.)

No, it's not HERC2 that regulates OCA2, it is a regulatory region which is located inside the HERC2 gene.

@Chris - Part of HERC2, then? If the question needs correcting, please do correct it.

It's not correct that human eye colour is determined by two genes. Eye color is a polygenic trait. See for example (Sulem,..., Stefansson, 2007).

A gene being dominant does not necessarily imply the gene is also common.
An easy counterexample is Huntington's disease. The gene is dominant, and only one mutant allele of huntingtin would result in development of the disease. However, the allele prevalence of the mutant is low in the general population.
In the absence of a selective advantage of green eyes over blue eyes, the two alleles of the gey gene should remain in genetic equilibrium, and therefore the number of people with green eyes will not increase. In fact, a similar misunderstanding applies to the disappearance of blondes/redheads. In both cases, the allele frequencies will remain unchanged in the absence of selection pressure.
The initial imbalance in the allele frequency could be due to many reasons. Population bottlenecks, genetic drift, and historical selection pressure could all be valid answers.


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How can Valonia ventricosa cells get so big?
Valonia ventricosa are single-celled algae that range between one and few centimetres. In rare cases, they can reach sizes exceeding 5cm. They range from grass-green to dark green, and some are even a blackish colour.

Weirdly, a lot of the literature covering these organisms seems to be pre-1950. This X-ray crystallography project in 1937 identified key structures in the cell wall of V. ventricosa:

It is found to consist of layers in which the cellulose chains in any
one layer are inclined to those in the preceding and subsequent layers
at an angle which is on the average rather less than a right angle.
The two sets of striations on the layers of the wall correspond closely to the
meridian and spiral directions of cellulose chains, while the
extinction directions, being defined both by the directions and by the
relative proportions of the two sets of cellulose chains, lie in
variable positions between. The development of the rhizoids has been
investigated and found to be associated with regions of the wall
adjacent to the poles of the spiral.

Although the authors hesitate to speculate on their function, has any progress in the field suggested the fibres identified in this 1948 Nature paper be involved in sustaining such a massive cell (Figure below)?

So it seems like the cell wall structure has been categorised long ago. But what allows these single-celled organisms to get so big? Is it the plant-like cell wall, or something else? I was under the impression that cells would burst or collapse well before reaching this size.

the problem is diffusion: 1) maybe cytoplasmic streaming via cytoskeleton? You'd need to somehow add bulk flow in order to correct for the limits of diffusion. 2) Also I'm guessing an immensely large vacuole in the center, thus keeping the layer of cytoplasm really thin in order to permit diffusion to be the dominant form of transport... all guesses here... I'm too lazy to actually read about this algae...

From what I could find, it seems like people aren't interested in publishing things about why its big. http://jmicro.oxfordjournals.org/content/early/2014/01/23/jmicro.dft083.full Is the most recent relevent paper I can find and again, it just discusses the cell surface strcture as analagous to plants. Nothing about how it aids the cell to achieve such sizes.

weird gaps in the literature... perhaps to motivate you to find your own and examine it under the microscope...

Its a bit expensive for me to get to a reef where these things grow :P But also it seems like thats all anyone has done and it doesn't tell them much. They have used crystallography, electron microscopy, atomic microscopy etc. From what I can tell all they have learned is that it looks pretty normal for an algae. My guess is that there needs to be something special in the cytoskeletal structure, but hopefully a specialist will come along and tell me why thats a silly idea!

Ventricaria ventricosa (previously called Valonia ventricosa) is not exactly a single cell. It has a coenocytic structure with multiple nuclei and chloroplasts. As Jasand Pruski correctly guessed the organism possesses a large central vacuole which is multilobular in structure (lobules radiating from a central spheroid region).
The entire cell contains several "cytoplasmic domains" with each domain having a nucleus and a few chloroplasts (See the figure below). Cytoplasmic domains are interconnected by cytoplasmic "bridges" that are supported by microtubules (like in axons). The peripheral cytoplasm (whose membrane is overlaid by the cell wall), is only about 40nm thick.

Fluorescent confocal micrograph of a cytoplasmic domain. From Shepherd et al. (2004) Protoplasma 223: 79–91. Here, n is nucleus c is chloroplast and v is vacuole.

So these are not huge cellular balloons that can burst easily. Nonetheless a huge structure like this is susceptible to injuries by shearing forces of water currents and by other organisms like fish which may try to feed on them. These organisms have some mechanisms other than the cytoplasmic organization that allows them to cope up with injuries:

When the outer membrane ruptures, then the cytoplasm contracts with the help of actin filaments that are attached to the former. Subsequently the membrane fuses, protoplasts form and then cell wall is regenerated. This movement is likely to be triggered by extracellular calcium.
A single cytoplasmic domain with nucleus and other essential organelles can regenerate an entire organism.
A muclilagenous layer made up of sulphated polysaccharides coats both the vacuolar and extracellular surfaces. During injury it impedes the movement of water and ions (by retaining them in the form of a gel) and therefore acts like a plug.

Other organisms like this (siphonous algae) also have similar mechanisms. Some even employ calcium carbonate to maintain rigidity.
REFERENCES:

Shepherd et al. (2004) Protoplasma 223: 79–91
Menzel (1988) Protoplasma 144: 73-91

Ah, fascinating! I'm familiar with coenocytic in terms of fungal hyphae structures. I'm still impressed at the shape of it, most of these other structures are still thin in one plane or another. Just to clarify anecdotally, these organisms are "solid" like a golf ball rather than hollow like a football?
I also read that crabs like to munch on them!

@GoodGravy They are not really solid because there is a central cavity i.e. the vacuole. See figure 2b-e in the first paper. From the optical sections it seems that the "cellular zone" is ~7µm thick. So they are indeed like footballs, with an outer layer (cell wall) the bladder with a central cavity. However unlike the bladder the cellular layer is relatively thicker and organized.

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


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Zinc and brewer's yeast
I'm hoping for some information relating to yeast nutrition (specifically Saccharomyces cerevisea) in beer fermentation.
Zinc is well-known to be necessary for yeast cultures to perform successful fermentations and since fermentable sugars derived from barley are often deficient in zinc, they are sometimes fortified with additions of zinc sulfate or zinc chloride. This guy tried zinc gluconate, a readily available dietary supplement for the same purpose, and found it to have very little, if any, positive effect on fermentation performance. As he even suggests at the end of his paper, could this be because yeast can't assimilate Zn from this molecule the same way it does from the other two?
Is this question better directed towards Chemistry SE?
Thanks in advance for any help I can get on this.

You can ask this question in homebrew.stackexchange.com

Thanks, I actually came here from the HBSE to ask this question.


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I photographed a couple of butterflies and birds in Argentina but can't identify them. What are my options?
I photographed a couple of birds and butterflies in Argentina and tried to identify them. I tried online species identification tools, looked in books, and just tried to find pictures on Google with similar animals. This worked for some of the pictures, but for others I couldn't find the correct species. So as a layman, what options do I have?
Here are the ones that I couldn't identify so far
1 (There seems to be a bird and a beetle in this picture. The bird could be a Thraupis Episcopus)

2 (A hummingbird but which one?)

3 (Seems to be the same hummingbird)

4 (No idea)

5 (No idea)

6 (No idea)

7 (No idea)

8 (No idea)

What most people do to identify is, well, Google "Birds (or butterflies) of Argentina" and narrow down the categories by beak type, tail type, etc. I know you have a dove, a hummingbird (should be easy), what I believe is a vulture, and one of the most common of parrots. That should start you off.

To 1: I am not quite sure if this is a beetle. It could be a piece of banana that was stuck to the tree. possibly to attract birds. Something black is sticking out of it close to the "center". And the bird also has this "don't touch my food"-look.

Each of these would probably be a good question by itself, but asking for 8 separate identifications is too broad for a single question. I think this should be broken apart into separate questions.

First, I think it is more useful to post separate questions, at least for each taxonomic group (birds, butterflies etc). To make a question a dumping ground for all sorts of species determination pictures is a bad idea.
That said, the butterflies seem to belong to the families Nymphalidae,  (nr 5) and Papilionidae (Swallowtails) (nr 7), judged by overall apperance. I'm not directly familiar with South American butterflies, but two likely species are:
Doxocopa agathina (Nr 5), or related species in the Doxocopa genus.

(from wikipedia commons)
Papilio thoas (Nr 7)
This is the King Swallowtail, your specimen probably of the subspecies P. t. brasiliensis which is found in Argentina. Sometimes the name Heraclides thoas is used. Pictures of subspecies can be found here: Butterflycorner.net. Your speciemen have lost the tail appendages (could be due to wear-and-tear or bird attacks). A related similar species is Papilio astyalus, which is also found in Argentina (pictures), but it usually has a broader yellow band.

(from wikipedia commons)
The bird in nr. 6 looks like a Black vulture (Coragyps atratus).

To answer your question as written, the best option I have for species ID is still to post to fora (such as this one), where experts (or interested amateurs like myself) can manually identify them. Computer identification, although much better nowadays, is still some way away from being able to recognise all species.
4 looks very much like a Mourning Dove Zenaida macroura, although its range seems to be limited to North America.
Going up its taxonomy I found the Eared Dove Zenaida auriculata which does live in Argentina.

8 looks like a collection of macaws, with the Blue and yellow macaw and the Scarlet macaw being visible.


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What is Trypsin?
I am currently helping a PhD student in his research lab. We have been using Trypsin for the past couple of weeks but I am unsure of its purpose.
I was wondering how Trypsin functioned and what it was usually used for?
The Trypsin we had been using apparently had "gone bad" and therefore we have to start the experiment over again. What could have caused it to not function properly?

Welcome to Biology S.E.! If you have additional questions, please visit The Help Center

How do you know that Trypsin has gone bad, when you don't understand it's function in the protocol (no pun intended)?

@Chris You know because the grad student tells you after his cell cultures stop working right.

@user137 This can be one of the reasons.

I don't see how "bad trypsin" will spoil a cell culture. The only step that trypsin is used in cell culture is for detaching cells from the cell plate/flask, and if the trypsin is not working, the cells will simply not detach, and you will just either add more trypsin or use a different batch of trypsin.

Trypsin is a protease, an enzyme that cuts other proteins. It is used in cell culture to help lift cells from a plate by cutting the proteins that hold the cells to the plate and to each other. Trypsin can go bad because a trypsin enzyme can cut other trypsins, eventually destroying the batch's enzyme activity. This is why trypsin must be kept frozen. Of course you have to thaw it out to use it, so it's best to split the trypsin stock into small aliquots, so you don't have to thaw out the whole bottle everytime you split your cells.


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Expression/Mechanism of ROR1 in healthy tissue
ROR1 is currently under investigation as a therapeutic target for cancer (1). A number of studies show different cancers may have their metastatic potential reduced, or become apoptotic through targeting or abrogation of ROR1 (1-3). ROR1 itself is show to have a number interactions (either through crosstalk or interaction) with some known tumorigenic markers; these include c-Met, PI3K, Akt, Wnt5a, EGF, c-Src (4-7). In terms of metastatic potential, interactions with vimentin, Snail/Slug, cadherins, ß-catenin, and CXCR4/CXCL12 were also identified (1, 8). Some of these are via expression of CREB. In terms of ROR1 is tissue, abnormalities that lead to death were noted in newborn mice that has ROR1 knocked down (9). A notable mechanism for ROR1 in development was in neuroprogenitor cells in which ROR1 regulation status determined whether these cells differentiated into neurons or not (10). It's also found that neural, heart, lung and kidney tissue in adults express some form or another of ROR1 (11). More recent studies suggest ROR1 downmodulation may present toxicity for some subsets of normal tissues (12).
The question, now: Are there any empirical studies that illuminate the potential mechanism of ROR1 in healthy, adult tissues? This is from a treatment toxicity standpoint, since the subsets of affected cells seem to be rather slim. I can understand why the effect on metastatic potential can be significant from the fetal neural cortex development (the need to migrate the neurons into position). We also see a truncated version of ROR1 in some instances. If anyone can shed some light, thank you in advance!
References

Cui B. et al. Targeting ROR1 inhibits epithelial-mesenchymal transition and metastasis.      Cancer. Res. 73, 3649–3660 (2012).
Hojjat-Farsangi, M., Ghaemimanesh, F., Daneshmanesh, A. H., Bayat, A. A., Mahmoudian, J., Jeddi-Tehrani, M., … Mellstedt, H. (2013). Inhibition of the Receptor Tyrosine Kinase ROR1 by Anti-ROR1 Monoclonal Antibodies and siRNA Induced Apoptosis of Melanoma Cells. PLoS ONE, 8. doi:10.1371/journal.pone.0061167
Daneshmanesh AH, Hojjat-Farsangi M, Sandin A, Khan AS, Moshfegh A, et al.. (2012) Monoclonal Antibody Against ROR1 In Chronic Lymphocytic Leukemia Cells Induced Apoptosis Via PI3-kinase/AKT/CREB pathway. 54th American Society of hematology (ASH), Atlanta, USA, 8–11 December.
T. Yamaguchi, K. Yanagisawa, R. Sugiyama, Y. Hosono, Y. Shimada, C. Arima, S. Kato, S. Tomida, M. Suzuki, H. Osada, T. Takahashi. NKX2-1/TITF1/TTF-1-induced ROR1 is required to sustain EGFR survival signaling in lung adenocarcinoma. Cancer Cell, 21 (2012), pp. 348–361
Fukuda T, Chen L, Endo T, Tang L, Lu D, Castro JE, Widhopf GF, II, Rassenti LZ, Cantwell MJ, Prussak CE, et al. Antisera induced by infusions of autologous Ad-CD154-leukemia B cells identify ROR1 as an oncofetal antigen and receptor for Wnt5a. Proc Natl Acad Sci USA. 2008;105:3047–3052. doi: 10.1073/pnas.0712148105.
Gentile A, Lazzari L, Benvenuti S, Trusolino L, Comoglio PM. Ror1 is a pseudokinase that is crucial for Met-driven tumorigenesis. Cancer Res 2011;71:3132–41.
Zhang S, Chen L, Cui B, Chuang HY, Yu J, Wang-Rodriguez J, et al. ROR1 is expressed in human breast cancer and associated with enhanced tumor-cell growth. PLoS ONE 2012;7:e31127.
Teicher BA, Fricker SP. CXCL12 (SDF-1)/CXCR4 pathway in cancer. Clin CancerRes. 2010;16(11):2927-31.
Nomi M, Oishi I, Kani S, Suzuki H, Matsuda T, Yoda A, et al. Loss of mRor1 enhances the heart and skeletal abnormalities in mRor2-deficient mice: redundant and pleiotropic functions of mRor1 and mRor2 receptor tyrosine kinases. Mol Cell Biol 2001;21:8329–35.
Endo M, Doi R, Nishita M, Minami Y. Ror family receptor tyrosine kinases regulate the maintenance of neural progenitor cells in the developing neocortex. J Cell Sci 2012;125:2017–29.
Reddy UR, Phatak S, Pleasure D. Human neural tissues express a truncated Ror1 receptor tyrosine kinase, lacking both extracellular and transmembrane domains. Oncogene 1996;13:1555–9.
Linked in text.

ROR1 knockout mice are unhealthy and die soon. ROR1 knockdown leads to shortened neurites but I guess this should not affect adults much. From this paper: … it is absent within most mature tissues. A low level of ROR1 expression is seen in adipose tissue and to a lesser degree in the pancreas, lung, and a subset of intermediate B cells

Examining the literature it'd seem that the ROR pathways incl. ROR1 and ROR2 are critical for developing tissues in the majority of cases. We also see relevance in the expression of ROR1/2, more specifically ROR2, in cases where taxic cell types are required to migrate, branch, etc. Most of the literature determines much of this occurs through a noncanonical Wnt signaling pathway.
Wnt5a–Ror–Dishevelled signaling constitutes a core developmental pathway that controls tissue morphogenesis
Ror2 Receptor Mediates Wnt11 Ligand Signaling and Affects Convergence and Extension Movements in Zebrafish
Ror2 regulates branching, differentiation, and actin-cytoskeletal dynamics within the mammary epithelium
Notwithstanding the abnormalities we see in neonates with knocked down ROR, is it wrong to assume we'd see developmental defects of branching tissues in developing (or juvenile) organisms such as lung, mammary, neural, glandular tissue, etc.? Some data in that respect would be interesting, but it's also illuminating given the presence of ROR in cancer metastasis and EMT events.


text:
How and why can cold inflict pain?
I was carrying a can of very cold liquid, had something heavy in my other hand so couldn't switch hands. After a few minutes, I started to feel very intense pain. I was very surprised. cold is just atoms moving slower. This makes more sense if you think about how heat, or burns can cause pain. But heat can cook tissue and disable it, it makes sense it would hurt.

What about frostbite? Did you read anything about injuries from the cold? What can you add to your question so that it isn't so broad?

also read about nociception. Extreme cold can activate pain pathways

I think your getting confused. Your assuming that it's actually the heat or cold that creates the feelings of pain.

I was very surprised. cold is just atoms moving slower.

Pain is a warning mechanism, stop doing that or you'll hurt yourself. It is not caused by the atoms in your nerves moving faster or slower in response to heat. Your nerves are triggered by a stimulus that could cause harm to your body and react by passing a pain signal to your nervous system. The heat (or lack of it) does not transmit up your nerves.

You could emphasise that its the lack of heat that causes pain.

One mechanism through which low temperatures cause pain is through vasoconstriction.
Cold environment causes constriction of blood vessels in the periphery. This will cause decreased blood flow and the muscles will cramp due to lack of oxygen. The cramping is due to the accumulation of lactic acid (due to activation of anaerobic pathways of metabolism) and carbon dioxide. Both these chemicals will lower the pH which cause pain.


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Why is iodine used for metabolic hormones?
Iodine and related biological iodine-carrying hormones are phylogenetically very old, at least according to Wikipedia. Humans use iodine as a metabolic indicator, as do axolotls and apparently most multicellular life.
So why? Growth hormones, sex hormones, et cetera don't require strange heavy elements not used for anything else. It's not a requirement of transcription factors that they contain iodine.
All I've got for hints is that selenium forms an essential part of deiodinases, as well as forming an essential part of thioredoxin reductase. Thioredoxin is a component used to reduce things around the cell, like thiols and RNA bits and so on and so forth, which I could see being worth the evolutionary cost of running down some selenium.
What's the point of iodine? People have iodine deficiency 'all the time' (it's common enough to be named). Is that a product of agriculture somehow? Are there any advantages to using iodine for metabolic hormones? If there are, what are they?

It's an interesting question, though I'm not sure it's answerable. This may be vaguely insightful (I have only read the abstract): http://www.ncbi.nlm.nih.gov/m/pubmed/7381861/?i=2&from=/684433/related

It may not be correct to say that iodine is a requirement of metabolic hormones; I imagine that the evolution of another system is entirely feasible. Perhaps it's a remnant of some species that had access to excess iodine, which provided a mechanism to easily create a different tyrosine-derived hormone to fill some niche.

There are two possiblities. Either iodine is useful in its own right in some way, or lack of iodine is not a concern. I don't know enough about iodine metabolism, excretion etc to know if iodine deficiency is even a thing in nonhuman animals. If it's not a thing, what is it about humans that makes them susceptible? Is it agriculture or something?

Thyroid hormone functions generally require they bind to specific receptor proteins, and some of these receptors undergo specific conformational changes that alter activation/repression dynamics in the nucleus. Iodines might assist in that respect, esp. given Canadianer's article.
http://www.vivo.colostate.edu/hbooks/pathphys/endocrine/thyroid/receptors.html

The specific receptor proteins are tuned to recognize thyroid hormones containing iodine, yes. Most transcription factors don't require a rare trace element, and there's a distinct fitness cost to it(at least in modern humans). So what's the payoff? Why do most multicellular organisms use such a specific and rare element? HGH, leptin, ghrelin, etcetera all don't require iodine. Other evolutionary solutions are possible

Interesting, but the question is too broad I think -- not all metabolic hormones contain iodine. (Insulin, glucacon, glucocorticoids, leptin are examples.) And thyroid hormones have effects on growth and development too. It would be better to phrase it specifically about thyroid hormones.

@Roland That's precisely what I mean. Not all metabolic hormones contain iodine, but some do. For some reason iodine is conserved even though it's not actually required for signaling, as demonstrated by HGH, leptin, etc. There's a drawback to using iodine(sometimes it's not there), and yet it's conserved. What's the benefit that balances out the fitness penalty of requiring iodine to grow properly?

Iodine in us
Iodine is found in two main hormones, T3 and T4. They affect every part of the body, and are important for cell-cell signaling. Wikipedia says:

The thyronines act on nearly every cell in the body. They act to increase the basal metabolic rate, affect protein synthesis, help regulate long bone growth (synergy with growth hormone) and neural maturation, and increase the body's sensitivity to catecholamines (such as adrenaline) by permissiveness. The thyroid hormones are essential to proper development and differentiation of all cells of the human body. These hormones also regulate protein, fat, and carbohydrate metabolism, affecting how human cells use energetic compounds. They also stimulate vitamin metabolism. Numerous physiological and pathological stimuli influence thyroid hormone synthesis.

Why do we have iodine in these hormones?
This is really what your question is. I have found several articles about this and what I found is Iodine is an important catalyst, and Iodotryosines evolved to be important hormones
First, of all, the use of iodine in organisms was ancient. Many prokaryotes and protists used it as a way to deal with reactive oxygen species. Iodide peroxidases were present in primitive oxygenic and photosynthetic Cyanobacteria about 3 - billion years ago. This is because Iodine is one of the most ancient antioxidants.
The thyroxine-like hormones seems to have evolved some 4 Mya in unicellular algae. However, its original function was not for cell-cell signaling as is the case for T3 and T4. It was originally to catalyze other biochemical reactions and scavaging  free radicals. This all came about when tyrosine was first created. Iodine reacts with the tyrosine, and forms iodotryosines that were important catalysts for many biochemical reactions.
The first use of Iodotryosines for regulation could have been for ATPase in the mitochondria for non-verterbrate organisms. Also, for vertebrates, the regulation of mtRNA was regulated by iodotryosines.
Iodotyrosines can diffuse between cells very easily, and the development of TH-receptors leaded to the development of thyroxine hormones. Such hormones were used first for embryological development, metamorphosis (if this is the correct term) of amphibians, and more. The rest is really evolution! These hormones are present in virtually all organisms (except prokaryotes).
Summary
In summary, the use of iodine in hormones started with iodine in the first cells as they provide protection against free radicals and reactive oxygen species, while catalyzing biochemical reactions. Iodotyrosines evolved to be important for regulation in cells and finally important in cell-cell signaling.
If you have any more questions, please ask in the comments or we can chat in the Biosphere.
References
These are my sources and there is much more information on these articles. Note that I am not chemically correct about the form of iodine used so these articles have the correct information
http://m.icb.oxfordjournals.org/content/early/2009/06/23/icb.icp053.full.pdf
http://ign.org/cm_data/2011_Venturi_Evolutionary_Significance_of_Iodine.pdf

Iodine helps balance out ROS production of metabolism, so when iodine is present, grow. That helps explain pretty much everything, I think. Nice answer.

Classical thyroid hormones implement a very flexible signaling mechanism. Basically, they comprise two aromatic rings that are connected via an oxygen atom. Optionally, they may contain organic side chains and inorganic iodine atoms.
In the case of iodothyronines, which are represented e.g. by the well-known thyroid hormones T4, T3 and 3,5-T2, the side chain contains an amino group and a carboxylate group. Therefore, iodothyronines are amino acids. Up to four different hydrogen atoms (two at every ring) may be replaced by iodine atoms, and the resulting pattern of iodination determines their biological activity. Generally, iodination of the inner ring and deiodination of the outer ring results in high biological activity (e.g. in T3 and 3,5-T2), whereas iodination of the outer ring and deiodination of the inner ring delivers a receptor-blocking thyroid hormone (e.g. reverse-T3). There are three deiodinases encoded by the DIO1, DIO2 and DIO3 genes that catalyze the "step-up" and "step-down" reactions to active or inactive thyroid hormones, respectively. Multiple molecular processes are able to differentially upregulate and downregulate tissue deiodinases. Therefore, thyroid hormones are subject to both global and local control.

Removal of the amino group results in iodothyroacetates. Their biological effects are similar to those of iodothyronines, but in addition to nuclear receptors they also have a strong effect on membrane-bound receptors, which are only weakly activated by iodothyronines.

Thyronamines lack the carboxylate group. Their biological effect is different to that of iodothyronines and iodothyroacetates. By activating the membrane-bound TAAR1 receptor they have an effect that is in most respects antagonistic to that of classical thyroid hormones. Thyronamines seem to be most active in deiodinated state.

Summarizing, both organic and anorganic modifications are able to modulate the effect of thyroid hormones. This mechanism is a very effective way to encode a high  grade of information entropy in rather small molecules.
References
Gereben B, Zavacki AM, Ribich S, Kim BW, Huang SA, Simonides WS, Zeöld A, Bianco AC. Cellular and molecular basis of deiodinase-regulated thyroid hormone signaling. Endocr Rev. 2008 Dec;29(7):898-938. doi: 10.1210/er.2008-0019. PMID: 18815314
Engler D, Burger AG. The deiodination of the iodothyronines and of their derivatives in man. Endocr Rev. 1984 Spring;5(2):151-84. PMID 6376077.
Piehl S, Hoefig CS, Scanlan TS, Köhrle J. Thyronamines--past, present, and future. Endocr Rev. 2011 Feb;32(1):64-80. doi: 10.1210/er.2009-0040. PMID 20880963.

This answer is great. It's technically complete and well-sourced. It doesn't actually answer the question I asked, but that is its only fault.

here is an interesting article:
The accumulation of radioactive iodine by Amphioxus
summarizing the abstract: it's about cephalocordates that are not vertebrate, so they are close relatives (most related to the ancestors of) the vertebrate. The specific cephalocordate in question is amphioxus.The article talks about a specific gland called the "endostyle" of Amphioxus and it explored the homology with the subpharyngeal gland of the larval form of lampreys (an agnathan, the most primitive of vertebrate) called ammocoete. The sub pharyngeal gland is sort of the same thing as the thyroid. In fact this sub pharyngeal gland or thyroid is a defining characteristic  of vertebrate. The abstract describes an experiment where they took the endostyle from amphioxus and implanted it into a salamander (and amphibian) and it had effects similar to the thyroid gland. This means that this mucous producing gland in the cephalocordates produces compounds that have effects similar to the thyroid
Why does the endostyle produce mucous? Because it is essential for their filter feeding (feeding by straining suspended matter and food particles from water).
Why concentrate iodine in the mucous, I don't know.
The other answers explain the function of iodine. This answer was to explain the evolution of iodine concentrating glands at the very beginning of our vertebrate ancestors.

Have a look at the article, I found an open source (linked above).

nice! full text definitely beats abstract...

I went back and reread this paper, and it looks like the thyroid started as a gland that secreted mucus into the gut, so any signaling molecules would have to be gut-resistant, ruling out proteins and so on. Still not sure why iodine exactly, but this has helped narrow it down for me substantially. Nice find.

yea, and just for a comparison I guess GI peptide horomones are secreted into the blood (or lymphatics?)... given high blood flow to the GI when eating the guts get some of the peptide horomone back... presumably endostyle secretions were secreted into the gut and not the blood...

you know I've never read anything about GI peptide horomones (CCK, secretin, gastrin, GLP, etc) in primitive cordates...


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What microscope/magnification would I need to observe P. Acnes bacteria?
I am currently attempting to grow a culture of P. Acnes bacteria.  Right now, my only hope in identifying colonies of the bacteria in the culture is to use a black light to find colonies that glow orange.  I am not sure whether or not this will work since nutrient agar may not provide them with something that helps them produce porphyrins.  It's also entirely possible that another form of bacteria contaminating the culture would produce the same effect.
I would like to entertain the possibility of buying a microscope for this project.  I have never owned a quality microscope(just toy ones in the past), so I don't really know what type of microscope or what magnification I'll need in order to correctly identify and observe the P. Acnes bacteria.
What would be interesting is if I could turn this into a pharmacological project; if I can verify that I have the correct bacteria(to a fair degree of certainty, anyway), I can see how the bacteria reacts to different chemicals and environments.

How a bacterium reacts to different chemicals and environments is often more useful in identification that microscopy. It's also cheaper. You may want to look into some differential/selective media and/or biochemical tests. Or just send it away for 16S sequencing.

I agree with canadianer that chemical tests are generally more useful for identification.  However, morphology does help and some staining techniques can be useful for identification (the Gram stain is the obvious one).  If you are looking for a microscope, look for a nice scope with a 100x oil-immersion objective and a 10x ocular lens (12x would be OK too). Zeiss, Nikon and Olympus are some old names that make good scopes - and there are more.


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background extraction in microscope analysis
I have taken microscope pictures for proteins in HeLa cells, in order to quantify the intensity (immunofluorescence). The proteins are both at the nuclear envelope, and in order to quantify the intensity I draw a line that goes across the whole cell,through the nucleus, and measure the intensity on that line (ImageJ). Which value should I use as background?

The area outside of the cell typically. Adjust contrast until the background black

and what about the cytoplasmic zone? (both proteins are nuclear) also, should I take an average of certain number of values?

It sounds to be in your best interest to set your analysis boundary around the cell but can you post a sample image so we can see your contrast issues

sorry but cannot upload any images. I consulted several people and I have been told to use outside cell as background as well. Thanks!


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Do people with congenital analgesia feel cold?
There are a few diseases that cause an insensitivity to pain. This question asks about the relationship between the cold and pain, which got me thinking:
Is shivering a response driven by the sensation of cold, or a response to the pain associated caused by the cold? This is easy to work out by considering people that do not experience pain.
The key here is if people with congenital analgesia (AKA CIPA, CIP) shiver then we may assume that it is the sensation of the cold, not the pain and the cold, that causes the shivering.

Do CIPA patients shiver in the cold?
Does this mean that the shivering is caused by sensation pathways or
pain pathways?

Disclaimer: I am not an anatomist and do not claim to have a working knowledge of the nervous system. Please point out any and all obvious errors in this question that might explain why this wouldn't be the case in the comments or as an answer if its a big error.

There's an awful lot on hyperthermia in CIPA individuals, but not a lot on hypothermia. My personal expectation would be a delayed reaction due to cold misperception, but an induced shivering response as core body T drops below critical values, because shivering is a motor reponse.

Thats interesting to note. I suppose hot things are more dangerous to CIPA sufferers than cold things, so thats where the research goes.

An apropos: I've read that some people who are born insensitive to pain is actually overly sensitive to cold. I read of the mother of a pain-insensitive boy who would soak him in cold water whenever he intentionally hurt himself, in an attempt to condition him to associate self-mutilation with something unpleasant

Interesting question. Here what I think (I am not an expert in congenital analgesia so take it with a grain of salt).
The pain provoked by an high temperature is mainly transmitted via the receptor TRPV1 (a Ca2+-channel nocireceptor) while cold sensation is driven by TRPM8 and possibly, for noxious cold, via TRPA1 (two similar types of Ca2+-channels). Those receptors are known as the temperature sensors. As an anecdote, TRPV1 is what give you a pungency sensation when eating spices while TRPM8/TRPA1 give you the cooling sensation from mint.
Mechanical pain is transmitted via other receptors, including TRP channels, but this is not fully understood at the molecular level.
As far as I know, the encoding of pain, and more generally physiological sensations, in the brain are also not yet fully understood but it is very likely that the pathways taken by TRPV1 differs from the one taken by TRPM8/A1 which would suggest that it is possible that CIPA individuals experience high-temperature pain and cold differently at the molecular level and therefore might respond, to some degree, to one but not the other. This also probably applies to mechanical pain vs temperature-driven pain.
I would actually not be too surprised if CIVA people shiver even if not feeling any temperature sensations. Would be interesting to have the opinion or even better the observations of experts in this field.
P.S. I know this is not a definitive answer but I have not enough reputation to comment.


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Do animals exist which have good vision, but see only grayscale?
In computer vision the color information is often discarded, as most object recognition tasks seem to work just as well on the greyscale image (even better, because there is less unnecessary information).
Do animals exist which have good vision (e.g. see sharp, many details), but only see greyscale / very limited colors?

When you say sharp and many details, this is hard to convert to zoological optometry. Cats can see fantastically clearly at night (practically as though it was daytime), but if anything is more than about 8 feet away its just a blurry motion with smells and sounds. Would you consider something like that great vision? Also, animals and grayscale eyesight always attracts myths and mistruths. If I hear one more person say dogs are colour blind...

@GoodGravy With "great vision" I wanted to make sure that I am not talking about insects / mules.

@GoodGravy - what is so upsetting about dogs being called color blind?

@ChrisStronks I actually didn't mean to write colour blind (I meant grayscale). They are colour blind when it comes to red. Dogs can however see blue and yellow. http://goo.gl/iKHaiF This is probably because they never had the selection pressure to forage berries. Practically speaking a good toy for a dog would be bright blue or bright yellow, whereas red won't really stand out on a green field. People with deuteranopia see in a similar way and its surprisingly common. Thats why you shouldn't use green and red themes for presentations (particularly a problem in graphs).

@GoodGravy - thanks for clarifying. They are color blind, in a way :)

@ChrisStronks They are categorically colour blind! But its the "Dogs see in black and white" line that isn't correct. In fact I think they see into the UV range where we don't so in some ways they see more than us (Even if it is so they can see other dog's pee)! livescience.com/43461-cats-and-dogs-see-in-ultraviolet.html

@moose: Why do you think that mules don't have good vision?  Though I've little experience with them, they seem not much different than horses, which have excellent vision.

@jamesqf Sorry, I wanted to write "moles".

Preamble & Overview.
This is a rather unsatisfying answer I'm afraid. I can't seem to find any animal that has exceptional eyesight and sees in monochrome.
Baring in mind the context of humans vs machines; machines cope better with shapes rather than colours however it generally appears that those animals which rely on exceptional eyesight to survive tend to see in colour and have other neurological systems to ease "data overload".
Animals that see in grey-scale.
Some pinnipeds (seals) see in grey-scale, but note that their survival doesn't seem to depend on visibility, and it is generally regarded as poor even in a typically healthy animal. According to SeaWorld, researchers have found blind seal mothers and pups that are otherwise perfectly healthy.
Dolphins are a similar story. It is so murky that they rely on bio-sonar. Fresh water dolphins are almost completely blind.
In fact, the more species that I have read about which have monochromatic vision, the more I see that these animals rely heavily on other senses.
Some land animals with "decent" monochromatic vision:

Lorisiformes
Bats
Raccoons
Nocturnal kinkajous

Note that these often have another much more acute sense like smell or hearing.
Surprisingly, there is also not necessarily a link between monochromatic vision and nocturnal state (there are some animals with dichromatic vision that are nocturnal, and some animals with monochromatic vision are crepuscular, or diurnal and visa versa).
From wiki:

Many species, such as all marine mammals, the owl monkey, and the Australian sea lion have monochromatic vision under normal conditions...

A trend I see is that animals that have exceptional eyesight tend to have also evolved some sort of colour differentiation.
Why not ditch the colour info to make it easier on the brain?
To bring this back to your context of machines I would say that identifying the difference between a ball, a chair, a human, and a car (the sort of things machines need to know about!) is much more dependent on shape than colour. A monochromatic person wouldn't struggle with that at all.
However in a "wild" environment telling the difference between grass and tiger stripes means that an animal with trichromatic vision may get to live another day whereas the animal with monochromatic vision might not see the tiger in time. Or spotting berries and fruit in some distant trees might mean food that would have otherwise gone unnoticed.
Those are obviously very narrow examples, but generally it seems animals always have one or more exceptional senses limited to smell, hearing, or colour vision (it would be great if someone could point out an exception to this in the comments, like touch or taste!).
You are right to hint that there is a lot of information in colour vision. Like your example with loss of colour in machines, data needs to be dumped very quickly in the human brain.
I'm not a neuroscientist, but I have read pop articles about how little we can remember with photo detail. Within seconds of looking at a scene all texture details are lost, most objects are forgotten about and all we can really recall are big shapes. But importantly, we would notice the tiger in the woods before forgetting and run for it! If we had no colour input, that wouldn't be the case.

Examples of more colour being used.
Hopefully the above demonstrates that colours are important to many animals. If anything it seems that more colours even than our perception of the EM spectrum are preferable, particularly into the UV range.
For prey identification reindeer rely on ultraviolet light to spot lichens that they eat. This same sight can spot the UV-absorbent urine of predators. This article has a few more examples.
Some birds of paradise like parrots have even more brilliant patters under UV light. Even starlings look to have an identifying pattern under UV light. Both those examples are thought to be involved in mate selection.

White light does not reveal the feathers' yellow fluorescence in images (left), but short wavelength illumination does (right). Photo: Science

This all hammers home that colour is more important to animals than machines and is involved in more than just camouflage.

Excellent answer! I enjoyed it.

I second One-Face's comment... :P I was completely unaware that racoons had monochromatic vision...

Most marine mammals, some nocturnal mammals, and some fossorial mammals are monochromats -- meaning they see in what is effectively greyscale. As previous commentators have mentioned, quantifying visual acuity is not a trivial matter. Still, I'd assume that under many measures a species such as the owl monkey--a monochromat--has quite good vision, at least at night.

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


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Identifying a creature that appears to be a worm wrapped in a cocoon
This creature was found on a bed. At first, I thought it was a piece of lint, but then it suddenly moved. I picked it up in a paper towel and put it in an eye cream containers, which it is currently in. I believe this means that it is pretty strong, since it appeared to have pulled itself all the way up from the floor, to the top of the bed, then across to the other side of a King-sized mattress.
It appears to be a worm wrapped in a cocoon. It is pretty short, being small enough to fit inside an eye cream container.
The creature is a pale yellow-white/cream, with brownish-red tips on each end (unless it can somehow turn around without exiting its casing). It looks from the side as if it has a rather flat face, one that comes to a slight bump at the bottom, but is pretty much flat. The casing is light grey, with some small portions that appear to be almost the same color as the organism, just slightly darker. There is an opening at each end of the casing, which the organism uses to slide slightly out. It has never fully come out of the casing. The edges of the openings at each end are white. The casing seems to either be made out of or covered in dust.
It can create a substance that is sticky and strong enough to support its weight. I cannot tell if the substance is created by the 'worm', or the 'cocoon'. A thread at each end of the casing is connected to the side of the container by the substance. When I accidentally detached one end of the casing, the entire thing began to shake violently when held so that one end was hanging. It wouldn't stop until I had turned it so that both ends were touching the side of the container. Within minutes, though, it had reattached the broken end. Minutes. Not hours, but one minute.
The holes at each end of the cocoon can either grow or shrink closed. I believe this allows us to tell which opening is in use. If it is nearly shut, it will come out the other end.
It appears to be nocturnal, since it doesn't move during the day, but it is very active at night. It also appears to react to light. If some is put on it, it will poke out to look around.
It has survived for four days straight without food, as far as we know. We put a small piece of lettuce in with it. However, there are two small, brownish things on the bottom of the container. This may be its excrement.
The creature moves by reaching out with its 'tentacle/worm', grabbing onto something (including the ground), and pulling itself forward.
I cannot tell if the creature is attaching to the container's side to climb, or because it is morphing. If that is the case, then the outer shell may be a cocoon. It did detach itself from the side of the container, and first hid under a ledge of lettuce, but now has wrapped itself in lettuce.
To summarize: can someone please help me identify this creature?

Reminds me of a bagworm, but the bag looks different. Of course, if this was living indoors it wouldn't have the normal material to build a bag with.

Welcome to Biology S.E.! If you have additional questions, please visit The Help Center. I think this is a very interesting question and I look forward to seeing it get answered!

It is almost certainly a bagworm, I also have an outstanding question about them in http://biology.stackexchange.com/questions/27961/identification-of-unknown-bagworm-singapore. I don't have a picture of a de-leafed cocoon, but I remember the de-leafed cocoon looking very much like your photo.

I don't think the picture is good enought for a species determination. However, also consider case moths (Coleophoridae), which have larvae that carry around a larval case for protection (similarly to bagworms). A key factor is whether the casing you see is the pupa used for metamorphosis or the case that larvae in some families carries around as protection. Also see this BioSE question.

Looks like an Indian mealmoth to me.

I think it's just a case bearing moth larva (Tinea pellionella).

Source: http://www.hantsmoths.org.uk/

As you might already know the source of an image must be added if it is borrowed from a different person/site.

That, I believe to be the larvae of an Indian Mealmoth Plodia interpunctella, but it could also be Tineola bisselliella or Tinea pellionella. It's definitely emerging from a pupa, and it's definitely a moth larva, but I'd need more information for an accurate identification.
To Google images

It doesn't have to be a pupa - consider that larvae of some moth families carry around a larval case (e.g. case moths (Coleophoridae)).


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Stockholm format to dot-brackets format?
I need to convert all my sequences in a Stockholm format into this:
hg19_11_6_Ala          ----------------.GG--gggaguggugu....gguuacgaaugUGGCCUCUGC-----AA.............................................................GCAGACA.........................G..CCUGGGUUCAAUU...........................
#=GR hg19_11_6_Ala  PP .................22..45677788888....899999999996777899988.....56.............................................................8999999.........................9..*************...........................

Into something like this:
 hg19_11_6_Ala         ................((..(((((((((((...)))))))))))))))))))))))....((................................)))))))))......)))).....................

Obviously, being coherent with the stockholm format. Any hint?

If what you want is to find a consensus structure for a group of alignments in stockholm format then you might try with
RNAalifold
 and for single sequence folding check RNAfold. Both have online servers and can also be run offline.
After you get the consensus structure update the stockholm file by adding  a structure consensus line as: #=GC SS_cons followed by the dot bracket notation.
A nice RNA structure editor that will make your life easier is EMACS when complemented with RALEE. It allows you to view and manipulate RNA structures, predict structure folding and color the alignments based on basepairs relationships. It will be worth it to invest time into mastering RALEE.


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Are some virus loads introduced to human cell but never triggered?
Is there a term or any evidence of phage DNA integrating into chromosomes/ DNA but never being triggered?
For example, could a virus that affected Neanderthals still infect human cells today but is never expressed, triggered, or executed?
How often is latent viral DNA ignored by the host?

There is viral DNA within our genomes. Embedded in the genomes of all vertebrates are the proviral remnants of previous retroviral infections. It is possible that some have conferred biological benefits.
Human endogenous retroviruses (HERVs) represent the proviral phase of exogenous retroviruses that have integrated into the germ line of their host. They are transmitted vertically through the germline and are thus inherited by successive generations in a Mendelian manner.
HERVs possess a similar genomic organisation to present day exogenous retroviruses such as human immunodeficiency virus (HIV) and human T cell leukaemia virus.
Although many are defective through the accumulation of mutations, deletions, and termination signals, some HERVs have been implicated in certain autoimmune diseases and cancers and might have a role in the etiology and pathology of disease.

Within humans, the most recently active ERVs are members of the HERV-K (HML2) family. This family first integrated into the genome of the common ancestor of humans and Old World monkeys at least 30 million years ago, and it contains >12 elements that have integrated since the divergence of humans and chimpanzees, as well as at least two that are polymorphic among humans.
Here we show that the HERV-K (HML2) family has increased in copy number predominantly via reinfection, and that the family has probably retained replication-competent and infectious members for >30 million years. We also present evidence for persistent reinfection by other ERV families within the human genome, and suggest that endogenous retrovirus families are often capable of extremely long periods of smoldering infection.

Long-term reinfection of the human genome by endogenous retroviruses
The viruses in all of us: characteristics and biological significance of human endogenous retrovirus sequences
Demystified . . . Human endogenous retroviruses


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How can a drone be male?
A drone bee is male and is the product of only a queen bee. How is it that the drone bee can be male. I know that a drone is produced by an unfertilized egg, but this does not explain where the two X chromosomes come from. To me, this means that the one X chromosome from the queen must some how be duplicated.

The drone bee is haploid, they only have 1 copy of each chromosome, so the chromosomes aren't duplicated. See this.

In the general case sex chromosomes in animals are different from the human XX/XY. Birds, some reptiles, some insects use ZW, where the female is ZW and the male is ZZ. Others use XO where XX is female and X is male. There are others. Fungi have hundreds of 'sexes' because they have a particularly weird system.

The short answer, which has already been pointed out by user137, is that females are diploid while males are haploid. Bees do not have sex chromosomes per se; rather sex is determined by the csd gene on chromosome III (csd stands for complementary sex determination). Diploid bees that are heterozygous at the csd locus (i.e. contain two different alleles (versions of a gene) for csd) are female (workers).
Bees that are haploid at the csd are males. Interestingly, diploid bees that are homozygous at the csd (i.e. contain two copies of the same csd allele) are also males. But in the honey bee, these bees do not survive as they are killed by workers before they mature. In some other haplodiploid species, however, both haploid and diploid males are viable (the bumble bee Bombus terrestris for example). Also note that diploid honey bee drones can be viable if they (somehow) make it to maturity without being killed by workers (e.g. see here).

Do you have a source for the diploid males?

Here is one source http://link.springer.com/article/10.1007%2FBF01240420

That's interesting, looks like 50% of all larva in those colonies are male, that would seriously handicap those colonies. Since the odds of diploid males goes up when inbreeding happens, do bees have some sort of defense against inbreeding? How many versions of the CSD gene are there? Because more versions would lead to reduced chances of diploid males. Also makes me want to know how the bee detects heterozygosity vs homozygosity.

Yes the honey bee csd is highly polymorphic, which reduces the odds of inbreeding (e.g. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1626638/). It's an interesting point within the context of bottlenecked populations (e.g. imagine an invasive bee swarm transferred by boat that has no conspecifics around) because, as you point out, if the population has low csd variability then it increases the probability that a diploid bee will be an inviable male rather than a viable worker. But as queens mate with multiple drones, a single invading queen can have multiple csd alleles in her spermatheca.

Also note that diploid honey bee drones can be viable if they (somehow) make it to maturity without being killed by workers (e.g. http://www.ncbi.nlm.nih.gov/pubmed/16475107). It looks like workers tell diploid and haploid males apart by pheromones.

@yidryi Feel free to add those links into the answer.


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How can the directionality of a protein structure be defined?
For a DNA molecule, you can define directionality using the convention of a 5'-3' direction on the Sense strand. However, using an N to C convention for a protein doesn't work since the ends may be on the same side and if the protein is unstructured then the N to C direction will change. I'm asking the question from the perspective of addressing PPIs. If I have two proteins that interact with each other, how do you quantitatively describe the relationship of the two proteins with respect to one another. We have formal ways to describing this using domains and residues but not for quaternary structures.
How would you mathematically define "up" for a protein structure?
I would imagine that using RDCs would be able to make some progress into this problem. At the moment it doesn't seem as if there is any convention in the structural biophysics community.

I am afraid that won't be that easy. One way I can think of is by finding the net dipole moment and making that as the axis. But I think PPIs are usually not in that global scale.


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What is the present tense verb form of apoptosis?
For example, if I want to say something along the lines of "this signaling pathway causes a cell to go through the process of apoptosis", but I want to shorten the phrase "go through the process of apoptosis" to one word, what would that word be? I've been saying "apoptose" so far but I'm not sure if that's correct.

Apoptosise? I think most people would just phrase it as you have.

Personally, I would say "undergo apoptosis" being both shorter and not risking coining new word forms.

According to Google Scholar, there were ~40000 hits for "apoptose" and ~120k hits for "undergo apoptosis" in published literature, both of which had significant numbers of high-impact articles.
Therefore, it is clear that both expressions are sufficiently used in literature for either to be used.
Personally, I would say "undergo apoptosis" being both shorter than your original phrase and not risking coining new word forms.


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Visualising a subset of the tree of life
I understand that many curated trees of life already exist (eg http://tolweb.org/tree/) but is there any website that allows one to input a list of organisms, and then produce the current best guess at their evolutionary relationships?
The best site I managed to find so far is http://itol.embl.de/itol.cgi, which allows you to select specific species from the main tree to plot into a sub-tree, but the tree itself is rather small, so more detailed comparisons cannot be made.

So you mean a site that can produce a phylogenetic tree for a group of chosen species, based on an underlying database of phylogenetic relationships?

@fileunderwater Yes, that would work.

I have a similar project, this option you need could be added in the future. Take a look: http://dao.url.ph/tree/tree.php

http://phylot.biobyte.de/ performs the requisite task (generating a phylogenetic tree based on the specific organisms provided, using the NCBI taxonomy tables).
For example, the input of tree elements

Trichomonas vaginalis,Trypanosoma brucei,Homo sapiens,Fibroporia
  radiculosa,Paramecium tetraurelia,Tetrahymena
  thermophila,Cryptosporidium muris,Cryptosporidium hominis,Blastocystis
  hominis

generates the tree

Really cool resource!