Wikipedia:Reference desk/Archives/Science/2008 May 9

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May 9

How many nucleotides are found in all of the exons of the CFTR gene?

How many nucleotides are found in all of the exons of the CFTR gene? —Preceding unsigned comment added by 65.29.80.238 (talk) 01:23, 9 May 2008 (UTC)

4575 [1] Someguy1221 (talk) 01:32, 9 May 2008 (UTC)

Well, there are non-protein coding sections within exons 5' and 3', but according to EBI Dbfetch (which is the data base I sometimes use in the lab), there are 4443 nucleotides in the mRNA [2]. Wisdom89 _{(T / ^C)} 04:57, 9 May 2008 (UTC)

The mRNA sequence is 4575 long if you end at the last translated codon. The EBI sequence left out the 5' untranslated region, 132 nucleotides long. Someguy1221 (talk) 09:19, 9 May 2008 (UTC)

Yes, you are correct, and hence my reference to 5 prime non-translated regions. This was just in case the user was possibly interested in just the coding region. Wisdom89 _{(T / ^C)} 11:16, 9 May 2008 (UTC)

Voyager Spacecraft

I've read that the Voyager spacecraft are at the edge of the Solar System and are slowing down. Scientists are saying this might be because of some interstellar wind that is pushing against them, making it hard for them to escape the Solar System. Could this not just be the same thing that rockets experience when attempting to reach 'escape velocity' from the Earth (sorry, I forget the correct term)? Could it not be that the Solar System has the same gravitational forces as the Earth, but on a much larger scale?--ChokinBako (talk) 02:32, 9 May 2008 (UTC)

That's quite true, the solar system (which can be greatly simplified to "the sun", for most purposes like these) does exert gravitational pull on Voyager. However, NASA et al have already accounted for this. What you've read likely means that there's an additional force of uncertain origin at play. — Lomn 02:35, 9 May 2008 (UTC)

The gravity from the Sun has been slowing Voyager down since it was launched. But it has plenty of velocity to leave the solar system and after a very, very long time reach some other star. Edison (talk) 03:55, 9 May 2008 (UTC)

I think the questioner may be refrring to the small unexplainned deceleration that has been detected in the Pioneer spacecraft - see our article on the Pioneer anomaly. 199.43.13.101 (talk) 11:05, 9 May 2008 (UTC)

(There's a great graph somewhere on WP of the probe's speed since its launch. I can't find it right now. If anyone has the link to it, it would be welcome.) 200.127.59.151 (talk) 17:57, 9 May 2008 (UTC)

Springtime for France

When does spring arrive in France ("arrive" in the phenological definition)? And when does it arrive in England? (although I imagine it arrives around the same time for both) 96.233.8.220 (talk)PrisonersOfLove —Preceding comment was added at 03:04, 9 May 2008 (UTC)

Would this be what you were looking for Spring (season)? Phenology deals with recording several natural events. It gives dates for a species, based on which next year's date can be predicted, e.g. to within about 55 days (-21, +34) for some flowers. So there is no fixed date. I assume that plants start blooming earlier in the southern part of France than in the northern part, which will be closer to southern England, since both are near the channel (gulf stream influence). But that's speculation. --71.236.23.111 (talk) 18:32, 9 May 2008 (UTC)

I just need to know when it gets warm and the flowers start blooming and it begins to *feel* like spring in those countries. Maybe someone who's lived there can help? —Preceding unsigned comment added by 96.233.8.220 (talk) 19:53, 9 May 2008 (UTC)

Varies heavily from year to year. Last year (in southern England), April was the closest thing we got to summer all year. This year April saw snowfall. See The Guardian letters page passim ad nauseam. Algebraist 08:59, 10 May 2008 (UTC)

France is a geographically diverse country. Marseille is on the Mediterranean. Calais is on the English channel. Alsace is inland. The climates are very different. Google "Marseille climate"[3], "calais climate"[4], and "Alsace climate"[5] -Arch dude (talk) 02:26, 11 May 2008 (UTC)

Why is there no Climate of France article?!!? It's even been redlinked on the List of basic France topics!!! Nimur (talk) 16:38, 14 May 2008 (UTC)

what is the term that refers to the earth's surface features?

the word comes from the latin term terra —Preceding unsigned comment added by Amandalsmithlpn (talk • contribs) 03:23, 9 May 2008 (UTC)

Terrain?--71.236.23.111 (talk) 08:45, 9 May 2008 (UTC)

Cancer

Is cancer just restricted to mammals and people, or can other living things get cancer? Our article makes no mention of other organisms besides humans getting cancer. I know that some trees can live hundreds of years, and I also know that "...cancer-promoting genetic abnormalities may be randomly acquired through errors in DNA replication, or are inherited, and thus present in all cells from birth.", so it stands to reason that really old trees that have undergone mitosis for ages would be susceptible to cancer (unlike insects who only live for a relatively short time). Thanks for all the info! PS-not specifically asking about old trees, just giving an example. I want to know can ANY living organism get cancer (in a nutshell). --71.98.26.52 (talk) 04:02, 9 May 2008 (UTC)

The difference between the way that plants and animals grow means that plants generally don't get cancer (because a huge increase in cell growth in a plant will just make a bigger plant, or one with more branches). However, the gall created by a gall wasp is, roughly speaking, a plant cancer. Confusing Manifestation(Say hi!) 04:13, 9 May 2008 (UTC)

As long as something is made of DNA, mutations are possible. Cancer, as we know it (e.g. tumors and neoplasms), may not be present in every animal or plant but there are other genetic diseases which resemble it. Regards, CycloneNimrod^Talk? 08:51, 9 May 2008 (UTC)

The misleading explanation is removed, thanks for the comments. Dr.Rajarshi (talk) 04:34, 10 May 2008 (UTC)

Unless I misread, but "uncontrolled cell growth" is not termed metastasis. Wisdom89 _{(T / ^C)} 11:13, 9 May 2008 (UTC)

Per Wisdom89, use 'Dr.' Rajarshi's information with caution. The process by which cells become malignant (cancerous) is called carcinogenesis, while the specific steps wherein growth regulation is lost may be called neoplasia. (Note that not all neoplasms are malignant.)

Metastasis meanwhile, is the spread of a malignant tumour from its original site to other locations within the body.

In my experience, the term cancer is used to describe malignant growths in mammals only; uncontrolled growths of cells do happen in other organisms, but usually go by other names. TenOfAllTrades(talk) 13:46, 9 May 2008 (UTC)

Plants do get cancer, but since plants don't have mobile cells, these cancers can't metastasize. --Carnildo (talk) 21:39, 9 May 2008 (UTC)

Interesting...thanks for all of the info. So I'm assuming other organisms which have mobile cells (and that live long) can get cancer that matastasizes, such as those sea turtles that live a hundred years? And I'm also assuming that insects, which live a relatively short time, have almost zilch chance of getting cancer? --71.117.40.7 (talk) 13:51, 10 May 2008 (UTC)

Book-name

What is a book-name?

The term is used in the article Spiny squirrel. Thank you. CBHA (talk) 04:18, 9 May 2008 (UTC)

Here[6] (scroll down) implies it's a "common name" that isn't in use but written down anyway for description purposes in the hope it catches on, as in: [It is] "desirable that well-chosen names be available... if no popular name be already available, a suitable book name will in time come into use as a common name." Julia Rossi (talk) 10:22, 9 May 2008 (UTC)

Meaning of a species name

In the article Bearded Barbet, the scientific name of this bird is Lybius dubius.

Why was it called dubius? Thanks, CBHA (talk) 05:04, 9 May 2008 (UTC)

There are quite a few species with 'dubius' in their name. The term is just what it seems: Latin for the similar word "dubious". My understanding is that species are given this name if the criteria for classifying them as a distinct species or placing them in a specific group is... well, dubious. According to this list of Latin terms used for species classification, the term can also mean "uncharacteristic". Dooky (talk) 09:15, 9 May 2008 (UTC)

Acute chest pain

What are some causes of acute chest pain that would not found by an echocardiogram or chest x-ray? Mac Davis (talk) 05:52, 9 May 2008 (UTC)

Chest pain might hold some clues. 71.236.23.111 (talk) 08:39, 9 May 2008 (UTC)

Just as a forewarning, please read this: Wikipedia:Medical disclaimer. Wisdom89 _{(T / ^C)} 11:10, 9 May 2008 (UTC)

Perhaps this can help you [7]. --Taraborn (talk) 14:36, 9 May 2008 (UTC)

Exothermic reaction

Alkalisation of cellulose with a mixture of ethyl alcohol & sodium hydroxide is an exothermic reaction. Can the heat generated be caluculated in terms of kcals using enthalpies of reactants?59.93.71.174 (talk) 12:11, 9 May 2008 (UTC)

It could be if you knew the products produced. In this case I suspect you may get a complex mixture including sugars and aldol condensation products, too complex to calculate. Graeme Bartlett (talk) 21:45, 9 May 2008 (UTC)

CO2 of fans

Is it more environmentally-friendly to have air-con in an office or for everyone to have electric fans blowing all day? 195.60.20.81 (talk) 14:33, 9 May 2008 (UTC)

It will probably depend on 1. the size of the office space (which gives you the power requirements for the central air), 2. the number of individuals in the office (which tells you how many electric fans there would be), and 3. assumptions about the efficiency of the technology in question (are we talking new, EnergyStar approved air conditioners, or one from decades back?). Not knowing any of those, I would estimate that central air is more energy-efficient under some conditions and individual fans are better for others. Which doesn't say much. --98.217.8.46 (talk) 16:19, 9 May 2008 (UTC)

: "Environmentally friendly" questions are always a tricky can of worms. What the outcome is depends more on who counts what how than comparable data. That's why I'm not going to drag up study A versus study B, but will give you a couple of factors to consider. First of all, if you get a real scorcher electric fans blowing all day are not going to provide the same level of comfort as an AC unit. They offer comparable performance only in moderate heat. This is particularly true if the heat is accompanied by high air humidity (the rule of thumb says to add 10 to the heat index for high humidity). Running an AC unit will actually dry the air. Airflow patterns for office buildings are usually designed with some degree (ideally a high degree) of care. Airflow patterns from individual fans are haphazard and chaotic. Fans cool by creating high volume air flow. This is a less efficient way of cooling than in the AC which uses a refrigeration cycle to actually remove the heat from the air. Central AC creates most of its noise away from your workers, individual fans running at full tilt can cause considerable noise pollution. Central AC can be kept on at a certain temperature setting overnight. If nighttime temperatures don't drop significantly enough the building will heat up overnight when your individual fans are turned off. This can actually lead to a much higher power consumption when the workers come back in the morning and run their fans to try and cool down the "oven". Such influences depend on individual structures and building materials and are therefore impossible to quantify on a general basis. Central AC can be adjusted following guidelines that take energy saving aspects into consideration. With individual fans you have to rely on the individual attitude of each worker. While we can calculate power consumption rates for a central AC at certain settings, calculating the overall power consumption for individual fans is highly arbitrary. Comparing both systems at maximum levels will not give realistic results. How much of an influence additional losses due to distributed power use for individual fans is I'll not consider now, that in any case would also depend on highly variable local factors. So far for power consumption of the units

Average life of an AC unit and individual fans is comparable at about 12 years. After that time you have only one AC unit to replace which will usually be removed by a professional and may be disposed of in ways with low environmental impact. Choosing the other option you end up with a pile of used fans that are usually disposed of in the ordinary trash. They can have some components that are environmentally taxing. Components that could theoretically be recycled, like e.g.metal components, will not be. Plastic recycling has recently come under fire, ironically from some environmental groups, because of the high energy expense, low efficiency and water use involved. AC units on the other hand often contain refrigerants that contribute significantly to the depletion of the ozone layer and/or are considered a health hazard. Fans with plastic components may emit Plasticizers and while the refrigerant in the AC is contained in a closed system any substance emitted by a fan will be emitted directly into the airflow hitting the worker. This also goes for any other substance detrimental to health that may be contained in the paint (e.g. heavy metals), insulation material, lubricants (hydrocarbon compounds) etc. If this wouldn't make the picture complex enough, comparing the environmental footprint of the manufacture and transport of the units opens a whole new chapter, with results influenced by such diverse factors as distance to the consumer, energy use and various sources of pollution involved in the acquisition of materials and the manufacturing process. Environmental impact of said pollutants and effectiveness of countermeasures. Not to mention packaging. So the answer is: yes or no or 42. ;-) (The above is neither medical nor legal or any other advice except for maybe looking very closely at all the factors before starting to point fingers.) 71.236.23.111 (talk) 17:44, 9 May 2008 (UTC)

Are one or more ceiling fans suitable for your office? Nil Einne (talk) 17:35, 11 May 2008 (UTC)

Sensitivity of Taq polymerase to heat

My lab supervisor (I'm an MSc student and she's a PhD student) often seems obsessive about keeping Taq polymerase on ice when it's not in the freezer and minimising the time spent between. I figured that if it still functions after being subject to 95 degrees C, then it ought to be fine for a few minutes at room temperature. The way that I was told do set up a PCR reaction was to insert the DNA samples into those strips of 0.2 ml tubes, and then add the 'master-mix' containing everything else. After three rounds of contaminated PCR reactions, presumably a result of contamination of the pipette tip used to add the master-mix, I decided to avoid the possibility altogether by adding the master-mix to all empty tubes and then adding the samples to the master-mix. Now that I've imaged the products, I see that almost all reactions failed except for a few which gave really light bands and the positive controls which worked fine. It could be that there were too many primers in the outside flanking mix (I'm doing nested PCR)... could it be that the Taq was at room temperature for about 15-20 minutes? ----Seans Potato Business 16:18, 9 May 2008 (UTC)

I keep Taq on ice while its out, but I've definitely had it in the master mix at room temperature for at least 15 minutes while filling a 96 well plate. I've also always gone mastermix first, then samples, because the mastermix has always been the larger volume, for me, and to avoid a simply excessive use of pipette tips. Have you tried any positive controls during your PCR runs? Someguy1221 (talk) 17:31, 9 May 2008 (UTC)

Yeah, the postive controls worked. I'm suspecting the samples. I will try it again with a greater quantity of sample and reduced water in the master-mix. ----Seans Potato Business 19:13, 9 May 2008 (UTC)

I agree with Someguy. I usually keep it on ice at all times, as it's become an automatic habit. However, whenever I do any type of PCR reaction (whether it's mutagenesis or straight up generating amplicons for subcloning), I always make the master mix without the enzyme. I add master mix, template, then lastly the enzyme. However, that being said, if you are getting "contaminated" looking lanes, it's most likely the primers and the annealing temperature. Very rarely does DNA contamination really affect the PCR reaction, at least in my experience. Don't get me wrong, it could, and you should wear gloves and use DNase/RNase free tips and tubes, but, I've never had that sort of problem if such precautions are being taken. Have you tried a gradient PCR? Wisdom89 _{(T / ^C)} 18:09, 9 May 2008 (UTC)

Oh, and just a recommendation, regular Taq Pol is good, but I would suggest trying to use Pfu turbo or ultra. Wisdom89 _{(T / ^C)} 18:10, 9 May 2008 (UTC)

The contaminations I talked about were in the water controls so it was likely the master-mix which was contaminated. The primers have all been optimised using gradient PCR to find the right annealing temperature and number of cycles. I don't have much say in the reagents we buy, particularly since Red Taq Pol usually works just fine. I'll try using more sample as per above and see how I go. I'll be back on Tuesday to report/whine. ----Seans Potato Business 19:13, 9 May 2008 (UTC)

Like the others, I always keep Taq on ice or in an ice block when not at -20. Its good lab practice. That said, most types of Taq Pol are pretty temperature resistant. I recall a student in our lab doing some PCR then leaving his Taq on the bench overnight and doing the rest the next day. Those amplified after 16hrs at room temperature worked just as well as those done immediately. If you store your Taq is small enough aliqouts, then some raised temperatures are unlikely to have much effect. However, if you store a large volume of Taq in one tube, you should always keep it cold, because eventually the Taq will begin die. I doubt very much Taq is the issue with your PCR. Sounds like a sample problem to me. Rockpocket 01:12, 10 May 2008 (UTC)

I actually went in yesterday to try it with more sample (16 ul instead of 4). Half of the reactions worked and half didn't at all. It's nested PCR and the outside is done with a mix of primers, to amplify a number of sequences. The product is diluted 1:1000 and then 4 ul of this is used in subsequent reactions (this is methylation-specific PCR)for different genes. We used seven primers in the outside reaction and the DNA is derived from paraffin-embedded tissue. It may be that there were too many flanking primers for the original sample. This whole thing is stupid... :/ --Seans Potato Business 21:32, 11 May 2008 (UTC)