Wikipedia:Reference desk/Archives/Science/2008 May 19

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[edit] May 19

[edit] Which genes flank TJP1

How do I find out which genes flank TJP1 in humans? I figure one of the many genomic databases would be able to help but they're terribly complicated and intimidating. ----Seans Potato Business 21:04, 11 May 2008 (UTC)

On the link you provided, scroll down to the section Genomic context. This will tell you the chromosome the gene is present on and it's location. By searching the position before it or after it should give you your answer. Regards, CycloneNimrodTalk? 21:11, 11 May 2008 (UTC)
Its actually a bit complicated this one. However, 5' of TJP1 appears to be necdin-like 2, while 3' is CHRNA7-FAM7A fusion isoform 1 (which is a very odd locus). There may be other genes in between, but they have not been characterized. Rockpocket 21:53, 11 May 2008 (UTC)
How did you get those? ----Seans Potato Business 21:59, 11 May 2008 (UTC)
Okay, this isn't working. I'd like to know in which order the genes TJP1, NDNL2, GREM1, SLC12A6 and SPRED1 occur. I know they're in the same region, but I want to determine if there are any genes between them and in what order the occur. If I search for each gene I get:

ndnl2 15q13.1

slc12a6 15q13-15

tjp1 15q13

grem1 15q13-15

spred1 15q14

Yet none of these shows up on the 'genomic context' diagram of any of the others. How can I interpret this mess? Does SPRED1 exist on an exon inside both GREM1 and SLC12A6 which both exist in exons of each other? I suppose one may be on the antisense strand, but there's going to be overlap somewhere here. ----Seans Potato Business 21:55, 11 May 2008 (UTC)
According to Ensembl (by searching for each gene on the human genome):
  • Ndnl2.. can be found on Chromosome 15 at location 27,347,645 - 27,349,325 and is anti-sense.
  • Tjp1.... can be found on Chromosome 15 at location 27,778,863 - 27,901,998 and is anti-sense.
  • Grem1.. can be found on Chromosome 15 at location 30,797,497 - 30,814,158 and is sense.
  • Slc12a6 can be found on Chromosome 15 at location 32,309,489 - 32,417,557 and is anti-sense.
  • Spred1. can be found on Chromosome 15 at location 36,331,808 - 36,433,526 and is sense.

Are there intervening genes? Yes in all cases, except between Ndn12 and Tjp1. Rockpocket 22:35, 11 May 2008 (UTC)

Okay, this is really helpful of you. Thanks. However, now I have a conflict; SPRED1, according to this is at 15q14 while GREM1 according to this is at 15q13-15. If 15q13-15 means 15q13 to 15q15, then why do those numbers you (kindly) provided not overlap? And how did you find out whether they were sense or anti-sense? --Seans Potato Business 22:48, 11 May 2008 (UTC)
The "q" refers to chromosome regions while the numbers (13-15) refer to cytogenetic bands identified by staining. That nomenclature is an old skool way of positioning genes on chromosomes and is not particularly accurate. Now we have a fully sequenced genome we can precisely identify exact positions of genes. In this case 15q13-15 means that Grem1 resides somewhere within bands 13-15, rather than meaning it spans that huge length. I used Ensembl to find the info, and identified the strand from that. For example, have a look at the diagram on the TJP1 page, under the "transcripts" sub-section. Find the thick blue line that says "DNA (contigs)". Now any gene identified above that line is on the forward strand (sense orientation) and any genes under that line is on the reverse strand (anti-sense). TJP1 is directly underneath the line, therefore it is anti-sense.
If you don't wish to use Ensembl, the NCBI site you were using gives the same info. On the Spred1 page, on the right hand side of the "genomic context" section there is a link to "See SPRED1 in MapViewer" If you follow that link [1], you can see that the Spred1 gene is located on the right hand side vertical line spanning roughly the same distance I provided (36331k to 36433k). If you want exact values, you can always zoom in by clicking on the gene. Note also the little black arrow beside the Spred1 gene name. The arrow points downwards, indicating the gene is on the sense strand. If it was to point upwards, you would know your gene of interest was anti-sense. Rockpocket 01:22, 12 May 2008 (UTC)
Just a couple more questions: how did you know that the little black arrow next to the gene name corresponds to sense/antisense? And, if we are able to define more precisely where a gene is located, why still quote 15q13-15 and not 15q13 or whatever? ----Seans Potato Business 22:32, 18 May 2008 (UTC)
Well I knew that something would indicate the direction of the gene and the arrow seemed a good candidate. So I checked to see if it was consistent with direction, and it does. Why quote the less detailed banding values? Probably because that page is only partially manually curated. A paper probably described the general position some time ago and no one has bothered to update the record with the exact position. Rockpocket 05:50, 20 May 2008 (UTC)

[edit] the brain

what part of the brain controls the pacemaker in your heart? (the real pacemaker-not an artificial one) —Preceding unsigned comment added by 97.115.18.248 (talk) 02:58, 19 May 2008 (UTC)

It's modulated by the autonomic nervous system, however the pacemaker cells of the sinoatrial node do not require any input from the CNS to induce the heart beat. Wisdom89 (T / C) 03:12, 19 May 2008 (UTC)
More specifically, the Vagus nerve is a parasympathetic cranial nerve that slows the rhtyhm of the heart at the SA node when stimulated. It descends form the brainstem, which is evolutionarily the most primitive part of the central nervous system. I'm not entirely sure how/if sympathetic ennervation occurs directly in the heart. The brain also commands the heart indirectly by orchestrating the release of hormones that have a global effect on the body, such as epinephrine. --Shaggorama (talk) 08:06, 19 May 2008 (UTC)
Since you mentioned it, sympathetic innervation impinges on the sinoatrial node, the AV node, as well as the myocardium itself to increase the speed of conduction, as well as the contractility of the ventricles. Wisdom89 (T / C) 17:43, 19 May 2008 (UTC)

[edit] Fluffy birds

Can birds fluff up their feathers at will, or is it just a reflex response to cold? —Preceding unsigned comment added by 84.66.70.50 (talk) 08:46, 19 May 2008 (UTC)

Both. Birds fluff up their feathers to trap air between then to act as an insulator. This is probably an automatic response, but they most defiantly can do it at will also. Have a look at this similar question. They sometimes also fluff them up when preening, to ensure they clean every layer, or to appear bigger to an opponent. Think outside the box 11:18, 19 May 2008 (UTC)
And often as a courtship ritual. --jpgordon∇∆∇∆ 13:32, 19 May 2008 (UTC)

Swans carry their baby chicks in their feathers on their back when the chicks feathers are not water proof to swim yet. Bed-Head-HairUser:BedHeadHairGirl12:56, 20 May 2008 (UTC)

  • You sure about that reason? Swans (like most water birds) are precocial -- the chicks can swim and feed themselves very soon after hatching. --jpgordon∇∆∇∆ 19:33, 25 May 2008 (UTC)

[edit] Solar Power - SILICON FEEDSTOCK

I am doing some reserch into solar power and its generation. I have searched companies and websites and find that they use SILICON FEEDSTOCK to manufacture solar cells. However none explain what the silicon feedstock is or the raw materialand processes used to manufacture the feed stock.

I would be grateful for any guidance.

Many thanks

Kusum Thanki —Preceding unsigned comment added by KusumThanki (talk • contribs) 10:44, 19 May 2008 (UTC)

One way to gather energy from the Sun is to use photovoltaic cells - these are just silicon chips (like computer chips). The raw material for making them is super-pure silicon. So the 'feedstock' for that manufacturing process is silicon which is purified, cast into cylinders then sliced to form 'wafers' onto which the circuitry is printed and etched. Silicon is a very common element - it makes up 25% of the earth's crust so it's everywhere around us. I believe that it's extracted from sand using coal or charcoal and then purified. Our article Silicon covers that fairly well. 70.116.10.189 (talk) 11:28, 19 May 2008 (UTC)
The silicon isn't cast into a cylinder; rather, a boule of silicon is grown using the Czochralski process. It's a time-intensive process which is one of the reasons why the silicon raw material is so expensive. (And because the boules are cylindrical, they slice out to form those inconveniently-shaped (rather area-wasteful) circular silicon wafers.) For a contrast, see amorphous silicon.
Atlant (talk) 13:00, 19 May 2008 (UTC)

[edit] plate tectonics

how is it possible for the continents to move? what are the consequences of drifting continents? what evidence exists to prove drifting continents? which hazards and opportunities result from continents on the move? if we stand on the beach,will we see how the land is moving?why? how fast is this movement? —Preceding unsigned comment added by 196.35.246.194 (talk) 13:58, 19 May 2008 (UTC)

I suggest reading the Plate tectonics article, and come back if you have any more questions. -- JSBillings 14:00, 19 May 2008 (UTC)
And Continental drift...--Cameron (t|p|c) 18:13, 19 May 2008 (UTC)

[edit] Mastubate

Do you know the technic of mastubate? —Preceding unsigned comment added by Aku orang ganteng (talk • contribs) 14:12, 19 May 2008 (UTC)

You are no doubt looking for our article on masturbation. For further advice, speak to a medical professional. TenOfAllTrades(talk) 15:03, 19 May 2008 (UTC)
Most likely a Sex therapist Nil Einne (talk) 18:07, 19 May 2008 (UTC)


[edit] DNA sequencing - why the plasmid?

If I want to sequence a length of DNA, why would I amplify by PCR and then clone into a vector for amplification within bacterial cells? Why can't I just use PCR for the amplification? What's the plasmid step all about? This is an example on such vector used by a research group whose paper I'm reading, before sequencing: "PCR products were cloned into plasmid vectors using the Topo TA cloning kit (Invitrogen, Carlsbad, CA, USA) following the manufacturer’s instructions. Five positive clones were purified from each test cell line using the Wizard Plus miniprep kit (Promega), and were then sequenced by the Applied Biosystems PRISM dye terminator cycle sequencing method" ----Seans Potato Business 15:55, 19 May 2008 (UTC)

These pages discuss some of the pros and cons of direct sequencing of PCR products. Direct sequencing of PCR products is much faster, but is prone to a number of pitfalls for the unwary experimenter. TenOfAllTrades(talk) 16:14, 19 May 2008 (UTC)

[edit] non-flammable wax

If there a substance that turns liquid at about the same temperature as wax but that is not flammable? —Preceding unsigned comment added by Taxa (talk • contribs) 17:07, 19 May 2008 (UTC)

Many solders might fit your description, but they're metallic, if that makes a difference. I suspect most non-metallics that melt at a reasonably low temperature are flammable to one degree or another, although the addition of flame retardants might affect that.
Atlant (talk) 17:26, 19 May 2008 (UTC)
Metallic again: Gallium, caesium, rubidium, francium. Rmhermen (talk) 22:14, 19 May 2008 (UTC)
Rubidium and francium will auto ignite in air, and most definitely are flammable. In the presence of a heat source, caesium might as well. Dragons flight (talk) 22:20, 19 May 2008 (UTC)
Low melting point solders melt at 90C, Wax melts at around 45C - so we need to do better than that. I can't think of anything that melts around 45C. The nearest that I'd suggest would be the plastic Polycaprolactone (sold in hobby stores as "Polymorph") which melts at 60C - but I don't know how flammable it is. Field's metal melts 62C, Wood's metal at 70C. Lipowitz's Alloy at 73C. Field's metal is relatively safe - but Wood's and Lipowitz's metals are toxic - so beware! More exotic: Rubidium melts at 40C and white Phosphorus at 44C...neither could be remotely described as "not flammable" though! Gallium might work - it melts in your hand at 30C and is thought to be non-toxic (although it's kinda tough to get off your hands)...but it'll melt at high room temperatures too! 70.116.10.189 (talk) 22:31, 19 May 2008 (UTC)
Let's back up a tick here...what's the application you have in mind for this material, and how "non-flammable" do you need (will be exposed to flame, vs will be heated strongly, vs just general safety concerns)? Is toxicity a concern? DMacks (talk) 22:42, 19 May 2008 (UTC)
Silicon based waxes would fit the bill. See Silicone oil --Shniken1 (talk) 23:18, 19 May 2008 (UTC)
Anything waxy with many halogen atoms in it would not burn, see flame retardant. Cacycle (talk) 01:10, 21 May 2008 (UTC)

[edit] Cost of DNA sequencing

Supposing one already owned the necessary hardware, how much would it cost, in terms of consumables, to sequence a sample of say, 200 basepairs? ----Seans Potato Business 20:27, 19 May 2008 (UTC)

To get an exact figure, you should pull out your Fisher Scientific/Sigma/Qiagen catalog(s) and look up exact costs for each item needed.
If you Google core sequencing facility or something similar, you'll be able to find price lists for various university labs, including the prices that they charge for internal academic users. Prices I've seen for a single sequencing reaction range from about 5 USD to 15 USD; some discounts are offered for large sample runs. Depending on how those core facilities are funded and subsidized, those figures probably represent a maximum cost of materials, but likely also include some amount of technician time and amortization of equipment costs.
In other words, the cost of sequencing a single 200 bp sample is trivial. TenOfAllTrades(talk) 20:44, 19 May 2008 (UTC)
Just from personal experience, DNA sequencing facilities typically charge customers between 6 and 12 U.S dollars per sample. This includes the reaction and the electrophoresis. Wisdom89 (T / C) 20:45, 19 May 2008 (UTC)

[edit] why does Microsoft lags behind Apple

Why Apples Iphone is such a success? why Microsft cant better than it, is microsoft techinally behind or something else —Preceding unsigned comment added by 198.109.30.86 (talk) 21:42, 19 May 2008 (UTC)

This isn't really a science question. Anyway, Microsoft has a long history of not leading, but rather entering a market segment only after an idea or product becomes successful, and then doing it (or marketing it) better. Internet Explorer, XBox, Zune, Microsoft Office... just wait. You can bet they aren't planning to cede the smart phone market to Apple. ~Amatulić (talk) 21:51, 19 May 2008 (UTC)
Microsoft is principly a software company, there are already phones which run windows mobile (I have one). Microsoft is more than willing to allow other companies to make the hardware while they write the software, but that doesn't mean they won't put out a phone built entirely in-house in the future. -- Mad031683 (talk) 23:29, 19 May 2008 (UTC)
Simple answer : Because Microsoft does not make phones. APL (talk) 17:56, 20 May 2008 (UTC)
More specifically, they don't make smart phones - I believe they're waiting until the market is bigger. They didn't make PDAs until Palm Pilots dominated that market. They didn't make portable music players until Apple iPods dominated that market. They didn't make video game consoles until fairly recently either. That was my point above: Microsoft innovates in the direction of already-existing BIG markets. Smart phones aren't yet dominant players in terms of total cell phone market penetration. Time will tell if Apple's iPhone and RIM's BlackBerry and other smart phone products become popular enough to spur Microsoft into selling similar hardware. ~Amatulić (talk) 18:18, 20 May 2008 (UTC)
Next time anyone wants to ask a question like this, there's a computing page for that purpose. 12:00, 21 May 2008 (UTC) —Preceding unsigned comment added by Cyberina 11 (talk • contribs)