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Everything posted by Greippi

  1. Putting aside the issue that you couldn't get the electron wavelength down to the size of a photon: Even if photons had a size, they move at 300 million m/s. Even if you could get a stationary photon, the Heisenburg uncertainty principle would prevent its observation. The theory is that photons have a dual nature - either particles or waves. It's a bit of a mistake to think of them as physical entities or something with substance.
  2. RNA is pretty unstable. Say, for example I'm trying to measure the concentration of DNA in a sample with a spectrophotometer but some RNA's "getting in the way", I just leave my sample sitting at room temperature for a bit (10 mins) and it'll have degraded sufficiently. This makes sense as in the cell, you don't want mRNA hanging around for too long, otherwise that wouldn't allow for very good control of e.g. protein expression levels. While the A-T base pair IS "stronger" than the A-U pair, this doesn't actually contribute much to the stability differences. Instead I would guess that the 2’ OH group on the ribose sugar makes RNA more prone to nucleophilic attack.
  3. First a disclaimer: a am not a geneticist. I'm a biochemist but I left genetics behind 3 years ago. However, I have just had to do some research on DNA microarrays, so I might be able to help! 1. Someone else will be able to answer this far more clearly than I can. 2. I think there's some misunderstanding going on here, because your statement doesn't seem to make sense. Back to the basics: when a gene is "turned" into a protein, first it is transcribed into mRNA, which is subsequently translated into a protein (each set of 3 base pairs in the mRNA codes for an amino acid in the protein). Usually an mRNA is not necessarily a direct complimentary copy of the gene as it undergoes processing before it is translated. Wikipedia has some good information on all this (search messenger RNA). So, different genes code for different proteins - at one point in the cell it may need more of a certain protein than another protein - each protein has different "expression levels". So a cell may be making more of a certain type of mRNA than another type. In the microarray, the expression levels of many different mRNAs can be compared, which gives information as to what the cell is doing at that particular time. If I've missed the point there, and you're talking about another sort of microarray experiment then I apologise. Microarrays can have other uses other than the study of gene expression (for example forensics), but since you're studying the proteome then i assume the gene expression use is key. 3. I can answer some questions here. What is your object of interest? Let's take the example of cancer cells. The genes in a cancerous cell are regulated differently to those in a normal cell. To study this, your genes of interest might be those involved in the cell cycle and proliferation. Your microarray would take all these genes from the cancer cell, and compare them against the normal cell. You could then see which genes are being upregulated and which are downregulated. It is easier to use DNA rather than RNA in an array experiment because DNA is more stable, RNA degrades very quickly. However, you can't just take the gene you're studying and put it on the array as it contains loads of rubbish that you're not interested in (mRNA is processed after transcription). So you can turn the mRNA back into DNA via the enzyme reverse transcriptase - and this DNA is called copyDNA. Colours - often a fluorescent tag is added to the DNA on the microarray (there are other sorts of tag, like radioactive etc). When comparing two different samples (e.g. the cancer cell vs the normal cell) different tags would be used for each - thus two different colours. You can compare the intensities of the colours after hybridization - the more intense colour of the two indicates that that sample has hybridized more strongly/best. 4. In any experiment you're going to get noise that can interfere with the data. You need to do some maths and processing to eliminate any noise that will give erroneous data. Okay, I've run out of time - I hope that helped a bit.
  4. I am no physicist, but photons are smaller than the wavelength of electrons. I'm not even sure a photon has "size".
  5. Think about what you're actually DOING to the liquid when you add more salt? - What are you adding when you add salt? - voltage = current * resistance
  6. E. coli like to grow at 37 celcius. I imagine using the heating pad will keep the petri dish at a decent enough temperature, ditto the oven if it's warm enough. Be careful not to get the temperature above that or you may well kill your bacteria. Usually I'd leave an agar plate of E.coli a day, if the temperature's lower than that then you may have to wait a couple of days. Do a trial run and see what happens. MAKE SURE THE PLATE DOESN'T GET OVERGROWN. Once you have a nice lawn of colonies it's ready to go. Milk, I'll hazard a guess: E. coli needs something to "eat" so it's usually grown in a medium containing nutrients. If there are no nutrients on the agar plate (i.e. if it's just pure agar and no medium like LB), then I imagine the milk will provide some nutrients. But be careful of contamination - there may be other types of bacteria in the milk, or you might get mold growing or something! Ampicillin: I'd ask a teacher to obtain it for you, there are companies that sell chemicals to science labs. Another thing: have you considered honey? It has great antibiotic properties - I did an experiment on that in my first year of uni. Manuka honey from Australia is the most effective, but I found that local honey had some antibiotic properties as well!
  7. My protocol is similar to the above. I've used it successfully for S17 and DH5alpha, as mentioned it'd be pretty much the same for other strains. Grow cells until they're in log phase (0.6 absorbance at 600nm) *keep the cells on ice/as cool as possible throughout the procedure* Spin cells down, obtain pellet Resuspend in 0.1M MgCl2 (I use 20ml) Spin down, obtain pellet Resuspend in 0.1M CaCl2 (I use 20ml) Spin down, obtain pellet Resuspend in 20% glycerol, 0.1M CaCl2 (I use 1ml) Aliquot. Snap freeze with liquid nitrogen. Store at -80C I've gotten better at making competent cells, it takes practice, - the first batch of S17s I made worked, but took a little longer than usual to grow up after transformation.
  8. Safety issues aside, here are some basic things you'll need off the top of my head: - lots of agar of various types. - lots of growth medium of various types (e.g. LB) - aseptic conditions (to prevent contamination of your samples), I'm sure you know how to do aseptic cultures. - incubators (37 degrees C I expect you'll need most often) with shakers. - bleach or something to kill the bugs (just bung in the conical or whatever you're using to grow the cultures up). My lab uses something awesome called Virkon. It's pink. To be honest, you don't need much to be able to culture microorganisms. I'd say the incubator/shaker s will be the most annoying thing to get hold of. How do you propose to get around the problem of getting a "pure" culture? Obviously from a skin swab there will be loads of different types of beasties on there, and you don't want your cultures taken over by the strongest of the bugs if you're looking for something else.
  9. Greippi

    About DNA ?

    Depends how you go about doing this, and what organism you're using, and how much genetic material you're putting in there. Chances are, the "embryo" will be unviable and not survive at all - just look at the hideously low success rate of an experiment like what was done with Dolly the sheep (and that wasn't even FOREIGN DNA).
  10. There's quite LOADS of literature on the topic. I haven't worked with them, but I'd go with whatever the general literature consensus is. Obviously it depends on WHAT protein you're extracting too - so it might be a bit trial and error finding the optimal technique for different proteins.
  11. To go RIGHT to basics: when you start looking at the numbers, you will soon realise this is unfeasable. The genome of HIV is nearly 10,000 base pairs long (influenza is 12,000). To mutate every single base in every possible combination..well I can't even be bothered to do the maths. It's ludicrous. Sure, there are certain segments of the genome that code for proteins that are detected by the immune system, which narrows it down a bit. But the number of permutations would just be insane.
  12. Well, this looks suspiciously like homework. All you need to do is plug the figures into your basic equation, so what part are you stuck on precisely? If it's not homework: was the spectrophotometer "zeroed" using clear solvent before measuring the uracil solution?
  13. Considering that cancer can be seen as "many different diseases" - i.e. it has many different triggers, there can't be a "one medicine cures all" solution.
  14. Other than the increased blood flow to capillaries, the other claims seem rather spurious to me. Water therapy had some popularity in Victorian England, and recent scientific studies have in fact shown the number of lymphocytes in circulation is increased after a cold water treatment, thus helping fight infection. After a brief search, I have found the following papers on that: "Effects of short-term hypothermal and contrast exposure on immunophysiological parameters of laboratory animals." PubMed ID: 19907753 Short term exposure to cold water increased bone marrow lymphocyte count. Contrast bathing (hot and cold alternating)stimulated cell-mediated immunity (but repressed innate immunity - which could be a good thing if an overwhelming innate response such as prolonged fever was exhausting the patient). "Immune changes in humans during cold exposure: effects of prior heating and exercise" IDS Number: 223WQ Found similar stimulation of the immune system after cold treatment.
  15. I think that would be sensible first distinction to make! Note: I said FIRST.
  16. There are many recently published papers on the topic. As jimmy said, the most common seem to be combination therapies with herpesviruses and radiotherapy.
  17. Some bacteria can become dormant as something known as an endospore, and can later become reactivated. These have been known to survive thousands of years. They are resistant to extremes of heat, freezing, radiation, dessiccation, many chemicals, and other extremely harsh conditions. To kill them, autoclaving at temperatures over 100 C for many hours can work, as well as treating with alkylating agents.
  18. Further to what's been said, The wavelength of light that can be used for photosynthesis depends on the types of pigments used, using many different types of pigments will increase the spectral width of the antenna. For example, purple photosynthetic bacteria have carotenoids (which absorb green light), as well as various chlorophylls. Proteins are used to fine-tune the absorbance characteristics of the pigments. Many organisms use the pigments best suited for their environment and what wavelengths of light are most abundant- for example red seaweeds can survive in low light conditions whereas green ones cannot.
  19. As excited as I am about the prospect of data analysis, I disagree passionately with your choice of bar graph format.
  20. Shh, it needed a thrilling title to lure people in.
  21. GAH, I was just too late in my submission.
  22. In short, a rock from a cliff in Devon was sent 300km high, exposed to the conditions of space, and then brought back down to Earth. It was found that one species had survived the trip - a photosynthetic cyanobactierium. Isolation of Novel Extreme-Tolerant Cyanobacteria from a Rock-Dwelling Microbial Community by Using Exposure to Low Earth Orbit
  23. If a protein is unfolded during the transport process then, no. Often proteins have a targetting sequence added on the end which tells the cell where it needs to go in the cell, this may interfere with the correct folding of a protein and thus make it less functional.
  24. Telomeres - a region of repetitive DNA that's stuck on the end of a chromosome. Each time a cell replicates, the telomere shortens, until after enough replications the telomere has all been "gobbled up" and genes at the end of the chromosome start being degraded. This limits the cell's capability to replicate endlessly. Cancer cells up-regulate the enzyme telomerase which elongates telomeres, creating the possiblity for an immortal cell line. Of course, in a human being this isn't desirable as naturally occurring mutations in the cell's DNA will eventually lead to a breakdown in cell proliferation control.
  25. Biochemistry in itself is a pretty huge field, so it's be an idea to look up the syllabus for the first year and see what topics will be covered - then we can give you some pointers.
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