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Everything posted by Greippi

  1. Kinetic studies have shown that finding the native conformation isn't the rate limiting step. The rate limiting step is actually the exclusion of water from the hydrophobic core of the protein. Are you referring to programs that will calculate 3D structure from amino acid sequence? As far as I was aware such algorithms are pretty much rubbish, although they're getting better. It is also worth noting that each intermediate in the folding pathway is not necessarily a step towards being more ordered - the structure does not necessarily get more native. For example, the protein BPTI containing 3 disulphide bonds. Its folding pathway is not a simple sequential process, the kinetically preferred mechanism involves intramolecular rearrangements using non-native disulphide bonds. This throws a bit of a spanner in the works for computer models that try and predict the folding pathway of a protein, and shows that the process is pretty complicated to understand.
  2. Exactly what experimental evidence do you have for that? The more classical explanations (while we don't fully understand it - especially type 2 and 3) have masses of empirical "evidence". Type 1 diabetes is autoimmune. Lymphocytes infiltrate the pancreas, and destroy pancreatic beta cells (those that sense glucose levels and produce insulin). Therefore you get a loss of insulin production. For type 2 and MODY (maturity onset diabetes of the young), are not autoimmune, but both have very strong genetic factors as well as environmental factors. From the genes that have a strong link to disease susceptibility, one can determine the biochemical pathways that are involved in these types of diabetes. For example, genes linked to disease susceptability in: tpe 2: CAPN10 - protease associated with insulin release from pancreatic cells. GCK - a hexokinase that increases metabolism of glucose GLUT2 - transports glucose into the cell, gene variants may disrupt glucose regulation. MODY: Most identified genes are transcription factors MODY1 - HNF4A - caauses abnormal regulation of transcription in beta cells, leading to a defect in the signalling of insulin secretion, beta cell mass or both. Glucokinase (MODY2) - decreases phosphorylation of glucose, leading to a defect in sensitivity of beta cells to glucose and defect in storage of flucose as glucogen in liver. Plus other genes involved in gene regulation.
  3. Never before have scientists been able to create an entire artificial genome (ie construct the DNA to contain the genes they want it to contain) and implant it in to a bacterial cell and to actually have it work as a "normal" bacterium. They've done similar with viruses though - I think it was the polio virus they "made" from scratch. HOWEVER: they still had to put the DNA into a pre-existing bacterium (that had had its original genetic material removed). They still aren't able to create an organism entirely from scratch (i.e. construct organelles, cell wall in vitro).
  4. On opening this thread my initial thought was "hah! so Venter's done it!" Turns out he has. Impressive stuff, will give the Science article a look later. If they've actually done it's pretty groundbreaking stuff, with massive implications.
  5. You should be fine. Looking at the safety data sheet it didn't look like you've got anywhere near a toxic dose. Note it says MAY cause cancer - so it's not certain. Seeing as it wasn't on your hands very long, and you're not going to have repeated skin exposure to it, I would say it's VERY unlikely. Generally with carcinogens, you're at risk if it's prolonged/repeated exposure.
  6. I always assumed the reason why targeting the gp120 never worked was because of the extremely high mutation rate - by the time you've worked out a vaccine against one type of it, it has mutated so it's completely different and the vaccine is no use. I also assume the paper referenced in that wikipedia article is work in progress (the targeting of the invariant region). CD proteins are found on white blood cells, MHC class 1 proteins are present on all nucleated cells, and class 2 on antigen-presenting cells. MHC present antigen to T cells.
  7. I'm confused about the late phase of the asthma response in which eosinophils are involved. My understanding is that eosinophils infiltrate the airways from the surrounding capillaries, causing inflammation. In time, epithelial cells are damaged and become hardened due to repetitive remodelling. To do this, they must first cross the endothelial cells that make up the capillaries via the adhesion cascade using various selectins (such as P-selectin on an endothelial cell), and integrins (such as VLA-4). But then how do they cross the epithelial cells to get inside the airways? Is there a similar adhesion cascade?
  8. Have you read the relevant literature? This paper has a large section titled "cell size and yield", including several hypotheses.
  9. Do you know how to read off maximal velocity (Vmax) from a michaelis-menton graph (plot rate against sucrose concentration)? Once you have Vmax, you can easily calculate Vmax/2 and thus read off Km. or, if you're familiar with it, it's easier to do this with a lineweaver-burke plot (plot the reciprocal of the rate and substrate concentration). To find the velocity (speed) of reaction for each sucrose concentration, you just need to work out how many mg of glucose are being produced per minute. Because the rate of glucose formation is the same as the rate of sucrose disappearance for the reasons I outlined above.
  10. As in you're not aware you're consciously making the decision to move the muscle.
  11. Quick response off the top of my head: Sometimes there is a stimulus, it's just subconscious. Other times, it's due to local stimuli - for example in some disorders involving involuntary muscle contraction, the neurotransmitter receptors may be more sensitive than normal (due to the fact that different neurotransmitters causing the receptor to be more or less sensitive, and an imbalance of neurotransmitters), resulting in contraction even at low concentrations of neurotransmitter.
  12. Did you do the first batch of PCR that worked a year ago? Most likely your DNA has degraded since then. How did you keep the DNA? If it was at -20C then generally your DNA is only good for up to half a year at most. At -80 you'll have better chances, but you still have to be careful when thawing it.
  13. I'm in a slightly different field and different country (UK), but one of the most important things is enthusiasm. Once you get to the interview stage, you can impress them with enthusiasm and your knowledge of the subject area (if you have a wide knowledge from your own reading it shows you're actually interested). You'll earn extra points if you've looked in to the work the lab does/has done and mention what you liked about it. Of course, they'll also be looking at just how well you'll fit in with the people who already work at the lab. I'm doing a masters before my PhD because I feel it will give me an edge over people who have just graduated from an ordinary degree. I would get more experience in the lab, and if I were to stay on in the same department I would be more familiar to the people working there. The people in my department who I would be working for if I did a PhD there agree - that extra lab experience is key. But then again, I understand that PhDs in America are a lot longer than those in the UK (ours are 3 years) so you may not want to "waste" time with a masters. I definitely feel that you should concentrate on getting more lab experience if you were to delay applying for a PhD though.
  14. The enzyme takes sucrose and converts it to glucose and fructose. In this reaction, one mole of sucrose produces one mole of glucose and one mole of fructose. So therefore the rate at which the sucrose disappears (goes down in concentration) and glucose appears is indicative of the rate at which the enzyme is working.
  15. So how exactly would you go about doing that? I'm interested. Probably because of the massive risk involved with tampering with such a complex and carefully balanced system.
  16. It is a LOT more complicated than that. It's individual-specific (no one's going to have the EXACT same proteins as you, except possibly a twin), hence why you have to give immunosuppressant drugs to someone who has received a transplant.
  17. If the device was used for several hours at a time, I'm pretty sure it would still be irritating to some extent. Now I'm wondering what on earth this device is haha.
  18. Have you checked the MSDS safety data? You probably have consulted similar as that would be the logical first port of call, but from what it says, you would be able to draw a logical conclusion from that depending on how the gas is stored. i.e. if it was in contact with the skin, it would be pretty mad as e.g. NO and N02 are corrosive. Especially as 200ppm is an insanely high concentration.
  19. Greippi


    Strength? Iridium is really brittle. Titanium is the strongest element, light too.
  20. Greippi


    Tungsten carbide is one of the hardest alloys. Boron is the hardest element, Cubic BC5 is not as hard as diamond, but much tougher. SiO2 or Al2O3 with zirconia are the toughest (most resistant to fracture).
  21. Greippi

    ear size

    A lot of it has to do with the shape of the actual ear itself (as in dogs, which can control their ears with muscles to maximise hearing depending on the circumstances). Dolphins have a huge hearing range (1-150kHz) and yet have no obvious big flappy ears! Desert animals often have large ears to lose heat (greater surface area with veins close to the surface).
  22. There are 60415 protein structures in the Protein Data Bank. We might as well do something with this knowledge! Designing proteins with new function could help create new biocatalysis for industry, or even have a role in therapy for disease.
  23. Oh okay, coincidentally that's pretty much what I might be doing next year.
  24. Yeah haha, tell me about it. More often than not it just falls apart or is nowhere near as good as the original enzyme. Hence another reason we need to improve our knowledge on/understanding of the forces holding a protein together/folding mechanism. CharonY, have you done this/worked on this sort of thing?
  25. I dared my boyfriend to eat a teabag and he nearly choked to death. Plus it was not a pleasant taste.
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