Reduction in cost of DNA analysis

Discussion in 'Biology & Genetics' started by Billy T, Jun 9, 2007.

  1. Billy T Use Sugar Cane Alcohol car Fuel Valued Senior Member

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    Thanks. Do you also know of Dr. Semelwise? Semilvise? etc -not sure of spelling anymore. As a woman you should. (I was wandering around in Budapest and discovered his statue, read his incredable history.) He gave himself "child birth fever" to prove the doctor's dirty hands were spreading it in the hospital (well before Pasture discovered germs) as they went form one woman to the next. When he still insistented that the doctors were "dirty" and they knew it was the women who were dirty "down there" they finally had him locked up in the asylem! Every woman should know him and his works.

    It seems your illustration is slightly mis leading about the location of the Telomere.

    I do not know why cells should divide less frequently on low calorie diet but they surely must is your weight goes up and down very few months by 20% so it is sort of that which makes me thin as I do.
     
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  3. S.A.M. uniquely dreadful Valued Senior Member

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    Why do you say so?
     
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  5. Billy T Use Sugar Cane Alcohol car Fuel Valued Senior Member

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    the telomere appears to be already in place near the lower right end yet more is still folding down from the foreground DNA.
     
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  7. S.A.M. uniquely dreadful Valued Senior Member

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    Thats just a representative diagram to show how one leads to the other.

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    The telomere is just the section at the end of the chromosome. The unfolding is for visualisation of the fine structure
     
  8. CharonZ Registered Senior Member

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    I think SAM did a great job explaining things (much better than my rush jobs)- yes I lurk a lot when I have to do computer work

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    .
    Less nutrients should not lead to reduction of cell divison, btw. You would have to have severe (possible lethal) nutrient limitation before cell cycles are getting disrupted.
    There are theories around, a recent one stating that it leads to oxidative stress which, paradoxically, may extend life-span (Ristow 2007 cell metabolism).

    Also regarding double stranded RNA (or dsRNA): some viruses possess dsRNA. Also siRNA is the framgentation product of dsRNA (by Dicer).

    Actually RNA has a another sugar backbone. DNA possess a desoxyribose as sugar and RNA ribose (hence "R" and "D"). And of course there is the exchange of a base thymidine-> uracil, however the sugar backbone is the "diagnostic" part.
    Other than that I do not think that there is much to comment on

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  9. Billy T Use Sugar Cane Alcohol car Fuel Valued Senior Member

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    Thanks again CharonZ
     
  10. Billy T Use Sugar Cane Alcohol car Fuel Valued Senior Member

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    I own stock in Teva, so received following news, illustrating the coming future of medicine. (Thanks to decreasing cost of DNA sequencing or more accurately, I think: "SNPing"):

    "... The new research, which deals with the genetic components of the response to Copaxone*, was recently published in the journal Pharmacogenetics and Genomics . It represents a significant step toward realizing this medical vision. In the collaborative study, Teva supplied DNA samples from drug-treated patients**, and the genetic tests were performed at the Crown Human Genome Center of the Weizmann Institute, headed by Prof. Doron Lancet of the Institute's Department of Molecular Genetics. The scientists used state-of-the-art equipment*** - the first of its kind in Israel - that allows for the rapid and accurate scanning of variations in the human genome. The scientists then examined the links between the genetic markers they found and the response of MS patients to Copaxone. They identified several genes that are tied to a positive response to the drug.

    "We analyzed the DNA sequences in 27 candidate genes from each patient participating in the trial," said Lancet, "and we identified two genes with a high potential for determining the response to Copaxone. In the future, it may be possible to use this method to scan the genome of MS sufferers, to predict the response levels in advance, and to optimize the dosage and treatment protocol to suit each patient personally."
    ----------------
    *Teva, is mainly a "generic drug seller," but Copaxone is a Teva developed drug and I think their biggest income producer by far - It has been shown to be the best (for MS) and with less adverse side effects (which were so bad with one competitor, based in Ireland, that for a year or two, their drug was off the market.)

    **I wonder if "informed consent" is required (in US or Israel) when patient ID is not told.

    ***I bet it was one of ILMN's machines as I known that one has been sold to researchers in Israel. Anyone with access to the published article and interest enough to read it, please let me know what equipment was used in the "SNPing." Thanks.
     
    Last edited by a moderator: Oct 11, 2007
  11. CharonZ Registered Senior Member

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    SNPing sounds nice (and is quite accurate actually), however it is generally referred to as "genotyping". The group in question uses traditionally genotyping methods coupled with a high throughput system that is mass spectrometer based (another completely different setup). They refer to it in the paper as sequenom:

    http://www.sequenom.com/seq_systems.html
     
  12. S.A.M. uniquely dreadful Valued Senior Member

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    Excess nutrients probably have inflammatory effects which may in turn lead to DNA damage and increased turnover and hence shortening of the telomere (speculation). The other side of the coin is when cell cycle continues in the presence of DNA damage and leads to carcinogenesis.
     
  13. Billy T Use Sugar Cane Alcohol car Fuel Valued Senior Member

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    Yes I liked the sound of it too. - Am I the first (as far as you know) to invent this "subdivison" of "genotyping" - I.e. "SNPing" is a subdivision of "genotyping" when you are looking / snooping for unusual variants in the base pairings. The phonetic similarity to "snooping" is also a natural re-inforcer of "SNPing," as is the English verb "TO SNIP," or cut small piece off of something larger. Thus, "SNPing" is an almost unavoidable extension of the English language. Hope it can keep the first three letters capital, as an exception, but doubt that will happen, but may if use is restricted to your field.
     
    Last edited by a moderator: Oct 11, 2007
  14. CharonZ Registered Senior Member

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    Actually I found that there are recent papers who used SNPing in a paper. I like "SNPing away at complex diseases."
    It has not yet become a technical term, though.

    (And SNP is, as you hinted at usually pronounce as "snip")
     
  15. CharonZ Registered Senior Member

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    Just to add this link regarding genome sequencing strategies. I haven't yet found the time to write something concise and intelligible up myself. It is a bit shortish and outdated (still refers to the human genome project) but overall readable.
     
  16. Billy T Use Sugar Cane Alcohol car Fuel Valued Senior Member

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    I do not understand well this field, but it seems personal medicine is moving closer with more cost reduction in genetic scanning:

    "When used with the recently launched Infinium® High-Density (HD) Human1M-Duo and Human610-Quad Genotyping BeadChips, and Illumina’s laboratory information management systems and automation options, the iScan System can complete genotyping studies up to six times faster than studies run on Illumina’s BeadStation.

    Illumina began shipping the iScan System in Q1 2008 to customers in both the academic and industrial sector. Among them were Scripps Genomics Medicine and Translational Science Institute and Cogenics™, a division of Clinical Data, Inc. ...“As our products become more complex, especially in the areas of high-density genotyping, copy number variation analysis, and gene expression profiling, it is important to have a scanner that keeps pace with the needs of genetic research,” says Jay Flatley, President and Chief Executive Officer of Illumina. “The iScan System offers researchers a next-generation microarray scanner that incorporates higher-performance optics and detection technology. Using our multi-sample iSelect™ BeadChip, researchers can process 120 samples in just 60 minutes, ... This directly translates into faster project completion, faster study publication, and reduced study costs.”

    Researchers at Scripps Genomics Medicine and Translational Science Institute are using the iScan System along with the Human610-Quad BeadChips to identify genetic determinants of cardiovascular disease towards more effective diagnostics and preventive strategies for this global health problem. After scanning fewer than 100 BeadChips, Scripps researchers have reported call rates averaging 99.8 percent, which are consistent with Illumina’s existing high call rates for the BeadStation.

    The iScan System is a high-resolution scanner that supports rapid, sensitive, and accurate imaging of Illumina’s BeadChip-based genetic analysis products. Using sub-micron resolution, assay automation, and laboratory information management systems options, researchers can produce up to 225 million genotypes per day. More information about the iScan System can be obtained at www.illumina.com/iScan.

    From: http://news.morningstar.com/newsnet/ViewNews.aspx?article=/BW/20080414005571_univ.xml

    PS I own shares in Illuminia. See Op and early posts. They have almost doubled since June 07 (or when I bought, which may be a few months earlier -too busy to check exactly). The people who do know field well like this company.
     
    Last edited by a moderator: Apr 19, 2008
  17. Billy T Use Sugar Cane Alcohol car Fuel Valued Senior Member

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    In addition to owning stock in ILMN I also have a position in QGEN. Both must be doing something right as share values are rapidly increasing.
    More details at www.qiagen.com & www.illumina.com

    Can anyone help be understand if the following is a "big deal" (seems to me to be) or just company hype?

    14May08: "QIAGEN and GENEART to develop, produce and commercialize a new product line for the enhanced production of all 35,000 human proteins. QIAgenes is the world's first comprehensive set of plasmids (small extra-chromosomal DNA molecules in bacteria) which serve as carriers ("vectors") for modified ("optimized") synthetic genes mapping the entire human genome. By using the QIAgenes set of plasmids and optimized genes for synthetic protein production in bacteria, academic and biomedical researchers, as well as biotech and pharmaceutical companies can more easily produce large amounts of proteins which play key roles in diseases such as cancer and their treatment.

    This new product line helps researchers develop new therapeutics, vaccines and accelerates drug screening processes.
    QIAgenes will be available starting May 19, 2008, through QIAGEN's web portal GeneGlobe, which already hosts the world's largest database of gene regulation and gene expression assays. The addition of synthetic genes is a synergistic extension of this offering, as the use of synthetic genes often follows the use of such assays. Additional variants of the synthetic genes, which are currently designed for E. coli bacteria only, are subject to future development.

    Scientists from both companies compared optimized and normal gene sequences of 100 different proteins from the five most common protein classes, thereby generating the most comprehensive validation study of its kind. The trial showed that QIAgenes solutions achieved very high success rates of more than 90% and yielded up to 50 times more protein than conventional methods using "normal" genes by providing optimized synthetic genes and purification methods. The first hurdle was to obtain an accurate high quality plasmid construct of any gene of choice, and second to produce the protein in sufficient amounts in bacteria. The market for synthetic DNA is currently estimated to be approximately US$ 80-100 million in revenues and to be growing by at least 30% per year. ..."
    Billy T compressed and edited the above from:
    http://news.morningstar.com/newsnet/ViewNews.aspx?article=/MWR/0396945_univ.xml
    If part is now nonsense, see above link and correct.

    Specifically, the part I made bold above. Can this "carrier" mean some coding for protiens is in a virus that could infect a cell and make it make or (as sRNAi block) some protien associated with genetic disease? I have interest in several other companies that are in the early stages of approaching disease therapy via this converion of viruses to "our side" in the war betweeen man and "bugs."
     
    Last edited by a moderator: May 15, 2008
  18. ElectricFetus Sanity going, going, gone Valued Senior Member

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    No the vector are used to infect a specfic bacteria, plasmid vectors aren't transmittable in people. The company is working on the mass production of human proteins via synthetic plasmids specifiably designed for protein production in a specific host, the host bacteria is also high modified for optimized protein production and susceptibility to plasmid infection.

    Say I want to study a human protein, I ask this company to produce it, they mass produce that protein and purify it easily, give it to me for a cheaper price then competitors. I study protein find how it cause disease, figure out cure, etc. This is not end level products like making cures, this is early level using for making products for understanding disease.
     
  19. Billy T Use Sugar Cane Alcohol car Fuel Valued Senior Member

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    Thanks. that was very helpful. I forget the name ot the molecular factory that the RNA information guides to make protiens, but from what you say I understand that in some sense QIAGEN is trying to "build better factories" in Bacteria (E-coli only now I think) to make specific protiens. If that is correct, or approximately so, where does the human RNA come from? (I think they are making human protiens.) Is RNA sort like a catalist in that it can be used many times to promote the same reaction. (So they don't need to inject much? or do they also modify the bacteira's DNA to make it make the needed RNA?) I have never had any courses in cellular biology - may not have been such course back when I was in university - physic was easy compared to all this stuff. Thanks again I really appreciate it.

    PS I have long thought that some day most chemical things man needs will be made by "bugs" for example even the monomers for plastics. BTW PetroBras is building new plant to make polyproplene etc. from alcohol, instead of oil etc. Do you think this joint project is a step towards that day? I.e. is this a "big deal" or just sales effort directed at researchers.
     
    Last edited by a moderator: May 15, 2008
  20. ElectricFetus Sanity going, going, gone Valued Senior Member

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    The RNA comes from people or is synthesized using a predesigned sequence feed to the computer the controls the RNA/DNA synthesizer. A gene in your body is made of DNA, it is transcribe to RNA, this "messenger" RNA is repeatedly translated into protein, RNA can have functions other then being used to make protein, it can in a few causes being an enzyme (proteins are usually responsible for enzyme or catalysis activity) it can in other cases regulate the rate a gene is transcribe or the rate a other mRNA is translated. For example "interference" RNA can bind to a prevent the translation of a mRNA, thus prevent the gene from producing its protein.

    We have already been making plastic from biomass, an excellent example though would be polylactides

    Modifying bacteria fermentation and synthesis pathways is in active research bot in academia and cooperations for the productions of fuels, plastics and pharmaceuticals. The only thing limiting these bioproducts is the price of oil and price of implementation, once it become cheaper to make biomass based products instead of petroleum ones, the next hurdle is the price of making factors to do it.
     
  21. CharonZ Registered Senior Member

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    Actually only relatively short RNA sequences can be synthesized de novo. However, for the expression of human proteins in bacteria one only needs the DNA sequence of the protein do be expressed (only using the exons). Of course proteins synthesized from bacteria sometimes have different properties (normally due to protein modification and/or folding).

    A lot of chemicals are produced by bacteria today. Examples include food additives (e.g. glutamate, lysine), pharmazeuticals (e.g. insuling) and so on.
     
  22. ElectricFetus Sanity going, going, gone Valued Senior Member

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  23. CharonZ Registered Senior Member

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    Well, I was talking about complete chemical synthesis of whole RNA strands. And not using RNA polymerases from DNA templates. Nonetheless for protein expression one seldom just uses the mRNA. It is kind of extremely inefficient.
     

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