Serving Science and Society Into the New Millenium (1998) / Chapter Skim
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Part I Enabling Research for Science and Technology: Biotechnology
Part I Enabling Research for Science and Technology: Biotechnology
Pages 11-30
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Part I Enabling Research for Science and Technology . Biotechnology
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For most people, trying to look directly at the information in DNA is like trying to translate hieroglyphics; even at the RNA level, for most of us, trying to make sense out of sequence data 13
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Most genes are present in a 1-to-1 ratio. However, at the level of gene expression or protein synthesis, dynamic ranges that are fairly formidable appear.
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And it is likely to continue many of the large pharmaceutical companies are beginning to mount substantial genome efforts of their own.
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, it is 1 gene per 30,000-50,000 base pairs. If one blindly decides to sequence human DNA today, functional units of information will be discovered at only 1/50 to 1/30 the rate for bacteria, if one does simple .
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Mutation detection, if one has to do it by direct DNA sequencing, is very inefficient because one has to sequence millions of base pairs to find 1 mutation. If someone can come up with a method of comparative sequencing that projects only the differences, we will gain an enormous economy of scale.
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Today, many of the methods are not user fnendly. Today, mutation detection usually requires accurate DNA sequencing.
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relatively simple MS can distinguish almost everything in 30-base DNA fragments. When confronted with a potentially novel sequencing method, people always ask, Has anything actually been sequenced with it?
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To demonstrate feasibility, we have sequenced 4 of the exons of p53 with mass spectrometry. We used a walking primary technique, because our read length is short and because we wanted to read through each primer in turn to make sure that the primers were not covering up mutations.
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The 3-dimensional structure of Streptavidin was the first novel structure solved by the multiple-wavelength anomalous dispersion method, which is uniquely enabled by cyclotron radiation and makes DOE's synchrotron sources an absolutely essential resource for any kind of modern structural biology. Streptavidin kills organisms because it interrupts a number of key metabolic pathways, including pyruvate metabolism and fatty acid biosynthesis; bacteria do not have a chance once this material is expressed inside them.
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Then, for example, when lacI is expressed, it also makes antisense strands against the streptavidin transcripts. When streptavidin is made, it makes antisense strands against lacI transcripts.
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What the genome project has done is open up a tremendous challenge. When the project was conceived, the notion was that we would have 100,000 genes to study in the year 2005, but we have 100,000 genes to study right now, and this is the enormous challenge that presents itself across a wide range of problems from information science through structural biology to plain biology.
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He began what later became the GenBank database. At that time, it was a pilot project called the Los Alamos Sequence Libraryi; Box 1 is from an early internal report at Los Alamos.
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If you look at the muscle transcriptional regulatory regions in general, you find that this geometry of spacing between the myoD family sites and mef2 family sites is important for muscle specificity and can be used to find some muscle-specific genes.5 If we combine the experimental studies of finding out where these sites are and the sequence-analysis studies of looking for the geometry of the patterns in the DNA, we will get to the point where we will be able to write computer programs that can look through the DNA and say, Here is a gene that is turned on in liver, here is a gene that is turned on in the atrium in the fetal heart, and so on. That approach will help in the challenge of finding the function of all the new genes that are turning up in the genome-sequencing projects.
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Synchrotron radiation has also enabled substantial biologic applications of other techniques, such as X-ray absorption spectroscopy and small-angle scattering, which provide information complementary to that obtained with crystallography. Synchrotron radiation is a polychromatic source, and its multiple wavelengths can be used to solve the phase problem in crystallography (which is necessary to visualize atomic structure)
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That also translates to increased demand and use of the synchrotron facilities because the same people want access for problems ranging from drug design to structures of modified enzymes with more-favorable industrial properties. Structural molecular-biology research integrates many parts of the BER portfolio, including relationship to the genome and environmental fields, such as bioremediation.
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The members of this family have similar structures and similar active sites, and those that are involved in chemical transformations catalyze similar reactions. We might expect to find other families that are unified by structure and function.
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Screening methods also require protein, and obtaining sufficient quantities is an in vitro challenge. Ultimately, refinements of these methods will be required if we are to turn sequence information into function information about the many gene sequences becoming available.
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