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Old 05-18-2014, 12:33 PM   #1
'lizbeth
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Post DNA The secret of Life

Excerpts from DNA The secret of Life by James D. Watson, Nobel prize winner Double Helix with Andrew Berry:

The most humbling aspect of the Human Genome Project so far has been the realization that we know remarkably little about what the vast majority of human genes do. To use the hard-won information properly requires us to devise methods for studying the function of genes on a genomewide scale. . .

Proteomics is the study of the proteins encoded by genes. Transcriptomics is devoted to determining where and when genes are expressed – that is, which genes are transcriptionally active in a given cell. If the genome is ultimately to be understood in its more dynamic reality, not as a mere set of instructions for life’s assembly but as the screenplay for life’s movie – all the drama described in the precise order it is meant to occur – then proteomics and transcriptomics provide the keys to glimpsing the live action. The more we learn, the more we see of Life, the Movie.

We have long appreciated that a protein is a great deal more in biological terms than the linear string of amino acids that compose it. How the string folds up to produce a distinctive three-dimensional configuration is really the key to its function – what proteomics seeks to know . . . Knowledge of a protein’s three-dimensional structure greatly assists the work of medical chemists in their hunt for new drugs that work, as many do, by inhibiting protein functioning . . .

All too often, however, the three dimensional structure itself provides no particular indication of that protein’s function. Important clues may come instead from studying how the mystery protein interacts with other known ones. A simple way to identify such interactions involves spotting out samples of a set of know proteins on a microscope slide and then dousing them with the mystery protein, which has been previously treated so it will fluoresce under UV light. Where our test protein “sticks” to a particular spot on the slide’s protein grid, it has become bound to the protein in that spot, causing it too to become fluorescent. Presumably, then, these two proteins are engineered to interact within the cell. . . .

To be continued
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Old 05-19-2014, 08:13 AM   #2
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Re: DNA The secret of Life

p220




. . . the functioning of all genes in a genome can be by measuring the relative amounts of their respective messenger RNA (mRNA) products. If you are interested in the genes being expressed in, say, a human liver cell, you isolate a sample of mRNAs from liver tissue. This represents a snapshot of the mRNA population in the liver cell: Very active genes, those most heavily transcribed and that produce many mRNA molecules, will be abundantly represented, whereas genes that are rarely transcribed will contribute only a few copies to the mRNA sample.
The key to transcriptomics is a surprisingly simple invention known as a DNA microarray. Imagine a microscope slide with a grid of 35,000 tiny dot-shaped wells etched onto it. Using precise micropipetting techniques, DNA sequences from just one gene are deposited in each well so that the grid contains every gene in the human genome. Critically, the location on the microscope slide of each gene’s DNA is known. . . . Using standard biochemical techniques, you can tag your live mRNAs with a chemical marker so, like the proteins mentioned above, they will fluoresce obligingly under UV light. Then comes the step where the power and simplicity of the technique becomes wonderfully apparent: you simply dump your sample of mRNAs onto the microarray with its minuscule chessboard of 35,000 gene filled wells. The very same base-pairing bonds that hold together the two strands of the double helix will compel each mRNA molecule to pair off with the gene from which it was derived. The complementarity is precise and foolproof: The mRNAs from gene X will bond only to the very spot occupied by gene X on the microarray. The next step is merely to observe which spots have picked up the fluorescent mRNAs. One spot on the microarray may show no fluorescence, implying that implying that there was no complementary mRNA in the sample – and thus, we may infer, no active transcription of that gene in the liver cell. On the other hand, a number of spots do fluoresce, some with particular intensity; this indicates that many mRNA molecules have bound to it. Conclusion: a very active gene. Thus, with a single simple experimental assay, you have identified every one of the genes active in the liver. And such molecular panoramas have been made possible thanks to the success of the Human Genome Project and the new mind-set it has ushered into biology: we no longer need to study bits and pieces – we can now see the whole picture in all its spectacular glory.

To be continued
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Old 05-19-2014, 08:20 AM   #3
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Post Re: DNA The secret of Life

Definition of mRNA

Messenger RNA 1. (Biochemistry) biochem a form of RNA, transcribed from a single strand of DNA, that carries genetic information required for protein synthesis from DNA to the ribosomes. Sometimes shortened to: mRNA


messenger RNAn. Abbr. mRNA The form of RNA that mediates the transfer of genetic information from the cell nucleus to ribosomes in the cytoplasm, where it serves as a template for protein synthesis. It is synthesized from a DNA template during the process of transcription.

The American Heritage® Dictionary of the English Language, Fourth Edition copyright ©2000 by Houghton Mifflin Company. Updated in 2009. Published by Houghton Mifflin Company. All rights reserved.

messenger RNAn1. (Biochemistry) biochem a form of RNA, transcribed from a single strand of DNA, that carries genetic information required for protein synthesis from DNA to the ribosomes. Sometimes shortened to: mRNA See also transfer RNA, genetic code

Collins English Dictionary – Complete and Unabridged © HarperCollins Publishers 1991, 1994, 1998, 2000, 2003


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Old 05-20-2014, 03:01 PM   #4
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Re: DNA The secret of Life

Transcriptomics is more than just another brilliant technical innovation. It promises to take us to a new level in the hunt for the genes that cause illness: using microarray technology we can discover the chemical basis for particular afflictions by studying the differences between healthy and diseases tissue as a function of gene expression. The logic is simple. We carry out microarray gene expression analysis on both normal and cancerous tissue, and spot the difference between the two, the genes being expressed in one and not the other. Once we can identify which genes are malfunctioning – either over- or underexpressing themselves in the cancerous tissue, for instance – we may be able to establish a target that can be attacked with pinpoint molecular therapies as opposed to broadly toxic radio-and chemotherapies that destroy health as well as diseased cells . . .

At Cold Spring Harbor Laboratory, Michael Wigler is using the method in yet another way: rather than adding RNA to a microarray and looking for gene expression, he is adding DNA from cancer cells to create a profile of the genetic diversity present in tumors. Many cancers are caused by chromosomal rearrangements – such as might occur when segments of a chromosome are inadvertently duplicated, leading to an excess in the number of genes that code for growth-promoting proteins. Other cancers arise due to the loss of genes coding for proteins that repress cell growth. Applying Wigler’s technique, clinicians biopsy cancerous and healthy tissues from the same person. DNA from the cancerous tissue is chemically tag with red dye white the DNA from the normal tissue is tagged green. Genes amplified in cancer cells are marked by red spots (because there are many more red-tagged molecules binding to that spot than green-tagged ones) while genes deleted in cancer cells show up as green spots on the microarray (because there is no red-tagged molecule to bind there). Such experiments already greatly expanded the list of genes know to contribute to breast cancer.
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Old 05-24-2014, 08:14 AM   #5
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Re: DNA The secret of Life

Thank you for this Elizabeth. It is a relief, emotionally, to read about the area where the real cure will lie. This is a scientific building blocks disease we have, and the next generation of women our age will hopefully have access to real cures, based on science students nowadays getting more committed and funded to put serious studies in motion that will save the lives of the next generation of b.c sufferers.
__________________
fall 2008: mammo of rt breast worrisome so am asked to redo mammo and have ultrasound of rt breast.I delay it til january 2009 and the results are "no cancer in rt breast. phew."
found plum sized lump in right breast the day before my dad died: April 17th 2011. saw it in mirror, while i was wearing a top, examining my figure after losing 10 lbs on dr. bernstein diet.
diagnosed may 10 2011

mast/lymphectomy: june 7 2011, 5/20 cancerous nodes. stage 3a before radiation oncologist during our first mtg on july 15th says he found cancer on the lymph node of my breast bone. Now stage 3b.
her2+++, EN-, PN-. Rt brst tumors:3 at onset, 4.5 cm was the big one
chemos: 3fec's followed by 3 taxotere, total of 18 wks chemo. sept: halfway thru chemo the mastectomy scar decides to open and ooze pus. (not healed before chemo) eventually with canasten powder sent by friend in ny (illegal in canada) it heals.
radiations:although scheduled to begin 25 january 2012, I am so terrified by it (rads cause other cancers) I don't start til february, miss a bunch, reschedule them all and finally finish 35 rads mid april. reason for 7 extra atop the 28 scheduled is that when i first met my rads oncologist he said he saw a tumor on the lymph node of my breastbone. extra 7 are special kind of beam used for that lymphnode. rads onc tells me nobody ever took so long to do rads so he cannot speak for effectiveness. trials had been done only on consecutive days so......we'll see.....
10 mos of herceptin started 6 wks into chemo. canadian onc says 10 mos is just as effective as the full yr recommended by dr. slamon......so we'll see..completed july 2012.
Sept 18 2012: reconstruction and 3 drains. fails. i wear antibiotic pouch on my job for two months and have 60 consecutive days visiting a nursing centre where they apply burn victims' silver paper and clean the oozing infection daily. silicone leaks out daily. plastic surgeon in caribbean. emergency dept wont remove "his" work. He finally appears and orders me in into an emergency removal of implant. I make him promise no drains and I get my way. No infection as a result. Chest looks like a map of Brazil. Had a perfectly good left breast on Sept 17th but surgeon wanted to "save another woman an operation" ? so he had crashed two operations together on my left breast, foregoing the intermediary operation where you install an expander. the first surgeon a year earlier had flat out refused to waste five hours on his feet taking both boobs. flat out refusal. between the canadian health system saving money and both these asses, I got screwed. who knows when i can next get enough time off work (i work for myself and have no substitute when my husband is on contract) to get boobs again. arrrgh.


I have a blog where I document this trip and vent.
www.nora'scancerblog.blogspot.com . I stopped the blog before radiation. I think the steroids made me more angry and depressed and i just hated reading it anymore
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