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August 15, 2004

Your genome on an iPod, but not your brain

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Posted by Zack Lynch

Up to now the biggest numbers game in biology had been run by the publicly financed Human Genome Project, which sequenced each of the three billion letters in the DNA code for a human being. "I know a neuroscientist who downloaded the Human Genome Project onto an Apple iPod," says Mark Boguski, an M.D. and Ph.D. who is a veteran of that project and who now directs the Brain Atlas Project at Allen Institute for Brain Science. "But that was 3 gigabytes, and we will be producing petabytes." Yes, your brain is very complex and this is why neuroinformatics will keep information technology vendors busy for many years to come.

Comments (0) + TrackBacks (0) | Category: Protein/Gene Chips

June 25, 2004

The Answer is in Your Blood (Part 2)

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Posted by Zack Lynch

This week's Science also has an interesting proteomics tid-bit, titled, "Written in the Blood." The piece confirms the diagnostic potential of blood. "Blood teems with telltale proteins that can reveal incipient prostate cancer, for example, and help show whether a patient is cruising for a heart attack. Researchers hoping to discover more of these bio-markers might start with this new collection from the National Cancer Institute in Frederick, Maryland. The database catalogs more than 1400 blood proteins isolated during a recent exhaustive analysis, the largest haul yet." This just goes to show that we still don't know all the proteins that exist in our blood, or for that matter in our brains, and that we are still in need of effective high-throughput methods of detecting and identifying them. Where is that protein chip anyway?

Comments (0) + TrackBacks (0) | Category: Protein/Gene Chips

November 20, 2003

Biochip Advances

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Posted by Zack Lynch

As I mentioned in Biochips, Brain Imaging and Behavior, further advances in biochips will be needed before effective neuroceuticals can be developed. Most importantly, no technology exists today to analyze proteins in an inexpensive and reliable manner.

FuturePundit's Biotech Advance Rates posts highlight the continually decreasing cost of biochips (take a look). I agree with him that the most exciting thing in biotechnology are advances in instrumentation and assay technologies. As he put it, "with a much better set of tools all discoveries could be made much sooner and with less effort and all treatments could be developed much more rapidly."

Comments (2) | Category: Protein/Gene Chips

June 19, 2003

Broad Support for "Y" Men Are Men

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Posted by Zack Lynch

Sex in humans is determined by the fact men carry one X chromosome and one Y chromosome in each cell, while women carry two Xs.


David Page of the Whitehead Institute has recently shown that Y chromosomes can repair its own genes in an experiment that denied the Y chromosome the benefits of recombining with the X.  The result was that the Y recombined with itself.  Dr. Page's team also found 78 active genes on the Y, contradicting earlier impressions of the chromosome as being a genetic wasteland apart from its male-determining gene.


In related news, MIT and Harvard announced today the formation of The Broad Institute whose purpose will be to fulfill the promise of the Human Genome Project for medicine.  As Charles M. Vest, president of MIT noted, “This venture will be an important nexus of Boston and Cambridge’s contributions in the future. We are deeply grateful to Eli and Edye Broad for their visionary commitment ($100m immediately) and for their extraordinary leadership as philanthropists." 

Comments (0) | Category: Protein/Gene Chips

June 18, 2003

Faster than a Speeding Gene

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Posted by Zack Lynch

Most people forget that we've only mapped the complete genome of a few people.  Although significant, the real breakthrough will come from population level analysis of genetic variation. 


The International HapMap Project is doing just this.  Haplotypes are genetic sequence blocks that are shared by many people.  Once these haplotypes are mapped it will form a powerful shortcut to identifying inherited gene sequences linked to disorders such as diabetes, heart disease and cancer.


Biomedical breakthroughs extending life and health are closer than we think. The aggressive timeline for the Human Genome Project started in 1990 was 15 years.  It was completed in 10.  What projects are being worked on now that will move much faster than most expect? 

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April 16, 2003

What is a gene?  Really.

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Posted by Zack Lynch

Now that the human genome has been sequenced it is time to return to simpler questions, like what is a gene?



  • In the early 1900s, a gene was as an abstract concept to explain the hereditary basis of traits. 
  • In the 1930s, Beadle introduced the concept of "one gene, one enzyme," which later became "one gene, one polypeptide."
  • Today, a gene is defined in molecular terms as "a complete chromosomal segment responsible for making a functional product."  For more detail, see this week's Science.

Sequencing the genome is just the first step in a much larger project Human Biology Project.  As Eric Lander of the Whitehead Institute reminds us, "starting today, the real serious analysis of things can begin."


Powered by faster gene chips the cost of genetic analysis continues to plummet. At the beginning of the project "it cost $10 to definitively identify a single base pair... and a highly trained technician could scan perhaps 10,000 base pairs in a day. Now the equivalent cost is 5 cents and lightning-fast robotic sequencers routinely process 10,000 base pairs a second."   Now that's progress.  Next step, sequencing the proteome.

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April 08, 2003

Evolution IS a Fact

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Posted by Zack Lynch

Other than my concern that Post Traumatic Stress Syndrome may eventually overtake depression as the leading global mental health problem, Richard Gayle's blog today on evolution tops my list of memes that deserve repeating.


We again have people rejecting textbooks because the books discuss evolution but not creationism. Evolution is a fact. It is the foundation upon which modern biology rests. Trying to pretend differently (as one of the Board members said "I do not believe that we evolved from anything other than human beings") only hurts the students and furthers ignorance. It does not reflect well on Tennessee. But then it was the state that outlawed the teaching of evolution, leading to the Scopes Trial.

Comments (0) | Category: Protein/Gene Chips

April 02, 2003

Biosimulation: Building upon the Past

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Posted by Zack Lynch

Like every technological revolution, the old is supporting the new.  Today's Protein Folding Project is leveraging the distributed computational capabilities of thousands of computers world-wide to unwind the hyper-complex problem of protein folding.  The emerging biological revolution is completely dependent on information technology, just as information technology would have been impossible without industrial age advances like electricity.


As Charles Delisi recently mentioned at a Santa Fe Institute meeting, "there is no way the past ten years of advances in genomics would have been possible without the computational capabilities brought forth by the microchip." 

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March 27, 2003

Biochips, Brain Imaging and Behavior

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Posted by Zack Lynch

Just as the Information Revolution has been driven by increasingly powerful microprocessors, the coming Biological Revolution will be driven by a "whole biochip" that enables consistent control over biological analysis and production.  This whole biochip will contain currently disparate and still developing technologies, making possible the inexpensive analysis of the three most important levels of biological analysis: DNA, RNA and proteins.


The convergence of information acquired from the whole biochip and advanced brain imaging technology will provide the resolution needed to develop new tools to influence human behavior. By combining data on cellular biochemical processes with information on the specific location of neuron interactions a robust understanding of how the human brain operates will emerge.

This information will represent a profound leap in our understanding of how each individual’s brain works giving rise to a whole new class of what today are referred to as neuropsychopharmaceuticals.  Tomorrow these neuroceuticals, as they will be called, will drive societal change.

Comments (3) | Category: Protein/Gene Chips

March 26, 2003

Protein Chips and My Wife

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Posted by Zack Lynch

My wife can attest to the Economist's just released technology report detailing the difficulties of developing a protein chip.  Three years ago she left a UCSF/Stanford's Doctoral program in Neuroscience with a post-doc friend to start a protein chip company, Aspira Biosystems.


Protein chips promise to accurately and inexpensively capture and identify proteins, just as gene chips now enable reliable and efficient genetic analysis.  The development of effective protein chips is a critical link in the development of personalized medicine.


Designing a protein chip is not easy, requiring expertise from a wide variety of disciplines including, protein chemistry, materials science and surface chemistry.  As the article poignantly declares, "a protein chip is to a gene chip what a supercomputer is to a calculator."


DNA is simpler to analyze than proteins for several reasons:



  • DNA has four building blocks, proteins have 20 amino acid building blocks
  • Genes code for the one purpose of producing proteins, proteins serve multiple purposes as enzymes, receptors, signaling agents
  • The genome is a relatively well-defined collection of about 40,000 genes, but the proteome is a loose collection of millions of proteins at different stages of change

Aspira's competitive advantage stems from their abilty to generate capture arrays with predictable specificity.  Thanks to incredible dedication and continued private and public funding, Aspira is poised to leap to the forefront of the burgeoning protein chip market. 


Obviously, I may be a bit biased on this topic.

Comments (0) | Category: Protein/Gene Chips