NCTimes.com Blogs

From SoCalTech

San Diego-based Tragara Pharmaceuticals, a developer of biopharmaceuticals aimed at cancer and inflammation treatments, has raised another $5M in a funding round, according to a regulatory filing by the firm last week. The filing indicates the equity funding comes as part of an ongoing, $10M fundraising effort by the company. No details on the funding have been announced by the firm. The firm has previously raised funding from Domain Associates, Proquest Investments, Mitsubishi, Morgenthaler Ventures, and Oxford Bioscience Partners. The firm last raised a large, $40M funding round in 2007.

Here’s the link to the SEC filing.

You didn’t know there was a book called “Stem Cells For Dummies”? There’s a Dummies book for everything else — acne; addiction & recovery; cast iron cooking; foreclosure investing …

Anyway, UCSD stem cell researcher Larry Goldstein has co-authored a book about stem cells. And he’s going to be talking about stem cells and signing his book the evening of Tuesday, March 2 at the Book Works, 2670 Via de la Valle, just east of I-5. The event starts at 7 p.m. and ends at 8 p.m.

The store’s number is (858) 755-3735.

Stem Cells For Dummies

Here’s more from the book’s blurb:

“A balanced, plain-English guide to this politically charged topic. This practical guide cuts away the hype and clearly presents the facts on stem cells. It explains what stem cells are and what they do, the legalities of harvesting them and using them in research, the latest research findings from the United States and abroad, and the prospects for medical stem cell therapies in the short and long term. It also discusses the ethical and moral considerations involved with the topic. But Goldstein presents us with the endless possibilities in using stem cells. Discover how stem cells are projected to make medical advances in the understanding and improved treatment of cancer, diabetes, heart disease, and more.”

Here’s more background about Goldstein from the Howard Hughes Medical Institute, where he is an investigator:

“Since the late 1990s, Lawrence Goldstein has been passionate about the promise of research with human embryonic stem cells—pliable, generic cells from the early embryo that scientists can convert into the body’s specialized cells to study basic biological processes, disease, and organ regeneration.
Goldstein became such an advocate for stem cells he helped write the California proposition that created a $3 billion funding organization in 2005 to support human stem cell research in the state. Voters supported the initiative because human embryonic stem cell research has been curtailed nationwide; the federal government has limited its financial support of research with these cells, citing the ethical problem of destroying embryos in performing the investigations.
When Goldstein first started promoting human embryonic stem cell research, he was acting to support the freedom of scientific inquiry to benefit society. Recently, though, Goldstein, funded by the Howard Hughes Medical Institute and the California program, has begun using human embryonic stem cells in his own laboratory. His research may demonstrate another example of the value of embryonic stem cells by helping to identify the cause of Alzheimer’s disease.
Goldstein studies the cellular machinery that moves material inside nerve cells and how problems with these conveyance systems might lead to Alzheimer’s and other neurodegenerative diseases. Embryonic stem cells, he says, are the only source of healthy human brain cells for his research. Extracting nerve cells from a living human brain for experimentation cannot be done.”

H/t to those industrious folks at Xconomy:

With all the froth around big tech company earnings, device announcements, and mobile app stores, it’s refreshing to see some long-term research in computing being funded. Google announced today it has awarded $1.35 million ($900,000 up front) to the University of Washington for work on mobile data collection for public health and environmental monitoring, and $100,000 to UC San Diego, for research on energy efficiency.
The awards are part of $5.7 million in the first Google Focused Awards Grants being given to a dozen projects led by 31 professors at 10 universities in the U.S. and U.K. The areas of research also include machine learning and privacy. The grants are for two to three years, and give the recipients “access to Google tools, technologies and expertise,” according to a blog post by Alfred Spector, Google’s vice president of research and special initiatives…
Meanwhile, the UCSD grant to computer scientists Tajana Simunic Rosing, Steven Swanson, and Amin Vahdat, is for studying energy efficiency in computing. Energy efficiency has been among the topics of interest at the UC San Diego campus of Calit2, the California Institute for Telecommunications and Information Technology. Calit2 director Larry Smarr views global warming as a serious environmental threat, and has highlighted efforts at UCSD and elsewhere to make data centers and other IT operations more energy-efficient.

Read the entire article at Xconomy

To get this to you as fast as possible, I’m going to give you the entire press release, plus the link to the entire report

The big news for San Diego County is that biomedical employment here has grown faster than in the state’s other biomed hubs. Here’s a chart:

California Biomedical Employment

The ACLU’s lawsuit against Myriad Genetics regarding two of its gene patents starts today. Friends of the Earth has issued a press release on this that contains several major inaccuracies often perpetuated in the media. I’ll reproduce the press release, with my corrections in italic.

Landmark Trial About Patenting Humans Begins Today
Humans can’t be patented.

NEW YORK CITY—The American Civil Liberties Union’s challenge of patents on two human genes associated with hereditary breast and ovarian cancer goes to trial here today.
Around 20 percent of the human genome has been patented by private interests.
Genes themselves, in a state of nature, cannot be patented.

The trial, which begins today, seeks a ruling on whether such patents violate the Patent Act and the Constitution. The defendant, Myriad Genetics holds the patents two human genes and charges $3,000 for its tests to determine whether the genes are present in individuals. These patents prevent other researchers from exploring connections between these genes and breast and ovarian cancer, or to come up with more effective and affordable tests.
Eric Hoffman, genetic engineering policy campaigner for Friends of the Earth, praised the ACLU for bringing the case to trial.
“Genetic material is the basis for all life. It has existed since the beginning of the living world,” Hoffman said. “The human genome is shared by all human beings, varying by only a fraction of a percent between people. This makes human genetic material a common good. Scientists are only beginning to understand the complexity of the human genome and by granting ownership over genes, the U.S. Patent and Trademark Office has limited the ability of scientists and health researchers to learn more about our bodies. This limits progress in fields that have the potential to benefit the health of all people.”
Patents do not grant ownership. They grant a legal monopoly on specified uses for a limited period. Patents do nothing to constrain the natural function of genes.

The trial beginning today is just one challenge confronting the corporations that are patenting human genes. Federal legislation, the “Genomic Research and Accessibility Act,” is soon expected to be introduced by Representative Xavier Becerra (D-CA). This bill prohibits the patenting of naturally occurring genes (nucleotide sequences), their functions, and their naturally occurring products, which the United States Patent and Trade Office has permitted since 1994.
“The Patent Office has erred in allowing corporations to patent parts of our bodies. We welcome Representative Becerra’s efforts to change this,” Hoffman said.
Again, patents are not made on the genes themselves, only on specified uses related to genes.

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I’ve written on gene patents over the years, and have taken the time to discuss with patent attorneys what patents can and cannot do. So while IANAL, I have a fair layman’s understanding of the subject:
– You cannot patent something in its natural state
– You may be able to patent a process or invention that uses something in nature..
– You cannot patent something that is obvious to someone knowledgeable in the field.

None of the above is meant as a statement on the wisdom of gene patents, which is a matter for philosophical and political debate. I’m simply correcting commonly held misconceptions about what gene patents do. No patent can grant ownership to some other entity over the natural functioning of your own genes.
*****************************************************************
For another view on gene patents, IP attorney Gene Quinn wrote in 2009 that the ACLU’s lawsuit is “frivolous”.

The ACLU should be sanctioned for its frivolous lawsuit challenging gene patents, which was filed Tuesday in the United States Federal District Court for the Southern District of New York. This lawsuit is nothing more than grandstanding, it presents frivolous arguments and outright lies. The ACLU would have you believe that the patents cover naturally occurring genes, which is simply not true, and the primary reason they should be sanctioned. The patents they are challenging relate to altered genes and diagnostic methods, so they are making assertions that are factually false, and challenging the patent system as being unconstitutional, which if successful would only bring an end to the biotechnology industry and perhaps even pharma. This would mean no new drugs, not diagnostic advances and hundreds of thousands of jobs lost, not to mention a stock market crash. . .
A diagnostic method does not naturally occur, but rather is a process conjured up by humans; and when something is “isolated” and “altered” it is not how God, the creator, spirits or luck (whichever you prefer) caused things to be naturally ordered. . .

The library of easily searchable compounds, that is. Researchers at Scripps’ Florida campus and the University of Texas Southwestern Medical Center say in a paper published in Cell that they have found a way to more efficiently search large libraries of compounds for the desired activity.

Here is Scripps’ press release:
JUPITER, FL, February 1, 2010 – The search for new drug compounds is probably worse than looking for a needle in a haystack because scientists are limited in the size of the haystacks they can rummage through—time and money make it virtually impossible to screen or search through super-large libraries of potential compounds. This is a serious problem, because there is enormous interest in identifying synthetic molecules that bind to proteins for applications in drug discovery, biology, and proteomics, and larger libraries should mean higher odds of success.
But large libraries come with large problems. Because even compounds with only modest affinity (binding to the target protein receptor with less force than those with high affinity) are usually marked as hits, researchers often end up with several hundred of them and, because of practical constraints involving time and money, no easy way to determine which might be the highest affinity or best compound to serve as a starting point to design a drug. These limitations and others have drastically blunted the use of very large libraries—monster libraries—in binding assays.
Now, in research published in the most recent issue of the journal Chemistry & Biology, Tom Kodadek, a professor at The Scripps Research Institute’s Florida campus, and his colleagues at Scripps Florida and the University of Texas Southwestern Medical Center have devised an innovative new way to solve this longstanding problem.
“Current methods severely limit the size of the libraries you can screen,” said Kodadek. “If you get 20 hits out of a 100,000 compound library, it’s feasible to re-synthesize each of those hits to test which are the most effective. But what if you want to screen 10 million compounds? It takes an impossible amount of time to re-synthesize promising compounds for further study. To find the most potent ligands, our new method stands head and shoulders over what is available to researchers today.”
Ligands are compounds that attach to proteins and alter their expression, potentially affecting a particular biomolecular activity, say, a protein pathway involved in a disease.
The new method displays millions of compounds on the surface of resin-based beads, each type of compound on a different bead. The hits are culled from the beads using a unique magnetic signature and then transferred to a microarray format—glass slides or silicon chips that can hold large numbers of compounds on their surface. The microarray format allows quantitative comparison of binding affinity that can be carried out without the need for tedious re-synthesis of many different compounds.
In the study, the team used mixed peptide/peptoid libraries—peptides make up proteins; peptoids are molecules closely related to, but more stable than peptides, making them more convenient for testing—but the method could be applied to any class of compound, according to Kodadek.

Changing the Paradigm
The Kodadek group’s method combines several different technical advances to enable this convenient and efficient screening.
These days, most active molecules are discovered through screening of two basic types. There are functional screens, in which small molecules are introduced into the wells of microtiter plates—flat plates with multiple wells that can reach as high as 9,600—and tested individually for their ability to alter the activity of an enzyme. Alternatively, there are binding assays, an approach first developed for bead-displayed peptide libraries, where each bead displays many copies of a single molecule.
“Our new method for screening synthetic libraries and characterizing the resultant hits combines many of the features of bead library screening and microarray-based analysis in a seamless fashion,” Kodadek said. “The new technique uses several million beads, each of which displays a unique ligand—theoretically as many as 64 million compounds. The target protein has an antibody attached to it that is covered with iron oxide particles—magnetic dust. If the peptoid ligand is a legitimate ligand, and attaches to the protein, we can pull it from the mass by using a magnetized centrifuge.”
The selected compounds are then removed from the beads through a unique cleaving process and attached to glass microarray slides. These arrays are mixed with different concentrations of the target protein, allowing the affinity strength of each compound on the array to be determined quickly and efficiently.
“This technology is relevant to custom libraries that are produced on beads,” Kodadek said. “Right now, that probably constitutes five percent of screening going on. My guess, however, is that ratio will change once researchers begin to adopt this new method.”
Adoption of this new technique will take time and something of a paradigm shift, Kodadek notes. The new screening technology monitors binding of the bead-immobilized molecule to the target protein; currently, the most widely used high-throughput screens monitor function of the compound. In addition, not all laboratories currently have the equipment and expertise necessary to make microarrays of small molecules.
“I think our method can revolutionize medicinal chemistry,” said Kodadek, “but this is only the first step.”
The first author of the study, “Seamless Bead to Microarray Screening: Rapid Identification of the Highest Affinity Protein Ligands from Large Combinatorial Libraries,” is John M. Astle of the University of Texas. In addition to Kodadek, other authors include Levi S. Simpson and Steven Connell of the University of Texas Southwestern Medical Center; and Yong Huang, M. Muralidhar Reddy, Rosemary Wilson, and Johnnie Wilson of The Scripps Research Institute.