Health,Stem Cells, and Technology

Thursday, March 31, 2016

A New Methylation Target - DNA methylation on N6-adenine in mammalian embryonic stem cells

A new means for environmental regulation of DNA in mammals has been discovered. A long held view by many scientist was that 5-methylcytosine is the only form of DNA methylation in mammalian genomes. In a new study published this week in Nature, Wu et al identify N6-methyladenine as another form of DNA modification in mouse embryonic stem cells.

The DNA of most organisms is composed of four standard bases and a small set of modified bases that are produced enzymatically from these four after DNA replication. One modified base, N6-methyladenine (N6mA), is prevalent in prokaryotes (bacteria and archaea), but whether it is found in mammals has remained unclear. In a paper online in Nature, Wu et the existence of N6mA in mouse stem cells. This exciting discovery is enhanced by the identification of an enzyme that removes methyl groups from N6mA, and by the finding that the modification is enriched in certain regulatory DNA sequences — data that together provide clues to N6mA's possible function in mammalian genomes.

The new study suggests that N6-methyladenine has developed a new role in epigenetic silencing in mammalian evolution distinct from its role in gene activation in other organisms. The results demonstrate that N6-methyladenine constitutes a crucial component of the epigenetic regulation repertoire in mammalian genomes. This is another mechanism by which the environment can regulate DNA by modifying the chemical structure of DNA by adding CH3, a methyl group, to the base. This in turn can suppress expression of the targeted DNA sequence.

UC Berkeley and Aduro Biotech launch new immunotherapy, vaccine effort

A good example of academia, government, and industry working together is exemplified by UC Berkeley cancer immunologists teaming with colleagues working on infectious disease to create a new Immunotherapeutics and Vaccine Research Initiative, fueled by $7.5 million in funding from Aduro Biotech Inc., a Berkeley company that develops immunotherapies for cancer and other diseases.

An excellent video explaining the science and the collaboration is available here.

Berkeley’s newest field site, Blue Oak Ranch Reserve for Integrative Biology

UC Berkeley’s newest research station, the Blue Oak Ranch Reserve, threw an open house to show off its new facilities, nestled amid rolling green, flower-studded hills east of San Jose.

The pristine reserve, operated by the campus for UC’s Natural Reserve System, has become a field research site for biologists interested in California’s oak woodlands, and comes complete with an embedded wireless sensing network that rivals many urban networks. Each of the nodes spread over the 3,280-acre reserve measures temperature, rain, sunshine, soil moisture and more, sending it back to the campus to be processed and analyzed. The system senses much more broadly the variation in those environmental conditions over the landscape than a single weather station. 

Blue Oak Ranch Reserve habitats support at least 130 species of birds, approximately 41 species of mammals, 7 species of amphibians, more 14 species of reptiles, 7 species of fish, and hundreds of species of invertebrates. Reserve streams and 17 ponds are Sensitive Aquatic Resource Areas habitats that support most of the reserve's rare species. River otter, California tiger salamander, foothill yellow-legged frog, and red-legged frog can all be found along reserve waterways. Riparian areas are utilized by more than ten species of neotropical migratory birds, including flycatchers, warblers, and vireos.

The Reserve is east of San Jose on the road that leads into the mountains to the University of California's Lick Observatory.BlueOakRanchReserve

Thursday, March 24, 2016

For The Love of Money: The NFL and Brain Injury

First, we should all be thankful for investigative reporting in general, and for that of the NY Times in particular. Without a well educated, well trained, and dedicated and experienced press we'd be in the dark about many things. Now, an investigation by The NY Times has found that the N.F.L.’s concussion research was far more flawed than previously known.

Confidential data obtained by The Times shows that more than 100 diagnosed concussions were omitted from the studies, including some severe injuries to stars like quarterbacks Steve Young and Troy Aikman. The committee then calculated the rates of concussions using the incomplete data, making the concussion rates appear less frequent than they actually were.

The Times article also says that a member of the concussion committee, Dr. Joseph Waeckerle, said he was unaware of the omissions. But he added: “If somebody made a human error or somebody assumed the data was absolutely correct and didn’t question it, well, we screwed up. If we found it wasn’t accurate and still used it, that’s not a screw-up; that’s a lie.”

According to an article in the Times today, a letter was received from a lawyer for the league that said “The N.F.L. is not the tobacco industry; it had no connection to the tobacco industry,” which he called “perhaps the most odious industry in American history.”

However, according to the Times, the records show that the two businesses shared lobbyists, lawyers and consultants. Personal correspondence underscored their friendships, including dinner invitations and a request for lobbying advice.

In 1997, to provide legal oversight for the committee, the league assigned Dorothy C. Mitchell, a young lawyer who had earlier defended the Tobacco Institute, the industry trade group. She had earned the institute’s “highest praise” for her work.

A co-owner of the Giants, Preston R. Tisch, also partly owned a leading cigarette company, Lorillard, and was a board member of both the Tobacco Institute and the Council for Tobacco Research, two entities that played a central role in misusing science to hide the risks of cigarettes.

The N.F.L.’s concussion committee began publishing its findings in 2003 in the medical journal Neurosurgery. Although the database used in the studies contained numerical codes for teams and players, The Times decoded it by cross-referencing team schedules and public injury reports.

Clearly, brain injury is a big problem in football, so much so that the NFL has felt compelled to cover-up the problem.

Wednesday, March 23, 2016

Collaboratories: The Design Academy San Diego

The Design Academy here in San Diego, CA is a collaboratory serving the needs of many organizations for, what I call, first-principles design solutions. The team is positioned and particularly adept at serving the needs of start-ups and small businesses. Chuck Pelly and Joan Gregor, the two co-founders, have years of experience designing many types of things, including cars, electronics, medical devices, websites, and many more.

In my article below, I describe a history of some important collaboratories serving special groups, and speak to the need for such collaboratories in the start-up and small business realms. We are fortunate to have this design team move their operations to San Diego where they are serving our very vibrant technology community.!blank-1/regv0

Tuesday, March 22, 2016

Dr. Andrew Grove, Ph.D., Intel CEO Who Helped Spur the Semiconductor Revolution Died Today

Dr. Andrew S. Grove, longtime chief executive and chairman of Intel Corporation, and one of the most acclaimed and influential personalities of the computer and Internet era, died on Monday at his home in Los Altos, Calif. He was 79.

Dr. Grove earned his Ph.D. at the University of California, Berkeley and was an early pioneer in the semiconductor revolution, helping to develop increasingly sophisticated chips to power computers. Intel’s microprocessors have also been essential for digital cameras, consumer electronic products, household appliances, toys, manufacturing equipment and a wide assortment of devices that depended on computerized functions.

Besides presiding over the development of Intel’s memory chips and microprocessors in laboratory research, Dr. Grove gained a reputation as an intensively effective manager who spurred associates and cowed rivals in a cutthroat, high-tech business world where companies rose and fell at startling speed. Dr. Grove’s famous slogan, “Only the Paranoid Survive,” became the title of his 1996 best seller describing his management style. He was also known for innovative business practices- Intel was the birthplace of nonhierarchical, open settings, and low-partitioned cubicles rather than traditional walled-in offices.

He was an inspiration to many of us in the science and technology world.

Saturday, March 19, 2016

CalTech Researchers Step Toward Silicon-Based Life

The Horta in StarTrek's 1967 episode the "The Devil in the Dark," and the Silman's in Dennis Noble's "The Music of Life," are silicon-based life forms. However, for life on Earth, carbon is key. All organisms build their cells from carbon-based molecules. Carbon forms the key component for all known life on Earth. Complex molecules are made up of carbon bonded with other elements, especially oxygen, hydrogen and nitrogen, and carbon is able to bond with all of these because of its four valence electrons. However, silicon is the second most abundant element in the earth's crust, much more abundant than number 15, carbon. Scientists have long speculated that because silicon atoms bond to other atoms in a manner similar to carbon, silicon could form the basis of an alternative biochemistry of life.

Dr. Frances Arnold, professor of chemistry at CalTech, reported in San Diego, California, this week at the semiannual meeting of the American Chemical Society that her lab has evolved a bacterial enzyme that efficiently incorporates silicon into simple hydrocarbons. This is a first for life.

Adopting silicon into our carbon-based biology, was performed by isolating a so-called thermophilic bacterium that grows in hot springs. Like most organisms, the bacterium contains an enzyme called cytochrome c, which shuttles electrons to other proteins, making it widely useful in biochemistry. Cytochrome c has a cluster of negatively charged amino acid side chains along a plane that creates a dipole moment  - the separation of positive and negative charge. The structure of the molecules and the resulting dipole are highly conserved in plants and animals.The dipole moment serves to orient proteins in their proper direction and enhances their abilities to bind to other molecules In some cases, however, cytochrome c in thermophilic bacteria works on silicon, and not just carbon. Professor Arnold tested their bacterium and found that in rare cases its cytochrome c also added silicon to hydrocarbons.

In nature, cytochrome c’s silicon reaction is so rare that it’s probably just a chance, low probability thermal event. To facilitate the silicon processing, the CalTech team incubated the bacteria with silicon and carbon compounds and genetically selected the organisms that produced the most hydrocarbons that incorporated silicon. After three rounds of this artificial selection, the enzymes had evolved to churn out silicon-containing hydrocarbons 2000 times as readily as natural cytochrome c.

For now, the silicon-spiked hydrocarbon compounds, called organosilanes, probably aren’t useful either to the bacteria or to industry. The short and stubby molecules are unlike the long chainlike versions that chemical companies make for uses such as adhesives, caulks, and sealants. But someday, evolved microbes may be able to produce complex silicon-based materials, such as those used in adhesives, using only a fraction of the energy chemical companies require today.

As for our Silmans and Hortas....Professor Arnold has now shown that the universe is capable of evolving such life forms, and maybe they're out there somewhere.