College of Natural Resources, UC Berkeley

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April 30, 2010

CNR Students Win Prestigious Scholarships

Congratulations to Emma Tome, a junior double majoring in Environmental Sciences and Geography, who was named as a recipient of the Udall Scholarship for 2010, and to Larry M. Cai, a junior majoring in Molecular Toxicology and minoring in Music, who was named as a recipient of the Barry M. Goldwater Scholarship for 2010. CNR is proud of these outstanding young scholars.


The Udall Scholarship awards $5,000 to sophomore- and junior-level college students committed to careers related to the environment, tribal public policy, or Native American health care. The Udall Foundation seeks future leaders across a wide spectrum of environmental fields, including policy, engineering, science, education, urban planning and renewal, business, health, justice, and economics. 80 scholarships are awarded nationwide.

The Barry M. Goldwater Scholarship provides $7,500 per year for educational expenses to sophomores and juniors majoring in math, science, and engineering. The purpose of the award is to encourage outstanding students to pursue careers and advanced degrees in these fields. The foundation awards up to 300 Goldwater Scholarships nationwide; UC Berkeley nominates four students for the award.

April 29, 2010

Mapping methylation's mysterious background


Alla Katsnelson

By chemically modifying and then sequencing the DNA of 17 different species, researchers in California say that they have come closer to understanding the mysteries surrounding DNA methylation. This is an essential process for the regulation of many cellular events in mammalian development.

Many plants, animals and fungi have their DNA altered by chemical modifications. Among these is methylation, the addition of a methyl group to cytosine, one of the four bases that make up DNA. But some organisms, such as flies, budding yeast and nematode worms, live perfectly well without this mechanism.

"One of the big mysteries of DNA methylation has been how come you have some organisms with DNA methylation and some without," says Daniel Zilberman, the senior author of a paper published in Science today1. "I wouldn't say we have provided the answer, but I would say we have provided a plausible version of an answer."

To do this, his team at the University of California, Berkeley, has determined the DNA methylation patterns of 17 organisms — five plants, seven animals and five fungi — choosing species in different parts of the evolutionary tree to reconstruct how methylation might have evolved. From this, the authors predict what the process may have looked like around 1.6 billion years ago in the last common ancestor of plants, animals and fungi.

They created genome-wide methylation maps for each species, using high-throughput sequencing in conjunction with a technique that chemically converts each cytosine base in a genome to another base, uracil, unless that cytosine is methylated — a process known as bisulphite sequencing.

"Previously, people had glimpses of DNA methylation in a variety of organisms, but what this [study] does is try to give a more global view, which is really valuable," says Eric Selker, a biologist at the University of Oregon in Eugune who was not involved in the study.

Mobile-DNA control

In mammals and plants, methylation has been widely observed in transposons — mobile pieces of DNA that can cause mutations in the genome — suggesting that the process may function to keep transposons in check. But in a recent study in plants, Zilberman's group also identified methylation in the middle of active genes2. The latest analysis extends the finding to other organisms, ranging from rice and the fungus Phycomyces to puffer fish to anemones1.

The fact that methylation occurs within active genes in many organisms suggests that it is an ancient phenomenon, says Zilberman. While DNA methylation in plants, fungi and vertebrates was concentrated in transposons, invertebrates showed the opposite pattern, with modifications occurring mainly in active genes.

What might explain that disparity, he says, is sex. In organisms that reproduce sexually, transposons — essentially genomic parasites — tend to be more aggressive in moving about the genome and wreaking mutational havoc. Conversely, in asexual organisms, transposons are generally quite tame; if they reduce the fitness of their host too much, they risk becoming extinct.

Ancestral enzymes

Zilberman proposes that the common ancestor of plants, animals and fungi carried enzymes that methylated both transposons and gene bodies. When animals split off from fungi, they were probably single-celled, asexually reproducing organisms with no need for a mechanism to control their transposons, so the enzyme that methylated transposons was lost. Vertebrates re-evolved it, but invertebrates did not — instead they developed other mechanisms to deal with their transposons.

However, not everyone agrees with this explanation.

"It is kind of a fun paper, but it has a lot of issues," says Timothy Bestor, a developmental geneticist at Columbia University in New York.

For a start, he says, the group's analysis doesn't distinguish between transposons that actually jump around the genome, as in mammals, and those that are so heavily mutated that they are pretty much stable, as in the Neurospora fungi. These two transposon types may well have different methylation patterns. Furthermore, says Bestor, the ancestral state suggested by Zilberman and his colleagues "is a fairly recent ancestral state" and doesn't explain where DNA methylation came from in the first place.

Another mystery remaining to be solved is why DNA methylation occurs in gene bodies at all, as it does not seem to interfere with gene expression, says Selker.

"I think the question of the future is, what the heck is this methylation doing?" he says.

April 28, 2010

Cal professor enlists volunteers in fight to save oaks


By Jonathan Morales
Contra Costa Times

Bill Hudson knew a major California environmental problem could be coming, literally, to his backyard.

The Orinda resident has a number of oaks on his property, so when he learned sudden oak death had crept over the Berkeley hills and into Contra Costa County, he decided to do something.

That's when he hooked up with UC Berkeley professor Matteo Garbelotto, who gives concerned residents such as Hudson the chance to help fight a tree-killing disease that has moved up and down the California coast.

Garbelotto organizes what he calls "SOD blitzes" in which volunteers scour their communities for signs of sudden oak death, helping researchers understand just how far the disease has spread.

"I'm concerned about it," Hudson said. "It's an important problem. (Garbelotto) needed some help and he's doing a lot of good work on it."

Garbelotto has organized several such blitzes each of the past two springs, and has several scheduled this April and May, including one in the East Bay later this month.

Sudden oak death was first introduced to California in Marin County in 1995, Garbelotto said. It has spread as far south as Monterey and as far north as Humboldt County, and even into parts of Oregon.

Several plants, like the California bay laurel, can carry sudden oak death but remain unaffected. It is often spread to oaks through rainwater that has come into contact with infected plants.

Because the area it affects is so large and, in many cases, economically unproductive, it's difficult to find funding for sudden oak death research, Garbelotto said.

Enter his army of volunteers.

They first head to UC Berkeley to learn which plants to examine and how to identify the disease. Then they spend the next couple of days collecting samples and returning them to Berkeley for testing, which is usually completed by October.

The process is by no means comprehensive, or even scientific. But Garbelotto said the volunteers' efforts are helpful because information on the disease's spread can lag.

"If you were to think, 'Oh, I know where sudden oak death is' and you're using data that was produced two years ago, probably you actually don't have a good idea where it is," he said.

The blitzes also benefit property owners by letting them know if their trees are infected. If detected early, Garbelotto said, there's a chance a property owner can rid the tree of the disease.

Hudson, the Orinda resident, admits he's helping out not just out of concern for the environment, but for his property, as well.

"I've got my own trees in my neighborhood, and that's where it impacts, so it's a mutually beneficial thing," he said.

Sudden oak death's impact stretches far beyond just the trees it infects, said Katie Palmieri, a spokeswoman for the California Mortality Task Force.

"You're losing food sources for the animals that live there, you're losing shade and screens in your urban-wildland interface area," she said. "It can impact water runoff qualities into the streams with soil erosion becoming more common."

Garbelotto said it's unusual for ordinary people to be able to get involved at the local level in battling what is very much a regional problem.

But when they do, he added, it amplifies the concerns already expressed by researchers, helping those concerns to be heard by government officials with the power to enact policies aimed at curbing the diseases's spread.

"Obviously the voice is heard," Garbelotto said, "not just (by) myself and a couple of other scientists, that this is important."

April 23, 2010

Can California fix the Delta before disaster strikes?


By Sarah Yang, Media Relations

When visiting Sherman Island in the Sacramento-San Joaquin River Delta, it is easy to forget the region's ever-present threat of catastrophic floods and instead revel in the West Coast's largest estuary, which supports farmers, anglers, and more than 700 native species of plants and animals, including some that are endangered.

"You drive out there and you see that cows are grazing, birds are chirping; but it's deceptive," said Robert Bea, professor of civil and environmental engineering at the University of California, Berkeley. "As you start to dig in, you find out how incredibly complex and vulnerable we've made this place."

At least 220 government agencies have jurisdiction in the Delta, which is home to half a million residents in 25 villages, towns and cities, including Sacramento, Stockton and Pittsburg. The region is under continual threat from floods, prevented only by a vast — and fragile — network of earthen levees.


Sherman Island, said Bea, is an example of a critical chokepoint in the Delta for the tangled networks of highways, railroads, and electrical, gas and telecommunication lines that serve as lifelines for the San Francisco Bay Area and large swaths of the state. The Delta also serves as the hub for aqueducts that channel drinking water for two-thirds of the state's population — more than 23 million people — and irrigation water for 3 million acres of agriculture responsible for half the nation's fruits and vegetables and one-quarter of its dairy products.

Today there are more than 1,100 miles of levees — longer than California's coastline — surrounding 837,000 acres of land in the Delta and Suisun Marsh. Many of those levees are now a century old.

The peat proved to be fertile ground for farms, but its exposure to oxygen and compaction literally sank the land as microbes gained access to the organic debris through the drainage of water. The land continues to sink at a rate of 1-3 inches per year.

Like most of the islands in the Delta, the land on Sherman Island sits 15-20 feet below sea level, a result of decades of subsidence.

Few know this better than biometeorologist Dennis Baldocchi, a UC Berkeley professor in the Department of Environmental Science, Policy & Management. Baldocchi came from a family of Delta farmers, starting with his grandparents who settled in Antioch after emigrating from Italy. Baldocchi's father grew almonds and walnuts in the Delta towns of Antioch and Oakley, while several aunts, uncles and cousins farmed asparagus, sugar beets, grains and other crops on Liberty and Sherman islands over the decades.

One of Baldocchi's aunts had fortunately moved out of her home on Sherman Island right before it was destroyed in a 1969 flood that resulted from a levee break. The home was never rebuilt, but Baldocchi's connection to the region remains. As a researcher, he has been studying the release of greenhouse gases in the Delta as methane and carbon dioxide are released from the peat.

When Baldocchi returns to Sherman Island for his research, he sees a landscape changed from his childhood memories.

"What strikes me most is the visual impression I get standing on a road today and seeing how much lower the fields are — 3 to 4 feet in many cases — from where they were 30 years ago when I was tramping through the fields pheasant hunting with my dad," said Baldocchi. "I can even see the markings on telephone poles from where the soil used to be. Those footings on the utility poles were probably buried in the peat when they were originally installed 70 to 80 years ago."

Exacerbating the vulnerability of the region is the continued development and population growth of the Delta. A 2007 report initiated by UC Berkeley's Department of Landscape Architecture and Environmental Planning noted that high housing prices throughout Northern California contributed to growth pressure in Delta communities. The report's authors noted that since the 2000 census, the towns and cities within the Delta have grown by 18 percent, with some, including Brentwood, Tracy and West Sacramento, experiencing growth of 25 percent.

April 21, 2010

Howler Monkey Census Reveals Population Holding Steady


Long before dawn on March 19 and 20, Katie Milton and a group of stalwart volunteers, each armed with flashlight and compass, spread out into the jungle to find 35 predetermined listening stations marked on their maps of the island.

Just before sunrise, howler monkeys launch into a chorus of howls, roars and barks. From 5:15 am until 6:30 am, each volunteer recorded the time and direction of these vocalizations and estimated the distance to each group that they could hear from their stations. As they walked back to the lab in the early morning light they noted locations of any monkey groups they saw.


“It amazes me that volunteers want to get up at 4 am to walk through the dark forest alone for an hour or more—but it is a thrill when they hear that first howl and know the dawn chorus is beginning,” said Katie Milton.

Continue reading "Howler Monkey Census Reveals Population Holding Steady" »

April 1, 2010

Prof. Reginald Barrett critiques the new report on the rare forest-dwelling Pacific fisher.

Wildlife experts allege that a new status report on the rare forest-dwelling Pacific fisher was altered by state officials to favor the logging industry.

The sleek and carnivorous fisher, a cousin of the weasel, has long been thought to favor old-growth forests, and its decline in the Sierra Nevada has been linked in part to logging that eliminated such habitat.

The Center for Biological Diversity petitioned the state to list the fisher as endangered.

The state Department of Fish and Game's recently published status review concludes the fisher does not warrant protection under the state Endangered Species Act, in part because of information that they appear able to survive in logged forests if some large trees are left uncut.

The outcome is politically sensitive. If the fisher is eventually recommended for protection by the state Fish and Game Commission, new logging restrictions could harm the timber industry.

Reginald Barrett, a professor of wildlife management at UC Berkeley and an expert on the fisher, on Friday sent the commission a 15-page critique of the final report.

Barrett in January reviewed a draft report, which he praised as supporting a conclusion to protect at least the southern Sierra Nevada fisher population as "threatened."

But in his Friday letter he called the final report "so different in content and tenor."

"It is evident that more emphasis was placed on timber industry input via personal communications and unpublished industry reports than the scientific literature," Barrett writes. "What I am concerned about is the fact that the Commission is being given a recommendation by DFG that has apparently gone beyond the expected biological, scientific information to include political and economic considerations."

Barrett did not respond to phone and e-mail requests for comment.

His letter highlights 21 sections that were deleted and 16 others added between the draft and final reports. The changes appear to strengthen arguments that the fisher population isn't harmed by logging, and to weaken support for protecting the species.

In numerous instances noted by Barrett, the final report deletes references to evidence that fishers depend on older and deeply shaded forests, and adds other information – largely based on unpublished studies – that fishers can survive in habitats altered by logging.

Eric Loft, chief of Fish and Game's wildlife branch, challenged as "not true" Barrett's suggestion that industry influenced the report. He said the report was an effort to provide the commission with the latest information – especially on the habitat question.

"Clearly, yes, it would be great if everything was peer-reviewed. But everything isn't peer-reviewed. It's the best available scientific information that we have," Loft said.

The reports are typically drafted by a staff-level biologist and then reviewed and finalized by department supervisors. In this case, the changes Barrett cites are alleged to have been made after staff completed the draft.

The draft was peer-reviewed individually by scientists, including Barrett. The final document has not received any peer review.

Loft said many of the changes referenced by Barrett were done to include information from a 2008 report, which evaluated the Center for Biological Diversity's original petition, so the two documents would be consistent.

"The draft document did undergo change to make sure we emphasized what we know ... versus what we think," Loft said. "We worked to avoid being overly speculative or draw conclusions that could not be substantiated by scientific information."

In a letter dated Friday, another wildlife biologist, Carlos Carroll, wrote the commission that the report "does not provide the level of scientifically rigorous review" needed for an informed decision.

Like Barrett, Carroll urges the commission to send the report back for more work.

"All I know is that the final report is not scientifically sound," Carroll told The Bee this week.

Much of the disputed anecdotal information came from a wildlife biologist who retired last year from Sierra Pacific Industries, the largest private landowner in California and a major player in the wood-products industry.

Sierra Pacific spokesman Mark Pawlicki denied that his company had any improper influence on the report.

"Here are the facts," Pawlicki said. "The Department of Fish and Game asked for more recent information that anyone has. We provided our input to the process just as other people have. Our input is no different than anyone else."

The Fish and Game Commission will discuss the report, and the fisher's conservation status, at its meeting April 7 in Monterey.


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Recent Posts

CNR Students Win Prestigious Scholarships
Mapping methylation's mysterious background
Cal professor enlists volunteers in fight to save oaks
Can California fix the Delta before disaster strikes?
Howler Monkey Census Reveals Population Holding Steady
Prof. Reginald Barrett critiques the new report on the rare forest-dwelling Pacific fisher.


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