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Amy Herr is first Faculty Director of Bakar Fellows

Department of Bioengineering - Wed, 01/18/2017 - 08:43
Professor Amy Herr has been named the the inaugural faculty director of the Bakar Fellows Program at UC Berkeley. The program fosters faculty entrepreneurship in the STEM+ fields including Engineering, Computer Science, Chemistry, Biological Sciences, Physical Sciences, and Architecture, to help professors translate their ground-breaking discoveries into practical solutions and contribute to Berkeley's entrepreneurial ecosystem. Herr was a member of the first class of Bakar Fellows in 2012.
Categories: Science News

Climate change could kill off parasites, destabilizing ecosystems

UC Berkeley Science News - Thu, 01/12/2017 - 14:48
Mass parasite extinction could create more virulent disease or alter the food web
Categories: Science News

Climate change could kill off parasites, destabilizing ecosystems

College of Natural Resources - Thu, 01/12/2017 - 12:46

Photogenic animals, from polar bears to people, aren’t the only creatures under threat from global climate change. A new review led by UC Berkeley suggests the phenomenon threatens parasites with extinction, which could have big consequences for ecosystems.

The vast majority of research into parasites and environment change focuses on how hosts, particularly humans, will be harmed. Few studies have addressed how the loss of parasite biodiversity may affect other aspects of host health, ecosystem connectedness and health  and biodiversity as a whole. Previous research suggests that parasites are up to 10 times more vulnerable to extinction than are their hosts.

In the new study, the researchers suggest that parasites are as prone to extinction due to climate change as any other taxonomic group. The study predicts that losing parasites could destabilize ecosystems in many ways, such as by increasing more virulent disease or by altering the food web or changing host physiology. The study found that parasites in hosts with variable internal temperatures, parasites of large-bodied hosts, host-specific parasites and parasites with complex life cycles will likely be the most vulnerable to extinction due to climate change.

“This is the first comprehensive review of how climate change may affect parasite biodiversity, from the point of view of parasite conservation,” said Carrie Cizauskas, who led the research as a postdoctoral affiliate in the lab of Wayne Getz, a professor of wildlife ecology in the Department of Environmental Science, Policy and Management. Colin Carlson, a graduate student in the same department, is co-lead author of the review.

The research was published today in the journal Royal Society Open Science.

Previous work from this group has called for further research into parasite vulnerability from parasites’ perspectives, rather than primarily focusing on hosts, and also outlined ways to potentially conserve parasites. In the new study, the authors outline actionable items for researching the vulnerability of parasites. A forthcoming review from Cizauskas and Carlson attempts to quantify these parasite extinction risks using existing data and modeling.

The team outlines a protocol for identifying vulnerable parasites by a set of key risk factors, including host specificity, parasite life cycle complexity and climatic tolerance. The next step involves identifying important unanswered questions in parasite ecology, such as how host phylogeny predicts parasite extinction, or whether parasite extinctions will be clustered in particular ecosystems. Finally, they suggest proposing how ecological disciplines may be used to identify gaps in parasite research data.

“Ultimately, our goal is for this review to act as a catalyst for further research efforts and discussions regarding the important and little-addressed topic of parasite vulnerability in the face of climate change,” Cizauskas said.

Read the story at the source.

 

Image: A parasite by the name of Schistorchis stenosomaDate: Thursday, January 12, 2017 - 12:45byline: By Brett Israel, UC Berkeley Media relations Legacy: section header item:  Date: Friday, January 20, 2017 - 12:45headline_position: Top Leftheadline_color_style: Normalheadline_width: Longcaption_color_style: Normalcaption_position: Bottom Left

BioE students featured in MEng newsletter

Department of Bioengineering - Mon, 01/09/2017 - 16:50
Bioengineering MEng students Sneha Balan and Nick Engel are featured on page 4 of the Winter MEng newsletter, for their Early Cancer Detection project and Alumni Innovation Award. Nick is also on the cover.
Categories: Science News

Snails travel far and wide, spreading disease along the way

UC Berkeley Science News - Mon, 01/09/2017 - 12:52
UC Berkeley-led study is the first to find genetic evidence for long-distance dispersal of disease-carrying snails.
Categories: Science News

Learning to live without plastic

UC Berkeley Science News - Mon, 01/09/2017 - 10:00
More than a dozen professors across a range of departments, from gender and women's studies to nuclear engineering, are working to incorporate content related to carbon neutrality, climate change and sustainability into their undergraduate course material.
Categories: Science News

Global warming hiatus disproved — again

College of Natural Resources - Thu, 01/05/2017 - 16:08
Melting ice bergs

A controversial paper published two years ago that concluded there was no detectable slowdown in ocean warming over the previous 15 years — widely known as the “global warming hiatus” — has now been confirmed using independent data in research led by researchers from UC Berkeley and Berkeley Earth, a non-profit research institute focused on climate change.

The 2015 analysis showed that the modern buoys now used to measure ocean temperatures tend to report slightly cooler temperatures than older ship-based systems, even when measuring the same part of the ocean at the same time. As buoy measurements have replaced ship measurements, this had hidden some of the real-world warming.

After correcting for this “cold bias,” researchers with the National Oceanic and Atmospheric Administration concluded in the journal Science that the oceans have actually warmed 0.12 degrees Celsius (0.22 degrees Fahrenheit) per decade since 2000, nearly twice as fast as earlier estimates of 0.07 degrees Celsius per decade. This brought the rate of ocean temperature rise in line with estimates for the previous 30 years, between 1970 and 1999.

This eliminated much of the global warming hiatus, an apparent slowdown in rising surface temperatures between 1998 and 2012. Many scientists, including the International Panel on Climate Change, acknowledged the puzzling hiatus, while those dubious about global warming pointed to it as evidence that climate change is a hoax.

Climate change skeptics attacked the NOAA researchers and a House of Representatives committee subpoenaed the scientists’ emails. NOAA agreed to provide data and respond to any scientific questions but refused to comply with the subpoena, a decision supported by scientists who feared the “chilling effect” of political inquisitions.

The new study, which uses independent data from satellites and robotic floats as well as buoys, concludes that the NOAA results were correct. The paper was published Jan. 4 in the online, open-access journal Science Advances.

“Our results mean that essentially NOAA got it right, that they were not cooking the books,” said lead author Zeke Hausfather, a graduate student in UC Berkeley’s Energy and Resources Group.

Long-term climate records

Hausfather said that years ago, mariners measured the ocean temperature by scooping up a bucket of water from the ocean and sticking a thermometer in it. In the 1950s, however, ships began to automatically measure water piped through the engine room, which typically is warm. Nowadays, buoys cover much of the ocean and that data is beginning to supplant ship data. But the buoys report slightly cooler temperatures because they measure water directly from the ocean instead of after a trip through a warm engine room...

Read the complete story at the UC Berkeley News site.

Image: Melting ice bergsDate: Thursday, January 5, 2017 - 16:00byline: Robert Sanders, UC Berkeley Media RelationsLegacy: section header item:  Date: Thursday, January 5, 2017 - 16:00headline_position: Top Leftheadline_color_style: Normalheadline_width: Longcaption_color_style: Normalcaption_position: Bottom Left

Arkin lab method may save lives during blood transfusion

Department of Bioengineering - Wed, 01/04/2017 - 16:42
After severe trauma, some patients in shock develop impaired coagulation. This is difficult to diagnose in crisis and makes blood transfusions dangerously challenging to manage. Professor Adam Arkin and collaborators have used dynamic modeling to demonstrate a method for calculating each patient’s transfusion requirements using only laboratory values that can be easily and quickly obtained in the emergency setting. This personalized information could help hospitals save lives at risk from acute traumatic coagulopathy and massive transfusion mortality.
Categories: Science News

Global warming hiatus disproved — again

UC Berkeley Science News - Wed, 01/04/2017 - 11:00
Study confirms steady warming of oceans for past 45 years
Categories: Science News

Fast radio burst tied to distant dwarf galaxy and, perhaps, magnetar

UC Berkeley Science News - Wed, 01/04/2017 - 10:00
First localization of mysterious bursts pinpoints galaxy 3 billion light years away
Categories: Science News

Downing in 2017 30 Under 30

Department of Bioengineering - Tue, 01/03/2017 - 12:41
Congratulations 2013 PhD Tim Downing, now a professor at UC Irvine, named to the 2017 Forbes 30 Under 30 for his work examining how extracellular signals can influence the final fate of cells.
Categories: Science News

BioE startup helps clean tech rise again

Department of Bioengineering - Wed, 12/28/2016 - 16:57
Lygos, a synthetic biology company founded by BioE PhD alumni Jeffrey Dietrich and Eric Steen, was featured in a New York Times article on the resurgence of companies using biology to produce cheap, safe and natural materials for fuel, cosmetics and other goods.
Categories: Science News

Liepmann lab team wins capstone award

Department of Bioengineering - Fri, 12/23/2016 - 10:50
Master of Engineering student Nicholas Engel won the Alumni Innovation Award at this year’s Fall Capstone Expo! Engel’s project, “Integrating Electronics into BioMEMS”, was developed with Professor Dorian Liepmann. It was selected by a panel of six M.Eng. alumni based upon the importance of the problem addressed, the creativity of the solution, and the impact of the […]
Categories: Science News

Compact CRISPR systems found in some of world’s smallest microbes

College of Natural Resources - Thu, 12/22/2016 - 09:48
A cryo-electron tomography image of an ultra-small bacteria similar

A cryo-electron tomography image of an ultra-small bacteria similar to the ones found to have small, compact CRISPR-Cas systems potentially suitable for laboratory gene-editing. The bacteria is less than 200 nanometers across (bar is 100 nanometers). The three objects near the bacteria are viruses, or phages, that attack bacteria. (Banfield lab image)

UC Berkeley scientists have discovered simple CRISPR systems similar to CRISPR-Cas9 — a gene-editing tool that has revolutionized biology — in previously unexplored bacteria that have eluded efforts to grow them in the laboratory.

The new systems are highly compact, befitting their presence in some of the smallest life forms on the planet. If these systems can be re-engineered like CRISPR-Cas9, their small size could make them easier to insert into cells to edit DNA, expanding the gene-editing toolbox available to researchers and physicians.

“These are particularly interesting because the key protein in these CRISPR systems is approximately the same as Cas9, but is not Cas9. It is part of a minimal system that has obvious potential for gene editing,” said Jill Banfield, a UC Berkeley professor of earth and planetary sciences and of environmental science, policy and management.

In CRISPR-Cas systems, the Cas protein is the scissors. When targeted to a specific sequence of DNA, the Cas protein binds and severs double-stranded DNA. The new discovery nearly doubles the number of simple and compact CRISPR-Cas systems potentially useful as laboratory and biomedical tools.

“The important thing here is that we found some of these CRISPR systems in a major branch of the bacterial tree, opening the door to a whole new world of microbes that are not cultured in the lab, so we don’t really know what they are and what their habits are,” said co-author Jennifer Doudna, a UC Berkeley professor of molecular and cell biology and of chemistry and a Howard Hughes Medical Institute investigator. Both Doudna and Banfield are faculty scientists at Lawrence Berkeley National Laboratory.

The team also found the first CRISPR-Cas9 system in some of the world’s smallest microbes: a nano-scale member of the archaea, which is a sister group to the bacteria.

The variety of uncultivable bacteria has only recently been recognized, in large part due to Banfield and her lab colleagues, who use metagenomic analysis to explore microbial diversity in exotic environments, from toxic pools in abandoned mines to the soil in Superfund contamination cleanup sites and the guts of premature infants. The majority of all bacterial life on the planet is basically unknown because these organisms cannot be cultivated in lab dishes, probably because they are symbionts and rely upon other microbes for nutrients needed to survive.

One of the new CRISPR proteins, dubbed CasY, was discovered in a massive group of recently recognized bacteria — what Banfield calls candidate phyla radiation (CPR) and which may contain half of all bacterial diversity — that live in geysers and in soil several feet underground. Another new one, CasX, was found in bacteria from known phyla living in groundwater and sediment. The two groups of nanoarchaea found to contain CRISPR-Cas9 were first described by Banfield from acid mine drainage.

Banfield, Doudna and their colleagues reported the findings today in the journal Nature.

Read the full story on the UC Berkeley News website. 

Image: Date: Thursday, December 22, 2016 - 09:45byline: Robert Sanders, UC Berkeley Media RelationsLegacy: section header item:  Date: Thursday, December 22, 2016 - 09:45headline_position: Top Leftheadline_color_style: Normalheadline_width: Longcaption_color_style: Normalcaption_position: Bottom Left

CRISPR Discovery: A Whole New World of Microbes

Department of Molecular and Cell Biology - Thu, 12/22/2016 - 08:36

MCB's Professor Jennifer Doudna, in collaboration with Professor Jill Banfield (of earth & planetary sciences and of ESPM), have "discovered simple CRISPR systems similar to CRISPR-Cas9 — a gene-editing tool that has revolutionized biology — in previously unexplored bacteria that have eluded efforts to grow them in the laboratory."

Read more...

Turning up the thermostat in tropics shows promise for energy and comfort

UC Berkeley Science News - Tue, 12/20/2016 - 16:00
Slightly upping indoor temperatures in tropical offices and arming workers with smart fans can save significantly on overall energy costs while maintaining employee comfort.
Categories: Science News

Jennifer Doudna: Luminary Award

Department of Molecular and Cell Biology - Tue, 12/20/2016 - 08:17

Professor Jennifer Doudna will be given a Luminary Award at the Precision Medicine World Conference on January 23rd-25th, 2017. Doudna will also be one of the key speakers at the conference -- read a recent PMWC Q&A with Professor Doudna.

Are you interested in attending the conference? PMWC has created a discount code for UC Berkeley attendees -- It is "berkeley_discount_pmwc2017" (expires on January 11, 2017). Or register here and have the code applied automatically. 

Read more...

From a single genetic mutation, secrets of ‘boy in the bubble’ disease revealed

UC Berkeley Science News - Thu, 12/15/2016 - 14:33
UC Berkeley was part of a research team that identified the cause of rare SCID case as a gene never before associated with the deadly immune system disorder
Categories: Science News