University of California, Merced - Jason Alvarez

Study: Drug-Resistant Cancer Cleverer Than Imagined

Anonymous — Wed, 04 Apr 2018 16:47:11 +0000

By Jason Alvarez, �鶹��

April 4, 2018

High-throughput screening in combination with systems biology analysis identifies cancer control elements and new drug targets of therapy resistance in malignant melanoma.

Precision medicine offers hope after a life-changing cancer diagnosis. But some cancers that initially respond to targeted chemotherapy become treatment-resistant — and the tumor itself is the culprit.

Now, new research from �鶹�� and UC Irvine is helping explain how therapy-resistant cancers arise — findings with important implications for the future of cancer therapy. The results are reported in a study published today in the journal BMC Systems Biology.

To understand how cancer becomes treatment resistant, a research team at the Systems Biology and Cancer Metabolism Lab, led by �鶹�� Professor Fabian V. Filipp of the School of Natural Sciences, compared genetic and metabolic pathways in treatment-responsive and treatment-resistant melanomas.

Melanoma is a cancer that originates in melanocytes, the cells that produce the skin pigment melanin. Though not the most common form of skin cancer, it is the most aggressive. And if it’s not caught and treated early, it’s also among the deadliest.

“Melanoma is usually induced by the sun — by UV damage,” Filipp said. “In the majority of cases, that UV damage changes a single target by causing point mutations.”

UV damage gives rise to point mutations — changes in a single letter of the 3 billion letter human genome. These mutations can interfere with signals that tell cells when to grow and divide and when to stop. Mutations in a protein called BRAF, the main focus of the new study, cause growth signals to be stuck in the “on” position and drive cancer development.

Professor Fabian V. Filipp is working on cancer genomics to fight therapy-resistant cancers.

Though scientists have managed to come up with drugs that target and turn off aberrant BRAF signaling, cancer cells are clever and learn to adapt to these BRAF-inhibitors.

“Today, many patients respond to cancer treatment very positively at first,” Filipp said. “Unfortunately, many ultimately develop resistance and metastases.”

Though chemotherapy might kill most of the cancer, tiny populations of drug-resistant cancer cells can survive and propagate. Unlike the more familiar case of antibiotic-resistant bacteria, where genetic mutations give rise to resistance, Filipp and his team found that many adaptations in treatment-resistant cancers aren’t the result of mutation.

“Cancer is a genomic disease. However, resistance to therapy might go beyond just cancer mutations,” Filipp explained. “Surprisingly, it was not new mutations that are causing resistance. The DNA stays the same, but cancer cells quickly adapt non-genomically to therapy and outsmart the drugs.”

Melanoma circumvents BRAF inhibitors not by changing the genes themselves, but by changing gene activity. Filipp and his team found that in treatment-resistant cancers, key regulatory genes were more active while important protective genes were less active when compared with treatment-responsive cancers.

Some of the genes with reduced activity were in the same signaling pathway as BRAF, the mutated protein that gave rise to the cancer and the main target of chemotherapy. Meanwhile, genes with increased activity were in metabolic pathways that allowed cancer cells to bypass BRAF altogether and continue to grow and divide. Cancer cells had essentially figured out how to survive by rewiring their metabolism in response to chemotherapy.

Daunting as this may sound, it actually offers hope to scientists and clinicians who want to treat chemo-resistant cancers.

“After this study, we now understand how some cancer drugs become ineffective,” Filipp said. “This suggests new ways of approaching therapy by looking at pathways beyond the genome and taking advantage of pathways in the epigenome and metabolism.”

Professor Fabian V. Filipp with his team working on precision targeting of malignant melanoma.

It’s a discovery that was made thanks in large part to contributions from students in Filipp’s lab.

“The work would have not been possible without an incredible team,” Filipp said. “Many graduate and undergraduate researchers contributed to the project — which was a collaborative effort between �鶹�� and the Cancer Center at UC Irvine.”

Efforts like this helped �鶹��’s graduate science programs break into the national rankings, said Dean of Natural Sciences Betsy Dumont.

“Groundbreaking research — like this new study from Professor Filipp’s lab, which may one day lead to new therapies for drug-resistant cancers — is why �鶹�� is now counted among the nation’s top graduate programs in biology,” she said.

Filipp is the recipient of the UC Cancer Research Coordinating Committee Award and part of a cancer research cluster at the Health Sciences Research Institute. Director of the Health Sciences Research Institute Professor Paul Brown, explained how Filipp’s interdisciplinary approach to cancer research provides a new path forward for tackling the disease.

“The research combines clinically-relevant models of cancer and uses state-of-the-art computational systems biology to identify ways to overcome cancer resistance.” Brown said. “Professor Filipp’s research demonstrates the advantages of taking a multi-disciplinary approach to research. The research is an important contribution to the treatment, control and prevention of cancer.”

In addition to breakthroughs in cancer research, Filipp is dedicated to promoting advanced graduate training and student mentoring. Filipp has developed cutting-edge training courses on cancer systems biology and is today hosting an International Bioengineering Symposium focused on metabolic engineering. The symposium features lectures by scientists from the U.S., Germany and Norway, strengthening bridges between American and European researchers.

“This is a great opportunity for early-career scientists to get involved into ongoing research at �鶹��,” Filipp said.

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Study: Kitchen and Culture Clash When Promoting Healthy Eating to Latinos

Anonymous — Thu, 22 Mar 2018 15:55:23 +0000

By Jason Alvarez, �鶹��

March 22, 2018

Professor Susana Ramirez

Latinos suffer from some of the highest obesity rates in the nation. Health officials have tried to intervene with messaging that encourages healthy eating and healthy behavior, but these campaigns have met with little success.

Now a new study from �鶹�� public health Professor Susana Ramirez suggests that efforts might be more successful if strategies encouraged Latinos to “decolonize their diet.”

Obesity risk among Latinos reflects a broader trend that public health experts have termed the “dietary acculturation paradox.”

“The paradox comes from epidemiological findings over the past 50 years that show that increased acculturation into mainstream U.S. culture is bad for your health,” Ramirez said. “If you look at immigrants born and raised in other countries who came to the U.S. as adults, they tend to be healthier than their American children.”

According to Ramirez, much of the problem stems from children of immigrants adopting American diets. These diets tend to be highly processed and high in unhealthy ingredients like fat, sodium and sugar. They're also low in healthy ingredients like fiber, complex carbohydrates and fresh fruits and vegetables.

This remains true despite gains in income and education, which are generally associated with better health outcomes. But Ramirez’s new study provides insight into why the acculturation paradox affects Latinos.

Ramirez and her collaborators surveyed young, bicultural women — ages 18-29; of Mexican descent; living in the Central Valley; fluent in English — about diet and cultural values.

“We started talking to this audience to learn about the factors that influence their decision-making around diet,” Ramirez said. “We also wanted to know what features of health messages are persuasive to this particular audience.”

Healthy living messages often don’t take culture into account. For me, that suggests a pretty radical approach to health communication, an approach that’s empowerment based.

Susana Ramirez

A number of themes emerged from the data. Ramirez found that participants were proud of their Mexican heritage, which they associated with family time, traditional Mexican cooking and the Spanish language. Though many participants admitted to a limited knowledge of traditional culinary techniques, and only a fraction spoke Spanish fluently, all three aspects of traditional culture were of tremendous personal significance.

“Thinking of themselves as Mexican is a source of pride for these second- and third-generation women,” Ramirez said.

Participants also reported a desire to eat healthy. They listed portion control, balanced meals, and fruits and vegetables as part of a healthy diet; fried foods and foods high in fat and sugar were seen as unhealthy. They were also able to identify specific consequences of unhealthy eating, including obesity and diabetes.

The findings suggested that the prevailing wisdom about healthy diets had reached the group, but those messages weren’t having the intended effect.

“Everybody was able to tell us what eating healthy was,” Ramirez said. “But we found that participants were saying ‘when I’m with my Mexican family and I’m expressing my Mexican culture, that is being unhealthy.’ Culture is at odds with health.”

Ramirez had identified a second paradox, one that pitted kitchen against culture. Though respondents viewed traditional Mexican cooking as essential to maintaining their ethnic identity, most described Mexican food as inherently unhealthy and incompatible with a healthy diet.

“Healthy-eating promoters often encourage traditional food. But there’s a disconnect there,” Ramirez said. “If you’re going to tell Latinos to eat their traditional foods, that’s priming them to think of unhealthy things. That can cause confusion.”

The solution, according to Ramirez, is a new approach to health communication — an approach that builds on the importance of Latino culture and frames the issue in ways that are relevant to the community.

“Healthy living messages often don’t take culture into account,” Ramirez said. “For me, that suggests a pretty radical approach to health communication, an approach that’s empowerment based.

“Talk about food and nutrition as rights they can advocate for in their community. Talk about how Latino populations are disproportionately targeted in marketing for junk food and fast food in their communities. It’s an approach that empowers young Latinas to decolonize their diet."

This study was supported with funding from the National Cancer Institute.

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Grad Programs Make U.S. News Rankings Debut

Anonymous — Tue, 20 Mar 2018 08:40:16 +0000

By Jason Alvarez, �鶹��

March 20, 2018

At less than 13 years old, the newest UC's rising national reputation has extended to its Graduate Division, with several science and engineering programs now ranked

Graduate programs in the natural sciences are among the many �鶹�� graduate programs included in the newest U.S. News rankings of Best Graduate Schools.

For the first time, �鶹��’s doctoral programs in the sciences have been ranked among the best in the nation, according to U.S. News & World Report’s 2019 edition of Best Graduate Schools.

The School of Engineering celebrated its third appearance in the rankings, and this year marks �鶹��’s first appearance in several science and engineering rankings. It was a banner year in particular for the natural sciences, with �鶹�� debuting in the rankings for chemistry (No. 122), mathematics (No. 144), physics (No. 146) and biology (No. 175).

U.S. News ranks graduate science programs based solely on peer assessment surveys sent to academics in each field, reflecting the growing prominence of �鶹�� faculty in the minds of scientists and academics nationwide.

“With four of our disciplines in the sciences debuting on this year’s list, it is clear that �鶹�� faculty and graduate students are being widely recognized for their significant contributions to science by experts and leaders in their respective fields,” said Dean of Natural Sciences Betsy Dumont.

Engineering school rankings are based in part on peer surveys, but also on other factors such as acceptance rate, research expenditures and number of Ph.D.s granted. �鶹��’s School of Engineering is ranked No. 132 in the nation.

Two engineering specialties were also ranked among the nation’s best, one for the first time. The environmental engineering program, which debuted on last year’s list, came in at No. 76. Mechanical engineering debuted at No. 126 in the rankings.

“The inclusion of the School of Engineering in U.S. News rankings for the third time reflects the growing reputation of the school and the quality of its faculty and graduate students,” said Dean of Engineering Mark Matsumoto. “The fact that we had a number of engineering specialties ranked, including environmental and mechanical engineering, further reflects the high esteem in which we’re held by engineers in every discipline.”

Having so many of our graduate programs counted among the nation’s best is an impressive feat for a university less than 13 years old. It’s especially impressive when one considers that every other university ranked is at least 30 years older than �鶹��.

Marjorie Zatz

Five other �鶹�� programs — bioengineering, computer engineering, computer science, electrical engineering, and materials science and engineering — also appeared for the first time in the Best Graduate Schools publication, but have not yet received a numerical ranking.

Disciplines spanning all three of �鶹��’s schools are now represented in the U.S. News graduate program rankings. The School of Social Sciences, Humanities and Arts appeared last year, when �鶹�� ranked No. 90 in psychology.

“Having so many of our graduate programs counted among the nation’s best is an impressive feat for a university less than 13 years old,” said Vice Provost and Graduate Dean Marjorie Zatz. “It’s especially impressive when one considers that every other university ranked is at least 30 years older than �鶹��. These rankings show that we are already seen as serious contenders when it comes to graduate education and research excellence.”

The rankings are a testament to �鶹��’s increasingly mature and prolific research enterprise. Many young faculty members are rising to prominence at �鶹��, as evidenced by the 16 NSF early-career awards they’ve received, which means roughly one in every 15 faculty members has won this prestigious award.

The university’s interdisciplinary approach to research can be seen in the Center for Cellular and Biomolecular Machines — funded by a $5 million grant from the National Science Foundation’s Centers of Research Excellence in Science and Technology (CREST) program — and the NASA-funded Merced nAnomaterials Center for Energy and Sensing (MACES). And in 2016, �鶹�� received two NSF Research Traineeship grants, in Innovations in Graduate Education and Intelligent Adaptive Systems.

�鶹��’s inclusion in the graduate school rankings also reflects a growing trend of national recognition for the university. In 2017, U.S. News ranked �鶹�� No. 165 on its Best Colleges list. That same year, Washington Monthly placed it in the top 10 for the success of its first-generation and underrepresented students; the Sierra Club ranked it No. 50 for sustainability; and College Raptor ranked it No. 12 among Hispanic-Serving Institutions. This is in addition to the many accolades the university has received in recent years.

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A Fruit Fly Walks Into a Bar ...

Anonymous — Mon, 05 Mar 2018 19:14:39 +0000

By Jason Alvarez, �鶹��

March 5, 2018

A drunk fruit fly. Fruit flies exposed to alcohol become uncoordinated, lose postural control and eventually pass out.

Editor’s note: Every year �鶹�� shines a spotlight on the cutting-edge research underway at the university. Research Week is an opportunity for the public to explore the groundbreaking work conducted by students and faculty. As part of Research Week, the Newsroom will highlight a few of these ongoing efforts. Tune in for new research stories all week long.

Humans aren’t the only species with a well-developed drinking culture. The social life of the humble fruit fly also revolves around alcohol.

Their favorite food, rotting fruit, ferments into a beer-strength quaff. Courtship often involves swarming boozy locales and getting frisky after imbibing. Flies also use alcohol as a palliative, taking to drink after repeated sexual rejection. And like humans, flies develop “drinking problems.”

Flies exposed to alcohol show behavioral changes associated with addiction. The biology behind these changes has long eluded scientists. But in a recent study published in Cell Reports, researchers at �鶹��, led by Professor Fred Wolf, identified a protein in a special kind of brain cell that’s essential to the development of alcohol tolerance and preference — key components of addiction.

“Addiction is a brain disease,” said Wolf, who's also a member of the Health Sciences Research Institute. “And we don’t have the big picture idea of what alcohol is doing in the brain.”

Wolf thinks flies might help.

Using fly brains to study addiction might seem fanciful. After all, what can they possibly tell us about our own brains? According to Wolf, a lot. That’s because flies and humans metabolize alcohol the same way. They also use the same chemicals in their brains’ reward systems.

“Flies are more like us than we’d like to believe,” Wolf said. “The structure of their brains looks very different, but when you get down to the molecular level, it’s basically the same.”

In this study, funded by the National Institutes of Health, Wolf took flies that had never been exposed to alcohol and liquored them up until they passed out. He gave them time to recover, then repeated the process.

Changes emerged after just one boozy experience. Flies needed more alcohol to reach the same level of inebriation the second time around. This is tolerance, a hallmark of addiction. Whether fly or human, frequent drinkers become desensitized to alcohol’s intoxicating effects.

But there’s more to addiction than tolerance. Preference is another defining symptom. Flies that have never imbibed shy away from alcohol. But after one exposure, they choose alcohol over alcohol-free foods.

Graduate student Kinsey Brock creates art that uses humor to explain the serious science underway in the Wolf Lab.

Wolf wanted to know why, so he scoured fly brains for molecular clues.

“Lots of things changed,” Wolf said. “But we started noticing one particular molecule at work in glial cells.”

That molecule was Akap200. Though it’s found in every kind of brain cell, it only responded to alcohol in glial cells.

Glia are one of two main types of brain cell — neurons are the other. Glia get short shrift because scientists have long thought of them as playing a supporting role in brain processes.

“Neurons transfer information from one place to another. They’re the business end of the brain, responsible for why we think and behave,” Wolf explained. “Glia are traditionally thought of as the brain’s scaffold. They give the nervous system its shape and keep the brain working optimally. But glia are often ignored because they sound boring when compared with neurons.”

Wolf’s work upends this narrative. His findings show that neurons aren’t the only part of the brain involved in adaptive learning. When it comes to alcohol-associated behavior, glia matter — but only those glia that comprise the blood-brain barrier (BBB), the gatekeeping structure that decides which molecules are allowed into the brain.

Akap200 catalyzed the remodeling of BBB glia after flies ingested alcohol. When Quantitative and Systems Biology graduate students Sarah Parkhurst and Pratik Adhikari inactivated Akap200, there was no remodeling and no behavioral change in response to alcohol. Akap200 in BBB glia was essential to learning this behavior.

“We know that these behaviors are coded in neurons,” Wolf said. “But we found that glia in the blood-brain barrier also control the brain’s ability to learn and change.”

The discovery also has implications for treating addiction with medication. The BBB is notoriously selective, and medicine often can’t make it across. Wolf’s findings suggest that crossing the barrier might not be necessary.

“If this discovery holds true in humans, it might make aspects of addiction treatment simpler,” Wolf said. “We wouldn’t need to get drugs into the brain, we would just need to target the blood-brain barrier.”

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Chancellor Inks Deal with Berkeley Lab to Promote Collaboration

Anonymous — Fri, 23 Feb 2018 22:28:44 +0000

By Jason Alvarez, University Communications

February 23, 2018

Chancellor Leland (left) and Berkeley Lab Director Michael Witherell sign MOU.

At a ceremony held earlier today, �鶹�� Chancellor Dorothy Leland and Lawrence Berkeley National Laboratory Director Michael Witherell signed a memorandum of understanding (MOU) to establish a formal partnership between the two organizations. The agreement sets terms for the appointment of joint faculty and the sharing of resources.

“This agreement formalizes and brings structure to what has already been a fruitful relationship between �鶹�� and Berkeley Lab,” �鶹�� Chancellor Dorothy Leland said. “When we combine our complementary strengths and our unique resources, there will be no limit to what we can achieve.”

The agreement is the first of its kind for �鶹��. Though the university has de facto working relationships with multiple Department of Energy National Laboratories, including research collaborations with Berkeley Lab and adjunct faculty at Lawrence Livermore National Lab, the MOU represents the first official partnership between �鶹�� and a national lab.

“This MOU formalizes Berkeley Lab and �鶹��’s commitment to build on existing relationships, and to look to the future in possibly creating joint programs between the two institutions to solve research questions in new and unique ways,” said Witherell.

The MOU will facilitate formal split appointments between �鶹�� and Berkeley Lab, according to �鶹�� Vice Chancellor for Research Sam Traina. Faculty employed under the terms of the agreement will receive official positions at both institutions. Recruitment, appraisal and tenure decisions will be made jointly. Startup costs and salaries will also be split evenly.

Chancellor Leland (seated left) with Berkeley Lab Director Michael Witherell (seated) and Berkeley Lab delegates at the MOU signing.

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NSF Taps Former Dean Juan Meza to Lead Division of Mathematical Sciences

Anonymous — Wed, 21 Feb 2018 21:33:58 +0000

By Jason Alvarez, �鶹��

February 21, 2018

Professor Juan Meza

The National Science Foundation (NSF) announced that they have selected former Dean of the School of Natural Sciences and Applied Mathematics Professor Juan Meza as the new Division Director for the Division of Mathematical Sciences (DMS).

Meza was selected from a pool of highly qualified candidates after a nationwide search. His appointment was based in part on his original contributions to the field of mathematical sciences, his demonstrated leadership in academia and his record of achievement in research administration.

“It’s a great honor to have been chosen to lead the Division of Mathematical Sciences, as it has a well-established record of funding a broad and excellent set of research and educational programs,” Meza said. “I’m looking forward to helping NSF and to continue their mission of supporting outstanding basic research.”

As DMS director, Meza will administer a portfolio of programs with an annual budget in excess of $230 million. He will lead a division whose mission is to fund groundbreaking research in mathematics and statistics, and support education and training in the mathematical sciences.

I’m looking forward to helping NSF and to continue their mission of supporting outstanding basic research.

Juan Meza

In addition to Meza’s many contributions to �鶹��, he has served on numerous federal advisory committees, including the NSF Mathematical and Physical Sciences Advisory Committee, the NSF Advanced Cyberinfrastructure Advisory Committee and the National Academies’ Board on Mathematical Sciences and their Applications. He also served as department head and senior scientist of high performance computing research at Lawrence Berkeley National Laboratory and was a distinguished member of the technical staff at Sandia National Laboratories.

“Dr. Meza’s selection is a testament to the high regard he is held in the mathematics and science community,” Provost Tom Peterson said. “He will be, in effect, one of the primary spokespersons nationally for basic research in mathematics. His presence in Washington during this IPA assignment will also bring further national and international recognition to his home institution, �鶹��.”

In his new position, Meza will serve as an Intergovernmental Personnel Act (IPA) assignee, an appointment that allows him to remain a member of the �鶹�� faculty while serving as DMS division director.

This is not the first time that Meza has held this type of assignment. When he worked at Sandia, he served as a detailee at Department of Energy headquarters in Washington D.C. as part of the Advanced Strategic Computing Initiative program.

“The first time I worked in D.C., it was a real learning experience,” Meza said. “It taught me much about how the federal agencies worked and how large federal programs were structured and run. I think that experience will be extremely useful as I start this new appointment."

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Pellissier Speaker to Discuss Substance Abuse and the Adolescent Brain

Anonymous — Mon, 12 Feb 2018 17:58:11 +0000

By Jason Alvarez, �鶹��

February 12, 2018

Professor Sandra A. Brown

California’s recent legalization of recreational marijuana and the nation’s ongoing opioid crisis have many parents worried that their own teenagers might succumb to the temptations of drugs and alcohol.

At this year’s installment of the Vital and Alice Pellissier Family Distinguished Lecture Series — “Alcohol, Drugs and the Adolescent Brain” — concerned parents and curious members of the community can hear Professor Sandra A. Brown explain what really happens to adolescent brains when teens inhale, ingest or imbibe.

It’s a subject Brown knows well as vice chancellor for research at UC San Diego and a distinguished professor of psychology and psychiatry. She’s spent decades studying the effects of drugs and alcohol on adolescent development and the adolescent brain.

“I’m quite interested in understanding how alcohol and drugs affect development and how this affects treatment for alcohol and drug problems,” Brown said.

At this year’s Pellissier Lecture — a jargon-free science talk intended for general audiences — Brown will highlight major findings from her decades of research. The talk, which is free and open to the public, is scheduled for 6:30 p.m. Thursday, Feb. 22, at the Art Kamangar Center at the Merced Theatre.

“Early on, I focused on understanding special problems and issues with adolescents and young adults,” Brown said. “I looked at how they fare after treatment and how they get better. We already knew that for adults, addiction could cause transient and longer-lasting effects.”

Though teenagers are resilient, Brown discovered that the neurocognitive impact on teens could also be significant.

“Even modest amounts of drug and alcohol use can have short-term effects — one week to a month — on the thinking ability of youth,” Brown says. “Since it’s their job to be in school and learn, we need a deeper appreciation of the fact that recreational substance use could have an impact on thinking abilities that could be a detriment to school performance.”

Even modest amounts of drug and alcohol use can have short-term effects...on the thinking ability of youth.

Sandra A. Brown

Since teenage brains are still developing, substance abuse at an early age can also have long-term consequences as teens progress into adulthood.

“Early heavy use influences brain development. This is especially true in frontal regions of brain,” Brown said. “Frontal lobes are involved in planning and self-control, some of the very things we think of as important during adolescent development.”

Though findings like these may prove worrisome, Brown sounds a more hopeful note when discussing teens and recovery.

“Many youths experiment with alcohol and drugs, and the vast majority work their way out of alcohol and drug use without ever receiving treatment,” Brown said. “There are many different ways. There’s not a single pathway to success.”

Brown’s talk will also highlight two ongoing NIH-funded efforts to monitor the health and behavior of youth over a decade.

“The idea is to take a look at youth before any of them use alcohol, nicotine, marijuana or any other substance, and then see what happens as some of them begin to use those substances over the course of adolescence,” Brown said.

However, Brown expects this study to uncover more than just factors associated with substance abuse.

“We’re following these youths on an annual basis to understand what leads to substance involvement,” Brown said. “But we’ll also be able to track other risks and disorders that unfold over adolescence, like obesity and mental health problems.”

She also notes that this study represents a new way of accelerating research that the government has funded.

“This project uses a new model for doing science called open science,” Brown said. “This means all data we gather will be released annually to the worldwide scientific community. We’re making this all available to get answers to scientific questions faster, and in doing so, ensure transparency and replicability of studies and findings.”

The annual Vital and Alice Pellissier Distinguished Speaker Series was made possible by a generous gift from the Pellissier family to �鶹��.

Attendees should RSVP online by Feb. 16 to reserve their space. For information, call 209-228-RSVP or email specialevents@ucmerced.edu.

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Scientists Explain Mechanisms Affecting Runoff Levels During Drought

Anonymous — Fri, 12 Jan 2018 21:01:20 +0000

Jason Alvarez, University Communications

January 12, 2018

Widespread tree mortality in Sierra Nevada forests was an important mechanism regulating water levels during California's recent drought. Photo courtesy of Margot Wholey.

Scientists at �鶹��’s Sierra Nevada Research Institute (SNRI), UC Irvine, UC Davis and the USDA Forest Service have enumerated the mechanisms that serve as master regulators of streamflow and drought intensity by studying California’s 2012-15 drought. Their findings are detailed in a new paper published in Scientific Reports.

Researchers used measurements from the Southern Sierra Critical Zone Observatory (CZO) in California’s Kings River Basin to pinpoint four distinct mechanisms responsible for regulating runoff levels during the recent drought. Runoff — water from precipitation, snowmelt and natural reservoirs that feeds into mountain streams and rivers — ultimately supplies much of the state’s water.

“Long-term measurements at the CZO allowed us to understand how the drought affected the amount of water supplied by mountains,” study coauthor and UC Irvine Professor Michael Goulden said. “This understanding is needed to more accurately forecast how future droughts will affect water supplies in California and in mountain headwaters around the world, and to help devise strategies to reduce the impact of drought.”

Two mechanisms — evapotranspiration and warming — decreased runoff levels and intensified the overall effects of the drought.

“Runoff in mountain rivers ultimately reflects the difference between precipitation, which occurs as both rain and snow, and water returned to the atmosphere through evapotranspiration, which is mainly water used by plants plus evaporation from soil,” said Roger Bales, SNRI director and lead author of the new study.

The drought was dominated by evapotranspiration, which varied little from year to year in Sierra Nevada forests, even as precipitation levels declined. As a result, more water was returned to the atmosphere than drained into nearby streams and rivers. This alone led to a 30 percent reduction in springtime runoff. The warming climate only made matters worse.

Temperatures were a full degree Celsius higher than they were the decade prior. This warming resulted in drier, hotter atmospheric conditions favorable to further evapotranspiration. Elevated temperatures ultimately led to an additional 5 percent reduction in runoff.

Wildfire and tree mortality helped mitigate the harmful effects of the drought. Photo courtesy of Emma McCorkle.

But the news wasn’t all bad for runoff levels. Scientists also described two processes that actually helped mitigate the drought’s harmful effects.

Local differences in precipitation and evapotranspiration resulted in 10 percent more runoff than might otherwise be expected. Even with rising temperatures, winter evapotranspiration remained low at colder, higher elevations. This meant that upslope meltwater, primarily from high-elevation snowpack, acted as a buffer against downslope declines in runoff.

And scientists identified another mechanism that helped reduce the drought’s overall impact. It was this fourth master regulator that proved most interesting to researchers.

Drought years were characterized by widespread tree mortality — the result of increased wildfire and drought-associated tree dieback. This had the effect of thinning forests, but also reduced forest-associated evapotranspiration, leading to a 15 percent increase in 2016 spring runoff.

“This fourth mechanism is potentially the most important in the southern Sierra Nevada, depending on how long the reduced evapotranspiration is sustained,” Bales said.

But Bales warns that tree mortality isn’t a sustainable long-term solution to drought.

”Rates of recovery following forest dieback or wildfire are uncertain in a warming, highly variable climate,” he said. “The 2012-15 drought may have a long-term legacy effect on Kings River flow if recovery is slow.”

Still, the findings demonstrate that the environment is able to maintain a balance in the face of severe drought, at least in the short term.

“We often think of drought as a one-way street, causing water shortages and creating desert-like conditions,” said Richard Yuretich, director of the National Science Foundation’s Critical Zone Observatories Program, which funded the research. “This analysis demonstrates that runoff from increased snowmelt at higher elevations and the loss of vegetation from wildfires can compensate for some of the decrease in rainfall.”

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LibraryCAVE Brings Virtual Reality and Big Data Into the Classroom

Anonymous — Wed, 20 Dec 2017 17:53:32 +0000

Jason Alvarez, University Communications

December 20, 2017

Professor Nicola Lercari wears 3-D glasses to navigate an ancient temple using �鶹��'s LibraryCAVE

Professor Nicola Lercari is leading his students on a tour of Palenque, the ancient Mesoamerican city that flourished at the peak of Maya civilization. They’re exploring the altar atop the Temple of the Cross, inspecting it from all angles and scrutinizing every detail.

But they’re not in Mexico. Lercari and his students are on the second floor of the �鶹�� Library, standing before a triptych of high-definition monitors, which they view through 3-D glasses. Lercari navigates the first-person, 360-degree panoramic tour using an Xbox controller. Passers-by stop to ask questions.

“It’s a new class,” explains teaching assistant Anais Guillem. “World Heritage 110: 3-D Modeling Cultural Heritage. And this is the LibraryCAVE.”

The LibraryCAVE is a smaller version of �鶹��’s Wide-Area Visualization Environment (WAVE) system, a 20-screen VR multiplex that allows researchers to navigate interactive 3-D renderings of complex structures. The WAVE is a powerful tool that can be used to explore ancient ruins or visualize the inner structure of the brain.

With only three screens, the LibraryCAVE is more compact but no less impressive. It can do much of what the WAVE does, but it serves a different purpose. Whereas the WAVE is primarily a research tool, the LibraryCAVE is meant to serve as a teaching tool. As such, it’s housed in full view of the public, en route to the library’s second floor stacks.

Though it’s only been up and running since last summer, Lercari has already incorporated the LibraryCAVE into World Heritage 110, part of the new World Heritage minor that SSHA instituted just this year. Though the course teaches students standard techniques in archaeological analysis — including methods for finding, reconstructing and interpreting historical sources — thanks to the LibraryCAVE, it also incorporates computer-aided design techniques more commonly associated with architecture and engineering.

Lercari teaches students to produce renderings of culturally significant world heritage sites in his 3-D Modeling Cultural Heritage class.

“We wanted an interactive virtual studio session like at architecture schools,” Lercari said. “Students present their work and have faculty and students comment on it.”

Over the course of the semester, Lercari asks his students to complete three projects of increasing complexity using Autodesk 3ds Max, a software platform widely-used for 3-D graphics. The students create 3-D models of Palenque’s Temple of the Cross and present their renderings on the LibraryCAVE, receiving feedback from Lercari to help them improve their digital drafting skills.

The LibraryCAVE is one of four CAVE kiosks in the UC system. Others are located at UC Berkeley’s Hearst Museum, UC San Diego’s Geisel Library and UCLA’s Fowler Museum. All four installations are part of the “At-Risk Cultural Heritage and the Digital Humanities” project, funded by a 2016 UC President’s Research Catalyst Award. According to the project abstract, its aim is “to use cyber-archaeology and digital humanities to document and safeguard virtually some of the most at-risk heritage objects and places.“

But the LibraryCAVE is also part of a broader trend reflecting the evolving role of libraries in the digital age.

“There’s lots of movement to digital and technological innovations happening in libraries nationwide,” University Librarian Haipeng Li said. “Libraries, particularly academic libraries, are changing from the traditional role of keeping books to broader roles that support teaching, research and learning. In the U.S., academic institutions are designing library spaces driven by technology to support these expanded roles.”

The library already offers digital curation and scholarship services. They also administer the Spatial Analysis and Research Center (SpARC), which consults on projects related to spatial data management, cartography and web mapping.

“In the future, we hope for an expanded role in data management,” Li said. “Data management is what librarians are good at.”

Though World Heritage 110 is the first class to employ the LibraryCAVE, both Lercari and Li look forward to helping other faculty incorporate it into their own syllabi.

“We wanted to make sure that it works for classes,” Li said. “This semester is like a pilot run. If successful, we can push the CAVE to other faculty who might find it useful.”

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Wells Fargo Gift Helps ‘Innovate to Grow’ Continue Fall Expansion

Anonymous — Tue, 12 Dec 2017 17:55:37 +0000

By Jason Alvarez, University Communications

December 12, 2017

Team Biocraft presents their concept for repurposing the woody debris on forest floors at the spring 2017 Innovate to Grow.

Innovate to Grow (I2G), the School of Engineering’s showcase for senior capstone projects and student ingenuity in engineering and entrepreneurship, is emerging as a twice-a-year event, thanks in large part to a $50,000 donation from Wells Fargo.

“Historically a spring-only event, this is the second straight year in which Innovate to Grow will be held at the end of the fall semester,” said Dean of Engineering Mark Matsumoto. “Wells Fargo’s gift is helping the school expand its Innovate to Grow offerings and provide more resources for the projects, allowing the School of Engineering to better meet student needs and experience.”

Scheduled for Dec. 15, this fall’s I2G will highlight the efforts of 13 teams presenting the results of their capstone projects. This fall event is the counterpart to the spring semester event that’s been held annually since 2012. The date for this year’s spring I2G is May 11, 2018.

The goal of the capstone project is to provide graduating seniors with hands-on, real-world experience that they don’t get from the classroom alone. Students assemble into teams with peers, faculty mentors, and external partners to tackle specific engineering challenges.

Students explain their capstone projects to judges at the spring 2017 Innovate to Grow poster session and prototype expo.

As in previous years, this fall’s teams worked with corporate, government and nonprofit partners — including major regional players like E&J Gallo, Del Monte, UCSF Fresno and the Turlock Irrigation District — to solve a variety of real-world engineering challenges. Some teams also worked with partners outside the Central Valley. One team, working jointly with San Diego County and the UC Division of Agriculture, is working to replace potentially harmful chemical pesticides with controlled hot water treatments. Another team is working with the Australian company T3 Energy, in collaboration with Super Insulated Green Building Technologies of Flagstaff, Arizona, to develop green bricks – building materials that are both load bearing and insulating. It’s technology that would bring down construction costs while maximizing energy efficiency.

I2G’s expansion into fall mirrors a school-wide trend to accommodate ever-increasing numbers of fall graduates. This semester, for example, marks the first time in university history that fall graduates will get their very own commencement ceremony.

“It was important that the School of Engineering expand its Innovate to Grow offerings to meet the growing demand from fall graduates,” Matsumoto said. “Seniors graduating from the School of Engineering gain valuable experience that prepares them for career entry through a capstone project; it was essential for the school to begin offering a fall event to accommodate fall graduates and the continued growth of the university.”

Innovate to Grow is free and open to the public. A complete schedule of events and a map of event locations can be found here. Further information on Innovate to Grow can be found on the I2G Website. Parking for the event is available at Lake Lot 2. Any additional questions about the event can be addressed to D.B. Quan at the School of Engineering.

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