Category Archives: Biochemistry

Judges at the Los Angeles County Science Fair named the top two winners of the competition on Saturday out of the more than a thousand students who had their experiments on display.

Kenneth Lee, a senior from Palos Verdes Peninsula High School, received the top sweepstakes prize for the senior-level division made up of high school students. He won for his project in the biochemistry and molecular biology category: "The Role of Testosterone in Hepatocyte Apoptosis in High Fat Diet-Induced Non-Alcoholic Fatty Liver Disease." His teacher on the project was Peter Starodub.

At the junior level for middle-schoolers, Raymond Gilmartin, an eight-grader at South Pasadena Middle School, took the sweepstakes prize. He had a project in the physics-aerodynamics and hydrodynamics category: "Spare the Environment, Spoiler the Car." His teacher on the project was Emily Hoffman.

Judges also awarded first-, second- and third-place medals, as well as honorable mention prizes, in a number of other categories, with animal physiology and biology, behavioral science, biochemistry and molecular biology, chemistry, engineering and mathematics and computer science, among them.

An exhibit hall at the Pasadena Convention Center was lined with rows of tri-fold poster boards featuring the projects, some of which will proceed to a statewide science fair and then on to the international level.

The science fair, in its 62nd year, had more students involved than in recent years, with 1,063 students taking part. The students came from public and private schools, as well as from those of the Archdiocese of Los Angeles. The number of girls participating has eclipsed the number of boys in recent years a trend that continued this year with 564 girls and 499 boys.

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L.A. County Science Fair names top student scientists

Benjamin Madej, a chemistry and biochemistry PhD student at the University of California, San Diego, has won the 2012-2013 Nvidia Graduate Fellowship Program award for his molecular dynamics research using graphics processing unit-based computing.

Madej will receive a $25,000 scholarship to further his research. Additionally, he will have access to Nvidia products, technology, and expertise.

His proposal focused on improving the Amber molecular dynamics GPU engine and extending the use of GPUs in other facets of molecular dynamics development and workflows. He is currently working on new methods for developing force fields used in molecular dynamics software, specifically the Amber MD package.

Biovest, a majority-owned subsidiary of Accentia Biopharmaceuticals, has tapped Brian Athey to be a member of its scientific advisory board.

Athey is a professor of biomedical informatics and was recently named chair of the department of computational medicine and bioinformatics at the University of Michigan's medical school (BI 1/20/2012). Additionally, he serves on Appistry's scientific and technology advisory board (BI 2/10/2012).

Athey is also one of the founders of the tranSMART project community which supports open source pharmaceutical data-sharing and -analysis software platforms.

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People in the News: Benjamin Madej and Brian Athey

(KATV, Source: UofA) Fayetteville - University of Arkansas Honors College students have led a campus-wide effort to plant a community garden that will provide fresh produce and flowers to the Full Circle Campus Food Pantry, a student-run emergency food assistance program recently honored at the White House. Two years of research and planning, along with countless hours of hands-on work with soil, compost and seedlings will culminate in the dedication of the new campus community garden at 3:30 p.m. on Monday, April 2.

Emily Crossfield, an honors biochemistry major in the J. William Fulbright College of Arts and Sciences has led the effort to get the garden in the ground. More than 50 students from multiple disciplines have worked together to design and plant the garden, fostering connections across campus. Crossfield said for her the project is as much about the people as the plants.

"I'm meeting people I never would have met otherwise," said Crossfield, who also serves as director of sustainability for the Associated Student Government. She sees the garden as an important tool for promoting community as the campus grows.

"As a freshman in a big class you can feel lost, but if you're working with 10 other students in the garden, you're going to get to know each other pretty well," she said.

Inspired by community gardens that she saw while studying in Berlin, Crossfield decided to plant a campus community garden as the capstone project required for her minor in sustainability. Her efforts have revolved around finding a good site and building partnerships across campus. The Associated Student Government and Residents' Interhall Congress have provided substantial funding for the garden, with additional support from the department of facilities management and two registered student organizations, GroGreen and the Horticulture Club.

"Emmy has worked hard to bring a lot of people together on this, and there have been lots of ups and downs," said Curt Rom, a professor of horticulture and honors program director for the Bumpers College. "She has provided the leadership to get this garden going."

The new garden builds on research by Samantha Jones, a recent honors graduate of Bumpers College who surveyed 86 universities with community gardens and visited six of them to document best practices in her honors thesis. Her feasibility study, directed by Rom, was undertaken after an earlier garden located at the university's Agricultural Research and Extension Center proved not to be sustainable.

The location of the new garden, close to two residence halls should help ensure ongoing support.

"You need the garden to be visible, where people pass by it, notice it and can easily take care of it," Crossfield said.

The site is not without challenges. Sandwiched between two four-story wings of Maple Hill, the garden is short on sunlight in certain areas and hampered by poor soil. The students have divided the small plot into three zones based on the amount of sunlight received, planting shade-loving perennials and herbs such as basil, rosemary and sage in the back of the garden. Two truckloads of topsoil and one truckload of compost, some of it recycled from residence hall food waste, have created a rich bed for growing broccoli, peppers, squash and tomatoes. One-half of the fresh produce will go to the student volunteers, while one-half will be donated to the Full Circle Campus Food Pantry. The students will also plant day lilies, cannas, irises and hostas to donate to the food pantry and to the chancellor's office for use at university events.

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Honors Students Lead Effort to Plant Campus Garden

Emily McFadden, a Westhampton College junior and biochemistry major, recently received the national Beckman Scholarship for outstanding undergraduate research in the chemistry and biological sciences.

The Beckman Scholars Program , established in 1997, was designed to provide scholarships that contribute significantly in advancing the education, research training and personal development of select students in biochemistry and its relative fields, according to the programs website. The nationwide scholarship is awarded to six undergraduate students each year.

McFadden, one of the six students selected to receive the scholarship in 2012 , said the $19,200 grant would cover her research costs for the next two summers and her senior year.

The grant funds travel to symposiums and conferences across the country where I can present my research, McFadden said. It also plays for supplies in my lab.

McFaddens research, which she has been conducting for the past year and a half, takes place in a Gottwald biochemistry lab with the help of a faculty mentor.

Ive been researching a specific enzyme involved in DNA repair, McFadden said. My upcoming project is looking at an alternative enzyme, and comparing the two to see how their efficiency in DNA repair is different.

McFadden said the final culmination of her research would take place next summer, when she would present her project results at the Beckman Scholars Conference in California.

Ill have the opportunity to show my work to the members of the Beckman Foundation, as well as any other scientists who may be interested in my findings, McFadden said.

Michelle Hamm , associate professor of chemistry at the University of Richmond , serves as McFaddens mentor and nominated McFadden to receive the scholarship.

Emily is a bright and talented student with a passion for science, Hamm said. The Beckman award is for future scientific leaders, and I thought that description fit Emily well.

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Westhampton junior receives national research scholarship

Public release date: 27-Mar-2012 [ | E-mail | Share ]

Contact: Jan Zverina jzverina@sdsc.edu 858-534-5111 University of California - San Diego

A graduate student working in the Walker Molecular Dynamics laboratory at the San Diego Supercomputer Center (SDSC) at the University of California, San Diego is a recipient of the 2012-2013 NVIDIA Graduate Fellowship Program award for his innovative molecular dynamics research using GPU (graphics processing unit) computing.

Benjamin Madej, a chemistry and biochemistry Ph.D. student at UC San Diego, will receive a $25,000 scholarship to further his research. Madej received his Bachelor of Science in biomedical engineering from Washington University in St. Louis, Missouri, and is currently working on new methods for developing force fields used in molecular dynamics software, specifically the AMBER MD package.

Madej's research proposal focused on not only improving the AMBER Molecular Dynamics GPU engine, but extending the use of GPUs to multiple facets of molecular dynamics development and workflow for new drug discovery.

"We are proud of Ben's achievement in being awarded this prestigious scholarship and recognition," said SDSC Director Michael Norman. "It is very gratifying to see such a high level of accomplishment in computational science as Ben pursues his doctorate here at UC San Diego."

"This fellowship is a testimony to Ben's past work, the importance of GPUs at the frontiers of molecular dynamics and drug discovery, and recognition of the future potential of his contributions to science. The GPU revolution is transforming the field and this fellowship provides vital support for us to continue this cutting-edge research," said Ross C. Walker, an assistant research professor with SDSC and head of the Walker Molecular Dynamics laboratory. Walker also is an adjunct assistant professor in UC San Diego's Department of Chemistry and Biochemistry, as well as an NVIDIA CUDA Fellow.

The NVIDIA Graduate Fellowship Program provides funding to Ph.D. students who are researching topics that will lead to major advances in the graphics and high-performance computing industries, and are investigating innovative ways of leveraging the power of GPUs. Recipients not only receive crucial funding for their research, but are provided access to NVIDIA products, technology, and expertise.

"This year the NVIDIA Foundation joined in our search for top Ph.D. students who are investigating innovative ways to leverage the power of the GPU, especially those that will ultimately benefit humanity," said Chandra Cheij, NVIDIA's research program manager. "Congratulations to Ben and SDSC for this significant achievement."

SDSC's Walker Molecular Dynamics lab is focused on computational chemistry, molecular biology, and high-performance computing. The lab is particularly interested in the development of efficient algorithms for parallel computation of Quantum Mechanical and hybrid Quantum/Molecular Mechanical (QM/MM) techniques, as well as improvements in the computational efficiency and accuracy of classical MM dynamics simulations.

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SDSC graduate student awarded NVIDIA Graduate Fellowship

Newswise Cigarette smoke cannot only cause cancer, but it's also responsible for the spread of it, according to research by UC Merced biochemistry Professor Henry Jay Forman.

Forman discovered tobacco smoke activates an enzyme called Src that causes cancer cells to spread to other parts of the body. The study will appear in the April 15 edition of Free Radical Biology and Medicine.

Cigarette smoke is the major cause of lung cancer, Forman said, but nearly half of lung cancer patients remain active smokers. Nonetheless, researchers haven't understood how cigarette smoke causes cancer to metastasize.

The lab was also able to prevent cigarette smoke from activating the enzyme by introducing an antioxidant. Forman's discovery could prove useful in the fight against cancer, as it creates more understanding on how it spreads and how antioxidants can help combat this.

Forman will present his findings on April 21 at the Experimental Biology 2012 conference in San Diego.

Forman coauthored the paper with a professor from the University of Padova in Italy. Forman served as a visiting professor during the summer while also conducting research.

In another paper, recently published in the Journal of Biological Chemistry, Forman collaborated with investigators at USC who are experts in looking at how cells maintain themselves using proteasome, which degrades old and damaged proteins. When cells are under oxidative stress, the proteasomes work faster to remove damaged proteins.

However, the lab discovered the signal used to increase a cell's defenses doesn't happen in old age, causing cells to die and turn malignant. The findings offer more insight into age-related problems, such as Alzheimer's disease. Both studies were supported by the National Institutes of Health.

Forman will continue his research this summer, focusing on three projects: understanding how differences in the expression of a particular enzyme increases human susceptibility to air pollution; studying how people with sickle cell trait may have a sickle cell crisis when doing severe exercise; and studying how cigarette smoke activates an enzyme that regulates changes in lung cancer cells that promote metastasis. The three projects are also funded by the National Institutes of Health.

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Continued Smoking Can Spread Cancer