Announcing the "new" MCSB MS/PhD Program

We are pleased to report that UC President Napolitano has approved the MCSB MS/PhD program! The program will start this September (2015) for students currently enrolled at UCI. This includes students who just finished the gateway program, as well as students currently enrolled in academic departments.  The fully approved proposal may be viewed from the following link: MCSB 050115

MCSB degreesSubject to approval by the MCSB Director in conjunction with the MCSB Executive Committee, current UCI students can transfer into the MCSB program this fall (2015) via the Change of Major form process. Full program details and specific transfer requirements, including resolving financial support issues, will be posted shortly on the MSCB website.

The stand-alone MCSB M.S./Ph.D. program builds on the success of the current MCB gateway graduate program and is the fulfillment of a 2005 HHMI grant obligation. The MCB gateway program will become the “Department Option” in the MCSB M.S./Ph.D. program, which will continue to provide students with a gateway opportunity. Students will now have the option to pursue their degree directly from the MCSB program by taking the MS/Ph.D. option.

Local high school students model watershed bacterial dynamics

"Is the water safe to swim in ?" That's the question that crossed the minds of Annie Chang and Daisy Chen, two 9th graders from Woodbridge High School, Irvine, and brother-sister team Hari and Anita Garg from University High School, Irvine after observing the confluence of pets, toddlers and river effluent at one of our local beaches last summer. They wondered whether certain sites in our local watershed harbor high concentrations of coliform bacteria that might elevate risks to human health. So they set out to find some answers. But what initially had seemed like a straight forward question, they quickly came to realize was a complex problem with no easy answers and no simple single methodology.

Under mentorship from Dr. Felix Grün (CCBS) and Dr. Michelle Digman (BME) they spent last summer collecting water samples along the ocean coastline, at river outlets and throughout Newport Bay, and analysing them for bacterial contaminants using a variety of quantitative laboratory techniques including bacterial colony forming plate and growth assays, species-specific qPCR, and applying a novel sensitive fluorescence particle counting instrument developed at UCI's Laboratory of Fluorescence Dynamics. Quantitative data on bacterial levels - along with real time weather, tidal and water flow data - were then used as input parameters for a research grade hydrodynamic and biogeochemical computational simulator (ELCOM-CAEDYM, Centre for Water Research, UWA) able to model the three-dimensional temporal and spatial dynamics of complex water transport processes and their ecological responses.

Annie and Daisy's modeling results, together with Hari and Anita's surveys, highlighted the highly dynamic (and sometimes surprising) interactions throughout our watershed. Notable was the distribution of high coliform counts in the Upper Bay around areas of freshwater input sources, e.g. runoff from marshes and golf courses, that were also subject to inefficient tidal flushing, and the rapid decline in viable bacterial counts at most ocean locations due to dilution effects and inhospitable growth conditions. So appearances aren't everything: the Upper Newport Bay ecological preserve might look tempting but is not a good place for a swim; swimming close to the Santa Ana river outlet ... well that depends on the time, tide and weather events.

2015IRWD winnersAnnie and Daisy won 1st Prize in Environmental Science for their project entitled "Multimethod Analysis and Spatial Modeling of Bacterial Dynamics in the Newport Bay Watershed" at the Orange County Science & Engineering Fair in April and took 4th place at the California statewide competition held at the Staples Center, Los Angeles in May. Their work also received recognition with additional awards from the Irvine Ranch Water District, Orange County Sea and Sage Audobon Society and the California Shore and Beach Preseveration Association. Hari and Anita Garg also excelled with their project entilted "Pathogen Detection in Southern California Water Using a Particle Counter" being recognized by a special IRWD award, a 3rd Place in the Biological Products section of the OCSEF and also going on to compete at the California statewide competition. Congratulations to all !


Chang Liu honored with the NIH New Innovator, the Dupont Early Career and Beckman Young Investigator Awards


Congratulations to Dr. Chang Liu who has just been recognized with a  NIH New Innovator Award for his research work on "A high-throughput continuous evolution system for in vivo biosensor engineering".

Dr. Liu was also recently named a recipient of the 2015 Dupont Young Professor grant awards. He joins the 2015 select group of outstanding faculty from 9 prestigious universities around the world honored for their contributions and potential to advance basic science knowledge that address global challenges in food, energy and environmental protection. Award recipients receive 2 years of grant support to help establish and develop their research careers.

In addition, Dr. Liu was also named one of eight recipients of the The 2015 Beckman Young Investigator's award. The Beckman Young Investigator (BYI) Program is intended to provide research support to the most promising young faculty members in the early stages of academic careers in the chemical and life sciences particularly to foster the invention of methods, instruments and materials that will open up new avenues of research in science.

Dr. Liu's research topic focuses on orthogonal replication and rapid evolution.


Jun Allard Receives NSF Career Award

Congratulations to Assistant Professor Jun Allard (Department of Mathematics and Physics & Astronomy) for receiving a 5-year NSF Career Award on the topic of "Mathematical Framework for Elucidating Mechanics at Immune Cell Interfaces."

Jun AllardDr. Allard's work will focus on developing mathematical models of the physical interactions at cell-cell interfaces, with particular emphasis on immune cells that need to decipher information - relevant to self and non-self recognition and disease processes - from transient dynamic cellular contacts. The dynamics at these interfaces involve an interplay between transport, mechanics and chemical kinetics, and play out over a range of length and time-scales, necessitating a combination of mathematical techniques, including systems of elliptic, parabolic and stochastic differential equations; computational fluid dynamics of liquid-structure interactions; Brownian dynamics; as well as Bayesian statistics that leverages quantitative experimental data. This work therefore aims to provide a deeper understanding of how cells overcome and exploit physical constraints to cell-cell contact, by developing a model that integrates motion of the intracellular and extracellular fluid, Brownian motion of molecules embedded in the cell's membranes and active forces. Dr. Allard will also explore the mechanism and evolutionary advantages of molecular clustering, and develop, validate and apply mesoscale models of large flexible biomolecules to decipher their mechanical properties and biological role. These mesoscale models are suitable to exploring timescales that all-atom molecular dynamics cannot, while capturing details that particle-based simulations miss.

Results from the work will have direct implications for understanding immune function, impacting research on autoimmune disease and immunotherapy. Students recruited to these projects will have the opportunity to gain exposure to contemporary work at the interface of mathematics, biology and physics.

2015 NSF Graduate Research Fellowship Awards

Congratulations to our MCSB graduate student award winners and honorable mentions.....

Award Winners:

Jaleal S. Sanjak for his project proposal "The Effects of Molecular Genetics Architecture and Deomgraphy on GWAS." Jaleal will be studying the "missing heritability" issue i.e. rare poylmorphisms with large effects that drive heritability of disease risk in humans, and which represents a significant problem for current genone wide association study (GWAS) approaches. He will develop and simulate predictive models that invoke population genetics theory and complex gene-gene interaction models to improve the predtictive power and GWAS study designs. He will be mentored by Professor Kevin Thornton, Department of Ecology and Evolutionary Biology.
Andrew J. Schaub for his project entitled "Engineering the Reductase Domain from the Non-Ribosomal Peptide Synthase Module in Myxalamid Biosynthesis System for Advanced Second-Generation Biofuel Production." Andrew will be studying methods to engineer improved metabolic pathways leading to polyketide synthesis that can be used for biofuel production. He will apply molecular dynamics (MD) simulations for the protein-protein interactions between the MxaA and PCP subunits bound to various alkyl-CoAs and polyketide mimics to guide the rational design and engineering of mutants able to accept different MxA upstream modules. His project mentors will be Professor Sheryl Tsai (Departments of Chemistry, Molecular Biology and Biochemistry and Pharmaceutical Sciences) and Professor Ray Luo (Departments of Molecular Biology and Biochemistry, Biomedical Engineering and Information and Computer Science).

Honorable Mentions:

Matthew Boyvn for his project entitled "Modeling Self-organization and Control in Motor Cargo Systems." Mathew hopes to investigate the properties that drive motor protein interactions with intracellular cargoes, and whether attachment/detachment occurs through stochastic events or is coordinated through various suspected mechanisms. He will use a combination of computational modeling and experimentation to address these questions. His mentor will be Professor Jun Allard (Department of Mathematics).
Anna LoPresti for her project entitled "An Evolutionary Model of Social Discounting and Implications for Climate Policy." Anna hopes to apply evolutionary theory to build a model of intergenerational social discounting in human populations related to implementation of policies addressing global climate change. In order to effectively tackle climate problems, current societies will have to forgo some benefits in order to provide future generations benefits, a process referred to as social discounting. This altruistic behavior is influenced by a combination of kin and group selection, and is subject to natural selection as well as the geogrpahic and temporal distributions of benefits and relatives in the future. Anna will be mentored by Professor Steven J. Davis (Department of Earth Systems Sciences).
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