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College of Science Research

Collaborative Research Awards 

Here in the College of Science, our curriculum emphasizes hands-on experience, real-world applications,  and opportunities to work closely with faculty on research projects. We believe that scientific research helps students develop critical reasoning skills and enhances understanding material covered in the classroom. The Collaborative Research Award seeks to promote interdisciplinary student-faculty research. Faculty from every department are encouraged to apply for this award.

Spring 2018 Winners

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Coastal Wetlands
Principal Investigator: Patty Oikawa, Assistant Professor, Earth and Environmental Sciences, CSU East Bay
Collaborator: Sara Knox, Earth System Science, Stanford University
Abstract: Coastal wetlands play significant roles in global C cycling yet are currently not well represented in Earth system models. We propose to improve estimates of carbon (C) sequestration in coastal tidal wetlands. We plan to leverage ongoing high frequency measurements of atmospheric C fluxes collected in the Hayward shoreline.These high frequency data include eddy covariance measurements of vertical fluxesof CO2 and CH4. Funding from the Collaborative Research Fund would provide critical ancillary soil data which will improve understanding of C cycling. We plan to expand thebiogeochemical PEPRMT model to predict atmospheric C exchange in tidal marshes using the continuous data streams measured at the tidal marsh in a model-data fusion approach. Our project will provide, to our knowledge, the first dataset to include multi-year continuous measurements of atmospheric C exchange in a tidal wetland in the San Francisco Bay. This rich dataset, analyses and modeling efforts will improve our ability to incorporate coastal tidal wetland C dynamics into the Earth system models.
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Transcriptomic Profiling and Domain Searches for Functional Characterization of Novel Virulence Determinants of Toxoplasma Pathogenesis
Principle Investigators: Ana Almeida, Ph.D. Biological Sciences, CSU East Bay 
Our collaborative proposal aims at studying the molecular mechanisms underlying host-parasite interactions during Toxoplasma gondii infection of the gastrointestinal tract. Toxoplasma gondii is a single-celled, eukaryotic pathogen of medical and veterinary importance, as it can infect humans and virtually all warm-blooded animals. Most Toxoplasma infections occur following ingestion of oocysts from environmental reservoirs as well as tissue cysts in raw and undercooked meat from infected animals. Horizontal transmission between intermediate hosts can also occur, for instance, when a human eats undercooked lamb. Although infection with Toxoplasma is usually self-limiting in healthy adult humans, severe disease does sometimes occur and there exists no effective therapy to treat a chronic infection. This presents serious challenges should a chronically infected individual become immunocompromised, as reactivation of tissue cysts can lead to severe complications, especially in HIV-AIDS and transplant patients. In addition, Toxoplasma can cross the placenta during pregnancy and infect the developing fetus to cause congenital toxoplasmosis, lifetime sequelae, and abortions. While Dr. Guiton’s lab will carry out the in vitro and in vivo studies to uncover the genes involved in T. gondii life cycle as well as modulation of host responses, Dr. Almeida’s lab will carry out in silico studies of candidate proteins in order to predict their involvement in infection and pathogenesis. Also, Dr. Almeida’s lab will provide bioinformatics support for the analysis of large-scale datasets generated by the experimental approaches performed on Dr. Guiton’s lab.
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Transcriptomic Profiling and Domain Searches for Functional Characterization of Novel Virulence Determinants of Toxoplasma Pathogenesis
Principle Investigators: Pascale Guiton, Ph.D., Biological Sciences, CSU East Bay
Abstract: Toxoplasma gondii is a unicellular parasite responsible for toxoplasmosis, a disease afflictingapproximately one third of the world human population. There presently exists no cure forchronic toxoplasmosis. During infection, usually following ingestion of contaminated food or water, the parasite invades the host cell and resides within a parasitophorous vacuole (PV). Toxoplasma in its host will interconvert between many developmental forms, each biochemically and functionally distinct. Toxoplasma possess stage-specific transcriptomes. They encompass a plethora of genes, including pep1, gra9, and rop23, that encode hypothetical proteins predicted to be secreted inside the PV and/or directly into the host cell. Preliminary evidence from my laboratory indicate that pep1-; gra9-, and rop23-defective mutant parasites are severely attenuated in virulence in mice, suggesting that PEP1, GRA9 and ROP23 may be novel virulence determinants of Toxoplasma. We postulate that Toxoplasma secretes these three developmentally regulated proteins at specific phases in the pathogenic process to modulate host processes.To address this hypothesis, my students will use standard molecular cloning techniques to engineer parasite mutants expressing a C-terminal-tagged version of each protein. This tag will be used as proxy in immunofluorescence assays to determine the subcellular locations of PEP1 and ROP23 in Toxoplasma and during infection of human intestinal epithelial cells (hIECs). Furthermore, we will infect hIECs with either parental and knockout mutant strains and perform RNA sequencing, in collaboration with Dr. Ana Almeida, to assess whether PEP1, GRA9, and/or ROP23 modulate host processes during Toxoplasma infection. Furthermore, Dr. Almeida’s group will conduct a variety of bioinformatic analyses to identify functional domains in these proteins that may provide clues as to their mechanisms of action during infection. Once completed, this work will expand our understanding of the pathogenicity of Toxoplasma and the therapeutic potentials offered by developmentally regulated virulence factors in the fight against toxoplasmosis.

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Politics at the Cutting Edge: Intergovernmental Policy Innovation in tAffordable Care Act
Primary Investigators: Ann C. Keller (University of California, Berkeley), Philip B. Rocco (Marquette University), Andrew S. Kelly Ph.D., Assistant Professor Health Sciences California State University, East Bay
Abstract: Following the 2016 election, Republicans defended proposals to repeal and replace the Affordable Care Act (ACA) by citing state governments’ unique capacity to carry out policyinnovation as “laboratories of democracy.” This paper examines the assumption that grants to states, in the current polarized context, will stimulate significant health policy innovations.In contrast to prior scholarship, we focus on the implementation of the ACA’s State Innovation Models (SIM) initiative.The SIM initiative is specifically geared towards incentivizing states to experiment with new models of payment and delivery that can improve health outcomes and/or reduce health-care costs. Drawing on a combination of quantitative and qualitative evidence, we find that, states’ participation in SIM is shaped by partisanship, administrative capacity, economic characteristics, and policy legacies. Our findings have important implications for future efforts to reform the ACA by delegating to state governments the responsibility for policy innovation. 

Fall 2017 Winners

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Time-resolved Microscopy of Semiconductor Quantum Ring Nanostructures
Principal Investigator: Ryan Smith, Associate Professor, Physics California State University, East Bay
Abstract: My collaborative work is being conducted with Prof. Jong Su Kim, who prepares samples at Yeungnam University in South Korea and participates in the interpretation of results. The research goal is to characterize the lifetimes of excited states of quantum rings, a novel class of solid-state nanostructures. Study of the dynamics in individual quantum rings will be accomplished through combining microscopy and pulsed laser spectroscopy techniques. Understanding dynamic light-matter interaction at small-spatial and short-time scales will permit the control of electronic configurations using states of light, thus opening new pathways for fundamental investigation and integration into novel nanotechnology devices such as quantum information storage devices. Shrinking technologies can translate to vast enhancements in device speed, flexibility, and strength. As the scale of solid state devices trends toward the single-atom limit, quantum confinement gives rise to many new challenges that arise at the intersection of solid state electronics and modern optics. Small length scales of nanoscale size systems (a nanometer is one billionth of a meter) implies that understanding short timescale physics (~10^-15 seconds, or femtoseconds) can lead to breakthroughs in control and utilization of light-matter interactions. Considering the importance of fast time scale processes to progress in nanomaterials, ultrafast spectroscopy techniques utilizing pulses ~10 femtoseconds in duration with a large spectral bandwidth are ideal for quantifying such processes in nanostructures. As the scale of solid-state optoelectronic devices trends toward the single-atom limit, it is critical to understand the effects of the quantum confinement of charges at this small length scale.
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Studying Gamma-ray Galaxies with the VERITAS Collaboration
Principle Investigators: Amy Furniss, Assistant ProfessorDepartment of Physics
Abstract: My collaborative project provided support for student and faculty travel the gamma-ray telescope VERITAS. This project allowed undergraduates to partake in cutting-edge gamma-ray astrophysics research using VERITAS, standing for Very Energetic Radiation Imaging Telescope Array System. The students and myself continue to participate in the local analysis of VERITAS data on extreme galaxies, complementing the hands on experience of operating the VERITAS instrument for the observing shift completed in March of 2018. The collaborative grant enables my continued membership in a large 100-pers on collaboration which utilizes and maintains the VERITAS instrument. This membership allows me to benefit from VERITAS data access and joint publication rights. The data that was taken and analyzed as part of this project will be included within a VERITAS extragalactic catalog, representing the first of its kind in a relatively young sub-field of astronomy. In addition to addressing high impact astrophysical questions on gamma-ray galaxies and the cosmological fields in our local universe, this project carried an overarching goal to involve students with the open questions relevant to particle astrophysics research, empirical observation, high performance instrumentation utilized by VERITAS, as well as instill the students with the sense of excitement that comes from working to answer fundamental questions about the Universe.
claudia_photo_ocean_2017.jpgNext-generation RNA Sequencing to Untangle Plant Responses to Nutrient Deficiencies
Principal Investigator : Claudia Uhde-Stone, Professor, Biological Sciences, California State University, East Bay
Abstract : Plants require nutrients, such as phosphorus, nitrogen, and iron, for growth and development. Phosphorus is one of the most limiting nutrients for crop production worldwide. Phosphorus fertilizer is usually applied as rock phosphate, a non-renewable resource which, by some estimates, may be depleted in 100-300 years. In order to develop crop plants that can grow with less fertilizer, researchers are taking a closer look at plants that are well adapted to nutrient-poor soils. White lupin can grow in poor soils where other plants can’t grow, and has become a model plant for the study of plant adaptations to nutrient deficiency. Still, not much is known about the processes by which white lupin senses nutrient deficiencies and initiates responses. Elevated sucrose (sugar) transport from shoot to root appears to act as long-distance signal, initiating nutrient starvation responses in the root. However, sucrose may not specify which nutrient stress the plant is experiencing. We hypothesize that sucrose acts as a general nutrient starvation signal, and that additional signals are needed to communicate the specific nature of the nutrient deficiency.  To untangle general and specific nutrient starvation responses, we propose to use next-generation RNA sequencing, a powerful tool for high-throughput analysis of gene expression (i.e. gene activity). Understanding how white lupin senses nutrient deficiencies and integrates specific and general nutrient starvation responses should be useful for developing plants that require less fertilizer while offering improved nutritional value for human consumption.
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