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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 2019

almeida
Can snail microbiome explain susceptibility to schistosomiasis infection? Understanding schistosomiasis through the lenses of Environmental Epidemiology
Principle Investigators: Dr. Ana Almeida, MD, , Ph.D. Department of Biological Sciences, CSU East Bay and Dr. Lucio Macedo Barbosa, MD, Ph.D, Department of Parasitology and Epidemiology Escola Baiana de Medicina e Saúde Pública (Salvador/Bahia, Brazil)
Abstract: Schistosomiasis is a disease caused by parasites of the genus Schistosoma, commonly known as blood- flukes. These parasitic worms spread via contact with contaminated water infested with infected freshwater snails. In 2015, the World Health Organization estimated that 252 million people were affected by schistosomiasis, and approximately 200,000 died as a consequence of this disease in the previous year. In tropical countries, where this disease is most commonly found, around 700 million people are exposed to schistosomiasis making it - second only to malaria - among the parasitic diseases with the greatest economic impact. The life cycle of a Schistosoma worm starts with the elimination of eggs with human feces or urine in a body of fresh water. Under optimal conditions, these eggs hatch as miracidia that, in turn, infect freshwater snails, their intermediate hosts. Inside the snail, the miracidia undergoes successive generation of sporocysts that are eliminated in water as cercariae. Cercariae penetrate the skin of humans, migrate to the liver portal system and other veins of the digestive system, mature into adult worms and, through sexual reproduction, form eggs that are eliminated in the water through contaminated feces or urine, completing the Schistosoma life cycle. Curiously, within a contaminated body of fresh water, less than 5% of snails are infected with sporocysts. The reasons why only a small number of snails are susceptible to miracidia infection are still unclear. In epidemiology, infectivity is the ability of a pathogen to establish an infection. More specifically, infectivity is a pathogen's capacity for horizontal transmission or, how frequently it spreads among hosts. Here, we hypothesize that miracidia infectivity is dependent on the snail specific microbiome. We expected that infected and non-infected snails harbor different microbiome compositions, and that these differences are capable of explaining the disparity in snail susceptibility within an endemic area. Also, we expect that snail microbiomes are influenced by geographical location (urban vs. rural areas), and but a similar patter of ‘potentially protective’ snail bacterial microbiome composition can be identified regardless of geographical location. In order to test these hypotheses we will compare the microbiome of infected and non-infected snails in four bodies of fresh water across urban and rural endemic areas in Bahia State, Brazil. We will use next- generation sequencing technologies to sequence the 16S rRNA gene of bacterial communities present in the snail’s body in order to characterize its microbiome. Alpha and beta diversity measurements such as disparity, evenness, and richness will be estimated from the sequencing data and compared within and between urban vs. rural and infected vs. non-infected snail populations. As a result of this project we will further characterize the microbiome of freshwater snails and its relationship to a major tropical parasitic disease, schistosomiasis. If a common microbiota is identified as protective to miracidia infection, public health measures can be planned on the basis of this information in order to help promote the establishment of a beneficial microbiome across snail populations within endemic areas. More data will certainly be required until such approaches can be taken, but the data generated in this project will shed a new light into future venues for combining Environmental Epidemiology and Public Health.
kocherzhenko
Modeling Thermally Activated Delayed Fluorescence In Bulk Molecular Materials
Principle Investigators: Dr. Aleksey Kocherzhenko Department of Chemistry and Biochemistry Collaborators: Pauline Germaux, chemistry major/computer science minor, CSU East Bay Antonios Alvertis, Cavendish Laboratory, University of Cambridge
Abstract: SThermally activated delayed fluorescence (TADF) is a physical process that holds promise for improving the energy efficiency of organic light-emitting diodes (OLEDs) used in displays of modern electronic devices and in lighting applications. It allows converting triplet excitons that cannot decay by emitting light to singlet excitons that can. TADF of individual molecules that exhibit it is commonly studied in solution, but in electronic devices such molecules form solid films. Interactions between molecules in a film (a) restrict molecular conformation and motion that have been shown to be important for TADF and (b) allow excitons to migrate within the material from one molecule to another, potentially reaching a molecule with a conformation in which TADF can occur efficiently. We propose to theoretically and computationally study these effects of intermolecular interactions in bulk organic solids on TADF from molecules that compose the solid. We will use classical molecular dynamics simulations to track conformational changes of molecules in the solid phase and will use simulations based on quantum dynamics models to track the migration of excitons within the solid. Based on our results, we hope to provide recommendations for designing solid films with optimal TADF properties for applications in next-generation OLEDs.

How To Apply

At Cal State East Bay, it is difficult for those who love to teach to sustain meaningful research programs without collaboration and resources of some kind, which support one’s focus on the research despite other priorities and interruptions. The collaborators might be one’s own students, other Cal State East Bay faculty, or collaborators might be from other universities, research laboratories, or companies, or some combination of these.
The purpose of these awards is to provide modest support that can increase the capacity of faculty members in the College of Science to sustain meaningful, productive long-term research programs, and to bring intellectual enrichment to their classroom, their department, and to the college and community. An October 15 submission deadline for tenured faculty provides sufficient time including summer for proposal preparation, including literature search, pilot research, and establishment of necessary collaborations and permissions. A March 15 submission deadline for untenured faculty gives new faculty nearly a whole academic year to prepare their proposal.
Proposals will be evaluated primarily based on scientific merit, and secondarily on the robustness of the collaboration envisioned and the project’s relevance to the interests and concerns of society at large. If there is to be an outside collaborator, that individual’s letter of commitment to the project and evaluation of the proposal must be included in the proposal. In the evaluation of scientific merit, the evaluation criteria should include the background and prior related work the researcher brings to the proposed project, the feasibility of the deliverables, and on the degree to which the proposed budget is designed to appropriately support the project. In other words, we will seek projects that are within the grasp of the researcher as demonstrated by prior work. The research can be in any of the fields within the programs of the College of Science, and the interdisciplinary element may include a related field inside or outside of the College of Science. Projects involving human subjects must show evidence of IRB approval, and projects involving animal subjects must show evidence of approval by the Animal Care Committee.
A progress report is due within a year of funding. A final report is due after a year and a half, and should include any manuscript or evidence that a scientific journal has accepted the resulting paper for publication. The quality of the final report will have a significant bearing on whether any future proposals by that person will be funded under this program.
A Review Committee consisting of Professor Emerita Joan Sieber (the convening and nonvoting member) and three faculty members from three different disciplines to be appointed by the College Dean will evaluate proposals.
Based on the experience of making awards for this first year of proposals, we wish to clarify the criteria for awards. Preference is given to proposals for research that:
  • Help prepare students for the science/technology workforce of tomorrow
  • Empower students as collaborators and potential co-authors of research
  • Focus on topics that are somehow of social significance, whatever the field of science or technology
  • Apply research to problems that span multiple disciplines, thus mirroring the current integration of fields of science/technology and their methodologies
  • Demonstrate your willingness to share the (modest) funding with other applicants by asking for the absolute minimum needed
  • Involve collaborators from other departments, and universities, or companies, research laboratories or agencies
  • Demonstrate that they are creatively drawing support from other resources as well
  • For example, Cal State East Bay’s Center for Student Research Scholar’s Program might also be used to provide support for student collaborators
It is not expected that any proposal would meet all of these criteria. This list of criteria is simply intended to indicate the kinds of qualities this small grant program is intended to support. To help clarify what is not supported, the following is a non-inclusive list of who should not submit a proposal to this program:
  • A scientist with lots of outside support should not apply, to add a little more money to the pot
  • Someone contemplating development of a whole new research direction for which they have not developed and tested their methodology
  • Someone wishing to pay students who would only help out with the investigator’s own obscure or isolated research program
  • A researcher wanting to receive a stipend for themselves.
For this round of funding, a total of $15,000 is available. The maximum award is $5,000 and partial awards may be funded. The awards can be used to support research related activities that include supplies & equipment, travel, conference attendance, and research assistant stipends. 
Future funding will give preference to programs that have continued to develop perhaps with prior funding from this small grant program.
Proposals from tenured faculty are due October 15 every year. A second round of funding will occur in the spring with a proposal deadline of March 15. Proposals should include an abstract, 3-page project description that includes methodology, specific outcomes and deliverables, and a timeline. In addition there should be a 1-page budget and budget narrative, and, where appropriate, a letter of support from an external collaborator, and any other relevant permissions (e.g., IRB approval, agreements from agencies to share information with the researchers). Awards will be announced within a few weeks of the submission due date, and funds will be available immediately thereafter.

Fall 2018 Winners

Claudia Uhde-Stone
Next-generation RNA sequencing to untangle plant responses to nutrient deficiencies
Principal Investigator: Claudia Uhde-Stone, Professor, Biological Sciences, CSU 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.
Michael Groziak
Organic and Medicinal Chemistry of Heterocycles and Nucleosides
Principle Investigators: Michael Groziak, Ph.D. Department of Chemistry & Biochemistry, CSU East Bay 
Abstract: The Groziak Group specializes in the organic and medicinal chemistry of heterocycles and nucleosides, developing new subclasses of these compounds to be used as biochemical tools, enzyme probes, and as potential biocidal, antiviral, or antitumor medicinal agents. Along the way, we enjoy developing new methodologies for the functionalization of heterocycles and for the synthesis of nucleosides. Most of the classes of compounds we investigate are chosen to advance biomedical research in areas like infectious diseases. Our lab’s day-to-day research efforts are focused on practicing the art of compound design, synthesis, and characterization. As a result of these efforts, we have gained extensive experience in the synthesis and characterization of stable boron heterocycles. One particular type of these boron heterocycles has been shown to exhibit good antibacterial properties, particularly against gram negative organisms, and we have synthesized a large number of them and have discovered a handful of new ones that possess good activity against the E. coli and M. smegmatis organisms. The present work continues this drug discovery effort with the fruitful collaboration between our synthetic organic chemistry group and an another CSU bacteria-specializing biology one. Compounds are prepared and chemically characterized here at CSUEB and then are sent down to CSULA for antibacterial testing. The overall goals of this collaborative project are to encourage medicinal chemists to investigate boron heterocycles more thoroughly as potential medicinal agents, and to discover new compounds that could potentially be used to develop new medicines for treating tuberculosis.
ken-curr
Isolation, Speciation and Characterization of the Microbiome from the Marine Nudibranch Tritonia tetraquetra
Principal Investigator: Ken Curr, Professor, Biological Sciences, CSU East Bay

Abstract:
Tritonia tetraquetra (Tritonia), formally known as Tritonia diomedea, is a marine nudibranch that resides along the coastal waters of the Pacific Ocean, whose natural habitat is constantly evolving due to environmental changes along coastal waters (i.e. ocean acidification, increased temperature, etc.). Because sea slugs do not have a protective coating, as do most other mollusks, they are very susceptible to the changes in local environments. As conditions change, so do pathogens that infect Tritonia. Importantly, the ability in the way Tritonia fights off infectious pathogens remains a mystery. Most pathogens enter the nudibranch through the intestinal track since it is the most efficient way for the pathogens to be exposed to internal tissues. Microflora can
inhibit infection by preventing pathogenic bacteria from taking residence on the intestinal wall. This study will focus on an arm of the innate immune system of Tritonia by identifying the microbiota that line their intestinal wall. The microbiota is a part of the innate immune response and is one of the primary mechanisms in which invertebrates protect themselves from foreign invaders.

Spring 2018 Winners

Patty Oikawa
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.
 Ana Almeida
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.
Pascale Guiton
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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Andrew S. Kelly
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

Ryan Smith
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.
Amy Furniss
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 Uhde-StoneNext-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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