CSCI Faculty Research
Collaborative Research Awards
Spring 2022 Winners
Optimal Sequence of Learning for
Memorizers Versus Rule-Finders
Principal Investigator:
Department of Psychology,
CSU East Bay
Abstract: Grouping information into different categories enables us to learn, remember, and integrate new information, but the optimal way to learn categorical information is unclear. Much research suggests that mixing up items from different categories (i.e., interleaving) is more effective for learning than is grouping items by category (i.e., blocking), particularly if the task involves memorization and/or classification based on perceptual similarity (see Kornell & Bjork, 2008). However, when a rule can be verbalized to explain categorization, blocking can be better than interleaving (Noh, Yan, Bjork, & Maddox, 2016). But, even when a rule defines category groupings, not all people find rules or even think to look for them. Within a single set of items, some people try to find rules, but some memorize the category-item pairs (Little & McDaniel, 2015). The proposed study examines optimal sequence as a function of the strategies that people use to learn, examining transfer performance at multiple time points (immediately and at a two-week delay). The results of the study have implications for optimizing learning in educational contexts.
This research will be conducted in collaboration with Jexy An Nepangue and Jayde Holt-Wyindon, two CSUEB students. We expect to submit an abstract to a conference and a manuscript to a journal by the end of the award period.
Understanding Potential Influence of Social, Cultural, and Historical Traumas on Health of Bangladeshis & Nepalese Northern California
Principal Investigator: Arnab Mukherjea, Dr.P.H., M.P.H.
Chair & Associate Professor Public Health, CSU East Bay
Abstract: The historical traumas related to the colonial partition of South Asia, including the indentured servitude and involuntary relocation of residents to outside the subcontinent, is well chronicled. The legacies of psychological and social harms caused by this event are compounded by diverse consequences related to prominent cultural hierarchies (e.g., caste, religious, gender, political, age, and minority status, among others) commonly found among native and migrant South Asian populations). What is unclear is the residual and cumulative impact of such traumas, as well as resulting individual and community resiliencies, on health status and disparities found among South Asians in the U.S. The purpose of this pilot research is to understand the breadth of traumas
that persist among communities of South Asian descent in the San Francisco Bay Area, distinguish adverse interpretations and effects of traumas between specific South Asian subgroups, identify social and cultural resiliencies that arise from legacies of trauma, and recognize potential influence of such contextual factors on relevant indicators of health in and among South Asian communities.
A qualitative orientation is employed in this study. In the form of focus groups, participants are stratified by South Asian subgroup (Asian Indian, Bangladeshi, Pakistani, Sri Lankan, and Indo-Fijian) and by gender. Each subgroup-gender dyad will have two focus groups conducted, for a total of 20 data collection events (6 –8 individuals per group) among the entire study sample (maximum of 96 people). Domains of inquiry include discussion of historical, migratory, and contemporary experiences and narrative of trauma and resilience, with a focus on contextual elements (e.g., gender norms, academic and economic pursuits and pressures, seeking of refuge from civil unrest/oppression, caste hierarchies, religious interactions, perceptions as a racial/ethnic minority in the U.S.). The approach to interpreting data will be constant comparative analysis, which will allow for refinement of concepts and thematically-relevant categorizations.
This pilot aims to add relevant and timely contributions to the scientific base of knowledge which elucidates previously-unknown influences on health, particularly for the growing population of aging individuals of South Asian descent in the U.S. Findings may provide directions multi-level targets for intervention design, particularly around structural and community-level facilitators and barriers for preventing disease, promoting well-being, and achieving health equity.
Particle Size, Mutation State, or Both? What Affects Apolipoprotein Exchange Rates on HDL?
Principal Investigator: Mark Borja
Department of Chemistry and Biochemistry, CSU East Bay
Abstract: High-density lipoprotein (HDL) is commonly known as the “good cholesterol” because healthy levels of this protein are associated with reduced risk of cardiovascular disease. Apolipoprotein A-I (apoA-I) is the main protein component of HDL, and is primarily responsible for HDL’s beneficial reverse cholesterol transport (RCT) activity. RCT activity is frequently measured using cell-based assays of cholesterol efflux. There is a strong association between the exchangeability (binding and releasing HDL) of apoA-I and cholesterol efflux. However, it is not known whether HDL particle size, along with the mutation state of apoA-I, impact the exchange rate of apoA-I. The purpose of this study is to investigate apoA-I exchange on three mutants of apoA-I which are associated with decreased HDL particle size (apoA-I Milano, apoA-I L75P, and apoA-I L174S), reduced HDL particle quantity, but increased capacity for cholesterol efflux capacity. The effect HDL particle size on apoA-I will be investigated in parallel because all three mutants of apoA-I have a tendency to naturally form smaller HDL particles.
This research will be conducted in collaboration with Dr. Jens Lagerstedt of Lund University, Sweden. The funding will be used toward the purchase of the necessary supplies for the project.
Analyzing Kitting’s pilot data on Novel Multidisciplinary Solutions to Global Climate Disruption: Persistence & Reflective Spectra of Upper Atmospheric Aerosols
Principal Investigator: Christopher Kitting
Department of Biological Sciences, CSU East Bay
Abstract: This multidisciplinary research has been expanding on my previous high-altitude Sierra work at UC’s Barcroft Lab and my two related, NASA atmospheric missions, on novel solutions to climate disruption including sea level rise. The work continues CSUEB’s Department of Biological Sciences monitoring and improving our environment, with five of us biology professors having published over ten reference and textbooks on the subject, with two of us using hundreds of thousand$ in research grants annually for >~20 consecutive years. Alas, then CSUEB then moved grant payments from its Foundation to cumbersome, restrictive CSUEB offices.
With half the proposed funding for this proposed project, this award deleted supplies and the proposed stipend for my preferred major collaborator (Director of Atmospheric Programs at US Air Force Academy). As noted in this award proposal, some details remain unsuitable for broad or web access, as with US Dept. of Defense.
I was able to substitute an analogous, local chair of Planetary Sciences and well-known climate and atmospheric expert from Cabrillo College (Santa Cruz/Aptos), Dr. Rick Nolthenius, who immediately helped inform my related, diverse CSUEB students about such expertise and opportunities, and now is recruiting such students to CSUEB.
An additional collaborator, East Bay Regional Parks wildlife steward (a former CSUEB Bio Sci MS student) David Riensche then helped complete our related journal manuscript on worsening local heat spells depleting shoreline breeding bird assemblages. Similarly, Kitting and his present MS student edited his Bio Sci thesis on solutions for wildlife during extreme weather, for format review later this summer.
I immediately presented other related findings at a virtual conference for Western Society of Naturalists: “Atmospheric persistence of reflective aerosols test #2: Hayabusa spacecraft fastest re-entry, with ablative organic heat shield.”
My spring ‘22 Conservation Bio Class offered these atmospheric options, including prep and field observations around our valuable Biology Ecological Preserve on our south campus. Several students became enthused, with options now integrated into the class. These outdoor class activities prevented at least one COVID risk and isolation for the class. We developed data tables based on our analogous environmental monitoring and on atmospheric data tables from Nolthenius. Weather did not cooperate during these spring semester atmospheric events, but my independent study undergrad there completed a research project on such prep for sea level rise, promptly published together with color illustrations in Tideline from USFWS, now Tide Rising, edited by SF Bay Wildlife Society: “Minimizing Human Impacts on Marsh Plants in a Wildlife Refuge.” By CL Kitting and Felicitas Jimenez, CSUEB Conservation Biology B. Sci. (plus author bios) Tide Rising (3:e) 2-3. 2022.
Univ. Calif. then approved my new atmospheric proposal for use of their Barcroft high altitude lab this summer (2022), but COVID then closed most such services at that remote lab, and my project there is being postponed one year. --after this award expires. Our analogous research and teaching productivity continue.
Studying Degradation of Modern Plastic Artworks using Surface-enhanced Raman Spectroscopy
Principal Investigator: Department of Chemistry & Biochemistry, CSU East Bay
Abstract: As an ever-increasing number of artworks made of plastics enter museum collections, it is critical to develop strategies to ensure the longevity of these objects, especially since many plastics already show visible signs of deterioration. Chemical characterization of plastic artworks is therefore necessary to inform conservation treatment strategies and to optimize storage conditions. The proposed research is a collaboration between the Zaleski laboratory at CSUEB, the Conservation Department at the Fine Arts Museums of San Francisco and the Broad Museum in Los Angeles. Specifically, we are proposing to use adsorbent surface-enhanced Raman spectroscopy (SERS) substrates recently developed in Dr. Zaleski’s laboratory to characterize the degradation of PVC-based postcards from the series Honey is Flowing by Joseph Beuys. The funding will be used to financially support a student researcher, travel to the museums for artwork analysis, and for the purchase of laboratory supplies.
How To Apply
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.
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, 缅北禁地’s Center for Student Research Scholar’s Program might also be used to provide support for student collaborators
- 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.
Future funding will give preference to programs that have continued to develop perhaps with prior funding from this small grant program.
Fall 2021 Winners
Metabolomic Analysis of Salinity Stressed Pistachios
Principal Investigators:
Department of Chemistry and Biochemistry, CSU East Bay
Abstract: With climate change non-saline water will become a scarce but necessary resource to maintain agriculture and therefore our food supply. Some plants, including pistachio trees, are able to withstand irrigation with saline water as in brackish but not ocean water. Shifting agricultural practices to more salt-tolerant plants could preserve freshwater resources. This project aims to elucidate the biochemical response of pistachio trees to salinity stress. My collaboration partners are Dr. Gary Baňuelos from the US Department of Agriculture – Agricultural Research Service (USDA-ARS), faculty and students at Fresno State, and five undergraduate research students at CSUEB. This collaboration is already well established. With the help of this grant, I seek to add a new research component in the form of a paid metabolomic pilot study. This pilot study will focus on phenolic compounds. In our previous work, we observed an increase in phenolic compounds in leaves of pistachio trees subjected to saline irrigation.Phenolic compounds serve as antioxidants and protect the plant tissue from radical oxygen species (ROS). An increase in ROS is a known consequence of salt-induced plant stress. With the help of the services from the Metabolomics Core Facility at UC Riverside we can find out which of the many plant phenolic compounds change in concentration as a response to salt stress. This pilot study will provide an excellent opportunity to train my research students in metabolomics (e.g.; how to obtain and evaluate data encompassing the many individual metabolites of an organism). We will use the data of the pilot study to design new experiments. We will quantify specific phenolic compounds selected from the metabolomic study and inspect the activity of enzymes involved in the transformation of these compounds. As my collaboration partners and I are moving forward with our study on the salt-tolerance of pistachio trees, we will apply for more funding. If this pilot study turns out to be successful, we will include metabolomic investigations for phenolics and other types of metabolites (e.g.; sugars, amino acids, lipids) in our next grant applications.
Progress Update:
This collaborative research award enabled me and my research team to conduct a metabolomic pilot study with pistachio leaf samples. The pistachio leaf samples stem from a salinity tolerance study conducted at the Agricultural Research Service - US Department of Agriculture (ARS-USDA) in Parlier, CA. My main collaborator, Dr. Gary Baňuelos, and his team planted pistachio trees into a research field site and irrigated these trees with water at different salinity levels. The goal of this study is to find a threshold for saline irrigation, so that pistachio growers can use low quality water (for example brackish water) for irrigation without damaging their pistachio orchards. Dr. Baňuelos’ team is sending pistachio leaf and nut samples to my research group at CSU East Bay for biochemical analysis. We aim to find biomarkers which are molecules that change in their concentration levels in response to salinity stress. A better molecular understanding of the plant’s stress response will enable us to better define the salinity threshold. Our preliminary results indicated that phenolic compounds might serve as biomarkers for salinity stress. To obtain more detailed information on individual phenolic compounds we decided to use the services of a metabolomic facility. Metabolomic facilities have instrumentation (liquid chromatography paired with mass spectrometry) and the expertise to survey large classes of smaller molecules, for example amino acids, lipids, sugars, and phenolic compounds, that make up the metabolism of an organism.
I obtained the collaborative research award in the middle of the Fall semester 2022. In Fall 2022 my undergraduate research team consisted of four students (Ryan Luu (CSR scholar), Michael Rivera, Esiason Rodriguez, and Quierra Shugart). By Spring 2023, I was able to recruit three additional students (Feliza Dao, Sabbu Shrestha, and Manmeet Kaur). In addition to sample preparation, my students learned about metabolomics and performed additional experiments to determine total antioxidant capacity and total concentration of phenolic compounds, photopigments, and soluble sugars.
The metabolomic study was carried out at the Metabolomic Facility of UC Riverside in April 2022. Dr. Amancio de Souza was my main point of contact. We sent 24 lyophilized pistachio leaf samples to the metabolomic facility. Lyophilization is used to preserve biological samples via a freeze-drying procedure. This sample treatment was recommended by Dr. Souza. An apparatus with a vacuum pump and cooling compartment was available in the research laboratory of my colleague Dr. Michael Groziak (Chemistry and Biochemistry Department, CSUEB). The metabolomic analysis conducted at UC Riverside resulted in the detection of 20 different phenolic compounds. Six of these compounds showed a weak dependency on salinity treatment. These compounds were myricetin 3-galactoside, myricetin 3-rutinoside, pinocembrin, naringenin, naringenin chalcone, and catechin.
My research group and I are currently conducting our own HPLC-based identification and quantification of phenolic compounds. HPLC stands for high-performance liquid chromatography. Since we do not have the same instrumentation as a metabolomics facility we can only detect phenolic compounds in our samples for which we have standards. A standard is a purchased pure compound that the experimenter is trying to detect and to quantify in the sample of interest. I used the remaining money from this award and funding provided by the Chemistry Department to purchase individual phenolic compounds. We leveraged the results of the metabolomic pilot study and consulted the scientific
literature to select our HPLC standards. This Fall semester (Fall 2022) my research team currently consists of four students (Takudzwa Chirenje (CSR scholar), Manmeet Kaur, Rebecca Chavez, Viral Chhaganbhai (graduate student)). We were able to corroborate the presence of catechin in the pistachio leaf samples. We discovered a significant catechin concentration increase in young pistachio leaves (leaves collected from the tip of a branch) of PG1 rootstocks irrigated with saline water. Older leaves of the same PG1 rootstock that were collected closer to the stem did not show any significant change of catechin concentration as a function of saline irrigation. This part of the research project is still ongoing. We are currently screening approximately 30 different phenolic compounds. In addition to the leaf samples that were sent to the metabolomic facility we are also investigating pistachio nut extracts and we will soon receive a new set of leaf samples from Dr. Baňuelos’ team.
I am happy to report that our HPLC-based work on phenolic compounds led to a new collaboration with my colleague Dr. Stephanie Zaleski (Chemistry and Biochemistry Department, CSUEB). Her group is using surface enhanced Raman spectroscopy (abbreviated SERS) to detect and quantify phenolic compounds. We are now sharing our reagents and results with each other. We already had one joint research group meeting and will host more so that our students can learn from each other. Dr. Zaleski’s group will apply the SERS technique to our pistachio leaf extracts. My research group already investigated the same extracts with HPLC. We will compare and contrast the advantages and limitations of both techniques with each other.
Spring 2021 Winners
Race in Political Discourse
Principal Investigators: Department of Psychology, CSU East Bay
Read the article:
Principal Investigators: Dr.Liz Kyonka Department of Psychology, CSU East Bay
Fall 2020 Winners
Investigator: Michael P. Groziak, Chemistry and Biochemistry
Project Title: Synthesis and Antibacterial Assay of New Boron Heterocycles
Collaborator: H. Howard Xu, Department of Biological Sciences, CSU Los Angeles
The proposed work is a drug discovery effort that seeks to continue a fruitful collaboration between a synthetic organic chemist and a bacteria-specializing biologist, with compounds prepared at CSUEB being sent down to CSULA for testing. Joint publications featuring student co-authors are the primary to be expected from this project. Our collaborative work began in 2010 and was supported by a Sieber Interdisciplinary Research Award. The Groziak and Xu Groups have examined more than 4 dozen compounds, found 6 new compounds with good antibacterial activity, and published 7 papers describing various aspects of their joint efforts (list at end). The first Sieber award, some Faculty Support Grants, and a 2018 Collaborative Research Award that enabled these accomplishments. With continuing College of Science Collaborative Research Award funding, targets will be synthesized, purified, characterized, and tested for antibacterial properties. These are analogs of a known antibacterial 4-toluenesulfonylated boron heterocycle (first compound shown below). A comparison of some of our past targets to this lead reveals a close structural resemblance. Our central hypothesis in the proposed work is that an acyl substituent can serve as a suitable replacement for the sulfonyl one, maintaining or even enhancing the enzyme inhibition known to be the mechanism of action of the known bactericidal boron heterocycle benchmark compound.The goal of this program is to help develop new anti-TB drugs which are becoming sorely needed due to the rise of multidrug-resistant strains of TB.
Spring 2020 Winners
Fall 2019 Winners
Fall 2018 Winners
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.
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
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.
Principal Investigators: Pascale Guiton, Ph.D., Biological Sciences, CSU East Bay
Abstract: Toxoplasma gondii is a unicellular parasite responsible for toxoplasmosis, a disease afflicting 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.
Fall 2017 Winners
Next-generation RNA Sequencing to Untangle Plant Responses to Nutrient Deficiencies