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BIO REU Projects

Epigenetics and biomineralization in the marine coccolithophorid, Emiliania huxleyi.

Dr. Betsy Read, Professor, Biological Sciences.

The goal of this project is to examine the plasticity of biomineralization in Emiliania huxleyi (E. huxleyi) and the potential role epigenetics may play in the process of calcification and coccolithogenesis.  Characterized by its elegantly sculpted cell coverings, otherwise known as coccoliths, this unicellular algal and most prominent coccolithophorid is one of the most productive CaCO3 secreting organisms on Earth. Considerable information about calcification in E. huxleyi has been gleaned from electron microscopy and ecophysiological studies. However, knowledge of the functional significance and molecular underpinnings of the process is lacking. The availability of the genome of E. huxleyi makes it feasible to examine the epigenome and its impact on biomineralization. To this end, the specific aims of the project are to: 1) profile landscape of histone post-translational modifications (PTMs), 2) define the genome-wide distribution and function of select histone marks, and 3) relate patterns of histone modification to changes in gene expression across calcifying and non-calcifying isogenic lines. Students will test the underlying hypotheses that plastic phenotypic changes in E. huxleyi, such as calcification, have an epigenetic component. This will be accomplished by students performing a comprehensive analysis of histone modifications using mass spectrometry of enzyme-digested histone preparations, and immunoblots of a broad range of available antibodies. The biological function of histone PTMs will be investigated by analyzing the distribution of a select number of histone marks across the E. huxleyi genome using chromatin immunoprecipitation and sequencing (ChIP-seq). The hypothesis that patterns of histone modification affect gene expression in ways that impact biomineralization in E. huxleyi will also be tested. Students will focus on a few histone marks with known functions in transcriptional activation or repression and compare ChIP- and RNA-seq results across calcifying and non-calcifying isogenic lines. This will enable genes involved in biomineralization to be identified, and the role of epigenetics in the regulation of calcification to be delineated.

Student Mentoring: In addition to using a variety of bioinformatics tools and techniques, students will purify histone proteins, perform western blots, carry out chromatin immunoprecipitation experiments, extract RNA, and prepare libraries for nucleic acid sequencing. Dr. Read led the Emiliania huxleyi (E. huxleyi) genome-sequencing project coordinating the efforts of ~ 75 research scientists. She has extensive experience training undergraduate students (~ 150 students; ~40% from underrepresented groups; 31 have pursued graduate work; 17 accepted into major graduate programs and one received an NSF fellowship for graduate studies). Students present their work at local, national, and international meetings. She has published more than 25 peer-reviewed papers, 14 of which include students as co-authors. 5 students have won research awards and/or research fellowships.


Effects of Heat Stress on Fibroblast Cell Migration from Multiple Animal Species.

Dr. Carlos Luna Lopez, Assistant Professor, Biological Sciences

This project focuses on the impact of climate change on the health and survivability of wild animal populations.  With a growing fusillade of environmental stressors, including habitat loss, global climate change and poaching, the biodiversity and survivability of dwindling wild populations are becoming increasingly at risk. The Luna lab is interested in discovering how stress factors such as heat can impact the physiological responses and plasticity of cells to maintain allostasis. Cellular response of heat stress includes changes in cytokine expression, apoptosis signaling, proliferation and the cell metabolism. Heat stress also affects cell adhesion and extra cellular matrix degradation, which delays wound healing. Changes in wound healing could significantly affect animal survival and the stability of their surrounding ecosystem.  For this project we will collaborate with the San Diego Zoo Wildlife Alliance, to apply scientific knowledge to fight against extinction. The Biodiversity Banking Team at the Beckman Center for Conservation Research will provide the team with fibroblast cells from a wide taxonomic range of species (birds, mammals, amphibian, fish, and more). Scratch assays will be applied to heat stressed cells to mimic wound healing and measure the changes in cell migration. RNA-Seq will be conducted to observe mRNA expression with specific attention to the molecular pathways responsible for cell proliferation, inflammation, cell adhesion and migration. Finally, we will study any correlations between changes in cellular behavior and cell transcriptomics. The underlying hypotheses are that heat stress will: 1) decreases cell decrease cell proliferation and increase rate of cell death, 2) initiate increased cellular stress response with increased production of heat shock protein, and 3) decrease wound healing and cell migration capability (TGF-b1, MMP2, MMP9, CTNNb1), cytokine production (IL-6, IL-1b) and fibroblast growth factor (FGF) 5 and 18.

Student Mentoring: Students will participate in all experimental procedures (cell culture, scratch assay, and RNA-seq), they will also participate in data analysis and result interpretation. Dr. Carlos Luna has mentored several undergraduate students that have gone to PhD programs or the Biotechnology industry. His students have been members of URISE, McNair and CSUPERB programs and participate in multiple scientific conferences. Dr. Luna works closely in diversity programs at CSUSM and is committed to the advancement of underrepresented students in science and engineering.


Employing MetaHiC to map the evolution of antibiotic resistance in microbial populations.

Dr. Elinne Becket. Assistant Professor, Biological Sciences

The overarching project goal is to delineate how genomes and microbial communities evolve in response to exogenous inputs, through taxonomic abundance changes and rapid evolution in the exchange of genetic information. The spread of microbial antibiotic resistance, particularly pathogenic microbes with multidrug resistance, is a global healthcare and ecological problem driven by the extensive medical and agricultural use of antibiotics. Microbial populations harbor reservoirs of antibiotic resistance known as the resistome, and are influenced by exposure to antibiotics, environmental/diet changes, or other factors. Microbial taxonomies and abundancies change in accordance to selective advantages conferred by specific environmental conditions; while resistance markers can be transmitted across species through horizontal gene transfer. In fact, many pathogenic microbes obtain genetic resistance determinants from resistant counterparts within a niche. Antibiotics in the environment also influence transmission, either by inducing transfer of elements or causing recipient cells to increase in competency. Therefore, we seek to elucidate changes in marine microbiome communities and resistome composition in response to common antibiotics seen in agricultural, urban waste, and stormwater runoff. This will be achieved by treating sampled populations with/without antibiotics and overlaying three NGS techniques: MetaHiC6 (to map the resistance elements to specific host organisms), long-read metagenomic sequencing (to measure global excision/insertion of resistance elements), and metatranscriptome sequencing (to assess competency and expression of resistance elements). Comparisons will be made of near-shore water samples close to and far from ocean sewage outlets to assess if pre-priming with antibiotics affects the movement of the resistome. The underlying hypotheses are: 1) exposure to antibiotics increases cell competency and resistance element transfer, 2) increases occur in distinct patterns depending on the antibiotic used, both in the cells within the population and the affected resistance elements, and 3) populations pre-primed with antibiotics (near sewage outlets) exhibit greater resistome mobility compared to those less-exposed.

Student mentoring: REU students will procure environmental samples, isolate and culture a variety of bacterial strains, and perform the MetaHiC analyses by preparing NGS libraries and using NGS/HiC bioinformatics tools. Students will acquire molecular biology and NGS skills, and learn data analysis methods with open-ended applications in ecological studies. Students will be competitive in their future careers with broad training in ecology, microbiology, molecular biology, and bioinformatics. Dr. Becket has mentored 49 undergraduates (22 at CSUSM; 27 at UCLA), 20 of whom have authored publications.


The developmental thermal environment as a driver of plasticity in the chorus frog, Pseudacris hypochondriaca.

Dr. Casey Mueller, Associate Professor, Biological Sciences

The long-term goal of the Mueller lab is to provide a mechanistic understanding of developmental phenotypic plasticity: 1) when plasticity occurs during ontogeny, and 2) how it influences animals directly and later in life. Despite recognition that the environment helps to create, sustain and alter phenotypes, physiological studies do not consistently integrate physiological data across all life stages. Such consideration is necessary to understand the breadth of environmental influence on organismal physiological phenotypes. Phenotypically plastic responses to the environment are typically examined in an immediate temporal context – how does an environmental variable alter the developing phenotype? Longer-term changes in phenotype are rarely comprehensively assessed or recognized. This major gap in knowledge needs to be addressed to gain an understanding of how long-term or permanent alterations in phenotype influence physiological responses to ecological changes later in life. This project will examine thermal responses during development of the Baja California chorus frog (Pseudacris hypochondriaca). The central hypothesis is that immediate responses (minutes to days) to temperature during development have long-term effects (days to months) that drive thermal physiology across life history. Students will examine the role of the developmental thermal environment by rearing chorus frogs in various temperature regimes, including fluctuating temperatures that mimic current field conditions, and those of climate change scenarios. They will perform physiological assays during embryonic, larval and post-metamorphic life stages. The work will provide an understanding of how developmental environments program thermal physiology of a vertebrate across all morphological life stages, including the metamorphic transition. Information gleaned from these thermal response studies will be applicable to other amphibian and vertebrate species and provide insight into the potential impacts of, and responses to, global climate change.

Student mentoring: In addition to gaining experience in field collection and maintenance of embryos and larvae students will perform morphological and physiological assays, micro dissections, respirometry measurements, swimming speed tests, and thermal tolerance assessments. Dr. Mueller has experience training students, having mentored 17 CSUSM undergraduates and two graduate students. Students are encouraged to present research findings at scientific conferences (9 presentations by 8 CSUSM students) and publish (4 CSUSM student co-authors). Four mentees are pursuing PhDs, and one a MD.


Voltage-gated ion channels in animal epithelia provide means for rapid plasticity and regulation of epithelial ion transport.

Dr. Dennis Kolosov, Assistant Professor, Biological Sciences.

Epithelia are tissues of multicellular organisms that specialize in directional transport of ions and water in and out of the animal. Faced with rapid changes in environmental and systemic variables, animals rely on epithelia to mount a rapid plastic response in a timely manner to maintain homeostasis. Recent work in our lab identified several novel molecular mechanisms used by epithelia of the insect ‘kidney’ to rapidly adjust ion transport in the face of rapidly changing environmental and systemic variables. These novel molecular mechanisms include the use of voltage-gated and mechanosensitive ion channels. Despite being very important for the function of animal epithelia, there is no consensus on how these channels regulate ion transport. In our lab, we study hydromineral balance of animals, which changes as a function of salt and water content of the diet and surrounding environment. Animals are subjected to varying degrees of environmental salinity and salt and water content in their food. Hypotheses being tested are: (i) voltage-gated ion channels regulate ion transport in the fish gill and in the Malpighian tubules of insects and are used to respond quickly to changes in environmental salinity and/or dietary ion and water, and (ii) different groups of voltage-gated ion channels regulate epithelial ion transport in a non-overlapping fashion. This project will use transcriptomics (RNAseq) to (i) identify the above-described ion channels expressed in insect Malpighian tubules and fish gill epithelium, and (ii) determine how these ion channels regulate transport. A mix of transcriptomic (RNAseq), molecular biology and electrophysiology techniques will detect expression of voltage-gated ion channels in Malpighian tubules of insects and gill epithelium of teleosts.

Student Mentoring: Students will extract RNA, perform cDNA synthesis, and conduct bioinformatics and computational analyses on NGS data. Students will learn quantitative methodologies such as qPCR and Western blotting, electrophysiology techniques, and bioassays for ion transport. Dr. Kolosov has trained ~25 undergraduates who routinely present their work scientific meetings. He has published more than 30 peer-reviewed papers, many of which include students co-authors.


Global change impacts on carbon and nutrient cycling in shrublandsand  terrestrial woodlands

Dr. George Vourlitis, Professor, Biological Sciences

The goal of two on-going longitudinal projects is to evaluate ecosystem responses to global change drivers such as climate, land use, and atmospheric changes in carbon (C) and nutrient (nitrogen (N) and phosphorus (P)) cycling in semi-arid shrublands and tropical woodlands.  The semi-arid shrubland research is  20-year field experiment that focuses on southern Californian chaparral and coastal sage scrub (CSS), and the impact of atmospheric N deposition on the C and N cycling. The hypothesis being tested is that C and N cycling and species composition in these shrublands are highly plastic and dependent upon atmospheric N deposition and annual variations in precipitation. Annual determination of net primary production (NPP) and species diversity and abundance are made across control and nitrogen exposed plots and compared in the California chaparral and CSS. Longitudinal research in tropical woodlands occurs in the savanna of the Brazilian Amazon Basin and Pantanal and probes the impact of climate change on C and nutrient cycling.  The underlying hypotheses are: 1) soil fertility and annual precipitation are important drivers of tree growth and C storage, and 2) climate change will cause a decline in C storage for these and other tropical forests and woodlands. Tree growth, stem growth, wood C storage are tracked for 434 trees located in upland and seasonally flooded (hyperseasonal) forests and woodlands of the Brazilian savanna of the southern Amazon Basin and Northern Pantanal of Mato Grosso, and correlated with measurements of rainfall, nutrient availability (P), and cations (K and Ca).  

Student Mentoring: Students will further these longitudinal studies and collect field samples, monitor species diversity and abundance, assist with the laboratory analysis of plant and soil samples, and select an aspect of each project to lead the data analysis and integration of results.  Dr. Vourlitis has mentored over 75 undergraduate students since 2010, 18 of which traveled to Brazil.  He has over 120 peer-reviewed publications, many of which include undergraduate students as co-authors.


Cellular dynamics of epidermal gd T cells in cytokine signaling.

Dr. Julie Jameson, Associate Professor, Biological Sciences

This project focuses on CCR6+ T-cell populations, their plasticity, and potential roles in the epidermis. Cytokine and chemokine receptor reception and cross-talk between gd T cells and keratinocytes in the skin is far more complex than we thought. Stress induces keratinocytes to express an unidentified receptor that activates skin-resident gd T cells to increase transcription of growth factors and cytokines with paracrine and autocrine functions. However, the impact of cytokine and chemokine reception during activation is little studied. Murine skin-resident gd T cells express CCR6 at varying levels after activation, however it is unknown how the ligand CCL20 regulates epidermal T cell activation. Based on previous studies we will test the hypotheses that (1) epidermal CCR6 expression modulates cellular function, and (2) that CCR6 acts as a regulatory switch in altering T cell functions such as cytokine production. NSF REU students will be involved in projects that test these hypotheses using RNAseq and flow cytometry and determine: 1) whether CCR6+ epidermal T cells represent a subset with distinct functionality, 2) how CCL20-CCR6 ligation regulates early versus late activation states in the cell, and 3) the role of NF-kB in mediating epidermal T cell dysfunction. Data will allow for the elucidation of signaling pathways and key processes that modulate T cell function in the skin.

Student Mentoring: Students will be involved in all aspects of the study and receive training in cellular and molecular biology techniques including: primary cell culture, qPCR, RNAseq, flow cytometry and immunofluorescent microscopy. Dr. Jameson has trained 48 undergraduates over the last 16 years, 60% from underrepresented minority groups in STEM, 65% women and 2 military veterans. Undergraduate and graduate students from her lab have presented their research at several national meetings. She has a long history of mentoring undergraduate students to join PhD programs


Chromosome rearrangements and mutagenesis initiated by microsatellite DNA repeats


Dr. Jane C. Kim, Assistant Professor, Biological Sciences

Microsatellites are simple DNA sequence repeats that are ubiquitous across all three domains of life and demonstrate substantial variability in length. Such microsatellite length polymorphisms influence gene expression, modulate chromatin configuration in eukaryotes, and facilitate population genetics studies. In humans, expansions of simple DNA repeats are the underlying cause of over 30 genetic diseases. Some microsatellite sequences, such as GAA trinucleotide repeats and interstitial telomeric repeats, have been shown to stimulate mitotic recombination or gross chromosomal rearrangements (GCRs). These events may result in loss of genetic material, gene fusion products, or new patterns of gene expression that may be harmful, beneficial, or neutral depending on the type of GCR. The objective of this research is to investigate how two model microsatellite sequences (CAG/CTG and CCTG/CAGG), contribute to genomic plasticity. This project will test the hypothesis that different microsatellite sequences stimulate gross chromosomal rearrangements at different rates, generating different patterns of genomic break points. Such break points will be assessed using Oxford Nanopore ultra-long read sequencing (>30 kb). A budding yeast reporter system, previously used to identify GAA microsatellite strains with GCRs, will be employed to select for chromosomal arm loss . This molecular phenotype is selected for on differential media and used to determine the rate of arm loss via a fluctuation assay. Rearrangements will be identified by comparing single reads to the reference genome of the background strain. Potential point mutations resulting from the repeats will be verified by Sanger sequencing. This research will contribute new information about genome instability instigated by CAG/CTG and CCTG/CAGG repeats and serve as a template for investigating complex genome rearrangements caused by other microsatellite sequences.

Student Mentoring: Students will receive laboratory training in molecular biology and genetics, gaining specific experience in molecular cloning, yeast genetics, nucleic acid biology, and bioinformatics analyses. Dr. Kim has mentored 13 CSUSM undergraduate students and five from a local community college participating in the BRIDGES to the Future program. Four of these students have matriculated to Ph.D. programs. Two undergraduates are co-authors on publications with Dr. Kim.


Environmental plasticity and the ecological genomics of desiccation in cyanobacteria found in the Anza Borrego Desert.

Dr. Rosalina Stancheva Hristova, Adjunct Professor, Biological Sciences

The arid Mediterranean climate of southern California is challenging for benthic cyanobacteria inhabiting intermittent streams. These desiccation-tolerant cyanobacteria possess remarkable plasticity undergoing physiological and morphological adaptations to survive frequent and prolong dry conditions, and quickly colonizing habitats when water is available. The aim of the project is to reveal the desiccation plasticity of filamentous Lynbgya-like cyanobacterium isolated from an intermittent stream in Anza Borrego Desert. Preliminary observations showed that filaments forms extensive extracellular polysaccharide sheaths, which may be multi-layred, colored and calcifying, depending on the conditions in the environment or in culture; potentially protecting the cells from desiccation and acting as sunscreen against extensive UV radiation. Desiccation experiments will be conducted to study the morphological changes of cellular and extracellular structures in this Lyngbya-like cyanobacterium.  During the last 5 years, genome sequences from three Lyngbya species from different ecological environments have become available which will makes it feasible to also examine adaptations to desiccation from a genomic perspective. This work is predicated on the hypothesis that significant and quantifiable structural and transcriptomic changes occur to afford the plasticity to meet the challenge of desiccation and rehydration in Lyngbya-like species.

Student Mentoring: Students will learn how to isolate and culture algae; perform detail morphometric analysis using microscopy, including SEM and TEM; isolate RNA and prepare RNASeq libraries; sequence and analyze sequence data, and perform quantitative PCR. Dr. Stancheva Hristova is the Chief Scientist of the California Algae Lab housed on the CSUSM campus, and has mentored more than 20 undergraduate students, including three previous REU students. Seven students are co-authors on her more than 20 published manuscripts


Planktonic community composition, growth and grazing rate estimates in San Diego, California across multiple time scales

Dr. Darcy Taniguchi, Assistant Professor, Biological Sciences

Unicellular marine plankton are vital components of marine ecosystems. They form the base of the marine food web, fix carbon and oxygen, and help regulate carbon sequestration. Characterizing the community composition and fundamental rates that control abundances are essential for understanding these organisms and predicting how plastic they and their ecosystems might be to future climatic conditions. Fundamental rates governing planktonic population dynamics are growth and grazing mortality. This proposed research aims to measure the growth and grazing mortality of phytoplankton and examine the bacterial and protistan community structure in marine waters off San Diego, California across multiple timescales. Student researchers will conduct serial dilution experiments of coastal San Diego waters to estimate planktonic growth and grazing mortality. To characterize the prokaryotic and eukaryotic community composition, students will take and analyze flow cytometry, acid Lugol’s, and epifluorescence microscopy samples. The rate estimates and associated community characterizations will be determined on a diel (day-night) cycle, and on a weekly basis over the summer for longer timepoint comparisons. Similar experiments performed during the summer 2021, will be used to compare the plasticity of fundamental rates and planktonic community structure over an interannual time period. This information will be integrated with environmental data, specifically sea surface temperature and nutrient concentrations, collected as part of the Southern California Coastal Ocean Observing System program. It is hypothesized that the community rates will vary most with the day-night cycle, given that light is a strong environmental driver. It is also hypothesized that the planktonic community structure will show greatest plasticity over the monthly and interannual timescales. This information will delineate how marine planktonic communities change over multiple timescales in this region of the California Current Ecosystem, and provide a mechanistic understanding of planktonic population dynamics in a nearshore marine ecosystem.

Student mentoring: Students will assist with sampling and serial dilution experiments, performing rate estimates, processing the acid Lugol’s and epifluorescence microscopy samples, and analyzing flow cytometry data to characterize the community composition. They will also acquire computer programing skills. Dr. Taniguchi has experience training 15 students in computational research projects and 3 students in rate estimate experiments. Of those students, ~80% have been from underrepresented groups in STEM, three have earned research scholarships/ awards, and many have presented work at conferences.

Understanding the impact of resource limitations during crucial life-stages

George Brusch, Assistant Professor, Biological Sciences

Research in the NET lab (Nutritional, Energetic, and Temperature physiology) investigates how animals respond to resource limitations. Given climatic predictions regarding precipitation patterns in many parts of the globe, our current focus is primarily on water limitations. We examine how water balance affects physiological functions such as immunocompetence, reproduction, and metabolism, as well as how animals mitigate potential negative effects. We use multiple levels of biological organization (communities, organisms, systems, cellular and molecular mechanisms) and a combination of field studies and manipulative laboratory experiments to understand the physiological implications of and adaptive responses to water limitation. By understanding how animals tolerate current instances of limited resource ability, we will be better able to predict how species will be impacted by future climate change and the variability in vulnerability among taxa.

Mentoring Students: The NET lab emphasizes training students in the scientific method, and they are typically involved in every step of the process (data collection, analyses, writing drafts of the manuscript). Dr. Brusch has mentored students on four different continents who have gone on to a myriad of professional and academic programs in the past (veterinary school, medical school, government positions, NGO, and the private sector). In addition to research experience, students are also asked to participate in a weekly reading group which helps students develop critical thinking skills and understand the depth of research that has come before them. Similarly, students typically attend seminars and local conferences as a group which sparks debate and elicits fresh ideas. The NET lab strives to connect with students from all backgrounds and encourage their development. We have worked with students in programs such as LSAMP and McNair and Dr. Brusch is especially excited to continue working with underrepresented students at CSU San Marcos.