Lab Members

Post-doctoral fellow

Thiago Bruce 

I am Post doc in Dinsdale´s Lab. I was born in Brazil and have PhD in genetics, Msc in Biotechnology and graduate in microbiology (2004). I have genuine interest in topics related to microbial molecular biology. I have been involved in research related to characterization and bioprospecting of microbial diversity. I had opportunity to handle with diverse approaches to characterize microbial communities from a variety of environments, searching for biocatalysts of industrial interest.Currently, im involved with Genotype to Phenotype Project. The lack of high-throughput phenotypic data is hindering our ability to describe the metabolic potential of microbes based on their genome annotation and our ability to predict gene complements from phenotypic analyses.The overall goal of this project is to improve our capability to reliably predict phenotype from genotype for microbial life across the bacterial kingdom. this project will result in genomic sequences, annotation and microbial metabolic models.

Shaili Johri Shaili Johri

 

PhD students 

 Matthew Haggerty

I am a PhD student in Ecology, I use metagenomics to identify differences in the composition of marine microbial communities in response to the environment. I have used sequence data to identify how microbial communities change with distance and environmental dissimilarity at a global scale. I have also applied these techniques to isolate potential super-heterotrophs implicated in coral reef decline and test the mechanisms regulating kelp decomposition.

 Michael Doane

I arrived to San Diego in summer of 2012 to begin a Master’s degree at San Diego State University. Growing up in Illinois, a landlocked region of the United States, I was always fascinated by the ocean. My trips to the ocean on vacation instilled a sense of intrigue and a shell collection to rival. I attended the University of Illinois at Urbana-Champaign as an undergraduate. From there, I ventured to Florida, working as a kayak guide in a wildlife refuge. It became apparent that I wanted to pursue research to answer many of the questions I could not answer for guest I would lead through the mangrove ecosystem in southwest Florida. I managed to secure a position as a researcher on a field project in Curacao, which made me realize my interest in field based investigation of coral ecosystems. It was here that I learned about San Diego State University. I know focus on the microbial communities that live on the skin of sharks, developing understanding for the role of microbes on sharks as well as how microbes interact with the skin of the shark.

 Megan Morris

PhD student in Ecology, applies metagenomics to study the role of microbes in the southern California kelp forests.

 


 Lais Lima 

I enrolled the Joint Doctoral Program in Ecology at SDSU/UC Davis in the fall 2016. Before I joined the Dinsdale lab, I received my Bachelor in Biological Sciences (University of Brasilia, 2011) and defended a Master’s in Marine Ecology (Federal Fluminense University, 2015) in Brazil, where I was born and raised. As a coral reef ecologist, I published my master’s thesis on the population ecology of an endemic coral species from Brazil advised by Dr. Ricardo Coutinho (IEAPM/UFF) and also conducted research on coral physiology in Bermuda, advised by Dr. Samantha de Putron (BIOS).

The aim of my PhD dissertation is to investigate the relationships between the holobiont physiological processes and the associated microbiome. I expect to address this aim by conducting in situ and laboratorial experiments in Caribbean coral reefs and in coastal ecosystems in California. The first part of my field and lab work will be conducted in the summer 2017 in Bermuda. In collaboration with the Bermuda Institute of Ocean Sciences (BIOS), I am sampling the coral microbiome across reef zones and subjecting corals from distinct thermal environments to heat-water treatments to assess whether the microbiome component enhances coral thermal resilience.  As a joint doctoral student, I am spending the 2017-2018 academic year at UC Davis under the Area of Emphasis “Ecotoxicology/Physiological Ecology”.

More information about my research interests and publications: https://www.researchgate.net/profile/Lais_Lima5

 Douglas Beattie

I am a visiting PhD candidate from the University of New South Wales, Australia. My research focuses on the role of viruses infecting the Sydney kelp Ecklonia radiata and the Californian giant kelp Macrocystis pyrifera. These are both primary habitat-forming brown alga along temperate rocky coastlines, and ongoing diebacks and disease have raised concern over the long-term health of these ecosystems and economic and commercial endeavors which rely on them.
Most medical or agricultural studies into viruses need the virus of interest to be isolated and grown on its own to enable further investigation. In contrast, we sequence the viral particles extracted directly from the kelp tissue. This provides genetic snapshots or Metagenomes of this community, where we can explore how different virus genes are affecting the health of the kelp.

 Amanda Alker 

I am currently a first year PhD rotation student in the Cell and Molecular Biology (CMB) Joint Doctoral program (JDP) with San Diego State University (SDSU) and University of California San Diego (UCSD). Originally from Florida, most of my previous research incorporated the use of molecular techniques to address both coral and microbial ecology. I was recently awarded the Graduate Research Fellowship (GRFP https://www.nsfgrfp.org/) funded by the National Science Foundation (NSF), to investigate the underlying mechanisms associated with bacterially-induced metamorphosis in coral larvae. I plan to use metagenomics, comparative genomics, and transcriptomics to elucidate these bacterially-mediated cues.

Graduate Students 

 Bhavya Nalagampalli Papudeshi 

I am a Bioinformatics graduate student in Dinsdale lab. My research includes optimization of metagenome assembly and binning tools to reconstruct population genomes.

 

 Dnyanada Pande 

I am a Master’s student in the Bionformatics and Medical Informatics program. Currently I am working on the analysis of viral metagenomes. The metagenomes have both single and double stranded viral sequences and I will be doing a comparative analysis between the above two mentioned types of viruses.

Rebecca de Wardt Rebecca DeWardt

When you grow up in Colorado, it is hard not to fall in love with camping, backpacking, hiking, and snowboarding.  My love of the outdoors has grown into a sense of duty to protect the worlds’ incredible and unique ecosystems.  This led me to attain a B.S. in Biology from the University of Colorado.  My studies as an undergrad piqued my interest in sustainability and biomimicry.  Currently, I am working towards attaining a M.S. in Cell and Molecular Biology.  My main research project focuses on linking genotypes to phenotypes through experimental analysis and metabolic modeling software.  The overarching goal of this project is to provide researches with a publicly available metabolic modeling tool to aid in understanding and bioengineering not well characterized bacterial species.  I am also working on tide pool microbiomes and am interested in their effects on host and ecological systems as well as exploring how microbiome signatures can be used as ecological bioindicators.

 Tucker Lopez

Marine microbes aid in the nutrition, reproduction, chemical defense, and immunity of associated organisms in marine ecosystems. As anthropogenic activity increases in coastal regions worldwide, marine microbial communities are shifting from symbiotic to pathogenic, causing further environmental detriment. Although the microbial genomic adaptations resulting from anthropogenic disturbance have been described, few studies have supported the genomic adaptation with evidence of phenotypic adaptations as well. My research explores the phenotypic adaptations in bacterial strains resulting from anthropogenic influence. Bacterial strains were isolated from four kelp forest regions offshore San Diego, California with different levels of anthropogenic disturbance. Because studies have shown that anthropogenic perturbations induce genomic changes in microbes, including transport of pollutant compounds out of the cell and utilization of contaminants as energy sources, we hypothesized that microbial strains isolated from higher anthropogenic disturbance areas would show phenotypic markers carbon, sulfur, phosphorous and nitrogen utilization. Utilization usage is tested using a 96-well phenotypic array plate with 72 carbon nutrient sources 24 sulfur, 10 phosphorus and 54 nitrogen  nutrient sources. Strains across the four kelp forest sampling locations, Catalina, Pt. Loma, La Jolla, & San Diego Bay have been tested to-date. The 96-well phenotypic array results are currently being analyzed to determine the nutrients that are being utilized among the Vibrio strains isolated from our areas of interest. As a result of this study, we will be better able to predict the changes that will occur in microbial communities, which has implications on the health of the associated environment and macro-organisms. This study is relevant as anthropogenic perturbations continue to increase in frequency and magnitude worldwide.

Reema Maniyar Reema Maniyar

I am a Master’s student in the Bionformatics and Medical Informatics program. My research focuses on developing a pipeline to identify phycotidnaviruses from metagenomes.

Undergraduate Students 

 Felicia Miller 

I am an undergrad biology student at San Diego State University who will graduate in the spring of 2017.  I am currently working on a tide pool project where I am taking samples from two locations, Mission Beach and Ocean Beach. From each location I am taking samples from three different microhabitats, hermit crabs, algae, and the water column and I’ll plating each sample on three different carbon sources, erythritol, cellobiose, and aspartic acid.  My hypothesis is that the microhabitats that I will sample from will determine the carbon usage rather than the location, which will infer that the microbial community of each microhabitat is conserved.  I am working under a COAST grant that I was awarded in the fall of 2015.

Taylor Cram

I am an undergraduate majoring in Microbiology at San Diego State University. I am currently working with microbial isolates that have been collected from La Jolla, Point Loma, Catalina, and San Diego Bay including both kelp and water samples. We will be plating the individual isolates on sodium alginate plate to see if the bacteria can use alginate as their carbon source.

Emma Billings Emma Billings 

Undergraduate in Biology

 

 

Natalie Frixione Natalie Frixione

Undergraduate in Biology

 Abigail Turnlund

I am an undergraduate majoring in Biology with an emphasis in Marine Biology at San Diego State University. Before attending San Diego State University, I first got involved in marine science by working at the Seymour Marine Discovery Center at Long Marine Lab at UC Santa Cruz. There I loved working with their swell sharks and plan on pursuing shark research in graduate school. Currently I am helping out with two projects in the lab, one looking at the role of microbes on sharks and the other linking genotypes to phenotypes for marine bacterial strains through experimental analysis.

 Alex A

I am an undergraduate majoring in Biology with a focus in Ecology at San Diego State University. Before the lab, I worked at SeaWorld as a Educator and was given the experience to interact with a variety of animals (thanks to trainers and aquarists!) which further fostered my love for ecology and the environment. Currently I’m on genotype to phenotype project which looks at marine bacteria strains through analytical assays and am very thankful for the research experience this lab has given me in the process.