Mixer presentations

Angela Garibaldi

Ph.D. candidate, Microbiology & Molecular Genetics, School of Medicine - Bioinformatics Support Group Organizer

Stacey Borrego, PhD

Research staff, Biological Chemistry, School of Medicine - Bioinformatics Support Group Organizer

Who we are: The Bioinformatics Support Group was founded in January 2018. Our goal in establishing this group was to bring biologists with different levels of experience together in a supportive community setting and to help orient beginners to get started. Over the course of our first session, meeting topics have ranged from HPC basics, Bash scripting, tutorials on RNA-seq programs, topics in the programming language R, and introductions to ChIP-seq and Metagenomics.

Collaboration Opportunities: We are thankful to the guest presenters that we have had over the past few months and we are actively looking for more. We do have topics in mind for presentations but we are open to any that are related to data analysis. Additionally, we have been fortunate to receive funding for our events from UCI organizations including the Institute for Genomics and Bioinformatics, the Cancer Research Institute, and the Research Cyberinfrastructure Center. We would like to host future events including workshops with invited speakers and would appreciate support to do so.

Contact Information: If you would like to collaborate with the us in any capacity or join our email list, please send an email to bioinformaticsSG@gmail.com

Presentation Slide

Mason Schechter

Research Staff, Biomedical Engineering, Samueli School of Engineering

I’m a junior specialist in the lab of Chang Liu in the Department of Biomedical Engineering. I’m going to describe two projects in the lab:

1. Orthogonal replication for in vivo continuous directed evolution: The lab has created yeast cells in which one to a few genes of the researcher’s choice evolve very quickly without affecting the normal functions of the yeast cell. This is achieved by expressing the genes of interest from a plasmid in the cell’s cytoplasm that is replicated by its own dedicated DNA polymerase; we have engineered this polymerase to have a variety of substitution error rates up to 100,000 times greater than the yeast genomic rate. The orthogonal replication system can be used to evolve the same gene or group of genes in many replicates under relevant selection conditions to analyze fitness landscapes on laboratory timescales. For all our experiments, we find lots of mutational paths leading to the target protein’s adaptation, and we would love to collaborate with computational biologists to extract insights about protein evolution and function from these large mutational datasets.

2. Cell history recording by ordered insertion (CHyROn): We have integrated a small synthetic locus into the genome of mammalian cells that continuously accumulates random inserted nucleotides in an ordered fashion. Because daughter cells inherit the inserted nucleotides accumulated by their ancestors, the sequence of the locus in any cell can be used to retrace its lineage relative to other cells in an organism or tissue. Alternatively, insertion of nucleotides can be made conditional on a cell stress; in a proof-of-concept experiment in tissue culture cells, we have shown that the lengths of insertions at the synthetic recording locus increase as a cell’s time in a hypoxia-mimicking drug increases. We would love to collaborate with computational biologists to reconstruct lineage and understand cell history from sequencing data recorded at the synthetic locus.

Xiangmin Xu, PhD

Associate Professor, Anatomy and Neurobiology, School of Medicine

Presenter information: Dr. Xiangmin Xu has received an accelerated promotion to Full Professor (effective July 1, 2018) in Anatomy and Neurobiology with joint appointments in Biomedical Engineering, Computer Science, and Microbiology and Molecular Genetics. He applies a strong background in biology, engineering and medicine to address fundamental questions in neuroscience. Dr. Xu’s research interest focuses on neural circuit organization and function in relation to the neurobiology of visual perception, learning and memory. His laboratory uses a multidisciplinary approach that combines electrophysiology, photostimulation and optical imaging, molecular genetics and viral tracing. Their analysis is further refined and informed by engineering and computational techniques.

Collaboration area of interest: Bioinformatic data analysis of TRAP-seq and FACS-sorted cells for RNA-seq; Use of systems biology approaches to interpret seq datasets, and extract relevant biological insights.

Relevant project information:

Project title: Neuregulin-1 based molecular mechanisms of cortical plasticity

The physiological aspects of experience-dependent critical period plasticity has been extensively studied. However the molecular mechanisms that translate visual deprivation into functional changes in circuit connections remain poorly understood. Neuregulin-1 (NRG1) signaling through its tyrosine kinase receptor ErbB4 is essential for the normal development of the nervous system, and has been involved in GABAergic synaptic plasticity, and neuropsychiatric disorders such as schizophrenia. NRG1 is widely expressed in excitatory neurons, inhibitory interneurons and glial cells in the visual cortex, while ErbB4 expression is largely restricted to parvalbumin-expressing (PV) neurons. We discovered recently that NRG1/ErbB4 signaling in PV neurons is critical for the initiation of critical period visual cortical plasticity by controlling excitatory synaptic inputs onto PV neurons and thus PV-cell mediated cortical inhibition that occurs following visual deprivation. Building on this discovery and our data showing that NRG1 effects depend on specific neuronal types and are modulated further by deprivation duration, we propose to provide a detailed analysis of NRG1 signaling actions implicated in visual cortical plasticity at the cellular and circuit levels. We start to plan PV- or excitatory- cell type specific TRAP-seq and FACS-sorted cells for RNA-seq at UCI genomic core. Using the state-of-art approaches including Next Generation Sequencing, we expect that the proposed research will advance our understanding of molecular mechanisms underlying visual cortical plasticity, and help to develop new therapeutic approaches to treat amblyopia and other neurodevelopmental disorders.

Erwin Strahsburger, PhD

Visiting Scholar, School of Medicine

Summary: Arsenobetaine (AB) is the only arsenic molecule not toxic for humans and is almost the same as glycine betaine (GB) but changing the nitrogen for an arsenic molecule. GB is an osmoprotectant molecule expressed in plants, animals, and microorganism as a response to osmotic stress, and AB apparently can exert the same role. In marine organisms AB is synthetized from arsenosugars or dimethylarsenic molecules, using the anabolic pathway of GB, meanwhile its catabolic pathway is unknown. A marine bacterium Paenibacillus sp. can metabolize arsenobetaine producing two metabolites; dimethylarsinoylacetate and dimethylarsinate. Only this last one is similar to the corresponding non-arsenic metabolite in GB catabolic pathway, therefore, maybe both catabolic pathways are not the same. On this sense, we like to collaborate to start a study driven to understand the evolution of glycine betaine catabolic pathway and determine according to structural protein analysis, if arsenobetaine or its intermediate can fix in these enzymes. The collaboration would involve a phylogenetic analysis of demethylases enzymes focusing mainly on marine bacteria, and protein structure analysis to model an AB molecule in the active site of enzymes of GB catabolic pathway. This information will allow us design primers, cloning and test in vitro these putative enzymes and propose a catabolic pathway for arsenobetaine.

Contact Information: estrahsb@uci.edu

Presentation Slide

Trina Norden-Krichmar, PhD

Assistant Professor, Department of Epidemiology, School of Medicine

Collaboration Goals: The focus of my lab is entirely on applied bioinformatics analyses and custom bioinformatics tool development. The goal of the lab’s current research is to investigate the genomic factors influencing health and disease. However, we are open to collaborations involving any type of genomic data, research focus, or organism.

Background: I have a B.S. in Biochemistry from University of Maryland, M.S. in Computer Science from George Washington University, and a Ph.D. in Marine Biology from the Scripps Institution of Oceanography at the University of California, San Diego. In addition to the laboratory skills acquired by my biological research, I also have over 15 years of experience working professionally as a computer programmer at IBM, the National Institutes of Health, and the Salk Institute. I have expertise performing bioinformatics analyses applied to projects involving RNA sequencing and gene expression microarrays, DNA sequencing and genotyping arrays, microRNAs, methylomics, proteomics, metagenomics, and metatranscriptomics. Additionally, I have experience teaching computer programming at the undergraduate, graduate, and professional levels.

Contact Information: If you are interested in collaborating, please feel free to send email to tnordenk@uci.edu.