Featured Spring 2019 Speakers

CaroSeptember 18th
Dr. Florencia Caro, Postdoctoral Fellow
Mekalanos Lab
Harvard University


"Lipoprotein transport inhibition induces Mega Outer Membrane Vesicle formation in Vibrio cholerae"



Genes necessary for the survival or reproduction of a cell are an attractive class of antibiotic targets. Studying essential genes by classical genetics, however, is inherently problematic because it is impossible to knock them out. Using CRISPR-interference (CRISPRi) knockdown in the human pathogen Vibrio cholerae we demonstrate that CRISPRi knockdown of 37 predicted essential genes inhibits viability, thus validating the products of these genes as drug target candidates. We show that V. cholerae is particularly vulnerable to lethal inhibition of the system for lipoprotein transport (Lol) a central hub for directing lipoproteins from the inner to the outer membrane (OM). Lol depletion makes cells prone to plasmolysis and elaborate membrane reorganization, during which the periplasm extrudes into a mega outer membrane vesicle or “MOMV” encased by OM which dynamically emerges specifically at plasmolysis sites. 

Dr. Florencia Caro Bio:

I come from Argentina, where I did my undergraduate degree at the University of Buenos Aires. For my PhD I joined the DeRisi lab at the University of California, San Francisco. My thesis work was centered on measuring mRNA translation on a genome-wide level in the Malaria parasite Plasmodium falciparum using ribosome profiling. My current work in the Mekalanos lab is centered on uncovering the genome-wide landscape of genetic interactions in V. cholerae and assessing the effects of essential gene depletion on bacteria survival.


CovarrubiasOctober 15th
Sergio Covarrubias
Postdoctoral Fellow and CRISPR Core Director
Carpenter Lab
Molecular, Cell and Developmental Biology
UC Santa Cruz

The UCSC CRISPR Core: High-Throughput Genetic Screens to Explore Pathways in Inflammation"



Chronic inflammation is at the core of a variety of human diseases including Rheumatoid Arthritis and certain cancers. There are numerous therapeutics available for treating inflammatory diseases, yet as many as 20-40% of patients don’t respond to treatment. Hence, there is a need for development of new drug targets that could regulate disease-relevant inflammatory pathways. Macrophages are important mediators of the inflammatory response, a process that is driven by the NF-kappa B (NF-kB) transcription factor. I will describe CRISPR-based systems I have developed for high-throughput screening for novel regulators of inflammation. We identified over 100 novel regulators of the NF-kB signaling and reveal interesting regulatory complexities of the tumor necrosis factor (TNF) signaling cascade. Additionally, I will describe how this same technology can be used to explore the dark matter of the genome probing for novel long noncoding RNAs that regulate macrophage differentiation. In the end, I will briefly discuss what the UCSC CRISPR Core is and how we are making this technology available to anyone.


Dr. Sergio Covarrubias Bio:

Sergio is currently a postdoctoral fellow and CRISPR Core Director in the laboratory of Susan Carpenter in the Department of Molecular, Cell and Developmental Biology at UC Santa Cruz.  He received his PhD from UC Berkeley in the area of Infectious Diseases and Immunity.  His current work focuses on using high-throughput CRISPR screening methods to dissect regulatory pathways involved in inflammation and host defense.


AChengOctober 22nd
Andrew Cheng
Sr. Scientist, Manufacturing,

Identification and Characterization of 4 years in a Startup"




Dr. Cheng has contributed to the development of a commercialized medical food probiotic shown to help people manage metabolic disorders, and shares his experience working at Pendulum Therapeutics, formerly known as Whole Biome.


Dr. Andrew Cheng Bio:

SAndrew Cheng is a senior scientist at Pendulum. He has over 10 years of research and experience in bacterial physiology and genetics. Andrew received his Ph.D. in microbiology and environmental toxicology at the University of California Santa Cruz studying biofilm formation in Vibrio cholerae. Prior to his academic training, Andrew was a senior research associate at Osel Inc. and helped develop a novel topical live biotherapeutic to prevent heterosexual transmission of HIV and bacterial vaginosis.

"I enjoy coming to work at Pendulum because: 1) I am enthusiastic to be at the forefront of microbiome research and develop interventions for microbiota dysbiosis, 2) I am part of an interdisciplinary team with unique backgrounds that unite to solve the mysteries of the microbiome, and 3) the culture of the Pendulum fosters both personal and career growth."


AdamspicNovember 5th
Walter Adams
Principal Investigator, Adams Lab
San Jose State University

"Two Truths and a PLY: Neutrophils, Epithelial Integrity, and a Toxin You Can’t Trust"



Dr. Walter Adams Bio:

Dr. Walter Adams is an Assistant Professor of Biological
Sciences at San Jose State University. Walter’s research
interests focus on the interplay between pathogenic bacteria
and the host immune response. The Adams Lab investigates
the Gram-positive respiratory pathogen S. pneumoniae and
the neutrophil immune response during infection.
Understanding how specific host and bacterial factors impact
the lung epithelium will help to develop novel treatments for
patients in the clinical setting.
Walter obtained his Ph.D. (2009) from UCSC in Microbiology and Environmental Toxicology in
the lab of Dr. Vicki Auerbuch Stone. His doctoral work focused on the role of the T3SS in
Yersinia pseudotuberculosis and the delivery of Yersinia effector proteins or HOTJEMs. During
his time at UCSC he participated in the IMSD and RMI Diversity programs and received the
Cota-Robles Diversity Fellowship.
Walter conducted his postdoctoral research in microbiology at Tufts University from 2015-2019
in the lab of Dr. John Leong. There he studied how the pore forming toxin pneumolysin
contributes to Streptococcus pneumoniae infection and its role in neutrophil migration. He was
awarded a Tufts IRACDA (formerly TEACRS) Postdoctoral Fellowship that provides
comprehensive training in undergraduate pedagogy, grant writing, mentoring, and science
In his spare time, Walter enjoys making science themed board games, playing the piano, and
telling really bad science jokes.


diazcastillophotoDecember 3rd
Dr. Carlos Diaz-Castillo

Researcher, Chamorro-Garcia Lab
UC Santa Cruz

"Mechanisms of biological diversity meets global health"




An inherent property of all biological systems is their ability to vary (i.e., biological variability). To understand the mechanisms of biological variability and its manifestation, diversity, is key for fields like evolutionary biology, inclusive approaches to human health and disease (e.g., precision medicine and global health), or bioengineering. However, we still understand very little on how biological variation is ultimately originated, how such variation is propagated through different levels of biological organization, how different types of variation interact, and how to translate the knowledge on the mechanisms of biological variability into practical applications. During my talk, I will illustrate how the use of integrative multidisciplinary analyses of datasets encompassing relevant biological diversity can be of great use to understand the mechanisms of biological variability/diversity and its potential application toward the preservation of human health.

Dr. Carlos Diaz-Castillo Bio:

I am originally from Madrid, Spain. I did my PhD on the Troponin C gene family of Drosophila melanogaster at the Universidad Autonoma de Madrid under the direction of Roberto Marco. As a postdoc in the Kent Golic lab at the University of Utah, I studied DNA sequence variation with regard to the heterochromatin/euchromatin compartmentalization of the D. melanogaster genome. As a postdoc in the Jose Ranz lab at the University of California, Irvine (UCI), I used analytical and chromosome engineering approaches to study gene order evolution and RNA-mediated gene duplications in the genus Drosophila. Still at UCI, I worked as Research Assistant at the David Gardiner and Susan Bryant lab focussing on the study of regenerative responses in salamanders, and collaborated with Raquel Chamorro-Garcia at the Bruce Blumberg lab on the study of mechanisms of transgenerational obesity. As independent researcher, I focus on the study of mechanisms of biological variability/diversity.


mcdermott.jpgDecember 10th
Dr. Tim McDermott


Montana State University

"Arsenic and the Gastrointestinal Tract Microbiome: "Design-Build-Test-Learn", Repeat"




Arsenic is a toxin, ranking first on the Agency for Toxic Substances and Disease Registry and the Environmental Protection Agency Priority List of Hazardous Substances. Chronic exposure increases the risk of a broad range of human illnesses, most notably cancer; however, there is significant variability in arsenic-induced disease among similarly exposed individuals. Human genetics is a known component, but it alone cannot account for the large inter-individual variability in presentation of arsenicosis symptoms. Given the well-established arsenic redox transformation activities of microorganisms, it is reasonable to imagine how the GIT microbiome composition variability among individuals could play a significant role in determining the fate, mobility and toxicity of arsenic, whether inhaled or ingested. This seminar will survey microbe-arsenic interactions in the context of the gut microbiome, as well as present results of current studies involving customized microbiomes in germ-free mice.

Dr. Tim McDermott Bio:

Tim McDermott is a microbial ecophysiologist.  His research program has two primary thrusts: 1) microbe-arsenic interactions in a broad array of environments, spanning from Yellowstone geothermal environments to the gut microbiome; and 2) methane cycling in freshwater environments, specifically Yellowstone Lake.