Curriculum Vitae – Adam Smith

Education

University of California | Berkeley

University of California | Berkeley
University of Colorado | Boulder

Doctor of Philosophy in Comparative Biochemistry, May 2022

Dissertation title: Genome-Wide Screen and Phenotypic Analysis of a Kaposi Sarcoma-Associated Herpesvirus Genome with Insights into Capsid Maturation.

Synopsis: Mutant library constructed by deleting every canonical and several uncanonical ORFs in a Kaposi-sarcoma associated herpesvirus (KSHV) genome using red-mediated mutagenesis. Phenotypic screening of mutants conducted by transfection of mutant viral BAC DNA into mammalian cells, followed by assessment of progeny generation, viral growth, viral gene expression, viral DNA replication, and capsid formation.

Worked with a team of two other graduate students to develop a coherent reverse genetics workflow and generated a library of KSHV mutants.
Developed methods to analyze the effects of mutations on the viral life
Independently designed and established protocols and conducted experiments for analysis of KSHV mutant phenotypes in multiple mammalian cell lines and primary cells, including, immunofluorescence and electron microscopy, multicolor flow-cytometry, ultracentrifugation, viral titration (TCID50, plaque, ect), RT-qPCR/qPCR, western blotting, ELISA, cloning, transfection and more.
Worked with core facility staff to troubleshoot and optimize drafted protocols.
Led a team of undergraduate students focused on protocol implementation and data generation.
Analyzed and managed large data sets and discovered novel drug targets.

Masters in Public Health in the division of Infectious Diseases and Vaccinology, May 2016

Thesis Title: Serotyping clinical Salmonella isolates using Fourier Transform Infrared Spectroscopy

Synopsis: Designed and created a database of FTIR spectra from an economically relevant sample of Salmonella serovars. Spectra were used in combination with unsupervised machine learning to create a modular artificial neural network (ANN) that classified unknown salmonella isolates. Validation of ANN classifications for unknown samples were done by classical serotyping and whole genome sequencing.

Project lead who set their own hours and project timeline.
Designed and constructed a database of FTIR spectra from clinically and economically relevant serovars.
Designed and optimized a modular Artificial Neural Network (ANN) for the classification of unknown isolates.
External validation of ANNs using whole genome sequencing (WGS) and traditional antisera testing.
Worked with third party vendors and CDPH leadership in design, construction, and validation of ANNs

Publications

1) 2,4-dichlorophenoxyacetic acid (2,4-D) and risk of non-Hodgkin lymphoma: a meta-analysis accounting for exposure levels

2,4-Dichlorophenoxyacetic acid (2,4-D) is one of the most commonly used selective herbicides in the world. A number of epidemiology studies have found an association between 2,4-D exposure and non-Hodgkin lymphoma (NHL) but these results are inconsistent and controversial. A previous meta-analysis found no clear association overall but did not specifically examine high-exposure groups. We conducted a systematic review and meta-analysis of the peer-reviewed epidemiologic studies of the associations between 2,4-D and NHL, with a particular focus on high-exposure groups, and evaluations of heterogeneity, dose-response, and bias. A total of 12 observational studies, 11 case-control studies, and one cohort study, were included. The summary relative risk for NHL using study results comparing subjects who were ever versus never exposed to 2,4-D was 1.38 (95% confidence interval (CI), 1.07–1.77). However, in analyses focusing on results from highly exposed groups, the summary relative risk for NHL was1.73 (95% CI, 1.10–2.72). No clear bias based on study design, exposure assessment methodology, or outcome misclassification was seen. Overall, these findings provide new evidence for an association between NHL and exposure to the herbicide 2,4-D.

doi: 10.1016/j.annepidem.2017.03.003

Kaposi’s sarcoma-associated herpesvirus (KSHV) is an opportunistic pathogen causing Kaposi’s sarcoma. It can establish latent infection, which can be reactivated to engage lytic infection for progeny production. KSHV contains a ~165 kilobase DNA genome predicted to encode at least 90 open reading frames (ORFs). In this report, we generated 91 KSHV mutants, each characterized by the disruption of a single viral ORF. The growth of these mutants in cultured cells was examined to systematically investigate the necessity of each ORF for viral latency, reactivation, and lytic replication. The salient features of our results are (a) 44 ORFs are essential for viral lytic replication in cultured cells and 47 are nonessential; (b) KSHV reactivation can be positively or negatively regulated by specific viral ORFs; and (c) ORFs identified to modulate viral reactivation encode functions modulating both innate and adoptive immune responses. The intersection of viral immunomodulatory genes controlling reactivation suggests that KSHV engages in a concerted effort to communicate and respond to the host immune system using a viral sensory network. Our results imply a novel mechanism in which reactivation of KSHV is actively controlled by the virus in response to its surrounding environment, leading to the opportunistic nature of viral diseases that are strongly correlated to the host’s immune status and conditions.

Manuscript pending submission — Full manuscript available upon request at authors discretion (adammsmi@berkeley.edu)
Target: Nature

Kaposi sarcoma-associated herpesvirus (KSHV) open reading frame 19 (ORF19) is conserved throughout human herpesviruses, however, very little is known about the role KSHV ORF19 plays in the viral lifecycle. In this study we investigated the role of KSHV ORF19 in the establishment and maintenance of viral latency, reactivation, viral lytic gene expression, lytic DNA replication, capsid formation, and progeny production. We created a KSHV ORF19 inactivation mutant (stop-ORF19) from a bacterial artificial chromosome containing the KSHV genome (BAC16), and we rescued the stop-ORF19 virus genotype (res-ORF19). stop-ORF19 virus was able to establish latency as determined by the expansion of transfected cell lines and the lack of infectious progeny in the cell and culture supernatant. stop-ORF19 virus had no defect in DNA replication and segregation during viral latency and induction confirmed stop-ORF19 was able to reactivate from latency. stop-ORF19 had no defect in lytic viral DNA replication. Tittering of induced cells and supernatants showed that stop-ORF19 virus produced no infectious progeny, while res-ORF19 virus produced progeny and grew like BAC16 virus. Transmission electron microscopy of induced stop-ORF19 virus infected cells revealed the accumulation of empty A-capsids that were retained in the nucleus, indicating that KSHV ORF19 plays a critical role in KSHV capsid maturation and possibly viral egress. Our results provide biological evidence complementing cryogenic electron microscopy (cryo-EM) structural data that indicate KSHV ORF19 helps retain the packaged genome inside of mature capsids by capping the portal vertex.

Manuscript pending submission — Full manuscript available upon request at authors discretion (adammsmi@berkeley.edu)
Target: PLOS Pathogens

Patents

Kaposi Sarcoma-associated herpesvirus gene function and methods for developing antivirals, anti-KSHV vaccines, and KSHV-based vectors, and compositions

Kaposi Sarcoma-associated herpesvirus gene function and methods for developing antivirals, anti-KSHV vaccines, and KSHV-based vectors, and compositions

Awards and Nominations

University of California Dissertation Year Fellowship Award

UC Berkeley is committed to recognizing and rewarding student’s contributions to diversifying the academy during their graduate careers and beyond. The purpose of this fellowship award is to provide funding to diverse doctoral students that allow them to prioritize and focus on completing the dissertation. Fellows will receive a $30,000 stipend, payment of in-state fees, travel allowance ($1,000 maximum) and $3,000 bonus for early dissertation filing. Student must have advanced to doctoral candidacy and completed two dissertation chapters or the equivalent, as confirmed by dissertation chair.

The Outstanding Graduate Student Instructor (OGSI) Award honors UC Berkeley GSIs each year for their outstanding work in teaching on the Berkeley campus. These OGSI recipients are nominated from within their teaching department. The GSI Teaching & Resource Center provides the award recipients certificates of distinction. Departments may only nominate up to 10% of the GSIs appointed by the department during the academic year.

2018

Entrepreneurship

Berkeley short I-Corps program

NSF I-Corps Training. Each month, NSF I-Corps Method offers a 1 week immersive course for university researchers and early stage startup founders. Received invitation/recommendation from teaching staff to apply to the national program.

This course features a series of lectures designed for students, post-docs, entrepreneurs, and investors with life sciences and tech backgrounds. This ten-week workshop will allow attendees to expand their knowledge and learn more about:

Intellectual Property law, including patent prosecution, litigation, trademarks, licensing, and commercial transactions
Business law, including raising funds, and company exit strategies
Regulatory law, including the FDA, privacy, and data security

Each session will explore more advanced topics in patent and life sciences law, such as US/EU patent drafting, small molecules, medical devices, biologics, FDA strategies, trade secrets, and licensing. Attendees will gain the hands-on knowledge scientists, engineers, entrepreneurs, and investors need to manage the legal aspects for launching and growing a startup including how to avoid common mistakes that can have serious consequences down the road.