Lauren Oldfield is an assistant professor in the Synthetic Biology department. Her diverse research interests include viral synthetic genomics for large DNA viruses and investigating the role of the microbiome in injury after pollution exposure.

In her postdoctoral research at the JCVI, she worked with Dr. Sanjay Vashee to develop synthetic genomics tools to improve researchers’ ability to manipulate herpesviruses. Through a strong collaboration with Dr. Prashant Desai they successfully implemented a novel synthetic genomics method to clone and assemble the HSV-1 genome from smaller overlapping genomic fragments and reconstitute infectious virus in tissue culture. By cloning the HSV-1 genome in fragments, the team can rapidly engineer changes to these fragments in parallel and reassemble full length genomes with a combination of mutant and wild-type parts. Dr. Oldfield is now working to expand these synthetic genomics tools to additional viruses and to new scientific and medical problems. Drs. Vashee and Oldfield also are working with collaborators to expand this system to other herpesviruses, including Epstein-Barr virus and human cytomegalovirus, and to viruses that are important agricultural pathogens.

She was also involved in other virus projects at JCVI studying Zika virus, rhinovirus, and enterovirus D68, and initiatives to look at the viral component of the microbiome and its contributions to cancer. As a graduate student under the direction of Dr. Graham Hatfull, a world renown bacteriophage expert, Dr. Oldfield studied several aspects of bacteriophage gene expression using RNA-Seq, promoter assays and characterizing the genetic switch for lytic versus lysogenic growth.

Dr. Oldfield is also a fellow in the Emerging Leaders in Biosecurity Initiative, which aims to provide education and networking to scientists and policy experts from academia, industry, nonprofits and government on issues of biosecurity.

Ongoing pilot projects will investigate the effects of ozone and particulate matter, respectively, on the microbiome in mouse model systems. Understanding the contribution of the microbiome may lead to diagnostics or treatments to help mitigate the effects of pollution exposure.

Dr. Oldfield received her PhD in Molecular Biology from the University of Pittsburgh and her BS in Biology from the University of Akron.

Research Priorities

Characterize and assess the phenotype of regions of repeated sequence in HSV-1
  • Determine the accurate sequence of the inverted structural repeats and smaller variable number tandem repeats of HSV-1
  • Isolate clones of these regions and assemble HSV-1 genomes with variants of the repeats
Understanding the role of the microbiome, including the resident virome, in the initiation and progression of cancer
  • Focus on the molecular mechanisms of herpesvirus oncogenesis
Bacteriophage-based diagnostics for antimicrobial resistance
  • Develop synthetic genomics assembly tools to rapidly manipulate bacteriophage genomes
  • Improve existing diagnostic phage to sensitively detect bacteria
Utilizing genomics to better understand viral outbreaks
  • Currently working with Zika virus and enterovirus D68

Publications

Optimization of qRT-PCR assay for zika virus detection in human serum and urine.
Virus research. 2019-04-02; 263.173-178.
PMID: 30742853
Rapid and efficient in vitro excision of BAC sequences from herpesvirus genomes using Cre-mediated recombination.
Journal of virological methods. 2018-11-01; 261.67-70.
PMID: 30092252
Whole genome sequencing, variant analysis, phylogenetics, and deep sequencing of Zika virus strains.
Scientific reports. 2018-10-26; 8.1: 15843.
PMID: 30367096
Contemporary Circulating Enterovirus D68 Strains Have Acquired the Capacity for Viral Entry and Replication in Human Neuronal Cells.
mBio. 2018-10-16; 9.5:
PMID: 30327438
Sequences of Zika Virus Genomes from a Pediatric Cohort in Nicaragua.
Genome announcements. 2018-06-14; 6.24:
PMID: 29903816
Whole-Genome Sequences of Zika Virus FLR Strains after Passage in Vero or C6/36 Cells.
Genome announcements. 2018-01-25; 6.4:
PMID: 29371358
Genome-wide engineering of an infectious clone of herpes simplex virus type 1 using synthetic genomics assembly methods.
Proceedings of the National Academy of Sciences of the United States of America. 2017-10-17; 114.42: E8885-E8894.
PMID: 28928148
Efficient size-independent chromosome delivery from yeast to cultured cell lines.
Nucleic acids research. 2017-04-20; 45.7: e50.
PMID: 27980064
The Human Microbiome and Cancer.
Cancer prevention research (Philadelphia, Pa.). 2017-04-01; 10.4: 226-234.
PMID: 28096237
An Unusual Phage Repressor Encoded by Mycobacteriophage BPs.
PloS one. 2015-09-02; 10.9: e0137187.
PMID: 26332854
Mutational analysis of the mycobacteriophage BPs promoter PR reveals context-dependent sequences for mycobacterial gene expression.
Journal of bacteriology. 2014-10-01; 196.20: 3589-97.
PMID: 25092027
Integration-dependent bacteriophage immunity provides insights into the evolution of genetic switches.
Molecular cell. 2013-01-24; 49.2: 237-48.
PMID: 23246436
BRED: a simple and powerful tool for constructing mutant and recombinant bacteriophage genomes.
PloS one. 2008-12-17; 3.12: e3957.
PMID: 19088849

Research Priorities

Characterize and assess the phenotype of regions of repeated sequence in HSV-1
  • Determine the accurate sequence of the inverted structural repeats and smaller variable number tandem repeats of HSV-1
  • Isolate clones of these regions and assemble HSV-1 genomes with variants of the repeats
Understanding the role of the microbiome, including the resident virome, in the initiation and progression of cancer
  • Focus on the molecular mechanisms of herpesvirus oncogenesis
Bacteriophage-based diagnostics for antimicrobial resistance
  • Develop synthetic genomics assembly tools to rapidly manipulate bacteriophage genomes
  • Improve existing diagnostic phage to sensitively detect bacteria
Utilizing genomics to better understand viral outbreaks
  • Currently working with Zika virus and enterovirus D68

Differences Between Men and Women and the Role of Microbiome In Asthma Onset

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Coronavirus Research

Overview of various projects related to the novel coronavirus pandemic.

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Designer Phage

Synthetic Engineering of Bacteriophage for Treatment of Wound Infections

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EV-D68 Replication in Human Neuronal Cells

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Synthetic Genomics to Generate a Stable Epstein-Barr Virus Infectious Clone

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Viral Synthetic Genomics to Engineer Large dsDNA Viruses

Rapid engineering of large dsDNA viruses using synthetic genomics assembly tools.

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Assembly of HSV-1

Use of cutting-edge synthetic genomics technology to revolutionize the study of herpesvirus biology.

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