Eric Beaudoin Email & Phone Number

Worcester, Ma, Us

Worcester, Massachusetts, United States

Systematically generated single gene deletions of predicted DNA methyltransferases in Bacillus subtilis 3610 using Gene Ontology databases. Generated clean deletions in B. subtilis 168 using natural competence, then moved them into 3610 using phage transduction. Predicted methylation activity by analyzing cross-conditional RNA relative abundance and mutant relative fitness. Characterized phenotypic differences in these strains in targeted conditions, performed targeted- and untargeted-metabolomics, and identified differences in DNA methylation through PacBio SMRT sequencing. Characterized spatial and temporal transcriptional heterogeneity within Bacillus subtilis biofilms using fluorescent transcriptional reporters. Compared these findings across media types. Dimensionally reduced data, writing scripts Matlab to linearize data and retrieve data on colony shape, size, and volume; and R to perform Principal Component Analysis (PCA).Identified novel, transcriptionally distinct subpopulations of B. subtilis and E. coli, as well as their relative abundances in populations, using flow cytometry. I used Python and SK-Learn to implement Gaussian Mixture Modeling (GMM), informed by AIC and BIC, to identify transcriptionally distinct subpopulations of cell communities. This program produces adaptive gates that can be input to a FACS, allowing integration with other downstream applications.Used MALDI-TOF Mass Spectrometry on a Phocaeicola (formerly Bacteroides) vulgatus transposon mutagenesis library to identify and predict gene functions. This was done using Python (Using PCA, Partial Least Squares Regression (PLS-DA), and Uniform Manifold Approximation and Projection (UMAP) for dimensionality reduction; GMM and K-means for clustering; and Compound Discoverer for metabolite prediction).Performed genome assembly of PacBio and Oxford Nanopore (ONP) long reads using SMRT Link and Canu, respectively. Identified Biosynthetic Gene Clusters (BGCs) with AntiSmash.

Chapel Hill, Nc

Began working in Dr. Elizabeth Shank's Lab. The lab moved to UMass Medical School in January 2020. Please see that listing for a complete list of my skills and projects

Raleigh-Durham, North Carolina Area

-Assisted in developing a photochemical mold remediation (PMR) solution that generates low levels of chlorine dioxide in solution for application in the remediation of building materials infected with microbial contaminants-Tested the effects of hydrogen peroxide vapor (HPV) as a means of decontaminating building materials infected with microbial contaminants-Measured the effects of airborne flame retardants on the oral microbiome-Engaged in the development, refinement, and implementation new standard operating procedures (SOPs) and miscellaneous operating procedures (MOPs) to optimize work flow within the lab, improve yields, and generate more accurate data-Improved spore recovery rates from concrete coupons from less than 1% to over 90% of the maximum theoretical yield-Developed a procedure to cheaply and quickly induce vegetative growth of spores on concrete coupons-Quantified differences in the efficacy of existing extraction protocols and advised the primary investigator on the optimal protocols to use for each situation-Assisted primary investigators with experimental design, work flow, and determination of required number of experimental replicates to ensure statistically valid results-Wrote a program that extracted experimental results from Excel spreadsheets and performed full statistical analyses automatically-Regular duties included preparing media, working solutions, and reagents; processing hazardous waste in compliance with federal and state regulations; making daily progress toward research goals; updating the lab notebook to log data and record progress; assisting in laboratory audits to ensure regulatory compliance; taking laboratory inventory; and submitting purchase requests in anticipation of upcoming research demands

-Processed high volumes of samples daily by executing SOPs; generating, logging, and interpreting data; and performing root cause analysis on anomalies as they arose-Checked nitrate, phosphate, TDS, conductivity, pH, and heavy metal levels in groundwater samples to ensure public safety, as well as compliance with state and federal regulations-Developed treatment strategies to help meet the specific needs of the public, customers, and stakeholders and bring water parameters within acceptable levels for the water’s intended use-Trained newly hired employees, regularly performing quality assurance (QA) checks on their findings to ensure accuracy

Durham, New Hampshire

-Utilized SYBR Green qPCR to detect low frequency, unculturable, or latent endophytes from environmental plant and soil samples-Applied pesticides, antimicrobial agents, and nutrient mixtures using a backpack sprayer on plants and soil, in field test plot and greenhouse settings, to quantify their impact on the relative health of the host-plant and soil microbial community-Used confocal microscopy to quantify the rate of infection of Phytophthora spp. in host roots, stems, and leaves when controlling for different levels of nutrients, water, and soil microbiome components-Cultured microbes from diseased plant tissue, extracted DNA, and sequenced 18S, ITS, GAPDH, actin, and beta-tubulin genes to determine the genus and species of the disease-causing agent -Identified the presence of CaBEN1 gene in in a local population of Colletotrichum acutatum that conveyed resistance to Benomyl, a commonly used fungicide-Updated laboratory notebook daily to ensure an accurate record of procedures and results existed for future researchers in the lab-Engage in general laboratory work such as the generation of media, working solutions, and reagents, as well as the maintenance of pure cell cultures and generation of inoculum.-Gave weekly or biweekly presentations on progress and research findings

Doctor Of Philosophy - Phd, Biological And Biomedical Sciences -- Systems, Computational, And And Quantitative Biology

Activities and Societies: Director of Communications -- UMass Chan Consulting Club President -- Microbiome Journal Club Continuation.

Doctor Of Philosophy - Phd, Microbial Interactions

Beginning of my PhD. Transferred to UMass Medical School with my academic advisor in January of 2020

Bachelor’S Degree, Genetics

Activities and Societies: American Phytopathological Society, Undergraduate Research Conference, Appalachian Mountain Club Presented.