Resume

• 2008

  Postdoc

  Division of Biological Sciences

  University of California San Diego

• 2004

  Salt Lake City

  UT

  •\tStudied circadian rhythms in cyanobacteria (Synechococcus elongatus). Focused on establishing the mechanism of circadian global gene regulation.\n•\tDemonstrated a circadian clock regulated chromosome compaction rhythm that matches that of a concurrent gene expression rhythm. This was a popular hypothesis in the field but

  until these studies

  the link had not been established.\no\tDeveloped an assay to look at chromosome compactions in live cells using fluorescent DNA dye & visualized using deconvolution fluorescent microscopy. \no\tResults were published in PNAS\n•\tEstablished a link between dark-induced chromosome compaction & phase shifts in gene expression rhythms using deconvolution fluorescent microscopy

  dark pulses

  & bioluminsecence.\no\t Used bioluminescence PkaiB::luc+ to follow circadian regulated gene expression after phase-shift with 5hr dark pulses.\no\tDemonstrated using deconvolution microscopy that dark treatments induce complete chromosome compaction.\no\tWas the first to establish that chromosome compaction has a role in circadian clock-regulated gene expression patterns & that the chromosome compaction state likely determines phase angle.\no\tResults were published in Bacterial Circadian Programs\n•\tInvestigated the role of SmcA in chromosome dynamics.\no\tConstructed an smcA3 allele and found that the smcA3 strain lacks dark-induced chromosome compaction & altered gene expression patterns in response to 5hr dark treatments.\no\tResults were published in Bacterial Circadian Programs\n•\tCollaborated with Jonathan Zehr’s UC Santa Cruz lab in studying diel cycling of DNA staining and nifH gene regulation in Crocosphaera watsonii (a unicellular cyanobacterium).\no\tResults were published in Environmental Microbiology.\n•\tResearch was supported by an individually earned NIH Genetics Training Grant.\n•\tServed as Chair of the Cell and Molecular Graduate Student Advisory Committee at the University of Utah for 1 year.

  Graduate Student

  Ph.D. Program

  University of Utah

  Salt Lake City

  UT

  Co-Lecturer BIOL 7160 \t\t\t\t\t\t\tSpring 2008\n•\tGraduate Level Microbiology: Special Topics. Co-Lecturer and course organizer. Professor: S. Parkinson

  Ph.D. Enrollment: 10 students.\n\nGuest Lecturer BIOL 3370 \t\t\t\t\t\tSpring 2008 and Spring 2007\n•\tMicrobial Biology undergraduate course. Guest lecturer for one lecture in 2008 and two lectures in 2007. Professor: S. Williams

  Ph.D. Enrollment: 50 students. \n\nTeaching Assistant BIOL 3370 \t\t\t\t\t\tSpring 2004 – 2006\n•\tMicrobial Biology undergraduate course. Duties included developing two lecture topics

  co-writing exams and grading. Professor: S. Williams

  Ph.D. Enrollment: 50-100 students.\n\nTeaching Assistant BIOL 5275 \t\t\t\t\t\tFall 2005\n•\tMicrobial Diversity

  Genomics

  and Evolution undergraduate lab course. Duties included assisting students with lab equipment

  developing experiments

  and grading. Professor: C. Dale

  Ph.D. Enrollment: 25 students.\n\nTeaching Assistant BIOL 5255 \t\t\t\t\t\tFall 2004\n•\tProkaryotic Genetics undergraduate lab course. Duties included assisting students with lab equipment

  experiments

  and grading. Professor: S. Parkinson

  Ph.D.\nEnrollment: 25 students.

  Teaching Experience

  University of Utah College of Science

  La Jolla

  CA

  Division of Biological Sciences

  Laboratory of Kit Pogliano

  Ph.D.\n•\tContinuation of postdoctoral project on microbial interspecies interactions and the mechanism of action of several antibiotics produced by Bacillus subtilis.

  Staff Research Associate IV

  UC San Diego

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  UC San Diego

  La Jolla

  CA

  Laboratory of Kit Pogliano

  PhD\n•\tCharacterized the role of SpoIID in peptidoglycan degradation during B. subtilis sporulation. \no\tDiscovered using membrane & DNA-intercalating fluorescent dyes along with deconvolution fluorescent microscopy that SpoIID is targeted to the sporulation septum

  where it interacts with SpoIIP & SpoIIM.\no\tChanged conserved amino acids in SpoIID to alanine. Characterized mutant strains via deconvolution fluorescent microscopy.\n•\tFound mutations that eliminated peptidoglycan degradation activity & showed increased septal localization

  reduced peptidoglycan degradation activity & caused uneven engulfment

  & destabilized the protein.\no\tResults were published in Journal of Bacteriology.\t\n•\tInvestigated outcomes of interaction between Bacillus subtilis & Gram Negatives isolated from soil samples with a side-by-side assay on different media types.\no\tDefined 3 morphologically distinct outcomes of interaction: coexistence

  lysis of neighboring colonies

  & colony invasion. Selected representative Gram-negative bacteria showing each of these outcomes.\no\tUsed a candidate gene approach to identify secreted molecules that are required for the total loss of viability in the Gram-negative species. \no\tVisualized side-by-side interactions of fluorescently labeled species using Leica fluorescent Stereomicroscope.\no\tMade crude extracts from the undomesticated B. subtilis (wild-type 3610) along with the secondary metabolites mutant strains (sfp

  srfA

  pks

  ppsB

  albA). Determined the minimum inhibitory dilution (MID) of crude extracts against E. coli lptD4213 using bacterial cytological profiling (BCP)

  which utilized fluorescent microscopy.\no\tCollaborated with a chemist (Gerry Newton) to purify secondary metabolites from crude extracts.\no\tDetermined mechanism of action of purified secondary metabolites using BCP.\no\tResults were published in The Journal of Antibiotics\n•\tWork was supported by an NIH post-doctoral fellowship

  Postdoctoral Fellow

  La Jolla

  CA

  BIMM 120 Lecturer Fall 2013\n•\tOrganized

  created lectures

  and taught core course in Bacteriology. Enrollment: 400 students.

  Lecturer

  UC San Diego

  AWIS

  University of Utah Biology Graduate Student Recruitment Award

  National Institute of Health Genetics Training Grant

  2006 – 2007 \tNational Institute of Health Genetics Training Grant

  National Institute of Health NRSA Postdoctoral Fellowship

  2009 – 2012 \tNational Institute of Health NRSA Postdoctoral Fellowship.

  UC San Diego Extension Back to Work Continuing Education Award

  2015\tUniversity of California San Diego Extension Back to Work Continuing Education Award. Was selected by the Association for Women in Science (AWIS) San Diego Chapter’s Back to Work Initiative. Award amount: $1000.

  University of Utah Continuing Biology Student Scholarship

  2002- 2003 University of Utah Continuing Biology Student Scholarship

  University of Utah

  Doctor of Philosophy (PhD)

  Thesis: The role of chromosome compaction in phase determination of circadian gene expression rhythms in the cyanobacterium Synechococcus elongatus.

  Biology

  Microbiology

  Bachelor's degree

  Biology

  General

  University of Utah

• 2003

  University of Utah

  PharmaScouts

  Inc.

  Salt Lake City

  UT

  •\tAided in establishing this laboratory at the University of Utah.\n•\tEstablished and implemented Standard Operating Procedures to streamline lab processes. 
\n•\tOrdered and controlled inventory of general lab supplies. 
\n•\tResearched and assesses lab equipment to be purchased. 
\n•\tBuilt and maintained relationships with vendors to find ideal lab products; negotiated prices with vendors. 
\n•\tFacilitated repairs of lab equipment as needed.\n•\tTroubleshot the growth of cyanobacteria after they were shipped from Texas A&M (had to fine tune the growth media to get them to survive in Utah).\n•\tPerformed experiments to study circadian rhythms in cyanobacteria (Synechococcus elongatus).\no\tUsed bioluminescence and known clock gene promoters

  such as PkaiB::luc+ to follow circadian regulated gene expression in various clock gene mutant strains.

  Laboratory Technician

  University of Utah

• Cell Culture

  PCR

  Recruiting

  Western Blotting

  University Teaching

  Biochemistry

  Microbiology

  Standard Molecular Biology

  Scientific Writing

  Life Sciences

  Molecular Cloning

  Fluorescence Microscopy

  Molecular Biology

  Bacterial Genetics

  Science

  Executive Search

  Cell Biology

  Fluorescence

  Genetics

  Molecular Microbiology

  Circadian rhythms in gene transcription imparted by chromosome compaction in the cyanobacterium Synechococcus elongatus

  Smith R.M. and Williams. S.B.

  Circadian rhythms in gene transcription imparted by chromosome compaction in the cyanobacterium Synechococcus elongatus

  Gutierrez J

  . Smith R.

  and Pogliano K.

  SpoIID-mediated peptidoglycan degradation is required throughout engulfment during Bacillus subtilis sporultation

  Smith R.M. and Williams

  S.B. \nIn J.L. Ditty

  S.R. Mackey

  & C.H. Johnson (Eds.) Bacterial Circadian Programs. Berlin: Springer-Verlag (invited review).

  Chromosome compaction: output and phase (book chapter in Bacterial Circadian Programs)

  Pennebaker K.

  Mackey K.R.

  Smith

  R.M

  Williams S.B.

  and Zehr J.P.

  Diel cycling of DNA staining and nifH gene regulation in the unicellular cyanobacterium Crocosphaera watsonii strain WH 8501

  Yang

  J.Y.

  Phelan

  R.S.

  Simkovsky

  R.

  Watrous

  J.D.

  Trial

  R.M.

  Fleming

  T.C.

  Wenter

  R.

  Moore

  B.S.

  Golden

  S.S.

  Pogliano

  K.

  and Dorrestein

  P.C. \nJournal of Bacteriology 2012 194(22): 6023-8.

  A primer on agar-based microbial imaging mass spectrometry.

  Poochit Nonejuie*

  Rachelle M Trial*

  Gerald L Newton

  Anne Lamsa

  Varahenage Ranmali Perera

  Julieta Aguilar

  Wei-Ting Liu

  Pieter C Dorrestein

  Joe Pogliano and Kit Pogliano\n*Indicates shared first author\n\n

  Application of bacterial cytological profiling to crude natural product extracts reveals the antibacterial arsenal of Bacillus subtilis

  Rachelle

  UC San Diego