Loren Axel Honaas
Work:
Department of Biology
The Pennsylvania State University
405 Life Sciences Building
University Park, PA 16802 USA
Work contact:
(814) 863-6413
lah338@psu.edu
Home:
Dr. Loren Honaas
2111 West College Avenue
State College, PA 16801
Home contact:
(814) 441-9592
lorenhonaas@gmail.com
Objective: N/A
Education:
Ph.D. The Pennsylvania State University (2013)
Plant Biology
B.S. Southeast Missouri State University (2003)
Major: Biology – emphasis on cell biology, molecular biology and microbiology
Minor: Chemistry
Current Position:
May 2013 – current: Postdoctoral Scholar - Department of Biology
Advisor: Dr. Claude dePamphilis
Previous Teaching assistantships/Guest Lectures:
Guest Lectures:
Symbiosis and Modified Organs in BIOL407 - March 2013
Teaching Assistantships, Penn State Biology Department:
Spring 2012: BIOL407- 3 sections
Spring 2011: BIOL407- 3 sections
Spring 2010: BIOL407- 2 sections
Duties:
Co-direct all lab activities
Write, administer and grade lab quizzes
Proctor and grade exams
Fill in and/or guest lecturing presenting original content
Spring 2009: BIO240W- 2 sections
Spring 2008: BIO240W- 2 sections
Fall 2007: BIO230W- 2 sections
Fall 2006: BIO230W- 1 section
Duties:
Prepare lectures with-in boundaries of course outline
Direct all lab/recitation activities
Prepare quizzes
Grade quizzes, 2 formal lab reports, all smaller writing assignments
Proctor exams
Hold 2 hour recitation/lab and office hours (2hrs) each week for each section of ~22
students
Previous positions:
June 2008-May 2013: Ph.D. Candidate - Penn State, The Huck Institutes of the Life
Sciences/Biology Department
PI: Dr. Claude dePamphilis
Duties:
Perform thesis research
Skills gained/refined:
WetBench:
RNA isolation/purification, mRNA purification, total RNA rRNA depletion, cDNA
synthesis, in vitro transcription, metal ion and nebulization fragmentation of nucleic
acids, 454 platform library preparation, Illumina platform library preparation, T7 based
linear mRNA amplification, quantitative Real Time PCR, sterile plant tissue culture,
Agrobacterium rhizogenes mediated transformation of Aristolochia fimbriata, sterile and
soil based co-culture of the parasitic plant Triphysaria versicolor with hosts Medicago
truncatula, Zea mays and Arabidopsis thaliana, fresh tissue cryo-sectioning, Laser
Pressure Catapult Micro-dissection (LPCM), Agilent Bioanalyzer, Qubit fluorometry,
and Nanodrop Spectroscopy based qualitative and quantitative assessment of total RNA,
mRNA, rRNA depleted RNA, cDNA, cRNA, 454FLX and Illumina PE mRNA-Seq
library cDNA
DryBench (bioinformatics):
Use of online tools for sequence database query (candidate and batch based), construction
and query of local BLAST databases, next generation sequence data read alignment using
BowTie II, Excel based manipulation of de novo transcriptome assembly outputs
including: annotations, read mapping results, and assembly statistics, use of R (custom
and borrowed scripts) to visualize and analyze de novo transcriptome and genomic
assembly outputs, use of R for statistical analysis of de novo transcriptome assembly
outputs, use of PERL for text file manipulation
Software:
MSDOS- and Linux-based OS, Microsoft Office Suite (esp. Word, PowerPoint and
Excel) Endnote, Adobe Acrobat, Inkscape, PERL, MEGAN, Image J, R, BowTie II,
various text editors, various web browsers, Geneious and various other DNA and Protein
analysis, alignment and assembly softwares, Unix/Linux commands, tree manipulation
with FigTree, various file transfer applications, Array Star (microarray data analysis),
various qRT-PCR data analysis applications (BioRad, ABI), image acquisition software
associated with epifluoresence, stereomicroscopy, time lapse and agarose gel imaging,
PALM RoboSoftware (Zeiss, LPCM), familiarity with other laser assisted microdissection associated applications (Leica, MMI), various LIMS, various file sharing
applications, various email clients, various other open source applications useful in
bioinformatics
August 2007-May 2008: Graduate Student - Penn State in The Huck Institutes of the Life
Sciences
PI: Dr. Richard Cyr
Duties:
Perform thesis research
Skills gained:
Epi-fluorescence time-course imaging, tobacco BY-2 tissue culture and transformation,
transformation vector design
August 2006- August 2007: Graduate Student - Penn State in The Huck Institutes of the
Life Sciences
PI: Dr. Sarah Assmann
Duties:
Perform thesis research
Skills gained:
Bright-field, epi-fluorescence and confocal imaging, plant electrophysiology, biolistic
transformation, basic quantitative image analysis
March 2004 – August 2005: Laboratory Technician, Donald Danforth Plant Science
Center
Supervisors: Drs. Christopher Taylor and Ulrich Hammes
Duties:
Maintain axenic root-knot nematode (Meloidogyne incognita) populations
Create, maintain propagate and screen promoter::scorable marker, protein fusion, and
knockout A. thaliana lines
Skills gained:
Plant Tissue Culture, PCR, dye terminator sequencing sample prep and analysis, cloning,
real-time PCR, A. thaliana transformation and GUS histochemical assays
1999-2003: Volunteer, Southeast Missouri State University Biology Department
Supervisors: Drs. Walter Lilly and Allen Gathman
Duties:
Maintinence of Schizophyllum commune lines
Generate Expressed Sequence Tags (ESTs)
Skills gained:
Isolation, purification and quantification of nucleic acids, fungal tissue culture, bacterial
transformation, gel electrophoresis, and DNA sequence analysis.
2000-2002: Student worker Southeast Missouri State University Biology Dept.
Supervisor: Dr. Joe Bidwell
Duties:
Set-up and maintenance of a Xenopus laevis colony
Skills gained:
Design and set-up of a system for care of laboratory animals
2000-2003: Student worker Southeast Missouri State University Biology Dept.
Supervisor: Dr. Maija Bluma
Duties: Preparation of materials for the microbiology teaching lab
General maintenance of microbiology teaching lab equipment
Disposal of biological waste
Skills gained:
Preparation of media, preparation of reagents
2002-2003: Student worker Southeast Missouri State University Biology Dept.
Supervisors: Drs. Walter Lilly and Allen Gathman
Duties:
Maintenance of Schizophyllum commune lines
Preparation of lab materials
General lab maintenance
Skills gained:
Preparation of media, preparation of reagents, fungal tissue culture
Summer 2003: Summer NSF REU intern, Donald Danforth Plant Science Center
Supervisor: Dr. Christopher Taylor
Project: Identification of essential root induction loci in Agrobacterium rhizogenes using
RNAi constructs against root induction loci
Skills gained:
Agrobacterium rhizogenes mediated soybean cotyledon and A. thaliana transformation,
GUS histochemical assays, PCR, nucleic acid isolation/purification, flavonoid
isolation/purification, basic fluorescence microscopy
Posters:
Collier R, Lutke WK, Honaas LA, Taylor CG (2003) Identification of Agrobacterium
rhizogenes genes essential for root induction in dicotyledonous plants. 24th Crown Gall
Meeting, Cornell University, Ithaca, New York. P. 19.
Honaas L, Wickett N, Wafula E, Zhang Y, Altman NS, Bao Y, McCombie WR, Schuster
SC, Taylor CG, Yoder JI, Landherr L, Wu B, dePamphilis CW (2009) Tissue specific
transcriptome studies in the parasitic plant Triphysaria versicolor using Next Generation
Sequencing technology. International Plant and Animal Genome Conference, San Diego,
CA January 9-13, 2010.
Honaas L, Wickett N, Wafula E, Zhang Y, Altman NS, Bao Y, McCombie WR, Schuster
SC, Taylor CG, Yoder JI, Landherr L, Wu B, dePamphilis CW (2010) Gene Discovery in
the Orobanchaceae. The Graduate Exhibition at Penn State, University Park, PA March
28th 2010.
Honaas L, Wickett N, Wafula E, Zhang Y, Altman NS, Bao Y, McCombie WR, Schuster
SC, Taylor CG, Yoder JI, Landherr L, Wu B, dePamphilis CW (2011) Functional Genomics
of a Generalist Parasitic Plant. 18th Plant Biology Symposium at Penn State, University
Park, PA May 18-21 2011.
Honaas L, Wickett N, Wafula E, Zhang Y, Altman NS, Bao Y, McCombie WR, Schuster
SC, Taylor CG, Yoder JI, Landherr L, Wu B, dePamphilis CW (2011) Functional Genomics
of a Generalist Parasitic Plant. 11th World Congress on Parasitic Plants, Martina Franca
Italy, June 8th 2011.
Honaas L, Wickett N, Wafula E, Zhang Y, Altman NS, Bao Y, McCombie WR, Schuster
SC, Taylor CG, Yoder JI, Landherr L, Wu B, dePamphilis CW (2011) Functional Genomics
of a Generalist Parasitic Plant. XVIII International Botanical Congress, Melbourne
Australia, 23-30 July 2011.
Honaas L, Wafula E, Der J, Wickett N, Zhang Y, Edgar P, Pires C, Altman N, dePamphilis
C (2013) Reference-based comparison of de novo transcriptome assembly tools. 6th Annual
Postdoc Research Exhibition at Pen State, University Park, PA Sep 12th 2013.
Honaas L, Wickett N, Wafula E, Zhang Y, Altman NS, Bao Y, McCombie WR, Schuster
SC,Taylor CG, Yoder JI, Landherr L, Wu B, dePamphilis CW (2013) Functional
Genomics of a Generalist Parasitic Plant. 4th Bioinformatics and Genomics Retreat
University Park, PA Oct 5th 2013.
Honaas L, Wafula EK, Ralph P, Zhang Y, Yang Z, Clermont K, Sheaffer L, Wickett N,
Huang K, Bao Y, Fernandez-Aparicio M, Das M, Bandaranayake P, Wu B, Collakova E,
Heath L, Timko M, Yoder J, dePamphilis CW, Westwood JH (2013) Evolutionary Gain
and Loss of Function in Parasitic Plant Genomes. The Plant & Animal Genome XXII
Conference San Diego, CA Jan 11-15 2014.
Presentations:
Guettler S, Lucchese S, Honaas L, (2001) Expressed sequence tags from Schizophyllum
commune grown under different nitrogen conditions. 9th annual Southeast Missouri State
University Student Research Conference, Cape Girardeau, MO April 10th-11th, 2001.
Honaas L & Wickett N (2009) The Parasitic Plant Genome Project: New insight into
parasitic weed biology and evolution. International Plant and Animal Genome Conference,
San Diego, CA January 10-14, 2009.
Honaas L (2009) Tissue specific transcriptome studies in the parasitic plant Triphysaria
versicolor. Plant Biology Seminar Series, Penn State, University Park PA Oct. 26th 2009
Honaas L (2010) The Front Line: Transcriptome Analysis at the Host-Parasite Interface.
Plant Biology Seminar Series, Penn State, University Park PA Oct. 4th 2010
Honaas L (2011) Functional Genomics of a Generalist Parasitic Plant. 11th World
Congress on Parasitic Plants, Martina Franca Italy, June 8th 2011
Honaas L (2011) Laser Pressure Catapult Micro-dissection. Laser Pressure Catapult Microdissection Work Shop, Virgina Tech, Blacksburg VA May 14th 2011.
Honaas L (2012) The Parasitic Plant Genome Project. Botany 2012: The Next Generation,
Columbus, Ohio, July 8th 2012.
Honaas L (2013) The Parasitic Plant Genome Project. IEB Seminar Series Westfälische
Wilhelms-Universität, Münster Germany, May 21st 2013.
Honaas L (2013) The Parasitic Plant Genome Project. MONOCOTS V: 5th International
Conference on Comparative Biology of Monocotyledons New York, NY July 12th 2013.
Honaas L (2013) Genome Scale Analysis of Laser Micro-Dissected Tissues Sheds Light on
Parasitic Plant-Host Plant Interactions. 13th World Congress on Parasitic Plants, Sheffield,
UK, July 16th 2013.
Publications:
Guettler S, Jackson EN, Lucchese SA, Honaas L, Green A, Hittinger CT, Tian Y, Lilly
WW, Gathman AC (2003) ESTs from the basidiomycete Schizophyllum commune grown on
nitrogen-replete and nitrogen limited media. Fungal Genet Biol. 39(2):191-8.
Hammes UZ, Nielsen E, Honaas LA, Taylor CG, Schachtman DP (2006) AtCAT6, a sinktissue-localized transporter for essential amino acids in Arabidopsis. The Plant Journal
(2006) 48, 414–426.
Wickett N, Honaas LA, Wafula E, Das M, Huang K, Wu B, Landherr L, Timko M, Yoder
J, Westwood J, dePamphilis C (2011) Transcriptomes of the Parasitic Plant Family
Orobanchaceae Reveal Surprising Conservation of Chlorophyll Synthesis. Current Biology
21, 2098–2104.
Westwood JH, dePamphilis CW, Das M, Fernández-Aparicio M, Honaas LA, Timko MP,
Wafula EK, Wickett NJ, Yoder JI (2012) The Parasitic Plant Genome Project: New Tools
for Understanding the Biology of Orobanche and Striga. Weed Science 60, 295-306.
Fernández-Aparicio M, Huang K, Wafula EK, Honaas LA, Wickett NJ, Timko MP,
dePamphilis CW, Yoder JI, Westwood JH (2012) Application of qRT-PCR and RNA-Seq
analysis for the identification of housekeeping genes useful for normalization of gene
expression values during Striga hermonthica development. Molecular Biology Reports.
Honaas LA, Wafula EK, Yang Z, Der JP, Wickett NJ, Altman NS, Taylor CG, Timko MP,
Westwood JH, dePamphilis CW (2013) Functional genomics of a generalist parasitic plant:
Laser microdissection of host-parasite interface reveals host-specific patterns of parasite
gene expression. BMC Plant Biology 13:9.
Zhang Y, Fernández-Aparicio M, Wafula EK, Das M, Jiao Y, Wickett NJ, Honaas LA,
Ralph PE, Wojciechowski MF, Timko MP, Yoder JI, Westwood JH, dePamphilis CW
(2013) Evolution of a horizontally acquired legume gene, albumin 1, in the parasitic plant
Phelipanche aegyptiaca and related species. BMC Evolutionary Biology 13:48.
Other print media:
Wickett, N., Honaas LA, Wafula EK, Timko MP, Yoder JI, Westwood JH, dePamphilis
CW, Exploring the causes and consequences of parasitism through stage specific
transcriptome sequencing in the parasitic plant family Orobanchaceae (2010) Conference
proceedings, Published
Bibliography: Botanical Society of America. Providence, RI
Awards/Honors:
Elected to membership of βββ Biological Honors Society, Iota Sigma chapter 2002
IBIOS 1st year Ph.D. Fellowship 2005-2006 ~ $33,000
Plant Physiology RA Fellowship Fall 2009 ~ $8000
Braddock Research Award 2010 -$1200
J. Ben and Helen Hill Memorial Fund Award 2011 - $600
Botanical Society of America - International Botanical Congress Travel Award 2011 $2000
Institute of Molecular Evolution and Genomics Travel Award 2011 - $300
European Weed Research Society Travel Award 2011 - €400
Intercollege Graduate Degree Program in Plant Biology Travel Award 2011- $450
Eva J. Pell Endowed Graduate Student Scholarship 2013 - $2500
Penn State PostDoc Society Travel Award 2013 - $250
Outreach:
Action Potential Summer Program July 2006
Capacity: Instructor “Magical Life in the Muggle World”
Duties: Responsible for leading all activities associated with “Magical Life in the Muggle
World” module (campers grade 7-9), direct undergraduate volunteers as helpers and manage
groups of kids and volunteers numbering 12-15
Bio-Days April 2006 and April 2007
Capacity: volunteer
Duties:
2006- Conduct demonstrations at the Plant Biology station
2007- Conduct demonstrations at the DNA station
Science U: iLove Science Camp February 2010
Capacity: Mentor for iLove Sience camp, 7th and 8th grade campers
Duties: Oversee activities done in a lab setting with special attention to lab safety and
proper use of Personal Protective Equipment.
Guest Presentation at Corl St. Elementary School, State College, PA February 2012
Capacity: Guest Speaker to the 5th grade class
Duties: Short presentation followed by hands on activities to inform students about the use
of microscopes in plant research.
78th Annual Pennsylvania Junior Academy of Science (PJAS) Competition May 2012
Capacity: Judge
Duties: Score student presentations, participate in brief question sessions following each
presentation, confer with other session judges for final scoring and nominate select
presentations (based on merit) for special awards.
Haunted-U Halloween Boot Camp October 2012
Capacity: Group Mentor 4th-6th grade
Duties: Oversee activities done in a lab setting with special attention to lab safety and
proper use of Personal Protective Equipment.
Upward Bound July 2013
Capacity: Instructor
Duties: Design, write, and implement a curriculum for a short course focused on plant
anatomy and technology used to study plant anatomy. Organize guests and field trips to
various places on campus. Direct an undergraduate assistant.