Alumni Symposium

Alumni Symposium

Alumni Symposium

In early September the NIH Biotechnology Training Program held its first Alumni Symposium to celebrate the past, present, and future of the program. The NIH – BTP is among the largest of its kind nationally and has trained more than 140 PhD students over its 25 year history at the U of M. September’s symposium included seminar presentations from 8 alumni of the program, a ‘Careers in Biotechnology’ Q & A panel with an additional 6 alumni, and a poster session that showcased the research of current trainees. The symposium was a great success for the 100+ in attendance, with engaging science and career talks, plenty of opportunities for networking, and optimism for the future of the program. A big thanks to all who made it possible!

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Symposium Program 

 

Opening Remarks

Mike Sadowsky PhD, UMN Director of BioTechnology Institute
Wei-Shou Hu PhD, UMN Professor of Chemical Engineering and Materials Science
Claudia Schmidt-Dannert PhD, UMN Professor of Biochemistry, Molecular Biology, and Biophysics

Science and Careers Session 1

Ross Carlson PhD, Montana State University (UMN ‘03) Professor of Chemical and Biological Engineering  
Nathan Lindquist PhD, Bethel University (UMN ‘10) Associate Professor of Physics
Emilie Rexeisen PhD, 3M Company (UMN ‘10) Senior Product Development Engineer
Chad Satori PhD, Medtronic (UMN ‘13) Senior Chemist

Careers in Biotechnology Q & A Panel

Susan Abu-Absi PhD, Bristol Myers Squibb (UMN ‘01) Director of Manufacturing Sciences and Technology
Jessica Eichmiller PhD, Alexandria Technical and Community College (UMN ‘12) Biology Instructor
Erin Marasco PhD, Cargill (UMN ‘08) Principal Scientist in Biotechnology
Betsy Martinez-Vaz PhD, Hamline University (UMN ‘01) Associate Professor and Co-Director of Biochemistry Aaron Wlaschin PhD, General Mills, Inc. (UMN ‘06) Senior Engineer II
Katie Wlaschin PhD, 3M Company (UMN ‘07) Advanced Research Specialist
David Umulis PhD, Purdue University (UMN ‘07) Associate Professor of Agricultural & Biological Engineering

Science and Careers Session 2

Derek Adams PhD, Evelo Biosciences (UMN ‘00) Senior Vice President, CMC
Benjamin Kidder PhD, Wayne State University (UMN ‘07) Assistant Professor of Oncology
Briana Kozlowicz PhD, Cargill (UMN ‘05) Senior Molecular Biotechnologist
James Wollack PhD, St Catherine University (UMN ‘03) Associate Professor of Chemistry

Student Poster Session

Alumni Network
Training Grant Symposium
Training Grant Symposium

Trainees

Trainees

Joe Buchman

Chemistry
jbuchman@umn.edu

Ben Hanson

Biochemistry, Molecular Biology, and Biophysics
Hans5090@umn.edu

Anh La

Biomedical Engineering
laxxx029@umn.edu

Rebecca Maysonet

Biochemistry, Molecular Biology, and Biophysics
Mayso004@umn.edu

Brian Mikolajczyk

Chemical Engineering and Materials Science
Mikol010@umn.edu

Sofie O’Brien

Biomedical Engineering
Bluvs002@umn.edu

Jennifer One

Biochemistry, Molecular Biology, and Biophysics
Onexx001@umn.edu

Kevin Ortiz-Rivera

Biomedical Engineering
Ortiz209@umn.edu

Seth Ritter

Chemical Engineering and Materials Science
Ritte120@umn.edu

Allison Siehr

Biomedical Engineering
siehr003@umn.edu

Molly Kupfer

Biomedical Engineering
kupfe018@umn.edu

Jeannette Caronia

Biomedical Engineering
caron100@umn.edu

Adeline Espinasse

Chemistry
espin109@umn.edu

 

Meghan McCann

Chemical Engineering and Materials Science
mccan234@umn.edu

Michael Maher

College of Biological Sciences
mmaher@umn.edu

Jason Jones

Biochemistry, Molecular Biology, and Biophysics
jone2616@umn.edu

Kelly Wallin

Biochemistry, Molecular Biology, and Biophysics
Walli241@umn.edu

Natalie Smith-Hudson

Chemistry
hudso283@umn.edu

Tim Horn

Biochemistry, Molecular Biology, and Biophysics
horn0399@umn.edu

Former Trainees

1995

David Mills

Bryce Pierson

Kristi Swope

1996

Paul August

Barbara Bensing

J. Nanette Paul

1997

Ronald Davies

David Reeder

Paul Sheldon

Ryan Taber

Florence Wu

1998

JJ Hahn

Daniel Jackson

Timothy Leaf

John McLaughlin

Frank Volkers

1999

Eric Eckwall

Paul Hermes

Scott Frykman

Shane Cain

Steven Wendell

Tammy Turek

2000

Claire Hypolite

Derek Adams

Jason Patzlaff

Julie Friend

Olav Lyngberg

2001

Susan Abu-Absi

Kevin Dolbeare

Aileen Green

Edmund Kao

Aaron Kelley

Betsy M. Martinez-Zayas

Barbara May

Jennifer Seffernick

Emmanouhl Tzanakakis

Michael Valley

Michelle Wagner

2002

Nicholas Abu-Absi

Jerry Johnson

Michael Paustian

Jessica West

2003

Adrian Anderson

Ross Carlson

Stephanie Groce

Simon Shannon

Brian Trammel

2004

Marcela De Leon Gatti

Lisa Herron-Olson

Robert Schwartz

2005

Jason Belter

James Kacmar

Briana Kozlowicz

Erik Pederson

Jack Staddon

2006

Kenneth Finley

Jeffrey (Clem) Fortman

Heather Haemig (Hrodey)

Patrick Hossler

Kevin Watts

Andrew Wilber

Aaron Wlaschin

2007

Charles Cameron

Benjamin Kiddler

Bobby Poe

Howard Salis

David Umulis

Katie Wlaschin

2008

Janelle Cockrell

Anthony Dodge

Jimmy Gosse

Allison Langham

Erin Marasco

2009

Matthew Hamilton

Anne Kantardijeff

Karen Olson

Jonathan Tomshine

James Wollack

2010

Daniel Coursolle

Amanda Degraw

Johnathan Gorke

Bree Hamman

Nathan Lindquist

Emilie Rexesien (Grzywa)

2011

Kelly Bouchonville

Janice Frias

Tyler Price

Tyler Yin

2012

Christina Brakken-Thal

Laura (Case) Cook

Daisy Cross

Jessica Eichmiller

Rachel Hillmer

Margaret Linak

Josh Ochocki

Jason Owens

Janet Rollefson Lawrence

2013

Richard Beck

Stephan Cameron

Sean Corum

Kevin DeRonne

John Haugner

Chris Kauffman

Joel Kooren

Chad Satori

Ilya Tikh

Katherine Volzing

Brett Waybrant

Adam Woodruff

2014

Nick Baltes

Sarah Bloch (Spainhour)

Timothy Johnson

Nicholas Kotloski

David Panus

Patrick Smadbeck

2015

Veronica Diaz-Rodriguez

Ian Gunsolus

Jeremiah Riesberg

2016

Sarah Gruba

Current Graduate Student

Brittany Bennett

Rebecca Breuer

Clairessa Brown

Joseph Buchman

David Chau

James Christenson

Heather Grundhofer

Amy Hauck

Sarah Hunt

Bryan Jones

Anh La

Amani Lee

Maria McClintock

Brian Mikolajczyk

Daniel Mohr

Lauren Otto

Carolyn Scott

Scott Simpkins

Lawrence Stern

Andrew Urick

Other Distinctions

Other Distinctions

Patents

Oh, San-hyun and Johnson, Timothy W. (2014) Method of forming individual metallic microstructuresPCT/US2013/030804

Baltes, Nicholas, Atkins, Paul, and Voytas, Daniel F. (2013) CRISPR/Cas reagents for the targeted modification of plant genomes. Notice of allowance issued.

Baltes, Nicholas, and Voytas, Daniel F. (2013) Conferring resistance to geminiviruses in plants using CRISPR/Cas

DiCosimo, R. Payne, M.S. Yin, T. (2012) Perhydrolases for enzymatic peracid generation, US Patent 8,334,120.

Baltes, Nicholas, and Voytas, Daniel F. (2012) Gene targeting in plants using DNA viruses.

 

Other Distinctions

James Christenson was the sole recipient of the Founder’s Award travel grant by the U.S. Enzyme Mechanism research community for 2017. There is only one award given each year to a graduate student or postdoc. In addition to a monetary award, he has been invited to present at the Enzyme Mechanisms Conference in January. James was an NIH BioTechnology Training Grant recipient and has been supported by MnDRIVE funds. He completed his research internship at BASF in Germany.

James was awarded for his research on bacteria biosynthesis of hydrocarbons, which has uncovered how microbes produce beta-lactone natural products. Beta-lactones are an emerging class of anti-obesity drugs, anti-cancer drugs, and next-generation antibiotics. James is a research associate in the Wackett and Wilmont labs.

John Haugner, received the Ross A. Gortner Award in 2015 and the University of Minnesota’s Graduate School Doctoral Dissertation Fellowship and Frederick J. Bollum Award in 2014. His research was published in Nature Chemical Biology and become a most read paper in the journal. John’s work enabled us to solve the 3D structure of an artificial enzyme created by in vitro evolution. This entirely new structure is highly dynamic and demonstrates that a small fold with suitable flexibility is sufficient to carry out enzymatic function, thereby challenging common views of how enzymes are supposed to look.

Sarah Hunt recently received an NIH Predoctoral Fellowship (F31 DK097947, “A theory of filtration and transport within the mesangium”).

Lauren Otto received an NSF Graduate Research Fellowship award after one year of being supported by this training program.

Rachel Hillmer received a Doctoral Dissertation Fellowship from the University for the 2014- 2015 academic year.

Sofie OBrien won first place for her poster “A Systems Analysis of Dual Signaling Control of Conjugative Drug Resistance Transfer in Enterococcus faecalis” in the Cellular and Molecular Bioengineering category at the Institute for Engineering in Medicine (IEM) conference on September 21, 2015.

Rebecca Maysonet was selected for the Carl Storm Underrepresented Minority Fellowship to attend the Applied and Environmental Microbiology Gordon Research Conference over summer 2015.

Ian Gunsolus received the Torske Klubben Fellowship, Doctoral Dissertation Fellowship, and the Robert L. Ferm Outstanding Graduate Teaching Assistant Award.

Joe Buchman received an NSF Graduate Research Fellowship.

Sarah Gruba received a top 25 Poster Presentation Award Bioanalytical Sensors GRC 2014, Minnesota Chapter of ACS travel grant for Fall ACS ($500), ACS Analytical Chemistry 75th Anniversary poster competition ($500).

Brian Mikolajczyk was a member of the five-student team that recently won first place at the 2015 U of M Global Health Case Competition. The competition brought 14 teams together to propose a bid to the International Olympic Committee highlighting their cities’ ability to host the 2024 Summer Olympic Games.

Brittany Bennett received the Microbial and Plant Genomics Institute Travel Award, 2014 and 2015 and the MICaB Student Service Award, 2015.

Internships

Internships

In our survey of current and former trainees, many ranked the industrial internships as a key component of the training grant program. Many report that it prepared them for positions in industry and some credit the experience with the networking opportunities that helped them find career placement after graduation.

Our trainees have ample opportunities to interact with industrial contacts. Members of our training faculty have strong research collaborations throughout the public and private sector. About 30% of BTI seminars (which are attended by our trainees) feature industry speakers. Several trainees participate in the Annual Meeting of the Minnesota Biotechnology Association where they present posters. The University also hosts biotechnology workshops and short courses, which trainees are encouraged to attend. The relevance of our training to industry and the quality of our trainees, however, is best illustrated by the high demand for our graduates from industry.

Internship Testimonials

I was able to do an internship with BASF in Ludwigshafen, Germany for three months. There were so many experiences from this internship that have made me a better scientist. I learned first hand what science looks like at a large European firm. It also allowed me to experience working with a lab group with completely different educations and backgrounds.

James Christenson, PhD Candidate, University of Minnesota, Current trainee

 

My most significant experiences connected with the NIH training grant was the internship I did at Cargill. Working at a large biotech corporation was informative. In addition to learning new skills like growing and doing genetics research on yeast, I also made important professional connections. After this experience, I am further convinced that a future in the industrial biotech industry is for me.

Bryan Jones, PhD Candidate, University of Minnesota, Former trainee

 

The industrial internship was a turning point for me in graduate school. It changed my perspective on my career path–I now know that I want to work in industry. I have the NIH Training Grant to thank for that.

Rachel Hillmer, PhD Candidate, University of Minnesota, Former trainee

 

Here are some of the companies in which interns have been placed over the past few years

3M
Abbott4 Laboratories
ACERA, Inc.
Advanced Tissue Sciences
Amgen
Ariad Pharmaceuticals
Bayer Corp.
Bristol-Myers Squibb
Cargill
Dow AgroSciences LLC
Dow Chemical		 Dupont
Ecolab
General Mills
Merck & Co.
PanVera Corporation
Pfizer
R&D Systems
Schering-Plough
SmithKline Beecham
USDA
Waters, Inc.
Publications

Publications

Publications

A total of 79 trainees were appointed to the training grant since 2006. They have authored 250 publications, including 125 first author publications.

45 trainees have graduated with a PhD and authored 205 publications, including 106 first author publications (~4.6 publications per trainee). One trainee has no publication; he finished his PhD early to work in industry.

4 trainees finished with a MS degree: 3 of them left without publications: 1 switched to Physics MS, 1 left program for personal reasons, 1 left for health reasons (the only one appointed to the current grant), 1 trainee finished with an MS to accept a job as an engineer at Nocatech, she coauthored one publication.

30 trainees appointed during this current grant are still pursuing their PhD research and 1 trainee is on a medical leave. They have so far published 45 publications, including 19 first author publications. 16 trainees are new entrants, including 11 who are currently taking their qualifying exams.

Ian Gonsolus

Former trainee Ian Gunsolus was interviewed on Minnesota’s KARE 11 News about chemicals used in the production of lithium batteries and their impact on soil bacteria. Working in the lab of training grant faculty member Christy Haynes, Gonsulas helped identify nickel and cobalt as the components most harmful to soil microbes.

Brittany Bennett

Bennett, B.D.; Brutinel, E.D.; and Gralnick, J.A. (2015) A ferrous iron exporter mediates iron resistance in Shewanella oneidensis MR-1. Appl. Environ. Microbiol. 81, 7938. PMCID: PMC4616933

Joseph Buchman

Kim, D.; Finkenstaedt-Quinn, S.; Hurley, K.; Buchman, J.T.; & Haynes, C.L. (2014) On-chip Evaluation of Platelet Adhesion and Aggregation upon Exposure to Mesoporous Silica Nanoparticles, Analyst, 139, 906. doi: 10.1039/C3AN01679J

Raju, R.; Chau, D.; Verfaillie, C.M.; & Hu, W.-S. (2013) The road to regenerative liver therapies: the triumphs, trials and tribulations. Biotechnol. Adv. 31, 1085. PMID: 24055818

James Christenson

Christenson, J., Jensen; M.; Seffernick, J.L.; Goblirsch, B.; Richman, J.; Mohamed, F.; Wilmot, C.; Wackett, L.P. (2016)Demonstration of an OleBCD protein complex in bacterial long-chain olefin biosynthesis. J. Bacteriol. (resubmission)

Heather Grundhofer

Grundhofer, H.M.; Kuhns, M.M.; & Arriaga, E.A. High Resolution Interrogation of Biological Systems via Mass Cytometry. Proteomics for Biological Discovery, 2nd Edition. Yates, J., Veenstra, T., Eds.; Wiley & Sons, In press.

Amy Hauck

Hauck, A., Olson, D. H., Burrill, J.S., and Bernlohr, D.A. (2015) Adipose Carbonylation And Mitochondrial Dysfunction in Protein Carbonylation-Principles, Analysis and Biological Implications (Q. Ros, Ed) Wiley & Co.

Hauck, A.K. & Bernlohr, D.A. (2016) Oxidative Stress and Lipotoxicity. J. Lipid Research, In press

Rachel Hillmer

Hillmer RA, Tsuda K, Rallapalli G, Asai S, Truman W, Papke MD, Sakakibara H, Jones JDG, Myers CL, Katagiri F. The Highly Buffered Arabidopsis Immune Signaling Network Hides the True Function of its Components. Submitted.

Hatsugai N, Hillmer R, Yamaoka S, Hara-Nishimura I, Katagiri F. The μ Subunit of Arabidopsis Adaptor Protein-2 Is Involved in Effector-Triggered Immunity Mediated by Membrane-Localized Resistance Proteins. (2016) Mol Plant Microbe Interact. Molecular Plant-Microbe Interactions. In press.

Hillmer RA, Katagiri F. Toward predictive modeling of large and complex biological signaling networks. (2016) Physiol Mol Plant Pathol. In press.

Bethke G, Thao A, Xiong G, Li B, Soltis NE, Hatsugai N, Hillmer RA, Katagiri F, Kliebenstein DJ, Pauly M, Glazebrook J. (2016) Pectin Biosynthesis Is Critical for Cell Wall Integrity and Immunity in Arabidopsis thaliana. Plant Cell. 28(2):537–56.

Hillmer RA. Systems biology for biologists. (2015) PLoS Pathog. 11(5):e1004786.

Kim Y, Tsuda K, Igarashi D, Hillmer RA, Sakakibara H, Myers CL, Katagiri F. (2014) Mechanisms underlying robustness and tunability in a plant immune signaling network. Cell Host Microbe. 15(1):84–94.

 

Sarah Hunt

Hunt, S.E., Dorfman, K.D., Segal, Y., and V.H. Barocas, A Computational Model of Flow and Species Transport in the Mesangium, AJP Renal, 310(3):F222-F229, 2016.

Bryan Jones

Jun Huang, Bryan J. Jones, Romas J. Kazlauskas (2015) Stabilization of an α/β-hydrolase by introducing proline residues: salicylic binding protein 2 from tobacco. Biochemistry 54, 4330-41;

Bryan Jones, Romas Kazlauskas (2015) The road to L. Nat. Chem. 6, 11-12h

Alissa Rauwerdink, Mark Lunzer, Titu Devamani, Bryan Jones, Joanna Mooney, Zhi-Jun Zhang, Jian-He Xu, Romas J. Kazlauskas, Antony M. Dean (2016) Evolution of a catalytic mechanism. Mol. Biol. Evol. 33, 000-000

Titu Devamani, Alissa M. Rauwerdink, Mark Lunzer, Bryan J. Jones, Joanna L. Mooney, Zhi-Jun Zhang, Maxilmilian Alaric O. Tan, Jian-He Xu, Antony M. Dean, Romas J. Kazlauskas (2016) Catalytic promiscuity of ancestral esterases and hydroxynitrile lyases. J. Am. Chem. Soc. 138, 1046-56;

Molly Kupfer

Kupfer ME and Ogle BM. Advanced imaging approaches for regenerative medicine: Emerging technologies for monitoring stem cell fate in vitro and in vivo. Biotechnology Journal. 10(10):1515-28. 2015.

Rebecca Maysonet Sanchez

Kane, A.L., E.D. Brutinel, H. Joo, R. Maysonet Sanchez, C.M. VanDrisse, N.J. Kotloski and J.A. Gralnick. 2016. Formate metabolism in Shewanella oneidensis generates proton motive force and prevents growth without an electron acceptor. J Bacteriol. 198(8):1337-1346. PMID: 26883823

Maria McClintock

McClintock MK, Kaznessis YN, Hackel BJ. (2016) Enterocin A mutants identified by saturation mutagenesis enhance potency towards vancomycin-resistant Enterococci. Biotechnol Bioeng. 113(2):414-23.

Daniel Mohr

Yoo D, Nguyen NC, Martin-Moreno L, Mohr DA, Carretero-Palacios S, Shaver J, Peraire J, Ebbesen TW, Oh SH. High-Throughput Fabrication of Resonant Metamaterials with Ultrasmall Coaxial Apertures via Atomic Layer Lithography. Nano Lett. 2016 Mar 9;16(3):2040-6. doi: 10.1021/acs.nanolett.6b00024. Epub 2016 Feb 29. PubMed PMID: 26910363; PubMed Central PMCID: PMC4789754.

Otto LM, Mohr DA, Johnson TW, Oh SH, Lindquist NC. Polarization interferometryfor real-time spectroscopic plasmonic sensing. Nanoscale. 2015 Mar 7;7(9):4226-33. doi: 10.1039/c4nr06586g. PubMed PMID: 25672889; PubMed Central PMCID: PMC4339257.

Lauren Otto

Kumar S, Johnson TW, Wood CK, Qu T, Wittenberg NJ, Otto LM, Shaver J, Long NJ, Victora RH, Edel JB, Oh SH. Template-Stripped Multifunctional Wedge and Pyramid Arrays for Magnetic Nanofocusing and Optical Sensing. ACS Appl Mater Interfaces. 2016 Feb 29. [Epub ahead of print] PubMed PMID: 26837912.

Freedman KJ, Otto LM, Ivanov AP, Barik A, Oh SH, Edel JB. Nanopore sensing at ultra-low concentrations using single-molecule dielectrophoretic trapping. Nat Commun. 2016 Jan 6;7:10217. doi: 10.1038/ncomms10217. PubMed PMID: 26732171; PubMed Central PMCID: PMC4729827.

Otto LM, Mohr DA, Johnson TW, Oh SH, Lindquist NC. Polarization interferometry for real-time spectroscopic plasmonic sensing. Nanoscale. 2015 Mar 7;7(9):4226-33. doi: 10.1039/c4nr06586g. PubMed PMID: 25672889; PubMed Central PMCID: PMC4339257.

Jose J, Kress S, Barik A, Otto LM, Shaver J, Johnson TW, Lapin ZJ, Bharadwaj P, Novotny L, Oh SH. Individual Template-Stripped Conductive Gold Pyramids for Tip-Enhanced Dielectrophoresis. ACS Photonics. 2014 May 21;1(5):464-470. Epub 2014 Apr 16. PubMed PMID: 25541619; PubMed Central PMCID: PMC4270414.

Barik A, Otto LM, Yoo D, Jose J, Johnson TW, Oh SH. Dielectrophoresis-enhanced plasmonic sensing with gold nanohole arrays. Nano Lett. 2014;14(4):2006-12. doi: 10.1021/nl500149h. Epub 2014 Mar 27. PubMed PMID: 24646075; PubMed Central PMCID: PMC4083195.

Lindquist NC, Johnson TW, Jose J, Otto LM, Oh SH. Ultrasmooth metallic films with buried nanostructures for backside reflection-mode plasmonic biosensing. Ann Phys. 2012 Nov;524(11):687-696. PubMed PMID: 24159227; PubMed Central PMCID: PMC3804426.

Carolyn Scott

Lindborg, B.A., Brekke, J.H., Vegoe, A.L., Ulrich, C.B., Haider, K.T., Subramaniam, S., Venhuizen, S.L., Eide, C.R., Orchard, P.J., Chen, W., Wang, Q., Pelaez, F., Scott, C.M., Kokkoli, E., Keirstead, S.A., Dutton, J.R., Tolar, J., and O’Brien, T.D. (2016). Rapid Induction of Cerebral Organoids from Human Induced Pluripotent Stem Cells Using a Chemically Defined Hydrogel and Defined Cell Culture Medium. Stem Cells Trans. Med., In press.

Scott, C.M., Forster C.L., and Kokkoli, E. (2015). 3D Cell Entrapment as a Function of the Weight Percent of Peptide-Amphiphile Hydrogels. Langmuir, 31 (22):6122-6129.

Lindborg, B.A., Brekke, J.H., Scott, C.M., Chai, Y.W., Ulrich, C., Sandquist, L., Kokkoli, E., and O’Brien, T.D. (2015). A Novel Chitosan-Hyaluronan Based Hydrogel-Hydrocolloid Supports In Vitro Culture and Differentiation of Human Mesenchymal Stem/Stromal Cells (MSCs). Tissue Eng. Part A, 21 (11-12):1952-1962.

Levine, R.M., Scott, C.M., and Kokkoli, E. (2013). Peptide Functionalized Nanoparticles for Nonviral Gene Delivery. Soft Matter, 9 (4):985-1004.

Scott Simpkins

Piotrowski JS, Simpkins SW, Li SC, Deshpande R, McIlwain SJ, Ong IM, Myers CL, Boone C, Andersen RJ, 2015, Chemical genomic profiling via barcode sequencing to predict compound mode of action,Methods Mol Biol, 1263, 299-318.

Lawrence Stern

Stern, L.A., Case, B.A., and Hackel, B.J., Alternative non-antibody protein scaffolds for molecular imaging of cancer Curr. Opin. Chem. Engr. 2013 2, 425-432. (PMID: 24358455)

Andrew Urick

W. C. Isley III, A. K. Urick, W. C. K. Pomerantz C. J. Cramer, The Prediction of 19F NMR in Proteins Mol.Pharm. Manuscript submitted

C. T. Gee, K. E. Arntson, A.K. Urick, N. K. Mishra, W. C. K. Pomerantz. 2016, Protein-Observed 19F NMR for Fragment Screening, Affinity Quantification, and Druggability Assessment Nat. Protoc. Accepted

A. K. Urick, L. M. L. Hawk, M. K. Cassel, N.K. Mishra, S.Liu, N. Adhikari, W. Zhang, C. O. dos Santos, J.L. Hall, and W. C. K. Pomerantz 2015, Dual screening of BPTF and Brd4 using protein-observed fluorine NMR uncovers new bromodomain probe molecules. ACS Chem. Biol. 10, 2246-56

N. K. Mishra, A. K. Urick, S. W. Ember, E. Schonbrunn, W. C. Pomerantz 2014 Fluorinated aromatic amino acids are sensitive probes for bromodomain ligand interactions, ACS Chem. Biol. 9 2755-60

Nicholas Baltes

Baltes NJ, Hummel AW, Konecna E, Cegan R, Bruns AN, Bisaro DM, Voytas DF. (2015). Conferring resistance to geminiviruses with the CRISPR-Cas prokaryotic immune system. Nature Plants. 15145: 1-4.

Cermak T, Baltes NJ, Cegan R, Zhang Y, Voytas DF (2015). High-frequency, precise modification of the tomato genome. Genome Biology. 16:232.

Lowder LG, Zhang D, Baltes NJ, Paul JW 3rd, Tang X, Zheng X, Voytas DF, Hsieh TF, Zhang Y, Qi Y (2015). A CRISPR/Cas9 toolbox for multiplexed plant genome editing and transcriptional regulation.Plant Physiol. 169:971-85.

Baltes NJ, Voytas DF (2015). Enabling plant synthetic biology through genome engineering. Trends in Biotechnology. 33:120-31.

Ali Z, Abul-faraj A, Li L, Ghosh N, Piatek M, Mahjoub A, Aouida M, Piatek A, Baltes NJ, Voytas DF, Dinesh-Kumar S, Hahfouz MM (2015). Efficient virus-mediated genome editing in plants using the CRISPR/Cas9 system. Mol. Plant. 8:1288-91.

Qi Y, Starker CG, Zhang F, Baltes NJ, Voytas DF (2014). Tailor-made mutations in Arabidopsis using zinc finger nucleases. Methods Mol Biol. 1062:193-209.

Baltes NJ, Gil-Humanes J, Cermak T, Atkins PA, Voytas DF (2014). DNA replicons for plant genome engineering. Plant Cell. 26:151-63.

Qi Y, Li X, Zhang Y, Starker CG, Baltes NJ, Zhang F, Sander JD, Reyon D, Joung JK, Voytas DF (2013).Targeted deletion and inversion of tandemly arrayed genes in Arabidopsis thaliana using zinc finger nucleases. G3. 3:1707-15.

Curtin SJ, Anderson JE, Starker CG, Baltes NJ, Mani D, Voytas DF, Stupar RM (2013). Targeted mutagenesis for functional analysis of gene duplication in legumes. Methods Mol Biol. 1069:25-42.

Curtin SJ, Zhang F, Sander JD, Haun WJ, Starker C, Baltes NJ, Reyon D, Dahlborg EJ, Goodwin MJ, Coffman AP, Dobbs D, Joung JK, Voytas DF, Stupar RM (2011). Targeted mutagenesis of duplicated genes in soybean with zinc finger nucleases. Plant Physiol. 156:466-73.

Sarah Bloch

Held, ME, Kolb, A, Perdue, S, Hsu, S, Bloch SE, Quin MB, Schmidt-Dannert, C, Engineering formation of multiple recombinant Eut protein nanocompartments in E. coli. SciReports 2016, 6:24359 DOI: 10.1038/srep24359

Bloch SE, Schmidt-Dannert C. Construction of a chimeric biosynthetic pathway for the de novo biosynthesis of rosmarinic acid in Eschericha coli. ChemBiochem 2014, 15:2393-2401.

Wawrzyn GT, Bloch SE, Schmidt-Dannert C. Discovery and characterization of terpenoid biosynthetic pathways of fungi. Methods Enzymol 2012; 515: 83-105. PMID: 22999171

Vick JE, Johnson ET, Choudhary S, Bloch SE, Lopez-Gellego F, Srivastava P, Tikh IB, Wawrzyn GT, Schmidt-Dannert C. Optimized compatible set of BioBrick™ vectors for metabolic pathway engineering. Appl Microbiol Biotechnol 2011; 92:1275–1286. PMID: 22033566

Stephan Cameron

Wackett, L.P., J. Frias, J.L. Seffernick, D. Sukovich, and S.M. Cameron (2007) Vibrio furnissii M1: Genomic and biochemical studies demonstrating the absence of an alkane-producing phenotype.Appl. Environ. Microbiol. 73: 7192-7198.

Cameron, S.M., K. Durchschein, J.E. Richman, M.J. Sadowsky and L.P. Wackett (2011) A new family of biuret hydrolases involved in s-triazine ring metabolism. ACS Catalysis 1(9):1075-1082.

Seffernick, J.L., J.S. Erickson, S.M. Cameron, S. Cho, A.G. Dodge, J. Richman, M.J. Sadowsky, and L.P. Wackett (2012) Defining the cyanuric acid hydrolase (AtzD)/barbiturase protein family. J. Bacteriol. 194:4579-4588.

Veronica Diaz-Rodriguez

Diaz-Rodriguez, V.; Ganusova, E.; Rappe, T. M.; Becker, J. M. & Distefano, M. D. (2015) Synthesis of Peptides Containing C-Terminal Esters Using Trityl Side-Chain Anchoring: Applications to the Synthesis of C-Terminal Ester Analogs of the Saccharomyces cerevisiae Mating Pheromone a-Factor.J. Org. Chem., 80, 11266. PMCID: in progress

Diaz-Rodriguez, V.; Mullen, D. G.; Ganusova, E.; Becker, J. M. & Distefano, M. D. (2012) Synthesis of Peptides Containing C-Terminal Methyl Esters Using Trityl Side-Chain Anchoring: Application to the Synthesis of a-Factor and a-Factor Analogs. Org. Lett., 14, 5648. PMCID: PMC3622458

Sarah Gruba

Finkenstaedt-Quinn, S.; Gruba, S.; & Haynes, C.L. (2016) Variations in Fusion Pore Formation in Cholesterol-Treated Platelets, Biophysical Journal, 110, 922 PMID: 26910428

Manning, B.M.; Meyer, A.F.; Gruba, S.M.; & Haynes, C.L. (2015) Single-Cell Analysis of Mast Cell Degranulation Induced by Airway Smooth Muscle-Secreted Chemokines, Biochimica et Biophysica Acta- General Subjects, 1850, 1862. PMID: 25986989

Gruba, S.M.; Koseoglu, S.; Meyer, A.F.; Meyer, B.M.; Maurer-Jones, M.A.; & Haynes, C.L. (2015) Platelet Membrane Variations and their Effects on δ-Granule Secretion Kinetics and Aggregation Spreading among Different Species, Biochimica et Biophysica Acta- Biomembranes, 1848, 1609. PMID: 25906946

Meyer, A.F.; Knutson, C.M.; Finkenstaedt-Quinn, S. A.; Gruba, S. M.; Meyer, B.M.; Thompson, J.W.; Maurer-Jones, M.A.; Halderman, S.; Tillman, A.S.; DeStefano, L.; & Haynes, C.L. (2014) Activities for Middle School Students To Sleuth a Chemistry Whodunit and Investigate the Scientific Method,Journal of Chemical Education, 91, 410.

Chan, J.D., Agbedanu, P.N., Zamanian, M., Gruba, S.M., Haynes, C.L., Day, T.A., Marchant, J.S., 2014, Death and Axes: Unexpected Ca2+ Entry Phenologs Predict New Anti-Schistosomal Agents,PLOS Pathogens, 10(2): e1003942.

Gruba, S.M., Meyer, A.F., Manning, B.M., Wang, Y., Thompson, J.W., Dalluge, J.J., and Haynes, C.L. (2014) Time- and Concentration-Dependent Effects of Exogenous Serotonin and Inflammatory Cytokines on Mast Cell Function, ACS Chemical Biology, 9, 503. PMID: 24586156

Ian Gunsolus

Hang, M.; Gunsolus, I.; Wayland, H.; Melby, E.; Mensch, A.; Hurley, K.; Pedersen, J.; Haynes, C.L.; Hamers, R. (2016) Impact of Nanoscale Lithium Nickel Manganese Cobalt Oxide (NMC) on the Bacterium Shewanella oneidensis MR-1, Chemistry of Materials, 28, 1092.

Gunsolus, I.L. & Haynes, C.L. (2016) Analytical Aspects of Nanotoxicology, Analytical Chemistry, 88 451. PMID: 26565109

Qiu, T. A.; Bozich, J. S.; Lohse, S. E.; Vartanian, A. M.; Jacob, L. M.; Meyer, B. M.; Gunsolus, I. L.; Niemuth, N. J.; Murphy, C. J.; Haynes, C. L.; & Klaper, R. D. (2015) Gene Expression Response of the Gram-negative Bacterium Shewanella oneidensis and the Water Flea Daphnia magna Exposed to Functionalized Gold Nanoparticles, Environmental Science: Nano, 2, 615.

Mousavi, M.P.S.; Gunsolus, I.; Perez de Jesus, C.E.; Lancaster, M.; Hussein, K.; Haynes, C.L.; Buhlmann, P. (2015) Dynamic Silver Speciation as Studied with Fluorous-phase Ion-selective Electrodes: Effect of Natural Organic Matter on the Toxicity and Speciation of Silver, Science of the Total Environment, 537, 453. PMID: 26284896

Jacobson, K.; Gunsolus, I.; Kuech, T.; Troiano, J.; Melby, E.; Lohse, S.; Hu, D.; Chrisler, W.; Murphy, C; Orr, G.; Geiger, F.; Haynes, C.L.; & Pedersen, J.A. (2015) Lipopolysaccharide Density and Structure Governs the Extent and Distance of Nanoparticle Interaction with Actual and Model Bacterial Outer Membranes, Environmental Science & Technology, 49, 10642. PMID: 26207769

Feng, Z.V., Gunsolus, I.L.; Qiu, T.A.; Hurley, K.R.; Nyberg, L.H.; Frew, H.; Johnson, K.P.; Vartanian, A.M.; Jacob, L.M.; Lohse, S.E.; Torelli, M.D.; Hamers, R.J.; Murphy, C.J.; & Haynes, C.L. (2015) Impacts of Gold Nanoparticle Charge and Ligand Type on Surface Binding and Toxicity to Gram-Negative and Gram-Positive Bacteria, Chemical Science, 6, 5186.

Gunsolus, I.L.; Mousavi, M.P.S.; Hussein, K.; Buhlmann, P.; & Haynes, C.L.; (2015) Effects of Humic and Fulvic Acids on Silver Nanoparticle Stability, Dissolution, and Toxicity, Environmental Science & Technology, 49, 8078. PMID: 26047330

Gunsolus, I.L.; Hu, D.; Mihai, C.; Lohse, S.E.; Lee, C.-S.; Torelli, M.D.; Hamers, R.J.; Murphy, C.J.; Orr, G.; and Haynes, C.L. (2014) Facile Method to Stain the Bacterial Cell Surface for Super-Resolution Fluorescence Microscopy, Analyst, 139(12) 3174-3178. PMID: 23701037

Maurer-Jones, M.A.; Gunsolus, I.; Meyer, B.; Christenson, C.; & Haynes, C.L. (2013) Impact of TiO2 Nanoparticles on Growth, Biofilm Formation, and Flavin Secretion in Shewanella oneidensis,Analytical Chemistry, 85, 5810. PMID: 23701037

Maurer-Jones, M.A.; Gunsolus, I.L.; Murphy, C.J.; & Haynes, C.L. (2013) Toxicity of Engineered Nanoparticles in the Environment, Analytical Chemistry, 85, 3036. PMID: 23427995

Timothy Johnson

Nicholls, D.P.; Oh S.H.; Johnson, T.W.; & Reitich, F. (2016) Launching surface plasmon waves via vanishingly small periodic gratings. J. Opt. Soc. Am. A Opt. Image. Sci. Vis. 33, 276. PMID: 26974896.

Kumar, S.; Johnson, T.W.; Wood, C.K.; Qu, T.; Wittenberg, N.J.; Otto, L.M.; Shaver, J.; Long, N.J.; Victora R.H.; Edel, J.B.; & Oh, S.H. (2016) Template-Stripped Multifunctional Wedge and Pyramid Arrays for Magnetic Nanofocusing and Optical Sensing. ACS Appl Mater Interfaces. [Epub ahead of print] PubMed PMID: 26837912.

Barik A, Cherukulappurath S, Wittenberg NJ, Johnson TW, Oh SH. Dielectrophoresis-Assisted Raman Spectroscopy of Intravesicular Analytes on Metallic Pyramids. Anal Chem. 2016 Feb 2;88(3):1704-10. doi:10.1021/acs.analchem.5b03719. Epub 2016 Jan 11. PubMed PMID: 26751756.

Yoo D, Johnson TW, Cherukulappurath S, Norris DJ, Oh SH. Template-Stripped Tunable Plasmonic Devices on Stretchable and Rollable Substrates. ACS Nano. 2015 Nov 24;9(11):10647-54. doi: 10.1021/acsnano.5b05279. Epub 2015 Oct 1. PubMed PMID: 26402066; PubMed Central PMCID: PMC4660390.

Otto LM, Mohr DA, Johnson TW, Oh SH, Lindquist NC.Polarization interferometry for real-time spectroscopic plasmonic sensing. Nanoscale. 2015 Mar 7;7(9):4226-33. doi: 10.1039/c4nr06586g. PubMed PMID: 25672889; PubMed Central PMCID: PMC4339257.

Kumar S, Cherukulappurath S, Johnson TW, Oh SH. Millimeter-Sized Suspended Plasmonic Nanohole Arrays for Surface-Tension-Driven Flow-Through SERS. Chem Mater. 2014 Nov 25;26(22):6523-6530. Epub 2014 Oct 20. PubMed PMID: 25678744; PubMed Central PMCID: PMC4311951.

Nicholls DP, Reitich F, Johnson TW, Oh SH. Fast high-order perturbation of surfaces methods for simulation of multilayer plasmonic devices and metamaterials. J Opt Soc Am A Opt Image Sci Vis. 2014 Aug 1;31(8):1820-31. doi: 10.1364/JOSAA.31.001820. PubMed PMID: 25121539.

Jose J, Kress S, Barik A, Otto LM, Shaver J, Johnson TW, Lapin ZJ, Bharadwaj P, Novotny L, Oh SH.Individual Template-Stripped Conductive Gold Pyramids for Tip-Enhanced Dielectrophoresis. ACS Photonics. 2014 May 21;1(5):464-470. Epub 2014 Apr 16. PubMed PMID: 25541619; PubMed Central PMCID: PMC4270414.

Wittenberg NJ, Johnson TW, Jordan LR, Xu X, Warrington AE, Rodriguez M, Oh SH. Formation of biomembrane microarrays with a squeegee-based assembly method. J Vis Exp. 2014 May 8;(87). doi: 10.3791/51501. PubMed PMID: 24837169; PubMed Central PMCID: PMC4032179.

Barik A, Otto LM, Yoo D, Jose J, Johnson TW, Oh SH. Dielectrophoresis-enhanced plasmonic sensing with gold nanohole arrays. Nano Lett. 2014;14(4):2006-12. doi: 10.1021/nl500149h. Epub 2014 Mar 27. PubMed PMID: 24646075; PubMed Central PMCID: PMC4083195.

Reitich F, Johnson TW, Oh SH, Meyer G. A fast and high-order accurate surface perturbation method for nanoplasmonic simulations: basic concepts, analytic continuation and applications. J Opt Soc Am A Opt Image Sci Vis. 2013 Nov 1;30(11):2175-87. doi: 10.1364/JOSAA.30.002175. PubMed PMID: 24322914.

Beams R, Smith D, Johnson TW, Oh SH, Novotny L, Vamivakas AN. Nanoscale fluorescence lifetime imaging of an optical antenna with a single diamond NV center. Nano Lett. 2013 Aug 14;13(8):3807-11. doi: 10.1021/nl401791v. Epub 2013 Jul 8. PubMed PMID: 23815462.

Im H, Bantz KC, Lee SH, Johnson TW, Haynes CL, Oh SH. Self-assembled plasmonic nanoring cavity arrays for SERS and LSPR biosensing. Adv Mater. 2013 May 21;25(19):2678-85. doi: 10.1002/adma.201204283. Epub 2013 Feb 22. PubMed PMID: 23436239.

Cherukulappurath S, Johnson TW, Lindquist NC, Oh SH. Template-stripped asymmetric metallic pyramids for tunable plasmonic nanofocusing. Nano Lett. 2013;13(11):5635-41. doi: 10.1021/nl403306n. Epub 2013 Oct 28. PubMed PMID: 24144067.

Lindquist NC, Johnson TW, Nagpal P, Norris DJ, Oh SH. Plasmonic nanofocusing with a metallic pyramid and an integrated C-shaped aperture. Sci Rep. 2013;3:1857. doi: 10.1038/srep01857. PubMed PMID: 23676841; PubMed Central PMCID: PMC3655335.

Lindquist NC, Johnson TW, Jose J, Otto LM, Oh SH. Ultrasmooth metallic films with buried nanostructures for backside reflection-mode plasmonic biosensing. Ann Phys. 2012 Nov;524(11):687-696. PubMed PMID: 24159227; PubMed Central PMCID: PMC3804426.

Johnson TW, Lapin ZJ, Beams R, Lindquist NC, Rodrigo SG, Novotny L, Oh SH. Highly reproducible near-field optical imaging with sub-20-nm resolution based on template-stripped gold pyramids. ACS Nano. 2012 Oct 23;6(10):9168-74. doi: 10.1021/nn303496g. Epub 2012 Sep 17. PubMed PMID: 22938087.

Wittenberg NJ, Johnson TW, Oh SH. High-density arrays of submicron spherical supported lipid bilayers. Anal Chem. 2012 Oct 2;84(19):8207-13. doi: 10.1021/ac3014274. Epub 2012 Sep 21. PubMed PMID: 22967217; PubMed Central PMCID: PMC3476481.

Wittenberg NJ, Im H, Johnson TW, Xu X, Warrington AE, Rodriguez M, Oh SH. Facile assembly of micro- and nanoarrays for sensing with natural cell membranes. ACS Nano. 2011 Sep 27;5(9):7555-64. doi: 10.1021/nn202554t. Epub 2011 Aug 17. PubMed PMID: 21842844; PubMed Central PMCID: PMC3183111.

Lindquist NC, Johnson TW, Norris DJ, Oh SH. Monolithic integration of continuously tunable plasmonic nanostructures. Nano Lett. 2011 Sep 14;11(9):3526-30. doi: 10.1021/nl2005737. Epub 2011 Aug 11. PubMed PMID: 21834564.

Im H, Lee SH, Wittenberg NJ, Johnson TW, Lindquist NC, Nagpal P, Norris DJ, Oh SH. Template-stripped smooth Ag nanohole arrays with silica shells for surface plasmon resonance biosensing. ACS Nano. 2011 Aug 23;5(8):6244-53. doi: 10.1021/nn202013v. Epub 2011 Jul 27. PubMed PMID: 21770414; PubMed Central PMCID: PMC3160512.

Nick Kotloski

Kane, A.L.; Brutinel, E.D.; Joo, H.; Maysonet Sanchez, R.; VanDrisse, C. M.; Kotloski, N.J.; & Gralnick, J. A. (2016) Formate metabolism in Shewanella oneidensis generates proton motive force and prevents growth without an electron acceptor. J Bacteriol. 198, 1337. PMID: 26883823

TerAvest, M.A.; Rosenbaum, M.A.; Kotloski, N.J.; Gralnick, J.A. & Angenent, L.T. 2014. Oxygen allows Shewanella oneidensis MR-1 to overcome mediator washout in a continuously-fed bioelectrochemical system. Biotechnol Bioeng. 111, 692. PMID: 24122485

Kotloski, N.J. & Gralnick, J.A. (2013) Flavin electron shuttles dominate extracellular electron transfer by Shewanella oneidensis. mBio. 4, e00553. PMCID: PMC3551548

Covington, E.D.; Gelbmann, C.B; Kotloski, N.J.; Gralnick, J.A. (2010) An essential role for UshA in processing of extracellular flavin electron shuttles by Shewanella oneidensis. Mol Microbiol. 78, 519. PMID: 20807196

Patrick Smadbeck

Smadbeck P. & Kaznessis, Y.N. (2015) On a theory of stability for nonlinear stochastic chemical reaction networks. J Chem Phys. 142, 184101. PMID: 25978877

Smadbeck, P. & Kaznessis Y.N. (2015) Chemical master equation closure for computer-aided synthetic biology. Methods Mol Biol.; 1244, 179. PMID: 25487098

Smadbeck, P. & Kaznessis, Y.N. (2014) Solution of Chemical Master Equations for Nonlinear Stochastic Reaction Networks. Curr. Opin. Chem. Eng. 5, 90. PMID: 25215268

Smadbeck, P. & Kaznessis, Y.N. (2013) A closure scheme for chemical master equations. Proc. Natl. Acad. Sci. USA. A110, 14261. PMID: 23940327

Smadbeck, P. & Kaznessis, Y. (2012) Stochastic model reduction using a modified Hill-type kinetic rate law. J. Chem. Phys. 137, 234109. PMID: 23267473

Smadbeck, P. & Kaznessis, Y.N. (2012) Efficient Moment Matrix Generation for Arbitrary Chemical Networks. Chem. Eng. Sci. 84, 612.

Adam Woodruff

Xiong M, Deng J, Woodruff A, Zhu M, Park S, Li H, Fu Y, Zhang K. (2012) A Bio-Catalytic Approach to Aliphatic Ketones. Sci. Rep.

Zhang, K., Woodruff A., Xiong M., Zhou, J. and Dhande, Y.K. (2011) A Synthetic Metabolic Pathway for Production of Platform Chemical Isobutyric Acid. ChemSusChem. Jul 8. 4(8):1068-70.

Ping Yu, Yi-Shu Tai, Adam P Woodruff, Mingyong Xiong, Kechun Zhang, (2012) Engineering artificial metabolic pathways for biosynthesis, Current Opinion in Chemical Engineering, Volume 1, Issue 4, Pages 373-379

Diversity

Diversity Outcomes

Our program has an excellent track record in mentoring and retaining under-represented minority trainees. We are pleased to see that our diversity enhancement strategies are beginning to show results. In this current grant period, and especially in the past year, we have significantly increased the number of URMs and disabled students. We added six under-represented minority students, four students in the past year alone, as trainees to the program, bringing the total to 25%. Two of the students are from Puerto Rico, one other student is Hispanic, one is American Indian, and two trainees are African-American. We also count three students with self-reported disabilities among our students; two of them were appointed to the training grant this past year. Under-represented minority participation in our program is twice the average for other graduate programs, especially engineering programs, reflecting our continuous efforts to recruit URM students to our training program.

Recruitment at the University of Puerto Rico

URM outreach and recruitment is a continuous, long-term effort and we have made steady gains over the years. In addition to our participation in conferences to present our program to under-represented minority undergraduate students from other universities, we have a sustained collaboration with the University of Puerto Rico. The training program not only goes to the University of Puerto Rico for recruitment but also contributes to their teaching and research, especially in areas where we have complementary strength.

For the past four years, training grant faculty visited the University of Puerto Rico annually. Our faculty gave seminars and classroom lectures and talked to students about opportunities available at the University of Minnesota. In the summer of 2015, we hosted a group of students from the University of Puerto Rico. Our trainees organized activities to introduce them to Minnesota, our graduate programs, and the biotechnology training grant. In the fall of 2015, Professors Hu and Smanski gave lectures at the University of Puerto Rico. They met with students and encouraged them to apply to our graduate programs. Professors Torres and Miazzo of the UPR and their students have visited the University of Minnesota multiple times to discuss collaborations and participate in Hu’s annual cell culture bioprocess technology course.