Christopher D. Herring

** ****** **., ******* ** 03748

phone: 603 - 276 - 0221

email: acat3z@r.postjobfree.com

Education

**** - **** **.*. ************, University of Wisconsin, Madison.

Major Advisor: Professor Fred Blattner.

Thesis: Introduction and Suppression of Amber Stop Codons in the Genome of

Escherichia coli.

Summary: As part of a functional genomics project in the bacterium Escherichia

coli, I developed a number of methods for the directed manipulation of the

genome, particularly the introduction of amber stop codons in essential genes.

The effects of these mutations were turned on and off by the use of a suppressor

tRNA, and the behavior of the resulting conditional lethal mutants were studied

in the context of evaluating different essential genes as targets for the

development of new antibiotics. The transcriptional side-effects from using the

suppressor tRNA were evaluated using microarrays, and a novel regulator for the

oxidation of formaldehyde was identified.

1991 - Dec. 1992 Bachelor of Science Degree in Biology with emphasis in Biotechnology.

Humboldt State University, Arcata, California USA

1988 -1990 San Diego State University, San Diego, California USA

Grants, Awards, and Fellowships

1) Co-PI: “Development of Thermoanaerobacterium saccharolyticum for conversion of lignocellulose

to ethanol,” grant from the Department of Energy Biomass Program to Mascoma Corporation for

$4.9 MM over 3 years.

2) NIH Ruth L. Kirschstein National Research Service Award postdoctoral fellowship

3) National Library of Medicine (NIH) Computation and Informatics in Biology and Medicine short-

term postdoctoral fellowship.

4) NIH Biotechnology Pre-doctoral Training Program Fellowship

5) Presidential Scholar, Humboldt State University

6) Letter of Commendation, National Merit Scholarship Program

Work Experience

July-Aug 2013 Scientist. Avitide, Inc. Lebanon, NH. Avitide is an early stage start-up working on

purifcation methods for protein therapeutics. I performed general molecular biology

and biochemistry for them on a short-term employment contract.

2011-current Adjunct Associate Professor, Thayer School of Engineering, Dartmouth College,

Hanover, New Hampshire. Co-taught Metabolic Engineering course and co-advised

graduate students with Professor Lee Lynd. I also acted as a liason between Mascoma

Corporation and Dartmouth college to monitor work done under a Sponsored Research

Agreement and was an activity leader at the BioEnergy Science Center.

2006-2013 Senior Research Scientist. Mascoma Corporation, Lebanon, NH. Mascoma is a spin-

off from Dartmouth College that develops biotechnology for conversion of grain and

cellulosic biomass to ethanol, and is particularly known for Consolidated

Bioprocessing. I joined Mascoma when it was a 12-person startup, managed 4-6 people

on a functional basis and directed work on thermophilic bacteria. As co-PI of a $4.9

MM grant from DOE, I helped develop T. saccharolyticum for conversion of pretreated

hardwood to ethanol. I was responsible for OMICs work performed in conjunction

with Oak Ridge National Lab, including microarray and metabolomic analysis.

2004-2006 Postdoctoral researcher. University of California San Diego, Department of

Bioengineering, laboratory of Bernhard Palsson. Projects: 1) investigation of systems

properties in data from gene expression measurements and an integrated model of

metabolism and regulation; 2) analysis of mutations acquired during adaptive evolution

in E. coli; 3) identification of RNA polymerase binding sites throughout the E. coli

genome using chromatin immunoprecipitation and microarrays (chIP-chip).

Summer 2004 Postdoctoral researcher. University of Wisconsin Madison, laboratories of Bob

Landick and Aseem Ansari in the departments of Bacteriology and Biochemistry.

Project: I worked to identify DNA binding sites of transcription factors throughout the

genome using chIP-chip.

Summer 2003 Intern. Scarab Genomics, Madison, Wisconsin. In fulfillment of the internship

requirements of the NIH Biotechnology Training Fellowship, I worked for Scarab

Genomics to engineer industrial strains of E. coli and collaborated with Dr. Bernhard

Palsson at UC San Diego on new strategies for metabolic engineering.

1999-2000 Teaching Assistant. University of Wisconsin, Department of Bacteriology. I

conducted short lectures and oversaw an introductory bacteriology laboratory course

for undergraduates, then assisted in the lectures and supervision of an upper division

undergraduate course in bacterial genetics.

1997 to 1998 Research Technician. University of Melbourne, Australia, Department of Surgery, Dr.

Wendy Cook’s lab. Project: Positional cloning of a tumor suppressor gene involved in

mouse myeloid leukemia.

1993 to 1997 Research Technician. Medical Biology Institute, La Jolla, California, Dr. Roy Riblet’s

lab. Projects: The cloning and characterization of the mouse Immunoglobulin Heavy-

chain (Igh) locus, and the positional cloning of stem cell regulatory genes, the SCID

gene, and the mouse herpes keratitis gene.

Summer 1992 Undergraduate Assistant. University of California, San Diego, Dr. Milton Saier’s lab.

Project: Identification and characterization of the phosphotransferase system of the

pathogen Listeria monocytogenes.

Summer 1991 Chemist. S-Cubed, San Diego, California. Project: Preparation and

spectrophotometric analysis of liquid and soil samples for trace metal contamination.

Publications

1) AJ Shaw, BB Miller, SR Rogers, WR Kenealy, A Meola, A Bhandiwad, WR Sillers, I Shikhare,

DA Hogsett, CD Herring. Anaerobic detoxification of acetic acid in a thermophilic ethanologen.

Submitted.

2) EB Mearls, DG Olson, CD Herring, LR Lynd. Development of a regulatable plasmid based gene

expression system for Clostridium thermocellum. Submitted.

3) DH Currie, B Raman, TJ Tschaplinski, ML Land, SD Brown, C Gowan, SS Fong, SF Covalla, DM

Klingeman, ZK Yang, NL Engle, CM Johnson, AJ Shaw, WR Kenealy, JR Mielenz, BH Davison,

DA Hogsett, CD Herring. Genome-scale resources for Thermoanaerobacterium saccharolyticum:

genome sequencing, transcriptomics, metabolite analysis, and metabolic modeling. In Preparation.

4) DH Currie, A Guss, CD Herring, R. Giannone, C. Johnson, P.K. Lankford, S. Brown, B. Hettich,

L.R. Lynd. A profile of Thermoanaerobacterium saccharolyticum secreted hydrolases and the

primary S-Layer protein. In Preparation.

5) CD Herring, P Thorne. Clostridium thermocellum releases coumaric acid during degradation of

untreated grasses by the action of an unknown enzyme. In preparation.

6) DH Currie, CD Herring, AM Guss, DG Olson, DA Hogsett and LR Lynd. Functional

heterologous expression of an engineered full length CipA from Clostridium thermocellum in

Thermoanaerobacterium saccharolyticum. Biotechnol Biofuels. 2013 6(1):32.

7) Deng Y, Olson DG, Zhou J, Herring CD, Joe Shaw A, Lynd LR. Redirecting carbon flux through

exogenous pyruvate kinase to achieve high ethanol yields in Clostridium thermocellum. Metab Eng.

2013. 15:151-8.

8) Tsakraklides V, Shaw AJ, Miller BB, Hogsett DA, Herring CD. Carbon catabolite repression in

Thermoanaerobacterium saccharolyticum. Biotechnol Biofuels. 2012. 26;5(1):85.

9) Shaw AJ, Covalla SF, Miller BB, Firliet BT, Hogsett DA, Herring CD. Urease expression in a

Thermoanaerobacterium saccharolyticum ethanologen allows high titer ethanol production. Metab

Eng. 2012. 14(5):528-32.

10) Podkaminer KK, Kenealy WR, Herring CD, Hogsett DA, Lynd LR. Ethanol and anaerobic

conditions reversibly inhibit commercial cellulase activity in thermophilic simultaneous

saccharification and fermentation (tSSF). Biotechnol Biofuels. 2012. 15;5(1):43.

11) Herring CD. Final Report on Development of Thermoanaerobacterium saccharolyticum for the

conversion of lignocellulose to ethanol. US Department of Energy Office of Science and Technical

Information Website: www.osti.gov/servlets/purl/1033560/

12) A.J. Shaw, S.F. Covalla, D.A. Hogsett, C.D. Herring. A marker removal system for

Thermoanaerobacterium saccharolyticum and development of markerless ethanologens. Appl.

Environ. Microbiol. 2011 Feb 11.

13) L.R. Lynd, D. Currie, N. Ciazza, C. Herring, N. Orem. Consolidated bioprocessing of cellulosic

biomass to ethanol using thermophilic bacteria. In Bioenergy, C.S. Harwood, A.L. Demain, J.D.

Wall (Eds.), ASM Press, 2008.

14) CD Herring. Introduction of conditional lethal amber mutations in Escherichia coli. In Gene

Essentiality at Genome Scale: Protocols and Bioinformatics, A.L. Osterman, S.Y. Gerdes (Eds.)

2008 Methods in Molecular Biology 416:323-334.

15) C.D. Herring, B.Ø. Palsson. An evaluation of Comparative Genome Sequencing (CGS) by

comparing two previously-sequenced bacterial genomes. 2007 BMC Genomics 8:274. Cited 9

times.

16) C.D. Herring*, A. Raghunathan*, C. Honisch*, T.R. Patel, M.K. Applebee, Thomas J. Albert, D.

van den Boom, C.R. Cantor, B.Ø. Palsson. Comparative genome sequencing of Escherichia coli

allows evolution to be observed on a laboratory timescale. 2006 Nature Genetics 38:1406-1412.

Cited 57 times. * Equal contributors.

17) J.L. Reed, T.R. Patel, K.H. Chen, A.R. Joyce, M.K. Applebee, C.D. Herring, O.T. Bui, E.M.

Knight, S.S. Fong and B.O. Palsson. Systems approach to refining genome annotation. 2006

Proceedings of the National Academy of Sciences USA. 103:174**-*****. Cited 48 times.

18) C.L.Barrett, C.D.Herring, J.L.Reed, B.Ø.Palsson. The transcriptional regulatory network for

metabolism in Escherichia coli attains few dominant functional states. 2005 Proceedings of the

National Academy of Sciences USA 102:191**-*****. Cited 41 times.

19) C.D.Herring, M.Raffaelle, T.E.Allen, E.Kanin, R.Landick, A.Z.Ansari, B.Ø.Palsson.

Immobilization of Escherichia coli RNA polymerase and location of binding sites using chromatin

immunoprecipitation and microarrays. 2005 Journal of Bacteriology. 187:6166-6174. Cited 33 x.

20) S.S.Fong, A.P.Burgard, C.D.Herring, E.M.Knight, F.R.Blattner, C.D.Maranas, B.O. Palsson. In

silico design and adaptive evolution of Escherichia coli for production of lactic acid. 2005

Biotechnology and Bioengineering. 91:643-648. Cited 41 times.

21) W.D. Cook, B.J. McCaw, C.D. Herring, D. John, S.L. Nutt, J.M. Adams. PU.1 is a suppressor of

myeloid leukemia, inactivated in mice by gene deletion and mutation of its DNA-binding domain.

2004 Blood. 104:3437-3444. Cited 47 times.

22) C.D.Herring, F.R.Blattner. Global transcriptional effects of a suppressor tRNA and inactivation of

the regulator FrmR. 2004 Journal of Bacteriology. 186:6714-6720. Cited 17 times.

23) C.D.Herring, F.R.Blattner. Conditional lethal amber mutations in essential Escherichia coli genes.

2004 Journal of Bacteriology 186: 2673-2681. Cited 19 times.

24) C.D.Herring, J.D.Glasner, F.R.Blattner. Gene replacement without selection: the introduction and

regulatable suppression of amber mutations in Escherichia Coli. 2003 Gene 311:153-163. Cited 31

times.

25) C.Chevillard, J.Ozaki, C.D.Herring, R.Riblet. A three-megabase yeast artificial chromosome

contig spanning the C57BL mouse Igh locus. 2002 Journal of Immunology 168(11):5659-66. Cited

27 times.

26) V.Kolisnychenko, G.Plunkett III, C.D.Herring, T.Fehér, J.Pósfai, F.R.Blattner, G. Pósfai.

Engineering a reduced Escherichia coli genome. 2002 Genome Research. 12(4):640-647. Cited 76

times.

27) C.D.Herring, C.Chevillard, R.Riblet. Vector-hexamer PCR Isolation of All Insert Ends from a

YAC Contig of the Mouse Igh Locus. 1998 Genome Research, 8(6):673-681. Cited 15 times.

28) R.Riblet, A.Tutter, J.Ozaki, and C.Herring. Immunoglobulin Genes and their Function. In Weir’s

Handbook of Experimental Immunology, Weir, D.M., Herzenberg, L.A., Herzenberg, L.A., and

Blackwell, C. [editors]. 1996 Blackwell Science, Cambridge, MA. Vol. 1:(3.1-3.3).

29) W.J.Mitchell, J.Reizer, C.Herring, C.Hoischen, M.H.Saier. Identification of a

Phosphoenolpyruvate:Fructose Phosphotransferase System (Fructose-1-Phosphate Forming) in

Listeria monocytogenes. 1993 Journal of Bacteriology 175:2758-2761. Cited 21 times.

Patents and applications

Dec. 2011 J Lo, AM Guss, PJ vav Dijken, AJ Shaw, DG Olson, CD Herring. Engineering

and Increase in Ethanol Production by Altering Cofactor Specificity. Provisional

Patent Application.

Oct. 2011 Y Deng, DG Olson, JP van Dijken, AJ Shaw, A Argyros, T Barrett, N Caiazza,

CD Herring, S Rogers, F Agbogbo. Engineering Microorganisms to Increase

Ethanol Production by Metabolic Redirection. Provisional Patent Application.

Dec. 2009 H.Hau, C.Rice, C.D.Herring, J.McBride, A.J.Shaw, E.Wiswall. Heterologous

biomass degrading enzyme expression in thermoanaerobacterium

saccharolyticum. Application PCT/US2009/069443.

July 2009 C.D.Herring, C.Liu, J.Bardsley. Flow-through biological conversion of

lignocellulosic biomass. Application PCT/US2009/004135.

Sept. 2008 N.Caiazza, A.Warner, C.Herring. Plasmids from thermophilic organisms,

vectors derived therefrom, and uses thereof. Application PCT/US2008/010545.

Aug. 2007 B.Palsson, C.D. Herring. Method for determining the genetic basis for

physiological changes in organisms. Application PCT/US2007/017283.

Sept. 2003 F.R.Blattner, G.Posfai, C.D.Herring, G.III Plunkett, J.Glasner, T.Twose.

Competent bacteria. US Patent 7,303,906.

Jan. 2002 F.R.Blattner, G.Pósfai, C.D.Herring, G.Plunkett, J.Glasner. Bacteria with

reduced genome. US Patent 6,989,265.

Presentations and Posters

June 2011 CD Herring. The role of OMICs in the Development of

Thermoanaerobacterium saccharolyticum for Production of Ethanol from

Pretreated Hardwood. Oral presentation at the Workshop on Complexity and

Systems Biology of Microbial Biofuels, University of Warwick, UK.

May 2011 CD Herring, B Raman, TJ Tschaplinski, ML Land, SD Brown, C Gowen, SS

Fong, SF Covalla, DM Klingeman, ZK Yang, NL Engle, CM Johnson, M

Rodriguez, AJ Shaw, WR Kenealy, JR Mielenz, BH Davison, DA Hogsett.

Analysis of the response of Thermoanaerobacterium saccharolyticum to

inhibitors and hemicellulose enabled by genome-scale resources. Oral

Presentation for the 33rd Symposium on Biotechnology for Fuels and

Chemicals, Seattle, WA.

June 2010 C.D.Herring, A.J.Shaw, W.R.Kenealy, W.R.Sillers, J.Bardsley, S.F.Covalla,

A.Foster, J.P.Johnson, S.R.Rogers, H.Xu, B.Raman, T.J.Tschaplinski,

D.M.Klingeman, Z.K.Yang, N.L. Engle, M.Rodriguez, C.M.Johnson, M. Land,

S.D.Brown, J.R.Mielenz, B.H.Davison, D.Hogsett. Development of

Thermoanaerobacterium saccharolyticum for fermentation of pretreated

hardwood. Oral Presentation for the 32nd Symposium on Biotechnology for

Fuels and Chemicals, Clearwater Beach, FL.

November 2008 C.D.Herring, A.J.Shaw, A.Warner. Re-sequencing of Thermoanaerobacterium

saccharolyticum adapted to growth in xylose medium. Poster for the Bioenergy

Science Center 2nd Annual Retreat, Chattanooga, TN.

August 2003 C.D.Herring, F.Blattner. Essential Gene Mutations in E. coli Regulated with an

Inducible Amber Suppressor tRNA. Poster for the 2003 Molecular Genetics of

Bacteria and Phages Meeting, Madison, WI.

May 2003 C.D.Herring, F.Blattner. Essential Gene Mutations in E. coli Regulated with an

Inducible Amber Suppressor tRNA. Poster for the 103rd General Meeting of the

American Society for Microbiology, Washington D.C.

Sept. 2002 C.D.Herring, F.Blattner. Technologies for Directed Mutation of Essential

Genes in E. coli. Poster for the 10th International Conference on Small

Genomes, Lake Arrowhead, CA.

Aug. 2000 C.D.Herring, et al. High-throughput Mutagenesis and Functional Genomics in

E. coli. Poster for the 8th International Conference on Small Genomes, Lake

Arrowhead, CA.

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