NIH Protein Biotechnology Training Program News & Rev iews

MESSAGE FROM THE

DIRECTOR ................. 1

2012 BIOTECHNOLOGY

SYMPOSIUM SPEAKERS 2 - 3

INTERNSHIP REPORTS AND

TRAINEE/TRAINER AWARDS,

PRESENTATIONS, AND

ACHIEVEMENTS .......... 4 - 7 News & Reviews WASHINGTON STATE UNIVERSITY NIH

BIOTECHNOLOGY TRAINING PROGRAM

Message from the Director Last September I took over the role of Direc-

tor of the Biotech Program from Dr. Ray

Reeves who served in that capacity for over

10 years. Ray did an outstanding job as Di-

rector and his enthusiasm and efforts on be-

half of the Program are evident in the Pro-

gram’s longstanding success and vitality. I

know everyone joins me in thanking Ray for

all his hard work and dedication-we really

do appreciate it! This transition year (the

23rd year of continuous NIH funding) was

filled with many noteworthy accomplish-

ments and successes of both trainees and the

faculty trainers. One of the main highlights

of the year is the fruition of the trainees

yearlong planning and organizational efforts:

the annual symposium. This year’s sympo-

sium “Cougs in Biotechnology” was held on

April 27, 2012 with former WSU graduates

including two past Biotech trainees as slated

speakers. The symposium was again a re-

sounding success with outstanding speakers

covering a broad range of topics from basic

and applied research to clinical trials, how

one turns ideas into products and product

marketing including: Drs. Brandon Placek

(Idaho State University), Jennifer Adair

(Fred Hutchinson Cancer Research Center),

Tracy Letain (AquaBella Organic Solu-

tions), Grant Norton (WSU Engineering;

who graciously stepped in at the very last

minute when one of the former Cougs was

unable to attend) and Mr. Kyle Armantrout

(Focus Diagnostics). A huge THANK YOU

to James Rosser (2011-2012 Forum Presi-

dent) and all the other officers and trainees

who did an amazing job organizing and exe-

cuting the symposium.

This year we saw a number of trainees grad-

uate including: McKenna Kyriss, PhD

(SMB; John Wyrick, PI), Dan Cuthbert-

son, PhD (MPS; Mark Lange, PI), Adam

Johnson, PhD (SMB; Margaret Black, PI),

Kaitlyn Morse, PhD (VMP; Wendy

Brown, PI), Laura Wayne, PhD (MPS;

John Browse, PI), Danny Bottenus, PhD

(CHEBE; Neil Ivory, PI), and Nate Tucker,

PhD (SMB; Eric Shelden, PI), Anna

Linsday, MS (SMB; Lisa Gloss, PI), Brian

Webb, MS (Chem; ChulHee Kang, PI), Sri

Nannapaneni, MS (CHEBE; Haluk

Beyenal, PI), and Tyler O’Dell, MS (Chem;

Cliff Berkman, PI). Congratulations to

each and every one of them!

In other trainee news: Seth Nydam (VMP)

was awarded a two-year, $75,000 fellowship

from the United States Department of Agri-

culture and Stacy Hathcox (SMB) was

awarded a fellowship from the Poncin Fel-

lowship Fund – way to go Seth and Stacy!

Kylie Allen (SMB) and Tim Harrington

(CHEBE) completed their internships and

James Rosser (SMB), Scott Schaeffer

(MPS), Seth Nydam (VMP), Jerome Bau-

bata (CHEBE), and Alan Budgeon (MPS)

are preforming their internships this summer.

Congratulations to faculty trainers as well

for their successes this year. Amit Dhingra

was promoted and awarded tenure; Norman

Lewis was elected to Scotland’s National

Academy of Science and Letters as Corre-

sponding Fellow to the Royal Society of

Edinburgh; Nancy Magnuson was named a

AAAS fellow and is also serving as Interim

Dean of The Graduate School and Vice

Provost for Research; and Mick Smerdon

received the WSU 2012 Eminent Faculty

Award (WSU’s highest honor).

We also welcomed several new faculty train-

ers to the Biotechnology Training Program

including Nehal Abu-Lail (CHEBE), Hec-

tor Aguilar-Carreno (VMP), Anthony Ni-

cola (VMP), Devendra Shah (VMP), Vive-

ka Vadyvaloo (VMP) and Ping Ye (SMB).

In other trainer news: Cliff Berkman

(Chem) was elected to serve on the Biotech-

nology Executive Steering Committee

(welcome Cliff!) and Wendy Brown (VMP)

has kindly agreed to substitute for Doug

Call (VMP) while he is on sabbatical leave

this next year (thank you Wendy!).

A BIG THANKS to Susan Bentjen who

helps us all advance in a forward direction

and who has helped me enormously transi-

tion smoothly into the Director position.

In closing let me remind you all that we are

coming to the end of the current funding

period in 2014 and therefore will be submit-

ting the competitive renewal this upcoming

January. We would like to thank you in ad-

vance for sending Susan Bentjen any re-

quested information in a timely fashion.

Have a great summer and I’ll see you at the

next Forum meeting in fall.

Margaret Black

2012 - 2013

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Symposium Speaker Profiles

Dr. Grant Norton GoNano Technologies, Inc.

Dr. Grant Norton is a professor at Washington State

University in The School of Mechanical

and Materials Engineering. Dr. Norton

obtained his Ph. D. in Materials from

Imperial College in London and served as

a postdoctoral researcher at Cornell

University. Prior to entering academia,

Professor Norton worked for two major

European multinationals: Cookson Group PLC and Heraeus GmbH. He has consulted

for a number of companies and

organizations including the United States Air Force and REC Silicon. In 2007 Dr.

Norton cofounded GoNano Technologies,

Inc., and currently serves as its Chief

Technology Officer. GoNano

Technologies focuses on producing and

finding new roles for Nanospring™

technology. This nanomaterial is currently

used in composites, catalysis,

pollution control, and sensory

technologies. GoNano is collaborating with many companies to expand the use of Nan-

ospring™ technology to animal

diagnostics, biosensors, and bioreactors.

BIOTECHNOLOGY

SYMPOSIUM

2012

The WSU NIH Biotechnology

program held our 21st

Annual Biotechnology

Symposium on April 27th

2012. We would like to thank

everyone who helped make

this year’s

symposium a great

success!

Dr. Adair completed her doctoral work in the laboratory of Dr. Reeves, School of Molecular

Biosciences, and graduated from WSU in 2005 with a

dissertation titled “Influence of HMGA-1 protein

overexpression on BRCA-1-mediated stabilization of p53 and excision repair.” Currently she is a Clinical Research

Associate at Fred Hutchinson Cancer Research Center in

Seattle, WA. Dr. Adair’s research is focused in the clinical applications of gene therapy for the treatment of cancer and

other genetic diseases, and her work, including preclinical

data generation and interpretation, has been submitted for

investigational new drug (IND) and Phase I clinical trials.

2012 BIOTECHNOLOGY

SYMPOSIUM CONTINUED ON PAGE………………3

INTERNSHIP REPORTS AND

TRAINEE/TRAINER AWARDS,

PRESENTATIONS AND

ACHIEVEMENTS .......... 4 –7

2

Dr. Jennifer Adair Focus Diagnostics

Symposium Speaker Profiles

Mr. Kyle Armantrout Focus Diagnostics

Mr. Armantrout, a WSU student from 1993-97, is the Senior Director of Global Marketing at Focus Diagnostics, a Division of Quest Diagnostics. Focus Diagnostics, Inc. engages in developing and providing infectious disease testing services, and manufacturing diagnostic products for biotechnology and pharmaceutical industries. It offers clinical reference laboratory services, including test listing, new tests, test updates, and certification services for complex diagnostics, infectious disease, autoimmune, and genetic testing, as well as diagnostic products, such as diagnostic test kits and reagents. The company also offers central laboratory and custom microbiology services. Mr. Armantrout has 14 years of industry focus and his work has led to multiple patents and patent applications resulting in an Edison Award for Innovation and a Medical Design Excellence Award.

Dr. Placek was a graduate student in

Dr. Lisa Gloss’ laboratory, School of Molecular

Biosciences. He graduated from WSU in 2004 with a

dissertation titled “Folding of the H2A-H2B dimer.” After

his graduation, he accepted a postdoctoral position at The

Wistar Institute, Philadelphia, PA, where he studied the role

of histone variant H3.3 on transcription during lytic

infection by Herpes Simplex Virus, HSV-1. Later he

undertook another project under the guidance of Dr. Shelley L. Berger at the University of Pennsylvania School of Med-

icine, and his research focused on chromatin

mechanisms underlying aging, gametogenesis, viral

infection, cancer (p53 regulation), and animal behavior.

Currently, he is a visiting Assistant Professor in the

Department of Biological Sciences at Idaho State

University.

INTERNSHIP REPORTS AND

TRAINEE/TRAINER AWARDS,

PRESENTATIONS AND

ACHIEVEMENTS .......... 4 - 7

3

Dr. Letain, Chief Technology Officer /

Microbiologist at AquaBella Organic Solutions,

Sebasto, CA, graduated from WSU in 1997. During her

graduate school career in the School of Molecular Biosciences at WSU she worked under the leadership of Dr.

Postle. For more than a decade, Dr. Letain’s focus has been

on environmental microbiology, and her research with soil and water covers a wide range of important topics. Dr.

Letain works on providing the research and explanation of

the natural science behind AquaBella's powerful products. She believes that her work with AquaBella Organic

Solutions will contribute to revitalizing the earth and

cleaning its waters.

Dr. Brandon Placek Idaho State University

Dr. Tracy Letain AquaBella Organic Solutions

Internship Reports

Kylie Allen

E.J. Gallo Winery, (Modesto, CA)

This past summer/fall of 2011 I completed an internship at E.J.

Gallo winery in an enology group under the supervision of Dr.

Chandra Richter. My first project was to assess the activity of a

commercially available beta-1,3-glucanase enzyme in wine. The company was interested in using this enzyme to enhance yeast

cell lysis during the aging process, thus improving mouthfeel

and aroma characteristics. We discovered that the glucanase

increased the concentration of polysaccharides responsible for

mouthfeel and mannoproteins capable of tannin stabilization in

the final wine. Studies are currently in progress to determine

whether addition of the enzyme during aging does in fact influ-

ence the quality of the final product. My main project was to

develop a real-time polymerase chain reaction protocol for de-

tection and identification of spoilage microbes in winemaking. I

developed primers and performed numerous controls for specif-

ic detection of various yeasts and bacteria found throughout the winemaking process. This method is currently being utilized at

the winery for rapid detection of spoilage organisms. Addition-

ally, I used an RT-PCR approach to track the population of mi-

crobes during a pinot noir cold soak. We found that a yeast na-

tive to grape vines proliferated during cold soak and could per-

haps be responsible for adding complexity to the wine. I enjoyed

the independence this internship allowed and I learned valuable

new techniques.

INTERNSHIP REPORTS AND

TRAINEE/TRAINER AWARDS,

PRESENTATIONS AND

ACHIEVEMENTS .......... 4 - 7

4

To learn more about E.J. Gallo Winery,

check out their website at:

http://www.gallo.com

Internship Reports

Timothy Harrington J.Craig Venter Institute (La Jolla, CA)

My internship was at the J. Craig Venter Institute in San Die-

go, CA, from May 16th through July 28th, 2011. The J. Craig

Venter Institute was started by Dr. Venter after he left Celera, and

after he sponsored the sequencing of the human genome. Natural-

ly, the institute still does a lot of genome sequencing, in addition to several other thrusts of research. While I was there, my main

project was under Jeff McLean, and involved investigations of

dental biofilms.

Dental biofilms are in everyone’s mouth, regardless of whether

one uses Listerine twice per day. There are at least 700 different

species of bacteria in the mouth, and certain ones dominate differ-

ent niches (under the tongue, behind the molars, etc.) They can

play good and bad roles in dental hygiene, and also have been

recently correlated with disease states in other parts of the body,

such as heart disease. One of the most important things dental

biofilms do is regulate the local pH of the saliva and the biofilms on the teeth. After an initial dose of sugar, the pH drops sharply

from around 7 to around 4.5, a pH which can cause tooth decay.

After several hours, the pH slowly rises back to 7. Since most of

the bacterial species in the mouth are unculturable in isolation, it

is unclear if there are bacteria that cause the pH drop, or, even

better, cause a rise in saliva pH. The grant I was working under

sought to decipher which organisms were doing what in the

mouth by using a technique called stable isotope probing, or SIP.

SIP has been around for a decade or so as a laboratory technique

for probing microbial communities. The basic concept is as fol-lows: First, a heavy-isotope labeled sugar (or amino acid, metabo-

lite, etc.) is fed to a community of microorganisms. The microor-

ganisms that can metabolize the heavy compound can start using

it as an energy source. Since they are constantly making RNA, the

RNA becomes almost immediately heavy-labeled with the heavy

isotope. Eventually, the cells divide and make an entire copy of

their genome, which is also all heavy-labeled. By purifying and

sequencing the RNA and DNA, it is possible to determine which

organisms can metabolize the compound(who they are), and what

RNA transcripts are most abundant at whatever state they are in

(what they are doing).

For our project with dental biofilms, we fed heavy-labeled glu-

cose to a biofilm community grown from saliva samples, while

they were kept at different pH values. The expected result was

that different microorganisms would be actively metabolizing the

sugar at pH 4.5 when compared to those at pH 7.0. After incubat-

ing for different time lengths (4, 8, 12, 16, 20 hours), the DNA

was isolated and loaded into an ultracentrifuge. The ultracentri-

fuge spun for 72 hours, separating the heavy DNA from the light

DNA. Afterwards, the column gradients were fractionated, and

the amount of DNA in each fraction was quantified. The first

phase of the project was identity, so the gene that was amplified

was the 16S rRNA gene, which is commonly used in phylogenet-ic analysis. We used a degenerate primer shown to work well

previously with dental biofilm communities, and performed PCR

on the heavy fractions. We then cloned the 16S genes into E. coli

in order to separate out the different 16S genes, and the amplified

them again for sequencing in Maryland. (Only one plasmid enters

an E. coli cell, so it only gets one 16S gene out of the ~700 in the

community. By counting different colonies, a statistical represen-

tation of the community can be obtained.) The future of the pro-

ject will involve mining the transcriptome under similar pH con-

ditions. The eventual goal is to separate the bacteria found in the

human dental biome into Santa’s good and naughty lists.

INTERNSHIP REPORTS AND

TRAINEE/TRAINER AWARDS,

PRESENTATIONS AND

ACHIEVEMENTS .......... 4- 7

5

To learn more about J. Craig

Venter Institute, check out

their website at:

http://www.jcvi.org

Trainee/Trainer Awards, Presentations, and

Achievements

Trainee Awards

Kim Hixon (Molecular Plant Sciences) Attended the prestigious 2011 Lindau Nobel Laureates Meeting in Ger-many

Stacy Hathcox (Molecular Biosciences)

Received a Poncin Fellowship from the Poncin Trust Scientific Committee.

Seth Nydam (Veterinary Microbiology and Pathology) Received a two-year , $75,000 fellowship from the United States Depart-ment Agriculture

Trainer Awards

Dr. Neil Ivory (Chemical Engineering) Named the inaugural Hohenschuh Distinguished Professor

Dr. Norm Lewis (Biological Chemistry) Elected to Scotland’s National Academy of Science and Letters as Corre-sponding Fellow to the Royal Society of Edinburgh

Dr. Nancy Margunson (Molecular Biosciences) Named a AAAS fellow and is also serving as interim dean of the gradu-ate school and vice provost for research

Dr. Mick Smerdon (Molecular Biosciences)

Received the WSU 2012 Eminent Faculty Award (WSU’s highest honor)

2012 Symposium Poster Winners

FIRST PLACE: James Rosser

(SMB, with Wenfeng An)

SECOND PLACE: Tom Jacroux

(CHEBE, with Wen-ji Dong)

THIRD PLACE: Tyson Euker

(SMB, with Mike Konkel)

Trainee Publications in 2011-2012

Kylie Allen Werner, W. J.; Allen, K. D.; Hu, K.; Helms, G. L.; Chen, B. S.; Wang, S.

C., In Vitro Phosphinate Methylation by PhpK from Kitasatospora phosalacinea. Biochemistry 2011, 50 (42), 8986-8988.

Joseph Agnes Agnes, J. T.; Brayton, K. A.; LaFollett, M.; Norimine, J.; Brown, W. C.; Palmer, G. H., Identification of Anaplasma marginale Outer Mem-brane Protein Antigens Conserved Between A. marginale Sensu Stricto Strains and the Live A. marginale subsp. centrale Vaccine. Infect Immun

2011, 79 (3), 1311-1318.

Jerome Babauta Babauta, J. T.; Nguyen, H. D.; Beyenal, H., Redox and pH Microenvi-ronments within Shewanella oneidensis MR-1 Biofilms Reveal an Elec-tron Transfer Mechanism. Environmental Science & Technology 2011, 45 (15), 6654-6660.

Sara Belchik Belchik, S. M.; Xun, L. Y., S-Glutathionyl-(Chloro)Hydroquinone Re-ductases: A New Class of Glutathione Transferases Functioning as Oxi-doreductases. Drug Metabolism Reviews 2011, 43 (2), 307-316.

Danny Bottenus Bottenus, D.; Hossan, M. R.; Ouyang, Y. X.; Dong, W. J.; Dutta, P.; Ivory, C. F., Preconcentration and Detection of the Phosphorylated Forms of Cardiac Troponin I in a Cascade Microchip by Cationic Iso-

tachophoresis. Lab Chip 2011, 11 (22), 3793-3801.

Bottenus, D.; Jubery, T. Z.; Dutta, P.; Ivory, C. F., 10 000-Fold Concen-tration Increase in Proteins in a Cascade Microchip Using Anionic ITP by a 3-D Numerical Simulation With Experimental Results. Electropho-resis 2011, 32 (5), 550-562.

Bottenus, D.; Jubery, T. Z.; Ouyang, Y. X.; Dong, W. J.; Dutta, P.; Ivo-

ry, C. F., 10,000-Fold Concentration Increase of the Biomarker Cardiac Troponin I in a Reducing Union Microfluidic Chip Using Cationic Iso-tachophoresis. Lab Chip 2011, 11 (5), 890-898.

Julie Burgal van Erp, H.; Bates, P. D.; Burgal, J.; Shockey, J.; Browse, J., Castor Phospholipid: Diacylglycerol Acyltransferase Facilitates Efficient Metab-olism of Hydroxy Fatty Acids in Transgenic Arabidopsis. Plant Physiolo-

gy 2011, 155 (2), 683-693.

Chris Detzel Detzel, C. J.; Van Wie, B. J., Use of a Centrifugal Bioreactor for Carti-laginous Tissue Formation from Isolated Chondrocytes. Biotechnol Progr 2011, 27 (2), 451-459.

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Trainee/Trainer Awards, Presentations, and

Achievements Trainee Publications in 2011-2012 (cont’d)

Timothy Harrington Harrington, T. D., Naber, N., Larson, A. G., Cooke, R., Rice, S. E., &

Pate, E. (2011). Analysis of the Interaction of the Eg5 Loop5 with the Nucleotide Site. Journal of Theoretical Biology, 289, 107–115.

Adam Johnson Johnson, A.J., Brown, M.B., and Black, M.E. (2011) Evaluation of a UCMK/dCK Fusion Enzyme for Gemcitabine-Mediated Cytotoxicity.

Biochemical and Biophysical Communications, Biochem Biophys Res

Commun. 2011 416(1-2):199-204.

Adam Johnson and Marilyn Sanchez-Bonilla Johnson, A. J.; Ardiani, A.; Sanchez-Bonilla, M.; Black, M. E., Com-parative Analysis of Enzyme and Pathway Engineering Strategies for

5FC-Mediated Suicide Gene Therapy Applications. Cancer Gene Ther 2011, 18 (8), 533-542.

Ben Kasten Ganguly, T., Kasten, B.B., Bucar, D-K., MacGillivray, L.R., Berkman, C.E., Benny, P.D. (2011) The Hydrazide/Hydrazone Click Reaction as a Biomolecule Labeling Strategy for M(CO)3 (M = Re, 99mTc) Radiophar-maceuticals. Chemical Communications, 47, 12846-12848.

Tyson Koepke

Koepke,T., Schaeffer,S., Krishnan,V., Jiwan,D., Whiting,M., Oraguz-ie,N. and Dhingra,A. (2012, In press) Rapid SNP and Haplotype Marker Development in Non-Model Crops Using 3'UTR Sequencing. BMC Ge-nomics (an open access journal). Koepke,T., Schaeffer,S., Krishnan,V., Jiwan,D., Whiting,M., Oraguz-ie,N. and Dhingra,A. (2012, In press) Rapid SNP and Haplotype Marker Development in Non-Model Crops Using 3'UTR Sequencing. BMC Ge-

nomics (an open access journal).

So Nagaoka Nagaoka, S. I.; Hodges, C. A.; Albertini, D. F.; Hunt, P. A., Oocyte-Specific Differences in Cell-Cycle Control Create an Innate Susceptibil-ity to Meiotic Errors. Curr Biol 2011, 21 (8), 651-657.

Ryan Renslow Renslow, R.; Lewandowski, Z.; Beyenal, H., Biofilm Image Reconstruc-tion for Assessing Structural Parameters. Biotechnol Bioeng 2011, 108

(6), 1383-1394.

Daniel Rieck Zhou, Z., K. L. Li, D. Rieck, Y. Ouyang, M. Chandra, and W. J. Dong. 2012. Published online Dec/31/2011. Structural dynamics of C-domain of cardiac troponin I protein in reconstituted thin filament. J. Biol. Chem. 287:7661-7674.

James Rosser Xie, Y.; Rosser, J. M.; Thompson, T. L.; Boeke, J. D.; An, W. F., Char-acterization of L1 Retrotransposition with High-Throughput Dual-Luciferase Assays. Nucleic Acids Res 2011, 39 (3), 1-11.

Rosser, J. M., and An, W. (2012 in press). L1 Expression and Regula-

tion in Humans and Rodents. (Review) Frontiers in Bioscience

Scott Schaeffer and Tyson Koepke Schaeffer S., Koepke T., and Dhingra A. (2012, in press). Tobacco: a Model Plant for Understanding the Mechanism of Abiotic Stress Toler-ance. In N. Tujeta et al. (ed). Improving Crop Resistance to Abiotic Stress. Weinheim, Germany: Wiley-VCH Verlag GmbH & Co. KG

Schaeffer S., Koepke T., and Dhingra A. (2012, in press). Tobacco: a Model Plant for Understanding the Mechanism of Abiotic Stress Toler-ance. In N. Tujeta et al. (ed). Improving Crop Resistance to Abiotic Stress. Weinheim, Germany: Wiley-VCH Verlag GmbH & Co. KG

Nathan Tucker Tucker, N. R.; Middleton, R. C.; Le, Q. P.; Shelden, E. A., HSF1 Is Essential for the Resistance of Zebrafish Eye and Brain Tissues to Hy-

poxia/Reperfusion Injury. Plos One 2011, 6 (7) 1-11.

Brian Webb Wang, W.; Perovic, I.; Chittuluru, J.; Kaganovich, A.; Nguyen, L. T. T.; Liao, J. L.; Auclair, J. R.; Johnson, D.; Landeru, A.; Simorellis, A. K.; Ju, S. L.; Cookson, M. R.; Asturias, F. J.; Agar, J. N.; Webb, B. N.; Kang, C. H.; Ringe, D.; Petsko, G. A.; Pochapsky, T. C.; Hoang, Q. Q., A Soluble Alpha-Synuclein Construct Forms a Dynamic Tetramer. P

Natl Acad Sci USA 2011, 108 (43), 17797-17802. .

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