Fall 2004 3 5 6 7 8 by gdf57j

VIEWS: 8 PAGES: 8

									Functional Genomic                                        Professor Hans Bohnert                                Fall 2004
Analysis of Germ Cell                                     is Interim Director of the                             IN THIS ISSUE
Development in Planarians                                 W.M. Keck Center
                                                                                                                        3
Dr. Phillip A. Newmark is an Assistant Professor in       When I arrived at UIUC more than 2 years            2004 Catherine Conner
                                                                                                              Outstanding Dissertation
the Department of Cell and Structural Biology. He         ago, the existence of the Biotechnology Center,        in Biotechnology
received his Ph.D. in Molecular, Cellular, and De-        specifically the W. M. Keck Center for Com-
velopmental Biology from the University of Colorado       parative and Functional Genomics, provided a                  5
at Boulder and performed postdoctoral research at the     significant attractor. The instruction, general      Affymetrix Workstation
                                                                                                                    Upgrade
University of Barcelona and the Carnegie Institution of   help, and specific trouble-shooting for my lab
Washington’s Department of Embryology. He joined          by the Keck folks have been superb. Who would                 6
the UIUC faculty in August 2001.                          not be impressed by the instrumentation and the        High Throughput
                                                                                                                   Proteomics at
                                                          expertise that is available? The Center supports     Biotechnology Center
Since the late nineteenth century, when Weis-
                                                          the role of faculty as teachers of new technolo-
mann proposed that an immortal germ line
was propagated from generation to generation,
                                                          gies, provides high-throughput platforms, and                 7
                                                          it is my sincere hope that this will continue and   Ryan Kim, New Director
producing a mortal soma at each generation,                                                                      of High-Throughput
                                                          expand even further. Recently, I have become            Sequencing and
biologists have been intrigued by the question
                                                          involved in an advisory role with the Compara-         Genotyping Unit of
of how the germ cell lineage is established.                                                                   the W.M. Keck Center
                                                          tive and Functional Genomics unit. After a few        for Comparative and
In addition to serving as a link between gen-
                                                          months, I can say that the day-to-day perfor-         Functional Genomics
erations, the germ cells represent an intriguing
                                                          mance is characterized by efficiency, compe-
example of cellular differentiation, in which
                                                          tence and easy communication, managed by the                  8
highly differentiated cell types maintain their                                                                Biotechnology Center
                                                          directors in the individual groups (http://www.            Personnel
totipotentiality and are capable of reproducing
                                                          biotech.uiuc.edu/keck.shtml) and the Biotech-
themselves indefinitely.
                                                          nology Center administration (http://www.
Two distinct modes of germ cell specification              biotech.uiuc.edu/).
are generally observed in animals. In the most
                                                           Taking stock, these URLs show the equipment
commonly studied invertebrates, Drosophila
                                                          and methodologies available, and—important-
and C. elegans, maternally supplied cytoplasmic
                                                          ly—this equipment is efficiently used by people,
determinants localized to the posterior of the
                                                          who love to interact with whoever wishes to use
embryo specify the germ cell lineage early in em-
                                                          these tools. In July 2003 a new DNA sequencer,
bryogenesis. Likewise, localized determinants
                                                          the ABI3730, arrived that resulted in longer
play a role in germ cell specification in many
                                                          read lengths of sequences, a higher sequencing
vertebrates (e.g., zebrafish, chickens, anuran am-
                                                          success rate, and faster turnover due to shorter
phibians). The specification of germ cells early
                                                          run times. Also this summer, a second ABI3730,
in embryogenesis by localized maternal deter-
                                                          funded through an NIH Shared Instrument
minants has been termed “determinate” germ                                                                      Dr. Hans Bohnert
                                                          Grant, went on line. We have recently lowered
cell specification. Alternatively, many organisms
                                                          sequencing costs as a result of the efficiency of
utilize inductive interactions to specify their
                                                          these instruments. The Keck Center has highly
germ cells relatively late in embryogenesis. This
                                                          competitive prices for DNA sequencing, analyz-
“epigenetic” specification is observed in mam-
mals as well as a wide range of basal invertebrate        ing the output, and database management. The

                                  continued on page 2                                   continued on page 4
                           2     Biotech Center News



Functional Genomic Analysis of Germ Cell Development in Planarians, continued from page 1

                         groups, such as sponges, cnidarians, and flat-       are resorbed, only to be regenerated when the
                         worms. Recently, tremendous strides have been       animal reaches the appropriate size after feeding
                         made in understanding the mechanisms of germ        is resumed. Following amputation of the head of
                                                   cell determination;       sexually mature animals, the testes are resorbed
                                                   however, the molec-       and are only reformed after the regeneration
                                                   ular mechanisms that      of the head is complete. Thus, inductive influ-
                                                   may link determi-         ences are important for sexual differentiation
                                                   nate and epigenetic       in planarians.
                                                   specification of germ
                                                                             The planarian Schmidtea mediterranea is the sub-
                                                   cells remain obscure.
                                                                             ject of our laboratory’s studies. A tremendous
                                                   Ongoing work in the
                                                                             advantage of using this species for studying
                                                   Newmark labora-
                                                                             germ cell specification and differentiation is that
                                                   tory seeks to expand
                                                                             genetic differences appear to be responsible for
                                                   our understanding
                                                                             determining the mode of reproduction. Thus,
                                                   of epigenetic speci-
                                                                             sexual and asexual strains of S. mediterranea can
                                                   fication of germ cell
                                                                             be distinguished by a chromosomal transloca-
Drs. Phillip Newmark,    fate using the freshwater planarian as a model
Ricardo Zayas, and
                                                                             tion present in the asexual strain. Individuals
                         organism.
Alvaro Hernandez (left                                                       harboring this translocation reproduce only by
to right)                Planarians are free-living, freshwater members      transverse fission and do not differentiate germ
                         of the phylum Platyhelminthes, the flatworms.        cells, somatic gonad, or the copulatory appara-
                         Flatworms are among the simplest animals with       tus; conversely, individuals lacking this translo-
                         three tissue layers (triploblasts) that display     cation are hermaphroditic and do not reproduce
                         bilateral symmetry, an anterior concentration       asexually. The genome of this species is currently
                         of neural tissue, and the organization of spe-      being sequenced by the Washington University
                         cialized tissues into organs. Planarians repro-     Genome Sequencing Center in St. Louis.
                         duce either asexually, by transverse fission, or
                                                                             With the goal of identifying genes required for
                         sexually, as cross-fertilizing hermaphrodites. In
                                                                             germ cell specification and differentiation, we
                         the asexual mode of reproduction, the worm
                                                                             are working with the Keck Center for Compara-
                         splits itself transversely into two fragments,
                                                                             tive and Functional Genomics to generate a col-
                         each of which regenerates the missing tissue,
                                                                             lection of expressed sequence tags (ESTs) from
                         thereby producing two planarians. In the sexual
                                                                             the sexual strain of S. mediterranea (supported
                         mode, hermaphrodites cross-fertilize, then lay
                                                                             by NSF CAREER Award IBN-0237825 to
                         egg capsules that contain several embryos. In
                                                                             PAN). Alvaro Hernandez at the Keck Center has
                         sexually reproducing planarians the germ cell
                                                                             produced the normalized and subtracted cDNA
                         lineage does not appear to be segregated during
                                                                             libraries that are being sequenced. To date we
                         embryogenesis; rather, when the planarian at-
                                                                             have sequenced over 13,000 ESTs; bioinformat-
                         tains sufficient size, gonads and the copulatory
                                                                             ics analyses by post-doc Ricardo Zayas reveal
                         apparatus are formed de novo in the appropriate
                                                                             that these ESTs represent over 6,500 unique
Planarian (courtesy of   regions of the worm.
                                                                             transcripts. We will sequence ~20,000 ESTs
Ricardo Zayas)           The planarians’ remarkable regenerative abilities   that should represent approximately 9-10,000
                         have led generations of biologists to study these   unique transcripts. These ESTs will be invalu-
                         organisms. When a planarian is cut transversely     able for the annotation of the S. mediterranea
                         and separated into two fragments, the anterior      genome.
                         fragment will regenerate a new posterior end
                                                                             The unique transcripts will be used to gener-
                         while the posterior fragment will regenerate
                                                                             ate micro-arrays for examining global gene
                         a new anterior end. The germ cell lineage
                                                                             expression patterns in both sexual and asexual
                         shows a similar plasticity. Thomas Hunt Mor-
                                                                             planarians, as well as during the process of sexual
                         gan showed that a planarian head fragment,
                                                                             development. Genes that are upregulated in
                         completely devoid of any germ line structures,
                                                                             the sexual strain or during sexual development
                         could regenerate functional gonads from the
                                                                             will be analyzed further by whole mount in situ
                         remaining somatic tissue. During the de-growth
                                                                             hybridization. Automation of this technique
                         (shrinkage) that is the planarian’s response to
                                                                             permits high-throughput analysis of up to 96
                         starvation, the gonads and copulatory apparatus
                                                                     Biotech Center News              3




different genes simultaneously, allowing us to
visualize – at single cell resolution in the whole
animal the cell types in which given genes are
expressed. In this manner we will be able to
identify genes expressed in the planarian germ
cells. To examine the role that these genes play
in germ cell development, we will use double-
stranded RNA-mediated interference (RNAi)
– a technique that is quite effective in planarians       The June 2004 Microarray Methods workshop offered hands-on
– to inhibit their expression and analyze the             microarray experimentation and analysis. The BTC regularly of-
resulting effects upon germ cell development.             fers several workshops including: Microarray Methods, Statistical
Ultimately, these experiments will provide in-            Analysis of Microarray Data, Bioinformatics, Biacore Basics, and
sight into the mechanisms by which germ cells             Flow Cytometry. These workshops focus on theory, experimental
are specified via inductive interactions and the           protocols, and data analysis to assist users in applications of the BTC’s
extent to which these mechanisms have been                instrumentation to their own research projects.
conserved evolutionarily.
          Dr. Phillip A. Newmark (pnewmark@uiuc.edu)




2004 Catherine Conner Outstanding Dissertation in Biotechnology

The Biotechnology Center has established the
Catherine Conner Outstanding Dissertation in Bio-
technology award in honor of Catherine Conner’s
campus service. Catherine Conner retired as the
Biotechnology Center’s Placement Director
in 2000 after 12 years of service. This annually
recurring award is funded through a founda-
tion established through the generous gifts of
Eli Lilly, GlaxoSmithKline, Colgate-Palmolive,
Monsanto, and Merck.
Each fall UIUC graduate students who are
within one year of finishing their Ph.D. disser-
tations that focus in the areas of biotechnology,
plant, microbial or animal genomics, functional
genomics, proteomics, bioinformatics, or bio-
engineering are encouraged to participate. The         Gregory Wallace the 2004 Conner Outstanding Dissertation in Biotechnology
                                                       awardee.
posters are due in December and the winner
is presented a $1,000 monetary award at the
January Biotechnology Job Fair. We encourage           Wallace. Greg is a Ph.D. student of Professor
qualified graduate students to call the Biotech-        Stephen Kaufman in the Department of Cell and
nology Office at (217) 333-1695 for further             Structural Biology. Greg’s award winning poster
information.                                           is entitled “α7β1 Integrin Promotes Muscle
                                                       Integrity, Regeneration, and Hypertrophy in
The 2004 Catherine Conner awardee is Greg
                                                       Rescued Dystrophic Mice.”
                            4      Biotech Center News



Professor Hans Bohnert is Interim Director of the W.M. Keck Center, continued from page 1

                          facilities for generating and analyzing spotted        university. The computational pipeline from
                          oligo and cDNA microarray slides and the               sequence to storage, analysis and integration
                          Affymetrix GeneChip workstation have been              into databases must be streamlined and results
                          upgraded during the last year. Utilization by          integrated into existing databases automatically.
                          the community has picked up; soon there will           We must participate in the development of new
                          be need for more instrumentation. New tools            high-throughput platforms, and new ways to
                          for data analysis, training opportunities and          visualize, measure and quantify gene structure,
 Biotechnology            workshops make this unit the genomics hub for          transcript expression, protein complexity, pro-
 Center at the
                          the campus community.                                  tein-substrate and metabolite interactions, and
 University of
 Illinois at Urbana-                                                             providing these tools to the community. Minia-
                          Also, a new service for creating custom normal-
 Champaign                                                                       turized and improved versions of platforms that
                          ized and subtracted cDNA libraries that greatly
                                                                                 are themselves only a few years old are coming
 Jonathan Sweedler,       reduce sequencing redundancy (http://www.bio-
 PhD • Director and                                                              on line.
                          tech.uiuc.edu/customlibrary.html). This service
 Lycan Professor of
                          originated from the recognition that faculty, not      Let me illustrate with the following example.
 Chemistry
                          restricted to Illinois, will benefit from expertly      Even though we have complete genome se-
 Mark Mikel,
 PhD • Associate          constructed, quality-controlled, and certified          quences for a few model organisms, it is recog-
 Director and Editor      gene libraries. From my own experience such            nized that populations, cultivars and ecotypes of
 Hans Bohnert,            libraries reduce project cost—measured as the          species can differ in gene complexity and, even
 PhD • Interim            number full-length sequences and unigenes—by           more so, in gene regulation. Large-scale geno-
 Director of the W.M.     at least an order of magnitude. The service, with      typing, SAGE and SNP-analysis, anchored on
 Keck Center for
                          competence that comes from experience, will            a model system genome sequence, will have to
 Comparative and
 Functional Genomics      free individual labs from having to acquire the        fill in gaps that describe the diversity of related
 and Professor of Crop    appropriate expertise. The Center’s education          species or population variants of model ge-
 Sciences and Plant       and training mission includes that you construct       nomes. Diversity will also require, for example,
 Biology                  your favorite cDNA (and other) library under           GeneChip experiments to be done in multi-
 Administrative           the watchful eyes of the experts.                      well format, each well with a subset or all genes
 Office • (217) 333-
                                                                                 printed or synthesized, to advance comparative
 1695 phone; (217)        These examples document expertise and ex-
 244-0466 (fax)                                                                  genomics. High-throughput quantification by
                          cellence of the Center for Comparative and
 To add a subscription,                                                          real-time PCR will become a platform similar
                          Functional Genomics. However, a facility such
 change an existing                                                              to microarray/GeneChip hybridizations. Con-
                          as this is doomed if it were to rest on its laurels.
 subscription, or be                                                             ceivably, one service by the Center can be the
 dropped from our         We have to think about where we would like to
                                                                                 design, synthesis, distribution, analysis and
 mailing list, please     be next year, and in five years. Science is driven
                                                                                 statistical examination of quantitative transcript
 email mmikel@uiuc.       by new technologies. These days new tools
 edu. The Biotech                                                                expression in 384-well or even larger formats.
                          are conceived and implemented within a few
 Center News is free                                                             Predictive computational tools for gene expres-
 of charge.
                          years or even months. As a service facility the
                                                                                 sion control, transcript maturation/splicing,
                          W.M. Keck Center has to play ball or become
                                                                                 posttranscriptional modification or interaction
                          outclassed and unnecessary and this means up-
                                                                                 propensity will generate greater demands on the
                          grading and changing constantly.
                                                                                 bioinformatics unit.
                          Here is a list of suggestions for the Center to
                                                                                 I imagine sequencing more model genomes to
                          prepare for. Easy to predict is high-throughput
                                                                                 be in the near future, and the need for cultivar-,
                          DNA sequencing to accelerate, with new tech-
                                                                                 population-, and related-species-specific gene
                          nologies that will streamline the pipeline from
                                                                                 collections is obvious and so is the application
                          clone to sequence into more highly automated
                                                                                 of high-throughput tools for analyses of biodi-
                          processes. The Center will have to adjust to such
                                                                                 versity. Generating and maintaining BAC/YAC/
                          changes in sequencing to continue to serve the
                                                                                 TAC-based gene collections, and their partial
                                                                      Biotech Center News              5




                                                           Affymetrix
sequencing, for populations of organisms might
well become a task for the Center.
                                                           Workstation
                                                           Upgrade
Another area of rapid technological and concep-
tual change center on the integration of different         The Functional Genom-
platforms, which will require enhanced interac-            ics Unit recently updat-
tions between several units in the Biotechnology           ed its Affymetrix system
Center. An important part to satisfy this require-         to the new GC3000
ment will be expanding our bioinformatics ca-              GeneChip Scanner
                                                                                       Affymetrix 3000 Workstation for processing and
pacity, developing strong interactions with the            bringing improved per- scanning GeneChips.
academic departments in computational science              formance, higher reso-
and engineering, and enhancing those interac-              lution and greater throughput to Affymetrix experimentation. The
tions that exist. In fostering such interaction, as        GC3000 scanner is compatible with higher density GeneChips used
much as in the support of ‘wet lab’ experimen-             in new organism releases that was not compatible with our previous
tation, I also imagine increased demand for the            scanner. In addition, the Affymetrix GC3000 will enable use of hu-
Center’s mission in training, consultation and             man, mouse and rat genomes each on a single high density GeneChip.
advising on prudent experimental strategy. I               Further cost savings have been realized by Affymetrix recently pricing
hope it is obvious that I am glad to serve the             The University of Illinois for a GeneChip volume discount. Please
                                                           contact Dr. Mark Band (markband@uiuc.edu, 217.244.3930) to dis-
unit and community.
                                                           cuss applications of GeneChip technology to your research. Assistance
Dr. Hans Bohnert (bohnerth@life.uiuc.edu)                  in design and analysis of Affymetrix experimentation is available from
                                                           Dr. Lei Liu Director of Bioinformatics. Dr. Liu can be contacted at
                                                           217.265.5061 or email leiliu@uiuc.edu.




   The Custom Oligonucleotide Synthesis Facility at the
   University of Illinois Biotechnology Center, offers a
   wide variety of oligo synthesis from scale sizes to special-         Cathy Chaoran Yu was awarded $200 for the best un-
   ized modifications, produced on the four column 394                   dergraduate Student Science Poster. Ms Yu’s Poster was
   ABI Synthesizer. Scale sizes offered are 40nmol, .2umol,             entitled Microclimate Changes in Soybeans Grown in Elevated
   1umol, and 10umol. OPC and PAGE purifications are                     Carbon Dioxide and Their Effects on Insect Herbivory. The
   available at the 40nmol and .2umol scales. Our more                  award was presented at the 2004 Biotech Job Fair last
   common modifications are dye labeled oligos such as                   January at the University of Illinois. The Kimberly-
   6-FAM, TET, HET, Cy3 and Cy5. Standard and special                   Clark Company, Pierce Biotechnology, Inc., and the
   ratio ambiguous bases are available, along with many                 Biotechnology Center Placement Office sponsored the
   other unique modifications. Call Lorie Rickords or Vir-               Poster Competition.
   ginia Lukas at 217.244.1007 for further information.
                          6     Biotech Center News



                        High Throughput Proteomics at Biotechnology Center

                        The instrumentation for high throughput
                        proteomics at the Protein Sciences Facility was
                        recently acquired using funding provided by
                        a Roy J. Carver Charitable Trust sponsored
                        scientific instrumentation grant. The newly
                        acquired instrumentation includes an Ettan 2-
                        D gel electrophoresis apparatus, a Typhoon™
                        9400 multilaser scanner for gel imaging/analysis,
                        a robotic sample handling workstation, and
DIGE Gel labeled with   an Ettan MALDI ToF Pro mass spectrometer
CyDyes˙ Cy2, Cy3, and   (MS). A number of high throughput proteomic
Cy5.                    research projects are currently under way and
                        more are planned.
                                                                             Research Specialists Karen Avenatti and Jennifer
                        The 2-D gel electrophoresis is with an Ettan         Showerman using Ettan sample handling workstation.
                        IPGphor Isoelectrofocusing first dimension
                        separation followed by a DALTsix electropho-         programmed to process up to 1152 samples per
                        resis second dimension separation. With the          batch from a maximum of 12 large format 2-D
                        Ettan DIGE (Fluorescence Difference in Gel           gels in less than 36 hours. For mass spectrom-
                        Electrophoresis) system samples are labeled with     etry analysis we utilize an Ettan MALDI ToF
                        CyDyes™ (Cy2, Cy3 and Cy5) and multiplexed           Pro MS that can process 288 samples/batch and
                        for co-separation during 2-D gel electrophore-       generate a protein identification list of the spots
                        sis. The samples, usually a treatment and control,   in about 6 hours.
                        are each labeled with either Cy3 or Cy5; plus a
                        Cy2 labeled internal standard for each treatment.    Another approach is to use multiple dimensional
                        The Cy2 labeled internal standard is an excellent    protein identification technology (MudPIT)
                        way to remove gel-to-gel variation. Following        to separate and identify proteins. MudPIT is a
                        2-D electrophoresis, gels are scanned with a         liquid chromatography based method capable
                        Molecular Dynamics Typhoon™ 9400 Imager              of resolving a mixture of digested peptides
                        with 3 direct excitable lasers and DeCyder™          using tandem ion-exchange chromatography
                        Differential analysis software automatically de-     with reverse phase chromatography coupled
                        tects, matches, and analyzes spots for very small    with electrospray ionization MS (e.g. Thermo
                        differences in protein abundance between the         LCQ, Micromass Q-ToF). In collaboration
                        two samples (Cy3/Cy5) on the same gel and            with the Mass Spectrometry Laboratory at the
                        between gels through Cy2 internal standards.         School of Chemical Sciences, we are able to offer
                        After DeCyder™ analysis identifies gel spots for      MudPIT analysis for complex protein samples.
                        picking the gel is transferred to the Ettan Sample   The Protein Sciences Facility also offers Edman
                        Handling Workstation (SHW). The SHW con-             Sequencing, standard 2-D gels, HPLC, FPLC,
                        sists of a video camera and three robotic units      and peptide synthesis services. We are planning
                        working together to excise selected protein          a short workshop in proteomics methodology
                        spots from gels for preparation for subsequent       that will cover these and other protocols and
                        analysis and identification. The gel plugs are        applications.
                        then destained, washed, trypsin digested, and                               Dr. Peter Yau (pmyau@uiuc.edu) is
                        spotted on a MALDI target. The SHW can be                     Director of Proteomics at the Biotechnology Center
                                                                     Biotech Center News             7




Ryan Kim, New Director of High-Throughput Sequencing and Genotyping Unit of
the W.M. Keck Center for Comparative and Functional Genomics
In February Dr. Ryan Kim and his family arrived in     microarray technology (Af-
Champaign from sunny La Jolla California in time       fymetrix GeneChip, cDNA-,
to experience an Illinois winter. Ryan Kim earned      oligo-, and promoter array) for
his Ph.D. in Molecular and Cell Biology from the       the prognosis of prostate and
University of California at Davis in 1997. Dr. Kim     ovarian cancer.
was previously Senior Research Scientist and Manager
                                                       The W. M. Keck Center for
of the Genomics Core at the Sidney Kimmel Cancer
                                                       Comparative and Functional
Center at La Jolla.
                                                       Genomics offers comprehen-
It is a great pleasure to be a part of the highly      sive services in DNA sequenc-
spirited, skilled, and dedicated DNA sequenc-          ing and genotyping, functional
ing team of the High-Throughput Sequencing             genomics, and bioinformatics.
and Genotyping Unit here at the W.M. Keck              The Sequencing and Geno-
                                                                                                       Dr. Ryan Kim
Center. I have extensive experience in molecular       typing Facility is fully staffed
biology and genomics in both plant and animal          and equipped to perform high throughput and
systems. During my post-doctoral training at           core DNA (plasmid, BAC, and PCR products)
Michigan State University my research included         sequencing, genotyping, synthesize custom
genome-wide expression profiling on regulatory          cDNA (normalized and subtracted plasmid)
genes that control the biosynthetic pathways of        libraries, and custom oligonucleotide synthesis
vitamin A and E in the marigold petal by using         (including modified oligos). Recently we ac-
high-throughput sequencing of a petal EST li-          quired second ABI 3730XL capillary sequencer.
brary and global gene expression profiling using        This sequencing platform offers state-of-the-art
spotted DNA microarray. This project resulted          sequencing by yielding longer read lengths,
in identification of developmentally regulated          higher success rates at lower input costs com-
genes and assignment of new functions to previ-        pared to previous sequencers. This acquisition
ously unknown genes. Many of these newly dis-          has substantially expanded our sequencing ca-
covered genes are tightly regulated during petal       pacity and contributed to lower pricing for our
development and may provide insight into their         sequencing services.
role in secondary metabolism. Most recently,
                                                       We offer quick turn around (often next day)
as a senior scientist and manager of Genomics
                                                       in both our core DNA sequencing (small scale
Core at Sidney Kimmel Cancer Center in San
                                                       sequencing and primer walking) and oligonu-
Diego, California, I acquired expertise using
                                                       cliotide synthesis services. We are continuously
high throughput applications of genomics in
                                                       improving and customizing our protocols to
cancer research. I investigated and established
                                                       expand high throughput capacity to be more
high throughput genotyping procedures (in situ
                                                       cost effective and offer higher quality DNA
PCR and extension on microarray slide) to de-
                                                       sequencing. Please feel free to stop by and visit
termine SNP genotypes of ≥8,000 human DNA
                                                       the laboratory. I look forward to working with
for prognosis of ovarian cancer. I also worked on
                                                       you and wish you continued success and growth
the development of high throughput analysis
                                                       of your research program.
of promoter activity and RNA stability using
                                                                            Dr. Ryan Kim (wrkim@uiuc.edu)

                                                                                                            The High-Throughput
                                                                                                            Sequencing and
                                                                                                            Genotyping Team
                           8   Biotech Center News



                       Biotechnology Center Personnel

                       This summer both Allison Reese and Evette Vlach began working in the
                       High Throughput DNA Sequencing Unit of the W.M. Keck Center. Ms.
                       Evette Vlach earned her B.S. degree in Ecology, Ethology, and Evolution
                       in 2000 from the University of Illinois. Evette was formerly at the Illinois
                       Natural History Survey where she worked on West Nile Virus in the state
                       of Illinois. In the Keck Center, Evette will be working on robotic colony
                       picking using the Genetix Q PIX. Ms Allison Reese earned her B.S. in
                       Animal Sciences, with a minor in Chemistry, in 2003 from the University
                       of Illinois. Allison was formerly an Academic Assistant in the College of
                       Agricultural, Consumer, and Environmental Sciences at UIUC. At the
                       Keck Center, Allison will be working on both Core DNA sequencing and
    Evette Vlach                                                                                      Dr. Jyothi Thimmapuram
                       robotic plasmid preps.
                       Dr. Jyothi Thimmapuram has joined the Bioinformatics Unit of the W.
                       M. Keck Center. Dr. Thimmapuram earned her Ph.D. in Physiology and
                       Molecular Biology from the University of Illinois in 1996. She brings
                       expertise in bioinformatics, functional genomics, and computer science
                       to assist the users of the Keck Center.
                       Mr. Al Bari has accepted the position of Laboratory Supervisor in the
                       Functional Genomics Unit. Al has extensive expertise in numerous ro-
                       botic applications. He has a leadership role in maintaining and using the
                       OmniGrid 100 in applications of printing oligonucleotide and cDNA
                       spotted microarray slides.
    Allison Reese                                                                                            Al Bari




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                                                                                                              U.S. Postage
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103 Observatory                                                                                             Champaign, IL
901 S. Mathews Avenue
Urbana, IL 61801
PHONE: (217) 333-1695
FAX: (217) 244-0466

								
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