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October 2005 Archive

ISU's Science Librarian - Andrea Dinkelman - October Newsletter (10/26/05 ts)
New books, etc. are cited in this on-line newsletter provided to us by Andrea. The entire newsletter is available here. A few new books in the BCB area include:

Mathematics and 21st century biology / Committee on Mathematical Sciences Research for DOE's Computational Biology
Board on Mathematical Sciences and Their Applications
Division on Engineering and Physical Sciences
National Research Council of the National Academies

Washington, DC : National Academies Press, c2005.
QH323.5 M376 2005
Online Book

Bioinformatics basics : applications in biological science and medicine / edited by Lukas K. Buehler, Hooman H. Rashidi.
Boca Raton : Taylor & Francis, 2005.
QH324.2 .R37 2005

Introduction to bioinformatics / Arthur M. Lesk.
Oxford ; New York : Oxford University Press, 2005.
QH507 L47 2005 Note: This is the second edition.
More Information

Information and its role in nature / J.G. Roederer.
Berlin : Springer, 2005.
QH507 R64x 2005

Computational genome analysis : an introduction / Richard C. Deonier, Simon Tavaré, Michael S. Waterman.
New York : Springer, 2005.
QH438.4.M33 D46 2005
More Information

Research Grants Received by BCB Faculty (10/26/05 ts)
Congratulations to the BCB faculty who have received grants in recent months. Here are just some of those grants which were noted in ISU's Research in Brief or the Plant Sciences Institute Update publications.

To Srinivas Aluru and Arun Somani, ECpE; Pat Schnable, Agron; and Robert Jernigan, BBMB; MRI: Acquisition of a 512 -Node Bluegene/L Supercomputer for Large-Scale Applications in Genomics and Systems Biology from the National Science Foundation, $600,00.
To Adam Bogdanove, Plant Path, Genomics of Rice Susceptibility to Bacterial Diseases from the National Science Foundation, $225,075
To Erik Vollbrecht and Volker Brendel, GDCB, VCA: A Two Component AC/DS Platform for Reverse and Forward Genetic Analysis in Maize from the Boyce Thompson Institute for Plant Research, Inc., $245,306
To Volker Brendel, GDCB, Database of Maize Genome Information from the USDA, $70,000
Philip Dixon, Stat, Statistical Analysis of Missouri River Fish Community Data from the Department of Interior, Fish and Wildlife Service, $4,717
To Vasant Honavar, Comp Sci; Drena Dobbs, GDCB; and Robert Jernigan, BBMB; Discovery of Protein Sequence Structural Function Relationships from the National Institutes of Health, $273,942
To Karin Dorman, Stat, Statistical, Computational, and Genetic Analysis of HIV Recombination from the National Institutes of Health, $237,216
To Heather Greenlee, BMS, Non-Invasive Antemortem Cocular Function Screening Test for Transmissible Spongiform Encephalopathy from the USDA, $175,091
To Mark Hargrove, BBMB, Structure and Function of Human Hexacoordinate Hemoglobins from the National Institutes of Health, $217,005
To W. Allen Miller, Plant Path, Mapping the sgRNA2 and sgRNA3 Promoters of BYDV from the National Institutes of Health, $29,751
To W. Allen Miller, Plant Path, Deciphering - 1 Frameshifting Cis Acting Domains in BYDV from the National Institutes of Health, $49,928
To Chris Minion, VMPM, Construction of Listeria Monocytogenes Microarrays from USDA, $16,000
To Marit Nilsen-Hamilton, BBMB, Tracking Stem Cells with Imagetags from the National Institutes of Health, $229,834
To Marit Nilsen-Hamilton, BBMB, Coupled Biological and Mathematical Models of Neuronal Pattern Formation f rom the National Institutes of Health, $285,586
To Reuben Peters, BBMB, Rice as a Model System for Investigating Diterpene Synthases from the USDA, $232,000
To Max Rothschild, An Sci, Discovery and Validation of Genetic Markers for Sow Longevity from the National Pork Board, $60,000
To Steven Lonergan, Elisabeth Lonergan and Max Rothschild, An Sci, Continued Selection for Rapid Growth: Implications for Pork Quality from the National Pork Board, $90,412
To Pat Schnable, Agron, VCA - A High-Density Genetic Map of Maize Transcripts from the National Science Foundation, $1,304,309
To Pat Schnable, Agron, Essential Nature of Fatty Acid Elongation in Plant Development from the National Science Foundation, $130,000
To Randy Shoemaker, Agron, SoyMap: An Integrated Map of Soybean for Resolution and Dissection of Multiple Genome Duplication Events from Purdue University, $194,708
To Dan Voytas, GDCB, A Highly Efficient Homologous Recombination System for Plants from the National Science Foundation, $463,267
To Dan Voytas, GDCB, IGERT - Computational Molecular Biology Training Group from the National Science Foundation, $588,144
To Jonathan Wendell and Joshua Udall, EEOB, Gene Expression in Polyploid Cotton from the USDA, $360,000
To Jonathan Wendell, EEOB, Comparative Evolutionary Genomics of Cotton from the National Science Foundation, $73,500
To Roger Wise and Steven Whitham, Pl Path; Dan Nettleton, Stat; and Julie Dickerson, ECpE; ISGA: Functional Genomics of Plant Disease Defense Pathways from the National Science Foundation, $548,380
To Diane Birt, FSHN, and Eve Wurtele, BBMB, Center for Research on Botanical Dietary Supplements from the National Institutes of Health, $171,905
To Edward Yu, Phys & Astro, Efflux Pump Mechanisms for Drug Recognition/Extrusion from the National Institutes of Health, $248,731

Biotech Career Day TODAY! (10/19/05 kmw)
Biotechnology Career Day 2005 is being held today, October 19, from 9 am to 3 pm in the Molecular Biology Building atrium. Don't miss this chance to learn about internship, job and post-doc opportunities in biotechnology-related fields!

Companies attending include:

Abbott & Associates
Biomedical Research Training Program - University of Nebraska
Cargill
Integrated DNA Technologies, Inc.
Iowa Careers Consortium
Kemin Industries
Lab Support
LAS Career Services
Monsanto
NewLink Genetics
Oklahoma Medical Research Foundation
Pioneer Hi-Bred International, Inc.
Sigma-Aldrich Corporation
University of Iowa Carver College of Medicine
University of Iowa College of Pharmacy

Baker Center Seminar Monday, October 17 (10/17/05 kmw)
Dr. Kevin Plaxco, University of CA Santa Barbara, presents My protein folds faster than yours: an experimentalist's view of protein folding theory at 1:10 pm today, Monday, October 17, in Alliant Energy-Lee Liu Auditorium in Howe Hall. The seminar is another in the Baker seminar series, which is co-sponsored by IGERT and the Laurence H. Baker Center for Bioinformatics and Biological Statistics.

Filing your Program of Study Committee Form (10/14/05 ts)
A bit of administrative business...if you entered ISU in Fall, 2004, it's time to file your Program of Study Committee form...Please talk with your major professor about membership choices for your committee. Then download the the Committee Appointment Form from the Grad College's site at: http://www.grad-college.iastate.edu/forms/forms.html.

Once you and your committee members sign the form, return it to Trish Stauble, if you are a BCB major, and she will get Srinivas Aluru's signature on the form as Director of Graduate Education (DOGE) for the major.

Again, for BCB majors, your major and co-major profs should be members of the BCB faculty. Let Trish know if you have any questions or concerns about this paperwork.

MGET Mini Grants Available (10/12/05 kmw)
Attention, MGET Fellows! Is there a conference you've been wanting to attend? A short course that would really give your research a boost? Computer software that would help you work magic with your results? An internship that would expand your horizons?

MGET has available mini grants to help enrich your PhD training. Requests for up to $1,000 will be considered. Just complete the application and submit it by the deadline; note that grants are available for Spring 2006 or Summer 2006. Funds must be expended by August 15, 2006. Questions? Contact Kathy.

MGET Fellowship Award Competition Announced (10/7/05 kmw)
We're pleased to announce the MGET Fellowship Award Competition. These awards will provide a six-month stipend of $11,500 beginning January 1, include full tuition (half paid by MGET, half by the Graduate College) and cover all standard fees for Spring 2006. All MGET PhD students whose two-year MGET fellowship support will have concluded by January 1 are eligible to apply.

Application deadline is November 11.

Dr. Jianpeng Ma to Present October 14 Baker Seminar (10/7/05 kmw)
Dr. Jianpeng Ma, Department of Biochemistry and Molecular Biology at Baylor College of Medicine, will present the October 14 Baker Center seminar at 12:10 pm in Alliant Energy-Lee Liu Auditorium in Howe Hall (1140 Howe Hall). The seminar, titled New methods for simulating, refining and modeling supermolecular complexes at multi-resolution and multi-length scales, is free and open to the ISU computational biology community. This seminar will be beamed live to New Mexico State University (NMSU) as part of the ISU-NMSU NSF-IGERT partnership. See the full slate of Baker Center seminars.

Pan Du, BCB Graduate Student, Presents Dissertation Research (10/6/05 ts)
Pan Du, PhD Student Co-Majoring in BCB and Electrical Engineering will present Multi-scale Genetic Network Inference based on Time Series Gene Expression Profiles at a seminar on Monday, October 10 at 9 a.m. in 2222 Coover. The seminar is open to the public.

Pan Du's co-major professors, Julie Dickerson and Dr. Eve Wurtele oversaw his research project which integrates multi-scale clustering and short-time correlation to estimate genetic regulatory networks with different time resolutions and detail levels.

Gene expression data are noisy and large scale. Clustering is widely used to group genes with similar pattern. The cluster centers can be used to infer the genetic networks among these clusters. This work introduces the Multi-scale Fuzzy K-means clustering algorithm to uncover groups of coregulated genes and capture the networks in different levels of detail.

Time series expression profiles provide dynamic information for inferring gene regulatory relationships. Large scale network inference, identifying the transient interactions and feedback loops as well as differentiating direct and indirect interactions are among the major challenges of genetic network inference. Pairwise time correlation can detect linear interactions between genes. Estimates of the time delay and direction of causality in the inferred network can also be made. Partial correlation and d-separation theory are combined to differentiate the direct and indirect interactions and identify feedback loops. Gene expression regulation can happen in specific time periods and conditions instead of across the whole expression profile. Short-time correlation can capture transient interactions.

The network discovery algorithm was validated using yeast cell cycle data. The algorithm successfully identified the yeast cell cycle development stages, cell cycle and negative feedback loops, and indicated how the networks dynamically changes over time. The inferred network reflects most interactions previously identified by genome-wide location analysis and matches extant literature results. The inferred network provides more detailed information about genes (or clusters) and the interactions among them. Interesting genes, clusters and interactions were identified, which match the literature and the gene ontology information and provide hypotheses for further studies.

Dean Adams, BCB Faculty member in EEOB, Presents Seminar (10/6/05 ts)
Dean Adams (Ecology, Environment and Organismal Biology), will present Ecology, Evolution, and the Nature of the Phenotype at the EEOB Seminar Series today. The seminar begins at 4:10 pm in 210 Bessey and is open to the public.

Dr. Adams' research is motivated by two-longstanding questions concerning how ecological and evolutionary forces generate and maintain species diversity and phenotypic diversity. His work is both empirical and theoretical, where computational, mathematical, statistical and quantitative morphological methods are integrated to examine ecological hypotheses from an evolutionary perspective. His empirical research examines species interactions, community organization, and the evolution of phenotypic diversity, largely in Plethodon salamanders. These studies examine patterns of phenotypic variation within and among populations, to understand the ecological and evolutionary processes responsible for generating phenotypic diversity, and regulating community structure. In his theoretical research, Dr. Adams develops new analytical tools for examining patterns of phenotypic variation, with current emphasis on a general analytical framework for assessing multivariate patterns of phenotypic change. This approach provides unifying perspective from which researchers studying phenotypic plasticity, biomechanics, ontogeny, and quantitative genetics, can explore the mechanistic processes underlying patterns of phenotypic change.

Dr. Chou at this Week's BCB Faculty Seminar (10/5/05 kmw)
Hui-Hsien Chou (Genetics, Development & Cell Biology and Computer Science), will present Daily bioinformatics - sampling the use of computers in everyday biological research at the BCB Faculty Seminar on Friday, October 7. The seminar will begin at 12:10 pm in E164 Lagomarcino and is open to the public.

First Thursday October 6 (10/5/05 kmw)
Our BCB-IGERT-MGET First Thursday supper and social will be held 5:00-6:30 pm on October 6 in 1102 Molecular Biology. To help us plan, please let us know whether you will be able to attend. We hope to see you there!

Goodies and Give-Aways! (10/5/05 kmw)
As part of customer service week October 3-7, the ISU student and scholar insurance office is having a customer appreciation day, Thursday October 6th. They promise goodies, give-aways and a drawing for all who fill out their brief customer service survey.

Upcoming Teaching Workshops for Grad Students (10/3/05 kmw)
This in from the Center for Excellence in Learning and Teaching (CELT):

The Center for Excellence in Learning and Teaching is presenting a series of workshops this fall especially for graduate students.

Graduate Student Focus: Grading will be held Wednesday, October 12, from 5-6:30 p.m. in Room 104 Lab of Mechanics (note location change from the Memorial Union). CELT assistant director Donna Kienzler will provide ideas for fast, fair and effective grading. Grading practices in different fields will also be addressed. A pizza dinner will be provided.

This semester's last Grad Student Focus seminar will be

Grad Student Focus: Classroom Discussion
Wednesday, November 2, 3:30-5 p.m.
South Ballroom, Memorial Union.

To register for any of these events, contact CELT at celt@iastate.edu or 294-5357.

October Birthdays (9/28/05; editied 1-4-07 kmw)
In October, we have more reasons than ever to celebrate!

Happy, happy birthday, everyone!

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