Conferences Topics for Dr. Hardies' sections.
Each of these is an assignment to try out one of the University's Bioinformatics software systems and give a presentation about it of ~30 min.to the class.

1) Demonstrate Vector NTI for tracking features on sequence as it is moved from one clone to another.

• This exercise requires a Microsoft Windows PC or a Mac OsX PC. The student will be given a sequence file corresponding to a protein expression clone, and a corresponding description of sequencing primers, vector/insert boundaries, etc.  Also some PCR primers will be stated to lift out subsections of the clone containing proposed protein domains.  The exercise is to create a Vector NTI version of the sequence with the features all marked, and then demonstrate the recombination with the sequence features attached. Details. Anyonya Guntur, Wed. March 16.

• This is to be done in Dr. Demeler's office on the SGI set up to run Insight II.  Take screen shots and explain both the process and describe the ease/difficulty of using the Insight II system. Details. Thomas Millstead, Wed. March 16.

• This is to be done with the Wisconsin GCG package running on the Bioinformatics Center's bioinf computer and accessed by ssh from a Microsoft Windows PC or MacOsX or by a computer running Linux Live..  A problem is given in which an insert is moved from one expression vector to another and poor expression is observed in the second vector.  The object is to use GCG mfold to look at mRNA secondary structure around the initiation site to see if the observations might be justified as a secondary structure problem.  Demonstrate screen shots of the various graphics available for secondary structure from this program.  Details. Jiayan Guo, Wed. March 16.

• This exercise requires a Microsoft Windows PC connected to the university network.  This is to be done on the site-licensed Oligo 6.0 system.  A failed  PCR primer pair for a particular experiment will be described.  The object will be to use Oligo 6.0 to analyze the problem primers and propose either better primers. Also suggest  altered conditions to save the failed primer pair. Details. James Trbovich, Mon. March 21.

• This is to be done with bioinformatics core facility software.  Details. Dhananjaya Nayak, Mon. March 21.

• This is to be done with the site-licensed LaserGene system.  The student will be given a couple of sets of sequence reads to assemble.  The student should examine the capability of the LaserGene system to assemble the data.  Then the student is requested to consult with Dr. Hardies to conduct a comparison of the LaserGene performance with that of phred/phrap running at the Bioinformatics core facility. Details. Renjing Wang, March 21.

CONFERENCE TOPICS for Dr. Henn's sections:
These will be ~30 minute presentations of the papers as indicated below.
For the following topics, expectations are (a) clear presentation of the genetic/cellular background of strains and methods, (b) presentation of key experimental data and results and (c) an overall summary of the impact of the results in the specific field of interest.

 (7) Murphy, B.A. et al. (2003) Transcription termination control of the S box system: direct measurement of S-adenosylmethionine by the leader RNA.  Proc. Natl. Acad. Sci. USA: 100:3083-3088.  [an example of the importance of riboswitch mechanisms for control of bacterial gene expression]. Jennifer De Luna, April 4.

 (8) Martin, D. E. et al. (2004) TOR regulates ribosomal protein gene expression via PKA and the forkhead transcription factor FHL1.  Cell 119:969-979.  [an example of the use of the yeast system for dissection of a signaling pathway]. Eugene Maes, April 4.

 (9) Outeiro, T.F., and S. Lindquist (2003) Yeast cells provide insight into alpha-synuclein biology and pathobiology.  Science 302:1772-1775.  and
Willinghaim, S. et al. (2003) Yeast genes that enhance the toxicity of a mutant huntingtin fragment or alpha-synuclein.  Science 302:1769-1772.  [examples of the use of the yeast system to examine the molecular basis for a human disease]. Jialu Liu, April 4.

 (10) Lee, T., and L. Luo (1999) Mosaic analysis with a repressible cell marker for studies of gene function in neuronal morphogenesis.  Neuron 22:451-461.  [an example of the application/development of a molecular genetic method in Drosophila]. Srikanth Polusani, April 13.

 (11) Leidel, S. et al. (2005) SAS-6 defines a protein family required for centrosome duplication in C. elegans and in human cells.  Nature Cell Biol. 7:115-125.  [an example of the use of siRNA and C. elegans to analyze human protein orthologs]. Qian Lu, April 13.

 (12) Sasaoka, G.Z. et al. (2004) Deletion of the PDGFR-? gene affects key fibroblast functions important for wound healing.  J. Biol. Chem. ; Epub ahead of print.  [an example of the application of Cre-lox technology to dissect a mammalian signaling pathway]. Duane Winkler, April 13.