BCBLab - Bioinformatics Consulting at ISU

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The BCBLab began in 2006 when BCB Graduate Students, Matthew Moscou (Roger Wise, major professor in Plant Pathology) and Yves Sucaet (Eve Wurtele, major professor in GDCB) were discussing their desire to do some consulting work on campus.  They had discussions with the BCB program coordinator and BCB faculty administrators, and out of those discussions and many others, the BCBLab was born.

The BCBLab provides a consulting experience for participants as they help life science researchers on campus integrate Big Data techniques and analysis into research projects. By working together to apply computational and bioinformatics solutions to biological problems through the BCBLab, our student body has created a vibrant learning community where they contribute to and learn from one another. Those who participate learn from the exchange of experience, knowledge, and resources with one another while making substantial contributions to on-going research efforts.

Past BCBLab projects have ranged from porting legacy Fortran applications to PHP/MySQL, to structure determination and microarray analysis. The BCBLab helped create the Iowa-mosquito.net, a web portal for mosquito surveillance information, 1969 to present. More recently, and importantly, a member of the BCBLab worked on TAL effector mediated genome editing in the course of a BCBLab project. This research was foundational to CRiSPR and the evolution of genome engineering ! Recent graduates from the program have highlighted such consulting experiences on their resumes to their benefit.

Below are some formation documents as well as some early progress reports on activities followed by more recent information on projects accomplished by the group.

BCBLab Proposal-May 10, 2006

BCBLab-Progress Report - May 2007

BCBLab Activity Summary 2007-2008

BCBLab Poster - March 2008

BCBLab Confidentiality Agreement

BCBLab - Rights and Responsibilities

Information on past projects

 

LIST OF BCBLab PROJECTS (2012-2013)

 

1. Dr. Ling Li (Dept. of Genetics, Development & Cell Biology)

 

Project: Identify one gene expression data from sequencing data (RNAseq): check if this gene is expressed under different conditions/in different species.

 

2. Dr. Gregory Phillips (Dept. of Veterinary Microbiology & Preventive Medicine)

 

Project: To enumerate the number of restriction enzyme recognition sites, or other short DNA sequences, in bacterial genomes of interest.  He would like to be able to access a sequenced genome from GenBank and then enter a short sequence, such as "GAATTC", and then have the program count the number of times this sequence occurs in the circular genome.

 

3. Jeanne M. Serb (Dept. of Ecology, Evolution and Organismal Biology)

 

Project: Scallop opsin protein structural analysis (The student who works on this project would earn authorship on the resulting publication)

 

All animals with light sensitivity possess a visual pigment composed of an apoprotein, opsin, and a light-sensitive chromophore derived from vitamin A. The opsin protein is composed of a series of amphipathic α-helices that span the photoreceptor membrane seven times (TM I-VII), forming a pocket within the membrane to enclose the chromophore (Findlay 1986; Hargrave 1991). The chromophore binding pocket (created by TM III, VI, and VII) is known to have a significant interaction with the chromophore (Wald 1968; Zhukovsky & Oprian 1989; Nakayama & Khorana 1990, 1991; Sakmar et al. 1991; Chan et al. 1992), which is covalently bound to opsin by a lysine residue (Lys-296) in the center of TM VII (Findlay 1986). Amino acid substitutions in the chromophore-binding pocket can have profound consequences by
altering the interaction between opsin and its
chromophore. Change of amino acid residues at just a few
positions of the chromophore binding pocket account for most of observed variation in
spectral sensitivity of visual pigments (Yokoyama 1995 and references within).

 

Our lab has identified two opsin copies in scallops that differ from one another by 45% of the amino acid sequence. We would like to predict the ramifications of these divergent sequences on protein structure. Preliminary protein structure prediction using Geneious v. 5.6 (Drummond et al. 2011) suggests these scallop opsin copies may also differ in how the protein folds to form the chromophore-binding pocket. However, more detailed modeling of these opsin proteins is needed.

 

There are two major aims for the project. First, to predict the protein structure for each scallop opsin copy (A1 vs. B1) using homology modeling (for example, SWISS-MODEL, Schede et al. 2003) with the crystal structures of bovine (Palczeski et al. 2000) and squid (Murakami & Kouyama 2008) opsin proteins. Second, to model the mutations observed in our 35 species dataset using the threaded structures and describe the biochemical implications of each mutation.

 

4. Julia A. Kuhlman (Dept. of Genetics, Development & Cell Biology)

The project would be on analyzing Next Gen sequencing data to discriminate SNPs from mutations.

Need to discuss with her sometime with the student. She is interested in taking a student for rotation also. But we could do a BCBLab project too on the downstream analysis of the data resulting from her experiments.

5.       Dean Adams (Dept. of Ecology, Evolution and Organismal Biology)

Project (Quoted from his mail): “I am finishing up a software package in R for distribution. One of the functions can take a very long time to run, particularly on large datasets. Thus, I wish to re-write the algebra for this routine in C++, and have R access the compiled C code. Unfortunately, while I program in R, Pascal, and Perl, I do not write C++.

 

I am looking for a BCB student with knowledge of C that can translate my R function into C, so that I can then run this function more efficiently and rapidly.  I expect the project will only be a few weeks’ tops, and would of course result in acknowledgement for the student as co-writer of this routine in R, and acknowledgement in the subsequent publications.”

6.       Christopher K. Tuggle (Dept. of Animal Science)

Project details not yet discussed. But a survey of the areas he works on should give an idea.

NOTE: I will be discussing with him tomorrow on the project. If any student is interested in his project, please mail me (ksankar@iastate.edu) and we can meet him together.