Department of Biology

Program

Molecular, Cellular & Developmental Biology

Research Area

Genomics and Bioinformatics

Education

Ph.D., Melbourne University, 1994Postdoctoral Fellow, National Institutes of Health, 1995-2000Postdoctoral Fellow, University of Geneva, 2000-2001

Research Description

A central process in the development of multi-cellular organisms is the specification and differentiation  of distinctive cell types.  My lab is focused on understanding how gene regulatory networks control developmental decisions.  We are taking a multidisciplinary approach -- incorporating genetics, molecular biology, genomics and bioinformatics -- to study regulatory networks controlling sex in two arthropod model organisms  -- the vinegar fly Drosophila melanogaster, and the freshwater crustacean Daphnia pulex. Sex specification and differentiation in the germline of Drosophila In Drosophila sex is determined by the number of X-chromosomes relative to the number of autosomes -- embryos with two X-chromosomes develop as females and those with one X-chromosome develop as males.  The most dramatic sexual dimorphism is found in the germline.  Germ cells differentiate to make either eggs or sperm with radically different cellular specializations.  This is reflected at the molecular level with germ cells showing dramatic sex-biased gene expression.  How is this regulated?  From previous studies we know that appropriate sexual differentiation of germ cells into female gametes requires: (i) a cell autonomous signal from the number of X chromosomes, (ii) a non-cell autonomous signal from the surrounding soma, and (iii) the function of several genes in the "germline sex-determination pathway",  So far these genes include: ovo, otu, stil, snf, and Sxl.  We are seeking to unravel this regulatory network in the following ways: Molecular structure and function of key regulatory genes.  To date, we have focused on molecular studies of ovo.  These studies have revealed that it encodes both an activator and a repressor transcription factor isoforms that bind to specific sites in the ovo and otu promoters and directly regulates their transcription.  We will be undertaking similar functional studies on new genes believed to participate in the germline sex-determination pathway (see point 3 below). Genome-wide germline gene regulation.  We have used EST sequencing and microarrays to investigate genome-wide sex-biased gene expression in the germline.  We are currently working to refine expression profiling techniques to identify genes that are co-regulated in specific cells at specific stages of oogeneisis.  This work is facilitated by the Drosophila Genomics Resource Center (DGRC) of which I am a co-Director.  Please see the DGRC web site at: http://dgrc.cgb.indiana.edu/. Identifying new players.  Our most recent work is implicating novel genes in this regulatory pathway.  Using microarrays we have identified genes showing altered expression in response to altered ovo transcription factor activity. We are following up on 22 genes that show the most dramatic responses.  These genes are either direct or indirect targets of OVO.  We are combining this analysis with the bioinformatic, identification of clustered OVO binding site motifs, and data mining various sources of functional information. Genomics of environmental sex determination and sexual/parthenogenetic oogenesis in Daphnia Daphnia has an intriguing reproductive cycle termed cyclical parthenogenesis.  Individual females are cued by environmental conditions to switch between parthenogenetic and sexual reproduction.  Additionally the sex of parthenogenetically produced embryos is also determined by environmental signals.  To facilitate the dissection of these developmental pathways we are working with a collaborative group to develop genomic resources of Daphnia pulex -- genome sequence, full length cDNA sequences, and microarrays [http://daphnia.cgb.indiana.edu/].  We are also taking a functional genomics approach to understanding the regulation of the reproductive cycle: The switch between male and female differentiation.  What is the regulatory pathway(s) that responds to environmental cue(s).  We are taking three approaches: (i) We have developed custom D. pulex microarrays and are using them to investigating sex-biased gene regulation.  So far, we have identified several hundred gene with sex-biased expression.  (ii) We have identified orthologs of the phylogenetically and functionally conserved doublesex gene which are candidates for a master regulator of sexual identity.  (iii)  We are investigating genes that respond early to crustacean analog of insect juvenile hormone, that normally triggers a switch from female sexual development.  Here we are taking advantage of mutant Daphnia isolates that fail to produce males. The switch between sexual and parthenogenetic oogenesis. Individual females can switch from parthenogenetic reproduction to sexual reproduction in response to environmental cues.  How is the switch in reproductive modes made?  Sexually produced eggs are normally laid in a state of developmental arrest, called diapause, which allows the eggs to survive adverse conditions.  Intriguingly, some strains have lost the ability to produce sexual eggs altogether, while others may produce diapause eggs parthenogenetically.  Distinguishing the genes involved in sexual, asexual, and diapause egg production is a focus of current research.

Select Publications

Costello, J. Dalkelic, M., Beason, S., Gelhausen, J., Patwardhan, R., Middha, S., Eads, B., and Andrews, J. 2009.  Gene networks in Drosophila melanogaster: Integrating experimental data to predict gene function.  Genome Biol.  10: R97.

Kijimoto, T., Costello, J., Tang, Z., Moczec, A.P. and Andrews, J.  2009.  EST and microarray analysis of horn development in Onthophagus beetles.  BMC Genomics 10: 504.

Colbourne, J. K., Eads, B. D., Shaw, J., Bohuski, E., Bauer, D. and Andrews, J. 2007.  Sampling Daphnia's expressed genes: preservation, expansion and invention of crustacean genes with reference to insect genomes.  BMC Genomics 8:217.

Eads, B. D., Colbourne, J. K. Bohuski, E. and Andrews, J. 2007. Profiling sex-biased gene expression during parthenogentic reproduction in Daphnia pulex.  BMC Genomics, BMC Genomics 2007, 8: 464.

Eads, B. D., Cash, A., Bogart, K., Costello, J. and Andrews, J.  2006.  Microarray hybridization troubleshooting.  Methods Enzymol. 411: 34049.

Parisi, M., Nuttall, R., Naiman, D., Bouffard, G., Malley, J., Andrews, J., 2003.  Eastman, S. and Oliver, B.  2003.  Paucity of genes on the Drosophila X-chromosome showing male-biased expression.  Science 299: 697-700.

Burr, A., Bogart, K., Conaty, J. and Andrews, J. 2006.  Automated liquid handling and high-throughput preparation of PCR amplified DNA for microarray fabrication. Methods Enzymol. 410: 99-120.

Andrews, J. and Oliver, B.  2002. Sex determination signals control ovo-B transcription in Drosophila melanogaster germ cells.  Genetics 160: 537-545.

Andrews, J., Bouffard, G. G., Cheadle, C., Lü, J., Becker, K. and Oliver, B. 2000.  Gene discovery using computational and microarray analysis of transcription in the Drosophila melanogaster testis.  2000.  Genome Research 10: 2030-2043.

Andrews, J., Garcia-Estefania, D., Delon, I., Lü, J., Mével-Ninio, M., Spierer, A., Payre, F., Pauli, D. and Oliver, B.  2000.  OVO transcription factors function antagonistically in the Drosophila female germline.  Development 127: 881-982.

View more publications »