Resume

• 2006

  NIH

  Bethesda

  MD

  Research Fellow

  NIH

  Assistant Professor

  Terre Haute

  Indiana Area

  Indiana State University

• 2003

  Shaad

  Ahmad

  Harvard Medical School

  Indiana State University

  Howard Hughes Medical Institute

  Howard Hughes Medical Institute

  Harvard Medical School

• 1988

  B.A. with High Honors

  Molecular Biology

  Ph.D.

  Developmental Biology

• Life Sciences

  Developmental Biology

  Systems Biology

  High Throughput Screening

  Confocal Microscopy

  In Vivo

  Microscopy

  Molecular Cloning

  Genetics

  Fluorescence Microscopy

  Mutagenesis

  Molecular Biology

  RNAi

  Identification and characterization of targets of the sex determination hierarchy in Drosophila melanogaster

  Identification and characterization of targets of the sex determination hierarchy in Drosophila melanogaster

  Signal transduction through multiple distinct pathways regulates and orchestrates the numerous biological processes comprising heart development. This review outlines the roles of the FGFR

  EGFR

  Wnt

  BMP

  Notch

  Hedgehog

  Slit/Robo

  and other signaling pathways during four sequential phases of Drosophila cardiogenesis-mesoderm migration

  cardiac mesoderm establishment

  differentiation of the cardiac mesoderm into distinct cardiac cell types

  and morphogenesis of the heart and its lumen based on the proper positioning and cell shape changes of these differentiated cardiac cells-and illustrates how these same cardiogenic roles are conserved in vertebrates. Mechanisms bringing about the regulation and combinatorial integration of these diverse signaling pathways in Drosophila are also described. This synopsis of our present state of knowledge of conserved signaling pathways in Drosophila cardiogenesis and the means by which it was acquired should facilitate our understanding of and investigations into related processes in vertebrates.

  Conserved signaling mechanisms in Drosophila heart development

  The development of a complex organ requires the specification of appropriate numbers of each of its constituent cell types

  as well as their proper differentiation and correct positioning relative to each other. During Drosophila cardiogenesis

  all three of these processes are controlled by jumeau (jumu) and Checkpoint suppressor homologue (CHES-1-like)

  two genes encoding forkhead transcription factors that we discovered utilizing an integrated genetic

  genomic

  and computational strategy for identifying genes expressed in the developing Drosophila heart. Both jumu and CHES-1-like are required during asymmetric cell division for the derivation of two distinct cardiac cell types from their mutual precursor and in symmetric cell divisions that produce yet a third type of heart cell. jumu and CHES-1-like control the division of cardiac progenitors by regulating the activity of Polo

  a kinase involved in multiple steps of mitosis. This pathway demonstrates how transcription factors integrate diverse developmental processes during organogenesis.

  Two Forkhead transcription factors regulate the division of cardiac progenitor cells by a Polo-dependent pathway

  A central issue in developmental biology is how the deployment of generic signaling proteins produces diverse specific outcomes. We show that Drosophila FGF is used

  only in males

  to recruit mesodermal cells expressing its receptor to become part of the genital imaginal disc. Male-specific deployment of FGF signaling is controlled by the sex determination regulatory gene doublesex. The recruited mesodermal cells become epithelial and differentiate into parts of the internal genitalia. Our results provide exceptions to two basic tenets of imaginal disc biology—that imaginal disc cells are derived from the embryonic ectoderm and belong to either an anterior or posterior compartment. The recruited mesodermal cells migrate into the disc late in development and are neither anterior nor posterior.

  Sex-specific deployment of FGF signaling in Drosophila recruits mesodermal cells into the male genital imaginal disc

  Cardiogenesis involves the coordinated regulation of multiple biological processes by a finite set of transcription factors (TFs). Here

  we show that the Forkhead TFs Checkpoint suppressor homologue (CHES-1-like) and Jumeau (Jumu)

  which govern cardiac progenitor cell divisions by regulating Polo kinase activity

  play an additional

  mutually redundant role in specifying the cardiac mesoderm (CM) as eliminating the functions of both Forkhead genes in the same Drosophila embryo results in defective hearts with missing hemisegments. This process is mediated by the Forkhead TFs regulating the fibroblast growth factor receptor Heartless (Htl) and the Wnt receptor Frizzled (Fz): CHES-1-like and jumu exhibit synergistic genetic interactions with htl and fz in CM specification

  thereby implying that they function through the same genetic pathways

  and transcriptionally activate the expression of both receptor-encoding genes. Furthermore

  ectopic overexpression of either htl or fz in the mesoderm partially rescues the defective CM specification phenotype in embryos lacking both Forkhead genes. Together

  these data emphasize the functional redundancy that leads to robustness in the cardiac progenitor specification process

  and illustrate the pleiotropic functions of Forkhead TFs in different aspects of cardiogenesis.

  Two Forkhead transcription factors regulate cardiac progenitor specification by controlling the expression of receptors of the fibroblast growth factor and Wnt signaling pathways

  The Drosophila heart is composed of two distinct cell types

  the contractile cardial cells (CCs) and the surrounding non-muscle pericardial cells (PCs)

  development of which is regulated by a network of conserved signaling molecules and transcription factors (TFs). Here

  we used machine learning with array-based chromatin immunoprecipitation (ChIP) data and TF sequence motifs to computationally classify cell type-specific cardiac enhancers. Extensive testing of predicted enhancers at single-cell resolution revealed the added value of ChIP data for modeling cell type-specific activities. Furthermore

  clustering the top-scoring classifier sequence features identified novel cardiac and cell type-specific regulatory motifs. For example

  we found that the Myb motif learned by the classifier is crucial for CC activity

  and the Myb TF acts in concert with two forkhead domain TFs and Polo kinase to regulate cardiac progenitor cell divisions. In addition

  differential motif enrichment and cis-trans genetic studies revealed that the Notch signaling pathway TF Suppressor of Hairless [Su(H)] discriminates PC from CC enhancer activities. Collectively

  these studies elucidate molecular pathways used in the regulatory decisions for proliferation and differentiation of cardiac progenitor cells

  implicate Su(H) in regulating cell fate decisions of these progenitors

  and document the utility of enhancer modeling in uncovering developmental regulatory subnetworks.

  Machine learning classification of cell-specific cardiac enhancers uncovers developmental subnetworks regulating progenitor cell division and cell fate specification

  Extending the upper limits of pulsed field DNA electrophoresis using programmed voltage gradients

  A common theme in developmental biology is the repeated use of the same gene in diverse spatial and temporal domains

  a process that generally involves transcriptional regulation mediated by multiple separate enhancers

  each with its own arrangement of transcription factor (TF)-binding sites and associated activities. Here

  by contrast

  we show that the expression of the Drosophila Nidogen (Ndg) gene at different embryonic stages and in four mesodermal cell types is governed by the binding of multiple cell-specific Forkhead (Fkh) TFs - including Biniou (Bin)

  Checkpoint suppressor homologue (CHES-1-like) and Jumeau (Jumu) - to three functionally distinguishable Fkh-binding sites in the same enhancer. Whereas Bin activates the Ndg enhancer in the late visceral musculature

  CHES-1-like cooperates with Jumu to repress this enhancer in the heart. CHES-1-like also represses the Ndg enhancer in a subset of somatic myoblasts prior to their fusion to form multinucleated myotubes. Moreover

  different combinations of Fkh sites

  corresponding to two different sequence specificities

  mediate the particular functions of each TF. A genome-wide scan for the occurrence of both classes of Fkh domain recognition sites in association with binding sites for known cardiac TFs showed an enrichment of combinations containing the two Fkh motifs in putative enhancers found within the noncoding regions of genes having heart expression. Collectively

  our results establish that different cell-specific members of a TF family regulate the activity of a single enhancer in distinct spatiotemporal domains

  and demonstrate how individual binding motifs for a TF class can differentially influence gene expression.

  Differential regulation of mesodermal gene expression by Drosophila cell type-specific Forkhead transcription factors

  There has recently been a revolution in our understanding of how the Drosophila sex-determination hierarchy generates somatic sexual dimorphism. Most significantly

  the sex hierarchy has been shown to modulate the activities of well-known signaling molecules (FGF

  Wnt and TGF beta proteins) and transcription factors (BAB and DAC) to direct various sex-specific aspects of growth and differentiation. As some of the genes encoding these proteins are also the targets of Hox gene action

  these and other findings are revealing the levels at which the sex determination and Hox patterning pathways are integrated to control growth

  morphogenesis and differentiation.

  Sex comes in from the cold