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Department of Molecular Biology|College of Agriculture and Natural Resources

Department of Molecular Biology
University of Wyoming
Dept. 3944
Laramie, WY 82071


Office: (307) 766-4961
Lab: (307) 766-4962
Fax: (307) 766-5098



In the broadest sense, we are trying to understand how genes and the proteins they encode control fundamental molecular and cellular processes during animal development. This is not only interesting from a biological standpoint but is also highly relevant to human health. This is because most genes that control fundamental biological processes are conserved across species and have been found to be misregulated or mutated in many human diseases. Thus, by understanding the normal functions of these genes and how they are regulated, we can gain deeper insights into the molecular causes of human disease. This knowledge can also help us to propose ways to counteract or alleviate the symptomatic outcomes of genetic defects or may be useful for accurately detecting and diagnosing human disease states.

The animal system that we use for most of our studies is the nematode Caenorhabditis elegans, a small transparent roundworm that is used by thousands or scientists around the world for biological and biomedical research. Many different tools can be applied to the study of this versatile nematode including genetics, genomics, whole genome sequencing, biochemistry, cell biology, biophysics, systems biology, and most recently, genome editing. Although we use all of these tools in our studies, genetics-based methods constitute the core our approach.

Our lab currently pursues two main research projects and one side project that are described briefly below. For more information, check out our published papers, which can be downloaded or linked to through our website. Our principle goal is to understand the functions and regulation of the extracellular matrix (ECM) during worm development. The ECM is a heterogeneous meshwork of many different kinds of secreted proteins, the identities, functions, and properties of which are still being worked out. More specifically, we are studying several protein signaling molecules and protein transport pathways that regulate the composition and functional–mechanical properties of the apical ECM of C. elegans epidermal cells. We also study how the ECM impacts developmental processes including embryonic morphogenesis and larval growth. These studies are relevant to a wide range of human disease processes including cancer metastasis and the genesis of birth defects and other types of genetic diseases.

Project #1. Characterizing novel functions of conserved NEK family kinases.

The NEK (NIMA-related) family of protein kinases are highly conserved in animal systems and have been widely implicated in human diseases including cancer and heart defects. Our studies in C. elegans have identified a previously unknown function for several NEK family members, NEKL-2 and NEKL-3, in promoting the remodeling and shedding of the outer epidermal ECM layer known as the cuticle (Figure 1). Similar to human skin, the C. elegans cuticle is a collagen-based layer that surrounds the animal on the outside and provides protection from the environment. Perturbation of NEKL-2 or NEKL-3 activity results in larvae that are unable to properly shed their old cuticle during molting cycles, leading to physical entrapment and growth arrest (Figure 1). Further studies in our lab have implicated NEKL-2 and NEKL-3 in regulating protein trafficking within the outermost epidermal cells that are responsible for degrading and re-synthesizing the cuticle during each molting cycle (Figure 2). Our studies have also identified several functional co-partners of the NEKLs along with candidate downstream targets that may be regulated by the NEKLs through phosphorylation. Further work on this project is expected to lead to a new understanding of the roles NEK family kinases play in protein trafficking and will result in the identification of new NEK pathway components and targets, which are largely unknown.

Figure 1

Figure 1. Model depicting the basic process of molting and the types of defects observed in molting-defective C. elegans mutants. In worms harboring severe disruption of function mutations in nekl-2 or nekl-3, L1/L2-stage larvae are trapped in a double cuticle, as observed in nekl-2(gk839) mutants. Alternatively, partial loss of function in nekl-2 or nekl-3 can lead to less severe molting defects, as seen for nekl-3(sv3) mutants, in which only a portion of the larva, the middle section, is encased within a double cuticle.

Figure 2

Figure 2. Working model for the roles of NEKL-2 and NEKL-3 in endocytosis and molting. Solid arrows between endocytic compartments indicate minus-end directed transport along MTs; dashed arrows, plus-end directed transport. For simplicity, bi-directional movement between compartments, which is normally quite extensive, has been omitted. Circled numbers with dotted arrows indicate proposed trafficking steps that may be controlled by NEKL-2 (1 and 2) or NEKL-3 (3–5). Also depicted are putative functional co-partners of the NEKLs (e.g., MLT-1–3), which may function as signaling scaffolds, and candidate downstream targets of the NEKLs (e.g., CDC-42 and BICD-1), which may control specific steps of endocytosis.

Project #2. Functions and regulation of the extracellular matrix in C. elegans embryos.

We recently reported on the discovery of a previously uncharacterized biomechanical force that operates during C. elegans embryogenesis. This force is caused by an inherent resistance of the embryonic foregut (pharynx) to elongation or stretch during early development (Figure 3). This resistance leads to an inward-pulling force on the anterior epidermis of the embryo, which must be counter-resisted in order for the embryo to maintain its normal shape and functions. These studies have led to the discovery of a role for FBN-1, a protein related to human fibrillins, as a structural component of the outer ECM (sheath) that attaches to the embryonic epidermis. Namely, FBN-1 helps the epidermis to resist pulling forces by the pharynx and also to resist circumferential constricting forces that are required to squeeze the embryo into its proper tube-like shape (Figure 3). Notably, human fibrillins are mutated in Marfan syndrome and several related diseases, leading to altered mechanical and functional properties of the ECM. Our studies have also highlighted the roles of several protein trafficking regulators and mRNA splicing factors that are involved in the production and transport of proteins that allow the epidermis to resist deformation by mechanical forces (Figure 4). Continued studies are expected to identify new proteins and pathways that are relevant to disease states caused by malfunctions in ECM components and other structural proteins as well as the regulatory networks that control their production and distribution.

Figure 3

Figure 3. Model for the pharyngeal pulling (yellow arrow) and circumferential squeezing (red arrows) forces that act on the embryonic epidermis and the apical ECM/sheath. For simplicity, the embryo is depicted as a tube; the pharynx is represented by the inner dark blue tube. Wild-type animals can resist both the pharyngeal pulling force and the circumferential constricted forces, the latter of which is required to squeeze the embryo into an elongated shape. When the sheath is moderately weakened, however, such as in mec-8; sym-4 mutants or when fbn-1 function is partially impaired, a “keyhole” phenotype is observed in which the anterior epidermis surrounding the future mouth is pulled inward by the pharynx. In cases where the sheath is more severely compromised, such as in mec-8; fbn-1 mutants, the depth of the keyhole is further increased and the much of the embryonic epidermis develops ingressions or furrows where radial constricting forces are acting.

Figure 4

Figure 4. Normal anterior morphogenesis and resistance to mechanical forces during development require the concerted functions of the ECM, cell adhesion molecules, and cytoskeletal proteins. Arrows indicate proposed regulation circuits; dashed lines, physical interactions. Blue proteins regulate the intracellular trafficking of ECM and/or transmembrane (TM) proteins critical for structural stability and cell adhesion. Green and red proteins include cytoskeletal, ECM, and TM proteins. MEC-8, an RNA-binding protein involved in alternative splicing, regulates ECM and TM proteins including FBN-1.

Project #3. Discovery and analysis of a conserved stress response pathway.

We have been working to understand the regulation of a highly conserved stress-response pathway that appears to operate in animal systems from worms and humans (Figure 5). This pathway, which has not been well studied in any system, responds to a very wide range of stressors including heat, oxidative, salt, and ethanol stress and has been termed ESRE (for ethanol- and stress-response element). We discovered that the Zn-finger protein, SLR-2/ZTF-24, acts upstream of a conserved histone demethylase, JMJC-1/NO66, to promote the expression of hundreds of genes containing the ESRE motif in their promoter–enhancer regions. In further genetic and biochemical studies we showed that ESRE gene expression is directly regulated by a conserved SWI/SNF-family nucleosome-remodeling complex termed PBAF, which was one of the first reports demonstrating regulation of a metazoan stress-response network by a nucleosome-remodeling complex. Further studies on this pathway have been directed towards identifying the protein(s) that binds directly to the ESRE and to identify other transcriptional regulators of this understudied stress pathway.

Figure 5

Figure 5. The ESRE pathway. On the left if depicted the major regulators of ESRE gene expression including SLR-2, JMJC-1, PBAF components, and the ESRE-binding protein (EBP), which acts on hundreds of ESRE-containing genes. On the right is shown the conserved ESRE binding sequences in worms, flies, and mice.

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