Research Areas - Department of Biochemistry | College of Medicine

Areas of Research

The Department of Biochemistry is a multidisciplinary program in basic science that encompasses a wide-range of advanced research topics utilizing cutting edge approaches in cellular and molecular biochemistry. The research faculty of the Department of Biochemistry is actively involved in one or more of the following major research areas:

Bone Biology and Skeletal Complications of Malignancies
The Department of Biology has unique programs that bring together a focus on the molecular, cellular and genetic models to understand regulatory mechanisms for the formation and homeostasis of bone and cartilage. Mechanisms regulating cell population in the MSK system are being addressed. Pathologic disorders currently being investigated include osteopetrosis, metastatic bone disease, chondrodysplasia related to dwarfism, rheumatoid and osteoarthritis, and bone loss related to age, embryonic malformations associated with disruption of signaling pathways and transcription factor networks. Analysis of bone tissue from humans and mouse models are supported by Core facilities that include genetic and proteomic analysis, specialized histology, in vivo molecular imaging, scanning and electron microscopy and high resolution micro-computed tomography.	Jane Lian - Lab Jonathan Gordon - Lab Janet Stein - Lab Gary Stein - Lab

Bone Biology and Skeletal Complications of Malignancies

The Department of Biology has unique programs that bring together a focus on the molecular, cellular and genetic models to understand regulatory mechanisms for the formation and homeostasis of bone and cartilage. Mechanisms regulating cell population in the MSK system are being addressed. Pathologic disorders currently being investigated include osteopetrosis, metastatic bone disease, chondrodysplasia related to dwarfism, rheumatoid and osteoarthritis, and bone loss related to age, embryonic malformations associated with disruption of signaling pathways and transcription factor networks. Analysis of bone tissue from humans and mouse models are supported by Core facilities that include genetic and proteomic analysis, specialized histology, in vivo molecular imaging, scanning and electron microscopy and high resolution micro-computed tomography.

Jane Lian - Lab
Jonathan Gordon - Lab
Janet Stein - Lab
Gary Stein - Lab

Cancer Biology and Pathology
Many cancers arise from defects in cell biology, including osteosarcoma and soft tissue sarcoma, leukemia and lymphoma, and carcinoma of the skin, liver, colon, breast and prostate. Research investigates cell growth regulation and the links between dysregulated cell growth, cancer, and aging. Topics include genetic and epigenetic regulation of oncogenes and tumor suppressors, and other factors that regulate the cell cycle, mediate cell senescence, control chromosome segregation, and govern cell motility. Links between chromatin structure and/or nuclear structure and tumorigenesis are being explored.	Christopher Berger - Lab Beth Bouchard - Lab Chris Francklyn - Lab Prachi Ghule - Lab Robert Hondal - Lab Robert Kelm - Lab Scott Morrical - Lab Erik Ruggles - Lab Gary Stein - Lab Janet Stein - Lab Russell Tracy - Lab

Cancer Biology and Pathology

Many cancers arise from defects in cell biology, including osteosarcoma and soft tissue sarcoma, leukemia and lymphoma, and carcinoma of the skin, liver, colon, breast and prostate. Research investigates cell growth regulation and the links between dysregulated cell growth, cancer, and aging. Topics include genetic and epigenetic regulation of oncogenes and tumor suppressors, and other factors that regulate the cell cycle, mediate cell senescence, control chromosome segregation, and govern cell motility. Links between chromatin structure and/or nuclear structure and tumorigenesis are being explored.

Christopher Berger - Lab
Beth Bouchard - Lab
Chris Francklyn - Lab
Prachi Ghule - Lab
Robert Hondal - Lab
Robert Kelm - Lab
Scott Morrical - Lab
Erik Ruggles - Lab
Gary Stein - Lab
Janet Stein - Lab
Russell Tracy - Lab

Cellular Structure and Function
The nucleus architecturally organizes nucleic acid metabolism. The DNA containing chromatin, an RNA containing nuclear matrix, and the nuclear lamina/envelope are interconnected structures. Subassemblies at their intersections spatially organize DNA replication, RNA transcription, RNA processing, the packaging of DNA into active or silenced chromatin, and other processes. Changes in these structural inter-relationships are a major driver of disease, including cancer and premature aging.	Gary Stein - Lab Janet Stein - Lab Jane Lian - Lab Delphine Quenet - Lab

Cellular Structure and Function

Cellular Structure and Function The nucleus architecturally organizes nucleic acid metabolism. The DNA containing chromatin, an RNA containing nuclear matrix, and the nuclear lamina/envelope are interconnected structures. Subassemblies at their intersections spatially organize DNA replication, RNA transcription, RNA processing, the packaging of DNA into active or silenced chromatin, and other processes. Changes in these structural inter-relationships are a major driver of disease, including cancer and premature aging.

Gary Stein - Lab
Janet Stein - Lab
Jane Lian - Lab
Delphine Quenet - Lab

Coagulation Biology and Disease
The Coagulation group (often referred to as ‘The Clotters’) is a large and close knit group of investigators who are studying all aspects of hemostasis. The work includes the identification, purification, kinetic characterization and structure determination of new clotting factors & inhibitors, pseudo in-vivo functional studies, cascade modeling, the role of the platelet and the identification of genetic risk markers. The Department has held an NIH Training Grant in Hemostasis for over 20 years to support both students and postdoctoral fellows.	Beth Bouchard - Lab Stephen Everse - Lab Robert Kelm - Lab Thomas Orfeo - Lab Jay Silveira - Lab Russell Tracy - Lab Paula Tracy - Lab

Coagulation Biology and Disease

he Coagulation group (often referred to as ‘The Clotters’) is a large and close knit group of investigators who are studying all aspects of hemostasis. The work includes the identification, purification, kinetic characterization and structure determination of new clotting factors & inhibitors, pseudo in-vivo functional studies, cascade modeling, the role of the platelet and the identification of genetic risk markers. The Department has held an NIH Training Grant in Hemostasis for over 20 years to support both students and postdoctoral fellows.

Beth Bouchard - Lab
Stephen Everse - Lab
Robert Kelm - Lab
Thomas Orfeo - Lab
Jay Silveira - Lab
Russell Tracy - Lab
Paula Tracy - Lab

Enzymology, Physical Biochemistry, and Structural Biology
Enzymes touch virtually every aspect of biochemistry. How an enzyme recognizes a substrate, cleaves it, and releases it are complex problems requiring a multi-disciplinary approach to understand. Many labs in the Department are taking a quantitative and/or structural approach to study enzymes in action. Research areas include: selenium containing enzymes, tRNA synthetases, enzymes and co-factors of the coagulation cascade, and DNA replication and recombination machines amongst others. The Department of Biochemistry, as part of the UVM College of Medicine’s Structural Biology Initiative, has embarked on a major program to establish structural biology as a core research discipline on this campus. This program has been facilitated by major grants to UVM from the Howard Hughes Medical Institute (HHMI) and from the Department of Energy (DOE). Ongoing projects include X-ray structures of: iron binding proteins, blood clotting factors, DNA-protein complexes involved in replication, recombination, and transcriptional regulation, and synthetase-tRNA complexes.	Beth Bouchard - Lab Christopher Berger - Lab Chris Francklyn - Lab Erik Ruggles - Lab Jay Silveira - Lab Paula Tracy - Lab Robert Hondal - Lab Robert Kelm - Lab Russell Tracy - Lab Saulius Butenas - Lab Scott Morrical - Lab Stephen Everse - Lab Thomas Orfeo - Lab

Enzymology, Physical Biochemistry, and Structural Biology

Enzymes touch virtually every aspect of biochemistry. How an enzyme recognizes a substrate, cleaves it, and releases it are complex problems requiring a multi-disciplinary approach to understand. Many labs in the Department are taking a quantitative and/or structural approach to study enzymes in action. Research areas include: selenium containing enzymes, tRNA synthetases, enzymes and co-factors of the coagulation cascade, and DNA replication and recombination machines amongst others. The Department of Biochemistry, as part of the UVM College of Medicine’s Structural Biology Initiative, has embarked on a major program to establish structural biology as a core research discipline on this campus. This program has been facilitated by major grants to UVM from the Howard Hughes Medical Institute (HHMI) and from the Department of Energy (DOE). Ongoing projects include X-ray structures of: iron binding proteins, blood clotting factors, DNA-protein complexes involved in replication, recombination, and transcriptional regulation, and synthetase-tRNA complexes.

Beth Bouchard - Lab
Christopher Berger - Lab
Chris Francklyn - Lab
Erik Ruggles - Lab
Jay Silveira - Lab
Paula Tracy - Lab
Robert Hondal - Lab
Robert Kelm - Lab
Russell Tracy - Lab
Saulius Butenas - Lab
Scott Morrical - Lab
Stephen Everse - Lab
Thomas Orfeo - Lab

Functional Nucleic Acid/Protein Interactions
How is a DNA replication fork assembled and regulated? How does a synthetase discriminate among dozens of tRNA species to find its one specific partner? How are DNA double-strand breaks repaired? Understanding mechanisms of transcription, translation, DNA replication, repair, and recombination are fundamentally important for predicting the stability or instability of genomes, for a molecular understanding of carcinogenesis, and for the design of new anti-tumor and anti-microbial agents. These and other important issues are being addressed by Biochemistry Faculty with interests in Nucleic Acid/Protein Interactions. Experimental approaches employed include thermodynamic, kinetic, and structural studies of DNA-protein and RNA-protein complexes, site directed mutagenesis of protein and nucleic acid components, plus biochemical assays for DNA synthesis, RNA synthesis, aminoacylation of tRNA, DNA recombination and repair.	Prachi Ghule - Lab Robert Kelm - Lab Scott Morrical - Lab Gary Stein - Lab Janet Stein - Lab Russell Tracy - Lab Delphine Quenet - Lab

Functional Nucleic Acid/Protein Interactions

How is a DNA replication fork assembled and regulated? How does a synthetase discriminate among dozens of tRNA species to find its one specific partner? How are DNA double-strand breaks repaired? Understanding mechanisms of transcription, translation, DNA replication, repair, and recombination are fundamentally important for predicting the stability or instability of genomes, for a molecular understanding of carcinogenesis, and for the design of new anti-tumor and anti-microbial agents. These and other important issues are being addressed by Biochemistry Faculty with interests in Nucleic Acid/Protein Interactions. Experimental approaches employed include thermodynamic, kinetic, and structural studies of DNA-protein and RNA-protein complexes, site directed mutagenesis of protein and nucleic acid components, plus biochemical assays for DNA synthesis, RNA synthesis, aminoacylation of tRNA, DNA recombination and repair.

Prachi Ghule - Lab
Robert Kelm - Lab
Scott Morrical - Lab
Gary Stein - Lab
Janet Stein - Lab
Russell Tracy - Lab
Delphine Quenet - Lab

Genetic and Epigenetic Regulatory Mechanisms
The complicated interplay between eukaryotic RNA polymerases, transcription factors, cofactors, histone modifying and ATP-dependent chromatin remodeling enzymes, and the structural proteins that comprise the chromatin ultimately results in the appropriate regulation of transcription initiation and elongation. Post-transcriptional regulation of gene expression by mRNA stability and microRNA function brings an added level of complexity to gene regulation.	Jane Lian - Lab Jonathan Gordon - Lab Gary Stein - Lab Prachi Ghule - Lab Janet Stein - Lab Delphine Quenet - Lab

Genetic and Epigenetic Regulatory Mechanisms

The complicated interplay between eukaryotic RNA polymerases, transcription factors, cofactors, histone modifying and ATP-dependent chromatin remodeling enzymes, and the structural proteins that comprise the chromatin ultimately results in the appropriate regulation of transcription initiation and elongation. Post-transcriptional regulation of gene expression by mRNA stability and microRNA function brings an added level of complexity to gene regulation.

Jane Lian - Lab
Jonathan Gordon - Lab
Gary Stein - Lab
Prachi Ghule - Lab
Janet Stein - Lab
Delphine Quenet - Lab