Research Areas - Department of Biochemistry | College of Medicine

Areas of Research

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

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, and colon, and, breast and prostate cancer. 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 factors that regulate cancer-compromised cell cycle control, mediate cell senescence, control chromosome segregation, cancer stem cells and govern cell motility. Links between chromatin structure and/or nuclear structure, higher order gene organization and tumorigenesis are being explored.	Christopher Berger - Lab Chris Francklyn - Lab Prachi Ghule - Lab Robert Hondal - Lab Robert Kelm - Lab Gary Stein - Lab Janet 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, and colon, and, breast and prostate cancer. 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 factors that regulate cancer-compromised cell cycle control, mediate cell senescence, control chromosome segregation, cancer stem cells and govern cell motility. Links between chromatin structure and/or nuclear structure, higher order gene organization and tumorigenesis are being explored.

Christopher Berger - Lab
Chris Francklyn - Lab
Prachi Ghule - Lab
Robert Hondal - Lab
Robert Kelm - Lab
Gary Stein - Lab
Janet 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 proliferation in the MSK system are being addressed. Competency for stem cell commitment to osteoblast differentiation is being examined. 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, epigenetic, 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 proliferation in the MSK system are being addressed. Competency for stem cell commitment to osteoblast differentiation is being examined. 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, epigenetic, 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

Cellular Structure and Function
Regulatory mechanisms that are operative in cancer stem cells which are treatment resistant and account for disease reoccurrence are being explored. 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 Regulatory mechanisms that are operative in cancer stem cells which are treatment resistant and account for disease reoccurrence are being explored. 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 is investigating 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.	Stephen Everse - Lab Robert Kelm - Lab Jay Silveira - 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 laboratories 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.	Christopher Berger - Lab Chris Francklyn - Lab Erik Ruggles - Lab Jay Silveira - Lab Robert Hondal - Lab Robert Kelm - Lab Stephen Everse - 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 laboratories 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.

Christopher Berger - Lab
Chris Francklyn - Lab
Erik Ruggles - Lab
Jay Silveira - Lab
Robert Hondal - Lab
Robert Kelm - Lab
Stephen Everse - 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 Gary Stein - Lab Janet Stein - 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
Gary Stein - Lab
Janet Stein - Lab
Delphine Quenet - Lab

Clinical and Translational Projects
The Department of Biochemistry provides leadership for the NNE-CTR, an NIH-funded program that supports clinical and translational investigation to address the health and healthcare challenges of Northern New England rurality. A data science initiative and a Pilot Project program to address prevention, early detection, and survivorship of chronic disease that includes cancer, cardiovascular disorders, musculoskeletal diseases, substance use disorders, and mental health. The Biochemistry Department leads and coordinates the Vermont Biomedical Research Network, an NIH-supported program that is building biochemical research structure throughout Vermont by facilitating the research capability of faculty and the education of undergraduate students in Biomedical research.

Clinical and Translational Projects

The Department of Biochemistry provides leadership for the NNE-CTR, an NIH-funded program that supports clinical and translational investigation to address the health and healthcare challenges of Northern New England rurality. A data science initiative and a Pilot Project program to address prevention, early detection, and survivorship of chronic disease that includes cancer, cardiovascular disorders, musculoskeletal diseases, substance use disorders, and mental health. The Biochemistry Department leads and coordinates the Vermont Biomedical Research Network, an NIH-supported program that is building biochemical research structure throughout Vermont by facilitating the research capability of faculty and the education of undergraduate students in Biomedical research.