Barbara Chadwick Hoopes (Associate Professor)

Department of Biology, Colgate University

Phone: 315.228.7344 Fax: 315.228.7997

E-Mail: BHoopes@mail.colgate.edu

Research Interests: Molecular genetics of gene expression in eukaryotes.  [Details]

Teaching Interests: Genetics, Molecular Techniques, Molecular Biology, courses in Scientific Perspectives. [Details]

Student Research   Publications  

Colgate Teaching & Research Directory  

Barbara Chadwick Hoopes

Research Interests:

My research interests are in the regulation of gene expression, focusing on the yeast Saccharomyces cerevisiae as a "model" organism.  One of the revolutions of the last decade has been our ability to determine the complete DNA sequence for a number of organisms, including humans.  Although many aspects of the genetic code are known, we still don't know exactly how the sequence of bases in DNA specifies how much of particular gene products are to be made, or in what types of cells or under what conditions.  It is this aspect of the genetic code that I am interested in.  My research is done as a collaboration with undergraduate students and is currently focused on two questions:

1) How is the expression of the class of proteins known as the General Transcription Factors regulated? 

2) How do organisms change gene expression to adapt to life at low temperature?

Current Projects in the Regulation of the General Transcription Factors

The General Transcription Factors are required for transcription of most, if not all, genes.  Our current research focuses on two proteins, TBP and TFIIB.  The TBP gene is unusual in that it has been reported to be translated by a mechanism called Internal Ribosomal Entry.  This means of translation is known to be important for viruses, but the significance of it to the normal cell (including yeast) is unclear.  Students have made mutations that should prevent translation of TBP by this mechanism and we are in the process of characterizing these mutations.  We have also examined an unusual structure of the TFIIB gene, which leads to the production of two RNA molecules [Image shown: Plate assays are used to test mutant yeast strains for sensitivity to cellular stresses (ethanol, in this case)].  We have found that although the relative amount of these two RNAs changes with cellular conditions, both of these RNAs provide similar amounts of TFIIB to the cell.  This work has added to our knowledge about what signals are used to specify the ends of genes and how the activity of the proteins involved in this process change with cellular conditions.  We are also interested in a puzzle: the transcription of the general transcription factors gene is fairly constant under a variety of conditions that others have shown change the level of transcription of at least 2000 of the 6000 yeast genes.  What is special about the DNA sequence of  the general transcription factor genes to allow for their invariant expression?  Experiments to address this question are currently in progress.

Current Projects in Low Temperature Adaptation

The process of transcription is inherently temperature dependent because unwinding of the DNA helix (which is necessary for transcription) is strongly affected by temperature.  In addition, TBP is highly temperature dependent in its function.  Our research on the adaptation of cells to low temperature has focused on two areas: 1) isolating general transcription factors from psychrophilic organisms that only live at low temperatures to compare them to yeast and mammalian proteins, and 2) using "whole genome expression assays" to look at the genes expressed by yeast at low temperatures.  We have isolated and sequenced a segment of the TBP gene from the snow alga, Chloromonas, and we will use this segment to help us isolate the remainder of the gene.  Similar experiments are ongoing for the TFIIB gene.  In the fall of 2000, I compared the expression of all 6000 yeast genes at 30oC to 10oC and have identified a number of genes that are more highly expressed at low temperatures (Image shown:  This false color image represents the relative levels of expression of 3000 individual yeast genes at 10 and 30 degrees. Genes that are more highly expressed at 10 degrees are shown as red and genes that are more highly expressed at 30 degrees are shown as green).  The increase in expression of some of these genes is a result of the cell's response to stress or to starvation (yeast starve in the midst of plenty at low temperature), but some of the genes whose expression increases seem to be specific to low temperature growth.  We are in the process of characterizing these genes. 

Teaching Interests:

[Student Research]In my classes I hope to help students appreciate the wonder of what is unknown about molecular genetics and biology.  I teach in the Molecules, Cells, and Genes class (BIOL212), where I have developed a four week investigative laboratory.  In this laboratory, students characterize an unknown mutation in yeast at both the cellular and molecular level, using both classical genetic tests and gene cloning and sequencing.  I also teach in our Molecular Analysis class (BIOL321), which is a laboratory intensive class that usually enrolls fewer than 16 students.  In this class we use a semester long investigative project to learn the theory and practice of molecular techniques in biology.  The senior seminar in Molecular Biology (BIOL450) really allows students to bring together everything they have learned in their four years here.  I enjoy this class because it is discussion oriented and full of students willing to argue with me.  I also teach a First Year Seminar that is part of the Scientific Perspectives section of the Core Curriculum called "Biotechnology and the New Genetics" that addresses the science, ethics, and economics behind various applications of biotechnology.

Student Research:

In the past few years, the following students have worked with me in the laboratory:

Recent Publications:

Hoopes, B.C., DiVisconte, M.J., Pantaleo, A. P.*, Mazzeo, J.* and Geier, S.  Functional analysis of the two SUA7 (TFIIB) transcripts of Saccharomyces cereivisiae. 
In preparation for Molecular and Cellular Biology.

Hoopes, B. C., DiVisconte, M. J. and Bowers, G. D.* (2000) The two  Saccharomyces cerevisiae SUA7 (TFIIB) transcripts differ at the 3'-end and respond differently to stress.  Nucleic Acids Research 28: 4435-4443.

Hoopes, B. C., leBlanc, J. F. and Hawley, D. K. (1998).  Contributions of the TATA box sequence to rate-limiting steps in transcription initiation by RNA polymerase II.  Journal of Molecular Biology 277: 1015-1031.

Starr, D. Barrry, Hoopes, B. C., and Hawley, D. K. (1995).  DNA bending is an important component of site-specific recognition by the TATA binding protein.  Journal of Molecular Biology 250: 434-446.