Tag Archive for biochemistry

Students, Alumni Present Research at Biophysical Meeting in San Francisco

Several Wesleyan students presented their work at the Biophysical Society 54th Annual Meeting Feb. 20-24 in San Francisco, Calif. More than 6,000 scientists from academia, government and industry attended. Olga Buzovetsky '10, pictured, presented her poster titled "Binding and Bending Parameters of Integration Host Factor to Holliday Junction." Her advisor is Ishita Mukerji, professor of molecular biology and biochemistry.

Several Wesleyan students and recent alumni presented their work at the Biophysical Society 54th Annual Meeting Feb. 20-24 in San Francisco, Calif. More than 6,000 scientists from academia, government and industry attended. Olga Buzovetsky '10, pictured, presented her poster titled "Binding and Bending Parameters of Integration Host Factor to Holliday Junction." Her advisor is Ishita Mukerji, professor of molecular biology and biochemistry.

Graduate student Sanchaita Das presented her poster titled, "Mapping SecA-SecY Interaction using In Vivo Photo-Cross Linking." Das's advisor is Don Oliver, the Daniel Ayres Professor of Biology, professor of molecular biology and biochemistry.

Graduate student Sanchaita Das presented her poster titled, "Mapping SecA-SecY Interaction using In Vivo Photo-Cross Linking." Das's advisor is Don Oliver, the Daniel Ayres Professor of Biology, professor of molecular biology and biochemistry.

Journal Films Molecular Biology and Biochemistry Methods

Molecular biology and biochemistry graduate student Jie Zhai explains a scene for videographer Kai-Jie Wang Dec. 15 inside the Hingorani Laboratory. Wang works for the Journal of Visualized Experiments, a peer reviewed, indexed journal devoted to the publication of biological research in a video format. He is filming a project at Wesleyan titled Application of Stopped-flow Kinetics Methods to Investigate the Mechanism of Action of a DNA Repair Protein.

Molecular biology and biochemistry graduate student Jie Zhai (left) explains a scene for videographer Kai-Jie Wang Dec. 15 inside the Hingorani Laboratory. Wang works for the Journal of Visualized Experiments (JoVE), a peer reviewed, indexed journal devoted to the publication of biological research in a video format. He is filming a project at Wesleyan titled "Application of Stopped-flow Kinetics Methods to Investigate the Mechanism of Action of a DNA Repair Protein."

Zhai and her peers use a KinTek-brand stopped-flow kinetics instrument to monitor the activities of DNA repair proteins in real-time. The JoVE video will explain how the lab uses the instrument so others can develop their own experiments on their own system. The equipment and film was supported by a National Science Foundation grant awarded to Manju Hingorani, associate professor of molecular biology and biochemistry.

Zhai and her peers use a KinTek-brand stopped-flow kinetics instrument to monitor the activities of DNA repair proteins in real-time. The JoVE video will explain how the lab uses the instrument so others can develop their own experiments on their own system. The equipment and film were supported by a National Science Foundation (NSF) grant awarded to Manju Hingorani, associate professor of molecular biology and biochemistry.

Molecular biology and biochemistry major Christopher Doucette '11 and graduate student F. Noah Biro also are featured in the JoVE video. The filmed experiments explain how they're able to monitor a protein binding with DNA by using a fluorescent 'reporter' marker.

Molecular biology and biochemistry major Christopher Doucette '11 and BA/MA student F. Noah Biro also are featured in the JoVE video. The filmed experiments explain how they're able to monitor a protein binding with DNA by using a fluorescent reporter molecule.

Biro explains how a chromatography system works in the lab's 'cold room.' Here, the students purify milligram quantities of a protein from E. coli host cells by ion exchange and chromatography. The JoVE film will be released in early 2010. (Photos by Olivia Bartlett Drake)

Biro explains how a chromatography system works in the lab's 'cold room.' Here, he purifies milligram quantities of a protein from E. coli host cells by ion exchange and chromatography. The JoVE film will be released in early 2010. (Photos by Olivia Bartlett Drake)

Hingorani, Royer Published in National Academy of Sciences

Manju Hingorani, associate professor of molecular biology and biochemistry, is the author of “S. cerevisiae Msh2-Msh6 DNA binding kinetics reveal a mechanism of targeting sites for DNA mismatch repair,” published in the Proceedings of the National Academy of Sciences ” Early Edition,” December 2009.

Dana Royer, assistant professor of earth and environmental sciences, is the author of “Fossil soils constrain ancient climate sensitivity,” published in the same journal.

Faculty, Students Present Research at Molecular Biophysics Program

Manju Hingorani, associate professor of molecular biology and biochemistry, speaks on DNA mismatch repair during the 10th annual Molecular Biophysics Program Sept. 24 at Wadsworth Mansion in Middletown. More than 70 students and faculty attended the day-long event.

Manju Hingorani, associate professor of molecular biology and biochemistry, speaks on DNA mismatch repair during the 10th annual Molecular Biophysics Program Sept. 24 at Wadsworth Mansion in Middletown. More than 70 students and faculty attended the day-long event.

Wilma Olson, the Mary I. Bunting Professor of Chemistry at Rutgers University, was the keynote speaker. She spoke about DNA Mechanics and Regulation. Olson is an expert on the influence of chemical architecture on the structure and properties of nucleic acids.

Wilma Olson, the Mary I. Bunting Professor of Chemistry at Rutgers University, was the keynote speaker. She spoke about DNA Mechanics and Regulation. Olson is an expert on the influence of chemical architecture on the structure and properties of nucleic acids.

At left, Michael Weir, director of the Hughes Program in the Life Sciences, professor of biology, and in center, Brian Northrop, assistant professor of chemistry, listen to Olson's presentation.

At left, Michael Weir, director of the Hughes Program in the Life Sciences, professor of biology, and in center, Brian Northrop, assistant professor of chemistry, listen to Olson's presentation.

Northrop also delivered a talk during the retreat titled 'Dynamic self-assembly as a route to new organic materials.'

Northrop also delivered a talk during the retreat titled 'Dynamic self-assembly as a route to new organic materials.'

During a poster session, molecular biology and biochemistry graduate student F. Noah Biro explains his DNA mismatch repair research titled "Developing Reporter Systems to Monitor the Structural Dynamics of MutS." Biro's faculty advisor is Manju Hingorani.

During a poster session, molecular biology and biochemistry graduate student F. Noah Biro explains his DNA mismatch repair research titled "Developing Reporter Systems to Monitor the Structural Dynamics of MutS." Biro's faculty advisor is Manju Hingorani.

Laurel Appel, director of the McNair Program, adjunct associate professor of biology, senior research associate, listens to Biro explain his research.

Laurel Appel, director of the McNair Program, adjunct associate professor of biology, senior research associate, listens to Biro explain his research.

Olson mingled with students during the Poster Session.

Olson mingled with students during the Poster Session.

Chemistry graduate student Daniel Czyzyk, center, explains his research titled "Heptosyltransferase I and its Role in Biofilm Formation." Czyzyk's advisor is Erika Taylor, assistant professor of chemistry.

Chemistry graduate student Daniel Czyzyk, center, explains his research titled "Heptosyltransferase I and its Role in Biofilm Formation." Czyzyk's advisor is Erika Taylor, assistant professor of chemistry.

David Beveridge, the University Professor of the Sciences and Mathematics, professor of chemistry, reads through the program schedule.

David Beveridge, the University Professor of the Sciences and Mathematics, professor of chemistry, reads through the program schedule.

Chemistry graduate student Sattanathan Paramasivan talks about his research titled "A mix and measure fluorescence screening assay for the exploration of selective quadruplex binders." Paramasivan's advisor is Philip Bolton, professor of chemistry.

Chemistry graduate student Sattanathan Paramasivan talks about his research titled "A mix and measure fluorescence screening assay for the exploration of selective quadruplex binders." Paramasivan's advisor is Philip Bolton, professor of chemistry.

Rich Olson, assistant professor of molecular biology and biochemistry, speaks on "Poring over the structural basis of Vibro cholerae cytolysin assembly."

Rich Olson, assistant professor of molecular biology and biochemistry, speaks on "Poring over the structural basis of Vibro cholerae cytolysin assembly."

Chemistry Department research assistant Elizabeth Wheatley, right, speaks to Olga Buzovetsky '10, about her research titled "A Molecular Dynamics Study of DNA Bending in the Integration Host Factor-DNA Complex." The complex of the protein IHF with oligometric DNA results in a highly-unusual structure in which the DNA is bent by nearly 180 degrees. Wheatley's advisor is David Beveridge.

Chemistry Department research assistant Elizabeth Wheatley, right, speaks to Olga Buzovetsky '10, about her research titled "A Molecular Dynamics Study of DNA Bending in the Integration Host Factor-DNA Complex." The complex of the protein IHF with oligometric DNA results in a highly-unusual structure in which the DNA is bent by nearly 180 degrees. Wheatley's advisor is David Beveridge.

Molecular biology and biochemistry graduate student Yan Li explains her research titled "Investigation of the Binding Interaction of S. cerevisiae MutS homologs MSH2-MSH6 and MSH4-MSH5 with Holliday Junctions." Yan's advisors are Ishita Mukerji, chair and professor of molecular biology and biochemistry, and Manju Hingorani. (Photos by Olivia Bartlett Drake and Manju Hingorani)

Molecular biology and biochemistry graduate student Yan Li explains her research titled "Investigation of the Binding Interaction of S. cerevisiae MutS homologs MSH2-MSH6 and MSH4-MSH5 with Holliday Junctions." Yan's advisors are Ishita Mukerji, chair and professor of molecular biology and biochemistry, and Manju Hingorani. (Photos by Olivia Bartlett Drake and Manju Hingorani)

Hughes Summer Research Program Begins with a Bash

Michael Weir, director of the Hughes Program in the Life Sciences, professor of biology, speaks to students at the 21st Hughes Summer Research Program pizza party May 27.

Michael Weir, director of the Hughes Program in the Life Sciences, professor of biology, speaks to students at a pizza party that launched the the 21st Hughes Summer Research Program May 27. Weir and Laurel Appel, director of the McNair Program, explained various seminars and workshops available to complement the students' summer-long research efforts.

The gathering allowed the students to meet and mingle with several faculty members including, at left, Ishita Mukerji, professor of molecular biology and biochemistry, and Manju Hingorani, associate professor of molecular biology and biochemistry.

The gathering allowed the students to meet and mingle with several faculty members including, at left, Ishita Mukerji, professor of molecular biology and biochemistry, and Manju Hingorani, associate professor of molecular biology and biochemistry.

Pizza party attendees included 58 Hughes Fellows, eight McNair Fellows, nine Mellon Fellows, six SCIC Fellows, 11 students supported by other funds, and volunteers who started their 10 week summer research projects.

Pizza party attendees included 58 Hughes Fellows, eight McNair Fellows, nine Mellon Fellows, six SCIC Fellows, 11 students supported by other funds, and volunteers who started their 10 week summer research projects.

Bill Nelligan, director of environmental halth, safety and sustainability, stands by empty pizza boxes from the party. Nelligan taught the fellows about safety issues. (Photos by Laurel Appel)

Bill Nelligan, director of environmental health, safety and sustainability, stands by empty pizza boxes from the party. Nelligan taught the fellows about safety issues in and around the labs. (Photos by Laurel Appel)

Students Explore Nursing Profession Through Documentary Film Course

Jacob Bricca, adjunct assistant professor of film studies, works with Laurenellen McCann '09 on a nursing profession film April 23. Bricca is co-teaching the spring semester course "Making the Science Documentary."

Jacob Bricca, adjunct assistant professor of film studies, works with Laurenellen McCann '09 on a nursing profession film April 23. Bricca is co-teaching the spring semester course "Making the Science Documentary." McCann's film is focused on an oncology nurse.

Baltimore native Esther McCready grew up in segregated, discriminatory world and was denied admission to the University of Maryland School of Nursing. At that time, the school did not admit “Negros.”

With help from NAACP civil rights leaders like Thurgood Marshall, she sued for admission to the university, and in April 1950, McCready won her right to attend classes.

In the spring semester course “Making the Science Documentary,” molecular biology and biochemistry major Christopher Doucette ’11 had the opportunity to interview and film McCready about being the first African American woman to attend Maryland’s School of Nursing. He also interviewed Rosetta Sands, the first African American dean in the University of Maryland’s undergraduate program.

“I asked these women about their stories and really analyzed how racial relations affected their school and working experience as nurses before, during and after the Civil Rights movement,” Doucette says. “I have always been interested in how science has been represented through both still and moving images, and this class really taught me how documentaries can be effective tools in conveying information and educating the public about pressing social and scientific issues.”

Doucette and his classmates Sarah Gillig ’09 and Vytaute Pivoriunaite ’12 traveled to the University of Maryland School of Nursing Living History Museum, where they conducted research on the history of nursing. Each student made his or her own film for the class, which was co-taught by Manju Hingorani, associate professor of molecular biology and biochemistry, and Jacob Bricca, adjunct assistant professor of film studies.

The science and film hybrid class, designated a Service Learning Course, is designed to introduce students to topics in the life sciences and the basics of documentary filmmaking, in order to teach students the skills and art of communicating science-related issues through visual media.

Students learn technical filmmaking skills such as composition, lighting and editing, and study science documentaries to understand functional models of non-fiction filmmaking. In complementary sessions, students learned about specific diseases, at the molecular, cellular, and human level, to develop a knowledge base that enables intellectual engagement with the nursing profession.

“I wanted students to gain an appreciation of the biological sciences at the molecular and organism level, learn about diseases like cancer and diabetes that have a devastating impact on so many people, and learn about biomedical research as it relates to the nursing profession,” Hingorani explains.

The 12 enrolled students worked under the guidance of Ann Anthony, a retired home care registered nurse and educator. Anthony made arrangements for the students to meet nurses working in hospice, oncology and palliative care at Middlesex Hospital; nurses working at the Joslin Diabetes Center in New London, Conn.; and a certified nurse specializing in wound care at Middlesex Hospital. Anthony also lectured on the history of the nursing profession, explaining how the nursing profession has evolved in the past 50 years.

“I was very impressed with the integrity and open-mindedness of all the Wesleyan students, and how serious they were in their projects,” Anthony says. “It was fascinating to see how these students with no medical or nursing background approached their films with a liberal arts perspective.”

Chris Skorik '09 edits his film on male nurses.

Chris Skorik '09 edits his film on male nurses.

Classmates Chris Skorik ’09, Kaitlin Halibozek ’10 and Elliott Skopin ’11 explored the role of gender in the field of nursing for their films. They interviewed two male nurses, one at Lawrence and Memorial Hospital in New London, and one from Middlesex Hospital, about their experiences in the profession.

“Nursing is currently dominated by about 90 percent females due to historical and cultural associations between the role females in society and nursing,” Skorik says. “As we had expected, they faced social barriers to their acceptance as nurses, especially early on in their careers. Confusion and occasional opposition was common from family members, for example ‘why aren’t you becoming a doctor instead?’ and from patients ‘wait, so you’re not my doctor?'”

All three students shot footage and interviews, and created three separate cuts based on their own preferences. From seven hours of raw footage, they created three, eight-minute documentaries highlighting different aspects of this interesting phenomenon.

This is the second iteration of “Making the Science Documentary” taught by Hingorani and Bricca. The first class, taught in Spring 2007, focused on four research labs at Wesleyan. The course is part of the interdisciplinary Science and Film Courses initiative begun in 2005 with support from Wesleyan’s Fund for Innovation, the National Science Foundation and the Howard Hughes Medical Institute.

Doucette’s film on African American nurses and Halibozek’s film on male nursing will be shown at the 2009 Nightingale Awards for Excellence in Nursing, Connecticut’s largest state-wide nursing recognition program on April 30. Doucette’s film will be shown at a gala in Hartford, and Halibozek’s film will be shown at a gala in New London.

Hingorani, Biro ’09 Co-Author Article on Metal Toxin

Manju Hingorani, associate professor of molecular biology and biochemistry, is the co-author of “Mechanism of Cadmium-mediated Inhibition of Msh2-Msh6 Function in DNA Mismatch Repair,” published in Biochemistry, March 25, 2009. Three undergraduates from three countries worked on the project in the Hingorani Lab at Wesleyan. They include Francis Noah Biro ’09; Markus Wieland, an exchange student from University of Konstanz; and Karan Hingorani, Manju Hingorani’s nephew from St. Xaviers College in Mumbai who did volunteer work in the lab. The project focused on how the heavy metal toxin Cadmium (found in cigarette smoke, industrial pollution, batteries, etc.) causes DNA damage and blocks DNA repair, which promotes development of cancer.

Hingorani also co-authored the article “Mechanism of ATP-Driven PCNA Clamp Loading by S. cerevisiae RFC,” published in the Journal of Molecular Biology, March 13, 2009.

Mukerji Awarded NSF Funding for Her DNA Research

Ishita Mukerji, professor of molecular biology and biochemistry, uses a UV resonance Raman spectrometer to measure molecular vibrations. She examines the structure of DNA, to understand how protein modulation of the structure can lead to tumors and other diseases.

Ishita Mukerji, professor of molecular biology and biochemistry, uses a UV resonance Raman spectrometer to measure molecular vibrations. She examines the structure of DNA, to understand how protein modulation of the structure can lead to tumors and other diseases.

Errors in genomic DNA can lead to tumors and other diseases. By probing specific DNA structures, Ishita Mukerji hopes to gain an understanding of how such medical conditions can be prevented or possibly cured.

Mukerji, professor of molecular biology and biochemistry, studies how different proteins recognize and bind to DNA. Specifically, she examines four-stranded DNA structures, known as “Holliday junctions,” which are involved in DNA repair and recombination. These are different from the common, two-stranded DNA.

On April 1, Mukerji will receive a four-year grant worth $798,368 from the National Science Foundation (NSF) to fund her research project, “Structure and Function of Holliday Junctions Complexed With Proteins Probed by Fluorescence and UV Raman Spectroscopic Methods.”

“Both DNA repair and recombination are vital functions of the cell, which are needed to maintaining a stable and active genome,” Mukerji explains. “Our goal is to study the structure of the junctions and how that relates to their function.”

Holliday junction structures can be changed by protein binding. Mukerji will examine how these structures are altered by proteins that are known to be involved in repair and recombination and are known to bind to junctions.

“These studies address the overall mechanism of how DNA recombination occurs in the cell and the function of these proteins,” she says.

Chemistry graduate students Andrew Moreno and Jon King, MBB graduate student Yan Li and molecular biology and biochemistry major Olga Buzovetsky ’10, will assist Mukerji with the ongoing research.

Two different methods are used to study the DNA interactions: fluorescence spectroscopy and a laser technique, UV resonance Raman spectroscopy. By using the fluorescence method, the Mukerji group can examine and compare the structure of the junction and the protein-binding sites. By using the Raman technique, which examines molecular vibrations, they can probe protein and ion binding sites.

Wesleyan’s Chemistry Department and Molecular Biology and Biochemistry Department own several fluorescence spectrometers, and Mukerji has built her own, specialized UV resonance Raman spectrometer.

Most of the proposed research will be completed in Mukerji’s lab, although some computational studies will be done in collaboration with David Beveridge, the University Professor of the Sciences and mathematics, professor of chemistry. She is also collaborating with the Hingorani lab (MBB department) to study how proteins involved in mismatch repair and meiotic recombination bind to Holliday junctions. One set of experiments will be conducted at SUNY Buffalo.

The group will also examine how the protein-junction complex either facilitates or suppresses certain processes.

“One theory that we have is that the proteins we are studying suppress recombination as a means of preserving or maintaining the genome.” Mukerji says. “This is an idea that will be tested with the proposed experiments.”

Faculty Teach Elementary Students DNA, Natural History

Michael Singer, assistant professor of biology, taught a workshop on "Biodiversity in Connecticut and Beyond" during the Middletown Minds in Motion program March 21 at Snow Elementary School.

Michael Singer, assistant professor of biology, taught a workshop on "Biodiversity in Connecticut and Beyond" during the Middletown Minds in Motion program March 21 at Snow Elementary School. Singer taught participants about natural history and the biologically diverse animals that inhabit Connecticut ecosystems, focusing on insects, reptiles and amphibians.

Ishita Mukerji, professor of molecular biology and biochemistry, taught a workshop titled "Who Done It? A DNA Investigation."

Ishita Mukerji, professor of molecular biology and biochemistry, taught a workshop titled "Who Done It? A DNA Investigation."

During a “Who Done It? A DNA Investigation,” elementary school aged children sported white lab coats and became “detectives” hoping to solve a crime.

The students learned about DNA structure by isolating DNA from wheat germ and comparing DNA samples from a ‘crime scene’ with the DNA from five suspects. They learn how DNA forensics actually works – just like on the television show “CSI.”

Faculty, Students Attend Biophysical Society Meeting

A group of Wesleyan faculty, graduate and undergraduate students, along with three post-docs from the Molecular Biology and Biochemistry and Chemistry departments, attended the 53rd Annual Biophysical Society Meeting in Boston.

Several labs contributed posters including those run by David Beveridge, the University Professor of the Sciences and Mathematics, professor of chemistry; Irina Russu, professor of chemistry; Manju Hingorani, associate professor of molecular biology and biochemistry; Don Oliver, the Daniel Ayres Professor of Biology, chair and professor of molecular biology and biochemistry; and Ishita Mukerji, professor of molecular biology and biochemistry.

Noah Biro ’09 was a co-author on a poster contributed by Hingorani lab. David Snydacker ’09 and Maiko Kondo ’07 were co-authors on posters contributed by Mukerji lab.

Mukerji was a speaker on a panel titled “Transition from Postdoc to Faculty.”

Mukerji Awarded $780K from National Science Foundation

Ishita Mukerji.

Ishita Mukerji.

Ishita Mukerji, professor of molecular biology and biochemistry, received a $798,368 grant from the National Science Foundation for her project “Structure and Function of Holliday Junctions complexed With Proteins Probed by Fluorescence and UV Raman Spectroscopic Methods.”

The grant is a continuing grant which has been approved on scientific / technical merit for approximately four years. The grant will be awarded April 1.