Tag Archive for biochemistry

Speakers, Poster Sessions at Annual Molecular Biophysics Program Retreat

Wesleyan’s Molecular Biophysics Program hosted its 18th annual retreat Sept. 28 at Wadsworth Mansion in Middletown. Wesleyan affiliated speakers included:

Professor Francis Starr, spoke about DNA junction dynamics and thermodynamics during the 18th annual Molecular Biophysics Retreat.

Professor Francis Starr spoke about DNA junction dynamics and thermodynamics during the 18th annual Molecular Biophysics Retreat.

  • Colin Smith, assistant professor of chemistry, on “An Atomistic View of Protein Dynamics and Allostery;”
  • Meng-Ju Renee Sher, assistant professor of physics, on “Tracking Electron Motions Using Terahertz Spectroscopy;”
  • Kelly Knee, PhD ’07, principle scientist for Pfizer’s Rare Disease Research Unit, on “Protein Folding Chaperones: Molecular Machines for Tricky Problems;”
  • and Francis Starr, professor of physics, director of the College of Integrative Sciences, on “DNA Four-Way Junction Dynamics and Thermodynamics: Lessons from Combining Simulations and Experiments.”

Arthur Palmer, the Robert Wood Johnson, Jr. Professor of Biochemistry and Molecular Biophysics at Columbia University Medical Center, delivered the keynote address on “Conformational dynamics in molecular recognition and catalysis: Lessons from ribonuclease H, AlkB, and GCN4.”

The day-long retreat also included two poster sessions, where undergraduates, graduate students and faculty shared their research with their peers and colleagues. The event concluded with a reception.

The Molecular Biophysics Training Program, Chemistry Department, and Molecular Biology and Biochemistry Department sponsored the event.

Photos of the retreat are below: (Photos by Olivia Drake)

Hingorani, Lui, Zhou PhD ’13 Published in Biological Chemistry Journal

Three scholars from the Molecular Biology and Biochemistry Department are co-authors of a study published in The Journal of Biological Chemistry in August 2017. The paper is titled “Linchpin DNA-binding residues serve as go/no-go controls in the replication factor C-catalyzed clamp loading mechanism.”

The co-authors, Manju Hingorani, chair and professor of molecular biology and biochemistry, professor of integrative sciences; Juan Liu, research associate; and Zayan Zhou, PhD ’13, performed the study on Replication Factor C (RFC) and proliferating cell nuclear antigen (PCNA), which are two essential proteins required for DNA replication and repair in all living organisms.

The researchers found new mechanistic information about how different parts of the RFC protein work together to load PCNA onto DNA (by “clamp loading”), which allows PCNA to help dozens of other proteins to replicate and repair DNA.

The Hingorani group investigates proteins responsible for DNA replication and repair. These proteins maintain genome and cell integrity, and their malfunction leads to cancer and other diseases.

Mukerji, Oliver Co-Author Study in PNAS on Basic Cell Function

In this illustration, SecA is shown in light gray and the SecYEG complex is in dark gray. The rainbow colored portion of SecA is the two helix finger. n cyan is a model of the hairpin.

In this illustration, the hairpin is highlighted in cyan. The hairpin is formed by the initiator part of a protein.

All cells — bacterial or human — secrete up to 10 or 20 percent of the proteins that they make. Human secreted proteins, for example, include components of serum, hormones, growth factors that promote cell development during embryogenesis and tissue remodeling, and proteins that provide the basis for immune cell signaling during infection or when fighting cancer.

The secretion process, however, isn’t an easy feat for cells, as they need to move the proteins across a membrane through a channel. Transport requires the formation of a hairpin, formed by an initiator protein.

In a recent study, Don Oliver, the Daniel Ayres Professor of Biology, professor of molecular biology and biochemistry, and Ishita Mukerji, the Fisk Professor of Natural Science, professor of molecular biology and biochemistry, explain the importance of where and why hairpins form and how they help proteins move across the cell.

The study, titled “Alignment of the protein substrate hairpin along the SecA two-helix finger primes protein transport in Escherichia coli,” brings together key areas of membrane biochemistry, structural biology and molecular biophysics, and has innovative applications of molecular genetics and fluorescence spectroscopy. It was published in the Aug. 7 issue of Proceedings of the National Academy of Sciences (PNAS).

Oppenheim ’02 Urges Cooperation, Preparation for Pandemic Threats

Ben Oppenheim ’02, a senior fellow at the Center on International Cooperation, as well as a consulting scientist with the start-up Metabiota, writes about the importance of international collective action for pandemic preparedness.

Ben Oppenheim ’02, a consulting scientist with Metabiota, a start-up focusing on epidemiological modeling and epidemic risk preparedness, was recently invited to participate in a workshop at the National Academy of Medicine. As a result, Oppenheim and his colleagues wrote an article published in Lancet Global Health titled “Financing of International Collective Action for Epidemic and Pandemic Preparedness,” based on these meetings. Also writing for the Brookings Institution, Oppenheim further explored the challenges of responding to global outbreaks, offering a four-point plan to protect the global poor during pandemics, with co-author Gavin Yamey.

“Post-Ebola and Zika, there’s been increasing worry—and debate—about how to prepare for epidemics and pandemics that threaten global health,” notes Oppenheim, who is also a senior fellow and visiting scholar at New York University’s Center on International Cooperation. “Cracking the problem means thinking through the ways that policy, economics, health, and other factors all intertwine. In the workshop, we were thinking about how to build incentives to improve disease surveillance and outbreak detection, as well as how to improve the legal and economic architecture to speed up the development of vaccines and therapeutics. All of this demands attention to everything from epidemiology, to financing, and to politics.”

Oppenheim also discussed the economic impacts of pandemics,

McAlear Visits Former Students Odede ’09, ’12, and Perel-Slater ’11 at Non-Profits in Africa

Professor Michael McAlear gathers with students at Shining Hope for Community, the nonprofit begun by Jessica ’09 and Kennedy ’12 Odede in Kibera, Africa. 

In 2010 Professor Michael McAlear first gathered with students at Shining Hope for Community, the nonprofit begun by Jessica ’09 and Kennedy ’12 Odede in Kibera, Kenya, offering a lecture on clean water. This year on his visit during spring break, he again gave a lecture to these students, now pre-teens and young teenagers, who filled his Q&A session with their concerns, interest, ideas, and a deep desire to learn.

In March, during Wesleyan’s spring break, Associate Professor of Molecular Biology and Biochemistry Michael McAlear took a trip to visit and catch up with three alumni whom he’d known when they were undergraduates, just beginning the nonprofits for which they are now known. McAlear doesn’t see them often: they live and work in Africa. All three had received Wesleyan’s Christopher Brodigan Award in their senior year, for research or work in Africa.

Kennedy Odede '12, Mike McAlear and Jessica ’09 Odede.

Pictured from left are Kennedy Odede ’12, Mike McAlear and Jessica Posner Odede ’09.

McAlear’s first stop was in Kibera, the largest slum in Kenya, and home of SHOFCO, Shining Hope for Community, the nonprofit begun by Jessica ’09 and Kennedy ’12 Odede. Linking education for girls with community services, the organization has grown since McAlear had last visited in 2010 to help set up the school, when it held only two classes of girls ages 6 and 7, and the group was building a clinic was built to honor Johanna Justin-Jinich ’10, the student slain in the spring of 2009. At that time, McAlear offered the young students a lecture on clean water and also became a sponsor for one little girl, a responsibility and relationship that is ongoing,

“I was overwhelmed by the need in Kibera— and the optimism and fearlessness of Kennedy and Jessica; you couldn’t help being swept up by that,” McAlear recalls. “They were so young and naïve that they didn’t know what they couldn’t do—so they just kept on doing things.”

Students Inducted into Honor Society, Win Awards At American Society for Biochemistry and Molecular Biology

Julianne Riggs in Chicago last month, where she attended the American Society for Biochemistry and Molecular Biology meeting.

Julianne Riggs ’17 in Chicago last month, where she attended the American Society for Biochemistry and Molecular Biology meeting.

Five Wesleyan seniors were inducted into the American Society for Biochemistry and Molecular Biology honor society at the ASBMB annual meeting in Chicago, April 22-26. They are: Jennifer Cascino ’17, Kaileen Fei ’17, Julianne Riggs ’17, Rachel Savage ’17 and Stacy Uchendu ’17.

The ASBMB Honor Society recognizes exceptional undergraduate juniors and seniors who are pursuing a degree in the molecular life sciences for their scholarly achievement, research accomplishments, and outreach activities. The mission of the society is to advance the science of biochemistry and molecular biology through organization of scientific meetings, advocacy for funding of basic research and education, support of science education at all levels, promotion of the diversity of individuals entering the scientific workforce, and publication of a number of scientific and educational journals, including the Journal of Biological Chemistry and the Journal of Lipid Research.

Bios of all the inductees, in alphabetical order, can be found here.

Riggs attended the meeting, where she took part in the induction ceremony and presented her research.

“Overall, it was a great experience. I got to present in the undergraduate poster competition and won honorable mention for best chromatin and gene expression poster. I also presented my poster to the general meeting,” she said. “It was a huge conference and there was so much going on. It was great to talk to people of all levels of science, get their perspectives on what it takes to be a scientist, and hear them passionately discuss their research projects. It was also wonderful to talk to people who were researching similar topics to mine, and get their advice and validation on my work.”

In addition, two students, Christine Little ’18 and Cody Hecht ’18, received ASBMB research awards. The $1,000 awards will support their research over the summer.

Faculty, Students, Alumnus Co-Author Paper in Biochemistry Journal

Wesleyan co-authors published a paper titled “The Stories Tryptophans Tell: Exploring Protein Dynamics of Heptosyltransferase I from Escherichia coli” in the January 2017 issue of Biochemistry.

The co-authors include chemistry graduate student Joy Cote; alumni Zarek Siegel ’16 and Daniel Czyzyk, PhD ’15; and faculty Erika Taylor, associate professor of chemistry; Ishita Mukerji, the Fisk Professor of Natural Science, professor of molecular biology and biochemistry.

Their paper investigates the intrinsic properties of Tryptophan amino acids found within the protein, Heptosyltransferase I, to understand the ways this protein moves during catalysis. Understanding the movement of this protein is an important step in developing its inhibitors.

When this protein is inactive, either because it was genetically altered or inhibited, hydrophobic antibiotics become more effective, so inhibitors could be useful in reactivating antibiotics that are current not effective against these bacteria.

While it is popularly believed that inhibiting a protein requires a compound to compete with the substrate, their paper argues that instead one can design a inhibitor to disrupt protein dynamics, preventing activity. The co-authors compare the function of this “protein dynamics disruptor” to a wedge holding open a door–once inserted, the inhibitor prevents the protein from performing its function.

Their research on Tryptophan residues also found that distant regions of the protein communicate whether or not they are binding their substrate to other regions.

“It would be like if your right hand knew that your left hand was holding a pencil just by the changes in the position of your left hand. We are currently pursuing computational studies to look for these motions via molecular dynamics experiments,” Taylor said.

Students Present Thesis Work at Biophysical Society Meeting

Three Wesleyan Molecular Biology and Biochemistry majors received the unique opportunity of presenting their thesis work at the 61st annual Biophysical Society meeting in New Orleans, Feb. 11-15.

Rachel Savage ’17 presented her senior honors thesis titled, “Investigation of the Melting Thermodynamics of a DNA 4-Way Junction: One Base at a Time,” which was done in collaboration with Francis Starr, professor of physics.

Rachel Savage ’17 presented her senior honors thesis titled, “Investigation of the Melting Thermodynamics of a DNA 4-Way Junction: One Base at a Time,” which was done in collaboration with Francis Starr, professor of physics.

Chemistry, Physics Students Attend Biomedical Research Conference

Contributed photo

From Nov. 9-12, two faculty members and five students from the physics and chemistry departments, attended the Annual Biomedical Research Conference for Minority Students in Tampa, Fla.

Candice Etson, assistant professor of physics, and Erika Taylor, associate professor of chemistry, were joined by McNair Scholars Luz Mendez ’17, Tatianna Pryce ’17, Stacy Uchendu ’17 and Hanna Morales ’17; and Wesleyan Mathematics and Science (WesMaSS) Scholar Helen Karimi ’19.

Students observed other research being performed around the nation by students who are members of underrepresented groups in Science, Technology, Engineering and Mathematics (STEM). In addition, the Wesleyan students presented their own research and Morales and Karimi were awarded Outstanding Poster Presentation Awards.

“Through the PIE Initiative, Wesleyan has a deliberate strategy to support underrepresented students and faculty in STEM fields by providing resources that increasing post-Wesleyan mentorship and exposure to research excellence, all of which were fulfilled through this conference,” said Antonio Farias, vice president for equity and inclusion/Title IX officer. “It cannot go without saying that without Professor Taylor’s and Professor Etson’s holistic mentorship approach, these type of opportunities for our young scholars would not be possible.”

RNA Splicing, Student Research Discussed at Biophysics, Biological Chemistry Retreat

The Molecular Biophysics Program, the Department of Chemistry and the Department of Molecular Biology and Biochemistry hosted the 17th Annual Molecular Biophysics and Biological Chemistry Retreat on Sept. 29 at Wadsworth Mansion in Middletown.

The event included several talks by Wesleyan faculty and two student research poster presentations.

Professor Anna Pyle delivered the keynote address titled “Structural and Mechanistic Insights into RNA Splicing.” Pyle is the Howard Hughes Medical Institute Investigator and the William Edward Gilbert Professor in the Departments of Molecular, Cellular and Developmental Biology and Chemistry at Yale University. Pyle studies the structure and function of large RNA molecules and RNA remodeling enzymes. A Howard Hughes Medical Institute Investigator since 1997 and the author of more than 150 publications, she uses a diverse set of biochemical and biophysical techniques, including crystallography and chemical probing, to understand the structural complexity of RNA architecture.

Photos of the retreat are below: (Photos by Will Barr ’19 and Gabi Hurlock ’20)

Biophysics Retreat at Wadsworth Mansion Sept 29, 2016. (Photo by Gabi Hurlock)

Hingorani Finishes Program Director Appointment with NSF

Manju Hingorani

Manju Hingorani

Manju Hingorani, professor of molecular biology and biochemistry, professor of integrative sciences, recently completed a two-year tenure working for the National Science Foundation’s Division of Molecular and Cellular Biosciences (MCB). Hingorani served as the program director of the MCB Genetic Mechanisms program.

Hingorani worked with investigator-driven proposals submitted to both the Genetic Mechanisms and the Cellular Dynamics and Function programs. As a rotating program director, Hingorani managed proposal reviews and awards and responded to inquiries from principal investigators conducting fundamental research related to the central dogma of biology.

Dierker, Mukerji Honored as Women of Innovation

Lisa Dierker

Lisa Dierker

Lisa Dierker, professor of psychology, director of pilot programs for the Center for Pedagogical Innovation, and Ishita Mukerji, the Fisk Professor of Natural Science, professor of molecular biology and biochemistry, professor of integrative sciences, were both honored at the 12th annual Women of Innovation Awards. Presented by the Connecticut Technology Council, the awards celebrate the energy, creativity and success of women and students from Connecticut’s science and technology community.

Both professors were honored in the category of Academic Innovation and Leadership. The celebration was held April 6 in Plantsville, Conn.

Dierker was honored for her work developing a curriculum to introduce students to a passion-driven, project-based course in applied statistics, data analysis and programming. Through a growing network of high schools, community colleges, and universities as well as a massive open online course (MOOC), she is dedicated to creating real access for women and other underserved populations, both locally and across the globe.

Ishita Mukerji

Ishita Mukerji

Mukerji was recognized for her research focused on the study of protein-DNA interactions to understand the mechanisms of gene expression, DNA replication and DNA repair. She previously served as dean of science and mathematics at Wesleyan, where she helped to establish the Wesleyan Math and Science Scholars program and the College of Integrative Sciences.