Tag Archive for Biology

NSF Supports Holmes’ Gene Expression Research

At right, Scott Holmes, associate professor of molecular biology and biochemistry, received a three-year grant to support his research gene expression. His lab uses a budding yeast for the studies.

At right, Scott Holmes, associate professor of molecular biology and biochemistry, received a three-year grant to support his research gene expression. His lab uses a budding yeast for the studies.

For the next three years, the National Science Foundation (NSF) will support gene expression research led by Scott Holmes, associate professor of molecular biology and biochemistry.

On March 2, the NSF awarded Holmes a $599,832, three-year grant for his studies on “Epigenetic Silencing of Gene Expression in Saccharomyces cerevisiae.”

Scott Holmes

Scott Holmes incorporates his research into the spring semester course Advanced Laboratory in Genetics and Molecular Biology.

Gene expression refers to the observable characteristics generated on a molecular level by a particular sequence of DNA or gene; epigenetic controls are essential in maintaining the specific patterns of gene expression that distinguish hundreds of distinct cell types in skin, muscles and other types of tissue.

“I’m thrilled to get the funding,” Holmes says. “It’s very timely for us, and it’s a testament to the great work that graduate and undergraduate students have done in the lab over the last few years.”

Holmes, currently working with four graduate and four undergraduate students, uses a simple budding yeast, Saccharomyces cerevisiae, to study gene expression. Yeast uses an epigenetic gene repression mechanism, known as “silencing” to control the genes responsible for determining cell type.

“Two organisms, or two cells within the same organism, can have identical genetic information, or the same DNA sequence, but can have very different characteristics and functions,” Holmes explains. “We want to know how the gene expression patterns that determine cell type are first established, and then propagated as cells divide.”

The DNA in cells is organized into structures known as chromosomes. A key mechanism for controlling whether genes are on or off is by altering the structure of the chromosome. Once established, these alterations can become a stable, heritable part of the chromosome.

The nature of these structures and the manner in which they are inherited is not clear, Holmes says. Studies conducted on yeast will reveal the basic mechanisms of epigenetic inheritance.

This is the ninth year the NSF has supported Holmes’s research on yeast. He incorporates this research into the spring semester course MB&B 294, Advanced Laboratory in Genetics and Molecular Biology, which is required for undergraduate majors in the MB&B Department.

“This course is designed to familiarize undergraduates with the methods and approaches of the field in the context of pursuing novel research questions,” Holmes explains.

He also has partnered with a local high school biology teacher to devise and implement lesson plans, focusing on key concepts in genetics. Advanced students from this high school also visit the research lab to shadow graduate students.

Scott Holmes Awarded NSF Grant

Scott Holmes, associate professor of molecular biology and biochemistry, received a grant from the National Science Foundation (NSF) on March 2. The three year grant, worth $599,832, will support his studies on “Epigenetic Silencing of Gene Expression in Saccharomyces cerevisiae.”

Read more on Holmes’s study here.

NS&B Alumni Speak to Students, Faculty About Post-Wesleyan Life

Dan Austin '08 speaks to students and faculty on "Research opportunities before graduate/medical school: The national Institutes of Health IRTA Post-Baccalaureate Fellowship," during the second Neuroscience and Behavior Symposium Feb. 20 in Exley Science Center. Austin was one of five NS&B alumni who returned to campus to speak at the symposium. While a student, Austin received university honors, the CBIA/CURE Bioscience Fellowship; and the Hawk Prize in Chemistry.

Dan Austin '08 speaks to students and faculty on "Research opportunities before graduate/medical school: The National Institutes of Health IRTA Post-Baccalaureate Fellowship," during the second Neuroscience and Behavior Symposium Feb. 20 in Exley Science Center. Austin was one of five NS&B alumni who returned to campus to speak at the symposium. While a student, Austin received university honors, the CBIA/CURE Bioscience Fellowship; and the Hawk Prize in Chemistry. He currently is a pre-doctorial fellow at the National Institutes of Health.

Faculty, Guests Discuss “Stem Cells into the Clinic”

Lori Gruen, associate professor of philosophy, associate professor of feminist, gender and sexuality studies, speaks during a symposium titled "Stem Cells into the Clinic: Biological, Ethical and Regulatory Concerns," Jan. 28 in the Goldsmith Family Cinema. The event was sponsored by the Dachs Chair, the Faust Lectures in Ethics, and the Ethics in Society Project.

Lori Gruen, associate professor of philosophy, associate professor of feminist, gender and sexuality studies, speaks during a symposium titled "Stem Cells into the Clinic: Biological, Ethical and Regulatory Concerns," Jan. 28 in the Goldsmith Family Cinema. The event was sponsored by the Dachs Chair, the Faust Lectures in Ethics, and the Ethics in Society Project.

Keynote speaker Bonnie Steinbock, professor of bioethics at the Union Graduate College-Mount Sinai School of Medicine, and professor of philosophy at the University of Albany spoke on “The Ethics of Stem Cell Policy." Her research focuses on the ethics of reproduction and genetics.

Keynote speaker Bonnie Steinbock, professor of bioethics at the Union Graduate College-Mount Sinai School of Medicine, and professor of philosophy at the University of Albany spoke on “The Ethics of Stem Cell Policy." Her research focuses on the ethics of reproduction and genetics.

Stephen Latham, deputy director of Yale University's Interdisciplinary Center for Bioethics, and Laura Grabel, the Lauren B. Dachs Professor of Science and Society, professor of biology, joined Gruen and Steinbock in a panel discussion of "Stem Cell Research in the Obama Era."

Stephen Latham, deputy director of Yale University's Interdisciplinary Center for Bioethics, and Laura Grabel, the Lauren B. Dachs Professor of Science and Society, professor of biology, joined Gruen and Steinbock in a panel discussion of "Stem Cell Research in the Obama Era."

Dr. Irving Weissman, professor of pathology and developmental biology at the Stanford School of Medicine and director of the Stanford Institute of Stem Cell Biology and Regenerative Medicine, spoke on “Normal and Neoplastic Stem Cells. Weissman’s research focuses on hematopoietic stem cell biology. Other speakers at the symposium included Gordon Carmichael, professor of genetics and developmental biology at the University of Connecticut Health Center, and Valerie Horsley, assistant professor of molecular, cellular and developmental biology at Yale University. Carmichael, who spoke on “Double Stranded and Noncoding RNAs in Human Embryonic Stem Cells” studies molecular signals which control the expression and function of mRNA molecules. Horsley, who spoke on “Intrinsic and Extrinsic Control of Skin Stem Cells," studies the cellular and molecular mechanisms that control stem cell activity and function within epithelia, the tissues that line internal organs and outer surfaces. (Photos by Olivia Bartlett Drake)

Dr. Irving Weissman, professor of pathology and developmental biology at the Stanford School of Medicine and director of the Stanford Institute of Stem Cell Biology and Regenerative Medicine, spoke on “Normal and Neoplastic Stem Cells. Weissman’s research focuses on hematopoietic stem cell biology. Other speakers at the symposium included Gordon Carmichael, professor of genetics and developmental biology at the University of Connecticut Health Center, and Valerie Horsley, assistant professor of molecular, cellular and developmental biology at Yale University. Carmichael, who spoke on “Double Stranded and Noncoding RNAs in Human Embryonic Stem Cells” studies molecular signals which control the expression and function of mRNA molecules. Horsley, who spoke on “Intrinsic and Extrinsic Control of Skin Stem Cells," studies the cellular and molecular mechanisms that control stem cell activity and function within epithelia, the tissues that line internal organs and outer surfaces. (Photos by Olivia Bartlett Drake)

5 Questions With … Michael Singer

Mike Singer, assistant professor of biology, pursues his interests in biodiversity and environmental conservation through teaching, research, outreach and personal activities.

Mike Singer, assistant professor of biology, pursues his interests in biodiversity and environmental conservation through teaching, research, outreach and personal activities.

This issue we ask 5 Questions of … Michael Singer, assistant professor of biology.

Q: Professor Singer, you are known around campus for being “the bug man,” or more specifically, “the caterpillar man.” What is your interest in entomology?

A: I’m generally interested in insects because of their diversity in form, function, and habits. Contrary to many people, I find most kinds of insects quite beautiful. They also have endless stories to tell. I’m particularly interested in a species of woolly bear caterpillar called Grammia incorrupta because of its polyphagous feeding behavior. (Polyphagous means that it eats many different kinds of plants.) Unlike most caterpillars, which have quite specialized diets, this one makes many choices about what it eats, and why it makes those choices is a subject of my research.

Q: Please give an example of plant-insect interaction and its role within ecology?

A:  I study the plant-insect interaction of herbivory (herbivores eating plants). Herbivory is very common and widespread in ecosystems, and most of it involves insects like caterpillars eating plants. Farmers and gardeners know this because they constantly try to keep insects from eating too much of their crop! In natural ecosystems, plants have to rely on other means of pest control. All plants make defensive chemicals to deter or poison herbivores, and most plants also rely on the natural enemies of herbivores, such as birds, spiders, and wasps, for protection from herbivores. This so-called tri-trophic interaction

Cohan Participates in Darwin Conference at University of Chicago

Fred Cohan, professor of biology, delivered a presentation titled “Darwin vs. Mayr on the Origin of Bacterial Species,” during a Darwin conference, celebrating the 200th anniversary of Charles Darwin’s birth. The event was held Oct. 29-31 at the University of Chicago. Cohan joined other evolutionary biologists, historians and philosophers who connected their work directly with Darwin. 2009 also marks the 150th anniversary of Darwin’s The Origin of Species.

Ph.D Candidate’s Bat Research Links 3 Biological Communities

Biology Ph.D. candidate Kate Miller records echolocation calls of bats at one of four study sites along Middletown's Coginchaug River. Miller hopes to identify which types of stream habitats have the most activity, and uncover critical habitats in Connecticut.  (Photos by Olivia Bartlett Drake)

Biology Ph.D. candidate Kate Miller records echolocation calls of bats at one of four study sites along Middletown's Coginchaug River. Miller hopes to identify which types of stream habitats have the most activity, and uncover critical habitats in Connecticut. (Photos by Olivia Bartlett Drake)

Biology Ph.D candidate Kate Miller treks through a wildflower-lined trail alongside Middletown’s Coginchaug River. She approaches a plastic garbage bin and a PCV pipe protruding from the ground.

“That’s my bat echolocation recorder,” she says. “It’s old but I’m not complaining. It was free and it works.” Miller credits Scott Reynolds, Ph.D, of North East Ecological Services in Concord, N.H. for the loan of the equipment.

Inside the crude setup is a 12-volt battery, an echolocation call recorder and lap-top computer. Every 1.5 seconds, the equipment translates the information into a graph and stores it as a data file on the laptop. Miller opens the lap top and examines the graph, which reveals recorded frequencies vs. time on two axis, in real-time.

The meadow is alive with audible sounds of songbirds, crickets and cicadas.

“Right now we’re picking up something with a 10 to 15 kilohertz frequency. We know that’s not a bat since their calls are usually between 25 and 80 kilohertz,” Miller explains, eyeing the lines on the graph. “Humans can only hear frequencies up to about 20 kilohertz.”

Building on studies that identify stream corridors as prime foraging habitats for bats, Miller hopes to identify which types of stream habitats have the most activity. She also hopes to determine whether or not the composition and abundance of “benthic macroinvertebrates” – mostly aquatic larvae that live on the stream bottom and hatch into flying insects the bats consume – is at all correlated

Undergraduates Present Summer Research at Poster Session

Hughes Fellow Juan Carlo Francisco '11 speaks to Michael Weir, director of the Hughes Program in the Life Sciences, professor of biology, about his project "Comparative Analysis of Ecotype Demarcation Algorithms" during the 2009 Summer Undergraduate Research Poster Presentations July 31 in Exley Science Center. Francisco's advisors were Danny Krizanc, professor of computer science, and Fred Cohan, professor of biology.

Hughes Fellow Juan Carlo Francisco '11 speaks to Michael Weir, director of the Hughes Program in the Life Sciences, professor of biology, about his project "Comparative Analysis of Ecotype Demarcation Algorithms" during the 2009 Summer Undergraduate Research Poster Presentations July 31 in Exley Science Center. Francisco's advisors were Danny Krizanc, professor of computer science, and Fred Cohan, professor of biology.

Hughes Fellow Danielle Mor ’10 speaks about her research titled “Identifying Migration Guidance Factors for Transplanted Neural Stem Cells in the Epileptic Hippocampus." Mor’s advisor is Laura Grabel, the Lauren B. Dachs Professor of Science and Society, professor of biology.

Hughes Fellow Danielle Mor ’10 speaks about her research titled “Identifying Migration Guidance Factors for Transplanted Neural Stem Cells in the Epileptic Hippocampus." Mor’s advisor is Laura Grabel, the Lauren B. Dachs Professor of Science and Society, professor of biology.

NSF, NIH Support Burke’s Development, Evolution Research

Ann

Ann Burke, associate professor of biology, received grants from the National Science Foundation and National Institutes of Health to study amphibian systems.

Ann Burke, associate professor of biology, recently received a three-year, $395,000 grant from the National Science Foundation (NSF) to study the development and evolution of the shoulder girdle using transgenic mice, frog and salamander.

The mice will be generated in collaboration with a lab at the University of Michigan and will allow Burke and her associates to turn off Hox genes, which are specific patterning genes, in specific sub populations of the embryonic mesoderm that make the musculoskeletal tissues.

Pictured is a three dimensional reconstruction of a mouse and chicken scapula. Ann Burke, associate professor of biology, received two grants that fund her research on the scapula's development.

Pictured is a three dimensional reconstruction of a mouse and chicken scapula. Burke is studying the scapula's development.

“Comparing the dynamics of gene expression and cell interactions during the formation of the pectoral region in a variety of embryos will help us understand the evolution of these musculoskeletal structures and the dramatic variations among vertebrate lineages associated with adaptations for different locomotor strategies, like swimming, scurrying, crawling and flying,” Burke explains.

The frog and salamander experiments will use transplants of mesoderm between wild type embryos and embryos that have Green Fluorescent Protein (GFP) expressed in all their cells, allowing Burke and her associates to fate map mesodermal cell populations.

Fate mapping is determining which cellular structures in the embryo give rise to which adult structures.

“We do this by transplanting the embryonic structure from a labeled embryo (GFP in this case) into the same spot in an unlabeled embryo, and tracing the ‘fate’ of the labeled cells, that is which adult structure they end up in,” Burke says.

Burke also received a two-year $100,000 grant from the National Institutes of Health (NIH) to use the same amphibian systems (salamander and frog) to develop a model system for understanding body wall defects in humans.

The grants will provide funds for a team of researchers at Wesleyan working with Professor Burke on these projects, including a postdoctoral fellow, graduate students and undergraduates.

“Receiving these two new federal grants, plus a grant from the Eppley foundation earlier this year, is a remarkable accomplishment in any year, but particularly this year as funding levels have dropped precipitously,” says Jan Naegele, professor of biology, professor of neuroscience and behavior.

Burke Awarded NSF, NIH Grants

Ann Burke, associate professor of biology, received a three-year, $395,000 grant from the National Science Foundation (NSF) to study the development and evolution of the shoulder girdle using transgenic mice, frog and salamander. She also received a two-year $100,000 grant from the National Institutes of Health (NIH) to use the same amphibian systems (salamander and frog) to develop a model system for understanding body wall defects in humans.The grants will provide funds for a team of researchers at Wesleyan working with Burke on these projects, including a postdoctoral fellow, graduate students and undergraduates.

5th Graders Sample Wesleyan Sciences

Brian Stewart, associate professor pf physics, demonstrates how liquid nitrogen looks like water but evaporates rapidly at room temperature. Fifth grade students from Snow Elementary School toured the Wesleyan sciences June 19.

Brian Stewart, associate professor pf physics, demonstrates how liquid nitrogen looks like water but evaporates rapidly at room temperature. Fifth grade students from Snow Elementary School toured the Wesleyan sciences June 19.

Vacek Miglus, lab technician and curator of the Physics Department, shows the students how various lamps are lit by a Tesla coil without being attached to wires. Brian Stewart is on the right.

Vacek Miglus, lab technician and curator of the Physics Department, shows the students how various lamps are lit by a Tesla coil without being attached to wires. Brian Stewart is on the right.

Laurel Appel, adjunct associate professor of biology, senior research associate and director of the McNair Program, watches DNA fibers come out of a solution as ice-cold alcohol meets the warm, salty, DNA solution. One of the students described the reaction as looking like a spiderweb.

Laurel Appel, adjunct associate professor of biology, senior research associate and director of the McNair Program, watches DNA fibers come out of a solution as ice-cold alcohol meets the warm, salty, DNA solution. One of the students described the reaction as looking like a spiderweb.

McNair fellow Kelley Miller '10, at right, helps the Snow Elementary School students isolate DNA from wheat germ. The recipe for this, and other experiments is online at http://lappel.web.wesleyan.edu/expts.htm.

McNair fellow Kelley Miller '10, at right, helps the Snow Elementary School students isolate DNA from wheat germ. The recipe for this, and other experiments is online at http://lappel.web.wesleyan.edu/expts.htm.

Astronomy graduate student Amy Langford, at right, teaches the students about Wesleyan's Alvan Clark 20-inch refractor telescope inside the observatory. (Photos by Olivia Bartlett)

Astronomy graduate student Amy Langford, at right, teaches the students about Wesleyan's Alvan Clark 20-inch refractor telescope inside the observatory. (Photos by Olivia Bartlett)

Marie Curie Fellowship Winner Studies Non-Native Plant at Wesleyan

The annual plant, Polygonum cespitosum, is becoming invasive in North America.

The annual plant, Polygonum cespitosum, is becoming invasive in North America.

For the next two years, researcher Silvia Matesanz of Segovia, Spain will be collaborating with Chair and Professor of Biology Sonia Sultan in her plant evolutionary ecology lab at Wesleyan. Matesanz was awarded the prestigious Marie Curie International Post-doctoral Fellowship from the European Commission. Matesanz, Sultan and biology BA/MA student Timothy Horgan-Kobelski ’09 will be studying an introduced annual plant called Polygonum cespitosum that is becoming invasive in North America.

The scientists are particularly interested in understanding the evolutionary dynamics of the plant’s spread. Sultan and her research group will provide Matesanz with evolutionary expertise, which will enhance her previous Ph.D. training in plant ecophysiology, or the physiological responses of plants to the environment.

A successful non-native plant such as Polygonum cespitosum can displace native species from areas into which it spreads, altering the functional properties of the local ecosystem and reducing biodiversity. A species with this kind of impact is considered to be invasive. Sultan and Matesanz wish to determine what characteristics of this species allow it to thrive in novel environments. Polygonum cespitosum was introduced to the United States from Asia at the beginning of the 20th century and has only recently become invasive.

Sonia Sultan

Sonia Sultan

“Many plants and animals are introduced into new regions but only a very small proportion of these become invasive,” Sultan said. “People are interested to know what it is about certain species that allow them to spread so successfully.”

Sultan said that most biologists agree that “individual plasticity” or flexibility is a common property among invasive species. For example, “a certain seed might develop into a functioning shade plant in the shade and a sun plant in the sun.” Sultan’s lab has been studying how New England Polygonum plants are rapidly evolving greater developmental plasticity for different habitats.

Matesanz stated that she was looking forward to focusing on the evolutionary aspects of plants, because she hadn’t explored that avenue of research as much during her PhD program at the Center of Environmental Sciences in Madrid.

“One purpose of these fellowships is for young scientists trained in Europe to increase their expertise by taking on project that use different approaches,” Sultan said.

Silvia Matesanz was awarded the prestigious Marie Curie International Post-doctoral Fellowship from the European Commission to conduct research at Wesleyan.

Silvia Matesanz was awarded the prestigious Marie Curie International Post-doctoral Fellowship from the European Commission to conduct research at Wesleyan.

Matesanz added, “I wanted to broaden my breadth of discipline. I wanted to come to a very top-notch lab and start doing different things. And, also, improve my English language.”

Sultan explained that the collaborative project is interdisciplinary because it uses Matesanz’s “expertise in understanding plant physiology combined with my expertise in thinking about the evolutionary process. So she brings a strength that I don’t have and we give her a strength that she doesn’t have yet,” she said.

The joint research project will involve greenhouse experiments, field studies, and microsatellite genetic analyses. The scientists will try to determine how the plants are evolving in New England by testing how plants from local populations of Polygonum develop and function in different controlled environments. By growing inbred plants of various genetic lines in contrasting conditions, Sultan and Matesanz can examine how plants with a given genetic makeup can respond to different environments.

“[Polygonum cespitosum’s] typical habitat in New England, which is similar to their habitat in their native Asian region, is shady paths and forests and also along shaded roadsides. Yet, we’re beginning to see them in open sites. They seem to be increasing their ecological range,” Sultan said.

Sultan and Matesanz expect to learn more about how the plants are evolving to tolerate sunny environments. In addition they will use molecular markers that reveal genetic differences at specific DNA sequences to track the spread and differentiation of the species in New England.

The team aim to publish several papers about their experiments and attend the Ecological Society of America conference to present their results.

Matesanz’s work in Sultan’s lab is part of the two-year outgoing phase of her fellowship. For the third year of her fellowship, she will return to Spain to complete the project in collaboration with her former PhD advisor, Fernando Valladares, at the Terrestrial Ecology group in Spain’s Institute of Natural Resources in Madrid.

Sultan said that another advantage of the Marie Curie International Post-doctoral Fellowship is that it encourages collaboration between labs in other countries.