Sharing MCB Science – Unraveling the relationship between DNA winding and chromatin topology

A 3D model of DNA wrapped around nucleosomes

A model of circular nucleosome array

Cells tackle the complex task of packaging all their DNA into a tiny nucleus by spooling it around nucleosomes, sets of 8 specialized proteins called histones. Historically there has been variation in estimates in the number of times that DNA winds around each nucleosome. This number is known from x-ray crystallography to be about 1.7 superhelical turns; however, previous examination of circular nucleosome arrays indicated to researchers that the number of turns is closer to one. The Grigoryev lab at Pennsylvania State University has proposed an explanation.

Through a more direct approach using a combination of electrophoresis and electron microscopy, Dr. Grigoryev and his lab, in collaboration with Dr. Zhurkin lab at NIH, discovered that the number of turns and the space between nucleosomes is actually quite variable within the same segment of DNA. Furthermore, the distance between nucleosomes seems to influence the number of turns DNA makes per each nucleosome. They also noted that this variability of chromosome spacing could be a mechanism which chromatin domains use to control DNA packing. The findings were published in Science Advances.
DNA packs tightly to fit into the cell nucleus, but how dense it is and how the density is distributed across the genome also influences higher level organization such as chromatin shape and even chromosome shape and structure. Shape and structure, in turn, influence how DNA interacts with the environment around it. For example, the density of DNA-packing influences whether regulatory proteins can properly interact with a gene and therefore whether the gene is expressed. Understanding the mechanisms behind how these changes are managed can provide a better look into how DNA functions, which can expand our ability to understand and manipulate genetic processes.

This work was funded by the Genetic Mechanisms cluster of the Division of Molecular and Cellular Biosciences, award #1516999.

Supplemental Funding Pays: Non-Academic Careers Class at UT-Knoxville

Although the Department of Biochemistry and Cellular and Molecular Biology (BCMB) at University of Tennessee, Knoxville, already had a well-established seminar series on career development, many faculty conversations revolved around how to introduce students to non-academic careers. The answer came in the form of a course named “Oh! The Places You’ll Go…with a PhD in Science.” Using a supplemental funding award (MCB 1616495), Dr. Maitreyi Das reimagined the seminar series.

“Oh! The Places You’ll Go…” built on the seminars by adding speakers from diverse career tracks and requiring students to prepare for each speaker through assigned reading, research on the speaker’s career field, and classroom discussion. After each seminar, students met with the speaker in an open forum to discuss the speaker’s career track, life events that led to the decision to pursue a particular expertise, and the logistics of transitioning to their non-academic specialty. The class also included segments on developing “soft skills,” led by Department Head Dr. Dan Roberts and Associate Department Head Dr. Gladys Alexandre. Skills developed included crafting an elevator pitch, assessing the need for and type of postdoctoral training, and interviewing skills.

Perhaps the most valuable change was requiring students to write an Individual Development Plan (IDP), says Dr. Das. Although the assignment was much more difficult for the students than initially anticipated, the exercise helped faculty realize that students did not know how to think about career development. The exercise helped students and faculty alike identify their respective strengths. The biggest benefit was that interactions between students, speakers, and faculty strengthened faculty commitment to helping students develop a career path. “It helped change department culture,” Dr. Das says.

“We expect this experience to provide a long-lasting impact on the ability of our departmental faculty to support and guide graduate students who wish to pursue different careers after their PhD,” says Dr. Das. “We also expect this course to become integrated into our Ph.D. training program. This program is helping students prepare for career paths they did not realize were available – let’s help our best people!”

Although the department of biochemistry and cellular and molecular biology (BCMB) at University of Tennessee, Knoxville, already had a well-established seminar series to introduce students to non-academic careers, conversation among faculty often revolved around how to do better prepare students for the workforce. Then, a panelist who’d recently served on an NSF merit review panel told Dr. Maitreyi Das, about supplemental funding offered by MCB. Dr. Das applied for the funding and used it to supplement the seminar series with intensive coursework. The MCB blog interviewed Dr. Das to learn more about the experience. Excerpts from that interview are posted below. What did you want to change about the seminar series? The previous seminar series (which the department plans to continue) invited a minimum of two speakers per semester to talk about their career paths. We focused on speakers whose PhDs have found success in non-traditional ways. However, attendance was optional; and neither students nor faculty seemed to be benefitting from the opportunity as much as expected. What was different about the course? Unlike the seminar series, which was optional, we required graduate students enrolled in the department’s PhD program to attend. We also required students to write an Individual Development Plan (IDP). Although this was much more difficult for them than we anticipated, there were several benefits: the exercise helped faculty understand that we have so much more work to do in helping students think about career development. Next, the IDP exercise helped both students and faculty become much more adept at identifying their strengths. Perhaps the biggest benefit was that interactions between students, speakers, and faculty increased faculty conversations and the will to do more to help students. It helped change department culture. Can you give us more details about the course? The course was named “Oh! The Places You’ll Go…with a PhD in Science!” It consisted of discussion and reading regarding each career track ahead of a visit and seminar by a selected speaker. Students then met in an open forum with each expert to discuss the speaker’s career track, life events that led to their decision to pursue particular expertise, as well as the logistics of how each got their start in their non-academic specialty. Apart from the valuable information that the students gathered, they also had the opportunity to network with the speakers. In the majority of instances, the speakers expressed enthusiasm for this effort and several even extended invitations to internships to interested students. In addition to these exercises, my colleagues [professors] Dan Roberts and Gladys Alexandre worked with the students on the development of their “soft” skills and provided tools to plan and prepare for the career of their choice. Topics discussed included developing and maintaining an individual development plan for goal setting and career planning, mentoring and networking, crafting an elevator pitch, postdoctoral training strategies in various settings and the need to assess whether a postdoc is required for a career. The students also engaged in group activities where they role-played various career tracks. What’s next? We expect this experience to provide a long-lasting impact on the ability of our departmental faculty to support and guide graduate students who wish to pursue different careers after their PhD, and expect this course to become integrated into our Ph.D. training program. Final thoughts? Let’s not limit our students to academia! This program is helping us to send scientists into the mainstream – let’s help our best people!

A few of the nearly 50 students enrolled in “Oh! The Places You’ll Go…with a PhD in Science pose with Dr. Das. Front, left to right: Udodirim Onwubiko, Brian Hercyk, Rosela Golloshi, Debalina Acharya. Back, left to right: Julie Rich, Dr. Maitreyi Das, Daniel DeGennaro, Kathleen King







mcb welcomes three new staff members

MCB has welcomed three new staff members to its ranks during the past several months. Dr. Manju Hingorani, who filled a rotator position as program director during 2014-2016, returns to MCB as a permanent program director in the Molecular Biophysics cluster. Allison Burrell, science assistant, joined MCB this past January; Bridget Johnson, program assistant, followed in March. Learn more about the unique experiences each brings to her respective role below. (more…)


The Division of Molecular and Cellular Biosciences is looking for a permanent Program Director for the Molecular Biophysics Cluster. The cluster funds research into the structure and dynamics of biomolecules with a goal to establish the fundamental principles that underlie biomolecular interactions, regulation of biological function at the atomic, near-atomic, and molecular levels. For more information and to apply visit  USAJobs before June 22, 2018.

Meet Dr. Basil Nikolau, Our New Division Director

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From the very start of my professional career, I’ve seen the National Science Foundation (NSF) as a major influence in shaping the direction of science. I’m excited for this opportunity to impact the processes that help guide the science priorities of the nation.

Since joining MCB as the newest Division Director several weeks ago, I am appreciative of the work done by my predecessors. I specifically want to thank Dr. Theresa Good for her excellent work as Acting Division Director for the past 16 months. Her commitment to keeping MCB moving forward maintained a sustainable platform on which to build. I look forward to working with a Deputy Division Director with so much experience and vision.

My career has come a long way since 1988, when I mailed 15 copies of my first 50-page grant application via Federal Express during my first year as an Assistant Professor at Iowa State University. Although that application was not funded, I was pleasantly surprised the next year when I received a call with the news of my first successful award to study biotin-containing enzymes in plants. That grant was the first in a series of projects, primarily NSF-funded, that built a research program focused on acetate (or acetyl-CoA) metabolism in plants.  Ultimately, we were successful in developing a program that provided the biocatalytic core of the NSF-funded Engineering Research Center for Biorenewable Chemicals (CBiRC).

Over the years, I have served at NSF as an ad hoc reviewer, a panelist, and as a member of various Committee of Visitors panels. I’ve been impressed by the dedication and collegiality of program officers and the administrative support staff as they work together serving a vibrant and diverse research community. Serving as Division Director will be an opportunity to give back to the organization that has supported my career. I see this role not only as an opportunity to support the NSF community but also to have a hand in contributing from the ground-up to the science priorities of the country.

During my time in MCB I look forward to supporting the strong scientific research programs this directorate is so well known for, as well as overseeing upcoming changes. The transition to the “No Deadlines” proposal submissions process, along with NSF’s “10 Big Ideas” and especially the “Rules of Life” initiative, are aimed at increasing the opportunities for NSF to fund research that crosses levels of biological organization. This is a pivotal time for NSF, and I feel fortunate to have this opportunity to lead MCB as we find ways to fund more complex, interdisciplinary projects that have the potential to dramatically advance the biological sciences. I also look forward to working with the great team in place here. Even after a few short weeks, I feel welcomed and impressed by just how efficient and dedicated the team here is.

Thank you,

Basil Nikolau

Better Communication, Better Science

Alexandre and Barnajeet
Dr. Gladys Alexandre, left, and REU participant Reena Barnajeet.

In 2015, researcher Dr. Gladys Alexandre learned something valuable: the addition of Reena Barnajeet, a hard of hearing student, to her lab improved the communication skills of everyone in the group. (more…)

Spotlight – Science and Technology Centers

Some scientific ideas are too big for one researcher or one university to tackle alone. To address such innovative and potentially transformative large-scale challenges, NSF periodically solicits proposals under the Science and Technology Centers (STCs): Integrative Partnerships program. Among the largest projects that MCB is involved with, each STC has a different approach to the research. However, they all have one thing in common: they bring together a range of people to work on one research or education project. The centers come from all areas of science, engineering, and education research funded by NSF. MCB assists in funding and managing several of the centers, including the Center for Cellular Construction (CCC) (award DBI 1548297).

The CCC is a partnership which brings together researchers in the San Francisco Bay area, which according to their website, aims to “engineer the physical structure and interactions of living cells, to turn them into living bioreactors and modules of novel self-organizing devices”.  The Center’s goal is to transition the field of cell biology to a quantitative discipline, combining classical cell biology with engineering to develop a design-build-test approach to understanding the rules governing cell behavior. Improving how we manipulate, control, and create cells could have impacts on a wide range of fields, including chemical production, materials engineering, biomedical engineering, basic scientific exploration, as well as various civil and consumer applications.

While the research area is exciting, it’s the partnerships that make this center unique; the center not only brings together university researchers, but also industry. The partnerships, which include the University of California, San Francisco; San Francisco State University; IBM Almaden Research Center; University of California, Berkeley; Stanford University; and The Exploratorium, are overseen by Center Director Dr. Wallace Marshall. These partnerships enable an exceptional approach to the research and create a strong and varied environment to train researchers of all ages, particularly important for addressing another of the Center’s goals to increase diversity of participation in research, education, and knowledge transfer.

CCC was one of four STCs funded in 2016 and one of 12 active centers in the U.S. Click here to monitor information about funding opportunities from the Office of Integrative Activities. Follow updates on MCB funding by visiting this page.