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Using stable MutS dimers and tetramers to quantitatively analyze DNA mismatch recognition and sliding clamp formation

Thu, 01/15/2015 - 2:42pm

The process of DNA mismatch repair is initiated when MutS recognizes mismatched DNA bases and starts the repair cascade. The Escherichia coli MutS protein exists in an equilibrium between dimers and tetramers, which has compromised biophysical analysis. To uncouple these states, we have generated stable dimers and tetramers, respectively. These proteins allowed kinetic analysis of DNA recognition and structural analysis of the full-length protein by X-ray crystallography and small angle X-ray scattering. Our structural data reveal that the tetramerization domains are flexible with respect to the body of the protein, resulting in mostly extended structures. Tetrameric MutS has a slow dissociation from DNA, which can be due to occasional bending over and binding DNA in its two binding sites. In contrast, the dimer dissociation is faster, primarily dependent on a combination of the type of mismatch and the flanking sequence. In the presence of ATP, we could distinguish two kinetic groups: DNA sequences where MutS forms sliding clamps and those where sliding clamps are not formed efficiently. Interestingly, this inability to undergo a conformational change rather than mismatch affinity is correlated with mismatch repair.

How to Speak Up and Be Heard: Self Advocacy

Mon, 01/12/2015 - 3:54pm

Self Advocacy is the ability to speak up for yourself and for the things that are important to you. This tip sheet offers advice and gives examples of how to self advocate at home, at school, at work and in the community.

Initiating Data Management Instruction to Graduate Students at the University of Houston Using the New England Collaborative Data Management Curriculum

Mon, 01/12/2015 - 10:16am

The need for graduate instruction on data management best practices across disciplines is a theme that has emerged from two campus-wide data management needs assessments that have been conducted at the UH Libraries since 2010. Graduate students are assigned numerous data management responsibilities over the course of their academic careers, but rarely receive formal training in this area. To address this need, the UH Libraries offered a workshop entitled Research Data Management 101 in April, 2014, and all graduate and professional students on campus were invited to attend. The New England Collaborative Data Management Curriculum (NECDMC) served as the basis for the workshop, and two general sessions were planned. A research group in the College of Natural Sciences & Mathematics requested a special session after advertisements for the workshop were distributed. One hundred and five individuals registered for the event, sixty-five signed into the workshop, and sixty-three completed the end-of-workshop assessment. The results from this assessment, general lessons learned, and plans for future sessions will be discussed.

The New England Collaborative Data Management Curriculum Pilot at the University of Manitoba: A Canadian Experience

Mon, 01/12/2015 - 10:16am

Canada’s federal funding agencies are following the directions of funding agencies in the United States and United Kingdom, and will soon require a data management plan in grant applications. The University of Manitoba Libraries in Canada has started planning and implementing research data services, and education is seen as a key component. In June 2014, the New England Collaborative Data Management Curriculum (NECDMC) (Lamar Soutter Library, University of Massachusetts Medical School 2014) was piloted and used to provide data management training for a group of subject librarians at the University of Manitoba Libraries, in combination with information about data-related policies of the Canadian funding agencies and the University of Manitoba. The seven NECDMC modules were delivered in a seminar style, with emphasis on group discussions and Canadian content. The benefits of NECDMC – adaptability and flexible framework – should be weighed against the challenges experienced in the pilot, mainly the significant amount of time needed to create local content and complement the existing curriculum. Overall, the pilot showed that NECDMC is a good, thorough introduction to data management, and that it is possible to adapt NECDMC to the local and Canadian settings in an effective way.

Gaining Traction in Research Data Management Support: A Case Study

Mon, 01/12/2015 - 10:16am

With the implementation of an institutional repository, librarians at the University of Vermont (UVM) began receiving inquiries about data management. In an effort to explore research data management roles for librarians at UVM the author led workshops based on Module One of the New England Collaborative Data Management Curriculum (NECDMC) with two audiences. In addition, the author consulted with faculty and staff from around the university to ascertain their support of research data management and integrate that information into the workshops. The first workshop was directed at UVM librarians and resulted in an understanding of their willingness to engage with research data management patron services. The second workshop was conducted for students and faculty. It built upon the first workshop and, in addition, experimented with a sixty-minute version of the NECDMC module. This second workshop will be added to an existing series of Dana Library workshops for graduate students and early-career researchers in fall 2014.

Lessons Learned From a Research Data Management Pilot Course at an Academic Library

Mon, 01/12/2015 - 10:15am

Setting and Objective:

From January-March 2014, three librarians from the University of Washington (UW) taught a course in research data management as a pilot for the New England Collaborative Data Management Curriculum (NECDMC). The goals of the workshops were to a) pilot the NECDMC curriculum to see how effective it was as an out-of-the box solution for teaching research data management (RDM), and b) to gauge interest in an RDM class among certain UW student populations, and c) to teach UW’s first RDM workshop offered to non-librarians.

Design and Methods:

The NECDMC consists of 7 modules that can be taught independently or as a series. UW decided to teach all seven modules consecutively, as one-hour long weekly workshops. Each module included a lecture and activity or discussion. We taught at one location on upper campus, and live-streamed the lecture to another location in the Health Sciences Library. Each module was assessed at the end of the class.

Results:

Interest in a research data management class is high; however, retention for a non-credit, 7-week class is low. Individual assessments show that students thought the content was important and well-delivered.

Conclusions:

Based on registration, graduate students at UW in many disciplines are interested in learning research data management skills. A non-credit, 7-week class had low retention; another type of class structure might increase retention. The NECDMC curriculum is an excellent framework, but modification to individual modules are necessary to provide a thorough and localized curriculum specific to one institution.

Building the New England Collaborative Data Management Curriculum

Mon, 01/12/2015 - 10:15am

The need for a curriculum designed for librarians to use for teaching STEM research data management skills to their constituents from diverse STEM disciplines has been widely identified. (Qin and D’Ignazio 2010). From 2012-2014, a collaborative group of New England librarians, led by a project team from the University of Massachusetts Medical School, developed lecture notes, presentation slides, assignments, readings, and case studies for teaching research data management. The New England Collaborative Data Management Curriculum (NECDMC) is unique in its flexibility; providing subject agnostic instructional materials in a modular format for teaching common data management best practices along with a suite of teaching cases illustrating data management in disciplinary contexts. This article is a follow-up to the “Teaching Research Data Management: An Undergraduate/Graduate Curriculum (Piorun et al. 2012) that was published in the Journal of eScience Librarianship.

What is Data Literacy?

Mon, 01/12/2015 - 10:15am

JESLIB Editor Elaine R. Martin introduces the articles in Volume 3, Issue 1 by discussing data literacy and the various forms of library services designed to support it. Martin highlights that librarians are already taking advantage of the opportunity to provide data support services and that the articles in this issue can serve as a point of reference for developing further data services and strategies for service development.

Building Data Services From the Ground Up: Strategies and Resources

Mon, 01/12/2015 - 10:15am

There is a scarcity of practical guidance for developing data services in an academic library. Data services, like many areas of research, require the expertise and resources of teams spanning many disciplines. While library professionals are embedded into the teaching activities of our institutions, fewer of us are embedded in research activities occurring across the full life cycle. The significant challenges of managing, preserving, and sharing data for reuse demand that we take a more active role. Providing support for funder data management plans is just one option in the data services landscape. Awareness of the institutional and library culture in which we operate places an emphasis on the importance of relationships. Understanding the various cultures in which our researchers operate is crucial for delivering data services that are relevant and utilized. The goal of this article is to guide data specialists through this landscape by providing key resources and strategies for developing locally relevant services and by pointing to active communities of librarians and researchers tackling the challenges associated with digital research data.