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Recent documents in eScholarship@UMMS
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Conserved chromosome 2q31 conformations are associated with transcriptional regulation of GAD1 GABA synthesis enzyme and altered in prefrontal cortex of subjects with schizophrenia

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

Little is known about chromosomal loopings involving proximal promoter and distal enhancer elements regulating GABAergic gene expression, including changes in schizophrenia and other psychiatric conditions linked to altered inhibition. Here, we map in human chromosome 2q31 the 3D configuration of 200 kb of linear sequence encompassing the GAD1 GABA synthesis enzyme gene locus, and we describe a loop formation involving the GAD1 transcription start site and intergenic noncoding DNA elements facilitating reporter gene expression. The GAD1-TSS(-50kbLoop) was enriched with nucleosomes epigenetically decorated with the transcriptional mark, histone H3 trimethylated at lysine 4, and was weak or absent in skin fibroblasts and pluripotent stem cells compared with neuronal cultures differentiated from them. In the prefrontal cortex of subjects with schizophrenia, GAD1-TSS(-50kbLoop) was decreased compared with controls, in conjunction with downregulated GAD1 expression. We generated transgenic mice expressing Gad2 promoter-driven green fluorescent protein-conjugated histone H2B and confirmed that Gad1-TSS(-55kbLoop), the murine homolog to GAD1-TSS(-50kbLoop), is a chromosomal conformation specific for GABAergic neurons. In primary neuronal culture, Gad1-TSS(-55kbLoop) and Gad1 expression became upregulated when neuronal activity was increased. We conclude that 3D genome architectures, including chromosomal loopings for promoter-enhancer interactions involved in the regulation of GABAergic gene expression, are conserved between the rodent and primate brain, and subject to developmental and activity-dependent regulation, and disordered in some cases with schizophrenia. More broadly, the findings presented here draw a connection between noncoding DNA, spatial genome architecture, and neuronal plasticity in development and disease.

Translational Regulation of Cytoplasmic mRNAs

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

Translation of the coding potential of a messenger RNA into a protein molecule is a fundamental process in all living cells and consumes a large fraction of metabolites and energy resources in growing cells. Moreover, translation has emerged as an important control point in the regulation of gene expression. At the level of gene regulation, translational control is utilized to support the specific life histories of plants, in particular their responses to the abiotic environment and to metabolites. This review summarizes the diversity of translational control mechanisms in the plant cytoplasm, focusing on specific cases where mechanisms of translational control have evolved to complement or eclipse other levels of gene regulation. We begin by introducing essential features of the translation apparatus. We summarize early evidence for translational control from the pre-Arabidopsis era. Next, we review evidence for translation control in response to stress, to metabolites, and in development. The following section emphasizes RNA sequence elements and biochemical processes that regulate translation. We close with a chapter on the role of signaling pathways that impinge on translation.

National trends in pancreaticoduodenal trauma: interventions and outcomes

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

OBJECTIVES: Pancreaticoduodenal trauma (PDT) is associated with substantial mortality and morbidity. In this study, contemporary trends were analysed using national data.

METHODS: The Nationwide Inpatient Sample for 1998-2009 was queried for patients with PDT. Interventions including any operation (Any-Op) and pancreas-specific surgery (PSURG) were identified. Trends in treatment and outcomes were determined [complications, length of stay (LoS), mortality] for the Any-Op, PSURG and non-operative (Non-Op) groups. Analyses included chi-squared tests, Cochran-Armitage trend tests and logistic regression.

RESULTS: A total of 27 216 patients (nationally weighted) with PDT were identified. Over time, the frequency of PDT increased by 8.3%, whereas the proportion of patients submitted to PSURG declined (from 21.7% to 19.8%; P = 0.0004) and the percentage of patients submitted to non-operative management increased (from 56.7% to 59.1%; P = 0.01). In the Non-Op group, mortality decreased from 9.7% to 8.6% (P < 0.001); morbidity and LoS remained unchanged at approximately 40% and approximately 12 days, respectively. In the PSURG group, mortality remained stable at approximately 15%, complications increased from 50.2% to 71.8% (P < 0.0001) and LoS remained stable at approximately 21 days. For all PDT patients, significant independent predictors of mortality included: the presence of combined pancreatic and duodenal injuries; penetrating trauma, and age over 50 years. Having any operation (Any-Op) was associated with mortality, but PSURG was not a predictor of death.

CONCLUSIONS: The utilization of operations for PDT has declined without affecting mortality, but operative morbidity increased significantly over the 12 years to 2009. The development of an evidence-based approach to invasive manoeuvres and an early multidisciplinary approach involving pancreatic surgeons may improve outcomes in patients with these morbid injuries.

Survival after hospital discharge for ST-segment elevation and non-ST-segment elevation acute myocardial infarction: a population-based study

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

BACKGROUND: Limited recent data are available describing differences in long-term survival, and factors affecting prognosis, after ST-segment elevation myocardial infarction (STEMI) and non-ST-segment elevation myocardial infarction (NSTEMI), especially from the more generalizable perspective of a population-based investigation. The objectives of this study were to examine differences in post-discharge prognosis after hospitalization for STEMI and NSTEMI, with a particular focus on factors associated with reduced long-term survival.

METHODS: We reviewed the medical records of residents of the Worcester, MA, USA metropolitan area hospitalized at eleven central Massachusetts medical centers for acute myocardial infarction (AMI) during 2001, 2003, 2005, and 2007.

RESULTS: A total of 3762 persons were hospitalized with confirmed AMI; of these, 2539 patients (67.5%) were diagnosed with NSTEMI. The average age of study patients was 70.3 years and 42.9% were women. Patients with NSTEMI experienced higher post-discharge death rates with 3-month, 1-year, and 2-year death rates of 12.6%, 23.5%, and 33.2%, respectively, compared to 6.1%, 11.5%, and 16.4% for patients with STEMI. After multivariable adjustment, patients with NSTEMI were significantly more likely to have died after hospital discharge (adjusted hazards ratio 1.28; 95% confidence interval 1.14-1.44). Several demographic (eg, older age) and clinical (eg, history of stroke) factors were associated with reduced long-term survival in patients with NSTEMI and STEMI.

CONCLUSIONS: The results of this study in residents of central Massachusetts suggest that patients with NSTEMI are at higher risk for dying after hospital discharge, and several subgroups are at particularly increased risk.

Blasticidin S inhibits translation by trapping deformed tRNA on the ribosome

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

The antibiotic blasticidin S (BlaS) is a potent inhibitor of protein synthesis in bacteria and eukaryotes. We have determined a 3.4-A crystal structure of BlaS bound to a 70StRNA ribosome complex and performed biochemical and single-molecule FRET experiments to determine the mechanism of action of the antibiotic. We find that BlaS enhances tRNA binding to the P site of the large ribosomal subunit and slows down spontaneous intersubunit rotation in pretranslocation ribosomes. However, the antibiotic has negligible effect on elongation factor G catalyzed translocation of tRNA and mRNA. The crystal structure of the antibiotic-ribosome complex reveals that BlaS impedes protein synthesis through a unique mechanism by bending the 3' terminus of the P-site tRNA toward the A site of the large ribosomal subunit. Biochemical experiments demonstrate that stabilization of the deformed conformation of the P-site tRNA by BlaS strongly inhibits peptidyl-tRNA hydrolysis by release factors and, to a lesser extent, peptide bond formation.

Successful treatment of mobile right atrial thrombus and acute pulmonary embolism with intravenous tissue plasminogen activator

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

An 89-year-old woman came with symptoms of progressively worsening dyspnoea at rest over the preceding week. She was normotensive, had elevated jugular venous pressure and clear lungs. ECG revealed atrial fibrillation with the rapid ventricular rate. Labs were significant for markedly elevated pro-brain natriuretic peptide of 43,000 pg/mL and troponin-T of 1 ng/mL. An urgent 2D echocardiogram was obtained, which revealed the severely dilated right atrium and a large linear mobile mass in the right atrium consistent with a thrombus. An emergent CT scan revealed multiple bilateral pulmonary emboli. She received intravenous tissue plasminogen activator. Repeat echocardiogram performed 6 h later showed no evidence of the right atrial thrombus. She was subsequently maintained on intravenous heparin and transitioned to Coumadin. Early recognition of this rare but potentially fatal complication is important as prompt treatment measures can help in preventing life-threatening complications of the right atrial thrombus.

Dynamics of survival of motor neuron (SMN) protein interaction with the mRNA-binding protein IMP1 facilitates its trafficking into motor neuron axons

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

Spinal muscular atrophy (SMA) is a lethal neurodegenerative disease specifically affecting spinal motor neurons. SMA is caused by the homozygous deletion or mutation of the survival of motor neuron 1 (SMN1) gene. The SMN protein plays an essential role in the assembly of spliceosomal ribonucleoproteins. However, it is still unclear how low levels of the ubiquitously expressed SMN protein lead to the selective degeneration of motor neurons. An additional role for SMN in the regulation of the axonal transport of mRNA-binding proteins (mRBPs) and their target mRNAs has been proposed. Indeed, several mRBPs have been shown to interact with SMN, and the axonal levels of few mRNAs, such as the beta-actin mRNA, are reduced in SMA motor neurons. In this study we have identified the beta-actin mRNA-binding protein IMP1/ZBP1 as a novel SMN-interacting protein. Using a combination of biochemical assays and quantitative imaging techniques in primary motor neurons, we show that IMP1 associates with SMN in individual granules that are actively transported in motor neuron axons. Furthermore, we demonstrate that IMP1 axonal localization depends on SMN levels, and that SMN deficiency in SMA motor neurons leads to a dramatic reduction of IMP1 protein levels. In contrast, no difference in IMP1 protein levels was detected in whole brain lysates from SMA mice, further suggesting neuron specific roles of SMN in IMP1 expression and localization. Taken together, our data support a role for SMN in the regulation of mRNA localization and axonal transport through its interaction with mRBPs such as IMP1.

Pediatric head injury and concussion

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

Children with head injuries frequently present to emergency departments. Even though most of these children have minor injuries, head injury is the most common cause of traumatic deaths in pediatric patients. The pediatric GCS and decision rules for obtaining head CT imaging help the provider evaluate head-injured infants and children. The provider must be vigilant to diagnose those who have life-threatening intracranial injuries or are victims of abusive head trauma. The goal of the emergency physician is to diagnose and treat the consequences of the primary injury and to limit or prevent secondary injury.

The Legionella pneumophila GTPase activating protein LepB accelerates Rab1 deactivation by a non-canonical hydrolytic mechanism

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

GTPase activating proteins (GAPs) from pathogenic bacteria and eukaryotic host organisms deactivate Rab GTPases by supplying catalytic arginine and glutamine fingers in trans and utilizing the cis-glutamine in the DXXGQ motif of the GTPase for binding rather than catalysis. Here, we report the transition state mimetic structure of the Legionella pneumophila GAP LepB in complex with Rab1 and describe a comprehensive structure-based mutational analysis of potential catalytic and recognition determinants. The results demonstrate that LepB does not simply mimic other GAPs but instead deploys an expected arginine finger in conjunction with a novel glutamic acid finger, which forms a salt bridge with an indispensible switch II arginine that effectively locks the cis-glutamine in the DXXGQ motif of Rab1 in a catalytically competent though unprecedented transition state configuration. Surprisingly, a heretofore universal transition state interaction with the cis-glutamine is supplanted by an elaborate polar network involving critical P-loop and switch I serines. LepB further employs an unusual tandem domain architecture to clamp a switch I tyrosine in an open conformation that facilitates access of the arginine finger to the hydrolytic site. Intriguingly, the critical P-loop serine corresponds to an oncogenic substitution in Ras and replaces a conserved glycine essential for the canonical transition state stereochemistry. In addition to expanding GTP hydrolytic paradigms, these observations reveal the unconventional dual finger and non-canonical catalytic network mechanisms of Rab GAPs as necessary alternative solutions to a major impediment imposed by substitution of the conserved P-loop glycine.

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.


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.


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.

Focused Outreach Final Report: Vermont (May 1, 2013 - April 30, 2014)

Fri, 01/09/2015 - 5:10pm

The National Network of Libraries of Medicine, New England Region (NN/LM NER) seeks to further the mission of the NN/LM, while increasing use of National Library of Medicine ( resources and services; and expanding collaboration with libraries through a Focused Health Information Outreach model. The mission of the National Network of Libraries of Medicine (NN/LM) is to advance the progress of medicine and improve the public health by providing all U.S. health professionals equal access to biomedical information and by improving the public's access to information to enable them to make informed decisions about their health.

The Focused Outreach Project connected underserved communities in Vermont with the resources and services of the National Library of Medicine. NER partnered with local libraries, public health agencies, school nurses, the state library, health education students, and community television. This year, the project transitioned to a train-the-trainer model. Project partners were identified following the Key Informant Interviews. NER staff worked with project partners to guide them through the project planning, proposal writing process, and initial NLM education. Project partners included:

  • Vermont State Library
  • Dana Medical Library
  • Middlebury Community TV
  • Vermont Agency of Education
  • Castleton State College Heath Education Department
  • Northeastern Vermont Regional Hospital Medical Library
  • Vermont School Nurse Health Information Access Project

Pre and post-evaluations showed that as a result of this project:

  • 92 consumers learned about MedlinePlus
  • 220 health information providers learned about MedlinePlus
  • 325 visitors at exhibits/health fairs learned more about the National Library of Medicine

Consumer post-evaluations showed that 79% reported that the trainings improved their ability to find information they could trust on the internetl: 64%were likely to use MedlinePlus in the future. Provider post-evaluations showed that 97% said the class improved their ability to find information they could trust on the internet; 100% were likely to use MedlinePlus in the future; and 62% were very likely to tell others about the NLM resources they learned.