Making Scholarly Profiles Work

A presentation on scholarly profiles given at the 2016 January Symposium at James Madison University

Peroxidase gene discovery from the horseradish transcriptome

BACKGROUND: Horseradish peroxidases (HRPs) from Armoracia rusticana have long been utilized as reporters in various diagnostic assays and histochemical stainings. Regardless of their increasing importance in the field of life sciences and suggested uses in medical applications, chemical synthesis and other industrial applications, the HRP isoenzymes, their substrate specificities and enzymatic properties are poorly characterized. Due to lacking sequence information of natural isoenzymes and the low levels of HRP expression in heterologous hosts, commercially available HRP is still extracted as a mixture of isoenzymes from the roots of A. rusticana. RESULTS: In this study, a normalized, size-selected A. rusticana transcriptome library was sequenced using 454 Titanium technology. The resulting reads were assembled into 14871 isotigs with an average length of 1133 bp. Sequence databases, ORF finding and ORF characterization were utilized to identify peroxidase genes from the 14871 isotigs generated by de novo assembly. The sequences were manually reviewed and verified with Sanger sequencing of PCR amplified genomic fragments, resulting in the discovery of 28 secretory peroxidases, 23 of them previously unknown. A total of 22 isoenzymes including allelic variants were successfully expressed in Pichia pastoris and showed peroxidase activity with at least one of the substrates tested, thus enabling their development into commercial pure isoenzymes. CONCLUSIONS: This study demonstrates that transcriptome sequencing combined with sequence motif search is a powerful concept for the discovery and quick supply of new enzymes and isoenzymes from any plant or other eukaryotic organisms. Identification and manual verification of the sequences of 28 HRP isoenzymes do not only contribute a set of peroxidases for industrial, biological and biomedical applications, but also provide valuable information on the reliability of the approach in identifying and characterizing a large group of isoenzymes

Lessons and Insights from CCAFS Results-Based Management Trial

Lessons learned from Flagship 4's Results-Based Management trial, based of an extensive survey to the trial project managers, coordinators and partners

Implementing GRACE Team Care in a Veterans Affairs Medical Center: Lessons Learned and Impacts Observed

In a randomized clinical trial, Geriatric Resources for Assessment and Care of Elders (GRACE), a model of care that works in collaboration with primary care providers (PCPs) and patient-centered medical homes to provide home-based geriatric care management focusing on geriatric syndromes and psychosocial problems commonly found in older adults, improved care quality and reduced acute care use for high-risk, low-income older adults. To assess the effect of GRACE at a Veterans Affairs (VA) Medical Center (VAMC), veterans aged 65 and older from Marion County, Indiana, with PCPs from four of five VAMC clinics who were not on hospice or dialysis were enrolled in GRACE after discharge home from an acute hospitalization. After an initial home-based transition visit to GRACE enrollees, the GRACE team returned to conduct a geriatric assessment. Guided by 12 protocols and input from an interdisciplinary panel and the PCP, the GRACE team developed and implemented a veteran-centric care plan. Hospitalized veterans from the fifth clinic, who otherwise met enrollment criteria, served as a usual-care comparison group. Demographic, comorbidity, and usage data were drawn from VA databases. The GRACE and comparison groups were similar in age, sex, and burden of comorbidity, although predicted risk of 1-year mortality in GRACE veterans was higher. Even so, GRACE enrollment was associated with 7.1% fewer emergency department visits, 14.8% fewer 30-day readmissions, 37.9% fewer hospital admissions, and 28.5% fewer total bed days of care, saving the VAMC an estimated $200,000 per year after program costs during the study for the 179 veterans enrolled in GRACE. Having engaged, enthusiastic VA leadership and GRACE staff; aligning closely with the medical home; and accommodating patient acuity were among the important lessons learned during implementation

Geodata Infrastructure for the Management of Railway Assets-Related Research Data

A system containing updated information on railway assets, including their condition, contributes significantly to the maintenance of railway networks and to ensure continuous service. The Institute of Transportation Systems (DLR-TS) of the German Aerospace Center (DLR) carries out research in the area of condition monitoring using in-service trains. Massive amounts of measurement data are collected from various sensors mounted railway vehicles. There is an ever-growing amount of data, as several terabytes of measurement data are collected every year as a part of multiple projects. Furthermore, static and semi-static data on railway networks such as the topology of the network, the infrastructure elements in the network and their conditions are also gathered. Here arises a need for sustainable management of the raw datasets and the generated results to make them Findable, Accessible, Interoperable and Reusable (FAIR) over time to researchers within the DLR, and other stakeholders such as project partners, funding organizations and the public. This poster addresses the topic of management of railway infrastructure and measurement data through the development of a system called “Transportation Infrastructure Data Platform” (TRIDAP) that enables the storage, analysis and sharing of data in a FAIR-compatible way. The platform is setup using open-source software such as PostgreSQL, Apache Kafka, Apache Spark, GeoServer, GeoNetwork and Prometheus to name a few. DLR-TS is actively developing this platform. Datasets from DLR-TS and few other DLR institutes are planned to be stored in the platform during the course of the DLR-funded cross-domain project “Digitaler Atlas 2.0”

Online-Marktplatz für regionale Lebensmittel in Sachsen: Bedarfs- und Machbarkeitsstudie für einen „Online-Marktplatz für regionale Lebensmittel in Sachsen“

Die Publikation informiert umfassend zum Thema „Online-Marktplatz für regionale Lebensmittel in Sachsen“. Anhand von drei potentiellen Geschäftsmodellen werden die Chancen und Risiken eines Online-Marktplatzes dargestellt. Detaillierte Analysen und Berechnungen zeigen die Möglichkeiten zur Umsetzung. Die Veröffentlichung richtet sich an Landwirte, Unternehmer des Ernährungsgewerbes und Akteure aus dem Online-Handel. Redaktionsschluss: 15.06.202

An exciton-polariton laser based on biologically produced fluorescent protein

We thank A. Clemens (TU Dresden, Germany) for technical support with protein preparation and C. Murawski (U St Andrews, UK) for support with TDAF deposition. We acknowledge support from the ERC Starting Grant ABLASE (640012), the Scottish Funding Council (via SUPA), the European Union Marie Curie Career Integration Grant (PCIG12-GA-2012-334407), studentship funding through the EPSRC CM-DTC (EP/L015110/1) and the EPSRC Hybrid Polaritonics program grant (EP/M025330/1). S.H. gratefully acknowledges support by the Royal Society and the Wolfson Foundation and M.S. gratefully acknowledges support from a MSCA IF (659213).Under adequate conditions, cavity-polaritons form a macroscopic coherent quantum state, known as polariton condensate (PC). Compared to Wannier-Mott polaritons in inorganic semiconductors, the localized Frenkel polaritons in organic emitter materials show weaker interaction with each other but stronger coupling to light, which recently enabled the first realization of a PC at room temperature. However, this required ultrafast optical pumping which limits the applications of organic PCs. Here, we demonstrate room-temperature PCs of cavity-polaritons in simple laminated microcavities filled with the biologically produced enhanced green fluorescent protein (eGFP). The unique molecular structure of eGFP prevents exciton annihilation even at high excitation densities, thus facilitating PCs under conventional nanosecond pumping. Condensation is clearly evidenced by a distinct threshold, an interaction-induced blueshift of the condensate, long-range coherence and the presence of a second threshold at higher excitation density which is associated with the onset of photon lasing.Publisher PDFPeer reviewe

Young people's response to six smartphone apps for anxiety and depression : focus group study

Background: Suicide is one of the most frequent causes of death in young people worldwide. Depression lies at the root of this issue, a condition that has a significant negative impact on the lives of those who experience it and on society more generally. However, 80% of affected young people do not obtain professional help for depression and other mental health issues. Therefore, a key challenge is to find innovative and appealing ways to engage young people in learning to manage their mental health. Research suggests that young people prefer to access anonymous Web-based programs rather than get face-to-face help, which has led to the development of numerous smartphone apps. However, the evidence indicates that not all of these apps are effective in engaging the interest of young people who are most in need of help. Objective: The study aimed to investigate young people’s response to six currently available smartphone apps for mental health and to identify features that young people like and dislike in such apps. Methods: Focus groups were conducted with 23 young people aged 13 to 25 years in which they viewed and used six smartphone apps for mental health. A general inductive approach following a realist paradigm guided data analysis. Results: The results revealed that young people value autonomy and the opportunity to personalize experiences with these apps above other things. Finding a balance between simplicity and informativeness is also an important factor. Conclusions: App developers need to consider using participant-design frameworks to ensure that smartphone apps are providing what young people want in a mental health app. Solutions to the need for personalization and increasing user engagement are also crucially needed

Structural mechanism for the recognition and ubiquitination of a single nucleosome residue by Rad6-Bre1

Cotranscriptional ubiquitination of histone H2B is key to gene regulation. The yeast E3 ubiquitin ligase Bre1 (human RNF20/40) pairs with the E2 ubiquitin conjugating enzyme Rad6 to monoubiquitinate H2B at Lys123. How this single lysine residue on the nucleosome core particle (NCP) is targeted by the Rad6-Bre1 machinery is unknown. Using chemical cross-linking and mass spectrometry, we identified the functional interfaces of Rad6, Bre1, and NCPs in a defined in vitro system. The Bre1 RING domain cross-links exclusively with distinct regions of histone H2B and H2A, indicating a spatial alignment of Bre1 with the NCP acidic patch. By docking onto the NCP surface in this distinct orientation, Bre1 positions the Rad6 active site directly over H2B Lys123. The Spt-Ada-Gcn5 acetyltransferase (SAGA) H2B deubiquitinase module competes with Bre1 for binding to the NCP acidic patch, indicating regulatory control. Our study reveals a mechanism that ensures site-specific NCP ubiquitination and fine-tuning of opposing enzymatic activities