Simple and efficient synthesis of 5′ pre-adenylated DNA using thermostable RNA ligase

We report a simple method of enzymatic synthesis of pre-adenylated DNA linkers/adapters for next-generation sequencing using thermostable RNA ligase from Methanobacterium thermoautotrophicum (MthRnl). Using RNA ligase for the reaction instead of the existing chemical or T4 DNA ligase-based methods allows quantitative conversion of 5′-phosphorylated single-stranded DNA (ssDNA) to the adenylated form. The MthRnl adenylation reaction is specific for ATP and either ssDNA or RNA. In the presence of Mg+2, the reaction has a pH optimum of 6.0–6.5. Unlike reactions that use T4 DNA ligase, this protocol does not require synthesis of a template strand for adenylation. The high yield of the reaction simplifies isolation and purification of the adenylated product. Conducting the adenylation reaction at the elevated temperature (65°C) reduces structural constraints, while increased ATP concentrations allow quantitative adenylation of DNA with a 3′-unprotected end

Évaluation des risques que comporte l’exposition aux gras trans au Canada

Trans fats are undesirable because they raise LDL-cholesterol and lower HDL-cholesterol levels in the blood, which can lead to an increased risk of coronary heart disease. In the mid-1990\u27s, researchers estimated that Canadians had one of the highest average trans fat intakes in the world, estimated to be approximately 3.7% of energy. The World Health Organization recommends that average intakes of trans fats should be less than 1% of total energy. As such Canada has pursued a multi-faceted approach to decrease trans fat levels in Canadian foods. Initiatives undertaken include: mandatory nutrition labelling, the establishment of a multi-stakeholder Trans Fat Task Force to develop recommendations and strategies to eliminate trans fat in Canadian foods, and most recently the monitoring of industry\u27s efforts in reducing trans fats from their food products. Collectively, these initiatives have proven successful as average trans fat intakes have been reduced to 1.42% of overall energy. Further reductions in trans fat levels in the Canadian food supply are needed to meet the target of 1% of energy, the associated public health objectives, and the protection of vulnerable populations.Les gras trans sont indésirables, car ils augmentent la concentration sanguine en cholestérol à lipoprotéines de faible densité et abaissent celle en cholestérol à lipoprotéines de haute densité, ce qui peut mener à un risque accru de coronaropathie. Au milieu des années 1990, les chercheurs ont estimé quʹau sein de la population canadienne les apports en gras trans comptaient au nombre des plus élevés au monde en atteignant environ 3,7% de l’apport énergétique. Selon la recommandation de l’Organisation mondiale de la santé, l’apport moyen en gras trans devrait être inférieur à 1% de l’apport énergétique total. Par conséquent, le Canada a adopté une démarche à volets multiples visant à diminuer la teneur en gras trans des aliments canadiens. Les initiatives entreprises sont les suivantes: l’étiquetage nutritionnel obligatoire, l’établissement dʹun groupe de travail multilatéral, soit le Groupe d’étude surles graisses trans, dans le but d’élaborer des recommandations et des stratégies ciblant l’élimination des gras trans dans l’approvisionnement alimentaire canadien et, plus récemment, la surveillance des efforts investis par l’industrie dans la diminution des gras trans contenus dans ses produits. De concert, ces initiatives ont été couronnées de succès alors que l’apport moyen en gras trans a atteint 1,42% de l’apport énergétique total. D’autres réductions de la teneur en gras trans de l’approvisionnement alimentaire au Canada sont essentielles pour atteindre pleinement la cible de 1% de l’apport énergétique ainsi que les objectifs afférents en matière de santé publique et de protection des populations vulnérables

Waveshifters and Scintillators for Ionizing Radiation Detection

Scintillation and waveshifter materials have been developed for the detection of ionizing radiation in an STTR program between Ludlum Measurements, Inc. and the University of Notre Dame. Several new waveshifter materials have been developed which are comparable in efficiency and faster in fluorescence decay than the standard material Y11 (K27) used in particle physics for several decades. Additionally, new scintillation materials useful for fiber tracking have been developed which have been compared to 3HF. Lastly, work was done on developing liquid scintillators and paint-on scintillators and waveshifters for high radiation environments

Development and Validation of Nomograms Predictive of Overall and Progression-Free Survival in Patients With Oropharyngeal Cancer

Purpose Treatment of oropharyngeal squamous cell carcinoma (OPSCC) is evolving toward risk-based modification of therapeutic intensity, which requires patient-specific estimates of overall survival (OS) and progression-free survival (PFS). Methods To develop and validate nomograms for OS and PFS, we used a derivation cohort of 493 patients with OPSCC with known p16 tumor status (surrogate of human papillomavirus) and cigarette smoking history (pack-years) randomly assigned to clinical trials using platinum-based chemoradiotherapy (NRG Oncology Radiation Therapy Oncology Group [RTOG] 0129 and 0522). Nomograms were created from Cox models and internally validated by use of bootstrap and cross-validation. Model discrimination was measured by calibration plots and the concordance index. Nomograms were externally validated in a cohort of 153 patients with OPSCC randomly assigned to a third trial, NRG Oncology RTOG 9003. Results Both models included age, Zubrod performance status, pack-years, education, p16 status, and T and N stage; the OS model also included anemia and age × pack-years interaction; and the PFS model also included marital status, weight loss, and p16 × Zubrod interaction. Predictions correlated well with observed 2-year and 5-year outcomes. The uncorrected concordance index was 0.76 (95% CI, 0.72 to 0.80) for OS and 0.70 (95% CI, 0.66 to 0.74) for PFS, and bias-corrected indices were similar. In the validation set, OS and PFS models were well calibrated, and OS and PFS were significantly different across tertiles of nomogram scores (log-rank P = .003;\u3c .001). Conclusion The validated nomograms provided useful prediction of OS and PFS for patients with OPSCC treated with primary radiation-based therapy

The process of recovery of people with mental illness: The perspectives of patients, family members and care providers: Part 1

<p>Abstract</p> <p>Background</p> <p>It is a qualitative design study that examines points of divergence and convergence in the perspectives on recovery of 36 participants or 12 triads. Each triad comprising a patient, a family member/friend, a care provider and documents the procedural, analytic of triangulating perspectives as a means of understanding the recovery process which is illustrated by four case studies. Variations are considered as they relate to individual characteristics, type of participant (patient, family, member/friend and care provider), and mental illness. This paper which is part of a larger study and is based on a qualitative research design documents the process of recovery of people with mental illness: Developing a Model of Recovery in Mental Health: A middle range theory.</p> <p><b>Methods</b></p> <p>Data were collected in field notes through semi-structured interviews based on three interview guides (one for patients, one for family members/friends, and one for caregivers). Cross analysis and triangulation methods were used to analyse the areas of convergence and divergence on the recovery process of all triads.</p> <p>Results</p> <p>In general, with the 36 participants united in 12 triads, two themes emerge from the cross-analysis process or triangulation of data sources (12 triads analysis in 12 cases studies). Two themes emerge from the analysis process of the content of 36 interviews with participants: (1) <it>Revealing dynamic context</it>, situating patients in their dynamic context; and (2) <it>Relationship issues in a recovery process</it>, furthering our understanding of such issues. We provide four case studies examples (among 12 cases studies) to illustrate the variations in the way recovery is perceived, interpreted and expressed in relation to the different contexts of interaction.</p> <p>Conclusion</p> <p>The perspectives of the three participants (patients, family members/friends and care providers) suggest that recovery depends on constructing meaning around mental illness experiences and that the process is based on each person's dynamic context (e.g., social network, relationship), life experiences and other social determinants (e.g., symptoms, environment). The findings of this study add to existing knowledge about the determinants of the recovery of persons suffering with a mental illness and significant other utilizing public mental health services in Montreal, Canada.</p

DMSO and Betaine Greatly Improve Amplification of GC-Rich Constructs in De Novo Synthesis

In Synthetic Biology, de novo synthesis of GC-rich constructs poses a major challenge because of secondary structure formation and mispriming. While there are many web-based tools for codon optimizing difficult regions, no method currently exists that allows for potentially phenotypically important sequence conservation. Therefore, to overcome these limitations in researching GC-rich genes and their non-coding elements, we explored the use of DMSO and betaine in two conventional methods of assembly and amplification. For this study, we compared the polymerase (PCA) and ligase-based (LCR) methods for construction of two GC-rich gene fragments implicated in tumorigenesis, IGF2R and BRAF. Though we found no benefit in employing either DMSO or betaine during the assembly steps, both additives greatly improved target product specificity and yield during PCR amplification. Of the methods tested, LCR assembly proved far superior to PCA, generating a much more stable template to amplify from. We further report that DMSO and betaine are highly compatible with all other reaction components of gene synthesis and do not require any additional protocol modifications. Furthermore, we believe either additive will allow for the production of a wide variety of GC-rich gene constructs without the need for expensive and time-consuming sample extraction and purification prior to downstream application

Genetic Architecture of Hybrid Male Sterility in Drosophila: Analysis of Intraspecies Variation for Interspecies Isolation

Background: The genetic basis of postzygotic isolation is a central puzzle in evolutionary biology. Evolutionary forces causing hybrid sterility or inviability act on the responsible genes while they still are polymorphic, thus we have to study these traits as they arise, before isolation is complete. Methodology/Principal Findings: Isofemale strains of D. mojavensis vary significantly in their production of sterile F 1 sons when females are crossed to D. arizonae males. We took advantage of the intraspecific polymorphism, in a novel design, to perform quantitative trait locus (QTL) mapping analyses directly on F1 hybrid male sterility itself. We found that the genetic architecture of the polymorphism for hybrid male sterility (HMS) in the F1 is complex, involving multiple QTL, epistasis, and cytoplasmic effects. Conclusions/Significance: The role of extensive intraspecific polymorphism, multiple QTL, and epistatic interactions in HMS in this young species pair shows that HMS is arising as a complex trait in this system. Directional selection alone would be unlikely to maintain polymorphism at multiple loci, thus we hypothesize that directional selection is unlikely to be the only evolutionary force influencing postzygotic isolation

CMS physics technical design report : Addendum on high density QCD with heavy ions

Peer reviewe