Exploration of the visual system: Part 1: Dissection of the mouse eye for RNA, protein, and histological analyses

Due to the power of genetics, the mouse has become a widely used animal model in vision research. However, its eyeball has an axial length of only about 2 mm. The present protocol describes how to easily dissect the small rodent eye post mortem. This allows collecting different tissues of the eye, i.e., cornea, lens, iris, retina, optic nerve, retinal pigment epithelium (RPE), and sclera. We further describe in detail how to process these eye samples in order to obtain high‐quality RNA for RNA expression profiling studies. Depending on the eye tissue to be analyzed, we present appropriate lysis buffers to prepare total protein lysates for immunoblot and immuno‐precipitation analyses. Fixation, inclusion, embedding, and cryosectioning of the globe for routine histological analyses (HE staining, DAPI staining, immunohistochemistry, in situ hybridization) is further presented. These basic protocols should allow novice investigators to obtain eye tissue samples rapidly for their experiments.

Self-avoiding random walks and Olbers' paradox

In this paper, we prove that a self-avoiding walk of infinite length provides a structure that would resolve Olbers' paradox. That is, if the stars of a universe were distributed like the vertices of an infinite random walk with each segment length of about a parsec, then the night sky could be as dark as actually observed on the Earth. Self-avoiding random walk structure can therefore resolve the Olbers' paradox even in a static universe.

Comparative analysis of the transcriptome across distant species.

The transcriptome is the readout of the genome. Identifying common features in it across distant species can reveal fundamental principles. To this end, the ENCODE and modENCODE consortia have generated large amounts of matched RNA-sequencing data for human, worm and fly. Uniform processing and comprehensive annotation of these data allow comparison across metazoan phyla, extending beyond earlier within-phylum transcriptome comparisons and revealing ancient, conserved features. Specifically, we discover co-expression modules shared across animals, many of which are enriched in developmental genes. Moreover, we use expression patterns to align the stages in worm and fly development and find a novel pairing between worm embryo and fly pupae, in addition to the embryo-to-embryo and larvae-to-larvae pairings. Furthermore, we find that the extent of non-canonical, non-coding transcription is similar in each organism, per base pair. Finally, we find in all three organisms that the gene-expression levels, both coding and non-coding, can be quantitatively predicted from chromatin features at the promoter using a 'universal model' based on a single set of organism-independent parameters.

Evaluating the Trabecular Micro-Bypass Stent Combined with Phacoemulsification Compared to Phacoemulsification Alone.

Aim: The aim of this study was to assess the effect of iStent (trabecular micro-bypass stent) implantation in combination with phacoemulsification on IOP and glaucoma medications and to compare this to the outcome of phacoemulsification alone. Patients and Methods: A retrospective consecutive comparative review was undertaken. 131 eyes with ocular hypertension and medically controlled glaucoma underwent phacoemulsification alone (n = 78 group I) or combined with gonioscopic-guided implantation of one iStent (n = 31, group II) or two iStents (n = 22, group III). Patients were assessed at postoperative weeks 1, 3 and 6, and months 3 and 6. Pre- and post-operative measures included visual acuity, IOP and glaucoma medications. Results: Post-operatively at 6 months, mean IOP decreased from 16.3 mmHg to 14.2 mmHg in group I (p < 0.01), from 16.7 mmHg to 15.1 mmHg in group II (p < 0.16) and from 17.0 to 13.8 in group III (p = 0.05). Mean glaucoma medication decreased from 1.9 to 1.6 in group I (8 %, p = 0.12), from 2.5 to 0.8 in group II (27 %, p = 0.04), and from 2.1 to 1.0 in group III (45 %, p < 0.01). Conclusions: iStent implantation resulted in similar IOP reduction to phacoemulsification alone but achieved a significantly greater reduction in glaucoma medications. This may improve compliance and quality of life, and reduce health care costs in patients with early to moderate glaucoma.

The TREAT-NMD DMD Global Database: Analysis of More than 7,000 Duchenne Muscular Dystrophy Mutations.

Analyzing the type and frequency of patient-specific mutations that give rise to Duchenne muscular dystrophy (DMD) is an invaluable tool for diagnostics, basic scientific research, trial planning, and improved clinical care. Locus-specific databases allow for the collection, organization, storage, and analysis of genetic variants of disease. Here, we describe the development and analysis of the TREAT-NMD DMD Global database (http://umd.be/TREAT_DMD/). We analyzed genetic data for 7,149 DMD mutations held within the database. A total of 5,682 large mutations were observed (80% of total mutations), of which 4,894 (86%) were deletions (1 exon or larger) and 784 (14%) were duplications (1 exon or larger). There were 1,445 small mutations (smaller than 1 exon, 20% of all mutations), of which 358 (25%) were small deletions and 132 (9%) small insertions and 199 (14%) affected the splice sites. Point mutations totalled 756 (52% of small mutations) with 726 (50%) nonsense mutations and 30 (2%) missense mutations. Finally, 22 (0.3%) mid-intronic mutations were observed. In addition, mutations were identified within the database that would potentially benefit from novel genetic therapies for DMD including stop codon read-through therapies (10% of total mutations) and exon skipping therapy (80% of deletions and 55% of total mutations).

Reliability of P-drive in occupational therapy following a short training session: A promising instrument measuring seniors' on-road driving competencies

Introduction Occupational therapists could play an important role in facilitating driving cessation for ageing drivers. This, however, requires an easy-to-learn, standardised on-road evaluation method. This study therefore investigates whether use of P-drive' could be reliably taught to occupational therapists via a short half-day training session. Method Using the English 26-item version of P-drive, two occupational therapists evaluated the driving ability of 24 home-dwelling drivers aged 70 years or over on a standardised on-road route. Experienced driving instructors' on-road, subjective evaluations were then compared with P-drive scores. Results Following a short half-day training session, P-drive was shown to have almost perfect between-rater reliability (ICC2,1=0.950, 95% CI 0.889 to 0.978). Reliability was stable across sessions including the training phase even if occupational therapists seemed to become slightly less severe in their ratings with experience. P-drive's score was related to the driving instructors' subjective evaluations of driving skills in a non-linear manner (R-2=0.445, p=0.021). Conclusion P-drive is a reliable instrument that can easily be taught to occupational therapists and implemented as a way of standardising the on-road driving test.

Internet-Based Brief Intervention to Prevent Unhealthy Alcohol Use among Young Men: A Randomized Controlled Trial.

Alcohol use is one of the leading modifiable morbidity and mortality risk factors among young adults. 2 parallel-group randomized controlled trial with follow-up at 1 and 6 months. Internet based study in a general population sample of young men with low-risk drinking, recruited between June 2012 and February 2013. Intervention: Internet-based brief alcohol primary prevention intervention (IBI). The IBI aims at preventing an increase in alcohol use: it consists of normative feedback, feedback on consequences, calorific value alcohol, computed blood alcohol concentration, indication that the reported alcohol use is associated with no or limited risks for health. Intervention group participants received the IBI. Control group (CG) participants completed only an assessment. Alcohol use (number of drinks per week), binge drinking prevalence. Analyses were conducted in 2014-2015. Of 4365 men invited to participate, 1633 did so; 896 reported low-risk drinking and were randomized (IBI: n = 451; CG: n = 445). At baseline, 1 and 6 months, the mean (SD) number of drinks/week was 2.4(2.2), 2.3(2.6), 2.5(3.0) for IBI, and 2.4(2.3), 2.8(3.7), 2.7(3.9) for CG. Binge drinking, absent at baseline, was reported by 14.4% (IBI) and 19.0% (CG) at 1 month and by 13.3% (IBI) and 13.0% (CG) at 6 months. At 1 month, beneficial intervention effects were observed on the number of drinks/week (p = 0.05). No significant differences were observed at 6 months. We found protective short term effects of a primary prevention IBI. Controlled-Trials.com ISRCTN55991918.

Molecular mechanism of a green-shifted, pH-dependent red fluorescent protein mKate variant.

Fluorescent proteins that can switch between distinct colors have contributed significantly to modern biomedical imaging technologies and molecular cell biology. Here we report the identification and biochemical analysis of a green-shifted red fluorescent protein variant GmKate, produced by the introduction of two mutations into mKate. Although the mutations decrease the overall brightness of the protein, GmKate is subject to pH-dependent, reversible green-to-red color conversion. At physiological pH, GmKate absorbs blue light (445 nm) and emits green fluorescence (525 nm). At pH above 9.0, GmKate absorbs 598 nm light and emits 646 nm, far-red fluorescence, similar to its sequence homolog mNeptune. Based on optical spectra and crystal structures of GmKate in its green and red states, the reversible color transition is attributed to the different protonation states of the cis-chromophore, an interpretation that was confirmed by quantum chemical calculations. Crystal structures reveal potential hydrogen bond networks around the chromophore that may facilitate the protonation switch, and indicate a molecular basis for the unusual bathochromic shift observed at high pH. This study provides mechanistic insights into the color tuning of mKate variants, which may aid the development of green-to-red color-convertible fluorescent sensors, and suggests GmKate as a prototype of genetically encoded pH sensors for biological studies.

Horaires de messes et promesses pastorales. Une enquête sociologique sur la pratique religieuse dans le décanat de Fribourg (Suisse)

Ce papier fournit et discute les résultats d'une grande enquête quantitative sur la pratique religieuse en ville de Fribourg. L'enquête a pu fournir de manière quantifiée les paramètres d'une situation, certes connue : baisse de la pratique, augmentation de la participation des migrants, vieillissement des fidèles et des prêtres. L'enquête aura aussi permis d'observer que certains styles de messes sont préférés à d'autres, que le sentiment d'appartenance est affecté par les réorganisations. Ces paramètres permettent de rendre visible une « révolution silencieuse » du catholicisme, pris dans un étau entre un certain conservatisme des fidèles - qui n'aiment pas que les choses changent - et une hiérarchie catholique - qui a ses lignes de conduites pastorales et éthiques -, que retiennent, chacun à leur façon, une partie des fidèles dans une pratique faible ou peu fréquente.

Erreurs innées du métabolisme: transition enfant-adulte [Inborn errors of metabolism: transition from childhood to adulthood].

Les erreurs innées du métabolisme (EIM) sont dues à des mutations de gènes codant pour des enzymes du métabolisme et sont classées selon trois grands groupes de maladies: 1) intoxications; 2) déficit énergétique et 3) déficit de synthèse ou catabolisme des maladies complexes. Le progrès thérapeutique des vingt dernières années a permis d'améliorer le pronostic des enfants atteints d'EIM. Ces enfants grandissent et doivent être pris en charge à l'adolescence et à l'âge adulte par des équipes spécialisées. Cette médecine métabolique pour adultes est une discipline relativement nouvelle avec une information limitée chez l'adulte. Les recommandations pédiatriques sont extrapolées à la prise en charge des adultes tout en intégrant les différentes étapes de vie (indépendance sociale, grossesse, vieillissement et éventuelles complications tardives). Inborn errors of metabolism (IEM) are due to mutations of genes coding for enzymes of intermediary metabolism and are classified into 3 broad categories: 1) intoxication, 2) energy defect and 3) cellular organelles synthesis or catabolism defect. Improvements of therapy over these last 20 years has improved prognosis of children with IEM. These children grow up and should have their transition to specialized adult care. Adult patients with IEM are a relatively new phenomenon with currently only limited knowledge. Extrapolated pediatric guidelines are applied to the adult population taking into account adult life stages (social independence, pregnancy, aging process and potential long-term complications).

Dual-Energy CT: Basic Principles, Technical Approaches, and Applications in Musculoskeletal Imaging (Part 2).

In recent years, technological advances have allowed manufacturers to implement dual-energy computed tomography (DECT) on clinical scanners. With its unique ability to differentiate basis materials by their atomic number, DECT has opened new perspectives in imaging. DECT has been successfully used in musculoskeletal imaging with applications ranging from detection, characterization, and quantification of crystal and iron deposits, to simulation of noncalcium (improving the visualization of bone marrow lesions) or noniodine images. Furthermore, the data acquired with DECT can be postprocessed to generate monoenergetic images of varying kiloelectron volts, providing new methods for image contrast optimization as well as metal artifact reduction. The first part of this article reviews the basic principles and technical aspects of DECT including radiation dose considerations. The second part focuses on applications of DECT to musculoskeletal imaging including gout and other crystal-induced arthropathies, virtual noncalcium images for the study of bone marrow lesions, the study of collagenous structures, applications in computed tomography arthrography, as well as the detection of hemosiderin and metal particles.