Factors influencing olfactory function in an adult general population sample: the CHRIS study.

The sense of smell allows for the assessment of the chemical composition of volatiles in our environment. Different factors are associated with reduced olfactory function, including age, sex, as well as health and lifestyle conditions. However, most studies that aimed at identifying the variables that drive olfactory function in the population suffered from methodological weaknesses in study designs and participant selection, such as the inclusion of convenience sample or only of certain age groups, or recruitment biases.

Antithrombin, Protein C, and Protein S: Genome and Transcriptome-Wide Association Studies Identify 7 Novel Loci Regulating Plasma Levels.

Background: Antithrombin, PC (protein C), and PS (protein S) are circulating natural anticoagulant proteins that regulate hemostasis and of which partial deficiencies are causes of venous thromboembolism. Previous genetic association studies involving antithrombin, PC, and PS were limited by modest sample sizes or by being restricted to candidate genes. In the setting of the Cohorts for Heart and Aging Research in Genomic Epidemiology consortium, we meta-analyzed across ancestries the results from 10 genome-wide association studies of plasma levels of antithrombin, PC, PS free, and PS total.

Genetic and Metabolic Determinants of Atrial Fibrillation in a General Population Sample: The CHRIS Study.

Atrial fibrillation (AF) is a supraventricular arrhythmia deriving from uncoordinated electrical activation with considerable associated morbidity and mortality. To expand the limited understanding of AF biological mechanisms, we performed two screenings, investigating the genetic and metabolic determinants of AF in the Cooperative Health Research in South Tyrol study. We found 110 AF cases out of 10,509 general population individuals.

Frequency of Heterozygous Parkin () Variants and Penetrance of Parkinson's Disease Risk Markers in the Population-Based CHRIS Cohort.

Mutations in the () gene are the most frequent cause of autosomal recessive early-onset Parkinson's disease (PD). Heterozygous mutation carriers might also be at increased risk for developing clinical symptoms of PD. Given the high frequency of heterozygous mutations in the general population, it is essential to have better estimates of the penetrance of these variants, and to investigate, which clinical and biochemical markers are present in carriers and thus potentially useful for identifying those individuals at greater risk of developing clinical symptoms later in life.

Sunitinib malate-loaded biodegradable microspheres for the prevention of corneal neovascularization in rats.

Corneal neovascularization (NV) predisposes patients to compromised corneal transparency and visional acuity. Sunitinib malate (Sunb-malate) targeting against multiple receptor tyrosine kinases, exerts potent antiangiogenesis. However, the rapid clearance of Sunb-malate eye drops administered through topical instillation limits its therapeutic efficacy and poses a challenge for potential patient compliance.

FlyBase at 25: looking to the future.

Since 1992, FlyBase (flybase.org) has been an essential online resource for the Drosophila research community. Concentrating on the most extensively studied species, Drosophila melanogaster, FlyBase includes information on genes (molecular and genetic), transgenic constructs, phenotypes, genetic and physical interactions, and reagents such as stocks and cDNAs.

Gene Model Annotations for Drosophila melanogaster: Impact of High-Throughput Data.

We report the current status of the FlyBase annotated gene set for Drosophila melanogaster and highlight improvements based on high-throughput data. The FlyBase annotated gene set consists entirely of manually annotated gene models, with the exception of some classes of small non-coding RNAs. All gene models have been reviewed using evidence from high-throughput datasets, primarily from the modENCODE project.

Gene Model Annotations for Drosophila melanogaster: The Rule-Benders.

In the context of the FlyBase annotated gene models in Drosophila melanogaster, we describe the many exceptional cases we have curated from the literature or identified in the course of FlyBase analysis. These range from atypical but common examples such as dicistronic and polycistronic transcripts, noncanonical splices, trans-spliced transcripts, noncanonical translation starts, and stop-codon readthroughs, to single exceptional cases such as ribosomal frameshifting and HAC1-type intron processing. In FlyBase, exceptional genes and transcripts are flagged with Sequence Ontology terms and/or standardized comments.

Corticosteroid-loaded biodegradable nanoparticles for prevention of corneal allograft rejection in rats.

Immunologic graft rejection is one of the main causes of short and long-term graft failure in corneal transplantation. Steroids are the most commonly used immunosuppressive agents for postoperative management and prevention of corneal graft rejection. However, steroids delivered in eye drops are rapidly cleared from the surface of the eye, so the required frequency of dosing for corneal graft rejection management can be as high as once every 2h.

FlyBase: introduction of the Drosophila melanogaster Release 6 reference genome assembly and large-scale migration of genome annotations.

Release 6, the latest reference genome assembly of the fruit fly Drosophila melanogaster, was released by the Berkeley Drosophila Genome Project in 2014; it replaces their previous Release 5 genome assembly, which had been the reference genome assembly for over 7 years. With the enormous amount of information now attached to the D. melanogaster genome in public repositories and individual laboratories, the replacement of the previous assembly by the new one is a major event requiring careful migration of annotations and genome-anchored data to the new, improved assembly.

Prevalence and severity of fuchs corneal dystrophy in Tangier Island.

Purpose: To investigate the clinical and genetic features of late-onset Fuchs corneal dystrophy (FCD) on Tangier, an island in the Chesapeake Bay with an isolated population of approximately 500 individuals.

Design: Observational, cross-sectional study.

Methods: A total of 156 individuals born to inhabitants of Tangier Island volunteered to undergo ophthalmic evaluation.

The Drosophila melanogaster transcriptome by paired-end RNA sequencing.

RNA-seq was used to generate an extensive map of the Drosophila melanogaster transcriptome by broad sampling of 10 developmental stages. In total, 142.2 million uniquely mapped 64-100-bp paired-end reads were generated on the Illumina GA II yielding 356× sequencing coverage.

Age-severity relationships in families linked to FCD2 with retroillumination photography.

Purpose: Fuchs corneal dystrophy (FCD) is a progressive disorder of the corneal endothelium and is pathologically defined by the presence of guttae, which are excrescences of the Descemet membrane. The present study was undertaken to investigate the age-severity relationship of the FCD2-linked disease phenotype using retroillumination photography and to compare it with the characteristics of FCD1.

Methods: Two large families with multiple affected members were recruited.

A rat model for choroidal neovascularization using subretinal lipid hydroperoxide injection.

The purpose of this study was to develop and characterize a rat model of choroidal neovascularization (CNV) as occurs in age-related macular degeneration. The lipid hydroperoxide 13(S)-hydroperoxy-9Z,11E-octadecadienoic acid (HpODE) is found in submacular Bruch's membrane in aged humans and has been reported to generate neovascularization in a rabbit model. Three weeks after a single subretinal injection of 30 microg of HpODE, eyes of Sprague-Dawley rats were harvested.

Progression of Fuchs corneal dystrophy in a family linked to the FCD1 locus.

Purpose: Fuchs corneal dystrophy (FCD) is a progressive corneal disease marked by the development of guttae, focal excrescences of Descemet's membrane. Retroillumination photography is a useful technique for illuminating the presence of guttae and has been used to document progression of disease. This study was undertaken to quantitatively assess disease progression in a cohort of individuals with late-onset FCD linked to chromosome 13.

Using Chado to store genome annotation data.

Chado is a relational database schema that can be used to manage a wide variety of biological information, including genome annotation, genetic, phenotypic, and expression data. Its flexibility comes from its use of "ontologies," which are controlled vocabularies that describe data types and the relationships among them. By changing its ontologies, Chado can be customized to suit many different needs.

A Chado case study: an ontology-based modular schema for representing genome-associated biological information.

Motivation: A few years ago, FlyBase undertook to design a new database schema to store Drosophila data. It would fully integrate genomic sequence and annotation data with bibliographic, genetic, phenotypic and molecular data from the literature representing a distillation of the first 100 years of research on this major animal model system. In developing this new integrated schema, FlyBase also made a commitment to ensure that its design was generic, extensible and available as open source, so that it could be employed as the core schema of any model organism data repository, thereby avoiding redundant software development and potentially increasing interoperability.

VectorBase: a home for invertebrate vectors of human pathogens.

VectorBase (http://www.vectorbase.org/) is a web-accessible data repository for information about invertebrate vectors of human pathogens.

Analysis and documentation of progression of Fuchs corneal dystrophy with retroillumination photography.

Purpose: Fuchs corneal dystrophy (FCD) is a degenerative disorder of the cornea that is characterized by the progressive accumulation of guttae, which are small excrescences of Descemet's membrane. We describe a method for documenting the location and number of guttae, and ask whether disease progression can be observed during relatively short periods.

Methods: Patients with FCD were imaged by standard retroillumination photography with a slit lamp.