Global selective sweep of a highly inbred genome of the cattle parasite Neospora caninum

Neospora caninum, a cyst-forming apicomplexan parasite, is a leading cause of neuromuscular diseases in dogs as well as fetal abortion in cattle worldwide. The importance of the domestic and sylvatic life cycles of Neospora, and the role of vertical transmission in the expansion and transmission of infection in cattle, is not sufficiently understood. To elucidate the population genomics of Neospora, we genotyped 50 isolates collected worldwide from a wide range of hosts using 19 linked and unlinked genetic markers. Phylogenetic analysis and genetic distance indices resolved a single genotype of N. caninum. Whole-genome sequencing of 7 isolates from 2 different continents identified high linkage disequilibrium, significant structural variation, but only limited polymorphism genome-wide, with only 5,766 biallelic single nucleotide polymorphisms (SNPs) total. Greater than half of these SNPs (∼3,000) clustered into 6 distinct haploblocks and each block possessed limited allelic diversity (with only 4 to 6 haplotypes resolved at each cluster). Importantly, the alleles at each haploblock had independently segregated across the strains sequenced, supporting a unisexual expansion model that is mosaic at 6 genomic blocks. Integrating seroprevalence data from African cattle, our data support a global selective sweep of a highly inbred livestock pathogen that originated within European dairy stock and expanded transcontinentally via unisexual mating and vertical transmission very recently, likely the result of human activities, including recurrent migration, domestication, and breed development of bovid and canid hosts within similar proximities

Evaluating Patterns of a White-Band Disease (WBD) Outbreak in Acropora palmata Using Spatial Analysis: A Comparison of Transect and Colony Clustering

. Likewise, there is little known about the spatiality of outbreaks. We examined the spatial patterns of WBD during a 2004 outbreak at Buck Island Reef National Monument in the US Virgin Islands. colonies with and without WBD.As the search for causation continues, surveillance and proper documentation of the spatial patterns may inform etiology, and at the same time assist reef managers in allocating resources to tracking the disease. Our results indicate that the spatial scale of data collected can drastically affect the calculation of prevalence and spatial distribution of WBD outbreaks. Specifically, we illustrate that higher resolution sampling resulted in more realistic disease estimates. This should assist in selecting appropriate sampling designs for future outbreak investigations. The spatial techniques used here can be used to facilitate other coral disease studies, as well as, improve reef conservation and management

Analysis combining correlated glaucoma traits identifies five new risk loci for open-angle glaucoma

Open-angle glaucoma (OAG) is a major cause of blindness worldwide. To identify new risk loci for OAG, we performed a genome-wide association study in 3,071 OAG cases and 6,750 unscreened controls, and meta-analysed the results with GWAS data for intraocular pressure (IOP) and optic disc parameters (the overall meta-analysis sample size varying between 32,000 to 48,000 participants), which are glaucoma-related traits. We identified and independently validated four novel genome-wide significant associations within or near MYOF and CYP26A1, LINC02052 and CRYGS, LMX1B, and LMO7 using single variant tests, one additional locus (C9) using gene-based tests, and two genetic pathways - “response to fluid shear stress” and “abnormal retina morphology” - in pathway-based tests. Interestingly, some of the new risk loci contribute to risk of other genetically-correlated eye diseases including myopia and age-related macular degeneration. To our knowledge, this study is the first integrative study to combine genetic data from OAG and its correlated traits to identify new risk variants and genetic pathways, highlighting the future potential of combining genetic data from genetically-correlated eye traits for the purpose of gene discovery and mapping

Prognostication of diffuse large B-cell lymphoma in the molecular era: moving beyond the IPI

Diffuse large B-cell lymphoma (DLBCL) is a heterogeneous disease with variable outcomes. Despite the majority of patients being cured with combination chemoimmunotherapy, up to 30% eventually succumb to the disease. Until recently, baseline prognostic assessment has centred on the International Prognostic Index (IPI), although this index is yet to impact strongly on treatment choice. Molecular features such as cell of origin, MYC and BCL-2 genetic alterations and protein overexpression were identified over a decade ago, yet their prognostic value is still not fully elucidated. Adding complexity are the plethora of new clinical, biological and molecular prognostic markers described in the recent literature, most of which lack independent validation, likely act as surrogate markers for those already in common use and have yet to substantially impact on therapeutic decision making. This review comprehensively assesses the value of individual prognostic markers in the clinical setting and their potential to predict response to novel agents, and ways to optimise their use in future research

FIMS database - supplementary files

Problem: Often spreadsheets are used as pseudo-databases for the storage of plot-based survey data, but they have major limitations in scalability, concurrent access and data retrieval. Paper-based surveys require time-consuming data entry. They contain potential inconsistencies (e.g. miss-spellings, abbreviations, missing values), particularly if coming from different observers due to unenforceable data standards. Methods: We analysed more than 30 years of data collected in the Northern Jarrah Forest (NJF) of south-western Australia, comprising c. 31,000 plots (c. 550,000 species records) and associated environmental variables stored across multiple spreadsheets in the development of our free and open source floristic information management system (FIMS). Data dictionaries were developed for each spreadsheet before being combined into a unified standard. OpenRefine software was used to ensure adherence to the standard, including correcting inconsistent field order in different files, removal of redundant or irrelevant fields, abolishing synonyms and abbreviations, and deleting incomplete rows. Database design and normalisation rules ensured the removal of repeating groups and the provision of fields for each retained attribute. Geometry was stored using spatial objects available in PostGIS whilst maintaining an otherwise relational database using PostgreSQL. Results: FIMS provides a spatial database system for storing, accessing and retrieving floristic survey data. FIMS includes a mobile data collection module for use on tablet technology with autonomous database synchronisation and one-step data entry to eliminate transcription and associated errors. Spatial data types enable the retrieval of data for viewing and analysis within most Geographic Information Systems and statistical software. It promotes portability and adaption to other locations and studies via the provision of all necessary code

A stereoselective synthesis of 1,6-diphenyl-1,3,5-hexatrienes utilising 4,4,6-trimethyl-2-vinyl-1,3,2-dioxaborinane as a two-carbon alkenyl building block.

A number of 1,6-diphenyl-1,3,5-hexatrienes of varying alkene geometries were stereoselectively prepared from just two starting materials: iodobenzene and 4,4,6-trimethyl-2-vinyl-1,3,2-dioxaborinane via a series of Heck, Suzuki-Miyaura and stereocontrolled iododeboronation reactions. These results demonstrate how 4,4,6-trimethyl-2-vinyl-1,3,2-dioxaborinane can be used as a genuine two-carbon vinyl-dianion building block in stereocontrolled polyene synthesis