An Improved Canine Genome and a Comprehensive Catalogue of Coding Genes and Non-Coding Transcripts

The domestic dog, Canis familiaris, is a well-established model system for mapping trait and disease loci. While the original draft sequence was of good quality, gaps were abundant particularly in promoter regions of the genome, negatively impacting the annotation and study of candidate genes. Here, we present an improved genome build, canFam3.1, which includes 85 MB of novel sequence and now covers 99.8% of the euchromatic portion of the genome. We also present multiple RNA-Sequencing data sets from 10 different canine tissues to catalog ∼175,000 expressed loci. While about 90% of the coding genes previously annotated by EnsEMBL have measurable expression in at least one sample, the number of transcript isoforms detected by our data expands the EnsEMBL annotations by a factor of four. Syntenic comparison with the human genome revealed an additional ∼3,000 loci that are characterized as protein coding in human and were also expressed in the dog, suggesting that those were previously not annotated in the EnsEMBL canine gene set. In addition to ∼20,700 high-confidence protein coding loci, we found ∼4,600 antisense transcripts overlapping exons of protein coding genes, ∼7,200 intergenic multi-exon transcripts without coding potential, likely candidates for long intergenic non-coding RNAs (lincRNAs) and ∼11,000 transcripts were reported by two different library construction methods but did not fit any of the above categories. Of the lincRNAs, about 6,000 have no annotated orthologs in human or mouse. Functional analysis of two novel transcripts with shRNA in a mouse kidney cell line altered cell morphology and motility. All in all, we provide a much-improved annotation of the canine genome and suggest regulatory functions for several of the novel non-coding transcripts

Genetic predisposition to mosaic Y chromosome loss in blood.

Mosaic loss of chromosome Y (LOY) in circulating white blood cells is the most common form of clonal mosaicism1-5, yet our knowledge of the causes and consequences of this is limited. Here, using a computational approach, we estimate that 20% of the male population represented in the UK Biobank study (n = 205,011) has detectable LOY. We identify 156 autosomal genetic determinants of LOY, which we replicate in 757,114 men of European and Japanese ancestry. These loci highlight genes that are involved in cell-cycle regulation and cancer susceptibility, as well as somatic drivers of tumour growth and targets of cancer therapy. We demonstrate that genetic susceptibility to LOY is associated with non-haematological effects on health in both men and women, which supports the hypothesis that clonal haematopoiesis is a biomarker of genomic instability in other tissues. Single-cell RNA sequencing identifies dysregulated expression of autosomal genes in leukocytes with LOY and provides insights into why clonal expansion of these cells may occur. Collectively, these data highlight the value of studying clonal mosaicism to uncover fundamental mechanisms that underlie cancer and other ageing-related diseases.This research has been conducted using the UK Biobank Resource under application 9905 and 19808. This work was supported by the Medical Research Council [Unit Programme number MC_UU_12015/2]. Full study-specific and individual acknowledgements can be found in the supplementary information

Rule-Based Models of the Interplay between Genetic and Environmental Factors in Childhood Allergy

Peer reviewe

A spatial energy consumption assessment for building stock supporting low carbon scenarios development

Energy saving, carbon emissions reduction strategies, and policies are the main concerns for the 21st century sustainable development. Policymakers have emphasized how the energy security promotes a transition towards low-carbon energy sources without undermining wellbeing. The Intergovernmental Panel on Climate Change (2014) estimates that almost 67% of the total global energy consumption is affected by activities in urban areas. Particularly, the existing buildings stock consumes about 40% of the total energy consumption in EU member states (2010/31/EU). Accordingly, it is crucial to understand the residential building energy profile. The goal of this work is, therefore, focusing on a method for assessing the energy consumption of residential sector. The methodology implemented for this work is based on a hybrid approach that is combined with two different categories top-down and bottom-up. It is mostly created by data collection from the technical maps, literature, and technical department of the municipality which are later transferred into the Geographic information system (GIS). GIS provides the urban energy maps for assessing saving scenarios and support decision making for policy implementation. Afterward, the model is able to assess the buildings energy consumption, depending on the Heating Degree Days, the compactness S/V, and the period of construction of buildings.It is fundamental to create a profile model to understand the current state of the energy consumption for building stock. This study began by calculating the energy consumption profile at the municipality scale with the use of GIS that can significantly help in the planning of actions in the future

A framework for selecting the best refurbishment alternative in renewable energies towards consumer stock ownership

The paper aims at presenting a guideline framework, called "Dossier", for selecting the best refurbishment in renewable energies alternative. It represents an ongoing work developed in the framework of “SCORE” (Supporting Consumer co- Ownership in Renewable Energies) Horizon 2020 project. The purpose of this project is (i) to overcome the use of energy from fossil sources in favour of renewable sources, (ii) to promote forms of efficiency and reduction of energy consumption, and (iii) to support the citizens’ participation, encouraging them to play an active role in the community. The “Dossier” represents a guideline in order to facilitate the project partners to uniformly collect information and data related to their case studies. Therefore, through this document, the refurbishment alternatives for each case study will be illustrated and, then, the use of a multi-criteria analysis (MCA) will allow the choice of the best one. The future step of this work is to exploit the defined business plan, considering the community’s financial contribution and the bank loan, in order to realize the best alternative solution effectively

Urban problems and patterns of change: The analysis of a downgraded industrial area in Turin

As it is well known, in Western countries cities are experiencing negative effects due to decentralization and deindustrialization, that have brought economic crisis and urban decline. In order to contrast such decline, urban regeneration is getting more and more important in the current political agenda. In fact, urban regeneration means not only building-restoration operations, but also programs aiming at eliminating social decline, increasing the quality of life of the inhabitants, supporting the valorization of cultural resources, protecting the environmental system, bringing economic development, and so on. Urban regeneration looks at urban areas as complex and dynamic systems, in which different processes (physical, social, environmental and economic) drive the transition and the generation of important changes. This paper aims to reflect on urban problems and regeneration operations, focusing in particular on the role of evaluation tools for supporting decision-making in this context. Starting from the analysis of a real case study related to a critical area in the city of Turin, the article will propose different evaluation tools able to produce a complete picture of the problem and to define possible long-term visions for the requalification of the site