The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics.

ABSTRACT: A global genome database of all of Earth’s species diversity could be a treasure trove of scientific discoveries. However, regardless of the major advances in genome sequencing technologies, only a tiny fraction of species have genomic information available. To contribute to a more complete planetary genomic database, scientists and institutions across the world have united under the Earth BioGenome Project (EBP), which plans to sequence and assemble high-quality reference genomes for all ∼1.5 million recognized eukaryotic species through a stepwise phased approach. As the initiative transitions into Phase II, where 150,000 species are to be sequenced in just four years, worldwide participation in the project will be fundamental to success. As the European node of the EBP, the European Reference Genome Atlas (ERGA) seeks to implement a new decentralised, accessible, equitable and inclusive model for producing high-quality reference genomes, which will inform EBP as it scales. To embark on this mission, ERGA launched a Pilot Project to establish a network across Europe to develop and test the first infrastructure of its kind for the coordinated and distributed reference genome production on 98 European eukaryotic species from sample providers across 33 European countries. Here we outline the process and challenges faced during the development of a pilot infrastructure for the production of reference genome resources, and explore the effectiveness of this approach in terms of high-quality reference genome production, considering also equity and inclusion. The outcomes and lessons learned during this pilot provide a solid foundation for ERGA while offering key learnings to other transnational and national genomic resource projects.info:eu-repo/semantics/publishedVersio

Impact assessment and remediation of anthropogenic interventions on fish populations - (FISHGUARD)

The disruption of longitudinal river connectivity by man-made obstacles and the stocking of fish communities with non-indigenous species or genotypes threaten the fish fauna of Belgian rivers to various extents. Obstacles impede migrations between habitats that are vital for populations, and they may restrict the gene flow between populations, thereby reducing the effective size and genetic diversity of populations and increasing the risk of local extinction. Restocking programs often involve the introduction of non-indigenous genotypes in native populations. Moreover, although stocking programs lead to the temporal and superficial enrichment of local fish communities or gene pools, they generally result in a loss of biodiversity on a regional or international scale through the homogenisation of communities and the breakdown of genetic differentiation between populations. Thus, stocking programs cannot compensate for the loss of free migration by artificial obstructions. The impact of these changes on fish populations remains largely unknown, which complicates the priorisation of spots to preserve and spots to restore. Here, we present an integrated study on Belgian waters, both in Flanders and Wallonia, which analyses fish communities, gene flow and migration patterns in the field, as well as the swimming and leaping performances of fishes under controlled conditions.Global change, Ecosystems and Biodiversit

Verstedelijking en biodiversiteit door een ecologische en evolutionaire bril

Our planet is urbanizing rapidly and Belgium (Flanders in particular) is characterized by a high degree of urbanization. Among biologists there is a growing interest to study the ecological and evolutionary consequences of urbanization since urban areas differ in multiple ways from the environments surrounding cities. During six years a consortium of Belgian biologists and their international network combined their efforts to study these impacts in a wide range of organisms, including both aquatic and terrestrial species and communities (e.g. bacteria, zooplankton, snails, butterflies and moths, grasshoppers, damselflies, fish, birds, etc.). This paper introduces the field of urban ecology and explores why evolutionary approaches are essential to unravel how organisms deal with these anthropogenic environmental conditions. We review in a highly selective way the ecological and evolutionary consequences of urbanization and introduce the aims and methods of the so called SPEEDY-project. More detailed case-studies from the project are presented in the other articles of this special volume on biodiversity and urbanization

Urbanisation and biodiversity through an ecological and evolutionary lens

Our planet is urbanizing rapidly and Belgium (Flanders in particular) is characterized by a high degree of urbanization. Among biologists there is a growing interest to study the ecological and evolutionary consequences of urbanization since urban areas differ in multiple ways from the environments surrounding cities. During six years a consortium of Belgian biologists and their international network combined their efforts to study these impacts in a wide range of organisms, including both aquatic and terrestrial species and communities (e.g. bacteria, zooplankton, snails, butterflies and moths, grasshoppers, damselflies, fish, birds, etc.). This paper introduces the field of urban ecology and explores why evolutionary approaches are essential to unravel how organisms deal with these anthropogenic environmental conditions. We review in a highly selective way the ecological and evolutionary consequences of urbanization and introduce the aims and methods of the so called SPEEDY-project. More detailed case-studies from the project are presented in the other articles of this special volume on biodiversity and urbanization.status: publishe

KU Leuven klimaatneutraal 2030

status: publishe

First-in-Human Study in Healthy Subjects with the Noncytotoxic Monoclonal Antibody OSE-127, a Strict Antagonist of IL-7Rα

International audienceAbstract OSE-127 is a humanized mAb targeting the IL-7Rα-chain (CD127), under development for inflammatory and autoimmune disease treatment. It is a strict antagonist of the IL-7R pathway, is not internalized by target cells, and is noncytotoxic. In this work, a first-in-human, phase I, randomized, double-blind, placebo-controlled, single-center study was carried out to determine the safety, pharmacokinetics, pharmacodynamics, and immunogenicity of OSE-127 administration. Sixty-three healthy subjects were randomly assigned to nine groups: six single ascending dose groups with i.v. administration (0.002–10 mg/kg), a single s.c. treatment group (1 mg/kg), and two double i.v. injection groups (6 or 10 mg/kg). Subjects were followed during <146 d. OSE-127’s pharmacokinetic half-life after a single dose increased from 4.6 (1 mg/kg) to 11.7 d (10 mg/kg) and, after a second dose, from 12.5 (6 mg/kg) to 16.25 d (10 mg/kg). Receptor occupancy was ≥95% at doses ≥0.02 mg/kg, and this saturation level was maintained >100 d after two i.v. infusions at 10 mg/kg. IL-7 consumption was inhibited by OSE-127 administration, as demonstrated by a decreased IL-7 pathway gene signature in peripheral blood cells and by ex vivo T lymphocyte restimulation experiments. OSE-127 was well tolerated, with no evidence of cytokine-release syndrome and no significant alteration of blood lymphocyte counts or subset populations. Altogether, the observed lack of significant lymphopenia or serious adverse events, concomitant with the dose-dependent inhibition of IL-7 consumption by target cells, highlights that OSE-127 may show clinical activity in IL-7R pathway–involved diseases

Conservation of Microstructure between a Sequenced Region of the Genome of Rice and Multiple Segments of the Genome of Arabidopsis thaliana

The nucleotide sequence was determined for a 340-kb segment of rice chromosome 2, revealing 56 putative protein-coding genes. This represents a density of one gene per 6.1 kb, which is higher than was reported for a previously sequenced segment of the rice genome. Sixteen of the putative genes were supported by matches to ESTs. The predicted products of 29 of the putative genes showed similarity to known proteins, and a further 17 genes showed similarity only to predicted or hypothetical proteins identified in genome sequence data. The region contains a few transposable elements: one retrotransposon, and one transposon. The segment of the rice genome studied had previously been identified as representing a part of rice chromosome 2 that may be homologous to a segment of Arabidopsis chromosome 4. We confirmed the conservation of gene content and order between the two genome segments. In addition, we identified a further four segments of the Arabidopsis genome that contain conserved gene content and order. In total, 22 of the 56 genes identified in the rice genome segment were represented in this set of Arabidopsis genome segments, with at least five genes present, in conserved order, in each segment. These data are consistent with the hypothesis that the Arabidopsis genome has undergone multiple duplication events. Our results demonstrate that conservation of the genome microstructure can be identified even between monocot and dicot species. However, the frequent occurrence of duplication, and subsequent microstructure divergence, within plant genomes may necessitate the integration of subsets of genes present in multiple redundant segments to deduce evolutionary relationships and identify orthologous genes

Vlaams Indicatorenboek 2019

Het Vlaams Indicatorenboek 2019 is een uitgave van het Expertisecentrum O&O Monitoring van de Vlaamse Gemeenschap in opdracht van de Vlaamse minister van Werk, Economie, Innovatie, en Sport en van de Vlaamse minister van Onderwijsstatus: publishe