Federating and querying heterogeneous and distributed Web APIs and triple stores

Today's international corporations such as BASF, a leading company in the crop protection industry, produce and consume more and more data that are often fragmented and accessible through Web APIs. In addition, part of the proprietary and public data of BASF's interest are stored in triple stores and accessible with the SPARQL query language. Homogenizing the data access modes and the underlying semantics of the data without modifying or replicating the original data sources become important requirements to achieve data integration and interoperability. In this work, we propose a federated data integration architecture within an industrial setup, that relies on an ontology-based data access method. Our performance evaluation in terms of query response time showed that most queries can be answered in under 1 second

Local rewiring of genome-nuclear lamina interactions by transcription

Transcriptionally inactive genes are often positioned at the nuclear lamina (NL), as part of large lamina-associated domains (LADs). Activation of such genes is often accompanied by repositioning toward the nuclear interior. How this process works and how it impacts flanking chromosomal regions are poorly understood. We addressed these questions by systematic activation or inactivation of individual genes, followed by detailed genome-wide analysis of NL interactions, replication timing, and transcription patterns. Gene activation inside LADs typically causes NL detachment of the entire transcription unit, but rarely more than 50-100 kb of flanking DNA, even when multiple neighboring genes are activated. The degree of detachment depends on the expression level and the length of the activated gene. Loss of NL interactions coincides with a switch from late to early replication timing, but the latter can involve longer stretches of DNA. Inactivation of active genes can lead to increased NL contacts. These extensive datasets are a resource for the analysis of LAD rewiring by transcription and reveal a remarkable flexibility of interphase chromosomes

Freshwater Seepage Into Sediments of the Shelf, Shelf Edge, and Continental Slope of the Canadian Beaufort Sea

Long‐term warming of the continental shelf of the Canadian Beaufort Sea caused by the transgression associated with the last deglaciation may be causing decomposition of relict offshore subsea permafrost and gas hydrates. To evaluate this possibility, pore waters from 118 sediment cores up to 7.3‐m long were taken on the shelf and slope and analyzed for chloride concentrations and δ180 and δD composition. We observed downcore decreases in pore waters Cl− concentration in sediments from all sites from the inner shelf (<20‐m water depth), from the shelf edge, from the outer slope (down to 1,000‐m water depths), and from localized shelf features such as midshelf pingo‐like features and inner shelf pockmarks. In contrast, pore water freshening is absent from all investigated cores of the Mackenzie Trough. Downcore pore waters Cl− concentration decreases indicate regional widespread freshwater seepage. Extrapolations to zero Cl− of pore water Cl− versus δ180 regression lines indicate that freshwaters in these environments carry different isotope signatures and thus are sourced from different reservoirs. These isotopic signatures indicate that freshening of shelf sediments pore waters is a result of downward infiltration of Mackenzie River water, freshening of shelf edge sediments is due to relict submarine permafrost degradation or gas hydrate decomposition under the shelf, and freshening of slope sediments is consistent with regional groundwater flow and submarine groundwater discharge as far as 150 km from shore. These results confirm ongoing decomposition of offshore permafrost and suggest extensive current groundwater discharge far from the coast

Osteoimmunology of Oral and Maxillofacial Diseases : Translational Applications Based on Biological Mechanisms

The maxillofacial skeleton is highly dynamic and requires a constant equilibrium between the bone resorption and bone formation. The field of osteoimmunology explores the interactions between bone metabolism and the immune response, providing a context to study the complex cellular and molecular networks involved in oro-maxillofacial osteolytic diseases. In this review, we present a framework for understanding the potential mechanisms underlying the immuno-pathobiology in etiologically-diverse diseases that affect the oral and maxillofacial region and share bone destruction as their common clinical outcome. These otherwise different pathologies share similar inflammatory pathways mediated by central cellular players, such as macrophages, T and B cells, that promote the differentiation and activation of osteoclasts, ineffective or insufficient bone apposition by osteoblasts, and the continuous production of osteoclastogenic signals by immune and local stromal cells. We also present the potential translational applications of this knowledge based on the biological mechanisms involved in the inflammation-induced bone destruction. Such applications can be the development of immune-based therapies that promote bone healing/regeneration, the identification of host-derived inflammatory/collagenolytic biomarkers as diagnostics tools, the assessment of links between oral and systemic diseases; and the characterization of genetic polymorphisms in immune or bone-related genes that will help diagnosis of susceptible individuals.Peer reviewe

Identification, Characterization, and Application of the Replicon Region of the Halophilic Temperate Sphaerolipovirus SNJ1

International audienceThe temperate haloarchaeal virus SNJ1 displays lytic and lysogenic life cycles. During the lysogenic cycle, the virus resides in its host, Natrinema sp. strain J7-1, in the form of an extrachromosomal circular plasmid, pHH205. In this study, a 3.9-kb region containing seven predicted genes organized in two operons was identified as the minimal replicon of SNJ1. Only RepA, encoded by open reading frame 11-12 (ORF11-12), was found to be essential for replication, and its expression increased during the lytic cycle. Sequence analysis suggested that RepA is a distant homolog of HUH endonucleases, a superfamily that includes rolling-circle replication initiation proteins from various viruses and plasmids. In addition to RepA, two genetic elements located within both termini of the 3.9-kb replicon were also required for SNJ1 replication. SNJ1 genome and SNJ1 replicon-based shuttle vectors were present at 1 to 3 copies per chromosome. However, the deletion of ORF4 significantly increased the SNJ1 copy number, suggesting that the product of ORF4 is a negative regulator of SNJ1 abundance. Shuttle vectors based on the SNJ1 replicon were constructed and validated for stable expression of heterologous proteins, both in J7 derivatives and in Natrinema pallidum JCM 8980(T), suggesting their broad applicability as genetic tools for Natrinema species. IMPORTANCE: Archaeal viruses exhibit striking morphological diversity and unique gene content. In this study, the minimal replicon of the temperate haloarchaeal virus SNJ1 was identified. A number of ORFs and genetic elements controlling virus genome replication, maintenance, and copy number were characterized. In addition, based on the replicon, a novel expression shuttle vector has been constructed and validated for protein expression and purification in Natrinema sp. CJ7 and Natrinema pallidum JCM 8980(T) This study not only provided mechanistic and functional insights into SNJ1 replication but also led to the development of useful genetic tools to investigate SNJ1 and other viruses infecting Natrinema species as well as their hosts

ORF4 of the temperate archaeal virus SNJ1 governs the lysis-lysogeny switch and superinfection immunity

International audienceRecent environmental and metagenomic studies have considerably increased the repertoire of archaeal viruses and suggested that they play important roles in nutrient cycling in the biosphere. However, very little is known about how they regulate their life cycles and interact with their hosts. Here, we report that the life cycle of the temperate haloarchaeal virus SNJ1 is controlled by the product ORF4, a small protein belonging to the antitoxin MazE superfamily. We show that ORF4 controls the lysis-lysogeny switch of SNJ1 and mediates superinfection immunity by repression of genomic DNA replication of the superinfecting viruses. Bioinformatic analysis shows that ORF4 is highly conserved in two SNJ1-like proviruses, suggesting that the mechanisms for lysis-lysogeny switch and superinfection immunity are conserved in this group of viruses. As lysis-lysogeny switch and superinfection immunity of archaeal viruses are poorly studied, we suggest that SNJ1 could serve as a model system to study these processes.IMPORTANCE Archaeal viruses are important parts of the virosphere. Understanding how they regulate their life cycles and interact with host cells provide crucial insights into their biological functions and the evolutionary histories of viruses. However, mechanistic studies of the life cycle of archaeal viruses are scarce due to a lack of genetic tools and demanding cultivation conditions. Here, we discover that the temperate haloarchaeal virus SNJ1, which infects Natrinema sp. J7, employs a lysis-lysogeny switch and establishes superinfection immunity like bacteriophages. We show that its ORF4 is critical for both processes and acts as a repressor of the replication of SNJ1.These results establish ORF4 as a master regulator of SNJ1 life cycle and provides novel insights on the regulation of life cycles by temperate archaeal viruses and on their interactions with host cells

DNA replication timing alterations identify common markers between distinct progeroid diseases

International audienc