Revealing the profound influence of diapause on gene expression: Insights from the annual transcriptome of the copepod Calanus finmarchicus.

Annual rhythms are observed in living organisms with numerous ecological implications. In the zooplanktonic copepod Calanus finmarchicus, such rhythms are crucial regarding its phenology, body lipid accumulation, and global carbon storage. Climate change drives annual biological rhythms out of phase with the prevailing environmental conditions with yet unknown but potentially catastrophic consequences.

A dual model of normal vs isogenic Nrf2-depleted murine epithelial cells to explore oxidative stress involvement.

Cancer-derived cell lines are useful tools for studying cellular metabolism and xenobiotic toxicity, but they are not suitable for modeling the biological effects of food contaminants or natural biomolecules on healthy colonic epithelial cells in a normal genetic context. The toxicological properties of such compounds may rely on their oxidative properties. Therefore, it appears to be necessary to develop a dual-cell model in a normal genetic context that allows to define the importance of oxidative stress in the observed toxicity.

Asterics: a simple tool for the ExploRation and Integration of omiCS data.

Background: The rapid development of omics acquisition techniques has induced the production of a large volume of heterogeneous and multi-level omics datasets, which require specific and sometimes complex analyses to obtain relevant biological information. Here, we present ASTERICS (version 2.5), a publicly available web interface for the analyses of omics datasets.

The Histone Chaperone Network Is Highly Conserved in .

The nucleosome is composed of histones and DNA. Prior to their deposition on chromatin, histones are shielded by specialized and diverse proteins known as histone chaperones. They escort histones during their entire cellular life and ensure their proper incorporation in chromatin.

Study of the colonic epithelial-mesenchymal dialogue through establishment of two activated or not mesenchymal cell lines: Activated and resting ones differentially modulate colonocytes in co-culture.

Continuous and rapid renewal of the colonic epithelium is crucial to resist the plethora of luminal deleterious agents. Subepithelial fibroblasts contribute to this turnover by regulating epithelial proliferation and differentiation. However, when intestinal homeostasis is disturbed, fibroblasts can acquire an activated phenotype and play a major role in the progression of intestinal pathologies.

Mosaic Evolution of Molecular Pathways for Sex Pheromone Communication in a Butterfly.

Unraveling the origin of molecular pathways underlying the evolution of adaptive traits is essential for understanding how new lineages emerge, including the relative contribution of conserved ancestral traits and newly evolved derived traits. Here, we investigated the evolutionary divergence of sex pheromone communication from moths (mostly nocturnal) to butterflies (mostly diurnal) that occurred ~119 million years ago. In moths, it is the females that typically emit pheromones to attract male mates, but in butterflies males emit pheromones that are used by females for mate choice.

SDR enzymes oxidize specific lipidic alkynylcarbinols into cytotoxic protein-reactive species.

Hundreds of cytotoxic natural or synthetic lipidic compounds contain chiral alkynylcarbinol motifs, but the mechanism of action of those potential therapeutic agents remains unknown. Using a genetic screen in haploid human cells, we discovered that the enantiospecific cytotoxicity of numerous terminal alkynylcarbinols, including the highly cytotoxic dialkynylcarbinols, involves a bioactivation by HSD17B11, a short-chain dehydrogenase/reductase (SDR) known to oxidize the C-17 carbinol center of androstan-3-alpha,17-beta-diol to the corresponding ketone. A similar oxidation of dialkynylcarbinols generates dialkynylketones, that we characterize as highly protein-reactive electrophiles.

Annual transcriptome of a key zooplankton species, the copepod .

The copepod (Crustacea, Copepoda) is a key zooplanktonic species with a crucial position in the North Atlantic food web and significant contributor to ocean carbon flux. Like many other high latitude animals, it has evolved a programmed arrested development called diapause to cope with long periods of limited food supply, while growth and reproduction are timed to take advantage of seasonal peaks in primary production. However, anthropogenic warming is inducing changes in the expected timing of phytoplankton blooms, suggesting phenological mismatches with negative consequences for the N.

Transcription-associated topoisomerase 2α (TOP2A) activity is a major effector of cytotoxicity induced by G-quadruplex ligands.

G-quadruplexes (G4) are non-canonical DNA structures found in the genome of most species including human. Small molecules stabilizing these structures, called G4 ligands, have been identified and, for some of them, shown to induce cytotoxic DNA double-strand breaks. Through the use of an unbiased genetic approach, we identify here topoisomerase 2α (TOP2A) as a major effector of cytotoxicity induced by two clastogenic G4 ligands, pyridostatin and CX-5461, the latter molecule currently undergoing phase I/II clinical trials in oncology.

Widely rhythmic transcriptome in during the high Arctic summer solstice period.

Solar light/dark cycles and seasonal photoperiods underpin daily and annual rhythms of life on Earth. Yet, the Arctic is characterized by several months of permanent illumination ("midnight sun"). To determine the persistence of 24h rhythms during the midnight sun, we investigated transcriptomic dynamics in the copepod during the summer solstice period in the Arctic, with the lowest diel oscillation and the highest altitude of the sun's position.

Life cycle assessment of fish and seafood processed products - A review of methodologies and new challenges.

Life cycle assessment (LCA) has been widely applied in many different sectors, but the marine products and seafood segment have received relatively little attention in the past. In recent decades, global fish production experienced sustained growth and peaked at about 179 million tonnes in 2018. Consequently, increased interest in the environmental implications of fishery products along the supply chain, namely from capture to end of life, was recently experienced by society, industry and policy-makers.

[Ga]Ga-PSMA-11 in prostate cancer: a comprehensive review.

Imaging of the prostate-specific membrane antigen (PSMA) has become an important tool for managing patients with recurrent prostate cancer, and one of the most frequently employed radiopharmaceuticals is [Ga]Ga-PSMA-11. Herein, we summarize the preclinical development and the clinical applications of [Ga]Ga-PSMA-11 and present side-by-side comparisons with other radiopharmaceuticals or imaging modalities, in order to assist imagers and clinicians in recommending, performing, and interpreting the results of [Ga]Ga-PSMA-11 PET scans in patients with prostate cancer.

Daily transcriptomes of the copepod Calanus finmarchicus during the summer solstice at high Arctic latitudes.

The zooplankter Calanus finmarchicus is a member of the so-called "Calanus Complex", a group of copepods that constitutes a key element of the Arctic polar marine ecosystem, providing a crucial link between primary production and higher trophic levels. Climate change induces the shift of C. finmarchicus to higher latitudes with currently unknown impacts on its endogenous timing.

MetaPopGen 2.0: A multilocus genetic simulator to model populations of large size.

Multilocus genetic processes in subdivided populations can be complex and difficult to interpret using theoretical population genetics models. Genetic simulators offer a valid alternative to study multilocus genetic processes in arbitrarily complex scenarios. However, the use of forward-in-time simulators in realistic scenarios involving high numbers of individuals distributed in multiple local populations is limited by computation time and memory requirements.

A future 1.2 °C increase in ocean temperature alters the quality of mangrove habitats for marine plants and animals.

Global climate stressors, like ocean warming and acidification, contribute to the erosion of structural complexity in marine foundation habitats by promoting the growth of low-relief turf, increasing grazing pressure on structurally complex marine vegetation, and by directly affecting the growth and survival of foundation species. Because mangrove roots are woody and their epibionts are used to ever-changing conditions in highly variable environments, mangrove habitats may be more resilient to global change stressors than other marine foundation species. Using a large-scale mesocosm experiment, we examined how ocean warming and acidification, under a reduced carbon emission scenario, affect the composition and structural complexity of mangrove epibiont communities and the use of mangrove habitat by juvenile fishes.

A comparative transcriptomic approach to understanding the formation of cork.

The transcriptome comparison of two oak species reveals possible candidates accounting for the exceptionally thick and pure cork oak phellem, such as those involved in secondary metabolism and phellogen activity. Cork oak, Quercus suber, differs from other Mediterranean oaks such as holm oak (Quercus ilex) by the thickness and organization of the external bark. While holm oak outer bark contains sequential periderms interspersed with dead secondary phloem (rhytidome), the cork oak outer bark only contains thick layers of phellem (cork rings) that accumulate until reaching a thickness that allows industrial uses.

Complete Genome Sequence and Annotation of the Strain HG001.

is an opportunistic Gram-positive pathogen responsible for a wide range of infections from minor skin abscesses to life-threatening diseases. Here, we report the draft genome assembly and current annotation of the HG001 strain, a derivative of the RN1 (NCT8325) strain with restored (a positive activator of SigB).

Reprogramming of DNA methylation is critical for nodule development in Medicago truncatula.

The legume-Rhizobium symbiosis leads to the formation of a new organ, the root nodule, involving coordinated and massive induction of specific genes. Several genes controlling DNA methylation are spatially regulated within the Medicago truncatula nodule, notably the demethylase gene, DEMETER (DME), which is mostly expressed in the differentiation zone. Here, we show that MtDME is essential for nodule development and regulates the expression of 1,425 genes, some of which are critical for plant and bacterial cell differentiation.

Sequencing and characterization of a multi-organ Arctic charr transcriptome: A toolbox for investigating polymorphism and seasonal life in a high Arctic fish.

The Arctic charr (Salvelinus alpinus L.) inhabits fresh water ecosystems of the high North. The species has developed a strong phenotypic plasticity and variability in life history characteristics which has made this species an attractive model for investigations on phenotype plasticity, morph formation and ecological speciation.

Whole-exome sequencing in osteosarcoma reveals important heterogeneity of genetic alterations.

Background: Whole-genome sequencing studies have recently shown that osteosarcomas (OSs) display high rates of structural variation, i.e. they contain many somatic mutations and copy number alterations.

Jflow: a workflow management system for web applications.

Summary: Biologists produce large data sets and are in demand of rich and simple web portals in which they can upload and analyze their files. Providing such tools requires to mask the complexity induced by the needed High Performance Computing (HPC) environment. The connection between interface and computing infrastructure is usually specific to each portal.

The BioMart community portal: an innovative alternative to large, centralized data repositories.

The BioMart Community Portal (www.biomart.org) is a community-driven effort to provide a unified interface to biomedical databases that are distributed worldwide.