Context-Dependent Dual Role of SKI8 Homologs in mRNA Synthesis and Turnover

Eukaryotic mRNA transcription and turnover is controlled by an enzymatic machinery that includes RNA polymerase II and the 3′ to 5′ exosome. The activity of these protein complexes is modulated by additional factors, such as the nuclear RNA polymerase II-associated factor 1 (Paf1c) and the cytoplasmic Superkiller (SKI) complex, respectively. Their components are conserved across uni- as well as multi-cellular organisms, including yeast, Arabidopsis, and humans. Among them, SKI8 displays multiple facets on top of its cytoplasmic role in the SKI complex. For instance, nuclear yeast ScSKI8 has an additional function in meiotic recombination, whereas nuclear human hSKI8 (unlike ScSKI8) associates with Paf1c. The Arabidopsis SKI8 homolog VERNALIZATION INDEPENDENT 3 (VIP3) has been found in Paf1c as well; however, whether it also has a role in the SKI complex remains obscure so far. We found that transgenic VIP3-GFP, which complements a novel vip3 mutant allele, localizes to both nucleus and cytoplasm. Consistently, biochemical analyses suggest that VIP3–GFP associates with the SKI complex. A role of VIP3 in the turnover of nuclear encoded mRNAs is supported by random-primed RNA sequencing of wild-type and vip3 seedlings, which indicates mRNA stabilization in vip3. Another SKI subunit homolog mutant, ski2, displays a dwarf phenotype similar to vip3. However, unlike vip3, it displays neither early flowering nor flower development phenotypes, suggesting that the latter reflect VIP3's role in Paf1c. Surprisingly then, transgenic ScSKI8 rescued all aspects of the vip3 phenotype, suggesting that the dual role of SKI8 depends on species-specific cellular context

Transcriptome Analysis of Female and Male Xiphophorus maculatus Jp 163 A

Background: Xiphophorus models are important for melanoma, sex determination and differentiation, ovoviviparity and evolution. To gain a global view of the molecular mechanism(s) whereby gene expression may influence sexual dimorphism in Xiphophorus and to develop a database for future studies, we performed a large-scale transcriptome study. Methodology/Principal Findings: The 454-FLX massively parallel DNA sequencing platform was employed to obtain 742,771 and 721,543 reads from 2 normalized cDNA libraries generated from whole adult female and male X. maculatus Jp 163 A, respectively. The reads assembled into 45,538 contigs (here, a "contig" is a set of contiguous sequences), of which, 11,918 shared homology to existing protein sequences. These numbers estimate that the contigs may cover 53% of the total number of Xiphophorus transcriptome. Putative translations were obtained for 11,918 cDNA contigs, of which, 3,049 amino acid sequences contain Pfam domains and 11,064 contigs encode secretory proteins. A total of 3,898 contigs were associated with 2,781 InterPro (IPR) entries and 5,411 contigs with 132 KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways. There were 10,446 contigs annotated with 69,778 gene ontology (GO) terms and the three corresponding organizing principles. Fifty-four potential sex differentially expressed genes have been identified from these contigs. Eight and nine of these contigs were confirmed by real-time PCR as female and male predominantly expressed genes respectively. Based on annotation results, 34 contigs were predicted to be differentially expressed in male and female and 17 of them were also confirmed by real-time PCR. Conclusions/Significance: This is the first report of an annotated overview of the transcriptome of X. maculatus and identification of sex differentially expressed genes. These data will be of interest to researchers using the Xiphophorus model. This work also provides an archive for future studies in molecular mechanisms of sexual dimorphism and evolution, and can be used in comparative studies of other fish

The Mayer-Rokitansky-Küster-Hauser syndrome (congenital absence of uterus and vagina) – phenotypic manifestations and genetic approaches

The Mayer-Rokitansky-Küster-Hauser (MRKH) syndrome affects at least 1 out of 4500 women and has for a long time been considered as a sporadic anomaly. Congenital absence of upper vagina and uterus is the prime feature of the disease which, in addition, is often found associated with unilateral renal agenesis or adysplasia as well as skeletal malformations (MURCS association). The phenotypic manifestations of MRKH overlap various other syndromes or associations and thus require accurate delineation. Since MRKH manifests itself in males, the term GRES syndrome (Genital, Renal, Ear, Skeletal) might be more appropriate when applied to both sexes. The MRKH syndrome, when described in familial aggregates, seems to be transmitted as an autosomal dominant trait with an incomplete degree of penetrance and variable expressivity. This suggests the involvement of either mutations in a major developmental gene or a limited chromosomal deletion. Until recently progress in understanding the genetics of MRKH syndrome has been slow, however, now HOX genes have been shown to play key roles in body patterning and organogenesis, and in particular during genital tract development. Expression and/or function defects of one or several HOX genes may account for this syndrome

Surface-Properties Characterization of Suspended Matter in the Ebro Delta (spain) - with an Application to Trace-Metal Sorption

International audienc

Surface-Properties of Suspended-Solids in Stratified Estuaries (krka River Estuary and Rhone River Delta)

International audienceThree surface parameters - specific surface area (SSA), heat of wetting (Hw), and cation exchange capacity (CEC) - of estuarine suspended solids were studied in relation to the organic matter (dissolved or particulate). Natural suspended solids were studied in two stratified river mouths - the Krka River estuary and the Rhone River delta. The same studies were performed with model solids, well defined by chemical composition and preparation (controlled pore glass, silanized controlled pore glass and calcite) after exposure to natural water samples from the Krka River estuary. On the basis of the studied parameters, the existence of two types of organic compounds that mediate the surface properties of particulates was indicated: (1) hydrophilic, with high density of functional groups, reactive and degradable, and coinciding with 'river type organic matter, and (2) hydrophobic, less reactive and thus more persistent, and coinciding prevalently with 'marine type organic matter'. Generally, it was found that high Hw values (100-300-mu-J cm-2) reflect the influence of surface functional groups that originate primarily from the reactive organics (adsorbed or particulate). An extreme value of Hw (523-mu-J cm-2) was found at a location of high biological productivity and high anthropogenic influence

Monitoring the propagation of SARS CoV2 variants by tracking identified mutation in wastewater using specific RT-qPCR

Since the end of 2020, the COVID-19 pandemic has experienced a major turning point with the appearance and rapid spread of new variants, causing a significant increase in the number of new cases requiring hospitalization. These so-called UK, South African or Brazilian variants are characterized by combinations of mutations which allow them to be distinguished from the variants which have circulated since the start of the epidemic. The impact of these variants on the functioning of healthcare systems requires monitoring the spread of these variants, which are more contagious, more lethal and may reinfect people who are already immune to a natural infection or to a vaccination. Monitoring the viral genome in wastewater has shown great value in early detection of the dynamics of virus spreading in populations. The sequencing of viral genomes is used in humans, but its application and interpretation on wastewater matrices are much more complex due to the diversity of circulating strains. Also this study demonstrates the possibility of following certain mutations found in these new variants by targeted RT-qPCR. This study is the first carried out in France demonstrating the spreading dynamics of the 69-70 deletion in the Spike protein of SARS-CoV-2

Several forms of SARS-CoV-2 RNA can be detected in wastewaters : implication for wastewater-based epidemiology and risk assessment

International audienceThe ongoing global pandemic of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been a public health emergency of international concern. Although SARS-CoV-2 is considered to be mainly transmitted by inhalation of contaminated droplets and aerosols, SARS-CoV-2 is also detected in human feces and in raw wastewaters suggesting that other routes of infection may exist. Monitoring SARS-CoV-2 genomes in wastewaters has been proposed as a complementary approach for tracing the dynamics of virus transmission within human population connected to wastewater network. The understanding on SARS-CoV-2 transmission through wastewater surveillance, the development of epidemic modeling and the evaluation of SARS-CoV-2 transmission from contaminated wastewater are largely limited by our knowledge on viral RNA genome persistence and virus infectivity preservation in such an environment. Using an integrity based RT-qPCR assay this study led to the discovery that SARS-CoV-2 RNA can persist under several forms in wastewaters, which provides important information on the presence of SARS-CoV-2 in raw wastewaters and associated risk assessment