Genetic Structure of Plasmodium falciparum and Elimination of Malaria, Comoros Archipelago

Elimination interventions should be implemented simultaneously throughout the entire archipelago

Early tumour response as a survival predictor in previously- treated patients receiving triplet hepatic artery infusion and intravenous cetuximab for unresectable liver metastases from wild-type KRAS colorectal cancer

Background: Early tumour shrinkage has been associated with improved survival in patients receiving cetuximab-based systemic chemotherapy for liver metastases from colorectal cancer (LM-CRC). We tested this hypothesis for previously treated LM-CRC patients receiving cetuximab (500 mg/m2) and triplet hepatic artery infusion (HAI) within European trial OPTILIV. Methods: Irinotecan (180 mg/m2), 5-fluorouracil (2800 mg/m2) and oxaliplatin (85 mg/m2) were given as chronomodulated or conventional delivery. Patients were retrospectively categorised as early responders (complete or partial RECIST response after three courses) or non-early responders (late or no response). Prognostic factors were determined using multivariate logistic or Cox regression models. Results: Response was assessed in 57 of 64 registered patients (89%), who had previously received one to three prior systemic chemotherapy protocols. An early response occurred at 6 weeks in 16 patients (28%; 9 men, 7 women), aged 33–76 years, with a median of 12 liver metastases (LMs) (2–50), involving five segments (1–8). Ten patients had a late response, and 31 patients had no response. Grade 3–4 fatigue selectively occurred in the non-early responders (0% versus 26%; p = 0.024). Early tumour response was jointly predicted by chronomodulation—odds ratio (OR): 6.0 (1.2–29.8; p = 0.029)—and LM diameter ≤57 mm—OR: 5.3 (1.1–25.0; p = 0.033). Early tumour response predicted for both R0-R1 liver resection—OR: 11.8 (1.4–100.2; p = 0.024) and overall survival—hazard ratio: 0.39 (0.17–0.88; p = 0.023) in multivariate analyses. Conclusions: Early tumour response on triplet HAI and systemic cetuximab predicted for complete macroscopic liver resection and prolonged survival for LM-CRC patients within a multicenter conversion-to-resection medicosurgical strategy. Confirmation is warranted for early response on HAI to guide decision making

Silencing-associated and meiosis-specific small RNA pathways in Paramecium tetraurelia

Distinct small RNA pathways are involved in the two types of homology-dependent effects described in Paramecium tetraurelia, as shown by a functional analysis of Dicer and Dicer-like genes and by the sequencing of small RNAs. The siRNAs that mediate post-transcriptional gene silencing when cells are fed with double-stranded RNA (dsRNA) were found to comprise two subclasses. DCR1-dependent cleavage of the inducing dsRNA generates ∼23-nt primary siRNAs from both strands, while a different subclass of ∼24-nt RNAs, characterized by a short untemplated poly-A tail, is strictly antisense to the targeted mRNA, suggestive of secondary siRNAs that depend on an RNA-dependent RNA polymerase. An entirely distinct pathway is responsible for homology-dependent regulation of developmental genome rearrangements after sexual reproduction. During early meiosis, the DCL2 and DCL3 genes are required for the production of a highly complex population of ∼25-nt scnRNAs from all types of germline sequences, including both strands of exons, introns, intergenic regions, transposons and Internal Eliminated Sequences. A prominent 5′-UNG signature, and a minor fraction showing the complementary signature at positions 21–23, indicate that scnRNAs are cleaved from dsRNA precursors as duplexes with 2-nt 3′ overhangs at both ends, followed by preferential stabilization of the 5′-UNG strand

Gene expression in a paleopolyploid: a transcriptome resource for the ciliate Paramecium tetraurelia

International audienceBACKGROUND: The genome of Paramecium tetraurelia, a unicellular model that belongs to the ciliate phylum, has been shaped by at least 3 successive whole genome duplications (WGD). These dramatic events, which have also been documented in plants, animals and fungi, are resolved over evolutionary time by the loss of one duplicate for the majority of genes. Thanks to a low rate of large scale genome rearrangement in Paramecium, an unprecedented large number of gene duplicates of different ages have been identified, making this organism an outstanding model to investigate the evolutionary consequences of polyploidization. The most recent WGD, with 51% of pre-duplication genes still in 2 copies, provides a snapshot of a phase of rapid gene loss that is not accessible in more ancient polyploids such as yeast. RESULTS: We designed a custom oligonucleotide microarray platform for P. tetraurelia genome-wide expression profiling and used the platform to measure gene expression during 1) the sexual cycle of autogamy, 2) growth of new cilia in response to deciliation and 3) biogenesis of secretory granules after massive exocytosis. Genes that are differentially expressed during these time course experiments have expression patterns consistent with a very low rate of subfunctionalization (partition of ancestral functions between duplicated genes) in particular since the most recent polyploidization event. CONCLUSIONS: A public transcriptome resource is now available for Paramecium tetraurelia. The resource has been integrated into the ParameciumDB model organism database, providing searchable access to the data. The microarray platform, freely available through NimbleGen Systems, provides a robust, cost-effective approach for genome-wide expression profiling in P. tetraurelia. The expression data support previous studies showing that at short evolutionary times after a whole genome duplication, gene dosage balance constraints and not functional change are the major determinants of gene retention

Functional outcomes in symptomatic versus asymptomatic patients undergoing incisional hernia repair: Replacing one problem with another? A prospective cohort study in 1312 patients

Background: Incisional hernias can be associated with pain or discomfort. Surgical repair especially mesh reinforcement, may likewise induce pain. The primary objective was to assess the incidence of pain after hernia repair in patients with and without pre-operative pain or discomfort. The secondary objectives were to determine the preferred mesh type, mesh location and surgical technique in minimizing postoperative pain or discomfort. Materials and methods: A registry-based prospective cohort study was performed, including patients undergoing incisional hernia repair between September 2011 and May 2019. Patients with a minimum follow-up of 3–6 months were included. The incidence of hernia related pain and discomfort was recorded perioperatively. Results: A total of 1312 patients were included. Pre-operatively, 1091 (83%) patients reported pain or discomfort. After hernia repair, 961 (73%) patients did not report pain or discomfort (mean follow-up = 11.1 months). Of the pre-operative asymptomatic patients (n = 221), 44 (20%, moderate or severe pain: n = 14, 32%) reported pain or discomfort after mean follow-up of 10.5 months. Of those patients initially reporting pain or discomfort (n = 1091), 307 (28%, moderate or severe pain: n = 80, 26%) still reported pain or discomfort after a mean follow-up of 11.3 months postoperatively. Conclusion: In symptomatic incisional hernia patients, hernia related complaints may be resolved in the majority of cases undergoing surgical repair. In asymptomatic incisional hernia patients, pain or discomfort may be induced in a considerable number of patients due to surgical repair and one should be aware if this postoperative complication

Multiscale Surface Self-Assembly of an Amyloid-like Peptide

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Overview of freshwater microbial eukaryotes diversity: a first analysis of publicly available metabarcoding data

International audienceAlthough they are widespread, diverse and involved in biogeochemical cycles, microbial eukaryotes attract less attention than their prokaryotic counterparts in environmental microbiology. In this study, we used publicly available 18S barcoding data to define biases that may limit such analyses and to gain an overview of the planktonic microbial eukaryotic diversity in freshwater ecosystems. The richness of the microbial eukaryotes was estimated to 100 798 operational taxonomic units (OTUs) delineating 1267 clusters or phylogenetic units (PUs, i.e. monophyletic groups of OTUs that are phylogenetically close). By summing the richness found in aquatic environments, we can predict the microbial eukaryotic richness to be around 200 000- 250 000 species. The molecular diversity of protists in freshwater environments is generally higher than that of the morphospecies and cultivated species catalogued in public databases. Amoebozoa, Viridiplantae, Ichthyosporea, and Cryptophyta are the most phylogenetically diverse taxa, and characterisation of these groups is still needed. A network analysis showed that Fungi, Stramenopiles and Viridiplantae play central role in lake ecosystems. Finally, this work provides guidance for compiling metabarcoding data and identifies missing data that should be obtained to increase our knowledge on microbial eukaryote diversity

Geographic distance and ecosystem size determine the distribution of smallest protists in lacustrine ecosystems.

International audienceUnderstanding the spatial distribution of aquatic microbial diversity and the underlying mechanisms causing differences in community composition is a challenging and central goal for ecologists. Recent insights into protistan diversity and ecology are increasing the debate over their spatial distribution. In this study, we investigate the importance of spatial and environmental factors in shaping the small protists community structure in lakes. We analyzed small protists community composition (beta-diversity) and richness (alpha-diversity) at regional scale by different molecular methods targeting the gene coding for 18S rRNA gene (T-RFLP and 454 pyrosequencing). Our results show a distance-decay pattern for rare and dominant taxa and the spatial distribution of the latter followed the prediction of the island biogeography theory. Furthermore, geographic distances between lakes seem to be the main force shaping the protists community composition in the lakes studied here. Finally, the spatial distribution of protists was discussed at the global scale (11 worldwide distributed lakes) by comparing these results with those present in the public database. UniFrac analysis showed 18S rRNA gene OTUs compositions significantly different among most of lakes, and this difference does not seem to be related to the trophic status