Determining gene flow and the influence of selection across the equatorial barrier of the East Pacific Rise in the tube-dwelling polychaete Alvinella pompejana

International audienceBackground: Comparative phylogeography recently performed on the mitochondrial cytochrome oxidase I (mtCOI) gene from seven deep-sea vent species suggested that the East Pacific Rise fauna has undergone a vicariant event with the emergence of a north/south physical barrier at the Equator 1-2 Mya. Within this specialised fauna, the tube-dwelling polychaete Alvinella pompejana showed reciprocal monophyly at mtCOI on each side of the Equator (9 degrees 50'N/7 degrees 25'S), suggesting potential, ongoing allopatric speciation. However, the development of a barrier to gene flow is a long and complex process. Secondary contact between previously isolated populations can occur when physical isolation has not persisted long enough to result in reproductive isolation between genetically divergent lineages, potentially leading to hybridisation and subsequent allelic introgression. The present study evaluates the strength of the equatorial barrier to gene flow and tests for potential secondary contact zones between A. pompejana populations by comparing the mtCOI gene with nuclear genes. Results: Allozyme frequencies and the analysis of nucleotide polymorphisms at three nuclear loci confirmed the north/south genetic differentiation of Alvinella pompejana populations along the East Pacific Rise. Migration was oriented north-to-south with a moderate allelic introgression between the two geographic groups over a narrow geographic range just south of the barrier. Multilocus analysis also indicated that southern populations have undergone demographic expansion as previously suggested by a multispecies approach. A strong shift in allozyme frequencies together with a high level of divergence between alleles and a low number of `hybrid' individuals were observed between the northern and southern groups using the phosphoglucomutase gene. In contrast, the S-adenosylhomocysteine hydrolase gene exhibited reduced diversity and a lack of population differentiation possibly due to a selective sweep or hitch-hiking. Conclusions: The equatorial barrier leading to the separation of East Pacific Rise vent fauna into two distinct geographic groups is still permeable to migration, with a probable north-to-south migration route for A. pompejana. This separation also coincides with demographic expansion in the southern East Pacific Rise. Our results suggest that allopatry resulting from ridge offsetting is a common mechanism of speciation for deep-sea hydrothermal vent organisms

Conjugating effects of symbionts and environmental factors on gene expression in deep-sea hydrothermal vent mussels.

International audienceABSTRACT: BACKGROUND: The deep-sea hydrothermal vent mussel Bathymodiolus azoricus harbors thiotrophic and methanotrophic symbiotic bacteria in its gills. While the symbiotic relationship between this hydrothermal mussel and these chemoautotrophic bacteria has been described, the molecular processes involved in the cross-talking between symbionts and host, in the maintenance of the symbiois, in the influence of environmental parameters on gene expression, and in transcriptome variation across individuals remain poorly understood. In an attempt to understand how, and to what extent, this double symbiosis affects host gene expression, we used a transcriptomic approach to identify genes potentially regulated by symbiont characteristics, environmental conditions or both. This study was done on mussels from two contrasting populations. RESULTS: Subtractive libraries allowed the identification of about 1000 genes putatively regulated by symbiosis and/or environmental factors. Microarray analysis showed that 120 genes (3.5% of all genes) were differentially expressed between the Menez Gwen (MG) and Rainbow (Rb) vent fields. The total number of regulated genes in mussels harboring a high versus a low symbiont content did not differ significantly. With regard to the impact of symbiont content, only 1% of all genes were regulated by thiotrophic (SOX) and methanotrophic (MOX) bacteria content in MG mussels whereas 5.6% were regulated in mussels collected at Rb. MOX symbionts also impacted a higher proportion of genes than SOX in both vent fields. When host transcriptome expression was analyzed with respect to symbiont gene expression, it was related to symbiont quantity in each field. CONCLUSIONS: Our study has produced a preliminary description of a transcriptomic response in a hydrothermal vent mussel host of both thiotrophic and methanotrophic symbiotic bacteria. This model can help to identify genes involved in the maintenance of symbiosis or regulated by environmental parameters. Our results provide evidence of symbiont effect on transcriptome regulation, with differences related to type of symbiont, even though the relative percentage of genes involved remains limited. Differences observed between the vent site indicate that environment strongly influences transcriptome regulation and impacts both activity and relative abundance of each symbiont. Among all these genes, those participating in recognition, the immune system, oxidative stress, and energy metabolism constitute new promising targets for extended studies on symbiosis and the effect of environmental parameters on the symbiotic relationships in B. azoricus

Studies on hemostasis in COVID-19 deserve careful reporting of the laboratory methods, their significance and their limitations

We read with much interest the recent observational study of Nougier et al., which aimed at studying thrombin generation (TG) and fibrinolysis profiles of COVID-19 patients admitted to an intensive care unit (ICU) or to an internal medicine ward and receiving various schemes of prophylactic heparin.[1] They reported that thrombin potential remained within normal range despite heparin and that fibrinolysis was decreased in relation with increased plasminogen activator inhibitor 1 (PAI-1) and thrombin-activatable fibrinolysis inhibitor (TAFI) antigen plasma levels. Using the rotational thromboelastometry (ROTEM) delta device with EXTEM reagents and the addition of 0.625µg/mL tPA (referred to as 'TEM-tPA'), they reported decreased clot lysis in COVID-19 patients, which was more pronounced in patients who presented a thrombotic event, compared to event-free patients

Staphylococcus aureus Bloodstream Infection and Endocarditis―A Prospective Cohort Study

Equipe CHU UB (EA) Pôle MERS CT3 Hors Enjeu The VIRSTA Study Group : Clinical centres: Besançon: Catherine Chirouze, Elodie Curlier, Cécile Descottes-Genon, Bruno Hoen, Isabelle Patry, Lucie Vettoretti. Dijon: Pascal Chavanet, Jean-Christophe Eicher, Sandrine Gohier-Treuvelot, Marie-Christine Greusard, Catherine Neuwirth, André Péchinot, Lionel Piroth. Lyon: Marie Célard, Catherine Cornu, François Delahaye, Malika Hadid, Pascale Rausch. Montpellier: Audrey Coma, Florence Galtier, Philippe Géraud, Hélène Jean-Pierre, Vincent Le Moing, Catherine Sportouch, Jacques Reynes. Nancy: Nejla Aissa, Thanh Doco- Lecompte, François Goehringer, Nathalie Keil, Lorraine Letranchant, Hepher Malela, Thierry May, Christine Selton-Suty. Nîmes: Nathalie Bedos, Jean-Philippe Lavigne, Catherine Lechiche, Albert Sotto. Paris: Xavier Duval, Emila Ilic Habensus, Bernard Iung, Catherine Leport, Pascale Longuet, Raymond Ruimy. Rennes: Eric Bellissant, Pierre-Yves Donnio, Fabienne Le Gac, Christian Michelet, Matthieu Revest, Pierre Tattevin, Elise Thebault. Coordination and statistical analyses: François Alla, Pierre Braquet, Marie-Line Erpelding, Laetitia Minary, Sarah Tubiana. Centre National de Référence des staphylocoques: Michèle Bès, Jérôme Etienne, Anne Tristan, François Vandenesch. Sponsor CHU de Montpellier: Sandrine Barbas, Christine Delonca, Virginie Sussmuth, Anne Verchère. Alain Makinson reviewed the manuscript for English correctness.International audienceOBJECTIVES: To update the epidemiology of S. aureus bloodstream infection (SAB) in a high-income country and its link with infective endocarditis (IE).METHODS: All consecutive adult patients with incident SAB (n = 2008) were prospectively enrolled between 2009 and 2011 in 8 university hospitals in France. RESULTS: SAB was nosocomial in 54%, non-nosocomial healthcare related in 18% and community-acquired in 26%. Methicillin resistance was present in 19% of isolates. SAB Incidence of nosocomial SAB was 0.159/1000 patients-days of hospitalization (95% confidence interval [CI] 0.111-0.219). A deep focus of infection was detected in 37%, the two most frequent were IE (11%) and pneumonia (8%). The higher rates of IE were observed in injecting drug users (IE: 38%) and patients with prosthetic (IE: 33%) or native valve disease (IE: 20%) but 40% of IE occurred in patients without heart disease nor injecting drug use. IE was more frequent in case of community-acquired (IE: 21%, adjusted odds-ratio (aOR) = 2.9, CI = 2.0-4.3) or non-nosocomial healthcare-related SAB (IE: 12%, aOR = 2.3, CI = 1.4-3.5). S. aureus meningitis (IE: 59%), persistent bacteremia at 48 hours (IE: 25%) and C-reactive protein > 190 mg/L (IE: 15%) were also independently associated with IE. Criteria for severe sepsis or septic shock were met in 30% of SAB without IE (overall in hospital mortality rate 24%) and in 51% of IE (overall in hospital mortality rate 35%).CONCLUSION: SAB is still a severe disease, mostly related to healthcare in a high-income country. IE is the most frequent complication and occurs frequently in patients without known predisposing condition

Variability among commercial batches of normal pooled plasma in lupus anticoagulant testing

Lupus anticoagulant (LA) testing requires normal pooled plasma (NPP) in performing mixing studies and can be used for normalized ratios of clotting times (CTs). The aims were to demonstrate whether significant differences in clotting times between two batches of a same commercial NPP (CRYOcheck™) directly affect NPP-based cut-off values. Diluted Russell Viper venom time (DRVVT) and activated partial thromboplastin time (aPTT) were used for LA testing. Screening, mixing and confirm tests were performed with Stago® instruments and reagents. Two batches of commercial NPP (A1291 and A1301 from CRYOcheck™; frozen) were compared in the determination of cut-off values. Cut-off values were defined as 99th percentile values of 60 healthy donors and compared with Mann-Whitney U test. Cut-off values obtained with the two NPP batches were significantly different for DRVVT (screen normalized ratio: 1.09 vs. 1.24, screen mix: 41.9 s vs. 38.9 s; index of circulating anticoagulant: 5.0 vs. 8.4; all had p-value <.001). On the contrary, no significant differences were observed for aPTT (screen normalized ratio: 1.32 vs. 1.34; p-value = .4068, screen mix: 37.8 s vs. 38.1 s; p-value = .1153) except for index of circulating anticoagulant: 9.6 versus 10.4 (p-value <.05). This study demonstrates that differences between two commercial NPP batches produced by a same manufacturer influenced LA cut-off values used for mixing studies and normalized ratios. Adequate cut-off setting, taking into account NPP CTs, is important to provide accurate conclusion about the presence or absence of a LA and avoid potential clinical impact

Congenital lung malformations: correlation between prenatal and postnatal imaging and pathological findings

Aim: Congenital lung malformations are a common finding during prenatal ultrasonography (US). Investigations were completed by means of prenatal MRI and postnatal computed tomographic (CT) scan. The purpose of this study was to compare these prenatal findings with postnatal findings and pathological findings after surgical resection.Materials and methods: Prenatal examinations and postnatal CTscan results of congenital malformations were compared with pathological findings.Results: From 2007 to 2013, 39 prenatally diagnosed congenital lung malformations were resected: 18 congenital cystic adenomatoid malformation, eight pulmonary sequestration, five bronchogenic cyst, one bronchial atresia and six complex lesions. Correlation between imaging and diagnosis was as follows: congenital cystic adenomatoid malformation was seen in 17/17 patients using postnatal CT, in 10/15 patients using prenatal MRI and in 17/18 patients using prenatal US. Correlation between imaging and diagnosis was as follows: bronchogenic cyst was seen in 3/5, 3/5 and 3/5 patients, pulmonary sequestration was seen in 7/9, 5/9 and 4/9 patients, and complex lesion was seen in 4/5, 3/6, and 2/6 patients using postnatal CT, prenatal MRI, and prenatal US,  respectively. Overall, 32/37 cases were diagnosed by means of postnatal CT, 21/36 cases were diagnosed by means of prenatal MRI and 26/39 cases were diagnosed by means of prenatal US.Conclusion: Discordance between imaging data and definitive diagnosis is not rare. Our results suggest that postnatal CT scan is the most sensible and specific examination. Before birth, US seems better compared with MRI for description of the lesion. MRI seems to be useful in case of complex lesions and pulmonary sequestration.Keywords: congenital lung malformation, imaging, prenata