Recommendations for the classification of germline variants in the exonuclease domain of POLE and POLD1

BackgroundGermline variants affecting the proofreading activity of polymerases epsilon and delta cause a hereditary cancer and adenomatous polyposis syndrome characterized by tumors with a high mutational burden and a specific mutational spectrum. In addition to the implementation of multiple pieces of evidence for the classification of gene variants, POLE and POLD1 variant classification is particularly challenging given that non-disruptive variants affecting the proofreading activity of the corresponding polymerase are the ones associated with cancer. In response to an evident need in the field, we have developed gene-specific variant classification recommendations, based on the ACMG/AMP (American College of Medical Genetics and Genomics/Association for Molecular Pathology) criteria, for the assessment of non-disruptive variants located in the sequence coding for the exonuclease domain of the polymerases.MethodsA training set of 23 variants considered pathogenic or benign was used to define the usability and strength of the ACMG/AMP criteria. Population frequencies, computational predictions, co-segregation data, phenotypic and tumor data, and functional results, among other features, were considered.ResultsGene-specific variant classification recommendations for non-disruptive variants located in the exonuclease domain of POLE and POLD1 were defined. The resulting recommendations were applied to 128 exonuclease domain variants reported in the literature and/or public databases. A total of 17 variants were classified as pathogenic or likely pathogenic, and 17 as benign or likely benign.ConclusionsOur recommendations, with room for improvement in the coming years as more information become available on carrier families, tumor molecular characteristics and functional assays, are intended to serve the clinical and scientific communities and help improve diagnostic performance, avoiding variant misclassifications

Experimental evidences for the use of two macroalgal species, Ascophyllum nodosum and Fucus vesiculosus as biomonitors of N sources

Proyecto ANILE (CTM2009-08396, CTM2010-08804-E) Plan Nacional de I+D+i y Proyecto RADIALES (IEO)Postprint2,263

The Tropical Seagrass Halophila stipulacea: Reviewing What We Know From Its Native and Invasive Habitats, Alongside Identifying Knowledge Gaps

Halophila stipulacea is a small tropical seagrass, native to the Red Sea, Persian Gulf, and the Indian Ocean. It invaded the Mediterranean Sea 150 years ago as a Lessepsian migrant, but so far has remained in insulated, small populations across this basin. Surprisingly, in 2002 it was reported in the Caribbean Sea, where within less than two decades it spread to most of the Caribbean Island nations and reaching the South American continent. Unlike its invasion of Mediterranean, in the Caribbean H. stipulacea creates large, continuous populations in many areas. Reports from the Caribbean demonstrated the invasiveness of H. stipulacea by showing that it displaces local Caribbean seagrass species. The motivation for this review comes from the necessity to unify the existing knowledge on several aspects of this species in its native and invasive habitats, identify knowledge gaps and develop a critical strategy to understand its invasive capacity and implement an effective monitoring and conservation plan to mitigate its potential spread outside its native ranges. We systematically reviewed 164 studies related to H. stipulacea to create the "Halophila stipulacea database." This allowed us to evaluate the current biological, ecological, physiological, biochemical, and molecular knowledge of H. stipulacea in its native and invasive ranges. Here we (i) discuss the possible environmental conditions and plant mechanisms involved in its invasiveness, (ii) assess the impact of H. stipulacea on native seagrasses and ecosystem functions in the invaded regions, (iii) predict the ability of this species to invade European and transoceanic coastal waters, (iv) identify knowledge gaps that should be addressed to better understand the biology and ecology of this species both in its native and non-native habitats, which would improve our ability to predict H. stipulacea's potential to expand into new areas in the future. Considering the predicted climate change scenarios and exponential human pressures on coastal areas, we stress the need for coordinated global monitoring and mapping efforts that will record changes in H. stipulacea and its associated communities over time, across its native, invasive and prospective distributional ranges. This will require the involvement of biologists, ecologists, economists, modelers, managers, and local stakeholder

Stable nitrogen isotopes in coastal macroalgae: geographic and anthropogenic variability

Proyectos ANILE (CTM2009-08396 and CTM2010-08804-E) del Plan Nacional de I+D+i y RADIALES del Instituto Español de Oceanografía (IEO). I.G.V. recibió un contrato FPI del Ministerio de Economía y CompetividadGrowing human population add to the natural nitrogen loads to coastal waters. As the excess nitrogen is readily incorporated in new biomass anthropogenic and natural nitrogen sources may be traced by the measurement of stable nitrogen isotopes (δ15N). In this study δ15N was determined in two species of macroalgae (Ascophyllum nodosum and Fucus vesiculosus), and in nitrate and ammonium to determine the relative importance of anthropogenic versus natural sources of nitrogen along the coast of NW Spain. Both algal species and nitrogen sources showed similar isotopic enrichment for a given site, but algal δ15N was not related to either inorganic nitrogen concentrations or δ15N in the water samples. The latter suggests that inorganic nitrogen inputs are variable and do not always leave an isotopic trace in macroalgae. However, a significant linear decrease in macroalgal δ15N along the coast is consistent with the differential effect of upwelling. Besides this geographic variability, the influence of anthropogenic nitrogen sources is evidenced by higher δ15N in macroalgae from rias and estuaries compared to those from open coastal areas and in areas with more than 15x103 inhabitants in the watershed. These results indicate that, in contrast with other studies, macroalgal δ15Nis not simply related to either inorganic nitrogen concentrations or human population size but depends on other factors as the upwelling or the efficiency of local waste treatment systems.Plan nacional I+D+i, IEOPreprint3,258

Participatory citizenship: critical perspectives on client-centred occupational therapy

Background/aims: This article aims to discuss client-centred practice, the current dominant approach within occupational therapy, in relation to participatory citizenship. Occupational therapists work within structures and policies that set boundaries on their engagement with clients, while working with complex, multidimensional social realities. Methods: The authors present a critical discussion shaped by their research, including a survey, discussions at workshops at international conferences, and critical engagement with the literature on occupational therapy, occupation, and citizenship. Conclusion: A focus on citizenship suggests reframing professional development based on the participation in public life of people as citizens of their society. While occupational therapists often refer to clients in the context of communities, groups, families, and wider society, the term client centred practice typically represents a particular view of the individual and may sometimes be too limited in application for a more systemic and societal approach. Significance: The authors question the individual focus which has, until recently, been typical of client-centred occupational therapy. Placing citizenship at the core of intervention is a transformative process that assumes all people are citizens and conceives of health as a collective issue, influencing the way we educate, do research, and practise. Key words: Collective, dis-citizenship, inequalities, professional development, participation, paradigms, occupational justice</p

International study to evaluate PCR methods for detection of Trypanosoma cruzi DNA in blood samples from Chagas disease patients

A century after its discovery, Chagas disease, caused by the parasite Trypanosoma cruzi, still represents a major neglected tropical threat. Accurate diagnostics tools as well as surrogate markers of parasitological response to treatment are research priorities in the field. The polymerase chain reaction (PCR) has been proposed as a sensitive laboratory tool for detection of T. cruzi infection and monitoring of parasitological treatment outcome. However, high variation in accuracy and lack of international quality controls has precluded reliable applications in the clinical practice and comparisons of data among cohorts and geographical regions. In an effort towards harmonization of PCR strategies, 26 expert laboratories from 16 countries evaluated their current PCR procedures against sets of control samples, composed by serial dilutions of T.cruzi DNA from culture stocks belonging to different lineages, human blood spiked with parasite cells and blood samples from Chagas disease patients. A high variability in sensitivities and specificities was found among the 48 reported PCR tests. Out of them, four tests with best performance were selected and further evaluated. This study represents a crucial first step towards device of a standardized operative procedure for T. cruzi PCR.Fil: Schijman, Alejandro G. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI-CONICET). Laboratorio de Biología Molecular de la Enfermedad de Chagas (LabMECh); Argentina.Fil: Bisio, Margarita. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI-CONICET). Laboratorio de Biología Molecular de la Enfermedad de Chagas (LabMECh); Argentina.Fil: Orellana, Liliana. Universidad de Buenos Aires. Instituto de Cálculo; Argentina.Fil: Sued, Mariela. Universidad de Buenos Aires. Instituto de Cálculo; Argentina.Fil: Duffy, Tomás. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI-CONICET). Laboratorio de Biología Molecular de la Enfermedad de Chagas (LabMECh); Argentina.Fil: Mejia Jaramillo, Ana M. Universidad de Antioquia. Grupo Chagas; Colombia.Fil: Cura, Carolina. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI-CONICET). Laboratorio de Biología Molecular de la Enfermedad de Chagas (LabMECh); Argentina.Fil: Auter, Frederic. French Blood Services; Francia.Fil: Veron, Vincent. Universidad de Parasitología. Laboratorio Hospitalario; Guayana Francesa.Fil: Qvarnstrom, Yvonne. Centers for Disease Control. Department of Parasitic Diseases; Estados Unidos.Fil: Deborggraeve, Stijn. Institute of Tropical Medicine; Bélgica.Fil: Hijar, Gisely. Instituto Nacional de Salud; Perú.Fil: Zulantay, Inés. Facultad de Medicina; Chile.Fil: Lucero, Raúl Horacio. Universidad Nacional del Nordeste; Argentina.Fil: Velázquez, Elsa. ANLIS Dr.C.G.Malbrán. Instituto Nacional de Parasitología Dr. Mario Fatala Chaben; Argentina.Fil: Tellez, Tatiana. Universidad Mayor de San Simon. Centro Universitario de Medicina Tropical; Bolivia.Fil: Sanchez Leon, Zunilda. Universidad Nacional de Asunción. Instituto de Investigaciones en Ciencias de la Salud; Paraguay.Fil: Galvão, Lucia. Faculdade de Farmácia; Brasil.Fil: Nolder, Debbie. Hospital for Tropical Diseases. London School of Tropical Medicine and Hygiene Department of Clinical Parasitology; Reino Unido.Fil: Monje Rumi, María. Universidad Nacional de Salta. Laboratorio de Patología Experimental; Argentina.Fil: Levi, José E. Hospital Sirio Libanês. Blood Bank; Brasil.Fil: Ramirez, Juan D. Universidad de los Andes. Centro de Investigaciones en Microbiología y Parasitología Tropical; Colombia.Fil: Zorrilla, Pilar. Instituto Pasteur; Uruguay.Fil: Flores, María. Instituto de Salud Carlos III. Centro de Mahahonda; España.Fil: Jercic, Maria I. Instituto Nacional De Salud. Sección Parasitología; Chile.Fil: Crisante, Gladys. Universidad de los Andes. Centro de Investigaciones Parasitológicas J.F. Torrealba; Venezuela.Fil: Añez, Néstor. Universidad de los Andes. Centro de Investigaciones Parasitológicas J.F. Torrealba; Venezuela.Fil: De Castro, Ana M. Universidade Federal de Goiás. Instituto de Patologia Tropical e Saúde Pública (IPTSP); Brasil.Fil: Gonzalez, Clara I. Universidad Industrial de Santander. Grupo de Inmunología y Epidemiología Molecular (GIEM); Colombia.Fil: Acosta Viana, Karla. Universidad Autónoma de Yucatán. Departamento de Biomedicina de Enfermedades Infecciosas y Parasitarias Laboratorio de Biología Celular; México.Fil: Yachelini, Pedro. Universidad Católica de Santiago del Estero. Instituto de Biomedicina; Argentina.Fil: Torrico, Faustino. Universidad Mayor de San Simon. Centro Universitario de Medicina Tropical; Bolivia.Fil: Robello, Carlos. Instituto Pasteur; Uruguay.Fil: Diosque, Patricio. Universidad Nacional de Salta. Laboratorio de Patología Experimental; Argentina.Fil: Triana Chavez, Omar. Universidad de Antioquia. Grupo Chagas; Colombia.Fil: Aznar, Christine. Universidad de Parasitología. Laboratorio Hospitalario; Guayana Francesa.Fil: Russomando, Graciela. Universidad Nacional de Asunción. Instituto de Investigaciones en Ciencias de la Salud; Paraguay.Fil: Büscher, Philippe. Institute of Tropical Medicine; Bélgica.Fil: Assal, Azzedine. French Blood Services; Francia.Fil: Guhl, Felipe. Universidad de los Andes. Centro de Investigaciones en Microbiología y Parasitología Tropical; Colombia.Fil: Sosa Estani, Sergio. ANLIS Dr.C.G.Malbrán. Centro Nacional de Diagnóstico e Investigación en Endemo-Epidemias; Argentina.Fil: DaSilva, Alexandre. Centers for Disease Control. Department of Parasitic Diseases; Estados Unidos.Fil: Britto, Constança. Instituto Oswaldo Cruz/FIOCRUZ. Laboratório de Biologia Molecular e Doenças Endêmicas; Brasil.Fil: Luquetti, Alejandro. Laboratório de Pesquisa de Doença de Chagas; Brasil.Fil: Ladzins, Janis. World Health Organization (WHO). Special Programme for Research and Training in Tropical Diseases (TDR); Suiza

International Study to Evaluate PCR Methods for Detection of Trypanosoma cruzi DNA in Blood Samples from Chagas Disease Patients

A century after its discovery, Chagas disease, caused by the parasite Trypanosoma cruzi, still represents a major neglected tropical threat. Accurate diagnostics tools as well as surrogate markers of parasitological response to treatment are research priorities in the field. The polymerase chain reaction (PCR) has been proposed as a sensitive laboratory tool for detection of T. cruzi infection and monitoring of parasitological treatment outcome. However, high variation in accuracy and lack of international quality controls has precluded reliable applications in the clinical practice and comparisons of data among cohorts and geographical regions. In an effort towards harmonization of PCR strategies, 26 expert laboratories from 16 countries evaluated their current PCR procedures against sets of control samples, composed by serial dilutions of T.cruzi DNA from culture stocks belonging to different lineages, human blood spiked with parasite cells and blood samples from Chagas disease patients. A high variability in sensitivities and specificities was found among the 48 reported PCR tests. Out of them, four tests with best performance were selected and further evaluated. This study represents a crucial first step towards device of a standardized operative procedure for T. cruzi PCR

Natural abundance of stable isotopes of macrophytes of NW Spain

The values of natural abundance of stable isotopes were measured in 22 species of macrophytes (18 macroalgae and 4 vascular plants) collected from the intertidal domain in NW Spain (NE Atlantic). This dataset contains the values of natural abundance of stable carbon and nitrogen isotopes in bulk samples and of nitrogen isotopes in amino acids