An Assessment of Different Genomic Approaches for Inferring Phylogeny of Listeria monocytogenes

Background/objectives: Whole genome sequencing (WGS) has proven to be a powerful subtyping tool for foodborne pathogenic bacteria like L. monocytogenes. The interests of genome-scale analysis for national surveillance, outbreak detection or source tracking has been largely documented. The genomic data however can be exploited with many different bioinformatics methods like single nucleotide polymorphism (SNP), core-genome multi locus sequence typing (cgMLST), whole-genome multi locus sequence typing (wgMLST) or multi locus predicted protein sequence typing (MLPPST) on either core-genome (cgMLPPST) or pan-genome (wgMLPPST). Currently, there are little comparisons studies of these different analytical approaches. Our objective was to assess and compare different genomic methods that can be implemented in order to cluster isolates of L. monocytogenes.Methods: The clustering methods were evaluated on a collection of 207 L. monocytogenes genomes of food origin representative of the genetic diversity of the Anses collection. The trees were then compared using robust statistical analyses.Results: The backward comparability between conventional typing methods and genomic methods revealed a near-perfect concordance. The importance of selecting a proper reference when calling SNPs was highlighted, although distances between strains remained identical. The analysis also revealed that the topology of the phylogenetic trees between wgMLST and cgMLST were remarkably similar. The comparison between SNP and cgMLST or SNP and wgMLST approaches showed that the topologies of phylogenic trees were statistically similar with an almost equivalent clustering.Conclusion: Our study revealed high concordance between wgMLST, cgMLST, and SNP approaches which are all suitable for typing of L. monocytogenes. The comparable clustering is an important observation considering that the two approaches have been variously implemented among reference laboratories

Current threats faced by amphibian populations in the southern cone of South America

In this work, we update and increase knowledge on the severity and extent of threats affecting 57 populations of 46 amphibian species from Chile and Argentina in southern South America. We analyzed the intrinsic conservation problems that directly impact these populations. We shared a questionnaire among specialists on threats affecting target amphibian populations with information on i) range, ii) historical occurrence and abundance, iii) population trends, iv) local extinctions, v) threats, and vi) ongoing and necessary conservation/research. We assessed association patterns between reported threats and population trends using multiple correspondence analysis. Since 2010, 25 of 57 populations have declined, while 16 experienced local extinctions. These populations were affected by 81% of the threat categories analyzed, with those related to agricultural activities and/or habitat modifications being the most frequently reported. Invasive species, emerging diseases, and activities related to grazing, ranching, or farming were the threats most associated with population declines. Low connectivity was the most frequent intrinsic conservation problem affecting 68% of the target populations, followed by low population numbers, affecting 60%. Ongoing monitoring activity was conducted in 32 (56%) populations and was the most frequent research activity. Threat mitigation was reported in 27 (47%) populations and was the most frequent ongoing management activity. We found that habitat management is ongoing in 5 (9%) populations. At least 44% of the amphibian populations surveyed in Chile and Argentina are declining. More information related to the effect of management actions to restore habitats, recover populations, and eliminate threats such as invasive species is urgently needed to reverse the conservation crisis facing amphibians in this Neotropical region.Fil: Kacoliris, Federico Pablo. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de La Plata. Facultad de Ciencias Naturales y Museo. División Zoología de Vertebrados. Sección Herpetología; ArgentinaFil: Berkunsky, Igor. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional del Centro de la Provincia de Buenos Aires. Facultad de Ciencias Exactas. Instituto Multidisciplinario de Ecosistemas y Desarrollo Sustentable; ArgentinaFil: Acosta, Juan Carlos. Universidad Nacional de San Juan. Facultad de Ciencias Exactas Físicas y Naturales. Departamento de Biología; ArgentinaFil: Acosta, Rodrigo. Universidad Nacional de San Juan. Facultad de Ciencias Exactas Físicas y Naturales. Departamento de Biología; ArgentinaFil: Agostini, Maria Gabriela. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Ecología, Genética y Evolución de Buenos Aires. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Ecología, Genética y Evolución de Buenos Aires; ArgentinaFil: Akmentins, Mauricio Sebastián. Universidad Nacional de Jujuy. Instituto de Ecorregiones Andinas. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Salta. Instituto de Ecorregiones Andinas; ArgentinaFil: Arellano, María Luz. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de La Plata. Facultad de Ciencias Naturales y Museo. División Zoología de Vertebrados. Sección Herpetología; ArgentinaFil: Azat, Claudio. Universidad Andrés Bello; ChileFil: Bach, Nadia Carla. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - San Luis. Instituto Multidisciplinario de Investigaciones Biológicas de San Luis. Universidad Nacional de San Luis. Facultad de Ciencias Físico Matemáticas y Naturales. Instituto Multidisciplinario de Investigaciones Biológicas de San Luis; ArgentinaFil: Blanco, Mirta Blanco. Universidad Nacional de San Juan. Facultad de Ciencias Exactas Físicas y Naturales. Departamento de Biología; ArgentinaFil: Calvo, Rodrigo. Universidad Nacional de La Plata. Facultad de Ciencias Naturales y Museo. División Zoología de Vertebrados. Sección Herpetología; ArgentinaFil: Charrier, Andres. Pontificia Universidad Católica de Chile; ChileFil: Corbalán, Valeria Elizabeth. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto Argentino de Investigaciones de las Zonas Áridas. Provincia de Mendoza. Instituto Argentino de Investigaciones de las Zonas Áridas. Universidad Nacional de Cuyo. Instituto Argentino de Investigaciones de las Zonas Áridas; ArgentinaFil: Correa, Claudio. Universidad de Concepción. Facultad de Ciencias Naturales y Oceanografía. Departamento de Zoología; ChileFil: Cuello, Maria Elena. Universidad Nacional del Comahue. Centro Regional Universitario Bariloche; ArgentinaFil: Deutsch, Camila. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Ecología, Genética y Evolución de Buenos Aires. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Ecología, Genética y Evolución de Buenos Aires; ArgentinaFil: Di Pietro, Diego Omar. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de La Plata. Facultad de Ciencias Naturales y Museo. División Zoología de Vertebrados. Sección Herpetología; ArgentinaFil: Gastón, María Soledad. Universidad Nacional de Jujuy. Instituto de Ecorregiones Andinas. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Salta. Instituto de Ecorregiones Andinas; ArgentinaFil: Gomez Alez, Rodrigo. Universidad Nacional de San Juan. Facultad de Ciencias Exactas Físicas y Naturales. Departamento de Biología; ArgentinaFil: Kaas, Camila. Universidad Nacional de La Plata. Facultad de Ciencias Naturales y Museo. División Zoología de Vertebrados. Sección Herpetología; ArgentinaFil: Kaas, Nicolas. Universidad Nacional de La Plata. Facultad de Ciencias Naturales y Museo. División Zoología de Vertebrados. Sección Herpetología; ArgentinaFil: Lobos, Gabriel. Universidad de Chile; ChileFil: Martínez, Tomás Agustín. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - San Juan; Argentina. Universidad Nacional de San Juan. Facultad de Ciencias Exactas Físicas y Naturales. Departamento de Biología; ArgentinaFil: Martínez Aguirre, Tomás. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de La Plata. Facultad de Ciencias Naturales y Museo. División Zoología de Vertebrados. Sección Herpetología; ArgentinaFil: Mora, Marta. Vida Nativa NGO; ChileFil: Nieva Cocilio, Rodrigo Alfredo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - San Juan; Argentina. Universidad Nacional de San Juan. Facultad de Ciencias Exactas Físicas y Naturales. Departamento de Biología; ArgentinaFil: Pastore, Hernán. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Administración de Parques Nacionales; ArgentinaFil: Pérez Iglesias, Juan Manuel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - San Luis. Instituto de Química de San Luis. Universidad Nacional de San Luis. Facultad de Química, Bioquímica y Farmacia. Instituto de Química de San Luis; Argentina. Universidad Nacional de San Luis. Facultad de Química, Bioquímica y Farmacia. Laboratorio de Biología; ArgentinaFil: Piaggio Kokot, Lia Elena. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - San Juan; Argentina. Universidad Nacional de San Juan. Facultad de Ciencias Exactas Físicas y Naturales. Departamento de Biología; ArgentinaFil: Rabanal, Felipe. Universidad Austral de Chile; ChileFil: Rodríguez Muñoz, Melina Jesús. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - San Juan; Argentina. Universidad Nacional de San Juan. Facultad de Ciencias Exactas Físicas y Naturales. Departamento de Biología; ArgentinaFil: Sanchez, Laura Cecilia. Provincia de Entre Ríos. Centro de Investigaciones Científicas y Transferencia de Tecnología a la Producción. Universidad Autónoma de Entre Ríos. Centro de Investigaciones Científicas y Transferencia de Tecnología a la Producción. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Centro de Investigaciones Científicas y Transferencia de Tecnología a la Producción; ArgentinaFil: Tala, Charif. Ministerio del Medio Ambiente de Chile; ChileFil: Ubeda, Carmen Adria. Universidad Nacional del Comahue. Centro Regional Universitario Bariloche; ArgentinaFil: Vaira, Marcos. Universidad Nacional de Jujuy. Instituto de Ecorregiones Andinas. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Salta. Instituto de Ecorregiones Andinas; ArgentinaFil: Velasco, Melina Alicia. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de La Plata. Facultad de Ciencias Naturales y Museo. División Zoología de Vertebrados. Sección Herpetología; ArgentinaFil: Vidal, Marcela. Universidad del Bio Bio. Facultad de Ciencias. Departamento de Ciencias Basicas; ChileFil: Williams, Jorge Daniel. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de La Plata. Facultad de Ciencias Naturales y Museo. División Zoología de Vertebrados. Sección Herpetología; Argentin

Creating a specialist protein resource network:a meeting report for the protein bioinformatics and community resources retreat

During 11–12 August 2014, a Protein Bioinformatics and Community Resources Retreat was held at the Wellcome Trust Genome Campus in Hinxton, UK. This meeting brought together the principal investigators of several specialized protein resources (such as CAZy, TCDB and MEROPS) as well as those from protein databases from the large Bioinformatics centres (including UniProt and RefSeq). The retreat was divided into five sessions: (1) key challenges, (2) the databases represented, (3) best practices for maintenance and curation, (4) information flow to and from large data centers and (5) communication and funding. An important outcome of this meeting was the creation of a Specialist Protein Resource Network that we believe will improve coordination of the activities of its member resources. We invite further protein database resources to join the network and continue the dialogue

Microwave-assisted extraction of phycobiliproteins from Porphyridium purpureum

In the present study, microwave-assisted extraction was first employed to extract the phycobiliproteins of Porphyridium purpureum (Pp). Freeze-dried Pp cells were subjected to microwave-assisted extraction (MAE) to extract phycoerythin (PE), phycocyanin (PC), and allophycocyanin (APC). MAE combined reproducibility and high extraction yields and allowed a 180- to 1,080-fold reduction of the extraction time compared to a conventional soaking process. The maximal PE extraction yield was obtained after 10-s MAE at 40 A degrees C, and PE was thermally damaged at temperatures higher than 40 A degrees C. In contrast, a flash irradiation for 10 s at 100 A degrees C was the best process to efficiently extract PC and APC, as it combined a high temperature necessary to extract them from the thylakoid membrane to a short exposure to thermal denaturation. The extraction order of the three phycobiliproteins was coherent with the structure of Pp phycobilisomes. Moreover, the absorption and fluorescence properties of MAE extracted phycobiliproteins were stable for several months after the microwave treatment. Scanning electron microscopy indicated that MAE at 100 A degrees C induced major changes in the Pp cell morphology, including fusion of the exopolysaccharidic cell walls and cytoplasmic membranes of adjacent cells. As a conclusion, MAE is a fast and high yield process efficient to extract and pre-purify phycobiliproteins, even from microalgae containing a thick exopolysaccharidic cell wall

Antiproliferative Activity of Cyanophora paradoxa Pigments in Melanoma, Breast and Lung Cancer Cells

The glaucophyte Cyanophora paradoxa (Cp) was chemically investigated to identify pigments efficiently inhibiting malignant melanoma, mammary carcinoma and lung adenocarcinoma cells growth. Cp water and ethanol extracts significantly inhibited the growth of the three cancer cell lines in vitro, at 100 mu g.mL(-1). Flash chromatography of the Cp ethanol extract, devoid of c-phycocyanin and allophycocyanin, enabled the collection of eight fractions, four of which strongly inhibited cancer cells growth at 100 mu g.mL(-1). Particularly, two fractions inhibited more than 90% of the melanoma cells growth, one inducing apoptosis in the three cancer cells lines. The detailed analysis of Cp pigment composition resulted in the discrimination of 17 molecules, ten of which were unequivocally identified by high resolution mass spectrometry. Pheophorbide a, beta-cryptoxanthin and zeaxanthin were the three main pigments or derivatives responsible for the strong cytotoxicity of Cp fractions in cancer cells. These data point to Cyanophora paradoxa as a new microalgal source to purify potent anticancer pigments, and demonstrate for the first time the strong antiproliferative activity of zeaxanthin and beta-cryptoxanthin in melanoma cells