Metagenomic analysis of historical herbarium specimens reveals a postmortem microbial community

Advances in DNA extraction and next-generation sequencing have made a vast number of historical herbarium specimens available for genomic investigation. These specimens contain not only genomic information from the individual plants themselves, but also from associated microorganisms such as bacteria and fungi. These microorganisms may have colonized the living plant (e.g., pathogens or host-associated commensal taxa) or may result from postmortem colonization that may include decomposition processes or contamination during sample handling. Here we characterize the metagenomic profile from shotgun sequencing data from herbarium specimens of two widespread plant species (Ambrosia artemisiifolia and Arabidopsis thaliana) collected up to 180 years ago. We used blast searching in combination with megan and were able to infer the metagenomic community even from the oldest herbarium sample. Through comparison with contemporary plant collections, we identify three microbial species that are nearly exclusive to herbarium specimens, including the fungus Alternaria alternata, which can comprise up to 7% of the total sequencing reads. This species probably colonizes the herbarium specimens during preparation for mounting or during storage. By removing the probable contaminating taxa, we observe a temporal shift in the metagenomic composition of the invasive weed Am. artemisiifolia. Our findings demonstrate that it is generally possible to use herbarium specimens for metagenomic analyses, but that the results should be treated with caution, as some of the identified species may be herbarium contaminants rather than representing the natural metagenomic community of the host plant

Historic sampling of a vanishing beast: Population structure and diversity in the Black Rhinoceros

The black rhinoceros (Diceros bicornis L.) is a critically endangered species historically distributed across sub-Saharan Africa. Hunting and habitat disturbance have diminished both its numbers and distribution since the 19th century, but a poaching crisis in the late 20th century drove them to the brink of extinction. Genetic and genomic assessments can greatly increase our knowledge of the species and inform management strategies. However, when a species has been severely reduced, with the extirpation and artificial admixture of several populations, it is extremely challenging to obtain an accurate understanding of historic population structure and evolutionary history from extant samples. Therefore, we generated and analyzed whole genomes from 63 black rhinoceros museum specimens collected between 1775 and 1981. Results showed that the black rhinoceros could be genetically structured into six major historic populations (Central Africa, East Africa, Northwestern Africa, Northeastern Africa, Ruvuma, and Southern Africa) within which were nested four further subpopulations (Maasailand, southwestern, eastern rift, and northern rift), largely mirroring geography, with a punctuated north–south cline. However, we detected varying degrees of admixture among groups and found that several geographical barriers, most prominently the Zambezi River, drove population discontinuities. Genomic diversity was high in the middle of the range and decayed toward the periphery. This comprehensive historic portrait also allowed us to ascertain the ancestry of 20 resequenced genomes from extant populations. Lastly, using insights gained from this unique temporal data set, we suggest management strategies, some of which require urgent implementation, for the conservation of the remaining black rhinoceros diversity

I Congresso Ibero-Americano de Bibliotecas Escolares

Actas de la primera edición del I Congreso Iberoamericano de Bibliotecas Escolares, CIBES 2015, organizado por la Universidad Carlos III de Madrid (España), la Universidad Estatal Paulista (Brasil) y el Ayuntamiento de Getafe (España). Celebrado: 21 - 23 de octubre de 2015 en la Universidad Estatal Paulista (Marília) y 26 - 28 de octubre de 2015 en la Universidad Carlos III de Madrid (Getafe)Universidad Carlos III de Madrid (España)Universidad Estatal Paulista (Brasil)Ayuntamiento de Getafe (España)Dimensiones y visiones de la biblioteca escolar en una Educación por competencias: la necesidad de una política estratégica / Miguel Ángel Marzal. -- Getafe ciudad educadora, lectora y escritora: Bibliotecas escolares / Lourdes Muñoz Santiuste. -- Presente y futuro: biblioteca escolar-CREA y proyectos interdisciplinares / Rosa Piquín. -- Cultura en información: un reto esencial de la biblioteca escolar / Mónica Baró. -- Bibliotecas escolares de Galicia: un mundo de oportunidades a favor de la Educación / Cristina Novoa. -- 10 años de la Red de Bibliotecas Escolares de Extremadura (REBEX) / Casildo Macías Pereira. -- Biblioteca Escolar y uso ético de la información para una Cultura de Paz / Ana Barrero Tíscar. -- Dinamización de la Biblioteca Escolar Plumita durante el curso escolar 2014/15 / María Antonia Cano Cañada. -- Experiencia de la creación de una biblioteca escolar / Susana Santos Martín. -- Grupo cooperativo Bibliotecas escolares en Red-Albacete / José Manuel Garrido Argandoña y Eva Leal Scasso. -- La BCREA "Juan Leiva". El fomento de la lectura desde la web social / Andrés Pulido Villar. -- Proceso de implantación de una herramienta de autoevaluación en la red de bibliotecas escolares de Extremadura (REBEX) / Casildo Macías Pereira. -- La biblioteca escolar: abriendo fronteras / Lorena Verónica Cabrera Orellana. -- O programa RBE e a avaliaçao das bibliotecas escolares: melhoria, desenvolvimiento e innovaçao / Elsa Conde. -- Profesional de Biblioteconomía y Documentación: esencial en la plantilla de la escuela / Pilar del Campo Puerta. -- Una mirada activa al proceso educativo desde la biblioteca escolar / María Jesús Fontela Fernández . -- Con otra mirada "La ilustración como vehículo de comunicación y aprendizaje en las bibliotecas escolares" / Pablo Jurado Sánchez-Galán. -- Fingertips. Recriar a biblioteca escolar na sala de aula / Rui Alfonso Mateus. -- Hablemos de libros. Cómo transformar una clase de literatura en una comunidad de interpretación de textos / Francisco César Díaz Rey. -- Inclusión social de familias inmigrantes a través de un programa de aprendizaje de la lengua castellana / Ana Carmen Tolino Fernández-Henarejos. -- O desenvolvimento de atividades de mediação de leitura em biblioteca escolar: o caso da biblioteca da Escola Sesc de Ensino Médio / Vagner Amaro. -- La biblioteca escolar. Proceso de enseñanza-aprendizaje de padres a hijos / Ana Carmen Tolino Fernández- Henarejos. -- Leo con y para los demás / Ismael Fernández Fernández, Ana María Moreno Vicente y Ana Beatriz Vicente Pérez. -- Nanas y arrullo. Poesía a la deriva / Bernardo Fuentes Navarrete y Carlos García-Romeral Pérez. -- Gestión y evaluación de servicios bibliotecarios para personas con dislexia: una biblioteca escolar inclusiva desde una perspectiva internacional / Carmen Jorge García-Reyes. -- Sueños lectores compartidos hechos realidad: la biblioteca escolar del C.E.I.P-S.E.S-A.A “LA PAZ” de Albacete / Ana Rosa Cabañero Tobarra, Juan Manuel Herráez, Eva Leal Scasso, María Marín Sánchez, Ana Belén Medrano Martínez y María José Nortes Ruipérez. -- El programa biblioteca escuela en Civican. La literatura como elemento motivador para la alfabetización informacional / Villar Arellano Yanguas. -- La competencia digital en el diseño curricular: desde la biblioteca al aula / Felicidad Campal García. -- O deselvomimento da pesquisa escolar por meio da competência em informaçao / Luciane de Fátima Cavalcante Beckman y Marta Leandro da Mata. -- Proyecto escolar de investigación documental "Te pillé leyendo" / José Manuel Garrido Argandoña. -- Aprender com a Biblioteca Escolar: formar para as literacias / Paula Correia y Isabel Mendinhos. -- Sucedió en el siglo XX / María Antonia Becerra Montalbán, Ángel Bernabé Muñoz y Sofía Vaz Romero. -- El Club de lectura en la nube / Belén Benito Blázquez y Ana Ordás García. -- Promover a leitura e a escrita na era digital: prácticas nas bibliotecas escolares / María Raquel Ramos. -- A biblioteca escolar e o desafío da interculturalidade: o projeto Ser + cidadao / María da Conceição Tomé. -- Cuando la competencia digital encontró a la alfabetización informacional o Mucho ruido y pocas nueces / Felicidad Campal García. -- Hora de ler, un programa para el fomento de la lectura en contexto educativo / Cristina Novoa. -- Hábitos de lectura para las competencias en información y alfabetización en información en bibliotecas escolares de Puerto Rico / Karen Denise Centeno Casillas. -- Repositorios digitales en las bibliotecas escolares andaluzas: situación, modelos y herramientas para su creación / Dolores Olmos Olmos y Andrés Pulido Villar. -- Trabajando las competencias clave con las aventuras de Mozarito en Extremadura / María Teresa Carballosa González y María Esther Nieto Vidal. -- Análisis de modelos de evaluación de la web de la biblioteca escolar / Raúl Cremades García. -- Emociónate con las historias: El bosque de las emociones e historias con mucho teatro / Esther Luis Pérez y Ana María Peromingo Fernández. -- Biblioteca escolar de innovación y continuación / E. María Guerrero Palacios y Silvia Mora Ramírez. -- Uso de estándares y licencias para la creación y difusión de contenidos en las bibliotecas escolares / José Luis Barreiro Cebey. -- La biblioteca escolar digital móvil / Javier Fernández Delgado. -- Uso de aplicaciones móviles para el desarrollo de la competencia lingüística. Proyecto Hansel App Gretel / Dolores Olmos Olmos. -- A memória e a mediação segundo Vigotski / Leda Maria Araújo, Patricia Celia Santana, Sueli Bortolin y Leticia Gorri Molina. -- Bibliotecas escolares como tema de estudo dos alunos de graduação em blioteconomia do Instituto de Ensino Superior da FUNLEC: estado da arte / Tiago Pereira Nocera y Rodrigo Pereira. -- Ações de mediação da leitura e da informação em bibliotecas escolares: um olhar sobre as bibliotecas dos Colégios de Aplicação / Tatyanne Christina Gonçalves Ferreira Valdez y Alberto Calil Júnior. -- Mediação pedagógica numa biblioteca de escola pública em Londrina / Rovilson José da Silva, Teba Silva Yllana y Sueli Bortolin. -- Utilização de categorias por cores em sistema de biblioteca voltado ao público infanto-juvenil / Liliana Giusti Serra. -- Atividades de ensino dos atos de leitura com crianças em risco social / Adriana Naomi Fukushima da Silva y Dagoberto Buim Arena. -- Biblioteca escolar: espaço de significados entre alunos, professores e bibliotecários / Rodrigo Barbosa Paulo, Marisa Xavier, Helen Castro Casarin y Creuza Barbaroto. -- A Biblioteca Escolar no Contexto da Legislação e do Processo Educativo / Eliane Lourdes da Silva Moro, Francisca Rosaline Leite Mota y Raimundo Martins de Lima. -- O jornal impresso como fonte de informação: a importância da formação de leitores críticos / Mariana Pícaro Cerigatto. -- Bibliotecas escolares no estado do Rio Grande do Sul: a trajetória de realização dos fóruns gaúchos pela melhoria das bibliotecas escolares / Eliane Lourdes da Silva Moro y Lizandra Brasil Estabel. -- O acesso à informação dos usuários surdos na biblioteca escolar / André Luís Onório Coneglian y Mayara Melo Santana. -- Aprendizagem coletiva de bibliotecários e a competência de pesquisa dos docentes: o caso do Instituto Federal do Espírito Santo / Maristela Almeida Mercandeli Rodrigues y Beatriz Quiroz Villardi. -- Biblioteca escolar: atores, parâmetros e competências / Mavi Galante Mancera Dall´Acqua Carvalho y Claudio Marcondes de Castro Filho. -- Estratégias de aprendizagem de escrita no Ensino Fundamental II / Érika Christina Kohle. -- Bebês e livros: leitura nas bebetecas. Kenia Adriana de Aquino Modesto Silva, Juliane Francischeti Martins Motoyama y Renata Junqueira de Souza. -- Práticas alternativas para organização de acervos nos espaços de leitura em ambientes escolares / Luciana Souza Gracioso, Ariovaldo Alves, Débora Nascimento, Suelen Redondo, Tainara Torika Kiri de Castro, Elizabete Angelon y Eduardo Barbosa. -- Reflexões sobre a modelagem e criação de uma Rede Virtual de Leitores para Bibliotecas Escolares / Carla Floriana Martins y Raoni Guerra Rajão. -- Biblioteca escolar: espaço de formação leitora? / Silvana Ferreira de Souza Balsan y Renata Junqueira de Souza. -- “Se a Biblioteca Escolar é minha mãe, o Google é meu pai”: representações da relação entre Biblioteca Escolar e Google no imaginário de alunos do ensino técnico / Adriana Bogliolo Sirihal-Duarte, Maria L. Amorim Antunes y Raquel Miranda Vilela Paiva. -- Desafios e propostas para a universalização das bibliotecas escolares no Brasil e na Espanha / Rodrigo Pereira, Daniela Spudeit y Fernanda de Sales. -- Bibliotecário educador: possibilidades de atuação no contexto da biblioteca escolar / André Carlos da Silva, Valéria Martin Valls y Mariana de Paula Silva. -- Uma ONG para Bibliotecas Escolares : estratégia para ampliar a igualdade e capacidade de acesso e uso da informação e educação escolar de qualidade / Suelen Camilo Ferreira y Luciana de Souza Gracioso. -- O aluno com deficência: o papel do bibliotecário na disponibilidade de recursos acessíveis na biblioteca escolar / Adriano de Sales Coelho, Rosilene de Melo Oliveira y Marcos Pastana Santos. -- Biblioteca digital virtual e o uso do tablete: uma possibilidade de construção de novas práticas de leitura na escola / Barbara Cibelli da Silva Monteagudo y Dagoberto Buim Arena. -- A importância da biblioteca na educação de crianças de 0 a 3 anos / Yngrid Karolline Mendonça Costa y Cyntia Graziella Guizelim Simões Girotto. -- Comportamento Informacional de adolescentes: a relação com bibliotecas e escolas / Nelson Sebastian Silva-Jerez y Helen de Castro S. Casarin

Genomic investigations of unexplained acute hepatitis in children

Since its first identification in Scotland, over 1,000 cases of unexplained paediatric hepatitis in children have been reported worldwide, including 278 cases in the UK1. Here we report an investigation of 38 cases, 66 age-matched immunocompetent controls and 21 immunocompromised comparator participants, using a combination of genomic, transcriptomic, proteomic and immunohistochemical methods. We detected high levels of adeno-associated virus 2 (AAV2) DNA in the liver, blood, plasma or stool from 27 of 28 cases. We found low levels of adenovirus (HAdV) and human herpesvirus 6B (HHV-6B) in 23 of 31 and 16 of 23, respectively, of the cases tested. By contrast, AAV2 was infrequently detected and at low titre in the blood or the liver from control children with HAdV, even when profoundly immunosuppressed. AAV2, HAdV and HHV-6 phylogeny excluded the emergence of novel strains in cases. Histological analyses of explanted livers showed enrichment for T cells and B lineage cells. Proteomic comparison of liver tissue from cases and healthy controls identified increased expression of HLA class 2, immunoglobulin variable regions and complement proteins. HAdV and AAV2 proteins were not detected in the livers. Instead, we identified AAV2 DNA complexes reflecting both HAdV-mediated and HHV-6B-mediated replication. We hypothesize that high levels of abnormal AAV2 replication products aided by HAdV and, in severe cases, HHV-6B may have triggered immune-mediated hepatic disease in genetically and immunologically predisposed children

Predicting sample success for large-scale ancient DNA studies on marine mammals

In recent years, non-human ancient DNA studies have begun to focus on larger sample sizes and whole genomes, offering the potential to reveal exciting and hitherto unknown answers to ongoing biological and archaeological questions. However, one major limitation to the feasibility of such studies is the substantial financial and time investments still required during sample screening, due to uncertainty regarding successful sample selection. This study investigates the effect of a wide range of sample properties including latitude, sample age, skeletal element, collagen preservation, and context on endogenous content and DNA damage profiles for 317 ancient and historic pinnipedsamples collected from across the North Atlantic. Using generalised linear and mixed-effectmodels, we found that a range of factors affected DNA preservation within each of the species under consideration. The most important findings were that endogenous content varied significantly according to context, the type of skeletal element, the collagen content and collection year. There also appears to be an effect of the sample’s geographic origin, with samples from the Arcticgenerally showing higher endogenous content and lower damage rates. Both latitude and sample age were found to have significant relationships with damage levels, but only for walrus samples. Sex, ontogenetic age and extraction material preparation were not found to have any significantrelationship with DNA preservation. Overall, the skeletal element and sample context were found to be the most influential factors and should therefore be considered when selecting samples for large-scale ancient genome studies

Obestatin signalling counteracts glucocorticoid‐induced skeletal muscle atrophy via NEDD4/KLF15 axis

International audienceBackground: A therapeutic approach for the treatment of glucocorticoid‐induced skeletal muscle atrophy should be based on the knowledge of the molecular mechanisms determining the unbalance between anabolic and catabolic processes and how to re‐establish this balance. Here, we investigated whether the obestatin/GPR39 system, an autocrine signalling system acting on myogenesis and with anabolic effects on the skeletal muscle, could protect against chronic glucocorticoid‐induced muscle atrophy.Methods: In this study, we used an in vivo model of muscle atrophy induced by the synthetic glucocorticoid dexamethasone to examine the liaison molecules that define the interaction between the glucocorticoid receptor and the obestatin/GPR39 systems. The findings were extended to in vitro effects on human atrophy using human KM155C25 myotubes.Results: KLF15 and FoxO transcription factors were identified as direct targets of obestatin signalling in the control of proteostasis in skeletal muscle. The KLF15‐triggered gene expression program, including atrogenes and FoxOs, was regulated via KLF15 ubiquitination by the E3 ubiquitin ligase NEDD4. Additionally, a specific pattern of FoxO post‐translational modification, including FoxO4 phosphorylation by Akt pathway, was critical in the regulation of the ubiquitin–proteasome system. The functional cooperativity between Akt and NEDD4 in the regulation of FoxO and KLF15 provides integrated cues to counteract muscle proteostasis and re‐establish protein synthesis.Conclusions: The effective control of FoxO activity in response to glucocorticoid is critical to counteract muscle‐related pathologies. These results highlight the potential of the obestatin/GPR39 system to fine‐tune the effects of glucocorticoids on skeletal muscle wasting

Historical population declines prompted significant genomic erosion in the northern and southern white rhinoceros (Ceratotherium simum)

Large vertebrates are extremely sensitive to anthropogenic pressure, and their populations are declining fast. The white rhinoceros (Ceratotherium simum) is a paradigmatic case: this African megaherbivore has suffered a remarkable decline in the last 150 years due to human activities. Its subspecies, the northern (NWR) and the southern white rhinoceros (SWR), however, underwent opposite fates: the NWR vanished quickly, while the SWR recovered after the severe decline. Such demographic events are predicted to have an erosive effect at the genomic level, linked to the extirpation of diversity, and increased genetic drift and inbreeding. However, there is little empirical data available to directly reconstruct the subtleties of such processes in light of distinct demographic histories. Therefore, we generated a whole-genome, temporal data set consisting of 52 resequenced white rhinoceros genomes, representing both subspecies at two time windows: before and during/after the bottleneck. Our data reveal previously unknown population structure within both subspecies, as well as quantifiable genomic erosion. Genome-wide heterozygosity decreased significantly by 10% in the NWR and 36% in the SWR, and inbreeding coefficients rose significantly by 11% and 39%, respectively. Despite the remarkable loss of genomic diversity and recent inbreeding it suffered, the only surviving subspecies, the SWR, does not show a significant accumulation of genetic load compared to its historical counterpart. Our data provide empirical support for predictions about the genomic consequences of shrinking populations, and our findings have the potential to inform the conservation efforts of the remaining white rhinoceroses

Historical population declines prompted significant genomic erosion in the northern and southern white rhinoceros (Ceratotherium simum)

Large vertebrates are extremely sensitive to anthropogenic pressure, and their populations are declining fast. The white rhinoceros (Ceratotherium simum) is a paradigmatic case: this African megaherbivore has suffered a remarkable decline in the last 150 years due to human activities. Its subspecies, the northern (NWR) and the southern white rhinoceros (SWR), however, underwent opposite fates: the NWR vanished quickly, while the SWR recovered after the severe decline. Such demographic events are predicted to have an erosive effect at the genomic level, linked to the extirpation of diversity, and increased genetic drift and inbreeding. However, there is little empirical data available to directly reconstruct the subtleties of such processes in light of distinct demographic histories. Therefore, we generated a whole-genome, temporal data set consisting of 52 resequenced white rhinoceros genomes, representing both subspecies at two time windows: before and during/after the bottleneck. Our data reveal previously unknown population structure within both subspecies, as well as quantifiable genomic erosion. Genome-wide heterozygosity decreased significantly by 10% in the NWR and 36% in the SWR, and inbreeding coefficients rose significantly by 11% and 39%, respectively. Despite the remarkable loss of genomic diversity and recent inbreeding it suffered, the only surviving subspecies, the SWR, does not show a significant accumulation of genetic load compared to its historical counterpart. Our data provide empirical support for predictions about the genomic consequences of shrinking populations, and our findings have the potential to inform the conservation efforts of the remaining white rhinoceroses.This work was supported by ERC Consolidator Grant 681396 “Extinction Genomics” to M.T.P.G. and by EMBO Short-Term Fellowship 7578 to F.S.B. The authors would like to acknowledge support from Science for Life Laboratory, the National Genomics Infrastructure (NGI), Sweden, the Knut and Alice Wallenberg Foundation and UPPMAX for providing assistance in massively parallel DNA sequencing and computational infrastructure. The authors are very grateful to all the museums who provided samples for this study: the American Museum of Natural History, the National Museums Scotland, the Natural History Museum at the National Museum Praha, the Natural History Museum Vienna, the Powell-Cotton Museum, the Royal Museum for Central Africa Tervuren, and the Swedish Museum of Natural History

Ancient and modern genomes unravel the evolutionary history of the rhinoceros family

Only five species of the once-diverse Rhinocerotidae remain, making the reconstruction of their evolutionary history a challenge to biologists since Darwin. We sequenced genomes from five rhinoceros species (three extinct and two living), which we compared to existing data from the remaining three living species and a range of outgroups. We identify an early divergence between extant African and Eurasian lineages, resolving a key debate regarding the phylogeny of extant rhinoceroses. This early Miocene (∼16 million years ago [mya]) split post-dates the land bridge formation between the Afro-Arabian and Eurasian landmasses. Our analyses also show that while rhinoceros genomes in general exhibit low levels of genome-wide diversity, heterozygosity is lowest and inbreeding is highest in the modern species. These results suggest that while low genetic diversity is a long-term feature of the family, it has been particularly exacerbated recently, likely reflecting recent anthropogenic-driven population declines.We thank the Natural History Museum at the University of Oslo for providing the Javan rhinoceros sample. We thank the Museum of the Institute of Plant and Animal Ecology (UB RAS, Ekaterinburg) for providing the sample of Siberian unicorn. M.T.P.G. was supported by European Research Council (ERC) Consolidator grant 681396 (Extinction Genomics). E.D.L. was supported by Independent Research Fund Denmark grant 8021-00218B . A.C. was supported by an Australian Research Council Laureate Fellowship ( FL140100260 ). T.M.B. is supported by funding from the ERC under the European Union’s Horizon 2020 research and innovation program (grant agreement 864203 ), grant BFU2017-86471-P ( MINECO /FEDER, UE), “Unidad de Excelencia María de Maeztu” funded by the AEI ( CEX2018-000792-M ), Howard Hughes International Early Career , and Secretaria d’Universitats i Recerca and CERCA Programme del Departament d’Economia i Coneixement de la Generalitat de Catalunya ( GRC 2017 SGR 880 ). L.D. was supported by the Swedish Research Council ( 2017-04647 ) and Formas ( 2018-01640 ). We thank Dmitry Bogdanov and Roger Hall for giving us permission to use their rhinoceros artwork