Organelle_PBA, a Pipeline for Assembling Chloroplast and Mitochondrial Genomes from PacBio DNA Sequencing Data

Background: The development of long-read sequencing technologies, such as single-molecule real-time (SMRT) sequencing by PacBio, has produced a revolution in the sequencing of small genomes. Sequencing organelle genomes using PacBio long-read data is a cost effective, straightforward approach. Nevertheless, the availability of simple-to-use software to perform the assembly from raw reads is limited at present. Results: We present Organelle-PBA, a Perl program designed specifically for the assembly of chloroplast and mitochondrial genomes. For chloroplast genomes, the program selects the chloroplast reads from a whole genome sequencing pool, maps the reads to a reference sequence from a closely related species, and then performs read correction and de novo assembly using Sprai. Organelle-PBA completes the assembly process with the additional step of scaffolding by SSPACE-LongRead. The program then detects the chloroplast inverted repeats and reassembles and re-orients the assembly based on the organelle origin of the reference. We have evaluated the performance of the software using PacBio reads from different species, read coverage, and reference genomes. Finally, we present the assembly of two novel chloroplast genomes from the species Picea glauca (Pinaceae) and Sinningia speciosa (Gesneriaceae). Conclusion: Organelle-PBA is an easy-to-use Perl-based software pipeline that was written specifically to assemble mitochondrial and chloroplast genomes from whole genome PacBio reads. The program is available at https://github.com/aubombarely/Organelle_PBA

Organelle_PBA, a Pipeline for Assembling Chloroplast and Mitochondrial Genomes from PacBio DNA Sequencing Data

Background: The development of long-read sequencing technologies, such as single-molecule real-time (SMRT) sequencing by PacBio, has produced a revolution in the sequencing of small genomes. Sequencing organelle genomes using PacBio long-read data is a cost effective, straightforward approach. Nevertheless, the availability of simple-to-use software to perform the assembly from raw reads is limited at present. Results: We present Organelle-PBA, a Perl program designed specifically for the assembly of chloroplast and mitochondrial genomes. For chloroplast genomes, the program selects the chloroplast reads from a whole genome sequencing pool, maps the reads to a reference sequence from a closely related species, and then performs read correction and de novo assembly using Sprai. Organelle-PBA completes the assembly process with the additional step of scaffolding by SSPACE-LongRead. The program then detects the chloroplast inverted repeats and reassembles and re-orients the assembly based on the organelle origin of the reference. We have evaluated the performance of the software using PacBio reads from different species, read coverage, and reference genomes. Finally, we present the assembly of two novel chloroplast genomes from the species Picea glauca (Pinaceae) and Sinningia speciosa (Gesneriaceae). Conclusion: Organelle-PBA is an easy-to-use Perl-based software pipeline that was written specifically to assemble mitochondrial and chloroplast genomes from whole genome PacBio reads. The program is available at https://github.com/aubombarely/Organelle_PBA

Estado, ciudadanía y grupos sociales en la sociedad rural andina : estudio de caso en la provincia de Quispicanchi-Cusco.

La tesis: “Estado, ciudadanía y grupos sociales en la sociedad rural andina” pretende, a partir de un estudio de caso en la provincia de Quispicanchi - Cusco, ser un acercamiento al estudio del funcionamiento del Estado en la sociedad rural peruana y la interacción de los diferentes grupos sociales a su interior. A partir del análisis de las instituciones estatales presentes a nivel provincial, en especial la subprefectura, gobernaciones, juzgados de paz y los gobiernos locales, se aborda el tema de las relaciones de poder al interior de la sociedad rural, las características de los nuevos poderes locales y su relación con los diferentes grupos sociales, en especial la población comunero campesina, tratando de establecer cuáles son las pautas de interacción presentes en esas relaciones, y en especial buscando identificar la presencia de elementos que puedan dar cuenta de la presencia y extensión de pautas de interacción ciudadanas. Como una de las principales conclusiones se propone la existencia de una “ciudadanía clientelista” en este tipo de espacios sociales, siendo éste un concepto que pretende por un lado reconocer la presencia y extensión de la ciudadanía en la sociedad rural, pero estableciendo los límites dados por una relación de dependencia entre la población campesina y los intermediarios políticos que en cierta medida controlan los mecanismos de acceso a las instituciones y los servicios estatales.Tesi

Nanopore sequencing of native adeno-associated virus (AAV) single-stranded DNA using a transposase-based rapid protocol

Radukic M, Brandt D, Haak M, Müller K, Kalinowski J. Nanopore sequencing of native adeno-associated virus (AAV) single-stranded DNA using a transposase-based rapid protocol. NAR Genomics and Bioinformatics. 2020;2(4): lqaa074.Next-generation sequencing of single-stranded DNA (ssDNA) enables transgene characterization of gene therapy vectors such as adeno-associated virus (AAV), but current library generation uses complicated and potentially biased second-strand synthesis. We report that libraries for nanopore sequencing of ssDNA can be conveniently created without second-strand synthesis using a transposase-based protocol. We show for bacteriophage M13 ssDNA that the MuA transposase has unexpected residual activity on ssDNA, explained in part by transposase action on transient double-stranded hairpins. In case of AAV, library creation is additionally aided by genome hybridization. We demonstrate the power of direct sequencing combined with nanopore long reads by characterizing AAV vector transgenes. Sequencing yielded reads up to full genome length, including GC-rich inverted terminal repeats. Unlike short-read techniques, single reads covered genome-genome and genome-contaminant fusions and other recombination events, whilst additionally providing information on epigenetic methylation. Single-nucleotide variants across the transgene cassette were revealed and secondary genome packaging signals were readily identified. Moreover, comparison of sequence abundance with quantitative polymerase chain reaction results demonstrated the technique's future potential for quantification of DNA impurities in AAV vector stocks. The findings promote direct nanopore sequencing as a fast and versatile platform for ssDNA characterization, such as AAV ssDNA in research and clinical settings

El elector latinoamericano del Siglo XXI : estudio comparado del comportamiento electoral en Brasil, Chile, México y Perú

El objetivo de la tesis es explicar los comportamientos electorales de los ciudadanos de América Latina, examinando cuatro casos relevantes desde una perspectiva de política comparada: Brasil, Chile, México y Perú. Para ello se ponen a prueba un conjunto de hipótesis derivadas de los modelos teóricos clásicos del comportamiento electoral (modelos sociológicos, sociopsicológicos, de la elección racional) en diálogo con los enfoques que enfatizan la importancia de la dimensión institucional en el comportamiento de los actores políticos y del elector. Para evaluar la pertinencia de las hipótesis formuladas se analiza la información proveniente de encuestas post electorales realizadas en los cuatro países seleccionados en el marco del proyecto internacional \Comparative Study of Electoral Systems". Se trabaja con 15 encuestas hechas a más de 24 mil electores, realizadas luego de las correspondientes elecciones presidenciales o parlamentarias que tuvieron lugar en los cuatro países entre 1997 y 2011. Entre los hallazgos principales, la investigación muestra que si bien la identificación partidaria tiene un efecto importante en el voto, ésta es relativamente débil en la mayoría de países y poco asociada a clivajes o divisiones sociales basadas en desigualdades socioeconómicas. En segundo lugar se encuentra que la evaluación de la distancia ideológica entre las preferencias del elector y la oferta electoral tiene efectos estadísticamente significativos en el comportamiento del elector, pero que su magnitud depende en gran medida del grado de polarización política que muestren los partidos en competencia. En tercer lugar, se confirma la hipótesis de que el desempeño del gobierno tiene un peso significativo en el voto a favor o en contra del partido de gobierno, pero que ello está mediado por las regla electorales (básicamente la posibilidad de reelección) y por el grado de consolidación del sistema de partidos.Tesi

Software-based Identification of Adaptation Needs in Global Production Networks

Internal and external influencing factors force companies to adapt their production networks to changing conditions, which entails a high level of complexity. To be competitive in the future, manufacturing companies have to minimize the required adaptation time between the occurrence of a change and the implementation of an adaptation. While some approaches deal with modelling and evaluating network configuration, there is a lack in identifying the need for adaptation. In practice, the creation of scenarios is often based on the experience and knowledge of the network designer. This paper presents an approach to systematically link perceived key figure changes to possible adaptation alternatives in network configuration. For this purpose, the relevant objects for network adaptations are first defined and adaptation alternatives are systematically described. Subsequently, these are combined with a set of key figures to derive suitable adaptation alternatives depending on their development. The approach is further implemented in a software-based prototype that enables the automated generation of adaptation alternatives in response to perceived changes and provides the user with a listing of possible alternatives prioritized by their utility. The validation with company data demonstrates that by earlier and automated identification of possible configuration adaptations, the adaptation time to changes can be reduced and the generated scenarios are less dependent on the individual experience of the user

Standards and Infrastructure for Innovation Data Exchange

This is the author's accepted manuscript. The original publication is available at http://www.sciencemag.org/content/338/6104/196.Economic growth relies in part on efficient advancement and application of research and development (R&D) knowledge. This requires access to data about science, in particular R&D inputs and outputs such as grants, patents, publications, and data sets, to support an understanding of how R&D information is produced and what affects its availability. But there is a cacophony of R&D-related data across countries, disciplines, data providers, and sectors. Burdened with data that are inconsistently specified, researchers and policy-makers have few incentives or mechanisms to share or interlink cleaned data sets. Access to these data is limited by a patchwork of laws, regulations, and practices that are unevenly applied and interpreted (1). A Web-based infrastructure for data sharing and analysis could help. We describe administrative and technical demands and opportunities to meet them. Data exchange standards are a first step

Functional connectivity of the Precuneus reflects effectiveness of visual restitution training in chronic hemianopia

Contains fulltext : 222045.pdf (publisher's version ) (Open Access

The Secret Life of Articles: From Download Metrics to Downstream Impact

Traditional citation and download metrics have long been the standard by which we measure the use and value of scholarly articles. However, these methods neglect the usage and real‐world impact of newer technologies to access, store, and share downloaded scholarly articles. This session’s speakers will share the results of interviews, focus groups, and an international survey with 1,000 scholars to investigate the ways in which they now access, store, share, and use downloaded scholarly articles. By identifying and measuring what traditional metrics fail to examine, the Beyond Downloads project attempts to capture a more complete picture of the use and value of scholarly articles, which is critical for librarians, publishers, and vendors to understand in developing scholarly tools and services. Complete usage can no longer be measured by traditional means alone. The speakers will discuss the findings of their research and the implications for metrics that take into account scholars’ changing access, reading, and sharing behaviors

Genome-Wide Assessment of Efficiency and Specificity in CRISPR/Cas9 Mediated Multiple Site Targeting in Arabidopsis

Simultaneous multiplex mutation of large gene families using Cas9 has the potential to revolutionize agriculture and plant sciences. The targeting of multiple genomic sites at once raises concerns about the efficiency and specificity in targeting. The model Arabidopsis thaliana is widely used in basic plant research. Previous work has suggested that the Cas9 off-target rate in Arabidopsis is undetectable. Here we use deep sequencing on pooled plants simultaneously targeting 14 distinct genomic loci to demonstrate that multiplex targeting in Arabidopsis is highly specific to on-target sites with no detectable off-target events. In addition, chromosomal translocations are extremely rare. The high specificity of Cas9 in Arabidopsis makes this a reliable method for clean mutant generation with no need to enhance specificity or adopt alternate Cas9 variants