Funcionalidad biológica de la resistencia al arsénico den la bacteria hipertolerante Pseudomonas putida KT2440

Tesis doctoral inédita. Universidad Autónoma de Madrid, Facultad de Ciencias, Departamento de Biología Molecular. Fecha de lectura: 30-10-200

Plan de negocios de “Después del Cole”: una plataforma web dedicada a la comunicación entre jóvenes entre 14 a 18 años y universidades e institutos en Lima Metropolitana

El presente plan de negocios bajo la razón social “ Después del Cole S.A.C“ tiene como fin el desarrollo de un ecosistema digital, el cual tiene como eje central a la website, en donde se brindará información relevante acerca de carreras profesionales y técnicas para los jóvenes, y a su vez, contenido de orientación vocacional sobre las carreras profesionales y las casas de estudios superiores en Lima Metropolitana (Universidad privadas e Institutos privados), las cuales están interesados en anunciar, contactar e interactuar con el segmento juvenil y el presente modelo de negocio será el medio ideal para ello. El plan de negocios se desarrolló en 8 capítulos: En el Capítulo I se plantea la idea del negocio, se trazan los objetivos, metodología de la investigación y la justificación. En el Capítulo II un marco teórico, en donde se analizan problemáticas de la educación peruana en búsqueda de oportunidades, con enfoque en el sector privado, universidades privadas e institutos técnicos, plataformas digitales, sitios web en el Perú, contenido digital, monetización y redes sociales. El Capítulo III presenta el análisis del negocio, en él encontramos el planteamiento del problema, análisis del entorno, análisis interno y el análisis Foda. El Capítulo IV corresponde a la validación de la idea del negocio a través de sondeos de mercado. En el Capítulo V se desarrolla el modelo de negocio y se establecen la Misión, Visión y Valores, el Value Proposition Canvas de Usuarios y Entidades Educativas, journey map y el lienzo del modelo de negocios canvas. El Capítulo VI desarrolla el plan de marketing y se presenta al mercado de consumidores, formulación estratégica y tácticas. El Capítulo VII muestra el plan de operaciones, en donde detallamos la definición de los servicios, políticas del servicio, información de la empresa, estrategia de operaciones, procesos y recursos humanos. Finalmente en el Capítulo VIII desarrollamos el plan económico financiero, donde se demuestra la viabilidad financiera del proyecto, el flujo de caja, estado de resultados y el estado financiero.The purpose of this business plan under the name of "Después del Cole S.A.C" is the development of a digital ecosystem, whose central axis is the web site, where relevant information about all the private universities and institutes from Metropolitan Lima and the professional and technical careers they hold will be provided for young people who are eager to start their professional studies. Additionally, as a content marketing strategy, this website will create digital content specialized in vocational guidance in order to converge the universities’ target with our platform. In such a manner, private institutes and universities will be interested in announcing, contacting, and interacting with our website’s public. This business plan is divided into 8 chapters. Chapter I, where presentation of the business idea, objectives, research methodology and justification are outlined. Chapter II, theoretical framework’s exposition, where we will study the main problems of Peruvian education with a focus on the private sector, private universities and technical institutes. Furthermore, study of digital platforms, websites in Peru, digital content, monetization and social networks. Chapter III presents the business analysis, where we decrypt the problem statement, environment analysis, internal analysis or SWOT analysis and other frameworks. Chapter IV corresponds to the validation of the business idea through market surveys. In Chapter V the business model is developed, this includes the Mission, Vision and Values, the Value Proposition Canvas for the website users and Educational Entities, the journey map and the business model canvas are also established. Chapter VI develops the marketing plan and it presents the consumer market, creative concepts for strategic formulation and tactics. Chapter VII shows the operations plan, where we detail the definition of services, service policies, company information, operations strategy, processes and human resources. Finally, in Chapter VIII we develop the financial economic plan, where the financial viability of the project is proven, the cash flow, the income statement and the financial statement are demonstrated.Trabajo de investigació

Minimum information about an uncultivated virus genome (MIUVIG)

This is the final version. Available on open access from Nature Research via the DOI in this recordNOTE: the full list of funders and grants is in the acknowledgements section of the articleWe present an extension of the Minimum Information about any (x) Sequence (MIxS) standard for reporting sequences of uncultivated virus genomes. Minimum Information about an Uncultivated Virus Genome (MIUViG) standards were developed within the Genomic Standards Consortium framework and include virus origin, genome quality, genome annotation, taxonomic classification, biogeographic distribution and in silico host prediction. Community-wide adoption of MIUViG standards, which complement the Minimum Information about a Single Amplified Genome (MISAG) and Metagenome-Assembled Genome (MIMAG) standards for uncultivated bacteria and archaea, will improve the reporting of uncultivated virus genomes in public databases. In turn, this should enable more robust comparative studies and a systematic exploration of the global virosphere.Simons Foundation InternationalNatural Environment Research Council (NERC

The role of plant growth promoting bacteria on arsenic removal: a review of existing perspectives

Phytobial remediation is an innovative tool that uses plants and microbes to mitigate Arsenic (As) contamination of the environment. Recently, plant growth-promoting bacteria (PGPB) that assists phytoremediation has been highly touted for both improving plant metal tolerance and promoting plant growth while achieving the goal of large-scale removal of As. This review focuses on the PGPB characteristics influencing plants and the mechanisms in which they function to overcome/lessen As-induced adversities. Several recent examples of mechanisms responsible for increasing the availability of As to plants and coping with As stresses facilitated by PGPB will be reviewed. Although drawbacks to phytoremediation have been reported, encouraging results have been developed with regular monitoring. Introducing PGPB-assisted phytoremediation of As in a field requires an assessment of the environmental effects of PGPB, especially with respect to the impacts on indigenous bacteria

Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection

Productivity of ruminant livestock depends on the rumen microbiota, which ferment indigestible plant polysaccharides into nutrients used for growth. Understanding the functions carried out by the rumen microbiota is important for reducing greenhouse gas production by ruminants and for developing biofuels from lignocellulose. We present 410 cultured bacteria and archaea, together with their reference genomes, representing every cultivated rumen-associated archaeal and bacterial family. We evaluate polysaccharide degradation, short-chain fatty acid production and methanogenesis pathways, and assign specific taxa to functions. A total of 336 organisms were present in available rumen metagenomic data sets, and 134 were present in human gut microbiome data sets. Comparison with the human microbiome revealed rumen-specific enrichment for genes encoding de novo synthesis of vitamin B12, ongoing evolution by gene loss and potential vertical inheritance of the rumen microbiome based on underrepresentation of markers of environmental stress. We estimate that our Hungate genome resource represents ?75% of the genus-level bacterial and archaeal taxa present in the rumen.publishersversionPeer reviewe

Unraveling the functional dark matter through global metagenomics

30 pages, 4 figures, 1 table, supplementary information https://doi.org/10.1038/s41586-023-06583-7.-- Data availability: All of the analysed datasets along with their corresponding sequences are available from the IMG system (http://img.jgi.doe.gov/). A list of the datasets used in this study is provided in Supplementary Data 8. All data from the protein clusters, including sequences, multiple alignments, HMM profiles, 3D structure models, and taxonomic and ecosystem annotation, are available through NMPFamsDB, publicly accessible at www.nmpfamsdb.org. The 3D models are also available at ModelArchive under accession code ma-nmpfamsdb.-- Code availability: Sequence analysis was performed using Tantan (https://gitlab.com/mcfrith/tantan), BLAST (https://blast.ncbi.nlm.nih.gov/Blast.cgi), LAST (https://gitlab.com/mcfrith/last), HMMER (http://hmmer.org/) and HH-suite3 (https://github.com/soedinglab/hh-suite). Clustering was performed using HipMCL (https://bitbucket.org/azadcse/hipmcl/src/master/). Additional taxonomic annotation was performed using Whokaryote (https://github.com/LottePronk/whokaryote), EukRep (https://github.com/patrickwest/EukRep), DeepVirFinder (https://github.com/jessieren/DeepVirFinder) and MMseqs2 (https://github.com/soedinglab/MMseqs2). 3D modelling was performed using AlphaFold2 (https://github.com/deepmind/alphafold) and TrRosetta2 (https://github.com/RosettaCommons/trRosetta2). Structural alignments were performed using TMalign (https://zhanggroup.org/TM-align/) and MMalign (https://zhanggroup.org/MM-align/). All custom scripts used for the generation and analysis of the data are available at Zenodo (https://doi.org/10.5281/zenodo.8097349)Metagenomes encode an enormous diversity of proteins, reflecting a multiplicity of functions and activities1,2. Exploration of this vast sequence space has been limited to a comparative analysis against reference microbial genomes and protein families derived from those genomes. Here, to examine the scale of yet untapped functional diversity beyond what is currently possible through the lens of reference genomes, we develop a computational approach to generate reference-free protein families from the sequence space in metagenomes. We analyse 26,931 metagenomes and identify 1.17 billion protein sequences longer than 35 amino acids with no similarity to any sequences from 102,491 reference genomes or the Pfam database3. Using massively parallel graph-based clustering, we group these proteins into 106,198 novel sequence clusters with more than 100 members, doubling the number of protein families obtained from the reference genomes clustered using the same approach. We annotate these families on the basis of their taxonomic, habitat, geographical and gene neighbourhood distributions and, where sufficient sequence diversity is available, predict protein three-dimensional models, revealing novel structures. Overall, our results uncover an enormously diverse functional space, highlighting the importance of further exploring the microbial functional dark matterWith the institutional support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S)Peer reviewe

The Standard European Vector Architecture (SEVA): a coherent platform for the analysis and deployment of complex prokaryotic phenotypes

The 'Standard European Vector Architecture' database (SEVA-DB, http://seva.cnb.csic.es) was conceived as a user-friendly, web-based resource and a material clone repository to assist in the choice of optimal plasmid vectors for de-constructing and re-constructing complex prokaryotic phenotypes. The SEVA-DB adopts simple design concepts that facilitate the swapping of functional modules and the extension of genome engineering options to microorganisms beyond typical laboratory strains. Under the SEVA standard, every DNA portion of the plasmid vectors is minimized, edited for flaws in their sequence and/or functionality, and endowed with physical connectivity through three inter-segment insulators that are flanked by fixed, rare restriction sites. Such a scaffold enables the exchangeability of multiple origins of replication and diverse antibiotic selection markers to shape a frame for their further combination with a large variety of cargo modules that can be used for varied end-applications. The core collection of constructs that are available at the SEVA-DB has been produced as a starting point for the further expansion of the formatted vector platform. We argue that adoption of the SEVA format can become a shortcut to fill the phenomenal gap between the existing power of DNA synthesis and the actual engineering of predictable and efficacious bacteria

Population and evolutionary dynamics in spatially structured seasonally varying environments

Increasingly imperative objectives in ecology are to understand and forecast population dynamic and evolutionary responses to seasonal environmental variation and change. Such population and evolutionary dynamics result from immediate and lagged responses of all key life-history traits, and resulting demographic rates that affect population growth rate, to seasonal environmental conditions and population density. However, existing population dynamic and eco-evolutionary theory and models have not yet fully encompassed within-individual and among-individual variation, covariation, structure and heterogeneity, and ongoing evolution, in a critical life-history trait that allows individuals to respond to seasonal environmental conditions: seasonal migration. Meanwhile, empirical studies aided by new animal-tracking technologies are increasingly demonstrating substantial within-population variation in the occurrence and form of migration versus year-round residence, generating diverse forms of 'partial migration' spanning diverse species, habitats and spatial scales. Such partially migratory systems form a continuum between the extreme scenarios of full migration and full year-round residence, and are commonplace in nature. Here, we first review basic scenarios of partial migration and associated models designed to identify conditions that facilitate the maintenance of migratory polymorphism. We highlight that such models have been fundamental to the development of partial migration theory, but are spatially and demographically simplistic compared to the rich bodies of population dynamic theory and models that consider spatially structured populations with dispersal but no migration, or consider populations experiencing strong seasonality and full obligate migration. Second, to provide an overarching conceptual framework for spatio-temporal population dynamics, we define a 'partially migratory meta-population' system as a spatially structured set of locations that can be occupied by different sets of resident and migrant individuals in different seasons, and where locations that can support reproduction can also be linked by dispersal. We outline key forms of within-individual and among-individual variation and structure in migration that could arise within such systems and interact with variation in individual survival, reproduction and dispersal to create complex population dynamics and evolutionary responses across locations, seasons, years and generations. Third, we review approaches by which population dynamic and eco-evolutionary models could be developed to test hypotheses regarding the dynamics and persistence of partially migratory meta-populations given diverse forms of seasonal environmental variation and change, and to forecast system-specific dynamics. To demonstrate one such approach, we use an evolutionary individual-based model to illustrate that multiple forms of partial migration can readily co-exist in a simple spatially structured landscape. Finally, we summarise recent empirical studies that demonstrate key components of demographic structure in partial migration, and demonstrate diverse associations with reproduction and survival. We thereby identify key theoretical and empirical knowledge gaps that remain, and consider multiple complementary approaches by which these gaps can be filled in order to elucidate population dynamic and eco-evolutionary responses to spatio-temporal seasonal environmental variation and change

ArsH protects Pseudomonas putida from oxidative damage caused by exposure to arsenic

The two As resistance arsRBC operons of Pseudomonas putida KT2440 are followed by a downstream gene called arsH that encodes an NADPH‐dependent flavin mononucleotide reductase. In this work, we show that the arsH1 and (to a lesser extent) arsH2 genes of P. putida KT2440 strengthened its tolerance to both inorganic As(V) and As(III) and relieved the oxidative stress undergone by cells exposed to either oxyanion. Furthermore, overexpression of arsH1 and arsH2 endowed P. putida with a high tolerance to the oxidative stress caused by diamide (a drainer of metabolic NADPH) in the absence of any arsenic. To examine whether the activity of ArsH was linked to a direct action on the arsenic compounds tested, arsH1 and arsH2 genes were expressed in Escherichia coli, which has an endogenous arsRBC operon but lacks an arsH ortholog. The resulting clones both deployed a lower production of reactive oxygen species (ROS) when exposed to As salts and had a superior endurance to physiological redox insults. These results suggest that besides the claimed direct action on organoarsenicals, ArsH contributes to relieve toxicity of As species by mediating reduction of ROS produced in vivo upon exposure to the oxyanion, e.g. by generating FMNH2 to fuel ROS‐quenching activities.UCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias Básicas::Centro de Investigaciones en Productos Naturales (CIPRONA)UCR::Vicerrectoría de Docencia::Ciencias Básicas::Facultad de Ciencias::Escuela de Químic