A Collaborating Centre for animal health economics in the Americas.

Countries in the Americas play a vital role in global livestock and aquaculture production. With international trade of livestock and aquaculture products becoming an important source of income for countries, there has been an increased interest in using animal health economics for advocacy and allocation of resources. This article discusses the development of a new Collaborating Centre for the Economics of Animal Health and the applications of the Global Burden of Animal Diseases (GBADs) framework in the Americas region. Incentives for the increased use of economics in animal health decision-making and examples from the Americas region are examined. The article then discusses the newly formed World Organisation for Animal Health Collaborating Centre in the Americas region. Finally, it reviews two ongoing case studies that are implementing the GBADs framework in Peru and the United States of America.

Les pays des Amériques jouent un rôle crucial dans la production mondiale d'animaux d'élevage, qu'il s'agisse d'espèces terrestres ou aquatiques. Le commerce international des produits issus de l'élevage et de l'aquaculture étant désormais une source importante de revenus pour les pays, la possibilité d'utiliser les concepts de l'économie de la santé animale à des fins de plaidoyer et d'allocation des ressources suscite un intérêt croissant. Les auteurs abordent la désignation d'un nouveau Centre collaborateur pour l'économie de la santé animale ainsi que les applications du programme " Impact mondial des maladies animales " (GBADs) dans la région des Amériques. Ils examinent les avantages d'une meilleure prise en compte de l'économie dans les prises de décision en matière de santé animale, illustrés par quelques exemples concrets relevés dans la région. Ils décrivent ensuite la création du nouveau Centre collaborateur de l'Organisation mondiale de la santé animale dans la région des Amériques. Enfin, ils présentent deux études de cas menées actuellement concernant la mise en oeuvre du programme GBADs respectivement au Pérou et aux Etats-Unis d'Amérique.

Los países de las Américas desempeñan un papel fundamental en la producción ganadera y acuícola mundial. Dado que el comercio internacional de productos ganaderos y acuícolas se ha convertido en una importante fuente de ingresos para los países, el interés por utilizar la economía de la sanidad animal en favor de la promoción y la asignación de recursos ha ido en aumento. En este artículo se analiza la creación de un nuevo Centro colaborador para la economía de la sanidad animal y las aplicaciones del marco del impacto global de las enfermedades animales (GBADs) en la región de las Américas. Se examinan los incentivos para un mayor uso de la economía en la toma de decisiones sobre sanidad animal, así como ejemplos de la región. A continuación, en el artículo se presenta el recién creado Centro colaborador de la Organización Mundial de Sanidad Animal en la región de las Américas. Por último, se examinan dos estudios de casos en los que se está poniendo en práctica el marco del GBADs en Perú y los Estados Unidos de América.

Entropy and Negative Specific Heat of Doped Graphene: Topological Phase Transitions and Nernst's Theorem Revisited.

This study explores the thermodynamic properties of doped graphene using an adapted electronic spectrum. We employed the one-electron tight-binding model to describe the hexagonal lattice structure. The dispersion relation for graphene is expressed in terms of the hopping energies using a compositional parameter that characterizes the different dopant atoms in the lattice. The focus of the investigation is on the impact of the compositions, specifically the presence of dopant atoms, on the energy spectrum, entropy, temperature, and specific heat of graphene. The numerical and analytical results reveal distinct thermodynamic behaviors influenced by the dopant composition, including topological transitions, inflection points in entropy, and specific heat divergences. In addition, the use of Boltzmann entropy and the revision of Nernst's theorem for doped graphene are introduced as novel aspects.

Room-temperature synthesis of bimetallic ZnCu-MOF-74 as an adsorbent for tetracycline removal from an aqueous solution.

The novel bimetallic MOF, ZnCu-MOF-74, has been evaluated for the remediation of tetracycline-contaminated water. ZnCu-MOF-74 was obtained at room temperature, avoiding high pressure and temperature. ZnCu-MOF-74 exhibited chemical stability in the 4-8 pH range. The adsorption result analysis was described using the Elovich kinetic model and the Langmuir adsorption isotherm, suggesting a physicochemical process. The maximum adsorption capacity was estimated at 775.66 mg g-1. The pH of the solution and the presence of ions such as NO3-, SO42-, Na+, Mg2+, Cl-, and Ca2+ had no influence on the removal of tetracycline. In addition, π-interactions and metal complexation were proposed as possible adsorption mechanisms through FT-IR and XPS. ZnCu-MOF-74 showed outstanding cyclability performance, preserving its adsorption capacity after 4 adsorption-desorption cycles, besides exhibiting chemical stability, proving the benefits of applying ZnCu-MOF-74 in the water treatment process.

Full-spectrum cannabidiol reduces UVB damage through the inhibition of TGF-ß1 and the NLRP3 inflammasome.

The thermodynamic characteristics, antioxidant potential, and photoprotective benefits of full-spectrum cannabidiol (FS-CBD) against UVB-induced cellular death were examined in this study. In silico analysis of CBD showed antioxidant capacity via proton donation and UV absorption at 209.09, 254.73, and 276.95 nm, according to the HAT and SPLET methodologies. FS-CBD protected against UVB-induced bacterial death for 30 min. FS-CBD protected against UVB-induced cell death by 42% (1.5 µg/mL) and 35% (3.5 µg/mL) in an in vitro keratinocyte cell model. An in vivo acute irradiated CD-1et/et mouse model (UVB-irradiated for 5 min) presented very low photoprotection when FS-CBD was applied cutaneously, as determined by histological analyses. In vivo skin samples showed that FS-CBD regulated inflammatory responses by inhibiting the inflammatory markers TGF-ß1 and NLRP3. The docking analysis showed that the CBD molecule had a high affinity for TGF-ß1 and NLRP3, indicating that protection against inflammation might be mediated by blocking these proinflammatory molecules. This result was corroborated by the docking interactions between CBD and TGF-ß1 and NLRP3, which resulted in a high affinity and inhibition of both proteins The present work suggested a FS-CBD moderate photoprotective agent against UVB light-induced skin damage and that this effect is partially mediated by its anti-inflammatory activity.

Mariner: explore the Hi-Cs.

MOTIVATION: 3D chromatin structure plays an important role in regulating gene expression and alterations to this structure can result in developmental abnormalities and disease. While genomic approaches like Hi-C and Micro-C can provide valuable insights in 3D chromatin architecture, the resulting datasets are extremely large and difficult to manipulate. RESULTS: Here, we present mariner, a rapid and memory efficient tool to extract, aggregate, and plot data from Hi-C matrices within the R/Bioconductor environment. Mariner simplifies the process of querying and extracting contacts from multiple Hi-C files using a parallel and block-processing approach. Modular functions allow complete workflow customization for advanced users, yet all-in-one functions are available for running the most common types of analyses. Finally, tight integration with existing Bioconductor infrastructure enables complete analysis and visualization of Hi-C data in R. AVAILABILITY AND IMPLEMENTATION: Available on GitHub at https://github.com/EricSDavis/mariner and on Bioconductor at https://www.bioconductor.org/packages/release/bioc/html/mariner.html.

Impact of airborne algicidal bacteria on marine phytoplankton blooms.

Ocean microbes are involved in global processes such as nutrient and carbon cycling. Recent studies indicated diverse modes of algal-bacterial interactions, including mutualism and pathogenicity, which have a substantial impact on ecology and oceanic carbon sequestration, and hence, on climate. However, the airborne dispersal and pathogenicity of bacteria in the marine ecosystem remained elusive. Here, we isolated an airborne algicidal bacterium, Roseovarius nubinhibens, emitted to the atmosphere as primary marine aerosol (referred also as sea spray aerosols) and collected above a coccolithophore bloom in the North Atlantic Ocean. The aerosolized bacteria retained infective properties and induced lysis of Gephyrocapsa huxleyi cultures.This suggests that the transport of marine bacteria through the atmosphere can effectively spread infection agents over vast oceanic regions, highlighting its significance in regulating the cell fate in algal blooms.

[Core data set for real world data in multiple sclerosis: customization for latin america from a global task force recommendation]. / Core data set para la generación de datos de la vida real en esclerosis múltiple: adaptación de una iniciativa global para América Latina.

INTRODUCTION: The primary objective of the core data set is to reduce heterogeneity and promote harmonization among data sources in EM, thereby reducing the time needed to execute real life data collection efforts. Recently, a group led by the Multiple Sclerosis Data Alliance has developed a core data set for collecting real-world data on multiple sclerosis (MS) globally. Our objective was to adapt this global data set to the needs of Latin America, so that it can be implemented by the registries already developed and in the process of development in the region. MATERIAL AND METHODS: A working group was formed regionally, the core data set created globally was adapted (translation process into Spanish, incorporation of regional variables and consensus on variables to be used). Consensus was obtained through the remote Delphi methodology of a round of questionnaires and remote discussion of the core data set variables. RESULTS: A total of 25 professionals from Latin America carried out the adaptation process between November 2022 and July 2023. Agreement was established on a core data set of nine categories and 45 variables, version 2023 to suggest its implementation in developed or developing registries, and MS cohorts in the region. CONCLUSION: The core data set seeks to harmonize the variables collected by registries and cohorts in MS in Latin America in order to facilitate said collection and allow collaboration between sources. Its implementation will facilitate real life data collection and collaboration in the region.

TITLE: Core data set para la generación de datos de la vida real en esclerosis múltiple: adaptación de una iniciativa global para América Latina.Introducción. Los objetivos primarios del core data set son reducir la heterogeneidad y promover la armonización entre las fuentes de datos en la esclerosis múltiple (EM), reduciendo así el tiempo necesario para ejecutar esfuerzos en la recolección de datos de vida real. Recientemente, un grupo liderado por la Multiple Sclerosis Data Alliance ha desarrollado un core data set para la recolección de datos del mundo real en EM a nivel global. Nuestro objetivo ha sido adaptar y consensuar este conjunto de datos globales a las necesidades de América Latina para que pueda ser implementado por los registros ya desarrollados y en proceso de desarrollo en la región. Material y métodos. Se conformó un grupo de trabajo regionalmente y se adaptó el core data set creado globalmente (proceso de traducción al español, incorporación de variables regionales y consenso sobre variables que se iban a utilizar). El consenso se obtuvo a través de la metodología Delphi remoto de ronda de cuestionarios y discusión a distancia de las variables del core data set. Resultados. Veinticinco profesionales de América Latina llevaron adelante el proceso de adaptación entre noviembre de 2022 y julio de 2023. Se estableció un acuerdo sobre un core data set de nueve categorías y 45 variables, versión 2023, con la sugerencia de implementarlo en registros desarrollados o en vías de desarrollo y cohortes de EM en la región. Conclusión. El core data set busca armonizar las variables recolectadas por los registros y las cohortes de EM en América Latina con el fin de facilitar dicha recolección y permitir una colaboración entre fuentes. Su implementación facilitará la recolección de datos de vida real y la colaboración en la región.

Clinical evaluation and treatment in men with low testosterone levels and prostate cancer.

INTRODUCTION: A high prevalence of low testosterone levels has been reported in men with prostate cancer. The use of testosterone therapy in men with a history of prostate cancer is still controversial, and there is uncertainty regarding the management of these patients. METHODS: We analyzed the European and American guidelines on this topic and presented the clinical experience in the management of patients with low testosterone levels and a history of prostate cancer in one of the world's leading cancer centers. RESULTS: According to the published evidence to date, testosterone therapy in men with prostate cancer does not increase the risk of prostate cancer recurrence in the short and medium term, but there is a lack of data on the long term. Symptomatic men with low testosterone levels who are candidates for this therapy need a thorough clinical evaluation before commencing testosterone therapy. Evaluation of prostate cancer history including type of treatment administered, pathologic stage of prostate cancer and prostate specific antigen should be requested before and during testosterone treatment to assess its trend. CONCLUSION: Prostate-specific antigen should remain undetectable after radical prostatectomy or stable after radiotherapy. Otherwise, it would be a sign of uncontrolled prostate cancer, and the patient may require cessation of testosterone therapy and referral to oncology for further evaluation.

Evaluation of the catalytic activity of Zn-MOF-74 for the alcoholysis of cyclohexene oxide.

In the present work, nanocrystalline Zn-MOF-74 is shown to be a heterogeneous catalyst for the acid-catalyzed ring-opening alcoholysis of cyclohexene oxide. The results corroborated that accessible open metal sites within the material are critical conditions (Zn(ii) Lewis acid sites) for this reaction. Zn-MOF-74 was tested at three different temperatures (30, 40, and 50 °C) for the alcoholysis reaction. Furthermore, the cyclohexene oxide conversion was 94% in less than two days. A comparison of the catalytic activity with different crystal sizes of Zn-MOF-74 and the homogenous phase, zinc acetate, was conducted. Zn-MOF-74 exhibited excellent catalytic cyclability for three cycles without losing its activity. The material showed chemical stability by retaining its crystalline structure after the reaction and cyclability process.

SU-101: a Bi(III)-based metal-organic framework as an efficient heterogeneous catalyst for the CO2 cycloaddition reaction.

A non-porous version of SU-101 (herein n-SU-101) was evaluated for the CO2 cycloaddition reaction. The findings revealed that open metal sites (Bi3+) are necessary for the reaction. n-SU-101 displays a high styrene oxide conversion of 96.6% under mild conditions (3 bar and 80 °C). The catalytic activity of n-SU-101 demonstrated its potential application for the cycloaddition of CO2 using styrene oxide.

MOF-based catalysts: insights into the chemical transformation of greenhouse and toxic gases.

Metal-organic framework (MOF)-based catalysts are outstanding alternative materials for the chemical transformation of greenhouse and toxic gases into high-add-value products. MOF catalysts exhibit remarkable properties to host different active sites. The combination of catalytic properties of MOFs is mentioned in order to understand their application. Furthermore, the main catalytic reactions, which involve the chemical transformation of CH4, CO2, NOx, fluorinated gases, O3, CO, VOCs, and H2S, are highlighted. The main active centers and reaction conditions for these reactions are presented and discussed to understand the reaction mechanisms. Interestingly, implementing MOF materials as catalysts for toxic gas-phase reactions is a great opportunity to provide new alternatives to enhance the air quality of our planet.

Maximal Ratio Combining Detection in OFDM Systems with Virtual Carriers Over V2V Channels.

This paper examines the performance of orthogonal frequency division multiplexing (OFDM) systems for vehicle-to-vehicle (V2V) communication channels. More specifically, a doubly selective channel under high intercarrier interference (ICI) is considered. Current solutions involve complex detection and/or reduced spectral efficiency receivers. This paper proposes the use of virtual carriers (VC) in an OFDM system with a low-complexity maximal ratio combining (MRC) detector to improve the bit error rate (BER) performance. The results show that VC provides diversity in received data, resulting in a ≥5 dB gain compared to previous OFDM systems with conventional linear/nonlinear detectors used as a reference. The detector presented in this paper has linear complexity, making it a suitable solution for real-time V2V communication systems.

Effects of an early rehabilitation program for adult cystic fibrosis patients during hospitalization: a randomized clinical trial.

There is little information on pulmonary rehabilitation in patients with cystic fibrosis (CF) with pulmonary exacerbation. This study aimed to evaluate the effects of an early rehabilitation program on lung function, muscle strength, inflammatory markers, and quality of life in adults with CF hospitalized for pulmonary exacerbation. In this randomized controlled trial, 19 patients were included in the intervention group and 15 in the control group. The intervention group underwent an early rehabilitation program for 14 days after admission. All patients underwent spirometry, one-repetition maximum tests (1RM), and the 6-min walk test, and answered the Revised Cystic Fibrosis Questionnaire (CFQ-R) for quality of life and the International Physical Activity Questionnaire. Serum levels of interleukin and tumor necrosis factor alpha (TNF-α) were measured. In the intervention group, there were increases in 1RM biceps (P=0.009), triceps (P=0.005), shoulder abductors (P=0.002), shoulder flexors (P=0.004), hamstrings (P<0.001), and quadriceps values (P<0.001). In addition, there were improvements in CFQ-R-emotion (P=0.002), treatment burden (P=0.002), vitality (P=0.011), and physical scores (P=0.026), and a reduction in the Borg resting fatigue score (P=0.037). The interleukins levels did not change after the intervention. In adult CF patients with pulmonary exacerbation, early hospital rehabilitation had a significant impact on improving resting fatigue, muscle strength, and quality of life.

Asociación de variables morfológicas de tipo de acromion con lesiones del manguito rotador por resonancia magnética nuclear / Association of morphological variables of acromion type with rotator cuff lesions by nuclear magnetic resonance

Resumen: Introducción: el acromion es una pequeña porción de la escápula que se extiende hacia la región anterior desde la espina de la escápula. Tradicionalmente se clasifica al acromion por la forma de su superficie inferior en un plano sagital. Se ha encontrado que la morfología acromial está rela-cionada con la lesión del manguito rotador. Objetivo: determinar la asociación entre el tipo de acromion con una mayor incidencia de ruptura de manguito rotador. Población de estudio: pacientes que acudan al Servicio de Traumatología y Ortopedia de un hospital privado de tercer nivel en la ciudad de Monterrey por hombro doloroso y a los cuales se les haya realizado una resonancia magnética simple de hombro. Material y métodos: se realizó un estudio de tipo transversal, retrospectivo y descriptivo, en el cual se revisaron 273 estudios de resonancia magnética en pacientes que cumplieran los criterios de inclusión. Se reportó el tipo de acromion según la clasificación morfológica en tipo I a IV y el estado del manguito rotador: sin ruptura, ruptura parcial o ruptura completa, haciendo una comparación entre hombro derecho e izquierdo. Resultados: se obtuvo un valor de p = 0.473 por lo que se concluye que no existe una asociación entre el tipo de acromion y el estado del manguito rotador. Conclusión: en el presente estudio, a diferencia de lo publicado en la literatura, se obtuvo que el acromion tipo II fue al que se asoció la mayoría de los casos con ruptura del manguito rotador.

Abstract: Introduction: the acromion is a small portion of the scapula that extends towards the anterior region from the spine of the scapula. Traditionally, the acromion is classified by the shape of its inferior surface in a sagittal plane. Acromial morphology has been found to be related to rotator cuff injury. Objective: to determine the association between the type of acromion with a higher incidence of rotator cuff rupture. Study population: patients who come to the Traumatology and Orthopedics Service of a third level hospital at Monterrey, Mexico, due to a painful shoulder and who have undergone a simple magnetic resonance of the shoulder. Material and methods: a cross-sectional, retrospective and descriptive study was carried out, in which 273 magnetic resonance studies were reviewed in patients who met the inclusion criteria. The type of acromion was reported according to the morphological classification in type I to IV and the state of the rotator cuff: without rupture, partial rupture or complete rupture, making a comparison between right and left shoulder. Results: in this study we found a value of p = 0.473 which concludes that there is no relation between the type of acromion and the injury of the rotator cuff. Conclusion: in the present study, unlike what has been published in the literature, it was found that type II acromion was the one that was associated in most cases with a rotator cuff tear.

Richer than Gold: the fungal biodiversity of Reserva Los Cedros, a threatened Andean cloud forest.

BACKGROUND: Globally, many undescribed fungal taxa reside in the hyperdiverse, yet undersampled, tropics. These species are under increasing threat from habitat destruction by expanding extractive industry, in addition to global climate change and other threats. Reserva Los Cedros is a primary cloud forest reserve of ~ 5256 ha, and is among the last unlogged watersheds on the western slope of the Ecuadorian Andes. No major fungal survey has been done there, presenting an opportunity to document fungi in primary forest in an underrepresented habitat and location. Above-ground surveys from 2008 to 2019 resulted in 1760 vouchered collections, cataloged and deposited at QCNE in Ecuador, mostly Agaricales sensu lato and Xylariales. We document diversity using a combination of ITS barcode sequencing and digital photography, and share the information via public repositories (GenBank & iNaturalist). RESULTS: Preliminary identifications indicate the presence of at least 727 unique fungal species within the Reserve, representing 4 phyla, 17 classes, 40 orders, 101 families, and 229 genera. Two taxa at Los Cedros have recently been recommended to the IUCN Fungal Red List Initiative (Thamnomyces chocöensis Læssøe and "Lactocollybia" aurantiaca Singer), and we add occurrence data for two others already under consideration (Hygrocybe aphylla Læssøe & Boertm. and Lamelloporus americanus Ryvarden). CONCLUSIONS: Plants and animals are known to exhibit exceptionally high diversity and endemism in the Chocó bioregion, as the fungi do as well. Our collections contribute to understanding this important driver of biodiversity in the Neotropics, as well as illustrating the importance and utility of such data to conservation efforts. RESUMEN: Antecedentes: A nivel mundial muchos taxones fúngicos no descritos residen en los trópicos hiper diversos aunque continúan submuestreados. Estas especies están cada vez más amenazadas por la destrucción del hábitat debido a la expansión de la industria extractivista además del cambio climático global y otras amenazas. Los Cedros es una reserva de bosque nublado primario de ~ 5256 ha y se encuentra entre las últimas cuencas hidrográficas no explotadas en la vertiente occidental de los Andes ecuatorianos. Nunca antes se ha realizado un estudio de diversidad micológica en el sitio, lo que significa una oportunidad para documentar hongos en el bosque primario, en hábitat y ubicación subrepresentatadas. El presente estudio recopila información entre el 2008 y 2019 muestreando material sobre todos los sustratos, reportando 1760 colecciones catalogadas y depositadas en el Fungario del QCNE de Ecuador, en su mayoría Agaricales sensu lato y Xylariales; además se documenta la diversidad mediante secuenciación de códigos de barras ITS y fotografía digital, la información está disponible en repositorios públicos digitales (GenBank e iNaturalist). RESULTADOS: La identificación preliminar indica la presencia de al menos 727 especies únicas de hongos dentro de la Reserva, que representan 4 filos, 17 clases, 40 órdenes, 101 familias y 229 géneros. Recientemente dos taxones en Los Cedros se recomendaron a la Iniciativa de Lista Roja de Hongos de la UICN (Thamnomyces chocöensis Læssøe y "Lactocollybia" aurantiaca Singer) y agregamos datos de presencia de otros dos que ya estaban bajo consideración (Hygrocybe aphylla Læssøe & Boertm. y Lamelloporus americanus Ryvarden). CONCLUSIONES: Se sabe que plantas y animales exhiben una diversidad y endemismo excepcionalmente altos en la bioregión del Chocó y los hongos no son la excepción. Nuestras colecciones contribuyen a comprender este importante promotor de la biodiversidad en el Neotrópico además de ilustrar la importancia y utilidad de dichos datos para los esfuerzos de conservación.

The Asociación Mexicana de Gastroenterología consensus on the diagnosis and treatment of acute pancreatitis in children and adolescents.

Acute pancreatitis (AP) and recurrent acute pancreatitis (RAP) are conditions, whose incidence is apparently on the rise. Despite the ever-increasing evidence regarding the management of AP in children and adults, therapeutic actions that could potentially affect having a poor prognosis in those patients, especially in the pediatric population, continue to be carried out. Therefore, the Asociación Mexicana de Gastroenterología convened a group of 24 expert pediatric gastroenterologists from different institutions and areas of Mexico, as well as 2 pediatric nutritionists and 2 specialists in pediatric surgery, to discuss different aspects of the epidemiology, diagnosis, and treatment of AP and RAP in the pediatric population. The aim of this document is to present the consensus results. Different AP topics were addressed by 6 working groups, each of which reviewed the information and formulated statements considered pertinent for each module, on themes involving recommendations and points of debate, concerning diagnostic or therapeutic approaches. All the statements were presented and discussed. They were then evaluated through a Delphi process, with electronic and anonymous voting, to determine the level of agreement on the statements. A total of 29 statements were formulated, all of which reached above 75% agreement in the first round of voting.

Open science resources from the Tara Pacific expedition across coral reef and surface ocean ecosystems.

The Tara Pacific expedition (2016-2018) sampled coral ecosystems around 32 islands in the Pacific Ocean and the ocean surface waters at 249 locations, resulting in the collection of nearly 58 000 samples. The expedition was designed to systematically study warm-water coral reefs and included the collection of corals, fish, plankton, and seawater samples for advanced biogeochemical, molecular, and imaging analysis. Here we provide a complete description of the sampling methodology, and we explain how to explore and access the different datasets generated by the expedition. Environmental context data were obtained from taxonomic registries, gazetteers, almanacs, climatologies, operational biogeochemical models, and satellite observations. The quality of the different environmental measures has been validated not only by various quality control steps, but also through a global analysis allowing the comparison with known environmental large-scale structures. Such publicly released datasets open the perspective to address a wide range of scientific questions.

Integrative omics framework for characterization of coral reef ecosystems from the Tara Pacific expedition.

Coral reef science is a fast-growing field propelled by the need to better understand coral health and resilience to devise strategies to slow reef loss resulting from environmental stresses. Key to coral resilience are the symbiotic interactions established within a complex holobiont, i.e. the multipartite assemblages comprising the coral host organism, endosymbiotic dinoflagellates, bacteria, archaea, fungi, and viruses. Tara Pacific is an ambitious project built upon the experience of previous Tara Oceans expeditions, and leveraging state-of-the-art sequencing technologies and analyses to dissect the biodiversity and biocomplexity of the coral holobiont screened across most archipelagos spread throughout the entire Pacific Ocean. Here we detail the Tara Pacific workflow for multi-omics data generation, from sample handling to nucleotide sequence data generation and deposition. This unique multidimensional framework also includes a large amount of concomitant metadata collected side-by-side that provide new assessments of coral reef biodiversity including micro-biodiversity and shape future investigations of coral reef dynamics and their fate in the Anthropocene.

Pervasive tandem duplications and convergent evolution shape coral genomes.

BACKGROUND: Over the last decade, several coral genomes have been sequenced allowing a better understanding of these symbiotic organisms threatened by climate change. Scleractinian corals are reef builders and are central to coral reef ecosystems, providing habitat to a great diversity of species. RESULTS: In the frame of the Tara Pacific expedition, we assemble two coral genomes, Porites lobata and Pocillopora cf. effusa, with vastly improved contiguity that allows us to study the functional organization of these genomes. We annotate their gene catalog and report a relatively higher gene number than that found in other public coral genome sequences, 43,000 and 32,000 genes, respectively. This finding is explained by a high number of tandemly duplicated genes, accounting for almost a third of the predicted genes. We show that these duplicated genes originate from multiple and distinct duplication events throughout the coral lineage. They contribute to the amplification of gene families, mostly related to the immune system and disease resistance, which we suggest to be functionally linked to coral host resilience. CONCLUSIONS: At large, we show the importance of duplicated genes to inform the biology of reef-building corals and provide novel avenues to understand and screen for differences in stress resilience.