Genomic variation in recently collected maize landraces from Mexico

AbstractThe present dataset comprises 36,931 SNPs genotyped in 46 maize landraces native to Mexico as well as the teosinte subspecies Zea maiz ssp. parviglumis and ssp. mexicana. These landraces were collected directly from farmers mostly between 2006 and 2010. We accompany these data with a short description of the variation within each landrace, as well as maps, principal component analyses and neighbor joining trees showing the distribution of the genetic diversity relative to landrace, geographical features and maize biogeography. High levels of genetic variation were detected for the maize landraces (HE=0.234 to 0.318 (mean 0.311), while slightly lower levels were detected in Zea m. mexicana and Zea m. parviglumis (HE=0.262 and 0.234, respectively). The distribution of genetic variation was better explained by environmental variables given by the interaction of altitude and latitude than by landrace identity. This dataset is a follow up product of the Global Native Maize Project, an initiative to update the data on Mexican maize landraces and their wild relatives, and to generate information that is necessary for implementing the Mexican Biosafety Law

Characterization of parabolic dunes of the oriental Pampean region, west center of the province of Buenos Aires (Argentina)

La región pampeana, especialmente la provincia de Buenos Aires, se caracteriza por la presencia de paisajes eólicos que, si bien responden a eventos producidos en el Cuaternario Superior, en la actualidad son reactivados por la actividad agropecuaria. El objetivo de este trabajo se centra en la detección y delimitación de un campo de médanos parabólicos parcialmente reactivados, ubicados en el centro oeste de dicha provincia, que si bien han sido mencionados en la literatura, no han sido objetode estudio detallado. Mediante la generación de un Modelo Digital de Elevaciones(MDE) a partir de imágenes SRTM (Shuttle Radar Topography Mission) se ha detectado un campo con un total de 254 médanos parabólicos que ocupan 20.200 km2,ubicados entre los 120 y 90 msnm. Los mismos presentan una dirección general SW-NE, con anchos que varían entre 2 y 5 km y alturas entre 2 y 6 m. Aplicando la herramienta Distancia Vertical al Curso (Vertical Distance to Channel Network,VDCN) del Software SAGA GIS 2.1.2 y una clasificación automática no supervisada en ArcGIS 10.1, se lograron discriminar los médanos de la planicie circundante. A partir de muestras de sedimento de un médano testigo ubicado en la localidad de 30 de Agosto (Buenos Aires), se establecieron claras diferencias en la granulometría en distintos sectores del mismo. La ubicación de estos médanos es clave en la configuración del escurrimiento y, en consecuencia, este paisaje arenoso tiene un rol importante en la configuración del espacio del área de estudio ya que se forman lagunas intermedanales someras cuyo desarrollo depende de las precipitaciones locales.The Pampean region is a fertile and extensive plain of Argentina. It has an extension of 613,532 km2 located within the temperate region, being also adjacent to the Atlantic Ocean. The latter generates low daily and annual thermal amplitudes than in other regions in similar latitudes. In addition, the region is characterized by the occurrence of long periods of floods and drought, which affect the availability of water resources (Aliaga et al., 2017). The Buenos Aires Province is especially characterized by the presence of aeolian landscapes that, even though they were developed in the past, they are currently being reactivated by agricultural activities. The antecedents indicate different dune morphologies within the province territory, mainly associated with sediment availability and wind direction (Iriondo and Kröhling, 1995; Isla et al., 2010; Zárate and Tripaldi 2012). The focus of this work is the detection, delimitation and characterization of a parabolic dune field located in the Middle West of the Buenos Aires Province (Fig. 1) for which no precedent has been found. Likewise, we also establish the relationship between the parabolic dunes and the distribution and evolution of the interdune shallow lakes associated with them. Through the generation of a Digital Elevation Model (DEM) from Shuttle Radar Topography Mission (SRTM) images, a field with 254 parabolic dunes that covers 20,200 km2 was detected (Fig. 1). It is located between 120 and 90 m above mean sea level, with SW-NE general orientation; widths between 2 and 5 km, and heights between 2 and 6 m. The Vertical Distance to Channel Network (VDCN) tool of the SAGA GIS 2.1.2 software was also employed (Fig. 3) and, additionally, an automatic unsupervised classification using ArcGIS 10.1 was carried out in order to discriminate the dunes from the surrounding plain. Grain size analysis were carried out in both dune and interdune areas. The analysis was performed employing a Mastersizer 2000 Laser Particle Analyzer, whose results were represented with the GRADISTAT v8 software. The results demonstrate clear differences between the interdune areas, having very fine materials, with respect to those obtained within the dune area, which varied depending on the sector and the depth of the sample, establishing differences in the various dune sectors. For example, an increase in finer materials in depth. Also revealed that they are fine sand dunes, but the bimodal curve obtained with fine materials suggests that its sediments respond to different climatic periods. The progressive increase of fine material inside the dune shows that there is a material redistribution. Simultaneously with the sampling, a flight with an unmanned aerial vehicle (UAV) was made, that allowed generating a set of videos and 360º panoramic photographs, later used in the generation of orthomosaics, dense point cloud and a threedimensional model (Fig. 6) using the SFM (Structure From Motion) method (Genchi et al., 2015). The method is based on sequential image acquisition, with a high overlap degree, and founded in the correlation of points identified in different images (Fernández and Gutiérrez, 2016). The images were optimized (USGS, 2016) obtaining a higher accuracy in the photograph parameters by correcting the distortions caused by the camera lens. Besides the method helps to improve the general model, whose scene geometry, camera location and orientation of the photographs were taken automatically but derived from the appropriate superposition (> 60 %). According to its morphology, the dunes were categorized into three classes (Table 1), being the symmetric dunes the most common, followed by the asymmetric dunes and, finally, those of lateral coalescence that, despite being inferior in quantity, possess greater spatial development, that is, have longer crestal lengths (Fig. 7). Bordering the margins of the dune field to the north, east and south we observed the typical longitudinal dunes characteristic of this Pampean region sector. According to Bagnold (1941), it is possible that some simple semilunar forms are deformed in longitudinal features when moving in areas with variable wind directions. The results demonstrate that there are 254 crests distributed in the area, with a density of 0.01 dunes/ km2, many of them are segmented due to natural process through the presence of small shallow lakes and temporary depressions whose approximate depth is 1 m (Fig. 4 and 5), but also increased by the removal of soils as a result of agricultural activity. The shallow lakes disposition allows inferring that, in presence of abundant rainfall; they can be connected and/or overflowed, flooding the surrounding areas. The location of these dunes is crucial in the spatial surface runoff configuration and, in consequence, this sandy landscape has an important role in the spatial configuration of the area generating risk conditions to both the local population and agricultural production.Fil: Contreras, Félix Ignacio. Universidad Nacional del Nordeste. Facultad de Ciencias Exactas y Naturales y Agrimensura; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Centro de Ecología Aplicada del Litoral. Universidad Nacional del Nordeste. Centro de Ecología Aplicada del Litoral; ArgentinaFil: Mavo Mastretta, Gian Marco. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Instituto Argentino de Oceanografía. Universidad Nacional del Sur. Instituto Argentino de Oceanografía; ArgentinaFil: Perillo, Gerardo Miguel E.. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Instituto Argentino de Oceanografía. Universidad Nacional del Sur. Instituto Argentino de Oceanografía; Argentina. Universidad Nacional del Sur. Departamento de Geología; ArgentinaFil: Piccolo, Maria Cintia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Instituto Argentino de Oceanografía. Universidad Nacional del Sur. Instituto Argentino de Oceanografía; Argentina. Universidad Nacional del Sur. Departamento de Geografía y Turismo; Argentin

Monitoring status and trends in genetic diversity for the Convention on Biological Diversity: An ongoing assessment of genetic indicators in nine countries

Recent scientific evidence shows that genetic diversity must be maintained, managed, and monitored to protect biodiversity and nature's contributions to people. Three genetic diversity indicators, two of which do not require DNA-based assessment, have been proposed for reporting to the Convention on Biological Diversity and other conservation and policy initiatives. These indicators allow an approximation of the status and trends of genetic diversity to inform policy, using existing demographic and geographic information. Application of these indicators has been initiated and here we describe ongoing efforts in calculating these indicators with examples. We specifically describe a project underway to apply these indicators in nine countries, provide example calculations, address concerns of policy makers and implementation challenges, and describe a roadmap for further development and deployment, incorporating feedback from the broader community. We also present guidance documents and data collection tools for calculating indicators. We demonstrate that Parties can successfully and cost-effectively report these genetic diversity indicators with existing biodiversity observation data, and, in doing so, better conserve the Earth's biodiversity

Genetic diversity Goals and Targets have improved, but remain insufficient for clear implementation of the post-2020 global biodiversity framework

Genetic diversity among and within populations of all species is necessary for people and nature to survive and thrive in a changing world. Over the past three years, commitments for conserving genetic diversity have become more ambitious and specific under the Convention on Biological Diversity’s (CBD) draft post-2020 global biodiversity framework (GBF). This Perspective article comments on how goals and targets of the GBF have evolved, the improvements that are still needed, lessons learned from this process, and connections between goals and targets and the actions and reporting that will be needed to maintain, protect, manage and monitor genetic diversity. It is possible and necessary that the GBF strives to maintain genetic diversity within and among populations of all species, to restore genetic connectivity, and to develop national genetic conservation strategies, and to report on these using proposed, feasible indicators

Consensus protocol for EEG and amplitude-integrated EEG assessment and monitoring in neonates

The aim of this work is to establish inclusive guidelines on electroencephalography (EEG) applicable to all neonatal intensive care units (NICUs). Guidelines on ideal EEG monitoring for neonates are available, but there are significant barriers to their implementation in many centres around the world. These include barriers due to limited resources regarding the availability of equipment and technical and interpretive round-the-clock personnel. On the other hand, despite its limitations, amplitude-integrated EEG (aEEG) (previously called Cerebral Function Monitor [CFM]) is a common alternative used in NICUs. The Italian Neonatal Seizure Collaborative Network (INNESCO), working with all national scientific societies interested in the field of neonatal clinical neurophysiology, performed a systematic literature review and promoted interdisciplinary discussions among experts (neonatologists, paediatric neurologists, neurophysiologists, technicians) between 2017 and 2020 with the aim of elaborating shared recommendations. A consensus statement on videoEEG (vEEG) and aEEG for the principal neonatal indications was established. The authors propose a flexible frame of recommendations based on the complementary use of vEEG and aEEG applicable to the various neonatal units with different levels of complexity according to local resources and specific patient features. Suggestions for promoting cooperation between neonatologists, paediatric neurologists, and neurophysiologists, organisational restructuring, and teleneurophysiology implementation are provided

Prebiotic and Probiotic Fortified Milk in Prevention of Morbidities among Children: Community-Based, Randomized, Double-Blind, Controlled Trial

HN019 to milk, in preventing diarrhea, respiratory infections and severe illnesses, in children aged 1–4 years as part of a four group study design, running two studies simultaneously. HN019 (PP; n = 312). Children were followed up for 1 year providing data for 1–4 years. Biweekly household surveillance was conducted to gather information on compliance and morbidity. Both study groups were comparable at baseline; compliance to intervention was similar. Overall, there was no effect of prebiotic and probiotic on diarrhea (6% reduction, 95% Confidence Interval [CI]: −1 to 12%; p = 0.08). Incidence of dysentery episodes was reduced by 21% (95% CI: 0 to 38%; p = 0.05). Incidence of pneumonia was reduced by 24% (95% CI: 0 to 42%; p = 0.05) and severe acute lower respiratory infection (ALRI) by 35% (95% CI: 0 to 58%; p = 0.05). Compared to children in Co group, children in PP group had 16% (95% CI: 5 to 26%, p = 0.004) and 5% (95% CI: 0 to 10%; p = 0.05) reduction in days with severe illness and high fever respectively.Milk can be a good medium for delivery of prebiotic and probiotic and resulted in significant reduction of dysentery, respiratory morbidity and febrile illness. Overall, impact of diarrhea was not significant. These findings need confirmation in other settings

Effect of allopurinol in addition to hypothermia treatment in neonates for hypoxic-ischemic brain injury on neurocognitive outcome (ALBINO): Study protocol of a blinded randomized placebo-controlled parallel group multicenter trial for superiority (phase III)

Background: Perinatal asphyxia and resulting hypoxic-ischemic encephalopathy is a major cause of death and long-term disability in term born neonates. Up to 20,000 infants each year are affected by HIE in Europe and even more in regions with lower level of perinatal care. The only established therapy to improve outcome in these infants is therapeutic hypothermia. Allopurinol is a xanthine oxidase inhibitor that reduces the production of oxygen radicals as superoxide, which contributes to secondary energy failure and apoptosis in neurons and glial cells after reperfusion of hypoxic brain tissue and may further improve outcome if administered in addition to therapeutic hypothermia. Methods: This study on the effects of ALlopurinol in addition to hypothermia treatment for hypoxic-ischemic Brain Injury on Neurocognitive Outcome (ALBINO), is a European double-blinded randomized placebo-controlled parallel group multicenter trial (Phase III) to evaluate the effect of postnatal allopurinol administered in addition to standard of care (including therapeutic hypothermia if indicated) on the incidence of death and severe neurodevelopmental impairment at 24 months of age in newborns with perinatal hypoxic-ischemic insult and signs of potentially evolving encephalopathy. Allopurinol or placebo will be given in addition to therapeutic hypothermia (where indicated) to infants with a gestational age 65 36 weeks and a birth weight 65 2500 g, with severe perinatal asphyxia and potentially evolving encephalopathy. The primary endpoint of this study will be death or severe neurodevelopmental impairment versus survival without severe neurodevelopmental impairment at the age of two years. Effects on brain injury by magnetic resonance imaging and cerebral ultrasound, electric brain activity, concentrations of peroxidation products and S100B, will also be studied along with effects on heart function and pharmacokinetics of allopurinol after iv-infusion. Discussion: This trial will provide data to assess the efficacy and safety of early postnatal allopurinol in term infants with evolving hypoxic-ischemic encephalopathy. If proven efficacious and safe, allopurinol could become part of a neuroprotective pharmacological treatment strategy in addition to therapeutic hypothermia in children with perinatal asphyxia. Trial registration: NCT03162653, www.ClinicalTrials.gov, May 22, 2017

Dynamics of Seed-Borne Rice Endophytes on Early Plant Growth Stages

Bacterial endophytes are ubiquitous to virtually all terrestrial plants. With the increasing appreciation of studies that unravel the mutualistic interactions between plant and microbes, we increasingly value the beneficial functions of endophytes that improve plant growth and development. However, still little is known on the source of established endophytes as well as on how plants select specific microbial communities to establish associations. Here, we used cultivation-dependent and -independent approaches to assess the endophytic bacterrial community of surface-sterilized rice seeds, encompassing two consecutive rice generations. We isolated members of nine bacterial genera. In particular, organisms affiliated with Stenotrophomonas maltophilia and Ochrobactrum spp. were isolated from both seed generations. PCR-based denaturing gradient gel electrophoresis (PCR-DGGE) of seed-extracted DNA revealed that approximately 45% of the bacterial community from the first seed generation was found in the second generation as well. In addition, we set up a greenhouse experiment to investigate abiotic and biotic factors influencing the endophytic bacterial community structure. PCR-DGGE profiles performed with DNA extracted from different plant parts showed that soil type is a major effector of the bacterial endophytes. Rice plants cultivated in neutral-pH soil favoured the growth of seed-borne Pseudomonas oryzihabitans and Rhizobium radiobacter, whereas Enterobacter-like and Dyella ginsengisoli were dominant in plants cultivated in low-pH soil. The seed-borne Stenotrophomonas maltophilia was the only conspicuous bacterial endophyte found in plants cultivated in both soils. Several members of the endophytic community originating from seeds were observed in the rhizosphere and surrounding soils. Their impact on the soil community is further discussed

Outlier SNPs detect weak regional structure against a background of genetic homogeneity in the Eastern Rock Lobster, Sagmariasus verreauxi

Genetic differentiation is characteristically weak in marine species making assessments of population connectivity and structure difficult. However, the advent of genomic methods has increased genetic resolution, enabling studies to detect weak, but significant population differentiation within marine species. With an increasing number of studies employing high resolution genome-wide techniques, we are realising that the connectivity of marine populations is often complex and quantifying this complexity can provide an understanding of the processes shaping marine species genetic structure and to inform long-term, sustainable management strategies. This study aims to assess the genetic structure, connectivity, and local adaptation of the Eastern Rock Lobster (Sagmariasus verreauxi), which has a maximum pelagic larval duration of 12 months and inhabits both subtropical and temperate environments. We used 645 neutral and 15 outlier SNPs to genotype lobsters collected from the only two known breeding populations and a third episodic population—encompassing S. verreauxi's known range. Through examination of the neutral SNP panel, we detected genetic homogeneity across the three regions, which extended across the Tasman Sea encompassing both Australian and New Zealand populations. We discuss differences in neutral genetic signature of S. verreauxi and a closely related, co-distributed rock lobster, Jasus edwardsii, determining a regional pattern of genetic disparity between the species, which have largely similar life histories. Examination of the outlier SNP panel detected weak genetic differentiation between the three regions. Outlier SNPs showed promise in assigning individuals to their sampling origin and may prove useful as a management tool for species exhibiting genetic homogeneity

Long-term genetic consequences of mammal reintroductions into an Australian conservation reserve

Available online 05 January 2018Reintroduction programs aim to restore self-sustaining populations of threatened species to their historic range. However, demographic restoration may not reflect genetic restoration, which is necessary for the long-term persistence of populations. Four threatened Australian mammals, the greater stick-nest rat (Leporillus conditor), greater bilby (Macrotis lagotis), burrowing bettong (Bettongia lesueur) and western barred bandicoot (Perameles bougainville), were reintroduced at Arid Recovery Reserve in northern South Australia over the last 18 years. These reintroductions have been deemed successful based on population growth and persistence, however the genetic consequences of the reintroductions are not known. We generated large single nucleotide polymorphism (SNP) datasets for each species currently at Arid Recovery and compared them to samples collected from founders. We found that average genetic diversity in all populations at the Arid Recovery Reserve are close to, or exceeding, the levels measured in the founders. Increased genetic diversity in two species was achieved by admixing slightly diverged and inbred source populations. Our results suggest that genetic diversity in translocated populations can be improved or maintained over relatively long time frames, even in small conservation reserves, and highlight the power of admixture as a tool for conservation management.Lauren C. White, Katherine E. Moseby, Vicki A. Thomson, Stephen C. Donnellan, Jeremy J. Austi