A Comprehensive Phylogenomic Platform for Exploring the Angiosperm Tree of Life.

The tree of life is the fundamental biological roadmap for navigating the evolution and properties of life on Earth, and yet remains largely unknown. Even angiosperms (flowering plants) are fraught with data gaps, despite their critical role in sustaining terrestrial life. Today, high-throughput sequencing promises to significantly deepen our understanding of evolutionary relationships. Here, we describe a comprehensive phylogenomic platform for exploring the angiosperm tree of life, comprising a set of open tools and data based on the 353 nuclear genes targeted by the universal Angiosperms353 sequence capture probes. The primary goals of this article are to (i) document our methods, (ii) describe our first data release, and (iii) present a novel open data portal, the Kew Tree of Life Explorer (https://treeoflife.kew.org). We aim to generate novel target sequence capture data for all genera of flowering plants, exploiting natural history collections such as herbarium specimens, and augment it with mined public data. Our first data release, described here, is the most extensive nuclear phylogenomic data set for angiosperms to date, comprising 3099 samples validated by DNA barcode and phylogenetic tests, representing all 64 orders, 404 families (96$\%$) and 2333 genera (17$\%$). A "first pass" angiosperm tree of life was inferred from the data, which totaled 824,878 sequences, 489,086,049 base pairs, and 532,260 alignment columns, for interactive presentation in the Kew Tree of Life Explorer. This species tree was generated using methods that were rigorous, yet tractable at our scale of operation. Despite limitations pertaining to taxon and gene sampling, gene recovery, models of sequence evolution and paralogy, the tree strongly supports existing taxonomy, while challenging numerous hypothesized relationships among orders and placing many genera for the first time. The validated data set, species tree and all intermediates are openly accessible via the Kew Tree of Life Explorer and will be updated as further data become available. This major milestone toward a complete tree of life for all flowering plant species opens doors to a highly integrated future for angiosperm phylogenomics through the systematic sequencing of standardized nuclear markers. Our approach has the potential to serve as a much-needed bridge between the growing movement to sequence the genomes of all life on Earth and the vast phylogenomic potential of the world's natural history collections. [Angiosperms; Angiosperms353; genomics; herbariomics; museomics; nuclear phylogenomics; open access; target sequence capture; tree of life.].

A nuclear phylogenomic study of the angiosperm order Myrtales, exploring the potential and limitations of the universal Angiosperms353 probe set.

PREMISE: To further advance the understanding of the species-rich, economically and ecologically important angiosperm order Myrtales in the rosid clade, comprising nine families, approximately 400 genera and almost 14,000 species occurring on all continents (except Antarctica), we tested the Angiosperms353 probe kit. METHODS: We combined high-throughput sequencing and target enrichment with the Angiosperms353 probe kit to evaluate a sample of 485 species across 305 genera (76% of all genera in the order). RESULTS: Results provide the most comprehensive phylogenetic hypothesis for the order to date. Relationships at all ranks, such as the relationship of the early-diverging families, often reflect previous studies, but gene conflict is evident, and relationships previously found to be uncertain often remain so. Technical considerations for processing HTS data are also discussed. CONCLUSIONS: High-throughput sequencing and the Angiosperms353 probe kit are powerful tools for phylogenomic analysis, but better understanding of the genetic data available is required to identify genes and gene trees that account for likely incomplete lineage sorting and/or hybridization events.

Zinc hyperaccumulation substitutes for defense failures beyond salicylate and jasmonate signaling pathways of Alternaria brassicicola attack in Noccaea caerulescens.

The hypothesis of metal defense as a substitute for a defective biotic stress signaling system in metal hyperaccumulators was tested using the pathosystem Alternaria brassicicola-Noccaea caerulescens under low (2 µM), medium (12 µM) and high (102 µM) Zn supply. Regardless the Zn supply, N. caerulescens responded to fungal attack with the activation of both HMA4 coding for a Zn transporter, and biotic stress signaling pathways. Salicylate, jasmonate, abscisic acid and indoleacetic acid concentrations, as well as biotic stress marker genes (PDF1.2, CHIB, LOX2, PR1 and BGL2) were activated 24 h upon inoculation. Based on the activation of defense genes 24 h after the inoculation an incompatible fungal-plant interaction could be predicted. Nonetheless, in the longer term (7 days) no effective protection against A. brassicicola was achieved in plants exposed to low and medium Zn supply. After 1 week the biotic stress markers were even further increased in these plants, and this compatible interaction was apparently not caused by a failure in the signaling of the fungal attack, but due to the lack of specificity in the type of the activated defense mechanisms. Only plants receiving high Zn exhibited an incompatible fungal interaction. High Zn accumulation in these plants, possibly in cooperation with high glucosinolate concentrations, substituted for the ineffective defense system and the interaction turned into incompatible. In a threshold-type response, these joint effects efficiently hampered fungal spread and, consequently decreased the biotic stress signaling.

Signal cross talk in Arabidopsis exposed to cadmium, silicon, and Botrytis cinerea.

The role of defence gene expression triggered by Cd toxicity in the plant's response to Botrytis cinerea was investigated in Arabidopsis thaliana Columbia 0. Silicon (0 or 1.5 mM) and Cd (0, 1 or 10 µM) were supplied to 3-month-old solution-cultured plants. After 3 days, half of the plants of each treatment were inoculated with Botrytis. Supplied Cd concentrations were below the toxicity threshold and did not cause shoot growth inhibition or evidence of oxidative stress, while Botrytis infection severely decreased plant growth in all treatments. The expression of marker genes PR1 and BGL2 for the salicylic acid (SA) and the PDF1.2 for the jasmonic acid-ethylene (JA-ET) signalling pathways was enhanced in 10 µM Cd-treated non-infected plants. Twenty hours after inoculation, PDF1.2 expression showed a strong increase in all treatments, while enhanced PR1, BGL2, and CHIB expression was only found 7 days after infection. A great synergistic effect of Cd and Botrytis on PDF1.2 expression was found in 10 µM Cd-treated plants. Silicon decreased PR1, BGL2, and CHIB, while increasing PDF1.2 expression, which indicates its role as a modulator of the signalling pathways involved in the plant's response to fungal infection. Botrytis growth decreased in 10 µM Cd-treated plants, which could be due to the combined effects of Cd and Botrytis activating the SA and JA-ET-mediated signalling pathways. Taken together, our results provide support for the view that Cd concentrations close to the toxicity threshold induce defence signalling pathways which potentiate the plant's response against fungal infection.

Complications associated with vertical bone augmentation techniques in implant dentistry: A systematic review of clinical studies published in the last ten years.

Vertical bone augmentation procedures are increasingly necessary in daily practice. However, it has been reported that vertical ridge augmentation is one of the least predictable techniques in terms of complications. The aim of this systematic review was to evaluate and compare complications in relation to the different procedures used for vertical bone augmentation prior to implant placement. This review was conducted according to PRISMA guidelines. An electronic search was carried out in four databases: The National Library of Medicine (MEDLINE/PubMed); Web of Science; SCOPUS; and Cochrane Central Register of Controlled Trials (CENTRAL). The Newcastle-Ottawa Quality Assessment Scale, the Cochrane Collaboration tool for assessing risk of bias, and The Joanna Briggs Institute Critical Appraisal tool were used to assess the quality of evidence in the studies reviewed. Twenty-five studies with a total of 749 vertically augmented sites were included in the review. Complication rates varied among the different procedures: 51.02% for distraction osteogenesis, 38.01% for bone blocks, and 16.80% for guided bone regeneration. Vertical bone augmentation procedures prior to implant placement are associated with frequent surgical complications and should be approached with caution due to their possible impact on clinical treatment success.

A Role for Zinc in Plant Defense Against Pathogens and Herbivores.

Pests and diseases pose a threat to food security, which is nowadays aggravated by climate change and globalization. In this context, agricultural policies demand innovative approaches to more effectively manage resources and overcome the ecological issues raised by intensive farming. Optimization of plant mineral nutrition is a sustainable approach to ameliorate crop health and yield. Zinc is a micronutrient essential for all living organisms with a key role in growth, development, and defense. Competition for Zn affects the outcome of the host-attacker interaction in both plant and animal systems. In this review, we provide a clear framework of the different strategies involving low and high Zn concentrations launched by plants to fight their enemies. After briefly introducing the most relevant macro- and micronutrients for plant defense, the functions of Zn in plant protection are summarized with special emphasis on superoxide dismutases (SODs) and zinc finger proteins. Following, we cover recent meaningful studies identifying Zn-related passive and active mechanisms for plant protection. Finally, Zn-based strategies evolved by pathogens and pests to counteract plant defenses are discussed.

Zinc triggers signaling mechanisms and defense responses promoting resistance to Alternaria brassicicola in Arabidopsis thaliana.

According to the elemental defense hypothesis the accumulation of trace elements by plants may substitute for organic defenses, while the joint effects hypothesis proposes that trace elements and organic defenses can have additive or synergistic effects against pathogens or herbivores. To evaluate these hypotheses the response of the pathosystem Alternaria brassicicola-Arabidopsis thaliana to control (2µM) and surplus (12µM) Zn was evaluated using the camalexin deficient mutant pad3-1 and mtp1-1, a mutant with impaired Zn vacuolar storage, along with the corresponding wildtypes. In vitro, a 50% inhibition of fungal growth was achieved by 440µM Zn. A. thaliana leaves could accumulate equivalent concentrations without harm. In fact, surplus Zn enhanced the resistance of A. thaliana to fungal attack in Columbia (Col-0), Wassilewskija (WS), and mtp1-1. However, surplus Zn was unable to protect pad3-1 demonstrating that Zn cannot substitute for camalexin, the main organic defense in A. thaliana. High, non phytotoxic leaf Zn concentrations enhanced the resistance to A. brassicicola of A. thaliana genotypes able to produce camalexin. This was mainly due to Zn-induced enhancement of the JA/ETH signaling pathway leading to enhanced PAD3 expression. These results support the joint effects hypothesis and highlight the importance of adequate Zn supply for reinforced pathogen resistance.

Characterization of Zinc and Cadmium Hyperaccumulation in Three Noccaea (Brassicaceae) Populations from Non-metalliferous Sites in the Eastern Pyrenees.

The Southern slope of the Pyrenees is the meridional limit for the distribution of several Noccaea populations. However, the systematic description of these populations and their hyperaccumulation mechanisms are not well established. Morphological and genetic analysis (ITS and 3 chloroplast regions) were used to identify Noccaea populations localized on non-metallicolous soils during a survey in the Catalonian Pyrenees. Cd and Zn concentrations were analyzed in soils and plants both sampled in the field and grown hydroponically. The expression of selected metal transporter genes was assessed by quantitative PCR. The populations were identified as Noccaea brachypetala (Jord.) F.K. Mey by conspicuous morphological traits. Principal component analysis provided a clear separation among N. brachypetala, Noccaea caerulescens J. Presl & C. Presl and Noccaea occitanica (Jord.) F.K. Mey., three Noccaea species reported in the Pyrenees. Contrastingly, ITS and cpDNA analyses were unable to clearly differentiate these taxa. Differences in the expression of the metal transporter genes HMA3, HMA4, and MTP1 between N. caerulescens and N. brachypetala, and those amongst the N. brachypetala populations suggest differences in the strategies for handling enhanced Cd and Zn availability. This is the first report demonstrating Cd and Zn hyperaccumulation by N. brachypetala both in the field and in hydroponics. This comprehensive study based on taxonomic, molecular, and physiological data allows both the correct identification of this species and the characterization of population differences in hyperaccumulation and tolerance of Zn and Cd.

Do toxic ions induce hormesis in plants?

The concept of hormesis in plants is critically reviewed, taking growth stimulation by low concentrations of toxic trace elements as a reference. The importance of both non-adaptive and adaptive mechanisms underlying ion-induced hormetic growth responses is highlighted. The activation of defense mechanisms by metal ions and pathogenic elicitors and the cross talk between the signals induced by metal ions and biotic stressors are considered. The production of reactive oxygen species and, consequently, the induction of stress-induced antioxidants, are key mechanisms in metal ion-induced hormesis in plants. It is concluded that in the current scientific literature, hormesis is used as an "umbrella" term that includes a wide range of different mechanisms. It is recommended that the term hormesis be used in plant toxicology as a descriptive term for the stimulated phase in growth response curves that is induced by low concentrations of toxic metal ions without evidence of the underlying mechanisms. If the mechanisms underlying the stimulated growth phase have been identified, specific terms, such as amelioration, defense gene activation, priming or acclimation, should be used.

[Stewardship of public health surveillance in the health system in Colombia: a case study]. / Rectoría de la vigilancia en salud pública en el sistema de seguridad social en salud de Colombia: estudio de casos.

INTRODUCTION: With the reform of the Colombian health system in 1993, public health surveillance continued to be a governmental responsibility under the stewardship of the Ministry of Social Protection along with state and local health authorities. OBJECTIVE: The effectiveness of the development and organization of state and municipality public health surveillance programs will be studied as they have evolved under the general social security system in Colombia. MATERIALS AND METHODS: Qualitative study and case-study method are applied to several institutions as they function in 5 states and 11 counties, ten years after the health system reforms. RESULTS: Public health authorities have reduced resources for providing advice, technical assistance, supervision and control of the process of the public health surveillance. Weaknesses in administrative control are common. Quantity and quality of human resources, as well as, staffing and financial resources are inadequate to meet the responsibilities that have been assigned to each state and county. The public health surveillance has prioritized the notification and registration of cases, and the strength of development of particular areas occasionally has been subject to the particular interests of officials in charge, particularly in the public hospitals. Little commitment or interest is shown by mayors, insurance companies, and institutions providing health services that are supposed to be involved with monitoring. A lack of cross-institutional collaboration is apparent in the development of health services surveillance. CONCLUSION: The implementation of public health surveillance at state and local levels is weak due to problems with the governmental stewardship. These weaknesses are manifested in the lack of regulation, financing and control of the health system.

Rectoría de la vigilancia en salud pública en el sistema de seguridad social en salud de Colombia: estudio de casos / Stewardship of public health surveillance in the health system in Colombia: a cases study

Introducción. Con la reforma del sistema de salud en Colombia, la vigilancia en salud pública continuó siendo una responsabilidad estatal, bajo la rectoría del Ministerio de la Protección Social y las autoridades sanitarias departamentales y locales. Objetivo. Comprender la manera como los departamentos y municipios han estructurado y desarrollado la vigilancia en salud pública en el marco del sistema general de seguridad en salud en Colombia, posterior a la reforma de 1993. Materiales y métodos. Se llevó a cabo un estudio cualitativo según el método de estudios de casos múltiples e institucionales en 5 departamentos y 11 municipios, en el año 2004, 10 años después de la reforma en salud. Resultados. Las autoridades sanitarias han reducido los recursos para asesoría, asistencia técnica, supervisión y control del proceso de la vigilancia en salud pública. Existen deficiencias en aspectos administrativos, la cantidad y calidad del recurso humano, la dotación y los recursos financieros para cumplir las responsabilidades que les han sido asignadas a los departamentos y a los municipios. La vigilancia en salud pública ha priorizado la notificación y el registro de los casos, y su desarrollo ha estado sujeto al interés de algunos funcionarios, principalmente de los hospitales públicos. Existe poco compromiso de los alcaldes, empresas aseguradoras, instituciones prestadoras de servicios de salud y del personal asistencial, para participar en la vigilancia. Falta acción intersectorial para el desarrollo de la vigilancia en salud. Conclusión. La implementación de la vigilancia en salud pública en el ámbito territorial es débil debido a problemas en la rectoría estatal, manifiestos en la falta de regulación, financiamiento y control en el sistema de salud.

Introduction. With the reform of the Colombian health system in 1993, public health surveillance continued to be a governmental responsibility under the stewardship of the Ministry of Social Protection along with state and local health authorities. Objective. The effectiveness of the development and organization of state and municipality public health surveillance programs will be studied as they have evolved under the general social security system in Colombia. Materials and methods. Qualitative study and case-study method are applied to several institutions as they function in 5 states and 11 counties, ten years after the health system reforms. Results. Public health authorities have reduced resources for providing advice, technical assistance, supervision and control of the process of the public health surveillance. Weaknesses in administrative control are common. Quantity and quality of human resources, as well as, staffing and financial resources are inadequate to meet the responsibilities that have been assigned to each state and county. The public health surveillance has prioritized the notification and registration of cases, and the strength of development of particular areas occasionally has been subject to the particular interests of officials in charge, particularly in the public hospitals. Little commitment or interest is shown by mayors, insurance companies, and institutions providing health services that are supposed to be involved with monitoring. A lack of cross-institutional collaboration is apparent in the development of health services surveillance. Conclusion. The implementation of public health surveillance at state and local levels is weak due to problems with the governmental stewardship. These weaknesses are manifested in the lack of regulation, financing and control of the health system.