Extremely low nucleotide diversity among thirty-six new chloroplast genome sequences from Aldama (Heliantheae, Asteraceae) and comparative chloroplast genomics analyses with closely related genera

Aldama (Heliantheae, Asteraceae) is a diverse genus in the sunflower family. To date, nearly 200 Asteraceae chloroplast genomes have been sequenced, but the plastomes of Aldama remain undescribed. Plastomes in Asteraceae usually show little sequence divergence, consequently, our hypothesis is that species of Aldama will be overall conserved. In this study, we newly sequenced 36 plastomes of Aldama and of five species belonging to other Heliantheae genera selected as outgroups (i.e., Dimerostemma asperatum, Helianthus tuberosus, Iostephane heterophylla, Pappobolus lanatus var. lanatus, and Tithonia diversifolia). We analyzed the structure and gene content of the assembled plastomes and performed comparative analyses within Aldama and with other closely related genera. As expected, Aldama plastomes are very conserved, with the overall gene content and orientation being similar in all studied species. The length of the plastome is also consistent and the junction between regions usually contain the same genes and have similar lengths. A large ~20 kb and a small ~3 kb inversion were detected in the Large Single Copy (LSC) regions of all assembled plastomes, similarly to other Asteraceae species. The nucleotide diversity is very low, with only 1,509 variable sites in 127,466 bp (i.e., 1.18% of the sites in the alignment of 36 Aldama plastomes, with one of the IRs removed, is variable). Only one gene, rbcL, shows signatures of positive selection. The plastomes of the selected outgroups feature a similar gene content and structure compared to Aldama and also present the two inversions in the LSC region. Deletions of different lengths were observed in the gene ycf2. Multiple SSRs were identified for the sequenced Aldama and outgroups. The phylogenetic analysis shows that Aldama is not monophyletic due to the position of the Mexican species A. dentata. All Brazilian species form a strongly supported clade. Our results bring new understandings into the evolution and diversity of plastomes at the species level

Elaboração e validação de protocolo para atendimento de pacientes com COVID-19 em centros de hemodiálise

Objetivo: Descrever a elaboração e validação de um protocolo para atendimento de pacientes suspeitos ou com Coronavirus Disease-19 (COVID-19) em hemodiálise.Método: Estudo metodológico conduzido de março a agosto/2020 em hospital do sul do Brasil. O estudo envolveu diagnóstico situacional, revisão da literatura, elaboração do protocolo e validação de conteúdo (abrangência, clareza e pertinência). Participaram da validação dez profissionais da equipe multidisciplinar com experiência no atendimento de pacientes com doença renal e um órgão oficial fiscalizatório de enfermagem. Obteve-se 100% de consenso entre os especialistas.Resultados: Foram elaborados: “Fluxo de atendimento para pacientes constituído de seis “etapas” e “Plano gerencial para centros de diálise”. A validação permitiu aprimorar e refinar o conteúdo atendendo preceitos de normas sanitárias, segurança e diretrizes clínicas.Considerações finais: A elaboração e validação do protocolo podem padronizar e nortear a prática clínica, promovendo a continuidade e a segurança no cuidado, podendo ser utilizado em outros centros. Palavras-chave: Diálise renal. Protocolos clínicos. Infecções por coronavírus. Estudo de validação. Segurança do paciente

Acquisition and diversification of tendrilled leaves in Bignonieae\ud (Bignoniaceae) involved changes in expression patterns of\ud SHOOTMERISTEMLESS (STM), LEAFY/FLORICAULA(LFY/\ud FLO), and PHANTASTICA(PHAN)

Leaves have undergone structural modifications over evolutionary time, and presently exist in many forms. For instance, in Fabaceae and Bignoniaceae, leaf parts can be modified into tendrils. Currently, no data are available on genic control of tendrilled leaf development outside Fabaceae. Here, we conducted a detailed study of three representatives of Bignonieae: Amphilophium buccinatorium, Dolichandra unguis-cati, and Bignonia callistegioides, bearing multifid, trifid, and simple-tendrilled leaves, respectively. We investigated the structure of their petioles, petiolules, leaflets, and tendrils through histological analyses. Additionally, the expression of SHOOTMERISTEMLESS (STM), PHANTASTICA (PHAN), and LEAFY/FLORICAULA (LFY/FLO) during leaf development was analyzed by in situ hybridizations. Tendrils share some anatomical similarities with leaflets, but not with other leaf parts. Transcripts of both STM and LFY/FLO were detected in leaf primordia, associated with regions from which leaflets and tendril branches originate. PHAN expression was found to be polarized in branched tendrils, but not in simple tendrils. In Bignonieae, tendrils are modified leaflets that, as a result of premature completion of development, become bladeless organs. Bignonieae leaves develop differently from those of peas, as both LFY/FLO and STM are expressed in developing leaves of Bignonieae. Moreover, PHAN is probably involved in tendril diversification in Bignonieae, as it has distinct expression patterns in different leaf types.(CNPq, Grant 140470/2007-7); (CAPES, Grant 4395-08-5

Radiation of the Tnt1 retrotransposon superfamily in three Solanaceae genera

Abstract\ud \ud \ud \ud Background\ud \ud Tnt1 was the first active plant retrotransposon identified in tobacco after nitrate reductase gene disruption. The Tnt1 superfamily comprises elements from Nicotiana (Tnt1 and Tto1) and Lycopersicon (Retrolyc1 and Tlc1) species. The study presented here was conducted to characterise Tnt1-related sequences in 20 wild species of Solanum and five cultivars of Solanum tuberosum.\ud \ud \ud \ud Results\ud \ud Tnt1-related sequences were amplified from total genomic DNA using a PCR-based approach. Purified fragments were cloned and sequenced, and clustering analysis revealed three groups that differ in their U3 region. Using a network approach with a total of 453 non-redundant sequences isolated from Solanum (197), Nicotiana (140) and Lycopersicon (116) species, it is demonstrated that the Tnt1 superfamily can be treated as a population to resolve previous phylogenetic multifurcations. The resulting RNAseH network revealed that sequences group according to the Solanaceae genus, supporting a strong association with the host genome, whereas tracing the U3 region sequence association characterises the modular evolutionary pattern within the Tnt1 superfamily. Within each genus, and irrespective of species, nearly 20% of Tnt1 sequences analysed are identical, indicative of being part of an active copy. The network approach enabled the identification of putative "master" sequences and provided evidence that within a genus these master sequences are associated with distinct U3 regions.\ud \ud \ud \ud Conclusion\ud \ud The results presented here support the hypothesis that the Tnt1 superfamily was present early in the evolution of Solanaceae. The evidence also suggests that the RNAseH region of Tnt1 became fixed at the host genus level whereas, within each genus, propagation was ensured by the diversification of the U3 region. Different selection pressures seemed to have acted on the U3 and RNAseH modules of ancestral Tnt1 elements, probably due to the distinct functions of these regions in the retrotransposon life cycle, resulting in both co evolution and adaptation of the element population with its host.M.E. Manetti is a recipient of a CAPES (Coordenação de Aperfeiçoamento de Pessoal de Nível Superior) Ph.D. fellowship. We thank Silvia Regina Blanco Ribeiro for sequencing and Myna Nakabashi for technical assistance. Financial support for the work presented here was provided to MAVS from FAPESP (Brazil), CNPq (Brazil) and USP (Brazil).M.E. Manetti is a recipient of a CAPES (Coordenação de Aperfeiçoamento de Pessoal de Nível Superior) Ph.D. fellowship. We thank Silvia Regina Blanco Ribeiro for sequencing and Myna Nakabashi for technical assistance. Financial support for the work presented here was provided to MAVS from FAPESP (Brazil), CNPq (Brazil) and USP (Brazil)

Plant degreening: evolution and expression of tomato\ud (Solanum lycopersicum) dephytylation enzymes

Chlorophyll is the most abundant pigment on earth and even though it is known that its high photo-excitability necessitates a tight regulation of its degradation pathway, to date there are still several steps in chlorophyll breakdown that remain obscure. In order to better understand the ‘degreening’ processes that accompany leaf senescence and fruit ripening, we characterized the enzyme-encoding genes involved in dephytylation from tomato (Solanum lycopersicum). A single pheophytinase (PPH) gene and four chlorophyllase (CLH) genes were identified in the tomato genome. A phenetic analysis revealed two groups of CLHs in eudicot species and further evolutionary analysis indicated that these enzymes are under diverse selection pressures. A comprehensive expression profile analysis also suggested functional specificity for these dephytylating enzymes. The integrated analysis allows us to propose three general roles for chlorophyll dephytylation: i) PPH, which is under high selective constraint, is responsible for chlorophyll degradation during developmentally programed physiological processes; ii) Group I CLHs, which are under relaxed selection constraint, respond to environmental and hormonal stimuli and play a role in plant adaptation plasticity; and iii) Group II CLHs, which are also under high selective constraint, are mostly involved in chlorophyll recycling.BSL and JA were recipients of FAPESP fellowships and MR was funded by a fellowship from CNPq. This work was supported by FAPESP2012-12531-8 (Brazil). The authors thank Rohm and Haas Company for generous donation of the 1-methylcyclopropene (SmartFresh®) used for the experiments

Migration and the Environment: Some Reflections on Current Legal Issues and Possible Ways Forward

The rationale behind the volume on Migration and the Environment: Some Reflections on Current Legal Issues and Possible Ways Forward is to provide a comprehensive and critical review of the major outcomes, implications and achievements on the relevant questions of international law on international migration and the environment. The ultimate objective of the volume is to foster the debate among experts, scholars and policy makers. To this end, the collected papers analyze from different perspectives the link between migration and the environment and the phenomenon of environment-related migration, discuss the extent to which people whose movements are induced by environmental factors are protected under the existing international legal framework, investigate the main legal issues and normative gaps and analyze the solutions at stak

Functional characterization of sugarcane mustang domesticated transposases and comparative diversity in sugarcane, rice, maize and sorghum

Transposable elements (TEs) account for a large portion of plant genomes, particularly in grasses, in which they correspond to 50%-80% of the genomic content. TEs have recently been shown to be a source of new genes and new regulatory networks. The most striking contribution of TEs is referred as "molecular domestication", by which the element coding sequence loses its movement capacity and acquires cellular function. Recently, domesticated transposases known as mustang and derived from the Mutator element have been described in sugarcane. In order to improve our understanding of the function of these proteins, we identified mustang genes from Sorghum bicolor and Zea mays and performed a phenetic analysis to assess the diversity and evolutionary history of this gene family. This analysis identified orthologous groups and showed that mustang genes are highly conserved in grass genomes. We also explored the transcriptional activity of sugarcane mustang genes in heterologous and homologous systems. These genes were found to be ubiquitously transcribed, with shoot apical meristem having the highest expression levels, and were downregulated by phytohormones. Together, these findings suggest the possible involvement of mustang proteins in the maintenance of hormonal homeostasis.Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPq), BrazilCNPq (Conselho Nacional de Desenvolvimento Cientifico e Tecnologico, Brazil)FAPESP (Fundacao de Amparo a Pesquisa do Estado de Sao Paulo, Brazil)Fundacao de Amparo a Pesquisa do Estado de Sao Paulo (FAPESP), BrazilCNPqCNPqFAPESPFAPES

Natural occurring epialleles determine vitamin E accumulation in tomato fruits

Vitamin E (VTE) content is a low heritability nutritional trait for which the genetic determinants are poorly understood. Here, we focus on a previously detected major tomato VTE quantitative trait loci (QTL; mQTL9-2-6) and identify the causal gene as one encoding a 2-methyl-6-phytylquinol methyltransferase (namely VTE3(1)) that catalyses one of the final steps in the biosynthesis of γ- and α-tocopherols, which are the main forms of VTE. By reverse genetic approaches, expression analyses, siRNA profiling and DNA methylation assays, we demonstrate that mQTL9-2-6 is an expression QTL associated with differential methylation of a SINE retrotransposon located in the promoter region of VTE3(1). Promoter DNA methylation can be spontaneously reverted leading to different epialleles affecting VTE3(1) expression and VTE content in fruits. These findings indicate therefore that naturally occurring epialleles are responsible for regulation of a nutritionally important metabolic QTL and provide direct evidence of a role for epigenetics in the determination of agronomic traits.L.Q. was recipient of a fellowship of Agencia Nacional de Promoción Científica y Tecnológica and Consejo Nacional de Investigaciones Científicas y Técnicas in Argentina and supported by a postdoctral fellowship from Investissements d’Avenir ANR-10-LABX-54 MEMO LIFE in France. J.A. and L.B. were recipients of a fellowship of Fundação à Amparo da Pesquisa do Estado de São Paulo (Brazil). J.V.C.d.S. was recipient of a fellowship of Conselho Nacional de Desenvolvimento Científico e Tecnológico (Brazil). R.A., L.B. and F.C. are members of Consejo Nacional de Investigaciones Científicas y Técnicas (Argentina). This work was carried out in compliance with current laws governing genetic experimentation in Brazil and in Argentina. This work was supported with grants from Instituto Nacional de Tecnologia Agropecuária, Consejo Nacional de Investigaciones Científicas y Técnicas and Agencia Nacional de Promoción Científica y Tecnológica (Argentina), Fundação à Amparo da Pesquisa do Estado de São Paulo, Conselho Nacional de Desenvolvimento Científico e Tecnológico and Universidade de São Paulo (Brazil); Max Planck Society (Germany); the Agence Nationale de la Recherche (Investissements d’Avenir ANR-10-LABX-54 MEMO LIFE and ANR-11-IDEX-0001-02 PSL* Research University to V.C.); and the European Union (EpiGeneSys FP7 Network of Excellence number 257082 to V.C. and the European Solanaceae Integrated Project FOOD-CT-2006-016214 to F.C., M.R. and A.R.F.)

Galacturonosyltransferase 4 silencing alters pectin composition and carbon partitioning in tomato

Pectin is a main component of the plant cell wall and is the most complex family of polysaccharides in nature. Its composition is essential for the normal growth and morphology pattern, as demonstrated by pectin-defective mutant phenotypes. Besides this basic role in plant physiology, in tomato, pectin structure contributes to very important quality traits such as fruit firmness. Sixty-seven different enzymatic activities have been suggested to be required for pectin biosynthesis, but only a few genes have been identified and studied so far. This study characterized the tomato galacturonosyltransferase (GAUT) family and performed a detailed functional study of the GAUT4 gene. The tomato genome harbours all genes orthologous to those described previously in Arabidopsis thaliana, and a transcriptional profile revealed that the GAUT4 gene was expressed at higher levels in developing organs. GAUT4-silenced tomato plants exhibited an increment in vegetative biomass associated with palisade parenchyma enlargement. Silenced fruits showed an altered pectin composition and accumulated less starch along with a reduced amount of pectin, which coincided with an increase in firmness. Moreover, the harvest index was dramatically reduced as a consequence of the reduction in the fruit weight and number. Altogether, these results suggest that, beyond its role in pectin biosynthesis, GAUT4 interferes with carbon metabolism, partitioning, and allocation. Hence, this cell-wall-related gene seems to be key in determining plant growth and fruit production in tomatoFil: Godoy, Fabiana de. Universidade de São Pablo. Departamento de Botânica; BrasilFil: Bermúdez, Luisa. Universidade de São Pablo. Departamento de Botânica; BrasilFil: Lira, Bruno Silvestre. Universidade de São Pablo. Departamento de Botânica; BrasilFil: Souza, Amanda Pereira de. Universidade de São Pablo. Departamento de Botânica; BrasilFil: Elbl, Paula. Universidade de São Pablo. Departamento de Botânica; BrasilFil: Demarco, Diego. Universidade de São Pablo. Departamento de Botânica; BrasilFil: Alseekh, Saleh. Max Planck Institute for Molecular Plant Physiology; AlemaniaFil: Insani, Ester Marina. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; ArgentinaFil: Buckeridge, Marcos. Universidade de São Pablo. Departamento de Botânica; BrasilFil: Almeida, Juliana. Universidade de São Pablo. Departamento de Botânica; BrasilFil: Grigioni, Gabriela Maria. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Tecnología de Alimentos; ArgentinaFil: Fernie, Alisdair Robert. Max Planck Institute for Molecular Plant Physiology; AlemaniaFil: Carrari, Fernando. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; ArgentinaFil: Rossi, Magdalena. Universidade de São Pablo. Departamento de Botânica; Brasi