Addressing Conservation Needs: Genetic Diversity and Population Ecology of the Endemic Tree Spondias tuberosa Arruda.

Spondias tuberosa Arruda (Anacardiaceae), popularly known as umbuzeiro or imbuzeiro, is a fruit tree native to the semiarid region of Brazil. The extractive harvesting of its fruits contributes significantly to the economy, generating an annual revenue of approximately $4,2 million. The present study aimed to assess the spatial pattern, allometric variations, fruit measurements, and genetic diversity of trees within a remaining forest of the Caatinga biome, with a focus on intrapopulation analysis. We used intersimple repeated sequence markers and the second-order function density of neighbours to determine the genetic and spatial structure. The density of neighbours was highest within a 10-meter radius. Biometric analyses revealed average fruit lengths of 31.12 mm (±0.22), diameters of 28.68 mm (±0.25), and fresh masses of 15.56 g (±0.33). Diaspores exhibited an average length, diameter, and thickness of 19.27 mm, 13.95 mm, and 11.14 mm, respectively, with a fresh mass of 2.28 g. Notably, the fresh mass demonstrated the highest coefficient of variation. Ten molecular markers were selected, generating 103 highly polymorphic loci (99.03%) with an average informative content of 0.45. Nei's diversity index (0.37) and Shannon's index (0.55) indicated moderate genetic diversity. Furthermore, Bayesian analysis revealed a population structure with two distinct genetic groups. The Infinite Allele and Mutation Step Models suggested a significant historical decline in population size, indicative of a genetic bottleneck. As a result, proactive in situ conservation strategies, including establishing protected natural areas, become essential, considering the socioeconomic significance of the species. Additionally, it is recommended to establish germplasm banks for ex situ conservation and the development of managed cultivation initiatives to reduce the pressure on native populations of S. tuberosa caused by extraction.

The 10-Item Physical Function Scale as a Sarcopenia Screening Tool for Patients on Hemodialysis.

OBJECTIVE: We investigated the accuracy of the 10-item Physical Function (PF-10) questions of the SF-36 quality of life questionnaire as a sarcopenia screening tool among patients on hemodialysis. METHODS: A cross-sectional, multicenter study that included adult patients on hemodialysis. The revised European Working Group on Sarcopenia in Older People was used to diagnose sarcopenia. The 10 questions about daily activities from the SF-36 quality of life questionnaire were used to appoint the PF-10, where the final score could range from 10 to 30, and the lower the worse the physical function. The PF-10 accuracy to identify confirmed sarcopenia (low muscle strength + low muscle mass) was assessed through a receiver operating characteristic curve and the cutoff was calculated using the Youden index. RESULTS: One hundred eighty-five patients were included (median 59 years; 45% female). Prevalence of confirmed sarcopenia was 31.4%. The median PF-10 score was 23 (interquartile range: 17-27) and a significant association with all sarcopenia measurements was found (all P < .05). The best cutoff calculated from the receiver operating characteristic curve was ≤26 points (area under the curve = 0.69, 95% confidence interval 0.61-0.77) with sensitivity and specificity of 96.6% and 71.0%, respectively. Moreover, patients with ≤26 points (n = 133, 72%) had a higher prevalence of low muscle strength by handgrip (53 vs. 19%; P < .001) and 5-time sit-to-stand (41 vs. 10%; P < .001), low gait speed (44 vs. 19%; P = .002), confirmed sarcopenia (39 vs. 11%; P < .001), and severe sarcopenia (26 vs. 4%; P = .001), but not low muscle mass (49 vs. 35%; P = .08), in comparison with those >26 points (n = 52, 28%). CONCLUSION: The PF-10 may be a useful physical dysfunction and sarcopenia screening tool in patients on hemodialysis. A PF-10 threshold of around 26 points appeared to display the fairest accuracy for diagnosing sarcopenia.

Unraveling the genetic diversity of Ceiba pubiflora (Malvaceae) in isolated limestone outcrops: Conservation strategies.

Seasonally Dry Tropical Forests (SDTFs) located on limestone outcrops are vulnerable to degradation caused by timber logging and limestone extraction for cement production. Some of these forests represent the last remnants of native vegetation cover, functioning as isolated islands. Ceiba pubiflora (Malvaceae) is a tree frequently found on limestone outcrops in the central region of Brazil. This study aimed to evaluate the genetic diversity and identify suitable populations for the establishment of Management Units (MUs) for conservation. Inter-simple sequence repeat markers were employed to assess the genetic diversity in ten populations sampled from the Caatinga, Cerrado, and Atlantic Forest biomes. The species exhibited substantial genetic diversity (HT = 0.345; PLP = 97.89%). Populations SAH, JAN, and MON demonstrated elevated rates of polymorphic loci (> 84.2%) along with notable genetic diversity (He > 0.325). Additionally, these populations were the primary contributors to gene flow. The analysis of molecular variance (AMOVA) indicated that most genetic variation occurs within populations (91.5%) than between them. In the Bayesian analysis, the ten populations were clustered into five groups, revealing the presence of at least three barriers to gene flow in the landscape: 1) the Central Plateau or Paranã River valley; 2) near the Espinhaço mountains or the São Francisco River valley; and 3) around the Mantiqueira mountain range, Chapada dos Veadeiros plateau, and disturbed areas. A positive and statistically significant correlation was observed between genetic (θB) and geographic distances (r = 0.425, p = 0.008). Based on these findings, we propose the establishment of Management Units in Minas Gerais state, encompassing the (1) southern region (MIN population), (2) central region (SAH population), and (3) north region (MON population), as well as in Goiás state, covering the (4) Central Plateau region. These units can significantly contribute to preserving the genetic diversity of these trees and protecting their habitat against ongoing threats.

Design and methodology of the SARCopenia trajectories and associations with adverse clinical outcomes in patients on HemoDialysis: the SARC-HD study.

BACKGROUND: Sarcopenia has been associated with adverse outcomes in patients with chronic kidney disease (CKD), particularly in those undergoing hemodialysis (HD). However, the trajectories across sarcopenia stages, their determinants, and associations with adverse clinical outcomes have yet to be comprehensively examined. METHODS: The SARC-HD is a multicenter, observational prospective cohort study designed to comprehensively investigate sarcopenia in patients on HD. Eligibility criteria include adult patients undergoing HD for ≥ 3 months. The primary objective is to investigate the trajectories of sarcopenia stages and their potential determinants. Secondary objectives include evaluating the association between sarcopenia and adverse clinical outcomes (i.e., falls, hospitalization, and mortality). Sarcopenia risk will be assessed by the SARC-F and SARC-CalF questionnaire. Sarcopenia traits (i.e., low muscle strength, low muscle mass, and low physical performance) will be defined according to the revised European Working Group on Sarcopenia in Older People and will be assessed at baseline and after 12 follow-up months. Patients will be followed-up at 3 monthly intervals for adverse clinical outcomes during 24 months. DISCUSSION: Collectively, we expect to provide relevant clinical findings for healthcare professionals from nephrology on the association between sarcopenia screening tools (i.e., SARC-F and SARC-CalF) with objective sarcopenia measurements, as well as to investigate predictors of trajectories across sarcopenia stages, and the impact of sarcopenia on adverse clinical outcomes. Hence, our ambition is that the data acquired from SARC-HD study will provide novel and valuable evidence to support an adequate screening and management of sarcopenia in patients on HD.

Inter-comparison of marine microbiome sampling protocols.

Research on marine microbial communities is growing, but studies are hard to compare because of variation in seawater sampling protocols. To help researchers in the inter-comparison of studies that use different seawater sampling methodologies, as well as to help them design future sampling campaigns, we developed the EuroMarine Open Science Exploration initiative (EMOSE). Within the EMOSE framework, we sampled thousands of liters of seawater from a single station in the NW Mediterranean Sea (Service d'Observation du Laboratoire Arago [SOLA], Banyuls-sur-Mer), during one single day. The resulting dataset includes multiple seawater processing approaches, encompassing different material-type kinds of filters (cartridge membrane and flat membrane), three different size fractionations (>0.22 µm, 0.22-3 µm, 3-20 µm and >20 µm), and a number of different seawater volumes ranging from 1 L up to 1000 L. We show that the volume of seawater that is filtered does not have a significant effect on prokaryotic and protist diversity, independently of the sequencing strategy. However, there was a clear difference in alpha and beta diversity between size fractions and between these and "whole water" (with no pre-fractionation). Overall, we recommend care when merging data from datasets that use filters of different pore size, but we consider that the type of filter and volume should not act as confounding variables for the tested sequencing strategies. To the best of our knowledge, this is the first time a publicly available dataset effectively allows for the clarification of the impact of marine microbiome methodological options across a wide range of protocols, including large-scale variations in sampled volume.

Thermostructural Evaluation of the Muriaé Watershed (Rio de Janeiro portion).

The hydrological basins can be considered sources of relevant information about the evolution of the Earth's crust since the relief forms that define the hydrographic channels are the resultant of the interaction between tectonics, pedogenics, intemperics and thermals processes. The geothermal field of Muriaé watershed was evaluated using eight (8) thermal logs and twenty-two (22) geochemical logs. The structural lineaments evidenced on the surface were interpreted jointly with the identification of sixty-five (65) magnetic lineaments from airborne magnetic data interpretation. The depths of these structures were range from the surface up to 4.5 km. The interpreted data allowed identification of regional tectonics features in the NE-SW direction, where the identified magnetic lineaments show a spatial correlation with accentuated topographic structures. The differences in the depths of the magnetic bodies found in conjunction with the heat flow distribution, evidence two distinct thermostructural zones: A1 (east part) presenting heat flow values within the average (approximately 60$\frac{mW.

The model diatom Phaeodactylum tricornutum provides insights into the diversity and function of microeukaryotic DNA methyltransferases.

Cytosine methylation is an important epigenetic mark involved in the transcriptional control of transposable elements in mammals, plants and fungi. The Stramenopiles-Alveolate-Rhizaria (SAR) lineages are a major group of ecologically important marine microeukaryotes, including the phytoplankton groups diatoms and dinoflagellates. However, little is known about their DNA methyltransferase diversity. Here, we performed an in-silico analysis of DNA methyltransferases found in marine microeukaryotes and showed that they encode divergent DNMT3, DNMT4, DNMT5 and DNMT6 enzymes. Furthermore, we found three classes of enzymes within the DNMT5 family. Using a CRISPR/Cas9 strategy we demonstrated that the loss of the DNMT5a gene correlates with a global depletion of DNA methylation and overexpression of young transposable elements in the model diatom Phaeodactylum tricornutum. The study provides a view of the structure and function of a DNMT family in the SAR supergroup using an attractive model species.

Characterization of a Marine Diatom Chitin Synthase Using a Combination of Meta-Omics, Genomics, and Heterologous Expression Approaches.

ß-Chitin has important ecological and physiological roles and potential for widespread applications, but the characterization of chitin-related enzymes from ß-chitin producers was rarely reported. Querying against the Tara Oceans Gene Atlas, 4,939 chitin-related unique sequences from 12 Pfam accessions were found in Bacillariophyta metatranscriptomes. Putative chitin synthase (CHS) sequences are decreasingly present in Crustacea (39%), Stramenopiles (16%) and Insecta (14%) from the Marine Atlas of Tara Oceans Unigenes version 1 Metatranscriptomes (MATOUv1+T) database. A CHS gene from the model diatom Thalassiosira pseudonana (Thaps3_J4413, designated TpCHS1) was identified. Homology analysis of TpCHS1 in Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP), PhycoCosm, and the PLAZA diatom omics data set showed that Mediophyceae and Thalassionemales species were potential new ß-chitin producers besides Thalassiosirales. TpCHS1 was overexpressed in Saccharomyces cerevisiae and Phaeodactylum tricornutum. In transgenic P. tricornutum lines, TpCHS1-eGFP localizes to the Golgi apparatus and plasma membrane and predominantly accumulates in the cleavage furrow during cell division. Enhanced TpCHS1 expression could induce abnormal cell morphology and reduce growth rates in P. tricornutum, which might be ascribed to the inhibition of the G2/M phase. S. cerevisiae was proved to be a better system for expressing large amounts of active TpCHS1, which effectively incorporates UDP-N-acetylglucosamine in radiometric in vitro assays. Our study expands the knowledge on chitin synthase taxonomic distribution in marine eukaryotic microbes, and is the first to collectively characterize an active marine diatom CHS which may play an important role during cell division. IMPORTANCE As the most abundant biopolymer in the oceans, the significance of chitin and its biosynthesis is rarely demonstrated in diatoms, which are the main contributors to the primary productivity of the oceans, ascribed to their huge biomass and efficient photosynthesis. We retrieved genes involved in chitin-based metabolism against the Tara Oceans Gene Atlas to expand our knowledge about their diversity and distribution in the marine environment. Potential new producers of chitin were found from the analysis of various algal transcriptome and genome databases. Heterologous expression confirms that Thalassiosira pseudonana contains an active chitin synthase (CHS) which may play an important role in the cell division process of diatoms. This study provides new insight into CHS geographic and taxonomic distribution in marine eukaryotic microbes, as well as into a new CHS functioning in the biosynthesis of ß-chitin in diatoms.

Convergent evolution and horizontal gene transfer in Arctic Ocean microalgae.

Microbial communities in the world ocean are affected strongly by oceanic circulation, creating characteristic marine biomes. The high connectivity of most of the ocean makes it difficult to disentangle selective retention of colonizing genotypes (with traits suited to biome specific conditions) from evolutionary selection, which would act on founder genotypes over time. The Arctic Ocean is exceptional with limited exchange with other oceans and ice covered since the last ice age. To test whether Arctic microalgal lineages evolved apart from algae in the global ocean, we sequenced four lineages of microalgae isolated from Arctic waters and sea ice. Here we show convergent evolution and highlight geographically limited HGT as an ecological adaptive force in the form of PFAM complements and horizontal acquisition of key adaptive genes. Notably, ice-binding proteins were acquired and horizontally transferred among Arctic strains. A comparison with Tara Oceans metagenomes and metatranscriptomes confirmed mostly Arctic distributions of these IBPs. The phylogeny of Arctic-specific genes indicated that these events were independent of bacterial-sourced HGTs in Antarctic Southern Ocean microalgae.

Population genomics of the neotropical palm Copernicia prunifera (Miller) H. E. Moore: Implications for conservation.

Copernicia prunifera (Miller) H. E. Moore is a palm tree native to Brazil. The products obtained from its leaf extracts are a source of income for local families and the agroindustry. Owing to the reduction of natural habitats and the absence of a sustainable management plan, the maintenance of the natural populations of this palm tree has been compromised. Therefore, this study aimed to evaluate the diversity and genetic structure of 14 C. prunifera populations using single nucleotide polymorphisms (SNPs) identified through genotyping-by-sequencing (GBS) to provide information that contributes to the conservation of this species. A total of 1,013 SNP markers were identified, of which 84 loci showed outlier behavior and may reflect responses to natural selection. Overall, the level of genomic diversity was compatible with the biological aspects of this species. The inbreeding coefficient (f) was negative for all populations, indicating excess heterozygotes. Most genetic variations occurred within populations (77.26%), and a positive correlation existed between genetic and geographic distances. The population structure evaluated through discriminant analysis of principal components (DAPC) revealed low genetic differentiation between populations. The results highlight the need for efforts to conserve C. prunifera as well as its distribution range to preserve its global genetic diversity and evolutionary potential.

Do anti-HIV drugs pose a threat to photosynthetic microorganisms?

We investigated the occurrence and risk assessment of three anti-HIV drugs [(tenofovir (TNF), lamivudine (LMV) and efavirenz (EFV)] in urban rivers from Curitiba (Brazil), as well as the individual and combined effects of their environmental representative concentrations on the freshwater periphytic species Synechococcus elongatus (Cyanobacteria) and Chlorococcum infusionum (Chlorophyta). The three studied drugs, except TNF, were found in 100% of the samples, and concentrations in samples ranged from 165 to 412 ng TNF L-1, 173-874 ng LMV L-1 and 13-1250 ng EFV L-1. Bioassays using artificial contaminated water showed that at environmental concentrations, TNF and LMV did not represent environmental risks to the studied photosynthetic organisms. However, EFV was shown to be toxic, affecting photosynthesis, respiration, and oxidative metabolism. The studied drugs demonstrated interactive effects. Indeed, when submitted to the combination of TNF and LMV, decreased photosynthesis was observed in C. infusionum cells. Moreover, the toxic effects of EFV were amplified in both species when TNF and/or LMV were added to the media. The simultaneous presence of TNF, LMV and EFV in environmental matrices associated with their interactive effects, lead to increased toxicological effects of water contaminated by anti-HIV drugs and thus to an ecological threat to photosynthetic microorganisms.

Comparison between radiographic methods of measuring flexibility in scoliosis / Comparação entre métodos radiográficos para medir a flexibilidade na escoliose / Comparación entre métodos radiográficos para medir la flexibilidad en la escoliosis

ABSTRACT Objective: To determine the preoperative radiographic method for measuring the Cobb angle that is closest to the postoperative result in patients with scoliotic deformity. Methods: Retrospective cohort study of radiographic spinal evaluation (preoperative posteroanterior (PA), bending, traction, traction under anesthesia and immediate postoperative posteroanterior (PO)) of 26 patients treated surgically for scoliotic deformities during the period from January 2017 to September 2019. The final mean Cobb angle and its decrease in relation to the PA value were evaluated in the three curves in patients with idiopathic (IS) and non-idiopathic scoliosis. Results: All the mean curve values were statistically significant, except for bending in non-idiopathic scoliosis (non-IS). The mean traction under anesthesia values were closer to the PO values. Regarding the delta (decrease) of the maneuvers in relation to the PA, no statistical significance was observed in the non-IS group. The traction under anesthesia maneuver had a greater delta in all curves. Conclusions: The traction under anesthesia maneuver in patients with idiopathic scoliosis is the method with the greatest flexibility and which best predicts the postoperative result. Level of evidence III; Diagnostic study.

RESUMO Objetivo: Objetivo: Determinar o método radiográfico pré-operatório para aferição do ângulo de Cobb que mais se aproxima dos resultados pós-operatórios em pacientes com deformidade escoliótica. Métodos: Estudo de coorte retrospectivo de avaliação radiográfica da coluna vertebral (posteroanterior pré-operatória [PA], inclinações, tração, tração com anestesia e posteroanterior pós-operatória imediata [PO]) de 26 pacientes com deformidades escolióticas no período de Janeiro de 2017 a Setembro de 2019 tratados com cirurgia . Avaliou-se a média final do ângulo de Cobb e a sua diminuição com relação ao PA nas três curvas em pacientes com escoliose idiopática (EI) e não idiopática. Resultados: Todas as médias das curvas têm significância estatística, exceto a inclinação na escoliose não idiopática (não EI). A tração com anestesia apresenta média de valores mais próximos ao PO. Com relação ao delta (diminuição) das manobras referentes ao PA, foi observado que não houve significância estatística nas não EI. A manobra de tração com anestesia tem delta maior em todas as curvas. Conclusões: A manobra de tração com anestesia em pacientes com escoliose idiopática configura-se como o método com maior flexibilidade e que melhor prediz o resultado pós-operatório. Nível de evidência III; Estudo diagnóstico.

RESUMEN Objetivo: Determinar el método radiográfico preoperatorio para medición del ángulo de Cobb que más se aproxima a los resultados postoperatorios en pacientes con deformidad escoliótica. Métodos: Estudio de cohorte retrospectivo de evaluación radiográfica de la columna vertebral (posteroanterior preoperatoria (PA), inclinaciones, tracción, tracción con anestesia y posteroanterior postoperatoria inmediata (PO)) de 26 pacientes con deformidades escolióticas en el período de enero de 2017 a septiembre de 2019 tratados con cirugía. Se evaluó el promedio final del ángulo de Cobb y su disminución con relación al PA en las tres curvas en pacientes con escoliosis idiopática (EI) y no idiopática. Resultados: Todos los promedios de las curvas tienen significancia estadística, excepto la inclinación en la escoliosis no idiopática (no EI). La tracción con anestesia presenta promedio de valores más próximos al PO. Con relación al delta (disminución) de las maniobras referentes al PA, se observó que no hubo significancia estadística en las no EI. La maniobra de tracción con anestesia tiene un delta mayor en todas las curvas. Conclusiones: La maniobra de tracción con anestesia en pacientes con escoliosis idiopática se configura como el método con mayor flexibilidad y que mejor predice el resultado postoperatorio.Nivel de evidencia III; Estudio diagnóstico.

Intra- and interobserver reproducibility of the radiographic evaluation of cranial parameters / Reprodutibilidade intra e interobservadores da avaliação radiográfica de parâmetros cranianos / Reproducibilidad intra e interobservadores de la evaluación radiográfica de parámetros craneales

ABSTRACT Objective: To evaluate the intra- and interobserver reproducibility of radiographic cranial parameters. Method: A study of the reproducibility of the radiographic cranial parameters (cranial incidence, cranial tilt, cranial slope and spinocervical angle) of 40 patients by 4 observers with different levels of experience. Results: Cranial incidence (CI) showed poor intraobserver concordance; for the other cranial parameters, good to excellent concordance was observed. In the assessment of interobserver concordance, all the parameters analyzed showed statistical significance, with good CI concordance. Conclusion: Cranial parameters are easily reproducible by orthopedists with different levels of experience. CI showed good interobserver concordance, but only reasonable intraobserver concordance among more experienced observers. Level of evidence IV; Diagnostic Study.

RESUMO Objetivo: Avaliar a reprodutibilidade intra e interobservadores dos parâmetros radiográficos cranianos. Métodos: Estudo de mensuração da reprodutibilidade da avaliação radiográfica de parâmetros cranianos (incidência craniana, inclinação craniana, slope craniano e ângulo espinocervical) de 40 pacientes, por quatro observadores com diferentes níveis de experiência em duas ocasiões distintas. Resultados: Na concordância intraobservador, a incidência craniana (IC) mostrou concordância ruim; nos demais parâmetros cranianos, observou-se concordância boa a excelente. Na avaliação de concordância interobservadores, todos os parâmetros analisados apresentaram significância estatística, com boa concordância da IC. Conclusão: Os parâmetros cranianos são facilmente reprodutíveis por ortopedistas em diferentes estágios de formação. A IC tem boa concordância interobservador, porém concordância apenas razoável na análise de intraobservadores mais experientes. Nível de evidência IV; Estudo Diagnóstico.

RESUMEN Objetivo: Evaluar la reproducibilidad intra e interobservadores de los parámetros radiográficos craneales. Métodos: Estudio de medición de la reproducibilidad de la evaluación radiográfica de parámetros craneales (incidencia craneal, inclinación craneal, slope craneal y ángulo espinocervical) de 40 pacientes, por cuatro observadores con diferentes niveles de experiencia en dos ocasiones distintas. Resultados: En la concordancia intraobservador, la incidencia craneal (IC) mostró concordancia mala; en los demás parámetros craneales, se observó concordancia de buena a excelente. En la evaluación de concordancia interobservadores, todos los parámetros analizados presentaron significancia estadística, con buena concordancia de la IC. Conclusión: Los parámetros craneales son fácilmente reproducibles por los ortopedistas en diferentes etapas de formación. La IC tiene buena concordancia interobservador, aunque concordancia sólo razonable en el análisis de intraobservadores con más experiencia. Nivel de evidencia IV; Estudio Diagnóstico.

Genome wide natural variation of H3K27me3 selectively marks genes predicted to be important for cell differentiation in Phaeodactylum tricornutum.

In multicellular organisms, Polycomb Repressive Complex2 (PRC2) is known to deposit tri-methylation of lysine 27 of histone H3 (H3K27me3) to establish and maintain gene silencing, critical for developmentally regulated processes. The PRC2 complex is absent in both widely studied model yeasts, which initially suggested that PRC2 arose with the emergence of multicellularity. However, its discovery in several unicellular species including microalgae questions its role in unicellular eukaryotes. Here, we use Phaeodactylum tricornutum enhancer of zeste E(z) knockouts and show that P. tricornutum E(z) is responsible for di- and tri-methylation of lysine 27 of histone H3. H3K27me3 depletion abolishes cell morphology in P. tricornutum providing evidence for its role in cell differentiation. Genome-wide profiling of H3K27me3 in fusiform and triradiate cells further revealed genes that may specify cell identity. These results suggest a role for PRC2 and its associated mark in cell differentiation in unicellular species, and highlight their ancestral function in a broader evolutionary context than currently is appreciated.

A comparative pan-genomic analysis of 53 C. pseudotuberculosis strains based on functional domains.

Corynebacterium pseudotuberculosis is a pathogenic bacterium with great veterinary and economic importance. It is classified into two biovars: ovis, nitrate-negative, that causes lymphadenitis in small ruminants and equi, nitrate-positive, causing ulcerative lymphangitis in equines. With the explosive growth of available genomes of several strains, pan-genome analysis has opened new opportunities for understanding the dynamics and evolution of C. pseudotuberculosis. However, few pan-genomic studies have compared biovars equi and ovis. Such studies have considered a reduced number of strains and compared entire genomes. Here we conducted an original pan-genome analysis based on protein sequences and their functional domains. We considered 53 C. pseudotuberculosis strains from both biovars isolated from different hosts and countries. We have analysed conserved domains, common domains more frequently found in each biovar and biovar-specific (unique) domains. Our results demonstrated that biovar equi is more variable; there is a significant difference in the number of proteins per strains, probably indicating the occurrence of more gene loss/gain events. Moreover, strains of biovar equi presented a higher number of biovar-specific domains, 77 against only eight in biovar ovis, most of them are associated with virulence mechanisms. With this domain analysis, we have identified functional differences among strains of biovars ovis and equi that could be related to niche-adaptation and probably help to better understanding mechanisms of virulence and pathogenesis. The distribution patterns of functional domains identified in this work might have impacts on bacterial physiology and lifestyle, encouraging the development of new diagnoses, vaccines, and treatments for C. pseudotuberculosis diseases.Communicated by Ramaswamy H. Sarma.

Correlation between the schanz screw insertion angle and the loss of kyphosis correction in thoracolumbar fractures / Correlação entre o ângulo de inserção do pino de schanz e a perda de correção da cifose em fraturas toracolombares / Correlación entre el ángulo de inserción del tornillo de schanz y la pérdida de corrección de la cifosis en fracturas toracolumbares

ABSTRACT Objective To compare the Schanz screw insertion angle and the loss of the regional kyphosis correction in thoracolumbar burst fractures following posterior short instrumentation surgery. Methods Patients with a thoracolumbar burst fracture between levels T11-L2 were divided into two groups (parallel and divergent) according to the angle formed between the Schanz screw and the vertebral plateau. Regional kyphosis was evaluated in preoperative, immediate postoperative and last follow-up radiographs. Results Of the 58 patients evaluated, 31 had a parallel assembly and 27 had a divergent assembly. When we analyzed the angle of kyphosis, no statistical difference was observed between the pre- and postoperative radiographs. However, a statistical difference in the last follow-up radiographs and in the final loss of the kyphosis correction was confirmed. Conclusion The insertion of Schanz screws with a divergent assembly presents better radiographic results with less loss of kyphosis correction angle when compared with the parallel assembly technique. Level of Evidence III; Retrospective cohort study.

RESUMO Objetivo Comparar o ângulo de inserção do pino de Schanz e os resultados da perda de correção da cifose regional nas fraturas toracolombares do tipo explosão após tratamento cirúrgico com instrumentação curta por via posterior. Métodos Os pacientes com fratura toracolombar do tipo explosão entre os níveis de T11-L2 foram divididos em dois grupos (paralelo e divergente) de acordo com o ângulo formado entre o pino de Schanz e o platô vertebral. Foi avaliada a cifose regional nas radiografias pré-operatória, pós-operatória imediata e do último acompanhamento. Resultados Dos 58 pacientes avaliados, 31 apresentaram uma montagem paralela e 27 uma montagem divergente. Ao analisarmos o ângulo da cifose, não se observou diferença estatística nas radiografias pré- e pós-operatória imediata. Porém, verificou-se uma diferença estatística nas radiografias do último acompanhamento e na perda final de correção da cifose. Conclusões A inserção do pino de Schanz com uma montagem divergente apresenta melhores resultados radiográficos com menor perda do ângulo de correção da cifose quando comparada com a técnica de montagem paralela. Nível de Evidência III; Estudo de coorte retrospectivo.

RESUMEN Objetivo Comparar el ángulo de inserción del tornillo de Schanz y los resultados de la pérdida de corrección de la cifosis regional en las fracturas toracolumbares del tipo explosión después del tratamiento quirúrgico con instrumentación corta por vía posterior. Métodos Los pacientes con fractura toracolumbar del tipo explosión entre los niveles de T11-L2 fueron divididos en dos grupos (paralelo y divergente) de acuerdo con el ángulo formado entre el tornillo de Schanz y la meseta vertebral. Fue evaluada la cifosis regional en las radiografías preoperatoria, posoperatoria inmediata y del último acompañamiento. Resultados De los 58 pacientes evaluados, 31 presentaron un montaje paralelo y 27 un montaje divergente. Al analizar el ángulo de la cifosis, no se observó diferencia estadística en las radiografías pre y postoperatoria inmediata. Sin embargo, se verificó una diferencia estadística en las radiografías del último acompañamiento y en la pérdida final de corrección de la cifosis. Conclusiones La inserción del tornillo de Schanz con un montaje divergente presenta mejores resultados radiográficos con menor pérdida del ángulo de corrección de la cifosis cuando comparada con la técnica de montaje paralelo. Nivel de Evidencia III; Estudio de cohorte retrospectivo.

Genome-enabled phylogenetic and functional reconstruction of an araphid pennate diatom Plagiostriata sp. CCMP470, previously assigned as a radial centric diatom, and its bacterial commensal.

Diatoms are an ecologically fundamental and highly diverse group of algae, dominating marine primary production in both open-water and coastal communities. The diatoms include both centric species, which may have radial or polar symmetry, and the pennates, which include raphid and araphid species and arose within the centric lineage. Here, we use combined microscopic and molecular information to reclassify a diatom strain CCMP470, previously annotated as a radial centric species related to Leptocylindrus danicus, as an araphid pennate species in the staurosiroid lineage, within the genus Plagiostriata. CCMP470 shares key ultrastructural features with Plagiostriata taxa, such as the presence of a sternum with parallel striae, and the presence of a highly reduced labiate process on its valve; and this evolutionary position is robustly supported by multigene phylogenetic analysis. We additionally present a draft genome of CCMP470, which is the first genome available for a staurosiroid lineage. 270 Pfams (19%) found in the CCMP470 genome are not known in other diatom genomes, which otherwise does not hold big novelties compared to genomes of non-staurosiroid diatoms. Notably, our DNA library contains the genome of a bacterium within the Rhodobacterales, an alpha-proteobacterial lineage known frequently to associate with algae. We demonstrate the presence of commensal alpha-proteobacterial sequences in other published algal genome and transcriptome datasets, which may indicate widespread and persistent co-occurrence.

A genomics approach reveals the global genetic polymorphism, structure, and functional diversity of ten accessions of the marine model diatom Phaeodactylum tricornutum.

Diatoms emerged in the Mesozoic period and presently constitute one of the main primary producers in the world's ocean and are of a major economic importance. In the current study, using whole genome sequencing of ten accessions of the model diatom Phaeodactylum tricornutum, sampled at broad geospatial and temporal scales, we draw a comprehensive landscape of the genomic diversity within the species. We describe strong genetic subdivisions of the accessions into four genetic clades (A-D) with constituent populations of each clade possessing a conserved genetic and functional makeup, likely a consequence of the limited dispersal of P. tricornutum in the open ocean. We further suggest dominance of asexual reproduction across all the populations, as implied by high linkage disequilibrium. Finally, we show limited yet compelling signatures of genetic and functional convergence inducing changes in the selection pressure on many genes and metabolic pathways. We propose these findings to have significant implications for understanding the genetic structure of diatom populations in nature and provide a framework to assess the genomic underpinnings of their ecological success and impact on aquatic ecosystems where they play a major role. Our work provides valuable resources for functional genomics and for exploiting the biotechnological potential of this model diatom species.

Access to RNA-sequencing data from 1,173 plant species: The 1000 Plant transcriptomes initiative (1KP).

BACKGROUND: The 1000 Plant transcriptomes initiative (1KP) explored genetic diversity by sequencing RNA from 1,342 samples representing 1,173 species of green plants (Viridiplantae). FINDINGS: This data release accompanies the initiative's final/capstone publication on a set of 3 analyses inferring species trees, whole genome duplications, and gene family expansions. These and previous analyses are based on de novo transcriptome assemblies and related gene predictions. Here, we assess their data and assembly qualities and explain how we detected potential contaminations. CONCLUSIONS: These data will be useful to plant and/or evolutionary scientists with interests in particular gene families, either across the green plant tree of life or in more focused lineages.

Meta-Omics Reveals Genetic Flexibility of Diatom Nitrogen Transporters in Response to Environmental Changes.

Diatoms (Bacillariophyta), one of the most abundant and diverse groups of marine phytoplankton, respond rapidly to the supply of new nutrients, often out-competing other phytoplankton. Herein, we integrated analyses of the evolution, distribution, and expression modulation of two gene families involved in diatom nitrogen uptake (DiAMT1 and DiNRT2), in order to infer the main drivers of divergence in a key functional trait of phytoplankton. Our results suggest that major steps in the evolution of the two gene families reflected key events triggering diatom radiation and diversification. Their expression is modulated in the contemporary ocean by seawater temperature, nitrate, and iron concentrations. Moreover, the differences in diversity and expression of these gene families throughout the water column hint at a possible link with bacterial activity. This study represents a proof-of-concept of how a holistic approach may shed light on the functional biology of organisms in their natural environment.