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.

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.

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.

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.

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.

Evaluation and improvements of clustering algorithms for detecting remote homologous protein families.

BACKGROUND: An important problem in computational biology is the automatic detection of protein families (groups of homologous sequences). Clustering sequences into families is at the heart of most comparative studies dealing with protein evolution, structure, and function. Many methods have been developed for this task, and they perform reasonably well (over 0.88 of F-measure) when grouping proteins with high sequence identity. However, for highly diverged proteins the performance of these methods can be much lower, mainly because a common evolutionary origin is not deduced directly from sequence similarity. To the best of our knowledge, a systematic evaluation of clustering methods over distant homologous proteins is still lacking. RESULTS: We performed a comparative assessment of four clustering algorithms: Markov Clustering (MCL), Transitive Clustering (TransClust), Spectral Clustering of Protein Sequences (SCPS), and High-Fidelity clustering of protein sequences (HiFix), considering several datasets with different levels of sequence similarity. Two types of similarity measures, required by the clustering sequence methods, were used to evaluate the performance of the algorithms: the standard measure obtained from sequence-sequence comparisons, and a novel measure based on profile-profile comparisons, used here for the first time. CONCLUSIONS: The results reveal low clustering performance for the highly divergent datasets when the standard measure was used. However, the novel measure based on profile-profile comparisons substantially improved the performance of the four methods, especially when very low sequence identity datasets were evaluated. We also performed a parameter optimization step to determine the best configuration for each clustering method. We found that TransClust clearly outperformed the other methods for most datasets. This work also provides guidelines for the practical application of clustering sequence methods aimed at detecting accurately groups of related protein sequences.

How predictable is the erectile function of patients with epilepsy?

INTRODUCTION: Erectile dysfunction (ED) is often reported by patients with epilepsy and may be related to endocrine system abnormalities, side effects of antiepileptic drugs, psychiatric comorbidities, and family or social difficulties. AIMS: This study aimed to identify independent predictor factors for ED in patients with epilepsy. MAIN OUTCOME MEASURES: the five-question form of the International Index of Erectile Function (IIEF-5). METHODS: Independent predictive factors for ED evaluated by the IIEF-5 questionnaire in 36 patients (mean age: 39 years) with focal epilepsy (mean: 6 seizures/month) were identified by multiple linear regression analysis. RESULTS: Eight (21.1%) patients were asymptomatic. Among the symptomatic patients, 11 (28.9%) had mild dysfunction, 10 (26.3%) had moderate dysfunction, and 9 (23.7%) showed severe ED. The multiple linear regression model including family income (B=0.005; p=0.05), education levels in years (B=0.54; p=0.03), depressive symptoms determined by HADS depression subscale (B=-0.49; p=0.03), and prolactin levels (B=-0.45; p=0.07) showed a moderate association (r=0.64) with the IIEF questionnaire and explained 41% (r(2)=0.41) of its variation. CONCLUSIONS: Erectile dysfunction is highly prevalent in patients with focal epilepsies. Education, depressive symptoms, and prolactin levels can predict erectile dysfunction in up to 41% of patients with epilepsy. This preliminary report justifies further efforts to make a large sample size study to identify independent biomarkers and therapeutic targets for ED treatment in patients with epilepsy.

Fast meta-analytic approximations for relational event models: applications to data streams and multilevel data.

Large relational-event history data stemming from large networks are becoming increasingly available due to recent technological developments (e.g. digital communication, online databases, etc). This opens many new doors to learn about complex interaction behavior between actors in temporal social networks. The relational event model has become the gold standard for relational event history analysis. Currently, however, the main bottleneck to fit relational events models is of computational nature in the form of memory storage limitations and computational complexity. Relational event models are therefore mainly used for relatively small data sets while larger, more interesting datasets, including multilevel data structures and relational event data streams, cannot be analyzed on standard desktop computers. This paper addresses this problem by developing approximation algorithms based on meta-analysis methods that can fit relational event models significantly faster while avoiding the computational issues. In particular, meta-analytic approximations are proposed for analyzing streams of relational event data, multilevel relational event data and potentially combinations thereof. The accuracy and the statistical properties of the methods are assessed using numerical simulations. Furthermore, real-world data are used to illustrate the potential of the methodology to study social interaction behavior in an organizational network and interaction behavior among political actors. The algorithms are implemented in the publicly available R package 'remx'.

Selectivity of a Copper Oxide CO2 Reduction Electrocatalyst Shifted by a Bioinspired pH-Sensitive Polymer.

A bioinspired polymeric membrane capable of shifting the selectivity of a copper oxide electrocatalyst in the CO2 reduction reaction is described. The membrane is deposited on top of copper oxide thin films from wet deposition techniques under controlled conditions of humidity and self-assembles into an arranged network of micrometer-sized pores throughout the polymer cross-section. The membrane was composed of a block copolymer with a precisely controlled ratio of poly-4-vinylpyridine and poly(methyl methacrylate) blocks (PMMA-b-P4VP). The intrinsic hydrophobicity, together with the porous nature of the membrane's surface, induces a Cassie-Baxter wetting transition above neutral pH, resulting in water repulsion from the catalyst surface. As a consequence, the catalyst's surface is shielded from surrounding water molecules under CO2 electroreduction reaction conditions, and CO2 molecules are preferentially located in the vicinity of the catalytically active area. The CO2 reduction reaction is therefore kinetically favored over the hydrogen evolution reaction (HER).

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.

Reactivity assessment of oligomeric systems associated with crystalline and amorphous cellulose for bioethanol production: a DFT study.

CONTEXT: The production of bioethanol from renewable raw materials is a decisive factor in the economic development of many countries. However, the complexity of the processes and the numerous experimental variables involved require a deeper understanding of the chemical reactions that take place during bioethanol production to define optimal parameters. Here, we have employed density functional theory-based calculations to investigate the local reactivity of oligomeric systems by considering crystalline and amorphous cellulose models to better understand some details regarding pulp pretreatment processes. Our results evidence a higher chemical susceptibility of amorphous portions of cellulose to chemicals typically employed in acid hydrolysis. Additionally, we observed that glucose monomers coming from cellulose hydrolysis may undergo oxidation, leading to the formation of byproducts such as hydroxymethylfurfural (HMF), acetic acid, formic acid, and levulinic acid. The analysis of local chemical softness indexes indicated that cellulose hydrolysis may be associated with intermediate chemical steps. Finally, we investigated the influence of distinct solvents (dielectric constants) on the local reactivity of the systems, evidencing a relevant role of the solvent dielectric constant for cellulose degradation in glucose. METHODS: Initial three-dimensional structures were constructed. Pre-optimizations were performed in a Hartree-Fock (HF) approach employing the PM7 semi-empirical hamiltonian. The structures were then re-optimized via density functional theory (DFT). The local reactivity study of the systems was conducted through the condensed-to-atoms Fukui indexes (CAFI). Systematic changes of the dielectric constants were also considered in geometry optimization and CAFI calculations to estimate the influence of solvents on the reactivity of the systems.

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.

Agreement between the EWGSOP2 and SDOC consensuses for sarcopenia in patients receiving hemodialysis: Findings of a cross sectional analysis from the SARC-HD study.

BACKGROUND: Differences in definitions and operational diagnoses for sarcopenia create difficulties in understanding the epidemiology of the disease. We examined the prevalences of sarcopenia using the revised European Working Group on Sarcopenia in Older People (EWGSOP2) and the Sarcopenia Definitions and Outcomes Consortium (SDOC) consensuses and analyzed their level of agreement in patients receiving hemodialysis. METHODS: Data from the SARCopenia trajectories and associations with clinical outcomes in patients receiving hemodialysis (SARC-HD) multicenter study in Brazil were analyzed. Muscle strength was assessed using handgrip strength, muscle mass by calf circumference, and physical performance by the 4-m gait speed test. Sarcopenia was diagnosed according to both the EWGSOP2 (low muscle strength plus low muscle mass) and the SDOC (low muscle strength plus low physical performance). The Cohen kappa statistic was used to determine the level of agreement between the consensuses. RESULTS: 838 patients (57.8 ± 15.0 years; 61% men) from 19 dialysis units were included. We found similar prevalences of sarcopenia between the consensuses (EWGSOP2, n = 128, 15.3%; SDOC, n = 105, 12.5%) but with weak agreement (50 of 233 patients, 21.5%; κ = 0.34, 95% CI 0.25-0.43). Agreement was also weak within age categories (≥60 years, κ = 0.34; <60 years, κ = 0.15; both P < 0.001). Of the 51 patients diagnosed by the EWGSOP2 criterion as having severe sarcopenia, all but 1 (98.0%) met the SDOC criterion for sarcopenia (κ = 0.61, 95% CI 0.52-0.70). Low muscle strength was more frequently diagnosed using the SDOC than with the EWGSOP2 (52.3% vs 25.9%). CONCLUSION: We found a weak agreement between the EWGSOP2 and SDOC consensuses for the diagnosis of sarcopenia in patients receiving hemodialysis. Although still weak, agreement was marginally better for older patients. These findings highlight the importance of a global and standardized conceptual diagnosis of sarcopenia.

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.

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.

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.

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.