Contrasting patterns of functional diversity in coffee root fungal communities associated with organic and conventionally managed fields

The structure and function of fungal communities in the coffee rhizosphere are influenced by crop environment. Because coffee can be grown along a management continuum from conventional application of pesticides and fertilizers in full sun to organic management in a shaded understory, we used coffee fields to hold host constant while comparing rhizosphere fungal communities under markedly different environmental conditions with regard to shade and inputs. We characterized the shade and soil environment in 25 fields under conventional, organic, or transitional management in two regions of Costa Rica. We amplified the internal transcribed spacer 2 (ITS2) region of fungal DNA from coffee roots in these fields and characterized the rhizosphere fungal community via high-throughput sequencing. Sequences were assigned to guilds to determine differences in functional diversity and trophic structure among coffee field environments. Organic fields had more shade, a greater richness of shade tree species, and more leaf litter and were less acidic, with lower soil nitrate availability and higher soil copper, calcium, and magnesium availability than conventionally managed fields, although differences between organic and conventionally managed fields in shade and calcium and magnesium availability depended on region. Differences in richness and community composition of rhizosphere fungi between organic and conventionally managed fields were also correlated with shade, soil acidity, and nitrate and copper availability. Trophic structure differed with coffee field management. Saprotrophs, plant pathogens, and mycoparasites were more diverse, and plant pathogens were more abundant, in organic than in conventionally managed fields, while saprotroph-plant pathogens were more abundant in conventionally managed fields. These differences reflected environmental differences and depended on region

Genetic variability and natural selection at the ligand domain of the Duffy binding protein in Brazilian Plasmodium vivax populations.

Background. Plasmodium vivax malaria is a major public health challenge in Latin America, Asia and Oceania, with 130-435 million clinical cases per year worldwide. Invasion of host blood cells by P. vivax mainly depends on a type I membrane protein called Duffy binding protein (PvDBP). The erythrocyte-binding motif of PvDBP is a 170 amino-acid stretch located in its cysteine-rich region II (PvDBPII), which is the most variable segment of the protein. Methods. To test whether diversifying natural selection has shaped the nucleotide diversity of PvDBPII in Brazilian populations, this region was sequenced in 122 isolates from six different geographic areas. A Bayesian method was applied to test for the action of natural selection under a population genetic model that incorporates recombination. The analysis was integrated with a structural model of PvDBPII, and T- and B-cell epitopes were localized on the 3-D structure. Results. The results suggest that: (i) recombination plays an important role in determining the haplotype structure of PvDBPII, and (ii) PvDBPII appears to contain neutrally evolving codons as well as codons evolving under natural selection. Diversifying selection preferentially acts on sites identified as epitopes, particularly on amino acid residues 417, 419, and 424, which show strong linkage disequilibrium. Conclusions. This study shows that some polymorphisms of PvDBPII are present near the erythrocyte-binding domain and might serve to elude antibodies that inhibit cell invasion. Therefore, these polymorphisms should be taken into account when designing vaccines aimed at eliciting antibodies to inhibit erythrocyte invasion

Morfotipos de novos isolados de microalgas da Coleção do Laboratório de Biotecnologia de Algas da Embrapa Agroenergia.

São reportados os procedimentos realizados com o objetivo de caracterizar os morfotipos obtidos de colônias de microalgas isoladadas em meio de cultura tendo como fonte principal de Nitrogênio o nitrato (meio BG11) ou amônio (meio BGUF). Estes isolados resultaram do crescimento de microalgas coletadas de lagoas ou poças de água ao longo da Estrada Parque Pantanal, no Mato Grosso do Sul, em viagem realizada em 11 de novembro de 2019. Após crescimento inicial em meio líquido, amostras foram riscadas em placas com meios semissólidos, com posterior repicagem de colônias selecionadas ao acaso para novo crescimento em meio líquido. Então, frações de 1 mL foram separadas, tratadas com solução fixadora (2,5% glutaraldeido em 0,1M cacodilato de sódio, pH 7,2) e montadas em lamínulas, para observação em Microscópio Óptico AxioImage Z2, marca Zeiss, em contraste de interferência diferencial. As microalgas presentes foram registradas digitalmente, usando‑se câmera digital IcC3 e o software Zen‑Zeiss, avaliando‑se os descritores morfológicos visíveis de núcleo, estrutura do talo, forma e cor. A fotodocumentação das microalgas isoladas resultou numa variedade significativa de morfotipos, com predominância de formas cocoides ou assemelhadas, em detrimento de formas filamentosas. Tal resultado indica que é necessário cuidado nos procedimentos iniciais de seleção para não serem isolados apenas microalgas de um macrogrupo específico, limitando‑se o enriquecimento da diversidade de algas numa coleção de diferentes espécies

Nonlinear vortex light beams supported and stabilized by dissipation

We describe nonlinear Bessel vortex beams as localized and stationary solutions with embedded vorticity to the nonlinear Schr\"odinger equation with a dissipative term that accounts for the multi-photon absorption processes taking place at high enough powers in common optical media. In these beams, power and orbital angular momentum are permanently transferred to matter in the inner, nonlinear rings, at the same time that they are refueled by spiral inward currents of energy and angular momentum coming from the outer linear rings, acting as an intrinsic reservoir. Unlike vortex solitons and dissipative vortex solitons, the existence of these vortex beams does not critically depend on the precise form of the dispersive nonlinearities, as Kerr self-focusing or self-defocusing, and do not require a balancing gain. They have been shown to play a prominent role in "tubular" filamentation experiments with powerful, vortex-carrying Bessel beams, where they act as attractors in the beam propagation dynamics. Nonlinear Bessel vortex beams provide indeed a new solution to the problem of the stable propagation of ring-shaped vortex light beams in homogeneous self-focusing Kerr media. A stability analysis demonstrates that there exist nonlinear Bessel vortex beams with single or multiple vorticity that are stable against azimuthal breakup and collapse, and that the mechanism that renders these vortexes stable is dissipation. The stability properties of nonlinear Bessel vortex beams explain the experimental observations in the tubular filamentation experiments.Comment: Chapter of boo

Preparo de meristemas apicais de cupuaçuzeiro (Theobroma grandiflorum) para estudos de expressão de genes por hibridização in situ.

O cupuaçuzeiro, Theobroma grandiflorum (Willd. ex Spreng.) Schum., é uma espécie nativa da Amazônia que produz uma das frutas mais populares da região, o cupuaçu. Sua polpa tem sabor e aroma muito apreciados, sendo utilizada na fabricação de uma grande diversidade de doces e na preparação de sucos. A partir das amêndoas é possível produzir o cupulate, produto similar ao chocolate. A cultura do cupuaçuzeiro tem relevante importância econômica para a região amazônica. Um dos entraves para esta cultura, no entanto, é a doença vassoura-de-bruxa (VB), causada pelo fungo Moniliophthora perniciosa, que compromete o desenvolvimento e a produção da planta. Este fungo acomete inicialmente as regiões meristemáticas do cupuaçuzeiro, particularmente o meristema da gema apical, causando superbrotamento, hipertrofia e hiperplasia dos tecidos, que acabam morrendo. Para maior entendimento do processo de infecção, genes relacionados à patogênese, particularmente os genes que codificam para as proteínas PR (pathogenesis-related), foram identificados em cupuaçuzeiro. Estudos de expressão temporal e espacial destes genes nos tecidos-alvo da infecção são necessários para acrescentar informações sobre a função de cada um no desenvolvimento da doença. Para tanto, torna-se necessário o estabelecimento de um método eficiente de hibridização in situ que permita identificar os locais e momentos específicos da expressão dos genes de interesse. Neste trabalho foi ajustada metodologia de hibridização in situ em gemas apicais de cupuaçuzeiros, desde a fixação e preparo do material vegetal até as condições de hibridização e pós-hibridização. Gemas apicais de galhos de cupuaçuzeiro foram coletadas e processadas para avaliação morfo-anatômica por microscopia de luz. Fragmento de cDNA de um gene de proteína do tipo PR foi clonado em pGEM®-T Easy e sondas de mRNA senso e antisenso marcadas com digoxigenina, produzidas por transcrição, foram utilizadas para a hibridização in situ em meristemas de cupuaçu. A técnica utilizada mostrou ser viável para a localização da expressão de genes neste tecido.bitstream/item/211640/1/Boletim-Cupuacu-35712.pd

Inspiratory Muscle Training in the Intensive Care Unit: A New Perspective

BACKGROUND: Prolonged use of mechanical ventilation (MV) leads to weakening of the respiratory muscles, especially in patients subjected to sedation, but this effect seems to be preventable or more quickly reversible using respiratory muscle training. The aims of the study were to assess variations in respiratory and hemodinamic parameters with electronic inspiratory muscle training (EIMT) in tracheostomized patients requiring MV and to compare these variations with those in a group of patients subjected to an intermittent nebulization program (INP). METHODS: This was a pilot, prospective, randomized study of tracheostomized patients requiring MV in one intensive care unit (ICU). Twenty-one patients were randomized: 11 into the INP group and 10 into the EIMT group. Two patients were excluded in experimental group because of hemodynamic instability. RESULTS: In the EIMT group, maximal inspiratory pressure (MIP) after training was significantly higher than that before (P = 0.017), there were no hemodynamic changes, and the total weaning time was shorter than in the INP group (P = 0.0192). CONCLUSION: The EIMT device is safe, promotes an increase in MIP, and leads to a shorter ventilator weaning time than that seen in patients treated using INP.info:eu-repo/semantics/publishedVersio

Enzyme classification with peptide programs: a comparative study

<p>Abstract</p> <p>Background</p> <p>Efficient and accurate prediction of protein function from sequence is one of the standing problems in Biology. The generalised use of sequence alignments for inferring function promotes the propagation of errors, and there are limits to its applicability. Several machine learning methods have been applied to predict protein function, but they lose much of the information encoded by protein sequences because they need to transform them to obtain data of fixed length.</p> <p>Results</p> <p>We have developed a machine learning methodology, called peptide programs (PPs), to deal directly with protein sequences and compared its performance with that of Support Vector Machines (SVMs) and BLAST in detailed enzyme classification tasks. Overall, the PPs and SVMs had a similar performance in terms of Matthews Correlation Coefficient, but the PPs had generally a higher precision. BLAST performed globally better than both methodologies, but the PPs had better results than BLAST and SVMs for the smaller datasets.</p> <p>Conclusion</p> <p>The higher precision of the PPs in comparison to the SVMs suggests that dealing with sequences is advantageous for detailed protein classification, as precision is essential to avoid annotation errors. The fact that the PPs performed better than BLAST for the smaller datasets demonstrates the potential of the methodology, but the drop in performance observed for the larger datasets indicates that further development is required.</p> <p>Possible strategies to address this issue include partitioning the datasets into smaller subsets and training individual PPs for each subset, or training several PPs for each dataset and combining them using a bagging strategy.</p