Interaction of insecticidal proteins from Pseudomonas spp. and Bacillus thuringiensis for boll weevil management.

Cotton crop yields are largely affected by infestations of Anthonomus grandis, which is its main pest. Although Bacillus thuringiensis (Bt) derived proteins can limit insect pest infestations, the diverse use of control methods becomes a viable alternative in order to prolong the use of technology in the field. One of the alternative methods to Bt technology has been the utilization of certain Pseudomonas species highly efficient in controlling coleopteran insects have been used to produce highly toxic insecticidal proteins. This study aimed to evaluate the toxicity of IPD072Aa and PIP-47Aa proteins, isolated from Pseudomonas spp., in interaction with Cry1Ia10, Cry3Aa, and Cry8B proteins isolated from B. thuringiensis, to control A. grandis in cotton crops. The genes IPD072Aa and PIP-47Aa were synthesized and cloned into a pET-SUMO expression vector. Moreover, Cry1Ia10, Cry3Aa, and Cry8B proteins were obtained by inducing recombinant E. coli clones, which were previously acquired by our research group from the Laboratory of Bacteria Genetics and Applied Biotechnology (LGBBA). These proteins were visualized in SDS-PAGE, quantified, and incorporated into an artificial diet to estimate their lethal concentrations (LC) through individual or combined bioassays. The results of individual toxicity revealed that IPD072Aa, PIP-47Aa, Cry1Ia10, Cry3Aa, and Cry8B were efficient in controlling A. grandis, with the latter being the most toxic. Regarding interaction assays, a high synergistic interaction was observed between Cry1Ia10 and Cry3Aa. All interactions involving Cry3Aa and PIP-47Aa, when combined with other proteins, showed a clear synergistic effect. Our findings highlighted that the tested proteins in combination, for the most part, increase toxicity against A. grandis neonate larvae, suggesting possible constructions for pyramiding cotton plants to the manage and the control boll weevils.

New proposal of viral genome representation applied in the classification of SARS-CoV-2 with deep learning.

BACKGROUND: In December 2019, the first case of COVID-19 was described in Wuhan, China, and by July 2022, there were already 540 million confirmed cases. Due to the rapid spread of the virus, the scientific community has made efforts to develop techniques for the viral classification of SARS-CoV-2. RESULTS: In this context, we developed a new proposal for gene sequence representation with Genomic Signal Processing techniques for the work presented in this paper. First, we applied the mapping approach to samples of six viral species of the Coronaviridae family, which belongs SARS-CoV-2 Virus. We then used the sequence downsized obtained by the method proposed in a deep learning architecture for viral classification, achieving an accuracy of 98.35%, 99.08%, and 99.69% for the 64, 128, and 256 sizes of the viral signatures, respectively, and obtaining 99.95% precision for the vectors with size 256. CONCLUSIONS: The classification results obtained, in comparison to the results produced using other state-of-the-art representation techniques, demonstrate that the proposed mapping can provide a satisfactory performance result with low computational memory and processing time costs.

A Novel Deep Neural Network Technique for Drug-Target Interaction.

Drug discovery (DD) is a time-consuming and expensive process. Thus, the industry employs strategies such as drug repositioning and drug repurposing, which allows the application of already approved drugs to treat a different disease, as occurred in the first months of 2020, during the COVID-19 pandemic. The prediction of drug-target interactions is an essential part of the DD process because it can accelerate it and reduce the required costs. DTI prediction performed in silico have used approaches based on molecular docking simulations, including similarity-based and network- and graph-based ones. This paper presents MPS2IT-DTI, a DTI prediction model obtained from research conducted in the following steps: the definition of a new method for encoding molecule and protein sequences onto images; the definition of a deep-learning approach based on a convolutional neural network in order to create a new method for DTI prediction. Training results conducted with the Davis and KIBA datasets show that MPS2IT-DTI is viable compared to other state-of-the-art (SOTA) approaches in terms of performance and complexity of the neural network model. With the Davis dataset, we obtained 0.876 for the concordance index and 0.276 for the MSE; with the KIBA dataset, we obtained 0.836 and 0.226 for the concordance index and the MSE, respectively. Moreover, the MPS2IT-DTI model represents molecule and protein sequences as images, instead of treating them as an NLP task, and as such, does not employ an embedding layer, which is present in other models.

Influence of the cultivation model on the posture and back pain prevalence of strawberry producers.

Introduction: Strawberry cultivation is an important source of income for Brazilian farmers. Cultivation can be done using the traditional model, in which producers must flex their trunk to handle seedlings, or using the hydroponic model, which involves an upright posture. Objectives: To verify the influence of cultivation model on posture and back pain prevalence among strawberry producers. Methods: A total of 26 strawberry producers who used traditional or hydroponic methods participated in the study. The angular values of the curvatures of the thoracic and lumbar spine in the sagittal plane were obtained using the "flexicurve" method, while pain prevalence was determined with Souza & Krieger's back pain questionnaire. The t-test for independent samples and the chi-square test were used to compare group results. Results: Growers using the traditional model had greater thoracic spine curvature (45.5 [SD, 26.2 ]) than those who used the hydroponic model (24.4 [SD, 10.3 ]). There was an association between thoracic spine classification and cervical pain, with a higher prevalence of thoracic kyphosis and cervical pain in the traditional model and a higher prevalence of normal curvature in the hydroponic model. Both groups reported a higher prevalence of pain in the lower back than in other locations. Conclusions: The cultivation model influenced posture and back pain prevalence in strawberry producers. Producers who use the traditional model have greater angulations of the thoracic spine, hyperkyphosis, lumbar straightening, and cervical pain than those who use the hydroponic model.

Introdução: O cultivo de morango é uma importante fonte de renda de agricultores brasileiros. Atualmente, o cultivo pode ser feito no modelo tradicional, em que o produtor flexiona o tronco para manusear a muda, ou no modelo hidropônico, em que ele adota uma postura ereta. Objetivos: Verificar a influência do modelo de cultivo na postura e na prevalência de dor na coluna vertebral em produtores de morango. Métodos: Participaram 26 produtores de morango de diferentes modelos de cultivo (tradicional e hidropônico). Os valores angulares das curvaturas da coluna torácica e lombar no plano sagital foram obtidos por meio do método "flexicurva", e a prevalência de dor foi medida através do questionário Informações sobre Dor nas Costas. Os modelos foram comparados com o teste t para amostras independentes, e a associação, com o teste de qui-quadrado. Resultados: Os produtores de morango que plantam a fruta no modelo tradicional apresentam maiores curvaturas na coluna torácica (45,5 ± 26,2 ) quando comparados aos que utilizam o modelo hidropônico (24,4 ± 10,3 ). Houve associação entre as classificações da coluna torácica e dor cervical, demonstrando maior prevalência de hipercifose torácica e dor na cervical no modelo tradicional e curvatura normal no hidropônico. Ambos os grupos apresentam maior prevalência de dor lombar. Conclusões: Pode-se concluir que há influência do modelo de cultivo na postura e na prevalência de dor na coluna vertebral em produtores de morango. Os produtores que manuseiam a fruta no modelo tradicional possuem maiores angulações na coluna torácica, prevalência de hipercifose, retificação lombar e dores na região cervical em comparação aos que manuseiam a fruta no modelo hidropônico.

Characterization of ruminal bacteria in grazing Nellore steers / Caracterización de bacterias ruminales en novillos Nelore en pastoreo / Caraterização bacteriana ruminal em novilhos Nelore em pastejo

Abstract Background: Rumen microorganisms have developed a series of complex interactions, representing one of the best examples of symbiosis between microorganisms in nature. Conventional taxonomic methods based on culture techniques are being replaced by molecular techniques that are faster and more accurate. Objective: To characterize rumen bacterial diversity of Nellore steers grazing on tropical pastures by sequencing the 16S rRNA gene using Illumina sequencing. Methods: Three rumen-cannulated Nellore steers were used. The liquid and solid fractions of the rumen contents were processed to extract metagenomic DNA, and the V1 and V2 hypervariable regions of the 16S rRNA gene were sequenced using Illumina sequencing. Results: A total of 11,407,000 reads of adequate quality were generated, and 812 operational taxonomic units (OTUs) were found at the species level. Twenty-seven phyla were identified, and the predominant phyla were Firmicutes (23%), Bacteroidetes (14%), Proteobacteria (10%), Spirochaetes (9%), Fibrobacteres (7%), Tenericutes (5%), and Actinobacteria (2%), which represented 70% of the total phyla identified in the rumen content. Conclusion: Rumen environment in grazing Nellore steers showed high bacterial diversity, with Firmicutes, Bacteroidetes, Proteobacteria, Spirochaetes, and Fibrobacteres as the predominant phyla.

Resumen Antecedentes: Los microorganismos ruminales han desarrollado una serie de interacciones complejas que representan uno de los mejores ejemplos de simbiosis entre microorganismos en la naturaleza. Los métodos taxonómicos tradicionales basados en técnicas de cultivo están siendo reemplazados por técnicas moleculares debido a su mayor velocidad y precisión. Objetivo: Caracterizar la diversidad bacteriana ruminal de novillos Nelore mantenidos en pasturas tropicales mediante la secuenciación del gen 16S RNA utilizando la plataforma de secuenciación Illumina. Métodos: Se utilizaron tres novillos Nelore fistulados en el rumen. Las fracciones líquida y sólida del contenido ruminal fueron procesadas para la extracción del DNA meta genómico y las regiones hipervariables V1 y V2 del gen 16S rRNA fueron secuenciadas usando la plataforma Illumina. Resultados: En total, se generaron 11.407.000 lecturas de calidad adecuada, y en el nivel de especie se encontraron 812 unidades taxonómicas operacionales (OTUs). Se identificaron veintisiete filos, predominantemente Firmicutes (23%), Bacteroidetes (14%), Proteobacteria (10%), Spirochaetes (9%), Fibrobacteres (7%), Tenericutes (5%) y Actinobacteria (2%), los cuales representaron el 70% de los filos identificados en el contenido ruminal. Conclusión: El ambiente ruminal de novillos Nelore en pastoreo presenta una alta diversidad de bacterias, con dominancia de los filos Firmicutes, Bacteroidetes, Proteobacteria, Spirochaetes y Fibrobacteres .

Resumo Antecedentes: Os microrganismos ruminais têm desenvolvido uma serie de complexas interações que representam um dos melhores exemplos de simbiose entre microrganismos na natureza. Os métodos taxonômicos tradicionais baseados em métodos de cultura vêm sendo substituídos por técnicas moleculares que apresentam maior velocidade a acurácia. Objetivo: Caracterizar a diversidade bacteriana ruminal em novilhos Nelore mantidos em pastagens tropicais mediante o sequenciamento do gene 16S rRNA utilizando a plataforma de sequenciamento Illumina. Métodos: Foram utilizados três novilhos Nelore fistulados no rúmen. A fração liquida e solida do conteúdo ruminal foram processadas para extrair o DNA metagenômico, e as regiões hipervariáveis V1 e V2 do gene 16S rRNA foram sequenciadas na plataforma Illumina. Resultados: No total foram geradas 11.407.000 leituras de qualidade adequada, e 812 unidades taxonomicas operacionais (OTUs) foram identificadas no nível de espécie. Foram identificados 27 filos, e houve predominância de Firmicutes (23%), Bacteroidetes (14%), Proteobacteria (10%), Spirochaetes (9%), Fibrobacteres (7%), Tenericutes (5%) e Actinobacteria (2 %), os quais representaram 70% dos filos identificados a partir do rúmen bovino. Conclusão: O ambiente ruminal em novilhos Nelore em pastejo apresentou alta diversidade bacteriana, com Firmicutes, Bacteroidetes, Proteobacteria, Spirochaetes e Fibrobacteres como filos predominantes.

Draft Genome Sequence of Bradyrhizobium elkanii TnphoA 33, a Producer of Polyhydroxyalkanoates.

The genus Bradyrhizobium comprises bacteria with the ability to form nitrogen-fixing symbioses with legumes. They are of great interest in agriculture, as well as for the production of biopolymers such as polyhydroxyalkanoates. Here, we report the draft genome assembly of Bradyrhizobium elkanii TnphoA 33 comprising 9 Mb, 1,124 contigs, and 9,418 open reading frames.

Influence of Vinasse Application in the Structure and Composition of the Bacterial Community of the Soil under Sugarcane Cultivation.

Although the use of vinasse as a waste helps replenish soil nutrients and improves the quality of the sugarcane crop, it is known that vinasse residues alter the diversity of bacteria naturally present in the soil. The actual impacts of vinasse application on the selection of bacterial taxa are not understood because no studies have addressed this phenomenon directly. Analysis of 16S rRNA gene clone sequences from four soil types showed that the soil planted with sugarcane and fertilized with vinasse has a high diversity of bacteria compared to other biomes, where Acidobacteria were the second most abundant phylum. Although the composition and structure of bacterial communities differ significantly in the four environments (Libshuff's test), forest soils and soil planted with sugarcane without vinasse fertilizer were similar to each other because they share at least 28 OTUs related to Rhizobiales, which are important agents involved in nitrogen fixation. OTUs belonging to Actinomycetales were detected more often in the soil that had vinasse applied, indicating that these groups are more favored by this type of land management.

Metagenomic Assembly and Draft Genome Sequence of an Uncharacterized Prevotella sp. from Nelore Rumen.

Prevotella is one of the most abundant genera in bovine rumen, although no genome has yet been assembled by a metagenomics approach applied to Brazilian Nelore. We report the draft genome sequence of Prevotella sp., comprising 2,971,040 bp, obtained using the Illumina sequencing platform. This genome includes 127 contigs and presents a low 48% GC.

Draft genome sequence of the nitrogen-fixing symbiotic bacterium Bradyrhizobium elkanii 587.

The draft sequence of the genome of Bradyrhizobium elkanii 587 is presented. This was obtained using Illumina Next-Gen DNA sequencing combined with Sanger sequencing. Genes for the pathways involved in biological nitrogen fixation (the nif gene cluster), nod genes including nodABC, and genes for the type III protein secretion system (T3SS) are present.

The antimicrobial activity of photodynamic therapy against Streptococcus mutans using different photosensitizers.

UNLABELLED: Several photosensitizers have been used against oral bacteria without standardization. Singlet oxygen ((1)O(2)) is an aggressive chemical species that can kill cells through apoptosis or necrosis. OBJECTIVE: to compare the antimicrobial activity of photodynamic therapy (PDT) with different photosensitizers at the same concentration against Streptococcus mutans. In addition, the (1)O(2) production of each photosensitizer was determined. The photosensitizers (163.5 µM) methylene blue (MB), toluidine blue ortho (TBO) and malachite green (MG) were activated with a light-emitting diode (LED; λ=636 nm), while eosin (EOS), erythrosine (ERI) and rose bengal (RB) were irradiated with a curing light (λ=570 nm). Light sources were operated at 24 J cm(-2). For each photosensitizer, 40 randomized assays (n=10 per condition) were performed under one of the following experimental conditions: no light irradiation or photosensitizer, irradiation only, photosensitizer only or irradiation in the presence of a photosensitizer. After treatment, serial dilutions of S. mutans were seeded onto brain heart infusion agar to determine viability in colony-forming units per milliliter (CFU mL(-1)). Generation of (1)O(2) was analyzed by tryptophan photooxidation, and the decay constant was estimated. Results were analyzed by one-way ANOVA and the Tukey-Kramer test (p<0.05). PDT with irradiation in the presence of the photosensitizers TBO and MG was effective in reducing S. mutans counts by 3 and 1.4 logs, respectively (p<0.01), compared to their respective untreated controls. MB generated 1.3 times more (1)O(2) than TBO, and both produced significantly higher concentrations of singlet oxygen than the other photosensitizers. Since in vitro bulk (1)O(2) production does not indicate that (1)O(2) was generated in the bacterial activity site, the bactericidal action against S. mutans cannot be related to in vitro singlet O(2) generation rate. In vitroS. mutans-experiments demonstrated TBO as the only photosensitizer that effectively reduced 99.9% of these microorganisms.