Discovery of antimicrobial peptides in the global microbiome with machine learning.

Novel antibiotics are urgently needed to combat the antibiotic-resistance crisis. We present a machine-learning-based approach to predict antimicrobial peptides (AMPs) within the global microbiome and leverage a vast dataset of 63,410 metagenomes and 87,920 prokaryotic genomes from environmental and host-associated habitats to create the AMPSphere, a comprehensive catalog comprising 863,498 non-redundant peptides, few of which match existing databases. AMPSphere provides insights into the evolutionary origins of peptides, including by duplication or gene truncation of longer sequences, and we observed that AMP production varies by habitat. To validate our predictions, we synthesized and tested 100 AMPs against clinically relevant drug-resistant pathogens and human gut commensals both in vitro and in vivo. A total of 79 peptides were active, with 63 targeting pathogens. These active AMPs exhibited antibacterial activity by disrupting bacterial membranes. In conclusion, our approach identified nearly one million prokaryotic AMP sequences, an open-access resource for antibiotic discovery.

Microbial population genomes from the Amazon River reveal possible modulation of the organic matter degradation process in tropical freshwaters.

Rivers connect the carbon cycle in land with that in aquatic ecosystems by transporting and transforming terrestrial organic matter (TeOM). The Amazon River receives huge loads of TeOM from the surrounding rainforest, promoting a substantial microbial heterotrophic activity and consequently, CO2 outgassing. In the Amazon River, microbes degrade up to 55% of the lignin present in the TeOM. Yet, the main microbial genomes involved in TeOM degradation were unknown. Here, we characterize 51 population genomes (PGs) representing some of the most abundant microbes in the Amazon River deriving from 106 metagenomes. The 51 reconstructed PGs are among the most abundant microbes in the Amazon River, and 53% of them are not able to degrade TeOM. Among the PGs capable of degrading TeOM, 20% were exclusively cellulolytic, while the others could also oxidize lignin. The transport and consumption of lignin oxidation byproducts seemed to be decoupled from the oxidation process, being apparently performed by different groups of microorganisms. By connecting the genomic features of abundant microbes in the Amazon River with the degradation machinery of TeOM, we suggest that a complex microbial consortium could explain the quick turnover of TeOM previously observed in this ecosystem.

Isohemigossypolone: Antiophidic properties of a naphthoquinone isolated from Pachira aquatica Aubl.

We investigated the antiophidic properties of isohemigossypolone (ISO), a naphthoquinone isolated from the outer bark of the Pachira aquatic Aubl. The inhibition of phospholipase A2, coagulant, fibrinogenolytic, hemorrhagic and myotoxic activities induced by Bothrops pauloensis venom (Pb) was investigated. For this, we use samples resulting from the incubation of Pb with ISO in different concentrations (1:1, 1:5 and 1:10 w/w), we also evaluated the condition of treatment using ISO after 15 min of venom inoculation. The activities of phospholipase A2, coagulant, fibrinogenolytic, hemorrhagic and myotoxic induced by the B. pauloensis venom were significantly inhibited when the ISO was pre-incubated with the crude venom. For in vivo neutralization tests, the results were observed even when the ISO was applied after 15 min of inoculation of the venom or metalloprotease (BthMP). Also, to identify the inhibition mechanism, we performed in silico assays, across simulations of molecular coupling and molecular dynamics, it was possible to identify the modes of interaction between ISO and bothropic toxins BmooMPα-I, Jararacussin-I and BNSP-7. The present study shows that naphthoquinone isohemigossypolone isolated from the P. aquatica plant inhibited part of the local and systemic damage caused by venom proteins, demonstrating the pharmacological potential of this compound in neutralizing the harmful effects caused by snakebites.

Uncovering the genomic potential of the Amazon River microbiome to degrade rainforest organic matter.

BACKGROUND: The Amazon River is one of the largest in the world and receives huge amounts of terrestrial organic matter (TeOM) from the surrounding rainforest. Despite this TeOM is typically recalcitrant (i.e. resistant to degradation), only a small fraction of it reaches the ocean, pointing to a substantial TeOM degradation by the river microbiome. Yet, microbial genes involved in TeOM degradation in the Amazon River were barely known. Here, we examined the Amazon River microbiome by analysing 106 metagenomes from 30 sampling points distributed along the river. RESULTS: We constructed the Amazon River basin Microbial non-redundant Gene Catalogue (AMnrGC) that includes ~ 3.7 million non-redundant genes, affiliating mostly to bacteria. We found that the Amazon River microbiome contains a substantial gene-novelty compared to other relevant known environments (rivers and rainforest soil). Genes encoding for proteins potentially involved in lignin degradation pathways were correlated to tripartite tricarboxylates transporters and hemicellulose degradation machinery, pointing to a possible priming effect. Based on this, we propose a model on how the degradation of recalcitrant TeOM could be modulated by labile compounds in the Amazon River waters. Our results also suggest changes of the microbial community and its genomic potential along the river course. CONCLUSIONS: Our work contributes to expand significantly our comprehension of the world's largest river microbiome and its potential metabolism related to TeOM degradation. Furthermore, the produced gene catalogue (AMnrGC) represents an important resource for future research in tropical rivers. Video abstract.

Recombinant expression, characterization and phylogenetic studies of novels cystatins-like proteins of sweet orange (Citrus sinensis) and clementine (Citrus clementina).

Phytocystatins are plant cystatins that are related to several physiological processes regulating endogenous cysteine proteases involved in seed development and germination, programmed cell death and response to stress conditions. In addition, phytocystatins can act in plant defense against exogenous peptidases from herbivorous insects, pathogens and nematodes. Considering that Citrus fruits are important to human nutrition and represent a high value crop in worldwide agriculture, in the present work, we performed the identification of putative cystatins from Citrus sinensis and from Citrus clementine and submitted them to phylogenetic analysis. Six cystatins from each species were identified as orthologous and classified into three well supported phylogenetic groups. Five cystatins representative of the phylogenetic groups were recombinantly expressed and the in vitro studies revealed them to be potent inhibitors against the cysteine peptidases papain, legumain, human cathepsins (B, L, S, K) and a cathepsin B-like from Diaphorina citri (the Asian Citrus psyllid). Our findings provide the C. clementina and C. sinensis cystatins classification and an enzyme-inhibitor interactions profile, which may reflect an evolutionary process of Citrus cystatins related to gene functions as initial germination rates and seedlings development as well associated to plant defense against pathogens, as insects and nematodes.

Flood Season Microbiota from the Amazon Basin Lakes: Analysis with Metagenome Sequencing.

Despite an apparent geographic separation of the Amazon water bodies, they are an interconnected system. During floods, the microbiota of rivers, lakes, and soil combines. This study used metagenomics sequencing to survey the microbiota of the Amazon Basin lakes during flood season, showing important patterns in microbial communities.

A transcriptomic survey of Migdolus fryanus (sugarcane rhizome borer) larvae.

Sugarcane, a major crop grown in the tropical and subtropical areas of the world, is produced mainly for sucrose, which is used as a sweetener or for the production of bioethanol. Among the numerous pests that significantly affect the yield of sugarcane, the sugarcane rhizome borer (Migdolus fryanus, a cerambycidae beetle) is known to cause severe damage to the crops in Brazil. The absence of molecular information about this insect reinforces the need for studies and an effective method to control this pest. In this study, RNA-Seq technology was employed to study different parts of M. fryanus larvae. The generated data will help in further investigations about the taxonomy, development, and adaptation of this insect. RNA was extracted from six different parts (head, fat body, integument, hindgut, midgut, and foregut) using Trizol methodology. Using Illumina paired-end sequencing technology and the Trinity platform, trimming and de novo assembly was performed, resulting in 44,567 contigs longer than 200 nt for a reunion of data from all transcriptomes, with a mean length of 1,095.27 nt. Transcripts were annotated using BLAST against different protein databanks (Uniprot/Swissprot, PFAM, KEEG, SignalP 4.1, Gene Ontology, and CAZY) and were compared for similarity using a Venn diagram. Differential expression patterns were studied for select genes through qPCR and FPKM comprising important protein families (digestive peptidases, glucosyl hydrolases, serine protease inhibitors and otopetrin), which allowed a better understanding of the insect's digestion, immunity and gravity sensorial mechanisms.

Epigenetic modifications and their relation to caste and sex determination and adult division of labor in the stingless bee Melipona scutellaris.

Stingless bees of the genus Melipona, have long been considered an enigmatic case among social insects for their mode of caste determination, where in addition to larval food type and quantity, the genotype also has a saying, as proposed over 50 years ago by Warwick E. Kerr. Several attempts have since tried to test his Mendelian two-loci/two-alleles segregation hypothesis, but only recently a single gene crucial for sex determination in bees was evidenced to be sex-specifically spliced and also caste-specifically expressed in a Melipona species. Since alternative splicing is frequently associated with epigenetic marks, and the epigenetic status plays a major role in setting the caste phenotype in the honey bee, we investigated here epigenetic chromatin modification in the stingless bee Melipona scutellaris. We used an ELISA-based methodology to quantify global methylation status and western blot assays to reveal histone modifications. The results evidenced DNA methylation/demethylation events in larvae and pupae, and significant differences in histone methylation and phosphorylation between newly emerged adult queens and workers. The epigenetic dynamics seen in this stingless bee species represent a new facet in the caste determination process in Melipona bees and suggest a possible mechanism that is likely to link a genotype component to the larval diet and adult social behavior of these bees.

Epigenetic modifications and their relation to caste and sex determination and adult division of labor in the stingless bee Melipona scutellaris

Abstract Stingless bees of the genus Melipona, have long been considered an enigmatic case among social insects for their mode of caste determination, where in addition to larval food type and quantity, the genotype also has a saying, as proposed over 50 years ago by Warwick E. Kerr. Several attempts have since tried to test his Mendelian two-loci/two-alleles segregation hypothesis, but only recently a single gene crucial for sex determination in bees was evidenced to be sex-specifically spliced and also caste-specifically expressed in a Melipona species. Since alternative splicing is frequently associated with epigenetic marks, and the epigenetic status plays a major role in setting the caste phenotype in the honey bee, we investigated here epigenetic chromatin modification in the stingless bee Melipona scutellaris. We used an ELISA-based methodology to quantify global methylation status and western blot assays to reveal histone modifications. The results evidenced DNA methylation/demethylation events in larvae and pupae, and significant differences in histone methylation and phosphorylation between newly emerged adult queens and workers. The epigenetic dynamics seen in this stingless bee species represent a new facet in the caste determination process in Melipona bees and suggest a possible mechanism that is likely to link a genotype component to the larval diet and adult social behavior of these bees.

Metagenome Sequencing of Prokaryotic Microbiota Collected from Rivers in the Upper Amazon Basin.

Tropical freshwater environments, like rivers, are important reservoirs of microbial life. This study employed metagenomic sequencing to survey prokaryotic microbiota in the Solimões, Purus, and Urucu Rivers of the Amazon Basin in Brazil. We report a rich and diverse microbial community.

Metagenomics Analysis of Microorganisms in Freshwater Lakes of the Amazon Basin.

The Amazon Basin is the largest hydrographic basin on the planet, and the dynamics of its aquatic microorganisms strongly impact global biogeochemical cycles. However, it remains poorly studied. This metagenome project was performed to obtain a snapshot of prokaryotic microbiota from four important lakes in the Amazon Basin.

Correlation between yield components in F6 soybean progenies derived from seven biparental crosses / Correlação entre caracteres em progênies F6 de soja provenientes de sete cruzamentos biparentais

Breeding programs strive to obtain cultivars with superior traits. The association between these characters, such as those estimated by correlation coeficients, are important to the breeding selection process. In this study we analyzed phenotypic and genotypic correlations between yield and other agronomic traits in soybean progenies derived from various crosses to support breeding line selection in the soybean breading program of the Federal University of Uberlandia (UFU). The experiment was carried out in the 2011/2012 growing season at the Capim Branco research station in Uberlandia, Minas Gerais, Brazil. Seventy-one soybean lines were evaluated using a randomized complete block design with three replications. In these plots plants were evaluated for the number of pods, grain yield per plant, number of days for flowering, plant height at flowering, number of days for maturity, plant height at maturity, height of the first pod insertion, number of grains per pod and grain yield per plant. The estimates for genotypic correlations were equal or greater than those for the phenotypic correlations for all the evaluated traits. This suggests a small effect of environmental factors on the trait expression. An exception of this behavior was the correlation between plant height at flowering and plant height at maturity. In this case, although the signs for the genotypic and phenotypic correlations were the same, the value for the last was greater than that for the former. The late flowering and late-maturing plants were taller. Also, selecting plants for higher number of pods ultimately contributed for the selection of plants with higher grain yield. The selection of late-flowering and late-maturing plants have yielded taller plantsin the same way that the selection for a higher pod number could promote the selection and improvement of grains yield trait.

O objetivo dos programas de melhoramento genético de qualquer cultura é a obtenção de cultivares que superem com vantagens as pré-existentes. Desse modo, o conhecimento das relações entre caracteres, tais como estimadas pelas correlações, tem apresentado grande importância para o sucesso dos processos de seleção no melhoramento. Os objetivos deste estudo foram avaliar as correlações fenotípicas e genotípicas entre caracteres agronômicos de linhagens de soja oriundas de diferentes cruzamentos, visando fornecer subsídios para fins de seleção a ser adotado no programa de melhoramento genético de soja da Universidade Federal de Uberlândia. O experimento foi conduzido em uma área experimental localizada na Fazenda Capim Branco, pertencente à Universidade Federal de Uberlândia, no município de Uberlândia, Minas Gerais, na safra 2011/2012. Foram avaliados 71 linhagens de soja em delineamento de blocos completos casualisados com três repetições. Avaliaram-se os caracteres: número total de vagens, produção de grãos por planta, número de dias para o florescimento, altura da planta no florescimento, número de dias para maturidade, altura da planta na maturidade, altura de inserção de primeira vagem, número de grãos por vagem e produção de grãos por planta. Para todos os caracteres, com exceção da correlação entre altura da planta no florescimento e maturidade em que a apesar de apresentarem mesma direção, a magnitude da correlação fenotípica superou a correlação genotípica, as correlações genotípicas foram superiores as fenotípicas e de igual sinal, indicando menor influência do ambiente na expressão dos caracteres. A seleção de plantas mais tardias no florescimento e maturidade, resulta em plantas mais altas nesses estádios de desenvolvimento, bem como a seleção de plantas com maior número de vagens favorece a seleção e melhoramento para o caractere produção de grãos por planta.

A novel ß-fructofuranosidase in Coleoptera: Characterization of a ß-fructofuranosidase from the sugarcane weevil, Sphenophorus levis.

ß-fructofuranosidases or invertases (EC 3.2.1.26) catalyze the hydrolysis of sucrose into fructose and glucose. ß-fructofuranosidases have been widely described in microorganisms, but were not known in the animal kingdom until very recently. There are studies reporting lepidopteran ß-fructofuranosidases, but no ß-fructofuranosidase gene sequence or encoding transcript has previously been identified in beetles. Considering the scarcity of functional studies on insect ß-fructofuranosidases and their apparent non-occurrence among coleopterans, the aim of the present study was to investigate the occurrence and characterize a ß-fructofuranosidase transcript identified in a cDNA library from the sugarcane weevil, Sphenophorus levis (Curculionidae). To validate that the ß-fructofuranosidase sequence (herein denominated Sl-ß-fruct) is indeed encoded by the S. levis genome, PCRs were performed using genomic DNA extracted from the larval fat body as well as DNA from the midgut with microbial content. Amplification of Sl-ß-fruct gene using larval fat body DNA indicated its presence in the insect's genomic DNA. The Sl-ß-fruct gene was cloned in Pichia pastoris to produce the recombinant enzyme (rSl-ß-fruct). Molecular weight of the recombinant protein was about 64 kDa, indicating possible glycosylation, since the theoretical weight was 54.8 kDa. The substrate specificity test revealed that rSl-ß-fruct hydrolyzes sucrose and raffinose, but not melibiose or maltose, thereby confirming invertase activity. The pH curve revealed greatest activity at pH 5.0, demonstrating rSl-ß-fruct to be an acidic ß-fructofuranosidase. Quantitative PCR (qRT-PCR) analyses indicated that the production of mRNA only occurs in the midgut and reaches the greatest expression level in 30-day-old larvae, which is the expected pattern for digestive enzymes. Chromatography of glycosidases from S. levis midguts showed two enzymes acting as ß-fructofuranosidase, indicating the presence of a Sl-ß-fruct isoform or a ß-fructofuranosidase from insect intestinal microbiota. Moreover, it was found that α-glucosidases do not act on sucrose hydrolysis. Phylogenetic analyses indicated this enzyme to be similar to enzymes found in other coleopteran and lepidopteran ß-fructofuranosidases, but also closely similar to bacterial enzymes, suggesting potential horizontal gene transfer. Despite this, the enzyme seems to be restricted to different groups of bacteria, which suggests distinct origin events. The present study expands the concept of the occurrence of ß-fructofuranosidase in insects. Despite the few descriptions of this gene in the animal kingdom, it is possible to state that ß-fructofuranosidase is crucial to the establishment of some insects throughout their evolutionary history, especially members of the Lepidoptera and Coleoptera clades.

Tollip or not Tollip: what are the evolving questions behind it?

Tollip plays an important role in the interleukin-1 receptor IL-1R and Toll pathways. As a modulator of the immune pathway, it indirectly controls the amount of antimicrobial peptides. This could indicate a vital step in maintaining animal immune systems and preventing infection. Evolutionary questions are crucial to understanding the conservation and functioning of the biochemical pathways like the Tollip-mediated one. Through an analysis of 36 sequences of the Tollip protein from different animal taxa, downloaded from Kyoto Encyclopedia of Genes and Genomes (KEGG) databank, we inferred diverse evolutionary parameters, such as molecular selection and structure conservation, by analyzing residue by residue, beyond the canonical parameters to this type of study, as maximum likelihood trees. We found that Tollip presented different trends in its evolving history. In primates, the protein is becoming more unstable, just the opposite is observed in the arthropod group. The most interesting finding was the concentration of positively selected residues at amino terminal ends. Some observed topological incongruences in maximum likelihood trees of complete and curated Tollip data sets could be explained through horizontal transfers, evidenced by recombination detection. These results suggest that there is more to be researched and understood about this protein.

Aspectos fisiológicos e bioquímicos de cultivares de soja submetidos a déficit hídrico induzido por PEG 6000 / Phisiological and biochemical aspects of soybean cultivars submitted to water deficit induced by PEG 6000

Na cultura da soja, o déficit hídrico é um dos fatores limitantes à obtenção da máxima produtividade. A identificação de genótipos com capacidade de tolerância à seca é fundamental para a solução desse problema. Objetivou-se, neste trabalho, analisar a qualidade fisiológica e as respostas bioquímicas de cultivares de soja (MG/BR 46 Conquista, UFUS Carajás, UFUS Impacta, UFUS Riqueza e UFUS Xavante) submetidas ao estresse hídrico com soluções de PEG 6000 em diferentes níveis de potencial osmótico (0; -0,1; -0,2; -0,3 e -0,4 MPa). Avaliou-se a qualidade fisiológica das cultivares por meio dos testes de comprimento de plântulas e biomassa fresca e seca de plântulas. As respostas bioquímicas foram avaliadas pela detecção do ácido indol-acético, pelo conteúdo de sacarose e pelo transporte de água nas plântulas. A cultivar UFUS Riqueza apresentou os melhores desempenhos nos testes de qualidade fisiológica, conteúdo de sacarose, absorção e velocidade de absorção de água em plântulas. A cultivar UFUS Xavante mostrou a maior concentração de AIA e o maior massa de plântulas no teste de transporte de água.

In soybean culture water deficit is one of the most limiting factors to the maximum yield obtained. Genotypes identification with drought tolerance capacity is fundamental to solve this problem. The objective in this paper was analyze the physiological quality and physiological and biochemical responses of soybeans cultivars (MG/BR 46 Conquista, UFUS Carajás, UFUS Impacta, UFUS Riqueza and UFUS Xavante) submitted to water stress with PEG 6000 solutions in different levels of osmotic potentials (0; -0,1; -0,2; -0,3 and -0,4 MPa). Physiological quality of cultivars were evaluated by seedling length test and fresh and dry biomass. The biochemical responses were evaluated by detection of indol-acetic acid (IAA), by saccharose content and seedling water transportation. UFUS Riqueza presented the best performance in physiological quality tests, saccharose content, absorption and water absorption velocity in seedling. UFUS Xavante showed the highest IAA's concentration and the greater weight of seedling in water transportation test.