Revision and annotation of DNA barcode records for marine invertebrates: Report of the 8th iBOL conference hackathon

The accuracy of specimen identification through DNA barcoding and metabarcoding relies on reference libraries containing records with reliable taxonomy and sequence quality. The considerable growth in barcode data requires stringent data curation, especially in taxonomically difficult groups such as marine invertebrates. A major effort in curating marine barcode data in the Barcode of Life Data Systems (BOLD) was undertaken during the 8th International Barcode of Life Conference (Trondheim, Norway, 2019). Major taxonomic groups (crustaceans, echinoderms, molluscs, and polychaetes) were reviewed to identify those which had disagreement between Linnaean names and Barcode Index Numbers (BINs). The records with disagreement were annotated with four tags: A) MIS-ID (misidentified, mislabeled, or contaminated records), b) AMBIG (ambiguous records unresolved with the existing data), c) COMPLEX (species names occurring in multiple BINs), and d) SHARE (barcodes shared between species). A total of 83,712 specimen records corresponding to 7,576 species were reviewed and 39% of the species were tagged (7% MIS-ID, 17% AMBIG, 14% COMPLEX, and 1% SHARE). High percentages (>50%) of AMBIG tags were recorded in gastropods, whereas COMPLEX tags dominated in crustaceans and polychaetes. The high proportion of tagged species reflects either flaws in the barcoding workflow (e.g., misidentification, cross-contamination) or taxonomic difficulties (e.g., synonyms, undescribed species). Although data curation is essential for barcode applications, such manual attempts to examine large datasets are unsustainable and automated solutions are extremely desirable.The hackathon was organized with financial support from the European Union COST Action DNAqua-Net (CA 15219 https://dnaqua.net/) in the scope of the 8th International Barcode of Life Conference in Trondheim, Norway on 16 June 2019. DNAqua-Net is acknowledged for the funding provided and the local conference organizers for all the logistical support that ensured a successful event. Tyler Elliot and the rest of the BOLD team are acknowledged for their help with data queries and analytics. The authors also thank the hackathon participants for vibrant discussions during and after the event: Berry van der Hoorn, Katrine Konsghavn, Guy Paz, Mouna Rifi, Malin Strand, Anne Helene Tandberg, Adam Wall, and Endre Willassen. Marcos A. L. Teixeira was supported by a PhD grant from the Portuguese Foundation for Science and Technology (FCT I.P.) co-financed by ESF (SFRH/BD/131527/2017). Financial support granted by FCT to Sofia Duarte (CEECIND/00667/2017) and to Pedro E. Vieira (project NIS-DNA, PTDC/BIA-BMA/29754/2017) is also acknowledged. Sanna Majaneva was financially supported by the Norwegian Taxonomy Initiative (project no. 70184235). The authors thank the five reviewers who provided valuable input into the earlier version of the manuscript

Production and release of heat-labile toxin by wild-type human-derived enterotoxigenic Escherichia coli

Production and release of heat-labile toxin (LT) by wild-type enterotoxigenic Escherichia coli (ETEC) strains, isolated from diarrheic and asymptomatic Brazilian children, was studied under in vitro and in vivo conditions. Based on a set of 26 genetically diverse LT+ enterotoxigenic E. coli strains, cell-bound LT concentrations varied from 49.8 to 2415 ng mL(-1). the amounts of toxin released in culture supernatants ranged from 0% to 50% of the total synthesized toxin. the amount of LT associated with secreted membrane vesicles represented < 5% of the total toxin detected in culture supernatants. ETEC strains secreting higher amounts of LT, but not those producing high intracellular levels of cell-bound toxin, elicited enhanced fluid accumulation in tied rabbit ileal loops, suggesting that the strain-specific differences in production and secretion of LT correlates with symptoms induced in vivo. However, no clear correlation was established between the ability to produce and secrete LT and the clinical symptoms of the infected individuals. the present results indicate that production and release of LT by wild-type human-derived ETEC strains are heterogeneous traits under both in vitro and in vivo growth conditions and may impact the clinical outcomes of infected individuals.Univ São Paulo, Dept Microbiol, Inst Ciencias Biomed, São Paulo, BrazilUniversidade Federal de São Paulo, Dept Microbiol Imunol & Parasitol, São Paulo, BrazilFdn Oswaldo Cruz, Escola Nacl Saude Publ, Rio de Janeiro, BrazilUniv São Paulo, Dept Patol, Fac Med Vet & Zootecn, São Paulo, BrazilInst Butantan, Div Desenvolvimento Tecnol & Prod, São Paulo, BrazilUniversidade Federal de São Paulo, Dept Microbiol Imunol & Parasitol, São Paulo, BrazilWeb of Scienc

Roles of non-coding RNA in sugarcane-microbe interaction

Studies have highlighted the importance of non-coding RNA regulation in plant-microbe interaction. However, the roles of sugarcane microRNAs (miRNAs) in the regulation of disease responses have not been investigated. Firstly, we screened the sRNA transcriptome of sugarcane infected with Acidovorax avenae. Conserved and novel miRNAs were identified. Additionally, small interfering RNAs (siRNAs) were aligned to differentially expressed sequences from the sugarcane transcriptome. Interestingly, many siRNAs aligned to a transcript encoding a coppertransporter gene whose expression was induced in the presence of A. avenae, while the siRNAs were repressed in the presence of A. avenae. Moreover, a long intergenic non-coding RNA was identified as a potential target or decoy of miR408. To extend the bioinformatics analysis, we carried out independent inoculations and the expression patterns of six miRNAs were validated by quantitative reverse transcription-PCR (qRT-PCR). Among these miRNAs, miR408—a copper- microRNA—was downregulated. The cleavage of a putative miR408 target, a laccase, was confirmed by a modified 50RACE (rapid amplification of cDNA ends) assay. MiR408 was also downregulated in samples infected with other pathogens, but it was upregulated in the presence of a beneficial diazotrophic bacteria. Our results suggest that regulation by miR408 is important in sugarcane sensing whether microorganisms are either pathogenic or beneficial, triggering specific miRNA-mediated regulatory mechanisms accordingly

Economic and climatic models for estimating coffee supply

O objetivo deste trabalho foi estimar a oferta cafeeira por meio da calibração de modelos estatísticos, com variáveis econômicas e climáticas, das principais regiões produtoras do Estado de São Paulo. As regiões estudadas foram Batatais, Caconde, Cássia dos Coqueiros, Cristais Paulista, Espírito Santo do Pinhal, Marília, Mococa e Osvaldo Cruz. Foram utilizados dados de oferta cafeeira, variáveis econômicas (crédito rural, crédito rural na agricultura e valor da produção) e variáveis climáticas (temperatura do ar, precipitação pluvial, evapotranspiração potencial, deficiência e excedente hídrico) de cada região, para o período de 2000–2014. Os modelos foram calibrados com uso de técnicas de regressão linear múltipla, e todas as combinações possíveis foram testadas para a seleção das variáveis. A oferta cafeeira foi a variável dependente, e as demais, as independentes. A acurácia e a precisão dos modelos foram analisadas pelo erro percentual médio e pelo coeficiente de determinação ajustado, respectivamente. As variáveis que mais influenciam a oferta cafeeira são o valor de produção e a temperatura do ar. É possível estimar a oferta cafeeira com regressões lineares múltiplas por meio de variáveis econômicas e elementos climáticos. Os modelos mais acurados são os calibrados para estimar a oferta cafeeira das regiões de Cássia dos Coqueiros e Osvaldo Cruz.The objective of this work was to estimate the coffee supply by calibrating statistical models with economic and climatic variables for the main producing regions of the state of São Paulo, Brazil. The regions were Batatais, Caconde, Cássia dos Coqueiros, Cristais Paulista, Espírito Santo do Pinhal, Marília, Mococa, and Osvaldo Cruz. Data on coffee supply, economic variables (rural credit, rural agricultural credit, and production value), and climatic variables (air temperature, rainfall, potential evapotranspiration, water deficit, and water surplus) for each region, during the period from 2000–2014, were used. The models were calibrated using multiple linear regression, and all possible combinations were tested for selecting the variables. Coffee supply was the dependent variable, and the other ones were considered independent. The accuracy and precision of the models were assessed by the mean absolute percentage error and the adjusted coefficient of determination, respectively. The variables that most affect coffee supply are production value and air temperature. Coffee supply can be estimated with multiple linear regressions using economic and climatic variables. The most accurate models are those calibrated to estimate coffee supply for the regions of Cássia dos Coqueiros and Osvaldo Cruz

Biochemical and genetic analysis of butyrylcholinesterase (BChE) in a family, due to prolonged neuromuscular blockade after the use of succinylcholine

Butyrylcholinesterase (BChE) is a plasma enzyme that catalyzes the hydrolysis of choline esters, including the muscle-relaxant succinylcholine and mivacurium. Patients who present sustained neuromuscular blockade after using succinylcholine usually carry BChE variants with reduced enzyme activity or an acquired BChE deficiency. We report here the molecular basis of the BCHE gene underlying the slow catabolism of succinylcholine in a patient who underwent endoscopic nasal surgery. We measured the enzyme activity of BChE and extracted genomic DNA in order to study the promoter region and all exons of the BCHE gene of the patient, her parents and siblings. PCR products were sequenced and compared with reference sequences from GenBank. We detected that the patient and one of her brothers have two homozygous mutations: nt1615 GCA > ACA (Ala539Thr), responsible for the K variant, and nt209 GAT > GGT (Asp70Gly), which produces the atypical variant A. Her parents and two of her brothers were found to be heterozygous for the AK allele, and another brother is homozygous for the normal allele. Sequence analysis of exon 1 including 5′UTR showed that the proband and her brother are homozygous for –116GG. The AK/AK genotype is considered the most frequent in hereditary hypocholinesterasemia (44%). This work demonstrates the importance of defining the phenotype and genotype of the BCHE gene in patients who are subjected to neuromuscular block by succinylcholine, because of the risk of prolonged neuromuscular paralysis

DNA Barcoding Bromeliaceae: Achievements and Pitfalls

<div><h3>Background</h3><p>DNA barcoding has been successfully established in animals as a tool for organismal identification and taxonomic clarification. Slower nucleotide substitution rates in plant genomes have made the selection of a DNA barcode for land plants a much more difficult task. The Plant Working Group of the Consortium for the Barcode of Life (CBOL) recommended the two-marker combination <em>rbcL</em>/<em>matK</em> as a pragmatic solution to a complex trade-off between universality, sequence quality, discrimination, and cost.</p> <h3>Methodology/Principal Findings</h3><p>It is expected that a system based on any one, or a small number of plastid genes will fail within certain taxonomic groups with low amounts of plastid variation, while performing well in others. We tested the effectiveness of the proposed CBOL Plant Working Group barcoding <em>markers</em> for land plants in identifying 46 bromeliad species, a group rich in endemic species from the endangered Brazilian Atlantic Rainforest. Although we obtained high quality sequences with the suggested primers, species discrimination in our data set was only 43.48%. Addition of a third marker, <em>trnH–psbA</em>, did not show significant improvement. This species identification failure in Bromeliaceaecould also be seen in the analysis of the GenBank's <em>matK</em> data set. Bromeliaceae's sequence divergence was almost three times lower than the observed for Asteraceae and Orchidaceae. This low variation rate also resulted in poorly resolved tree topologies. Among the three Bromeliaceae subfamilies sampled, Tillandsioideae was the only one recovered as a monophyletic group with high bootstrap value (98.6%). Species paraphyly was a common feature in our sampling.</p> <h3>Conclusions/Significance</h3><p>Our results show that although DNA barcoding is an important tool for biodiversity assessment, it tends to fail in taxonomy complicated and recently diverged plant groups, such as Bromeliaceae. Additional research might be needed to develop markers capable to discriminate species in these complex botanical groups.</p> </div