cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.20018168.v1
title: Diversity of bacteriocins in the microbiome of the Tucuruí Hydroelectric Power Plant water reservoir and three-dimensional structure prediction of a zoocin

description: Abstract Bacteriocins are antimicrobial peptides expressed by bacteria through ribosomal activity. In this study, we analyzed the diversity of bacteriocin-like genes in the Tucuruí-HPP using a whole-metagenome shotgun sequencing approach. Three layers of the water column were analyzed (photic, aphotic and sediment). Detection of bacteriocin-like genes was performed with blastx using the BAGEL4 database as subject sequences. In order to calculate the abundance of bacteriocin-like genes we also determined the number of 16S rRNA genes using blastn. Taxonomic analysis was performed using RAST server and the metagenome was assembled using IDBA-UD in order to recover the full sequence of a zoocin which had its three-dimensional structure determined. The photic zone presented the highest number of reads affiliated to bacteriocins. The most abundant bacteriocins were sonorensin, Klebicin D , pyocin and colicin. The zoocin model was composed of eight anti-parallel β-sheets and two α-helices with a Zn2+ ion in the active site. This model was considerably stable during 10 ns of molecular dynamics simulation. We observed a high diversity of bacteriocins in the Tucuruí-HPP, demonstrating that the environment is an inexhaustible source for prospecting these molecules. Finally, the zoocin model can be used for further studies of substrate binding and molecular mechanisms involving peptidoglycan degradation.
DOI: 10.6084/m9.figshare.20018166.v1
title: Genomic analysis of Enterococcus durans LAB18S, a potential probiotic strain isolated from cheese

description: Abstract Gut microbiota exerts a fundamental role in human health and increased evidence supports the beneficial role of probiotic microorganisms in the maintenance of intestinal health. Enterococcus durans LAB18S was previously isolated from soft cheese and showed some desirable in vitro probiotic properties, for that reason its genome was sequenced and evaluated for genes that can be relevant for probiotic activity and are involved in selenium metabolism. Genome sequencing was performed using the Illumina MiSeq System. A variety of genes potentially associated with probiotic properties, including adhesion capability, viability at low pH, bile salt resistance, antimicrobial activity, and utilization of prebiotic fructooligosaccharides (FOS) were identified. The strain showed tolerance to acid pH and bile salts, exhibited antimicrobial activity and thrived on prebiotic oligosaccharides. Six genes involved in selenium metabolism were predicted. Analysis of the SECIS element showed twelve known selenoprotein candidates. E. durans LAB18S was the only food isolate showing absence of plasmids, virulence and antimicrobial resistance genes, when compared with other 30 E. durans genomes. The results of this study provide evidence supporting the potential of E. durans LAB18S as alternative for probiotic formulations.
DOI: 10.6084/m9.figshare.20018171
title: Perspectives in Myrtaceae evolution from plastomes and nuclear phylogenies

description: Abstract Myrtaceae is a large and species-rich family of woody eudicots, with prevalent distribution in the Southern Hemisphere. Classification and taxonomy of species belonging to this family is quite challenging, sometimes with difficulty in species identification and producing phylogenies with low support for species relationships. Most of the current knowledge comes from few molecular markers, such as plastid genes and intergenic regions, which can be difficult to handle and produce conflicting results. Based on plastid protein-coding sequences and nuclear markers, we present a topology for the phylogenetic relationships among Myrtaceae tribes. Our phylogenetic estimate offers a contrasting topology over previous analysis with fewer markers. Plastome phylogeny groups the tribes Syzygieae and Eucalypteae and individual chloroplast genes produce divergent topologies, especially among species within Myrteae tribe, but also in regard to the grouping of Syzygieae and Eucalypteae. Results are consistent and reproducible with both nuclear and organellar datasets. It confronts previous data about the deep nodes of Myrtaceae phylogeny.
DOI: 10.6084/m9.figshare.20018171.v1
title: Perspectives in Myrtaceae evolution from plastomes and nuclear phylogenies

description: Abstract Myrtaceae is a large and species-rich family of woody eudicots, with prevalent distribution in the Southern Hemisphere. Classification and taxonomy of species belonging to this family is quite challenging, sometimes with difficulty in species identification and producing phylogenies with low support for species relationships. Most of the current knowledge comes from few molecular markers, such as plastid genes and intergenic regions, which can be difficult to handle and produce conflicting results. Based on plastid protein-coding sequences and nuclear markers, we present a topology for the phylogenetic relationships among Myrtaceae tribes. Our phylogenetic estimate offers a contrasting topology over previous analysis with fewer markers. Plastome phylogeny groups the tribes Syzygieae and Eucalypteae and individual chloroplast genes produce divergent topologies, especially among species within Myrteae tribe, but also in regard to the grouping of Syzygieae and Eucalypteae. Results are consistent and reproducible with both nuclear and organellar datasets. It confronts previous data about the deep nodes of Myrtaceae phylogeny.
DOI: 10.6084/m9.figshare.20018172
title: In the screening of alternative insecticides to control Aedes aegytpti larvae 2-methylanthraquinone showed no genotoxicity and low toxicity to zebrafish (Danio rerio)

description: Abstract The threats posed by insecticide resistance to Aedes aegypti in the context of controlling dengue have led to an urgent search for an environmentally safer alternative chemical with more effective larvicidal properties. Among many molecules tested, 2-methylanthraquinone showed the lowest LC50 for A. aegypti in a previous study and the highest LC50 for zebrafish embryos. Embryos were exposed at concentrations of 1.0, 2.19, 4.78, 10.46, 22.87, 50.0 and 100.0 mg/L, and malformations and mortality were significantly observed only at the highest exposures of 50 and 100 mg/L after 96 h. Micronucleus test and comet assay in zebrafish adults were both negative after exposures at 6.25, 12.5, 25.0, 50.0 and 100.0 mg/L for 96 h. Several biochemical biomarkers were analyzed in adults, and 2-methylanthraquinone did not interfere with acetylcholinesterase activity. The lactate dehydrogenase activity was higher at concentrations of 25 and 100 mg/L. Glutathione-S-Transferase (GST) activities were tested in the gill and body (muscle tail). The gill was more sensitive than body for GST activity after exposure to 2-methylanthraquinone, showing the highest activities, and 2-methylanthraquinone showed low toxicity to a non-target organism.
DOI: 10.6084/m9.figshare.20018172.v1
title: In the screening of alternative insecticides to control Aedes aegytpti larvae 2-methylanthraquinone showed no genotoxicity and low toxicity to zebrafish (Danio rerio)

description: Abstract The threats posed by insecticide resistance to Aedes aegypti in the context of controlling dengue have led to an urgent search for an environmentally safer alternative chemical with more effective larvicidal properties. Among many molecules tested, 2-methylanthraquinone showed the lowest LC50 for A. aegypti in a previous study and the highest LC50 for zebrafish embryos. Embryos were exposed at concentrations of 1.0, 2.19, 4.78, 10.46, 22.87, 50.0 and 100.0 mg/L, and malformations and mortality were significantly observed only at the highest exposures of 50 and 100 mg/L after 96 h. Micronucleus test and comet assay in zebrafish adults were both negative after exposures at 6.25, 12.5, 25.0, 50.0 and 100.0 mg/L for 96 h. Several biochemical biomarkers were analyzed in adults, and 2-methylanthraquinone did not interfere with acetylcholinesterase activity. The lactate dehydrogenase activity was higher at concentrations of 25 and 100 mg/L. Glutathione-S-Transferase (GST) activities were tested in the gill and body (muscle tail). The gill was more sensitive than body for GST activity after exposure to 2-methylanthraquinone, showing the highest activities, and 2-methylanthraquinone showed low toxicity to a non-target organism.
DOI: 10.6084/m9.figshare.19929974.v2
title: RC04.zip

description: Sample data for quasi periodic signal (superposition of sine waves; angular frequency ratio equals golden number)
DOI: 10.6084/m9.figshare.19929968.v2
title: RC03.zip

description: Sample data for quasi periodic signal (superposition of sine waves; angular frequency ratio equals PI)
DOI: 10.5281/zenodo.6618550
title: Raw Data for Fairly flexible: Brown-tufted capuchins and a squirrel monkey adjust their motor responses in a foraging task

description: Raw Data for Manuscript entitled: Fairly flexible: Brown-tufted capuchins and a squirrel monkey adjust their motor responses in a foraging task
DOI: 10.5281/zenodo.6618549
title: Raw Data for Fairly flexible: Brown-tufted capuchins and a squirrel monkey adjust their motor responses in a foraging task

description: Raw Data for Manuscript entitled: Fairly flexible: Brown-tufted capuchins and a squirrel monkey adjust their motor responses in a foraging task
DOI: 10.5066/p9avkjvy
title: Porphyry copper deposits and prospects in the Andes Mountains of South America

description: The Andes Mountains of South America host significant porphyry copper deposits. The region is the major global source of copper and an area of active mining, exploration, and development. The Andes region was included in USGS global compilations of porphyry deposits published by Singer and others in 2005 and 2008. Since that time, many new discoveries and new resource data have become available. This compilation includes new and updated location, references, and grade and tonnage data for porphyry copper deposits in the Andes along with grade and tonnage data from the previous compilations. The data release includes a data table, references, and shapefiles of porphyry copper locations and political boundaries.
DOI: 10.6084/m9.figshare.20018195.v1
title: High-quality genome assembly of Pseudocercospora ulei the main threat to natural rubber trees

description: Abstract Pseudocercospora ulei is the causal agent of South American Leaf Blight (SALB), the main disease affecting Hevea brasiliensis rubber tree, a native species to the Amazon. Rubber tree is a major crop in South American countries and SALB disease control strategies would benefit from the availability of genomic resources for the fungal pathogen. Here, we assembled and annotated the P. ulei genome. Shotgun sequencing was performed using second and third generation sequencing technologies. We present the first P. ulei high-quality genome assembly, the largest among Mycosphaerellaceae, with 93.8 Mbp, comprising 215 scaffolds, an N50 of 2.8 Mbp and a BUSCO gene completeness of 97.5%. We identified 12,745 protein-coding gene models in the P. ulei genome with 756 genes encoding secreted proteins and 113 genes encoding effector candidates. Most of the genome (80%) is composed of repetitive elements dominated by retrotransposons of the Gypsy superfamily. P. ulei has the largest genome size among Mycosphaerellaceae, with the highest TE content. In conclusion, we have established essential genomic resources for a wide range of studies on P. ulei and related species.
DOI: 10.6084/m9.figshare.20018195
title: High-quality genome assembly of Pseudocercospora ulei the main threat to natural rubber trees

description: Abstract Pseudocercospora ulei is the causal agent of South American Leaf Blight (SALB), the main disease affecting Hevea brasiliensis rubber tree, a native species to the Amazon. Rubber tree is a major crop in South American countries and SALB disease control strategies would benefit from the availability of genomic resources for the fungal pathogen. Here, we assembled and annotated the P. ulei genome. Shotgun sequencing was performed using second and third generation sequencing technologies. We present the first P. ulei high-quality genome assembly, the largest among Mycosphaerellaceae, with 93.8 Mbp, comprising 215 scaffolds, an N50 of 2.8 Mbp and a BUSCO gene completeness of 97.5%. We identified 12,745 protein-coding gene models in the P. ulei genome with 756 genes encoding secreted proteins and 113 genes encoding effector candidates. Most of the genome (80%) is composed of repetitive elements dominated by retrotransposons of the Gypsy superfamily. P. ulei has the largest genome size among Mycosphaerellaceae, with the highest TE content. In conclusion, we have established essential genomic resources for a wide range of studies on P. ulei and related species.
DOI: 10.6084/m9.figshare.20018199
title: Mosquito long non-coding RNAs are enriched with Transposable Elements

description: Abstract Long non-coding RNAs (lncRNAs) lack coding capacity and mounting evidence suggests that they have a regulatory role in diverse organisms. Most knowledge about lncRNAs comes from studies on vertebrates, including a structural association between lncRNAs and transposable elements (TEs). TE sequences are genomic parasites found in all branches of life and are particularly active and abundant in insect genomes. Here we investigate the contribution of TEs to lncRNA biogenesis in Aedes albopictus and Culex quinquefasciatus. We found that a large fraction of lncRNA loci co-occurs with TE loci in both species. Around 40% of A. albopictus and 52% of C. quinquefasciatus lncRNAs show some association with TEs. Most of the lncRNA/TE associations are represented by TE-derived sequences that are expressed as one or all exons of lncRNAs, including five lncRNAs that seem to influence immune-related genes involved in antiviral response. The contribution of TEs to lncRNAs also varies among the different types of TEs. The Gypsi superfamily is particularly enriched in lncRNAs sequences. In sum, this study demonstrates that transposable elements substantially contribute to lncRNAs biogenesis in A. albopictus and C. quinquefasciatus and may have an impact on regulatory modulation in these species.
DOI: 10.6084/m9.figshare.20018199.v1
title: Mosquito long non-coding RNAs are enriched with Transposable Elements

description: Abstract Long non-coding RNAs (lncRNAs) lack coding capacity and mounting evidence suggests that they have a regulatory role in diverse organisms. Most knowledge about lncRNAs comes from studies on vertebrates, including a structural association between lncRNAs and transposable elements (TEs). TE sequences are genomic parasites found in all branches of life and are particularly active and abundant in insect genomes. Here we investigate the contribution of TEs to lncRNA biogenesis in Aedes albopictus and Culex quinquefasciatus. We found that a large fraction of lncRNA loci co-occurs with TE loci in both species. Around 40% of A. albopictus and 52% of C. quinquefasciatus lncRNAs show some association with TEs. Most of the lncRNA/TE associations are represented by TE-derived sequences that are expressed as one or all exons of lncRNAs, including five lncRNAs that seem to influence immune-related genes involved in antiviral response. The contribution of TEs to lncRNAs also varies among the different types of TEs. The Gypsi superfamily is particularly enriched in lncRNAs sequences. In sum, this study demonstrates that transposable elements substantially contribute to lncRNAs biogenesis in A. albopictus and C. quinquefasciatus and may have an impact on regulatory modulation in these species.
DOI: 10.6084/m9.figshare.20018204
title: Gene Expression Analysis Platform (GEAP): A highly customizable, fast, versatile and ready-to-use microarray analysis platform

description: Abstract There are still numerous challenges to be overcome in microarray data analysis because advanced, state-of-the-art analyses are restricted to programming users. Here we present the Gene Expression Analysis Platform, a versatile, customizable, optimized, and portable software developed for microarray analysis. GEAP was developed in C# for the graphical user interface, data querying, storage, results filtering and dynamic plotting, and R for data processing, quality analysis, and differential expression. Through a new automated system that identifies microarray file formats, retrieves contents, detects file corruption, and solves dependencies, GEAP deals with datasets independently of platform. GEAP covers 32 statistical options, supports quality assessment, differential expression from single and dual-channel experiments, and gene ontology. Users can explore results by different plots and filtering options. Finally, the entire data can be saved and organized through storage features, optimized for memory and data retrieval, with faster performance than R. These features, along with other new options, are not yet present in any microarray analysis software. GEAP accomplishes data analysis in a faster, straightforward, and friendlier way than other similar software, while keeping the flexibility for sophisticated procedures. By developing optimizations, unique customizations and new features, GEAP is destined for both advanced and non-programming users.
DOI: 10.6084/m9.figshare.20018204.v1
title: Gene Expression Analysis Platform (GEAP): A highly customizable, fast, versatile and ready-to-use microarray analysis platform

description: Abstract There are still numerous challenges to be overcome in microarray data analysis because advanced, state-of-the-art analyses are restricted to programming users. Here we present the Gene Expression Analysis Platform, a versatile, customizable, optimized, and portable software developed for microarray analysis. GEAP was developed in C# for the graphical user interface, data querying, storage, results filtering and dynamic plotting, and R for data processing, quality analysis, and differential expression. Through a new automated system that identifies microarray file formats, retrieves contents, detects file corruption, and solves dependencies, GEAP deals with datasets independently of platform. GEAP covers 32 statistical options, supports quality assessment, differential expression from single and dual-channel experiments, and gene ontology. Users can explore results by different plots and filtering options. Finally, the entire data can be saved and organized through storage features, optimized for memory and data retrieval, with faster performance than R. These features, along with other new options, are not yet present in any microarray analysis software. GEAP accomplishes data analysis in a faster, straightforward, and friendlier way than other similar software, while keeping the flexibility for sophisticated procedures. By developing optimizations, unique customizations and new features, GEAP is destined for both advanced and non-programming users.
DOI: 10.6084/m9.figshare.19945745.v2
title: Supporting Data 3 (Data S3): PANTHER Protein Class LxCxE proteins

description: PANTHER Protein Class analysis of LxCxE-containing proteins for key Viridiplantae clades.
DOI: 10.6084/m9.figshare.19945745
title: Supporting Data 4 (Data S4): PANTHER Protein Class LxCxE proteins

description: PANTHER Protein Class analysis of LxCxE-containing proteins for key Viridiplantae clades.
DOI: 10.6084/m9.figshare.19945745.v4
title: Supporting Data 4 (Data S4): PANTHER Protein Class LxCxE proteins

description: PANTHER Protein Class analysis of LxCxE-containing proteins for key Viridiplantae clades.
DOI: 10.6084/m9.figshare.19945745.v3
title: Supporting Data 3 (Data S4): PANTHER Protein Class LxCxE proteins

description: PANTHER Protein Class analysis of LxCxE-containing proteins for key Viridiplantae clades.
DOI: 10.6084/m9.figshare.20018208
title: Common BMI and diabetes-related genetic variants: A pilot study among indigenous people in the Brazilian Amazon

description: Abstract This study was carried out to investigate the frequency of genetic variants related to body mass index (BMI) and type 2 diabetes (T2D) and evaluating the potential impact of risk alleles on susceptibility to these disorders in six indigenous peoples from Brazilian Amazon region. The majority of Fst values for pairwise population comparisons among the indigenous groups are low or moderate. The indigenous people show high values of differentiation with Africans, Europeans and Southeast Asians and moderate values with East Asian and American populations, as expected. The allelic frequencies among indigenous indicate that the majority of associations observed with T2D in continental populations can be replicated in native Amazonians. The genetic risk scores calculated for T2D in indigenous are high and similar to those calculated for Americans and East Asians, while the estimates obtained for obesity are low, probably due to the low frequencies of the risk allele of the FTO gene found in our samples. ADRB3-rs4994 and ABCC8-rs1799854 genes showed a significant association with BMI and waist circumference, and the KCNJ11-rs5219 gene with hyperglycemia. These results emphasize the importance of knowing the genetic variability underlying complex genetic diseases in indigenous peoples and the search for particular or rare variants.
DOI: 10.6084/m9.figshare.20018208.v1
title: Common BMI and diabetes-related genetic variants: A pilot study among indigenous people in the Brazilian Amazon

description: Abstract This study was carried out to investigate the frequency of genetic variants related to body mass index (BMI) and type 2 diabetes (T2D) and evaluating the potential impact of risk alleles on susceptibility to these disorders in six indigenous peoples from Brazilian Amazon region. The majority of Fst values for pairwise population comparisons among the indigenous groups are low or moderate. The indigenous people show high values of differentiation with Africans, Europeans and Southeast Asians and moderate values with East Asian and American populations, as expected. The allelic frequencies among indigenous indicate that the majority of associations observed with T2D in continental populations can be replicated in native Amazonians. The genetic risk scores calculated for T2D in indigenous are high and similar to those calculated for Americans and East Asians, while the estimates obtained for obesity are low, probably due to the low frequencies of the risk allele of the FTO gene found in our samples. ADRB3-rs4994 and ABCC8-rs1799854 genes showed a significant association with BMI and waist circumference, and the KCNJ11-rs5219 gene with hyperglycemia. These results emphasize the importance of knowing the genetic variability underlying complex genetic diseases in indigenous peoples and the search for particular or rare variants.
DOI: 10.6084/m9.figshare.19799173.v1
title: Supporting Data 4 (Data S4): Predicted LxCxE-containing Transcription Associated Proteins (TAPs)

description: Contains seqIDs and hmmscan scores files for transcription associated proteins (transcription factors, chromatin modifiers and putative regulators) encoding the RBR LxCxE interacting motif for 28 representative species across Viridiplantae.
DOI: 10.6084/m9.figshare.19799173.v2
title: Supporting Data 4 (Data S5): Predicted LxCxE-containing Transcription Associated Proteins (TAPs)

description: Contains seqIDs and hmmscan scores files for transcription associated proteins (transcription factors, chromatin modifiers and putative regulators) encoding the RBR LxCxE interacting motif for 28 representative species across Viridiplantae.