A method to find groups of orthogous genes across multiple genomes

In this work we propose a simple method to obtain groups of homologous genes across multiple (k) organisms, called kGC. Our method takes as input all-against-all Blastp comparisons and produces groups of homologous sequences. First, homologies among groups of paralogs of all the k compared genomes are found, followed by homologies of groups among k - 1 genomes and so on, until groups belonging exclusively to only one genome, that is, groups of one genome not presenting strong similarities with any group of any other genome, are identified. We have used our method to determine homologous groups across six Actinobacterial complete genomes. To validate kGC, we first investigate the Pfam classification of the homologous groups, and after compare our results with those produced by OrthoMCL. Although kGC is much simpler than OrthoMCL it presented similar results with respect to Pfam classification

Targeted and Untargeted Approaches Unravel Novel Candidate Genes and Diagnostic SNPs for Quantitative Resistance of the Potato (Solanum tuberosum L.) to Phytophthora infestans Causing the Late Blight Disease

The oomycete Phytophthora infestans causes late blight of potato, which can completely destroy the crop. Therefore, for the past 160 years, late blight has been the most important potato disease worldwide. The identification of cultivars with high and durable field resistance to P. infestans is an objective of most potato breeding programs. This type of resistance is polygenic and therefore quantitative. Its evaluation requires multi-year and location trials. Furthermore, quantitative resistance to late blight correlates with late plant maturity, a negative agricultural trait. Knowledge of the molecular genetic basis of quantitative resistance to late blight not compromised by late maturity is very limited. It is however essential for developing diagnostic DNA markers that facilitate the efficient combination of superior resistance alleles in improved cultivars. We used association genetics in a population of 184 tetraploid potato cultivars in order to identify single nucleotide polymorphisms (SNPs) that are associated with maturity corrected resistance (MCR) to late blight. The population was genotyped for almost 9000 SNPs from three different sources. The first source was candidate genes specifically selected for their function in the jasmonate pathway. The second source was novel candidate genes selected based on comparative transcript profiling (RNA-Seq) of groups of genotypes with contrasting levels of quantitative resistance to P. infestans. The third source was the first generation 8.3k SolCAP SNP genotyping array available in potato for genome wide association studies (GWAS). Twenty seven SNPs from all three sources showed robust association with MCR. Some of those were located in genes that are strong candidates for directly controlling quantitative resistance, based on functional annotation. Most important were: a lipoxygenase (jasmonate pathway), a 3-hydroxy-3-methylglutaryl coenzyme A reductase (mevalonate pathway), a P450 protein (terpene biosynthesis), a transcription factor and a homolog of a major gene for resistance to P. infestans from the wild potato species Solanum venturii. The candidate gene approach and GWAS complemented each other as they identified different genes. The results of this study provide new insight in the molecular genetic basis of quantitative resistance in potato and a toolbox of diagnostic SNP markers for breeding applications.</p

Latin American aquatic mammals : an overview of 12 years focusing on molecular techniques applied to conservation

Ecological information useful for conservation purposes have benefitted from recent and rapid advancements in genetic techniques, revealing unknown aspects of behavior, natural history, population structure and demography of several aquatic mammal species, many of them with conservation concerns. Molecular markers have been used to define management units, to settle taxonomic uncertainties, to control illegal wildlife trade, among others, providing valuable information to decision-making to conserve and manage aquatic mammals. We review genetic studies applied to conservation-related issues involving natural populations of more than 40 species of aquatic mammals in Latin America, covering four taxonomic groups. The main goal was to assess which genetic approaches have been used and to identify gaps in genetic research relating to geographic areas and species. We reviewed studies published in peer-reviewed journals between 2011 and 2022, and found that most were focused on population structure, phylogeography, gene flow and dispersal movements. The review revealed that researchers need to increase and improve the knowledge in those species which face major conservation concern. Scarce findings were related to forensics and its application to wildlife trade. In the era of next-generation-sequencing techniques, just a few studies used genomics as a tool for monitoring gene diversity, an important goal to help us predict how species will cope with climate change events. Looking to the future we suggest which species, geographic areas and genetic studies should be prioritized in a scenario of climate change and increased human threats (e.g., fishery bycatch, habitat degradation, etc.) and the urgent need for conservation actions. Finally, we highlight the benefits of the collaborative works and the necessity of generating a conservation genetic network, with an open agenda to discuss the local and regional problematics. All in all, we strongly emphasize the generation of critical information towards the effective conservation and management of aquatic mammals in Latin America.Peer reviewe

Functional characterization and target discovery of glycoside hydrolases from the digestome of the lower termite Coptotermes gestroi

<p>Abstract</p> <p>Background</p> <p>Lignocellulosic materials have been moved towards the forefront of the biofuel industry as a sustainable resource. However, saccharification and the production of bioproducts derived from plant cell wall biomass are complex and lengthy processes. The understanding of termite gut biology and feeding strategies may improve the current state of biomass conversion technology and bioproduct production.</p> <p>Results</p> <p>The study herein shows comprehensive functional characterization of crude body extracts from <it>Coptotermes gestroi </it>along with global proteomic analysis of the termite's digestome, targeting the identification of glycoside hydrolases and accessory proteins responsible for plant biomass conversion. The crude protein extract from <it>C. gestroi </it>was enzymatically efficient over a broad pH range on a series of natural polysaccharides, formed by glucose-, xylose-, mannan- and/or arabinose-containing polymers, linked by various types of glycosidic bonds, as well as ramification types. Our proteomic approach successfully identified a large number of relevant polypeptides in the <it>C. gestroi </it>digestome. A total of 55 different proteins were identified and classified into 29 CAZy families. Based on the total number of peptides identified, the majority of components found in the <it>C. gestroi </it>digestome were cellulose-degrading enzymes. Xylanolytic enzymes, mannan- hydrolytic enzymes, pectinases and starch-degrading and debranching enzymes were also identified. Our strategy enabled validation of liquid chromatography with tandem mass spectrometry recognized proteins, by enzymatic functional assays and by following the degradation products of specific 8-amino-1,3,6-pyrenetrisulfonic acid labeled oligosaccharides through capillary zone electrophoresis.</p> <p>Conclusions</p> <p>Here we describe the first global study on the enzymatic repertoire involved in plant polysaccharide degradation by the lower termite <it>C. gestroi</it>. The biochemical characterization of whole body termite extracts evidenced their ability to cleave all types of glycosidic bonds present in plant polysaccharides. The comprehensive proteomic analysis, revealed a complete collection of hydrolytic enzymes including cellulases (GH1, GH3, GH5, GH7, GH9 and CBM 6), hemicellulases (GH2, GH10, GH11, GH16, GH43 and CBM 27) and pectinases (GH28 and GH29).</p

Mass Spectrometry-Based (GeLC-MS/MS) Comparative Proteomic Analysis of Endoscopically (ePFT) Collected Pancreatic and Gastroduodenal Fluids

Objectives: The secretin-stimulated endoscopic pancreatic function test (ePFT) allows for the safe collection of gastroduodenal and pancreatic fluid from the duodenum. We test the hypothesis that these endoscopically collected fluids have different proteomes. As such, we aim to show that the ePFT method can be used to collect fluid enriched in pancreatic proteins to test for pancreatic function. Methods: Gastroduodenal and pancreatic fluid were collected sequentially from chronic pancreatitis patients undergoing an ePFT. Proteins from each fluid type were extracted using previously published optimized methods and subjected to GeLC-MS/MS analysis for protein identification and bioinformatics analysis. Results: Mass spectrometry analysis identified proteins that were exclusive in either gastroduodenal (46) or pancreatic fluid (234). Subsequent quantitative analysis revealed proteins that were differentially abundant with statistical significance. As expected, proteolytic enzymes and protease inhibitors were among the differentially detected proteins. The proteases pepsinogens and gastrin were enriched in gastroduodenal fluid, while common pancreatic enzymes (e.g., aminopeptidase N, chymotrypsin C, elastase-3A, trypsin, and carboxypeptidase A1, and elastase 2B) were found in greater abundance in pancreatic fluid. Similarly for protease inhibitors, members of the cystatin family were exclusive to gastroduodenal fluid, while serpins A11, B4, and D1 were exclusive to pancreatic fluid. Conclusions: We have shown that ePFT collection coupled with mass spectrometry can be used to identify differentially detected proteins in gastroduodenal and pancreatic fluids. The data obtained using GeLC-MS/MS techniques provide further evidence supporting the feasibility of using ePFT-collected fluid to study specific diseases of the upper gastrointestinal tract, such as chronic pancreatitis

Optical fiber relative humidity sensor based on a FBG with a di-ureasil coating

In this work we proposed a relative humidity (RH) sensor based on a Bragg grating written in an optical fiber, associated with a coating of organo-silica hybrid material prepared by the sol-gel method. The organo-silica-based coating has a strong adhesion to the optical fiber and its expansion is reversibly affected by the change in the RH values (15.0–95.0%) of the surrounding environment, allowing an increased sensitivity (22.2 pm/%RH) and durability due to the presence of a siliceous-based inorganic component. The developed sensor was tested in a real structure health monitoring essay, in which the RH inside two concrete blocks with different porosity values was measured over 1 year. The results demonstrated the potential of the proposed optical sensor in the monitoring of civil engineering structures