A5054990791- Genomics and Phylogenetic Studies
- Environmental DNA in Biodiversity Studies
- Microbial Community Ecology and Physiology
- Enzyme Production and Characterization
- Ichthyology and Marine Biology
- Biofuel production and bioconversion
- Molecular Biology Techniques and Applications
- Fish Biology and Ecology Studies
- Fish biology, ecology, and behavior
- Single-cell and spatial transcriptomics
- RNA and protein synthesis mechanisms
- Fish Ecology and Management Studies
- Educational theories and practices
- Cell Image Analysis Techniques
- Microbial Metabolic Engineering and Bioproduction
- Fern and Epiphyte Biology
- Latin American socio-political dynamics
- Carbohydrate Chemistry and Synthesis
- Advertising and Communication Studies
- Congenital heart defects research
- Morphological variations and asymmetry
- Higher Education and Sustainability
- Advanced Fluorescence Microscopy Techniques
- Seed Germination and Physiology
- Communication and COVID-19 Impact
University of Guelph
2020-2023
McGill University
2017-2023
Universidad del Valle
2009-2017
Dalhousie University
2012-2017
McGill Genome Centre
2017
Canadian Institute for Advanced Research
2015
Abstract The effective use of metabarcoding in biodiversity science has brought important analytical challenges due to the need generate accurate taxonomic assignments. assignment sequences genus or species level is critical for surveys and biomonitoring, but it particularly challenging as researchers must select approach that best recovers information on composition. This study evaluates performance accuracy seven methods recovering composition mock communities by using COI barcode...
Abstract Metagenomics and total RNA sequencing (total RNA-Seq) have the potential to improve taxonomic identification of diverse microbial communities, which could allow for incorporation microbes into routine ecological assessments. However, these target-PCR-free techniques require more testing optimization. In this study, we processed metagenomics RNA-Seq data from a commercially available mock community using 672 data-processing workflows, identified most accurate tools, compared their...
ABSTRACT Optical pooled screening (OPS) is a highly scalable method for linking image-based phenotypes with cellular perturbations. However, it has thus far been restricted to relatively low-plex phenotypic readouts in cancer cell lines culture, due limitations associated situ sequencing (ISS) of perturbation barcodes. Here, we developed PerturbView, an OPS technology that leverages vitro transcription (IVT) amplify barcodes prior ISS, enabling screens multiplexed across diverse systems,...
Assessing protein modularity is important to understand evolution. Still the question of existence a sub-domain modular architecture remains. We propose graph-theory approach with significance and power testing identify modules in structures. In first step, clusters are determined by optimizing partition that maximizes score. Second, each cluster tested for significance. Significant referred as modules. Evolutionary identified analyzing homologous Dynamic inferred from sets snapshots...
ABSTRACT In order to investigate zoogeographical patterns of the marine elasmobranch species Colombia, richness Pacific and Caribbean their subareas (Coastal Pacific, Oceanic Coastal Caribbean, Caribbean) was analyzed. The areas shared 10 families, genera 16 sharks, eight three four batoids. Carcharhinidae had highest contribution shark richness, whereas Rajidae Urotrygonidae greatest batoid in respectively. Most elasmobranchs were associated with benthic coastal habitats. similarity...
Aquatic ecosystems offer a continuum of water flow from headwater streams to inland lakes and coastal marine systems. This spatial connectivity influences the structure, function dynamics aquatic communities, which are among most threatened degraded on Earth. Here, we determine resolution environmental DNA (eDNA) in dendritic freshwater networks, use as model for connected metacommunities. Our intensive sampling campaign comprised over 420 eDNA samples across 21 lakes, allowing us analyse...
Huperzia brevifolia is one of the dominant species genus living in paramos and superparamos from Colombian Andes. A detailed study sporangium's ontogeny sporogenesis was carried out using specimens collected at 4200m above sea level, Parque Natural Nacional El Cocuy, Colombia. Small pieces caulinar axis bearing sporangia were fixed, dehydrated, paraffin embedded, sectioned a rotatory microtome, stained common Safranin O-Fast Green technique; handmade cross sections also made, with aqueous...
ABSTRACT Metagenomics and total RNA sequencing (total RNA-Seq) have the potential to improve taxonomic identification of diverse microbial communities, which could allow for incorporation microbes into routine freshwater assessments. However, these targeted-PCR- free techniques require more testing optimization. In this study, we processed metagenomics RNA-Seq data from a commercially available mock community using 768 data-processing workflows, identified most accurate tools, compared their...
ABSTRACT The effective use of metabarcoding in biodiversity science has brought important analytical challenges due to the need generate accurate taxonomic assignments. assignment sequences a generic or species level is critical for surveys and biomonitoring, but it particularly challenging. Researchers must select approach that best recovers information on composition. This study evaluates performance accuracy seven methods recovering composition mock communities which vary number specimen...
The 5S rDNA gene is a non-coding RNA that can be found in 2 copies (type I and type II) bony cartilaginous fish. Previous studies have pointed out II paralog derived from I. We analyzed the molecular organization of elasmobranchs. Although structure supposed to highly conserved, our results show secondary this group possesses some variability different than consensus structure. One these differences Selachii an internal loop at nucleotides 7 112. These mutations observed transcribed region...
The Glycoside Hydrolase Family 13 (GH13) is both evolutionarily diverse and relevant to many industrial applications. Its members hydrolyze starch into smaller carbohydrates of the family have been bioengineered improve catalytic function under environments. We introduce a framework analyze response selection GH13 protein structures given some phylogenetic simulated dynamic information. find that TIM-barrel (a conserved fold consisting eight α-helices parallel β-strands alternate along...
ABSTRACT Aim To examine the species richness, distribution and macroecological patterns of elasmobranch assemblages across a broad latitudinal gradient in Eastern Pacific Ocean (EPO). Location The study area encompasses coast American continent, spanning from 65°N to 60°S, extending coastline approximately 1000 km offshore, encompassing oceanic archipelagos. Taxon Elasmobranchs. Methods Utilising established ranges 190 (comprising 89 sharks 101 rays), we assessed richness spatial these EPO....
Urotrygon rogersi is a stingray of the order Myliobatiformes, with benthic habits and trophic preference for crustaceans, frequently caught in trawling fisheries.Such frequency could change morphometric relationships (possible associations between variables) this species; therefore, 41 variables more commonly used batoids were studied.The collinearity correlation evaluated among mothers, offspring mothers.The subject to descriptive statistics, variable transformation, test, multivariate...
Abstract Summary Amplicons to Global Gene ( A 2 G ) is a Python wrapper that uses MAFFT and an “Amplicon Gene” strategy align very large numbers of sequences while improving alignment accuracy. It specially developed deal with conserved genes, where traditional aligners introduce significant amount gaps. leverages the add option global reference gene local region. Both these references can be consensus trusted sources. Efficient parallelization tasks allows number (> 500K) in reasonable...
Community structure detection is an important tool in graph analysis. This can be done, among other ways, by solving for the partition set which optimizes modularity scores . Here it shown that topological constraints correlation graphs induce over-fragmentation of community structures. A refinement step to this optimization based on Linear Discriminant Analysis (LDA) and a statistical test significance proposed. In structured simulation constrained topology, novel approach performs better...
Abstract A phenotype is defined as an organism’s physical traits. In the macroscopic world, animal’s shape a phenotype. Geometric morphometrics (GM) can be used to analyze its shape. Let’s pose protein structures microscopic three dimensional shapes, and apply principles of GM analysis macromolecules. this paper we introduce way 1) abstract structure shape; 2) align shapes; 3) perform statistical establish patterns variation in datasets. We show that general procrustes superimposition (GPS)...
Abstract Aquatic ecosystems offer a continuum of water flow from headwater streams to inland lakes and coastal marine systems. This spatial connectivity influences the structure, function dynamics aquatic communities, which are among most threatened degraded on earth. Environmental DNA achieves biodiversity surveys in these habitats high-throughput, spatially integrated way. Here, we determine resolution eDNA dendritic freshwater networks that typical habitats. Our intensive sampling...