OTUsBiodiversityBiologyDiversitySequencesPhylogenySequence similarityMorphologicalEcologyApproachesMicrobialDelimitationIdentified to species levelPhylaOrganismsSimilarityMethodsDetectionAssessBenthicMorphologyFaecalAnalysesIdentificationSimulationsDynamicsIncreasinglyAnalysisLackStudiesBiologicalStudyResultsResearchSystemsGroups
OTUs14
- In other words, OTUs are pragmatic proxies for "species" (microbial or metazoan) at different taxonomic levels, in the absence of traditional systems of biological classification as are available for macroscopic organisms. (wikipedia.org)
- For several years, OTUs have been the most commonly used units of diversity, especially when analysing small subunit 16S (for prokaryotes) or 18S rRNA (for eukaryotes) marker gene sequence datasets. (wikipedia.org)
- Assignment of 16S rRNA gene sequences to operational taxonomic units (OTUs) is a computational bottleneck in the process of analyzing microbial communities. (nih.gov)
- DNA sequences were organized into operational taxonomic units (OTUs) and identified using a database derived from the National Center for Biotechnology Information. (cdc.gov)
- Seven other bacterial operational taxonomic units (OTUs) were detected using clone libraries. (nih.gov)
- These clusters, or operational taxonomic units (OTUs), are widely used as an analytical unit in microbial ecology studies [ 1 ]. (biomedcentral.com)
- 1991). The method of depicting the results of a phenetic analysis is by way of a branching diagram called a dendrogram drawn by cluster analysis which is a method for grouping operational taxonomic units (OTUs). (scialert.net)
- These genomes represent 12,556 novel candidate species-level operational taxonomic units (OTUs), representing a resource that captures a broad phylogenetic and functional diversity of uncultivated bacteria and archaea. (nature.com)
- The large numbers of taxonomically unassigned molecular operational taxonomic units (OTUs) were not equally distributed among phyla, with nematodes and platyhelminthes being the most poorly characterized from a taxonomic perspective. (id-gene.com)
- Even so, the effectiveness of molecular analysis will depend on the records readily available in databases and libraries of barcode sequences of known species [21], representing a further analytical obstacle, because the taxonomic operational units (OTUs) vary according to the resolution in the genes analyzed [9]. (axlinhibitor.com)
- This results in total DNA that reveals higher alpha diversity through observed operational taxonomic units (OTUs) in downstream testing. (qiagen.com)
- A total of 111 operational taxonomic units (OTUs) were retained after bioinformatic analysis: 1 OTU assigned to family level, 36 OTUs to genius level and 74 OTUs to species level. (gov.pt)
- More than a fifth (21%) of the eukaryotic Operational Taxonomic Units (OTUs) found are ascribed to pathogenic (within 11 Phyla) and potential pathogenic (within 1 phylum, the Chytridiomycota) microorganisms. (hes-so.ch)
- 16S identified scores of operational taxonomic units (OTUs). (nih.gov)
Biodiversity6
- This course is being delivered by Dr. Owen S. Wangensteen, an expert in the application of molecular techniques to the study of marine ecological issues and biodiversity assessment of marine benthic ecosystems, including high-throughput sequencing and bioinformatics. (bioblogia.net)
- This workshop is mainly aimed at researchers and technical workers with a background in ecology, biodiversity or community biology who want to use molecular tools for biodiversity research and at researchers in other areas of bioinformatics who want to learn ecological applications for biodiversity-assessment. (bioblogia.net)
- While the data obtained here reveal pronounced heterogeneity and vast amounts of unknown biodiversity in the deep sea, they also expose the difficulties in exploiting metabarcoding datasets resulting from the lack of taxonomic knowledge and appropriate reference databases. (id-gene.com)
- The first null hypothesis was that typical taxonomic distinctness index with the assemblages captured by ARMS reflects the taxonomic diversity of the known species in every single area, working with Ocean Biodiversity Details Technique (OBIS) and Felder and Camp (2009) [24] as a baseline. (axlinhibitor.com)
- We reached these conclusions through a comparison of the theoretical foundations of two molecular approaches seeking to assess biodiversity: metagenomics (mostly used on prokaryotes and protists) and DNA barcoding (mostly used on multicellular eukaryotes), and by pragmatic considerations of the issues caused by the 'species problem' in biodiversity studies. (biomedcentral.com)
- Part of the problem is that analyses of biodiversity require both a clear definition of the term biodiversity, e.g. what are the relevant units of biodiversity considered, and a consensus on the methods relevant to quantify these units. (biomedcentral.com)
Biology3
- QIAamp PowerFecal Pro DNA Kits are intended for molecular biology applications. (qiagen.com)
- While macroscopic anatomy is required for the representation of diseases and procedures, subcellular anatomy has become increasingly important for molecular biology. (nih.gov)
- NAMD is a parallel molecular dynamics program for UNIX platforms designed for high-performance simulations in structural biology. (nih.gov)
Diversity9
- Molecular Sequence Typing Reveals Genotypic Diversity among Escherichia coli Isolates Recovered from a Cantaloupe Packinghouse in Northwestern Mexico. (cdc.gov)
- Methods: To assess the Trichoptera diversity of the area within and around the Mount Halimun Salak National Park (MHSNP or Taman Nasional Gunung Halimun Salak) in West Java (Indonesia), we conducted a molecular-morphological study on Trichoptera diversity using larvae from a benthic survey and adults from hand-netting. (bvsalud.org)
- Conclusions: This study provides an example of how molecular approaches can benefit the exploration of hidden diversity in unexplored areas and can be a valuable tool to link life stages. (bvsalud.org)
- Genetic diversity at molecular levels represents slightly different sequences. (scialert.net)
- We investigated the diversity of anguillid eels on the western Indonesian islands of Sumatra and Java using automated molecular classification and genetic species delimitation methods to explore temporal patterns of glass eel cohorts entering inland waters. (seafdec.id)
- Rejecting this hypothesis suggests that the diversity of taxonomic categories collected with ARMS doesn't represent what was anticipated for the area. (axlinhibitor.com)
- Morphological and molecular analyses of ectomycorrhizal diversity in a man-made T. melanosporum plantation: Description of novel truffle-like morphotypes. (inia.es)
- In particular, Faith[ 6 , 10 ] suggested to account for the whole hierarchy of bio- specifics (from lower-level genetic units to higher clades) and for within species diversity. (biomedcentral.com)
- When compared, both at the level of genus and species-level operational taxonomic units (OTU), β-diversity measures of faecal microbiota from cases and controls significantly differed ( figure 1 ). (bmj.com)
Sequences2
- Citation: Cruz M. Á, Arias S. & Terrazas T. 2016: Molecular phylogeny and taxonomy of the genus Disocactus (Cactaceae), based on the DNA sequences of six chloroplast markers. (researchgate.net)
- Each sample is expected to yield taxon-specific marker sequences that can be matched to a high-quality database of marker sequences with known taxonomic identity, to give a taxonomic breakdown reflecting the community composition. (peerj.com)
Phylogeny1
- This study present the first comprehensive molecular phylogeny for the genus Trochulus Chemnitz, 1786 (until recently Trichia , Hartmann 1840) based on mitochondrial and nuclear loci. (biomedcentral.com)
Sequence similarity1
- Bonin A , Guerrieri A , Ficetola GF (2023) Optimal sequence similarity thresholds for clustering of molecular operational taxonomic units in DNA metabarcoding studies. (argaly.com)
Morphological2
- In addition to morphological identification, we applied four different molecular taxon delimitation approaches (Generalized Mixed Yule Coalescent, Bayesian Poisson Tree Processes, Automatic Barcode Gap Discovery and Assemble Species by Automatic Partitioning) based on DNA barcoding of Cytochrome-C-Oxidase I (COI). (bvsalud.org)
- Consequently, Lyngbya , as currently intended, is a polyphyletic group, probably including several cryptogenera (i.e., lineages that cannot be distinguished by morphology and / or ecology, but only using molecular methods), comprising well-delimitated clades, which lack morphological exclusive characters ( Komárek 2016 ). (e-algae.org)
Ecology3
- Molecular Ecology. (wikipedia.org)
- The operational taxonomic unit (OTU) is widely used in microbial ecology. (biomedcentral.com)
- Molecular Ecology Resources , 23: 368-381. (argaly.com)
Approaches3
- A vast number of diverse microorganisms have thus far eluded cultivation and remain accessible only through cultivation-independent molecular approaches. (nature.com)
- Second, such metagenomic data should be studied with novel inclusive network-based approaches, designed to draw inferences both on the many units and on the many processes present in the environments. (biomedcentral.com)
- To solve this issue, the application of molecular approaches with successful bioindicators like foraminifera is promising. (hes-so.ch)
Microbial1
- Characterizing indoor microbial communities using molecular methods provides insight into bacterial assemblages present in environments that can influence occupants' health. (cdc.gov)
Delimitation1
- Results: The molecular delimitation detected 72 to 81 Operational Taxonomic Units (OTU). (bvsalud.org)
Identified to species level1
- Wombat ticks were sourced from wildlife hospitals and sanctuaries across Australia and identified to species level using taxonomic keys. (biomedcentral.com)
Phyla1
- This comprehensive catalog includes 52,515 metagenome-assembled genomes representing 12,556 novel candidate species-level operational taxonomic units spanning 135 phyla. (nature.com)
Organisms3
- The term was originally introduced in 1963 by Robert R. Sokal and Peter H. A. Sneath in the context of numerical taxonomy, where an "operational taxonomic unit" is simply the group of organisms currently being studied. (wikipedia.org)
- Alternatively, the suitability and biological representativeness on the organisms captured with ARMS may be evaluated by estimating the taxonomic distinctness and testing for deviations from expectations contemplating the species already registered inside the region [19]. (axlinhibitor.com)
- In general, the current protocols for processing biological samples collected with ARMS focus on the usage of molecular methods for example DNA barcoding and metabarcoding to recognize and quantify organisms [2,eight,202]. (axlinhibitor.com)
Similarity1
- By selecting an appropriate range of similarity to represent a given level in the taxonomic hierarchy, the taxonomists may then recognize species, genera, etc. (scialert.net)
Methods3
- 2) Methods: To investigate the molecular basis of radula diversification and its contribution to lineage divergence, we used tissue-specific transcriptomes of two sympatric Tylomelania sarasinorum ecomorphs. (bvsalud.org)
- Determine the Azores Woodpigeon's diet and its spatio-temporal variation, by analysing non-invasive samples (faeces) collected on the islands of Pico and Terceira, during two years, using molecular and micro-histological methods. (gov.pt)
- Psi4 is an ab-initio electronic structure code that supports various methods for calculating energies and gradients of molecular systems. (nih.gov)
Detection2
- Balamurugan R, Chittaranjan SP, Chandragunasekaran AM and Ramakrishna BS 2009 Molecular detection of the ruminal bacterium, Butyrivibrio fibrisolvens , in feces from rural residences of Southern India. (springer.com)
- Through new sensors and sophisticated molecular detection tools we have designed novel interventions to reduce antibiotic resistance and virulence of bacteria that survive in our buildings. (nih.gov)
Assess1
- Most importantly, the out there taxonomic records are extra accessible and comparable than the molecular ones, which would make it a lot easier to assess the suitability of ARMS as a sampling strategy. (axlinhibitor.com)
Benthic2
- Traditional morpho-taxonomic studies suggest that the ocean floor hosts extraordinarily diverse benthic communities. (id-gene.com)
- To ascertain this, we analyzed the species richness, taxonomic representativeness, and relative abundance of sessile benthic groups. (axlinhibitor.com)
Morphology1
- Laboratory parasitism rates, sex ratios, morphology, molecular diagnosis and implications for agriculture are discussed. (pensoft.net)
Faecal1
- Results are preliminary and consist of the molecular analysis of a first set of faecal samples (366 samples collected on Pico between May 2021 and January 2022, three seasons: summer, autumn and winter). (gov.pt)
Analyses1
- However, sampling protocols, molecular procedures and data analyses need to be validated before such tools can be routinely applied. (hes-so.ch)
Identification2
- With molecular identification techniques ever more evolving, analysis of arthropod communities has accelerated. (bvsalud.org)
- 2010. The UNITE database for molecular identification of fungi - recent updates and future perspectives. (inia.es)
Simulations1
- Classical molecular AS1842856 dynamics simulations are applied to the study of amorphous silicon regrowth in a nanodevice. (nartpathway.com)
Dynamics2
Increasingly1
- For example, it has become increasingly clear since the advancement of molecular barcoding techniques that many species of Rickettsia , Francisella , and Coxiella , which are generally considered pathogens of medical and veterinary importance, have evolved as non-pathogenic endosymbionts of ticks [ 9 ]. (biomedcentral.com)
Analysis2
- Molecular analysis of the t(2;8)/MYC-IGK translocation in high-grade lymphoma/leukemia by long-distance inverse PCR. (pcrgrade.com)
- It contains interactive tools to visualize a dataset's distribution of per-particle variability, generate density maps for exploratory analysis, extract particle subsets for use with other tools and generate trajectories to visualize molecular motions. (nih.gov)
Lack1
- However, in many areas, caddisflies remain understudied due to lack of taxonomic expertise. (bvsalud.org)
Studies1
- Environmental DNA (eDNA) metabarcoding offers a powerful tool to complement morpho-taxonomic studies. (id-gene.com)
Biological1
- COHH are expected to create an environment conducive to interdisciplinary and reciprocally beneficial collaborations among biomedical scientists (e.g., epidemiologists, pharmacologists, toxicologists, microbiologists, cell and molecular biologists) and ocean scientists (e.g., biological and physical oceanographers, geochemists, and ecologists) with the common goal of improving our knowledge of the impacts of the ocean on human health. (nih.gov)
Study1
- The objective of this study is to provide an operational definition of principles with which well-formed ontologies should comply. (nih.gov)
Results2
- 4) Conclusions: Our results are in line with diversifying selection on the radula driving Tylomelania ecomorph divergence and indicate that some molecular pathways may be especially prone to adaptive diversification, even across phylogenetically distant animal groups. (bvsalud.org)
- Our results reveal a quasiparticle renormalization at low energy scales (effective mass m(*) = 1.9 m(e)) and omega(2) www.selleckchem.com/products/mln-4924.html dependence of the imaginary part of the self energy, limited by a kink at similar to 50 meV arising from coupling to molecular vibrations. (nartpathway.com)
Research1
- European Journal of Operational Research, 309(1):252-270. (uzh.ch)
Systems2
Groups1
- An operational taxonomic unit (OTU) is an operational definition used to classify groups of closely related individuals. (wikipedia.org)