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Aquatic Macroinvertebrate DNA Barcoding
DNA barcoding is an alternative method to the traditional morphological taxonomic classification, and has frequently been used to identify species of aquatic macroinvertebrates (generally considered those large enough to be seen without magnification). Many are crucial indicator organisms in the bioassessment of freshwater (e.g.: Ephemeroptera, Plecoptera, Trichoptera) and marine (e.g. Annelida, Echinoderms, Molluscs) ecosystems. Since its introduction, the field of DNA barcoding has matured to bridge the gap between traditional taxonomy and molecular systematics. This technique has the ability to provide more detailed taxonomic information, particularly for cryptic, small, or rare species. DNA barcoding involves specific targeting of gene regions that are found and conserved in most animal species, but have high variation between members of different species. Accurate diagnosis depends on low intraspecific variation compared with that between species, a short DNA sequence suc ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Taxonomic Classification
In biology, taxonomy () is the scientific study of naming, defining ( circumscribing) and classifying groups of biological organisms based on shared characteristics. Organisms are grouped into taxa (singular: taxon) and these groups are given a taxonomic rank; groups of a given rank can be aggregated to form a more inclusive group of higher rank, thus creating a taxonomic hierarchy. The principal ranks in modern use are domain, kingdom, phylum (''division'' is sometimes used in botany in place of ''phylum''), class, order, family, genus, and species. The Swedish botanist Carl Linnaeus is regarded as the founder of the current system of taxonomy, as he developed a ranked system known as Linnaean taxonomy for categorizing organisms and binomial nomenclature for naming organisms. With advances in the theory, data and analytical technology of biological systematics, the Linnaean system has transformed into a system of modern biological classification intended to reflect the evolut ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
16S Ribosomal RNA
16 S ribosomal RNA (or 16 S rRNA) is the RNA component of the 30S subunit of a prokaryotic ribosome (SSU rRNA). It binds to the Shine-Dalgarno sequence and provides most of the SSU structure. The genes coding for it are referred to as 16S rRNA gene and are used in reconstructing phylogenies, due to the slow rates of evolution of this region of the gene. Carl Woese and George E. Fox were two of the people who pioneered the use of 16S rRNA in phylogenetics in 1977. Multiple sequences of the 16S rRNA gene can exist within a single bacterium. Functions * Like the large (23S) ribosomal RNA, it has a structural role, acting as a scaffold defining the positions of the ribosomal proteins. * The 3-end contains the anti- Shine-Dalgarno sequence, which binds upstream to the AUG start codon on the mRNA. The 3-end of 16S RNA binds to the proteins S1 and S21 which are known to be involved in initiation of protein synthesis * Interacts with 23S, aiding in the binding of the two ribosomal s ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Sequencing
In genetics and biochemistry, sequencing means to determine the primary structure (sometimes incorrectly called the primary sequence) of an unbranched biopolymer. Sequencing results in a symbolic linear depiction known as a sequence which succinctly summarizes much of the atomic-level structure of the sequenced molecule. DNA sequencing DNA sequencing is the process of determining the nucleotide order of a given DNA fragment. So far, most DNA sequencing has been performed using the chain termination method developed by Frederick Sanger. This technique uses sequence-specific termination of a DNA synthesis reaction using modified nucleotide substrates. However, new sequencing technologies such as pyrosequencing are gaining an increasing share of the sequencing market. More genome data are now being produced by pyrosequencing than Sanger DNA sequencing. Pyrosequencing has enabled rapid genome sequencing. Bacterial genomes can be sequenced in a single run with several times cover ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Algae DNA Barcoding
DNA barcoding of algae is commonly used for species identification and phylogenetic studies. Algae form a phylogenetically heterogeneous group, meaning that the application of a single universal barcode/ marker for species delimitation is unfeasible, thus different markers/barcodes are applied for this aim in different algal groups. Diatoms Diatom DNA barcoding is a method for taxonomical identification of diatoms even to species level. It is conducted using DNA or RNA followed by amplification and sequencing of specific, conserved regions in the diatom genome followed by taxonomic assignment. One of the main challenges of identifying diatoms is that it is often collected as a mixture of diatoms from several species. DNA metabarcoding is the process of identifying the individual species from a mixed sample of environmental DNA (also called eDNA) which is DNA extracted straight from the environment such as in soil or water samples. A newly applied method is diatom DNA m ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Fish DNA Barcoding
DNA barcoding methods for fish are used to identify groups of fish based on DNA sequences within selected regions of a genome. These methods can be used to study fish, as genetic material, in the form of environmental DNA (eDNA) or cells, is freely diffused in the water. This allows researchers to identify which species are present in a body of water by collecting a water sample, extracting DNA from the sample and isolating DNA sequences that are specific for the species of interest. Barcoding methods can also be used for biomonitoring and food safety validation, DNA barcoding in diet assessment, animal diet assessment, assessment of food webs and species distribution, and for detection of invasive species. In fish research, barcoding can be used as an alternative to traditional sampling methods. Barcoding methods can often provide information without damage to the studied animal. Aquatic environments have unique properties that affect how genetic material from organisms is distri ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Taxonomic Resolution
DNA barcoding is a method of species identification using a short section of DNA from a specific gene or genes. The premise of DNA barcoding is that by comparison with a reference library of such DNA sections (also called "DNA sequence, sequences"), an individual sequence can be used to uniquely identify an organism to species, just as a supermarket scanner uses the familiar black stripes of the Universal Product Code, UPC barcode to identify an item in its stock against its reference database. These "barcodes" are sometimes used in an effort to identify unknown species or parts of an organism, simply to catalog as many Taxon, taxa as possible, or to compare with traditional taxonomy in an effort to determine species boundaries. Different gene regions are used to identify the different organismal groups using barcoding. The most commonly used barcode region for animals and some protists is a portion of the Cytochrome c oxidase subunit I, cytochrome ''c'' oxidase I (COI or Cytochr ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Environmental Monitoring
Environmental monitoring describes the processes and activities that need to take place to characterize and monitor the quality of the environment. Environmental monitoring is used in the preparation of environmental impact assessments, as well as in many circumstances in which human activities carry a risk of harmful effects on the natural environment. All monitoring strategies and programs have reasons and justifications which are often designed to establish the current status of an environment or to establish trends in environmental parameters. In all cases, the results of monitoring will be reviewed, analyzed statistically, and published. The design of a monitoring program must therefore have regard to the final use of the data before monitoring starts. Environmental monitoring includes monitoring of air quality, soils and water quality. Air quality monitoring Air pollutants are atmospheric substances—both naturally occurring and anthropogenic—which may potentially ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Environmental DNA
Environmental DNA or eDNA is DNA that is collected from a variety of environmental samples such as soil, seawater, snow or air, rather than directly sampled from an individual organism. As various organisms interact with the environment, DNA is expelled and accumulates in their surroundings from various sources. In recent years, eDNA has been used as a tool to detect endangered wildlife that were otherwise unseen. In 2020, human health researchers began repurposing eDNA techniques to track the COVID-19 pandemic. Example sources of eDNA include, but are not limited to, feces, mucus, gametes, shed skin, carcasses and hair. Samples can be analyzed by high-throughput DNA sequencing methods, known as metagenomics, metabarcoding, and single-species detection, for rapid monitoring and measurement of biodiversity. In order to better differentiate between organisms within a sample, DNA metabarcoding is used in which the sample is analyzed and uses previously studied DNA librari ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Next-generation Sequencing
Massive parallel sequencing or massively parallel sequencing is any of several high-throughput approaches to DNA sequencing using the concept of massively parallel processing; it is also called next-generation sequencing (NGS) or second-generation sequencing. Some of these technologies emerged between 1994 and 1998 and have been commercially available since 2005. These technologies use miniaturized and parallelized platforms for sequencing of 1 million to 43 billion short reads (50 to 400 bases each) per instrument run. Many NGS platforms differ in engineering configurations and sequencing chemistry. They share the technical paradigm of massive parallel sequencing via spatially separated, clonally amplified DNA templates or single DNA molecules in a flow cytometry, flow cell. This design is very different from that of Sanger sequencing—also known as capillary sequencing or first-generation sequencing—which is based on electrophoretic separation of chain-termination products produ ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
DNA Sequencing
DNA sequencing is the process of determining the nucleic acid sequence – the order of nucleotides in DNA. It includes any method or technology that is used to determine the order of the four bases: adenine, guanine, cytosine, and thymine. The advent of rapid DNA sequencing methods has greatly accelerated biological and medical research and discovery. Knowledge of DNA sequences has become indispensable for basic biological research, DNA Genographic Projects and in numerous applied fields such as medical diagnosis, biotechnology, forensic biology, virology and biological systematics. Comparing healthy and mutated DNA sequences can diagnose different diseases including various cancers, characterize antibody repertoire, and can be used to guide patient treatment. Having a quick way to sequence DNA allows for faster and more individualized medical care to be administered, and for more organisms to be identified and cataloged. The rapid speed of sequencing attained with modern D ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Metabarcoding
Metabarcoding is the barcoding of DNA/RNA (or eDNA/ eRNA) in a manner that allows for the simultaneous identification of many taxa within the same sample. The main difference between barcoding and metabarcoding is that metabarcoding does not focus on one specific organism, but instead aims to determine species composition within a sample. A barcode consists of a short variable gene region (for example, see different markers/barcodes) which is useful for taxonomic assignment flanked by highly conserved gene regions which can be used for primer design. This idea of general barcoding originated in 2003 from researchers at the University of Guelph. The metabarcoding procedure, like general barcoding, proceeds in order through stages of DNA extraction, PCR amplification, sequencing and data analysis. Different genes are used depending if the aim is to barcode single species or metabarcoding several species. In the latter case, a more universal gene is used. Metabarcoding does ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
18S Ribosomal RNA
18S ribosomal RNA (abbreviated 18S rRNA) is a part of the ribosomal RNA. The S in 18S represents Svedberg units. 18S rRNA is an SSU rRNA, a component of the eukaryotic ribosomal small subunit (40S). 18S rRNA is the structural RNA for the small component of eukaryotic cytoplasmic ribosomes, and thus one of the basic components of all eukaryotic cells. 18S rRNA is the eukaryotic cytosolic homologue of 16S ribosomal RNA in prokaryotes and plastids. 18S rRNA is also a homologue of 12S ribosomal RNA in mitochondria. The genes coding for 18S rRNA are referred to as 18S rRNA genes. Sequence data from these genes is widely used in molecular analysis to reconstruct the evolutionary history of organisms, especially in vertebrates, as its slow evolutionary rate makes it suitable to reconstruct ancient divergences. Uses in phylogeny The small subunit (SSU) 18S rRNA gene is one of the most frequently used genes in phylogenetic studies and an important marker for random target polymerase ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
