MetagenomicsMetagenomics is the study of genetic material recovered directly from environmental or clinical samples by a method called sequencing. The broad field may also be referred to as environmental genomics, ecogenomics, community genomics or microbiomics. While traditional microbiology and microbial genome sequencing and genomics rely upon cultivated clonal cultures, early environmental gene sequencing cloned specific genes (often the 16S rRNA gene) to produce a profile of diversity in a natural sample.
Shotgun sequencingIn genetics, shotgun sequencing is a method used for sequencing random DNA strands. It is named by analogy with the rapidly expanding, quasi-random shot grouping of a shotgun. The chain-termination method of DNA sequencing ("Sanger sequencing") can only be used for short DNA strands of 100 to 1000 base pairs. Due to this size limit, longer sequences are subdivided into smaller fragments that can be sequenced separately, and these sequences are assembled to give the overall sequence.
Whole genome sequencingWhole genome sequencing (WGS), also known as full genome sequencing, complete genome sequencing, or entire genome sequencing, is the process of determining the entirety, or nearly the entirety, of the DNA sequence of an organism's genome at a single time. This entails sequencing all of an organism's chromosomal DNA as well as DNA contained in the mitochondria and, for plants, in the chloroplast. Whole genome sequencing has largely been used as a research tool, but was being introduced to clinics in 2014.
Genome projectGenome projects are scientific endeavours that ultimately aim to determine the complete genome sequence of an organism (be it an animal, a plant, a fungus, a bacterium, an archaean, a protist or a virus) and to annotate protein-coding genes and other important genome-encoded features. The genome sequence of an organism includes the collective DNA sequences of each chromosome in the organism. For a bacterium containing a single chromosome, a genome project will aim to map the sequence of that chromosome.
Sewage treatmentSewage treatment (or domestic wastewater treatment, municipal wastewater treatment) is a type of wastewater treatment which aims to remove contaminants from sewage to produce an effluent that is suitable to discharge to the surrounding environment or an intended reuse application, thereby preventing water pollution from raw sewage discharges. Sewage contains wastewater from households and businesses and possibly pre-treated industrial wastewater. There are a high number of sewage treatment processes to choose from.
Secondary treatmentSecondary treatment (mostly biological wastewater treatment) is the removal of biodegradable organic matter (in solution or suspension) from sewage or similar kinds of wastewater. The aim is to achieve a certain degree of effluent quality in a sewage treatment plant suitable for the intended disposal or reuse option. A "primary treatment" step often precedes secondary treatment, whereby physical phase separation is used to remove settleable solids.
Human Genome ProjectThe Human Genome Project (HGP) was an international scientific research project with the goal of determining the base pairs that make up human DNA, and of identifying, mapping and sequencing all of the genes of the human genome from both a physical and a functional standpoint. It started in 1990 and was completed in 2003. It remains the world's largest collaborative biological project. Planning for the project started after it was adopted in 1984 by the US government, and it officially launched in 1990.
Wastewater treatmentWastewater treatment is a process which removes and eliminates contaminants from wastewater and converts this into an effluent that can be returned to the water cycle. Once returned to the water cycle, the effluent creates an acceptable impact on the environment or is reused for various purposes (called water reclamation). The treatment process takes place in a wastewater treatment plant. There are several kinds of wastewater which are treated at the appropriate type of wastewater treatment plant.
Reference genomeA reference genome (also known as a reference assembly) is a digital nucleic acid sequence database, assembled by scientists as a representative example of the set of genes in one idealized individual organism of a species. As they are assembled from the sequencing of DNA from a number of individual donors, reference genomes do not accurately represent the set of genes of any single individual organism. Instead a reference provides a haploid mosaic of different DNA sequences from each donor.
Industrial wastewater treatmentIndustrial wastewater treatment describes the processes used for treating wastewater that is produced by industries as an undesirable by-product. After treatment, the treated industrial wastewater (or effluent) may be reused or released to a sanitary sewer or to a surface water in the environment. Some industrial facilities generate wastewater that can be treated in sewage treatment plants.
Sequence assemblyIn bioinformatics, sequence assembly refers to aligning and merging fragments from a longer DNA sequence in order to reconstruct the original sequence. This is needed as DNA sequencing technology might not be able to 'read' whole genomes in one go, but rather reads small pieces of between 20 and 30,000 bases, depending on the technology used. Typically, the short fragments (reads) result from shotgun sequencing genomic DNA, or gene transcript (ESTs).
Comparative genomicsComparative genomics is a field of biological research in which the genomic features of different organisms are compared. The genomic features may include the DNA sequence, genes, gene order, regulatory sequences, and other genomic structural landmarks. In this branch of genomics, whole or large parts of genomes resulting from genome projects are compared to study basic biological similarities and differences as well as evolutionary relationships between organisms.
Point mutationA point mutation is a genetic mutation where a single nucleotide base is changed, inserted or deleted from a DNA or RNA sequence of an organism's genome. Point mutations have a variety of effects on the downstream protein product—consequences that are moderately predictable based upon the specifics of the mutation. These consequences can range from no effect (e.g. synonymous mutations) to deleterious effects (e.g. frameshift mutations), with regard to protein production, composition, and function.
GenomeIn the fields of molecular biology and genetics, a genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding genes, other functional regions of the genome such as regulatory sequences (see non-coding DNA), and often a substantial fraction of junk DNA with no evident function. Almost all eukaryotes have mitochondria and a small mitochondrial genome.
MicrobiomeA microbiome () is the community of microorganisms that can usually be found living together in any given habitat. It was defined more precisely in 1988 by Whipps et al. as "a characteristic microbial community occupying a reasonably well-defined habitat which has distinct physio-chemical properties. The term thus not only refers to the microorganisms involved but also encompasses their theatre of activity". In 2020, an international panel of experts published the outcome of their discussions on the definition of the microbiome.
Water treatmentWater treatment is any process that improves the quality of water to make it appropriate for a specific end-use. The end use may be drinking, industrial water supply, irrigation, river flow maintenance, water recreation or many other uses, including being safely returned to the environment. Water treatment removes contaminants and undesirable components, or reduces their concentration so that the water becomes fit for its desired end-use. This treatment is crucial to human health and allows humans to benefit from both drinking and irrigation use.
Decentralized wastewater systemDecentralized wastewater systems (also referred to as decentralized wastewater treatment systems) convey, treat and dispose or reuse wastewater from small and low-density communities, buildings and dwellings in remote areas, individual public or private properties. Wastewater flow is generated when appropriate water supply is available within the buildings or close to them. Decentralized wastewater systems treat, reuse or dispose the effluent in relatively close vicinity to its source of generation.
Nonsense mutationIn genetics, a nonsense mutation is a point mutation in a sequence of DNA that results in a premature stop codon, or a nonsense codon in the transcribed mRNA, and in leading to a truncated, incomplete, and nonfunctional protein product. Nonsense mutation is not always harmful, the functional effect of a nonsense mutation depends on many aspects, such as the location of the stop codon within the coding DNA. For example, the effect of a nonsense mutation depends on the proximity of the nonsense mutation to the original stop codon, and the degree to which functional subdomains of the protein are affected.
GenomicsGenomics is an interdisciplinary field of biology focusing on the structure, function, evolution, mapping, and editing of genomes. A genome is an organism's complete set of DNA, including all of its genes as well as its hierarchical, three-dimensional structural configuration. In contrast to genetics, which refers to the study of individual genes and their roles in inheritance, genomics aims at the collective characterization and quantification of all of an organism's genes, their interrelations and influence on the organism.
Agricultural wastewater treatmentAgricultural wastewater treatment is a farm management agenda for controlling pollution from confined animal operations and from surface runoff that may be contaminated by chemicals in fertilizer, pesticides, animal slurry, crop residues or irrigation water. Agricultural wastewater treatment is required for continuous confined animal operations like milk and egg production. It may be performed in plants using mechanized treatment units similar to those used for industrial wastewater.
