MetatranscriptomicsMetatranscriptomics is the set of techniques used to study gene expression of microbes within natural environments, i.e., the metatranscriptome. While metagenomics focuses on studying the genomic content and on identifying which microbes are present within a community, metatranscriptomics can be used to study the diversity of the active genes within such community, to quantify their expression levels and to monitor how these levels change in different conditions (e.g., physiological vs. pathological conditions in an organism).
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.
PhosphoritePhosphorite, phosphate rock or rock phosphate is a non-detrital sedimentary rock that contains high amounts of phosphate minerals. The phosphate content of phosphorite (or grade of phosphate rock) varies greatly, from 4% to 20% phosphorus pentoxide (P2O5). Marketed phosphate rock is enriched ("beneficiated") to at least 28%, often more than 30% P2O5. This occurs through washing, screening, de-liming, magnetic separation or flotation. By comparison, the average phosphorus content of sedimentary rocks is less than 0.
Phosphorus cycleThe phosphorus cycle is the biogeochemical cycle that describes the movement of phosphorus through the lithosphere, hydrosphere, and biosphere. Unlike many other biogeochemical cycles, the atmosphere does not play a significant role in the movement of phosphorus, because phosphorus and phosphorus-based compounds are usually solids at the typical ranges of temperature and pressure found on Earth. The production of phosphine gas occurs in only specialized, local conditions.
Gene expression profilingIn the field of molecular biology, gene expression profiling is the measurement of the activity (the expression) of thousands of genes at once, to create a global picture of cellular function. These profiles can, for example, distinguish between cells that are actively dividing, or show how the cells react to a particular treatment. Many experiments of this sort measure an entire genome simultaneously, that is, every gene present in a particular cell. Several transcriptomics technologies can be used to generate the necessary data to analyse.
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.
Activated sludgeThe activated sludge process is a type of biological wastewater treatment process for treating sewage or industrial wastewaters using aeration and a biological floc composed of bacteria and protozoa. It uses air (or oxygen) and microorganisms to biologically oxidize organic pollutants, producing a waste sludge (or floc) containing the oxidized material. The activated sludge process for removing carbonaceous pollution begins with an aeration tank where air (or oxygen) is injected into the waste water.
Pyridoxal phosphatePyridoxal phosphate (PLP, pyridoxal 5'-phosphate, P5P), the active form of vitamin B6, is a coenzyme in a variety of enzymatic reactions. The International Union of Biochemistry and Molecular Biology has catalogued more than 140 PLP-dependent activities, corresponding to ~4% of all classified activities. The versatility of PLP arises from its ability to covalently bind the substrate, and then to act as an electrophilic catalyst, thereby stabilizing different types of carbanionic reaction intermediates.
Triphenyl phosphateTriphenyl phosphate (TPhP) is the chemical compound with the formula OP(OC6H5)3. It is the simplest aromatic organophosphate. This colourless solid is the ester (triester) of phosphoric acid and phenol. It is used as a plasticizer and a fire retardant in a wide variety of settings and products. Triphenyl phosphate is prepared by the SN2 reaction of phosphorus oxychloride and phenol. Triphenyl phosphate has been used widely as a flame retardant and plasticizer.
Transcriptomics technologiesTranscriptomics technologies are the techniques used to study an organism's transcriptome, the sum of all of its RNA transcripts. The information content of an organism is recorded in the DNA of its genome and expressed through transcription. Here, mRNA serves as a transient intermediary molecule in the information network, whilst non-coding RNAs perform additional diverse functions. A transcriptome captures a snapshot in time of the total transcripts present in a cell.
Carbon sequestrationCarbon sequestration (or carbon storage) is the process of storing carbon in a carbon pool. Carbon sequestration is a naturally occurring process but it can also be enhanced or achieved with technology, for example within carbon capture and storage projects. There are two main types of carbon sequestration: geologic and biologic (also called biosequestration). Carbon dioxide (CO2) is naturally captured from the atmosphere through biological, chemical, and physical processes.
PhosphateIn chemistry, a phosphate is an anion, salt, functional group or ester derived from a phosphoric acid. It most commonly means orthophosphate, a derivative of orthophosphoric acid, aka. phosphoric acid . The phosphate or orthophosphate ion [PO4]3− is derived from phosphoric acid by the removal of three protons H+. Removal of one proton gives the dihydrogen phosphate ion [H2PO4]− while removal of two ions gives the hydrogen phosphate ion [HPO4]2−. These names are also used for salts of those anions, such as ammonium dihydrogen phosphate and trisodium phosphate.
Glyceraldehyde 3-phosphate dehydrogenaseGlyceraldehyde 3-phosphate dehydrogenase (abbreviated GAPDH) () is an enzyme of about 37kDa that catalyzes the sixth step of glycolysis and thus serves to break down glucose for energy and carbon molecules. In addition to this long established metabolic function, GAPDH has recently been implicated in several non-metabolic processes, including transcription activation, initiation of apoptosis, ER to Golgi vesicle shuttling, and fast axonal, or axoplasmic transport. In sperm, a testis-specific isoenzyme GAPDHS is expressed.
Abundance (ecology)In ecology, local abundance is the relative representation of a species in a particular ecosystem. It is usually measured as the number of individuals found per sample. The ratio of abundance of one species to one or multiple other species living in an ecosystem is referred to as relative species abundances. Both indicators are relevant for computing biodiversity. A variety of sampling methods are used to measure abundance. For larger animals, these may include spotlight counts, track counts and roadkill counts, as well as presence at monitoring stations.
Constructed wetlandA constructed wetland is an artificial wetland to treat sewage, greywater, stormwater runoff or industrial wastewater. It may also be designed for land reclamation after mining, or as a mitigation step for natural areas lost to land development. Constructed wetlands are engineered systems that use the natural functions of vegetation, soil, and organisms to provide secondary treatment to wastewater. The design of the constructed wetland has to be adjusted according to the type of wastewater to be treated.
GlycogenGlycogen is a multibranched polysaccharide of glucose that serves as a form of energy storage in animals, fungi, and bacteria. It is the main storage form of glucose in the human body. Glycogen functions as one of two forms of energy reserves, glycogen being for short-term and the other form being triglyceride stores in adipose tissue (i.e., body fat) for long-term storage. In humans, glycogen is made and stored primarily in the cells of the liver and skeletal muscle.
MicrobiotaMicrobiota are the range of microorganisms that may be commensal, mutualistic, or pathogenic found in and on all multicellular organisms, including plants. Microbiota include bacteria, archaea, protists, fungi, and viruses, and have been found to be crucial for immunologic, hormonal, and metabolic homeostasis of their host. The term microbiome describes either the collective genomes of the microbes that reside in an ecological niche or within the microbes themselves.
Human Microbiome ProjectThe Human Microbiome Project (HMP) was a United States National Institutes of Health (NIH) research initiative to improve understanding of the microbiota involved in human health and disease. Launched in 2007, the first phase (HMP1) focused on identifying and characterizing human microbiota. The second phase, known as the Integrative Human Microbiome Project (iHMP) launched in 2014 with the aim of generating resources to characterize the microbiome and elucidating the roles of microbes in health and disease states.
MetabolismMetabolism (məˈtæbəlɪzəm, from μεταβολή metabolē, "change") is the set of life-sustaining chemical reactions in organisms. The three main functions of metabolism are: the conversion of the energy in food to energy available to run cellular processes; the conversion of food to building blocks for proteins, lipids, nucleic acids, and some carbohydrates; and the elimination of metabolic wastes. These enzyme-catalyzed reactions allow organisms to grow and reproduce, maintain their structures, and respond to their environments.
Carbon cycleThe carbon cycle is that part of the biogeochemical cycle by which carbon is exchanged among the biosphere, pedosphere, geosphere, hydrosphere, and atmosphere of Earth. Other major biogeochemical cycles include the nitrogen cycle and the water cycle. Carbon is the main component of biological compounds as well as a major component of many minerals such as limestone. The carbon cycle comprises a sequence of events that are key to making Earth capable of sustaining life.
