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Archaeal Richmond Mine Acidophilic Nanoorganisms
Archaeal Richmond Mine acidophilic nanoorganisms (ARMAN) were first discovered in an extremely acidic mine located in northern California ( Richmond Mine at Iron Mountain) by Brett Baker in Jill Banfield's laboratory at the University of California Berkeley. These novel groups of archaea named ARMAN-1, ARMAN-2 (''Candidatus Micrarchaeum acidiphilum'' ARMAN-2), and ARMAN-3 were missed by previous PCR-based surveys of the mine community because the ARMANs have several mismatches with commonly used PCR primers for 16S rRNA genes. Baker ''et al.'' detected them in a later study using shotgun sequencing of the community. The three groups were originally thought to represent three unique lineages deeply branched within the Euryarchaeota, a subgroup of the Archaea. However, based on a more complete archaeal genomic tree, they were assigned to a new superphylum named DPANN. The ARMAN groups now comprise deeply divergent phyla named Micrarchaeota and Parvarchaeota. Their 16S rRNA ge ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Archaea
Archaea ( ; singular archaeon ) is a domain of single-celled organisms. These microorganisms lack cell nuclei and are therefore prokaryotes. Archaea were initially classified as bacteria, receiving the name archaebacteria (in the Archaebacteria kingdom), but this term has fallen out of use. Archaeal cells have unique properties separating them from the other two domains, Bacteria and Eukaryota. Archaea are further divided into multiple recognized phyla. Classification is difficult because most have not been isolated in a laboratory and have been detected only by their gene sequences in environmental samples. Archaea and bacteria are generally similar in size and shape, although a few archaea have very different shapes, such as the flat, square cells of ''Haloquadratum walsbyi''. Despite this morphological similarity to bacteria, archaea possess genes and several metabolic pathways that are more closely related to those of eukaryotes, notably for the enzymes involved ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Thermoplasmatales
In alpha taxonomy, taxonomy, the Thermoplasmatales are an order (biology), order of the Thermoplasmata. All are acidophiles, growing optimally at pH below 2. ''Picrophilus'' is currently the most acidophile, acidophilic of all known organisms, being capable of growing at a pH of -0.06. Many of these organisms do not contain a cell wall, although this is not true in the case of ''Picrophilus''. Most members of the Thermotoplasmata are thermophilic. Phylogeny The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN) and National Center for Biotechnology Information (NCBI). See also * List of Archaea genera References * Further reading Scientific journals * * * * Scientific books * * Scientific databases External links Archaea taxonomic orders Euryarchaeota {{Euryarchaeota-stub ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Euryarchaea
Euryarchaeota (from Ancient Greek ''εὐρύς'' eurús, "broad, wide") is a phylum of archaea. Euryarchaeota are highly diverse and include methanogens, which produce methane and are often found in intestines, halobacteria, which survive extreme concentrations of salt, and some extremely thermophilic aerobes and anaerobes, which generally live at temperatures between 41 and 122 °C. They are separated from the other archaeans based mainly on rRNA sequences and their unique DNA polymerase. Description The ''Euryarchaeota'' are diverse in appearance and metabolic properties. The phylum contains organisms of a variety of shapes, including both rods and cocci. ''Euryarchaeota'' may appear either gram-positive or gram-negative depending on whether pseudomurein is present in the cell wall. ''Euryarchaeota'' also demonstrate diverse lifestyles, including methanogens, halophiles, sulfate-reducers, and extreme thermophiles in each. Others live in the ocean, suspended with plankton ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Self-Organizing Map
A self-organizing map (SOM) or self-organizing feature map (SOFM) is an unsupervised machine learning technique used to produce a low-dimensional (typically two-dimensional) representation of a higher dimensional data set while preserving the topological structure of the data. For example, a data set with p variables measured in n observations could be represented as clusters of observations with similar values for the variables. These clusters then could be visualized as a two-dimensional "map" such that observations in proximal clusters have more similar values than observations in distal clusters. This can make high-dimensional data easier to visualize and analyze. An SOM is a type of artificial neural network but is trained using competitive learning rather than the error-correction learning (e.g., backpropagation with gradient descent) used by other artificial neural networks. The SOM was introduced by the Finnish professor Teuvo Kohonen in the 1980s and therefore is sometim ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Joint Genome Institute
The U.S. Department of Energy (DOE) Joint Genome Institute (JGI), first located in Walnut Creek then Berkeley, California, was created in 1997 to unite the expertise and resources in genome mapping, DNA sequencing, technology development, and information sciences pioneered at the DOE genome centers at Lawrence Berkeley National Laboratory (Berkeley Lab), Lawrence Livermore National Laboratory (LLNL) and Los Alamos National Laboratory (LANL). As a DOE Office of Science User Facility of Berkeley Lab, the JGI staff is composed of employees from Berkeley Lab, LLNL and the HudsonAlpha Institute for Biotechnology. The JGI also collaborates with other DOE-supported programs and facilities, such as the Environmental Molecular Sciences Laboratory at Pacific Northwest National Laboratory (PNNL), the National Energy Research Scientific Computing Center, or NERSC, and the DOE Bioenergy Research Centers. History In 1999, the University of California, which manages the three national labs for ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Ribosomes
Ribosomes ( ) are macromolecular machines, found within all cells, that perform biological protein synthesis (mRNA translation). Ribosomes link amino acids together in the order specified by the codons of messenger RNA (mRNA) molecules to form polypeptide chains. Ribosomes consist of two major components: the small and large ribosomal subunits. Each subunit consists of one or more ribosomal RNA (rRNA) molecules and many ribosomal proteins (RPs or r-proteins). The ribosomes and associated molecules are also known as the ''translational apparatus''. Overview The sequence of DNA that encodes the sequence of the amino acids in a protein is transcribed into a messenger RNA chain. Ribosomes bind to messenger RNAs and use their sequences for determining the correct sequence of amino acids to generate a given protein. Amino acids are selected and carried to the ribosome by transfer RNA (tRNA) molecules, which enter the ribosome and bind to the messenger RNA chain via an anti-cod ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Virus
A virus is a submicroscopic infectious agent that replicates only inside the living cells of an organism. Viruses infect all life forms, from animals and plants to microorganisms, including bacteria and archaea. Since Dmitri Ivanovsky's 1892 article describing a non-bacterial pathogen infecting tobacco plants and the discovery of the tobacco mosaic virus by Martinus Beijerinck in 1898,Dimmock p. 4 more than 9,000 virus species have been described in detail of the millions of types of viruses in the environment. Viruses are found in almost every ecosystem on Earth and are the most numerous type of biological entity. The study of viruses is known as virology, a subspeciality of microbiology. When infected, a host cell is often forced to rapidly produce thousands of copies of the original virus. When not inside an infected cell or in the process of infecting a cell, viruses exist in the form of independent particles, or ''virions'', consisting of (i) the genetic material, i. ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Biofilms
A biofilm comprises any syntrophic consortium of microorganisms in which cells stick to each other and often also to a surface. These adherent cells become embedded within a slimy extracellular matrix that is composed of extracellular polymeric substances (EPSs). The cells within the biofilm produce the EPS components, which are typically a polymeric conglomeration of extracellular polysaccharides, proteins, lipids and DNA. Because they have three-dimensional structure and represent a community lifestyle for microorganisms, they have been metaphorically described as "cities for microbes". Biofilms may form on living or non-living surfaces and can be prevalent in natural, industrial, and hospital settings. They may constitute a microbiome or be a portion of it. The microbial cells growing in a biofilm are physiologically distinct from planktonic cells of the same organism, which, by contrast, are single cells that may float or swim in a liquid medium. Biofilms can form ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Cryo-electron Tomography
Electron cryotomography (CryoET) is an imaging technique used to produce high-resolution (~1–4 nm) three-dimensional views of samples, often (but not limited to) biological macromolecules and cells. CryoET is a specialized application of transmission electron cryomicroscopy (CryoTEM) in which samples are imaged as they are tilted, resulting in a series of 2D images that can be combined to produce a 3D reconstruction, similar to a CT scan of the human body. In contrast to other electron tomography techniques, samples are imaged under cryogenic conditions (< −150 °C). For cellular material, the structure is immobilized in non-crystalline, vitreous ice, allowing them to be imaged without dehydration or chemical fixation, which would otherwise disrupt or distort biological structures. Description of technique [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Rio Tinto (river)
The Río Tinto (, ''red river'' or Tinto River) is a river in southwestern Spain that rises in the Sierra Morena mountains of Andalusia. It flows generally south-southwest, reaching the Gulf of Cádiz at Huelva. The Rio Tinto river has a unique red and orange colour derived from its chemical makeup that is extremely acidic and with very high levels of iron and heavy metals. The river maintains its colour for an approximate length of 50 kilometres. After the 50 kilometre mark, the chemistry that makes the Rio Tinto river so unique appears to slowly decline, as does the odd colouring. The location where the chemistry of the river is altered is near a town called Niebla. The river's chemistry begins to significantly change following the town of Niebla owing to the fact that the Rio Tinto blends itself with other streams that are connected to the Atlantic Ocean. The river is approximately long and is located within the Iberian Pyrite Belt. This area has large amounts of ore and sul ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Acid Mine Drainage
Acid mine drainage, acid and metalliferous drainage (AMD), or acid rock drainage (ARD) is the outflow of acidic water from metal mines or coal mines. Acid rock drainage occurs naturally within some environments as part of the rock weathering process but is exacerbated by large-scale earth disturbances characteristic of mining and other large construction activities, usually within rocks containing an abundance of sulfide minerals. Areas where the earth has been disturbed (e.g. construction sites, subdivisions, and transportation corridors) may create acid rock drainage. In many localities, the liquid that drains from coal stocks, coal handling facilities, coal washeries, and coal waste tips can be highly acidic, and in such cases it is treated as acid rock drainage. This liquid often contains highly toxic metals, such as copper or iron. These, combined with reduced pH, have a detrimental impact on the streams aquatic environments. The same type of chemical reactions and pr ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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