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Earth Microbiome Project
The 'Earth Microbiome Project'' (EMP) is an initiative founded by Janet Jansson, Jack Gilbert and Rob Knight in 2010 to collect natural samples and to analyze the microbial community around the globe. Microbes are highly abundant, diverse, and have an important role in the ecological system. For example, the ocean contains an estimated 1.3 × 1028 archaeal cells, 3.1 × 1028 bacterial cells, and 1 × 1030 virus particles. The bacterial diversity, a measure of the number of ''types'' of bacteria in a community, is estimated to be about 160 for a mL of ocean water, 6,400–38,000 for a g of soil, and 70 for a mL of sewage works. Yet , it was estimated that the total global environmental DNA sequencing effort had produced less than 1 percent of the total DNA found in a liter of seawater or a gram of soil, and the specific interactions between microbes are largely unknown. The EMP aims to process as many as 200,000 samples in different biomes, generati ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Rob Knight (biologist)
Rob Knight (born 1976 in Dunedin, New Zealand) is a professor at the University of California, San Diego and the co-founder of the American Gut Project. He is also a co-founder of the Earth Microbiome Project, and his lab's research involves the development of laboratory and computational techniques to characterize the microbiomes of humans, animals, and the environment. In 2015, he received the Vilcek Prize for Creative Promise in Biomedical Science. Knight completed a BSc in biochemistry at the University of Otago and a PhD in Ecology and Evolutionary Biology at Princeton University in 2001, where his thesis was "The Origin and Evolution of the Genetic Code." Until 2014, he was a professor at the University of Colorado Boulder. He did an IAmA on Reddit and co-taught an online microbiome course on Coursera. He gave a TED Talk in 2014 on the role microbes play on our health. Later this idea was expanded into the book ''Follow Your Gut: The Enormous Impact of Tiny Microbes'', ... [...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] |
High-throughput 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 DNA ... [...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] |
Phylogenetic Tree
A phylogenetic tree (also phylogeny or evolutionary tree Felsenstein J. (2004). ''Inferring Phylogenies'' Sinauer Associates: Sunderland, MA.) is a branching diagram or a tree showing the evolutionary relationships among various biological species or other entities based upon similarities and differences in their physical or genetic characteristics. All life on Earth is part of a single phylogenetic tree, indicating common ancestry. In a ''rooted'' phylogenetic tree, each node with descendants represents the inferred most recent common ancestor of those descendants, and the edge lengths in some trees may be interpreted as time estimates. Each node is called a taxonomic unit. Internal nodes are generally called hypothetical taxonomic units, as they cannot be directly observed. Trees are useful in fields of biology such as bioinformatics, systematics, and phylogenetics. ''Unrooted'' trees illustrate only the relatedness of the leaf nodes and do not require the ancestral root to b ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Ribosomal Database Project
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-codon ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
BLAST
Blast or The Blast may refer to: * Explosion, a rapid increase in volume and release of energy in an extreme manner *Detonation, an exothermic front accelerating through a medium that eventually drives a shock front Film * ''Blast'' (1997 film), starring Andrew Divoff * ''Blast'' (2000 film), starring Liesel Matthews * ''Blast'' (2004 film), an action comedy film * ''Blast!'' (1972 film) or ''The Final Comedown'', an American drama * ''BLAST!'' (2008 film), a documentary about the BLAST telescope * '' A Blast'', a 2014 film directed by Syllas Tzoumerkas Magazines * ''Blast'' (magazine), a 1914–15 literary magazine of the Vorticist movement * ''Blast'' (U.S. magazine), a 1933–34 American short-story magazine * ''The Blast'' (magazine), a 1916–17 American anarchist periodical Music * Blast (American band), a hardcore punk band * Blast (Russian band), an indie band * ''Blast'' (album), by Holly Johnson, 1989 * ''The Blast'' (album), by Yuvan Shankar Raja, 1999 * " ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Bioinformatics
Bioinformatics () is an interdisciplinary field that develops methods and software tools for understanding biological data, in particular when the data sets are large and complex. As an interdisciplinary field of science, bioinformatics combines biology, chemistry, physics, computer science, information engineering, mathematics and statistics to analyze and interpret the biological data. Bioinformatics has been used for '' in silico'' analyses of biological queries using computational and statistical techniques. Bioinformatics includes biological studies that use computer programming as part of their methodology, as well as specific analysis "pipelines" that are repeatedly used, particularly in the field of genomics. Common uses of bioinformatics include the identification of candidates genes and single nucleotide polymorphisms (SNPs). Often, such identification is made with the aim to better understand the genetic basis of disease, unique adaptations, desirable properties (e ... [...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] |
Multiple Displacement Amplification
Multiple displacement amplification (MDA) is a DNA amplification technique. This method can rapidly amplify minute amounts of DNA samples to a reasonable quantity for genomic analysis. The reaction starts by annealing random hexamer primers to the template: DNA synthesis is carried out by a high fidelity enzyme, preferentially Φ29 DNA polymerase. Compared with conventional PCR amplification techniques, MDA does not employ sequence-specific primers but amplifies all DNA, generates larger-sized products with a lower error frequency, and works at a constant temperature. MDA has been actively used in whole genome amplification (WGA) and is a promising method for application to single cell genome sequencing and sequencing-based genetic studies. Background Many biological and forensic cases involving genetic analysis require sequencing of DNA from minute amounts of sample, such as DNA from uncultured single cells or trace amounts of tissue collected from crime scenes. Conventiona ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Polymerase Chain Reaction
The polymerase chain reaction (PCR) is a method widely used to rapidly make millions to billions of copies (complete or partial) of a specific DNA sample, allowing scientists to take a very small sample of DNA and amplify it (or a part of it) to a large enough amount to study in detail. PCR was invented in 1983 by the American biochemist Kary Mullis at Cetus Corporation; Mullis and biochemist Michael Smith (chemist), Michael Smith, who had developed other essential ways of manipulating DNA, were jointly awarded the Nobel Prize in Chemistry in 1993. PCR is fundamental to many of the procedures used in genetic testing and research, including analysis of Ancient DNA, ancient samples of DNA and identification of infectious agents. Using PCR, copies of very small amounts of DNA sequences are exponentially amplified in a series of cycles of temperature changes. PCR is now a common and often indispensable technique used in medical laboratory research for a broad variety of applications ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Water Filtering
Water (chemical formula ) is an Inorganic compound, inorganic, transparent, tasteless, odorless, and Color of water, nearly colorless chemical substance, which is the main constituent of Earth's hydrosphere and the fluids of all known living organisms (in which it acts as a solvent). It is vital for all known forms of life, despite not providing food energy, food, energy or organic micronutrients. Its chemical formula, H2O, indicates that each of its molecules contains one oxygen and two hydrogen atoms, connected by covalent bonds. The hydrogen atoms are attached to the oxygen atom at an angle of 104.45°. "Water" is also the name of the liquid state of H2O at standard temperature and pressure. A number of natural states of water exist. It forms precipitation in the form of rain and aerosols in the form of fog. Clouds consist of suspended droplets of water and ice, its solid state. When finely divided, crystalline ice may precipitate in the form of snow. The gaseous state of ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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