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PICRUSt
PICRUSt is a bioinformatics software package. The name is an abbreviation for ''Phylogenetic Investigation of Communities by Reconstruction of Unobserved States.'' The tool serves in the field of metagenomic analysis where it allows inference of the functional profile of a microbial community based on marker gene survey along one or more samples. In essence, PICRUSt takes a user supplied operational taxonomic unit table (typically referred to as an OTU table), representing the marker gene sequences (most commonly a 16S ribosomal RNA, 16S Cluster analysis, cluster) accompanied with its relative abundance in each of the samples. The output of PICRUSt is a sample by functional-gene-count matrix, telling the count of each functional-gene in each of the samples surveyed. The ability of PICRUSt to estimate the functional-gene profile for a given sample relies on a set of known sequenced genomes. This could also be thought of as an automated alternative to manually researching the gene ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Human Microbiome
The human microbiome is the aggregate of all microbiota that reside on or within human tissues and biofluids along with the corresponding anatomical sites in which they reside, including the skin, mammary glands, seminal fluid, uterus, ovarian follicles, lung, saliva, oral mucosa, conjunctiva, biliary tract, and gastrointestinal tract. Types of human microbiota include bacteria, archaea, fungi, protists and viruses. Though micro-animals can also live on the human body, they are typically excluded from this definition. In the context of genomics, the term ''human microbiome'' is sometimes used to refer to the collective genomes of resident microorganisms; however, the term '' human metagenome'' has the same meaning. Humans are colonized by many microorganisms, with approximately the same order of magnitude of non-human cells as human cells. Some microorganisms that colonize humans are commensal, meaning they co-exist without harming humans; others have a mutualistic relation ... [...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] |
Wagner Parsimony
Wilhelm Richard Wagner ( ; ; 22 May 181313 February 1883) was a German composer, theatre director, polemicist, and conductor who is chiefly known for his operas (or, as some of his mature works were later known, "music dramas"). Unlike most opera composers, Wagner wrote both the libretto and the music for each of his stage works. Initially establishing his reputation as a composer of works in the romantic vein of Carl Maria von Weber and Giacomo Meyerbeer, Wagner revolutionised opera through his concept of the ''Gesamtkunstwerk'' ("total work of art"), by which he sought to synthesise the poetic, visual, musical and dramatic arts, with music subsidiary to drama. He described this vision in a series of essays published between 1849 and 1852. Wagner realised these ideas most fully in the first half of the four-opera cycle ''Der Ring des Nibelungen'' (''The Ring of the Nibelung''). His compositions, particularly those of his later period, are notable for their complex textures, ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Evolutionary Comparative Genomics
Evolution is change in the heredity, heritable Phenotypic trait, characteristics of biological populations over successive generations. These characteristics are the Gene expression, expressions of genes, which are passed on from parent to offspring during reproduction. Genetic variability, Variation tends to exist within any given population as a result of genetic mutation and genetic recombination, recombination. Evolution occurs when evolutionary processes such as natural selection (including sexual selection) and genetic drift act on this variation, resulting in certain characteristics becoming more common or more rare within a population. The evolutionary pressures that determine whether a characteristic is common or rare within a population constantly change, resulting in a change in heritable characteristics arising over successive generations. It is this process of evolution that has given rise to biodiversity at every level of biological organisation, including the l ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Microbial Mats
A microbial mat is a multi-layered sheet of microorganisms, mainly bacteria and archaea, or bacteria alone. Microbial mats grow at interfaces between different types of material, mostly on submerged or moist surfaces, but a few survive in deserts. A few are found as endosymbionts of animals. Although only a few centimetres thick at most, microbial mats create a wide range of internal chemical environments, and hence generally consist of layers of microorganisms that can feed on or at least tolerate the dominant chemicals at their level and which are usually of closely related species. In moist conditions mats are usually held together by slimy substances secreted by the microorganisms. In many cases some of the bacteria form tangled webs of filaments which make the mat tougher. The best known physical forms are flat mats and stubby pillars called stromatolites, but there are also spherical forms. Microbial mats are the earliest form of life on Earth for which there is good fossi ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Guerrero Negro
Guerrero Negro is the largest town located in the municipality of Mulegé in the Mexican state of Baja California Sur (BCS). It had a population of 14,316 in the 2015 census. The town is served by Guerrero Negro Airport. Whale Festival The town has a celebration each year to hail the annual arrival of the gray whales that calve in the lagoons of Baja California Sur (BCS). This festival occurs during the first half of February. The port of San Blas, also in BCS, has a similar festival on February 24 and 25. Saltworks operation Guerrero Negro was founded in 1957 when Daniel Ludwig built a salt works there to supply the demand of salt in the western United States. The salt mine was established around the Ojo de Liebre coastal lagoon to take advantage of its strong salinity. This company, called Exportadora de Sal, S.A., of C.V. ("Salt Exporters, Inc."), eventually became the greatest salt mine in the world, with a production of seven million tons of salt per year, expo ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Human Microbiome Project
The 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. The program received $170 million in funding by the NIH Common Fund from 2007 to 2016. Important components of the HMP were culture-independent methods of microbial community characterization, such as metagenomics (which provides a broad genetic perspective on a single microbial community), as well as extensive whole genome sequencing (which provides a "deep" genetic perspective on certain aspects of a given microbial community, ''i.e.'' of individual bacterial spe ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Shotgun Metagenomics
A shotgun (also known as a scattergun, or historically as a fowling piece) is a long-barreled firearm designed to shoot a straight-walled cartridge known as a shotshell, which usually discharges numerous small pellet-like spherical sub-projectiles called shot, or sometimes a single solid projectile called a slug. Shotguns are most commonly smoothbore firearms, meaning that their gun barrels have no rifling on the inner wall, but rifled barrels for shooting slugs (slug barrels) are also available. Shotguns come in a wide variety of calibers and gauges ranging from 5.5 mm (.22 inch) to up to , though the 12-gauge (18.53 mm or 0.729 in) and 20-gauge (15.63 mm or 0.615 in) bores are by far the most common. Almost all are breechloading, and can be single-barreled, double-barreled, or in the form of a combination gun. Like rifles, shotguns also come in a range of different action types, both single-shot and repeating. For non-repeating designs, o ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Metagenome
Metagenomics 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. Such work revealed that the vast majority of microbial biodiversity had been missed by cultivation-based methods. Because of its ability to reveal the previously hidden diversity of microscopic life, metagenomics offers a powerful lens for viewing the microbial world that has the potential to revolutionize understanding of the entire living world. As the price of DNA sequencing continues to fall, metagenomics now allows microbial ecology to be investigated at a much greater scale ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
16S RRNA
16S rRNA may refer to: * 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 rR ..., the prokaryotic ribosomal subunit * Mitochondrially encoded 16S RNA, the eukaryotic ribosomal subunit {{Short pages monitor ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Lack Of Genomic Data
Lack may refer to: Places * Lack, County Fermanagh, a townland in Northern Ireland * Lack, Poland * Łąck, Poland * Lack Township, Juniata County, Pennsylvania, US Other uses * Lack (surname) * Lack (manque), a term in Lacan's psychoanalytic philosophy * "Lack" (song), by Porno Graffitti, 2003 See also * Lakh, a term in India for 100,000 * Lac (other) * Lak (other) * Henrietta Lacks Henrietta Lacks (born Loretta Pleasant; August 1, 1920 – October 4, 1951) Note: Some sources report her birthday as August 2, 1920, vs. August 1, 1920. was an African-American woman whose cancer cells are the source of the HeLa cell line ... (1920–1951), African-American woman whose cancer cells are the source of the immortalized HeLa cell line * 359426 Lacks, a main-belt asteroid named after Henrietta Lacks {{disambiguation ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Phylogenetic Inference
Computational phylogenetics is the application of computational algorithms, methods, and programs to phylogenetic "tribe, clan, race", and wikt:γενετικός, γενετικός [] "origin, source, birth") is the study of the evolutionary history and relationships among or within groups ... "tribe, clan, race", and wikt:γενετικός, γενετικός [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
